Fix API naming/consistency quirks in Flow and Fit - #4
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Standardizes coords -> coordinates across distances.py and graph_construction.py, lets Flow accept plain arrays/Series (not just DataFrame/named-Series) for scores and distances, de-duplicates the fit-failure bookkeeping shared by the three saturation Fit subclasses, fixes _calculate_fraction_not_converged's missing return values, and renames Flow.flow()'s `measures` parameter to `score_names` so it stops being conflated with compute_centrality_measures's fixed centrality vocabulary (it actually accepts arbitrary score-column names). Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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Summary
coords->coordinatesacrossdistances.py/graph_construction.pyFlownow accepts plain arrays/pd.Seriesforscores/distances, not onlyDataFrame/named-SeriesFitsubclasses via a newFit._finalize_fit()_calculate_fraction_not_converged's missingreturn(previously always returnedNonedespite its-> floatannotation)Flow.flow()'smeasuresparameter toscore_names, since it accepts arbitrary score-column names (e.g.log1p_total_counts, gene names), not the fixed centrality vocabulary thatcompute_centrality_measurescorrectly callsmeasuresCLAUDE.mdclaims (networkx fallback, missingdistance_to_alpha_shapeentry)Test plan
pytest tests/— 111 passed, 1 skippedFlow.from_distances_and_scoreswith plainnp.ndarrayscores/distancesmeasures=keyword now correctly raisesTypeErroronFlow.flow()Note: no consuming code outside this repo passes
coords=/measures=as keywords for the renamed functions (verified via grep acrosstruncated_graphs); the one exception,Flow.flow(measures=...), is being updated in a companion PR ontruncated_graphs.🤖 Generated with Claude Code