Fix slide_cells edge cases in region_extract (#60) - #61
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Two edge-case bugs in scf.tl.slide_cells reported in #60: 1. When the first principal point already exceeds the window, inds[0] is 0 and the pps_region slice [:0] returns an empty window, producing a NaN pt_cur that breaks the recursion. Keep at least that point. 2. In the two-branch case, a branch may run out of cells for the current pseudotime, making its pt_cur NaN and crashing the recursive call. Only recurse into branches that still have cells to extract. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_0152pVAvAhGXQuWepi4YbWYn
Newer pandas makes pd.Series(dtype=str) a strict StringDtype that rejects the integer milestone ids assigned to it, breaking test_pipeline. Use dtype=object (values are cast to str later anyway). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
…rogram Assign str(pos_idx) instead of int into the string-typed seg_pos column; it is cast back to int right after. Fixes test_pipeline under newer pandas. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
- milestones plot: drop removed dtype kwarg from sc.AnnData() - get_activation: use label access (x["start"]/x["end"]) instead of positional x[0]/x[1], which no longer falls back on a labeled Series - slide_cors: fill diagonal on a writable numpy copy since DataFrame.values is now read-only Reproduced against a fresh env (pandas 3.0.3, anndata 0.13.1); full test suite passes. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #61 +/- ##
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- Coverage 80.75% 80.73% -0.02%
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Files 40 40
Lines 4078 4085 +7
Branches 512 514 +2
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+ Hits 3293 3298 +5
Misses 529 529
- Partials 256 258 +2
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Two edge-case bugs in scf.tl.slide_cells reported in #60:
When the first principal point already exceeds the window, inds[0]
is 0 and the pps_region slice [:0] returns an empty window, producing
a NaN pt_cur that breaks the recursion. Keep at least that point.
In the two-branch case, a branch may run out of cells for the current
pseudotime, making its pt_cur NaN and crashing the recursive call.
Only recurse into branches that still have cells to extract.
Co-Authored-By: Claude Opus 4.8 noreply@anthropic.com
Claude-Session: https://claude.ai/code/session_0152pVAvAhGXQuWepi4YbWYn