Automatically reindex and align phases to a common origin - #359
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This was referenced Aug 22, 2026
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! This PR was vibe-coded.
Stack
Part 9 of 11 for #31. Depends on #358. Merge bottom-up.
Next branch: codex/phase-alignment-10-alignment-options.
What this implements
Adds OriginShiftCandidate, PhaseAlignmentResult, and the first public align_phases() orchestration. It validates two isomorphous merged DataSets, automatically performs correlation reindexing when the moving metric admits an ambiguity, searches only symmetry-allowed origins, applies the selected Phenix-sign shift to a copy, and returns ranked diagnostics.
Tests
End-to-end tests cover three real space-group fixtures, automatic P 61 reindexing before origin fitting, exact phase recovery, the Phenix sign convention, result types, and nonmutation.
Reviewer focus
Related: #31 and #174.