ci: install the declared test group in the conda job - #1375
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The PETSc/SLEPc + R job hand-rolled its test dependencies in the workflow instead of using the `test` dependency group every other job installs, so the two drifted: the list carried `leidenalg`, which nothing uses (cellrank pins `flavor="igraph"` in `_cluster_X`, and the plotting tests pass the same flavor), while `pytest-timeout` — which that job's `--timeout=600` needs — was missing from the group. Add `pytest-timeout` to the group and install it with `pip install -e '.[plot]' --group test`, matching the cookiecutter-scverse layout where CI installs declared groups and never ad-hoc package lists. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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Stacked on #1371 — GitHub retargets this to
mainonce that merges.Problem
The
PETSc / SLEPc + Rjob hand-rolls its test dependencies in the workflow:pip install pytest pytest-cov pytest-mock pytest-timeout coverage igraph leidenalg pillowEvery other job installs the
testdependency group frompyproject.toml, so the two drifted in both directions:leidenalgis dead weight. It appears exactly once in the repo — that line._cluster_Xpinssc.tl.leiden(..., flavor="igraph")and the plotting tests passclustering_kwargs={"flavor": "igraph"}, so onlyigraph(already in the group) is ever needed. It was added in CI workflow modernization #1291 (Feb 2026).pytest-timeoutis missing from the group, even though it is a real test dependency — the conda job runspytest --timeout=600, andhatch test -- --timeout=…fails locally because the hatch envs don't have it.Changes
pytest-timeoutin thetestdependency group.pip install -e '.[plot]' --group test(pip on the runner is 26.2.1;--groupneeds ≥ 25.1).This matches cookiecutter-scverse, whose test workflow installs declared groups only (
hatch env create+hatch run …:run-cov) and never an ad-hoc package list.Note the conda job now also gets
jax,moscotandscvelofrom the group, so the tests that currently skip there run under the PETSc/SLEPc + R stack too — more coverage, at the cost of a somewhat longer install.🤖 Generated with Claude Code