migrate to hatch + uv

.coveragerc

@@ -1,28 +1,13 @@
-# .coveragerc to control coverage.py
 [run]
-branch = True
-source = biocframe
-# omit = bad_file.py
-
-[paths]
-source =
-    src/
-    */site-packages/
+source = src
+omit = tests/*
 
 [report]
-# Regexes for lines to exclude from consideration
 exclude_lines =
-    # Have to re-enable the standard pragma
     pragma: no cover
-
-    # Don't complain about missing debug-only code:
     def __repr__
-    if self\.debug
-
-    # Don't complain if tests don't hit defensive assertion code:
+    if self.debug:
     raise AssertionError
     raise NotImplementedError
-
-    # Don't complain if non-runnable code isn't run:
     if 0:
     if __name__ == .__main__.:

.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@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+      - uses: pre-commit/action@v3.0.1

.github/workflows/publish-pypi.yml

@@ -1,52 +1,101 @@
-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
 
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+
       - 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: uv tool install tox --with tox-uv
 
-      - 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@v4
+
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.12
+
+      - name: Install tox
+        run: uv tool install tox --with tox-uv
 
       - name: Build docs
-        run: |
-          tox -e docs
+        run: tox -e docs
+
+      - name: Add .nojekyll
+        run: touch ./docs/_build/html/.nojekyll
 
-      - run: touch ./docs/_build/html/.nojekyll
+      - name: Upload Pages artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: ./docs/_build/html
 
-      - name: GH Pages Deployment
-        uses: JamesIves/github-pages-deploy-action@v4
+  publish-pypi:
+    name: Publish to PyPI
+    needs: build-and-test
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/biocframe
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+    steps:
+      - name: Download all the dists
+        uses: actions/download-artifact@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: 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@v4

.github/workflows/run-tests.yml

@@ -38,21 +38,25 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v5
-        id: setup-python
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python }}
 
+      - name: Install tox
+        run: uv tool install tox --with tox-uv
+
       - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install tox coverage
+        run: uv sync --all-extras --python ${{ matrix.python }}
 
       - 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
+        run: |
+          tox -e default -- --cov --cov-branch --cov-report=xml
 
       - name: Check for codecov token availability
         id: codecov-check

.gitignore

@@ -52,3 +52,59 @@ MANIFEST
 .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 0.8.0
+
+- Package migrated to hatch+uv using the `hatchit` package.
+
 ## Version 0.7.0 - 0.7.3
 
 - Major update to type hints throughout the module for better type safety and consistency.