github action for integration pipeline #7
Workflow file for this run
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| name: Tutorials CI | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| env: | |
| debug: 'true' | |
| jobs: | |
| integration: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-latest"] # , "macos-latest", "windows-latest" | |
| python-version: ["3.9"] | |
| steps: | |
| # - uses: actions/checkout@v4 | |
| - name: Download Conda YAML file | |
| run: curl -o pipeline_env.yaml https://raw.githubusercontent.com/DendrouLab/panpipes/main/pipeline_env.yaml | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniforge-version: latest | |
| auto-activate-base: true | |
| auto-update-conda: true | |
| channels: conda-forge | |
| channel-priority: strict | |
| activate-environment: pipeline_env | |
| environment-file: pipeline_env.yaml # consider moving to etc/pipeline_env.yaml | |
| # Note: the pinned versions in pipeline_env.yaml are not respected during the miniconda step above | |
| - name: Pin version of pip dependencies | |
| shell: bash -el {0} | |
| run: pip install --force-reinstall -v \ | |
| boto3==1.34.34 \ | |
| botocore==1.34.34 \ | |
| flax==0.8.0 \ | |
| fonttools==4.47.2 \ | |
| jax==0.4.23 \ | |
| jaxlib==0.4.23 \ | |
| numpy==1.22.4 \ | |
| orbax-checkpoint==0.5.2 \ | |
| pytorch-lightning==2.1.4 | |
| - name: Conda info | |
| if: env.debug == 'true' | |
| shell: bash -el {0} | |
| run: conda info | |
| - name: Conda list | |
| if: env.debug == 'true' | |
| shell: pwsh | |
| run: conda list | |
| # Note: all three files are renamed during the download to trim the "subsample_" prefix | |
| - name: Preparing the data | |
| run: | | |
| mkdir -p teaseq/integration && cd teaseq/integration | |
| curl -L -o teaseq.h5mu https://figshare.com/ndownloader/files/44471927 | |
| # Note: we run the following to test that the commands works | |
| # However, the following task will replacing the file anyway | |
| - name: Preparing the configuration file | |
| shell: bash -el {0} | |
| run: | | |
| cd teaseq/integration | |
| panpipes integration config | |
| - name: Edit the submission file | |
| run: | | |
| cd teaseq/integration | |
| curl -o pipeline.yml https://panpipes-tutorials.readthedocs.io/en/latest/_downloads/f834fdb0a65979b0e4d11d6d75188a8e/pipeline.yml | |
| - name: Replace template contents in configuration file | |
| run: | | |
| cd teaseq/ingest | |
| sed -i 's+/Users/fabiola.curion/Documents/devel/miniconda3/envs/pipeline_env+pipeline_env+g' pipeline.yml | |
| - name: File tree | |
| if: env.debug == 'true' | |
| run: tree | |
| - name: Review pipeline tasks | |
| shell: bash -el {0} | |
| run: | | |
| cd teaseq/integration | |
| panpipes integration show full --local | |
| - name: Run pipeline tasks | |
| shell: bash -el {0} | |
| run: | | |
| cd teaseq/integration | |
| panpipes integration make full --local | |
| - name: File tree | |
| if: env.debug == 'true' | |
| run: tree |