First draft of GitHub Actions #9
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: Ingestion CI | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| env: | |
| debug: 'true' | |
| jobs: | |
| build: | |
| 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 | |
| - 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 | |
| - 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 | |
| #- name: Run tests | |
| # shell: bash -el {0} | |
| # run: | | |
| # python -m pytest tests/ | |
| - name: Preparing the data | |
| run: | | |
| mkdir -p teaseq/ingest/data.dir | |
| curl -o teaseq/ingest/data.dir/subsample_adt.h5ad https://figshare.com/ndownloader/files/41671551 | |
| curl -o teaseq/ingest/data.dir/subsample_atac.h5ad https://figshare.com/ndownloader/files/41671554 | |
| curl -o teaseq/ingest/data.dir/subsample_rna.h5ad https://figshare.com/ndownloader/files/41671557 | |
| - name: Preparing the configuration file | |
| run: panpipes ingest config |