fixing local tests, make geneformer paths relative #11
Workflow file for this run
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| name: "BioNeMo Recipes CI" | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - "pull-request/[0-9]+" | |
| - "dependabot/**" | |
| merge_group: | |
| types: [checks_requested] | |
| schedule: | |
| - cron: "0 7 * * *" # Runs at 7 AM UTC daily (12 AM MST) | |
| defaults: | |
| run: | |
| shell: bash -x -e -u -o pipefail {0} | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| changed-dirs: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| any_changed: ${{ steps.changed-files.outputs.any_changed }} | |
| all_changed_files: ${{ steps.changed-files.outputs.all_changed_files }} | |
| dirs: ${{ steps.set-dirs.outputs.dirs }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Get changed files | |
| id: changed-files | |
| uses: step-security/changed-files@v46 | |
| with: | |
| json: true | |
| matrix: true | |
| base_sha: main | |
| dir_names: true | |
| dir_names_max_depth: 2 | |
| files: | | |
| models/** | |
| recipes/** | |
| .github/workflows/unit-tests-recipes.yml | |
| - id: set-dirs | |
| run: | | |
| # Get all recipe and model directories | |
| ALL_DIRS=$(ls -d recipes/*/ models/*/ 2>/dev/null | jq -R -s -c 'split("\n")[:-1] | map(rtrimstr("/"))') | |
| CHANGED_FILES='${{ steps.changed-files.outputs.all_changed_files }}' | |
| # Filter directories to only those that have changed files. Then assign a Docker image to each. | |
| # Currently, AMPLIFY is the only folder that needs a custom base image, since we have to support both TE and | |
| # xformers-based models for golden value testing. The rest of the models use the default pytorch image. | |
| DIRS=$(echo "$ALL_DIRS" | jq -c --argjson changed "$CHANGED_FILES" ' | |
| map(select(. as $dir | $changed | index($dir) != null)) | | |
| map({ | |
| dir: ., | |
| image: ( | |
| if . == "models/amplify" then | |
| "svcbionemo023/bionemo-framework:amplify-model-devcontainer-082025" | |
| else | |
| "nvcr.io/nvidia/pytorch:25.06-py3" | |
| end | |
| ) | |
| }) | |
| ') | |
| echo "dirs=$DIRS" >> $GITHUB_OUTPUT | |
| - name: Show output | |
| run: | | |
| echo '${{ toJSON(steps.changed-files.outputs) }}' | |
| echo '${{ toJSON(steps.set-dirs.outputs) }}' | |
| shell: | |
| bash | |
| unit-tests: | |
| needs: changed-dirs | |
| runs-on: linux-amd64-gpu-l4-latest-1 | |
| container: | |
| image: ${{ matrix.recipe.image }} | |
| strategy: | |
| matrix: | |
| recipe: ${{ fromJson(needs.changed-dirs.outputs.dirs) }} | |
| fail-fast: false | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| sparse-checkout: '${{ matrix.recipe.dir }}' | |
| sparse-checkout-cone-mode: false | |
| - name: Install dependencies | |
| working-directory: ${{ matrix.recipe.dir }} | |
| # | |
| run: | | |
| if [ -f pyproject.toml ] || [ -f setup.py ]; then | |
| PIP_CONSTRAINT= pip install -e . | |
| echo "Installed ${{ matrix.recipe.dir }} as editable package" | |
| elif [ -f requirements.txt ]; then | |
| PIP_CONSTRAINT= pip install -r requirements.txt | |
| echo "Installed ${{ matrix.recipe.dir }} from requirements.txt" | |
| else | |
| echo "No pyproject.toml, setup.py, or requirements.txt found in ${{ matrix.recipe.dir }}" | |
| exit 1 | |
| fi | |
| - name: Run tests | |
| working-directory: ${{ matrix.recipe.dir }} | |
| run: pytest -v . |