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Add gpu and docs extras to tox setup #17

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Add gpu and docs extras to tox setup

Add gpu and docs extras to tox setup #17

Workflow file for this run

.github/workflows/ci-cd.yml at cb6f1ea
# File: .github/workflows/release.yml
# This workflow handles:
# 1. For Pull Requests:
# - Runs all tests
# - Verifies documentation builds
# 2. For Pre-releases:
# - Runs all tests
# - Builds documentation
# - Deploys documentation to GitHub Pages
# - Publishes package to PyPI
# - If everything passes:
# - Updates the release to a full release (removes pre-release status)
name: Test, Docs & Publish
on:
# Run on pull requests to main branch to verify changes
pull_request:
branches:
- main
# Run when a new release is published to deploy docs and package
release:
types: [published]
permissions:
contents: write # Needed to update release status
pages: write # Needed for docs deployment
id-token: write # Needed for docs deployment
jobs:
test:
if: github.event_name == 'pull_request' || (github.event_name == 'release' && github.event.release.prerelease == true)
runs-on: ubuntu-latest
strategy:
matrix:
python-version: ['3.8', '3.13'] # Test on limit versions (3.8 and latest)
steps:
- name: Checkout repository
uses: actions/checkout@v4
with:
fetch-depth: 0 # Fetch full repository history, including all tags
- name: Verify available tags
run: git tag -l
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
cache: "pip" # Enables automatic pip caching
# Cache test data
- name: Cache test data
uses: actions/cache@v4
with:
path: data/
key: snputils-test-data-${{ hashFiles('snputils/snp/io/read/__test__/conftest.py') }}
- name: Install dependencies
run: |
python -m pip install --upgrade pip
python -m pip install tox tox-gh-actions
- name: Run tests
run: python -m tox
build-docs:
# Only build documentation after tests have passed
needs: test
if: needs.test.result == 'success' && (github.event_name == 'pull_request' || (github.event_name == 'release' && github.event.release.prerelease == true))
runs-on: ubuntu-latest
steps:
- name: Checkout repository
uses: actions/checkout@v4
with:
fetch-depth: 0 # Fetch full repository history, including all tags
- name: Verify available tags
run: git tag -l
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: '3.13' # Ensure this is the latest Python version so the cached deps are used
cache: 'pip'
- name: Install package with docs dependencies
run: |
python -m pip install --upgrade pip
python -m pip install '.[docs]'
# Build documentation and verify it builds correctly
# DOC_ALLOW_EXEC=1 allows executing code examples in docstrings
- name: Build documentation
run: DOC_ALLOW_EXEC=1 pdoc --docformat google -o docs/ snputils
# Upload Pages artifact if this is a release
- name: Upload Pages artifact
if: github.event_name == 'release'
uses: actions/upload-pages-artifact@v3
with:
path: docs/
deploy:
needs: [test, build-docs]
if: needs.build-docs.result == 'success' && github.event_name == 'release' && github.event.release.prerelease == true
runs-on: ubuntu-latest
environment:
name: github-pages
url: ${{ steps.deployment.outputs.page_url }}
steps:
# Deploy documentation to GitHub Pages
- name: Deploy to GitHub Pages
id: deployment
uses: actions/deploy-pages@v4
# Build and publish to PyPI
- name: Checkout repository
uses: actions/checkout@v4
with:
fetch-depth: 0 # Fetch full repository history, including all tags
- name: Verify available tags
run: git tag -l
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: '3.13' # Ensure this is the latest Python version so the cached deps are used
cache: 'pip'
- name: Install build dependencies
run: |
python -m pip install --upgrade pip
python -m pip install build
- name: Build package
run: python -m build
- name: Publish package to PyPI
uses: pypa/gh-action-pypi-publish@release/v1
with:
user: __token__
password: ${{ secrets.PYPI_API_TOKEN }}
# Update the release to a full release and mark it as latest
- name: Mark Release as Final and Latest
if: success()
env:
GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
run: |
gh release edit ${{ github.event.release.tag_name }} --prerelease=false --latest