test_linux_custom_dataloader.yml

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] @ ."

      - name: Install Specific Branch of Repository
        env:
          GH_TOKEN: ${{ secrets.GH_TOKEN }}
        run: |
          git config --global url."https://${GH_TOKEN}:x-oauth-basic@github.com/".insteadOf "https://github.com/"
          #pip install git+https://github.com/ebezzi/cellxgene-census.git@ebezzi/census-scvi-datamodule
          git clone --single-branch --branch ebezzi/census-scvi-datamodule https://github.com/ebezzi/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 }}