[Working version for Small 2d and BRT] Small 2D and BRT fixes #586
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Python Test and Package | |
| on: | |
| push: | |
| branches: | |
| - dev | |
| tags: | |
| - "v*" | |
| pull_request: | |
| branches: | |
| - dev | |
| env: | |
| HEDWIG_ENV: dev | |
| jobs: | |
| docs: | |
| runs-on: ubuntu-latest | |
| name: Docs | |
| needs: test | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.8 | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install -r docs/requirements.txt | |
| - name: Build Sphinx Documentation | |
| run: | | |
| make -C docs html | |
| - name: Upload documentation | |
| if: github.event_name == 'push' | |
| uses: actions/upload-artifact@v1 | |
| with: | |
| name: sphinx-docs | |
| path: docs/_build/html | |
| - name: Update gh-pages | |
| if: github.ref == 'refs/heads/dev' | |
| run: | | |
| rm docs/_build/html/.buildinfo | |
| touch docs/_build/html/.nojekyll | |
| git update-ref refs/heads/${TARGET_BRANCH} origin/${TARGET_BRANCH} | |
| ./.github/workflows/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: ${{ secrets.github_token }} | |
| TARGET_BRANCH: "gh-pages" | |
| test: | |
| runs-on: ubuntu-latest | |
| name: Check coverage | |
| permissions: | |
| # Gives the action the necessary permissions for publishing new | |
| # comments in pull requests. | |
| pull-requests: write | |
| # Gives the action the necessary permissions for pushing data to the | |
| # python-coverage-comment-action branch, and for editing existing | |
| # comments (to avoid publishing multiple comments in the same PR) | |
| contents: write | |
| strategy: | |
| matrix: | |
| python-version: ["3.8"] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - uses: actions/setup-java@v3 | |
| with: | |
| distribution: 'zulu' | |
| java-version: '17' | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.8 | |
| - name: Create LFS file list | |
| run: | | |
| git lfs ls-files -l | cut -d' ' -f1 | sort > .lfs-assets-id | |
| - name: Restore LFS cache | |
| uses: actions/cache@v2 | |
| id: lfs-cache | |
| with: | |
| path: .git/lfs | |
| key: lfs-v1-${{ hashFiles('.lfs-assets-id') }} | |
| restore-keys: lfs-v1- | |
| - name: Git LFS Pull | |
| run: | | |
| git lfs pull | |
| - name: Install dependencies | |
| run: | | |
| sudo apt -y update && sudo apt -y install libgl-dev graphicsmagick libblosc1 | |
| IMOD=imod_4.11.24_RHEL7-64_CUDA10.1.sh | |
| export IMOD_DIR=/usr/local/IMOD | |
| export PATH=$IMOD_DIR/bin:$PATH | |
| wget https://bio3d.colorado.edu/imod/AMD64-RHEL5/${IMOD} && sudo sh ${IMOD} -yes && rm -f ${IMOD} | |
| BIO2R_V=0.7.0 | |
| BIO2R_Z=bioformats2raw-${BIO2R_V}.zip | |
| export BIO2R_DIR=/usr/local/BIO2R | |
| export PATH=$BIO2R_DIR/bioformats2raw-${BIO2R_V}/bin:$PATH | |
| wget https://github.com/glencoesoftware/bioformats2raw/releases/download/v${BIO2R_V}/${BIO2R_Z} && sudo unzip ${BIO2R_Z} -d ${BIO2R_DIR} && rm -f ${BIO2R_Z} | |
| python -m pip install --upgrade pip | |
| pip install -e . -r requirements-dev.txt | |
| - name: Directory setup | |
| run: | | |
| cp .env.sample .env | |
| - name: Test Coverage | |
| continue-on-error: true | |
| run: | | |
| BIO2R_V=0.7.0 | |
| export BIO2R_DIR=/usr/local/BIO2R/bioformats2raw-${BIO2R_V} | |
| export IMOD_DIR=/usr/local/IMOD | |
| export PATH=$BIO2R_DIR/bin:$IMOD_DIR/bin:$PATH | |
| python -m pytest -v --log-cli-level=INFO -m "not (slow or localdata)" | |
| - name: Coverage Badge | |
| uses: tj-actions/coverage-badge-py@v2 | |
| - name: Coverage comment | |
| id: coverage_comment | |
| uses: py-cov-action/python-coverage-comment-action@v3 | |
| with: | |
| GITHUB_TOKEN: ${{ github.token }} | |
| - name: Store Pull Request comment to be posted | |
| uses: actions/upload-artifact@v3 | |
| if: steps.coverage_comment.outputs.COMMENT_FILE_WRITTEN == 'true' | |
| with: | |
| # If you use a different name, update COMMENT_ARTIFACT_NAME accordingly | |
| name: python-coverage-comment-action | |
| # If you use a different name, update COMMENT_FILENAME accordingly | |
| path: python-coverage-comment-action.txt |