Remove support for Python 3.8 (#3)

.github/workflows/publish-pypi.yml

@@ -0,0 +1,49 @@
+name: Publish to PyPI
+
+on:
+  push:
+    tags: "*"
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - 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/run-tests.yml

@@ -0,0 +1,33 @@
+name: Test the library
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+
+    name: Python ${{ matrix.python-version }}
+    steps:
+      - 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

@@ -0,0 +1,32 @@
+exclude: '^docs/conf.py'
+
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v5.0.0
+  hooks:
+  - id: trailing-whitespace
+  - id: check-added-large-files
+  - id: check-ast
+  - id: check-json
+  - id: check-merge-conflict
+  - id: check-xml
+  - id: check-yaml
+  - id: debug-statements
+  - id: end-of-file-fixer
+  - id: requirements-txt-fixer
+  - 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/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.8.2
+  hooks:
+    - id: ruff
+      args: [--fix, --exit-non-zero-on-fix]
+    - id: ruff-format
+
+## Check for misspells in documentation files:
+# - repo: https://github.com/codespell-project/codespell
+#   rev: v2.2.5
+#   hooks:
+#   - id: codespell

CHANGELOG.md

@@ -1,4 +1,12 @@
 # Changelog
 
-## Version 0.1 (development)
+## Version 0.2.0
 
+- chore: Remove Python 3.8 (EOL).
+- Add support for Python 3.13.
+- precommit: Replace docformatter with ruff's formatter.
+
+
+## Version 0.1 
+
+- Initial release.

docs/conf.py

@@ -304,4 +304,15 @@
     "multiassayexperiment": ("https://biocpy.github.io/MultiAssayExperiment/", None),
 }
 
-print(f"loading configurations for {project} {version} ...", file=sys.stderr)
+print(f"loading configurations for {project} {version} ...", file=sys.stderr)
+
+# -- Biocsetup configuration -------------------------------------------------
+
+autodoc_default_options = {
+    "special-members": True,
+    "undoc-members": True,
+    "exclude-members": "__weakref__, __dict__, __str__, __module__",
+}
+
+autosummary_generate = True
+autosummary_imported_members = True

docs/requirements.txt

@@ -3,6 +3,7 @@
 # under `install_requires` in `setup.cfg` is also listed here!
 # sphinx_rtd_theme
 myst-parser[linkify]
+myst-nb
 sphinx>=3.2.1
 furo
-sphinx-autodoc-typehints
+sphinx-autodoc-typehints

pyproject.toml

@@ -7,3 +7,19 @@ build-backend = "setuptools.build_meta"
 # For smarter version schemes and other configuration options,
 # check out https://github.com/pypa/setuptools_scm
 version_scheme = "no-guess-dev"
+
+[tool.ruff]
+line-length = 120
+src = ["src"]
+exclude = ["tests"]
+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

@@ -41,17 +41,17 @@ 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
 # new major versions. This works if the required packages follow Semantic Versioning.
 # For more information, check out https://semver.org/.
 install_requires =
     importlib-metadata; python_version<"3.8"
-    dolomite_base>=0.2.4
-    dolomite_sce>=0.1.2
-    dolomite_se>=0.1.3
+    dolomite-base>=0.4.2
+    dolomite_sce>=0.3.0
+    dolomite_se>=0.3.0
     multiassayexperiment>=0.4.2
     biocutils
     pandas