Custom dataloader registry support #11
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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') || | |
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: ["3.11"] | |
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] @ ." | |
python -m pip install tiledbsoma | |
- name: Install Specific Branch of Repository | |
env: | |
GH_TOKEN: ${{ secrets.GH_TOKEN }} | |
run: | | |
git config --global url."https://${GH_TOKEN}:[email protected]/".insteadOf "https://github.com/" | |
#pip install git+https://github.com/ori-kron-wis/cellxgene-census.git@ebezzi/census-scvi-datamodule | |
git clone --single-branch --branch ebezzi/census-scvi-datamodule https://github.com/ori-kron-wis/cellxgene-census.git | |
#cd cellxgene-census | |
#python -m pip install | |
- 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 }} |