Merge pull request #154 from MC-kit/devel

Add export to pandas and duckdb

.flake8

@@ -57,15 +57,19 @@ exclude=
     *.egg-info
     .cache
     .eggs
+    notebooks/dvp/*.py
+    .nox
+    .idea
+
 per-file-ignores =
     benchmarks/*:S101,DAR101
     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

.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

.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

.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
 
@@ -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@v1.8.3
         with:
           user: __token__
           password: ${{ secrets.PYPI_TOKEN }}
 
       - name: Publish package on TestPyPI
         if: "! steps.check-version.outputs.tag"
-        uses: pypa/gh-action-pypi-publish@v1.6.4
+        uses: pypa/gh-action-pypi-publish@v1.8.3
         with:
           user: __token__
           password: ${{ secrets.TEST_PYPI_TOKEN }}

.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'

.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/[email protected]
@@ -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
@@ -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
 
@@ -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
@@ -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
 
@@ -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
@@ -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/[email protected]
@@ -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

.gitignore

@@ -134,3 +134,9 @@ dmypy.json
 
 # A soundbox work and data folder
 wrk/
+
+
+# poetry local config
+/poetry.toml
+
+

.pre-commit-config.yaml

@@ -81,12 +81,14 @@ repos:
         entry: poetry run black
         language: system
         types: [python]
+        exclude: ^notebooks
     # Lint
-    -   id: flake8
-        name: flake8
-        entry: poetry run flake8
+    -   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

benchmarks/test_inventory.py

@@ -2,18 +2,29 @@
 
 See https://pytest-benchmark.readthedocs.io/en/latest/index.html
 """
+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")
 
 
 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

docs/source/conf.py

@@ -1,26 +1,28 @@
-# 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 --------------------------------------------------------------
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # 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 ---------------------------------------------------