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We have to activate the environment before running poetry. --- tools/reset-pyenv | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/tools/reset-pyenv b/tools/reset-pyenv index 0a8e3ba..39c91fc 100755 --- a/tools/reset-pyenv +++ b/tools/reset-pyenv @@ -4,16 +4,18 @@ env="xpypact" pkg="${env//-/_}" +last_python="3.11.2" eval "$(pyenv init -)" -pyenv local "$env" "3.10.10" "3.9.16" "3.8.16" +pyenv local "$last_python" pyenv virtualenv-delete -f "$env" -pyenv virtualenv "3.11.2" "$env" +pyenv virtualenv "$last_python" "$env" pyenv rehash pyenv shell "$env" poetry env info poetry install pyenv shell --unset +pyenv local "$env" "3.10.10" "3.9.16" "3.8.16" pyenv rehash python -c "import ${pkg}; print(${pkg}.__version__)" From 84fbbd36d24c2410e91b94599dc31b629b25c94e Mon Sep 17 00:00:00 2001 From: dvp Date: Sun, 12 Mar 2023 13:45:53 +0300 Subject: [PATCH 03/32] bump: version xpypact 0.1.12a0 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git 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{file = "typeguard-2.13.3-py3-none-any.whl", hash = "sha256:5e3e3be01e887e7eafae5af63d1f36c849aaa94e3a0112097312aabfa16284f1"}, - {file = "typeguard-2.13.3.tar.gz", hash = "sha256:00edaa8da3a133674796cf5ea87d9f4b4c367d77476e185e80251cc13dfbb8c4"}, + {file = "typeguard-3.0.1-py3-none-any.whl", hash = "sha256:15628045c830abf68533247afd2cb04683b5ce6f4e30d5401a5ef6f5182280de"}, + {file = "typeguard-3.0.1.tar.gz", hash = "sha256:beb0e67c5dc76eea4a6d00a6606d444d899589908362960769d0c4a1d32bca70"}, ] +[package.dependencies] +importlib-metadata = {version = ">=3.6", markers = "python_version < \"3.10\""} +typing-extensions = {version = ">=4.4.0", markers = "python_version < \"3.11\""} + [package.extras] -doc = ["sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"] -test = ["mypy", "pytest", "typing-extensions"] +doc = ["packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"] +test = ["mypy (>=0.991)", "pytest (>=7)"] [[package]] name = "typer" @@ -2797,14 +2801,14 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] [[package]] name = "virtualenv" -version = "20.20.0" +version = "20.21.0" description = "Virtual Python Environment builder" category = "dev" optional = false python-versions = ">=3.7" files = [ - {file = "virtualenv-20.20.0-py3-none-any.whl", hash = "sha256:3c22fa5a7c7aa106ced59934d2c20a2ecb7f49b4130b8bf444178a16b880fa45"}, - {file = "virtualenv-20.20.0.tar.gz", hash = "sha256:a8a4b8ca1e28f864b7514a253f98c1d62b64e31e77325ba279248c65fb4fcef4"}, + {file = "virtualenv-20.21.0-py3-none-any.whl", hash = "sha256:31712f8f2a17bd06234fa97fdf19609e789dd4e3e4bf108c3da71d710651adbc"}, + {file = "virtualenv-20.21.0.tar.gz", hash = "sha256:f50e3e60f990a0757c9b68333c9fdaa72d7188caa417f96af9e52407831a3b68"}, ] [package.dependencies] From 14d463118e00cc97638b3cc6b64aa43741784562 Mon Sep 17 00:00:00 2001 From: dvp Date: Thu, 16 Mar 2023 20:47:02 +0300 Subject: [PATCH 05/32] build: sync with similar mckit-nuclides files --- .github/workflows/release.yml | 4 ++-- .github/workflows/tests.yml | 8 ++++---- pyproject.toml | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 5700711..4ccfa44 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -71,14 +71,14 @@ jobs: - name: Publish package on PyPI if: steps.check-version.outputs.tag - uses: pypa/gh-action-pypi-publish@v1.6.4 + uses: pypa/gh-action-pypi-publish@v1.7.1 with: user: __token__ password: ${{ secrets.PYPI_TOKEN }} - name: Publish package on TestPyPI if: "! steps.check-version.outputs.tag" - uses: pypa/gh-action-pypi-publish@v1.6.4 + uses: pypa/gh-action-pypi-publish@v1.7.1 with: user: __token__ password: ${{ secrets.TEST_PYPI_TOKEN }} diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 693329c..d3e54cc 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -55,7 +55,7 @@ jobs: - name: Load poetry cache id: cached-poetry-dependencies - uses: actions/cache@v3.2.6 + uses: actions/cache@v3.3.1 with: path: | .cache/pypoetry @@ -106,7 +106,7 @@ jobs: - name: Load poetry cache id: cached-poetry-dependencies - uses: actions/cache@v3.2.6 + uses: actions/cache@v3.3.1 with: path: | .cache/pypoetry @@ -158,7 +158,7 @@ jobs: - name: Load poetry cache id: cached-poetry-dependencies - uses: actions/cache@v3.2.6 + uses: actions/cache@v3.3.1 with: path: | .cache/pypoetry @@ -201,7 +201,7 @@ jobs: - name: Load poetry cache id: cached-poetry-dependencies - uses: actions/cache@v3.2.6 + uses: actions/cache@v3.3.1 with: path: | .cache/pypoetry diff --git a/pyproject.toml b/pyproject.toml index 4997745..4f8e26f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -31,7 +31,7 @@ classifiers = [ ] [build-system] -requires = ["poetry-core>=1.1.0"] +requires = ["poetry-core >= 1.1.0"] build-backend = "poetry.core.masonry.api" # [tool.poetry.scripts] From 361c87abdcc451b01d62b14a3c2d05cabef296b6 Mon Sep 17 00:00:00 2001 From: dvp Date: Mon, 20 Mar 2023 22:50:54 +0300 Subject: [PATCH 06/32] dependencies: poetry update (dev only) --- poetry.lock | 30 +++++++++++++++--------------- 1 file changed, 15 insertions(+), 15 deletions(-) diff --git a/poetry.lock b/poetry.lock index 2e0435d..3d38306 100644 --- a/poetry.lock +++ b/poetry.lock @@ -14,14 +14,14 @@ files = [ [[package]] name = "argcomplete" -version = "2.1.1" +version = "2.1.2" description = "Bash tab completion for argparse" category = "dev" optional = false python-versions = ">=3.6" files = [ - {file = "argcomplete-2.1.1-py3-none-any.whl", hash = "sha256:17041f55b8c45099428df6ce6d0d282b892471a78c71375d24f227e21c13f8c5"}, - {file = "argcomplete-2.1.1.tar.gz", hash = "sha256:72e08340852d32544459c0c19aad1b48aa2c3a96de8c6e5742456b4f538ca52f"}, + {file = "argcomplete-2.1.2-py3-none-any.whl", hash = "sha256:4ba9cdaa28c361d251edce884cd50b4b1215d65cdc881bd204426cdde9f52731"}, + {file = "argcomplete-2.1.2.tar.gz", hash = "sha256:fc82ef070c607b1559b5c720529d63b54d9dcf2dcfc2632b10e6372314a34457"}, ] [package.extras] @@ -736,14 +736,14 @@ flake8 = ">=2" [[package]] name = "flake8-comprehensions" -version = "3.10.1" +version = "3.11.0" description = "A flake8 plugin to help you write better list/set/dict comprehensions." category = "dev" optional = false python-versions = ">=3.7" files = [ - {file = "flake8-comprehensions-3.10.1.tar.gz", hash = "sha256:412052ac4a947f36b891143430fef4859705af11b2572fbb689f90d372cf26ab"}, - {file = "flake8_comprehensions-3.10.1-py3-none-any.whl", hash = "sha256:d763de3c74bc18a79c039a7ec732e0a1985b0c79309ceb51e56401ad0a2cd44e"}, + {file = "flake8_comprehensions-3.11.0-py3-none-any.whl", hash = "sha256:820b6463d4964249b7380432f3aac2f26d4a86c7d52cbe9d53dfd9e1caf01b33"}, + {file = "flake8_comprehensions-3.11.0.tar.gz", hash = "sha256:d06a95fdf2dabf6a7632550fed4a10d0449d00473875b1e4b167ca84d4daee59"}, ] [package.dependencies] @@ -1093,14 +1093,14 @@ files = [ [[package]] name = "importlib-metadata" -version = "6.0.0" +version = "6.1.0" description = "Read metadata from Python packages" category = "dev" optional = false python-versions = ">=3.7" files = [ - {file = "importlib_metadata-6.0.0-py3-none-any.whl", hash = "sha256:7efb448ec9a5e313a57655d35aa54cd3e01b7e1fbcf72dce1bf06119420f5bad"}, - {file = "importlib_metadata-6.0.0.tar.gz", hash = "sha256:e354bedeb60efa6affdcc8ae121b73544a7aa74156d047311948f6d711cd378d"}, + {file = "importlib_metadata-6.1.0-py3-none-any.whl", hash = "sha256:ff80f3b5394912eb1b108fcfd444dc78b7f1f3e16b16188054bd01cb9cb86f09"}, + {file = "importlib_metadata-6.1.0.tar.gz", hash = "sha256:43ce9281e097583d758c2c708c4376371261a02c34682491a8e98352365aad20"}, ] [package.dependencies] @@ -1766,14 +1766,14 @@ testing = ["pytest", "pytest-benchmark"] [[package]] name = "pre-commit" -version = "3.1.1" +version = "3.2.0" description = "A framework for managing and maintaining multi-language pre-commit hooks." category = "dev" optional = false python-versions = ">=3.8" files = [ - {file = "pre_commit-3.1.1-py2.py3-none-any.whl", hash = "sha256:b80254e60668e1dd1f5c03a1c9e0413941d61f568a57d745add265945f65bfe8"}, - {file = "pre_commit-3.1.1.tar.gz", hash = "sha256:d63e6537f9252d99f65755ae5b79c989b462d511ebbc481b561db6a297e1e865"}, + {file = "pre_commit-3.2.0-py2.py3-none-any.whl", hash = "sha256:f712d3688102e13c8e66b7d7dbd8934a6dda157e58635d89f7d6fecdca39ce8a"}, + {file = "pre_commit-3.2.0.tar.gz", hash = "sha256:818f0d998059934d0f81bb3667e3ccdc32da6ed7ccaac33e43dc231561ddaaa9"}, ] [package.dependencies] @@ -2744,14 +2744,14 @@ files = [ [[package]] name = "types-setuptools" -version = "67.6.0.0" +version = "67.6.0.5" description = "Typing stubs for setuptools" category = "dev" optional = false python-versions = "*" files = [ - {file = "types-setuptools-67.6.0.0.tar.gz", hash = "sha256:70b5e6a379e9fccf6579871a93ca3301a46252e3ae66957ec64281a2b6a812d9"}, - {file = "types_setuptools-67.6.0.0-py3-none-any.whl", hash = "sha256:d669a80ee8e37eb1697dc31a23d41ea2c48a635464e2c7e6370dda811459b466"}, + {file = "types-setuptools-67.6.0.5.tar.gz", hash = "sha256:3a708e66c7bdc620e4d0439f344c750c57a4340c895a4c3ed2d0fc4ae8eb9962"}, + {file = "types_setuptools-67.6.0.5-py3-none-any.whl", hash = "sha256:dae5a4a659dbb6dba57773440f6e2dbdd8ef282dc136a174a8a59bd33d949945"}, ] [[package]] From fd70b9e6c9148a760609b4213fc6e25b2c05aada Mon Sep 17 00:00:00 2001 From: dvp Date: Wed, 22 Mar 2023 12:09:05 +0300 Subject: [PATCH 07/32] feat: won't scale by mass dose rates Resolved TODO to check if mass or point source is fixed (1g) --- src/xpypact/TimeStep.py | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/src/xpypact/TimeStep.py b/src/xpypact/TimeStep.py index 3434522..4d2da25 100644 --- a/src/xpypact/TimeStep.py +++ b/src/xpypact/TimeStep.py @@ -13,7 +13,15 @@ @dataclass class DoseRate: - """Dose rate attributes.""" + """Dose rate attributes. + + Don't scale by mass, for point source mass is always 1g, for contact dose mass is meaningless. + + Attrs: + type: "Plain source" for contact dose or "Point source" + distance: specified for "point source", meters + mass: mass for point source, always 1g + """ type: str = "" distance: float = 0.0 @@ -22,9 +30,8 @@ class DoseRate: def __post_init__(self) -> None: """Correct wrong value coming from FISPACT.""" - # TODO dvp: check behaviour with FISPACT v.5 and try to correct scenarios. if self.mass == 0.0: - # According to FISPACT manual (v.4) + # According to FISPACT manual (both v.4 and v.5 (p.63)) # should be 1 gram always, but FISPACT shows 0 at the first step # and less, than 1 in the following steps. Fixing here. self.mass = 1.0e-3 From 5d2ddf13bf378eaac88a1ca739fbf3008605bda5 Mon Sep 17 00:00:00 2001 From: dvp Date: Wed, 22 Mar 2023 19:21:07 +0300 Subject: [PATCH 08/32] feat: add notebooks for prototyping --- .flake8 | 1 + notebooks/dvp/try_ducdb.ipynb | 2881 +++++++++++++++++++++++++++++++++ notebooks/dvp/try_ducdb.py | 380 +++++ notebooks/poetry.lock | 2509 ++++++++++++++++++++++++++++ notebooks/pyproject.toml | 19 + poetry.lock | 103 +- 6 files changed, 5845 insertions(+), 48 deletions(-) create mode 100644 notebooks/dvp/try_ducdb.ipynb create mode 100644 notebooks/dvp/try_ducdb.py create mode 100644 notebooks/poetry.lock create mode 100644 notebooks/pyproject.toml diff --git a/.flake8 b/.flake8 index a62c9b1..36c9561 100644 --- a/.flake8 +++ b/.flake8 @@ -57,6 +57,7 @@ exclude= *.egg-info .cache .eggs + notebooks/dvp/*.py per-file-ignores = benchmarks/*:S101,DAR101 noxfile.py:ANN,DAR101 diff --git a/notebooks/dvp/try_ducdb.ipynb b/notebooks/dvp/try_ducdb.ipynb new file mode 100644 index 0000000..2e8290f --- /dev/null +++ b/notebooks/dvp/try_ducdb.ipynb @@ -0,0 +1,2881 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "id": "250d384f-b617-4bde-8d6e-5bfea316e21f", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "%config Completer.use_jedi = False" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "id": "49812848-cb6d-487a-bcdf-927e86781ae9", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "import xpypact as xp" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "id": "5e40fc05-d196-4ab9-b4df-ec6166ee5611", + "metadata": { + "tags": [] + }, + "outputs": [ + { + "data": { + "text/plain": [ + "'0.1.12a0'" + ] + }, + "execution_count": 5, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "xp.__version__" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "id": "982fbe50-fd22-499a-98d9-910f6d0c72d7", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "from pathlib import Path" + ] + }, + { + "cell_type": "code", + "execution_count": 19, + "id": "bf81c238-8be8-4f93-b3e4-155bb46e21e8", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "root_dir = Path(\"~\", \"dev\", \"xpypact\").expanduser()" + ] + }, + { + "cell_type": "code", + "execution_count": 20, + "id": "c0811f45-0503-4302-9890-62803b49cabe", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "json_path = root_dir / \"tests/data/Ag-1.json\"\n", + "assert json_path.exists()" + ] + }, + { + "cell_type": "code", + "execution_count": 23, + "id": "57fecf87-b03f-48e4-bfe4-beee3d661355", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "from xpypact.Inventory import Inventory, from_json\n", + "import xpypact.data_arrays as da" + ] + }, + { + "cell_type": "code", + "execution_count": 24, + "id": "c13bb091-11ad-4e08-bbad-7cba93475e4b", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "inventory = from_json(json_path)" + ] + }, + { + "cell_type": "code", + "execution_count": 25, + "id": "e471ce43-3860-430d-b669-7a1211bb5d06", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "ds = da.create_dataset(inventory)" + ] + }, + { + "cell_type": "code", + "execution_count": 26, + "id": "eaa7c75f-119c-493c-b038-dbd615b72c6f", + "metadata": { + "tags": [] + }, + "outputs": [ + { + "data": { + "text/html": [ + "
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'm' '' '' ''\n", + " elapsed_time (time_step_number) float64 0.0 6.312e+07\n", + " zai (nuclide) int64 471050 471051 ... 441030 441040\n", + " * timestamp (timestamp) datetime64[ns] 2020-07-12T23:01:19\n", + "Data variables: (12/31)\n", + " irradiation_time (time_step_number) float64 0.0 6.312e+07\n", + " cooling_time (time_step_number) float64 0.0 0.0\n", + " duration (time_step_number) float64 0.0 6.312e+07\n", + " flux (time_step_number) float64 0.0 2.445e+10\n", + " total_atoms (time_step_number) float64 5.578e+21 5.578e+21\n", + " total_activity (time_step_number) float64 0.0 6.123e+09\n", + " ... ...\n", + " nuclide_alpha_heat (time_step_number, nuclide) float64 nan nan ... 0.0\n", + " nuclide_beta_heat (time_step_number, nuclide) float64 nan nan ... 0.0\n", + " nuclide_gamma_heat (time_step_number, nuclide) float64 nan nan ... 0.0\n", + " nuclide_dose (time_step_number, nuclide) float64 nan nan ... 0.0\n", + " nuclide_ingestion (time_step_number, nuclide) float64 nan nan ... 0.0\n", + " nuclide_inhalation (time_step_number, nuclide) float64 nan nan ... 0.0\n", + "Attributes:\n", + " run_name: * Material Ag, fluxes 1\n", + " flux_name: 55.F9.10 11-L2-02W HFS_GLRY_08_U\n", + " dose_rate_type: Point source\n", + " dose_rate_distance: 1.0" + ] + }, + "execution_count": 26, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ds" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "3d2db9b3-09d8-4bf7-bc4b-8ec13cc8105b", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": 28, + "id": "79beed07-0f86-485b-be23-97d7e8f33abb", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "import duckdb as db" + ] + }, + { + "cell_type": "code", + "execution_count": 46, + "id": "ee7bf9aa-13a8-419d-b39e-c90493094148", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "db_path = root_dir / \"wrk/try-duckdb.duckdb\"\n", + "db_path.parent.mkdir(parents=True, exist_ok=True)" + ] + }, + { + "cell_type": "code", + "execution_count": 48, + "id": "99a86bdc-84e1-4cd3-b7b7-4e63b6428086", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "con = db.connect(str(db_path))" + ] + }, + { + "cell_type": "code", + "execution_count": 153, + "id": "d9e1ddfb-398e-4cea-b01d-fb0e53242776", + "metadata": { + "tags": [] + }, + "outputs": [ + { + "data": { + "text/plain": [ + "" + ] + }, + "execution_count": 153, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# con.execute(\"drop table rundata\")\n", + "# con.execute(\"drop table if exists timestep_gamma\")\n", + "con.execute(\"drop table if exists timestep_nuclide\")\n", + "# con.execute(\"drop table if exists timestep\")\n", + "con.execute(\"drop table nuclide\")\n" + ] + }, + { + "cell_type": "code", + "execution_count": 154, + "id": "c402d3a1-e77a-4b24-accc-a19588ccdf54", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "def create_tables(con):\n", + " sql = \"\"\"\n", + " \n", + " CREATE TABLE IF NOT EXISTS rundata (\n", + " timestamp varchar NOT NULL,\n", + " run_name varchar NOT NULL,\n", + " flux_name varchar NOT NULL,\n", + " dose_rate_type varchar NOT NULL,\n", + " dose_rate_distance real NOT NULL\n", + " );\n", + "\n", + " CREATE TABLE IF NOT EXISTS timestep(\n", + " id integer PRIMARY KEY,\n", + " elapsed_time real not null,\n", + " irradiation_time real not null,\n", + " cooling_time real not null,\n", + " duration real not null,\n", + " flux real not null,\n", + " total_atoms real not null,\n", + " total_activity real not null,\n", + " total_alpha_activity real not null,\n", + " total_beta_activity real not null,\n", + " total_gamma_activity real not null,\n", + " total_mass real not null,\n", + " total_heat real not null,\n", + " total_alpha_heat real not null,\n", + " total_beta_heat real not null,\n", + " total_gamma_heat real not null,\n", + " total_ingest1ion_dose real not null,\n", + " total_inhalation_dose real not null,\n", + " total_dose_rate real not null\n", + " );\n", + " \n", + " CREATE TABLE IF NOT EXISTS nuclide(\n", + " element varchar(2) not null,\n", + " mass_number integer not null check(0 < mass_number), -- A\n", + " state varchar(1) not null,\n", + " zai integer not null check(10010 <= zai) unique,\n", + " half_life real not null check(0 <= half_life),\n", + " primary key(element, mass_number, state)\n", + " );\n", + " \n", + " CREATE TABLE IF NOT EXISTS timestep_nuclide(\n", + " timestep_id integer not null,\n", + " element varchar(2) not null,\n", + " mass_number integer not null,\n", + " state varchar(1) not null,\n", + " atoms real not null,\n", + " grams real not null,\n", + " activity real not null,\n", + " alpha_activity real not null,\n", + " beta_activity real not null,\n", + " gamma_activity real not null,\n", + " heat real not null,\n", + " alpha_heat real not null,\n", + " beta_heat real not null,\n", + " gamma_heat real not null,\n", + " dose real not null,\n", + " ingestion real not null,\n", + " inhalation real not null,\n", + " primary key(timestep_id, element, mass_number, state),\n", + " foreign key(timestep_id) references timestep(id),\n", + " foreign key(element, mass_number, state) references nuclide(element, mass_number, state) \n", + " );\n", + "\n", + " CREATE TABLE IF NOT EXISTS timestep_gamma(\n", + " timestep_id integer not null,\n", + " boundary real not null check(0 <= boundary),\n", + " intensity real not null, \n", + " primary key(timestep_id, boundary),\n", + " foreign key(timestep_id) references timestep(id),\n", + " );\n", + "\"\"\"\n", + " con.execute(sql)" + ] + }, + { + "cell_type": "code", + "execution_count": 155, + "id": "25f6867e-397a-4e98-a363-74b6af739c88", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "create_tables(con)" + ] + }, + { + "cell_type": "code", + "execution_count": 85, + "id": "db019e1c-bebd-4993-a1b5-274cf00a2ceb", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "# con.execute(\"delete from rundata\")" + ] + }, + { + "cell_type": "code", + "execution_count": 81, + "id": "29716201-70f8-40d2-8da7-85689714ec32", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "def save_rundata(con, ds):\n", + " sql = \"\"\"\n", + " INSERT INTO rundata values(?, ?, ?, ?, ?)\n", + " \"\"\"\n", + " con.execute(sql, ( \n", + " ds.coords[\"timestamp\"].item(),\n", + " ds.attrs[\"run_name\"],\n", + " ds.attrs[\"flux_name\"],\n", + " ds.attrs[\"dose_rate_type\"],\n", + " ds.attrs[\"dose_rate_distance\"]\n", + " ))\n", + " con.commit()" + ] + }, + { + "cell_type": "code", + "execution_count": 83, + "id": "c789eedd-580c-4383-8bf1-cc943562a3aa", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "save_rundata(con, ds)" + ] + }, + { + "cell_type": "code", + "execution_count": 84, + "id": "1c650134-edf3-44dd-aa90-ddde6a3987a7", + "metadata": { + "tags": [] + }, + "outputs": [ + { + "data": { + 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timestamprun_nameflux_namedose_rate_typedose_rate_distance
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" + ], + "text/plain": [ + " timestamp run_name \\\n", + "0 1594594879000000000 * Material Ag, fluxes 1 \n", + "\n", + " flux_name dose_rate_type dose_rate_distance \n", + "0 55.F9.10 11-L2-02W HFS_GLRY_08_U Point source 1.0 " + ] + }, + "execution_count": 84, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "con.execute(\"select * from rundata\").df()" + ] + }, + { + "cell_type": "code", + "execution_count": 114, + "id": "cf8661b6-d9cb-4431-8b40-f14072409d5a", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "def save_timesteps(con, ds):\n", + " timesteps_df = ds[\n", + " [\n", + " \"time_step_number\",\n", + " \"elapsed_time\",\n", + " \"irradiation_time\",\n", + " \"cooling_time\",\n", + " \"duration\",\n", + " \"flux\",\n", + " \"total_atoms\",\n", + " \"total_activity\",\n", + " \"total_alpha_activity\",\n", + " \"total_beta_activity\",\n", + " \"total_gamma_activity\",\n", + " \"total_mass\",\n", + " \"total_heat\",\n", + " \"total_alpha_heat\",\n", + " \"total_beta_heat\",\n", + " \"total_gamma_heat\",\n", + " \"total_ingest1ion_dose\",\n", + " \"total_inhalation_dose\",\n", + " \"total_dose_rate\",\n", + " ]\n", + " ].to_pandas().reset_index()\n", + " sql = \"insert into timestep select * from timesteps_df\"\n", + " con.execute(sql)\n", + " con.commit()" + ] + }, + { + "cell_type": "code", + "execution_count": 115, + "id": "78154d84-9df4-417d-a35f-60252575aae6", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "save_timesteps(con, ds)" + ] + }, + { + "cell_type": "code", + "execution_count": 116, + "id": "bf73ee32-d132-418f-8e77-969d779b780a", + "metadata": { + "tags": [] + }, + "outputs": [ + { + "data": { + "text/html": [ + "
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13Ag111m4711116.480000e+01
14Cd1064810602.082800e+26
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16Cd1084810801.293860e+25
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33Pd1094610904.932430e+04
34Pd109m4610912.814000e+02
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37Rh102m4510211.797120e+07
38Rh1034510300.000000e+00
39Rh103m4510313.366840e+03
40Rh1044510404.230000e+01
41Rh104m4510412.604000e+02
42Rh1054510501.272960e+05
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44Rh106m4510617.920000e+03
45Ru1024410200.000000e+00
46Ru1034410303.392060e+06
47Ru1044410400.000000e+00
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" + ], + "text/plain": [ + " element mass_number state zai nuclide_half_life\n", + "0 Ag 105 471050 3.568320e+06\n", + "1 Ag 105 m 471051 4.338000e+02\n", + "2 Ag 106 471060 1.440000e+03\n", + "3 Ag 106 m 471061 7.309440e+05\n", + "4 Ag 107 471070 0.000000e+00\n", + "5 Ag 107 m 471071 4.430000e+01\n", + "6 Ag 108 471080 1.440000e+02\n", + "7 Ag 108 m 471081 1.319110e+10\n", + "8 Ag 109 471090 0.000000e+00\n", + "9 Ag 109 m 471091 3.970000e+01\n", + "10 Ag 110 471100 2.456000e+01\n", + "11 Ag 110 m 471101 2.158100e+07\n", + "12 Ag 111 471110 6.436800e+05\n", + "13 Ag 111 m 471111 6.480000e+01\n", + "14 Cd 106 481060 2.082800e+26\n", + "15 Cd 107 481070 2.347200e+04\n", + "16 Cd 108 481080 1.293860e+25\n", + "17 Cd 109 481090 3.996860e+07\n", + "18 Cd 110 481100 0.000000e+00\n", + "19 Cd 111 481110 0.000000e+00\n", + "20 Cd 111 m 481111 2.924400e+03\n", + "21 Cd 112 481120 0.000000e+00\n", + "22 H 1 10010 0.000000e+00\n", + "23 H 2 10020 0.000000e+00\n", + "24 H 3 10030 3.891050e+08\n", + "25 He 3 20030 0.000000e+00\n", + "26 He 4 20040 0.000000e+00\n", + "27 Pd 104 461040 0.000000e+00\n", + "28 Pd 105 461050 0.000000e+00\n", + "29 Pd 106 461060 0.000000e+00\n", + "30 Pd 107 461070 2.051200e+14\n", + "31 Pd 107 m 461071 2.130000e+01\n", + "32 Pd 108 461080 0.000000e+00\n", + "33 Pd 109 461090 4.932430e+04\n", + "34 Pd 109 m 461091 2.814000e+02\n", + "35 Pd 110 461100 1.893460e+25\n", + "36 Rh 102 451020 9.158400e+07\n", + "37 Rh 102 m 451021 1.797120e+07\n", + "38 Rh 103 451030 0.000000e+00\n", + "39 Rh 103 m 451031 3.366840e+03\n", + "40 Rh 104 451040 4.230000e+01\n", + "41 Rh 104 m 451041 2.604000e+02\n", + "42 Rh 105 451050 1.272960e+05\n", + "43 Rh 106 451060 3.000000e+01\n", + "44 Rh 106 m 451061 7.920000e+03\n", + "45 Ru 102 441020 0.000000e+00\n", + "46 Ru 103 441030 3.392060e+06\n", + "47 Ru 104 441040 0.000000e+00" + ] + }, + "execution_count": 131, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ds[[\"element\", \"mass_number\", \"state\", \"zai\", \"nuclide_half_life\"]].to_pandas().reset_index(drop=True)" + ] + }, + { + "cell_type": "code", + "execution_count": 156, + "id": "c5fdb6e7-00b7-40f1-9d8d-f755dd768a97", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "def save_nuclides(con, ds):\n", + " nuclides_df = ds[[\"element\", \"mass_number\", \"state\", \"zai\", \"nuclide_half_life\"]].to_pandas().reset_index(drop=True)\n", + " sql = \"insert into nuclide select * from nuclides_df\"\n", + " con.execute(sql)\n", + " con.commit()" + ] + }, + { + "cell_type": "code", + "execution_count": 157, + "id": "2cd4e47d-1ec3-493c-b655-8a83917deea5", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "save_nuclides(con, ds)" + ] + }, + { + "cell_type": "code", + "execution_count": 160, + "id": "1f6cbb0e-e893-4d88-a744-989d9b39e0a4", + "metadata": { + "tags": [] + }, + "outputs": [ + { + "data": { + "text/html": [ + "
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elementmass_numberstatezaihalf_life
0Ag1054710503.568320e+06
1Ag105m4710514.338000e+02
2Ag1064710601.440000e+03
3Ag106m4710617.309440e+05
4Ag1074710700.000000e+00
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" + ], + "text/plain": [ + " element mass_number state zai half_life\n", + "0 Ag 105 471050 3.568320e+06\n", + "1 Ag 105 m 471051 4.338000e+02\n", + "2 Ag 106 471060 1.440000e+03\n", + "3 Ag 106 m 471061 7.309440e+05\n", + "4 Ag 107 471070 0.000000e+00" + ] + }, + "execution_count": 160, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "con.execute(\"select * from nuclide\").df().head()" + ] + }, + { + "cell_type": "code", + "execution_count": 166, + "id": "01216ae8-6108-4909-a332-44afbe8fb2c3", + "metadata": { + "tags": [] + }, + "outputs": [ + { + "data": { + "text/html": [ + "
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<xarray.Dataset>\n",
+       "Dimensions:                 (time_step_number: 2, nuclide: 48, timestamp: 1)\n",
+       "Coordinates:\n",
+       "  * time_step_number        (time_step_number) int64 1 2\n",
+       "  * nuclide                 (nuclide) object MultiIndex\n",
+       "  * element                 (nuclide) object 'Ag' 'Ag' 'Ag' ... 'Ru' 'Ru' 'Ru'\n",
+       "  * mass_number             (nuclide) int64 105 105 106 106 ... 106 102 103 104\n",
+       "  * state                   (nuclide) object '' 'm' '' 'm' '' ... 'm' '' '' ''\n",
+       "    elapsed_time            (time_step_number) float64 0.0 6.312e+07\n",
+       "    zai                     (nuclide) int64 471050 471051 ... 441030 441040\n",
+       "  * timestamp               (timestamp) datetime64[ns] 2020-07-12T23:01:19\n",
+       "Data variables: (12/31)\n",
+       "    irradiation_time        (time_step_number) float64 0.0 6.312e+07\n",
+       "    cooling_time            (time_step_number) float64 0.0 0.0\n",
+       "    duration                (time_step_number) float64 0.0 6.312e+07\n",
+       "    flux                    (time_step_number) float64 0.0 2.445e+10\n",
+       "    total_atoms             (time_step_number) float64 5.578e+21 5.578e+21\n",
+       "    total_activity          (time_step_number) float64 0.0 6.123e+09\n",
+       "    ...                      ...\n",
+       "    nuclide_alpha_heat      (time_step_number, nuclide) float64 nan nan ... 0.0\n",
+       "    nuclide_beta_heat       (time_step_number, nuclide) float64 nan nan ... 0.0\n",
+       "    nuclide_gamma_heat      (time_step_number, nuclide) float64 nan nan ... 0.0\n",
+       "    nuclide_dose            (time_step_number, nuclide) float64 nan nan ... 0.0\n",
+       "    nuclide_ingestion       (time_step_number, nuclide) float64 nan nan ... 0.0\n",
+       "    nuclide_inhalation      (time_step_number, nuclide) float64 nan nan ... 0.0\n",
+       "Attributes:\n",
+       "    run_name:            * Material Ag, fluxes 1\n",
+       "    flux_name:           55.F9.10 11-L2-02W HFS_GLRY_08_U\n",
+       "    dose_rate_type:      Point source\n",
+       "    dose_rate_distance:  1.0
" + ], + "text/plain": [ + "\n", + "Dimensions: (time_step_number: 2, nuclide: 48, timestamp: 1)\n", + "Coordinates:\n", + " * time_step_number (time_step_number) int64 1 2\n", + " * nuclide (nuclide) object MultiIndex\n", + " * element (nuclide) object 'Ag' 'Ag' 'Ag' ... 'Ru' 'Ru' 'Ru'\n", + " * mass_number (nuclide) int64 105 105 106 106 ... 106 102 103 104\n", + " * state (nuclide) object '' 'm' '' 'm' '' ... 'm' '' '' ''\n", + " elapsed_time (time_step_number) float64 0.0 6.312e+07\n", + " zai (nuclide) int64 471050 471051 ... 441030 441040\n", + " * timestamp (timestamp) datetime64[ns] 2020-07-12T23:01:19\n", + "Data variables: (12/31)\n", + " irradiation_time (time_step_number) float64 0.0 6.312e+07\n", + " cooling_time (time_step_number) float64 0.0 0.0\n", + " duration (time_step_number) float64 0.0 6.312e+07\n", + " flux (time_step_number) float64 0.0 2.445e+10\n", + " total_atoms (time_step_number) float64 5.578e+21 5.578e+21\n", + " total_activity (time_step_number) float64 0.0 6.123e+09\n", + " ... ...\n", + " nuclide_alpha_heat (time_step_number, nuclide) float64 nan nan ... 0.0\n", + " nuclide_beta_heat (time_step_number, nuclide) float64 nan nan ... 0.0\n", + " nuclide_gamma_heat (time_step_number, nuclide) float64 nan nan ... 0.0\n", + " nuclide_dose (time_step_number, nuclide) float64 nan nan ... 0.0\n", + " nuclide_ingestion (time_step_number, nuclide) float64 nan nan ... 0.0\n", + " nuclide_inhalation (time_step_number, nuclide) float64 nan nan ... 0.0\n", + "Attributes:\n", + " run_name: * Material Ag, fluxes 1\n", + " flux_name: 55.F9.10 11-L2-02W HFS_GLRY_08_U\n", + " dose_rate_type: Point source\n", + " dose_rate_distance: 1.0" + ] + }, + "execution_count": 166, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ds" + ] + }, + { + "cell_type": "code", + "execution_count": 203, + "id": "b9679cc0-5621-4367-a4a9-0176745b9a65", + "metadata": { + "tags": [] + }, + "outputs": [ + { + "ename": "ValueError", + "evalue": "cannot remove index(es) 'nuclide', which would corrupt the following index built from coordinates 'nuclide', 'element', 'mass_number', 'state':\nPandasIndex(MultiIndex([('Ag', 105, ''),\n ('Ag', 105, 'm'),\n ('Ag', 106, ''),\n ('Ag', 106, 'm'),\n ('Ag', 107, ''),\n ('Ag', 107, 'm'),\n ('Ag', 108, ''),\n ('Ag', 108, 'm'),\n ('Ag', 109, ''),\n ('Ag', 109, 'm'),\n ('Ag', 110, ''),\n ('Ag', 110, 'm'),\n ('Ag', 111, ''),\n ('Ag', 111, 'm'),\n ('Cd', 106, ''),\n ('Cd', 107, ''),\n ('Cd', 108, ''),\n ('Cd', 109, ''),\n ('Cd', 110, ''),\n ('Cd', 111, ''),\n ('Cd', 111, 'm'),\n ('Cd', 112, ''),\n ( 'H', 1, ''),\n ( 'H', 2, ''),\n ( 'H', 3, ''),\n ('He', 3, ''),\n ('He', 4, ''),\n ('Pd', 104, ''),\n ('Pd', 105, ''),\n ('Pd', 106, ''),\n ('Pd', 107, ''),\n ('Pd', 107, 'm'),\n ('Pd', 108, ''),\n ('Pd', 109, ''),\n ('Pd', 109, 'm'),\n ('Pd', 110, ''),\n ('Rh', 102, ''),\n ('Rh', 102, 'm'),\n ('Rh', 103, ''),\n ('Rh', 103, 'm'),\n ('Rh', 104, ''),\n ('Rh', 104, 'm'),\n ('Rh', 105, ''),\n ('Rh', 106, ''),\n ('Rh', 106, 'm'),\n ('Ru', 102, ''),\n ('Ru', 103, ''),\n ('Ru', 104, '')],\n name='nuclide'))", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mValueError\u001b[0m Traceback (most recent call last)", + "Cell \u001b[0;32mIn[203], line 19\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[43mds\u001b[49m\u001b[43m[\u001b[49m\u001b[43m[\u001b[49m\n\u001b[1;32m 2\u001b[0m \u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mtime_step_number\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 3\u001b[0m \u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43melement\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 4\u001b[0m \u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mmass_number\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 5\u001b[0m \u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mstate\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 6\u001b[0m \u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mnuclide_atoms\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 7\u001b[0m \u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mnuclide_grams\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 8\u001b[0m \u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mnuclide_activity\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 9\u001b[0m \u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mnuclide_alpha_activity\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 10\u001b[0m \u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mnuclide_beta_activity\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 11\u001b[0m \u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mnuclide_gamma_activity\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 12\u001b[0m \u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mnuclide_heat\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 13\u001b[0m \u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mnuclide_alpha_heat\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 14\u001b[0m \u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mnuclide_beta_heat\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 15\u001b[0m \u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mnuclide_gamma_heat\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 16\u001b[0m \u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mnuclide_dose\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 17\u001b[0m \u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mnuclide_ingestion\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 18\u001b[0m \u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mnuclide_inhalation\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[0;32m---> 19\u001b[0m \u001b[43m]\u001b[49m\u001b[43m]\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mto_array\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdrop_indexes\u001b[49m\u001b[43m(\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mtime_step_number\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mnuclide\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 20\u001b[0m \u001b[38;5;66;03m# .reset_coords(names=[\"time_step_number\", \"nuclide\"])\u001b[39;00m\n\u001b[1;32m 21\u001b[0m \u001b[38;5;66;03m# .stack(dimensions={\"tsn\": [\"time_step_number\", \"element\", \"mass_number\", \"state\"]})\u001b[39;00m\n", + "File \u001b[0;32m~/.pyenv/versions/3.11.2/envs/xpypact/lib/python3.11/site-packages/xarray/core/dataarray.py:3017\u001b[0m, in \u001b[0;36mDataArray.drop_indexes\u001b[0;34m(self, coord_names, errors)\u001b[0m\n\u001b[1;32m 2995\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mdrop_indexes\u001b[39m(\n\u001b[1;32m 2996\u001b[0m \u001b[38;5;28mself\u001b[39m: T_DataArray,\n\u001b[1;32m 2997\u001b[0m coord_names: Hashable \u001b[38;5;241m|\u001b[39m Iterable[Hashable],\n\u001b[1;32m 2998\u001b[0m \u001b[38;5;241m*\u001b[39m,\n\u001b[1;32m 2999\u001b[0m errors: ErrorOptions \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mraise\u001b[39m\u001b[38;5;124m\"\u001b[39m,\n\u001b[1;32m 3000\u001b[0m ) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m T_DataArray:\n\u001b[1;32m 3001\u001b[0m \u001b[38;5;250m \u001b[39m\u001b[38;5;124;03m\"\"\"Drop the indexes assigned to the given coordinates.\u001b[39;00m\n\u001b[1;32m 3002\u001b[0m \n\u001b[1;32m 3003\u001b[0m \u001b[38;5;124;03m Parameters\u001b[39;00m\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 3015\u001b[0m \u001b[38;5;124;03m A new dataarray with dropped indexes.\u001b[39;00m\n\u001b[1;32m 3016\u001b[0m \u001b[38;5;124;03m \"\"\"\u001b[39;00m\n\u001b[0;32m-> 3017\u001b[0m ds \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_to_temp_dataset\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdrop_indexes\u001b[49m\u001b[43m(\u001b[49m\u001b[43mcoord_names\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43merrors\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43merrors\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 3018\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_from_temp_dataset(ds)\n", + "File \u001b[0;32m~/.pyenv/versions/3.11.2/envs/xpypact/lib/python3.11/site-packages/xarray/core/dataset.py:5155\u001b[0m, in \u001b[0;36mDataset.drop_indexes\u001b[0;34m(self, coord_names, errors)\u001b[0m\n\u001b[1;32m 5150\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m unindexed_coords:\n\u001b[1;32m 5151\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mValueError\u001b[39;00m(\n\u001b[1;32m 5152\u001b[0m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mthose coordinates do not have an index: \u001b[39m\u001b[38;5;132;01m{\u001b[39;00munindexed_coords\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 5153\u001b[0m )\n\u001b[0;32m-> 5155\u001b[0m \u001b[43massert_no_index_corrupted\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mxindexes\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcoord_names\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43maction\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mremove index(es)\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m\n\u001b[1;32m 5157\u001b[0m variables \u001b[38;5;241m=\u001b[39m {}\n\u001b[1;32m 5158\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m name, var \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_variables\u001b[38;5;241m.\u001b[39mitems():\n", + "File \u001b[0;32m~/.pyenv/versions/3.11.2/envs/xpypact/lib/python3.11/site-packages/xarray/core/indexes.py:1506\u001b[0m, in \u001b[0;36massert_no_index_corrupted\u001b[0;34m(indexes, coord_names, action)\u001b[0m\n\u001b[1;32m 1504\u001b[0m common_names_str \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m, \u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;241m.\u001b[39mjoin(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mk\u001b[38;5;132;01m!r}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;28;01mfor\u001b[39;00m k \u001b[38;5;129;01min\u001b[39;00m common_names)\n\u001b[1;32m 1505\u001b[0m index_names_str \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m, \u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;241m.\u001b[39mjoin(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mk\u001b[38;5;132;01m!r}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;28;01mfor\u001b[39;00m k \u001b[38;5;129;01min\u001b[39;00m index_coords)\n\u001b[0;32m-> 1506\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mValueError\u001b[39;00m(\n\u001b[1;32m 1507\u001b[0m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mcannot \u001b[39m\u001b[38;5;132;01m{\u001b[39;00maction\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mcommon_names_str\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m, which would corrupt \u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 1508\u001b[0m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mthe following index built from coordinates \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mindex_names_str\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m:\u001b[39m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 1509\u001b[0m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mindex\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 1510\u001b[0m )\n", + "\u001b[0;31mValueError\u001b[0m: cannot remove index(es) 'nuclide', which would corrupt the following index built from coordinates 'nuclide', 'element', 'mass_number', 'state':\nPandasIndex(MultiIndex([('Ag', 105, ''),\n ('Ag', 105, 'm'),\n ('Ag', 106, ''),\n ('Ag', 106, 'm'),\n ('Ag', 107, ''),\n ('Ag', 107, 'm'),\n ('Ag', 108, ''),\n ('Ag', 108, 'm'),\n ('Ag', 109, ''),\n ('Ag', 109, 'm'),\n ('Ag', 110, ''),\n ('Ag', 110, 'm'),\n ('Ag', 111, ''),\n ('Ag', 111, 'm'),\n ('Cd', 106, ''),\n ('Cd', 107, ''),\n ('Cd', 108, ''),\n ('Cd', 109, ''),\n ('Cd', 110, ''),\n ('Cd', 111, ''),\n ('Cd', 111, 'm'),\n ('Cd', 112, ''),\n ( 'H', 1, ''),\n ( 'H', 2, ''),\n ( 'H', 3, ''),\n ('He', 3, ''),\n ('He', 4, ''),\n ('Pd', 104, ''),\n ('Pd', 105, ''),\n ('Pd', 106, ''),\n ('Pd', 107, ''),\n ('Pd', 107, 'm'),\n ('Pd', 108, ''),\n ('Pd', 109, ''),\n ('Pd', 109, 'm'),\n ('Pd', 110, ''),\n ('Rh', 102, ''),\n ('Rh', 102, 'm'),\n ('Rh', 103, ''),\n ('Rh', 103, 'm'),\n ('Rh', 104, ''),\n ('Rh', 104, 'm'),\n ('Rh', 105, ''),\n ('Rh', 106, ''),\n ('Rh', 106, 'm'),\n ('Ru', 102, ''),\n ('Ru', 103, ''),\n ('Ru', 104, '')],\n name='nuclide'))" + ] + } + ], + "source": [ + "ds[[\n", + "\"time_step_number\",\n", + "\"element\",\n", + "\"mass_number\",\n", + "\"state\",\n", + "\"nuclide_atoms\",\n", + "\"nuclide_grams\",\n", + "\"nuclide_activity\",\n", + "\"nuclide_alpha_activity\",\n", + "\"nuclide_beta_activity\",\n", + "\"nuclide_gamma_activity\",\n", + "\"nuclide_heat\",\n", + "\"nuclide_alpha_heat\",\n", + "\"nuclide_beta_heat\",\n", + "\"nuclide_gamma_heat\",\n", + "\"nuclide_dose\",\n", + "\"nuclide_ingestion\",\n", + "\"nuclide_inhalation\",\n", + "]].to_array().drop_indexes([\"time_step_number\", \"nuclide\"])\n", + "# .reset_coords(names=[\"time_step_number\", \"nuclide\"])\n", + "# .stack(dimensions={\"tsn\": [\"time_step_number\", \"element\", \"mass_number\", \"state\"]})" + ] + }, + { + "cell_type": "code", + "execution_count": 186, + "id": "526610bb-be7b-4ce7-8cc9-0bcdb00588f2", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "def save_timestep_nucludes(con, ds):\n", + " timesteps_nuclides_df = ds[[\n", + " \"time_step_number\",\n", + " \"element\",\n", + " \"mass_number\",\n", + " \"state\",\n", + " \"nuclide_atoms\",\n", + " \"nuclide_grams\",\n", + " \"nuclide_activity\",\n", + " \"nuclide_alpha_activity\",\n", + " \"nuclide_beta_activity\",\n", + " \"nuclide_gamma_activity\",\n", + " \"nuclide_heat\",\n", + " \"nuclide_alpha_heat\",\n", + " \"nuclide_beta_heat\",\n", + " \"nuclide_gamma_heat\",\n", + " \"nuclide_dose\",\n", + " \"nuclide_ingestion\",\n", + " \"nuclide_inhalation\",\n", + " ]].to_dataframe().reset_index(drop=True)\n", + " sql = \"insert into timestep_nuclide select * from timesteps_nuclides_df\"\n", + " con.execute(sql)\n", + " con.commit()" + ] + }, + { + "cell_type": "code", + "execution_count": 187, + "id": "de4b9bd0-02e4-48f5-bec3-bb92c67682d0", + "metadata": { + "tags": [] + }, + "outputs": [ + { + "ename": "BinderException", + "evalue": "Binder Error: table timestep_nuclide has 17 columns but 18 values were supplied", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mBinderException\u001b[0m Traceback (most recent call last)", + "Cell \u001b[0;32mIn[187], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[43msave_timestep_nucludes\u001b[49m\u001b[43m(\u001b[49m\u001b[43mcon\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mds\u001b[49m\u001b[43m)\u001b[49m\n", + "Cell \u001b[0;32mIn[186], line 22\u001b[0m, in \u001b[0;36msave_timestep_nucludes\u001b[0;34m(con, ds)\u001b[0m\n\u001b[1;32m 2\u001b[0m timesteps_nuclides_df \u001b[38;5;241m=\u001b[39m ds[[\n\u001b[1;32m 3\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mtime_step_number\u001b[39m\u001b[38;5;124m\"\u001b[39m,\n\u001b[1;32m 4\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124melement\u001b[39m\u001b[38;5;124m\"\u001b[39m,\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 19\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mnuclide_inhalation\u001b[39m\u001b[38;5;124m\"\u001b[39m,\n\u001b[1;32m 20\u001b[0m ]]\u001b[38;5;241m.\u001b[39mto_dataframe()\u001b[38;5;241m.\u001b[39mreset_index(drop\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m)\n\u001b[1;32m 21\u001b[0m sql \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124minsert into timestep_nuclide select * from timesteps_nuclides_df\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[0;32m---> 22\u001b[0m \u001b[43mcon\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mexecute\u001b[49m\u001b[43m(\u001b[49m\u001b[43msql\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 23\u001b[0m con\u001b[38;5;241m.\u001b[39mcommit()\n", + "\u001b[0;31mBinderException\u001b[0m: Binder Error: table timestep_nuclide has 17 columns but 18 values were supplied" + ] + } + ], + "source": [ + "save_timestep_nucludes(con, ds)" + ] + }, + { + "cell_type": "code", + "execution_count": 41, + "id": "def18203-fed9-472d-a69c-b653dbf9a7b2", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "con.close()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "01b93a4e-7cd9-42cd-9c2f-1ddbe9d83810", + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.11.2" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/notebooks/dvp/try_ducdb.py b/notebooks/dvp/try_ducdb.py new file mode 100644 index 0000000..767a59e --- /dev/null +++ b/notebooks/dvp/try_ducdb.py @@ -0,0 +1,380 @@ +#!/usr/bin/env python +# coding: utf-8 + +# In[1]: + + +get_ipython().run_line_magic("config", "Completer.use_jedi = False") + + +# In[3]: + + +import xpypact as xp + +# In[5]: + + +xp.__version__ + + +# In[11]: + + +from pathlib import Path + +# In[19]: + + +root_dir = Path("~", "dev", "xpypact").expanduser() + + +# In[20]: + + +json_path = root_dir / "tests/data/Ag-1.json" +assert json_path.exists() + + +# In[23]: + + +import xpypact.data_arrays as da + +from xpypact.Inventory import Inventory, from_json + +# In[24]: + + +inventory = from_json(json_path) + + +# In[25]: + + +ds = da.create_dataset(inventory) + + +# In[26]: + + +ds + + +# In[ ]: + + +# In[28]: + + +import duckdb as db + +# In[46]: + + +db_path = root_dir / "wrk/try-duckdb.duckdb" +db_path.parent.mkdir(parents=True, exist_ok=True) + + +# In[48]: + + +con = db.connect(str(db_path)) + + +# In[153]: + + +# con.execute("drop table rundata") +# con.execute("drop table if exists timestep_gamma") +con.execute("drop table if exists timestep_nuclide") +# con.execute("drop table if exists timestep") +con.execute("drop table nuclide") + + +# In[154]: + + +def create_tables(con): + sql = """ + + CREATE TABLE IF NOT EXISTS rundata ( + timestamp varchar NOT NULL, + run_name varchar NOT NULL, + flux_name varchar NOT NULL, + dose_rate_type varchar NOT NULL, + dose_rate_distance real NOT NULL + ); + + CREATE TABLE IF NOT EXISTS timestep( + id integer PRIMARY KEY, + elapsed_time real not null, + irradiation_time real not null, + cooling_time real not null, + duration real not null, + flux real not null, + total_atoms real not null, + total_activity real not null, + total_alpha_activity real not null, + total_beta_activity real not null, + total_gamma_activity real not null, + total_mass real not null, + total_heat real not null, + total_alpha_heat real not null, + total_beta_heat real not null, + total_gamma_heat real not null, + total_ingest1ion_dose real not null, + total_inhalation_dose real not null, + total_dose_rate real not null + ); + + CREATE TABLE IF NOT EXISTS nuclide( + element varchar(2) not null, + mass_number integer not null check(0 < mass_number), -- A + state varchar(1) not null, + zai integer not null check(10010 <= zai) unique, + half_life real not null check(0 <= half_life), + primary key(element, mass_number, state) + ); + + CREATE TABLE IF NOT EXISTS timestep_nuclide( + timestep_id integer not null, + element varchar(2) not null, + mass_number integer not null, + state varchar(1) not null, + atoms real not null, + grams real not null, + activity real not null, + alpha_activity real not null, + beta_activity real not null, + gamma_activity real not null, + heat real not null, + alpha_heat real not null, + beta_heat real not null, + gamma_heat real not null, + dose real not null, + ingestion real not null, + inhalation real not null, + primary key(timestep_id, element, mass_number, state), + foreign key(timestep_id) references timestep(id), + foreign key(element, mass_number, state) references nuclide(element, mass_number, state) + ); + + CREATE TABLE IF NOT EXISTS timestep_gamma( + timestep_id integer not null, + boundary real not null check(0 <= boundary), + intensity real not null, + primary key(timestep_id, boundary), + foreign key(timestep_id) references timestep(id), + ); +""" + con.execute(sql) + + +# In[155]: + + +create_tables(con) + + +# In[85]: + + +# con.execute("delete from rundata") + + +# In[81]: + + +def save_rundata(con, ds): + sql = """ + INSERT INTO rundata values(?, ?, ?, ?, ?) + """ + con.execute( + sql, + ( + ds.coords["timestamp"].item(), + ds.attrs["run_name"], + ds.attrs["flux_name"], + ds.attrs["dose_rate_type"], + ds.attrs["dose_rate_distance"], + ), + ) + con.commit() + + +# In[83]: + + +save_rundata(con, ds) + + +# In[84]: + + +con.execute("select * from rundata").df() + + +# In[114]: + + +def save_timesteps(con, ds): + timesteps_df = ( + ds[ + [ + "time_step_number", + "elapsed_time", + "irradiation_time", + "cooling_time", + "duration", + "flux", + "total_atoms", + "total_activity", + "total_alpha_activity", + "total_beta_activity", + "total_gamma_activity", + "total_mass", + "total_heat", + "total_alpha_heat", + "total_beta_heat", + "total_gamma_heat", + "total_ingest1ion_dose", + "total_inhalation_dose", + "total_dose_rate", + ] + ] + .to_pandas() + .reset_index() + ) + sql = "insert into timestep select * from timesteps_df" + con.execute(sql) + con.commit() + + +# In[115]: + + +save_timesteps(con, ds) + + +# In[116]: + + +con.execute("select * from timestep").df() + + +# In[131]: + + +ds[ + ["element", "mass_number", "state", "zai", "nuclide_half_life"] +].to_pandas().reset_index(drop=True) + + +# In[156]: + + +def save_nuclides(con, ds): + nuclides_df = ( + ds[["element", "mass_number", "state", "zai", "nuclide_half_life"]] + .to_pandas() + .reset_index(drop=True) + ) + sql = "insert into nuclide select * from nuclides_df" + con.execute(sql) + con.commit() + + +# In[157]: + + +save_nuclides(con, ds) + + +# In[160]: + + +con.execute("select * from nuclide").df().head() + + +# In[166]: + + +ds + + +# In[203]: + + +ds[ + [ + """Time_step_number.""", + """Element.""", + """Mass_number.""", + """State.""", + """Nuclide_atoms.""", + """Nuclide_grams.""", + """Nuclide_activity.""", + """Nuclide_alpha_activity.""", + """Nuclide_beta_activity.""", + """Nuclide_gamma_activity.""", + """Nuclide_heat.""", + """Nuclide_alpha_heat.""", + """Nuclide_beta_heat.""", + """Nuclide_gamma_heat.""", + """Nuclide_dose.""", + """Nuclide_ingestion.""", + 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"cells": [ { "cell_type": "code", - "execution_count": 1, + "execution_count": 233, "id": "250d384f-b617-4bde-8d6e-5bfea316e21f", "metadata": { "tags": [] @@ -14,7 +14,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 234, "id": "49812848-cb6d-487a-bcdf-927e86781ae9", "metadata": { "tags": [] @@ -26,7 +26,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 235, "id": "5e40fc05-d196-4ab9-b4df-ec6166ee5611", "metadata": { "tags": [] @@ -38,7 +38,7 @@ "'0.1.12a0'" ] }, - "execution_count": 5, + "execution_count": 235, "metadata": {}, "output_type": "execute_result" } @@ -49,7 +49,7 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": 236, "id": "982fbe50-fd22-499a-98d9-910f6d0c72d7", "metadata": { "tags": [] @@ -61,7 +61,7 @@ }, { "cell_type": "code", - "execution_count": 19, + "execution_count": 237, "id": "bf81c238-8be8-4f93-b3e4-155bb46e21e8", "metadata": { "tags": [] @@ -73,20 +73,20 @@ }, { "cell_type": "code", - "execution_count": 20, + "execution_count": 238, "id": "c0811f45-0503-4302-9890-62803b49cabe", "metadata": { "tags": [] }, "outputs": [], "source": [ - "json_path = root_dir / \"tests/data/Ag-1.json\"\n", + "json_path = root_dir / \"wrk/Alloy718-Co04-104_2_1_1.json\"\n", "assert json_path.exists()" ] }, { "cell_type": "code", - "execution_count": 23, + "execution_count": 239, "id": "57fecf87-b03f-48e4-bfe4-beee3d661355", "metadata": { "tags": [] @@ -99,7 +99,7 @@ }, { "cell_type": "code", - "execution_count": 24, + "execution_count": 240, "id": "c13bb091-11ad-4e08-bbad-7cba93475e4b", "metadata": { "tags": [] @@ -111,7 +111,7 @@ }, { "cell_type": "code", - "execution_count": 25, + "execution_count": 241, "id": "e471ce43-3860-430d-b669-7a1211bb5d06", "metadata": { "tags": [] @@ -123,7 +123,7 @@ }, { "cell_type": "code", - "execution_count": 26, + "execution_count": 242, "id": "eaa7c75f-119c-493c-b038-dbd615b72c6f", "metadata": { "tags": [] @@ -496,389 +496,610 @@ " fill: currentColor;\n", "}\n", "
<xarray.Dataset>\n",
-       "Dimensions:                 (time_step_number: 2, nuclide: 48, timestamp: 1)\n",
+       "Dimensions:                 (time_step_number: 65, nuclide: 215,\n",
+       "                             gamma_boundaries: 25, timestamp: 1)\n",
        "Coordinates:\n",
-       "  * time_step_number        (time_step_number) int64 1 2\n",
+       "  * time_step_number        (time_step_number) int64 1 2 3 4 5 ... 62 63 64 65\n",
        "  * nuclide                 (nuclide) object MultiIndex\n",
-       "  * element                 (nuclide) object 'Ag' 'Ag' 'Ag' ... 'Ru' 'Ru' 'Ru'\n",
-       "  * mass_number             (nuclide) int64 105 105 106 106 ... 106 102 103 104\n",
-       "  * state                   (nuclide) object '' 'm' '' 'm' '' ... 'm' '' '' ''\n",
-       "    elapsed_time            (time_step_number) float64 0.0 6.312e+07\n",
-       "    zai                     (nuclide) int64 471050 471051 ... 441030 441040\n",
-       "  * timestamp               (timestamp) datetime64[ns] 2020-07-12T23:01:19\n",
-       "Data variables: (12/31)\n",
-       "    irradiation_time        (time_step_number) float64 0.0 6.312e+07\n",
-       "    cooling_time            (time_step_number) float64 0.0 0.0\n",
-       "    duration                (time_step_number) float64 0.0 6.312e+07\n",
-       "    flux                    (time_step_number) float64 0.0 2.445e+10\n",
-       "    total_atoms             (time_step_number) float64 5.578e+21 5.578e+21\n",
-       "    total_activity          (time_step_number) float64 0.0 6.123e+09\n",
+       "  * element                 (nuclide) object 'Al' 'Al' 'Al' ... 'Zr' 'Zr' 'Zr'\n",
+       "  * mass_number             (nuclide) int64 26 27 28 29 30 40 ... 93 94 95 96 97\n",
+       "  * state                   (nuclide) object '' '' '' '' '' ... '' '' '' '' ''\n",
+       "  * gamma_boundaries        (gamma_boundaries) float64 1e-11 0.01 ... 14.0 20.0\n",
+       "    elapsed_time            (time_step_number) float64 0.0 6.312e+07 ... 3.2e+10\n",
+       "    zai                     (nuclide) int64 130260 130270 ... 400960 400970\n",
+       "  * timestamp               (timestamp) datetime64[ns] 2022-02-21T01:52:47\n",
+       "Data variables: (12/32)\n",
+       "    irradiation_time        (time_step_number) float64 0.0 ... 4.207e+08\n",
+       "    cooling_time            (time_step_number) float64 0.0 0.0 ... 3.158e+10\n",
+       "    duration                (time_step_number) float64 0.0 ... 2.84e+10\n",
+       "    flux                    (time_step_number) float64 0.0 2.445e+10 ... 0.0 0.0\n",
+       "    total_atoms             (time_step_number) float64 1.045e+22 ... 1.045e+22\n",
+       "    total_activity          (time_step_number) float64 0.01099 ... 3.152e+04\n",
        "    ...                      ...\n",
-       "    nuclide_alpha_heat      (time_step_number, nuclide) float64 nan nan ... 0.0\n",
-       "    nuclide_beta_heat       (time_step_number, nuclide) float64 nan nan ... 0.0\n",
-       "    nuclide_gamma_heat      (time_step_number, nuclide) float64 nan nan ... 0.0\n",
-       "    nuclide_dose            (time_step_number, nuclide) float64 nan nan ... 0.0\n",
-       "    nuclide_ingestion       (time_step_number, nuclide) float64 nan nan ... 0.0\n",
-       "    nuclide_inhalation      (time_step_number, nuclide) float64 nan nan ... 0.0\n",
+       "    nuclide_beta_heat       (time_step_number, nuclide) float64 nan 0.0 ... nan\n",
+       "    nuclide_gamma_heat      (time_step_number, nuclide) float64 nan 0.0 ... nan\n",
+       "    nuclide_dose            (time_step_number, nuclide) float64 nan 0.0 ... nan\n",
+       "    nuclide_ingestion       (time_step_number, nuclide) float64 nan 0.0 ... nan\n",
+       "    nuclide_inhalation      (time_step_number, nuclide) float64 nan 0.0 ... nan\n",
+       "    gamma                   (time_step_number, gamma_boundaries) float64 0.0 ...\n",
        "Attributes:\n",
-       "    run_name:            * Material Ag, fluxes 1\n",
-       "    flux_name:           55.F9.10 11-L2-02W HFS_GLRY_08_U\n",
+       "    run_name:            * Material Alloy718-Co04, fluxes 104_2_1_1\n",
+       "    flux_name:           90-degrees bend\n",
        "    dose_rate_type:      Point source\n",
-       "    dose_rate_distance:  1.0
    • time_step_number
      PandasIndex
      PandasIndex(Int64Index([ 1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11, 12, 13, 14, 15, 16, 17,\n",
+       "            18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34,\n",
+       "            35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51,\n",
+       "            52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65],\n",
+       "           dtype='int64', name='time_step_number'))
    • nuclide
      element
      mass_number
      state
      PandasMultiIndex
      PandasIndex(MultiIndex([('Al', 26,  ''),\n",
+       "            ('Al', 27,  ''),\n",
+       "            ('Al', 28,  ''),\n",
+       "            ('Al', 29,  ''),\n",
+       "            ('Al', 30,  ''),\n",
+       "            ('Ar', 40,  ''),\n",
+       "            ( 'B', 10,  ''),\n",
+       "            ( 'B', 11,  ''),\n",
+       "            ('Be',  9,  ''),\n",
+       "            ('Be', 10,  ''),\n",
+       "            ...\n",
+       "            ('Zr', 89,  ''),\n",
+       "            ('Zr', 89, 'm'),\n",
+       "            ('Zr', 90,  ''),\n",
+       "            ('Zr', 91,  ''),\n",
+       "            ('Zr', 92,  ''),\n",
+       "            ('Zr', 93,  ''),\n",
+       "            ('Zr', 94,  ''),\n",
+       "            ('Zr', 95,  ''),\n",
+       "            ('Zr', 96,  ''),\n",
+       "            ('Zr', 97,  '')],\n",
+       "           name='nuclide', length=215))
    • gamma_boundaries
      PandasIndex
      PandasIndex(Float64Index([9.999999747378751e-12,                  0.01,\n",
+       "                               0.02,  0.049999999999999996,\n",
+       "                0.09999999999999999,   0.19999999999999998,\n",
+       "                                0.3,   0.39999999999999997,\n",
+       "                                0.6,    0.7999999999999999,\n",
+       "                                1.0,                  1.22,\n",
+       "                               1.44,                  1.66,\n",
+       "                                2.0,                   2.5,\n",
+       "                                3.0,                   4.0,\n",
+       "                                5.0,                   6.5,\n",
+       "                                8.0,                  10.0,\n",
+       "                               12.0,                  14.0,\n",
+       "                               20.0],\n",
+       "             dtype='float64', name='gamma_boundaries'))
    • timestamp
      PandasIndex
      PandasIndex(DatetimeIndex(['2022-02-21 01:52:47'], dtype='datetime64[ns]', name='timestamp', freq='D'))
  • run_name :
    * Material Alloy718-Co04, fluxes 104_2_1_1
    flux_name :
    90-degrees bend
    dose_rate_type :
    Point source
    dose_rate_distance :
    1.0
    • " ], "text/plain": [ "\n", - "Dimensions: (time_step_number: 2, nuclide: 48, timestamp: 1)\n", + "Dimensions: (time_step_number: 65, nuclide: 215,\n", + " gamma_boundaries: 25, timestamp: 1)\n", "Coordinates:\n", - " * time_step_number (time_step_number) int64 1 2\n", + " * time_step_number (time_step_number) int64 1 2 3 4 5 ... 62 63 64 65\n", " * nuclide (nuclide) object MultiIndex\n", - " * element (nuclide) object 'Ag' 'Ag' 'Ag' ... 'Ru' 'Ru' 'Ru'\n", - " * mass_number (nuclide) int64 105 105 106 106 ... 106 102 103 104\n", - " * state (nuclide) object '' 'm' '' 'm' '' ... 'm' '' '' ''\n", - " elapsed_time (time_step_number) float64 0.0 6.312e+07\n", - " zai (nuclide) int64 471050 471051 ... 441030 441040\n", - " * timestamp (timestamp) datetime64[ns] 2020-07-12T23:01:19\n", - "Data variables: (12/31)\n", - " irradiation_time (time_step_number) float64 0.0 6.312e+07\n", - " cooling_time (time_step_number) float64 0.0 0.0\n", - " duration (time_step_number) float64 0.0 6.312e+07\n", - " flux (time_step_number) float64 0.0 2.445e+10\n", - " total_atoms (time_step_number) float64 5.578e+21 5.578e+21\n", - " total_activity (time_step_number) float64 0.0 6.123e+09\n", + " * element (nuclide) object 'Al' 'Al' 'Al' ... 'Zr' 'Zr' 'Zr'\n", + " * mass_number (nuclide) int64 26 27 28 29 30 40 ... 93 94 95 96 97\n", + " * state (nuclide) object '' '' '' '' '' ... '' '' '' '' ''\n", + " * gamma_boundaries (gamma_boundaries) float64 1e-11 0.01 ... 14.0 20.0\n", + " elapsed_time (time_step_number) float64 0.0 6.312e+07 ... 3.2e+10\n", + " zai (nuclide) int64 130260 130270 ... 400960 400970\n", + " * timestamp (timestamp) datetime64[ns] 2022-02-21T01:52:47\n", + "Data variables: (12/32)\n", + " irradiation_time (time_step_number) float64 0.0 ... 4.207e+08\n", + " cooling_time (time_step_number) float64 0.0 0.0 ... 3.158e+10\n", + " duration (time_step_number) float64 0.0 ... 2.84e+10\n", + " flux (time_step_number) float64 0.0 2.445e+10 ... 0.0 0.0\n", + " total_atoms (time_step_number) float64 1.045e+22 ... 1.045e+22\n", + " total_activity (time_step_number) float64 0.01099 ... 3.152e+04\n", " ... ...\n", - " nuclide_alpha_heat (time_step_number, nuclide) float64 nan nan ... 0.0\n", - " nuclide_beta_heat (time_step_number, nuclide) float64 nan nan ... 0.0\n", - " nuclide_gamma_heat (time_step_number, nuclide) float64 nan nan ... 0.0\n", - " nuclide_dose (time_step_number, nuclide) float64 nan nan ... 0.0\n", - " nuclide_ingestion (time_step_number, nuclide) float64 nan nan ... 0.0\n", - " nuclide_inhalation (time_step_number, nuclide) float64 nan nan ... 0.0\n", + " nuclide_beta_heat (time_step_number, nuclide) float64 nan 0.0 ... nan\n", + " nuclide_gamma_heat (time_step_number, nuclide) float64 nan 0.0 ... nan\n", + " nuclide_dose (time_step_number, nuclide) float64 nan 0.0 ... nan\n", + " nuclide_ingestion (time_step_number, nuclide) float64 nan 0.0 ... nan\n", + " nuclide_inhalation (time_step_number, nuclide) float64 nan 0.0 ... nan\n", + " gamma (time_step_number, gamma_boundaries) float64 0.0 ...\n", "Attributes:\n", - " run_name: * Material Ag, fluxes 1\n", - " flux_name: 55.F9.10 11-L2-02W HFS_GLRY_08_U\n", + " run_name: * Material Alloy718-Co04, fluxes 104_2_1_1\n", + " flux_name: 90-degrees bend\n", " dose_rate_type: Point source\n", " dose_rate_distance: 1.0" ] }, - "execution_count": 26, + "execution_count": 242, "metadata": {}, "output_type": "execute_result" } @@ -889,226 +1110,8 @@ }, { "cell_type": "code", - "execution_count": null, - "id": "3d2db9b3-09d8-4bf7-bc4b-8ec13cc8105b", - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [] - }, - { - "cell_type": "code", - "execution_count": 28, - "id": "79beed07-0f86-485b-be23-97d7e8f33abb", - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "import duckdb as db" - ] - }, - { - "cell_type": "code", - "execution_count": 46, - "id": "ee7bf9aa-13a8-419d-b39e-c90493094148", - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "db_path = root_dir / \"wrk/try-duckdb.duckdb\"\n", - "db_path.parent.mkdir(parents=True, exist_ok=True)" - ] - }, - { - "cell_type": "code", - "execution_count": 48, - "id": "99a86bdc-84e1-4cd3-b7b7-4e63b6428086", - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "con = db.connect(str(db_path))" - ] - }, - { - "cell_type": "code", - "execution_count": 153, - "id": "d9e1ddfb-398e-4cea-b01d-fb0e53242776", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "data": { - "text/plain": [ - "" - ] - }, - "execution_count": 153, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "# con.execute(\"drop table rundata\")\n", - "# con.execute(\"drop table if exists timestep_gamma\")\n", - "con.execute(\"drop table if exists timestep_nuclide\")\n", - "# con.execute(\"drop table if exists timestep\")\n", - "con.execute(\"drop table nuclide\")\n" - ] - }, - { - "cell_type": "code", - "execution_count": 154, - "id": "c402d3a1-e77a-4b24-accc-a19588ccdf54", - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "def create_tables(con):\n", - " sql = \"\"\"\n", - " \n", - " CREATE TABLE IF NOT EXISTS rundata (\n", - " timestamp varchar NOT NULL,\n", - " run_name varchar NOT NULL,\n", - " flux_name varchar NOT NULL,\n", - " dose_rate_type varchar NOT NULL,\n", - " dose_rate_distance real NOT NULL\n", - " );\n", - "\n", - " CREATE TABLE IF NOT EXISTS timestep(\n", - " id integer PRIMARY KEY,\n", - " elapsed_time real not null,\n", - " irradiation_time real not null,\n", - " cooling_time real not null,\n", - " duration real not null,\n", - " flux real not null,\n", - " total_atoms real not null,\n", - " total_activity real not null,\n", - " total_alpha_activity real not null,\n", - " total_beta_activity real not null,\n", - " total_gamma_activity real not null,\n", - " total_mass real not null,\n", - " total_heat real not null,\n", - " total_alpha_heat real not null,\n", - " total_beta_heat real not null,\n", - " total_gamma_heat real not null,\n", - " total_ingest1ion_dose real not null,\n", - " total_inhalation_dose real not null,\n", - " total_dose_rate real not null\n", - " );\n", - " \n", - " CREATE TABLE IF NOT EXISTS nuclide(\n", - " element varchar(2) not null,\n", - " mass_number integer not null check(0 < mass_number), -- A\n", - " state varchar(1) not null,\n", - " zai integer not null check(10010 <= zai) unique,\n", - " half_life real not null check(0 <= half_life),\n", - " primary key(element, mass_number, state)\n", - " );\n", - " \n", - " CREATE TABLE IF NOT EXISTS timestep_nuclide(\n", - " timestep_id integer not null,\n", - " element varchar(2) not null,\n", - " mass_number integer not null,\n", - " state varchar(1) not null,\n", - " atoms real not null,\n", - " grams real not null,\n", - " activity real not null,\n", - " alpha_activity real not null,\n", - " beta_activity real not null,\n", - " gamma_activity real not null,\n", - " heat real not null,\n", - " alpha_heat real not null,\n", - " beta_heat real not null,\n", - " gamma_heat real not null,\n", - " dose real not null,\n", - " ingestion real not null,\n", - " inhalation real not null,\n", - " primary key(timestep_id, element, mass_number, state),\n", - " foreign key(timestep_id) references timestep(id),\n", - " foreign key(element, mass_number, state) references nuclide(element, mass_number, state) \n", - " );\n", - "\n", - " CREATE TABLE IF NOT EXISTS timestep_gamma(\n", - " timestep_id integer not null,\n", - " boundary real not null check(0 <= boundary),\n", - " intensity real not null, \n", - " primary key(timestep_id, boundary),\n", - " foreign key(timestep_id) references timestep(id),\n", - " );\n", - "\"\"\"\n", - " con.execute(sql)" - ] - }, - { - "cell_type": "code", - "execution_count": 155, - "id": "25f6867e-397a-4e98-a363-74b6af739c88", - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "create_tables(con)" - ] - }, - { - "cell_type": "code", - "execution_count": 85, - "id": "db019e1c-bebd-4993-a1b5-274cf00a2ceb", - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "# con.execute(\"delete from rundata\")" - ] - }, - { - "cell_type": "code", - "execution_count": 81, - "id": "29716201-70f8-40d2-8da7-85689714ec32", - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "def save_rundata(con, ds):\n", - " sql = \"\"\"\n", - " INSERT INTO rundata values(?, ?, ?, ?, ?)\n", - " \"\"\"\n", - " con.execute(sql, ( \n", - " ds.coords[\"timestamp\"].item(),\n", - " ds.attrs[\"run_name\"],\n", - " ds.attrs[\"flux_name\"],\n", - " ds.attrs[\"dose_rate_type\"],\n", - " ds.attrs[\"dose_rate_distance\"]\n", - " ))\n", - " con.commit()" - ] - }, - { - "cell_type": "code", - "execution_count": 83, - "id": "c789eedd-580c-4383-8bf1-cc943562a3aa", - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "save_rundata(con, ds)" - ] - }, - { - "cell_type": "code", - "execution_count": 84, - "id": "1c650134-edf3-44dd-aa90-ddde6a3987a7", + "execution_count": 287, + "id": "6f923a0d-5ef8-4dea-8157-98f6049ddb26", "metadata": { "tags": [] }, @@ -1116,952 +1119,93 @@ { "data": { "text/html": [ - "
    \n", - "\n", - "\n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - "
    timestamprun_nameflux_namedose_rate_typedose_rate_distance
    01594594879000000000* Material Ag, fluxes 155.F9.10 11-L2-02W HFS_GLRY_08_UPoint source1.0
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    " - ], - "text/plain": [ - " id elapsed_time irradiation_time cooling_time duration flux \\\n", - "0 1 0.0 0.0 0.0 0.0 0.000000e+00 \n", - "1 2 63115200.0 63115200.0 0.0 63115200.0 2.445200e+10 \n", + ".xr-header {\n", + " padding-top: 6px;\n", + " padding-bottom: 6px;\n", + " margin-bottom: 4px;\n", + " border-bottom: solid 1px var(--xr-border-color);\n", + "}\n", "\n", - " total_atoms total_activity total_alpha_activity total_beta_activity \\\n", - "0 5.577957e+21 0.000000e+00 0.0 0.0 \n", - "1 5.577957e+21 6.123276e+09 0.0 0.0 \n", + ".xr-header > div,\n", + ".xr-header > ul {\n", + " display: inline;\n", + " margin-top: 0;\n", + " margin-bottom: 0;\n", + "}\n", "\n", - " total_gamma_activity total_mass total_heat total_alpha_heat \\\n", - "0 0.0 0.000999 0.000000 0.0 \n", - "1 0.0 0.000999 0.000001 0.0 \n", + ".xr-obj-type,\n", + ".xr-array-name {\n", + " margin-left: 2px;\n", + " margin-right: 10px;\n", + "}\n", "\n", - " total_beta_heat total_gamma_heat total_ingest1ion_dose \\\n", - "0 0.000000e+00 0.000000e+00 0.000000 \n", - "1 9.894924e-07 1.135242e-07 0.544602 \n", + ".xr-obj-type {\n", + " color: var(--xr-font-color2);\n", + "}\n", "\n", - " total_inhalation_dose total_dose_rate \n", - "0 0.000000 0.000000 \n", - "1 2.323375 0.000092 " - ] - }, - "execution_count": 116, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "con.execute(\"select * from timestep\").df()" - ] - }, - { - "cell_type": "code", - "execution_count": 131, - "id": "44222193-149a-4661-8eef-00b46d5c6a90", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "data": { - "text/html": [ - "
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    elementmass_numberstatezainuclide_half_life
    0Ag1054710503.568320e+06
    1Ag105m4710514.338000e+02
    2Ag1064710601.440000e+03
    3Ag106m4710617.309440e+05
    4Ag1074710700.000000e+00
    5Ag107m4710714.430000e+01
    6Ag1084710801.440000e+02
    7Ag108m4710811.319110e+10
    8Ag1094710900.000000e+00
    9Ag109m4710913.970000e+01
    10Ag1104711002.456000e+01
    11Ag110m4711012.158100e+07
    12Ag1114711106.436800e+05
    13Ag111m4711116.480000e+01
    14Cd1064810602.082800e+26
    15Cd1074810702.347200e+04
    16Cd1084810801.293860e+25
    17Cd1094810903.996860e+07
    18Cd1104811000.000000e+00
    19Cd1114811100.000000e+00
    20Cd111m4811112.924400e+03
    21Cd1124811200.000000e+00
    22H1100100.000000e+00
    23H2100200.000000e+00
    24H3100303.891050e+08
    25He3200300.000000e+00
    26He4200400.000000e+00
    27Pd1044610400.000000e+00
    28Pd1054610500.000000e+00
    29Pd1064610600.000000e+00
    30Pd1074610702.051200e+14
    31Pd107m4610712.130000e+01
    32Pd1084610800.000000e+00
    33Pd1094610904.932430e+04
    34Pd109m4610912.814000e+02
    35Pd1104611001.893460e+25
    36Rh1024510209.158400e+07
    37Rh102m4510211.797120e+07
    38Rh1034510300.000000e+00
    39Rh103m4510313.366840e+03
    40Rh1044510404.230000e+01
    41Rh104m4510412.604000e+02
    42Rh1054510501.272960e+05
    43Rh1064510603.000000e+01
    44Rh106m4510617.920000e+03
    45Ru1024410200.000000e+00
    46Ru1034410303.392060e+06
    47Ru1044410400.000000e+00
    \n", - "
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    elementmass_numberstatezaihalf_life
    0Ag1054710503.568320e+06
    1Ag105m4710514.338000e+02
    2Ag1064710601.440000e+03
    3Ag106m4710617.309440e+05
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    " - ], - "text/plain": [ - " element mass_number state zai half_life\n", - "0 Ag 105 471050 3.568320e+06\n", - "1 Ag 105 m 471051 4.338000e+02\n", - "2 Ag 106 471060 1.440000e+03\n", - "3 Ag 106 m 471061 7.309440e+05\n", - "4 Ag 107 471070 0.000000e+00" - ] - }, - "execution_count": 160, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "con.execute(\"select * from nuclide\").df().head()" - ] - }, - { - "cell_type": "code", - "execution_count": 166, - "id": "01216ae8-6108-4909-a332-44afbe8fb2c3", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "data": { - "text/html": [ - "
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    <xarray.DataArray 'timestamp' (timestamp: 1)>\n",
+       "array(['2022-02-21T01:52:47.000000000'], dtype='datetime64[ns]')\n",
+       "Coordinates:\n",
+       "  * timestamp  (timestamp) datetime64[ns] 2022-02-21T01:52:47\n",
+       "Attributes:\n",
+       "    long description:  FISPACT datasets can be merged and then selected by ti...
    " + ], + "text/plain": [ + "\n", + "array(['2022-02-21T01:52:47.000000000'], dtype='datetime64[ns]')\n", + "Coordinates:\n", + " * timestamp (timestamp) datetime64[ns] 2022-02-21T01:52:47\n", + "Attributes:\n", + " long description: FISPACT datasets can be merged and then selected by ti..." + ] + }, + "execution_count": 287, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ds.timestamp" + ] + }, + { + "cell_type": "code", + "execution_count": 243, + "id": "79beed07-0f86-485b-be23-97d7e8f33abb", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "import duckdb as db" + ] + }, + { + "cell_type": "code", + "execution_count": 384, + "id": "ee7bf9aa-13a8-419d-b39e-c90493094148", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "db_path = root_dir / \"wrk/try-duckdb.duckdb\"\n", + "db_path.parent.mkdir(parents=True, exist_ok=True)\n", + "if db_path.exists():\n", + " db_path.unlink()" + ] + }, + { + "cell_type": "code", + "execution_count": 385, + "id": "99a86bdc-84e1-4cd3-b7b7-4e63b6428086", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "con = db.connect(str(db_path))" + ] + }, + { + "cell_type": "code", + "execution_count": 386, + "id": "c74de5dc-5b72-4e1a-a105-3c629995a5af", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "material_id = 100\n", + "case_id = 3" + ] + }, + { + "cell_type": "code", + "execution_count": 387, + "id": "d9e1ddfb-398e-4cea-b01d-fb0e53242776", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "def drop_tables(con):\n", + " con.execute(\"drop table if exists timestep_gamma\")\n", + " con.execute(\"drop table if exists timestep_nuclide\")\n", + " con.execute(\"drop table if exists timestep\")\n", + " con.execute(\"drop table if exists nuclide\")\n", + " con.execute(\"drop table if exists rundata\")" + ] + }, + { + "cell_type": "code", + "execution_count": 395, + "id": "c402d3a1-e77a-4b24-accc-a19588ccdf54", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "def create_tables(con):\n", + " sql = \"\"\" \n", + " CREATE TABLE IF NOT EXISTS rundata (\n", + " material_id uinteger not null,\n", + " case_id uinteger not null,\n", + " timestamp timestamp not null,\n", + " run_name varchar not null,\n", + " flux_name varchar NOT NULL,\n", + " dose_rate_type varchar NOT NULL,\n", + " dose_rate_distance real NOT NULL,\n", + " primary key(material_id, case_id)\n", + " );\n", + "\n", + " CREATE TABLE IF NOT EXISTS timestep(\n", + " id uinteger PRIMARY KEY,\n", + " elapsed_time float4 not null,\n", + " irradiation_time float4 not null,\n", + " cooling_time float4 not null,\n", + " duration float4 not null,\n", + " flux float4 not null,\n", + " total_atoms float4 not null,\n", + " total_activity float4 not null,\n", + " total_alpha_activity float4 not null,\n", + " total_beta_activity float4 not null,\n", + " total_gamma_activity float4 not null,\n", + " total_mass float4 not null,\n", + " total_heat float4 not null,\n", + " total_alpha_heat float4 null,\n", + " total_beta_heat float4 not null,\n", + " total_gamma_heat float4 not null,\n", + " total_ingest1ion_dose float4 not null,\n", + " total_inhalation_dose float4 not null,\n", + " total_dose_rate float4 not null,\n", + " material_id uinteger not null,\n", + " case_id uinteger not null,\n", + " foreign key(material_id, case_id) references rundata(material_id, case_id) \n", + " );\n", + "\n", + " \n", + " CREATE TABLE IF NOT EXISTS nuclide(\n", + " element varchar(2) not null,\n", + " mass_number usmallint not null check(0 < mass_number),\n", + " state varchar(1) not null,\n", + " zai integer not null check(10010 <= zai) unique,\n", + " half_life float4 not null check(0 <= half_life),\n", + " primary key(element, mass_number, state)\n", + " );\n", + " \n", + " CREATE TABLE IF NOT EXISTS timestep_nuclide(\n", + " timestep_id uinteger not null,\n", + " element varchar(2) not null,\n", + " mass_number usmallint not null,\n", + " state varchar(1) not null,\n", + " atoms float4 not null,\n", + " grams float4 not null,\n", + " activity float4 not null,\n", + " alpha_activity float4 not null,\n", + " beta_activity float4 not null,\n", + " gamma_activity float4 not null,\n", + " heat float4 not null,\n", + " alpha_heat float4 not null,\n", + " beta_heat float4 not null,\n", + " gamma_heat float4 not null,\n", + " dose float4 not null,\n", + " ingestion float4 not null,\n", + " inhalation float4 not null,\n", + " primary key(timestep_id, element, mass_number, state),\n", + " foreign key(timestep_id) references timestep(id),\n", + " foreign key(element, mass_number, state) references nuclide(element, mass_number, state) \n", + " );\n", + "\n", + " CREATE TABLE IF NOT EXISTS timestep_gamma(\n", + " timestep_id uinteger not null,\n", + " boundary real not null check(0 <= boundary),\n", + " intensity real not null, \n", + " primary key(timestep_id, boundary),\n", + " foreign key(timestep_id) references timestep(id),\n", + " );\n", + " \"\"\"\n", + " con.execute(sql)" + ] + }, + { + "cell_type": "code", + "execution_count": 396, + "id": "25f6867e-397a-4e98-a363-74b6af739c88", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "# drop_tables(con)\n", + "create_tables(con)" + ] + }, + { + "cell_type": "code", + "execution_count": 402, + "id": "29716201-70f8-40d2-8da7-85689714ec32", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "def save_rundata(con, ds):\n", + " sql = \"\"\"\n", + " INSERT INTO rundata values(?, ?, ?, ?, ?)\n", + " \"\"\"\n", + " con.execute(sql, ( \n", + " material_id,\n", + " case_id,\n", + " ds.coords[\"timestamp\"].item(),\n", + " ds.attrs[\"run_name\"],\n", + " ds.attrs[\"flux_name\"],\n", + " ds.attrs[\"dose_rate_type\"],\n", + " ds.attrs[\"dose_rate_distance\"]\n", + " ))\n", + " con.commit()" + ] + }, + { + "cell_type": "code", + "execution_count": 403, + "id": "4d71d862-2960-455d-be85-c5d9394a160d", + "metadata": { + "tags": [] + }, + 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    table_catalogtable_schematable_nametable_typeself_referencing_column_namereference_generationuser_defined_type_cataloguser_defined_type_schemauser_defined_type_nameis_insertable_intois_typedcommit_action
    0try-duckdbmainrundataBASE TABLENaNNaNNaNNaNNaNYESNONaN
    1try-duckdbmaintimestepBASE TABLENaNNaNNaNNaNNaNYESNONaN
    2try-duckdbmainnuclideBASE TABLENaNNaNNaNNaNNaNYESNONaN
    3try-duckdbmaintimestep_nuclideBASE TABLENaNNaNNaNNaNNaNYESNONaN
    4try-duckdbmaintimestep_gammaBASE TABLENaNNaNNaNNaNNaNYESNONaN
    \n", + "
    " + ], + "text/plain": [ + " table_catalog table_schema table_name table_type \\\n", + "0 try-duckdb main rundata BASE TABLE \n", + "1 try-duckdb main timestep BASE TABLE \n", + "2 try-duckdb main nuclide BASE TABLE \n", + "3 try-duckdb main timestep_nuclide BASE TABLE \n", + "4 try-duckdb main timestep_gamma BASE TABLE \n", + "\n", + " self_referencing_column_name reference_generation \\\n", + "0 NaN NaN \n", + "1 NaN NaN \n", + "2 NaN NaN \n", + "3 NaN NaN \n", + "4 NaN NaN \n", + "\n", + " user_defined_type_catalog user_defined_type_schema \\\n", + "0 NaN NaN \n", + "1 NaN NaN \n", + "2 NaN NaN \n", + "3 NaN NaN \n", + "4 NaN NaN \n", + "\n", + " user_defined_type_name is_insertable_into is_typed commit_action \n", + "0 NaN YES NO NaN \n", + "1 NaN YES NO NaN \n", + "2 NaN YES NO NaN \n", + "3 NaN YES NO NaN \n", + "4 NaN YES NO NaN " + ] + }, + "execution_count": 403, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "con.execute(\"select * from information_schema.tables\").df()" + ] + }, + { + "cell_type": "code", + "execution_count": 400, + "id": "c789eedd-580c-4383-8bf1-cc943562a3aa", + "metadata": { + "tags": [] + }, + "outputs": [ + { + "ename": "BinderException", + "evalue": "Binder Error: table rundata has 7 columns but 5 values were supplied", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mBinderException\u001b[0m Traceback (most recent call last)", + "Cell \u001b[0;32mIn[400], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[43msave_rundata\u001b[49m\u001b[43m(\u001b[49m\u001b[43mcon\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mds\u001b[49m\u001b[43m)\u001b[49m\n", + "Cell \u001b[0;32mIn[397], line 5\u001b[0m, in \u001b[0;36msave_rundata\u001b[0;34m(con, ds)\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21msave_rundata\u001b[39m(con, ds):\n\u001b[1;32m 2\u001b[0m sql \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m\"\"\"\u001b[39m\n\u001b[1;32m 3\u001b[0m \u001b[38;5;124m INSERT INTO rundata values(?, ?, ?, ?, ?)\u001b[39m\n\u001b[1;32m 4\u001b[0m \u001b[38;5;124m \u001b[39m\u001b[38;5;124m\"\"\"\u001b[39m\n\u001b[0;32m----> 5\u001b[0m \u001b[43mcon\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mexecute\u001b[49m\u001b[43m(\u001b[49m\u001b[43msql\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43m(\u001b[49m\u001b[43m \u001b[49m\n\u001b[1;32m 6\u001b[0m \u001b[43m \u001b[49m\u001b[43mds\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcoords\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mtimestamp\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m]\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mitem\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 7\u001b[0m \u001b[43m \u001b[49m\u001b[43mds\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mattrs\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mrun_name\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 8\u001b[0m \u001b[43m \u001b[49m\u001b[43mds\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mattrs\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mflux_name\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 9\u001b[0m \u001b[43m \u001b[49m\u001b[43mds\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mattrs\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mdose_rate_type\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 10\u001b[0m \u001b[43m \u001b[49m\u001b[43mds\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mattrs\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mdose_rate_distance\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m]\u001b[49m\n\u001b[1;32m 11\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 12\u001b[0m con\u001b[38;5;241m.\u001b[39mcommit()\n", + "\u001b[0;31mBinderException\u001b[0m: Binder Error: table rundata has 7 columns but 5 values were supplied" + ] + } + ], + "source": [ + "save_rundata(con, ds)" + ] + }, + { + "cell_type": "code", + "execution_count": 254, + "id": "1c650134-edf3-44dd-aa90-ddde6a3987a7", + "metadata": { + "tags": [] + }, + "outputs": [ + { + "data": { + "text/html": [ + "
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    timestamprun_nameflux_namedose_rate_typedose_rate_distance
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    elementmass_numberstatezaihalf_life
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    3Al291302903.936000e+02
    4Al301303003.650000e+00
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    211Zr944009401.893460e+23
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    " + ], + "text/plain": [ + " element mass_number state zai half_life\n", + "0 Al 26 130260 2.262630e+13\n", + "1 Al 27 130270 0.000000e+00\n", + "2 Al 28 130280 1.344600e+02\n", + "3 Al 29 130290 3.936000e+02\n", + "4 Al 30 130300 3.650000e+00\n", + ".. ... ... ... ... ...\n", + "210 Zr 93 400930 4.828210e+13\n", + "211 Zr 94 400940 1.893460e+23\n", + "212 Zr 95 400950 5.532360e+06\n", + "213 Zr 96 400960 1.230750e+27\n", + "214 Zr 97 400970 6.027840e+04\n", + "\n", + "[215 rows x 5 columns]" + ] + }, + "execution_count": 285, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "con.execute(\"select * from nuclide\").df()" + ] + }, + { + "cell_type": "code", + "execution_count": 263, + "id": "526610bb-be7b-4ce7-8cc9-0bcdb00588f2", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "def save_timestep_nucludes(con, ds):\n", + " columns = [\n", + " \"time_step_number\",\n", + " \"element\",\n", + " \"mass_number\",\n", + " \"state\",\n", + " \"nuclide_atoms\",\n", + " \"nuclide_grams\",\n", + " \"nuclide_activity\",\n", + " \"nuclide_alpha_activity\",\n", + " \"nuclide_beta_activity\",\n", + " \"nuclide_gamma_activity\",\n", + " \"nuclide_heat\",\n", + " \"nuclide_alpha_heat\",\n", + " \"nuclide_beta_heat\",\n", + " \"nuclide_gamma_heat\",\n", + " \"nuclide_dose\",\n", + " \"nuclide_ingestion\",\n", + " \"nuclide_inhalation\",\n", + " ]\n", + " tn = ds[columns].to_dataframe().reset_index(\"time_step_number\")[columns].fillna(0.0)\n", + " sql = \"insert into timestep_nuclide select * from tn\"\n", + " con.execute(sql)\n", + " con.commit()" + ] + }, + { + "cell_type": "code", + "execution_count": 264, + "id": "de4b9bd0-02e4-48f5-bec3-bb92c67682d0", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "save_timestep_nucludes(con, ds)" + ] + }, + { + "cell_type": "code", + "execution_count": 265, + "id": "13094d05-fcad-40c3-b53d-34dfb8f84a4e", + "metadata": { + "tags": [] + }, + "outputs": [ + { + "data": { + "text/html": [ + "
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    timestep_idelementmass_numberstateatomsgramsactivityalpha_activitybeta_activitygamma_activityheatalpha_heatbeta_heatgamma_heatdoseingestioninhalation
    01Al260.000000e+000.000000e+000.000000e+000.00.000000e+000.00.000000e+000.00.000000e+000.00.00.000000e+000.000000e+00
    11Al271.785556e+208.000000e-030.000000e+000.00.000000e+000.00.000000e+000.00.000000e+000.00.00.000000e+000.000000e+00
    21Al280.000000e+000.000000e+000.000000e+000.00.000000e+000.00.000000e+000.00.000000e+000.00.00.000000e+000.000000e+00
    31Al290.000000e+000.000000e+000.000000e+000.00.000000e+000.00.000000e+000.00.000000e+000.00.00.000000e+000.000000e+00
    41Al300.000000e+000.000000e+000.000000e+000.00.000000e+000.00.000000e+000.00.000000e+000.00.00.000000e+000.000000e+00
    ......................................................
    1397065Zr936.327286e+139.761411e-099.083574e-010.09.083574e-010.02.791257e-180.02.791257e-180.00.09.991931e-102.270894e-08
    1397165Zr947.058445e+111.100659e-102.583916e-120.02.583916e-120.04.734377e-280.04.734377e-280.00.02.480559e-202.842307e-20
    1397265Zr950.000000e+000.000000e+000.000000e+000.00.000000e+000.00.000000e+000.00.000000e+000.00.00.000000e+000.000000e+00
    1397365Zr961.091942e+101.739020e-126.149716e-180.06.149716e-180.03.301027e-330.03.301027e-330.00.01.721921e-251.906412e-25
    1397465Zr970.000000e+000.000000e+000.000000e+000.00.000000e+000.00.000000e+000.00.000000e+000.00.00.000000e+000.000000e+00
    \n", + "

    13975 rows × 17 columns

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    " + ], + "text/plain": [ + " timestep_id element mass_number state atoms grams \\\n", + "0 1 Al 26 0.000000e+00 0.000000e+00 \n", + "1 1 Al 27 1.785556e+20 8.000000e-03 \n", + "2 1 Al 28 0.000000e+00 0.000000e+00 \n", + "3 1 Al 29 0.000000e+00 0.000000e+00 \n", + "4 1 Al 30 0.000000e+00 0.000000e+00 \n", + "... ... ... ... ... ... ... \n", + "13970 65 Zr 93 6.327286e+13 9.761411e-09 \n", + "13971 65 Zr 94 7.058445e+11 1.100659e-10 \n", + "13972 65 Zr 95 0.000000e+00 0.000000e+00 \n", + "13973 65 Zr 96 1.091942e+10 1.739020e-12 \n", + "13974 65 Zr 97 0.000000e+00 0.000000e+00 \n", + "\n", + " activity alpha_activity beta_activity gamma_activity \\\n", + "0 0.000000e+00 0.0 0.000000e+00 0.0 \n", + "1 0.000000e+00 0.0 0.000000e+00 0.0 \n", + "2 0.000000e+00 0.0 0.000000e+00 0.0 \n", + "3 0.000000e+00 0.0 0.000000e+00 0.0 \n", + "4 0.000000e+00 0.0 0.000000e+00 0.0 \n", + "... ... ... ... ... \n", + "13970 9.083574e-01 0.0 9.083574e-01 0.0 \n", + "13971 2.583916e-12 0.0 2.583916e-12 0.0 \n", + "13972 0.000000e+00 0.0 0.000000e+00 0.0 \n", + "13973 6.149716e-18 0.0 6.149716e-18 0.0 \n", + "13974 0.000000e+00 0.0 0.000000e+00 0.0 \n", + "\n", + " heat alpha_heat beta_heat gamma_heat dose ingestion \\\n", + "0 0.000000e+00 0.0 0.000000e+00 0.0 0.0 0.000000e+00 \n", + "1 0.000000e+00 0.0 0.000000e+00 0.0 0.0 0.000000e+00 \n", + "2 0.000000e+00 0.0 0.000000e+00 0.0 0.0 0.000000e+00 \n", + "3 0.000000e+00 0.0 0.000000e+00 0.0 0.0 0.000000e+00 \n", + "4 0.000000e+00 0.0 0.000000e+00 0.0 0.0 0.000000e+00 \n", + "... ... ... ... ... ... ... \n", + "13970 2.791257e-18 0.0 2.791257e-18 0.0 0.0 9.991931e-10 \n", + "13971 4.734377e-28 0.0 4.734377e-28 0.0 0.0 2.480559e-20 \n", + "13972 0.000000e+00 0.0 0.000000e+00 0.0 0.0 0.000000e+00 \n", + "13973 3.301027e-33 0.0 3.301027e-33 0.0 0.0 1.721921e-25 \n", + "13974 0.000000e+00 0.0 0.000000e+00 0.0 0.0 0.000000e+00 \n", + "\n", + " inhalation \n", + "0 0.000000e+00 \n", + "1 0.000000e+00 \n", + "2 0.000000e+00 \n", + "3 0.000000e+00 \n", + "4 0.000000e+00 \n", + "... ... \n", + "13970 2.270894e-08 \n", + "13971 2.842307e-20 \n", + "13972 0.000000e+00 \n", + "13973 1.906412e-25 \n", + "13974 0.000000e+00 \n", + "\n", + "[13975 rows x 17 columns]" + ] + }, + "execution_count": 265, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "con.execute(\"select * from timestep_nuclide\").df()" + ] + }, + { + "cell_type": "code", + "execution_count": 276, + "id": "a5ea7054-9a19-43e0-ab96-c4472f2422ad", + "metadata": { + "tags": [] + }, + "outputs": [ + { + "data": { + "text/html": [ + "
    \n", + "
    <xarray.Dataset>\n",
-       "Dimensions:                 (time_step_number: 2, nuclide: 48, timestamp: 1)\n",
-       "Coordinates:\n",
-       "  * time_step_number        (time_step_number) int64 1 2\n",
-       "  * nuclide                 (nuclide) object MultiIndex\n",
-       "  * element                 (nuclide) object 'Ag' 'Ag' 'Ag' ... 'Ru' 'Ru' 'Ru'\n",
-       "  * mass_number             (nuclide) int64 105 105 106 106 ... 106 102 103 104\n",
-       "  * state                   (nuclide) object '' 'm' '' 'm' '' ... 'm' '' '' ''\n",
-       "    elapsed_time            (time_step_number) float64 0.0 6.312e+07\n",
-       "    zai                     (nuclide) int64 471050 471051 ... 441030 441040\n",
-       "  * timestamp               (timestamp) datetime64[ns] 2020-07-12T23:01:19\n",
-       "Data variables: (12/31)\n",
-       "    irradiation_time        (time_step_number) float64 0.0 6.312e+07\n",
-       "    cooling_time            (time_step_number) float64 0.0 0.0\n",
-       "    duration                (time_step_number) float64 0.0 6.312e+07\n",
-       "    flux                    (time_step_number) float64 0.0 2.445e+10\n",
-       "    total_atoms             (time_step_number) float64 5.578e+21 5.578e+21\n",
-       "    total_activity          (time_step_number) float64 0.0 6.123e+09\n",
-       "    ...                      ...\n",
-       "    nuclide_alpha_heat      (time_step_number, nuclide) float64 nan nan ... 0.0\n",
-       "    nuclide_beta_heat       (time_step_number, nuclide) float64 nan nan ... 0.0\n",
-       "    nuclide_gamma_heat      (time_step_number, nuclide) float64 nan nan ... 0.0\n",
-       "    nuclide_dose            (time_step_number, nuclide) float64 nan nan ... 0.0\n",
-       "    nuclide_ingestion       (time_step_number, nuclide) float64 nan nan ... 0.0\n",
-       "    nuclide_inhalation      (time_step_number, nuclide) float64 nan nan ... 0.0\n",
-       "Attributes:\n",
-       "    run_name:            * Material Ag, fluxes 1\n",
-       "    flux_name:           55.F9.10 11-L2-02W HFS_GLRY_08_U\n",
-       "    dose_rate_type:      Point source\n",
-       "    dose_rate_distance:  1.0
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    time_step_numbergamma_boundariesgamma
    011.000000e-110.000000e+00
    111.000000e-023.156906e-11
    212.000000e-020.000000e+00
    315.000000e-020.000000e+00
    411.000000e-015.480877e-10
    ............
    1620658.000000e+000.000000e+00
    1621651.000000e+010.000000e+00
    1622651.200000e+010.000000e+00
    1623651.400000e+010.000000e+00
    1624652.000000e+010.000000e+00
    \n", + "

    1625 rows × 3 columns

    \n", + "" ], "text/plain": [ - "\n", - "Dimensions: (time_step_number: 2, nuclide: 48, timestamp: 1)\n", - "Coordinates:\n", - " * time_step_number (time_step_number) int64 1 2\n", - " * nuclide (nuclide) object MultiIndex\n", - " * element (nuclide) object 'Ag' 'Ag' 'Ag' ... 'Ru' 'Ru' 'Ru'\n", - " * mass_number (nuclide) int64 105 105 106 106 ... 106 102 103 104\n", - " * state (nuclide) object '' 'm' '' 'm' '' ... 'm' '' '' ''\n", - " elapsed_time (time_step_number) float64 0.0 6.312e+07\n", - " zai (nuclide) int64 471050 471051 ... 441030 441040\n", - " * timestamp (timestamp) datetime64[ns] 2020-07-12T23:01:19\n", - "Data variables: (12/31)\n", - " irradiation_time (time_step_number) float64 0.0 6.312e+07\n", - " cooling_time (time_step_number) float64 0.0 0.0\n", - " duration (time_step_number) float64 0.0 6.312e+07\n", - " flux (time_step_number) float64 0.0 2.445e+10\n", - " total_atoms (time_step_number) float64 5.578e+21 5.578e+21\n", - " total_activity (time_step_number) float64 0.0 6.123e+09\n", - " ... ...\n", - " nuclide_alpha_heat (time_step_number, nuclide) float64 nan nan ... 0.0\n", - " nuclide_beta_heat (time_step_number, nuclide) float64 nan nan ... 0.0\n", - " nuclide_gamma_heat (time_step_number, nuclide) float64 nan nan ... 0.0\n", - " nuclide_dose (time_step_number, nuclide) float64 nan nan ... 0.0\n", - " nuclide_ingestion (time_step_number, nuclide) float64 nan nan ... 0.0\n", - " nuclide_inhalation (time_step_number, nuclide) float64 nan nan ... 0.0\n", - "Attributes:\n", - " run_name: * Material Ag, fluxes 1\n", - " flux_name: 55.F9.10 11-L2-02W HFS_GLRY_08_U\n", - " dose_rate_type: Point source\n", - " dose_rate_distance: 1.0" + " time_step_number gamma_boundaries gamma\n", + "0 1 1.000000e-11 0.000000e+00\n", + "1 1 1.000000e-02 3.156906e-11\n", + "2 1 2.000000e-02 0.000000e+00\n", + "3 1 5.000000e-02 0.000000e+00\n", + "4 1 1.000000e-01 5.480877e-10\n", + "... ... ... ...\n", + "1620 65 8.000000e+00 0.000000e+00\n", + "1621 65 1.000000e+01 0.000000e+00\n", + "1622 65 1.200000e+01 0.000000e+00\n", + "1623 65 1.400000e+01 0.000000e+00\n", + "1624 65 2.000000e+01 0.000000e+00\n", + "\n", + "[1625 rows x 3 columns]" ] }, - "execution_count": 166, + "execution_count": 276, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "ds" + "ds.gamma.to_dataframe().reset_index()[[\"time_step_number\", \"gamma_boundaries\", \"gamma\"]]" ] }, { "cell_type": "code", - "execution_count": 203, - "id": "b9679cc0-5621-4367-a4a9-0176745b9a65", + "execution_count": 277, + "id": "6d10e66a-6550-4cbc-828b-4438cbdab443", "metadata": { "tags": [] }, - "outputs": [ - { - "ename": "ValueError", - "evalue": "cannot remove index(es) 'nuclide', which would corrupt the following index built from coordinates 'nuclide', 'element', 'mass_number', 'state':\nPandasIndex(MultiIndex([('Ag', 105, ''),\n ('Ag', 105, 'm'),\n ('Ag', 106, ''),\n ('Ag', 106, 'm'),\n ('Ag', 107, ''),\n ('Ag', 107, 'm'),\n ('Ag', 108, ''),\n ('Ag', 108, 'm'),\n ('Ag', 109, ''),\n ('Ag', 109, 'm'),\n ('Ag', 110, ''),\n ('Ag', 110, 'm'),\n ('Ag', 111, ''),\n ('Ag', 111, 'm'),\n ('Cd', 106, ''),\n ('Cd', 107, ''),\n ('Cd', 108, ''),\n ('Cd', 109, ''),\n ('Cd', 110, ''),\n ('Cd', 111, ''),\n ('Cd', 111, 'm'),\n ('Cd', 112, ''),\n ( 'H', 1, ''),\n ( 'H', 2, ''),\n ( 'H', 3, ''),\n ('He', 3, ''),\n ('He', 4, ''),\n ('Pd', 104, ''),\n ('Pd', 105, ''),\n ('Pd', 106, ''),\n ('Pd', 107, ''),\n ('Pd', 107, 'm'),\n ('Pd', 108, ''),\n ('Pd', 109, ''),\n ('Pd', 109, 'm'),\n ('Pd', 110, ''),\n ('Rh', 102, ''),\n ('Rh', 102, 'm'),\n ('Rh', 103, ''),\n ('Rh', 103, 'm'),\n ('Rh', 104, ''),\n ('Rh', 104, 'm'),\n ('Rh', 105, ''),\n ('Rh', 106, ''),\n ('Rh', 106, 'm'),\n ('Ru', 102, ''),\n ('Ru', 103, ''),\n ('Ru', 104, '')],\n name='nuclide'))", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mValueError\u001b[0m Traceback (most recent call last)", - "Cell \u001b[0;32mIn[203], line 19\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[43mds\u001b[49m\u001b[43m[\u001b[49m\u001b[43m[\u001b[49m\n\u001b[1;32m 2\u001b[0m \u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mtime_step_number\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 3\u001b[0m \u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43melement\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 4\u001b[0m \u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mmass_number\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 5\u001b[0m \u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mstate\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 6\u001b[0m \u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mnuclide_atoms\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 7\u001b[0m \u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mnuclide_grams\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 8\u001b[0m \u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mnuclide_activity\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 9\u001b[0m \u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mnuclide_alpha_activity\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 10\u001b[0m \u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mnuclide_beta_activity\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 11\u001b[0m \u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mnuclide_gamma_activity\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 12\u001b[0m \u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mnuclide_heat\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 13\u001b[0m \u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mnuclide_alpha_heat\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 14\u001b[0m \u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mnuclide_beta_heat\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 15\u001b[0m \u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mnuclide_gamma_heat\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 16\u001b[0m \u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mnuclide_dose\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 17\u001b[0m \u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mnuclide_ingestion\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 18\u001b[0m \u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mnuclide_inhalation\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[0;32m---> 19\u001b[0m \u001b[43m]\u001b[49m\u001b[43m]\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mto_array\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdrop_indexes\u001b[49m\u001b[43m(\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mtime_step_number\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mnuclide\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 20\u001b[0m \u001b[38;5;66;03m# .reset_coords(names=[\"time_step_number\", \"nuclide\"])\u001b[39;00m\n\u001b[1;32m 21\u001b[0m \u001b[38;5;66;03m# .stack(dimensions={\"tsn\": [\"time_step_number\", \"element\", \"mass_number\", \"state\"]})\u001b[39;00m\n", - "File \u001b[0;32m~/.pyenv/versions/3.11.2/envs/xpypact/lib/python3.11/site-packages/xarray/core/dataarray.py:3017\u001b[0m, in \u001b[0;36mDataArray.drop_indexes\u001b[0;34m(self, coord_names, errors)\u001b[0m\n\u001b[1;32m 2995\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mdrop_indexes\u001b[39m(\n\u001b[1;32m 2996\u001b[0m \u001b[38;5;28mself\u001b[39m: T_DataArray,\n\u001b[1;32m 2997\u001b[0m coord_names: Hashable \u001b[38;5;241m|\u001b[39m Iterable[Hashable],\n\u001b[1;32m 2998\u001b[0m \u001b[38;5;241m*\u001b[39m,\n\u001b[1;32m 2999\u001b[0m errors: ErrorOptions \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mraise\u001b[39m\u001b[38;5;124m\"\u001b[39m,\n\u001b[1;32m 3000\u001b[0m ) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m T_DataArray:\n\u001b[1;32m 3001\u001b[0m \u001b[38;5;250m \u001b[39m\u001b[38;5;124;03m\"\"\"Drop the indexes assigned to the given coordinates.\u001b[39;00m\n\u001b[1;32m 3002\u001b[0m \n\u001b[1;32m 3003\u001b[0m \u001b[38;5;124;03m Parameters\u001b[39;00m\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 3015\u001b[0m \u001b[38;5;124;03m A new dataarray with dropped indexes.\u001b[39;00m\n\u001b[1;32m 3016\u001b[0m \u001b[38;5;124;03m \"\"\"\u001b[39;00m\n\u001b[0;32m-> 3017\u001b[0m ds \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_to_temp_dataset\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdrop_indexes\u001b[49m\u001b[43m(\u001b[49m\u001b[43mcoord_names\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43merrors\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43merrors\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 3018\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_from_temp_dataset(ds)\n", - "File \u001b[0;32m~/.pyenv/versions/3.11.2/envs/xpypact/lib/python3.11/site-packages/xarray/core/dataset.py:5155\u001b[0m, in \u001b[0;36mDataset.drop_indexes\u001b[0;34m(self, coord_names, errors)\u001b[0m\n\u001b[1;32m 5150\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m unindexed_coords:\n\u001b[1;32m 5151\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mValueError\u001b[39;00m(\n\u001b[1;32m 5152\u001b[0m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mthose coordinates do not have an index: \u001b[39m\u001b[38;5;132;01m{\u001b[39;00munindexed_coords\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 5153\u001b[0m )\n\u001b[0;32m-> 5155\u001b[0m \u001b[43massert_no_index_corrupted\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mxindexes\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcoord_names\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43maction\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mremove index(es)\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m\n\u001b[1;32m 5157\u001b[0m variables \u001b[38;5;241m=\u001b[39m {}\n\u001b[1;32m 5158\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m name, var \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_variables\u001b[38;5;241m.\u001b[39mitems():\n", - "File \u001b[0;32m~/.pyenv/versions/3.11.2/envs/xpypact/lib/python3.11/site-packages/xarray/core/indexes.py:1506\u001b[0m, in \u001b[0;36massert_no_index_corrupted\u001b[0;34m(indexes, coord_names, action)\u001b[0m\n\u001b[1;32m 1504\u001b[0m common_names_str \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m, \u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;241m.\u001b[39mjoin(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mk\u001b[38;5;132;01m!r}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;28;01mfor\u001b[39;00m k \u001b[38;5;129;01min\u001b[39;00m common_names)\n\u001b[1;32m 1505\u001b[0m index_names_str \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m, \u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;241m.\u001b[39mjoin(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mk\u001b[38;5;132;01m!r}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;28;01mfor\u001b[39;00m k \u001b[38;5;129;01min\u001b[39;00m index_coords)\n\u001b[0;32m-> 1506\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mValueError\u001b[39;00m(\n\u001b[1;32m 1507\u001b[0m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mcannot \u001b[39m\u001b[38;5;132;01m{\u001b[39;00maction\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mcommon_names_str\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m, which would corrupt \u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 1508\u001b[0m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mthe following index built from coordinates \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mindex_names_str\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m:\u001b[39m\u001b[38;5;130;01m\\n\u001b[39;00m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 1509\u001b[0m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mindex\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 1510\u001b[0m )\n", - "\u001b[0;31mValueError\u001b[0m: cannot remove index(es) 'nuclide', which would corrupt the following index built from coordinates 'nuclide', 'element', 'mass_number', 'state':\nPandasIndex(MultiIndex([('Ag', 105, ''),\n ('Ag', 105, 'm'),\n ('Ag', 106, ''),\n ('Ag', 106, 'm'),\n ('Ag', 107, ''),\n ('Ag', 107, 'm'),\n ('Ag', 108, ''),\n ('Ag', 108, 'm'),\n ('Ag', 109, ''),\n ('Ag', 109, 'm'),\n ('Ag', 110, ''),\n ('Ag', 110, 'm'),\n ('Ag', 111, ''),\n ('Ag', 111, 'm'),\n ('Cd', 106, ''),\n ('Cd', 107, ''),\n ('Cd', 108, ''),\n ('Cd', 109, ''),\n ('Cd', 110, ''),\n ('Cd', 111, ''),\n ('Cd', 111, 'm'),\n ('Cd', 112, ''),\n ( 'H', 1, ''),\n ( 'H', 2, ''),\n ( 'H', 3, ''),\n ('He', 3, ''),\n ('He', 4, ''),\n ('Pd', 104, ''),\n ('Pd', 105, ''),\n ('Pd', 106, ''),\n ('Pd', 107, ''),\n ('Pd', 107, 'm'),\n ('Pd', 108, ''),\n ('Pd', 109, ''),\n ('Pd', 109, 'm'),\n ('Pd', 110, ''),\n ('Rh', 102, ''),\n ('Rh', 102, 'm'),\n ('Rh', 103, ''),\n ('Rh', 103, 'm'),\n ('Rh', 104, ''),\n ('Rh', 104, 'm'),\n ('Rh', 105, ''),\n ('Rh', 106, ''),\n ('Rh', 106, 'm'),\n ('Ru', 102, ''),\n ('Ru', 103, ''),\n ('Ru', 104, '')],\n name='nuclide'))" - ] - } - ], + "outputs": [], "source": [ - "ds[[\n", - "\"time_step_number\",\n", - "\"element\",\n", - "\"mass_number\",\n", - "\"state\",\n", - "\"nuclide_atoms\",\n", - "\"nuclide_grams\",\n", - "\"nuclide_activity\",\n", - "\"nuclide_alpha_activity\",\n", - "\"nuclide_beta_activity\",\n", - "\"nuclide_gamma_activity\",\n", - "\"nuclide_heat\",\n", - "\"nuclide_alpha_heat\",\n", - "\"nuclide_beta_heat\",\n", - "\"nuclide_gamma_heat\",\n", - "\"nuclide_dose\",\n", - "\"nuclide_ingestion\",\n", - "\"nuclide_inhalation\",\n", - "]].to_array().drop_indexes([\"time_step_number\", \"nuclide\"])\n", - "# .reset_coords(names=[\"time_step_number\", \"nuclide\"])\n", - "# .stack(dimensions={\"tsn\": [\"time_step_number\", \"element\", \"mass_number\", \"state\"]})" + "def save_gamma_spectra(con, ds):\n", + " columns = [\"time_step_number\", \"gamma_boundaries\", \"gamma\"]\n", + " tg = ds.gamma.to_dataframe().reset_index()[columns]\n", + " sql = \"insert into timestep_gamma select * from tg\"\n", + " con.execute(sql)\n", + " con.commit()" ] }, { "cell_type": "code", - "execution_count": 186, - "id": "526610bb-be7b-4ce7-8cc9-0bcdb00588f2", + "execution_count": 278, + "id": "fc882c1d-9402-4cc5-a316-f8f0ca25a5e1", "metadata": { "tags": [] }, "outputs": [], "source": [ - "def save_timestep_nucludes(con, ds):\n", - " timesteps_nuclides_df = ds[[\n", - " \"time_step_number\",\n", - " \"element\",\n", - " \"mass_number\",\n", - " \"state\",\n", - " \"nuclide_atoms\",\n", - " \"nuclide_grams\",\n", - " \"nuclide_activity\",\n", - " \"nuclide_alpha_activity\",\n", - " \"nuclide_beta_activity\",\n", - " \"nuclide_gamma_activity\",\n", - " \"nuclide_heat\",\n", - " \"nuclide_alpha_heat\",\n", - " \"nuclide_beta_heat\",\n", - " \"nuclide_gamma_heat\",\n", - " \"nuclide_dose\",\n", - " \"nuclide_ingestion\",\n", - " \"nuclide_inhalation\",\n", - " ]].to_dataframe().reset_index(drop=True)\n", - " sql = \"insert into timestep_nuclide select * from timesteps_nuclides_df\"\n", - " con.execute(sql)\n", - " con.commit()" + "save_gamma_spectra(con, ds)" ] }, { "cell_type": "code", - "execution_count": 187, - "id": "de4b9bd0-02e4-48f5-bec3-bb92c67682d0", + "execution_count": 283, + "id": "398ae012-c5df-4793-9b19-60395bbff7a7", "metadata": { "tags": [] }, "outputs": [ { - "ename": "BinderException", - "evalue": "Binder Error: table timestep_nuclide has 17 columns but 18 values were supplied", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mBinderException\u001b[0m Traceback (most recent call last)", - "Cell \u001b[0;32mIn[187], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[43msave_timestep_nucludes\u001b[49m\u001b[43m(\u001b[49m\u001b[43mcon\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mds\u001b[49m\u001b[43m)\u001b[49m\n", - "Cell \u001b[0;32mIn[186], line 22\u001b[0m, in \u001b[0;36msave_timestep_nucludes\u001b[0;34m(con, ds)\u001b[0m\n\u001b[1;32m 2\u001b[0m timesteps_nuclides_df \u001b[38;5;241m=\u001b[39m ds[[\n\u001b[1;32m 3\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mtime_step_number\u001b[39m\u001b[38;5;124m\"\u001b[39m,\n\u001b[1;32m 4\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124melement\u001b[39m\u001b[38;5;124m\"\u001b[39m,\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 19\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mnuclide_inhalation\u001b[39m\u001b[38;5;124m\"\u001b[39m,\n\u001b[1;32m 20\u001b[0m ]]\u001b[38;5;241m.\u001b[39mto_dataframe()\u001b[38;5;241m.\u001b[39mreset_index(drop\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m)\n\u001b[1;32m 21\u001b[0m sql \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124minsert into timestep_nuclide select * from timesteps_nuclides_df\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[0;32m---> 22\u001b[0m \u001b[43mcon\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mexecute\u001b[49m\u001b[43m(\u001b[49m\u001b[43msql\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 23\u001b[0m con\u001b[38;5;241m.\u001b[39mcommit()\n", - "\u001b[0;31mBinderException\u001b[0m: Binder Error: table timestep_nuclide has 17 columns but 18 values were supplied" - ] + "data": { + "text/html": [ + "
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    " + ], + "text/plain": [ + " boundary intensity\n", + "0 1.000000e-11 0.000000e+00\n", + "1 1.000000e-02 4.204333e+05\n", + "2 2.000000e-02 8.981064e+04\n", + "3 5.000000e-02 1.969102e+04\n", + "4 1.000000e-01 2.891012e+06\n", + "5 2.000000e-01 7.068460e+06\n", + "6 3.000000e-01 1.825296e+06\n", + "7 4.000000e-01 1.259209e+06\n", + "8 6.000000e-01 8.268742e+06\n", + "9 8.000000e-01 9.028931e+05\n", + "10 1.000000e+00 5.304670e+07\n", + "11 1.220000e+00 6.488259e+07\n", + "12 1.440000e+00 6.590924e+07\n", + "13 1.660000e+00 5.267068e+05\n", + "14 2.000000e+00 7.746914e+06\n", + "15 2.500000e+00 4.308211e+06\n", + "16 3.000000e+00 1.930387e+06\n", + "17 4.000000e+00 7.964872e+04\n", + "18 5.000000e+00 1.688151e+01\n", + "19 6.500000e+00 0.000000e+00\n", + "20 8.000000e+00 0.000000e+00\n", + "21 1.000000e+01 0.000000e+00\n", + "22 1.200000e+01 0.000000e+00\n", + "23 1.400000e+01 0.000000e+00\n", + "24 2.000000e+01 0.000000e+00" + ] + }, + "execution_count": 284, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "con.execute(\"select boundary, intensity from timestep_gamma where timestep_id = 42\").df()" ] }, { "cell_type": "code", - "execution_count": 41, + "execution_count": 286, "id": "def18203-fed9-472d-a69c-b653dbf9a7b2", "metadata": { "tags": [] diff --git a/notebooks/dvp/try_ducdb.py b/notebooks/dvp/try_ducdb.py index 767a59e..f480e6d 100644 --- a/notebooks/dvp/try_ducdb.py +++ b/notebooks/dvp/try_ducdb.py @@ -1,189 +1,203 @@ #!/usr/bin/env python # coding: utf-8 -# In[1]: +# In[233]: get_ipython().run_line_magic("config", "Completer.use_jedi = False") -# In[3]: +# In[234]: import xpypact as xp -# In[5]: +# In[235]: xp.__version__ -# In[11]: +# In[236]: from pathlib import Path -# In[19]: +# In[237]: root_dir = Path("~", "dev", "xpypact").expanduser() -# In[20]: +# In[238]: -json_path = root_dir / "tests/data/Ag-1.json" +json_path = root_dir / "wrk/Alloy718-Co04-104_2_1_1.json" assert json_path.exists() -# In[23]: +# In[239]: import xpypact.data_arrays as da from xpypact.Inventory import Inventory, from_json -# In[24]: +# In[240]: inventory = from_json(json_path) -# In[25]: +# In[241]: ds = da.create_dataset(inventory) -# In[26]: +# In[242]: ds -# In[ ]: +# In[287]: + +ds.timestamp -# In[28]: + +# In[243]: import duckdb as db -# In[46]: +# In[384]: db_path = root_dir / "wrk/try-duckdb.duckdb" db_path.parent.mkdir(parents=True, exist_ok=True) +if db_path.exists(): + db_path.unlink() -# In[48]: +# In[385]: con = db.connect(str(db_path)) -# In[153]: +# In[386]: + + +material_id = 100 +case_id = 3 + + +# In[387]: -# con.execute("drop table rundata") -# con.execute("drop table if exists timestep_gamma") -con.execute("drop table if exists timestep_nuclide") -# con.execute("drop table if exists timestep") -con.execute("drop table nuclide") +def drop_tables(con): + con.execute("drop table if exists timestep_gamma") + con.execute("drop table if exists timestep_nuclide") + con.execute("drop table if exists timestep") + con.execute("drop table if exists nuclide") + con.execute("drop table if exists rundata") -# In[154]: +# In[395]: def create_tables(con): sql = """ - CREATE TABLE IF NOT EXISTS rundata ( - timestamp varchar NOT NULL, - run_name varchar NOT NULL, + material_id uinteger not null, + case_id uinteger not null, + timestamp timestamp not null, + run_name varchar not null, flux_name varchar NOT NULL, dose_rate_type varchar NOT NULL, - dose_rate_distance real NOT NULL + dose_rate_distance real NOT NULL, + primary key(material_id, case_id) ); CREATE TABLE IF NOT EXISTS timestep( - id integer PRIMARY KEY, - elapsed_time real not null, - irradiation_time real not null, - cooling_time real not null, - duration real not null, - flux real not null, - total_atoms real not null, - total_activity real not null, - total_alpha_activity real not null, - total_beta_activity real not null, - total_gamma_activity real not null, - total_mass real not null, - total_heat real not null, - total_alpha_heat real not null, - total_beta_heat real not null, - total_gamma_heat real not null, - total_ingest1ion_dose real not null, - total_inhalation_dose real not null, - total_dose_rate real not null + id uinteger PRIMARY KEY, + elapsed_time float4 not null, + irradiation_time float4 not null, + cooling_time float4 not null, + duration float4 not null, + flux float4 not null, + total_atoms float4 not null, + total_activity float4 not null, + total_alpha_activity float4 not null, + total_beta_activity float4 not null, + total_gamma_activity float4 not null, + total_mass float4 not null, + total_heat float4 not null, + total_alpha_heat float4 null, + total_beta_heat float4 not null, + total_gamma_heat float4 not null, + total_ingest1ion_dose float4 not null, + total_inhalation_dose float4 not null, + total_dose_rate float4 not null, + material_id uinteger not null, + case_id uinteger not null, + foreign key(material_id, case_id) references rundata(material_id, case_id) ); + CREATE TABLE IF NOT EXISTS nuclide( element varchar(2) not null, - mass_number integer not null check(0 < mass_number), -- A + mass_number usmallint not null check(0 < mass_number), state varchar(1) not null, zai integer not null check(10010 <= zai) unique, - half_life real not null check(0 <= half_life), + half_life float4 not null check(0 <= half_life), primary key(element, mass_number, state) ); CREATE TABLE IF NOT EXISTS timestep_nuclide( - timestep_id integer not null, + timestep_id uinteger not null, element varchar(2) not null, - mass_number integer not null, + mass_number usmallint not null, state varchar(1) not null, - atoms real not null, - grams real not null, - activity real not null, - alpha_activity real not null, - beta_activity real not null, - gamma_activity real not null, - heat real not null, - alpha_heat real not null, - beta_heat real not null, - gamma_heat real not null, - dose real not null, - ingestion real not null, - inhalation real not null, + atoms float4 not null, + grams float4 not null, + activity float4 not null, + alpha_activity float4 not null, + beta_activity float4 not null, + gamma_activity float4 not null, + heat float4 not null, + alpha_heat float4 not null, + beta_heat float4 not null, + gamma_heat float4 not null, + dose float4 not null, + ingestion float4 not null, + inhalation float4 not null, primary key(timestep_id, element, mass_number, state), foreign key(timestep_id) references timestep(id), foreign key(element, mass_number, state) references nuclide(element, mass_number, state) ); CREATE TABLE IF NOT EXISTS timestep_gamma( - timestep_id integer not null, + timestep_id uinteger not null, boundary real not null check(0 <= boundary), intensity real not null, primary key(timestep_id, boundary), foreign key(timestep_id) references timestep(id), ); -""" + """ con.execute(sql) -# In[155]: +# In[396]: +# drop_tables(con) create_tables(con) -# In[85]: - - -# con.execute("delete from rundata") - - -# In[81]: +# In[402]: def save_rundata(con, ds): @@ -193,6 +207,8 @@ def save_rundata(con, ds): con.execute( sql, ( + material_id, + case_id, ds.coords["timestamp"].item(), ds.attrs["run_name"], ds.attrs["flux_name"], @@ -203,19 +219,25 @@ def save_rundata(con, ds): con.commit() -# In[83]: +# In[403]: + + +con.execute("select * from information_schema.tables").df() + + +# In[400]: save_rundata(con, ds) -# In[84]: +# In[254]: con.execute("select * from rundata").df() -# In[114]: +# In[255]: def save_timesteps(con, ds): @@ -251,27 +273,19 @@ def save_timesteps(con, ds): con.commit() -# In[115]: +# In[256]: save_timesteps(con, ds) -# In[116]: +# In[257]: con.execute("select * from timestep").df() -# In[131]: - - -ds[ - ["element", "mass_number", "state", "zai", "nuclide_half_life"] -].to_pandas().reset_index(drop=True) - - -# In[156]: +# In[258]: def save_nuclides(con, ds): @@ -285,93 +299,97 @@ def save_nuclides(con, ds): con.commit() -# In[157]: +# In[259]: save_nuclides(con, ds) -# In[160]: +# In[285]: -con.execute("select * from nuclide").df().head() +con.execute("select * from nuclide").df() -# In[166]: +# In[263]: -ds +def save_timestep_nucludes(con, ds): + columns = [ + "time_step_number", + "element", + "mass_number", + "state", + "nuclide_atoms", + "nuclide_grams", + "nuclide_activity", + "nuclide_alpha_activity", + "nuclide_beta_activity", + "nuclide_gamma_activity", + "nuclide_heat", + "nuclide_alpha_heat", + "nuclide_beta_heat", + "nuclide_gamma_heat", + "nuclide_dose", + "nuclide_ingestion", + "nuclide_inhalation", + ] + tn = ds[columns].to_dataframe().reset_index("time_step_number")[columns].fillna(0.0) + sql = "insert into timestep_nuclide select * from tn" + con.execute(sql) + con.commit() -# In[203]: - - -ds[ - [ - """Time_step_number.""", - """Element.""", - """Mass_number.""", - """State.""", - """Nuclide_atoms.""", - """Nuclide_grams.""", - """Nuclide_activity.""", - """Nuclide_alpha_activity.""", - """Nuclide_beta_activity.""", - """Nuclide_gamma_activity.""", - """Nuclide_heat.""", - """Nuclide_alpha_heat.""", - """Nuclide_beta_heat.""", - """Nuclide_gamma_heat.""", - """Nuclide_dose.""", - """Nuclide_ingestion.""", - """Nuclide_inhalation.""", - ] -].to_array().drop_indexes(["time_step_number", "nuclide"]) -# .reset_coords(names=["time_step_number", "nuclide"]) -# .stack(dimensions={"tsn": ["time_step_number", "element", "mass_number", "state"]}) +# In[264]: -# In[186]: +save_timestep_nucludes(con, ds) -def save_timestep_nucludes(con, ds): - timesteps_nuclides_df = ( - ds[ - [ - "time_step_number", - "element", - "mass_number", - "state", - "nuclide_atoms", - "nuclide_grams", - "nuclide_activity", - "nuclide_alpha_activity", - "nuclide_beta_activity", - "nuclide_gamma_activity", - "nuclide_heat", - "nuclide_alpha_heat", - "nuclide_beta_heat", - "nuclide_gamma_heat", - "nuclide_dose", - "nuclide_ingestion", - "nuclide_inhalation", - ] - ] - .to_dataframe() - .reset_index(drop=True) - ) - sql = "insert into timestep_nuclide select * from timesteps_nuclides_df" +# In[265]: + + +con.execute("select * from timestep_nuclide").df() + + +# In[276]: + + +ds.gamma.to_dataframe().reset_index()[["time_step_number", "gamma_boundaries", "gamma"]] + + +# In[277]: + + +def save_gamma_spectra(con, ds): + columns = ["time_step_number", "gamma_boundaries", "gamma"] + tg = ds.gamma.to_dataframe().reset_index()[columns] + sql = "insert into timestep_gamma select * from tg" con.execute(sql) con.commit() -# In[187]: +# In[278]: -save_timestep_nucludes(con, ds) +save_gamma_spectra(con, ds) + + +# In[283]: + + +con.execute("select * from timestep_gamma").df() + + +# In[284]: + + +con.execute( + "select boundary, intensity from timestep_gamma where timestep_id = 42" +).df() -# In[41]: +# In[286]: con.close() From 49fb3f4b3b2e4d63a383919106bf91b7bf899f94 Mon Sep 17 00:00:00 2001 From: dvp Date: Thu, 23 Mar 2023 19:37:37 +0300 Subject: [PATCH 10/32] feat: continue notebook for prototyping with duckdb - add material and case --- notebooks/dvp/try_ducdb.ipynb | 2514 ++++++++++++++++++++++++++++----- notebooks/dvp/try_ducdb.py | 141 +- 2 files changed, 2247 insertions(+), 408 deletions(-) diff --git a/notebooks/dvp/try_ducdb.ipynb b/notebooks/dvp/try_ducdb.ipynb index 4ea1a3d..a2036ed 100644 --- a/notebooks/dvp/try_ducdb.ipynb +++ b/notebooks/dvp/try_ducdb.ipynb @@ -111,7 +111,7 @@ }, { "cell_type": "code", - "execution_count": 241, + "execution_count": 469, "id": "e471ce43-3860-430d-b669-7a1211bb5d06", "metadata": { "tags": [] @@ -123,7 +123,7 @@ }, { "cell_type": "code", - "execution_count": 242, + "execution_count": 470, "id": "eaa7c75f-119c-493c-b038-dbd615b72c6f", "metadata": { "tags": [] @@ -526,14 +526,14 @@ " run_name: * Material Alloy718-Co04, fluxes 104_2_1_1\n", " flux_name: 90-degrees bend\n", " dose_rate_type: Point source\n", - " dose_rate_distance: 1.0
  • run_name :
    * Material Alloy718-Co04, fluxes 104_2_1_1
    flux_name :
    90-degrees bend
    dose_rate_type :
    Point source
    dose_rate_distance :
    1.0
    • " ], "text/plain": [ "\n", @@ -1099,7 +1099,7 @@ " dose_rate_distance: 1.0" ] }, - "execution_count": 242, + "execution_count": 470, "metadata": {}, "output_type": "execute_result" } @@ -1110,8 +1110,8 @@ }, { "cell_type": "code", - "execution_count": 287, - "id": "6f923a0d-5ef8-4dea-8157-98f6049ddb26", + "execution_count": 417, + "id": "8dbfda08-8776-4733-9215-9d569fb24a34", "metadata": { "tags": [] }, @@ -1487,7 +1487,7 @@ "Coordinates:\n", " * timestamp (timestamp) datetime64[ns] 2022-02-21T01:52:47\n", "Attributes:\n", - " long description: FISPACT datasets can be merged and then selected by ti..." + " long description: FISPACT datasets can be merged and then selected by ti..." ], "text/plain": [ "\n", @@ -1498,7 +1498,7 @@ " long description: FISPACT datasets can be merged and then selected by ti..." ] }, - "execution_count": 287, + "execution_count": 417, "metadata": {}, "output_type": "execute_result" } @@ -1561,7 +1561,1477 @@ }, { "cell_type": "code", - "execution_count": 387, + "execution_count": 475, + "id": "dd2fb504-eb9a-48ee-bab2-2a512630797a", + "metadata": { + "tags": [] + }, + "outputs": [ + { + "data": { + "text/html": [ + "
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    " + ], + "text/plain": [ + "\n", + "array([[[0.00000000e+00, 6.31152000e+07, 3.78691200e+08, 3.78691200e+08,\n", + " 4.20662808e+08, 4.20662808e+08, 4.20663208e+08, 4.20663208e+08,\n", + " 4.20663608e+08, 4.20663608e+08, 4.20664008e+08, 4.20664008e+08,\n", + " 4.20664408e+08, 4.20664408e+08, 4.20664808e+08, 4.20664808e+08,\n", + " 4.20665208e+08, 4.20665208e+08, 4.20665608e+08, 4.20665608e+08,\n", + " 4.20666008e+08, 4.20666008e+08, 4.20666408e+08, 4.20666408e+08,\n", + " 4.20666808e+08, 4.20666808e+08, 4.20667208e+08, 4.20667208e+08,\n", + " 4.20667608e+08, 4.20667608e+08, 4.20668008e+08, 4.20668008e+08,\n", + " 4.20668408e+08, 4.20668408e+08, 4.20668808e+08, 4.20668808e+08,\n", + " 4.20669208e+08, 4.20669208e+08, 4.20669608e+08, 4.20669608e+08,\n", + " 4.20670008e+08, 4.20670008e+08, 4.20670408e+08, 4.20670408e+08,\n", + " 4.20670808e+08, 4.20670808e+08, 4.20670808e+08, 4.20670808e+08,\n", + " 4.20670808e+08, 4.20670808e+08, 4.20670808e+08, 4.20670808e+08,\n", + " 4.20670808e+08, 4.20670808e+08, 4.20670808e+08, 4.20670808e+08,\n", + " 4.20670808e+08, 4.20670808e+08, 4.20670808e+08, 4.20670808e+08,\n", + " 4.20670808e+08, 4.20670808e+08, 4.20670808e+08, 4.20670808e+08,\n", + " 4.20670808e+08]]])\n", + "Coordinates:\n", + " * material_id (material_id) int64 100\n", + " * case_id (case_id) int64 3\n", + " * time_step_number (time_step_number) int64 1 2 3 4 5 6 ... 60 61 62 63 64 65\n", + " elapsed_time (time_step_number) float64 0.0 6.312e+07 ... 3.2e+10\n", + "Attributes:\n", + " units: s" + ] + }, + "execution_count": 476, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ds.irradiation_time" + ] + }, + { + "cell_type": "code", + "execution_count": 446, "id": "d9e1ddfb-398e-4cea-b01d-fb0e53242776", "metadata": { "tags": [] @@ -1578,7 +3048,7 @@ }, { "cell_type": "code", - "execution_count": 395, + "execution_count": 447, "id": "c402d3a1-e77a-4b24-accc-a19588ccdf54", "metadata": { "tags": [] @@ -1599,7 +3069,9 @@ " );\n", "\n", " CREATE TABLE IF NOT EXISTS timestep(\n", - " id uinteger PRIMARY KEY,\n", + " material_id uinteger not null,\n", + " case_id uinteger not null,\n", + " time_step_number uinteger not null,\n", " elapsed_time float4 not null,\n", " irradiation_time float4 not null,\n", " cooling_time float4 not null,\n", @@ -1618,8 +3090,7 @@ " total_ingest1ion_dose float4 not null,\n", " total_inhalation_dose float4 not null,\n", " total_dose_rate float4 not null,\n", - " material_id uinteger not null,\n", - " case_id uinteger not null,\n", + " primary key(material_id, case_id, time_step_number),\n", " foreign key(material_id, case_id) references rundata(material_id, case_id) \n", " );\n", "\n", @@ -1634,7 +3105,9 @@ " );\n", " \n", " CREATE TABLE IF NOT EXISTS timestep_nuclide(\n", - " timestep_id uinteger not null,\n", + " material_id uinteger not null,\n", + " case_id uinteger not null,\n", + " time_step_number uinteger not null,\n", " element varchar(2) not null,\n", " mass_number usmallint not null,\n", " state varchar(1) not null,\n", @@ -1651,17 +3124,19 @@ " dose float4 not null,\n", " ingestion float4 not null,\n", " inhalation float4 not null,\n", - " primary key(timestep_id, element, mass_number, state),\n", - " foreign key(timestep_id) references timestep(id),\n", + " primary key(material_id, case_id, time_step_number, element, mass_number, state),\n", + " foreign key(material_id, case_id, time_step_number) references timestep(material_id, case_id, time_step_number),\n", " foreign key(element, mass_number, state) references nuclide(element, mass_number, state) \n", " );\n", "\n", " CREATE TABLE IF NOT EXISTS timestep_gamma(\n", - " timestep_id uinteger not null,\n", + " material_id uinteger not null,\n", + " case_id uinteger not null,\n", + " time_step_number uinteger not null,\n", " boundary real not null check(0 <= boundary),\n", " intensity real not null, \n", - " primary key(timestep_id, boundary),\n", - " foreign key(timestep_id) references timestep(id),\n", + " primary key(material_id, case_id, time_step_number, boundary),\n", + " foreign key(material_id, case_id, time_step_number) references timestep(material_id, case_id, time_step_number),\n", " );\n", " \"\"\"\n", " con.execute(sql)" @@ -1669,20 +3144,20 @@ }, { "cell_type": "code", - "execution_count": 396, + "execution_count": 448, "id": "25f6867e-397a-4e98-a363-74b6af739c88", "metadata": { "tags": [] }, "outputs": [], "source": [ - "# drop_tables(con)\n", + "drop_tables(con)\n", "create_tables(con)" ] }, { "cell_type": "code", - "execution_count": 402, + "execution_count": 449, "id": "29716201-70f8-40d2-8da7-85689714ec32", "metadata": { "tags": [] @@ -1691,12 +3166,12 @@ "source": [ "def save_rundata(con, ds):\n", " sql = \"\"\"\n", - " INSERT INTO rundata values(?, ?, ?, ?, ?)\n", + " INSERT INTO rundata values(?, ?, ?, ?, ?, ?, ?)\n", " \"\"\"\n", " con.execute(sql, ( \n", - " material_id,\n", - " case_id,\n", - " ds.coords[\"timestamp\"].item(),\n", + " ds.material_id.item(),\n", + " ds.case_id.item(),\n", + " ds.timestamp.dt.strftime(\"%Y-%m-%d %H:%M:%S\").item(),\n", " ds.attrs[\"run_name\"],\n", " ds.attrs[\"flux_name\"],\n", " ds.attrs[\"dose_rate_type\"],\n", @@ -1707,194 +3182,19 @@ }, { "cell_type": "code", - "execution_count": 403, - "id": "4d71d862-2960-455d-be85-c5d9394a160d", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "data": { - "text/html": [ - "
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    table_catalogtable_schematable_nametable_typeself_referencing_column_namereference_generationuser_defined_type_cataloguser_defined_type_schemauser_defined_type_nameis_insertable_intois_typedcommit_action
    0try-duckdbmainrundataBASE TABLENaNNaNNaNNaNNaNYESNONaN
    1try-duckdbmaintimestepBASE TABLENaNNaNNaNNaNNaNYESNONaN
    2try-duckdbmainnuclideBASE TABLENaNNaNNaNNaNNaNYESNONaN
    3try-duckdbmaintimestep_nuclideBASE TABLENaNNaNNaNNaNNaNYESNONaN
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    \n", - "
    " - ], - "text/plain": [ - " table_catalog table_schema table_name table_type \\\n", - "0 try-duckdb main rundata BASE TABLE \n", - "1 try-duckdb main timestep BASE TABLE \n", - "2 try-duckdb main nuclide BASE TABLE \n", - "3 try-duckdb main timestep_nuclide BASE TABLE \n", - "4 try-duckdb main timestep_gamma BASE TABLE \n", - "\n", - " self_referencing_column_name reference_generation \\\n", - "0 NaN NaN \n", - "1 NaN NaN \n", - "2 NaN NaN \n", - "3 NaN NaN \n", - "4 NaN NaN \n", - "\n", - " user_defined_type_catalog user_defined_type_schema \\\n", - "0 NaN NaN \n", - "1 NaN NaN \n", - "2 NaN NaN \n", - "3 NaN NaN \n", - "4 NaN NaN \n", - "\n", - " user_defined_type_name is_insertable_into is_typed commit_action \n", - "0 NaN YES NO NaN \n", - "1 NaN YES NO NaN \n", - "2 NaN YES NO NaN \n", - "3 NaN YES NO NaN \n", - "4 NaN YES NO NaN " - ] - }, - "execution_count": 403, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "con.execute(\"select * from information_schema.tables\").df()" - ] - }, - { - "cell_type": "code", - "execution_count": 400, + "execution_count": 451, "id": "c789eedd-580c-4383-8bf1-cc943562a3aa", "metadata": { "tags": [] }, - "outputs": [ - { - "ename": "BinderException", - "evalue": "Binder Error: table rundata has 7 columns but 5 values were supplied", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mBinderException\u001b[0m Traceback (most recent call last)", - "Cell \u001b[0;32mIn[400], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[43msave_rundata\u001b[49m\u001b[43m(\u001b[49m\u001b[43mcon\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mds\u001b[49m\u001b[43m)\u001b[49m\n", - "Cell \u001b[0;32mIn[397], line 5\u001b[0m, in \u001b[0;36msave_rundata\u001b[0;34m(con, ds)\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21msave_rundata\u001b[39m(con, ds):\n\u001b[1;32m 2\u001b[0m sql \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m\"\"\"\u001b[39m\n\u001b[1;32m 3\u001b[0m \u001b[38;5;124m INSERT INTO rundata values(?, ?, ?, ?, ?)\u001b[39m\n\u001b[1;32m 4\u001b[0m \u001b[38;5;124m \u001b[39m\u001b[38;5;124m\"\"\"\u001b[39m\n\u001b[0;32m----> 5\u001b[0m \u001b[43mcon\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mexecute\u001b[49m\u001b[43m(\u001b[49m\u001b[43msql\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43m(\u001b[49m\u001b[43m \u001b[49m\n\u001b[1;32m 6\u001b[0m \u001b[43m \u001b[49m\u001b[43mds\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcoords\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mtimestamp\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m]\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mitem\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 7\u001b[0m \u001b[43m \u001b[49m\u001b[43mds\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mattrs\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mrun_name\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 8\u001b[0m \u001b[43m \u001b[49m\u001b[43mds\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mattrs\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mflux_name\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 9\u001b[0m \u001b[43m \u001b[49m\u001b[43mds\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mattrs\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mdose_rate_type\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 10\u001b[0m \u001b[43m \u001b[49m\u001b[43mds\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mattrs\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mdose_rate_distance\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m]\u001b[49m\n\u001b[1;32m 11\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 12\u001b[0m con\u001b[38;5;241m.\u001b[39mcommit()\n", - "\u001b[0;31mBinderException\u001b[0m: Binder Error: table rundata has 7 columns but 5 values were supplied" - ] - } - ], + "outputs": [], "source": [ "save_rundata(con, ds)" ] }, { "cell_type": "code", - "execution_count": 254, + "execution_count": 452, "id": "1c650134-edf3-44dd-aa90-ddde6a3987a7", "metadata": { "tags": [] @@ -1921,6 +3221,8 @@ " \n", " \n", " \n", + " material_id\n", + " case_id\n", " timestamp\n", " run_name\n", " flux_name\n", @@ -1931,7 +3233,9 @@ " \n", " \n", " 0\n", - " 1645408367000000000\n", + " 100\n", + " 3\n", + " 2022-02-21 01:52:47\n", " * Material Alloy718-Co04, fluxes 104_2_1_1\n", " 90-degrees bend\n", " Point source\n", @@ -1942,14 +3246,17 @@ "" ], "text/plain": [ - " timestamp run_name \\\n", - "0 1645408367000000000 * Material Alloy718-Co04, fluxes 104_2_1_1 \n", + " material_id case_id timestamp \\\n", + "0 100 3 2022-02-21 01:52:47 \n", + "\n", + " run_name flux_name dose_rate_type \\\n", + "0 * Material Alloy718-Co04, fluxes 104_2_1_1 90-degrees bend Point source \n", "\n", - " flux_name dose_rate_type dose_rate_distance \n", - "0 90-degrees bend Point source 1.0 " + " dose_rate_distance \n", + "0 1.0 " ] }, - "execution_count": 254, + "execution_count": 452, "metadata": {}, "output_type": "execute_result" } @@ -1960,7 +3267,7 @@ }, { "cell_type": "code", - "execution_count": 255, + "execution_count": 455, "id": "cf8661b6-d9cb-4431-8b40-f14072409d5a", "metadata": { "tags": [] @@ -1970,6 +3277,8 @@ "def save_timesteps(con, ds):\n", " timesteps_df = ds[\n", " [\n", + " \"material_id\",\n", + " \"case_id\",\n", " \"time_step_number\",\n", " \"elapsed_time\",\n", " \"irradiation_time\",\n", @@ -1990,7 +3299,7 @@ " \"total_inhalation_dose\",\n", " \"total_dose_rate\",\n", " ]\n", - " ].to_pandas().reset_index()\n", + " ].to_dataframe().reset_index()\n", " sql = \"insert into timestep select * from timesteps_df\"\n", " con.execute(sql)\n", " con.commit()" @@ -1998,7 +3307,7 @@ }, { "cell_type": "code", - "execution_count": 256, + "execution_count": 456, "id": "78154d84-9df4-417d-a35f-60252575aae6", "metadata": { "tags": [] @@ -2010,7 +3319,7 @@ }, { "cell_type": "code", - "execution_count": 257, + "execution_count": 457, "id": "bf73ee32-d132-418f-8e77-969d779b780a", "metadata": { "tags": [] @@ -2037,7 +3346,9 @@ " \n", " \n", " \n", - " id\n", + " material_id\n", + " case_id\n", + " time_step_number\n", " elapsed_time\n", " irradiation_time\n", " cooling_time\n", @@ -2045,7 +3356,7 @@ " flux\n", " total_atoms\n", " total_activity\n", - " total_alpha_activity\n", + " ...\n", " total_beta_activity\n", " total_gamma_activity\n", " total_mass\n", @@ -2061,6 +3372,8 @@ " \n", " \n", " 0\n", + " 100\n", + " 3\n", " 1\n", " 0.000000e+00\n", " 0.0\n", @@ -2069,7 +3382,7 @@ " 0.000000e+00\n", " 1.045481e+22\n", " 1.099260e-02\n", - " 0.000000e+00\n", + " ...\n", " 1.099260e-02\n", " 0.000000e+00\n", " 0.001\n", @@ -2083,6 +3396,8 @@ " \n", " \n", " 1\n", + " 100\n", + " 3\n", " 2\n", " 6.311520e+07\n", " 63115200.0\n", @@ -2091,7 +3406,7 @@ " 2.445200e+10\n", " 1.045481e+22\n", " 2.268685e+07\n", - " 6.921229e-15\n", + " ...\n", " 1.476443e+07\n", " 7.922416e+06\n", " 0.001\n", @@ -2105,6 +3420,8 @@ " \n", " \n", " 2\n", + " 100\n", + " 3\n", " 3\n", " 3.786912e+08\n", " 378691200.0\n", @@ -2113,7 +3430,7 @@ " 1.882800e+11\n", " 1.045484e+22\n", " 2.005898e+08\n", - " 3.384520e-12\n", + " ...\n", " 1.391144e+08\n", " 6.147540e+07\n", " 0.001\n", @@ -2127,6 +3444,8 @@ " \n", " \n", " 3\n", + " 100\n", + " 3\n", " 4\n", " 3.997401e+08\n", " 378691200.0\n", @@ -2135,7 +3454,7 @@ " 0.000000e+00\n", " 1.045484e+22\n", " 5.064473e+07\n", - " 3.389543e-12\n", + " ...\n", " 5.005196e+07\n", " 5.927796e+05\n", " 0.001\n", @@ -2149,6 +3468,8 @@ " \n", " \n", " 4\n", + " 100\n", + " 3\n", " 5\n", " 4.417117e+08\n", " 420662816.0\n", @@ -2157,7 +3478,7 @@ " 3.790000e+11\n", " 1.045484e+22\n", " 3.644599e+08\n", - " 4.926714e-12\n", + " ...\n", " 2.411954e+08\n", " 1.232645e+08\n", " 0.001\n", @@ -2190,9 +3511,13 @@ " ...\n", " ...\n", " ...\n", + " ...\n", + " ...\n", " \n", " \n", " 60\n", + " 100\n", + " 3\n", " 61\n", " 7.573741e+08\n", " 420670816.0\n", @@ -2201,7 +3526,7 @@ " 0.000000e+00\n", " 1.045484e+22\n", " 1.021210e+07\n", - " 4.950759e-12\n", + " ...\n", " 9.725966e+06\n", " 4.861311e+05\n", " 0.001\n", @@ -2215,6 +3540,8 @@ " \n", " \n", " 61\n", + " 100\n", + " 3\n", " 62\n", " 1.388526e+09\n", " 420670816.0\n", @@ -2223,7 +3550,7 @@ " 0.000000e+00\n", " 1.045484e+22\n", " 2.140445e+06\n", - " 4.950759e-12\n", + " ...\n", " 1.934185e+06\n", " 2.062603e+05\n", " 0.001\n", @@ -2237,6 +3564,8 @@ " \n", " \n", " 62\n", + " 100\n", + " 3\n", " 63\n", " 2.019678e+09\n", " 420670816.0\n", @@ -2245,7 +3574,7 @@ " 0.000000e+00\n", " 1.045484e+22\n", " 1.354644e+06\n", - " 4.950759e-12\n", + " ...\n", " 1.266816e+06\n", " 8.782794e+04\n", " 0.001\n", @@ -2259,6 +3588,8 @@ " \n", " \n", " 63\n", + " 100\n", + " 3\n", " 64\n", " 3.597558e+09\n", " 420670816.0\n", @@ -2267,7 +3598,7 @@ " 0.000000e+00\n", " 1.045484e+22\n", " 8.909484e+05\n", - " 4.950759e-12\n", + " ...\n", " 8.798868e+05\n", " 1.106160e+04\n", " 0.001\n", @@ -2281,6 +3612,8 @@ " \n", " \n", " 64\n", + " 100\n", + " 3\n", " 65\n", " 3.199940e+10\n", " 420670816.0\n", @@ -2289,7 +3622,7 @@ " 0.000000e+00\n", " 1.045484e+22\n", " 3.152101e+04\n", - " 4.950759e-12\n", + " ...\n", " 3.071513e+04\n", " 8.058719e+02\n", " 0.001\n", @@ -2303,48 +3636,48 @@ " \n", " \n", "\n", - "

    65 rows × 19 columns

    \n", + "

    65 rows × 21 columns

    \n", "" ], "text/plain": [ - " id elapsed_time irradiation_time cooling_time duration \\\n", - "0 1 0.000000e+00 0.0 0.000000e+00 0.000000e+00 \n", - "1 2 6.311520e+07 63115200.0 0.000000e+00 6.311520e+07 \n", - "2 3 3.786912e+08 378691200.0 0.000000e+00 3.155760e+08 \n", - "3 4 3.997401e+08 378691200.0 2.104892e+07 2.104892e+07 \n", - "4 5 4.417117e+08 420662816.0 2.104892e+07 4.197161e+07 \n", - ".. .. ... ... ... ... \n", - "60 61 7.573741e+08 420670816.0 3.367033e+08 2.209032e+08 \n", - "61 62 1.388526e+09 420670816.0 9.678553e+08 6.311520e+08 \n", - "62 63 2.019678e+09 420670816.0 1.599007e+09 6.311520e+08 \n", - "63 64 3.597558e+09 420670816.0 3.176887e+09 1.577880e+09 \n", - "64 65 3.199940e+10 420670816.0 3.157873e+10 2.840184e+10 \n", - "\n", - " flux total_atoms total_activity total_alpha_activity \\\n", - "0 0.000000e+00 1.045481e+22 1.099260e-02 0.000000e+00 \n", - "1 2.445200e+10 1.045481e+22 2.268685e+07 6.921229e-15 \n", - "2 1.882800e+11 1.045484e+22 2.005898e+08 3.384520e-12 \n", - "3 0.000000e+00 1.045484e+22 5.064473e+07 3.389543e-12 \n", - "4 3.790000e+11 1.045484e+22 3.644599e+08 4.926714e-12 \n", - ".. ... ... ... ... \n", - "60 0.000000e+00 1.045484e+22 1.021210e+07 4.950759e-12 \n", - "61 0.000000e+00 1.045484e+22 2.140445e+06 4.950759e-12 \n", - "62 0.000000e+00 1.045484e+22 1.354644e+06 4.950759e-12 \n", - "63 0.000000e+00 1.045484e+22 8.909484e+05 4.950759e-12 \n", - "64 0.000000e+00 1.045484e+22 3.152101e+04 4.950759e-12 \n", - "\n", - " total_beta_activity total_gamma_activity total_mass total_heat \\\n", - "0 1.099260e-02 0.000000e+00 0.001 1.994928e-19 \n", - "1 1.476443e+07 7.922416e+06 0.001 2.522555e-09 \n", - "2 1.391144e+08 6.147540e+07 0.001 2.601587e-08 \n", - "3 5.005196e+07 5.927796e+05 0.001 1.072963e-08 \n", - "4 2.411954e+08 1.232645e+08 0.001 4.388052e-08 \n", - ".. ... ... ... ... \n", - "60 9.725966e+06 4.861311e+05 0.001 3.030422e-09 \n", - "61 1.934185e+06 2.062603e+05 0.001 2.260388e-10 \n", - "62 1.266816e+06 8.782794e+04 0.001 2.303827e-11 \n", - "63 8.798868e+05 1.106160e+04 0.001 6.016502e-12 \n", - "64 3.071513e+04 8.058719e+02 0.001 3.465519e-12 \n", + " material_id case_id time_step_number elapsed_time irradiation_time \\\n", + "0 100 3 1 0.000000e+00 0.0 \n", + "1 100 3 2 6.311520e+07 63115200.0 \n", + "2 100 3 3 3.786912e+08 378691200.0 \n", + "3 100 3 4 3.997401e+08 378691200.0 \n", + "4 100 3 5 4.417117e+08 420662816.0 \n", + ".. ... ... ... ... ... \n", + "60 100 3 61 7.573741e+08 420670816.0 \n", + "61 100 3 62 1.388526e+09 420670816.0 \n", + "62 100 3 63 2.019678e+09 420670816.0 \n", + "63 100 3 64 3.597558e+09 420670816.0 \n", + "64 100 3 65 3.199940e+10 420670816.0 \n", + "\n", + " cooling_time duration flux total_atoms total_activity \\\n", + "0 0.000000e+00 0.000000e+00 0.000000e+00 1.045481e+22 1.099260e-02 \n", + "1 0.000000e+00 6.311520e+07 2.445200e+10 1.045481e+22 2.268685e+07 \n", + "2 0.000000e+00 3.155760e+08 1.882800e+11 1.045484e+22 2.005898e+08 \n", + "3 2.104892e+07 2.104892e+07 0.000000e+00 1.045484e+22 5.064473e+07 \n", + "4 2.104892e+07 4.197161e+07 3.790000e+11 1.045484e+22 3.644599e+08 \n", + ".. ... ... ... ... ... \n", + "60 3.367033e+08 2.209032e+08 0.000000e+00 1.045484e+22 1.021210e+07 \n", + "61 9.678553e+08 6.311520e+08 0.000000e+00 1.045484e+22 2.140445e+06 \n", + "62 1.599007e+09 6.311520e+08 0.000000e+00 1.045484e+22 1.354644e+06 \n", + "63 3.176887e+09 1.577880e+09 0.000000e+00 1.045484e+22 8.909484e+05 \n", + "64 3.157873e+10 2.840184e+10 0.000000e+00 1.045484e+22 3.152101e+04 \n", + "\n", + " ... total_beta_activity total_gamma_activity total_mass total_heat \\\n", + "0 ... 1.099260e-02 0.000000e+00 0.001 1.994928e-19 \n", + "1 ... 1.476443e+07 7.922416e+06 0.001 2.522555e-09 \n", + "2 ... 1.391144e+08 6.147540e+07 0.001 2.601587e-08 \n", + "3 ... 5.005196e+07 5.927796e+05 0.001 1.072963e-08 \n", + "4 ... 2.411954e+08 1.232645e+08 0.001 4.388052e-08 \n", + ".. ... ... ... ... ... \n", + "60 ... 9.725966e+06 4.861311e+05 0.001 3.030422e-09 \n", + "61 ... 1.934185e+06 2.062603e+05 0.001 2.260388e-10 \n", + "62 ... 1.266816e+06 8.782794e+04 0.001 2.303827e-11 \n", + "63 ... 8.798868e+05 1.106160e+04 0.001 6.016502e-12 \n", + "64 ... 3.071513e+04 8.058719e+02 0.001 3.465519e-12 \n", "\n", " total_alpha_heat total_beta_heat total_gamma_heat \\\n", "0 0.000000e+00 1.994919e-19 8.784190e-25 \n", @@ -2372,50 +3705,206 @@ "63 1.548528e-04 1.769614e-03 2.999845e-09 \n", "64 2.518117e-05 6.220313e-04 2.701462e-09 \n", "\n", - "[65 rows x 19 columns]" + "[65 rows x 21 columns]" + ] + }, + "execution_count": 457, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "con.execute(\"select * from timestep\").df()" + ] + }, + { + "cell_type": "code", + "execution_count": 458, + "id": "c5fdb6e7-00b7-40f1-9d8d-f755dd768a97", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "def save_nuclides(con, ds):\n", + " nuclides_df = ds[[\"element\", \"mass_number\", \"state\", \"zai\", \"nuclide_half_life\"]].to_pandas().reset_index(drop=True)\n", + " sql = \"insert or ignore into nuclide select * from nuclides_df\"\n", + " con.execute(sql)\n", + " con.commit()" + ] + }, + { + "cell_type": "code", + "execution_count": 459, + "id": "2cd4e47d-1ec3-493c-b655-8a83917deea5", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "save_nuclides(con, ds)" + ] + }, + { + "cell_type": "code", + "execution_count": 460, + "id": "1f6cbb0e-e893-4d88-a744-989d9b39e0a4", + "metadata": { + "tags": [] + }, + "outputs": [ + { + "data": { + "text/html": [ + "
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    " + ], + "text/plain": [ + " element mass_number state zai half_life\n", + "0 Al 26 130260 2.262630e+13\n", + "1 Al 27 130270 0.000000e+00\n", + "2 Al 28 130280 1.344600e+02\n", + "3 Al 29 130290 3.936000e+02\n", + "4 Al 30 130300 3.650000e+00\n", + ".. ... ... ... ... ...\n", + "210 Zr 93 400930 4.828210e+13\n", + "211 Zr 94 400940 1.893460e+23\n", + "212 Zr 95 400950 5.532360e+06\n", + "213 Zr 96 400960 1.230750e+27\n", + "214 Zr 97 400970 6.027840e+04\n", + "\n", + "[215 rows x 5 columns]" ] }, - "execution_count": 257, + "execution_count": 460, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "con.execute(\"select * from timestep\").df()" - ] - }, - { - "cell_type": "code", - "execution_count": 258, - "id": "c5fdb6e7-00b7-40f1-9d8d-f755dd768a97", - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "def save_nuclides(con, ds):\n", - " nuclides_df = ds[[\"element\", \"mass_number\", \"state\", \"zai\", \"nuclide_half_life\"]].to_pandas().reset_index(drop=True)\n", - " sql = \"insert into nuclide select * from nuclides_df\"\n", - " con.execute(sql)\n", - " con.commit()" - ] - }, - { - "cell_type": "code", - "execution_count": 259, - "id": "2cd4e47d-1ec3-493c-b655-8a83917deea5", - "metadata": { - "tags": [] - }, - "outputs": [], - "source": [ - "save_nuclides(con, ds)" + "con.execute(\"select * from nuclide\").df()" ] }, { "cell_type": "code", - "execution_count": 285, - "id": "1f6cbb0e-e893-4d88-a744-989d9b39e0a4", + "execution_count": 508, + "id": "1161cef3-d3cf-4c2f-aa2d-2c1ea9ee9208", "metadata": { "tags": [] }, @@ -2441,53 +3930,149 @@ " \n", " \n", " \n", + " material_id\n", + " case_id\n", + " time_step_number\n", " element\n", " mass_number\n", " state\n", + " nuclide_atoms\n", + " nuclide_grams\n", + " nuclide_activity\n", + " nuclide_alpha_activity\n", + " ...\n", + " nuclide_gamma_activity\n", + " nuclide_heat\n", + " nuclide_alpha_heat\n", + " nuclide_beta_heat\n", + " nuclide_gamma_heat\n", + " nuclide_dose\n", + " nuclide_ingestion\n", + " nuclide_inhalation\n", + " elapsed_time\n", " zai\n", - " half_life\n", " \n", " \n", " \n", " \n", " 0\n", + " 0\n", + " 0\n", + " 0\n", " Al\n", " 26\n", " \n", + " 0.000000e+00\n", + " 0.000000e+00\n", + " 0.000000e+00\n", + " 0.0\n", + " ...\n", + " 0.0\n", + " 0.000000e+00\n", + " 0.0\n", + " 0.000000e+00\n", + " 0.0\n", + " 0.0\n", + " 0.000000e+00\n", + " 0.000000e+00\n", + " 0.000000e+00\n", " 130260\n", - " 2.262630e+13\n", " \n", " \n", " 1\n", + " 0\n", + " 0\n", + " 0\n", " Al\n", " 27\n", " \n", - " 130270\n", + " 1.785556e+20\n", + " 8.000000e-03\n", + " 0.000000e+00\n", + " 0.0\n", + " ...\n", + " 0.0\n", " 0.000000e+00\n", + " 0.0\n", + " 0.000000e+00\n", + " 0.0\n", + " 0.0\n", + " 0.000000e+00\n", + " 0.000000e+00\n", + " 0.000000e+00\n", + " 130270\n", " \n", " \n", " 2\n", + " 0\n", + " 0\n", + " 0\n", " Al\n", " 28\n", " \n", + " 0.000000e+00\n", + " 0.000000e+00\n", + " 0.000000e+00\n", + " 0.0\n", + " ...\n", + " 0.0\n", + " 0.000000e+00\n", + " 0.0\n", + " 0.000000e+00\n", + " 0.0\n", + " 0.0\n", + " 0.000000e+00\n", + " 0.000000e+00\n", + " 0.000000e+00\n", " 130280\n", - " 1.344600e+02\n", " \n", " \n", " 3\n", + " 0\n", + " 0\n", + " 0\n", " Al\n", " 29\n", " \n", + " 0.000000e+00\n", + " 0.000000e+00\n", + " 0.000000e+00\n", + " 0.0\n", + " ...\n", + " 0.0\n", + " 0.000000e+00\n", + " 0.0\n", + " 0.000000e+00\n", + " 0.0\n", + " 0.0\n", + " 0.000000e+00\n", + " 0.000000e+00\n", + " 0.000000e+00\n", " 130290\n", - " 3.936000e+02\n", " \n", " \n", " 4\n", + " 0\n", + " 0\n", + " 0\n", " Al\n", " 30\n", " \n", + " 0.000000e+00\n", + " 0.000000e+00\n", + " 0.000000e+00\n", + " 0.0\n", + " ...\n", + " 0.0\n", + " 0.000000e+00\n", + " 0.0\n", + " 0.000000e+00\n", + " 0.0\n", + " 0.0\n", + " 0.000000e+00\n", + " 0.000000e+00\n", + " 0.000000e+00\n", " 130300\n", - " 3.650000e+00\n", " \n", " \n", " ...\n", @@ -2496,76 +4081,261 @@ " ...\n", " ...\n", " ...\n", + " ...\n", + " ...\n", + " ...\n", + " ...\n", + " ...\n", + " ...\n", + " ...\n", + " ...\n", + " ...\n", + " ...\n", + " ...\n", + " ...\n", + " ...\n", + " ...\n", + " ...\n", + " ...\n", " \n", " \n", - " 210\n", + " 13970\n", + " 0\n", + " 0\n", + " 64\n", " Zr\n", " 93\n", " \n", + " 6.327286e+13\n", + " 9.761411e-09\n", + " 9.083574e-01\n", + " 0.0\n", + " ...\n", + " 0.0\n", + " 2.791257e-18\n", + " 0.0\n", + " 2.791257e-18\n", + " 0.0\n", + " 0.0\n", + " 9.991931e-10\n", + " 2.270893e-08\n", + " 3.199940e+10\n", " 400930\n", - " 4.828210e+13\n", " \n", " \n", - " 211\n", + " 13971\n", + " 0\n", + " 0\n", + " 64\n", " Zr\n", " 94\n", " \n", + " 7.058445e+11\n", + " 1.100659e-10\n", + " 2.583916e-12\n", + " 0.0\n", + " ...\n", + " 0.0\n", + " 4.734377e-28\n", + " 0.0\n", + " 4.734377e-28\n", + " 0.0\n", + " 0.0\n", + " 2.480559e-20\n", + " 2.842307e-20\n", + " 3.199940e+10\n", " 400940\n", - " 1.893460e+23\n", " \n", " \n", - " 212\n", + " 13972\n", + " 0\n", + " 0\n", + " 64\n", " Zr\n", " 95\n", " \n", + " 0.000000e+00\n", + " 0.000000e+00\n", + " 0.000000e+00\n", + " 0.0\n", + " ...\n", + " 0.0\n", + " 0.000000e+00\n", + " 0.0\n", + " 0.000000e+00\n", + " 0.0\n", + " 0.0\n", + " 0.000000e+00\n", + " 0.000000e+00\n", + " 3.199940e+10\n", " 400950\n", - " 5.532360e+06\n", " \n", " \n", - " 213\n", + " 13973\n", + " 0\n", + " 0\n", + " 64\n", " Zr\n", " 96\n", " \n", + " 1.091942e+10\n", + " 1.739020e-12\n", + " 6.149716e-18\n", + " 0.0\n", + " ...\n", + " 0.0\n", + " 3.301027e-33\n", + " 0.0\n", + " 3.301027e-33\n", + " 0.0\n", + " 0.0\n", + " 1.721921e-25\n", + " 1.906412e-25\n", + " 3.199940e+10\n", " 400960\n", - " 1.230750e+27\n", " \n", " \n", - " 214\n", + " 13974\n", + " 0\n", + " 0\n", + " 64\n", " Zr\n", " 97\n", " \n", + " 0.000000e+00\n", + " 0.000000e+00\n", + " 0.000000e+00\n", + " 0.0\n", + " ...\n", + " 0.0\n", + " 0.000000e+00\n", + " 0.0\n", + " 0.000000e+00\n", + " 0.0\n", + " 0.0\n", + " 0.000000e+00\n", + " 0.000000e+00\n", + " 3.199940e+10\n", " 400970\n", - " 6.027840e+04\n", " \n", " \n", "\n", - "

    215 rows × 5 columns

    \n", + "

    13975 rows × 21 columns

    \n", "" ], "text/plain": [ - " element mass_number state zai half_life\n", - "0 Al 26 130260 2.262630e+13\n", - "1 Al 27 130270 0.000000e+00\n", - "2 Al 28 130280 1.344600e+02\n", - "3 Al 29 130290 3.936000e+02\n", - "4 Al 30 130300 3.650000e+00\n", - ".. ... ... ... ... ...\n", - "210 Zr 93 400930 4.828210e+13\n", - "211 Zr 94 400940 1.893460e+23\n", - "212 Zr 95 400950 5.532360e+06\n", - "213 Zr 96 400960 1.230750e+27\n", - "214 Zr 97 400970 6.027840e+04\n", - "\n", - "[215 rows x 5 columns]" + " material_id case_id time_step_number element mass_number state \\\n", + "0 0 0 0 Al 26 \n", + "1 0 0 0 Al 27 \n", + "2 0 0 0 Al 28 \n", + "3 0 0 0 Al 29 \n", + "4 0 0 0 Al 30 \n", + "... ... ... ... ... ... ... \n", + "13970 0 0 64 Zr 93 \n", + "13971 0 0 64 Zr 94 \n", + "13972 0 0 64 Zr 95 \n", + "13973 0 0 64 Zr 96 \n", + "13974 0 0 64 Zr 97 \n", + "\n", + " nuclide_atoms nuclide_grams nuclide_activity nuclide_alpha_activity \\\n", + "0 0.000000e+00 0.000000e+00 0.000000e+00 0.0 \n", + "1 1.785556e+20 8.000000e-03 0.000000e+00 0.0 \n", + "2 0.000000e+00 0.000000e+00 0.000000e+00 0.0 \n", + "3 0.000000e+00 0.000000e+00 0.000000e+00 0.0 \n", + "4 0.000000e+00 0.000000e+00 0.000000e+00 0.0 \n", + "... ... ... ... ... \n", + "13970 6.327286e+13 9.761411e-09 9.083574e-01 0.0 \n", + "13971 7.058445e+11 1.100659e-10 2.583916e-12 0.0 \n", + "13972 0.000000e+00 0.000000e+00 0.000000e+00 0.0 \n", + "13973 1.091942e+10 1.739020e-12 6.149716e-18 0.0 \n", + "13974 0.000000e+00 0.000000e+00 0.000000e+00 0.0 \n", + "\n", + " ... nuclide_gamma_activity nuclide_heat nuclide_alpha_heat \\\n", + "0 ... 0.0 0.000000e+00 0.0 \n", + "1 ... 0.0 0.000000e+00 0.0 \n", + "2 ... 0.0 0.000000e+00 0.0 \n", + "3 ... 0.0 0.000000e+00 0.0 \n", + "4 ... 0.0 0.000000e+00 0.0 \n", + "... ... ... ... ... \n", + "13970 ... 0.0 2.791257e-18 0.0 \n", + "13971 ... 0.0 4.734377e-28 0.0 \n", + "13972 ... 0.0 0.000000e+00 0.0 \n", + "13973 ... 0.0 3.301027e-33 0.0 \n", + "13974 ... 0.0 0.000000e+00 0.0 \n", + "\n", + " nuclide_beta_heat nuclide_gamma_heat nuclide_dose nuclide_ingestion \\\n", + "0 0.000000e+00 0.0 0.0 0.000000e+00 \n", + "1 0.000000e+00 0.0 0.0 0.000000e+00 \n", + "2 0.000000e+00 0.0 0.0 0.000000e+00 \n", + "3 0.000000e+00 0.0 0.0 0.000000e+00 \n", + "4 0.000000e+00 0.0 0.0 0.000000e+00 \n", + "... ... ... ... ... \n", + "13970 2.791257e-18 0.0 0.0 9.991931e-10 \n", + "13971 4.734377e-28 0.0 0.0 2.480559e-20 \n", + "13972 0.000000e+00 0.0 0.0 0.000000e+00 \n", + "13973 3.301027e-33 0.0 0.0 1.721921e-25 \n", + "13974 0.000000e+00 0.0 0.0 0.000000e+00 \n", + "\n", + " nuclide_inhalation elapsed_time zai \n", + "0 0.000000e+00 0.000000e+00 130260 \n", + "1 0.000000e+00 0.000000e+00 130270 \n", + "2 0.000000e+00 0.000000e+00 130280 \n", + "3 0.000000e+00 0.000000e+00 130290 \n", + "4 0.000000e+00 0.000000e+00 130300 \n", + "... ... ... ... \n", + "13970 2.270893e-08 3.199940e+10 400930 \n", + "13971 2.842307e-20 3.199940e+10 400940 \n", + "13972 0.000000e+00 3.199940e+10 400950 \n", + "13973 1.906412e-25 3.199940e+10 400960 \n", + "13974 0.000000e+00 3.199940e+10 400970 \n", + "\n", + "[13975 rows x 21 columns]" ] }, - "execution_count": 285, + "execution_count": 508, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "con.execute(\"select * from nuclide\").df()" + "columns = [\n", + " \"material_id\",\n", + " \"case_id\",\n", + " \"time_step_number\",\n", + " \"element\",\n", + " \"mass_number\",\n", + " \"state\",\n", + " \"nuclide_atoms\",\n", + " \"nuclide_grams\",\n", + " \"nuclide_activity\",\n", + " \"nuclide_alpha_activity\",\n", + " \"nuclide_beta_activity\",\n", + " \"nuclide_gamma_activity\",\n", + " \"nuclide_heat\",\n", + " \"nuclide_alpha_heat\",\n", + " \"nuclide_beta_heat\",\n", + " \"nuclide_gamma_heat\",\n", + " \"nuclide_dose\",\n", + " \"nuclide_ingestion\",\n", + " \"nuclide_inhalation\",\n", + "]\n", + "# tn = ds[columns].to_dataframe().reset_index(\n", + "# [\n", + "# \"material_id\", \"case_id\", \"time_step_number\",\n", + "# ]\n", + "# )\n", + "# tn = tn.reset_index(\n", + "# [\"element\", \"mass_number\", \"state\"]\n", + "# )\n", + "\n", + "# .reset_index()\n", + "# .reset_index(\"time_step_number\")[columns].fillna(0.0)\n", + "# tn.reset_index(allow_duplicates=True)\n", + "ds[columns].reset_index([\"material_id\", \"case_id\", \"time_step_number\", \"nuclide\"]).to_dataframe().reset_index(\n", + " [\n", + " \"material_id\", \"case_id\", \"time_step_number\",\n", + " ]\n", + ").reset_index(drop=True).fillna(0.0)\n" ] }, { @@ -2579,6 +4349,8 @@ "source": [ "def save_timestep_nucludes(con, ds):\n", " columns = [\n", + " \"material_id\",\n", + " \"case_id\",\n", " \"time_step_number\",\n", " \"element\",\n", " \"mass_number\",\n", diff --git a/notebooks/dvp/try_ducdb.py b/notebooks/dvp/try_ducdb.py index f480e6d..1727c60 100644 --- a/notebooks/dvp/try_ducdb.py +++ b/notebooks/dvp/try_ducdb.py @@ -49,19 +49,19 @@ inventory = from_json(json_path) -# In[241]: +# In[469]: ds = da.create_dataset(inventory) -# In[242]: +# In[470]: ds -# In[287]: +# In[417]: ds.timestamp @@ -94,7 +94,20 @@ case_id = 3 -# In[387]: +# In[475]: + + +ds = ds.expand_dims(dim={"material_id": [material_id], "case_id": [case_id]}) +ds + + +# In[476]: + + +ds.irradiation_time + + +# In[446]: def drop_tables(con): @@ -105,7 +118,7 @@ def drop_tables(con): con.execute("drop table if exists rundata") -# In[395]: +# In[447]: def create_tables(con): @@ -122,7 +135,9 @@ def create_tables(con): ); CREATE TABLE IF NOT EXISTS timestep( - id uinteger PRIMARY KEY, + material_id uinteger not null, + case_id uinteger not null, + time_step_number uinteger not null, elapsed_time float4 not null, irradiation_time float4 not null, cooling_time float4 not null, @@ -141,8 +156,7 @@ def create_tables(con): total_ingest1ion_dose float4 not null, total_inhalation_dose float4 not null, total_dose_rate float4 not null, - material_id uinteger not null, - case_id uinteger not null, + primary key(material_id, case_id, time_step_number), foreign key(material_id, case_id) references rundata(material_id, case_id) ); @@ -157,7 +171,9 @@ def create_tables(con): ); CREATE TABLE IF NOT EXISTS timestep_nuclide( - timestep_id uinteger not null, + material_id uinteger not null, + case_id uinteger not null, + time_step_number uinteger not null, element varchar(2) not null, mass_number usmallint not null, state varchar(1) not null, @@ -174,42 +190,44 @@ def create_tables(con): dose float4 not null, ingestion float4 not null, inhalation float4 not null, - primary key(timestep_id, element, mass_number, state), - foreign key(timestep_id) references timestep(id), + primary key(material_id, case_id, time_step_number, element, mass_number, state), + foreign key(material_id, case_id, time_step_number) references timestep(material_id, case_id, time_step_number), foreign key(element, mass_number, state) references nuclide(element, mass_number, state) ); CREATE TABLE IF NOT EXISTS timestep_gamma( - timestep_id uinteger not null, + material_id uinteger not null, + case_id uinteger not null, + time_step_number uinteger not null, boundary real not null check(0 <= boundary), intensity real not null, - primary key(timestep_id, boundary), - foreign key(timestep_id) references timestep(id), + primary key(material_id, case_id, time_step_number, boundary), + foreign key(material_id, case_id, time_step_number) references timestep(material_id, case_id, time_step_number), ); """ con.execute(sql) -# In[396]: +# In[448]: -# drop_tables(con) +drop_tables(con) create_tables(con) -# In[402]: +# In[449]: def save_rundata(con, ds): sql = """ - INSERT INTO rundata values(?, ?, ?, ?, ?) + INSERT INTO rundata values(?, ?, ?, ?, ?, ?, ?) """ con.execute( sql, ( - material_id, - case_id, - ds.coords["timestamp"].item(), + ds.material_id.item(), + ds.case_id.item(), + ds.timestamp.dt.strftime("%Y-%m-%d %H:%M:%S").item(), ds.attrs["run_name"], ds.attrs["flux_name"], ds.attrs["dose_rate_type"], @@ -219,31 +237,27 @@ def save_rundata(con, ds): con.commit() -# In[403]: - - -con.execute("select * from information_schema.tables").df() - - -# In[400]: +# In[451]: save_rundata(con, ds) -# In[254]: +# In[452]: con.execute("select * from rundata").df() -# In[255]: +# In[455]: def save_timesteps(con, ds): timesteps_df = ( ds[ [ + "material_id", + "case_id", "time_step_number", "elapsed_time", "irradiation_time", @@ -265,7 +279,7 @@ def save_timesteps(con, ds): "total_dose_rate", ] ] - .to_pandas() + .to_dataframe() .reset_index() ) sql = "insert into timestep select * from timesteps_df" @@ -273,19 +287,19 @@ def save_timesteps(con, ds): con.commit() -# In[256]: +# In[456]: save_timesteps(con, ds) -# In[257]: +# In[457]: con.execute("select * from timestep").df() -# In[258]: +# In[458]: def save_nuclides(con, ds): @@ -294,28 +308,81 @@ def save_nuclides(con, ds): .to_pandas() .reset_index(drop=True) ) - sql = "insert into nuclide select * from nuclides_df" + sql = "insert or ignore into nuclide select * from nuclides_df" con.execute(sql) con.commit() -# In[259]: +# In[459]: save_nuclides(con, ds) -# In[285]: +# In[460]: con.execute("select * from nuclide").df() +# In[508]: + + +columns = [ + "material_id", + "case_id", + "time_step_number", + "element", + "mass_number", + "state", + "nuclide_atoms", + "nuclide_grams", + "nuclide_activity", + "nuclide_alpha_activity", + "nuclide_beta_activity", + "nuclide_gamma_activity", + "nuclide_heat", + "nuclide_alpha_heat", + "nuclide_beta_heat", + "nuclide_gamma_heat", + "nuclide_dose", + "nuclide_ingestion", + "nuclide_inhalation", +] +# tn = ds[columns].to_dataframe().reset_index( +# [ +# "material_id", "case_id", "time_step_number", +# ] +# ) +# tn = tn.reset_index( +# ["element", "mass_number", "state"] +# ) + +# .reset_index() +# .reset_index("time_step_number")[columns].fillna(0.0) +# tn.reset_index(allow_duplicates=True) +ds[columns].reset_index( + ["material_id", "case_id", "time_step_number", "nuclide"] +).to_dataframe().reset_index( + [ + "material_id", + "case_id", + "time_step_number", + ] +).reset_index( + drop=True +).fillna( + 0.0 +) + + # In[263]: def save_timestep_nucludes(con, ds): columns = [ + "material_id", + "case_id", "time_step_number", "element", "mass_number", From b68c61296c63b00efb89f4e8ccc13f334edb2296 Mon Sep 17 00:00:00 2001 From: dvp Date: Fri, 24 Mar 2023 17:08:05 +0300 Subject: [PATCH 11/32] notebook: duckdb prototyping in progress --- notebooks/dvp/try_ducdb.ipynb | 939 +++++++++++++++++++--------------- notebooks/dvp/try_ducdb.py | 80 +-- 2 files changed, 574 insertions(+), 445 deletions(-) diff --git a/notebooks/dvp/try_ducdb.ipynb b/notebooks/dvp/try_ducdb.ipynb index a2036ed..12d27ba 100644 --- a/notebooks/dvp/try_ducdb.ipynb +++ b/notebooks/dvp/try_ducdb.ipynb @@ -3110,20 +3110,24 @@ " time_step_number uinteger not null,\n", " element varchar(2) not null,\n", " mass_number usmallint not null,\n", + " \n", " state varchar(1) not null,\n", " atoms float4 not null,\n", " grams float4 not null,\n", " activity float4 not null,\n", " alpha_activity float4 not null,\n", + " \n", " beta_activity float4 not null,\n", " gamma_activity float4 not null,\n", " heat float4 not null,\n", " alpha_heat float4 not null,\n", " beta_heat float4 not null,\n", + " \n", " gamma_heat float4 not null,\n", " dose float4 not null,\n", " ingestion float4 not null,\n", " inhalation float4 not null,\n", + " \n", " primary key(material_id, case_id, time_step_number, element, mass_number, state),\n", " foreign key(material_id, case_id, time_step_number) references timestep(material_id, case_id, time_step_number),\n", " foreign key(element, mass_number, state) references nuclide(element, mass_number, state) \n", @@ -3144,7 +3148,7 @@ }, { "cell_type": "code", - "execution_count": 448, + "execution_count": 512, "id": "25f6867e-397a-4e98-a363-74b6af739c88", "metadata": { "tags": [] @@ -3157,7 +3161,7 @@ }, { "cell_type": "code", - "execution_count": 449, + "execution_count": 513, "id": "29716201-70f8-40d2-8da7-85689714ec32", "metadata": { "tags": [] @@ -3182,7 +3186,7 @@ }, { "cell_type": "code", - "execution_count": 451, + "execution_count": 514, "id": "c789eedd-580c-4383-8bf1-cc943562a3aa", "metadata": { "tags": [] @@ -3194,7 +3198,7 @@ }, { "cell_type": "code", - "execution_count": 452, + "execution_count": 515, "id": "1c650134-edf3-44dd-aa90-ddde6a3987a7", "metadata": { "tags": [] @@ -3256,7 +3260,7 @@ "0 1.0 " ] }, - "execution_count": 452, + "execution_count": 515, "metadata": {}, "output_type": "execute_result" } @@ -3267,7 +3271,7 @@ }, { "cell_type": "code", - "execution_count": 455, + "execution_count": 516, "id": "cf8661b6-d9cb-4431-8b40-f14072409d5a", "metadata": { "tags": [] @@ -3307,7 +3311,7 @@ }, { "cell_type": "code", - "execution_count": 456, + "execution_count": 517, "id": "78154d84-9df4-417d-a35f-60252575aae6", "metadata": { "tags": [] @@ -3319,7 +3323,7 @@ }, { "cell_type": "code", - "execution_count": 457, + "execution_count": 518, "id": "bf73ee32-d132-418f-8e77-969d779b780a", "metadata": { "tags": [] @@ -3708,7 +3712,7 @@ "[65 rows x 21 columns]" ] }, - "execution_count": 457, + "execution_count": 518, "metadata": {}, "output_type": "execute_result" } @@ -3719,7 +3723,7 @@ }, { "cell_type": "code", - "execution_count": 458, + "execution_count": 533, "id": "c5fdb6e7-00b7-40f1-9d8d-f755dd768a97", "metadata": { "tags": [] @@ -3727,7 +3731,16 @@ "outputs": [], "source": [ "def save_nuclides(con, ds):\n", - " nuclides_df = ds[[\"element\", \"mass_number\", \"state\", \"zai\", \"nuclide_half_life\"]].to_pandas().reset_index(drop=True)\n", + " nuclides_df = ds[[\"element\", \"mass_number\", \"state\", \"zai\", \"nuclide_half_life\"]] \\\n", + " .reset_index([\"material_id\", \"case_id\"]) \\\n", + " .to_dataframe() \\\n", + " .reset_index(\n", + " [\n", + " \"material_id\", \"case_id\"\n", + " ],\n", + " drop=True\n", + " ) \\\n", + " .reset_index(drop=True)\n", " sql = \"insert or ignore into nuclide select * from nuclides_df\"\n", " con.execute(sql)\n", " con.commit()" @@ -3735,7 +3748,7 @@ }, { "cell_type": "code", - "execution_count": 459, + "execution_count": 534, "id": "2cd4e47d-1ec3-493c-b655-8a83917deea5", "metadata": { "tags": [] @@ -3747,7 +3760,7 @@ }, { "cell_type": "code", - "execution_count": 460, + "execution_count": 535, "id": "1f6cbb0e-e893-4d88-a744-989d9b39e0a4", "metadata": { "tags": [] @@ -3892,7 +3905,7 @@ "[215 rows x 5 columns]" ] }, - "execution_count": 460, + "execution_count": 535, "metadata": {}, "output_type": "execute_result" } @@ -3903,7 +3916,7 @@ }, { "cell_type": "code", - "execution_count": 508, + "execution_count": 559, "id": "1161cef3-d3cf-4c2f-aa2d-2c1ea9ee9208", "metadata": { "tags": [] @@ -3912,387 +3925,485 @@ { "data": { "text/html": [ - "
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    <xarray.Dataset>\n",
+       "Dimensions:           (material_id: 1, case_id: 1, time_step_number: 65,\n",
+       "                       nuclide: 215)\n",
+       "Coordinates:\n",
+       "  * material_id       (material_id) int64 100\n",
+       "  * case_id           (case_id) int64 3\n",
+       "  * time_step_number  (time_step_number) int64 1 2 3 4 5 6 ... 60 61 62 63 64 65\n",
+       "  * element           (nuclide) object 'Al' 'Al' 'Al' 'Al' ... 'Zr' 'Zr' 'Zr'\n",
+       "  * mass_number       (nuclide) int64 26 27 28 29 30 40 10 ... 92 93 94 95 96 97\n",
+       "  * state             (nuclide) object '' '' '' '' '' '' ... '' '' '' '' '' ''\n",
+       "  * nuclide           (nuclide) object MultiIndex\n",
+       "    elapsed_time      (time_step_number) float64 0.0 6.312e+07 ... 3.2e+10\n",
+       "    zai               (nuclide) int64 130260 130270 130280 ... 400960 400970\n",
+       "Data variables:\n",
+       "    *empty*\n",
+       "Attributes:\n",
+       "    run_name:            * Material Alloy718-Co04, fluxes 104_2_1_1\n",
+       "    flux_name:           90-degrees bend\n",
+       "    dose_rate_type:      Point source\n",
+       "    dose_rate_distance:  1.0
    " ], "text/plain": [ - " material_id case_id time_step_number element mass_number state \\\n", - "0 0 0 0 Al 26 \n", - "1 0 0 0 Al 27 \n", - "2 0 0 0 Al 28 \n", - "3 0 0 0 Al 29 \n", - "4 0 0 0 Al 30 \n", - "... ... ... ... ... ... ... \n", - "13970 0 0 64 Zr 93 \n", - "13971 0 0 64 Zr 94 \n", - "13972 0 0 64 Zr 95 \n", - "13973 0 0 64 Zr 96 \n", - "13974 0 0 64 Zr 97 \n", - "\n", - " nuclide_atoms nuclide_grams nuclide_activity nuclide_alpha_activity \\\n", - "0 0.000000e+00 0.000000e+00 0.000000e+00 0.0 \n", - "1 1.785556e+20 8.000000e-03 0.000000e+00 0.0 \n", - "2 0.000000e+00 0.000000e+00 0.000000e+00 0.0 \n", - "3 0.000000e+00 0.000000e+00 0.000000e+00 0.0 \n", - "4 0.000000e+00 0.000000e+00 0.000000e+00 0.0 \n", - "... ... ... ... ... \n", - "13970 6.327286e+13 9.761411e-09 9.083574e-01 0.0 \n", - "13971 7.058445e+11 1.100659e-10 2.583916e-12 0.0 \n", - "13972 0.000000e+00 0.000000e+00 0.000000e+00 0.0 \n", - "13973 1.091942e+10 1.739020e-12 6.149716e-18 0.0 \n", - "13974 0.000000e+00 0.000000e+00 0.000000e+00 0.0 \n", - "\n", - " ... nuclide_gamma_activity nuclide_heat nuclide_alpha_heat \\\n", - "0 ... 0.0 0.000000e+00 0.0 \n", - "1 ... 0.0 0.000000e+00 0.0 \n", - "2 ... 0.0 0.000000e+00 0.0 \n", - "3 ... 0.0 0.000000e+00 0.0 \n", - "4 ... 0.0 0.000000e+00 0.0 \n", - "... ... ... ... ... \n", - "13970 ... 0.0 2.791257e-18 0.0 \n", - "13971 ... 0.0 4.734377e-28 0.0 \n", - "13972 ... 0.0 0.000000e+00 0.0 \n", - "13973 ... 0.0 3.301027e-33 0.0 \n", - "13974 ... 0.0 0.000000e+00 0.0 \n", - "\n", - " nuclide_beta_heat nuclide_gamma_heat nuclide_dose nuclide_ingestion \\\n", - "0 0.000000e+00 0.0 0.0 0.000000e+00 \n", - "1 0.000000e+00 0.0 0.0 0.000000e+00 \n", - "2 0.000000e+00 0.0 0.0 0.000000e+00 \n", - "3 0.000000e+00 0.0 0.0 0.000000e+00 \n", - "4 0.000000e+00 0.0 0.0 0.000000e+00 \n", - "... ... ... ... ... \n", - "13970 2.791257e-18 0.0 0.0 9.991931e-10 \n", - "13971 4.734377e-28 0.0 0.0 2.480559e-20 \n", - "13972 0.000000e+00 0.0 0.0 0.000000e+00 \n", - "13973 3.301027e-33 0.0 0.0 1.721921e-25 \n", - "13974 0.000000e+00 0.0 0.0 0.000000e+00 \n", - "\n", - " nuclide_inhalation elapsed_time zai \n", - "0 0.000000e+00 0.000000e+00 130260 \n", - "1 0.000000e+00 0.000000e+00 130270 \n", - "2 0.000000e+00 0.000000e+00 130280 \n", - "3 0.000000e+00 0.000000e+00 130290 \n", - "4 0.000000e+00 0.000000e+00 130300 \n", - "... ... ... ... \n", - "13970 2.270893e-08 3.199940e+10 400930 \n", - "13971 2.842307e-20 3.199940e+10 400940 \n", - "13972 0.000000e+00 3.199940e+10 400950 \n", - "13973 1.906412e-25 3.199940e+10 400960 \n", - "13974 0.000000e+00 3.199940e+10 400970 \n", - "\n", - "[13975 rows x 21 columns]" + "\n", + "Dimensions: (material_id: 1, case_id: 1, time_step_number: 65,\n", + " nuclide: 215)\n", + "Coordinates:\n", + " * material_id (material_id) int64 100\n", + " * case_id (case_id) int64 3\n", + " * time_step_number (time_step_number) int64 1 2 3 4 5 6 ... 60 61 62 63 64 65\n", + " * element (nuclide) object 'Al' 'Al' 'Al' 'Al' ... 'Zr' 'Zr' 'Zr'\n", + " * mass_number (nuclide) int64 26 27 28 29 30 40 10 ... 92 93 94 95 96 97\n", + " * state (nuclide) object '' '' '' '' '' '' ... '' '' '' '' '' ''\n", + " * nuclide (nuclide) object MultiIndex\n", + " elapsed_time (time_step_number) float64 0.0 6.312e+07 ... 3.2e+10\n", + " zai (nuclide) int64 130260 130270 130280 ... 400960 400970\n", + "Data variables:\n", + " *empty*\n", + "Attributes:\n", + " run_name: * Material Alloy718-Co04, fluxes 104_2_1_1\n", + " flux_name: 90-degrees bend\n", + " dose_rate_type: Point source\n", + " dose_rate_distance: 1.0" ] }, - "execution_count": 508, + "execution_count": 559, "metadata": {}, "output_type": "execute_result" } @@ -4319,28 +4430,23 @@ " \"nuclide_ingestion\",\n", " \"nuclide_inhalation\",\n", "]\n", - "# tn = ds[columns].to_dataframe().reset_index(\n", + "# ds[columns].reset_index([\"material_id\", \"case_id\"])\n", + "\n", + "ds[columns].coords.to_dataset()\n", + "# .reset_index([\"elapsed_time\", \"zai\"])\n", + "# .reset_coords()\n", + "# .drop_indexes([\"material_id\", \"case_id\", \"time_step_number\", \"nuclide\"])\n", + "# .reset_index([\"material_id\", \"case_id\", \"time_step_number\", \"nuclide\"])\n", + "# .to_dataframe().reset_index(\n", "# [\n", "# \"material_id\", \"case_id\", \"time_step_number\",\n", "# ]\n", - "# )\n", - "# tn = tn.reset_index(\n", - "# [\"element\", \"mass_number\", \"state\"]\n", - "# )\n", - "\n", - "# .reset_index()\n", - "# .reset_index(\"time_step_number\")[columns].fillna(0.0)\n", - "# tn.reset_index(allow_duplicates=True)\n", - "ds[columns].reset_index([\"material_id\", \"case_id\", \"time_step_number\", \"nuclide\"]).to_dataframe().reset_index(\n", - " [\n", - " \"material_id\", \"case_id\", \"time_step_number\",\n", - " ]\n", - ").reset_index(drop=True).fillna(0.0)\n" + "# ).reset_index(drop=True)[columns].fillna(0.0)\n" ] }, { "cell_type": "code", - "execution_count": 263, + "execution_count": 540, "id": "526610bb-be7b-4ce7-8cc9-0bcdb00588f2", "metadata": { "tags": [] @@ -4369,7 +4475,11 @@ " \"nuclide_ingestion\",\n", " \"nuclide_inhalation\",\n", " ]\n", - " tn = ds[columns].to_dataframe().reset_index(\"time_step_number\")[columns].fillna(0.0)\n", + " tn = ds[columns].reset_index([\"material_id\", \"case_id\", \"time_step_number\", \"nuclide\"]).to_dataframe().reset_index(\n", + " [\n", + " \"material_id\", \"case_id\", \"time_step_number\",\n", + " ]\n", + " ).reset_index(drop=True)[columns].fillna(0.0)\n", " sql = \"insert into timestep_nuclide select * from tn\"\n", " con.execute(sql)\n", " con.commit()" @@ -4377,12 +4487,25 @@ }, { "cell_type": "code", - "execution_count": 264, + "execution_count": 541, "id": "de4b9bd0-02e4-48f5-bec3-bb92c67682d0", "metadata": { "tags": [] }, - "outputs": [], + "outputs": [ + { + "ename": "ConstraintException", + "evalue": "Constraint Error: Violates foreign key constraint because key \"material_id: 0, case_id: 0, time_step_number: 0\" does not exist in the referenced table", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mConstraintException\u001b[0m Traceback (most recent call last)", + "Cell \u001b[0;32mIn[541], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[43msave_timestep_nucludes\u001b[49m\u001b[43m(\u001b[49m\u001b[43mcon\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mds\u001b[49m\u001b[43m)\u001b[49m\n", + "Cell \u001b[0;32mIn[540], line 29\u001b[0m, in \u001b[0;36msave_timestep_nucludes\u001b[0;34m(con, ds)\u001b[0m\n\u001b[1;32m 23\u001b[0m tn \u001b[38;5;241m=\u001b[39m ds[columns]\u001b[38;5;241m.\u001b[39mreset_index([\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mmaterial_id\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mcase_id\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mtime_step_number\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mnuclide\u001b[39m\u001b[38;5;124m\"\u001b[39m])\u001b[38;5;241m.\u001b[39mto_dataframe()\u001b[38;5;241m.\u001b[39mreset_index(\n\u001b[1;32m 24\u001b[0m [\n\u001b[1;32m 25\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mmaterial_id\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mcase_id\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mtime_step_number\u001b[39m\u001b[38;5;124m\"\u001b[39m,\n\u001b[1;32m 26\u001b[0m ]\n\u001b[1;32m 27\u001b[0m )\u001b[38;5;241m.\u001b[39mreset_index(drop\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m)[columns]\u001b[38;5;241m.\u001b[39mfillna(\u001b[38;5;241m0.0\u001b[39m)\n\u001b[1;32m 28\u001b[0m sql \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124minsert into timestep_nuclide select * from tn\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[0;32m---> 29\u001b[0m \u001b[43mcon\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mexecute\u001b[49m\u001b[43m(\u001b[49m\u001b[43msql\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 30\u001b[0m con\u001b[38;5;241m.\u001b[39mcommit()\n", + "\u001b[0;31mConstraintException\u001b[0m: Constraint Error: Violates foreign key constraint because key \"material_id: 0, case_id: 0, time_step_number: 0\" does not exist in the referenced table" + ] + } + ], "source": [ "save_timestep_nucludes(con, ds)" ] diff --git a/notebooks/dvp/try_ducdb.py b/notebooks/dvp/try_ducdb.py index 1727c60..cb90a76 100644 --- a/notebooks/dvp/try_ducdb.py +++ b/notebooks/dvp/try_ducdb.py @@ -176,20 +176,24 @@ def create_tables(con): time_step_number uinteger not null, element varchar(2) not null, mass_number usmallint not null, + state varchar(1) not null, atoms float4 not null, grams float4 not null, activity float4 not null, alpha_activity float4 not null, + beta_activity float4 not null, gamma_activity float4 not null, heat float4 not null, alpha_heat float4 not null, beta_heat float4 not null, + gamma_heat float4 not null, dose float4 not null, ingestion float4 not null, inhalation float4 not null, + primary key(material_id, case_id, time_step_number, element, mass_number, state), foreign key(material_id, case_id, time_step_number) references timestep(material_id, case_id, time_step_number), foreign key(element, mass_number, state) references nuclide(element, mass_number, state) @@ -208,14 +212,14 @@ def create_tables(con): con.execute(sql) -# In[448]: +# In[512]: drop_tables(con) create_tables(con) -# In[449]: +# In[513]: def save_rundata(con, ds): @@ -237,19 +241,19 @@ def save_rundata(con, ds): con.commit() -# In[451]: +# In[514]: save_rundata(con, ds) -# In[452]: +# In[515]: con.execute("select * from rundata").df() -# In[455]: +# In[516]: def save_timesteps(con, ds): @@ -287,25 +291,27 @@ def save_timesteps(con, ds): con.commit() -# In[456]: +# In[517]: save_timesteps(con, ds) -# In[457]: +# In[518]: con.execute("select * from timestep").df() -# In[458]: +# In[533]: def save_nuclides(con, ds): nuclides_df = ( ds[["element", "mass_number", "state", "zai", "nuclide_half_life"]] - .to_pandas() + .reset_index(["material_id", "case_id"]) + .to_dataframe() + .reset_index(["material_id", "case_id"], drop=True) .reset_index(drop=True) ) sql = "insert or ignore into nuclide select * from nuclides_df" @@ -313,19 +319,19 @@ def save_nuclides(con, ds): con.commit() -# In[459]: +# In[534]: save_nuclides(con, ds) -# In[460]: +# In[535]: con.execute("select * from nuclide").df() -# In[508]: +# In[559]: columns = [ @@ -349,34 +355,21 @@ def save_nuclides(con, ds): "nuclide_ingestion", "nuclide_inhalation", ] -# tn = ds[columns].to_dataframe().reset_index( +# ds[columns].reset_index(["material_id", "case_id"]) + +ds[columns].coords.to_dataset() +# .reset_index(["elapsed_time", "zai"]) +# .reset_coords() +# .drop_indexes(["material_id", "case_id", "time_step_number", "nuclide"]) +# .reset_index(["material_id", "case_id", "time_step_number", "nuclide"]) +# .to_dataframe().reset_index( # [ # "material_id", "case_id", "time_step_number", # ] -# ) -# tn = tn.reset_index( -# ["element", "mass_number", "state"] -# ) - -# .reset_index() -# .reset_index("time_step_number")[columns].fillna(0.0) -# tn.reset_index(allow_duplicates=True) -ds[columns].reset_index( - ["material_id", "case_id", "time_step_number", "nuclide"] -).to_dataframe().reset_index( - [ - "material_id", - "case_id", - "time_step_number", - ] -).reset_index( - drop=True -).fillna( - 0.0 -) +# ).reset_index(drop=True)[columns].fillna(0.0) -# In[263]: +# In[540]: def save_timestep_nucludes(con, ds): @@ -401,13 +394,26 @@ def save_timestep_nucludes(con, ds): "nuclide_ingestion", "nuclide_inhalation", ] - tn = ds[columns].to_dataframe().reset_index("time_step_number")[columns].fillna(0.0) + tn = ( + ds[columns] + .reset_index(["material_id", "case_id", "time_step_number", "nuclide"]) + .to_dataframe() + .reset_index( + [ + "material_id", + "case_id", + "time_step_number", + ] + ) + .reset_index(drop=True)[columns] + .fillna(0.0) + ) sql = "insert into timestep_nuclide select * from tn" con.execute(sql) con.commit() -# In[264]: +# In[541]: save_timestep_nucludes(con, ds) From 04b665c1432dd88540ecd5ce33a07c6c45525e96 Mon Sep 17 00:00:00 2001 From: dvp Date: Fri, 24 Mar 2023 17:09:52 +0300 Subject: [PATCH 12/32] dependecies: poetry update --- poetry.lock | 96 ++++++++++++++++++++++++++--------------------------- 1 file changed, 48 insertions(+), 48 deletions(-) diff --git a/poetry.lock b/poetry.lock index a390b1e..cc0c8c0 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.4.0 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.4.1 and should not be changed by hand. 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+version = "2.17.1" description = "python code static checker" category = "dev" optional = false python-versions = ">=3.7.2" files = [ - {file = "pylint-2.17.0-py3-none-any.whl", hash = "sha256:e097d8325f8c88e14ad12844e3fe2d963d3de871ea9a8f8ad25ab1c109889ddc"}, - {file = "pylint-2.17.0.tar.gz", hash = "sha256:1460829b6397cb5eb0cdb0b4fc4b556348e515cdca32115f74a1eb7c20b896b4"}, + {file = "pylint-2.17.1-py3-none-any.whl", hash = "sha256:8660a54e3f696243d644fca98f79013a959c03f979992c1ab59c24d3f4ec2700"}, + {file = "pylint-2.17.1.tar.gz", hash = "sha256:d4d009b0116e16845533bc2163493d6681846ac725eab8ca8014afb520178ddd"}, ] [package.dependencies] @@ -2695,14 +2695,14 @@ toml = ">=0.10.2" [[package]] name = "typeguard" -version = "3.0.1" +version = "3.0.2" description = "Run-time type checker for Python" category = "dev" optional = false python-versions = ">=3.7.4" files = [ - {file = "typeguard-3.0.1-py3-none-any.whl", hash = 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a/.github/constraints.txt +++ b/.github/constraints.txt @@ -1,5 +1,5 @@ pip==23.0.1 nox==2022.11.21 -poetry==1.4.0 +poetry==1.4.1 virtualenv==20.16.5 # restricted by poetry on Windows, current 20.17.1 wheel-0.38.4 diff --git a/.github/workflows/labeler.yml b/.github/workflows/labeler.yml index 5e1da55..149f097 100644 --- a/.github/workflows/labeler.yml +++ b/.github/workflows/labeler.yml @@ -26,7 +26,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out the repository - uses: actions/checkout@v3.3.0 + uses: actions/checkout@v3.4.0 - name: Sync GitHub Issue Labels uses: crazy-max/ghaction-github-labeler@v4 diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 4ccfa44..333871e 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -27,7 +27,7 @@ jobs: steps: - name: Check out the repository - uses: actions/checkout@v3.3.0 + uses: actions/checkout@v3.4.0 with: fetch-depth: 2 # need previous revision to define tag @@ -71,14 +71,14 @@ jobs: - name: Publish package on PyPI if: steps.check-version.outputs.tag - uses: pypa/gh-action-pypi-publish@v1.7.1 + uses: pypa/gh-action-pypi-publish@v1.8.1 with: user: __token__ password: ${{ secrets.PYPI_TOKEN }} - name: Publish package on TestPyPI if: "! steps.check-version.outputs.tag" - uses: pypa/gh-action-pypi-publish@v1.7.1 + uses: pypa/gh-action-pypi-publish@v1.8.1 with: user: __token__ password: ${{ secrets.TEST_PYPI_TOKEN }} diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index d3e54cc..e0155c7 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -36,7 +36,7 @@ jobs: !contains(github.event.head_commit.message, '[skip_ci]') steps: - name: Check out the repository - uses: actions/checkout@v3.3.0 + uses: actions/checkout@v3.4.0 - name: Set up Python 3.10 # on 3.11 pip install in unstable: "canonicalize" fails occasionally uses: actions/setup-python@v4.5.0 @@ -137,7 +137,7 @@ jobs: steps: - name: Checkout repository - uses: actions/checkout@v3.3.0 + uses: actions/checkout@v3.4.0 with: fetch-depth: 1 @@ -187,7 +187,7 @@ jobs: steps: - name: Check out the repository - uses: actions/checkout@v3.3.0 + uses: actions/checkout@v3.4.0 - name: Set up Python 3.11 uses: actions/setup-python@v4.5.0 diff --git a/pyproject.toml b/pyproject.toml index 4f8e26f..2fc1038 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -31,7 +31,7 @@ classifiers = [ ] [build-system] -requires = ["poetry-core >= 1.1.0"] +requires = ["poetry-core >= 1.5.2"] build-backend = "poetry.core.masonry.api" # [tool.poetry.scripts] @@ -43,7 +43,7 @@ Changelog = "https://github.com/MC-kit/xpypact/releases" [tool.poetry.dependencies] -python = ">=3.8,<4.0" +python = ">=3.8.1,<4.0" h5netcdf = ">=0.13.1" mckit-nuclides = {version = ">=0.1.1", allow-prereleases = true} numpy = ">=1.24.2" @@ -105,13 +105,13 @@ numpy = ">=1.23.2" [tool.poetry.group.flake8.dependencies] darglint = ">=1.8.1" -flake8 = ">=4.0.1" #TODO dvp: update with flake8-eradicate +flake8 = ">=6.0.0" #flake8 = ">=6.0.0" flake8-adjustable-complexity = ">=0.0.6" flake8-annotations = ">=2.6.2" flake8-annotations-coverage = ">=0.0.6" flake8-bandit = ">=4.1.1" -flake8-bugbear = ">=22.3.23" +flake8-bugbear = ">=23.3.23" flake8-builtins = ">=1.5.3" flake8-class-attributes-order = ">=0.1.3" flake8-cognitive-complexity = ">=0.1.0" @@ -119,7 +119,7 @@ flake8-colors = ">=0.1.9" flake8-commas = ">=2.1.0" flake8-comprehensions = ">=3.10.0" flake8-docstrings = ">=1.6.0" -flake8-eradicate = ">=1.4.0" +# flake8-eradicate = ">=1.4.0" #TODO dvp: return with flake8-eradicate update flake8-expression-complexity = ">=0.0.11" flake8-functions = ">=0.0.7" flake8-import-order = ">=0.18.1" From 037815ef803b65eb0d0d230bf2a1c18cf0049d83 Mon Sep 17 00:00:00 2001 From: dvp Date: Mon, 27 Mar 2023 07:49:08 +0300 Subject: [PATCH 14/32] dependencies: poetry update (dev only) --- poetry.lock | 229 +++++++++++++++++++++++++++------------------------- 1 file changed, 117 insertions(+), 112 deletions(-) diff --git a/poetry.lock b/poetry.lock index 3d38306..f2a1666 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.4.0 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.4.1 and should not be changed by hand. [[package]] name = "alabaster" @@ -54,14 +54,14 @@ files = [ [[package]] name = "astroid" -version = "2.15.0" +version = "2.15.1" description = "An abstract syntax tree for Python with inference support." category = "dev" optional = false python-versions = ">=3.7.2" files = [ - {file = "astroid-2.15.0-py3-none-any.whl", hash = "sha256:e3e4d0ffc2d15d954065579689c36aac57a339a4679a679579af6401db4d3fdb"}, - {file = "astroid-2.15.0.tar.gz", hash = "sha256:525f126d5dc1b8b0b6ee398b33159105615d92dc4a17f2cd064125d57f6186fa"}, + {file = "astroid-2.15.1-py3-none-any.whl", hash = "sha256:89860bda98fe2bbd1f5d262229be7629d778ce280de68d95d4a73d1f592ad268"}, + {file = "astroid-2.15.1.tar.gz", hash = "sha256:af4e0aff46e2868218502789898269ed95b663fba49e65d91c1e09c966266c34"}, ] [package.dependencies] @@ -543,19 +543,19 @@ testing = ["pre-commit"] [[package]] name = "filelock" -version = "3.10.0" +version = "3.10.6" description = "A platform independent file lock." category = "dev" optional = false 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{file = "pre_commit-3.2.0-py2.py3-none-any.whl", hash = "sha256:f712d3688102e13c8e66b7d7dbd8934a6dda157e58635d89f7d6fecdca39ce8a"}, - {file = "pre_commit-3.2.0.tar.gz", hash = "sha256:818f0d998059934d0f81bb3667e3ccdc32da6ed7ccaac33e43dc231561ddaaa9"}, + {file = "pre_commit-3.2.1-py2.py3-none-any.whl", hash = "sha256:a06a7fcce7f420047a71213c175714216498b49ebc81fe106f7716ca265f5bb6"}, + {file = "pre_commit-3.2.1.tar.gz", hash = "sha256:b5aee7d75dbba21ee161ba641b01e7ae10c5b91967ebf7b2ab0dfae12d07e1f1"}, ] [package.dependencies] @@ -1821,14 +1792,14 @@ typer = ">=0.4.1,<0.8.0" [[package]] name = "pycodestyle" -version = "2.9.1" +version = "2.10.0" description = "Python style guide checker" category = "dev" optional = false python-versions = ">=3.6" files = [ - {file = "pycodestyle-2.9.1-py2.py3-none-any.whl", hash = "sha256:d1735fc58b418fd7c5f658d28d943854f8a849b01a5d0a1e6f3f3fdd0166804b"}, - {file = "pycodestyle-2.9.1.tar.gz", hash = "sha256:2c9607871d58c76354b697b42f5d57e1ada7d261c261efac224b664affdc5785"}, + {file = "pycodestyle-2.10.0-py2.py3-none-any.whl", hash = "sha256:8a4eaf0d0495c7395bdab3589ac2db602797d76207242c17d470186815706610"}, + {file = "pycodestyle-2.10.0.tar.gz", hash = "sha256:347187bdb476329d98f695c213d7295a846d1152ff4fe9bacb8a9590b8ee7053"}, ] [[package]] @@ -1919,14 +1890,14 @@ toml = ["tomli (>=1.2.3)"] [[package]] name = "pyflakes" -version = "2.5.0" +version = "3.0.1" description = "passive checker of Python programs" category = "dev" optional = false python-versions = ">=3.6" files = [ - {file = "pyflakes-2.5.0-py2.py3-none-any.whl", hash = "sha256:4579f67d887f804e67edb544428f264b7b24f435b263c4614f384135cea553d2"}, - {file = "pyflakes-2.5.0.tar.gz", hash = "sha256:491feb020dca48ccc562a8c0cbe8df07ee13078df59813b83959cbdada312ea3"}, + {file = "pyflakes-3.0.1-py2.py3-none-any.whl", hash = "sha256:ec55bf7fe21fff7f1ad2f7da62363d749e2a470500eab1b555334b67aa1ef8cf"}, + {file = "pyflakes-3.0.1.tar.gz", hash = "sha256:ec8b276a6b60bd80defed25add7e439881c19e64850afd9b346283d4165fd0fd"}, ] [[package]] @@ -2103,14 +2074,14 @@ six = ">=1.5" [[package]] name = "pytz" -version = "2022.7.1" +version = "2023.2" description = "World timezone definitions, modern and historical" category = "main" optional = false python-versions = "*" files = [ - {file = "pytz-2022.7.1-py2.py3-none-any.whl", hash = "sha256:78f4f37d8198e0627c5f1143240bb0206b8691d8d7ac6d78fee88b78733f8c4a"}, - {file = "pytz-2022.7.1.tar.gz", hash = "sha256:01a0681c4b9684a28304615eba55d1ab31ae00bf68ec157ec3708a8182dbbcd0"}, + {file = "pytz-2023.2-py2.py3-none-any.whl", hash = "sha256:8a8baaf1e237175b02f5c751eea67168043a749c843989e2b3015aa1ad9db68b"}, + {file = "pytz-2023.2.tar.gz", hash = "sha256:a27dcf612c05d2ebde626f7d506555f10dfc815b3eddccfaadfc7d99b11c9a07"}, ] [[package]] @@ -2985,5 +2956,5 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more [metadata] lock-version = "2.0" -python-versions = ">=3.8,<4.0" -content-hash = "6398c04f3b966965cfb936b0d477dafedaf7f53481db8a090d576b53e14e9dc1" +python-versions = ">=3.8.1,<4.0" +content-hash = "6a94d46546d761f4aa966b6e06f2649c9776f6349cfe42d2fd6430be27c14a0f" From 6e75e6e2bf4c21c2e4a90d4de3ebe70a5408e4c6 Mon Sep 17 00:00:00 2001 From: dvp Date: Mon, 27 Mar 2023 10:50:47 +0300 Subject: [PATCH 16/32] dependencies: poetry update --- poetry.lock | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/poetry.lock b/poetry.lock index a8bd79a..f2cb20f 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2616,14 +2616,14 @@ files = [ [[package]] name = "tomlkit" -version = "0.11.6" +version = "0.11.7" description = "Style preserving TOML library" category = "dev" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" files = [ - {file = "tomlkit-0.11.6-py3-none-any.whl", hash = "sha256:07de26b0d8cfc18f871aec595fda24d95b08fef89d147caa861939f37230bf4b"}, - {file = "tomlkit-0.11.6.tar.gz", hash = "sha256:71b952e5721688937fb02cf9d354dbcf0785066149d2855e44531ebdd2b65d73"}, + {file = "tomlkit-0.11.7-py3-none-any.whl", hash = "sha256:5325463a7da2ef0c6bbfefb62a3dc883aebe679984709aee32a317907d0a8d3c"}, + {file = "tomlkit-0.11.7.tar.gz", hash = "sha256:f392ef70ad87a672f02519f99967d28a4d3047133e2d1df936511465fbb3791d"}, ] [[package]] From ed66665c29a20970ac4d9ac7953db972bd0c0c47 Mon Sep 17 00:00:00 2001 From: dvp Date: Mon, 27 Mar 2023 11:18:28 +0300 Subject: [PATCH 17/32] build: git ignore poetry local config --- .gitignore | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/.gitignore b/.gitignore index e2acb02..8bd070d 100644 --- a/.gitignore +++ b/.gitignore @@ -134,3 +134,9 @@ dmypy.json # A soundbox work and data folder wrk/ + + +# poetry local config +/poetry.toml + + From e2be64a067c08f3c2680c946387539c1f735665c Mon Sep 17 00:00:00 2001 From: dvp Date: Mon, 27 Mar 2023 12:31:55 +0300 Subject: [PATCH 18/32] notebook: duckdb prototype is done --- notebooks/dvp/try_ducdb.ipynb | 5766 +++++++++++++++------------------ notebooks/dvp/try_ducdb.py | 189 +- 2 files changed, 2694 insertions(+), 3261 deletions(-) diff --git a/notebooks/dvp/try_ducdb.ipynb b/notebooks/dvp/try_ducdb.ipynb index 12d27ba..ba8d453 100644 --- a/notebooks/dvp/try_ducdb.ipynb +++ b/notebooks/dvp/try_ducdb.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "code", - "execution_count": 233, + "execution_count": 1, "id": "250d384f-b617-4bde-8d6e-5bfea316e21f", "metadata": { "tags": [] @@ -14,7 +14,7 @@ }, { "cell_type": "code", - "execution_count": 234, + "execution_count": 2, "id": "49812848-cb6d-487a-bcdf-927e86781ae9", "metadata": { "tags": [] @@ -26,7 +26,7 @@ }, { "cell_type": "code", - "execution_count": 235, + "execution_count": 3, "id": "5e40fc05-d196-4ab9-b4df-ec6166ee5611", "metadata": { "tags": [] @@ -38,7 +38,7 @@ "'0.1.12a0'" ] }, - "execution_count": 235, + "execution_count": 3, "metadata": {}, "output_type": "execute_result" } @@ -49,7 +49,7 @@ }, { "cell_type": "code", - "execution_count": 236, + "execution_count": 4, "id": "982fbe50-fd22-499a-98d9-910f6d0c72d7", "metadata": { "tags": [] @@ -61,7 +61,7 @@ }, { "cell_type": "code", - "execution_count": 237, + "execution_count": 5, "id": "bf81c238-8be8-4f93-b3e4-155bb46e21e8", "metadata": { "tags": [] @@ -73,7 +73,7 @@ }, { "cell_type": "code", - "execution_count": 238, + "execution_count": 6, "id": "c0811f45-0503-4302-9890-62803b49cabe", "metadata": { "tags": [] @@ -86,7 +86,7 @@ }, { "cell_type": "code", - "execution_count": 239, + "execution_count": 7, "id": "57fecf87-b03f-48e4-bfe4-beee3d661355", "metadata": { "tags": [] @@ -99,7 +99,7 @@ }, { "cell_type": "code", - "execution_count": 240, + "execution_count": 8, "id": "c13bb091-11ad-4e08-bbad-7cba93475e4b", "metadata": { "tags": [] @@ -111,7 +111,7 @@ }, { "cell_type": "code", - "execution_count": 469, + "execution_count": 9, "id": "e471ce43-3860-430d-b669-7a1211bb5d06", "metadata": { "tags": [] @@ -123,7 +123,7 @@ }, { "cell_type": "code", - "execution_count": 470, + "execution_count": 10, "id": "eaa7c75f-119c-493c-b038-dbd615b72c6f", "metadata": { "tags": [] @@ -526,14 +526,14 @@ " run_name: * Material Alloy718-Co04, fluxes 104_2_1_1\n", " flux_name: 90-degrees bend\n", " dose_rate_type: Point source\n", - " dose_rate_distance: 1.0
  • run_name :
    * Material Alloy718-Co04, fluxes 104_2_1_1
    flux_name :
    90-degrees bend
    dose_rate_type :
    Point source
    dose_rate_distance :
    1.0
    • " ], "text/plain": [ "\n", @@ -1099,7 +1099,7 @@ " dose_rate_distance: 1.0" ] }, - "execution_count": 470, + "execution_count": 10, "metadata": {}, "output_type": "execute_result" } @@ -1110,8 +1110,60 @@ }, { "cell_type": "code", - "execution_count": 417, - "id": "8dbfda08-8776-4733-9215-9d569fb24a34", + "execution_count": 12, + "id": "79beed07-0f86-485b-be23-97d7e8f33abb", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "import duckdb as db" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "id": "ee7bf9aa-13a8-419d-b39e-c90493094148", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "db_path = root_dir / \"wrk/try-duckdb.duckdb\"\n", + "db_path.parent.mkdir(parents=True, exist_ok=True)\n", + "if db_path.exists():\n", + " db_path.unlink()" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "id": "99a86bdc-84e1-4cd3-b7b7-4e63b6428086", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "con = db.connect(str(db_path))" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "id": "c74de5dc-5b72-4e1a-a105-3c629995a5af", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "material_id = 100\n", + "case_id = 3" + ] + }, + { + "cell_type": "code", + "execution_count": 16, + "id": "dd2fb504-eb9a-48ee-bab2-2a512630797a", "metadata": { "tags": [] }, @@ -1482,2940 +1534,2206 @@ " stroke: currentColor;\n", " fill: currentColor;\n", "}\n", - "
    <xarray.DataArray 'timestamp' (timestamp: 1)>\n",
-       "array(['2022-02-21T01:52:47.000000000'], dtype='datetime64[ns]')\n",
-       "Coordinates:\n",
-       "  * timestamp  (timestamp) datetime64[ns] 2022-02-21T01:52:47\n",
-       "Attributes:\n",
-       "    long description:  FISPACT datasets can be merged and then selected by ti...
    " - ], - "text/plain": [ - "\n", - "array(['2022-02-21T01:52:47.000000000'], dtype='datetime64[ns]')\n", + "
    <xarray.Dataset>\n",
+       "Dimensions:                 (material_id: 1, case_id: 1, time_step_number: 65,\n",
+       "                             nuclide: 215, gamma_boundaries: 25, timestamp: 1)\n",
        "Coordinates:\n",
-       "  * timestamp  (timestamp) datetime64[ns] 2022-02-21T01:52:47\n",
+       "  * material_id             (material_id) int64 100\n",
+       "  * case_id                 (case_id) int64 3\n",
+       "  * time_step_number        (time_step_number) int64 1 2 3 4 5 ... 62 63 64 65\n",
+       "  * nuclide                 (nuclide) object MultiIndex\n",
+       "  * element                 (nuclide) object 'Al' 'Al' 'Al' ... 'Zr' 'Zr' 'Zr'\n",
+       "  * mass_number             (nuclide) int64 26 27 28 29 30 40 ... 93 94 95 96 97\n",
+       "  * state                   (nuclide) object '' '' '' '' '' ... '' '' '' '' ''\n",
+       "  * gamma_boundaries        (gamma_boundaries) float64 1e-11 0.01 ... 14.0 20.0\n",
+       "    elapsed_time            (time_step_number) float64 0.0 6.312e+07 ... 3.2e+10\n",
+       "    zai                     (nuclide) int64 130260 130270 ... 400960 400970\n",
+       "  * timestamp               (timestamp) datetime64[ns] 2022-02-21T01:52:47\n",
+       "Data variables: (12/32)\n",
+       "    irradiation_time        (material_id, case_id, time_step_number) float64 ...\n",
+       "    cooling_time            (material_id, case_id, time_step_number) float64 ...\n",
+       "    duration                (material_id, case_id, time_step_number) float64 ...\n",
+       "    flux                    (material_id, case_id, time_step_number) float64 ...\n",
+       "    total_atoms             (material_id, case_id, time_step_number) float64 ...\n",
+       "    total_activity          (material_id, case_id, time_step_number) float64 ...\n",
+       "    ...                      ...\n",
+       "    nuclide_beta_heat       (material_id, case_id, time_step_number, nuclide) float64 ...\n",
+       "    nuclide_gamma_heat      (material_id, case_id, time_step_number, nuclide) float64 ...\n",
+       "    nuclide_dose            (material_id, case_id, time_step_number, nuclide) float64 ...\n",
+       "    nuclide_ingestion       (material_id, case_id, time_step_number, nuclide) float64 ...\n",
+       "    nuclide_inhalation      (material_id, case_id, time_step_number, nuclide) float64 ...\n",
+       "    gamma                   (material_id, case_id, time_step_number, gamma_boundaries) float64 ...\n",
        "Attributes:\n",
-       "    long description:  FISPACT datasets can be merged and then selected by ti..."
-      ]
-     },
-     "execution_count": 417,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "ds.timestamp"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 243,
-   "id": "79beed07-0f86-485b-be23-97d7e8f33abb",
-   "metadata": {
-    "tags": []
-   },
-   "outputs": [],
-   "source": [
-    "import duckdb as db"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 384,
-   "id": "ee7bf9aa-13a8-419d-b39e-c90493094148",
-   "metadata": {
-    "tags": []
-   },
-   "outputs": [],
-   "source": [
-    "db_path = root_dir / \"wrk/try-duckdb.duckdb\"\n",
-    "db_path.parent.mkdir(parents=True, exist_ok=True)\n",
-    "if db_path.exists():\n",
-    "    db_path.unlink()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 385,
-   "id": "99a86bdc-84e1-4cd3-b7b7-4e63b6428086",
-   "metadata": {
-    "tags": []
-   },
-   "outputs": [],
-   "source": [
-    "con = db.connect(str(db_path))"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 386,
-   "id": "c74de5dc-5b72-4e1a-a105-3c629995a5af",
-   "metadata": {
-    "tags": []
-   },
-   "outputs": [],
-   "source": [
-    "material_id = 100\n",
-    "case_id = 3"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 475,
-   "id": "dd2fb504-eb9a-48ee-bab2-2a512630797a",
-   "metadata": {
-    "tags": []
-   },
-   "outputs": [
-    {
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-       "    flux_name:           90-degrees bend\n",
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-       "\n",
-       "Dimensions:                 (material_id: 1, case_id: 1, time_step_number: 65,\n",
-       "                             nuclide: 215, gamma_boundaries: 25, timestamp: 1)\n",
-       "Coordinates:\n",
-       "  * material_id             (material_id) int64 100\n",
-       "  * case_id                 (case_id) int64 3\n",
-       "  * time_step_number        (time_step_number) int64 1 2 3 4 5 ... 62 63 64 65\n",
-       "  * nuclide                 (nuclide) object MultiIndex\n",
-       "  * element                 (nuclide) object 'Al' 'Al' 'Al' ... 'Zr' 'Zr' 'Zr'\n",
-       "  * mass_number             (nuclide) int64 26 27 28 29 30 40 ... 93 94 95 96 97\n",
-       "  * state                   (nuclide) object '' '' '' '' '' ... '' '' '' '' ''\n",
-       "  * gamma_boundaries        (gamma_boundaries) float64 1e-11 0.01 ... 14.0 20.0\n",
-       "    elapsed_time            (time_step_number) float64 0.0 6.312e+07 ... 3.2e+10\n",
-       "    zai                     (nuclide) int64 130260 130270 ... 400960 400970\n",
-       "  * timestamp               (timestamp) datetime64[ns] 2022-02-21T01:52:47\n",
-       "Data variables: (12/32)\n",
-       "    irradiation_time        (material_id, case_id, time_step_number) float64 ...\n",
-       "    cooling_time            (material_id, case_id, time_step_number) float64 ...\n",
-       "    duration                (material_id, case_id, time_step_number) float64 ...\n",
-       "    flux                    (material_id, case_id, time_step_number) float64 ...\n",
-       "    total_atoms             (material_id, case_id, time_step_number) float64 ...\n",
-       "    total_activity          (material_id, case_id, time_step_number) float64 ...\n",
-       "    ...                      ...\n",
-       "    nuclide_beta_heat       (material_id, case_id, time_step_number, nuclide) float64 ...\n",
-       "    nuclide_gamma_heat      (material_id, case_id, time_step_number, nuclide) float64 ...\n",
-       "    nuclide_dose            (material_id, case_id, time_step_number, nuclide) float64 ...\n",
-       "    nuclide_ingestion       (material_id, case_id, time_step_number, nuclide) float64 ...\n",
-       "    nuclide_inhalation      (material_id, case_id, time_step_number, nuclide) float64 ...\n",
-       "    gamma                   (material_id, case_id, time_step_number, gamma_boundaries) float64 ...\n",
-       "Attributes:\n",
-       "    run_name:            * Material Alloy718-Co04, fluxes 104_2_1_1\n",
-       "    flux_name:           90-degrees bend\n",
-       "    dose_rate_type:      Point source\n",
-       "    dose_rate_distance:  1.0"
-      ]
-     },
-     "execution_count": 475,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "ds =ds.expand_dims(dim={\"material_id\": [material_id], \"case_id\": [case_id]})\n",
-    "ds"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 476,
-   "id": "7a9969f8-6583-444f-82ec-2c76ed8cf8cb",
-   "metadata": {
-    "tags": []
-   },
-   "outputs": [
-    {
-     "data": {
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-       "\n",
-       "\n",
-       "\n",
-       "\n",
-       "\n",
-       "
    <xarray.DataArray 'irradiation_time' (material_id: 1, case_id: 1,\n",
-       "                                      time_step_number: 65)>\n",
-       "array([[[0.00000000e+00, 6.31152000e+07, 3.78691200e+08, 3.78691200e+08,\n",
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-       "         4.20670808e+08]]])\n",
-       "Coordinates:\n",
-       "  * material_id       (material_id) int64 100\n",
-       "  * case_id           (case_id) int64 3\n",
-       "  * time_step_number  (time_step_number) int64 1 2 3 4 5 6 ... 60 61 62 63 64 65\n",
-       "    elapsed_time      (time_step_number) float64 0.0 6.312e+07 ... 3.2e+10\n",
-       "Attributes:\n",
-       "    units:    s
    "
-      ],
-      "text/plain": [
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-       "         4.20670008e+08, 4.20670008e+08, 4.20670408e+08, 4.20670408e+08,\n",
-       "         4.20670808e+08, 4.20670808e+08, 4.20670808e+08, 4.20670808e+08,\n",
-       "         4.20670808e+08, 4.20670808e+08, 4.20670808e+08, 4.20670808e+08,\n",
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-       "         4.20670808e+08]]])\n",
-       "Coordinates:\n",
-       "  * material_id       (material_id) int64 100\n",
-       "  * case_id           (case_id) int64 3\n",
-       "  * time_step_number  (time_step_number) int64 1 2 3 4 5 6 ... 60 61 62 63 64 65\n",
-       "    elapsed_time      (time_step_number) float64 0.0 6.312e+07 ... 3.2e+10\n",
-       "Attributes:\n",
-       "    units:    s"
-      ]
-     },
-     "execution_count": 476,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "ds.irradiation_time"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 446,
-   "id": "d9e1ddfb-398e-4cea-b01d-fb0e53242776",
-   "metadata": {
-    "tags": []
-   },
-   "outputs": [],
-   "source": [
-    "def drop_tables(con):\n",
-    "    con.execute(\"drop table if exists timestep_gamma\")\n",
-    "    con.execute(\"drop table if exists timestep_nuclide\")\n",
-    "    con.execute(\"drop table if exists timestep\")\n",
-    "    con.execute(\"drop table if exists nuclide\")\n",
-    "    con.execute(\"drop table if exists rundata\")"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 447,
-   "id": "c402d3a1-e77a-4b24-accc-a19588ccdf54",
-   "metadata": {
-    "tags": []
-   },
-   "outputs": [],
-   "source": [
-    "def create_tables(con):\n",
-    "    sql = \"\"\" \n",
-    "    CREATE TABLE IF NOT EXISTS rundata (\n",
-    "        material_id uinteger not null,\n",
-    "        case_id uinteger not null,\n",
-    "        timestamp timestamp not null,\n",
-    "        run_name varchar not null,\n",
-    "        flux_name varchar NOT NULL,\n",
-    "        dose_rate_type varchar NOT NULL,\n",
-    "        dose_rate_distance real NOT NULL,\n",
-    "        primary key(material_id, case_id)\n",
-    "    );\n",
-    "\n",
-    "    CREATE TABLE IF NOT EXISTS timestep(\n",
-    "        material_id  uinteger not null,\n",
-    "        case_id      uinteger not null,\n",
-    "        time_step_number uinteger not null,\n",
-    "        elapsed_time float4 not null,\n",
-    "        irradiation_time float4 not null,\n",
-    "        cooling_time float4 not null,\n",
-    "        duration float4 not null,\n",
-    "        flux float4 not null,\n",
-    "        total_atoms float4 not null,\n",
-    "        total_activity float4 not null,\n",
-    "        total_alpha_activity float4 not null,\n",
-    "        total_beta_activity float4 not null,\n",
-    "        total_gamma_activity float4 not null,\n",
-    "        total_mass float4 not null,\n",
-    "        total_heat float4 not null,\n",
-    "        total_alpha_heat float4 null,\n",
-    "        total_beta_heat float4 not null,\n",
-    "        total_gamma_heat float4 not null,\n",
-    "        total_ingest1ion_dose float4 not null,\n",
-    "        total_inhalation_dose float4 not null,\n",
-    "        total_dose_rate float4 not null,\n",
-    "        primary key(material_id, case_id, time_step_number),\n",
-    "        foreign key(material_id, case_id) references rundata(material_id, case_id) \n",
-    "    );\n",
-    "\n",
-    "    \n",
-    "    CREATE TABLE IF NOT EXISTS nuclide(\n",
-    "        element varchar(2) not null,\n",
-    "        mass_number usmallint not null check(0 < mass_number),\n",
-    "        state varchar(1) not null,\n",
-    "        zai integer not null check(10010 <= zai) unique,\n",
-    "        half_life float4 not null check(0 <= half_life),\n",
-    "        primary key(element, mass_number, state)\n",
-    "    );\n",
-    "    \n",
-    "    CREATE TABLE IF NOT EXISTS timestep_nuclide(\n",
-    "        material_id  uinteger not null,\n",
-    "        case_id      uinteger not null,\n",
-    "        time_step_number uinteger not null,\n",
-    "        element varchar(2) not null,\n",
-    "        mass_number usmallint not null,\n",
-    "        \n",
-    "        state varchar(1) not null,\n",
-    "        atoms float4 not null,\n",
-    "        grams float4 not null,\n",
-    "        activity float4 not null,\n",
-    "        alpha_activity float4 not null,\n",
-    "        \n",
-    "        beta_activity float4 not null,\n",
-    "        gamma_activity float4 not null,\n",
-    "        heat float4 not null,\n",
-    "        alpha_heat float4 not null,\n",
-    "        beta_heat float4 not null,\n",
-    "        \n",
-    "        gamma_heat float4 not null,\n",
-    "        dose float4 not null,\n",
-    "        ingestion float4 not null,\n",
-    "        inhalation float4 not null,\n",
-    "        \n",
-    "        primary key(material_id, case_id, time_step_number, element, mass_number, state),\n",
-    "        foreign key(material_id, case_id, time_step_number) references timestep(material_id, case_id, time_step_number),\n",
-    "        foreign key(element, mass_number, state) references nuclide(element, mass_number, state) \n",
-    "    );\n",
-    "\n",
-    "    CREATE TABLE IF NOT EXISTS timestep_gamma(\n",
-    "        material_id  uinteger not null,\n",
-    "        case_id      uinteger not null,\n",
-    "        time_step_number uinteger not null,\n",
-    "        boundary real not null check(0 <= boundary),\n",
-    "        intensity real not null, \n",
-    "        primary key(material_id, case_id, time_step_number, boundary),\n",
-    "        foreign key(material_id, case_id, time_step_number) references timestep(material_id, case_id, time_step_number),\n",
-    "    );\n",
-    "    \"\"\"\n",
-    "    con.execute(sql)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 512,
-   "id": "25f6867e-397a-4e98-a363-74b6af739c88",
-   "metadata": {
-    "tags": []
-   },
-   "outputs": [],
-   "source": [
-    "drop_tables(con)\n",
-    "create_tables(con)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 513,
-   "id": "29716201-70f8-40d2-8da7-85689714ec32",
-   "metadata": {
-    "tags": []
-   },
-   "outputs": [],
-   "source": [
-    "def save_rundata(con, ds):\n",
-    "    sql = \"\"\"\n",
-    "        INSERT INTO rundata values(?, ?, ?, ?, ?, ?, ?)\n",
-    "    \"\"\"\n",
-    "    con.execute(sql, (    \n",
-    "        ds.material_id.item(),\n",
-    "        ds.case_id.item(),\n",
-    "        ds.timestamp.dt.strftime(\"%Y-%m-%d %H:%M:%S\").item(),\n",
-    "        ds.attrs[\"run_name\"],\n",
-    "        ds.attrs[\"flux_name\"],\n",
-    "        ds.attrs[\"dose_rate_type\"],\n",
-    "        ds.attrs[\"dose_rate_distance\"]\n",
-    "    ))\n",
-    "    con.commit()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 514,
-   "id": "c789eedd-580c-4383-8bf1-cc943562a3aa",
-   "metadata": {
-    "tags": []
-   },
-   "outputs": [],
-   "source": [
-    "save_rundata(con, ds)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 515,
-   "id": "1c650134-edf3-44dd-aa90-ddde6a3987a7",
-   "metadata": {
-    "tags": []
-   },
-   "outputs": [
-    {
-     "data": {
-      "text/html": [
-       "
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    material_idcase_idtimestamprun_nameflux_namedose_rate_typedose_rate_distance
    010032022-02-21 01:52:47* Material Alloy718-Co04, fluxes 104_2_1_190-degrees bendPoint source1.0
    \n",
-       "
    "
-      ],
-      "text/plain": [
-       "   material_id  case_id           timestamp  \\\n",
-       "0          100        3 2022-02-21 01:52:47   \n",
-       "\n",
-       "                                     run_name        flux_name dose_rate_type  \\\n",
-       "0  * Material Alloy718-Co04, fluxes 104_2_1_1  90-degrees bend   Point source   \n",
-       "\n",
-       "   dose_rate_distance  \n",
-       "0                 1.0  "
-      ]
-     },
-     "execution_count": 515,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "con.execute(\"select * from rundata\").df()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 516,
-   "id": "cf8661b6-d9cb-4431-8b40-f14072409d5a",
-   "metadata": {
-    "tags": []
-   },
-   "outputs": [],
-   "source": [
-    "def save_timesteps(con, ds):\n",
-    "    timesteps_df = ds[\n",
-    "        [\n",
-    "            \"material_id\",\n",
-    "            \"case_id\",\n",
-    "            \"time_step_number\",\n",
-    "            \"elapsed_time\",\n",
-    "            \"irradiation_time\",\n",
-    "            \"cooling_time\",\n",
-    "            \"duration\",\n",
-    "            \"flux\",\n",
-    "            \"total_atoms\",\n",
-    "            \"total_activity\",\n",
-    "            \"total_alpha_activity\",\n",
-    "            \"total_beta_activity\",\n",
-    "            \"total_gamma_activity\",\n",
-    "            \"total_mass\",\n",
-    "            \"total_heat\",\n",
-    "            \"total_alpha_heat\",\n",
-    "            \"total_beta_heat\",\n",
-    "            \"total_gamma_heat\",\n",
-    "            \"total_ingest1ion_dose\",\n",
-    "            \"total_inhalation_dose\",\n",
-    "            \"total_dose_rate\",\n",
-    "        ]\n",
-    "    ].to_dataframe().reset_index()\n",
-    "    sql = \"insert into timestep select * from timesteps_df\"\n",
-    "    con.execute(sql)\n",
-    "    con.commit()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 517,
-   "id": "78154d84-9df4-417d-a35f-60252575aae6",
-   "metadata": {
-    "tags": []
-   },
-   "outputs": [],
-   "source": [
-    "save_timesteps(con, ds)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 518,
-   "id": "bf73ee32-d132-418f-8e77-969d779b780a",
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    material_idcase_idtime_step_numberelapsed_timeirradiation_timecooling_timedurationfluxtotal_atomstotal_activity...total_beta_activitytotal_gamma_activitytotal_masstotal_heattotal_alpha_heattotal_beta_heattotal_gamma_heattotal_ingest1ion_dosetotal_inhalation_dosetotal_dose_rate
    0100310.000000e+000.00.000000e+000.000000e+000.000000e+001.045481e+221.099260e-02...1.099260e-020.000000e+000.0011.994928e-190.000000e+001.994919e-198.784190e-255.288239e-129.131853e-127.484415e-22
    1100326.311520e+0763115200.00.000000e+006.311520e+072.445200e+101.045481e+222.268685e+07...1.476443e+077.922416e+060.0012.522555e-091.316125e-304.443058e-102.078249e-091.225884e-027.370374e-021.774444e-06
    2100333.786912e+08378691200.00.000000e+003.155760e+081.882800e+111.045484e+222.005898e+08...1.391144e+086.147540e+070.0012.601587e-086.436155e-283.691712e-092.232416e-081.498245e-011.057001e+001.854623e-05
    3100343.997401e+08378691200.02.104892e+072.104892e+070.000000e+001.045484e+225.064473e+07...5.005196e+075.927796e+050.0011.072963e-086.445708e-285.938637e-101.013577e-088.618334e-027.240407e-017.931148e-06
    4100354.417117e+08420662816.02.104892e+074.197161e+073.790000e+111.045484e+223.644599e+08...2.411954e+081.232645e+080.0014.388052e-089.368928e-287.024670e-093.685585e-082.313087e-011.522821e+003.102856e-05
    ..................................................................
    601003617.573741e+08420670816.03.367033e+082.209032e+080.000000e+001.045484e+221.021210e+07...9.725966e+064.861311e+050.0013.030422e-099.414649e-281.199240e-102.910498e-092.524398e-022.288691e-012.231632e-06
    611003621.388526e+09420670816.09.678553e+086.311520e+080.000000e+001.045484e+222.140445e+06...1.934185e+062.062603e+050.0012.260388e-109.414649e-281.325084e-112.127880e-102.034489e-031.899889e-021.650785e-07
    621003632.019678e+09420670816.01.599007e+096.311520e+080.000000e+001.045484e+221.354644e+06...1.266816e+068.782794e+040.0012.303827e-119.414649e-284.691881e-121.834639e-113.442937e-043.528395e-031.529847e-08
    631003643.597558e+09420670816.03.176887e+091.577880e+090.000000e+001.045484e+228.909484e+05...8.798868e+051.106160e+040.0016.016502e-129.414649e-282.779170e-123.237332e-121.548528e-041.769614e-032.999845e-09
    641003653.199940e+10420670816.03.157873e+102.840184e+100.000000e+001.045484e+223.152101e+04...3.071513e+048.058719e+020.0013.465519e-129.414649e-283.548016e-133.110717e-122.518117e-056.220313e-042.701462e-09
    \n",
-       "
    65 rows × 21 columns
    \n",
-       "
    "
-      ],
-      "text/plain": [
-       "    material_id  case_id  time_step_number  elapsed_time  irradiation_time  \\\n",
-       "0           100        3                 1  0.000000e+00               0.0   \n",
-       "1           100        3                 2  6.311520e+07        63115200.0   \n",
-       "2           100        3                 3  3.786912e+08       378691200.0   \n",
-       "3           100        3                 4  3.997401e+08       378691200.0   \n",
-       "4           100        3                 5  4.417117e+08       420662816.0   \n",
-       "..          ...      ...               ...           ...               ...   \n",
-       "60          100        3                61  7.573741e+08       420670816.0   \n",
-       "61          100        3                62  1.388526e+09       420670816.0   \n",
-       "62          100        3                63  2.019678e+09       420670816.0   \n",
-       "63          100        3                64  3.597558e+09       420670816.0   \n",
-       "64          100        3                65  3.199940e+10       420670816.0   \n",
-       "\n",
-       "    cooling_time      duration          flux   total_atoms  total_activity  \\\n",
-       "0   0.000000e+00  0.000000e+00  0.000000e+00  1.045481e+22    1.099260e-02   \n",
-       "1   0.000000e+00  6.311520e+07  2.445200e+10  1.045481e+22    2.268685e+07   \n",
-       "2   0.000000e+00  3.155760e+08  1.882800e+11  1.045484e+22    2.005898e+08   \n",
-       "3   2.104892e+07  2.104892e+07  0.000000e+00  1.045484e+22    5.064473e+07   \n",
-       "4   2.104892e+07  4.197161e+07  3.790000e+11  1.045484e+22    3.644599e+08   \n",
-       "..           ...           ...           ...           ...             ...   \n",
-       "60  3.367033e+08  2.209032e+08  0.000000e+00  1.045484e+22    1.021210e+07   \n",
-       "61  9.678553e+08  6.311520e+08  0.000000e+00  1.045484e+22    2.140445e+06   \n",
-       "62  1.599007e+09  6.311520e+08  0.000000e+00  1.045484e+22    1.354644e+06   \n",
-       "63  3.176887e+09  1.577880e+09  0.000000e+00  1.045484e+22    8.909484e+05   \n",
-       "64  3.157873e+10  2.840184e+10  0.000000e+00  1.045484e+22    3.152101e+04   \n",
-       "\n",
-       "    ...  total_beta_activity  total_gamma_activity  total_mass    total_heat  \\\n",
-       "0   ...         1.099260e-02          0.000000e+00       0.001  1.994928e-19   \n",
-       "1   ...         1.476443e+07          7.922416e+06       0.001  2.522555e-09   \n",
-       "2   ...         1.391144e+08          6.147540e+07       0.001  2.601587e-08   \n",
-       "3   ...         5.005196e+07          5.927796e+05       0.001  1.072963e-08   \n",
-       "4   ...         2.411954e+08          1.232645e+08       0.001  4.388052e-08   \n",
-       "..  ...                  ...                   ...         ...           ...   \n",
-       "60  ...         9.725966e+06          4.861311e+05       0.001  3.030422e-09   \n",
-       "61  ...         1.934185e+06          2.062603e+05       0.001  2.260388e-10   \n",
-       "62  ...         1.266816e+06          8.782794e+04       0.001  2.303827e-11   \n",
-       "63  ...         8.798868e+05          1.106160e+04       0.001  6.016502e-12   \n",
-       "64  ...         3.071513e+04          8.058719e+02       0.001  3.465519e-12   \n",
-       "\n",
-       "    total_alpha_heat  total_beta_heat  total_gamma_heat  \\\n",
-       "0       0.000000e+00     1.994919e-19      8.784190e-25   \n",
-       "1       1.316125e-30     4.443058e-10      2.078249e-09   \n",
-       "2       6.436155e-28     3.691712e-09      2.232416e-08   \n",
-       "3       6.445708e-28     5.938637e-10      1.013577e-08   \n",
-       "4       9.368928e-28     7.024670e-09      3.685585e-08   \n",
-       "..               ...              ...               ...   \n",
-       "60      9.414649e-28     1.199240e-10      2.910498e-09   \n",
-       "61      9.414649e-28     1.325084e-11      2.127880e-10   \n",
-       "62      9.414649e-28     4.691881e-12      1.834639e-11   \n",
-       "63      9.414649e-28     2.779170e-12      3.237332e-12   \n",
-       "64      9.414649e-28     3.548016e-13      3.110717e-12   \n",
-       "\n",
-       "    total_ingest1ion_dose  total_inhalation_dose  total_dose_rate  \n",
-       "0            5.288239e-12           9.131853e-12     7.484415e-22  \n",
-       "1            1.225884e-02           7.370374e-02     1.774444e-06  \n",
-       "2            1.498245e-01           1.057001e+00     1.854623e-05  \n",
-       "3            8.618334e-02           7.240407e-01     7.931148e-06  \n",
-       "4            2.313087e-01           1.522821e+00     3.102856e-05  \n",
-       "..                    ...                    ...              ...  \n",
-       "60           2.524398e-02           2.288691e-01     2.231632e-06  \n",
-       "61           2.034489e-03           1.899889e-02     1.650785e-07  \n",
-       "62           3.442937e-04           3.528395e-03     1.529847e-08  \n",
-       "63           1.548528e-04           1.769614e-03     2.999845e-09  \n",
-       "64           2.518117e-05           6.220313e-04     2.701462e-09  \n",
-       "\n",
-       "[65 rows x 21 columns]"
-      ]
-     },
-     "execution_count": 518,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "con.execute(\"select * from timestep\").df()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 533,
-   "id": "c5fdb6e7-00b7-40f1-9d8d-f755dd768a97",
-   "metadata": {
-    "tags": []
-   },
-   "outputs": [],
-   "source": [
-    "def save_nuclides(con, ds):\n",
-    "    nuclides_df = ds[[\"element\", \"mass_number\", \"state\", \"zai\", \"nuclide_half_life\"]] \\\n",
-    "    .reset_index([\"material_id\", \"case_id\"]) \\\n",
-    "    .to_dataframe() \\\n",
-    "    .reset_index(\n",
-    "        [\n",
-    "            \"material_id\", \"case_id\"\n",
-    "        ],\n",
-    "        drop=True\n",
-    "    ) \\\n",
-    "    .reset_index(drop=True)\n",
-    "    sql = \"insert or ignore into nuclide select * from nuclides_df\"\n",
-    "    con.execute(sql)\n",
-    "    con.commit()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 534,
-   "id": "2cd4e47d-1ec3-493c-b655-8a83917deea5",
-   "metadata": {
-    "tags": []
-   },
-   "outputs": [],
-   "source": [
-    "save_nuclides(con, ds)"
-   ]
-  },
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-   "execution_count": 535,
-   "id": "1f6cbb0e-e893-4d88-a744-989d9b39e0a4",
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    elementmass_numberstatezaihalf_life
    0Al261302602.262630e+13
    1Al271302700.000000e+00
    2Al281302801.344600e+02
    3Al291302903.936000e+02
    4Al301303003.650000e+00
    ..................
    210Zr934009304.828210e+13
    211Zr944009401.893460e+23
    212Zr954009505.532360e+06
    213Zr964009601.230750e+27
    214Zr974009706.027840e+04
    \n",
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    215 rows × 5 columns
    \n",
-       "
    "
-      ],
-      "text/plain": [
-       "    element  mass_number state     zai     half_life\n",
-       "0        Al           26        130260  2.262630e+13\n",
-       "1        Al           27        130270  0.000000e+00\n",
-       "2        Al           28        130280  1.344600e+02\n",
-       "3        Al           29        130290  3.936000e+02\n",
-       "4        Al           30        130300  3.650000e+00\n",
-       "..      ...          ...   ...     ...           ...\n",
-       "210      Zr           93        400930  4.828210e+13\n",
-       "211      Zr           94        400940  1.893460e+23\n",
-       "212      Zr           95        400950  5.532360e+06\n",
-       "213      Zr           96        400960  1.230750e+27\n",
-       "214      Zr           97        400970  6.027840e+04\n",
-       "\n",
-       "[215 rows x 5 columns]"
-      ]
-     },
-     "execution_count": 535,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "con.execute(\"select * from nuclide\").df()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 559,
-   "id": "1161cef3-d3cf-4c2f-aa2d-2c1ea9ee9208",
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+       "      \n",
+       "      \n",
+       "      \n",
+       "    \n",
+       "    \n",
+       "      \n",
+       "      \n",
+       "      \n",
+       "      \n",
+       "      \n",
+       "    \n",
+       "    \n",
+       "      \n",
+       "      \n",
+       "      \n",
+       "      \n",
+       "      \n",
+       "    \n",
+       "    \n",
+       "      \n",
+       "      \n",
+       "      \n",
+       "      \n",
+       "      \n",
+       "    \n",
+       "  \n",
+       "
    material_idcase_idtime_step_number0
    0100310.0
    11003263115200.0
    210033378691200.0
    310034378691200.0
    410035420662808.0
    ...............
    60100361420670808.0
    61100362420670808.0
    62100363420670808.0
    63100364420670808.0
    64100365420670808.0
    \n",
+       "
    65 rows × 4 columns
    \n",
+       "
    "
+      ],
+      "text/plain": [
+       "    material_id  case_id  time_step_number            0\n",
+       "0           100        3                 1          0.0\n",
+       "1           100        3                 2   63115200.0\n",
+       "2           100        3                 3  378691200.0\n",
+       "3           100        3                 4  378691200.0\n",
+       "4           100        3                 5  420662808.0\n",
+       "..          ...      ...               ...          ...\n",
+       "60          100        3                61  420670808.0\n",
+       "61          100        3                62  420670808.0\n",
+       "62          100        3                63  420670808.0\n",
+       "63          100        3                64  420670808.0\n",
+       "64          100        3                65  420670808.0\n",
+       "\n",
+       "[65 rows x 4 columns]"
+      ]
+     },
+     "execution_count": 20,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "ds.irradiation_time.stack({\"idx\":[\"material_id\", \"case_id\", \"time_step_number\"]}).to_pandas().reset_index()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 21,
+   "id": "d9e1ddfb-398e-4cea-b01d-fb0e53242776",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "def drop_tables(con):\n",
+    "    con.execute(\"drop table if exists timestep_gamma\")\n",
+    "    con.execute(\"drop table if exists timestep_nuclide\")\n",
+    "    con.execute(\"drop table if exists timestep\")\n",
+    "    con.execute(\"drop table if exists nuclide\")\n",
+    "    con.execute(\"drop table if exists rundata\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 22,
+   "id": "c402d3a1-e77a-4b24-accc-a19588ccdf54",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "def create_tables(con):\n",
+    "    sql = \"\"\" \n",
+    "    CREATE TABLE IF NOT EXISTS rundata (\n",
+    "        material_id uinteger not null,\n",
+    "        case_id uinteger not null,\n",
+    "        timestamp timestamp not null,\n",
+    "        run_name varchar not null,\n",
+    "        flux_name varchar NOT NULL,\n",
+    "        dose_rate_type varchar NOT NULL,\n",
+    "        dose_rate_distance real NOT NULL,\n",
+    "        primary key(material_id, case_id)\n",
+    "    );\n",
+    "\n",
+    "    CREATE TABLE IF NOT EXISTS timestep(\n",
+    "        material_id  uinteger not null,\n",
+    "        case_id      uinteger not null,\n",
+    "        time_step_number uinteger not null,\n",
+    "        elapsed_time float4 not null,\n",
+    "        irradiation_time float4 not null,\n",
+    "        cooling_time float4 not null,\n",
+    "        duration float4 not null,\n",
+    "        flux float4 not null,\n",
+    "        total_atoms float4 not null,\n",
+    "        total_activity float4 not null,\n",
+    "        total_alpha_activity float4 not null,\n",
+    "        total_beta_activity float4 not null,\n",
+    "        total_gamma_activity float4 not null,\n",
+    "        total_mass float4 not null,\n",
+    "        total_heat float4 not null,\n",
+    "        total_alpha_heat float4 null,\n",
+    "        total_beta_heat float4 not null,\n",
+    "        total_gamma_heat float4 not null,\n",
+    "        total_ingest1ion_dose float4 not null,\n",
+    "        total_inhalation_dose float4 not null,\n",
+    "        total_dose_rate float4 not null,\n",
+    "        primary key(material_id, case_id, time_step_number),\n",
+    "        foreign key(material_id, case_id) references rundata(material_id, case_id) \n",
+    "    );\n",
+    "\n",
+    "    \n",
+    "    CREATE TABLE IF NOT EXISTS nuclide(\n",
+    "        element varchar(2) not null,\n",
+    "        mass_number usmallint not null check(0 < mass_number),\n",
+    "        state varchar(1) not null,\n",
+    "        zai integer not null check(10010 <= zai) unique,\n",
+    "        half_life float4 not null check(0 <= half_life),\n",
+    "        primary key(element, mass_number, state)\n",
+    "    );\n",
+    "    \n",
+    "    CREATE TABLE IF NOT EXISTS timestep_nuclide(\n",
+    "        material_id  uinteger not null,\n",
+    "        case_id      uinteger not null,\n",
+    "        time_step_number uinteger not null,\n",
+    "        element varchar(2) not null,\n",
+    "        mass_number usmallint not null,\n",
+    "        \n",
+    "        state varchar(1) not null,\n",
+    "        atoms float4 not null,\n",
+    "        grams float4 not null,\n",
+    "        activity float4 not null,\n",
+    "        alpha_activity float4 not null,\n",
+    "        \n",
+    "        beta_activity float4 not null,\n",
+    "        gamma_activity float4 not null,\n",
+    "        heat float4 not null,\n",
+    "        alpha_heat float4 not null,\n",
+    "        beta_heat float4 not null,\n",
+    "        \n",
+    "        gamma_heat float4 not null,\n",
+    "        dose float4 not null,\n",
+    "        ingestion float4 not null,\n",
+    "        inhalation float4 not null,\n",
+    "        \n",
+    "        primary key(material_id, case_id, time_step_number, element, mass_number, state),\n",
+    "        foreign key(material_id, case_id, time_step_number) references timestep(material_id, case_id, time_step_number),\n",
+    "        foreign key(element, mass_number, state) references nuclide(element, mass_number, state) \n",
+    "    );\n",
+    "\n",
+    "    CREATE TABLE IF NOT EXISTS timestep_gamma(\n",
+    "        material_id  uinteger not null,\n",
+    "        case_id      uinteger not null,\n",
+    "        time_step_number uinteger not null,\n",
+    "        boundary real not null check(0 <= boundary),\n",
+    "        intensity real not null, \n",
+    "        primary key(material_id, case_id, time_step_number, boundary),\n",
+    "        foreign key(material_id, case_id, time_step_number) references timestep(material_id, case_id, time_step_number),\n",
+    "    );\n",
+    "    \"\"\"\n",
+    "    con.execute(sql)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 23,
+   "id": "25f6867e-397a-4e98-a363-74b6af739c88",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "drop_tables(con)\n",
+    "create_tables(con)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 24,
+   "id": "29716201-70f8-40d2-8da7-85689714ec32",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "def save_rundata(con, ds):\n",
+    "    sql = \"\"\"\n",
+    "        INSERT INTO rundata values(?, ?, ?, ?, ?, ?, ?)\n",
+    "    \"\"\"\n",
+    "    con.execute(sql, (    \n",
+    "        ds.material_id.item(),\n",
+    "        ds.case_id.item(),\n",
+    "        ds.timestamp.dt.strftime(\"%Y-%m-%d %H:%M:%S\").item(),\n",
+    "        ds.attrs[\"run_name\"],\n",
+    "        ds.attrs[\"flux_name\"],\n",
+    "        ds.attrs[\"dose_rate_type\"],\n",
+    "        ds.attrs[\"dose_rate_distance\"]\n",
+    "    ))\n",
+    "    con.commit()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 25,
+   "id": "c789eedd-580c-4383-8bf1-cc943562a3aa",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "save_rundata(con, ds)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 26,
+   "id": "1c650134-edf3-44dd-aa90-ddde6a3987a7",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "
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+       "\n",
+       "\n",
+       "  \n",
+       "    \n",
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+       "
    material_idcase_idtimestamprun_nameflux_namedose_rate_typedose_rate_distance
    010032022-02-21 01:52:47* Material Alloy718-Co04, fluxes 104_2_1_190-degrees bendPoint source1.0
    \n",
+       "
    "
+      ],
+      "text/plain": [
+       "   material_id  case_id           timestamp  \\\n",
+       "0          100        3 2022-02-21 01:52:47   \n",
        "\n",
-       ".xr-index-preview {\n",
-       "  grid-column: 2 / 5;\n",
-       "  color: var(--xr-font-color2);\n",
-       "}\n",
+       "                                     run_name        flux_name dose_rate_type  \\\n",
+       "0  * Material Alloy718-Co04, fluxes 104_2_1_1  90-degrees bend   Point source   \n",
        "\n",
-       ".xr-var-name,\n",
-       ".xr-var-dims,\n",
-       ".xr-var-dtype,\n",
-       ".xr-preview,\n",
-       ".xr-attrs dt {\n",
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-       "  overflow: hidden;\n",
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-       "  padding-right: 10px;\n",
-       "}\n",
+       "   dose_rate_distance  \n",
+       "0                 1.0  "
+      ]
+     },
+     "execution_count": 26,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "con.execute(\"select * from rundata\").df()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 27,
+   "id": "cf8661b6-d9cb-4431-8b40-f14072409d5a",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "def save_timesteps(con, ds):\n",
+    "    timesteps_df = ds[\n",
+    "        [\n",
+    "            \"material_id\",\n",
+    "            \"case_id\",\n",
+    "            \"time_step_number\",\n",
+    "            \"elapsed_time\",\n",
+    "            \"irradiation_time\",\n",
+    "            \"cooling_time\",\n",
+    "            \"duration\",\n",
+    "            \"flux\",\n",
+    "            \"total_atoms\",\n",
+    "            \"total_activity\",\n",
+    "            \"total_alpha_activity\",\n",
+    "            \"total_beta_activity\",\n",
+    "            \"total_gamma_activity\",\n",
+    "            \"total_mass\",\n",
+    "            \"total_heat\",\n",
+    "            \"total_alpha_heat\",\n",
+    "            \"total_beta_heat\",\n",
+    "            \"total_gamma_heat\",\n",
+    "            \"total_ingest1ion_dose\",\n",
+    "            \"total_inhalation_dose\",\n",
+    "            \"total_dose_rate\",\n",
+    "        ]\n",
+    "    ].to_dataframe().reset_index()\n",
+    "    sql = \"insert into timestep select * from timesteps_df\"\n",
+    "    con.execute(sql)\n",
+    "    con.commit()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 28,
+   "id": "78154d84-9df4-417d-a35f-60252575aae6",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "save_timesteps(con, ds)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 29,
+   "id": "bf73ee32-d132-418f-8e77-969d779b780a",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [
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    material_idcase_idtime_step_numberelapsed_timeirradiation_timecooling_timedurationfluxtotal_atomstotal_activity...total_beta_activitytotal_gamma_activitytotal_masstotal_heattotal_alpha_heattotal_beta_heattotal_gamma_heattotal_ingest1ion_dosetotal_inhalation_dosetotal_dose_rate
    0100310.000000e+000.00.000000e+000.000000e+000.000000e+001.045481e+221.099260e-02...1.099260e-020.000000e+000.0011.994928e-190.000000e+001.994919e-198.784190e-255.288239e-129.131853e-127.484415e-22
    1100326.311520e+0763115200.00.000000e+006.311520e+072.445200e+101.045481e+222.268685e+07...1.476443e+077.922416e+060.0012.522555e-091.316125e-304.443058e-102.078249e-091.225884e-027.370374e-021.774444e-06
    2100333.786912e+08378691200.00.000000e+003.155760e+081.882800e+111.045484e+222.005898e+08...1.391144e+086.147540e+070.0012.601587e-086.436155e-283.691712e-092.232416e-081.498245e-011.057001e+001.854623e-05
    3100343.997401e+08378691200.02.104892e+072.104892e+070.000000e+001.045484e+225.064473e+07...5.005196e+075.927796e+050.0011.072963e-086.445708e-285.938637e-101.013577e-088.618334e-027.240407e-017.931148e-06
    4100354.417117e+08420662816.02.104892e+074.197161e+073.790000e+111.045484e+223.644599e+08...2.411954e+081.232645e+080.0014.388052e-089.368928e-287.024670e-093.685585e-082.313087e-011.522821e+003.102856e-05
    ..................................................................
    601003617.573741e+08420670816.03.367033e+082.209032e+080.000000e+001.045484e+221.021210e+07...9.725966e+064.861311e+050.0013.030422e-099.414649e-281.199240e-102.910498e-092.524398e-022.288691e-012.231632e-06
    611003621.388526e+09420670816.09.678553e+086.311520e+080.000000e+001.045484e+222.140445e+06...1.934185e+062.062603e+050.0012.260388e-109.414649e-281.325084e-112.127880e-102.034489e-031.899889e-021.650785e-07
    621003632.019678e+09420670816.01.599007e+096.311520e+080.000000e+001.045484e+221.354644e+06...1.266816e+068.782794e+040.0012.303827e-119.414649e-284.691881e-121.834639e-113.442937e-043.528395e-031.529847e-08
    631003643.597558e+09420670816.03.176887e+091.577880e+090.000000e+001.045484e+228.909484e+05...8.798868e+051.106160e+040.0016.016502e-129.414649e-282.779170e-123.237332e-121.548528e-041.769614e-032.999845e-09
    641003653.199940e+10420670816.03.157873e+102.840184e+100.000000e+001.045484e+223.152101e+04...3.071513e+048.058719e+020.0013.465519e-129.414649e-283.548016e-133.110717e-122.518117e-056.220313e-042.701462e-09
    \n",
+       "
    65 rows × 21 columns
    \n",
+       "
    "
+      ],
+      "text/plain": [
+       "    material_id  case_id  time_step_number  elapsed_time  irradiation_time  \\\n",
+       "0           100        3                 1  0.000000e+00               0.0   \n",
+       "1           100        3                 2  6.311520e+07        63115200.0   \n",
+       "2           100        3                 3  3.786912e+08       378691200.0   \n",
+       "3           100        3                 4  3.997401e+08       378691200.0   \n",
+       "4           100        3                 5  4.417117e+08       420662816.0   \n",
+       "..          ...      ...               ...           ...               ...   \n",
+       "60          100        3                61  7.573741e+08       420670816.0   \n",
+       "61          100        3                62  1.388526e+09       420670816.0   \n",
+       "62          100        3                63  2.019678e+09       420670816.0   \n",
+       "63          100        3                64  3.597558e+09       420670816.0   \n",
+       "64          100        3                65  3.199940e+10       420670816.0   \n",
        "\n",
-       ".xr-var-attrs-in:checked ~ .xr-var-attrs,\n",
-       ".xr-var-data-in:checked ~ .xr-var-data,\n",
-       ".xr-index-data-in:checked ~ .xr-index-data {\n",
-       "  display: block;\n",
-       "}\n",
+       "    cooling_time      duration          flux   total_atoms  total_activity  \\\n",
+       "0   0.000000e+00  0.000000e+00  0.000000e+00  1.045481e+22    1.099260e-02   \n",
+       "1   0.000000e+00  6.311520e+07  2.445200e+10  1.045481e+22    2.268685e+07   \n",
+       "2   0.000000e+00  3.155760e+08  1.882800e+11  1.045484e+22    2.005898e+08   \n",
+       "3   2.104892e+07  2.104892e+07  0.000000e+00  1.045484e+22    5.064473e+07   \n",
+       "4   2.104892e+07  4.197161e+07  3.790000e+11  1.045484e+22    3.644599e+08   \n",
+       "..           ...           ...           ...           ...             ...   \n",
+       "60  3.367033e+08  2.209032e+08  0.000000e+00  1.045484e+22    1.021210e+07   \n",
+       "61  9.678553e+08  6.311520e+08  0.000000e+00  1.045484e+22    2.140445e+06   \n",
+       "62  1.599007e+09  6.311520e+08  0.000000e+00  1.045484e+22    1.354644e+06   \n",
+       "63  3.176887e+09  1.577880e+09  0.000000e+00  1.045484e+22    8.909484e+05   \n",
+       "64  3.157873e+10  2.840184e+10  0.000000e+00  1.045484e+22    3.152101e+04   \n",
        "\n",
-       ".xr-var-data > table {\n",
-       "  float: right;\n",
-       "}\n",
+       "    ...  total_beta_activity  total_gamma_activity  total_mass    total_heat  \\\n",
+       "0   ...         1.099260e-02          0.000000e+00       0.001  1.994928e-19   \n",
+       "1   ...         1.476443e+07          7.922416e+06       0.001  2.522555e-09   \n",
+       "2   ...         1.391144e+08          6.147540e+07       0.001  2.601587e-08   \n",
+       "3   ...         5.005196e+07          5.927796e+05       0.001  1.072963e-08   \n",
+       "4   ...         2.411954e+08          1.232645e+08       0.001  4.388052e-08   \n",
+       "..  ...                  ...                   ...         ...           ...   \n",
+       "60  ...         9.725966e+06          4.861311e+05       0.001  3.030422e-09   \n",
+       "61  ...         1.934185e+06          2.062603e+05       0.001  2.260388e-10   \n",
+       "62  ...         1.266816e+06          8.782794e+04       0.001  2.303827e-11   \n",
+       "63  ...         8.798868e+05          1.106160e+04       0.001  6.016502e-12   \n",
+       "64  ...         3.071513e+04          8.058719e+02       0.001  3.465519e-12   \n",
        "\n",
-       ".xr-var-name span,\n",
-       ".xr-var-data,\n",
-       ".xr-index-name div,\n",
-       ".xr-index-data,\n",
-       ".xr-attrs {\n",
-       "  padding-left: 25px !important;\n",
-       "}\n",
+       "    total_alpha_heat  total_beta_heat  total_gamma_heat  \\\n",
+       "0       0.000000e+00     1.994919e-19      8.784190e-25   \n",
+       "1       1.316125e-30     4.443058e-10      2.078249e-09   \n",
+       "2       6.436155e-28     3.691712e-09      2.232416e-08   \n",
+       "3       6.445708e-28     5.938637e-10      1.013577e-08   \n",
+       "4       9.368928e-28     7.024670e-09      3.685585e-08   \n",
+       "..               ...              ...               ...   \n",
+       "60      9.414649e-28     1.199240e-10      2.910498e-09   \n",
+       "61      9.414649e-28     1.325084e-11      2.127880e-10   \n",
+       "62      9.414649e-28     4.691881e-12      1.834639e-11   \n",
+       "63      9.414649e-28     2.779170e-12      3.237332e-12   \n",
+       "64      9.414649e-28     3.548016e-13      3.110717e-12   \n",
        "\n",
-       ".xr-attrs,\n",
-       ".xr-var-attrs,\n",
-       ".xr-var-data,\n",
-       ".xr-index-data {\n",
-       "  grid-column: 1 / -1;\n",
-       "}\n",
+       "    total_ingest1ion_dose  total_inhalation_dose  total_dose_rate  \n",
+       "0            5.288239e-12           9.131853e-12     7.484415e-22  \n",
+       "1            1.225884e-02           7.370374e-02     1.774444e-06  \n",
+       "2            1.498245e-01           1.057001e+00     1.854623e-05  \n",
+       "3            8.618334e-02           7.240407e-01     7.931148e-06  \n",
+       "4            2.313087e-01           1.522821e+00     3.102856e-05  \n",
+       "..                    ...                    ...              ...  \n",
+       "60           2.524398e-02           2.288691e-01     2.231632e-06  \n",
+       "61           2.034489e-03           1.899889e-02     1.650785e-07  \n",
+       "62           3.442937e-04           3.528395e-03     1.529847e-08  \n",
+       "63           1.548528e-04           1.769614e-03     2.999845e-09  \n",
+       "64           2.518117e-05           6.220313e-04     2.701462e-09  \n",
        "\n",
-       "dl.xr-attrs {\n",
-       "  padding: 0;\n",
-       "  margin: 0;\n",
-       "  display: grid;\n",
-       "  grid-template-columns: 125px auto;\n",
-       "}\n",
+       "[65 rows x 21 columns]"
+      ]
+     },
+     "execution_count": 29,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "con.execute(\"select * from timestep\").df()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 55,
+   "id": "9b2d9205-284f-48bf-8817-04dce78e16fd",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
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+       "
    elementmass_numberstatezainuclide_half_life
    0Al261302602.262630e+13
    1Al271302700.000000e+00
    2Al281302801.344600e+02
    3Al291302903.936000e+02
    4Al301303003.650000e+00
    ..................
    210Zr934009304.828210e+13
    211Zr944009401.893460e+23
    212Zr954009505.532360e+06
    213Zr964009601.230750e+27
    214Zr974009706.027840e+04
    \n",
+       "
    215 rows × 5 columns
    \n",
+       "
    "
+      ],
+      "text/plain": [
+       "    element  mass_number state     zai  nuclide_half_life\n",
+       "0        Al           26        130260       2.262630e+13\n",
+       "1        Al           27        130270       0.000000e+00\n",
+       "2        Al           28        130280       1.344600e+02\n",
+       "3        Al           29        130290       3.936000e+02\n",
+       "4        Al           30        130300       3.650000e+00\n",
+       "..      ...          ...   ...     ...                ...\n",
+       "210      Zr           93        400930       4.828210e+13\n",
+       "211      Zr           94        400940       1.893460e+23\n",
+       "212      Zr           95        400950       5.532360e+06\n",
+       "213      Zr           96        400960       1.230750e+27\n",
+       "214      Zr           97        400970       6.027840e+04\n",
        "\n",
-       ".xr-attrs dt:hover span {\n",
-       "  display: inline-block;\n",
-       "  background: var(--xr-background-color);\n",
-       "  padding-right: 10px;\n",
-       "}\n",
+       "[215 rows x 5 columns]"
+      ]
+     },
+     "execution_count": 55,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "columns_all = [\"element\", \"mass_number\", \"state\", \"zai\", \"nuclide_half_life\"]\n",
+    "columns = [\"zai\", \"nuclide_half_life\"]\n",
+    "ds[columns].to_dataframe()[columns].reset_index()[columns_all]\n",
+    "# .unstack(\"nuclide\") \n",
+    "# .stack({\"idx\": [\"material_id\", \"case_id\", \"element\", \"mass_number\", \"state\"]}) \\\n",
+    "# .to_dataframe()\n",
+    "\n",
+    "# \\\n",
+    "#     .reset_index([\"material_id\", \"case_id\"]) \\\n",
+    "#     .to_dataframe() \\\n",
+    "#     .reset_index(\n",
+    "#         [\n",
+    "#             \"material_id\", \"case_id\"\n",
+    "#         ],\n",
+    "#         drop=True\n",
+    "#     ) \\\n",
+    "#     .reset_index(drop=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 56,
+   "id": "c5fdb6e7-00b7-40f1-9d8d-f755dd768a97",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "def save_nuclides(con, ds):\n",
+    "    columns_all = [\"element\", \"mass_number\", \"state\", \"zai\", \"nuclide_half_life\"]\n",
+    "    columns = [\"zai\", \"nuclide_half_life\"]\n",
+    "    nuclides_df = ds[columns].to_dataframe()[columns].reset_index()[columns_all]\n",
+    "    sql = \"insert or ignore into nuclide select * from nuclides_df\"\n",
+    "    con.execute(sql)\n",
+    "    con.commit()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 57,
+   "id": "2cd4e47d-1ec3-493c-b655-8a83917deea5",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "save_nuclides(con, ds)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 58,
+   "id": "1f6cbb0e-e893-4d88-a744-989d9b39e0a4",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "
    \n",
+       "
    <xarray.Dataset>\n",
-       "Dimensions:           (material_id: 1, case_id: 1, time_step_number: 65,\n",
-       "                       nuclide: 215)\n",
-       "Coordinates:\n",
-       "  * material_id       (material_id) int64 100\n",
-       "  * case_id           (case_id) int64 3\n",
-       "  * time_step_number  (time_step_number) int64 1 2 3 4 5 6 ... 60 61 62 63 64 65\n",
-       "  * element           (nuclide) object 'Al' 'Al' 'Al' 'Al' ... 'Zr' 'Zr' 'Zr'\n",
-       "  * mass_number       (nuclide) int64 26 27 28 29 30 40 10 ... 92 93 94 95 96 97\n",
-       "  * state             (nuclide) object '' '' '' '' '' '' ... '' '' '' '' '' ''\n",
-       "  * nuclide           (nuclide) object MultiIndex\n",
-       "    elapsed_time      (time_step_number) float64 0.0 6.312e+07 ... 3.2e+10\n",
-       "    zai               (nuclide) int64 130260 130270 130280 ... 400960 400970\n",
-       "Data variables:\n",
-       "    *empty*\n",
-       "Attributes:\n",
-       "    run_name:            * Material Alloy718-Co04, fluxes 104_2_1_1\n",
-       "    flux_name:           90-degrees bend\n",
-       "    dose_rate_type:      Point source\n",
-       "    dose_rate_distance:  1.0
    "
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+       "  \n",
+       "
    elementmass_numberstatezaihalf_life
    0Al261302602.262630e+13
    1Al271302700.000000e+00
    2Al281302801.344600e+02
    3Al291302903.936000e+02
    4Al301303003.650000e+00
    ..................
    210Zr934009304.828210e+13
    211Zr944009401.893460e+23
    212Zr954009505.532360e+06
    213Zr964009601.230750e+27
    214Zr974009706.027840e+04
    \n",
+       "
    215 rows × 5 columns
    \n",
+       ""
+      ],
+      "text/plain": [
+       "    element  mass_number state     zai     half_life\n",
+       "0        Al           26        130260  2.262630e+13\n",
+       "1        Al           27        130270  0.000000e+00\n",
+       "2        Al           28        130280  1.344600e+02\n",
+       "3        Al           29        130290  3.936000e+02\n",
+       "4        Al           30        130300  3.650000e+00\n",
+       "..      ...          ...   ...     ...           ...\n",
+       "210      Zr           93        400930  4.828210e+13\n",
+       "211      Zr           94        400940  1.893460e+23\n",
+       "212      Zr           95        400950  5.532360e+06\n",
+       "213      Zr           96        400960  1.230750e+27\n",
+       "214      Zr           97        400970  6.027840e+04\n",
+       "\n",
+       "[215 rows x 5 columns]"
+      ]
+     },
+     "execution_count": 58,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "con.execute(\"select * from nuclide\").df()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 91,
+   "id": "1161cef3-d3cf-4c2f-aa2d-2c1ea9ee9208",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [
+    {
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+       "
    material_idcase_idtime_step_numberelementmass_numberstatenuclide_atomsnuclide_gramsnuclide_activitynuclide_alpha_activitynuclide_beta_activitynuclide_gamma_activitynuclide_heatnuclide_alpha_heatnuclide_beta_heatnuclide_gamma_heatnuclide_dosenuclide_ingestionnuclide_inhalation
    010031Al260.000000e+000.000000e+000.0000000.00.0000000.00.000000e+000.00.000000e+000.000000e+000.000000e+000.000000e+000.000000e+00
    110032Al261.110297e+114.791169e-120.0034010.00.0034010.01.675088e-180.02.173910e-191.457697e-181.085307e-151.190471e-116.802694e-11
    210033Al264.381537e+121.890728e-100.1342270.00.1342270.06.610360e-170.08.578851e-185.752474e-174.282920e-144.697929e-102.684531e-09
    310034Al264.381534e+121.890726e-100.1342260.00.1342260.06.610355e-170.08.578846e-185.752471e-174.282917e-144.697926e-102.684529e-09
    410035Al265.523492e+122.383506e-100.1692100.00.1692100.08.333209e-170.01.081475e-177.251735e-175.399172e-145.922345e-103.384197e-09
    ............................................................
    13970100361Zr970.000000e+000.000000e+000.0000000.00.0000000.00.000000e+000.00.000000e+000.000000e+000.000000e+000.000000e+000.000000e+00
    13971100362Zr970.000000e+000.000000e+000.0000000.00.0000000.00.000000e+000.00.000000e+000.000000e+000.000000e+000.000000e+000.000000e+00
    13972100363Zr970.000000e+000.000000e+000.0000000.00.0000000.00.000000e+000.00.000000e+000.000000e+000.000000e+000.000000e+000.000000e+00
    13973100364Zr970.000000e+000.000000e+000.0000000.00.0000000.00.000000e+000.00.000000e+000.000000e+000.000000e+000.000000e+000.000000e+00
    13974100365Zr970.000000e+000.000000e+000.0000000.00.0000000.00.000000e+000.00.000000e+000.000000e+000.000000e+000.000000e+000.000000e+00
    \n",
+       "
    13975 rows × 19 columns
    \n",
+       "
    "
       ],
       "text/plain": [
-       "\n",
-       "Dimensions:           (material_id: 1, case_id: 1, time_step_number: 65,\n",
-       "                       nuclide: 215)\n",
-       "Coordinates:\n",
-       "  * material_id       (material_id) int64 100\n",
-       "  * case_id           (case_id) int64 3\n",
-       "  * time_step_number  (time_step_number) int64 1 2 3 4 5 6 ... 60 61 62 63 64 65\n",
-       "  * element           (nuclide) object 'Al' 'Al' 'Al' 'Al' ... 'Zr' 'Zr' 'Zr'\n",
-       "  * mass_number       (nuclide) int64 26 27 28 29 30 40 10 ... 92 93 94 95 96 97\n",
-       "  * state             (nuclide) object '' '' '' '' '' '' ... '' '' '' '' '' ''\n",
-       "  * nuclide           (nuclide) object MultiIndex\n",
-       "    elapsed_time      (time_step_number) float64 0.0 6.312e+07 ... 3.2e+10\n",
-       "    zai               (nuclide) int64 130260 130270 130280 ... 400960 400970\n",
-       "Data variables:\n",
-       "    *empty*\n",
-       "Attributes:\n",
-       "    run_name:            * Material Alloy718-Co04, fluxes 104_2_1_1\n",
-       "    flux_name:           90-degrees bend\n",
-       "    dose_rate_type:      Point source\n",
-       "    dose_rate_distance:  1.0"
+       "       material_id  case_id  time_step_number element  mass_number state  \\\n",
+       "0              100        3                 1      Al           26         \n",
+       "1              100        3                 2      Al           26         \n",
+       "2              100        3                 3      Al           26         \n",
+       "3              100        3                 4      Al           26         \n",
+       "4              100        3                 5      Al           26         \n",
+       "...            ...      ...               ...     ...          ...   ...   \n",
+       "13970          100        3                61      Zr           97         \n",
+       "13971          100        3                62      Zr           97         \n",
+       "13972          100        3                63      Zr           97         \n",
+       "13973          100        3                64      Zr           97         \n",
+       "13974          100        3                65      Zr           97         \n",
+       "\n",
+       "       nuclide_atoms  nuclide_grams  nuclide_activity  nuclide_alpha_activity  \\\n",
+       "0       0.000000e+00   0.000000e+00          0.000000                     0.0   \n",
+       "1       1.110297e+11   4.791169e-12          0.003401                     0.0   \n",
+       "2       4.381537e+12   1.890728e-10          0.134227                     0.0   \n",
+       "3       4.381534e+12   1.890726e-10          0.134226                     0.0   \n",
+       "4       5.523492e+12   2.383506e-10          0.169210                     0.0   \n",
+       "...              ...            ...               ...                     ...   \n",
+       "13970   0.000000e+00   0.000000e+00          0.000000                     0.0   \n",
+       "13971   0.000000e+00   0.000000e+00          0.000000                     0.0   \n",
+       "13972   0.000000e+00   0.000000e+00          0.000000                     0.0   \n",
+       "13973   0.000000e+00   0.000000e+00          0.000000                     0.0   \n",
+       "13974   0.000000e+00   0.000000e+00          0.000000                     0.0   \n",
+       "\n",
+       "       nuclide_beta_activity  nuclide_gamma_activity  nuclide_heat  \\\n",
+       "0                   0.000000                     0.0  0.000000e+00   \n",
+       "1                   0.003401                     0.0  1.675088e-18   \n",
+       "2                   0.134227                     0.0  6.610360e-17   \n",
+       "3                   0.134226                     0.0  6.610355e-17   \n",
+       "4                   0.169210                     0.0  8.333209e-17   \n",
+       "...                      ...                     ...           ...   \n",
+       "13970               0.000000                     0.0  0.000000e+00   \n",
+       "13971               0.000000                     0.0  0.000000e+00   \n",
+       "13972               0.000000                     0.0  0.000000e+00   \n",
+       "13973               0.000000                     0.0  0.000000e+00   \n",
+       "13974               0.000000                     0.0  0.000000e+00   \n",
+       "\n",
+       "       nuclide_alpha_heat  nuclide_beta_heat  nuclide_gamma_heat  \\\n",
+       "0                     0.0       0.000000e+00        0.000000e+00   \n",
+       "1                     0.0       2.173910e-19        1.457697e-18   \n",
+       "2                     0.0       8.578851e-18        5.752474e-17   \n",
+       "3                     0.0       8.578846e-18        5.752471e-17   \n",
+       "4                     0.0       1.081475e-17        7.251735e-17   \n",
+       "...                   ...                ...                 ...   \n",
+       "13970                 0.0       0.000000e+00        0.000000e+00   \n",
+       "13971                 0.0       0.000000e+00        0.000000e+00   \n",
+       "13972                 0.0       0.000000e+00        0.000000e+00   \n",
+       "13973                 0.0       0.000000e+00        0.000000e+00   \n",
+       "13974                 0.0       0.000000e+00        0.000000e+00   \n",
+       "\n",
+       "       nuclide_dose  nuclide_ingestion  nuclide_inhalation  \n",
+       "0      0.000000e+00       0.000000e+00        0.000000e+00  \n",
+       "1      1.085307e-15       1.190471e-11        6.802694e-11  \n",
+       "2      4.282920e-14       4.697929e-10        2.684531e-09  \n",
+       "3      4.282917e-14       4.697926e-10        2.684529e-09  \n",
+       "4      5.399172e-14       5.922345e-10        3.384197e-09  \n",
+       "...             ...                ...                 ...  \n",
+       "13970  0.000000e+00       0.000000e+00        0.000000e+00  \n",
+       "13971  0.000000e+00       0.000000e+00        0.000000e+00  \n",
+       "13972  0.000000e+00       0.000000e+00        0.000000e+00  \n",
+       "13973  0.000000e+00       0.000000e+00        0.000000e+00  \n",
+       "13974  0.000000e+00       0.000000e+00        0.000000e+00  \n",
+       "\n",
+       "[13975 rows x 19 columns]"
       ]
      },
-     "execution_count": 559,
+     "execution_count": 91,
      "metadata": {},
      "output_type": "execute_result"
     }
    ],
    "source": [
     "columns = [\n",
-    "    \"material_id\",\n",
-    "    \"case_id\",\n",
-    "    \"time_step_number\",\n",
-    "    \"element\",\n",
-    "    \"mass_number\",\n",
-    "    \"state\",\n",
+    "    # \"material_id\",\n",
+    "    # \"case_id\",\n",
+    "    # \"time_step_number\",\n",
+    "    # \"element\",\n",
+    "    # \"mass_number\",\n",
+    "    # \"state\",\n",
     "    \"nuclide_atoms\",\n",
     "    \"nuclide_grams\",\n",
     "    \"nuclide_activity\",\n",
@@ -4430,9 +3748,19 @@
     "    \"nuclide_ingestion\",\n",
     "    \"nuclide_inhalation\",\n",
     "]\n",
+    "columns_all = [\n",
+    "    \"material_id\",\n",
+    "    \"case_id\",\n",
+    "    \"time_step_number\",\n",
+    "    \"element\",\n",
+    "    \"mass_number\",\n",
+    "    \"state\",\n",
+    "] + columns\n",
+    "\n",
+    "ds[columns].stack(idx=(\"material_id\", \"case_id\", \"time_step_number\")).to_dataframe()[columns].reset_index()[columns_all].fillna(0.0)\n",
     "# ds[columns].reset_index([\"material_id\", \"case_id\"])\n",
     "\n",
-    "ds[columns].coords.to_dataset()\n",
+    "# ds[columns].coords.to_dataset()\n",
     "# .reset_index([\"elapsed_time\", \"zai\"])\n",
     "# .reset_coords()\n",
     "# .drop_indexes([\"material_id\", \"case_id\", \"time_step_number\", \"nuclide\"])\n",
@@ -4446,7 +3774,15 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 540,
+   "execution_count": null,
+   "id": "bdcce70a-bf6c-40a5-9b19-e95145d22b6e",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 92,
    "id": "526610bb-be7b-4ce7-8cc9-0bcdb00588f2",
    "metadata": {
     "tags": []
@@ -4455,12 +3791,6 @@
    "source": [
     "def save_timestep_nucludes(con, ds):\n",
     "    columns = [\n",
-    "        \"material_id\",\n",
-    "        \"case_id\",\n",
-    "        \"time_step_number\",\n",
-    "        \"element\",\n",
-    "        \"mass_number\",\n",
-    "        \"state\",\n",
     "        \"nuclide_atoms\",\n",
     "        \"nuclide_grams\",\n",
     "        \"nuclide_activity\",\n",
@@ -4475,11 +3805,20 @@
     "        \"nuclide_ingestion\",\n",
     "        \"nuclide_inhalation\",\n",
     "    ]\n",
-    "    tn = ds[columns].reset_index([\"material_id\", \"case_id\", \"time_step_number\", \"nuclide\"]).to_dataframe().reset_index(\n",
-    "        [\n",
-    "            \"material_id\", \"case_id\", \"time_step_number\",\n",
-    "        ]\n",
-    "    ).reset_index(drop=True)[columns].fillna(0.0)\n",
+    "    columns_all = [\n",
+    "        \"material_id\",\n",
+    "        \"case_id\",\n",
+    "        \"time_step_number\",\n",
+    "        \"element\",\n",
+    "        \"mass_number\",\n",
+    "        \"state\",\n",
+    "    ] + columns\n",
+    "\n",
+    "    tn = ds[columns] \\\n",
+    "        .stack(idx=(\"material_id\", \"case_id\", \"time_step_number\")) \\\n",
+    "        .to_dataframe()[columns] \\\n",
+    "        .reset_index()[columns_all] \\\n",
+    "        .fillna(0.0)\n",
     "    sql = \"insert into timestep_nuclide select * from tn\"\n",
     "    con.execute(sql)\n",
     "    con.commit()"
@@ -4487,32 +3826,19 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 541,
+   "execution_count": 93,
    "id": "de4b9bd0-02e4-48f5-bec3-bb92c67682d0",
    "metadata": {
     "tags": []
    },
-   "outputs": [
-    {
-     "ename": "ConstraintException",
-     "evalue": "Constraint Error: Violates foreign key constraint because key \"material_id: 0, case_id: 0, time_step_number: 0\" does not exist in the referenced table",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[0;31mConstraintException\u001b[0m                       Traceback (most recent call last)",
-      "Cell \u001b[0;32mIn[541], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[43msave_timestep_nucludes\u001b[49m\u001b[43m(\u001b[49m\u001b[43mcon\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mds\u001b[49m\u001b[43m)\u001b[49m\n",
-      "Cell \u001b[0;32mIn[540], line 29\u001b[0m, in \u001b[0;36msave_timestep_nucludes\u001b[0;34m(con, ds)\u001b[0m\n\u001b[1;32m     23\u001b[0m tn \u001b[38;5;241m=\u001b[39m ds[columns]\u001b[38;5;241m.\u001b[39mreset_index([\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mmaterial_id\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mcase_id\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mtime_step_number\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mnuclide\u001b[39m\u001b[38;5;124m\"\u001b[39m])\u001b[38;5;241m.\u001b[39mto_dataframe()\u001b[38;5;241m.\u001b[39mreset_index(\n\u001b[1;32m     24\u001b[0m     [\n\u001b[1;32m     25\u001b[0m         \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mmaterial_id\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mcase_id\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mtime_step_number\u001b[39m\u001b[38;5;124m\"\u001b[39m,\n\u001b[1;32m     26\u001b[0m     ]\n\u001b[1;32m     27\u001b[0m )\u001b[38;5;241m.\u001b[39mreset_index(drop\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m)[columns]\u001b[38;5;241m.\u001b[39mfillna(\u001b[38;5;241m0.0\u001b[39m)\n\u001b[1;32m     28\u001b[0m sql \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124minsert into timestep_nuclide select * from tn\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[0;32m---> 29\u001b[0m \u001b[43mcon\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mexecute\u001b[49m\u001b[43m(\u001b[49m\u001b[43msql\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m     30\u001b[0m con\u001b[38;5;241m.\u001b[39mcommit()\n",
-      "\u001b[0;31mConstraintException\u001b[0m: Constraint Error: Violates foreign key constraint because key \"material_id: 0, case_id: 0, time_step_number: 0\" does not exist in the referenced table"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "save_timestep_nucludes(con, ds)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 265,
+   "execution_count": 94,
    "id": "13094d05-fcad-40c3-b53d-34dfb8f84a4e",
    "metadata": {
     "tags": []
@@ -4539,7 +3865,9 @@
        "  \n",
        "    \n",
        "      \n",
-       "      timestep_id\n",
+       "      material_id\n",
+       "      case_id\n",
+       "      time_step_number\n",
        "      element\n",
        "      mass_number\n",
        "      state\n",
@@ -4561,103 +3889,113 @@
        "  \n",
        "    \n",
        "      0\n",
+       "      100\n",
+       "      3\n",
        "      1\n",
        "      Al\n",
        "      26\n",
        "      \n",
        "      0.000000e+00\n",
        "      0.000000e+00\n",
-       "      0.000000e+00\n",
+       "      0.000000\n",
        "      0.0\n",
-       "      0.000000e+00\n",
+       "      0.000000\n",
        "      0.0\n",
        "      0.000000e+00\n",
        "      0.0\n",
        "      0.000000e+00\n",
-       "      0.0\n",
-       "      0.0\n",
+       "      0.000000e+00\n",
+       "      0.000000e+00\n",
        "      0.000000e+00\n",
        "      0.000000e+00\n",
        "    \n",
        "    \n",
        "      1\n",
-       "      1\n",
+       "      100\n",
+       "      3\n",
+       "      2\n",
        "      Al\n",
-       "      27\n",
+       "      26\n",
        "      \n",
-       "      1.785556e+20\n",
-       "      8.000000e-03\n",
-       "      0.000000e+00\n",
-       "      0.0\n",
-       "      0.000000e+00\n",
+       "      1.110297e+11\n",
+       "      4.791169e-12\n",
+       "      0.003401\n",
        "      0.0\n",
-       "      0.000000e+00\n",
-       "      0.0\n",
-       "      0.000000e+00\n",
+       "      0.003401\n",
        "      0.0\n",
+       "      1.675088e-18\n",
        "      0.0\n",
-       "      0.000000e+00\n",
-       "      0.000000e+00\n",
+       "      2.173910e-19\n",
+       "      1.457697e-18\n",
+       "      1.085307e-15\n",
+       "      1.190471e-11\n",
+       "      6.802694e-11\n",
        "    \n",
        "    \n",
        "      2\n",
-       "      1\n",
+       "      100\n",
+       "      3\n",
+       "      3\n",
        "      Al\n",
-       "      28\n",
+       "      26\n",
        "      \n",
-       "      0.000000e+00\n",
-       "      0.000000e+00\n",
-       "      0.000000e+00\n",
-       "      0.0\n",
-       "      0.000000e+00\n",
+       "      4.381537e+12\n",
+       "      1.890728e-10\n",
+       "      0.134227\n",
        "      0.0\n",
-       "      0.000000e+00\n",
-       "      0.0\n",
-       "      0.000000e+00\n",
+       "      0.134227\n",
        "      0.0\n",
+       "      6.610360e-17\n",
        "      0.0\n",
-       "      0.000000e+00\n",
-       "      0.000000e+00\n",
+       "      8.578851e-18\n",
+       "      5.752475e-17\n",
+       "      4.282920e-14\n",
+       "      4.697929e-10\n",
+       "      2.684531e-09\n",
        "    \n",
        "    \n",
        "      3\n",
-       "      1\n",
+       "      100\n",
+       "      3\n",
+       "      4\n",
        "      Al\n",
-       "      29\n",
+       "      26\n",
        "      \n",
-       "      0.000000e+00\n",
-       "      0.000000e+00\n",
-       "      0.000000e+00\n",
-       "      0.0\n",
-       "      0.000000e+00\n",
+       "      4.381534e+12\n",
+       "      1.890726e-10\n",
+       "      0.134226\n",
        "      0.0\n",
-       "      0.000000e+00\n",
-       "      0.0\n",
-       "      0.000000e+00\n",
+       "      0.134226\n",
        "      0.0\n",
+       "      6.610355e-17\n",
        "      0.0\n",
-       "      0.000000e+00\n",
-       "      0.000000e+00\n",
+       "      8.578846e-18\n",
+       "      5.752471e-17\n",
+       "      4.282917e-14\n",
+       "      4.697926e-10\n",
+       "      2.684529e-09\n",
        "    \n",
        "    \n",
        "      4\n",
-       "      1\n",
+       "      100\n",
+       "      3\n",
+       "      5\n",
        "      Al\n",
-       "      30\n",
+       "      26\n",
        "      \n",
-       "      0.000000e+00\n",
-       "      0.000000e+00\n",
-       "      0.000000e+00\n",
-       "      0.0\n",
-       "      0.000000e+00\n",
+       "      5.523492e+12\n",
+       "      2.383506e-10\n",
+       "      0.169210\n",
        "      0.0\n",
-       "      0.000000e+00\n",
-       "      0.0\n",
-       "      0.000000e+00\n",
+       "      0.169210\n",
        "      0.0\n",
+       "      8.333209e-17\n",
        "      0.0\n",
-       "      0.000000e+00\n",
-       "      0.000000e+00\n",
+       "      1.081475e-17\n",
+       "      7.251735e-17\n",
+       "      5.399172e-14\n",
+       "      5.922345e-10\n",
+       "      3.384197e-09\n",
        "    \n",
        "    \n",
        "      ...\n",
@@ -4678,169 +4016,181 @@
        "      ...\n",
        "      ...\n",
        "      ...\n",
+       "      ...\n",
+       "      ...\n",
        "    \n",
        "    \n",
        "      13970\n",
-       "      65\n",
+       "      100\n",
+       "      3\n",
+       "      61\n",
        "      Zr\n",
-       "      93\n",
+       "      97\n",
        "      \n",
-       "      6.327286e+13\n",
-       "      9.761411e-09\n",
-       "      9.083574e-01\n",
-       "      0.0\n",
-       "      9.083574e-01\n",
-       "      0.0\n",
-       "      2.791257e-18\n",
+       "      0.000000e+00\n",
+       "      0.000000e+00\n",
+       "      0.000000\n",
        "      0.0\n",
-       "      2.791257e-18\n",
+       "      0.000000\n",
        "      0.0\n",
+       "      0.000000e+00\n",
        "      0.0\n",
-       "      9.991931e-10\n",
-       "      2.270894e-08\n",
+       "      0.000000e+00\n",
+       "      0.000000e+00\n",
+       "      0.000000e+00\n",
+       "      0.000000e+00\n",
+       "      0.000000e+00\n",
        "    \n",
        "    \n",
        "      13971\n",
-       "      65\n",
+       "      100\n",
+       "      3\n",
+       "      62\n",
        "      Zr\n",
-       "      94\n",
+       "      97\n",
        "      \n",
-       "      7.058445e+11\n",
-       "      1.100659e-10\n",
-       "      2.583916e-12\n",
-       "      0.0\n",
-       "      2.583916e-12\n",
-       "      0.0\n",
-       "      4.734377e-28\n",
+       "      0.000000e+00\n",
+       "      0.000000e+00\n",
+       "      0.000000\n",
        "      0.0\n",
-       "      4.734377e-28\n",
+       "      0.000000\n",
        "      0.0\n",
+       "      0.000000e+00\n",
        "      0.0\n",
-       "      2.480559e-20\n",
-       "      2.842307e-20\n",
+       "      0.000000e+00\n",
+       "      0.000000e+00\n",
+       "      0.000000e+00\n",
+       "      0.000000e+00\n",
+       "      0.000000e+00\n",
        "    \n",
        "    \n",
        "      13972\n",
-       "      65\n",
+       "      100\n",
+       "      3\n",
+       "      63\n",
        "      Zr\n",
-       "      95\n",
+       "      97\n",
        "      \n",
        "      0.000000e+00\n",
        "      0.000000e+00\n",
-       "      0.000000e+00\n",
+       "      0.000000\n",
        "      0.0\n",
-       "      0.000000e+00\n",
+       "      0.000000\n",
        "      0.0\n",
        "      0.000000e+00\n",
        "      0.0\n",
        "      0.000000e+00\n",
-       "      0.0\n",
-       "      0.0\n",
+       "      0.000000e+00\n",
+       "      0.000000e+00\n",
        "      0.000000e+00\n",
        "      0.000000e+00\n",
        "    \n",
        "    \n",
        "      13973\n",
-       "      65\n",
+       "      100\n",
+       "      3\n",
+       "      64\n",
        "      Zr\n",
-       "      96\n",
+       "      97\n",
        "      \n",
-       "      1.091942e+10\n",
-       "      1.739020e-12\n",
-       "      6.149716e-18\n",
-       "      0.0\n",
-       "      6.149716e-18\n",
-       "      0.0\n",
-       "      3.301027e-33\n",
+       "      0.000000e+00\n",
+       "      0.000000e+00\n",
+       "      0.000000\n",
        "      0.0\n",
-       "      3.301027e-33\n",
+       "      0.000000\n",
        "      0.0\n",
+       "      0.000000e+00\n",
        "      0.0\n",
-       "      1.721921e-25\n",
-       "      1.906412e-25\n",
+       "      0.000000e+00\n",
+       "      0.000000e+00\n",
+       "      0.000000e+00\n",
+       "      0.000000e+00\n",
+       "      0.000000e+00\n",
        "    \n",
        "    \n",
        "      13974\n",
+       "      100\n",
+       "      3\n",
        "      65\n",
        "      Zr\n",
        "      97\n",
        "      \n",
        "      0.000000e+00\n",
        "      0.000000e+00\n",
-       "      0.000000e+00\n",
+       "      0.000000\n",
        "      0.0\n",
-       "      0.000000e+00\n",
+       "      0.000000\n",
        "      0.0\n",
        "      0.000000e+00\n",
        "      0.0\n",
        "      0.000000e+00\n",
-       "      0.0\n",
-       "      0.0\n",
+       "      0.000000e+00\n",
+       "      0.000000e+00\n",
        "      0.000000e+00\n",
        "      0.000000e+00\n",
        "    \n",
        "  \n",
        "\n",
-       "
    13975 rows × 17 columns
    \n",
+       "
    13975 rows × 19 columns
    \n",
        ""
       ],
       "text/plain": [
-       "       timestep_id element  mass_number state         atoms         grams  \\\n",
-       "0                1      Al           26        0.000000e+00  0.000000e+00   \n",
-       "1                1      Al           27        1.785556e+20  8.000000e-03   \n",
-       "2                1      Al           28        0.000000e+00  0.000000e+00   \n",
-       "3                1      Al           29        0.000000e+00  0.000000e+00   \n",
-       "4                1      Al           30        0.000000e+00  0.000000e+00   \n",
-       "...            ...     ...          ...   ...           ...           ...   \n",
-       "13970           65      Zr           93        6.327286e+13  9.761411e-09   \n",
-       "13971           65      Zr           94        7.058445e+11  1.100659e-10   \n",
-       "13972           65      Zr           95        0.000000e+00  0.000000e+00   \n",
-       "13973           65      Zr           96        1.091942e+10  1.739020e-12   \n",
-       "13974           65      Zr           97        0.000000e+00  0.000000e+00   \n",
-       "\n",
-       "           activity  alpha_activity  beta_activity  gamma_activity  \\\n",
-       "0      0.000000e+00             0.0   0.000000e+00             0.0   \n",
-       "1      0.000000e+00             0.0   0.000000e+00             0.0   \n",
-       "2      0.000000e+00             0.0   0.000000e+00             0.0   \n",
-       "3      0.000000e+00             0.0   0.000000e+00             0.0   \n",
-       "4      0.000000e+00             0.0   0.000000e+00             0.0   \n",
-       "...             ...             ...            ...             ...   \n",
-       "13970  9.083574e-01             0.0   9.083574e-01             0.0   \n",
-       "13971  2.583916e-12             0.0   2.583916e-12             0.0   \n",
-       "13972  0.000000e+00             0.0   0.000000e+00             0.0   \n",
-       "13973  6.149716e-18             0.0   6.149716e-18             0.0   \n",
-       "13974  0.000000e+00             0.0   0.000000e+00             0.0   \n",
-       "\n",
-       "               heat  alpha_heat     beta_heat  gamma_heat  dose     ingestion  \\\n",
-       "0      0.000000e+00         0.0  0.000000e+00         0.0   0.0  0.000000e+00   \n",
-       "1      0.000000e+00         0.0  0.000000e+00         0.0   0.0  0.000000e+00   \n",
-       "2      0.000000e+00         0.0  0.000000e+00         0.0   0.0  0.000000e+00   \n",
-       "3      0.000000e+00         0.0  0.000000e+00         0.0   0.0  0.000000e+00   \n",
-       "4      0.000000e+00         0.0  0.000000e+00         0.0   0.0  0.000000e+00   \n",
-       "...             ...         ...           ...         ...   ...           ...   \n",
-       "13970  2.791257e-18         0.0  2.791257e-18         0.0   0.0  9.991931e-10   \n",
-       "13971  4.734377e-28         0.0  4.734377e-28         0.0   0.0  2.480559e-20   \n",
-       "13972  0.000000e+00         0.0  0.000000e+00         0.0   0.0  0.000000e+00   \n",
-       "13973  3.301027e-33         0.0  3.301027e-33         0.0   0.0  1.721921e-25   \n",
-       "13974  0.000000e+00         0.0  0.000000e+00         0.0   0.0  0.000000e+00   \n",
-       "\n",
-       "         inhalation  \n",
-       "0      0.000000e+00  \n",
-       "1      0.000000e+00  \n",
-       "2      0.000000e+00  \n",
-       "3      0.000000e+00  \n",
-       "4      0.000000e+00  \n",
-       "...             ...  \n",
-       "13970  2.270894e-08  \n",
-       "13971  2.842307e-20  \n",
-       "13972  0.000000e+00  \n",
-       "13973  1.906412e-25  \n",
-       "13974  0.000000e+00  \n",
-       "\n",
-       "[13975 rows x 17 columns]"
+       "       material_id  case_id  time_step_number element  mass_number state  \\\n",
+       "0              100        3                 1      Al           26         \n",
+       "1              100        3                 2      Al           26         \n",
+       "2              100        3                 3      Al           26         \n",
+       "3              100        3                 4      Al           26         \n",
+       "4              100        3                 5      Al           26         \n",
+       "...            ...      ...               ...     ...          ...   ...   \n",
+       "13970          100        3                61      Zr           97         \n",
+       "13971          100        3                62      Zr           97         \n",
+       "13972          100        3                63      Zr           97         \n",
+       "13973          100        3                64      Zr           97         \n",
+       "13974          100        3                65      Zr           97         \n",
+       "\n",
+       "              atoms         grams  activity  alpha_activity  beta_activity  \\\n",
+       "0      0.000000e+00  0.000000e+00  0.000000             0.0       0.000000   \n",
+       "1      1.110297e+11  4.791169e-12  0.003401             0.0       0.003401   \n",
+       "2      4.381537e+12  1.890728e-10  0.134227             0.0       0.134227   \n",
+       "3      4.381534e+12  1.890726e-10  0.134226             0.0       0.134226   \n",
+       "4      5.523492e+12  2.383506e-10  0.169210             0.0       0.169210   \n",
+       "...             ...           ...       ...             ...            ...   \n",
+       "13970  0.000000e+00  0.000000e+00  0.000000             0.0       0.000000   \n",
+       "13971  0.000000e+00  0.000000e+00  0.000000             0.0       0.000000   \n",
+       "13972  0.000000e+00  0.000000e+00  0.000000             0.0       0.000000   \n",
+       "13973  0.000000e+00  0.000000e+00  0.000000             0.0       0.000000   \n",
+       "13974  0.000000e+00  0.000000e+00  0.000000             0.0       0.000000   \n",
+       "\n",
+       "       gamma_activity          heat  alpha_heat     beta_heat    gamma_heat  \\\n",
+       "0                 0.0  0.000000e+00         0.0  0.000000e+00  0.000000e+00   \n",
+       "1                 0.0  1.675088e-18         0.0  2.173910e-19  1.457697e-18   \n",
+       "2                 0.0  6.610360e-17         0.0  8.578851e-18  5.752475e-17   \n",
+       "3                 0.0  6.610355e-17         0.0  8.578846e-18  5.752471e-17   \n",
+       "4                 0.0  8.333209e-17         0.0  1.081475e-17  7.251735e-17   \n",
+       "...               ...           ...         ...           ...           ...   \n",
+       "13970             0.0  0.000000e+00         0.0  0.000000e+00  0.000000e+00   \n",
+       "13971             0.0  0.000000e+00         0.0  0.000000e+00  0.000000e+00   \n",
+       "13972             0.0  0.000000e+00         0.0  0.000000e+00  0.000000e+00   \n",
+       "13973             0.0  0.000000e+00         0.0  0.000000e+00  0.000000e+00   \n",
+       "13974             0.0  0.000000e+00         0.0  0.000000e+00  0.000000e+00   \n",
+       "\n",
+       "               dose     ingestion    inhalation  \n",
+       "0      0.000000e+00  0.000000e+00  0.000000e+00  \n",
+       "1      1.085307e-15  1.190471e-11  6.802694e-11  \n",
+       "2      4.282920e-14  4.697929e-10  2.684531e-09  \n",
+       "3      4.282917e-14  4.697926e-10  2.684529e-09  \n",
+       "4      5.399172e-14  5.922345e-10  3.384197e-09  \n",
+       "...             ...           ...           ...  \n",
+       "13970  0.000000e+00  0.000000e+00  0.000000e+00  \n",
+       "13971  0.000000e+00  0.000000e+00  0.000000e+00  \n",
+       "13972  0.000000e+00  0.000000e+00  0.000000e+00  \n",
+       "13973  0.000000e+00  0.000000e+00  0.000000e+00  \n",
+       "13974  0.000000e+00  0.000000e+00  0.000000e+00  \n",
+       "\n",
+       "[13975 rows x 19 columns]"
       ]
      },
-     "execution_count": 265,
+     "execution_count": 94,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -4851,7 +4201,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 276,
+   "execution_count": 98,
    "id": "a5ea7054-9a19-43e0-ab96-c4472f2422ad",
    "metadata": {
     "tags": []
@@ -4878,6 +4228,8 @@
        "  \n",
        "    \n",
        "      \n",
+       "      material_id\n",
+       "      case_id\n",
        "      time_step_number\n",
        "      gamma_boundaries\n",
        "      gamma\n",
@@ -4886,30 +4238,40 @@
        "  \n",
        "    \n",
        "      0\n",
+       "      100\n",
+       "      3\n",
        "      1\n",
        "      1.000000e-11\n",
        "      0.000000e+00\n",
        "    \n",
        "    \n",
        "      1\n",
+       "      100\n",
+       "      3\n",
        "      1\n",
        "      1.000000e-02\n",
        "      3.156906e-11\n",
        "    \n",
        "    \n",
        "      2\n",
+       "      100\n",
+       "      3\n",
        "      1\n",
        "      2.000000e-02\n",
        "      0.000000e+00\n",
        "    \n",
        "    \n",
        "      3\n",
+       "      100\n",
+       "      3\n",
        "      1\n",
        "      5.000000e-02\n",
        "      0.000000e+00\n",
        "    \n",
        "    \n",
        "      4\n",
+       "      100\n",
+       "      3\n",
        "      1\n",
        "      1.000000e-01\n",
        "      5.480877e-10\n",
@@ -4919,71 +4281,83 @@
        "      ...\n",
        "      ...\n",
        "      ...\n",
+       "      ...\n",
+       "      ...\n",
        "    \n",
        "    \n",
        "      1620\n",
+       "      100\n",
+       "      3\n",
        "      65\n",
        "      8.000000e+00\n",
        "      0.000000e+00\n",
        "    \n",
        "    \n",
        "      1621\n",
+       "      100\n",
+       "      3\n",
        "      65\n",
        "      1.000000e+01\n",
        "      0.000000e+00\n",
        "    \n",
        "    \n",
        "      1622\n",
+       "      100\n",
+       "      3\n",
        "      65\n",
        "      1.200000e+01\n",
        "      0.000000e+00\n",
        "    \n",
        "    \n",
        "      1623\n",
+       "      100\n",
+       "      3\n",
        "      65\n",
        "      1.400000e+01\n",
        "      0.000000e+00\n",
        "    \n",
        "    \n",
        "      1624\n",
+       "      100\n",
+       "      3\n",
        "      65\n",
        "      2.000000e+01\n",
        "      0.000000e+00\n",
        "    \n",
        "  \n",
        "\n",
-       "
    1625 rows × 3 columns
    \n",
+       "
    1625 rows × 5 columns
    \n",
        ""
       ],
       "text/plain": [
-       "      time_step_number  gamma_boundaries         gamma\n",
-       "0                    1      1.000000e-11  0.000000e+00\n",
-       "1                    1      1.000000e-02  3.156906e-11\n",
-       "2                    1      2.000000e-02  0.000000e+00\n",
-       "3                    1      5.000000e-02  0.000000e+00\n",
-       "4                    1      1.000000e-01  5.480877e-10\n",
-       "...                ...               ...           ...\n",
-       "1620                65      8.000000e+00  0.000000e+00\n",
-       "1621                65      1.000000e+01  0.000000e+00\n",
-       "1622                65      1.200000e+01  0.000000e+00\n",
-       "1623                65      1.400000e+01  0.000000e+00\n",
-       "1624                65      2.000000e+01  0.000000e+00\n",
-       "\n",
-       "[1625 rows x 3 columns]"
+       "      material_id  case_id  time_step_number  gamma_boundaries         gamma\n",
+       "0             100        3                 1      1.000000e-11  0.000000e+00\n",
+       "1             100        3                 1      1.000000e-02  3.156906e-11\n",
+       "2             100        3                 1      2.000000e-02  0.000000e+00\n",
+       "3             100        3                 1      5.000000e-02  0.000000e+00\n",
+       "4             100        3                 1      1.000000e-01  5.480877e-10\n",
+       "...           ...      ...               ...               ...           ...\n",
+       "1620          100        3                65      8.000000e+00  0.000000e+00\n",
+       "1621          100        3                65      1.000000e+01  0.000000e+00\n",
+       "1622          100        3                65      1.200000e+01  0.000000e+00\n",
+       "1623          100        3                65      1.400000e+01  0.000000e+00\n",
+       "1624          100        3                65      2.000000e+01  0.000000e+00\n",
+       "\n",
+       "[1625 rows x 5 columns]"
       ]
      },
-     "execution_count": 276,
+     "execution_count": 98,
      "metadata": {},
      "output_type": "execute_result"
     }
    ],
    "source": [
-    "ds.gamma.to_dataframe().reset_index()[[\"time_step_number\", \"gamma_boundaries\", \"gamma\"]]"
+    "ds.gamma.to_dataframe().reset_index()[[\"material_id\", \"case_id\", \"time_step_number\", \"gamma_boundaries\", \"gamma\"]]"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 277,
+   "execution_count": 99,
    "id": "6d10e66a-6550-4cbc-828b-4438cbdab443",
    "metadata": {
     "tags": []
@@ -4991,7 +4365,7 @@
    "outputs": [],
    "source": [
     "def save_gamma_spectra(con, ds):\n",
-    "    columns = [\"time_step_number\", \"gamma_boundaries\", \"gamma\"]\n",
+    "    columns = [\"material_id\", \"case_id\", \"time_step_number\", \"gamma_boundaries\", \"gamma\"]\n",
     "    tg = ds.gamma.to_dataframe().reset_index()[columns]\n",
     "    sql = \"insert into timestep_gamma select * from tg\"\n",
     "    con.execute(sql)\n",
@@ -5000,7 +4374,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 278,
+   "execution_count": 100,
    "id": "fc882c1d-9402-4cc5-a316-f8f0ca25a5e1",
    "metadata": {
     "tags": []
@@ -5012,7 +4386,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 283,
+   "execution_count": 101,
    "id": "398ae012-c5df-4793-9b19-60395bbff7a7",
    "metadata": {
     "tags": []
@@ -5039,7 +4413,9 @@
        "  \n",
        "    \n",
        "      \n",
-       "      timestep_id\n",
+       "      material_id\n",
+       "      case_id\n",
+       "      time_step_number\n",
        "      boundary\n",
        "      intensity\n",
        "    \n",
@@ -5047,30 +4423,40 @@
        "  \n",
        "    \n",
        "      0\n",
+       "      100\n",
+       "      3\n",
        "      1\n",
        "      1.000000e-11\n",
        "      0.000000e+00\n",
        "    \n",
        "    \n",
        "      1\n",
+       "      100\n",
+       "      3\n",
        "      1\n",
        "      1.000000e-02\n",
        "      3.156906e-11\n",
        "    \n",
        "    \n",
        "      2\n",
+       "      100\n",
+       "      3\n",
        "      1\n",
        "      2.000000e-02\n",
        "      0.000000e+00\n",
        "    \n",
        "    \n",
        "      3\n",
+       "      100\n",
+       "      3\n",
        "      1\n",
        "      5.000000e-02\n",
        "      0.000000e+00\n",
        "    \n",
        "    \n",
        "      4\n",
+       "      100\n",
+       "      3\n",
        "      1\n",
        "      1.000000e-01\n",
        "      5.480877e-10\n",
@@ -5080,60 +4466,72 @@
        "      ...\n",
        "      ...\n",
        "      ...\n",
+       "      ...\n",
+       "      ...\n",
        "    \n",
        "    \n",
        "      1620\n",
+       "      100\n",
+       "      3\n",
        "      65\n",
        "      8.000000e+00\n",
        "      0.000000e+00\n",
        "    \n",
        "    \n",
        "      1621\n",
+       "      100\n",
+       "      3\n",
        "      65\n",
        "      1.000000e+01\n",
        "      0.000000e+00\n",
        "    \n",
        "    \n",
        "      1622\n",
+       "      100\n",
+       "      3\n",
        "      65\n",
        "      1.200000e+01\n",
        "      0.000000e+00\n",
        "    \n",
        "    \n",
        "      1623\n",
+       "      100\n",
+       "      3\n",
        "      65\n",
        "      1.400000e+01\n",
        "      0.000000e+00\n",
        "    \n",
        "    \n",
        "      1624\n",
+       "      100\n",
+       "      3\n",
        "      65\n",
        "      2.000000e+01\n",
        "      0.000000e+00\n",
        "    \n",
        "  \n",
        "\n",
-       "
    1625 rows × 3 columns
    \n",
+       "
    1625 rows × 5 columns
    \n",
        ""
       ],
       "text/plain": [
-       "      timestep_id      boundary     intensity\n",
-       "0               1  1.000000e-11  0.000000e+00\n",
-       "1               1  1.000000e-02  3.156906e-11\n",
-       "2               1  2.000000e-02  0.000000e+00\n",
-       "3               1  5.000000e-02  0.000000e+00\n",
-       "4               1  1.000000e-01  5.480877e-10\n",
-       "...           ...           ...           ...\n",
-       "1620           65  8.000000e+00  0.000000e+00\n",
-       "1621           65  1.000000e+01  0.000000e+00\n",
-       "1622           65  1.200000e+01  0.000000e+00\n",
-       "1623           65  1.400000e+01  0.000000e+00\n",
-       "1624           65  2.000000e+01  0.000000e+00\n",
-       "\n",
-       "[1625 rows x 3 columns]"
+       "      material_id  case_id  time_step_number      boundary     intensity\n",
+       "0             100        3                 1  1.000000e-11  0.000000e+00\n",
+       "1             100        3                 1  1.000000e-02  3.156906e-11\n",
+       "2             100        3                 1  2.000000e-02  0.000000e+00\n",
+       "3             100        3                 1  5.000000e-02  0.000000e+00\n",
+       "4             100        3                 1  1.000000e-01  5.480877e-10\n",
+       "...           ...      ...               ...           ...           ...\n",
+       "1620          100        3                65  8.000000e+00  0.000000e+00\n",
+       "1621          100        3                65  1.000000e+01  0.000000e+00\n",
+       "1622          100        3                65  1.200000e+01  0.000000e+00\n",
+       "1623          100        3                65  1.400000e+01  0.000000e+00\n",
+       "1624          100        3                65  2.000000e+01  0.000000e+00\n",
+       "\n",
+       "[1625 rows x 5 columns]"
       ]
      },
-     "execution_count": 283,
+     "execution_count": 101,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -5144,7 +4542,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 284,
+   "execution_count": 103,
    "id": "680defd9-9305-4459-b1a2-357ed1e476e3",
    "metadata": {
     "tags": []
@@ -5334,13 +4732,13 @@
        "24  2.000000e+01  0.000000e+00"
       ]
      },
-     "execution_count": 284,
+     "execution_count": 103,
      "metadata": {},
      "output_type": "execute_result"
     }
    ],
    "source": [
-    "con.execute(\"select boundary, intensity from timestep_gamma where timestep_id = 42\").df()"
+    "con.execute(\"select boundary, intensity from timestep_gamma where time_step_number = 42\").df()"
    ]
   },
   {
diff --git a/notebooks/dvp/try_ducdb.py b/notebooks/dvp/try_ducdb.py
index cb90a76..18572e4 100644
--- a/notebooks/dvp/try_ducdb.py
+++ b/notebooks/dvp/try_ducdb.py
@@ -1,78 +1,72 @@
 #!/usr/bin/env python
 # coding: utf-8
 
-# In[233]:
+# In[1]:
 
 
 get_ipython().run_line_magic("config", "Completer.use_jedi = False")
 
 
-# In[234]:
+# In[2]:
 
 
 import xpypact as xp
 
-# In[235]:
+# In[3]:
 
 
 xp.__version__
 
 
-# In[236]:
+# In[4]:
 
 
 from pathlib import Path
 
-# In[237]:
+# In[5]:
 
 
 root_dir = Path("~", "dev", "xpypact").expanduser()
 
 
-# In[238]:
+# In[6]:
 
 
 json_path = root_dir / "wrk/Alloy718-Co04-104_2_1_1.json"
 assert json_path.exists()
 
 
-# In[239]:
+# In[7]:
 
 
 import xpypact.data_arrays as da
 
 from xpypact.Inventory import Inventory, from_json
 
-# In[240]:
+# In[8]:
 
 
 inventory = from_json(json_path)
 
 
-# In[469]:
+# In[9]:
 
 
 ds = da.create_dataset(inventory)
 
 
-# In[470]:
+# In[10]:
 
 
 ds
 
 
-# In[417]:
-
-
-ds.timestamp
-
-
-# In[243]:
+# In[12]:
 
 
 import duckdb as db
 
-# In[384]:
+# In[13]:
 
 
 db_path = root_dir / "wrk/try-duckdb.duckdb"
@@ -81,33 +75,37 @@
     db_path.unlink()
 
 
-# In[385]:
+# In[14]:
 
 
 con = db.connect(str(db_path))
 
 
-# In[386]:
+# In[15]:
 
 
 material_id = 100
 case_id = 3
 
 
-# In[475]:
+# In[16]:
 
 
 ds = ds.expand_dims(dim={"material_id": [material_id], "case_id": [case_id]})
 ds
 
 
-# In[476]:
+# How to transform xarray to pandas saving indexes as columns
 
+# In[20]:
 
-ds.irradiation_time
 
+ds.irradiation_time.stack(
+    {"idx": ["material_id", "case_id", "time_step_number"]}
+).to_pandas().reset_index()
 
-# In[446]:
+
+# In[21]:
 
 
 def drop_tables(con):
@@ -118,7 +116,7 @@ def drop_tables(con):
     con.execute("drop table if exists rundata")
 
 
-# In[447]:
+# In[22]:
 
 
 def create_tables(con):
@@ -212,14 +210,14 @@ def create_tables(con):
     con.execute(sql)
 
 
-# In[512]:
+# In[23]:
 
 
 drop_tables(con)
 create_tables(con)
 
 
-# In[513]:
+# In[24]:
 
 
 def save_rundata(con, ds):
@@ -241,19 +239,19 @@ def save_rundata(con, ds):
     con.commit()
 
 
-# In[514]:
+# In[25]:
 
 
 save_rundata(con, ds)
 
 
-# In[515]:
+# In[26]:
 
 
 con.execute("select * from rundata").df()
 
 
-# In[516]:
+# In[27]:
 
 
 def save_timesteps(con, ds):
@@ -291,56 +289,74 @@ def save_timesteps(con, ds):
     con.commit()
 
 
-# In[517]:
+# In[28]:
 
 
 save_timesteps(con, ds)
 
 
-# In[518]:
+# In[29]:
 
 
 con.execute("select * from timestep").df()
 
 
-# In[533]:
+# In[55]:
+
+
+columns_all = ["element", "mass_number", "state", "zai", "nuclide_half_life"]
+columns = ["zai", "nuclide_half_life"]
+ds[columns].to_dataframe()[columns].reset_index()[columns_all]
+# .unstack("nuclide")
+# .stack({"idx": ["material_id", "case_id", "element", "mass_number", "state"]}) \
+# .to_dataframe()
+
+# \
+#     .reset_index(["material_id", "case_id"]) \
+#     .to_dataframe() \
+#     .reset_index(
+#         [
+#             "material_id", "case_id"
+#         ],
+#         drop=True
+#     ) \
+#     .reset_index(drop=True)
+
+
+# In[56]:
 
 
 def save_nuclides(con, ds):
-    nuclides_df = (
-        ds[["element", "mass_number", "state", "zai", "nuclide_half_life"]]
-        .reset_index(["material_id", "case_id"])
-        .to_dataframe()
-        .reset_index(["material_id", "case_id"], drop=True)
-        .reset_index(drop=True)
-    )
+    columns_all = ["element", "mass_number", "state", "zai", "nuclide_half_life"]
+    columns = ["zai", "nuclide_half_life"]
+    nuclides_df = ds[columns].to_dataframe()[columns].reset_index()[columns_all]
     sql = "insert or ignore into nuclide select * from nuclides_df"
     con.execute(sql)
     con.commit()
 
 
-# In[534]:
+# In[57]:
 
 
 save_nuclides(con, ds)
 
 
-# In[535]:
+# In[58]:
 
 
 con.execute("select * from nuclide").df()
 
 
-# In[559]:
+# In[91]:
 
 
 columns = [
-    "material_id",
-    "case_id",
-    "time_step_number",
-    "element",
-    "mass_number",
-    "state",
+    # "material_id",
+    # "case_id",
+    # "time_step_number",
+    # "element",
+    # "mass_number",
+    # "state",
     "nuclide_atoms",
     "nuclide_grams",
     "nuclide_activity",
@@ -355,9 +371,21 @@ def save_nuclides(con, ds):
     "nuclide_ingestion",
     "nuclide_inhalation",
 ]
+columns_all = [
+    "material_id",
+    "case_id",
+    "time_step_number",
+    "element",
+    "mass_number",
+    "state",
+] + columns
+
+ds[columns].stack(idx=("material_id", "case_id", "time_step_number")).to_dataframe()[
+    columns
+].reset_index()[columns_all].fillna(0.0)
 # ds[columns].reset_index(["material_id", "case_id"])
 
-ds[columns].coords.to_dataset()
+# ds[columns].coords.to_dataset()
 # .reset_index(["elapsed_time", "zai"])
 # .reset_coords()
 # .drop_indexes(["material_id", "case_id", "time_step_number", "nuclide"])
@@ -369,17 +397,14 @@ def save_nuclides(con, ds):
 # ).reset_index(drop=True)[columns].fillna(0.0)
 
 
-# In[540]:
+# In[ ]:
+
+
+# In[92]:
 
 
 def save_timestep_nucludes(con, ds):
     columns = [
-        "material_id",
-        "case_id",
-        "time_step_number",
-        "element",
-        "mass_number",
-        "state",
         "nuclide_atoms",
         "nuclide_grams",
         "nuclide_activity",
@@ -394,18 +419,20 @@ def save_timestep_nucludes(con, ds):
         "nuclide_ingestion",
         "nuclide_inhalation",
     ]
+    columns_all = [
+        "material_id",
+        "case_id",
+        "time_step_number",
+        "element",
+        "mass_number",
+        "state",
+    ] + columns
+
     tn = (
         ds[columns]
-        .reset_index(["material_id", "case_id", "time_step_number", "nuclide"])
-        .to_dataframe()
-        .reset_index(
-            [
-                "material_id",
-                "case_id",
-                "time_step_number",
-            ]
-        )
-        .reset_index(drop=True)[columns]
+        .stack(idx=("material_id", "case_id", "time_step_number"))
+        .to_dataframe()[columns]
+        .reset_index()[columns_all]
         .fillna(0.0)
     )
     sql = "insert into timestep_nuclide select * from tn"
@@ -413,52 +440,60 @@ def save_timestep_nucludes(con, ds):
     con.commit()
 
 
-# In[541]:
+# In[93]:
 
 
 save_timestep_nucludes(con, ds)
 
 
-# In[265]:
+# In[94]:
 
 
 con.execute("select * from timestep_nuclide").df()
 
 
-# In[276]:
+# In[98]:
 
 
-ds.gamma.to_dataframe().reset_index()[["time_step_number", "gamma_boundaries", "gamma"]]
+ds.gamma.to_dataframe().reset_index()[
+    ["material_id", "case_id", "time_step_number", "gamma_boundaries", "gamma"]
+]
 
 
-# In[277]:
+# In[99]:
 
 
 def save_gamma_spectra(con, ds):
-    columns = ["time_step_number", "gamma_boundaries", "gamma"]
+    columns = [
+        "material_id",
+        "case_id",
+        "time_step_number",
+        "gamma_boundaries",
+        "gamma",
+    ]
     tg = ds.gamma.to_dataframe().reset_index()[columns]
     sql = "insert into timestep_gamma select * from tg"
     con.execute(sql)
     con.commit()
 
 
-# In[278]:
+# In[100]:
 
 
 save_gamma_spectra(con, ds)
 
 
-# In[283]:
+# In[101]:
 
 
 con.execute("select * from timestep_gamma").df()
 
 
-# In[284]:
+# In[103]:
 
 
 con.execute(
-    "select boundary, intensity from timestep_gamma where timestep_id = 42"
+    "select boundary, intensity from timestep_gamma where time_step_number = 42"
 ).df()
 
 

From f43d3291426ca49619eb76770f4b6c2d5c0e98d5 Mon Sep 17 00:00:00 2001
From: dvp 
Date: Mon, 27 Mar 2023 19:22:33 +0300
Subject: [PATCH 19/32] notebook: duckdb prototype is done

---
 notebooks/dvp/try_ducdb.ipynb | 2 +-
 notebooks/dvp/try_ducdb.py    | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/notebooks/dvp/try_ducdb.ipynb b/notebooks/dvp/try_ducdb.ipynb
index ba8d453..2ae9ebf 100644
--- a/notebooks/dvp/try_ducdb.ipynb
+++ b/notebooks/dvp/try_ducdb.ipynb
@@ -4743,7 +4743,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 286,
+   "execution_count": 104,
    "id": "def18203-fed9-472d-a69c-b653dbf9a7b2",
    "metadata": {
     "tags": []
diff --git a/notebooks/dvp/try_ducdb.py b/notebooks/dvp/try_ducdb.py
index 18572e4..eeb7281 100644
--- a/notebooks/dvp/try_ducdb.py
+++ b/notebooks/dvp/try_ducdb.py
@@ -497,7 +497,7 @@ def save_gamma_spectra(con, ds):
 ).df()
 
 
-# In[286]:
+# In[104]:
 
 
 con.close()

From eb91621af40c96eaa74af09d919a7ad1ca4c0325 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 28 Mar 2023 11:56:55 +0000
Subject: [PATCH 20/32] build(deps): bump actions/checkout from 3.3.0 to 3.5.0

Bumps [actions/checkout](https://github.com/actions/checkout) from 3.3.0 to 3.5.0.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](https://github.com/actions/checkout/compare/v3.3.0...v3.5.0)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] 
---
 .github/workflows/labeler.yml | 2 +-
 .github/workflows/release.yml | 2 +-
 .github/workflows/tests.yml   | 8 ++++----
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/labeler.yml b/.github/workflows/labeler.yml
index 5e1da55..3a7babe 100644
--- a/.github/workflows/labeler.yml
+++ b/.github/workflows/labeler.yml
@@ -26,7 +26,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out the repository
-        uses: actions/checkout@v3.3.0
+        uses: actions/checkout@v3.5.0
 
       - name: Sync GitHub Issue Labels
         uses: crazy-max/ghaction-github-labeler@v4
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 4ccfa44..4bff35f 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -27,7 +27,7 @@ jobs:
 
     steps:
       - name: Check out the repository
-        uses: actions/checkout@v3.3.0
+        uses: actions/checkout@v3.5.0
         with:
           fetch-depth: 2    # need previous revision to define tag
 
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index d3e54cc..4e80520 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -36,7 +36,7 @@ jobs:
       !contains(github.event.head_commit.message, '[skip_ci]')
     steps:
       - name: Check out the repository
-        uses: actions/checkout@v3.3.0
+        uses: actions/checkout@v3.5.0
 
       - name: Set up Python 3.10  # on 3.11 pip install in unstable: "canonicalize" fails occasionally
         uses: actions/setup-python@v4.5.0
@@ -85,7 +85,7 @@ jobs:
     needs: lint
     steps:
       - name: Check out the repository
-        uses: actions/checkout@v3.3.0
+        uses: actions/checkout@v3.5.0
         with:
           fetch-depth: 1
 
@@ -137,7 +137,7 @@ jobs:
     steps:
 
       - name: Checkout repository
-        uses: actions/checkout@v3.3.0
+        uses: actions/checkout@v3.5.0
         with:
           fetch-depth: 1
 
@@ -187,7 +187,7 @@ jobs:
     steps:
 
       - name: Check out the repository
-        uses: actions/checkout@v3.3.0
+        uses: actions/checkout@v3.5.0
 
       - name: Set up Python 3.11
         uses: actions/setup-python@v4.5.0

From d59f6e554d5c3b42b8e8e882455c70b29682a824 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 28 Mar 2023 11:56:58 +0000
Subject: [PATCH 21/32] build(deps): bump actions/stale from 7 to 8

Bumps [actions/stale](https://github.com/actions/stale) from 7 to 8.
- [Release notes](https://github.com/actions/stale/releases)
- [Changelog](https://github.com/actions/stale/blob/main/CHANGELOG.md)
- [Commits](https://github.com/actions/stale/compare/v7...v8)

---
updated-dependencies:
- dependency-name: actions/stale
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] 
---
 .github/workflows/stale.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/stale.yml b/.github/workflows/stale.yml
index 5dd2ae0..0a639eb 100644
--- a/.github/workflows/stale.yml
+++ b/.github/workflows/stale.yml
@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/stale@v7
+    - uses: actions/stale@v8
       with:
         repo-token: ${{ secrets.MCKIT_GITHUB_TOKEN }}
         stale-issue-message: 'Stale issue message'

From ff5ebdca99ec87e184f52a49a7945220042d24c8 Mon Sep 17 00:00:00 2001
From: dvp 
Date: Tue, 28 Mar 2023 18:11:36 +0300
Subject: [PATCH 22/32] build: add ruff as major linter

---
 .pre-commit-config.yaml    |   12 +-
 docs/source/conf.py        |   26 +-
 notebooks/dvp/try_ducdb.py |   14 +-
 noxfile.py                 |   15 +
 poetry.lock                | 1097 +++++++++++++++++++++++++++++++++++-
 pyproject.toml             |   60 +-
 6 files changed, 1182 insertions(+), 42 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index ec90ea1..140f1d3 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -82,12 +82,16 @@ repos:
         language: system
         types: [python]
     # Lint
-    -   id: flake8
-        name: flake8
-        entry: poetry run flake8
+    # -   id: flake8
+    #     name: flake8
+    #     entry: poetry run flake8
+    #     language: system
+    #     types: [python]
+    -   id: ruff
+        name: ruff
+        entry: poetry run ruff --force-exclude --fix --config pyproject.toml
         language: system
         types: [python]
-# Also code format the docs
 #    -   id: blacken-docs
 #        name: blacken-docs
 #        entry: poetry run blacken-docs
diff --git a/docs/source/conf.py b/docs/source/conf.py
index 32025e2..acf91dd 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -1,8 +1,8 @@
-# Configuration file for the Sphinx documentation builder.
-#
-# This file only contains a selection of the most common options. For a full
-# list see the documentation:
-# https://www.sphinx-doc.org/en/master/usage/configuration.html
+from typing import Dict, List
+
+import sys
+
+from pathlib import Path
 
 # -- Path setup --------------------------------------------------------------
 
@@ -10,17 +10,19 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
-import sys
-
-from pathlib import Path
 
 pkg_path = Path("..", "..", "src").absolute()
 assert pkg_path.exists(), f"Invalid path {pkg_path}"
 sys.path.insert(0, str(pkg_path))
 
-from typing import Dict, List
+import xpypact  # noqa: E402
+
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
 
-import mckit_nuclides
 
 # -- Project information -----------------------------------------------------
 
@@ -35,9 +37,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = mckit_nuclides.__version__.rsplit(".", maxsplit=1)[0]
+version = xpypact.__version__.rsplit(".", maxsplit=1)[0]
 # The full version, including alpha/beta/rc tags.
-release = mckit_nuclides.__version__
+release = xpypact.__version__
 
 
 # -- General configuration ---------------------------------------------------
diff --git a/notebooks/dvp/try_ducdb.py b/notebooks/dvp/try_ducdb.py
index eeb7281..b9d8bd0 100644
--- a/notebooks/dvp/try_ducdb.py
+++ b/notebooks/dvp/try_ducdb.py
@@ -41,7 +41,7 @@
 
 import xpypact.data_arrays as da
 
-from xpypact.Inventory import Inventory, from_json
+from xpypact.Inventory import from_json
 
 # In[8]:
 
@@ -255,7 +255,7 @@ def save_rundata(con, ds):
 
 
 def save_timesteps(con, ds):
-    timesteps_df = (
+    (
         ds[
             [
                 "material_id",
@@ -329,7 +329,7 @@ def save_timesteps(con, ds):
 def save_nuclides(con, ds):
     columns_all = ["element", "mass_number", "state", "zai", "nuclide_half_life"]
     columns = ["zai", "nuclide_half_life"]
-    nuclides_df = ds[columns].to_dataframe()[columns].reset_index()[columns_all]
+    ds[columns].to_dataframe()[columns].reset_index()[columns_all]
     sql = "insert or ignore into nuclide select * from nuclides_df"
     con.execute(sql)
     con.commit()
@@ -428,7 +428,7 @@ def save_timestep_nucludes(con, ds):
         "state",
     ] + columns
 
-    tn = (
+    (
         ds[columns]
         .stack(idx=("material_id", "case_id", "time_step_number"))
         .to_dataframe()[columns]
@@ -471,7 +471,7 @@ def save_gamma_spectra(con, ds):
         "gamma_boundaries",
         "gamma",
     ]
-    tg = ds.gamma.to_dataframe().reset_index()[columns]
+    ds.gamma.to_dataframe().reset_index()[columns]
     sql = "insert into timestep_gamma select * from tg"
     con.execute(sql)
     con.commit()
@@ -492,9 +492,7 @@ def save_gamma_spectra(con, ds):
 # In[103]:
 
 
-con.execute(
-    "select boundary, intensity from timestep_gamma where time_step_number = 42"
-).df()
+con.execute("select boundary, intensity from timestep_gamma where time_step_number = 42").df()
 
 
 # In[104]:
diff --git a/noxfile.py b/noxfile.py
index fb8d2b6..54f4f19 100644
--- a/noxfile.py
+++ b/noxfile.py
@@ -297,6 +297,21 @@ def xdoctest(s: Session) -> None:
     s.run("python", "-m", "xdoctest", *args)
 
 
+@session(python="3.11")
+def ruff(s: Session) -> None:
+    """Run ruff linter."""
+    args = s.posargs or ["src", "tests"]
+    s.run(
+        "poetry",
+        "install",
+        "--no-root",
+        "--only",
+        "main,ruff",
+        external=True,
+    )
+    s.run("ruff", *args)
+
+
 @session(name="docs-build", python="3.11")
 def docs_build(s: Session) -> None:
     """Build the documentation."""
diff --git a/poetry.lock b/poetry.lock
index f2cb20f..574cedb 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -12,6 +12,18 @@ files = [
     {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"},
 ]
 
+[[package]]
+name = "appdirs"
+version = "1.4.4"
+description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
+category = "dev"
+optional = false
+python-versions = "*"
+files = [
+    {file = "appdirs-1.4.4-py2.py3-none-any.whl", hash = "sha256:a841dacd6b99318a741b166adb07e19ee71a274450e68237b4650ca1055ab128"},
+    {file = "appdirs-1.4.4.tar.gz", hash = "sha256:7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41"},
+]
+
 [[package]]
 name = "argcomplete"
 version = "2.1.2"
@@ -130,6 +142,40 @@ test = ["beautifulsoup4 (>=4.8.0)", "coverage (>=4.5.4)", "fixtures (>=3.0.0)",
 toml = ["tomli (>=1.1.0)"]
 yaml = ["PyYAML"]
 
+[[package]]
+name = "beautifulsoup4"
+version = "4.12.0"
+description = "Screen-scraping library"
+category = "dev"
+optional = false
+python-versions = ">=3.6.0"
+files = [
+    {file = "beautifulsoup4-4.12.0-py3-none-any.whl", hash = "sha256:2130a5ad7f513200fae61a17abb5e338ca980fa28c439c0571014bc0217e9591"},
+    {file = "beautifulsoup4-4.12.0.tar.gz", hash = "sha256:c5fceeaec29d09c84970e47c65f2f0efe57872f7cff494c9691a26ec0ff13234"},
+]
+
+[package.dependencies]
+soupsieve = ">1.2"
+
+[package.extras]
+html5lib = ["html5lib"]
+lxml = ["lxml"]
+
+[[package]]
+name = "beniget"
+version = "0.4.1"
+description = "Extract semantic information about static Python code"
+category = "dev"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+files = [
+    {file = "beniget-0.4.1-py3-none-any.whl", hash = "sha256:cb061256631313f9d06031b824f7f403baecaf609b2d3d14d43f23356cf143f2"},
+    {file = "beniget-0.4.1.tar.gz", hash = "sha256:75554b3b8ad0553ce2f607627dad3d95c60c441189875b98e097528f8e23ac0c"},
+]
+
+[package.dependencies]
+gast = ">=0.5.0,<0.6.0"
+
 [[package]]
 name = "black"
 version = "22.12.0"
@@ -166,6 +212,41 @@ d = ["aiohttp (>=3.7.4)"]
 jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"]
 uvloop = ["uvloop (>=0.15.2)"]
 
+[[package]]
+name = "bleach"
+version = "6.0.0"
+description = "An easy safelist-based HTML-sanitizing tool."
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "bleach-6.0.0-py3-none-any.whl", hash = "sha256:33c16e3353dbd13028ab4799a0f89a83f113405c766e9c122df8a06f5b85b3f4"},
+    {file = "bleach-6.0.0.tar.gz", hash = "sha256:1a1a85c1595e07d8db14c5f09f09e6433502c51c595970edc090551f0db99414"},
+]
+
+[package.dependencies]
+six = ">=1.9.0"
+webencodings = "*"
+
+[package.extras]
+css = ["tinycss2 (>=1.1.0,<1.2)"]
+
+[[package]]
+name = "cattrs"
+version = "22.2.0"
+description = "Composable complex class support for attrs and dataclasses."
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "cattrs-22.2.0-py3-none-any.whl", hash = "sha256:bc12b1f0d000b9f9bee83335887d532a1d3e99a833d1bf0882151c97d3e68c21"},
+    {file = "cattrs-22.2.0.tar.gz", hash = "sha256:f0eed5642399423cf656e7b66ce92cdc5b963ecafd041d1b24d136fdde7acf6d"},
+]
+
+[package.dependencies]
+attrs = ">=20"
+exceptiongroup = {version = "*", markers = "python_version < \"3.11\""}
+
 [[package]]
 name = "certifi"
 version = "2022.12.7"
@@ -178,6 +259,83 @@ files = [
     {file = "certifi-2022.12.7.tar.gz", hash = "sha256:35824b4c3a97115964b408844d64aa14db1cc518f6562e8d7261699d1350a9e3"},
 ]
 
+[[package]]
+name = "cffi"
+version = "1.15.1"
+description = "Foreign Function Interface for Python calling C code."
+category = "dev"
+optional = false
+python-versions = "*"
+files = [
+    {file = "cffi-1.15.1-cp27-cp27m-macosx_10_9_x86_64.whl", hash = "sha256:a66d3508133af6e8548451b25058d5812812ec3798c886bf38ed24a98216fab2"},
+    {file = "cffi-1.15.1-cp27-cp27m-manylinux1_i686.whl", hash = "sha256:470c103ae716238bbe698d67ad020e1db9d9dba34fa5a899b5e21577e6d52ed2"},
+    {file = "cffi-1.15.1-cp27-cp27m-manylinux1_x86_64.whl", hash = "sha256:9ad5db27f9cabae298d151c85cf2bad1d359a1b9c686a275df03385758e2f914"},
+    {file = "cffi-1.15.1-cp27-cp27m-win32.whl", hash = "sha256:b3bbeb01c2b273cca1e1e0c5df57f12dce9a4dd331b4fa1635b8bec26350bde3"},
+    {file = "cffi-1.15.1-cp27-cp27m-win_amd64.whl", hash = "sha256:e00b098126fd45523dd056d2efba6c5a63b71ffe9f2bbe1a4fe1716e1d0c331e"},
+    {file = "cffi-1.15.1-cp27-cp27mu-manylinux1_i686.whl", hash = "sha256:d61f4695e6c866a23a21acab0509af1cdfd2c013cf256bbf5b6b5e2695827162"},
+    {file = "cffi-1.15.1-cp27-cp27mu-manylinux1_x86_64.whl", hash = "sha256:ed9cb427ba5504c1dc15ede7d516b84757c3e3d7868ccc85121d9310d27eed0b"},
+    {file = "cffi-1.15.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:39d39875251ca8f612b6f33e6b1195af86d1b3e60086068be9cc053aa4376e21"},
+    {file = "cffi-1.15.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:285d29981935eb726a4399badae8f0ffdff4f5050eaa6d0cfc3f64b857b77185"},
+    {file = "cffi-1.15.1-cp310-cp310-manylinux_2_12_i686.manylinux2010_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:3eb6971dcff08619f8d91607cfc726518b6fa2a9eba42856be181c6d0d9515fd"},
+    {file = "cffi-1.15.1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:21157295583fe8943475029ed5abdcf71eb3911894724e360acff1d61c1d54bc"},
+    {file = "cffi-1.15.1-cp310-cp310-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:5635bd9cb9731e6d4a1132a498dd34f764034a8ce60cef4f5319c0541159392f"},
+    {file = "cffi-1.15.1-cp310-cp310-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:2012c72d854c2d03e45d06ae57f40d78e5770d252f195b93f581acf3ba44496e"},
+    {file = "cffi-1.15.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:dd86c085fae2efd48ac91dd7ccffcfc0571387fe1193d33b6394db7ef31fe2a4"},
+    {file = "cffi-1.15.1-cp310-cp310-musllinux_1_1_i686.whl", hash = "sha256:fa6693661a4c91757f4412306191b6dc88c1703f780c8234035eac011922bc01"},
+    {file = "cffi-1.15.1-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:59c0b02d0a6c384d453fece7566d1c7e6b7bae4fc5874ef2ef46d56776d61c9e"},
+    {file = "cffi-1.15.1-cp310-cp310-win32.whl", hash = "sha256:cba9d6b9a7d64d4bd46167096fc9d2f835e25d7e4c121fb2ddfc6528fb0413b2"},
+    {file = "cffi-1.15.1-cp310-cp310-win_amd64.whl", hash = "sha256:ce4bcc037df4fc5e3d184794f27bdaab018943698f4ca31630bc7f84a7b69c6d"},
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+]
+
+[package.dependencies]
+pycparser = "*"
+
 [[package]]
 name = "cfgv"
 version = "3.3.1"
@@ -428,6 +586,36 @@ files = [
     {file = "darglint-1.8.1.tar.gz", hash = "sha256:080d5106df149b199822e7ee7deb9c012b49891538f14a11be681044f0bb20da"},
 ]
 
+[[package]]
+name = "defusedxml"
+version = "0.7.1"
+description = "XML bomb protection for Python stdlib modules"
+category = "dev"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+files = [
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+    {file = "defusedxml-0.7.1.tar.gz", hash = "sha256:1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69"},
+]
+
+[[package]]
+name = "deprecated"
+version = "1.2.13"
+description = "Python @deprecated decorator to deprecate old python classes, functions or methods."
+category = "dev"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+files = [
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+    {file = "Deprecated-1.2.13.tar.gz", hash = "sha256:43ac5335da90c31c24ba028af536a91d41d53f9e6901ddb021bcc572ce44e38d"},
+]
+
+[package.dependencies]
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+
+[package.extras]
+dev = ["PyTest", "PyTest (<5)", "PyTest-Cov", "PyTest-Cov (<2.6)", "bump2version (<1)", "configparser (<5)", "importlib-metadata (<3)", "importlib-resources (<4)", "sphinx (<2)", "sphinxcontrib-websupport (<2)", "tox", "zipp (<2)"]
+
 [[package]]
 name = "dill"
 version = "0.3.6"
@@ -455,6 +643,18 @@ files = [
     {file = "distlib-0.3.6.tar.gz", hash = "sha256:14bad2d9b04d3a36127ac97f30b12a19268f211063d8f8ee4f47108896e11b46"},
 ]
 
+[[package]]
+name = "docstring-to-markdown"
+version = "0.12"
+description = "On the fly conversion of Python docstrings to markdown"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+files = [
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+]
+
 [[package]]
 name = "docutils"
 version = "0.19"
@@ -529,16 +729,31 @@ files = [
 [package.extras]
 testing = ["pre-commit"]
 
+[[package]]
+name = "fastjsonschema"
+version = "2.16.3"
+description = "Fastest Python implementation of JSON schema"
+category = "dev"
+optional = false
+python-versions = "*"
+files = [
+    {file = "fastjsonschema-2.16.3-py3-none-any.whl", hash = "sha256:04fbecc94300436f628517b05741b7ea009506ce8f946d40996567c669318490"},
+    {file = "fastjsonschema-2.16.3.tar.gz", hash = "sha256:4a30d6315a68c253cfa8f963b9697246315aa3db89f98b97235e345dedfb0b8e"},
+]
+
+[package.extras]
+devel = ["colorama", "json-spec", "jsonschema", "pylint", "pytest", "pytest-benchmark", "pytest-cache", "validictory"]
+
 [[package]]
 name = "filelock"
-version = "3.10.6"
+version = "3.10.7"
 description = "A platform independent file lock."
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "filelock-3.10.6-py3-none-any.whl", hash = "sha256:52f119747b2b9c4730dac715a7b1ab34b8ee70fd9259cba158ee53da566387ff"},
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+    {file = "filelock-3.10.7.tar.gz", hash = "sha256:892be14aa8efc01673b5ed6589dbccb95f9a8596f0507e232626155495c18105"},
 ]
 
 [package.extras]
@@ -939,6 +1154,30 @@ files = [
 [package.dependencies]
 flake8 = ">=3.6"
 
+[[package]]
+name = "frilouz"
+version = "0.0.2"
+description = "Python AST parser adapter with partial error recovery"
+category = "dev"
+optional = false
+python-versions = "*"
+files = [
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+    {file = "frilouz-0.0.2.tar.gz", hash = "sha256:ba7922f36500f6ea4a68e87f9cd24fe4a011a98673cb7ab4c7c3efcd33647a59"},
+]
+
+[[package]]
+name = "gast"
+version = "0.5.3"
+description = "Python AST that abstracts the underlying Python version"
+category = "dev"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+files = [
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+    {file = "gast-0.5.3.tar.gz", hash = "sha256:cfbea25820e653af9c7d1807f659ce0a0a9c64f2439421a7bba4f0983f532dea"},
+]
+
 [[package]]
 name = "gitdb"
 version = "4.0.10"
@@ -1131,6 +1370,26 @@ pipfile-deprecated-finder = ["pip-shims (>=0.5.2)", "pipreqs", "requirementslib"
 plugins = ["setuptools"]
 requirements-deprecated-finder = ["pip-api", "pipreqs"]
 
+[[package]]
+name = "jedi"
+version = "0.18.2"
+description = "An autocompletion tool for Python that can be used for text editors."
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+files = [
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+    {file = "jedi-0.18.2.tar.gz", hash = "sha256:bae794c30d07f6d910d32a7048af09b5a39ed740918da923c6b780790ebac612"},
+]
+
+[package.dependencies]
+parso = ">=0.8.0,<0.9.0"
+
+[package.extras]
+docs = ["Jinja2 (==2.11.3)", "MarkupSafe (==1.1.1)", "Pygments (==2.8.1)", "alabaster (==0.7.12)", "babel (==2.9.1)", "chardet (==4.0.0)", "commonmark (==0.8.1)", "docutils (==0.17.1)", "future (==0.18.2)", "idna (==2.10)", "imagesize (==1.2.0)", "mock (==1.0.1)", "packaging (==20.9)", "pyparsing (==2.4.7)", "pytz (==2021.1)", "readthedocs-sphinx-ext (==2.1.4)", "recommonmark (==0.5.0)", "requests (==2.25.1)", "six (==1.15.0)", "snowballstemmer (==2.1.0)", "sphinx (==1.8.5)", "sphinx-rtd-theme (==0.4.3)", "sphinxcontrib-serializinghtml (==1.1.4)", "sphinxcontrib-websupport (==1.2.4)", "urllib3 (==1.26.4)"]
+qa = ["flake8 (==3.8.3)", "mypy (==0.782)"]
+testing = ["Django (<3.1)", "attrs", "colorama", "docopt", "pytest (<7.0.0)"]
+
 [[package]]
 name = "jinja2"
 version = "3.1.2"
@@ -1149,6 +1408,85 @@ MarkupSafe = ">=2.0"
 [package.extras]
 i18n = ["Babel (>=2.7)"]
 
+[[package]]
+name = "jsonschema"
+version = "4.17.3"
+description = "An implementation of JSON Schema validation for Python"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "jsonschema-4.17.3-py3-none-any.whl", hash = "sha256:a870ad254da1a8ca84b6a2905cac29d265f805acc57af304784962a2aa6508f6"},
+    {file = "jsonschema-4.17.3.tar.gz", hash = "sha256:0f864437ab8b6076ba6707453ef8f98a6a0d512a80e93f8abdb676f737ecb60d"},
+]
+
+[package.dependencies]
+attrs = ">=17.4.0"
+importlib-resources = {version = ">=1.4.0", markers = "python_version < \"3.9\""}
+pkgutil-resolve-name = {version = ">=1.3.10", markers = "python_version < \"3.9\""}
+pyrsistent = ">=0.14.0,<0.17.0 || >0.17.0,<0.17.1 || >0.17.1,<0.17.2 || >0.17.2"
+
+[package.extras]
+format = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3987", "uri-template", "webcolors (>=1.11)"]
+format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "uri-template", "webcolors (>=1.11)"]
+
+[[package]]
+name = "jupyter-client"
+version = "8.1.0"
+description = "Jupyter protocol implementation and client libraries"
+category = "dev"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "jupyter_client-8.1.0-py3-none-any.whl", hash = "sha256:d5b8e739d7816944be50f81121a109788a3d92732ecf1ad1e4dadebc948818fe"},
+    {file = "jupyter_client-8.1.0.tar.gz", hash = "sha256:3fbab64100a0dcac7701b1e0f1a4412f1ccb45546ff2ad9bc4fcbe4e19804811"},
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+importlib-metadata = {version = ">=4.8.3", markers = "python_version < \"3.10\""}
+jupyter-core = ">=4.12,<5.0.0 || >=5.1.0"
+python-dateutil = ">=2.8.2"
+pyzmq = ">=23.0"
+tornado = ">=6.2"
+traitlets = ">=5.3"
+
+[package.extras]
+docs = ["ipykernel", "myst-parser", "pydata-sphinx-theme", "sphinx (>=4)", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling"]
+test = ["codecov", "coverage", "ipykernel (>=6.14)", "mypy", "paramiko", "pre-commit", "pytest", "pytest-cov", "pytest-jupyter[client] (>=0.4.1)", "pytest-timeout"]
+
+[[package]]
+name = "jupyter-core"
+version = "5.3.0"
+description = "Jupyter core package. A base package on which Jupyter projects rely."
+category = "dev"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "jupyter_core-5.3.0-py3-none-any.whl", hash = "sha256:d4201af84559bc8c70cead287e1ab94aeef3c512848dde077b7684b54d67730d"},
+    {file = "jupyter_core-5.3.0.tar.gz", hash = "sha256:6db75be0c83edbf1b7c9f91ec266a9a24ef945da630f3120e1a0046dc13713fc"},
+]
+
+[package.dependencies]
+platformdirs = ">=2.5"
+pywin32 = {version = ">=300", markers = "sys_platform == \"win32\" and platform_python_implementation != \"PyPy\""}
+traitlets = ">=5.3"
+
+[package.extras]
+docs = ["myst-parser", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling", "traitlets"]
+test = ["ipykernel", "pre-commit", "pytest", "pytest-cov", "pytest-timeout"]
+
+[[package]]
+name = "jupyterlab-pygments"
+version = "0.2.2"
+description = "Pygments theme using JupyterLab CSS variables"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "jupyterlab_pygments-0.2.2-py2.py3-none-any.whl", hash = "sha256:2405800db07c9f770863bcf8049a529c3dd4d3e28536638bd7c1c01d2748309f"},
+    {file = "jupyterlab_pygments-0.2.2.tar.gz", hash = "sha256:7405d7fde60819d905a9fa8ce89e4cd830e318cdad22a0030f7a901da705585d"},
+]
+
 [[package]]
 name = "lazy-object-proxy"
 version = "1.9.0"
@@ -1259,6 +1597,22 @@ files = [
 six = "*"
 tornado = {version = "*", markers = "python_version > \"2.7\""}
 
+[[package]]
+name = "lsprotocol"
+version = "2023.0.0a1"
+description = "Python implementation of the Language Server Protocol."
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "lsprotocol-2023.0.0a1-py3-none-any.whl", hash = "sha256:133c339a7cccb299a5b357f9b8ef6aebe27616e0daf4ba54e63476afe0e12e47"},
+    {file = "lsprotocol-2023.0.0a1.tar.gz", hash = "sha256:32edfd4856abba1349bf5a070567445b3d7286951afba3644b472629796f82d0"},
+]
+
+[package.dependencies]
+attrs = "*"
+cattrs = "*"
+
 [[package]]
 name = "markupsafe"
 version = "2.1.2"
@@ -1349,6 +1703,42 @@ numpy = ">=1.24.2"
 openpyxl = ">=3.0.9"
 pandas = ">=1.4.1"
 
+[[package]]
+name = "memestra"
+version = "0.2.1"
+description = "Memestra checks code for places where deprecated functions are called"
+category = "dev"
+optional = false
+python-versions = ">=3.4"
+files = [
+    {file = "memestra-0.2.1-py3-none-any.whl", hash = "sha256:cd3ea54ca2a5b48763b58954d882b15b94b2a1abe2d830c3863bf8082a3e24ea"},
+    {file = "memestra-0.2.1.tar.gz", hash = "sha256:eac8707fd0680df64ccb48ad3fc7ac34fe28bfa7f0e8b2693b763965a8700d9c"},
+]
+
+[package.dependencies]
+beniget = "*"
+frilouz = "*"
+gast = "*"
+nbconvert = "*"
+nbformat = "*"
+pyyaml = "*"
+
+[package.extras]
+dev = ["pytest"]
+test = ["pytest"]
+
+[[package]]
+name = "mistune"
+version = "2.0.5"
+description = "A sane Markdown parser with useful plugins and renderers"
+category = "dev"
+optional = false
+python-versions = "*"
+files = [
+    {file = "mistune-2.0.5-py2.py3-none-any.whl", hash = "sha256:bad7f5d431886fcbaf5f758118ecff70d31f75231b34024a1341120340a65ce8"},
+    {file = "mistune-2.0.5.tar.gz", hash = "sha256:0246113cb2492db875c6be56974a7c893333bf26cd92891c85f63151cee09d34"},
+]
+
 [[package]]
 name = "mr-proper"
 version = "0.0.7"
@@ -1441,6 +1831,90 @@ files = [
     {file = "mypy_extensions-1.0.0.tar.gz", hash = "sha256:75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782"},
 ]
 
+[[package]]
+name = "nbclient"
+version = "0.7.2"
+description = "A client library for executing notebooks. Formerly nbconvert's ExecutePreprocessor."
+category = "dev"
+optional = false
+python-versions = ">=3.7.0"
+files = [
+    {file = "nbclient-0.7.2-py3-none-any.whl", hash = "sha256:d97ac6257de2794f5397609df754fcbca1a603e94e924eb9b99787c031ae2e7c"},
+    {file = "nbclient-0.7.2.tar.gz", hash = "sha256:884a3f4a8c4fc24bb9302f263e0af47d97f0d01fe11ba714171b320c8ac09547"},
+]
+
+[package.dependencies]
+jupyter-client = ">=6.1.12"
+jupyter-core = ">=4.12,<5.0.0 || >=5.1.0"
+nbformat = ">=5.1"
+traitlets = ">=5.3"
+
+[package.extras]
+dev = ["pre-commit"]
+docs = ["autodoc-traits", "mock", "moto", "myst-parser", "nbclient[test]", "sphinx (>=1.7)", "sphinx-book-theme"]
+test = ["ipykernel", "ipython", "ipywidgets", "nbconvert (>=7.0.0)", "pytest (>=7.0)", "pytest-asyncio", "pytest-cov (>=4.0)", "testpath", "xmltodict"]
+
+[[package]]
+name = "nbconvert"
+version = "7.2.10"
+description = "Converting Jupyter Notebooks"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "nbconvert-7.2.10-py3-none-any.whl", hash = "sha256:e41118f81698d3d59b3c7c2887937446048f741aba6c367c1c1a77810b3e2d08"},
+    {file = "nbconvert-7.2.10.tar.gz", hash = "sha256:8eed67bd8314f3ec87c4351c2f674af3a04e5890ab905d6bd927c05aec1cf27d"},
+]
+
+[package.dependencies]
+beautifulsoup4 = "*"
+bleach = "*"
+defusedxml = "*"
+importlib-metadata = {version = ">=3.6", markers = "python_version < \"3.10\""}
+jinja2 = ">=3.0"
+jupyter-core = ">=4.7"
+jupyterlab-pygments = "*"
+markupsafe = ">=2.0"
+mistune = ">=2.0.3,<3"
+nbclient = ">=0.5.0"
+nbformat = ">=5.1"
+packaging = "*"
+pandocfilters = ">=1.4.1"
+pygments = ">=2.4.1"
+tinycss2 = "*"
+traitlets = ">=5.0"
+
+[package.extras]
+all = ["nbconvert[docs,qtpdf,serve,test,webpdf]"]
+docs = ["ipykernel", "ipython", "myst-parser", "nbsphinx (>=0.2.12)", "pydata-sphinx-theme", "sphinx (==5.0.2)", "sphinxcontrib-spelling"]
+qtpdf = ["nbconvert[qtpng]"]
+qtpng = ["pyqtwebengine (>=5.15)"]
+serve = ["tornado (>=6.1)"]
+test = ["ipykernel", "ipywidgets (>=7)", "pre-commit", "pytest", "pytest-dependency"]
+webpdf = ["pyppeteer (>=1,<1.1)"]
+
+[[package]]
+name = "nbformat"
+version = "5.8.0"
+description = "The Jupyter Notebook format"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "nbformat-5.8.0-py3-none-any.whl", hash = "sha256:d910082bd3e0bffcf07eabf3683ed7dda0727a326c446eeb2922abe102e65162"},
+    {file = "nbformat-5.8.0.tar.gz", hash = "sha256:46dac64c781f1c34dfd8acba16547024110348f9fc7eab0f31981c2a3dc48d1f"},
+]
+
+[package.dependencies]
+fastjsonschema = "*"
+jsonschema = ">=2.6"
+jupyter-core = "*"
+traitlets = ">=5.1"
+
+[package.extras]
+docs = ["myst-parser", "pydata-sphinx-theme", "sphinx", "sphinxcontrib-github-alt", "sphinxcontrib-spelling"]
+test = ["pep440", "pre-commit", "pytest", "testpath"]
+
 [[package]]
 name = "nodeenv"
 version = "1.7.0"
@@ -1669,6 +2143,34 @@ files = [
 attrs = "*"
 flake8 = ">3.0.0"
 
+[[package]]
+name = "pandocfilters"
+version = "1.5.0"
+description = "Utilities for writing pandoc filters in python"
+category = "dev"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+files = [
+    {file = "pandocfilters-1.5.0-py2.py3-none-any.whl", hash = "sha256:33aae3f25fd1a026079f5d27bdd52496f0e0803b3469282162bafdcbdf6ef14f"},
+    {file = "pandocfilters-1.5.0.tar.gz", hash = "sha256:0b679503337d233b4339a817bfc8c50064e2eff681314376a47cb582305a7a38"},
+]
+
+[[package]]
+name = "parso"
+version = "0.8.3"
+description = "A Python Parser"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "parso-0.8.3-py2.py3-none-any.whl", hash = "sha256:c001d4636cd3aecdaf33cbb40aebb59b094be2a74c556778ef5576c175e19e75"},
+    {file = "parso-0.8.3.tar.gz", hash = "sha256:8c07be290bb59f03588915921e29e8a50002acaf2cdc5fa0e0114f91709fafa0"},
+]
+
+[package.extras]
+qa = ["flake8 (==3.8.3)", "mypy (==0.782)"]
+testing = ["docopt", "pytest (<6.0.0)"]
+
 [[package]]
 name = "pathspec"
 version = "0.10.3"
@@ -1708,6 +2210,18 @@ files = [
 [package.dependencies]
 flake8 = ">=5.0.0"
 
+[[package]]
+name = "pkgutil-resolve-name"
+version = "1.3.10"
+description = "Resolve a name to an object."
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "pkgutil_resolve_name-1.3.10-py3-none-any.whl", hash = "sha256:ca27cc078d25c5ad71a9de0a7a330146c4e014c2462d9af19c6b828280649c5e"},
+    {file = "pkgutil_resolve_name-1.3.10.tar.gz", hash = "sha256:357d6c9e6a755653cfd78893817c0853af365dd51ec97f3d358a819373bbd174"},
+]
+
 [[package]]
 name = "platformdirs"
 version = "3.2.0"
@@ -1802,6 +2316,18 @@ files = [
     {file = "pycodestyle-2.10.0.tar.gz", hash = "sha256:347187bdb476329d98f695c213d7295a846d1152ff4fe9bacb8a9590b8ee7053"},
 ]
 
+[[package]]
+name = "pycparser"
+version = "2.21"
+description = "C parser in Python"
+category = "dev"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+files = [
+    {file = "pycparser-2.21-py2.py3-none-any.whl", hash = "sha256:8ee45429555515e1f6b185e78100aea234072576aa43ab53aefcae078162fca9"},
+    {file = "pycparser-2.21.tar.gz", hash = "sha256:e644fdec12f7872f86c58ff790da456218b10f863970249516d60a5eaca77206"},
+]
+
 [[package]]
 name = "pydantic"
 version = "1.10.7"
@@ -1900,6 +2426,28 @@ files = [
     {file = "pyflakes-3.0.1.tar.gz", hash = "sha256:ec8b276a6b60bd80defed25add7e439881c19e64850afd9b346283d4165fd0fd"},
 ]
 
+[[package]]
+name = "pygls"
+version = "1.0.1"
+description = "a pythonic generic language server (pronounced like \"pie glass\")."
+category = "dev"
+optional = false
+python-versions = "<4,>=3.7"
+files = [
+    {file = "pygls-1.0.1-py3-none-any.whl", hash = "sha256:adacc96da77598c70f46acfdfd1481d3da90cd54f639f7eee52eb6e4dbd57b55"},
+    {file = "pygls-1.0.1.tar.gz", hash = "sha256:f3ee98ddbb4690eb5c755bc32ba7e129607f14cbd313575f33d0cea443b78cb2"},
+]
+
+[package.dependencies]
+lsprotocol = "*"
+typeguard = ">=2.10.0,<3"
+
+[package.extras]
+dev = ["bandit (==1.7.4)", "flake8 (==4.0.1)", "mypy (==0.961)"]
+docs = ["sphinx (==5.0.1)", "sphinx-rtd-theme (==1.0.0)"]
+test = ["mock (==4.0.3)", "pytest (==7.1.2)", "pytest-asyncio (==0.18.3)"]
+ws = ["websockets (>=10.0.0,<11.0.0)"]
+
 [[package]]
 name = "pygments"
 version = "2.14.0"
@@ -1945,6 +2493,78 @@ typing-extensions = {version = ">=3.10.0", markers = "python_version < \"3.10\""
 spelling = ["pyenchant (>=3.2,<4.0)"]
 testutils = ["gitpython (>3)"]
 
+[[package]]
+name = "pyls-isort"
+version = "0.2.2"
+description = "Isort plugin for python-lsp-server"
+category = "dev"
+optional = false
+python-versions = "*"
+files = [
+    {file = "pyls-isort-0.2.2.tar.gz", hash = "sha256:2192bd2203db00459f85eb329521feba58af63075d2dd10a051a4eccd000bba0"},
+]
+
+[package.dependencies]
+isort = "*"
+python-lsp-server = "*"
+
+[[package]]
+name = "pyls-memestra"
+version = "0.0.16"
+description = "Memestra plugin for the Python Language Server"
+category = "dev"
+optional = false
+python-versions = "*"
+files = [
+    {file = "pyls-memestra-0.0.16.tar.gz", hash = "sha256:ccc543776b81e339f0dfccf7c9bd0db7ba901f97461d36d004864efeaa35fedf"},
+    {file = "pyls_memestra-0.0.16-py3-none-any.whl", hash = "sha256:59dea636aa061026b51a01607fae3c678c19c18678b865cddc34e84491ab3ec1"},
+]
+
+[package.dependencies]
+Deprecated = "*"
+memestra = "*"
+python-lsp-server = "*"
+
+[[package]]
+name = "pylsp-mypy"
+version = "0.6.6"
+description = "Mypy linter for the Python LSP Server"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "pylsp-mypy-0.6.6.tar.gz", hash = "sha256:aa5d547b25ca431b5b17689c495c55aa374b19b35c59746987e417044fb722ce"},
+    {file = "pylsp_mypy-0.6.6-py3-none-any.whl", hash = "sha256:46666ffa282e1b44b86b3b03f55b95ca12df82af77c88cf4b85fba3d532b7290"},
+]
+
+[package.dependencies]
+mypy = "*"
+python-lsp-server = ">=1.7.0"
+tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""}
+
+[package.extras]
+test = ["coverage", "pytest", "pytest-cov", "tox"]
+
+[[package]]
+name = "pylsp-rope"
+version = "0.1.11"
+description = "Extended refactoring capabilities for Python LSP Server using Rope."
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "pylsp-rope-0.1.11.tar.gz", hash = "sha256:48aadf993dafa5e8fca1108b4a5431314cf80bc78cffdd56400ead9c407553be"},
+    {file = "pylsp_rope-0.1.11-py3-none-any.whl", hash = "sha256:71fb08dc6ead9a69202f2e7c5f7bbc5ada037a0f0722d7eb2d1f8cac2c9a18af"},
+]
+
+[package.dependencies]
+python-lsp-server = "*"
+rope = ">=0.21.0"
+
+[package.extras]
+dev = ["build", "pytest", "twine"]
+test = ["pytest"]
+
 [[package]]
 name = "pyparsing"
 version = "3.0.9"
@@ -1960,6 +2580,43 @@ files = [
 [package.extras]
 diagrams = ["jinja2", "railroad-diagrams"]
 
+[[package]]
+name = "pyrsistent"
+version = "0.19.3"
+description = "Persistent/Functional/Immutable data structures"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+files = [
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+
+[package.dependencies]
+cffi = {version = "*", markers = "implementation_name == \"pypy\""}
+
 [[package]]
 name = "requests"
 version = "2.28.2"
@@ -2190,6 +3056,25 @@ typing-extensions = {version = ">=4.0.0,<5.0", markers = "python_version < \"3.9
 [package.extras]
 jupyter = ["ipywidgets (>=7.5.1,<8.0.0)"]
 
+[[package]]
+name = "rope"
+version = "1.7.0"
+description = "a python refactoring library..."
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+files = [
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+[package.dependencies]
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+
+[package.extras]
+dev = ["build (>=0.7.0)", "pre-commit (>=2.20.0)", "pytest (>=7.0.1)", "pytest-timeout (>=2.1.0)"]
+doc = ["pytoolconfig[doc]", "sphinx (>=4.5.0)", "sphinx-autodoc-typehints (>=1.18.1)", "sphinx-rtd-theme (>=1.0.0)"]
+
 [[package]]
 name = "rstcheck"
 version = "6.1.2"
@@ -2300,6 +3185,54 @@ files = [
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 ]
 
+[[package]]
+name = "ruff"
+version = "0.0.259"
+description = "An extremely fast Python linter, written in Rust."
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+files = [
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+]
+
+[[package]]
+name = "ruff-lsp"
+version = "0.0.24"
+description = "A Language Server Protocol implementation for Ruff."
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+files = [
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+]
+
+[package.dependencies]
+lsprotocol = ">=2023.0.0a1"
+pygls = ">=1.0.1"
+ruff = ">=0.0.253"
+typing-extensions = "*"
+
+[package.extras]
+dev = ["black (==22.12.0)", "mypy (==0.991)", "python-lsp-jsonrpc (==1.0.0)"]
+
 [[package]]
 name = "safety"
 version = "2.3.5"
@@ -2389,6 +3322,18 @@ files = [
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 ]
 
+[[package]]
+name = "soupsieve"
+version = "2.4"
+description = "A modern CSS selector implementation for Beautiful Soup."
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+files = [
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+]
+
 [[package]]
 name = "sphinx"
 version = "6.1.3"
@@ -2590,6 +3535,25 @@ files = [
 [package.dependencies]
 pbr = ">=2.0.0,<2.1.0 || >2.1.0"
 
+[[package]]
+name = "tinycss2"
+version = "1.2.1"
+description = "A tiny CSS parser"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+files = [
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+    {file = "tinycss2-1.2.1.tar.gz", hash = "sha256:8cff3a8f066c2ec677c06dbc7b45619804a6938478d9d73c284b29d14ecb0627"},
+]
+
+[package.dependencies]
+webencodings = ">=0.4"
+
+[package.extras]
+doc = ["sphinx", "sphinx_rtd_theme"]
+test = ["flake8", "isort", "pytest"]
+
 [[package]]
 name = "toml"
 version = "0.10.2"
@@ -2647,6 +3611,22 @@ files = [
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 ]
 
+[[package]]
+name = "traitlets"
+version = "5.9.0"
+description = "Traitlets Python configuration system"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "traitlets-5.9.0-py3-none-any.whl", hash = "sha256:9e6ec080259b9a5940c797d58b613b5e31441c2257b87c2e795c5228ae80d2d8"},
+    {file = "traitlets-5.9.0.tar.gz", hash = "sha256:f6cde21a9c68cf756af02035f72d5a723bf607e862e7be33ece505abf4a3bad9"},
+]
+
+[package.extras]
+docs = ["myst-parser", "pydata-sphinx-theme", "sphinx"]
+test = ["argcomplete (>=2.0)", "pre-commit", "pytest", "pytest-mock"]
+
 [[package]]
 name = "tryceratops"
 version = "1.1.0"
@@ -2666,23 +3646,19 @@ toml = ">=0.10.2"
 
 [[package]]
 name = "typeguard"
-version = "3.0.2"
+version = "2.13.3"
 description = "Run-time type checker for Python"
 category = "dev"
 optional = false
-python-versions = ">=3.7.4"
+python-versions = ">=3.5.3"
 files = [
-    {file = "typeguard-3.0.2-py3-none-any.whl", hash = "sha256:bbe993854385284ab42fd5bd3bee6f6556577ce8b50696d6cb956d704f286c8e"},
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+    {file = "typeguard-2.13.3-py3-none-any.whl", hash = "sha256:5e3e3be01e887e7eafae5af63d1f36c849aaa94e3a0112097312aabfa16284f1"},
+    {file = "typeguard-2.13.3.tar.gz", hash = "sha256:00edaa8da3a133674796cf5ea87d9f4b4c367d77476e185e80251cc13dfbb8c4"},
 ]
 
-[package.dependencies]
-importlib-metadata = {version = ">=3.6", markers = "python_version < \"3.10\""}
-typing-extensions = {version = ">=4.4.0", markers = "python_version < \"3.11\""}
-
 [package.extras]
-doc = ["packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"]
-test = ["mypy (>=0.991)", "pytest (>=7)"]
+doc = ["sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"]
+test = ["mypy", "pytest", "typing-extensions"]
 
 [[package]]
 name = "typer"
@@ -2710,14 +3686,14 @@ test = ["black (>=22.3.0,<23.0.0)", "coverage (>=6.2,<7.0)", "isort (>=5.0.6,<6.
 
 [[package]]
 name = "types-docutils"
-version = "0.19.1.6"
+version = "0.19.1.7"
 description = "Typing stubs for docutils"
 category = "dev"
 optional = false
 python-versions = "*"
 files = [
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+    {file = "types-docutils-0.19.1.7.tar.gz", hash = "sha256:cb6e0dd1c895c723002ec4dc8334bf9df04726ef0cf13f5597501578b47eef30"},
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 ]
 
 [[package]]
@@ -2760,6 +3736,81 @@ files = [
 mypy-extensions = ">=0.3.0"
 typing-extensions = ">=3.7.4"
 
+[[package]]
+name = "ujson"
+version = "5.7.0"
+description = "Ultra fast JSON encoder and decoder for Python"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+files = [
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+    {file = "ujson-5.7.0-pp39-pypy39_pp73-win_amd64.whl", hash = "sha256:4c592eb91a5968058a561d358d0fef59099ed152cfb3e1cd14eee51a7a93879e"},
+    {file = "ujson-5.7.0.tar.gz", hash = "sha256:e788e5d5dcae8f6118ac9b45d0b891a0d55f7ac480eddcb7f07263f2bcf37b23"},
+]
+
 [[package]]
 name = "urllib3"
 version = "1.26.15"
@@ -2798,6 +3849,18 @@ platformdirs = ">=2.4,<4"
 docs = ["furo (>=2022.12.7)", "proselint (>=0.13)", "sphinx (>=6.1.3)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=22.12)"]
 test = ["covdefaults (>=2.2.2)", "coverage (>=7.1)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23)", "pytest (>=7.2.1)", "pytest-env (>=0.8.1)", "pytest-freezegun (>=0.4.2)", "pytest-mock (>=3.10)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)"]
 
+[[package]]
+name = "webencodings"
+version = "0.5.1"
+description = "Character encoding aliases for legacy web content"
+category = "dev"
+optional = false
+python-versions = "*"
+files = [
+    {file = "webencodings-0.5.1-py2.py3-none-any.whl", hash = "sha256:a0af1213f3c2226497a97e2b3aa01a7e4bee4f403f95be16fc9acd2947514a78"},
+    {file = "webencodings-0.5.1.tar.gz", hash = "sha256:b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923"},
+]
+
 [[package]]
 name = "wrapt"
 version = "1.15.0"
@@ -2957,4 +4020,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.8.1,<4.0"
-content-hash = "6a94d46546d761f4aa966b6e06f2649c9776f6349cfe42d2fd6430be27c14a0f"
+content-hash = "f27445064962e71a6f6142162cd36f44fa133f172a97a52420e8e6bf33e07775"
diff --git a/pyproject.toml b/pyproject.toml
index 2fc1038..ad29467 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -145,10 +145,21 @@ sphinx-autodoc-typehints = ">=1.19.5"
 sphinx-autobuild = ">=2021.3.14"
 
 
+[tool.poetry.group.pylsp.dependencies]
+pylsp-mypy = ">=0.6.6"
+pyls-isort = ">=0.2.2"
+python-lsp-black = ">=1.2.1"
+pyls-memestra = ">=0.0.16"
+pylsp-rope = ">=0.1.11"
+ruff-lsp = "^0.0.24"
+
+[tool.poetry.group.ruff.dependencies]
+ruff = ">=0.0.259"
+
 [tool.isort]
 atomic = true
 ensure_newline_before_comments = true
-known_first_party = "xpypact"
+known_first_party = "src"
 known_third_party = "mpl_toolkits,matplotlib,numpy,scipy"
 known_typing = "typing,types,typing_extensions,mypy,mypy_extensions"
 sections = "FUTURE,TYPING,STDLIB,THIRDPARTY,FIRSTPARTY,LOCALFOLDER"
@@ -362,3 +373,50 @@ summary-quotes-same-line = true
 good-names-rgxs=["."]  # a single character variable is okay
 logging-format-style="new"   # use {} in logging messages
 deprecated-modules=["six"]
+
+[tool.ruff]
+# Same as Black.
+line-length = 100
+
+# show an enumeration of all autofixed lint violations
+show-fixes = true
+
+# show source code snippets when reporting violations
+show-source = true
+
+src = ["src", "test"]
+
+# Allow unused variables when underscore-prefixed.
+# dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
+dummy-variable-rgx = "^_$"
+exclude = [
+  "docs/source/conf.py",
+  "__pycache__",
+  "adhoc",
+  "wrk",
+  "*.egg-info",
+  ".cache",
+  "notebooks/dvp/*.py"
+]
+# Assume Python 3.10.
+# target-version = "py310"
+
+[tool.ruff.per-file-ignores]
+"__init__.py" = ["E402"]
+"src/xpypact/Fluxes.py" = ["F811"]
+
+[tool.ruff.mccabe]
+# Unlike Flake8, default to a complexity level of 10.
+max-complexity = 10
+
+[tool.ruff.flake8-type-checking]
+strict = true
+
+[tool.ruff.isort]
+known-first-party = ["src"]
+known-third-party = ["mpl_toolkits", "matplotlib", "numpy", "scipy"]
+required-imports = ["from __future__ import annotations"]
+
+[tool.ruff.pydocstyle]
+# Use Google-style docstrings.
+convention = "google"

From e46f823383669fea7b773804c652c66633ec265f Mon Sep 17 00:00:00 2001
From: dvp 
Date: Tue, 28 Mar 2023 19:05:43 +0300
Subject: [PATCH 23/32] build: add ruff as major linter

---
 .flake8        |  3 +++
 pyproject.toml | 57 ++++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 60 insertions(+)

diff --git a/.flake8 b/.flake8
index 36c9561..5df8e51 100644
--- a/.flake8
+++ b/.flake8
@@ -58,6 +58,9 @@ exclude=
     .cache
     .eggs
     notebooks/dvp/*.py
+    .nox
+    .idea
+
 per-file-ignores =
     benchmarks/*:S101,DAR101
     noxfile.py:ANN,DAR101
diff --git a/pyproject.toml b/pyproject.toml
index ad29467..9285e64 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -375,6 +375,63 @@ logging-format-style="new"   # use {} in logging messages
 deprecated-modules=["six"]
 
 [tool.ruff]
+#see full list: https://beta.ruff.rs/docs/rules/#pyflakes-f
+select= [
+  "A",
+  "B",
+  "C",
+  "D",
+  "E",
+  "F",
+  "G",
+  "I",
+  "N",
+  "PIE",
+  "PT",
+  "PL",
+  "PLC",
+  "PLE",
+  "PLR",
+  "PLW",
+  "PYI",
+  "Q",
+  "R",
+  "S",
+  "T",
+  "U",
+  "W",
+  "YTT"
+]
+
+# Ignore rules that currently fail on the codebase
+ignore = [
+    # "E401",  # Multiple imports on one line
+    "E402",  # Module level import not at top of file
+    "E501",  # Line too long ( > 88 characters)
+    # "E701",  # Multiple statements on one line (colon)
+    # "E702",  # Multiple statements on one line (semicolon)
+    # "E703",  # Statement ends with an unnecessary semicolon
+    # "E704",  # Multiple statements on one line (def)
+    # "E711",  # Comparison to `None` should be `cond is not None`
+    # "E712",  # Comparison to `` should be `cond is `
+    # "E713",  # Test for membership should be `not in`
+    # "E714",  # Test for object identity should be `is not`
+    # "E721",  # Do not compare types, use `isinstance()`
+    # "E722",  # Do not use bare `except`
+    # "E731",  # Do not assign a `lambda` expression, use a `def`
+    # "E741",  # Ambiguous variable name: ``
+    # "E743",  # Ambiguous function name: ``
+    # "F401",  # `` imported but unused
+    # "F403",  # `from  import *` used; unable to detect undefined names
+    # "F405",  # `` may be undefined, or defined from star imports: ``
+    # "F523",  # `.format` call has unused arguments at position(s): 
+    # "F601",  # Dictionary key literal `''` repeated
+    # "F811",  # Redefinition of unused `` from line 
+    # "F821",  # Undefined name `VARIABLE`
+    # "F823",  # Local variable `VARIABLE` referenced before assignment
+    # "F841",  # Local variable `VARIABLE` is assigned to but never used
+]
+
 # Same as Black.
 line-length = 100
 

From f21f29d1a4489579acf9aa10b633e1060c855917 Mon Sep 17 00:00:00 2001
From: dvp 
Date: Wed, 29 Mar 2023 14:22:18 +0300
Subject: [PATCH 24/32] build: fix ruff config and warnings

---
 .flake8                                       |  4 +-
 .pre-commit-config.yaml                       |  1 +
 benchmarks/test_inventory.py                  |  8 +++-
 notebooks/dvp/try_ducdb.py                    |  6 ++-
 noxfile.py                                    |  4 +-
 pyproject.toml                                | 39 ++++++++++++++++++-
 src/xpypact/__init__.py                       |  2 +
 src/xpypact/data_arrays.py                    | 25 ++++++------
 src/xpypact/{Fluxes.py => fluxes.py}          | 17 +++++---
 src/xpypact/{Inventory.py => inventory.py}    | 21 +++++-----
 src/xpypact/{Nuclide.py => nuclide.py}        |  8 ++--
 src/xpypact/{RunData.py => run_data.py}       |  2 +-
 src/xpypact/{TimeStep.py => time_step.py}     | 30 +++++++-------
 src/xpypact/utils/io.py                       |  5 ++-
 src/xpypact/utils/resource.py                 |  5 +--
 src/xpypact/utils/types.py                    |  2 +
 tests/conftest.py                             |  6 ++-
 tests/test_data_arrays.py                     | 13 ++++---
 tests/{test_Fluxes.py => test_fluxes.py}      | 21 +++++-----
 .../{test_Inventory.py => test_inventory.py}  |  8 ++--
 tests/test_package.py                         |  5 ++-
 tests/{test_RunData.py => test_run_data.py}   |  5 ++-
 tests/utils/test_resource.py                  |  9 +++--
 tools/clear-prev-dist-info.py                 |  8 ++--
 24 files changed, 162 insertions(+), 92 deletions(-)
 rename src/xpypact/{Fluxes.py => fluxes.py} (96%)
 rename src/xpypact/{Inventory.py => inventory.py} (93%)
 rename src/xpypact/{Nuclide.py => nuclide.py} (91%)
 rename src/xpypact/{RunData.py => run_data.py} (87%)
 rename src/xpypact/{TimeStep.py => time_step.py} (87%)
 rename tests/{test_Fluxes.py => test_fluxes.py} (90%)
 rename tests/{test_Inventory.py => test_inventory.py} (93%)
 rename tests/{test_RunData.py => test_run_data.py} (86%)

diff --git a/.flake8 b/.flake8
index 5df8e51..18f9bf8 100644
--- a/.flake8
+++ b/.flake8
@@ -66,10 +66,10 @@ per-file-ignores =
     noxfile.py:ANN,DAR101
     tools/clear-prev-dist-info.py:S404,S603,S607
     tests/*:ANN,B950,DAR100,D100,D101,D102,D103,D104,DAR101,DAR103,S101
-    src/xpypact/Inventory.py:F811
+    src/xpypact/inventory.py:F811
     src/xpypact/data_arrays.py:ANN401,PD011
     src/xpypact/utils/resource.py:ANN202
-    src/xpypact/Fluxes.py:F811
+    src/xpypact/fluxes.py:F811
 ignore-decorators=click,pytest
 docstring-convention = google
 rst-roles = class,const,func,meth,mod,ref
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 140f1d3..1a2979d 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -81,6 +81,7 @@ repos:
         entry: poetry run black
         language: system
         types: [python]
+        exclude: ^notebooks
     # Lint
     # -   id: flake8
     #     name: flake8
diff --git a/benchmarks/test_inventory.py b/benchmarks/test_inventory.py
index d8bc456..0a3ee96 100644
--- a/benchmarks/test_inventory.py
+++ b/benchmarks/test_inventory.py
@@ -2,11 +2,15 @@
 
 See https://pytest-benchmark.readthedocs.io/en/latest/index.html
 """
+from __future__ import annotations
+
 import bz2
 
-from xpypact.Inventory import Inventory, from_json
+from xpypact.inventory import Inventory, from_json
 from xpypact.utils.resource import path_resolver
 
+EXPECTED_TIME_STEPS = 65
+
 data_path_resolver = path_resolver("benchmarks")
 
 with bz2.open(data_path_resolver("data/Ag-1.json.bz2")) as fid:
@@ -16,4 +20,4 @@
 def test_load_from_string(benchmark) -> None:
     """Loading from string."""
     inventory: Inventory = benchmark(from_json, AG_1_TEXT)
-    assert len(inventory.inventory_data) == 65
+    assert len(inventory.inventory_data) == EXPECTED_TIME_STEPS
diff --git a/notebooks/dvp/try_ducdb.py b/notebooks/dvp/try_ducdb.py
index b9d8bd0..b9bb8c0 100644
--- a/notebooks/dvp/try_ducdb.py
+++ b/notebooks/dvp/try_ducdb.py
@@ -41,7 +41,7 @@
 
 import xpypact.data_arrays as da
 
-from xpypact.Inventory import from_json
+from xpypact.inventory import from_json
 
 # In[8]:
 
@@ -492,7 +492,9 @@ def save_gamma_spectra(con, ds):
 # In[103]:
 
 
-con.execute("select boundary, intensity from timestep_gamma where time_step_number = 42").df()
+con.execute(
+    "select boundary, intensity from timestep_gamma where time_step_number = 42"
+).df()
 
 
 # In[104]:
diff --git a/noxfile.py b/noxfile.py
index 54f4f19..ddce4d1 100644
--- a/noxfile.py
+++ b/noxfile.py
@@ -4,7 +4,7 @@
 """
 from __future__ import annotations
 
-from typing import Final, List
+from typing import Final
 
 import re
 import shutil
@@ -207,7 +207,7 @@ def isort(s: Session) -> None:
         "profiles/*.py",
         "adhoc/*.py",
     ]
-    files_to_process: List[str] = sum((glob(p, recursive=True) for p in search_patterns), [])
+    files_to_process: list[str] = sum((glob(p, recursive=True) for p in search_patterns), [])
     if files_to_process:
         s.run(
             "poetry",
diff --git a/pyproject.toml b/pyproject.toml
index 9285e64..9eb1475 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -375,6 +375,7 @@ logging-format-style="new"   # use {} in logging messages
 deprecated-modules=["six"]
 
 [tool.ruff]
+target-version = "py38"
 #see full list: https://beta.ruff.rs/docs/rules/#pyflakes-f
 select= [
   "A",
@@ -405,9 +406,20 @@ select= [
 
 # Ignore rules that currently fail on the codebase
 ignore = [
+    "ANN001", # ANN001 Missing type annotation for function argument: doesn't allow to use functools dispatching
+    "ANN002", # ANN002 Missing type annotation for *drop_items: ... as above
+    "ANN101", # ANN101 Missing type annotation for self in method
+    "ANN102", # ANN102 Missing type annotation for cls in classmethod
+    "ANN202", # ANN202 Missing return type annotation for protected function: ... dispatching
+    "ANN204", # ANN204 Missing return type annotation for special method
+    "B905",   # B905 `zip()` without an explicit `strict=` parameter - ignore while support 3.8, 3.9
+    # "C812",   # C812 Missing trailing comma: black compatibility
+    "D105",   # D105 Missing docstring in magic method (__hash__, __eq__)
+    "D107",   # Missing docstring in __init__
+    # "E203",   # E203: Whitespace before ‘:'
     # "E401",  # Multiple imports on one line
     "E402",  # Module level import not at top of file
-    "E501",  # Line too long ( > 88 characters)
+    "E501",  # Line too long ( > 100 characters)
     # "E701",  # Multiple statements on one line (colon)
     # "E702",  # Multiple statements on one line (semicolon)
     # "E703",  # Statement ends with an unnecessary semicolon
@@ -430,6 +442,18 @@ ignore = [
     # "F821",  # Undefined name `VARIABLE`
     # "F823",  # Local variable `VARIABLE` referenced before assignment
     # "F841",  # Local variable `VARIABLE` is assigned to but never used
+
+    "I001",  # import order is controlled by isort
+    # "I101",
+    # "I201",
+    # "I202",
+
+# ignore some questionable pandas-vet warnings
+    # "PD005", # use operator instead of method
+    # "PD008", # We use at() to access single values
+    # "PD009", # And we use iat()
+    # "W503",  # Line break before binary operator: for compatibility with black settings
+    "PT019",   # Fixture `_bin` without value is injected as parameter (false positive?)
 ]
 
 # Same as Black.
@@ -460,7 +484,14 @@ exclude = [
 
 [tool.ruff.per-file-ignores]
 "__init__.py" = ["E402"]
-"src/xpypact/Fluxes.py" = ["F811"]
+"src/xpypact/fluxes.py" = ["F811"]
+"benchmarks/*" = ["S101"]
+"noxfile.py" = ["ANN"]
+"tests/*" = ["ANN", "D100", "D101", "D102", "D103", "D104",  "PLR2004", "S101"]
+"src/xpypact/inventory.py" = ["F811"]
+"src/xpypact/data_arrays.py" = ["ANN401", "PD011"]
+"src/xpypact/utils/resource.py" = ["ANN202"]
+"tools/*" = ["T201"]
 
 [tool.ruff.mccabe]
 # Unlike Flake8, default to a complexity level of 10.
@@ -474,6 +505,10 @@ known-first-party = ["src"]
 known-third-party = ["mpl_toolkits", "matplotlib", "numpy", "scipy"]
 required-imports = ["from __future__ import annotations"]
 
+
+[tool.ruff.flake8-pytest-style]
+parametrize-names-type = "list"
+
 [tool.ruff.pydocstyle]
 # Use Google-style docstrings.
 convention = "google"
diff --git a/src/xpypact/__init__.py b/src/xpypact/__init__.py
index 1be5d81..1fda642 100644
--- a/src/xpypact/__init__.py
+++ b/src/xpypact/__init__.py
@@ -2,6 +2,8 @@
 
 Wraps FISPACT workflow. Transforms FISPACT output to xarray datasets.
 """
+from __future__ import annotations
+
 from importlib import metadata as _meta
 from importlib.metadata import PackageNotFoundError, version
 
diff --git a/src/xpypact/data_arrays.py b/src/xpypact/data_arrays.py
index c8fd4b8..b25506c 100644
--- a/src/xpypact/data_arrays.py
+++ b/src/xpypact/data_arrays.py
@@ -15,7 +15,7 @@
 """
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, Any, Literal, TextIO, Tuple, Union, cast
+from typing import TYPE_CHECKING, Any, Literal, TextIO, cast
 
 from functools import reduce
 from pathlib import Path
@@ -30,9 +30,9 @@
 from mckit_nuclides.elements import ELEMENTS_TABLE
 from mckit_nuclides.nuclides import NUCLIDES_TABLE
 from xarray.core.accessor_dt import DatetimeAccessor
-from xpypact.Inventory import Inventory
-from xpypact.Inventory import from_json as inventory_from_json
-from xpypact.TimeStep import TimeStep
+from xpypact.inventory import Inventory
+from xpypact.inventory import from_json as inventory_from_json
+from xpypact.time_step import TimeStep
 from xpypact.utils.types import MayBePath
 
 if TYPE_CHECKING:  # pragma: no cover
@@ -70,18 +70,18 @@
 ]
 
 
-def _make_var(value, dtype=float) -> Tuple[str, ArrayLike]:
+def _make_var(value, dtype=float) -> tuple[str, ArrayLike]:
     value = np.array([value], dtype=dtype)
     return "time_step_number", value
 
 
-def _make_nuclide_var(getter, nuclides, dtype=float) -> Tuple[str, ArrayLike]:
+def _make_nuclide_var(getter, nuclides, dtype=float) -> tuple[str, ArrayLike]:
     return "nuclide", np.fromiter(map(getter, nuclides), dtype=dtype)
 
 
 def _make_time_step_and_nuclide_var(
     getter, nuclides, dtype=float
-) -> Tuple[Tuple[str, str], ArrayLike]:
+) -> tuple[tuple[str, str], ArrayLike]:
     _data = np.fromiter(map(getter, nuclides), dtype=dtype)
     return ("time_step_number", "nuclide"), _data.reshape(1, _data.size)
 
@@ -148,8 +148,7 @@ def _add_time_step_record(_ds: xr.Dataset, ts: TimeStep) -> xr.Dataset:
         coords["gamma_boundaries"] = gamma_boundaries
 
     tsr = xr.Dataset(data_vars=data_vars, coords=coords)
-    _ds = xr.merge([_ds, tsr])
-    return _ds
+    return xr.merge([_ds, tsr])
 
 
 def create_dataset(inventory: Inventory) -> xr.Dataset:
@@ -337,8 +336,7 @@ def scale_by_mass(ds: xr.Dataset, scale: float) -> xr.Dataset:
         A new dataset with scaled columns.
     """
     columns = [x for x in SCALABLE_COLUMNS if x in ds.variables]
-    scaled = ds.merge(ds[columns] * scale, overwrite_vars=columns, join="exact")
-    return scaled
+    return ds.merge(ds[columns] * scale, overwrite_vars=columns, join="exact")
 
 
 def _encode_multiindex(ds: xr.Dataset, idx_name: str) -> xr.Dataset:
@@ -402,11 +400,10 @@ def load_nc(
         The loaded dataset
     """
     encoded = xr.load_dataset(cn, engine=engine, **kwargs)
-    ds = _decode_to_multiindex(encoded, "nuclide")
-    return ds
+    return _decode_to_multiindex(encoded, "nuclide")
 
 
-def from_json(path: Union[str, Path, TextIO]) -> xr.Dataset:
+def from_json(path: str | Path | TextIO) -> xr.Dataset:
     """Load Dataset from the FISPACT JSON output.
 
     Args:
diff --git a/src/xpypact/Fluxes.py b/src/xpypact/fluxes.py
similarity index 96%
rename from src/xpypact/Fluxes.py
rename to src/xpypact/fluxes.py
index f99bf4b..3714500 100644
--- a/src/xpypact/Fluxes.py
+++ b/src/xpypact/fluxes.py
@@ -1,6 +1,9 @@
 """The Class to represent FISPACT fluxes file content."""
-from typing import Callable, TextIO, Tuple, cast
+from __future__ import annotations
 
+from typing import TextIO, cast
+
+from collections.abc import Callable
 from dataclasses import dataclass
 from io import StringIO, TextIOBase
 from pathlib import Path
@@ -13,6 +16,8 @@
 from xpypact.utils.io import print_cols
 from xpypact.utils.types import NDArrayFloat
 
+FISPACT_709_BINS_NUMBER = 709
+
 # pylint: disable=function-redefined
 
 LAST_TWO_DECADES = np.fromstring(
@@ -232,7 +237,7 @@ def is_709_fluxes(fluxes: Fluxes) -> bool:
     Returns:
         bool: True, if fluxes are 709 kind of fluxes.
     """
-    return fluxes.energy_bins is FISPACT_709_BINS and fluxes.fluxes.size == 709
+    return fluxes.energy_bins is FISPACT_709_BINS and fluxes.fluxes.size == FISPACT_709_BINS_NUMBER
 
 
 def are_fluxes_equal(a: Fluxes, b: Fluxes) -> bool:
@@ -285,7 +290,7 @@ def are_fluxes_close(
 
 def read_fluxes(
     stream: TextIO,
-    define_bins_and_fluxes: Callable[[NDArrayFloat], Tuple[NDArrayFloat, NDArrayFloat]],
+    define_bins_and_fluxes: Callable[[NDArrayFloat], tuple[NDArrayFloat, NDArrayFloat]],
 ) -> Fluxes:
     """Load Fluxes from a stream.
 
@@ -407,7 +412,7 @@ class ArbitraryFluxesDataSizeError(FluxesDataSizeError):
     """The number of float values from arb_flux file should be odd."""
 
 
-def define_arb_bins_and_fluxes(data: NDArrayFloat) -> Tuple[NDArrayFloat, NDArrayFloat]:
+def define_arb_bins_and_fluxes(data: NDArrayFloat) -> tuple[NDArrayFloat, NDArrayFloat]:
     """Extract energy bins and values of arbitrary flux.
 
     Args:
@@ -434,7 +439,7 @@ class StandardFluxesDataSizeError(FluxesDataSizeError):
     """Invalid data for standard FISPACT 709-group fluxes."""
 
 
-def define_709_bins_and_fluxes(data: NDArrayFloat) -> Tuple[NDArrayFloat, NDArrayFloat]:
+def define_709_bins_and_fluxes(data: NDArrayFloat) -> tuple[NDArrayFloat, NDArrayFloat]:
     """Strategy to define energy bins and values of standard 709 group flux.
 
     Args:
@@ -446,7 +451,7 @@ def define_709_bins_and_fluxes(data: NDArrayFloat) -> Tuple[NDArrayFloat, NDArra
     Raises:
         StandardFluxesDataSizeError: if size of data is not 709.
     """
-    if data.size != 709:
+    if data.size != FISPACT_709_BINS_NUMBER:
         raise StandardFluxesDataSizeError()
     return FISPACT_709_BINS, data[::-1]
 
diff --git a/src/xpypact/Inventory.py b/src/xpypact/inventory.py
similarity index 93%
rename from src/xpypact/Inventory.py
rename to src/xpypact/inventory.py
index dfb1964..4f4e097 100644
--- a/src/xpypact/Inventory.py
+++ b/src/xpypact/inventory.py
@@ -1,10 +1,11 @@
 """Classes to load information from FISPACT output JSON file."""
 from __future__ import annotations
 
-from typing import Any, Callable, Iterable, cast
+from typing import Any, cast
 
 import io
 
+from collections.abc import Callable, Iterable
 from dataclasses import dataclass
 from functools import singledispatch
 from pathlib import Path
@@ -13,10 +14,12 @@
 
 import orjson as json
 
-from xpypact.RunData import RunData
-from xpypact.TimeStep import TimeStep
+from xpypact.run_data import RunData
+from xpypact.time_step import TimeStep
 from xpypact.utils.types import NDArrayFloat
 
+FLOAT_ZERO = 0.0
+
 
 @dataclass
 class RunDataCorrected:
@@ -47,21 +50,21 @@ def __str__(self) -> str:
 
 
 def _create_json_inventory_data_mapper() -> Callable[[dict[str, Any]], TimeStep]:
-    prev_irradiation_time = prev_cooling_time = prev_elapsed_time = 0.0
+    prev_irradiation_time = prev_cooling_time = prev_elapsed_time = FLOAT_ZERO
     number = 1
 
     def json_inventory_data_mapper(jts: dict[str, Any]) -> TimeStep:
         nonlocal number, prev_irradiation_time, prev_cooling_time, prev_elapsed_time
         ts = TimeStep.from_json(jts)
         duration = ts.irradiation_time - prev_irradiation_time
-        if duration == 0.0:
+        if duration == FLOAT_ZERO:
             duration = ts.cooling_time - prev_cooling_time
-        if duration < 0.0:
+        if duration < FLOAT_ZERO:
             raise InventoryNonMonotonicTimesError()  # pragma: no cover
         ts.duration = duration
         prev_elapsed_time = ts.elapsed_time = prev_elapsed_time + duration
-        if duration == 0.0:
-            ts.flux = 0.0
+        if duration == FLOAT_ZERO:
+            ts.flux = FLOAT_ZERO
         ts.number = number
         number += 1
         prev_irradiation_time, prev_cooling_time = (
@@ -104,7 +107,7 @@ def meta_info(self) -> RunDataCorrected:
         )
 
     @classmethod
-    def from_json(cls, json_dict: dict[str, Any]) -> "Inventory":
+    def from_json(cls, json_dict: dict[str, Any]) -> Inventory:
         """Construct Inventory instance from JSON dictionary.
 
         Args:
diff --git a/src/xpypact/Nuclide.py b/src/xpypact/nuclide.py
similarity index 91%
rename from src/xpypact/Nuclide.py
rename to src/xpypact/nuclide.py
index 1b0faff..caaec6c 100644
--- a/src/xpypact/Nuclide.py
+++ b/src/xpypact/nuclide.py
@@ -5,6 +5,8 @@
 
 from dataclasses import dataclass
 
+FLOAT_ZERO = 0.0
+
 try:
     from scipy.constants import Avogadro
 except ImportError:  # pragma: no cover
@@ -44,9 +46,9 @@ def __post_init__(self) -> None:
         _z = z(self.element)
         if self.zai == 0:
             self.zai = _z * 10000 + self.isotope * 10
-            if self.state != "":
+            if self.state:
                 self.zai += 1
-        if self.atoms == 0.0 and 0.0 < self.grams:
+        if self.atoms == FLOAT_ZERO and FLOAT_ZERO < self.grams:
             self.atoms = Avogadro * self.grams / get_nuclide_mass(_z, self.isotope)
 
     @property
@@ -59,7 +61,7 @@ def a(self) -> int:
         return self.isotope
 
     @classmethod
-    def from_json(cls, json_dict: dict[str, Any]) -> "Nuclide":
+    def from_json(cls, json_dict: dict[str, Any]) -> Nuclide:
         """Construct the Nuclide from JSON dictionary.
 
         Args:
diff --git a/src/xpypact/RunData.py b/src/xpypact/run_data.py
similarity index 87%
rename from src/xpypact/RunData.py
rename to src/xpypact/run_data.py
index 06003b9..c32ceea 100644
--- a/src/xpypact/RunData.py
+++ b/src/xpypact/run_data.py
@@ -13,7 +13,7 @@ class RunData:
     flux_name: str
 
     @classmethod
-    def from_json(cls, json_dict: dict[str, str]) -> "RunData":
+    def from_json(cls, json_dict: dict[str, str]) -> RunData:
         """Construct RunData instance from JSON.
 
         Args:
diff --git a/src/xpypact/TimeStep.py b/src/xpypact/time_step.py
similarity index 87%
rename from src/xpypact/TimeStep.py
rename to src/xpypact/time_step.py
index 4d2da25..7cc3340 100644
--- a/src/xpypact/TimeStep.py
+++ b/src/xpypact/time_step.py
@@ -1,15 +1,17 @@
 """Classes to read a FISPACT time step attributes from JSON."""
 from __future__ import annotations
 
-from typing import Any, Optional
+from typing import Any
 
 from dataclasses import dataclass, field
 
 import numpy as np
 
-from xpypact.Nuclide import Nuclide
+from xpypact.nuclide import Nuclide
 from xpypact.utils.types import NDArrayFloat
 
+FLOAT_ZERO = 0.0
+
 
 @dataclass
 class DoseRate:
@@ -23,14 +25,14 @@ class DoseRate:
         mass: mass for point source, always 1g
     """
 
-    type: str = ""
+    type: str = ""  # noqa: A003
     distance: float = 0.0
     mass: float = 0.0
     dose: float = 0.0
 
     def __post_init__(self) -> None:
         """Correct wrong value coming from FISPACT."""
-        if self.mass == 0.0:
+        if self.mass == FLOAT_ZERO:
             # According to FISPACT manual (both v.4 and v.5 (p.63))
             # should be 1 gram always, but FISPACT shows 0 at the first step
             # and less, than 1 in the following steps. Fixing here.
@@ -52,7 +54,7 @@ class GammaSpectrum:
     intensities: NDArrayFloat
 
     @classmethod
-    def from_json(cls, json: dict[str, list[float]]) -> "GammaSpectrum":
+    def from_json(cls, json: dict[str, list[float]]) -> GammaSpectrum:
         """Construct GammaSpectrum instance from JSON dictionary.
 
         Args:
@@ -95,22 +97,22 @@ class TimeStep:  # pylint: disable=too-many-instance-attributes
     inhalation_dose: float = 0.0
     dose_rate: DoseRate = field(default_factory=DoseRate)
     nuclides: list[Nuclide] = field(default_factory=list)
-    gamma_spectrum: Optional[GammaSpectrum] = None
+    gamma_spectrum: GammaSpectrum | None = None
 
     def __post_init__(self) -> None:  # noqa: ignore[CAC001]
         """Correct data missed in FISPACT-4."""
         # workarounds for FISPACT v.4
-        if self.total_mass == 0.0:
+        if self.total_mass == FLOAT_ZERO:
             self.total_mass = 1e-3 * sum(n.grams for n in self.nuclides)
-        if self.total_atoms == 0.0:
+        if self.total_atoms == FLOAT_ZERO:
             self.total_atoms = sum(n.atoms for n in self.nuclides)
-        if self.total_activity == 0.0:
+        if self.total_activity == FLOAT_ZERO:
             self.total_activity = sum(n.activity for n in self.nuclides)
-        if self.alpha_activity == 0.0:
+        if self.alpha_activity == FLOAT_ZERO:
             self.alpha_activity = sum(n.alpha_activity for n in self.nuclides)
-        if self.beta_activity == 0.0:
+        if self.beta_activity == FLOAT_ZERO:
             self.beta_activity = sum(n.beta_activity for n in self.nuclides)
-        if self.gamma_activity == 0.0:
+        if self.gamma_activity == FLOAT_ZERO:
             self.gamma_activity = sum(n.gamma_activity for n in self.nuclides)
 
     @property
@@ -129,10 +131,10 @@ def is_cooling(self) -> bool:
         Returns:
             Is the irradiation flux zero?
         """
-        return self.flux == 0.0
+        return self.flux == FLOAT_ZERO
 
     @classmethod
-    def from_json(cls, json_dict: dict[str, Any]) -> "TimeStep":
+    def from_json(cls, json_dict: dict[str, Any]) -> TimeStep:
         """Construct TimeStep instance from JSON dictionary.
 
         Args:
diff --git a/src/xpypact/utils/io.py b/src/xpypact/utils/io.py
index fe7278d..b88aa19 100644
--- a/src/xpypact/utils/io.py
+++ b/src/xpypact/utils/io.py
@@ -1,9 +1,12 @@
 """Output utilities."""
+from __future__ import annotations
 
-from typing import Any, Iterable, TextIO
+from typing import Any, TextIO
 
 import sys
 
+from collections.abc import Iterable
+
 
 def print_cols(
     seq: Iterable[Any], fid: TextIO = sys.stdout, max_columns: int = 6, fmt: str = "{}"
diff --git a/src/xpypact/utils/resource.py b/src/xpypact/utils/resource.py
index e14c534..d5b65f6 100644
--- a/src/xpypact/utils/resource.py
+++ b/src/xpypact/utils/resource.py
@@ -1,10 +1,9 @@
 """Utility methods to access a package data."""
 from __future__ import annotations
 
-from typing import Callable
-
 import sys
 
+from collections.abc import Callable
 from pathlib import Path
 
 if sys.version_info >= (3, 9):
@@ -21,6 +20,6 @@ def path_resolver(package: Package) -> Callable[[str], Path | Traversable]:
         package: the package below which the data is stored.
 
     Returns:
-        callable which appends the argument to the package folder adt returns as Path.
+        callable which appends the argument to the package folder as Path.
     """
     return files(package).joinpath
diff --git a/src/xpypact/utils/types.py b/src/xpypact/utils/types.py
index 49f19e9..6b62e7e 100644
--- a/src/xpypact/utils/types.py
+++ b/src/xpypact/utils/types.py
@@ -1,4 +1,6 @@
 """Utility types for the package."""
+from __future__ import annotations
+
 from typing import Union
 
 import os
diff --git a/tests/conftest.py b/tests/conftest.py
index 54e35b0..4c4cf0c 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import os
 
 from pathlib import Path
@@ -17,8 +19,8 @@ def data() -> Path:
     return path_resolver("tests")("data")
 
 
-@pytest.fixture
-def cd_tmpdir(tmpdir):
+@pytest.fixture()
+def cd_tmpdir(tmpdir):  # noqa: PT004
     """Temporarily switch to temp directory.
 
     Args:
diff --git a/tests/test_data_arrays.py b/tests/test_data_arrays.py
index a4221b5..df59614 100644
--- a/tests/test_data_arrays.py
+++ b/tests/test_data_arrays.py
@@ -15,8 +15,7 @@
 import xarray as xr
 import xpypact.data_arrays as da
 
-from pytest import approx
-from xpypact.Inventory import Inventory, from_json
+from xpypact.inventory import Inventory, from_json
 
 
 @pytest.fixture(scope="module")
@@ -41,9 +40,9 @@ def test_first_time_step(ds):
     ts = ts.isel(nuclide=(ts.nuclide_atoms > 0.0))
     assert ts.nuclide.size == 2, "Only Ag107 and Ag109 present before irradiation"
     assert ts.nuclide_grams.units == "g"
-    assert ts.nuclide_grams.sum().item() == approx(1.0, rel=1e-3), "Expected 1g mass"
+    assert ts.nuclide_grams.sum().item() == pytest.approx(1.0, rel=1e-3), "Expected 1g mass"
     assert ts.total_mass.units == "kg"
-    assert ts.total_mass == approx(1e-3, rel=1e-3), "Total mass is to be about 0.001kg"
+    assert ts.total_mass == pytest.approx(1e-3, rel=1e-3), "Total mass is to be about 0.001kg"
 
 
 def test_elapsed_time(ds: xr.Dataset, inventory: Inventory) -> None:
@@ -78,7 +77,9 @@ def test_atomic_masses_column(ds: xr.Dataset) -> None:
     argentum = ds.sel(nuclide=("Ag", 111, ""))
     assert argentum.element == "Ag"
     a = argentum.a
-    assert a.item() == approx(110.905, rel=1e-4), " the Ag atomic mass is to be about 110.905"
+    assert a.item() == pytest.approx(
+        110.905, rel=1e-4
+    ), " the Ag atomic mass is to be about 110.905"
 
 
 def test_scale_by_mass(ds):
@@ -171,7 +172,7 @@ def test_inventory_with_gamma(data):
     with bz2.open(data / "with-gamma.json.bz2") as fid:
         ds = da.from_json(fid.read().decode("utf-8"))
         assert ds.gamma is not None
-        assert ds.gamma.sel(time_step_number=2, gamma_boundaries=1.0).item() == approx(
+        assert ds.gamma.sel(time_step_number=2, gamma_boundaries=1.0).item() == pytest.approx(
             17857.24443195
         )
 
diff --git a/tests/test_Fluxes.py b/tests/test_fluxes.py
similarity index 90%
rename from tests/test_Fluxes.py
rename to tests/test_fluxes.py
index b901143..fafe5e1 100644
--- a/tests/test_Fluxes.py
+++ b/tests/test_fluxes.py
@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 from typing import Any
 
 from copy import copy, deepcopy
@@ -10,7 +12,7 @@
 
 import pytest
 
-from xpypact.Fluxes import (
+from xpypact.fluxes import (
     Fluxes,
     StandardFluxesDataSizeError,
     are_fluxes_close,
@@ -45,7 +47,7 @@ def test_flux_constructor():
     assert flux.norm == 2.0
     assert not is_709_fluxes(flux)
     assert are_fluxes_close(flux, flux)
-    with pytest.raises(ValueError) as exc_info:
+    with pytest.raises(ValueError, match="Incompatible sizes of bins and fluxes") as exc_info:
         Fluxes(ebins[:-2], bins, "test")
     assert exc_info.type == ValueError
     assert exc_info.value.args[0].startswith("Incompatible sizes of bins and fluxes")
@@ -59,7 +61,7 @@ def test_flux_constructor():
 
 
 @pytest.mark.parametrize(
-    "_bin, expected_e0, expected_e1,expected_flux",
+    ["_bin", "expected_e0", "expected_e1", "expected_flux"],
     [
         (0, 1e-5, 1e6, 1),
         (1, 1e6, 1e7, 90),
@@ -93,7 +95,7 @@ def assert_one(_: Any, f: Any) -> Any:
 
 
 @pytest.mark.parametrize(
-    "_bin, expected_e0, expected_e1,expected_flux",
+    ["_bin", "expected_e0", "expected_e1", "expected_flux"],
     [
         (0, 1.1e-5, 0.25, 3.600000e05),
         (6, 7.800000e06, 1.410000e07, 2.870000e03),
@@ -114,7 +116,7 @@ def fluxes_1(data):
 
 
 @pytest.mark.parametrize(
-    "_bin, expected_e0, expected_e1,expected_flux",
+    ["_bin", "expected_e0", "expected_e1", "expected_flux"],
     [
         (0, 1e-5, 1.0471e-5, 1.8182e-3),
         (1, 1.0471e-5, 1.0965e-5, 1.8182e-3),
@@ -154,14 +156,15 @@ def test_print_arbitrary_fluxes(data, arb_flux_1):
 
 def test_define_arb_flux_fail():
     data = np.linspace(1, 10, 4)
-    with pytest.raises(ValueError):
+    with pytest.raises(
+        ValueError, match="The number of float values from arb_flux file should be odd."
+    ):
         define_arb_bins_and_fluxes(data)
 
 
 def test_print_709_fluxes_fail(arb_flux_1):
-    with pytest.raises(ValueError) as exc_info:
-        stream = StringIO()
-        print_709_fluxes(arb_flux_1, stream, max_columns=3)
+    with pytest.raises(ValueError, match="Expected 709-group fluxes.") as exc_info:
+        print_709_fluxes(arb_flux_1, StringIO(), max_columns=3)
     assert str(exc_info.value) == "Expected 709-group fluxes."
 
 
diff --git a/tests/test_Inventory.py b/tests/test_inventory.py
similarity index 93%
rename from tests/test_Inventory.py
rename to tests/test_inventory.py
index d4f7575..30d3b3c 100644
--- a/tests/test_Inventory.py
+++ b/tests/test_inventory.py
@@ -1,11 +1,13 @@
 """Test loading Inventory from FISPACT JSON file."""
+from __future__ import annotations
+
 import bz2
 
 import pytest
 
-from xpypact.Inventory import Inventory, RunDataCorrected, from_json  # extract_times,
-from xpypact.RunData import RunData
-from xpypact.TimeStep import DoseRate, TimeStep
+from xpypact.inventory import Inventory, RunDataCorrected, from_json  # extract_times,
+from xpypact.run_data import RunData
+from xpypact.time_step import DoseRate, TimeStep
 
 SECONDS_PER_YEAR = int(365.24 * 24 * 3600)
 
diff --git a/tests/test_package.py b/tests/test_package.py
index d84e4f8..13f6600 100644
--- a/tests/test_package.py
+++ b/tests/test_package.py
@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import re
 import sys
 
@@ -16,8 +18,7 @@ def find_version_from_project_toml():
     toml_path = Path(__file__).parent.parent / "pyproject.toml"
     assert toml_path.exists()
     pyproject = tomllib.loads(toml_path.read_text())
-    version = pyproject["tool"]["poetry"]["version"]
-    return version
+    return pyproject["tool"]["poetry"]["version"]
 
 
 _VERSION_NORM_PATTERN = re.compile(r"-(?P.)[^.]*\.(?P.*)$")
diff --git a/tests/test_RunData.py b/tests/test_run_data.py
similarity index 86%
rename from tests/test_RunData.py
rename to tests/test_run_data.py
index af0b12b..8a78c4d 100644
--- a/tests/test_RunData.py
+++ b/tests/test_run_data.py
@@ -1,12 +1,13 @@
 """Tests for FISPACT header."""
+from __future__ import annotations
 
 import pytest
 
-from xpypact.RunData import RunData
+from xpypact.run_data import RunData
 
 
 @pytest.mark.parametrize(
-    "inp, expected",
+    ["inp", "expected"],
     [
         (
             {
diff --git a/tests/utils/test_resource.py b/tests/utils/test_resource.py
index 5abcd67..5df5a80 100644
--- a/tests/utils/test_resource.py
+++ b/tests/utils/test_resource.py
@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 from pathlib import Path
 
 import pytest
@@ -9,7 +11,7 @@
 
 # noinspection PyCompatibility
 @pytest.mark.parametrize(
-    "package, resource, expected",
+    ["package", "resource", "expected"],
     [
         ("tests", "data/Ag-1.json", "data/Ag-1.json"),
     ],
@@ -22,7 +24,7 @@ def test_path_resolver(package, resource, expected) -> None:
 
 
 @pytest.mark.parametrize(
-    "package, resource, expected",
+    ["package", "resource", "expected"],
     [
         ("tests", "data/not_existing", "tests/data/not_existing"),
         ("xpypact", "data/not_existing", "xpypact/data/not_existing"),
@@ -36,8 +38,7 @@ def test_path_resolver_when_resource_doesnt_exist(package, resource, expected) -
 
 def test_path_resolver_when_package_doesnt_exist() -> None:
     with pytest.raises(ModuleNotFoundError):
-        resolver = path_resolver("not_existing")
-        resolver("something.txt")
+        path_resolver("not_existing")("something.txt")
 
 
 def test_path_resolver_local() -> None:
diff --git a/tools/clear-prev-dist-info.py b/tools/clear-prev-dist-info.py
index f72f265..3a0a0f5 100755
--- a/tools/clear-prev-dist-info.py
+++ b/tools/clear-prev-dist-info.py
@@ -5,7 +5,9 @@
 Should be fixed in poetry 1.2, but it's not available yet.
 Run this if test_package() fails on pytest run.
 """
-from typing import Optional, TypeVar
+from __future__ import annotations
+
+from typing import TypeVar
 
 import shutil
 import site
@@ -22,7 +24,7 @@
 PathLike = TypeVar("PathLike", str, Path)
 
 
-def search_upwards_for_file(filename: PathLike) -> Optional[Path]:
+def search_upwards_for_file(filename: PathLike) -> Path | None:
     """Search upward from the current directory for a `filename`.
 
     Args:
@@ -54,7 +56,7 @@ def get_project_name() -> str:
     """
     pyproject_path = search_upwards_for_file("pyproject.toml")
     if pyproject_path is None:
-        raise EnvironmentError(
+        raise OSError(
             "Illegal directory: cannot find file pyproject.toml "
             f"from current directory: {Path.cwd()}"
         )

From 9e78ed0e1dbfcd0105998d8cd4782a890d04df85 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 29 Mar 2023 11:38:30 +0000
Subject: [PATCH 25/32] build(deps): bump pypa/gh-action-pypi-publish from
 1.7.1 to 1.8.3

Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.7.1 to 1.8.3.
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.7.1...v1.8.3)

---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] 
---
 .github/workflows/release.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 5439096..871fe84 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -71,14 +71,14 @@ jobs:
 
       - name: Publish package on PyPI
         if: steps.check-version.outputs.tag
-        uses: pypa/gh-action-pypi-publish@v1.8.1
+        uses: pypa/gh-action-pypi-publish@v1.8.3
         with:
           user: __token__
           password: ${{ secrets.PYPI_TOKEN }}
 
       - name: Publish package on TestPyPI
         if: "! steps.check-version.outputs.tag"
-        uses: pypa/gh-action-pypi-publish@v1.8.1
+        uses: pypa/gh-action-pypi-publish@v1.8.3
         with:
           user: __token__
           password: ${{ secrets.TEST_PYPI_TOKEN }}

From 8060d139cf0abf0a384c363d11e516d325473186 Mon Sep 17 00:00:00 2001
From: dvp 
Date: Wed, 29 Mar 2023 14:46:57 +0300
Subject: [PATCH 26/32] test: use ruff in precommit depdencies instead of
 flake8

---
 noxfile.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/noxfile.py b/noxfile.py
index ddce4d1..ca325fb 100644
--- a/noxfile.py
+++ b/noxfile.py
@@ -115,7 +115,7 @@ def precommit(s: Session) -> None:
         "install",
         "--no-root",
         "--only",
-        "pre_commit,style,isort,black,flake8",
+        "pre_commit,style,isort,black,ruff",
         external=True,
     )
     s.run("pre-commit", *args)

From 6e3b4fbad78cddb28c8ee742dedaed62029e71e4 Mon Sep 17 00:00:00 2001
From: dvp 
Date: Wed, 29 Mar 2023 14:48:46 +0300
Subject: [PATCH 27/32] docs: remove obsolete reference

---
 noxfile.py | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/noxfile.py b/noxfile.py
index ca325fb..b0e3bac 100644
--- a/noxfile.py
+++ b/noxfile.py
@@ -1,7 +1,4 @@
-"""Nox sessions.
-
-See `Cjolowicz's article `_
-"""
+"""Nox sessions."""
 from __future__ import annotations
 
 from typing import Final

From 1f51fc8f1cdc4591170f4ef1e72154933466909b Mon Sep 17 00:00:00 2001
From: dvp 
Date: Sun, 2 Apr 2023 15:26:19 +0300
Subject: [PATCH 28/32] feat: implemented export to duckdb

---
 poetry.lock                              |  59 +-
 pyproject.toml                           |   1 +
 src/xpypact/__init__.py                  |  28 +
 src/xpypact/dao/__init__.py              |   6 +
 src/xpypact/dao/api.py                   |   6 +
 src/xpypact/dao/duckdb/__init__.py       |   6 +
 src/xpypact/dao/duckdb/create_schema.sql |  85 +++
 src/xpypact/dao/duckdb/implementation.py | 167 +++++
 src/xpypact/data_frames.py               | 190 ++++++
 tests/conftest.py                        |  16 +
 tests/data/Ag-with-gamma.json            | 797 +++++++++++++++++++++++
 tests/test_data_arrays.py                |  14 +-
 tests/test_data_frames.py                |  69 ++
 tests/test_duckdb_dao.py                 |  54 ++
 14 files changed, 1488 insertions(+), 10 deletions(-)
 create mode 100644 src/xpypact/dao/__init__.py
 create mode 100644 src/xpypact/dao/api.py
 create mode 100644 src/xpypact/dao/duckdb/__init__.py
 create mode 100644 src/xpypact/dao/duckdb/create_schema.sql
 create mode 100644 src/xpypact/dao/duckdb/implementation.py
 create mode 100644 src/xpypact/data_frames.py
 create mode 100644 tests/data/Ag-with-gamma.json
 create mode 100644 tests/test_data_frames.py
 create mode 100644 tests/test_duckdb_dao.py

diff --git a/poetry.lock b/poetry.lock
index ee21036..90d01f2 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -687,6 +687,63 @@ toml = "*"
 conda = ["pyyaml"]
 pipenv = ["pipenv"]
 
+[[package]]
+name = "duckdb"
+version = "0.7.1"
+description = "DuckDB embedded database"
+category = "main"
+optional = false
+python-versions = "*"
+files = [
+    {file = "duckdb-0.7.1-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:3e0170be6cc315c179169dfa3e06485ef7009ef8ce399cd2908f29105ef2c67b"},
+    {file = "duckdb-0.7.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:6360d41023e726646507d5479ba60960989a09f04527b36abeef3643c61d8c48"},
+    {file = "duckdb-0.7.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:578c269d7aa27184e8d45421694f89deda3f41fe6bd2a8ce48b262b9fc975326"},
+    {file = "duckdb-0.7.1-cp310-cp310-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:36aae9a923c9f78da1cf3fcf75873f62d32ea017d4cef7c706d16d3eca527ca2"},
+    {file = "duckdb-0.7.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:630e0122a02f19bb1fafae00786350b2c31ae8422fce97c827bd3686e7c386af"},
+    {file = "duckdb-0.7.1-cp310-cp310-musllinux_1_1_i686.whl", hash = "sha256:9b9ca2d294725e523ce207bc37f28787478ae6f7a223e2cf3a213a2d498596c3"},
+    {file = "duckdb-0.7.1-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:0bd89f388205b6c99b62650169efe9a02933555ee1d46ddf79fbd0fb9e62652b"},
+    {file = "duckdb-0.7.1-cp310-cp310-win32.whl", hash = "sha256:a9e987565a268fd8da9f65e54621d28f39c13105b8aee34c96643074babe6d9c"},
+    {file = "duckdb-0.7.1-cp310-cp310-win_amd64.whl", hash = "sha256:5d986b5ad1307b069309f9707c0c5051323e29865aefa059eb6c3b22dc9751b6"},
+    {file = "duckdb-0.7.1-cp311-cp311-macosx_10_9_universal2.whl", hash = "sha256:54606dfd24d7181d3098030ca6858f6be52f3ccbf42fff05f7587f2d9cdf4343"},
+    {file = "duckdb-0.7.1-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:bd9367ae650b6605ffe00412183cf0edb688a5fc9fbb03ed757e8310e7ec3b6c"},
+    {file = "duckdb-0.7.1-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:aaf33aeb543c7816bd915cd10141866d54f92f698e1b5712de9d8b7076da19df"},
+    {file = "duckdb-0.7.1-cp311-cp311-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:2e56b0329c38c0356b40449917bab6fce6ac27d356257b9a9da613d2a0f064e0"},
+    {file = "duckdb-0.7.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:604b8b476d6cc6bf91625d8c2722ef9c50c402b3d64bc518c838d6c279e6d93b"},
+    {file = "duckdb-0.7.1-cp311-cp311-musllinux_1_1_i686.whl", hash = "sha256:32a268508c6d7fdc99d5442736051de74c28a5166c4cc3dcbbf35d383299b941"},
+    {file = "duckdb-0.7.1-cp311-cp311-musllinux_1_1_x86_64.whl", hash = "sha256:90794406fa2111414877ee9db154fef940911f3920c312c1cf69947621737c8d"},
+    {file = "duckdb-0.7.1-cp311-cp311-win32.whl", hash = "sha256:bf20c5ee62cbbf10b39ebdfd70d454ce914e70545c7cb6cb78cb5befef96328a"},
+    {file = "duckdb-0.7.1-cp311-cp311-win_amd64.whl", hash = "sha256:bb2700785cab37cd1e7a76c4547a5ab0f8a7c28ad3f3e4d02a8fae52be223090"},
+    {file = "duckdb-0.7.1-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:b09741cfa31388b8f9cdf5c5200e0995d55a5b54d2d1a75b54784e2f5c042f7f"},
+    {file = "duckdb-0.7.1-cp36-cp36m-win32.whl", hash = "sha256:766e6390f7ace7f1e322085c2ca5d0ad94767bde78a38d168253d2b0b4d5cd5c"},
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+    {file = "duckdb-0.7.1-cp39-cp39-win_amd64.whl", hash = "sha256:066885e1883464ce3b7d1fd844f9431227dcffe1ee39bfd2a05cd6d53f304557"},
+    {file = "duckdb-0.7.1.tar.gz", hash = "sha256:a7db6da0366b239ea1e4541fcc19556b286872f5015c9a54c2e347146e25a2ad"},
+]
+
 [[package]]
 name = "et-xmlfile"
 version = "1.1.0"
@@ -4020,4 +4077,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.8.1,<4.0"
-content-hash = "f27445064962e71a6f6142162cd36f44fa133f172a97a52420e8e6bf33e07775"
+content-hash = "d262cdfaa5f5ddb156180ea2302918b0743c171eb4fa5e6899f03f6c7ab3e4a3"
diff --git a/pyproject.toml b/pyproject.toml
index 9eb1475..4cc3c46 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -52,6 +52,7 @@ orjson = ">=3.6.7"
 pandas = ">=1.4.1"
 xarray = ">=2022.3.0"
 multipledispatch = ">=0.6.0"
+duckdb = "^0.7.1"
 
 [tool.poetry.group.dev.dependencies]
 Pygments = ">=2.10.0"
diff --git a/src/xpypact/__init__.py b/src/xpypact/__init__.py
index 1fda642..b0eb716 100644
--- a/src/xpypact/__init__.py
+++ b/src/xpypact/__init__.py
@@ -7,6 +7,15 @@
 from importlib import metadata as _meta
 from importlib.metadata import PackageNotFoundError, version
 
+from .data_arrays import from_json, scale_by_flux, scale_by_mass
+from .data_frames import (
+    get_gamma,
+    get_nuclides,
+    get_run_data,
+    get_time_steps,
+    get_timestep_nuclides,
+)
+
 try:
     __version__ = version(__name__)
 except PackageNotFoundError:  # pragma: no cover
@@ -19,3 +28,22 @@
 __license__ = __meta_data__["License"]
 __summary__ = __meta_data__["Summary"]
 __copyright__ = f"Copyright 2021 {__author__}"
+
+__all__ = [
+    "__version__",
+    "__distribution__",
+    "__meta_data__",
+    "__author__",
+    "__author_email__",
+    "__license__",
+    "__summary__",
+    "__copyright__",
+    "get_run_data",
+    "get_gamma",
+    "get_nuclides",
+    "get_timestep_nuclides",
+    "get_time_steps",
+    "from_json",
+    "scale_by_flux",
+    "scale_by_mass",
+]
diff --git a/src/xpypact/dao/__init__.py b/src/xpypact/dao/__init__.py
new file mode 100644
index 0000000..d6fd546
--- /dev/null
+++ b/src/xpypact/dao/__init__.py
@@ -0,0 +1,6 @@
+"""Interface and implementations of data access objects (DAO)."""
+from __future__ import annotations
+
+from .api import DataAccessInterface
+
+__all__ = ["DataAccessInterface"]
diff --git a/src/xpypact/dao/api.py b/src/xpypact/dao/api.py
new file mode 100644
index 0000000..aafbe92
--- /dev/null
+++ b/src/xpypact/dao/api.py
@@ -0,0 +1,6 @@
+"""Interface to data access facilities."""
+from __future__ import annotations
+
+
+class DataAccessInterface:
+    """Abstract DAO."""
diff --git a/src/xpypact/dao/duckdb/__init__.py b/src/xpypact/dao/duckdb/__init__.py
new file mode 100644
index 0000000..557463e
--- /dev/null
+++ b/src/xpypact/dao/duckdb/__init__.py
@@ -0,0 +1,6 @@
+"""DAO implementation for DuckDB."""
+from __future__ import annotations
+
+from .implementation import DuckDBDAO
+
+__all__ = ["DuckDBDAO"]
diff --git a/src/xpypact/dao/duckdb/create_schema.sql b/src/xpypact/dao/duckdb/create_schema.sql
new file mode 100644
index 0000000..206d646
--- /dev/null
+++ b/src/xpypact/dao/duckdb/create_schema.sql
@@ -0,0 +1,85 @@
+CREATE TABLE IF NOT EXISTS rundata (
+    material_id uinteger not null,
+    case_id varchar not null,
+    timestamp timestamp not null,
+    run_name varchar not null,
+    flux_name varchar NOT NULL,
+    dose_rate_type varchar NOT NULL,
+    dose_rate_distance real NOT NULL,
+    primary key(material_id, case_id)
+);
+
+CREATE TABLE IF NOT EXISTS timestep(
+    material_id  uinteger not null,
+    case_id      varchar not null,
+    time_step_number uinteger not null,
+    elapsed_time float4 not null,
+    irradiation_time float4 not null,
+    cooling_time float4 not null,
+    duration float4 not null,
+    flux float4 not null,
+    atoms float4 not null,
+    activity float4 not null,
+    alpha_activity float4 not null,
+    beta_activity float4 not null,
+    gamma_activity float4 not null,
+    mass float4 not null,
+    heat float4 not null,
+    alpha_heat float4 null,
+    beta_heat float4 not null,
+    gamma_heat float4 not null,
+    ingest1ion_dose float4 not null,
+    inhalation_dose float4 not null,
+    dose_rate float4 not null,
+    primary key(material_id, case_id, time_step_number),
+    foreign key(material_id, case_id) references rundata(material_id, case_id)
+);
+
+
+CREATE TABLE IF NOT EXISTS nuclide(
+    element varchar(2) not null,
+    mass_number usmallint not null check(0 < mass_number),
+    state varchar(1) not null,
+    zai integer not null check(10010 <= zai) unique,
+    half_life float4 not null check(0 <= half_life),
+    primary key(element, mass_number, state)
+);
+
+CREATE TABLE IF NOT EXISTS timestep_nuclide(
+    material_id  uinteger not null,
+    case_id      varchar not null,
+    time_step_number uinteger not null,
+    element varchar(2) not null,
+    mass_number usmallint not null,
+
+    state varchar(1) not null,
+    atoms float4 not null,
+    grams float4 not null,
+    activity float4 not null,
+    alpha_activity float4 not null,
+
+    beta_activity float4 not null,
+    gamma_activity float4 not null,
+    heat float4 not null,
+    alpha_heat float4 not null,
+    beta_heat float4 not null,
+
+    gamma_heat float4 not null,
+    dose float4 not null,
+    ingestion float4 not null,
+    inhalation float4 not null,
+
+    primary key(material_id, case_id, time_step_number, element, mass_number, state),
+    foreign key(material_id, case_id, time_step_number) references timestep(material_id, case_id, time_step_number),
+    foreign key(element, mass_number, state) references nuclide(element, mass_number, state)
+);
+
+CREATE TABLE IF NOT EXISTS timestep_gamma(
+    material_id  uinteger not null,
+    case_id      varchar not null,
+    time_step_number uinteger not null,
+    boundary real not null check(0 <= boundary),
+    rate real not null,
+    primary key(material_id, case_id, time_step_number, boundary),
+    foreign key(material_id, case_id, time_step_number) references timestep(material_id, case_id, time_step_number),
+);
diff --git a/src/xpypact/dao/duckdb/implementation.py b/src/xpypact/dao/duckdb/implementation.py
new file mode 100644
index 0000000..ea40b41
--- /dev/null
+++ b/src/xpypact/dao/duckdb/implementation.py
@@ -0,0 +1,167 @@
+"""Code to implement DuckDB DAO."""
+from __future__ import annotations
+
+from dataclasses import dataclass, field
+from pathlib import Path
+
+import duckdb as db
+import pandas as pd
+import xarray as xr
+
+from xpypact import get_gamma, get_nuclides, get_run_data, get_time_steps, get_timestep_nuclides
+from xpypact.utils.resource import path_resolver
+
+from ...dao import DataAccessInterface
+
+
+# noinspection SqlNoDataSourceInspection
+@dataclass
+class DuckDBDAO(DataAccessInterface):
+    """Implementation of DataAccessInterface for DuckDB."""
+
+    path: Path | None = None
+    read_only: bool = False
+    config: dict | None = None
+    con: db.DuckDBPyConnection = field(init=False)
+
+    def __enter__(self):
+        if self.path is not None:
+            self.path.parent.mkdir(parents=True, exist_ok=True)
+        database_name = str(self.path) if self.path else ":memory:"
+        # duckdb.connect(... config=None) - doesn't work
+        if self.config is None:
+            self.con = db.connect(database_name, self.read_only)
+        else:
+            self.con = db.connect(database_name, self.read_only, self.config)
+        if not self.read_only:
+            self.create_schema()
+        return self
+
+    def __exit__(self, exc_type, exc_val, exc_tb):
+        self.con.close()
+
+    def get_tables_info(self):
+        """Get information on tables in schema."""
+        return self.con.execute("select * from information_schema.tables").df()
+
+    def create_schema(self) -> None:
+        """Create tables to store xpypact dataset.
+
+        Retain existing tables.
+        """
+        sql_path: Path = path_resolver(__package__)("create_schema.sql")
+        sql = sql_path.read_text(encoding="utf-8")
+        self.con.execute(sql)
+
+    def drop_schema(self):
+        """Drop our DB objects."""
+        tables = [
+            "timestep_nuclide",
+            "timestep_gamma",
+            "timestep",
+            "nuclide",
+            "rundata",
+        ]
+        for table in tables:
+            self.con.execute(f"drop table if exists {table}")
+
+    def save(self, ds: xr.Dataset, material_id=1, case_id="") -> None:
+        """Save xpypact dataset to database.
+
+        Args:
+            ds: xpypact dataset to save
+            material_id: additional key to distinguish multiple FISPACT run
+            case_id: second additional key
+        """
+        self._save_run_data(ds, material_id, case_id)
+        self._save_nuclides(ds)
+        self._save_time_steps(ds)
+        self._save_time_step_nuclides(ds)
+        self._save_gamma(ds)
+
+    def load_rundata(self) -> pd.DataFrame:
+        """Load FISPACT run data as table.
+
+        Returns:
+            FISPACT run data
+        """
+        return self.con.execute("select * from rundata").df()
+
+    def load_nuclides(self) -> pd.DataFrame:
+        """Load nuclide table.
+
+        Returns:
+            time nuclide
+        """
+        return self.con.execute("select * from nuclide").df()
+
+    def load_time_steps(self) -> pd.DataFrame:
+        """Load time step table.
+
+        Returns:
+            time step table
+        """
+        return self.con.execute("select * from timestep").df()
+
+    def load_time_step_nuclides(self) -> pd.DataFrame:
+        """Load time step x nuclides table.
+
+        Returns:
+            time step x nuclides table
+        """
+        return self.con.execute("select * from timestep_nuclide").df()
+
+    def load_gamma(self, time_step_number: int = None) -> pd.DataFrame:
+        """Load time step x gamma table.
+
+        Args:
+            time_step_number: filter for time_step_number
+
+        Returns:
+            time step x gamma table
+        """
+        sql = "select * from timestep_gamma"
+        if time_step_number is not None:
+            sql += f" where time_step_number == {time_step_number}"
+        return self.con.execute(sql).df()
+
+    def _save_run_data(self, ds: xr.Dataset, material_id=1, case_id=""):
+        _table = get_run_data(ds)
+        _table = _add_material_and_case_columns(_table, material_id, case_id)
+        self.con.execute("insert into rundata from _table")
+        self.con.commit()
+
+    def _save_nuclides(self, ds: xr.Dataset):
+        _table = get_nuclides(ds)  # noqa: F841 - used below
+        sql = "insert or ignore into nuclide select * from _table"
+        self.con.execute(sql)
+        self.con.commit()
+
+    def _save_time_steps(self, ds: xr.Dataset, material_id=1, case_id=""):
+        _table = get_time_steps(ds)
+        _table = _add_material_and_case_columns(_table, material_id, case_id)
+        self.con.execute("insert into timestep from _table")
+        self.con.commit()
+
+    def _save_time_step_nuclides(self, ds: xr.Dataset, material_id=1, case_id=""):
+        _table = get_timestep_nuclides(ds)
+        _table = _add_material_and_case_columns(_table, material_id, case_id)
+        self.con.execute("insert into timestep_nuclide from _table")
+        self.con.commit()
+
+    def _save_gamma(self, ds: xr.Dataset, material_id=1, case_id=""):
+        _table = get_gamma(ds)
+        _table = _add_material_and_case_columns(_table, material_id, case_id)
+        self.con.execute("insert into timestep_gamma from _table")
+        self.con.commit()
+
+
+def _add_material_and_case_columns(
+    table: pd.DataFrame, material_id: int, case_id: str
+) -> pd.DataFrame:
+    columns = table.columns.values
+    table["material_id"] = material_id
+    table["case_id"] = case_id
+    new_columns = ["material_id", "case_id"]
+    new_columns.extend(columns)
+    return table[new_columns]
diff --git a/src/xpypact/data_frames.py b/src/xpypact/data_frames.py
new file mode 100644
index 0000000..b6a5a3b
--- /dev/null
+++ b/src/xpypact/data_frames.py
@@ -0,0 +1,190 @@
+"""Export xpypact dataset to pandas dataframes.
+
+This can be used to store the data in databases or parquet datasets.
+"""
+from __future__ import annotations
+
+import pandas as pd
+
+from xarray import Dataset
+
+
+def get_run_data(ds: Dataset) -> pd.DataFrame:
+    """Extract FISPACT run data as dataframe.
+
+    Args:
+        ds: xpypact dataset loaded from FISPACT output JSON file
+
+    Returns:
+        pd.DataFrame: one row table with the run data
+    """
+    return pd.DataFrame.from_dict(
+        {
+            "timestamp": ds.timestamp,
+            "run_name": ds.attrs["run_name"],
+            "flux_name": ds.attrs["flux_name"],
+            "dose_rate_type": ds.attrs["dose_rate_type"],
+            "dose_rate_distance": ds.attrs["dose_rate_distance"],
+        }
+    )
+
+
+def get_time_steps(ds: Dataset) -> pd.DataFrame:
+    """Extract time steps table from xpypact dataset.
+
+    Drops "total_" prefix from column names.
+
+    Args:
+        ds: xpypact dataset to extract from
+
+    Returns:
+        Time step totals table.
+    """
+    return (
+        ds[
+            [
+                "time_step_number",
+                "elapsed_time",
+                "irradiation_time",
+                "cooling_time",
+                "duration",
+                "flux",
+                "total_atoms",
+                "total_activity",
+                "total_alpha_activity",
+                "total_beta_activity",
+                "total_gamma_activity",
+                "total_mass",
+                "total_heat",
+                "total_alpha_heat",
+                "total_beta_heat",
+                "total_gamma_heat",
+                "total_ingest1ion_dose",
+                "total_inhalation_dose",
+                "total_dose_rate",
+            ]
+        ]
+        .to_dataframe()
+        .reset_index()
+        .rename(
+            columns={
+                "total_atoms": "atoms",
+                "total_activity": "activity",
+                "total_alpha_activity": "alpha_activity",
+                "total_beta_activity": "beta_activity",
+                "total_gamma_activity": "gamma_activity",
+                "total_mass": "mass",
+                "total_heat": "heat",
+                "total_alpha_heat": "alpha_heat",
+                "total_beta_heat": "beta_heat",
+                "total_gamma_heat": "gamma_heat",
+                "total_ingest1ion_dose": "ingest1ion_dose",
+                "total_inhalation_dose": "inhalation_dose",
+                "total_dose_rate": "dose_rate",
+            }
+        )
+    )
+
+
+def get_nuclides(ds: Dataset) -> pd.DataFrame:
+    """Extract nuclides table from xpypact dataset.
+
+    Sets 'half_life' column name instead 'nuclide_half_life'.
+
+    Args:
+        ds: xpypact dataset to extract from
+
+    Returns:
+        Nuclide table
+    """
+    columns_all = ["element", "mass_number", "state", "zai", "nuclide_half_life"]
+    columns = ["zai", "nuclide_half_life"]
+    return (
+        ds[columns]
+        .to_dataframe()[columns]
+        .reset_index()[columns_all]
+        .rename(columns={"nuclide_half_life": "half_life"})
+    )
+
+
+def get_timestep_nuclides(ds: Dataset) -> pd.DataFrame:
+    """Extract timestep X nuclides table from xpypact dataset.
+
+    Removes "nuclide_" prefix from column names.
+
+    Args:
+        ds: xpypact dataset to extract from
+
+    Returns:
+        Time step x Nuclide table
+    """
+    columns = [
+        "nuclide_atoms",
+        "nuclide_grams",
+        "nuclide_activity",
+        "nuclide_alpha_activity",
+        "nuclide_beta_activity",
+        "nuclide_gamma_activity",
+        "nuclide_heat",
+        "nuclide_alpha_heat",
+        "nuclide_beta_heat",
+        "nuclide_gamma_heat",
+        "nuclide_dose",
+        "nuclide_ingestion",
+        "nuclide_inhalation",
+    ]
+    columns_all = [
+        "time_step_number",
+        "element",
+        "mass_number",
+        "state",
+    ] + columns
+
+    return (
+        ds[columns]
+        .to_dataframe()[columns]
+        .reset_index()[columns_all]
+        .fillna(0.0)
+        .rename(
+            columns={
+                "nuclide_atoms": "atoms",
+                "nuclide_grams": "grams",
+                "nuclide_activity": "activity",
+                "nuclide_alpha_activity": "alpha_activity",
+                "nuclide_beta_activity": "beta_activity",
+                "nuclide_gamma_activity": "gamma_activity",
+                "nuclide_heat": "heat",
+                "nuclide_alpha_heat": "alpha_heat",
+                "nuclide_beta_heat": "beta_heat",
+                "nuclide_gamma_heat": "gamma_heat",
+                "nuclide_dose": "dose",
+                "nuclide_ingestion": "ingestion",
+                "nuclide_inhalation": "inhalation",
+            }
+        )
+    )
+
+
+def get_gamma(ds: Dataset) -> pd.DataFrame | None:
+    """Extract timestep X gamma table from xpypact dataset.
+
+    Set column names to "boundary" and "rate".
+
+    Args:
+        ds: xpypact dataset to extract from
+
+    Returns:
+        Time step x gamma rate table
+    """
+    if "gamma" not in ds:
+        return None
+    columns = [
+        "time_step_number",
+        "gamma_boundaries",
+        "gamma",
+    ]
+    return (
+        ds.gamma.to_dataframe()
+        .reset_index()[columns]
+        .rename(columns={"gamma_boundaries": "boundary", "gamma": "rate"})
+    )
diff --git a/tests/conftest.py b/tests/conftest.py
index 4c4cf0c..3823a43 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,10 +1,12 @@
 from __future__ import annotations
 
+import bz2
 import os
 
 from pathlib import Path
 
 import pytest
+import xpypact.data_arrays as da
 
 from xpypact.utils.resource import path_resolver
 
@@ -34,3 +36,17 @@ def cd_tmpdir(tmpdir):  # noqa: PT004
         yield
     finally:
         os.chdir(old_dir)
+
+
+@pytest.fixture()
+def dataset_with_gamma(data):
+    """Load dataset with gamma information.
+
+    Args:
+        data: fixture - path to test data
+
+    Returns:
+        Dataset with gamma information.
+    """
+    with bz2.open(data / "with-gamma.json.bz2") as fid:
+        return da.from_json(fid.read().decode("utf-8"))
diff --git a/tests/data/Ag-with-gamma.json b/tests/data/Ag-with-gamma.json
new file mode 100644
index 0000000..c20259a
--- /dev/null
+++ b/tests/data/Ag-with-gamma.json
@@ -0,0 +1,797 @@
+{
+  "run_data": {
+    "timestamp": "23:01:19 12 July 2020",
+    "run_name": "* Material Ag, fluxes 1",
+    "flux_name": "55.F9.10 11-L2-02W HFS_GLRY_08_U"
+  },
+  "inventory_data": [
+    {
+      "irradiation_time": 0.0E+0,
+      "cooling_time": 0.0E+0,
+      "flux": 0.22204460492503131E-15,
+      "total_heat": 0.0E+0,
+      "alpha_heat": 0.0E+0,
+      "beta_heat": 0.0E+0,
+      "gamma_heat": 0.0E+0,
+      "ingestion_dose": 0.0E+0,
+      "inhalation_dose": 0.0E+0,
+      "dose_rate": {
+        "type": "",
+        "distance": 0.0E+0,
+        "mass": 0.0E+0,
+        "dose": 0.0E+0
+      },
+      "nuclides": [
+        {
+          "element": "Ag",
+          "isotope": 107,
+          "state": "",
+          "half_life": 0.0E+0,
+          "grams": 0.51331081722407967E+0,
+          "activity": 0.0E+0,
+          "heat": 0.0E+0,
+          "alpha_heat": 0.0E+0,
+          "beta_heat": 0.0E+0,
+          "gamma_heat": 0.0E+0,
+          "dose": 0.0E+0,
+          "ingestion": 0.0E+0,
+          "inhalation": 0.0E+0
+        },
+        {
+          "element": "Ag",
+          "isotope": 109,
+          "state": "",
+          "half_life": 0.0E+0,
+          "grams": 0.48580881498719353E+0,
+          "activity": 0.0E+0,
+          "heat": 0.0E+0,
+          "alpha_heat": 0.0E+0,
+          "beta_heat": 0.0E+0,
+          "gamma_heat": 0.0E+0,
+          "dose": 0.0E+0,
+          "ingestion": 0.0E+0,
+          "inhalation": 0.0E+0
+        }
+      ]
+    },
+    {
+      "irradiation_time": 0.631152E+8,
+      "cooling_time": 0.0E+0,
+      "flux": 0.24452E+11,
+      "total_heat": 0.11030165034397161E-5,
+      "alpha_heat": 0.0E+0,
+      "beta_heat": 0.98949233746662077E-6,
+      "gamma_heat": 0.11352416597309523E-6,
+      "ingestion_dose": 0.54460209506958901E+0,
+      "inhalation_dose": 0.23233747877698998E+1,
+      "dose_rate": {
+        "type": "Point source",
+        "distance": 0.1E+1,
+        "mass": 0.99912027864633153E-3,
+        "dose": 0.91720603767081113E-4
+      },
+      "nuclides": [
+        {
+          "element": "H",
+          "isotope": 1,
+          "state": "",
+          "half_life": 0.0E+0,
+          "grams": 0.11468776343339874E-10,
+          "activity": 0.0E+0,
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+          "alpha_heat": 0.0E+0,
+          "beta_heat": 0.0E+0,
+          "gamma_heat": 0.0E+0,
+          "dose": 0.0E+0,
+          "ingestion": 0.0E+0,
+          "inhalation": 0.0E+0
+        },
+        {
+          "element": "H",
+          "isotope": 2,
+          "state": "",
+          "half_life": 0.0E+0,
+          "grams": 0.25119780426357819E-11,
+          "activity": 0.0E+0,
+          "heat": 0.0E+0,
+          "alpha_heat": 0.0E+0,
+          "beta_heat": 0.0E+0,
+          "gamma_heat": 0.0E+0,
+          "dose": 0.0E+0,
+          "ingestion": 0.0E+0,
+          "inhalation": 0.0E+0
+        },
+        {
+          "element": "H",
+          "isotope": 3,
+          "state": "",
+          "half_life": 0.389105E+9,
+          "grams": 0.61154162665727945E-12,
+          "activity": 0.21751901447801447E+3,
+          "heat": 0.19890508451476908E-15,
+          "alpha_heat": 0.0E+0,
+          "beta_heat": 0.19890508451476908E-15,
+          "gamma_heat": 0.0E+0,
+          "dose": 0.0E+0,
+          "ingestion": 0.91357987602394283E-8,
+          "inhalation": 0.56554942406295335E-7
+        },
+        {
+          "element": "He",
+          "isotope": 3,
+          "state": "",
+          "half_life": 0.0E+0,
+          "grams": 0.35721237859544966E-13,
+          "activity": 0.0E+0,
+          "heat": 0.0E+0,
+          "alpha_heat": 0.0E+0,
+          "beta_heat": 0.0E+0,
+          "gamma_heat": 0.0E+0,
+          "dose": 0.0E+0,
+          "ingestion": 0.0E+0,
+          "inhalation": 0.0E+0
+        },
+        {
+          "element": "He",
+          "isotope": 4,
+          "state": "",
+          "half_life": 0.0E+0,
+          "grams": 0.12570001773575198E-10,
+          "activity": 0.0E+0,
+          "heat": 0.0E+0,
+          "alpha_heat": 0.0E+0,
+          "beta_heat": 0.0E+0,
+          "gamma_heat": 0.0E+0,
+          "dose": 0.0E+0,
+          "ingestion": 0.0E+0,
+          "inhalation": 0.0E+0
+        },
+        {
+          "element": "Ru",
+          "isotope": 102,
+          "state": "",
+          "half_life": 0.0E+0,
+          "grams": 0.34983189029929211E-16,
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+          "inhalation": 0.0E+0
+        },
+        {
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+          "ingestion": 0.14469533622422684E-9,
+          "inhalation": 0.5946383692505783E-9
+        },
+        {
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+          "inhalation": 0.0E+0
+        },
+        {
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+          "ingestion": 0.55270123294340411E-11,
+          "inhalation": 0.36138156848736712E-10
+        },
+        {
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+          "heat": 0.93334328316713467E-12,
+          "alpha_heat": 0.0E+0,
+          "beta_heat": 0.33793493233943999E-13,
+          "gamma_heat": 0.89954978993319077E-12,
+          "dose": 0.81006482658430914E-9,
+          "ingestion": 0.49751094120993204E-5,
+          "inhalation": 0.85741251565658307E-5
+        },
+        {
+          "element": "Ag",
+          "isotope": 105,
+          "state": "m",
+          "half_life": 0.43380000000000001E+3,
+          "grams": 0.88840159621411246E-15,
+          "activity": 0.81488270636557409E+4,
+          "heat": 0.34676243773644742E-13,
+          "alpha_heat": 0.0E+0,
+          "beta_heat": 0.33082240902939207E-13,
+          "gamma_heat": 0.15940028707055333E-14,
+          "dose": 0.38122859413734422E-11,
+          "ingestion": 0.2607624614610379E-8,
+          "inhalation": 0.22001833514054075E-8
+        },
+        {
+          "element": "Ag",
+          "isotope": 106,
+          "state": "",
+          "half_life": 0.144E+4,
+          "grams": 0.25623373600250572E-12,
+          "activity": 0.70133653490005806E+6,
+          "heat": 0.13590704348967376E-9,
+          "alpha_heat": 0.0E+0,
+          "beta_heat": 0.56578886814995987E-10,
+          "gamma_heat": 0.79328156674677776E-10,
+          "dose": 0.68125282717686622E-7,
+          "ingestion": 0.2244276902712498E-4,
+          "inhalation": 0.1122138451356249E-4
+        },
+        {
+          "element": "Ag",
+          "isotope": 106,
+          "state": "m",
+          "half_life": 0.730944E+6,
+          "grams": 0.10051383627008998E-9,
+          "activity": 0.54199388899810566E+6,
+          "heat": 0.24025308516506763E-9,
+          "alpha_heat": 0.0E+0,
+          "beta_heat": 0.10658197883348133E-11,
+          "gamma_heat": 0.23918726537673284E-9,
+          "dose": 0.19452980153336471E-6,
+          "ingestion": 0.81299084059091218E-3,
+          "inhalation": 0.59619326705375971E-3
+        },
+        {
+          "element": "Ag",
+          "isotope": 107,
+          "state": "",
+          "half_life": 0.0E+0,
+          "grams": 0.51329420065723108E+0,
+          "activity": 0.0E+0,
+          "heat": 0.0E+0,
+          "alpha_heat": 0.0E+0,
+          "beta_heat": 0.0E+0,
+          "gamma_heat": 0.0E+0,
+          "dose": 0.0E+0,
+          "ingestion": 0.0E+0,
+          "inhalation": 0.0E+0
+        },
+        {
+          "element": "Ag",
+          "isotope": 107,
+          "state": "m",
+          "half_life": 0.44299999999999997E+2,
+          "grams": 0.660879448591702E-13,
+          "activity": 0.58249936752201235E+7,
+          "heat": 0.85773096274286314E-10,
+          "alpha_heat": 0.0E+0,
+          "beta_heat": 0.73894663405594378E-10,
+          "gamma_heat": 0.11878432868691933E-10,
+          "dose": 0.29753303272889411E-7,
+          "ingestion": 0.54172442794571284E-6,
+          "inhalation": 0.34949961438007276E-6
+        },
+        {
+          "element": "Ag",
+          "isotope": 108,
+          "state": "",
+          "half_life": 0.144E+3,
+          "grams": 0.53604771440652259E-10,
+          "activity": 0.14400313919500124E+10,
+          "heat": 0.1449731546271876E-6,
+          "alpha_heat": 0.0E+0,
+          "beta_heat": 0.1397069370170044E-6,
+          "gamma_heat": 0.5266217610183196E-8,
+          "dose": 0.43097570399810856E-5,
+          "ingestion": 0.86401882000791984E-4,
+          "inhalation": 0.54721190958031695E-4
+        },
+        {
+          "element": "Ag",
+          "isotope": 108,
+          "state": "m",
+          "half_life": 0.131911E+11,
+          "grams": 0.48618486571333499E-6,
+          "activity": 0.14257764140518595E+6,
+          "heat": 0.37602632648470844E-10,
+          "alpha_heat": 0.0E+0,
+          "beta_heat": 0.36643184732535899E-12,
+          "gamma_heat": 0.37236200801145486E-10,
+          "dose": 0.31746662995780599E-7,
+          "ingestion": 0.32792857070626361E-3,
+          "inhalation": 0.52753726619406398E-2
+        },
+        {
+          "element": "Ag",
+          "isotope": 109,
+          "state": "",
+          "half_life": 0.0E+0,
+          "grams": 0.48575518606565266E+0,
+          "activity": 0.0E+0,
+          "heat": 0.0E+0,
+          "alpha_heat": 0.0E+0,
+          "beta_heat": 0.0E+0,
+          "gamma_heat": 0.0E+0,
+          "dose": 0.0E+0,
+          "ingestion": 0.0E+0,
+          "inhalation": 0.0E+0
+        },
+        {
+          "element": "Ag",
+          "isotope": 109,
+          "state": "m",
+          "half_life": 0.39700000000000003E+2,
+          "grams": 0.58283960068471687E-13,
+          "activity": 0.56271566234365366E+7,
+          "heat": 0.79372851869381988E-10,
+          "alpha_heat": 0.0E+0,
+          "beta_heat": 0.6918691639319512E-10,
+          "gamma_heat": 0.1018593547618687E-10,
+          "dose": 0.27438457466793909E-7,
+          "ingestion": 0.45017252197514684E-6,
+          "inhalation": 0.28698498466571095E-6
+        },
+        {
+          "element": "Ag",
+          "isotope": 110,
+          "state": "",
+          "half_life": 0.24559999999999999E+2,
+          "grams": 0.28952987609614811E-10,
+          "activity": 0.44773339984219284E+10,
+          "heat": 0.86982623942326058E-6,
+          "alpha_heat": 0.0E+0,
+          "beta_heat": 0.84734570354017081E-6,
+          "gamma_heat": 0.22480535883089762E-7,
+          "dose": 0.18626136845818681E-4,
+          "ingestion": 0.30445871261786826E-2,
+          "inhalation": 0.19252536310458365E-2
+        },
+        {
+          "element": "Ag",
+          "isotope": 110,
+          "state": "m",
+          "half_life": 0.21581E+8,
+          "grams": 0.10964187218367905E-5,
+          "activity": 0.19295647152856052E+9,
+          "heat": 0.87629689879889588E-7,
+          "alpha_heat": 0.0E+0,
+          "beta_heat": 0.2233097849885987E-8,
+          "gamma_heat": 0.85396592030003597E-7,
+          "dose": 0.6843052221354352E-4,
+          "ingestion": 0.5402781221378381E+0,
+          "inhalation": 0.23154776785464328E+1
+        },
+        {
+          "element": "Ag",
+          "isotope": 111,
+          "state": "",
+          "half_life": 0.64368E+6,
+          "grams": 0.10471451900220665E-11,
+          "activity": 0.61229306518999847E+4,
+          "heat": 0.37022379971382907E-12,
+          "alpha_heat": 0.0E+0,
+          "beta_heat": 0.34424324931120938E-12,
+          "gamma_heat": 0.25980550402619689E-13,
+          "dose": 0.21307903061641942E-10,
+          "ingestion": 0.79598098262857418E-5,
+          "inhalation": 0.10408982289691157E-4
+        },
+        {
+          "element": "Ag",
+          "isotope": 111,
+          "state": "m",
+          "half_life": 0.64799999999999997E+2,
+          "grams": 0.1010031095388864E-15,
+          "activity": 0.58665421084955906E+4,
+          "heat": 0.59108494057051247E-13,
+          "alpha_heat": 0.0E+0,
+          "beta_heat": 0.52643521171169564E-13,
+          "gamma_heat": 0.64649728858816768E-14,
+          "dose": 0.1671967925860669E-10,
+          "ingestion": 0.12906392809737019E-8,
+          "inhalation": 0.13493046413993241E-8
+        },
+        {
+          "element": "Cd",
+          "isotope": 106,
+          "state": "",
+          "half_life": 0.20828000000000001E+27,
+          "grams": 0.38922197013032626E-10,
+          "activity": 0.73655032273496197E-15,
+          "heat": 0.32688315447555532E-30,
+          "alpha_heat": 0.0E+0,
+          "beta_heat": 0.32688315447555532E-30,
+          "gamma_heat": 0.0E+0,
+          "dose": 0.0E+0,
+          "ingestion": 0.3535441579976322E-22,
+          "inhalation": 0.11048255231810652E-21
+        },
+        {
+          "element": "Cd",
+          "isotope": 107,
+          "state": "",
+          "half_life": 0.23472E+5,
+          "grams": 0.19523358677244556E-15,
+          "activity": 0.32477102542653306E+2,
+          "heat": 0.14317397600348717E-15,
+          "alpha_heat": 0.0E+0,
+          "beta_heat": 0.32646370634266384E-16,
+          "gamma_heat": 0.11052760536922079E-15,
+          "dose": 0.30709031342403621E-12,
+          "ingestion": 0.20135804341068232E-8,
+          "inhalation": 0.26955995988620265E-8
+        },
+        {
+          "element": "Cd",
+          "isotope": 108,
+          "state": "",
+          "half_life": 0.129386E+26,
+          "grams": 0.15813025497622825E-4,
+          "activity": 0.47278839390078124E-8,
+          "heat": 0.2060343686886307E-24,
+          "alpha_heat": 0.0E+0,
+          "beta_heat": 0.2060343686886307E-24,
+          "gamma_heat": 0.0E+0,
+          "dose": 0.0E+0,
+          "ingestion": 0.2222105425231277E-16,
+          "inhalation": 0.70918256554511287E-16
+        },
+        {
+          "element": "Cd",
+          "isotope": 109,
+          "state": "",
+          "half_life": 0.399686E+8,
+          "grams": 0.59080382436402523E-11,
+          "activity": 0.56657162401414041E+3,
+          "heat": 0.18934283050730958E-14,
+          "alpha_heat": 0.0E+0,
+          "beta_heat": 0.51854453083456525E-15,
+          "gamma_heat": 0.13748837742385306E-14,
+          "dose": 0.46274824006278327E-11,
+          "ingestion": 0.11331432159808012E-5,
+          "inhalation": 0.45892300310124533E-5
+        },
+        {
+          "element": "Cd",
+          "isotope": 110,
+          "state": "",
+          "half_life": 0.0E+0,
+          "grams": 0.52852819343633571E-4,
+          "activity": 0.0E+0,
+          "heat": 0.0E+0,
+          "alpha_heat": 0.0E+0,
+          "beta_heat": 0.0E+0,
+          "gamma_heat": 0.0E+0,
+          "dose": 0.0E+0,
+          "ingestion": 0.0E+0,
+          "inhalation": 0.0E+0
+        },
+        {
+          "element": "Cd",
+          "isotope": 111,
+          "state": "",
+          "half_life": 0.0E+0,
+          "grams": 0.30241515766100312E-9,
+          "activity": 0.0E+0,
+          "heat": 0.0E+0,
+          "alpha_heat": 0.0E+0,
+          "beta_heat": 0.0E+0,
+          "gamma_heat": 0.0E+0,
+          "dose": 0.0E+0,
+          "ingestion": 0.0E+0,
+          "inhalation": 0.0E+0
+        },
+        {
+          "element": "Cd",
+          "isotope": 111,
+          "state": "m",
+          "half_life": 0.29244000000000001E+4,
+          "grams": 0.65830389339780975E-15,
+          "activity": 0.84726643488654486E+3,
+          "heat": 0.53792205630193643E-13,
+          "alpha_heat": 0.0E+0,
+          "beta_heat": 0.14877060433432532E-13,
+          "gamma_heat": 0.3891514519676111E-13,
+          "dose": 0.3325050339232257E-10,
+          "ingestion": 0.93199309669773339E-7,
+          "inhalation": 0.12708996399026879E-6
+        },
+        {
+          "element": "Cd",
+          "isotope": 112,
+          "state": "",
+          "half_life": 0.0E+0,
+          "grams": 0.69587465556908194E-15,
+          "activity": 0.0E+0,
+          "heat": 0.0E+0,
+          "alpha_heat": 0.0E+0,
+          "beta_heat": 0.0E+0,
+          "gamma_heat": 0.0E+0,
+          "dose": 0.0E+0,
+          "ingestion": 0.0E+0,
+          "inhalation": 0.0E+0
+        }
+      ]
+    }
+    ]
+}
\ No newline at end of file
diff --git a/tests/test_data_arrays.py b/tests/test_data_arrays.py
index df59614..7450099 100644
--- a/tests/test_data_arrays.py
+++ b/tests/test_data_arrays.py
@@ -2,8 +2,6 @@
 
 from typing import cast
 
-import bz2
-
 from copy import deepcopy
 
 import numpy as np
@@ -168,13 +166,11 @@ def test_net_cdf_writing_with_group_and_appending(cd_tmpdir, ds):
     assert actual.total_dose_rate.attrs["units"] == "Sv/h"
 
 
-def test_inventory_with_gamma(data):
-    with bz2.open(data / "with-gamma.json.bz2") as fid:
-        ds = da.from_json(fid.read().decode("utf-8"))
-        assert ds.gamma is not None
-        assert ds.gamma.sel(time_step_number=2, gamma_boundaries=1.0).item() == pytest.approx(
-            17857.24443195
-        )
+def test_inventory_with_gamma(dataset_with_gamma):
+    assert dataset_with_gamma.gamma is not None
+    assert dataset_with_gamma.gamma.sel(
+        time_step_number=2, gamma_boundaries=1.0
+    ).item() == pytest.approx(17857.24443195)
 
 
 if __name__ == "__main__":
diff --git a/tests/test_data_frames.py b/tests/test_data_frames.py
new file mode 100644
index 0000000..0637dfc
--- /dev/null
+++ b/tests/test_data_frames.py
@@ -0,0 +1,69 @@
+from __future__ import annotations
+
+import pandas as pd
+import pytest
+import xarray as xr
+import xpypact.data_arrays as da
+
+from xpypact.data_frames import (
+    get_gamma,
+    get_nuclides,
+    get_run_data,
+    get_time_steps,
+    get_timestep_nuclides,
+)
+from xpypact.inventory import Inventory, from_json
+
+
+@pytest.fixture(scope="module")
+def inventory(data) -> Inventory:
+    return from_json(data / "Ag-1.json")
+
+
+@pytest.fixture(scope="module")
+def ds(inventory: Inventory) -> xr.Dataset:
+    return da.create_dataset(inventory)
+
+
+def test_get_run_data(ds):
+    run_data = get_run_data(ds)
+    assert isinstance(run_data, pd.DataFrame)
+    assert run_data["timestamp"].item() == pd.Timestamp("2020-07-12 23:01:19")
+    assert run_data["run_name"].item() == "* Material Ag, fluxes 1"
+
+
+def test_get_time_steps(ds):
+    time_steps = get_time_steps(ds)
+    assert isinstance(time_steps, pd.DataFrame)
+    assert "time_step_number" in time_steps.columns
+    assert time_steps.iloc[1].flux == 0.24452e11
+    assert time_steps.iloc[1].heat == 1.103016503439716e-06, "Should have column 'heat'"
+
+
+def test_get_nuclides(ds):
+    nuclides = get_nuclides(ds)
+    nuclides = nuclides.set_index(["element", "mass_number", "state"])
+    assert nuclides.loc[("H", 1, "")].half_life == 0.0
+
+
+def test_get_timestep_nuclides(ds):
+    timestep_nuclides = get_timestep_nuclides(ds)
+    timestep_nuclides = timestep_nuclides.set_index(
+        ["time_step_number", "element", "mass_number", "state"]
+    )
+    assert timestep_nuclides.loc[2, "H", 1, ""].grams == 0.11468776343339874e-10
+
+
+def test_get_gamma_with_dataset_without_gamma(ds):
+    gamma = get_gamma(ds)
+    assert gamma is None
+
+
+def test_get_gamma_with_dataset_with_gamma(dataset_with_gamma):
+    gamma = get_gamma(dataset_with_gamma)
+    gamma = gamma.set_index(["time_step_number", "boundary"])
+    assert gamma.loc[2, 1.0].rate == pytest.approx(17857.24443195)
+
+
+if __name__ == "__main__":
+    pytest.main()
diff --git a/tests/test_duckdb_dao.py b/tests/test_duckdb_dao.py
new file mode 100644
index 0000000..e8182fe
--- /dev/null
+++ b/tests/test_duckdb_dao.py
@@ -0,0 +1,54 @@
+from __future__ import annotations
+
+import pandas as pd
+import pytest
+
+from duckdb import InvalidInputException
+from xpypact.dao.duckdb import DuckDBDAO as DataAccessObject
+
+
+def test_ddl(tmp_path):
+    with DataAccessObject(tmp_path / "test-ddl.duckdb") as dao:
+        tables = dao.get_tables_info()
+        assert 5 == len(tables)
+        table_names = tables["table_name"]
+        for name in ["rundata", "timestep", "nuclide", "timestep_nuclide", "timestep_gamma"]:
+            assert name in table_names.values
+        dao.drop_schema()
+        tables = dao.get_tables_info()
+        assert 0 == len(tables)
+        dao.create_schema()
+        tables = dao.get_tables_info()
+        assert 5 == len(tables)
+    with DataAccessObject(tmp_path / "test-ddl.duckdb", read_only=True) as dao:
+        tables = dao.get_tables_info()
+        assert 5 == len(tables)
+        with pytest.raises(InvalidInputException, match="Cannot execute statement"):
+            dao.drop_schema()
+
+
+def test_save(dataset_with_gamma):
+    with DataAccessObject(config={"default_null_order": "nulls_last"}) as dao:
+        dao.save(dataset_with_gamma)
+        run_data = dao.load_rundata()
+        assert run_data["timestamp"].item() == pd.Timestamp("2022-02-21 01:52:45")
+        assert run_data["run_name"].item() == "* Material Cu, fluxes 104_2_1_1"
+        nuclides = dao.load_nuclides()
+        nuclides = nuclides.set_index(["element", "mass_number", "state"])
+        assert not nuclides.loc["Cu"].empty
+        time_steps = dao.load_time_steps()
+        assert not time_steps.empty
+        time_steps = time_steps.set_index("time_step_number")
+        assert not time_steps.loc[2].empty
+        time_step_nuclides = dao.load_time_step_nuclides()
+        assert not time_step_nuclides.empty
+        time_step_nuclides = time_step_nuclides.set_index(
+            ["time_step_number", "element", "mass_number", "state"]
+        )
+        assert not time_step_nuclides.loc[2, "Cu"].empty
+        gamma = dao.load_gamma()
+        assert not gamma.empty
+        gamma = gamma.set_index(["time_step_number", "boundary"])
+        assert not gamma.loc[2, 1.0].empty
+        gamma2 = dao.load_gamma(2)
+        assert not gamma2.empty

From 8c8b483ff569d9acfbcf06d738f07c4a3d6e1095 Mon Sep 17 00:00:00 2001
From: dvp 
Date: Sun, 2 Apr 2023 15:26:52 +0300
Subject: [PATCH 29/32] bump: version xpypact 0.2.0

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 4cc3c46..fbccddf 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "xpypact"
-version = "0.1.12a0"
+version = "0.2.0"
 description = "\"Python tools to work with elements and isotopes\""
 authors = ["dvp "]
 license = "MIT"

From c3ff9d14adc21c7c8b9edd0e55d7e237b98001b1 Mon Sep 17 00:00:00 2001
From: dvp 
Date: Sun, 2 Apr 2023 17:22:39 +0300
Subject: [PATCH 30/32] style: more ruff linters

---
 poetry.lock                              | 44 ++++++------
 pyproject.toml                           | 79 ++++++++++++++--------
 src/xpypact/dao/api.py                   | 86 +++++++++++++++++++++++-
 src/xpypact/dao/duckdb/implementation.py | 24 ++++---
 src/xpypact/data_arrays.py               | 26 ++++---
 src/xpypact/data_frames.py               | 18 +++--
 src/xpypact/fluxes.py                    | 41 +++++------
 src/xpypact/inventory.py                 | 16 +++--
 src/xpypact/nuclide.py                   |  6 +-
 src/xpypact/time_step.py                 | 14 ++--
 src/xpypact/utils/io.py                  | 14 ++--
 src/xpypact/utils/resource.py            | 16 +++--
 src/xpypact/utils/types.py               |  1 -
 tests/conftest.py                        |  4 +-
 tests/test_data_arrays.py                | 16 +++--
 tests/test_data_frames.py                | 12 +++-
 tests/test_duckdb_dao.py                 | 17 +++--
 tests/test_fluxes.py                     |  7 +-
 tests/test_inventory.py                  |  7 +-
 tests/test_package.py                    |  2 +-
 tests/test_run_data.py                   |  2 +-
 tests/utils/test_resource.py             |  8 +--
 22 files changed, 306 insertions(+), 154 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 90d01f2..8710cd4 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1163,14 +1163,14 @@ flake8-simplify = ">=0.18.2"
 
 [[package]]
 name = "flake8-simplify"
-version = "0.19.3"
+version = "0.20.0"
 description = "flake8 plugin which checks for code that can be simplified"
 category = "dev"
 optional = false
 python-versions = ">=3.6.1"
 files = [
-    {file = "flake8_simplify-0.19.3-py3-none-any.whl", hash = "sha256:1057320e9312d75849541fee822900d27bcad05b2405edc84713affee635629e"},
-    {file = "flake8_simplify-0.19.3.tar.gz", hash = "sha256:2fb083bf5142a98d9c9554755cf2f56f8926eb4a33eae30c0809041b1546879e"},
+    {file = "flake8_simplify-0.20.0-py3-none-any.whl", hash = "sha256:599a47824726c93fadcf0274e569daed45052e38cd906360d9080eaa3bd76d61"},
+    {file = "flake8_simplify-0.20.0.tar.gz", hash = "sha256:7b8796bbea8aed45f56621c389d0556cc86f0afa5d992581139451240a8fbeca"},
 ]
 
 [package.dependencies]
@@ -3244,29 +3244,29 @@ files = [
 
 [[package]]
 name = "ruff"
-version = "0.0.259"
+version = "0.0.260"
 description = "An extremely fast Python linter, written in Rust."
 category = "dev"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "ruff-0.0.259-py3-none-macosx_10_7_x86_64.whl", hash = "sha256:f3938dc45e2a3f818e9cbd53007265c22246fbfded8837b2c563bf0ebde1a226"},
-    {file = "ruff-0.0.259-py3-none-macosx_10_9_x86_64.macosx_11_0_arm64.macosx_10_9_universal2.whl", hash = "sha256:22e1e35bf5f12072cd644d22afd9203641ccf258bc14ff91aa1c43dc14f6047d"},
-    {file = "ruff-0.0.259-py3-none-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:d2fb20e89e85d147c85caa807707a1488bccc1f3854dc3d53533e89b52a0c5ff"},
-    {file = "ruff-0.0.259-py3-none-manylinux_2_17_armv7l.manylinux2014_armv7l.whl", hash = "sha256:49e903bcda19f6bb0725a962c058eb5d61f40d84ef52ed53b61939b69402ab4e"},
-    {file = "ruff-0.0.259-py3-none-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:71f0ef1985e9a6696fa97da8459917fa34bdaa2c16bd33bd5edead585b7d44f7"},
-    {file = "ruff-0.0.259-py3-none-manylinux_2_17_ppc64.manylinux2014_ppc64.whl", hash = "sha256:7cfef26619cba184d59aa7fa17b48af5891d51fc0b755a9bc533478a10d4d066"},
-    {file = "ruff-0.0.259-py3-none-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:79b02fa17ec1fd8d306ae302cb47fb614b71e1f539997858243769bcbe78c6d9"},
-    {file = "ruff-0.0.259-py3-none-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:428507fb321b386dda70d66cd1a8aa0abf51d7c197983d83bb9e4fa5ee60300b"},
-    {file = "ruff-0.0.259-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:c5fbaea9167f1852757f02133e5daacdb8c75b3431343205395da5b10499927a"},
-    {file = "ruff-0.0.259-py3-none-musllinux_1_2_aarch64.whl", hash = "sha256:40ae87f2638484b7e8a7567b04a7af719f1c484c5bf132038b702bb32e1f6577"},
-    {file = "ruff-0.0.259-py3-none-musllinux_1_2_armv7l.whl", hash = "sha256:29e2b77b7d5da6a7dd5cf9b738b511355c5734ece56f78e500d4b5bffd58c1a0"},
-    {file = "ruff-0.0.259-py3-none-musllinux_1_2_i686.whl", hash = "sha256:5b3c1beacf6037e7f0781d4699d9a2dd4ba2462f475be5b1f45cf84c4ba3c69d"},
-    {file = "ruff-0.0.259-py3-none-musllinux_1_2_x86_64.whl", hash = "sha256:daaea322e7e85f4c13d82be9536309e1c4b8b9851bb0cbc7eeb15d490fd46bf9"},
-    {file = "ruff-0.0.259-py3-none-win32.whl", hash = "sha256:38704f151323aa5858370a2f792e122cc25e5d1aabe7d42ceeab83da18f0b456"},
-    {file = "ruff-0.0.259-py3-none-win_amd64.whl", hash = "sha256:aa9449b898287e621942cc71b9327eceb8f0c357e4065fecefb707ef2d978df8"},
-    {file = "ruff-0.0.259-py3-none-win_arm64.whl", hash = "sha256:e4f39e18702de69faaaee3969934b92d7467285627f99a5b6ecd55a7d9f5d086"},
-    {file = "ruff-0.0.259.tar.gz", hash = "sha256:8b56496063ab3bfdf72339a5fbebb8bd46e5c5fee25ef11a9f03b208fa0562ec"},
+    {file = "ruff-0.0.260-py3-none-macosx_10_7_x86_64.whl", hash = "sha256:c559650b623f3fbdc39c7ed1bcb064765c666a53ee738c53d1461afbf3f23db2"},
+    {file = "ruff-0.0.260-py3-none-macosx_10_9_x86_64.macosx_11_0_arm64.macosx_10_9_universal2.whl", hash = "sha256:90ff1479e292a84c388a8a035d223247ddeea5f6760752a9142b88b6d59ac334"},
+    {file = "ruff-0.0.260-py3-none-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:25584d1b9f445fde72651caab97e7430a4c5bfd2a0ce9af39868753826cba10d"},
+    {file = "ruff-0.0.260-py3-none-manylinux_2_17_armv7l.manylinux2014_armv7l.whl", hash = "sha256:8032e35357384a29791c75194a71e314031171eb0731fcaa872dfaf4c1f4470a"},
+    {file = "ruff-0.0.260-py3-none-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:1e4fa7293f97c021825b3b72f2bf53f0eb4f59625608a889678c1fc6660f412d"},
+    {file = "ruff-0.0.260-py3-none-manylinux_2_17_ppc64.manylinux2014_ppc64.whl", hash = "sha256:8bec0271e2c8cd36bcf915cb9f6a93e40797a3ff3d2cda4ca87b7bed9e598472"},
+    {file = "ruff-0.0.260-py3-none-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:3e075a61aaff8ebe56172217f0ac14c5df9637b289bf161ac697445a9003d5c2"},
+    {file = "ruff-0.0.260-py3-none-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:f8678f54eb2696481618902a10c3cb28325f3323799af99997ad6f06005ea4f5"},
+    {file = "ruff-0.0.260-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:57d9f0bfdef739b76aa3112b9182a214f0f34589a2659f88353492c7670fe2fe"},
+    {file = "ruff-0.0.260-py3-none-musllinux_1_2_aarch64.whl", hash = "sha256:3ec1f77219ba5adaa194289cb82ba924ff2ed931fd00b8541d66a1724c89fbc9"},
+    {file = "ruff-0.0.260-py3-none-musllinux_1_2_armv7l.whl", hash = "sha256:aae2170a7ec6f7fc4a73db30aa7aa7fce936176bf66bf85f77f69ddd1dd4a665"},
+    {file = "ruff-0.0.260-py3-none-musllinux_1_2_i686.whl", hash = "sha256:5f847b72ef994ab88e9da250c7eb5cbb3f1555b92a9f22c5ed1c27a44b7e98d6"},
+    {file = "ruff-0.0.260-py3-none-musllinux_1_2_x86_64.whl", hash = "sha256:6dd705d4eff405c2b70513188fbff520f49db6df91f0d5e8258c5d469efa58bc"},
+    {file = "ruff-0.0.260-py3-none-win32.whl", hash = "sha256:3866a96b2ef92c7d837ba6bf8fc9dd125a67886f1c5512ad6fa5d5fefaceff87"},
+    {file = "ruff-0.0.260-py3-none-win_amd64.whl", hash = "sha256:0733d524946decbd4f1e63f7dc26820f5c1e6c31da529ba20fb995057f8e79b1"},
+    {file = "ruff-0.0.260-py3-none-win_arm64.whl", hash = "sha256:12542a26f189a5a10c719bfa14d415d0511ac05e5c9ff5e79cc9d5cc50b81bc8"},
+    {file = "ruff-0.0.260.tar.gz", hash = "sha256:ea8f94262f33b81c47ee9d81f455b144e94776f5c925748cb0c561a12206eae1"},
 ]
 
 [[package]]
@@ -4077,4 +4077,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.8.1,<4.0"
-content-hash = "d262cdfaa5f5ddb156180ea2302918b0743c171eb4fa5e6899f03f6c7ab3e4a3"
+content-hash = "e890862398264672a03751c20463cb4f89762c8e6cc8c94590d0af040c0a22e6"
diff --git a/pyproject.toml b/pyproject.toml
index fbccddf..fb3e21e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -44,6 +44,7 @@ Changelog = "https://github.com/MC-kit/xpypact/releases"
 
 [tool.poetry.dependencies]
 python = ">=3.8.1,<4.0"
+duckdb = ">=0.7.1"
 h5netcdf = ">=0.13.1"
 mckit-nuclides = {version = ">=0.1.1", allow-prereleases = true}
 numpy = ">=1.24.2"
@@ -52,7 +53,6 @@ orjson = ">=3.6.7"
 pandas = ">=1.4.1"
 xarray = ">=2022.3.0"
 multipledispatch = ">=0.6.0"
-duckdb = "^0.7.1"
 
 [tool.poetry.group.dev.dependencies]
 Pygments = ">=2.10.0"
@@ -248,7 +248,7 @@ omit = ["*_tab.py", "**/__init__.py"]
 show_missing = true
 skip_covered = true
 fail_under = 100
-omit = ["*_tab.py", "**/__init__.py"]
+omit = ["*_tab.py", "**/__init__.py", "**/types.py"]
 # Regexes for lines to exclude from consideration
 exclude_lines = [
     # Have to re-enable the standard pragma
@@ -262,6 +262,7 @@ exclude_lines = [
     # Don't complain if non-runnable code isn't run:
     "if 0:",
     "if __name__ == .__main__.:",
+    "if TYPE_CHECKING:",
 ]
 ignore_errors = true
 sort = "Cover"
@@ -379,30 +380,52 @@ deprecated-modules=["six"]
 target-version = "py38"
 #see full list: https://beta.ruff.rs/docs/rules/#pyflakes-f
 select= [
-  "A",
-  "B",
-  "C",
-  "D",
-  "E",
-  "F",
-  "G",
-  "I",
-  "N",
-  "PIE",
-  "PT",
-  "PL",
-  "PLC",
-  "PLE",
-  "PLR",
-  "PLW",
-  "PYI",
-  "Q",
-  "R",
-  "S",
-  "T",
-  "U",
-  "W",
-  "YTT"
+    "A", # flake8-builtins
+    "ANN", # flake8-annotations
+    "ARG", # flake8-unused-arguments
+    "B", # flake8-bugbear
+    "BLE", # flake8-blind-except
+    "C4", # flake8-comprehensions
+    "C90", # mccabe
+    "COM", # flake8-commas
+    "DJ", # flake8-django
+    "D", # pydocstyle
+    "DTZ", # flake8-datetimez
+    "EM", # flake8-errmsg
+    "ERA", # eradicate
+    "E", # pycodestyle
+    "EXE", # flake8-executable
+    "FBT", # flake8-boolean-trap
+    "F", # Pyflakes
+    "G", # flake8-logging-format
+    "ICN", # flake8-import-conventions
+    "I", # isort
+    "INP", # flake8-no-pep420
+    "ISC", # flake8-implicit-str-concat
+    "N", # pep8-naming
+    "NPY", # NumPy-specific rules
+    "PD", # pandas-vet
+    "PGH", # pygrep-hooks
+    "PIE", # flake8-pie
+    "PL", # Pylint
+    "PT", # flake8-pytest-style
+    "PTH", # flake8-use-pathlib
+    "PYI", # flake8-pyi
+    "Q", # flake8-quotes
+    "RET", # flake8-return
+    "RSE", # flake8-raise
+    "RUF", # Ruff-specific rules
+    "S", # flake8-bandit
+    "SIM", # flake8-simplify
+    "SLF", # flake8-self
+    "T10", # flake8-debugger
+    "T20", # flake8-print
+    "TCH", # flake8-type-checking
+    "TID", # flake8-tidy-imports
+    "TRY", # tryceratops
+    "UP", # pyupgrade
+    "W", # pycodestyle 2
+    "YTT", # flake8-2020
 ]
 
 # Ignore rules that currently fail on the codebase
@@ -419,8 +442,8 @@ ignore = [
     "D107",   # Missing docstring in __init__
     # "E203",   # E203: Whitespace before ‘:'
     # "E401",  # Multiple imports on one line
-    "E402",  # Module level import not at top of file
-    "E501",  # Line too long ( > 100 characters)
+    # "E402",  # Module level import not at top of file
+    # "E501",  # Line too long ( > 100 characters)
     # "E701",  # Multiple statements on one line (colon)
     # "E702",  # Multiple statements on one line (semicolon)
     # "E703",  # Statement ends with an unnecessary semicolon
diff --git a/src/xpypact/dao/api.py b/src/xpypact/dao/api.py
index aafbe92..65b19de 100644
--- a/src/xpypact/dao/api.py
+++ b/src/xpypact/dao/api.py
@@ -1,6 +1,90 @@
 """Interface to data access facilities."""
 from __future__ import annotations
 
+from typing import TYPE_CHECKING
 
-class DataAccessInterface:
+from abc import ABC, abstractmethod
+
+if TYPE_CHECKING:
+    import pandas as pd
+    import xarray as xr
+
+
+class DataAccessInterface(ABC):
     """Abstract DAO."""
+
+    @abstractmethod
+    def __enter__(self):
+        """Use DAO as context manager."""
+
+    @abstractmethod
+    def __exit__(self, exc_type, exc_val, exc_tb):
+        """Use DAO as context manager."""
+
+    @abstractmethod
+    def get_tables_info(self) -> pd.DataFrame:
+        """Get information on tables in schema."""
+
+    @abstractmethod
+    def create_schema(self) -> None:
+        """Create tables to store xpypact dataset.
+
+        Retain existing tables.
+        """
+
+    @abstractmethod
+    def drop_schema(self) -> None:
+        """Drop our DB objects."""
+
+    @abstractmethod
+    def save(self, ds: xr.Dataset, material_id=1, case_id="") -> None:
+        """Save xpypact dataset to database.
+
+        Args:
+            ds: xpypact dataset to save
+            material_id: additional key to distinguish multiple FISPACT run
+            case_id: second additional key
+        """
+
+    @abstractmethod
+    def load_rundata(self) -> pd.DataFrame:
+        """Load FISPACT run data as table.
+
+        Returns:
+            FISPACT run data
+        """
+
+    @abstractmethod
+    def load_nuclides(self) -> pd.DataFrame:
+        """Load nuclide table.
+
+        Returns:
+            time nuclide
+        """
+
+    @abstractmethod
+    def load_time_steps(self) -> pd.DataFrame:
+        """Load time step table.
+
+        Returns:
+            time step table
+        """
+
+    @abstractmethod
+    def load_time_step_nuclides(self) -> pd.DataFrame:
+        """Load time step x nuclides table.
+
+        Returns:
+            time step x nuclides table
+        """
+
+    @abstractmethod
+    def load_gamma(self, time_step_number: int | None = None) -> pd.DataFrame:
+        """Load time step x gamma table.
+
+        Args:
+            time_step_number: filter for time_step_number
+
+        Returns:
+            time step x gamma table
+        """
diff --git a/src/xpypact/dao/duckdb/implementation.py b/src/xpypact/dao/duckdb/implementation.py
index ea40b41..0e4bdb4 100644
--- a/src/xpypact/dao/duckdb/implementation.py
+++ b/src/xpypact/dao/duckdb/implementation.py
@@ -1,17 +1,21 @@
 """Code to implement DuckDB DAO."""
 from __future__ import annotations
 
+from typing import TYPE_CHECKING, cast
+
 from dataclasses import dataclass, field
 from pathlib import Path
 
 import duckdb as db
-import pandas as pd
-import xarray as xr
 
 from xpypact import get_gamma, get_nuclides, get_run_data, get_time_steps, get_timestep_nuclides
+from xpypact.dao import DataAccessInterface
 from xpypact.utils.resource import path_resolver
 
-from ...dao import DataAccessInterface
+if TYPE_CHECKING:
+
+    import pandas as pd
+    import xarray as xr
 
 
 # noinspection SqlNoDataSourceInspection
@@ -40,7 +44,7 @@ def __enter__(self):
     def __exit__(self, exc_type, exc_val, exc_tb):
         self.con.close()
 
-    def get_tables_info(self):
+    def get_tables_info(self) -> pd.DataFrame:
         """Get information on tables in schema."""
         return self.con.execute("select * from information_schema.tables").df()
 
@@ -49,11 +53,11 @@ def create_schema(self) -> None:
 
         Retain existing tables.
         """
-        sql_path: Path = path_resolver(__package__)("create_schema.sql")
+        sql_path: Path = cast(Path, path_resolver(__package__)("create_schema.sql"))
         sql = sql_path.read_text(encoding="utf-8")
         self.con.execute(sql)
 
-    def drop_schema(self):
+    def drop_schema(self) -> None:
         """Drop our DB objects."""
         tables = [
             "timestep_nuclide",
@@ -111,7 +115,7 @@ def load_time_step_nuclides(self) -> pd.DataFrame:
         """
         return self.con.execute("select * from timestep_nuclide").df()
 
-    def load_gamma(self, time_step_number: int = None) -> pd.DataFrame:
+    def load_gamma(self, time_step_number: int | None = None) -> pd.DataFrame:
         """Load time step x gamma table.
 
         Args:
@@ -157,9 +161,11 @@ def _save_gamma(self, ds: xr.Dataset, material_id=1, case_id=""):
 
 
 def _add_material_and_case_columns(
-    table: pd.DataFrame, material_id: int, case_id: str
+    table: pd.DataFrame,
+    material_id: int,
+    case_id: str,
 ) -> pd.DataFrame:
-    columns = table.columns.values
+    columns = table.columns.to_numpy()
     table["material_id"] = material_id
     table["case_id"] = case_id
     new_columns = ["material_id", "case_id"]
diff --git a/src/xpypact/data_arrays.py b/src/xpypact/data_arrays.py
index b25506c..7bc57c7 100644
--- a/src/xpypact/data_arrays.py
+++ b/src/xpypact/data_arrays.py
@@ -18,7 +18,6 @@
 from typing import TYPE_CHECKING, Any, Literal, TextIO, cast
 
 from functools import reduce
-from pathlib import Path
 
 import numpy as np
 
@@ -30,12 +29,11 @@
 from mckit_nuclides.elements import ELEMENTS_TABLE
 from mckit_nuclides.nuclides import NUCLIDES_TABLE
 from xarray.core.accessor_dt import DatetimeAccessor
-from xpypact.inventory import Inventory
 from xpypact.inventory import from_json as inventory_from_json
-from xpypact.time_step import TimeStep
-from xpypact.utils.types import MayBePath
 
 if TYPE_CHECKING:  # pragma: no cover
+    from pathlib import Path
+
     try:
         from dask.delayed import Delayed
     except ImportError:
@@ -45,6 +43,10 @@
     except ImportError:
         DaskDataFrame = None
 
+    from xpypact.inventory import Inventory
+    from xpypact.time_step import TimeStep
+    from xpypact.utils.types import MayBePath
+
 SCALABLE_COLUMNS = [
     "total_mass",
     "total_heat",
@@ -80,7 +82,9 @@ def _make_nuclide_var(getter, nuclides, dtype=float) -> tuple[str, ArrayLike]:
 
 
 def _make_time_step_and_nuclide_var(
-    getter, nuclides, dtype=float
+    getter,
+    nuclides,
+    dtype=float,
 ) -> tuple[tuple[str, str], ArrayLike]:
     _data = np.fromiter(map(getter, nuclides), dtype=dtype)
     return ("time_step_number", "nuclide"), _data.reshape(1, _data.size)
@@ -111,13 +115,16 @@ def _add_time_step_record(_ds: xr.Dataset, ts: TimeStep) -> xr.Dataset:
         "nuclide_grams": _make_time_step_and_nuclide_var(lambda n: n.grams, ts.nuclides),
         "nuclide_activity": _make_time_step_and_nuclide_var(lambda n: n.activity, ts.nuclides),
         "nuclide_alpha_activity": _make_time_step_and_nuclide_var(
-            lambda n: n.alpha_activity, ts.nuclides
+            lambda n: n.alpha_activity,
+            ts.nuclides,
         ),
         "nuclide_beta_activity": _make_time_step_and_nuclide_var(
-            lambda n: n.beta_activity, ts.nuclides
+            lambda n: n.beta_activity,
+            ts.nuclides,
         ),
         "nuclide_gamma_activity": _make_time_step_and_nuclide_var(
-            lambda n: n.gamma_activity, ts.nuclides
+            lambda n: n.gamma_activity,
+            ts.nuclides,
         ),
         "nuclide_heat": _make_time_step_and_nuclide_var(lambda n: n.heat, ts.nuclides),
         "nuclide_alpha_heat": _make_time_step_and_nuclide_var(lambda n: n.alpha_heat, ts.nuclides),
@@ -252,7 +259,8 @@ def get_atomic_numbers(ds: xr.Dataset) -> ArrayLike:
 
 
 def add_atomic_number_coordinate(
-    ds: xr.Dataset, coordinate_name: str = "atomic_number"
+    ds: xr.Dataset,
+    coordinate_name: str = "atomic_number",
 ) -> xr.Dataset:
     """Add coordinate for Z.
 
diff --git a/src/xpypact/data_frames.py b/src/xpypact/data_frames.py
index b6a5a3b..f092ffd 100644
--- a/src/xpypact/data_frames.py
+++ b/src/xpypact/data_frames.py
@@ -4,9 +4,12 @@
 """
 from __future__ import annotations
 
+from typing import TYPE_CHECKING
+
 import pandas as pd
 
-from xarray import Dataset
+if TYPE_CHECKING:
+    from xarray import Dataset
 
 
 def get_run_data(ds: Dataset) -> pd.DataFrame:
@@ -25,7 +28,7 @@ def get_run_data(ds: Dataset) -> pd.DataFrame:
             "flux_name": ds.attrs["flux_name"],
             "dose_rate_type": ds.attrs["dose_rate_type"],
             "dose_rate_distance": ds.attrs["dose_rate_distance"],
-        }
+        },
     )
 
 
@@ -81,7 +84,7 @@ def get_time_steps(ds: Dataset) -> pd.DataFrame:
                 "total_ingest1ion_dose": "ingest1ion_dose",
                 "total_inhalation_dose": "inhalation_dose",
                 "total_dose_rate": "dose_rate",
-            }
+            },
         )
     )
 
@@ -133,12 +136,7 @@ def get_timestep_nuclides(ds: Dataset) -> pd.DataFrame:
         "nuclide_ingestion",
         "nuclide_inhalation",
     ]
-    columns_all = [
-        "time_step_number",
-        "element",
-        "mass_number",
-        "state",
-    ] + columns
+    columns_all = ["time_step_number", "element", "mass_number", "state", *columns]
 
     return (
         ds[columns]
@@ -160,7 +158,7 @@ def get_timestep_nuclides(ds: Dataset) -> pd.DataFrame:
                 "nuclide_dose": "dose",
                 "nuclide_ingestion": "ingestion",
                 "nuclide_inhalation": "inhalation",
-            }
+            },
         )
     )
 
diff --git a/src/xpypact/fluxes.py b/src/xpypact/fluxes.py
index 3714500..c8695f2 100644
--- a/src/xpypact/fluxes.py
+++ b/src/xpypact/fluxes.py
@@ -1,9 +1,8 @@
 """The Class to represent FISPACT fluxes file content."""
 from __future__ import annotations
 
-from typing import TextIO, cast
+from typing import TYPE_CHECKING, TextIO, cast
 
-from collections.abc import Callable
 from dataclasses import dataclass
 from io import StringIO, TextIOBase
 from pathlib import Path
@@ -14,10 +13,14 @@
 
 from multipledispatch import dispatch
 from xpypact.utils.io import print_cols
-from xpypact.utils.types import NDArrayFloat
 
 FISPACT_709_BINS_NUMBER = 709
 
+if TYPE_CHECKING:
+    from collections.abc import Callable
+
+    from xpypact.utils.types import NDArrayFloat
+
 # pylint: disable=function-redefined
 
 LAST_TWO_DECADES = np.fromstring(
@@ -174,10 +177,11 @@ def __post_init__(self) -> None:
             ValueError: if sizes of bins and fluxes are not compatible.
         """
         if self.fluxes.size != self.energy_bins.size - 1:
-            raise ValueError(
+            msg = (
                 "Incompatible sizes of bins and fluxes, "
-                f"{self.fluxes.size} and {self.energy_bins.size}"
+                f"{self.fluxes.size} and {self.energy_bins.size}",
             )
+            raise ValueError(msg)
 
     @property
     def total(self) -> float:
@@ -264,7 +268,7 @@ def are_fluxes_close(
     b: Fluxes,
     rtol: float = 1.0e-5,
     atol: float = 1.0e-8,
-    equal_nan: bool = False,
+    equal_nan: bool = False,  # noqa: FBT - not worse than in allclose()
 ) -> bool:
     """Compare data of fluxes approximately.
 
@@ -426,7 +430,7 @@ def define_arb_bins_and_fluxes(data: NDArrayFloat) -> tuple[NDArrayFloat, NDArra
     """
     sz = data.size
     if sz & 1 == 0:
-        raise ArbitraryFluxesDataSizeError()
+        raise ArbitraryFluxesDataSizeError
     bins_end = sz // 2 + 1
     energy_bins = data[:bins_end]
     fluxes = data[bins_end:]
@@ -452,24 +456,19 @@ def define_709_bins_and_fluxes(data: NDArrayFloat) -> tuple[NDArrayFloat, NDArra
         StandardFluxesDataSizeError: if size of data is not 709.
     """
     if data.size != FISPACT_709_BINS_NUMBER:
-        raise StandardFluxesDataSizeError()
+        raise StandardFluxesDataSizeError
     return FISPACT_709_BINS, data[::-1]
 
 
-def print_fluxes(fluxes: Fluxes, fid: TextIO, arbitrary: bool, max_columns: int = 5) -> None:
-    """Print fluxes for FISPACT.
+def _print_bin_values(fluxes: Fluxes, fid: TextIO, max_columns: int = 5) -> None:
+    """Print fluxes bins for FISPACT.
 
     Args:
-        fluxes: to print
+        fluxes: to print bins from
         fid: a stream to print to
         arbitrary: if True - arbitrary, otherwise 709
         max_columns: max columns in output
     """
-    if arbitrary:
-        sequence = fluxes.energy_bins[::-1]
-        column = print_cols(sequence, fid, max_columns, fmt="{:.6e}")
-        if column != 0:
-            print(file=fid)
     sequence = fluxes.fluxes[::-1]
     column = print_cols(sequence, fid, max_columns, fmt="{:.5e}")
     if column != 0:
@@ -494,8 +493,8 @@ def print_709_fluxes(fluxes: Fluxes, fid: TextIO, max_columns: int = 7) -> None:
         NotA709Error: if not a valid 709 group "Fluxes" object is provided.
     """
     if not is_709_fluxes(fluxes):
-        raise NotA709Error()
-    print_fluxes(fluxes, fid, False, max_columns)
+        raise NotA709Error
+    _print_bin_values(fluxes, fid, max_columns)
 
 
 def print_arbitrary_fluxes(fluxes: Fluxes, fid: TextIO, max_columns: int = 5) -> None:
@@ -506,4 +505,8 @@ def print_arbitrary_fluxes(fluxes: Fluxes, fid: TextIO, max_columns: int = 5) ->
         fid: output stream
         max_columns: max number of columns in a row
     """
-    print_fluxes(fluxes, fid, True, max_columns)
+    sequence = fluxes.energy_bins[::-1]
+    column = print_cols(sequence, fid, max_columns, fmt="{:.6e}")
+    if column != 0:
+        print(file=fid)
+    _print_bin_values(fluxes, fid, max_columns)
diff --git a/src/xpypact/inventory.py b/src/xpypact/inventory.py
index 4f4e097..e3d1d7c 100644
--- a/src/xpypact/inventory.py
+++ b/src/xpypact/inventory.py
@@ -1,14 +1,13 @@
 """Classes to load information from FISPACT output JSON file."""
 from __future__ import annotations
 
-from typing import Any, cast
+from typing import TYPE_CHECKING, Any, cast
 
-import io
+import io  # noqa: TCH003 - needed for dispatch
 
-from collections.abc import Callable, Iterable
 from dataclasses import dataclass
 from functools import singledispatch
-from pathlib import Path
+from pathlib import Path  # noqa: TCH003 - needed for dispatch
 
 import numpy as np
 
@@ -16,7 +15,12 @@
 
 from xpypact.run_data import RunData
 from xpypact.time_step import TimeStep
-from xpypact.utils.types import NDArrayFloat
+
+if TYPE_CHECKING:
+
+    from collections.abc import Callable, Iterable
+
+    from xpypact.utils.types import NDArrayFloat
 
 FLOAT_ZERO = 0.0
 
@@ -60,7 +64,7 @@ def json_inventory_data_mapper(jts: dict[str, Any]) -> TimeStep:
         if duration == FLOAT_ZERO:
             duration = ts.cooling_time - prev_cooling_time
         if duration < FLOAT_ZERO:
-            raise InventoryNonMonotonicTimesError()  # pragma: no cover
+            raise InventoryNonMonotonicTimesError  # pragma: no cover
         ts.duration = duration
         prev_elapsed_time = ts.elapsed_time = prev_elapsed_time + duration
         if duration == FLOAT_ZERO:
diff --git a/src/xpypact/nuclide.py b/src/xpypact/nuclide.py
index caaec6c..6fc6ecf 100644
--- a/src/xpypact/nuclide.py
+++ b/src/xpypact/nuclide.py
@@ -5,8 +5,6 @@
 
 from dataclasses import dataclass
 
-FLOAT_ZERO = 0.0
-
 try:
     from scipy.constants import Avogadro
 except ImportError:  # pragma: no cover
@@ -17,6 +15,8 @@
 
 __all__ = ["Avogadro", "Nuclide"]
 
+FLOAT_ZERO = 0.0
+
 
 @dataclass
 class Nuclide:  # pylint: disable=too-many-instance-attributes
@@ -48,7 +48,7 @@ def __post_init__(self) -> None:
             self.zai = _z * 10000 + self.isotope * 10
             if self.state:
                 self.zai += 1
-        if self.atoms == FLOAT_ZERO and FLOAT_ZERO < self.grams:
+        if self.atoms == FLOAT_ZERO and self.grams > FLOAT_ZERO:
             self.atoms = Avogadro * self.grams / get_nuclide_mass(_z, self.isotope)
 
     @property
diff --git a/src/xpypact/time_step.py b/src/xpypact/time_step.py
index 7cc3340..bea6e8b 100644
--- a/src/xpypact/time_step.py
+++ b/src/xpypact/time_step.py
@@ -1,14 +1,16 @@
 """Classes to read a FISPACT time step attributes from JSON."""
 from __future__ import annotations
 
-from typing import Any
+from typing import TYPE_CHECKING, Any
 
 from dataclasses import dataclass, field
 
 import numpy as np
 
 from xpypact.nuclide import Nuclide
-from xpypact.utils.types import NDArrayFloat
+
+if TYPE_CHECKING:
+    from xpypact.utils.types import NDArrayFloat  # pragma: no cover
 
 FLOAT_ZERO = 0.0
 
@@ -82,7 +84,6 @@ class TimeStep:  # pylint: disable=too-many-instance-attributes
     duration: float = 0.0
     elapsed_time: float = 0.0
     flux: float = 0.0
-    # TODO dvp: compute the values in case of FISPACT v.4 to maintain same logic.
     total_atoms: float = 0.0  # FISPACT 5.0
     total_activity: float = 0.0  # -/-
     alpha_activity: float = 0.0  # -/-
@@ -99,7 +100,7 @@ class TimeStep:  # pylint: disable=too-many-instance-attributes
     nuclides: list[Nuclide] = field(default_factory=list)
     gamma_spectrum: GammaSpectrum | None = None
 
-    def __post_init__(self) -> None:  # noqa: ignore[CAC001]
+    def __post_init__(self) -> None:
         """Correct data missed in FISPACT-4."""
         # workarounds for FISPACT v.4
         if self.total_mass == FLOAT_ZERO:
@@ -146,10 +147,7 @@ def from_json(cls, json_dict: dict[str, Any]) -> TimeStep:
         json_dose_rate = json_dict.pop("dose_rate")
         dose_rate = DoseRate(**json_dose_rate)
         json_nuclides = json_dict.pop("nuclides")
-        if json_nuclides:
-            nuclides = [Nuclide.from_json(n) for n in json_nuclides]
-        else:
-            nuclides = []  # pragma: no cover
+        nuclides = [Nuclide.from_json(n) for n in json_nuclides] if json_nuclides else []
         json_gamma_spectrum = json_dict.pop("gamma_spectrum", None)
         if json_gamma_spectrum:
             gamma_spectrum = GammaSpectrum.from_json(json_gamma_spectrum)
diff --git a/src/xpypact/utils/io.py b/src/xpypact/utils/io.py
index b88aa19..33bca1c 100644
--- a/src/xpypact/utils/io.py
+++ b/src/xpypact/utils/io.py
@@ -1,15 +1,19 @@
 """Output utilities."""
 from __future__ import annotations
 
-from typing import Any, TextIO
+from typing import TYPE_CHECKING, Any, TextIO
 
 import sys
 
-from collections.abc import Iterable
+if TYPE_CHECKING:
+    from collections.abc import Iterable
 
 
 def print_cols(
-    seq: Iterable[Any], fid: TextIO = sys.stdout, max_columns: int = 6, fmt: str = "{}"
+    seq: Iterable[Any],
+    fid: TextIO = sys.stdout,
+    max_columns: int = 6,
+    fmt: str = "{}",
 ) -> int:
     """Print sequence in columns.
 
@@ -22,10 +26,10 @@ def print_cols(
     Returns:
         int: the number of the last column printed on the last row
     """
-    i = 0  # noqa: ignore[SIM113]
+    i = 0
     for s in seq:
         print(fmt.format(s), file=fid, end="")
-        if (0 < i) and (i % max_columns == 0):
+        if (i > 0) and (i % max_columns == 0):
             print(file=fid)
         else:
             print(" ", file=fid, end="")
diff --git a/src/xpypact/utils/resource.py b/src/xpypact/utils/resource.py
index d5b65f6..1719fe8 100644
--- a/src/xpypact/utils/resource.py
+++ b/src/xpypact/utils/resource.py
@@ -1,16 +1,20 @@
 """Utility methods to access a package data."""
 from __future__ import annotations
 
-import sys
+from typing import TYPE_CHECKING
 
-from collections.abc import Callable
-from pathlib import Path
+import sys
 
 if sys.version_info >= (3, 9):
-    from importlib.abc import Traversable
-    from importlib.resources import Package, files
+    from importlib.resources import files
 else:
-    from importlib_resources import files
+    from importlib_resources import files  # pragma: no cover
+
+if TYPE_CHECKING:
+    from collections.abc import Callable
+    from importlib.abc import Traversable
+    from importlib.resources import Package
+    from pathlib import Path
 
 
 def path_resolver(package: Package) -> Callable[[str], Path | Traversable]:
diff --git a/src/xpypact/utils/types.py b/src/xpypact/utils/types.py
index 6b62e7e..2b7b496 100644
--- a/src/xpypact/utils/types.py
+++ b/src/xpypact/utils/types.py
@@ -10,6 +10,5 @@
 from numpy.typing import NDArray
 
 MayBePath = Union[str, os.PathLike, None]
-
 NDArrayFloat = NDArray[np.float_]
 NDArrayInt = NDArray[np.int_]
diff --git a/tests/conftest.py b/tests/conftest.py
index 3823a43..6a46923 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,5 +1,7 @@
 from __future__ import annotations
 
+from typing import cast
+
 import bz2
 import os
 
@@ -18,7 +20,7 @@ def data() -> Path:
     Returns:
         Path to tests/data directory
     """
-    return path_resolver("tests")("data")
+    return cast(Path, path_resolver("tests")("data"))
 
 
 @pytest.fixture()
diff --git a/tests/test_data_arrays.py b/tests/test_data_arrays.py
index 7450099..3755d37 100644
--- a/tests/test_data_arrays.py
+++ b/tests/test_data_arrays.py
@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-from typing import cast
+from typing import TYPE_CHECKING, cast
 
 from copy import deepcopy
 
@@ -10,11 +10,13 @@
 
 import pandas as pd
 import pytest
-import xarray as xr
 import xpypact.data_arrays as da
 
 from xpypact.inventory import Inventory, from_json
 
+if TYPE_CHECKING:
+    import xarray as xr
+
 
 @pytest.fixture(scope="module")
 def inventory(data) -> Inventory:
@@ -76,7 +78,8 @@ def test_atomic_masses_column(ds: xr.Dataset) -> None:
     assert argentum.element == "Ag"
     a = argentum.a
     assert a.item() == pytest.approx(
-        110.905, rel=1e-4
+        110.905,
+        rel=1e-4,
     ), " the Ag atomic mass is to be about 110.905"
 
 
@@ -147,7 +150,7 @@ def test_scale_by_flux_on_dose_rate(ds):
     assert_equal(actual.attrs, ds.attrs)
 
 
-def test_net_cdf_writing(cd_tmpdir, ds):
+def test_net_cdf_writing(cd_tmpdir, ds):  # noqa: ARG001
     assert ds.total_dose_rate is not None
     da.save_nc(ds, "Ag-1.nc")
     actual = da.load_nc("Ag-1.nc")
@@ -156,7 +159,7 @@ def test_net_cdf_writing(cd_tmpdir, ds):
     assert actual.total_dose_rate.attrs["units"] == "Sv/h"
 
 
-def test_net_cdf_writing_with_group_and_appending(cd_tmpdir, ds):
+def test_net_cdf_writing_with_group_and_appending(cd_tmpdir, ds):  # noqa: ARG001
     group = "some-group"
     assert ds.total_dose_rate is not None
     da.save_nc(ds, "Ag-1.nc", mode="a", group=group)
@@ -169,7 +172,8 @@ def test_net_cdf_writing_with_group_and_appending(cd_tmpdir, ds):
 def test_inventory_with_gamma(dataset_with_gamma):
     assert dataset_with_gamma.gamma is not None
     assert dataset_with_gamma.gamma.sel(
-        time_step_number=2, gamma_boundaries=1.0
+        time_step_number=2,
+        gamma_boundaries=1.0,
     ).item() == pytest.approx(17857.24443195)
 
 
diff --git a/tests/test_data_frames.py b/tests/test_data_frames.py
index 0637dfc..7c10492 100644
--- a/tests/test_data_frames.py
+++ b/tests/test_data_frames.py
@@ -1,8 +1,9 @@
 from __future__ import annotations
 
+from typing import TYPE_CHECKING
+
 import pandas as pd
 import pytest
-import xarray as xr
 import xpypact.data_arrays as da
 
 from xpypact.data_frames import (
@@ -12,7 +13,12 @@
     get_time_steps,
     get_timestep_nuclides,
 )
-from xpypact.inventory import Inventory, from_json
+from xpypact.inventory import from_json
+
+if TYPE_CHECKING:
+    import xarray as xr
+
+    from xpypact.inventory import Inventory
 
 
 @pytest.fixture(scope="module")
@@ -49,7 +55,7 @@ def test_get_nuclides(ds):
 def test_get_timestep_nuclides(ds):
     timestep_nuclides = get_timestep_nuclides(ds)
     timestep_nuclides = timestep_nuclides.set_index(
-        ["time_step_number", "element", "mass_number", "state"]
+        ["time_step_number", "element", "mass_number", "state"],
     )
     assert timestep_nuclides.loc[2, "H", 1, ""].grams == 0.11468776343339874e-10
 
diff --git a/tests/test_duckdb_dao.py b/tests/test_duckdb_dao.py
index e8182fe..b34dd82 100644
--- a/tests/test_duckdb_dao.py
+++ b/tests/test_duckdb_dao.py
@@ -10,19 +10,19 @@
 def test_ddl(tmp_path):
     with DataAccessObject(tmp_path / "test-ddl.duckdb") as dao:
         tables = dao.get_tables_info()
-        assert 5 == len(tables)
+        assert len(tables) == 5
         table_names = tables["table_name"]
         for name in ["rundata", "timestep", "nuclide", "timestep_nuclide", "timestep_gamma"]:
-            assert name in table_names.values
+            assert name in table_names.to_numpy()
         dao.drop_schema()
         tables = dao.get_tables_info()
-        assert 0 == len(tables)
+        assert len(tables) == 0
         dao.create_schema()
         tables = dao.get_tables_info()
-        assert 5 == len(tables)
+        assert len(tables) == 5
     with DataAccessObject(tmp_path / "test-ddl.duckdb", read_only=True) as dao:
         tables = dao.get_tables_info()
-        assert 5 == len(tables)
+        assert len(tables) == 5
         with pytest.raises(InvalidInputException, match="Cannot execute statement"):
             dao.drop_schema()
 
@@ -43,7 +43,12 @@ def test_save(dataset_with_gamma):
         time_step_nuclides = dao.load_time_step_nuclides()
         assert not time_step_nuclides.empty
         time_step_nuclides = time_step_nuclides.set_index(
-            ["time_step_number", "element", "mass_number", "state"]
+            [
+                "time_step_number",
+                "element",
+                "mass_number",
+                "state",
+            ],
         )
         assert not time_step_nuclides.loc[2, "Cu"].empty
         gamma = dao.load_gamma()
diff --git a/tests/test_fluxes.py b/tests/test_fluxes.py
index fafe5e1..1e4f8dc 100644
--- a/tests/test_fluxes.py
+++ b/tests/test_fluxes.py
@@ -47,10 +47,8 @@ def test_flux_constructor():
     assert flux.norm == 2.0
     assert not is_709_fluxes(flux)
     assert are_fluxes_close(flux, flux)
-    with pytest.raises(ValueError, match="Incompatible sizes of bins and fluxes") as exc_info:
+    with pytest.raises(ValueError, match="Incompatible sizes of bins and fluxes"):
         Fluxes(ebins[:-2], bins, "test")
-    assert exc_info.type == ValueError
-    assert exc_info.value.args[0].startswith("Incompatible sizes of bins and fluxes")
     ebins, bins = define_709_bins_and_fluxes(np.ones(709, dtype=float))
     f709 = Fluxes(ebins, bins, "test 709")
     assert f709.total == 709
@@ -157,7 +155,8 @@ def test_print_arbitrary_fluxes(data, arb_flux_1):
 def test_define_arb_flux_fail():
     data = np.linspace(1, 10, 4)
     with pytest.raises(
-        ValueError, match="The number of float values from arb_flux file should be odd."
+        ValueError,
+        match="The number of float values from arb_flux file should be odd.",
     ):
         define_arb_bins_and_fluxes(data)
 
diff --git a/tests/test_inventory.py b/tests/test_inventory.py
index 30d3b3c..375aef5 100644
--- a/tests/test_inventory.py
+++ b/tests/test_inventory.py
@@ -1,14 +1,19 @@
 """Test loading Inventory from FISPACT JSON file."""
 from __future__ import annotations
 
+from typing import TYPE_CHECKING
+
 import bz2
 
 import pytest
 
-from xpypact.inventory import Inventory, RunDataCorrected, from_json  # extract_times,
+from xpypact.inventory import Inventory, from_json
 from xpypact.run_data import RunData
 from xpypact.time_step import DoseRate, TimeStep
 
+if TYPE_CHECKING:
+    from xpypact.inventory import RunDataCorrected
+
 SECONDS_PER_YEAR = int(365.24 * 24 * 3600)
 
 
diff --git a/tests/test_package.py b/tests/test_package.py
index 13f6600..826934f 100644
--- a/tests/test_package.py
+++ b/tests/test_package.py
@@ -32,5 +32,5 @@ def test_package():
     """This test checks if only current version is installed in working environment."""
     version = find_version_from_project_toml()
     assert __version__ == normalize_version(
-        version
+        version,
     ), "Run 'poetry install' and, if this doesn't help, run `tools/clear-prev-dist-info.py`"
diff --git a/tests/test_run_data.py b/tests/test_run_data.py
index 8a78c4d..ea23df3 100644
--- a/tests/test_run_data.py
+++ b/tests/test_run_data.py
@@ -20,7 +20,7 @@
                 run_name="* Material Ag, fluxes 1",
                 flux_name="55.F9.10 11-L2-02W HFS_GLRY_08_U",
             ),
-        )
+        ),
     ],
 )
 def test_from_json(inp, expected):
diff --git a/tests/utils/test_resource.py b/tests/utils/test_resource.py
index 5df5a80..8c1dc99 100644
--- a/tests/utils/test_resource.py
+++ b/tests/utils/test_resource.py
@@ -24,13 +24,13 @@ def test_path_resolver(package, resource, expected) -> None:
 
 
 @pytest.mark.parametrize(
-    ["package", "resource", "expected"],
+    ["package", "resource"],
     [
-        ("tests", "data/not_existing", "tests/data/not_existing"),
-        ("xpypact", "data/not_existing", "xpypact/data/not_existing"),
+        ("tests", "data/not_existing"),
+        ("xpypact", "data/not_existing"),
     ],
 )
-def test_path_resolver_when_resource_doesnt_exist(package, resource, expected) -> None:
+def test_path_resolver_when_resource_doesnt_exist(package, resource) -> None:
     resolver = path_resolver(package)
     actual = resolver(resource)
     assert not Path(actual).exists(), f"The resource {resource!r} should not be available"

From c52b863c9c42937387c13b85a02443398b54c09e Mon Sep 17 00:00:00 2001
From: dvp 
Date: Sun, 2 Apr 2023 17:33:22 +0300
Subject: [PATCH 31/32] build: sync with mckit-nuclides similar files

---
 .pre-commit-config.yaml      | 6 +-----
 pyproject.toml               | 5 +++--
 tests/test_fluxes.py         | 6 +++---
 tests/test_run_data.py       | 2 +-
 tests/utils/test_resource.py | 4 ++--
 tools/reset-pyenv            | 8 +++++---
 6 files changed, 15 insertions(+), 16 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index c0b3dd7..aac2609 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -83,16 +83,12 @@ repos:
         types: [python]
         exclude: ^notebooks
     # Lint
-    # -   id: flake8
-    #     name: flake8
-    #     entry: poetry run flake8
-    #     language: system
-    #     types: [python]
     -   id: ruff
         name: ruff
         entry: poetry run ruff --force-exclude --fix --config pyproject.toml
         language: system
         types: [python]
+        exclude: ^notebooks
 # Also code format the docs
 #    -   id: blacken-docs
 #        name: blacken-docs
diff --git a/pyproject.toml b/pyproject.toml
index fb3e21e..579d87c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -476,8 +476,9 @@ ignore = [
     # "PD005", # use operator instead of method
     # "PD008", # We use at() to access single values
     # "PD009", # And we use iat()
-    # "W503",  # Line break before binary operator: for compatibility with black settings
     "PT019",   # Fixture `_bin` without value is injected as parameter (false positive?)
+
+    # "W503",  # Line break before binary operator: for compatibility with black settings
 ]
 
 # Same as Black.
@@ -531,7 +532,7 @@ required-imports = ["from __future__ import annotations"]
 
 
 [tool.ruff.flake8-pytest-style]
-parametrize-names-type = "list"
+parametrize-names-type = "csv"
 
 [tool.ruff.pydocstyle]
 # Use Google-style docstrings.
diff --git a/tests/test_fluxes.py b/tests/test_fluxes.py
index 1e4f8dc..64fbbaa 100644
--- a/tests/test_fluxes.py
+++ b/tests/test_fluxes.py
@@ -59,7 +59,7 @@ def test_flux_constructor():
 
 
 @pytest.mark.parametrize(
-    ["_bin", "expected_e0", "expected_e1", "expected_flux"],
+    "_bin,expected_e0,expected_e1,expected_flux",
     [
         (0, 1e-5, 1e6, 1),
         (1, 1e6, 1e7, 90),
@@ -93,7 +93,7 @@ def assert_one(_: Any, f: Any) -> Any:
 
 
 @pytest.mark.parametrize(
-    ["_bin", "expected_e0", "expected_e1", "expected_flux"],
+    "_bin,expected_e0,expected_e1,expected_flux",
     [
         (0, 1.1e-5, 0.25, 3.600000e05),
         (6, 7.800000e06, 1.410000e07, 2.870000e03),
@@ -114,7 +114,7 @@ def fluxes_1(data):
 
 
 @pytest.mark.parametrize(
-    ["_bin", "expected_e0", "expected_e1", "expected_flux"],
+    "_bin,expected_e0,expected_e1,expected_flux",
     [
         (0, 1e-5, 1.0471e-5, 1.8182e-3),
         (1, 1.0471e-5, 1.0965e-5, 1.8182e-3),
diff --git a/tests/test_run_data.py b/tests/test_run_data.py
index ea23df3..af31c83 100644
--- a/tests/test_run_data.py
+++ b/tests/test_run_data.py
@@ -7,7 +7,7 @@
 
 
 @pytest.mark.parametrize(
-    ["inp", "expected"],
+    "inp,expected",
     [
         (
             {
diff --git a/tests/utils/test_resource.py b/tests/utils/test_resource.py
index 8c1dc99..4de9488 100644
--- a/tests/utils/test_resource.py
+++ b/tests/utils/test_resource.py
@@ -11,7 +11,7 @@
 
 # noinspection PyCompatibility
 @pytest.mark.parametrize(
-    ["package", "resource", "expected"],
+    "package,resource,expected",
     [
         ("tests", "data/Ag-1.json", "data/Ag-1.json"),
     ],
@@ -24,7 +24,7 @@ def test_path_resolver(package, resource, expected) -> None:
 
 
 @pytest.mark.parametrize(
-    ["package", "resource"],
+    "package,resource",
     [
         ("tests", "data/not_existing"),
         ("xpypact", "data/not_existing"),
diff --git a/tools/reset-pyenv b/tools/reset-pyenv
index 39c91fc..d6993fc 100755
--- a/tools/reset-pyenv
+++ b/tools/reset-pyenv
@@ -1,9 +1,10 @@
 #!/bin/bash
 
+. ~/.bash-functions.rc
+
 # set -exu
 
-env="xpypact"
-pkg="${env//-/_}"
+env=($(pyenv local))[1]
 last_python="3.11.2"
 
 eval "$(pyenv init -)"
@@ -17,7 +18,8 @@ poetry install
 pyenv shell --unset
 pyenv local "$env" "3.10.10" "3.9.16" "3.8.16"
 pyenv rehash
-python -c "import ${pkg}; print(${pkg}.__version__)"
 
+pkg=($(ls src))[1]
+python -c "import ${pkg}; print(${pkg}.__version__)" && success "Environment $env is reset"
 
 # vim: set ts=4 sw=4 tw=92 ss=0 ft=sh et ai :

From 316a1c5ca7729cb394d0a00e2c64f698e91af4dd Mon Sep 17 00:00:00 2001
From: dvp 
Date: Sun, 2 Apr 2023 17:45:53 +0300
Subject: [PATCH 32/32] style: fix I001

---
 benchmarks/test_inventory.py  | 11 +++++++++--
 noxfile.py                    | 10 +++++++---
 pyproject.toml                |  5 ++++-
 tools/clear-prev-dist-info.py |  5 +++--
 4 files changed, 23 insertions(+), 8 deletions(-)

diff --git a/benchmarks/test_inventory.py b/benchmarks/test_inventory.py
index 0a3ee96..100662e 100644
--- a/benchmarks/test_inventory.py
+++ b/benchmarks/test_inventory.py
@@ -4,16 +4,23 @@
 """
 from __future__ import annotations
 
+from typing import TYPE_CHECKING, cast
+
 import bz2
 
-from xpypact.inventory import Inventory, from_json
+from pathlib import Path
+
+from xpypact.inventory import from_json
 from xpypact.utils.resource import path_resolver
 
+if TYPE_CHECKING:
+    from xpypact.inventory import Inventory
+
 EXPECTED_TIME_STEPS = 65
 
 data_path_resolver = path_resolver("benchmarks")
 
-with bz2.open(data_path_resolver("data/Ag-1.json.bz2")) as fid:
+with bz2.open(cast(Path, data_path_resolver("data/Ag-1.json.bz2"))) as fid:
     AG_1_TEXT = fid.read().decode("utf-8")
 
 
diff --git a/noxfile.py b/noxfile.py
index b0e3bac..4d66505 100644
--- a/noxfile.py
+++ b/noxfile.py
@@ -1,7 +1,7 @@
 """Nox sessions."""
 from __future__ import annotations
 
-from typing import Final
+from typing import TYPE_CHECKING, Final
 
 import re
 import shutil
@@ -13,7 +13,10 @@
 
 import nox
 
-from nox import Session, session
+from nox import session
+
+if TYPE_CHECKING:
+    from nox import Session
 
 nox.options.sessions = (
     "safety",
@@ -98,7 +101,8 @@ def activate_virtualenv_in_precommit_hooks(s: Session) -> None:
         return
 
     for hook in filter(
-        lambda x: not x.name.endswith(".sample") and x.is_file(), hook_dir.iterdir()
+        lambda x: not x.name.endswith(".sample") and x.is_file(),
+        hook_dir.iterdir(),
     ):
         _update_hook(hook, virtualenv, s)
 
diff --git a/pyproject.toml b/pyproject.toml
index 579d87c..2238eef 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -516,7 +516,10 @@ exclude = [
 "src/xpypact/inventory.py" = ["F811"]
 "src/xpypact/data_arrays.py" = ["ANN401", "PD011"]
 "src/xpypact/utils/resource.py" = ["ANN202"]
-"tools/*" = ["T201"]
+"tools/*" = [
+    "T201",
+    "INP001",  # file ... is part of implicit namespace ... add __init__.py - there are no modules in tools
+]
 
 [tool.ruff.mccabe]
 # Unlike Flake8, default to a complexity level of 10.
diff --git a/tools/clear-prev-dist-info.py b/tools/clear-prev-dist-info.py
index 3a0a0f5..6021b8e 100755
--- a/tools/clear-prev-dist-info.py
+++ b/tools/clear-prev-dist-info.py
@@ -56,10 +56,11 @@ def get_project_name() -> str:
     """
     pyproject_path = search_upwards_for_file("pyproject.toml")
     if pyproject_path is None:
-        raise OSError(
+        msg = (
             "Illegal directory: cannot find file pyproject.toml "
-            f"from current directory: {Path.cwd()}"
+            f"from current directory: {Path.cwd()}",
         )
+        raise OSError(msg)
     pyproject = tomllib.loads(pyproject_path.read_text())
     name: str = pyproject["tool"]["poetry"]["name"].replace("-", "_")
     print(f"Package {name} is found in {pyproject_path.absolute()}")