From d9aedc19f6c4e25c46e187779854954c63aacd9c Mon Sep 17 00:00:00 2001 From: dvp Date: Fri, 9 Sep 2022 18:04:25 +0300 Subject: [PATCH 01/17] build: sync configuration with mckit-meshes --- .flake8 | 4 ++++ .github/workflows/labeler.yml | 2 +- .github/workflows/tests.yml | 5 +++-- .pre-commit-config.yaml | 10 +++++++++- noxfile.py | 19 ++----------------- poetry.lock | 34 +--------------------------------- pyproject.toml | 14 ++++++-------- 7 files changed, 26 insertions(+), 62 deletions(-) diff --git a/.flake8 b/.flake8 index e6f7873..7dc1b09 100644 --- a/.flake8 +++ b/.flake8 @@ -22,6 +22,10 @@ ignore= E501 # W503: Line break before binary operator: for compatibility with black settings W503 + # import is controlled by isort + I100 + I201 + I202 exclude= .git __pycache__ diff --git a/.github/workflows/labeler.yml b/.github/workflows/labeler.yml index 6b89109..8a6426f 100644 --- a/.github/workflows/labeler.yml +++ b/.github/workflows/labeler.yml @@ -24,7 +24,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out the repository - uses: actions/checkout@v2 + uses: actions/checkout@v2.4.0 - name: Sync GitHub Issue Labels uses: crazy-max/ghaction-github-labeler@v4 diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 8b0cbf7..8405fc6 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -11,6 +11,7 @@ on: - "**.yaml" - "**.yml" - "**.toml" + - "**/data/**" - ".github/constraints.txt" pull_request: branches: @@ -119,8 +120,8 @@ jobs: with: python-version: ${{ matrix.python-version }} architecture: x64 - - name: Checkout submodules - run: git submodule update --init --recursive --depth=1 +# - name: Checkout submodules +# run: git submodule update --init --recursive --depth=1 - name: Install nox run: pip install --constraint=.github/constraints.txt nox - name: Install poetry diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 072db55..4c8a777 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -87,7 +87,6 @@ repos: # entry: poetry run blacken-docs # language: system - # Checking for common mistakes #- repo: https://github.com/pre-commit/pygrep-hooks # rev: "v1.9.0" @@ -116,6 +115,15 @@ repos: # types: [file] # files: (\.cmake|CMakeLists.txt)(.in)?$ +# Check static types with mypy +#- repo: https://github.com/pre-commit/mirrors-mypy +# rev: "v0.942" +# hooks: +# - id: mypy +# args: [--show-error-codes] +# exclude: ^(tests|docs)/ +# additional_dependencies: [nox, rich] + # Checks the manifest for missing files (native support) #- repo: https://github.com/mgedmin/check-manifest # rev: "0.48" diff --git a/noxfile.py b/noxfile.py index 54d3878..2e174d8 100644 --- a/noxfile.py +++ b/noxfile.py @@ -25,7 +25,7 @@ ) -NAME_RGX = re.compile(r'name\s*=\s*"(?P[_a-zA-Z]*)"') +NAME_RGX = re.compile(r'name\s*=\s*"(?P[-_a-zA-Z]+)"') def find_my_name() -> str: @@ -270,7 +270,6 @@ def mypy(s: Session) -> None: "main,mypy", external=True, ) - # s.install(*MYPY_DEPS) s.run("mypy", *args) if not s.posargs: s.run("mypy", f"--python-executable={sys.executable}", "noxfile.py") @@ -280,18 +279,11 @@ def mypy(s: Session) -> None: def xdoctest(s: Session) -> None: """Run examples with xdoctest.""" args = s.posargs or ["all"] - # s.run( - # "poetry", - # "install", - # "--no-dev", - # external=True, - # ) - # s.install("xdoctest[colors]") s.run( "poetry", "install", "--only", - "xdoctest", + "main,xdoctest", external=True, ) s.run("python", "-m", "xdoctest", package, *args) @@ -319,13 +311,6 @@ def docs_build(s: Session) -> None: def docs(s: Session) -> None: """Build and serve the documentation with live reloading on file changes.""" args = s.posargs or ["--open-browser", "docs/source", "docs/_build"] - # s.run( - # "poetry", - # "install", - # "--no-dev", - # external=True, - # ) - # s.install("sphinx-autobuild", *SPHINX_DEPS) s.run( "poetry", "install", diff --git a/poetry.lock b/poetry.lock index 98d0038..fd39ada 100644 --- a/poetry.lock +++ b/poetry.lock @@ -796,14 +796,6 @@ category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" -[[package]] -name = "py-cpuinfo" -version = "8.0.0" -description = "Get CPU info with pure Python 2 & 3" -category = "dev" -optional = false -python-versions = "*" - [[package]] name = "pycln" version = "2.1.1" @@ -906,23 +898,6 @@ tomli = ">=1.0.0" [package.extras] testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "xmlschema"] -[[package]] -name = "pytest-benchmark" -version = "3.4.1" -description = "A ``pytest`` fixture for benchmarking code. It will group the tests into rounds that are calibrated to the chosen timer." -category = "dev" -optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" - -[package.dependencies] -py-cpuinfo = "*" -pytest = ">=3.8" - -[package.extras] -aspect = ["aspectlib"] -elasticsearch = ["elasticsearch"] -histogram = ["pygal", "pygaljs"] - [[package]] name = "pytest-cache" version = "1.0" @@ -1570,7 +1545,7 @@ testing = ["func-timeout", "jaraco.itertools", "pytest (>=6)", "pytest-black (>= [metadata] lock-version = "1.1" python-versions = ">=3.8,<4.0" -content-hash = "7f0d0fff5670e4b549fe32ba7bf715ef4f8a78214b9d205a468951cbb0a0d4a6" +content-hash = "482ce9552716820606a3649acddf90967aa2a0f2eaf329eaccffe4dce478b3a4" [metadata.files] alabaster = [ @@ -2097,9 +2072,6 @@ py = [ {file = "py-1.11.0-py2.py3-none-any.whl", hash = "sha256:607c53218732647dff4acdfcd50cb62615cedf612e72d1724fb1a0cc6405b378"}, {file = "py-1.11.0.tar.gz", hash = "sha256:51c75c4126074b472f746a24399ad32f6053d1b34b68d2fa41e558e6f4a98719"}, ] -py-cpuinfo = [ - {file = "py-cpuinfo-8.0.0.tar.gz", hash = "sha256:5f269be0e08e33fd959de96b34cd4aeeeacac014dd8305f70eb28d06de2345c5"}, -] pycln = [ {file = "pycln-2.1.1-py3-none-any.whl", hash = "sha256:d90fad498563b309e570615d610e44399ef842d4644ba06925e4d46a8a691013"}, {file = "pycln-2.1.1.tar.gz", hash = "sha256:255a135935796761958dd3349822ccc71ce3052464c4d81e119df0106bbaf882"}, @@ -2166,10 +2138,6 @@ pytest = [ {file = "pytest-7.1.3-py3-none-any.whl", hash = "sha256:1377bda3466d70b55e3f5cecfa55bb7cfcf219c7964629b967c37cf0bda818b7"}, {file = "pytest-7.1.3.tar.gz", hash = "sha256:4f365fec2dff9c1162f834d9f18af1ba13062db0c708bf7b946f8a5c76180c39"}, ] -pytest-benchmark = [ - {file = "pytest-benchmark-3.4.1.tar.gz", hash = "sha256:40e263f912de5a81d891619032983557d62a3d85843f9a9f30b98baea0cd7b47"}, - {file = "pytest_benchmark-3.4.1-py2.py3-none-any.whl", hash = "sha256:36d2b08c4882f6f997fd3126a3d6dfd70f3249cde178ed8bbc0b73db7c20f809"}, -] pytest-cache = [ {file = "pytest-cache-1.0.tar.gz", hash = "sha256:be7468edd4d3d83f1e844959fd6e3fd28e77a481440a7118d430130ea31b07a9"}, ] diff --git a/pyproject.toml b/pyproject.toml index ca2a21f..c447eeb 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -47,12 +47,12 @@ Pygments = ">=2.10.0" nox = ">=2022.1.7" tomli = ">=2.0.1" -[tool.poetry.group.profile] -optional = true +#[tool.poetry.group.profile] +#optional = true -[tool.poetry.group.profile.dependencies] +#[tool.poetry.group.profile.dependencies] # TODO dvp: apply yappi: https://coderzcolumn.com/tutorials/python/yappi-yet-another-python-profiler -yappi = ">=1.3.2" +#yappi = ">=1.3.2" [tool.poetry.group.safety.dependencies] safety = ">=1.10.3" @@ -70,7 +70,6 @@ pycln = {version = "^2.1.1", extras = ["click"]} [tool.poetry.group.test.dependencies] pytest = ">=7.0.1" -pytest-benchmark = ">=3.4.1" pytest-cache = ">=1.0" pytest-cov = ">=3.0.0" pytest-mock = ">=3.6.1" @@ -96,7 +95,7 @@ numpy = ">=1.23.2" darglint = ">=1.8.1" flake8 = ">=4.0.1" flake8-annotations = ">=2.6.2" -flake8-bandit = ">=2.1.2" +flake8-bandit = ">=3.0.0" flake8-bugbear = ">=22.1.11" flake8-builtins = ">=1.5.3" flake8-colors = ">=0.1.9" @@ -113,7 +112,7 @@ tryceratops = ">=1.0.1" sphinx = ">=5.0.2" sphinx-autodoc-typehints = ">=1.12.0" sphinx-autorun = ">=1.1.1" -sphinx-click = ">=3.0.2" +sphinx-click = ">=4.0.3" sphinx-rtd-theme = ">=1.0.0" sphinxcontrib-napoleon = ">=0.7" @@ -245,7 +244,6 @@ module = [ "loguru", "multipledispatch", "nox", - "nox_poetry", "numpy.testing", "pandas", "pytest", From 70955cc1bd132ab1a0cfe205c208ec88068c1b68 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 9 Sep 2022 15:05:16 +0000 Subject: [PATCH 02/17] build(deps): bump sphinx-click from 3.0.2 to 4.3.0 Bumps [sphinx-click](https://github.com/click-contrib/sphinx-click) from 3.0.2 to 4.3.0. - [Release notes](https://github.com/click-contrib/sphinx-click/releases) - [Commits](https://github.com/click-contrib/sphinx-click/compare/3.0.2...4.3.0) --- updated-dependencies: - dependency-name: sphinx-click dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- docs/requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/requirements.txt b/docs/requirements.txt index b52cfc6..bc4a2ab 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -2,6 +2,6 @@ sphinx==4.2.0 sphinx-autobuild==2021.3.14 sphinx-autodoc-typehints==1.12.0 sphinx-autorun==1.1.1 -sphinx-click==3.0.2 +sphinx-click==4.3.0 sphinx-rtd-theme==1.0.0 sphinxcontrib-napoleon==0.7 From cbf554bda082283899fda1b1fd31b53433e280b5 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 9 Sep 2022 15:05:19 +0000 Subject: [PATCH 03/17] build(deps): bump sphinx-autodoc-typehints from 1.12.0 to 1.19.2 Bumps [sphinx-autodoc-typehints](https://github.com/tox-dev/sphinx-autodoc-typehints) from 1.12.0 to 1.19.2. - [Release notes](https://github.com/tox-dev/sphinx-autodoc-typehints/releases) - [Changelog](https://github.com/tox-dev/sphinx-autodoc-typehints/blob/main/CHANGELOG.md) - [Commits](https://github.com/tox-dev/sphinx-autodoc-typehints/compare/1.12.0...1.19.2) --- updated-dependencies: - dependency-name: sphinx-autodoc-typehints dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- docs/requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/requirements.txt b/docs/requirements.txt index b52cfc6..fa415c0 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,6 +1,6 @@ sphinx==4.2.0 sphinx-autobuild==2021.3.14 -sphinx-autodoc-typehints==1.12.0 +sphinx-autodoc-typehints==1.19.2 sphinx-autorun==1.1.1 sphinx-click==3.0.2 sphinx-rtd-theme==1.0.0 From 4f3d83869d4d8d24d7e6e21f95a8a36c95497480 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 9 Sep 2022 15:05:21 +0000 Subject: [PATCH 04/17] build(deps): bump sphinx from 4.2.0 to 5.1.1 Bumps [sphinx](https://github.com/sphinx-doc/sphinx) from 4.2.0 to 5.1.1. - [Release notes](https://github.com/sphinx-doc/sphinx/releases) - [Changelog](https://github.com/sphinx-doc/sphinx/blob/5.x/CHANGES) - [Commits](https://github.com/sphinx-doc/sphinx/compare/v4.2.0...v5.1.1) --- updated-dependencies: - dependency-name: sphinx dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- docs/requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/requirements.txt b/docs/requirements.txt index b52cfc6..9179dfc 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,4 +1,4 @@ -sphinx==4.2.0 +sphinx==5.1.1 sphinx-autobuild==2021.3.14 sphinx-autodoc-typehints==1.12.0 sphinx-autorun==1.1.1 From 2266758be7f5d0e0e207a0424a2b189fee08c2de Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 12 Sep 2022 11:19:22 +0000 Subject: [PATCH 05/17] build(deps): bump numpy from 1.23.2 to 1.23.3 Bumps [numpy](https://github.com/numpy/numpy) from 1.23.2 to 1.23.3. - [Release notes](https://github.com/numpy/numpy/releases) - [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst) - [Commits](https://github.com/numpy/numpy/compare/v1.23.2...v1.23.3) --- updated-dependencies: - dependency-name: numpy dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- poetry.lock | 109 +++++++++++++++------------------------------------- 1 file changed, 30 insertions(+), 79 deletions(-) diff --git a/poetry.lock b/poetry.lock index fd39ada..1741cd5 100644 --- a/poetry.lock +++ b/poetry.lock @@ -653,7 +653,7 @@ tox_to_nox = ["jinja2", "tox"] [[package]] name = "numpy" -version = "1.23.2" +version = "1.23.3" description = "NumPy is the fundamental package for array computing with Python." category = "main" optional = false @@ -1519,17 +1519,6 @@ runtime-strict = ["six (==1.11.0)"] tests = ["cmake", "codecov", "ninja", "pybind11", "pytest", "pytest", "pytest", "pytest", "pytest", "pytest", "pytest-cov", "pytest-cov", "pytest-cov", "pytest-cov", "scikit-build", "typing"] tests-strict = ["cmake (==3.21.2)", "codecov (==2.0.15)", "ninja (==1.10.2)", "pybind11 (==2.7.1)", "pytest (==4.6.0)", "pytest (==4.6.0)", "pytest (==4.6.0)", "pytest (==4.6.0)", "pytest (==4.6.0)", "pytest (==6.2.5)", "pytest-cov (==2.8.1)", 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Sep 2022 11:29:40 +0000 Subject: [PATCH 06/17] build(deps): bump actions/checkout from 2.4.0 to 3.0.2 Bumps [actions/checkout](https://github.com/actions/checkout) from 2.4.0 to 3.0.2. - [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/v2.4.0...v3.0.2) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... 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 8a6426f..282f363 100644 --- a/.github/workflows/labeler.yml +++ b/.github/workflows/labeler.yml @@ -24,7 +24,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out the repository - uses: actions/checkout@v2.4.0 + uses: actions/checkout@v3.0.2 - 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 16afbc3..b90ba49 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -12,7 +12,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out the repository - uses: actions/checkout@v3 + uses: actions/checkout@v3.0.2 with: fetch-depth: 2 diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 8405fc6..020cf94 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 + uses: actions/checkout@v3.0.2 - name: Set up Python 3.10 uses: actions/setup-python@v4.2.0 @@ -76,7 +76,7 @@ jobs: needs: lint steps: - name: Check out the repository - uses: actions/checkout@v3 + uses: actions/checkout@v3.0.2 - name: Set up Python 3.10 uses: actions/setup-python@v4.2.0 @@ -115,7 +115,7 @@ jobs: python-version: ['3.8', '3.9', '3.10'] steps: - name: Checkout repository - uses: actions/checkout@v3 + uses: actions/checkout@v3.0.2 - uses: actions/setup-python@v4.2.0 with: python-version: ${{ matrix.python-version }} @@ -139,7 +139,7 @@ jobs: needs: tests steps: - name: Check out the repository - uses: actions/checkout@v3 + uses: actions/checkout@v3.0.2 - name: Set up Python 3.10 uses: actions/setup-python@v4.2.0 From 974ce3d5e05ff86316ab34db0a91d21ce95a06f5 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 20 Sep 2022 11:36:19 +0000 Subject: [PATCH 07/17] build(deps): bump release-drafter/release-drafter from 5.15.0 to 5.21.0 Bumps [release-drafter/release-drafter](https://github.com/release-drafter/release-drafter) from 5.15.0 to 5.21.0. - [Release notes](https://github.com/release-drafter/release-drafter/releases) - [Commits](https://github.com/release-drafter/release-drafter/compare/v5.15.0...v5.21.0) --- updated-dependencies: - dependency-name: release-drafter/release-drafter dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- .github/workflows/release-drafter.yml | 2 +- .github/workflows/release.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/release-drafter.yml b/.github/workflows/release-drafter.yml index bd1b77f..cedc822 100644 --- a/.github/workflows/release-drafter.yml +++ b/.github/workflows/release-drafter.yml @@ -7,6 +7,6 @@ jobs: draft_release: runs-on: ubuntu-latest steps: - - uses: release-drafter/release-drafter@v5 + - uses: release-drafter/release-drafter@v5.21.0 env: GITHUB_TOKEN: ${{ secrets.MCKIT_GITHUB_TOKEN }} diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 16afbc3..9484005 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -70,7 +70,7 @@ jobs: repository_url: https://test.pypi.org/legacy/ - name: Publish the release notes - uses: release-drafter/release-drafter@v5.15.0 + uses: release-drafter/release-drafter@v5.21.0 with: publish: ${{ steps.check-version.outputs.tag != '' }} tag: ${{ steps.check-version.outputs.tag }} From 647d9973558d7bfbc5edc351a076d9288f3b0fd3 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 26 Sep 2022 11:28:03 +0000 Subject: [PATCH 08/17] build(deps): bump pandas from 1.4.4 to 1.5.0 Bumps [pandas](https://github.com/pandas-dev/pandas) from 1.4.4 to 1.5.0. - [Release notes](https://github.com/pandas-dev/pandas/releases) - [Changelog](https://github.com/pandas-dev/pandas/blob/main/RELEASE.md) - [Commits](https://github.com/pandas-dev/pandas/compare/v1.4.4...v1.5.0) --- updated-dependencies: - dependency-name: pandas dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- poetry.lock | 112 +++++++++++++++++----------------------------------- 1 file changed, 37 insertions(+), 75 deletions(-) diff --git a/poetry.lock b/poetry.lock index fd39ada..6118f35 100644 --- a/poetry.lock +++ b/poetry.lock @@ -691,7 +691,7 @@ pyparsing = ">=2.0.2,<3.0.5 || >3.0.5" [[package]] name = "pandas" -version = "1.4.4" +version = "1.5.0" description = "Powerful data structures for data analysis, time series, and statistics" category = "main" optional = false @@ -699,10 +699,8 @@ python-versions = ">=3.8" [package.dependencies] numpy = [ - {version = ">=1.18.5", markers = "platform_machine != \"aarch64\" and platform_machine != \"arm64\" and python_version < \"3.10\""}, - {version = ">=1.19.2", markers = "platform_machine == \"aarch64\" and python_version < \"3.10\""}, - {version = ">=1.20.0", markers = "platform_machine == \"arm64\" and python_version < \"3.10\""}, {version = ">=1.21.0", markers = "python_version >= \"3.10\""}, + {version = 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"sha256:c26779cbba3947823c260354adaab4e91ca8c18888aa2b740f503844b88f1813"}, - {file = "types_setuptools-65.3.0-py3-none-any.whl", hash = "sha256:f69210049580939c70386252b776eb75ff4b6de488e7d766b9398669b7de68af"}, + {file = "types-setuptools-65.4.0.0.tar.gz", hash = "sha256:d9021d6a70690b34e7bd2947e7ab10167c646fbf062508cb56581be2e2a1615e"}, + {file = "types_setuptools-65.4.0.0-py3-none-any.whl", hash = "sha256:ce178b3f7dbd6c0e67f8eee7ae29c1be280ade7e5188bdd9e620843de4060d85"}, ] typing-extensions = [ {file = "typing_extensions-4.3.0-py3-none-any.whl", hash = "sha256:25642c956049920a5aa49edcdd6ab1e06d7e5d467fc00e0506c44ac86fbfca02"}, diff --git a/pyproject.toml b/pyproject.toml index c447eeb..0c601bf 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "xpypact" -version = "0.1.5" +version = "0.1.6a0" description = "\"Python tools to work with elements and isotopes\"" authors = ["dvp "] license = "MIT" @@ -121,7 +121,7 @@ sphinx-autobuild = ">=2021.3.14" [build-system] -requires = ["poetry-core>=1.0.0"] +requires = ["poetry-core>=1.1.0"] build-backend = "poetry.core.masonry.api" [tool.isort] @@ -222,9 +222,9 @@ sort = "Cover" # MyPy config # See https://mypy.readthedocs.io/en/stable/config_file.html#using-a-pyproject-toml-file [tool.mypy] -python_version = 3.9 +python_version = 3.10 # strict = true # TODO dvp: uncomment this to get strict control -follow_imports = "skip" +follow_imports = "silent" # namespace_packages = true warn_return_any = true warn_unused_configs = true diff --git a/tools/reset-pyenv b/tools/reset-pyenv index 57a7279..8b5632b 100755 --- a/tools/reset-pyenv +++ b/tools/reset-pyenv @@ -3,7 +3,7 @@ # set -exu pyenv virtualenv-delete -f xpypact -pyenv virtualenv 3.10.6 xpypact +pyenv virtualenv 3.10.7 xpypact pyenv rehash poetry install pyenv rehash From b31884bfa4eace24a30014ff838db38724ad601f Mon Sep 17 00:00:00 2001 From: dvp Date: Tue, 4 Oct 2022 11:11:07 +0300 Subject: [PATCH 11/17] fix: saving to nedcdif for the xarray version 2022.9.0 --- src/xpypact/data_arrays.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/xpypact/data_arrays.py b/src/xpypact/data_arrays.py index e64aefc..40440fe 100644 --- a/src/xpypact/data_arrays.py +++ b/src/xpypact/data_arrays.py @@ -372,7 +372,8 @@ def _encode_multiindex(ds: xr.Dataset, idx_name: str) -> xr.Dataset: coordinate = ds.indexes[idx_name].to_frame().reset_index(drop=True) columns = coordinate.columns.values columns_to_drop = (idx_name, *columns) - encoded = ds.reset_index(columns_to_drop).reset_coords(columns_to_drop, drop=True) + encoded = ds.reset_index(columns_to_drop, drop=True) + # encoded = encoded.reset_coords(columns_to_drop, drop=True) encoded.attrs[idx_name + "_columns"] = columns for c in columns: encoded.attrs[idx_name + f"_{c}"] = coordinate[c].values @@ -380,7 +381,7 @@ def _encode_multiindex(ds: xr.Dataset, idx_name: str) -> xr.Dataset: def _decode_to_multiindex(encoded: xr.Dataset, idx_name: str) -> xr.Dataset: - columns = encoded.attrs[idx_name + "_columns"] + columns = encoded.attrs.pop(idx_name + "_columns") mi_columns = [encoded.attrs.pop(idx_name + f"_{c}") for c in columns] mi = pd.MultiIndex.from_arrays(mi_columns, names=columns) encoded.coords[idx_name] = mi From 125a43193f8f46a4c0831c629bdf2b2f30a3d062 Mon Sep 17 00:00:00 2001 From: dvp Date: Tue, 4 Oct 2022 11:33:39 +0300 Subject: [PATCH 12/17] style: make mypy happy --- pyproject.toml | 2 +- src/xpypact/data_arrays.py | 10 +++++----- src/xpypact/utils/types.py | 6 ++++++ 3 files changed, 12 insertions(+), 6 deletions(-) create mode 100644 src/xpypact/utils/types.py diff --git a/pyproject.toml b/pyproject.toml index 0c601bf..d3744ca 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -222,7 +222,7 @@ sort = "Cover" # MyPy config # See https://mypy.readthedocs.io/en/stable/config_file.html#using-a-pyproject-toml-file [tool.mypy] -python_version = 3.10 +python_version = "3.10" # strict = true # TODO dvp: uncomment this to get strict control follow_imports = "silent" # namespace_packages = true diff --git a/src/xpypact/data_arrays.py b/src/xpypact/data_arrays.py index 40440fe..6e7d12c 100644 --- a/src/xpypact/data_arrays.py +++ b/src/xpypact/data_arrays.py @@ -30,6 +30,7 @@ from .Inventory import Inventory from .Inventory import from_json as inventory_from_json from .TimeStep import TimeStep +from .utils.types import MayBePath SCALABLE_COLUMNS = [ "total_mass", @@ -243,7 +244,7 @@ def get_timestamp(ds: xr.Dataset) -> DatetimeAccessor: Returns: accessor to timestamp """ - return ds.timestamp[0].dt + return ds.timestamp[0].dt # type: ignore[no-any-return] def get_atomic_numbers(ds: xr.Dataset) -> np.ndarray: @@ -373,7 +374,6 @@ def _encode_multiindex(ds: xr.Dataset, idx_name: str) -> xr.Dataset: columns = coordinate.columns.values columns_to_drop = (idx_name, *columns) encoded = ds.reset_index(columns_to_drop, drop=True) - # encoded = encoded.reset_coords(columns_to_drop, drop=True) encoded.attrs[idx_name + "_columns"] = columns for c in columns: encoded.attrs[idx_name + f"_{c}"] = coordinate[c].values @@ -391,7 +391,7 @@ def _decode_to_multiindex(encoded: xr.Dataset, idx_name: str) -> xr.Dataset: # noinspection PyShadowingBuiltins def save_nc( ds: xr.Dataset, - path: str | Path | None = None, + path: MayBePath = None, mode: Literal["w", "a"] = "w", format: Literal["NETCDF4", "NETCDF4_CLASSIC", "NETCDF3_64BIT", "NETCDF3_CLASSIC"] | None = None, @@ -423,8 +423,8 @@ def save_nc( see :py:meth:`xarray.Dataset.to_netcdf()` """ encoded = _encode_multiindex(ds, "nuclide") - return encoded.to_netcdf( # type: ignore[no-any-return] - path, + return encoded.to_netcdf( # type: ignore[misc] + path, # type: ignore[arg-type] mode, format, group, diff --git a/src/xpypact/utils/types.py b/src/xpypact/utils/types.py new file mode 100644 index 0000000..567648f --- /dev/null +++ b/src/xpypact/utils/types.py @@ -0,0 +1,6 @@ +"""Utility types for the package.""" +from typing import Union + +import os + +MayBePath = Union[str, os.PathLike, None] From cacfde1d38869b1f0e43315661303720bb42d240 Mon Sep 17 00:00:00 2001 From: dvp Date: Tue, 4 Oct 2022 11:37:11 +0300 Subject: [PATCH 13/17] build: poetry update (dev deps only) --- poetry.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/poetry.lock b/poetry.lock index 55a10a6..cb6bced 100644 --- a/poetry.lock +++ b/poetry.lock @@ -450,7 +450,7 @@ numpy = ">=1.14.5" [[package]] name = "identify" -version = "2.5.5" +version = "2.5.6" description = "File identification library for Python" category = "dev" optional = false @@ -1775,8 +1775,8 @@ h5py = [ {file = "h5py-3.7.0.tar.gz", hash = "sha256:3fcf37884383c5da64846ab510190720027dca0768def34dd8dcb659dbe5cbf3"}, ] identify = [ - {file = "identify-2.5.5-py2.py3-none-any.whl", hash = "sha256:ef78c0d96098a3b5fe7720be4a97e73f439af7cf088ebf47b620aeaa10fadf97"}, - {file = "identify-2.5.5.tar.gz", hash = "sha256:322a5699daecf7c6fd60e68852f36f2ecbb6a36ff6e6e973e0d2bb6fca203ee6"}, + {file = "identify-2.5.6-py2.py3-none-any.whl", hash = "sha256:b276db7ec52d7e89f5bc4653380e33054ddc803d25875952ad90b0f012cbcdaa"}, + {file = "identify-2.5.6.tar.gz", hash = "sha256:6c32dbd747aa4ceee1df33f25fed0b0f6e0d65721b15bd151307ff7056d50245"}, ] idna = [ {file = "idna-3.4-py3-none-any.whl", hash = "sha256:90b77e79eaa3eba6de819a0c442c0b4ceefc341a7a2ab77d7562bf49f425c5c2"}, From 2bbde5aa03f6a0b908ea6578d96a34184b3710ed Mon Sep 17 00:00:00 2001 From: dvp Date: Tue, 4 Oct 2022 12:04:29 +0300 Subject: [PATCH 14/17] test: refactor nox xdoctest command --- noxfile.py | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/noxfile.py b/noxfile.py index 2e174d8..2d26def 100644 --- a/noxfile.py +++ b/noxfile.py @@ -147,7 +147,6 @@ def tests(s: Session) -> None: "main,test,xdoctest,coverage", external=True, ) - # s.install("pytest", "pygments", "coverage[toml]") try: s.run("coverage", "run", "--parallel", "-m", "pytest", *s.posargs) finally: @@ -171,7 +170,6 @@ def coverage(s: Session) -> None: "coverage", external=True, ) - # s.install("coverage[toml]") if not s.posargs and any(Path().glob(".coverage.*")): s.run("coverage", "combine") @@ -190,7 +188,6 @@ def typeguard(s: Session) -> None: "main,test,typeguard", external=True, ) - # s.install("pytest", "typeguard", "pygments") s.run("pytest", f"--typeguard-packages={package}", *s.posargs) @@ -275,10 +272,10 @@ def mypy(s: Session) -> None: s.run("mypy", f"--python-executable={sys.executable}", "noxfile.py") -@session(python=supported_pythons) +@session(python="3.10") def xdoctest(s: Session) -> None: """Run examples with xdoctest.""" - args = s.posargs or ["all"] + args = s.posargs or ["--quiet", "-m", package] s.run( "poetry", "install", @@ -286,7 +283,7 @@ def xdoctest(s: Session) -> None: "main,xdoctest", external=True, ) - s.run("python", "-m", "xdoctest", package, *args) + s.run("python", "-m", "xdoctest", *args) @session(name="docs-build", python="3.10") From 9d708ce9ed2f0bf46719cc5a581788eed25e0174 Mon Sep 17 00:00:00 2001 From: dvp Date: Tue, 4 Oct 2022 12:05:01 +0300 Subject: [PATCH 15/17] bump: version xpypact 0.1.6 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index d3744ca..c1d50bb 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "xpypact" -version = "0.1.6a0" +version = "0.1.6" description = "\"Python tools to work with elements and isotopes\"" authors = ["dvp "] license = "MIT" From c0ba700d1eff52defd2dbe27e29448ef53cb8e7a Mon Sep 17 00:00:00 2001 From: dvp Date: Tue, 4 Oct 2022 12:56:05 +0300 Subject: [PATCH 16/17] build: update flake8-bandit --- .pre-commit-config.yaml | 7 +++++++ pyproject.toml | 5 ++--- 2 files changed, 9 insertions(+), 3 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 4c8a777..127ed28 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -87,6 +87,13 @@ repos: # entry: poetry run blacken-docs # language: system +#- repo: https://github.com/sirosen/texthooks +# rev: "0.3.1" +# hooks: +# - id: fix-ligatures +# - id: fix-smartquotes + + # Checking for common mistakes #- repo: https://github.com/pre-commit/pygrep-hooks # rev: "v1.9.0" diff --git a/pyproject.toml b/pyproject.toml index c1d50bb..4753df1 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -95,12 +95,12 @@ numpy = ">=1.23.2" darglint = ">=1.8.1" flake8 = ">=4.0.1" flake8-annotations = ">=2.6.2" -flake8-bandit = ">=3.0.0" +flake8-bandit = ">=4.1.1" flake8-bugbear = ">=22.1.11" flake8-builtins = ">=1.5.3" flake8-colors = ">=0.1.9" flake8-commas = ">=2.1.0" -flake8-comprehensions = "^3.10.0" +flake8-comprehensions = ">=3.10.0" flake8-docstrings = ">=1.6.0" flake8-import-order = ">=0.18.1" flake8-print = ">=5.0.0" @@ -254,7 +254,6 @@ ignore_missing_imports = true [tool.tryceratops] include = ["src"] -#exclude = [".nox"] #ignore = ["TC002", "TC200", "TC300"] experimental = true From 52429b9b848dcc31cc57a83c7f633b392fb572e7 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 4 Oct 2022 11:46:36 +0000 Subject: [PATCH 17/17] build(deps): bump actions/checkout from 3.0.2 to 3.1.0 Bumps [actions/checkout](https://github.com/actions/checkout) from 3.0.2 to 3.1.0. - [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/v3.0.2...v3.1.0) --- 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 282f363..a9d7539 100644 --- a/.github/workflows/labeler.yml +++ b/.github/workflows/labeler.yml @@ -24,7 +24,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out the repository - uses: actions/checkout@v3.0.2 + uses: actions/checkout@v3.1.0 - 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 3c902e7..10df488 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -12,7 +12,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out the repository - uses: actions/checkout@v3.0.2 + uses: actions/checkout@v3.1.0 with: fetch-depth: 2 diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 020cf94..b28e0ab 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@v3.0.2 + uses: actions/checkout@v3.1.0 - name: Set up Python 3.10 uses: actions/setup-python@v4.2.0 @@ -76,7 +76,7 @@ jobs: needs: lint steps: - name: Check out the repository - uses: actions/checkout@v3.0.2 + uses: actions/checkout@v3.1.0 - name: Set up Python 3.10 uses: actions/setup-python@v4.2.0 @@ -115,7 +115,7 @@ jobs: python-version: ['3.8', '3.9', '3.10'] steps: - name: Checkout repository - uses: actions/checkout@v3.0.2 + uses: actions/checkout@v3.1.0 - uses: actions/setup-python@v4.2.0 with: python-version: ${{ matrix.python-version }} @@ -139,7 +139,7 @@ jobs: needs: tests steps: - name: Check out the repository - uses: actions/checkout@v3.0.2 + uses: actions/checkout@v3.1.0 - name: Set up Python 3.10 uses: actions/setup-python@v4.2.0