chore: remove Python 3.8 support

.github/workflows/pypi-publish.yml

@@ -9,43 +9,44 @@ on:
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v2
-      with:
-        python-version: 3.9
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install flake8 pytest tox
-    # - name: Lint with flake8
-    #   run: |
-    #     # stop the build if there are Python syntax errors or undefined names
-    #     flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-    #     # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-    #     # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Test with tox
-      run: |
-        tox
-    - name: Build docs
-      run: |
-        tox -e docs
-    - run: touch ./docs/_build/html/.nojekyll
-    - name: GH Pages Deployment
-      uses: JamesIves/[email protected]
-      with:
-        branch: gh-pages # The branch the action should deploy to.
-        folder: ./docs/_build/html
-        clean: true # Automatically remove deleted files from the deploy branch
-    - name: Build Project and Publish
-      run: |
-        python -m tox -e clean,build
-    - name: Publish package
-      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
-      with:
-        user: __token__
-        password: ${{ secrets.PYPI_PASSWORD }}
+      - uses: actions/checkout@v4
+
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.11
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install tox
+
+      - name: Test with tox
+        run: |
+          tox
+
+      - name: Build docs
+        run: |
+          tox -e docs
+
+      - run: touch ./docs/_build/html/.nojekyll
+
+      - name: GH Pages Deployment
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          branch: gh-pages # The branch the action should deploy to.
+          folder: ./docs/_build/html
+          clean: true # Automatically remove deleted files from the deploy branch
+
+      - name: Build Project and Publish
+        run: |
+          python -m tox -e clean,build
+
+      - name: Publish package
+        uses: pypa/[email protected]
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_PASSWORD }}

.github/workflows/pypi-test.yml

@@ -1,40 +1,33 @@
-# This workflow will install Python dependencies, run tests and lint with a single version of Python
-# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
-
-name: Test the library
+name: Run tests
 
 on:
   push:
-    branches: [ master ]
+    branches: [master]
   pull_request:
-    branches: [ master ]
+    branches: [master]
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ '3.8', '3.9', '3.10', '3.11', '3.12' ]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
 
     name: Python ${{ matrix.python-version }}
     steps:
-    - uses: actions/checkout@v2
-    - name: Setup Python
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-        cache: 'pip'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install flake8 pytest tox
-    # - name: Lint with flake8
-    #   run: |
-    #     # stop the build if there are Python syntax errors or undefined names
-    #     flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-    #     # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-    #     # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Test with tox
-      run: |
-        tox
+      - uses: actions/checkout@v4
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: "pip"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install tox
+
+      - name: Test with tox
+        run: |
+          tox

.pre-commit-config.yaml

@@ -17,26 +17,27 @@ repos:
   - id: mixed-line-ending
     args: ['--fix=auto']  # replace 'auto' with 'lf' to enforce Linux/Mac line endings or 'crlf' for Windows
 
-- repo: https://github.com/PyCQA/docformatter
-  rev: v1.7.5
-  hooks:
-    - id: docformatter
-      additional_dependencies: [tomli]
-      args: [--in-place, --wrap-descriptions=120, --wrap-summaries=120]
-      # --config, ./pyproject.toml
+# - repo: https://github.com/PyCQA/docformatter
+#   rev: master
+#   hooks:
+#     - id: docformatter
+#       additional_dependencies: [tomli]
+#       args: [--in-place, --wrap-descriptions=120, --wrap-summaries=120]
+#       # --config, ./pyproject.toml
 
-- repo: https://github.com/psf/black
-  rev: 24.8.0
-  hooks:
-  - id: black
-    language_version: python3
+# - repo: https://github.com/psf/black
+#   rev: 24.8.0
+#   hooks:
+#   - id: black
+#     language_version: python3
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
   rev: v0.6.8
   hooks:
     - id: ruff
       args: [--fix, --exit-non-zero-on-fix]
+    - id: ruff-format
 
 ## If like to embrace black styles even in the docs:
 # - repo: https://github.com/asottile/blacken-docs

CHANGELOG.md

@@ -1,5 +1,10 @@
 # Changelog
 
+## Version 0.5.0
+
+- chore: Remove Python 3.8 (EOL)
+- precommit: Replace docformatter with ruff's formatter
+
 ## Version 0.4.7
 
 - Fix package version issues to support Python<=3.9. Mostly related to how anndata dependencies are versioned in the MuData package discussed [here](https://github.com/scverse/mudata/issues/82).

pyproject.toml

@@ -16,6 +16,10 @@ extend-ignore = ["F821"]
 [tool.ruff.pydocstyle]
 convention = "google"
 
+[tool.ruff.format]
+docstring-code-format = true
+docstring-code-line-length = 20
+
 [tool.ruff.per-file-ignores]
 "__init__.py" = ["E402", "F401"]
 

setup.cfg

@@ -41,7 +41,7 @@ package_dir =
     =src
 
 # Require a min/specific Python version (comma-separated conditions)
-python_requires = >=3.8
+python_requires = >=3.9
 
 # Add here dependencies of your project (line-separated), e.g. requests>=2.2,<3.0.
 # Version specifiers like >=2.2,<3.0 avoid problems due to API changes in