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ci: windows #364

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fb37e3c
ci: try out windows
tristan-f-r Jul 29, 2025
f25d482
Merge branch '4-core' into windows-ci
tristan-f-r Jul 29, 2025
cf40bf3
ci: typo
tristan-f-r Jul 29, 2025
ced0339
test: ignore cytoscape, attempt pca windows fix
tristan-f-r Jul 29, 2025
c9319ae
fix: use correct datatype
tristan-f-r Jul 29, 2025
2ea7737
ci: dbg
tristan-f-r Jul 29, 2025
0a2415c
fix: paths and more paths
tristan-f-r Jul 29, 2025
416baa6
Merge branch 'main' into windows-ci
tristan-f-r Sep 6, 2025
c271322
fix: type pca_chosen_pathway
tristan-f-r Sep 6, 2025
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18 changes: 18 additions & 0 deletions .github/workflows/test-spras.yml
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Expand Up @@ -25,6 +25,24 @@ jobs:
shell: bash --login {0}
run: conda list

test_windows:
name: Run weakened windows tests
runs-on: windows-latest
steps:
- name: Checkout repository
uses: actions/checkout@v4
- name: Install conda environment
uses: conda-incubator/setup-miniconda@v2
with:
activate-environment: spras
environment-file: environment.yml
auto-activate-base: false
miniconda-version: 'latest'
- name: Run tests
shell: bash --login {0}
# Verbose output and disable stdout and stderr capturing
run: pytest -vs --ignore=test/AllPairs --ignore=test/BowTieBuilder --ignore=test/DOMINO --ignore=test/MEO --ignore=test/MinCostFlow --ignore=test/OmicsIntegrator1 --ignore=--ignore=test/OmicsIntegrator2 --ignore=test/PathLinker --ignore=test/ResponseNet --ignore=test/RWR --ignore=test/ST_RWR
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@tristan-f-r tristan-f-r Jul 29, 2025

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This could be a good time to begin moving algorithms to their own folder.

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@tristan-f-r tristan-f-r Sep 6, 2025

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#391.

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@agitter agitter Oct 3, 2025

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Why do we have to ignore so many tests?

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@tristan-f-r tristan-f-r Oct 4, 2025

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Docker doesn't work on windows in GitHub CI. It would be good to at least test anything in Windows that doesn't rely on docker. [Earlier, I believe you had issues running SPRAS tests on Windows because of path issues with the analysis tests]

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@agitter agitter Oct 4, 2025

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The windows-2025 runner lists these tools

  • Docker 27.5.1
  • Docker Compose v2 2.32.2
  • Docker-wincred 0.9.3

Did Docker not work?


# Runs the test code and Snakemake workflow in the conda environment
test:
name: Run tests
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