Migrate package to hatch

.coveragerc

@@ -1,8 +1,8 @@
 # .coveragerc to control coverage.py
 [run]
 branch = True
-source = spatialexperiment
-# 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

@@ -1,55 +1,91 @@
-# 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: 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 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@v5
         with:
-          python-version: 3.11
+          python-version: 3.12
+
+      - name: Install tox
+        run: python -m pip install tox
 
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install tox
+      - name: Test
+        run: tox -e default
 
-      - name: Test with tox
-        run: |
-          tox
+      - name: Build Project
+        run: tox -e build
+
+      - 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
 
-      - name: Build Project and Publish
-        run: |
-          python -m tox -e clean,build
+  publish-pypi:
+    name: Publish to PyPI
+    needs: build-and-test
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/spatialexperiment
+    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/
 
-      # This uses the trusted publisher workflow so no token is required.
-      - name: Publish to PyPI
+      - 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

@@ -28,29 +28,26 @@
   test:
     strategy:
       matrix:
-        python: ["3.10", "3.11", "3.12", "3.13"]
+        python: ["3.10", "3.11", "3.12", "3.13", "3.14"]
         platform:
           - ubuntu-latest
           # - macos-latest
           # - windows-latest
     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

@@ -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

@@ -17,16 +17,46 @@ 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: 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/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:
+# - repo: https://github.com/asottile/blacken-docs
+#   rev: v1.13.0
+#   hooks:
+#   - id: blacken-docs
+#     additional_dependencies: [black]
+
 ## Check for misspells in documentation files:
 # - repo: https://github.com/codespell-project/codespell
 #   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 0.2.0
+
+- Migrate package to hatch.
+
 ## Version 0.1.0
 
 - Migrating changes from SCE, replace `validate` with `_validate`.