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- path metric with n_neighbors collected leaves on discovery rather than in distance order, so farther leaves could displace closer ones; nodes are now collected when popped from the queue and ties are broken randomly - single-string obs flagged the query node instead of its neighbors Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Add loaders for the mouse embryo lineage tracing datasets, point the Zenodo record at the new version, and add a --slow-tests flag so the large dataset tests only run on request. Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Add get_depth_key and use it in clades, n_extant, tree_distance, tree_neighbors, ancestral_linkage and fitness, matching pycea.pl. Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Treat True/False as 1/0 for the mean and sum methods so internal nodes get the fraction and number of True leaves. Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Add a tutorial using the colgan26 dataset to the docs, and remove the autoreload magic and stale execution count from the growth dynamics tutorial. Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
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Files 37 37
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Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
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Summary
pycea.datasets.colgan26(mouse embryo lineage atlas, E7.5-E10.0, with optionalembryossubsetting) andpycea.datasets.yu26(DNA Typewriter mouse lineage). Both load slimmed h5td files from the updated Zenodo record (23195576). Docs and bib entries included, and a--slow-testsflag gates the large-dataset tests.colgan26to the docs.tree_neighborsfixes:metric="path"withn_neighborscollected leaves on discovery rather than in distance order, so farther leaves could displace closer ones (138/300 random trees in a brute-force comparison). Nodes are now collected when popped from the queue, and ties are broken randomly.metric="lca"was checked against brute force and needed no change.obsflagged the queried node instead of its neighbors.depth_key: now defaults totdata.uns["default_depth"](falling back to"depth") inclades,n_extant,tree_distance,tree_neighbors,ancestral_linkageandfitness, matchingpycea.pl.ancestral_linkage: single-target mode stores per-cell results intdata.obs['{key_added}_linkage']whenkey_addedis given. This changes the output column for callers passingkey_addedwithtarget.ancestral_states: supports boolean data.meanandsumtreatTrue/Falseas 1/0.Test plan
pytest tests/passes (225 passed, 5 skipped) before the last two commits;test_ancestral_states.py,test_ancestral_linkage.pyandtest_default_depth.pypass after themtest_colgan26passes with--internet-tests --slow-teststest_yu26has not passed yet: the download hit a disk quota error on the author's home directory (environment limit, not a loader bug)🤖 Generated with Claude Code