feat: implement Decipher model in external #2325
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: test (cuda) | |
| on: | |
| push: | |
| branches: [main, "[0-9]+.[0-9]+.x"] #this is new | |
| 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 "cuda tests" or "all tests" or if scheduled or manually triggered | |
| if: >- | |
| ( | |
| contains(github.event.pull_request.labels.*.name, 'cuda tests') || | |
| contains(github.event.pull_request.labels.*.name, 'all tests') || | |
| contains(github.event_name, 'schedule') || | |
| contains(github.event_name, 'workflow_dispatch') | |
| ) | |
| runs-on: [self-hosted, Linux, X64, CUDA] | |
| defaults: | |
| run: | |
| shell: bash -e {0} # -e to fail on error | |
| container: | |
| image: ghcr.io/scverse/scvi-tools:py3.12-cu12-base | |
| #image: ghcr.io/scverse/scvi-tools:py3.12-cu12-${{ env.BRANCH_NAME }}-base | |
| options: --user root --gpus all | |
| name: integration | |
| env: | |
| OS: ${{ matrix.os }} | |
| PYTHON: ${{ matrix.python }} | |
| steps: | |
| #- name: Get the current branch name | |
| # id: vars | |
| # run: echo "BRANCH_NAME=$(echo $GITHUB_REF | awk -F'/' '{print $3}')" >> $GITHUB_ENV | |
| - 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] @ ." | |
| python -m pip install jax[cuda] | |
| python -m pip install nvidia-nccl-cu12 | |
| - name: Run pytest | |
| env: | |
| MPLBACKEND: agg | |
| PLATFORM: ${{ matrix.os }} | |
| DISPLAY: :42 | |
| COLUMNS: 120 | |
| run: | | |
| coverage run -m pytest -v --color=yes --accelerator cuda --devices auto | |
| coverage report | |
| - uses: codecov/codecov-action@v4 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} |