Backport PR #3816 on branch 1.4.x (Fix: list of metrics to be recorded in autotune as well as removal of MLX from CUDA installation) #2860
Workflow file for this run
This file contains hidden or 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: test (custom dataloaders) | |
| on: | |
| push: | |
| branches: [main, "[0-9]+.[0-9]+.x"] | |
| pull_request: | |
| branches: [main, "[0-9]+.[0-9]+.x"] | |
| types: [labeled, synchronize, opened] | |
| schedule: | |
| - cron: "0 10 * * *" # runs at 10:00 UTC (03:00 PST) every day | |
| workflow_dispatch: | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| # if PR has label "custom_dataloader" or "all tests" or if scheduled or manually triggered | |
| if: >- | |
| ( | |
| contains(github.event.pull_request.labels.*.name, 'custom_dataloader') || | |
| contains(github.event.pull_request.labels.*.name, 'all tests') || | |
| (contains(github.event_name, 'schedule') && github.repository == 'scverse/scvi-tools') || | |
| contains(github.event_name, 'workflow_dispatch') | |
| ) | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: bash -e {0} # -e to fail on error | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest] | |
| python: ["3.13"] | |
| name: integration | |
| env: | |
| OS: ${{ matrix.os }} | |
| PYTHON: ${{ matrix.python }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python }} | |
| cache: "pip" | |
| cache-dependency-path: "**/pyproject.toml" | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip wheel uv | |
| python -m uv pip install --system "scvi-tools[tests,dataloaders] @ ." | |
| - name: Run specific custom dataloader pytest | |
| env: | |
| MPLBACKEND: agg | |
| PLATFORM: ${{ matrix.os }} | |
| DISPLAY: :42 | |
| COLUMNS: 120 | |
| run: | | |
| coverage run -m pytest -v --color=yes --custom-dataloader-tests | |
| coverage report | |
| - uses: codecov/codecov-action@v4 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| flags: custom_dataloader |