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fix: add scanpy2 extra #42

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Merged
flying-sheep merged 2 commits into from
Jul 24, 2026
Merged

fix: add scanpy2 extra #42

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b86dab1
fix: add scanpy2 extra
flying-sheep Jul 24, 2026
043ba0a
more bump
flying-sheep Jul 24, 2026
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16 changes: 8 additions & 8 deletions .github/workflows/integration-test.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -26,31 +26,31 @@ jobs:
- {name: "spatialdata", extras: ""}
- {name: "scirpy", extras: ""}
- {name: "muon", extras: ""}
- {name: "scanpy", extras: ""}
- {name: "scanpy", extras: "scanpy2"}
- {name: "squidpy", extras: ""}
- {name: "scvi-tools", extras: ""}
- {name: "pertpy", extras: "de"}
- {name: "decoupler", extras: ""}
- {name: "SnapATAC2", extras: ""}
- {name: "rapids-singlecell", extras: "rapids-cu13", gpu: true}
exclude:
- { python: 3.12, is_pre: true }
- { python: "3.12", is_pre: true }

defaults:
run:
shell: bash -el {0}
shell: bash -leo pipefail {0}

runs-on: ${{ matrix.package.gpu && format('cirun-aws-gpu--{0}', github.run_id) || 'ubuntu-latest' }}

steps:

- uses: actions/checkout@v4
- uses: actions/checkout@v7
with:
fetch-depth: 0
filter: blob:none
path: integration-testing

- uses: actions/checkout@v4
- uses: actions/checkout@v7
with:
repository: scverse/${{ matrix.package.name }}
fetch-depth: 0
Expand All @@ -69,7 +69,7 @@ jobs:
echo "LD_LIBRARY_PATH=/usr/local/cuda/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}" >> $GITHUB_ENV

- name: Install Python
uses: actions/setup-python@v6
uses: actions/setup-python@v7
with:
python-version: ${{ matrix.python }}

Expand Down Expand Up @@ -131,7 +131,7 @@ jobs:
- name: Generate tokens
id: app-token
if: always()
uses: actions/create-github-app-token@v2
uses: actions/create-github-app-token@v3
with:
app-id: ${{ vars.ISSUE_CREATOR_APP_ID }}
private-key: ${{ secrets.ISSUE_CREATOR_PRIVATE_KEY }}
Expand All @@ -140,7 +140,7 @@ jobs:
# https://github.com/scverse/gpu-ci-config/issues/4
- name: Install GitHub CLI
if: matrix.package.gpu
uses: sersoft-gmbh/setup-gh-cli-action@v2
uses: sersoft-gmbh/setup-gh-cli-action@v3
with:
version: stable

Expand Down
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