(feat): add nightly cron job

.github/workflows/integration-test.yml

@@ -0,0 +1,101 @@
+name: Integration test
+
+on:
+  schedule:
+    - cron: "0 0 * * *"  # Run daily at midnight UTC
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    strategy:
+      fail-fast: false
+      matrix:
+        python: ["3.10", "3.12"]
+        package: ["mudata", "spatialdata", "scirpy", "muon", "scanpy", "squidpy", "scvi-tools"]
+
+    defaults:
+      run:
+        shell: bash -el {0}
+
+    runs-on: ubuntu-latest
+
+    env:
+      # This env variable is used by the `gh` CLI
+      GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          filter: blob:none
+          path: integration-testing
+
+      - uses: actions/checkout@v4
+        with:
+          repository: scverse/${{ matrix.package }}
+          fetch-depth: 0
+          filter: blob:none
+          path: ${{ matrix.package }}
+
+      - name: Install Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python }}
+
+      - name: Install UV
+        uses: hynek/setup-cached-uv@v2
+
+      - name: Install AnnData + test dep
+        run: |
+          uv pip install --compile --system ".[test]" git+https://github.com/scverse/anndata -c ../integration-testing/constraints.txt -v 
+        working-directory: ${{ matrix.package }}
+
+      - name: Set failure type for install
+        if: failure()
+        run: |
+          echo "Installation failed for ${{ matrix.package }}"
+          echo "failure_type=install" >> $GITHUB_ENV
+
+      - name: Env list
+        run: uv pip freeze
+
+      - name: Run test
+        run: |
+          pytest
+        working-directory: ${{ matrix.package }}
+
+      - name: Set failure type for test
+        if: failure() && env.failure_type != 'install'
+        run: |
+          echo "Test failed for ${{ matrix.package }}"
+          echo "failure_type=test" >> $GITHUB_ENV
+
+      - name: Check for open failure issue
+        if: failure() && github.event_name == 'schedule'
+        id: find_issue
+        run: |
+          ISSUE_TITLE="Integration Testing CI ${failure_type^} Failure on python ${{ matrix.python }}"
+          echo "Checking for existing issue: $ISSUE_TITLE"
+          ISSUE_COUNT=$(gh issue list --repo scverse/${{ matrix.package }} --state open --search "${ISSUE_TITLE}" --json number --jq 'length')
+          if [[ "$ISSUE_COUNT" -gt 0 ]]; then
+            echo "${failure_type^} failure issue already exists for today."
+            echo "issue_exists=true" >> $GITHUB_ENV
+          else
+            echo "issue_exists=false" >> $GITHUB_ENV
+            echo "issue_title=$ISSUE_TITLE" >> $GITHUB_ENV
+          fi
+
+      - name: Report failure issue
+        if: failure() && env.issue_exists == 'false' && github.event_name == 'schedule'
+        run: |
+          RUN_URL="${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}"
+          ISSUE_BODY="The daily CI failed on ${failure_type} for ${{ matrix.package }} failed.  Please go to [the logs of the integration testing repo](${RUN_URL}) to review. @scverse/anndata"
+          gh issue create --repo scverse/${{ matrix.package }} --title "${{ env.issue_title }}" --body "${ISSUE_BODY}"

constraints.txt

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+# uv backtracking is broken so we need to lower bound these
+numba>=0.60.0
+mofapy2>=0.7.1