docs: refresh DE docstring pseudobulk examples#996
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The example code in EdgeR/PyDESeq2 docstrings still called PseudobulkSpace.compute() with the long-removed `min_cells` and `min_counts` parameters, so anyone copy-pasting the example hit a TypeError. Replace each example with the current PseudobulkSpace.compute(target_col=..., groups_col=..., layer_key=..., mode=...) call that actually runs. Co-Authored-By: Claude Opus 4.7 (1M context) <[email protected]>
Lets MyST/sphinx cross-references like {func}`~decoupler.op.collectri`
in the DE tutorial resolve to decoupler's docs instead of dropping to
plain text. decoupler publishes its objects.inv at decoupler.readthedocs.io
(not decoupler-py.readthedocs.io, which has an empty inventory).
Co-Authored-By: Claude Opus 4.7 (1M context) <[email protected]>
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…sweep Points docs/tutorials/notebooks at scverse/pertpy-tutorials@7ae61d5 (merge commit of scverse/pertpy-tutorials#60), which contains the companion DE narrative additions and the intersphinx sweep that consumes the new decoupler entry added to docs/conf.py in this PR. Co-Authored-By: Claude Opus 4.7 (1M context) <[email protected]>
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Summary
Two small docs-only changes tied together by issue #615:
Examplesblocks inpertpy/tools/_differential_gene_expression/_base.py(5 occurrences acrossEdgeR/PyDESeq2plot andcompare_groupsdocstrings) so they use the currentPseudobulkSpace.compute(...)signature. The previous examples passed the long-removedmin_cells=10/min_counts=1000kwargs, so anyone copy-pasting them hitTypeError: compute() got an unexpected keyword argument 'min_cells'. Reported by @mschilli87 in Improve DE tutorial #615.decouplertodocs/conf.py'sintersphinx_mappingso MyST cross-references like{func}~decoupler.op.collectri`` (introduced in the companion tutorials PR de: clarify model choice, design matrices, and result interpretation pertpy-tutorials#60) resolve to decoupler's docs.