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CI: put pysceptre's scripts/ on PYTHONPATH for the Nextflow DAG step #3

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Merged
emattei merged 3 commits into from
Sep 28, 2026
Merged

CI: put pysceptre's scripts/ on PYTHONPATH for the Nextflow DAG step #3

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9d522b5
Put pysceptre's scripts/ on PYTHONPATH in the CI Nextflow DAG step
emattei Sep 26, 2026
ba2e315
Declare anndata and mudata in pyproject.toml, as pixi.toml already does
emattei Sep 28, 2026
a49baea
Run the CI stub under -profile stub, whose resource caps fit the runner
emattei Sep 28, 2026
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7 changes: 6 additions & 1 deletion .github/workflows/test.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -41,8 +41,13 @@ jobs:
- name: Nextflow DAG
# Catches a rewiring mistake without running anything. The stub needs the synthetic
# dataset, which is generated rather than committed.
# pysceptre's scripts/ (sceptre_io, which watteg-make-test-data imports) is not in its
# wheel, so it is fetched at the pinned tag and put on PYTHONPATH, as the container does.
run: |
git clone --quiet --depth 1 --branch v0.2.0 \
https://github.com/broadinstitute/pysceptre.git /tmp/pysceptre
export PYTHONPATH=/tmp/pysceptre/scripts
curl -fsSL https://get.nextflow.io | bash
uv run watteg-make-test-data --out tests/data/synthetic.h5mu
./nextflow run . -profile standard -params-file config/test.yml -stub-run \
./nextflow run . -profile stub -params-file config/test.yml -stub-run \
--samplesheet assets/samplesheet_synthetic.csv --outdir /tmp/stub
2 changes: 2 additions & 0 deletions pyproject.toml
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Expand Up @@ -11,6 +11,8 @@ dependencies = [
"pandas>=2.0",
"h5py>=3.8",
"pyarrow>=14",
"anndata", # reading the .h5mu pysceptre's export writes (pixi.toml has them too)
"mudata",
"pysceptre",
]

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