[Working version for Small 2d and BRT] Small 2D and BRT fixes #593
Workflow file for this run
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| 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 |