Migrate to hatch for packaging

.coveragerc

@@ -1,8 +1,8 @@
 # .coveragerc to control coverage.py
 [run]
 branch = True
-source = biocutils
-# omit = bad_file.py
+source = src
+omit = tests/*
 
 [paths]
 source =

.github/dependabot.yml

@@ -0,0 +1,15 @@
+version: 2
+updates:
+ - package-ecosystem: "github-actions"
+ directory: "/"
+ schedule:
+ interval: "weekly"
+ labels:
+ - "dependencies"
+
+ - package-ecosystem: "pip"
+ directory: "/"
+ schedule:
+ interval: "weekly"
+ labels:
+ - "dependencies"

.github/workflows/pre-commit.yml

@@ -0,0 +1,16 @@
+name: pre-commit
+
+on:
+ pull_request:
+ push:
+ branches: [main]
+
+jobs:
+ pre-commit:
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/checkout@v7
+ - uses: actions/setup-python@v5
+ with:
+ python-version: '3.12'
+ - uses: pre-commit/action@v3.0.1

.github/workflows/publish-pypi.yml

@@ -1,52 +1,91 @@
-name: Publish to PyPI
+name: Publish to PyPI and GitHub Pages
 
 on:
  push:
  tags: "*"
 
 jobs:
- build:
+ build-and-test:
+ name: Build and Test
  runs-on: ubuntu-latest
- permissions:
- id-token: write
- repository-projects: write
- contents: write
- pages: write
-
  steps:
- - uses: actions/checkout@v4
+ - uses: actions/checkout@v7
 
  - name: Set up Python 3.12
  uses: actions/setup-python@v5
  with:
  python-version: 3.12
 
- - name: Install dependencies
- run: |
- python -m pip install --upgrade pip
- pip install tox
+ - name: Install tox
+ run: python -m pip install tox
 
- - name: Test with tox
- run: |
- tox
+ - name: Test
+ run: tox -e default
 
- - name: Build Project and Publish
- run: |
- python -m tox -e clean,build
+ - name: Build Project
+ run: tox -e build
 
- # This uses the trusted publisher workflow so no token is required.
- - name: Publish to PyPI
- uses: pypa/gh-action-pypi-publish@release/v1
+ - name: Store the distribution packages
+ uses: actions/upload-artifact@v4
+ with:
+ name: python-package-distributions
+ path: dist/
+
+ build-docs:
+ name: Build Documentation
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/checkout@v7
+
+ - name: Set up Python 3.12
+ uses: actions/setup-python@v5
+ with:
+ python-version: 3.12
+
+ - name: Install tox
+ run: python -m pip install tox
 
  - name: Build docs
- run: |
- tox -e docs
+ run: tox -e docs
 
- - run: touch ./docs/_build/html/.nojekyll
+ - name: Add .nojekyll
+ run: touch ./docs/_build/html/.nojekyll
 
- - name: GH Pages Deployment
- uses: JamesIves/github-pages-deploy-action@v4
+ - name: Upload Pages artifact
+ uses: actions/upload-pages-artifact@v5
  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
+ path: ./docs/_build/html
+
+ publish-pypi:
+ name: Publish to PyPI
+ needs: build-and-test
+ runs-on: ubuntu-latest
+ environment:
+ name: pypi
+ url: https://pypi.org/p/biocutils
+ permissions:
+ id-token: write # IMPORTANT: mandatory for trusted publishing
+ steps:
+ - name: Download all the dists
+ uses: actions/download-artifact@v8
+ with:
+ name: python-package-distributions
+ path: dist/
+
+ - name: Publish package to PyPI
+ uses: pypa/gh-action-pypi-publish@release/v1
+
+ deploy-pages:
+ name: Deploy GitHub Pages
+ needs: build-docs
+ runs-on: ubuntu-latest
+ permissions:
+ pages: write
+ id-token: write
+ environment:
+ name: github-pages
+ url: ${{ steps.deployment.outputs.page_url }}
+ steps:
+ - name: Deploy to GitHub Pages
+ id: deployment
+ uses: actions/deploy-pages@v5

.github/workflows/run-tests.yml

@@ -36,21 +36,18 @@
  runs-on: ${{ matrix.platform }}
  name: Python ${{ matrix.python }}, ${{ matrix.platform }}
  steps:
- - uses: actions/checkout@v4
+ - uses: actions/checkout@v7
 
- - uses: actions/setup-python@v5
-id: setup-python
+ - name: Set up Python
+uses: actions/setup-python@v5
  with:
  python-version: ${{ matrix.python }}
 
- - name: Install dependencies
- run: |
- python -m pip install --upgrade pip
- pip install tox coverage
+ - name: Install tox
+ run: python -m pip install tox coverage
 
  - name: Run tests
  run: >-
- pipx run --python '${{ steps.setup-python.outputs.python-path }}'
  tox
  -- -rFEx --durations 10 --color yes --cov --cov-branch --cov-report=xml # pytest args
 
@@ -65,9 +62,9 @@
  fi
 
  - name: Upload coverage reports to Codecov with GitHub Action
- uses: codecov/codecov-action@v5
+ uses: codecov/codecov-action@v7
  if: ${{ steps.codecov-check.outputs.codecov == 'true' }}
-env:
-CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+with:
+token: ${{ secrets.CODECOV_TOKEN }}
  slug: ${{ github.repository }}
  flags: ${{ matrix.platform }} - py${{ matrix.python }}

.gitignore

@@ -53,3 +53,59 @@ docs/html
 .venv*/
 .conda*/
 .python-version
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*$py.class
+# C extensions
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+# PyInstaller
+*.manifest
+*.spec
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.cache
+nosetests.xml
+*.cover
+*.py,cover
+.hypothesis/
+cover/
+# Sphinx documentation
+docs/_build/
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+# mypy, ruff, etc
+.mypy_cache/
+.ruff_cache/
+.pyre/
+# Editors
+.vscode/
+.idea/
+*.swp
+*.swo

.pre-commit-config.yaml

@@ -33,10 +33,12 @@ repos:
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
  # Ruff version.
- rev: v0.15.6
+ rev: v0.16.2
  hooks:
- - id: ruff
- args: [--fix, --exit-non-zero-on-fix]
+ # Run the linter.
+ - id: ruff-check
+ args: [--fix, --exit-zero]
+ # Run the formatter.
  - id: ruff-format
 
 ## If like to embrace black styles even in the docs:
@@ -51,3 +53,10 @@ repos:
 # rev: v2.2.5
 # hooks:
 # - id: codespell
+
+- repo: https://github.com/PyCQA/bandit
+ rev: 1.7.9
+ hooks:
+ - id: bandit
+ args: ["-c", "pyproject.toml"]
+ additional_dependencies: ["bandit[toml]"]

CHANGELOG.md

@@ -1,5 +1,9 @@
 # Changelog
 
+## Version 0.5.0
+
+- Migate the package to `hatch`.
+
 ## Version 0.4.0 - 0.4.2
 
 - Implemented R's `split()` utility to split a sequence by a grouping factor.