ENH: Reset index after ITK filters, keep ITK object and python interface consistent #14
Workflow file for this run
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| name: ci-pytest | |
| # Fast tests with cached antspy build designed to test changes in the python code | |
| # Builds on Linux only, with a single python version | |
| on: | |
| push: | |
| branches: | |
| - master | |
| pull_request: | |
| branches: | |
| - master | |
| workflow_dispatch: | |
| env: | |
| # Updates or changes to this, or the runner OS or arch will invalidate the cache | |
| python_version: '3.10' # Python version to use for testing - update when needed | |
| jobs: | |
| test: | |
| runs-on: ubuntu-20.04 | |
| # Default shell needs to be bash for conda | |
| # https://github.com/conda-incubator/setup-miniconda?tab=readme-ov-file#important | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| steps: | |
| - name: Setup Miniconda | |
| uses: conda-incubator/setup-miniconda@030178870c779d9e5e1b4e563269f3aa69b04081 # v3.0.3, devs recommend using hash | |
| with: | |
| miniconda-version: "latest" | |
| python-version: ${{ env.python_version }} | |
| auto-update-conda: true | |
| activate-environment: "test-env" | |
| - name: Configure Conda to use only .tar.bz2 | |
| run: | | |
| conda config --set use_only_tar_bz2 true | |
| - name: Checkout code | |
| uses: actions/checkout@v4 # Checkout PR code to 'antspy-pr' | |
| with: | |
| path: antspy-pr | |
| - name: Load conda environment from cache if available | |
| id: cache-env | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/conda-env.tar.bz2 | |
| key: >- | |
| ${{ runner.os }}-conda-${{ env.python_version }}- | |
| ${{ hashFiles('antspy-pr/ants/environment.yml', 'antspy-pr/ants/requirements.txt', 'antspy-pr/ants/setup.py', | |
| 'antspy-pr/ants/scripts/configure_ITK.sh', 'antspy-pr/ants/scripts/configure_ANTsPy.sh', | |
| 'antspy-pr/ants/lib/*') }} | |
| - name: Unpack cached environment | |
| if: steps.cache-env.outputs.cache-hit == 'true' | |
| run: | | |
| mkdir -p ${CONDA}/envs/antspy-env | |
| tar -xjf ~/conda-env.tar.bz2 -C ${CONDA}/envs/antspy-env | |
| conda activate antspy-env | |
| conda-unpack | |
| - name: Install dependencies and ANTsPy from PR | |
| if: steps.cache-env.outputs.cache-hit != 'true' | |
| run: | | |
| conda create -n antspy-env python=${{ env.python_version }} -y | |
| conda activate antspy-env | |
| conda install -c conda-forge conda-pack | |
| conda info | |
| pip install ./antspy-pr | |
| conda list | |
| antspy-pr/tests/run_tests.sh | |
| conda pack -n antspy-env -o ~/conda-env.tar.bz2 | |
| - name: Cache Conda environment | |
| if: steps.cache-env.outputs.cache-hit != 'true' | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/conda-env.tar.bz2 | |
| key: >- | |
| ${{ runner.os }}-conda-${{ env.python_version }}- | |
| ${{ hashFiles('antspy-pr/ants/environment.yml', 'antspy-pr/ants/requirements.txt', 'antspy-pr/ants/setup.py', | |
| 'antspy-pr/ants/scripts/configure_ITK.sh', 'antspy-pr/ants/scripts/configure_ANTsPy.sh', | |
| 'antspy-pr/ants/lib/*') }}) }} | |
| - name: Replace installed ANTsPy with PR code | |
| if: steps.cache-env.outputs.cache-hit == 'true' | |
| run: | | |
| conda activate antspy-env | |
| echo "List of installed packages in cached env:" | |
| conda list | |
| ANTS_SITE_PACKAGES="${CONDA}/envs/antspy-env/lib/python${{ env.python_version }}/site-packages/ants" | |
| for d in contrib core learn registration segmentation utils viz; do | |
| rm -rf $ANTS_SITE_PACKAGES/$d; | |
| cp -r antspy-pr/ants/$d $ANTS_SITE_PACKAGES/$d; | |
| done | |
| find $ANTS_SITE_PACKAGES -name '__pycache__' -exec rm -rf {} + | |
| - name: Run tests | |
| if: steps.cache-env.outputs.cache-hit == 'true' | |
| run: | | |
| conda activate antspy-env | |
| bash antspy-pr/tests/run_tests.sh |