Merge branch 'main' into v0.4

Author: tobiasraabe

.github/workflows/main.yml

@@ -5,9 +5,6 @@ concurrency:
   group: ${{ github.head_ref || github.run_id }}
   cancel-in-progress: true
 
-env:
-  CONDA_EXE: mamba
-
 on:
   push:
     branches:
@@ -18,6 +15,21 @@ on:
 
 jobs:
 
+  run-type-checking:
+
+    name: Run tests for type-checking
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version-file: .python-version
+          allow-prereleases: true
+          cache: pip
+      - run: pip install tox-uv
+      - run: tox -e typing
+
   run-tests:
 
     name: Run tests for ${{ matrix.os }} on ${{ matrix.python-version }}
@@ -31,33 +43,29 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: actions/setup-python@v5
         with:
-          auto-update-conda: false
           python-version: ${{ matrix.python-version }}
-          channels: conda-forge,nodefaults
-          miniforge-variant: Mambaforge
-
-      - name: Install core dependencies.
-        shell: bash -l {0}
-        run: mamba install -c conda-forge tox-conda coverage
+          cache: pip
+          allow-prereleases: true
+      - run: pip install tox-uv
 
       # Unit, integration, and end-to-end tests.
 
       - name: Run unit tests and doctests.
         shell: bash -l {0}
-        run: tox -e pytest -- -m "unit or (not integration and not end_to_end)" --cov=./ --cov-report=xml -n auto
+        run: tox -e test -- -m "unit or (not integration and not end_to_end)" --cov=./ --cov-report=xml -n auto
 
-      - name: Upload coverage report for unit tests and doctests.
-        if: runner.os == 'Linux' && matrix.python-version == '3.8'
-        shell: bash -l {0}
-        run: bash <(curl -s https://codecov.io/bash) -F unit -c
+      - name: Upload unit test coverage reports to Codecov with GitHub Action
+        uses: codecov/codecov-action@v4
+        with:
+          flags: unit
 
       - name: Run end-to-end tests.
         shell: bash -l {0}
-        run: tox -e pytest -- -m end_to_end --cov=./ --cov-report=xml -n auto
+        run: tox -e test -- -m end_to_end --cov=./ --cov-report=xml -n auto
 
-      - name: Upload coverage reports of end-to-end tests.
-        if: runner.os == 'Linux' && matrix.python-version == '3.8'
-        shell: bash -l {0}
-        run: bash <(curl -s https://codecov.io/bash) -F end_to_end -c
+      - name: Upload end_to_end test coverage reports to Codecov with GitHub Action
+        uses: codecov/codecov-action@v4
+        with:
+          flags: end_to_end

.github/workflows/publish-to-pypi.yml

@@ -1,36 +1,91 @@
-name: PyPI
+name: Publish Python 🐍 distribution 📦 to PyPI
 
 on: push
 
 jobs:
-  build-n-publish:
-    name: Build and publish Python 🐍 distributions 📦 to PyPI
+  build:
+    name: Build distribution 📦
     runs-on: ubuntu-latest
+
     steps:
     - uses: actions/checkout@v4
-
-    - name: Set up Python 3.8
-      uses: actions/setup-python@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.8
-
+        python-version: "3.x"
     - name: Install pypa/build
       run: >-
-        python -m
+        python3 -m
         pip install
         build
         --user
-
     - name: Build a binary wheel and a source tarball
-      run: >-
-        python -m
-        build
-        --sdist
-        --wheel
-        --outdir dist/
+      run: python3 -m build
+    - name: Store the distribution packages
+      uses: actions/upload-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
 
+  publish-to-pypi:
+    name: Publish Python 🐍 distribution 📦 to PyPI
+    if: startsWith(github.ref, 'refs/tags/')  # only publish to PyPI on tag pushes
+    needs:
+    - build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/pytask-stata
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
     - name: Publish distribution 📦 to PyPI
-      if: startsWith(github.ref, 'refs/tags')
-      uses: pypa/gh-action-pypi-publish@master
+      uses: pypa/gh-action-pypi-publish@release/v1
+
+  github-release:
+    name: >-
+      Sign the Python 🐍 distribution 📦 with Sigstore
+      and upload them to GitHub Release
+    needs:
+    - publish-to-pypi
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: write  # IMPORTANT: mandatory for making GitHub Releases
+      id-token: write  # IMPORTANT: mandatory for sigstore
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Sign the dists with Sigstore
+      uses: sigstore/[email protected]
       with:
-        password: ${{ secrets.PYPI_API_TOKEN }}
+        inputs: >-
+          ./dist/*.tar.gz
+          ./dist/*.whl
+    - name: Create GitHub Release
+      env:
+        GITHUB_TOKEN: ${{ github.token }}
+      run: >-
+        gh release create
+        '${{ github.ref_name }}'
+        --repo '${{ github.repository }}'
+        --notes ""
+    - name: Upload artifact signatures to GitHub Release
+      env:
+        GITHUB_TOKEN: ${{ github.token }}
+      # Upload to GitHub Release using the `gh` CLI. `dist/` contains the built
+      # packages, and the sigstore-produced signatures and certificates.
+      run: >-
+        gh release upload
+        '${{ github.ref_name }}' dist/**
+        --repo '${{ github.repository }}'

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.6.0
     hooks:
     -   id: check-added-large-files
         args: [--maxkb=25]
@@ -24,61 +24,29 @@ repos:
     -   id: python-no-log-warn
     -   id: python-use-type-annotations
     -   id: text-unicode-replacement-char
--   repo: https://github.com/asottile/reorder-python-imports
-    rev: v3.12.0
-    hooks:
-    -   id: reorder-python-imports
-        args: [--py38-plus, --add-import, from __future__ import annotations]
--   repo: https://github.com/asottile/setup-cfg-fmt
-    rev: v2.5.0
-    hooks:
-    -   id: setup-cfg-fmt
--   repo: https://github.com/psf/black
-    rev: 23.9.1
-    hooks:
-    -   id: black
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.0.292
+    rev: v0.4.4
     hooks:
     -   id: ruff
+    -   id: ruff-format
 -   repo: https://github.com/dosisod/refurb
-    rev: v1.21.0
+    rev: v2.0.0
     hooks:
     -   id: refurb
-        args: [--ignore, FURB126]
--   repo: https://github.com/econchick/interrogate
-    rev: 1.5.0
-    hooks:
-    -   id: interrogate
-        args: [-v, --fail-under=40, src, tests]
 -   repo: https://github.com/executablebooks/mdformat
     rev: 0.7.17
     hooks:
     -   id: mdformat
         additional_dependencies:
         - mdformat-gfm
         - mdformat-black
-        args: [--wrap, '88']
+        args: [--wrap, "88"]
 -   repo: https://github.com/codespell-project/codespell
     rev: v2.2.6
     hooks:
     -   id: codespell
--   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.5.1
-    hooks:
-    -   id: mypy
-        additional_dependencies:
-        - attrs
-        - pytask
-        - types-setuptools
-        pass_filenames: false
--   repo: https://github.com/mgedmin/check-manifest
-    rev: '0.49'
-    hooks:
-    -   id: check-manifest
-        args: [--no-build-isolation]
-        additional_dependencies: [setuptools-scm, toml]
 -   repo: meta
     hooks:
     -   id: check-hooks-apply
     -   id: check-useless-excludes
+    # -   id: identity  # Prints all files passed to pre-commits. Debugging.

.python-version

@@ -0,0 +1 @@
+3.12.2

pyproject.toml

@@ -2,11 +2,54 @@
 requires = ["setuptools>=45", "wheel", "setuptools_scm[toml]>=6.0"]
 build-backend = "setuptools.build_meta"
 
+[project]
+name = "pytask_stata"
+description = "Execute do-files with Stata and pytask."
+authors = [{ name = "Tobias Raabe", email = "[email protected]" }]
+license = { text = "MIT" }
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3 :: Only",
+]
+requires-python = ">=3.8"
+dependencies = ["click", "pytask>=0.3,<0.4"]
+dynamic = ["version"]
+
+[project.readme]
+file = "README.md"
+content-type = "text/markdown"
+
+[project.optional-dependencies]
+test = ["pytest", "pytest-cov", "pytest-xdist"]
+typing = ["mypy"]
+
+[project.urls]
+Homepage = "https://github.com/pytask-dev/pytask-stata"
+Documentation = "https://github.com/pytask-dev/pytask-stata"
+Github = "https://github.com/pytask-dev/pytask-stata"
+Tracker = "https://github.com/pytask-dev/pytask-stata/issues"
+Changelog = "https://github.com/pytask-dev/pytask-stata/blob/main/CHANGES.md"
+
+[project.entry-points]
+pytask = { pytask_stata = "pytask_stata.plugin" }
+
+[tool.setuptools]
+include-package-data = true
+package-dir = { "" = "src" }
+zip-safe = false
+platforms = ["any"]
+license-files = ["LICENSE"]
+
+[tool.setuptools.packages.find]
+where = ["src"]
+namespaces = false
 
 [tool.setuptools_scm]
 write_to = "src/pytask_stata/_version.py"
 
-
 [tool.mypy]
 files = ["src", "tests"]
 check_untyped_defs = true
@@ -17,54 +60,36 @@ no_implicit_optional = true
 warn_redundant_casts = true
 warn_unused_ignores = true
 
-
 [[tool.mypy.overrides]]
 module = "tests.*"
 disallow_untyped_defs = false
 ignore_errors = true
 
-
 [tool.ruff]
 target-version = "py38"
-select = ["ALL"]
 fix = true
-extend-ignore = [
-    "I",  # ignore isort
-    "TRY",
-    # Numpy docstyle
-    "D107",
-    "D203",
-    "D212",
-    "D213",
-    "D402",
-    "D413",
-    "D415",
-    "D416",
-    "D417",
-    # Others.
-    "D404",  # Do not start module docstring with "This".
-    "RET504",  # unnecessary variable assignment before return.
-    "S101",  # raise errors for asserts.
-    "B905",  # strict parameter for zip that was implemented in py310.
-    "ANN101",  # type annotating self
-    "ANN102",  # type annotating cls
-    "FBT",  # flake8-boolean-trap
-    "EM",  # flake8-errmsg
-    "ANN401",  # flake8-annotate typing.Any
-    "PD",  # pandas-vet
-    "COM812",  # trailing comma missing, but black takes care of that
-]
+unsafe-fixes = true
 
+[tool.ruff.lint]
+select = ["ALL"]
+ignore = [
+    "ANN101",
+    "ANN102",
+    "ANN401", # flake8-annotate typing.Any
+    "COM812", # Comply with ruff-format.
+    "ISC001", # Comply with ruff-format.
+]
 
-[tool.ruff.per-file-ignores]
-"tests/*" = ["D", "ANN"]
+[tool.ruff.lint.per-file-ignores]
+"tests/*" = ["D", "ANN", "S101"]
 "__init__.py" = ["D104"]
 
+[tool.ruff.lint.isort]
+force-single-line = true
 
-[tool.ruff.pydocstyle]
+[tool.ruff.lint.pydocstyle]
 convention = "numpy"
 
-
 [tool.pytest.ini_options]
 # Do not add src since it messes with the loading of pytask-parallel as a plugin.
 testpaths = ["tests"]