Cookpa patch 6 #2
Workflow file for this run
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| name: ci-pytest | |
| on: pull_request | |
| env: | |
| # Changing either of these two things will invalidate the cache and cause a full re-install | |
| # of ANTsPy and its dependencies | |
| # Update this hash whenever there is a change that affects ANTsPy libraries or dependencies | |
| # Updates or changes to the runner OS or arch will also invalidate the cache | |
| python_version: '3.9' # Python version to use for testing - update when needed | |
| jobs: | |
| test: | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Setup Miniconda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| python-version: ${{ env.python_version }} | |
| activate-environment: antspy-env | |
| - name: Load conda environment from cache if available | |
| id: cache-env | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/conda-env.tar.gz | |
| key: >- | |
| ${{ runner.os }}-conda-${{ env.python_version }}- | |
| ${{ hashFiles('environment.yml', 'requirements.txt', 'setup.py', | |
| 'scripts/configure_ITK.sh', 'scripts/configure_ANTsPy.sh') }} | |
| - name: Unpack cached environment | |
| if: steps.cache-env.outputs.cache-hit == 'true' | |
| run: | | |
| tar -xzf ~/conda-env.tar.gz -C ${CONDA}/envs/antspy-env | |
| - name: Checkout ANTsPy at specific commit | |
| if: steps.cache-env.outputs.cache-hit != 'true' | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: ANTsX/ANTsPy | |
| ref: ${{ env.antspy_ref_hash }} | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| path: antspy-temp | |
| - name: Install dependencies and ANTsPy from commit | |
| if: steps.cache-env.outputs.cache-hit != 'true' | |
| run: | | |
| source $CONDA/etc/profile.d/conda.sh | |
| conda install -c conda-forge conda-pack | |
| conda create -n antspy-env python=${{ env.python_version }} -y | |
| conda activate antspy-env | |
| pip install ./antspy-temp | |
| # Pack the environment | |
| conda deactivate | |
| conda pack -n antspy-env -o ~/conda-env.tar.gz | |
| - name: Cache Conda environment | |
| if: steps.cache-env.outputs.cache-hit != 'true' | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/conda-env.tar.gz | |
| key: >- | |
| ${{ runner.os }}-conda-${{ env.python_version }}- | |
| ${{ hashFiles('environment.yml', 'requirements.txt', 'setup.py', | |
| 'scripts/configure_ITK.sh', 'scripts/configure_ANTsPy.sh') }} | |
| - uses: actions/checkout@v4 # Checkout PR code to 'antspy-pr' | |
| with: | |
| path: antspy-pr | |
| - name: Replace installed ANTsPy with PR code | |
| run: | | |
| source $CONDA/etc/profile.d/conda.sh | |
| conda activate antspy-env | |
| ANTS_SITE_PACKAGES=$(python -c "import os, ants; print(os.path.dirname(ants.__file__))") | |
| rm -rf $ANTS_SITE_PACKAGES/ants | |
| cp -r antspy-pr/ants $ANTS_SITE_PACKAGES/ants | |
| - name: Run tests | |
| run: | | |
| source $CONDA/etc/profile.d/conda.sh | |
| conda activate antspy-env | |
| bash antspy-pr/tests/run_tests.sh |