Update to sckit learn 1.3 #123
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name: Python Test and Package | |
on: | |
push: | |
branches: | |
- master | |
tags: | |
- 'v*' | |
pull_request: | |
branches: | |
- master | |
jobs: | |
linting: | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v3 | |
- name: Set up Python 3.8 | |
uses: actions/setup-python@v3 | |
with: | |
python-version: 3.8 | |
- name: Install tools | |
run: | | |
python -m pip install --upgrade pip | |
pip install black flake8 | |
- name: Lint with black | |
run: | | |
python -m black --check --diff . | |
- name: Lint with flake8 | |
run: | | |
# stop the build for flake8 issues | |
python -m flake8 . --show-source --statistics | |
test: | |
needs: linting | |
runs-on: ubuntu-latest | |
strategy: | |
matrix: | |
python-version: [3.8, 3.9] | |
steps: | |
- uses: actions/checkout@v3 | |
with: | |
fetch-depth: 0 | |
- name: Create LFS file list | |
run: | | |
git lfs ls-files -l | cut -d' ' -f1 | sort > .lfs-assets-id | |
- name: Restore LFS cache | |
uses: actions/cache@v3 | |
id: lfs-cache | |
with: | |
path: .git/lfs | |
key: lfs-v1-${{ hashFiles('.lfs-assets-id') }} | |
restore-keys: | |
lfs-v1- | |
- name: Git LFS Pull | |
run: | | |
git lfs pull | |
- name: Set up Python ${{ matrix.python-version }} | |
uses: actions/setup-python@v4 | |
with: | |
python-version: ${{ matrix.python-version }} | |
- name: Install dependencies | |
run: | | |
python -m pip install --upgrade pip | |
pip install -e .[dev] | |
env: | |
PIP_EXTRA_INDEX_URL: https://${{secrets.ARTIFACTORY_RO_USER}}:${{secrets.ARTIFACTORY_RO_TOKEN}}@artifactory.niaid.nih.gov/artifactory/api/pypi/bcbb-pypi/simple | |
- name: Test with pytest | |
run: | | |
python -m pytest --junitxml=junit/test-results-${{ matrix.python-version }}.xml | |
- name: Upload pytest test results | |
uses: actions/upload-artifact@v1 | |
with: | |
name: pytest-results-${{ matrix.python-version }} | |
path: junit/test-results-${{ matrix.python-version }}.xml | |
# Use always() to always run this step to publish test results when there are test failures | |
if: ${{ always() }} | |
package_docs: | |
needs: test | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v3 | |
with: | |
fetch-depth: 0 | |
- name: Create LFS file list | |
run: | | |
git lfs ls-files -l | cut -d' ' -f1 | sort > .lfs-assets-id | |
- name: Restore LFS cache | |
uses: actions/cache@v3 | |
id: lfs-cache | |
with: | |
path: .git/lfs | |
key: lfs-v1-${{ hashFiles('.lfs-assets-id') }} | |
restore-keys: | | |
lfs-v1- | |
- name: Git LFS Pull | |
run: | | |
git lfs pull | |
- name: Set up Python 3.9 | |
uses: actions/setup-python@v4 | |
with: | |
python-version: 3.9 | |
- name: Install dependencies | |
run: | | |
python -m pip install --upgrade pip | |
python -m pip install build | |
- name: Build package | |
run: | | |
python -m build | |
ls -la dist | |
- name: Upload package | |
if: github.event_name == 'push' | |
uses: actions/upload-artifact@v3 | |
with: | |
name: python-packages | |
path: dist | |
- name: Build Sphinx Documentation | |
run: | | |
# install so that setuptools_scm generate version for package | |
pip install -r docs/requirements.txt -e . | |
make -C docs html | |
env: | |
PIP_EXTRA_INDEX_URL: https://${{secrets.ARTIFACTORY_RO_USER}}:${{secrets.ARTIFACTORY_RO_TOKEN}}@artifactory.niaid.nih.gov/artifactory/api/pypi/bcbb-pypi/simple | |
- name: Upload documentation | |
if: github.event_name == 'push' | |
uses: actions/upload-artifact@v3 | |
with: | |
name: sphinx-docs | |
path: docs/_build/html | |
- name: Update gh-pages | |
if: github.ref == 'refs/heads/master' | |
run: | | |
rm docs/_build/html/.buildinfo | |
touch docs/_build/html/.nojekyll | |
git update-ref refs/heads/${TARGET_BRANCH} origin/${TARGET_BRANCH} | |
./utils/update-gh-pages.sh docs/_build/html | |
repo_uri="https://x-access-token:${GITHUB_TOKEN}@github.com/${GITHUB_REPOSITORY}.git" | |
git push $repo_uri ${TARGET_BRANCH} | |
env: | |
GITHUB_TOKEN: ${{ secrets.github_token }} | |
TARGET_BRANCH: 'gh-pages' | |
publish_release: | |
if: startsWith(github.ref, 'refs/tags/v') | |
needs: package_docs | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/download-artifact@v3 | |
id: download | |
with: | |
name: python-packages | |
- name: Extract Python Packages | |
id: files | |
run: | | |
cd ${{steps.download.outputs.download-path}} | |
echo ::set-output name=file1::$(ls tbpcxr*any.whl) | |
echo ::set-output name=file2::$(ls tbpcxr*.tar.gz) | |
- name: Create Release | |
id: create_release | |
uses: actions/create-release@v1 | |
env: | |
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
with: | |
tag_name: ${{ github.ref }} | |
release_name: Release ${{ github.ref }} | |
draft: false | |
prerelease: false | |
- name: Upload Release Asset Wheel | |
if: startsWith(github.ref, 'refs/tags/v') | |
uses: actions/upload-release-asset@v1 | |
env: | |
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
with: | |
# This pulls from the CREATE RELEASE step above, referencing it's ID to get its outputs object, which include | |
# a `upload_url`. See this blog post for more info: | |
# https://jasonet.co/posts/new-features-of-github-actions/#passing-data-to-future-steps | |
upload_url: ${{ steps.create_release.outputs.upload_url }} | |
asset_path: ${{steps.download.outputs.download-path}}/${{steps.files.outputs.file1}} | |
asset_name: ${{steps.files.outputs.file1}} | |
asset_content_type: application/octet-stream | |
- name: Upload Release Asset Source | |
if: startsWith(github.ref, 'refs/tags/v') | |
uses: actions/upload-release-asset@v1 | |
env: | |
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
with: | |
upload_url: ${{ steps.create_release.outputs.upload_url }} | |
asset_path: ${{steps.download.outputs.download-path}}/${{steps.files.outputs.file2}} | |
asset_name: ${{steps.files.outputs.file2}} | |
asset_content_type: application/octet-stream | |
- name: bcbb-pypi upload | |
run: | | |
python -m pip install twine | |
python -m twine check ${{steps.download.outputs.download-path}}/* | |
python -m twine upload ${{steps.download.outputs.download-path}}/* | |
env: | |
TWINE_REPOSITORY_URL: https://artifactory.niaid.nih.gov/artifactory/api/pypi/bcbb-pypi | |
TWINE_PASSWORD: ${{secrets.BCBB_PYPI_PASSWORD}} | |
TWINE_USERNAME: ${{secrets.BCBB_PYPI_USERNAME}} |