[Sync] Reorganize output directories + deduplicate snakefiles + bugfixes #8
Workflow file for this run
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| name: test | |
| # run unit and integration tests for the ProteinCartography package | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| # 'synchronize' means the PR was updated with new commits | |
| types: [opened, reopened, labeled, synchronize] | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Setup conda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniforge-variant: Mambaforge | |
| miniforge-version: latest | |
| python-version: "3.9" | |
| use-mamba: true | |
| activate-environment: test-env | |
| auto-activate-base: false | |
| # note: the docs claim `use-only-tar-bz2` must be set to true | |
| # in order for package caching to work properly, | |
| # but this results in many package-not-found errors, | |
| # so we set it to false and do not use package caching | |
| use-only-tar-bz2: false | |
| - name: Cache the conda env | |
| uses: actions/cache@v2 | |
| id: cache-conda-env | |
| with: | |
| path: ${{ env.CONDA }}/envs | |
| key: | |
| conda-${{ runner.os }}--${{ runner.arch }}--${{ hashFiles('envs/cartography_test.yml') }} | |
| - name: Create the conda env from which to run snakemake | |
| run: | | |
| mamba env update -n test-env -f envs/cartography_test.yml | |
| if: steps.cache-conda-env.outputs.cache-hit != 'true' | |
| - name: Cache the conda envs created by snakemake | |
| uses: actions/cache@v2 | |
| id: cache-snakemake-conda-envs | |
| with: | |
| path: .snakemake/conda | |
| key: | |
| conda-${{ runner.os }}--${{ runner.arch }}--${{ hashFiles('envs/*.yml') }} | |
| - name: Create the snakemake conda envs | |
| run: | | |
| snakemake --configfile demo/search-mode/config_actin.yml --use-conda --conda-create-envs-only --cores 1 | |
| if: steps.cache-snakemake-conda-envs.outputs.cache-hit != 'true' | |
| - name: Run the tests | |
| run: | | |
| make test | |
| - name: Run the tests without mocks | |
| if: contains(github.event.pull_request.labels.*.name, 'run-slow-tests') | |
| run: | | |
| make test-without-mocks |