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Detect Wyckoff positions automatically from coordinates#189

Merged

AndrewSazonov merged 55 commits into

developeasyscience/diffraction-lib:developfrom

wyckoff-letter-detectioneasyscience/diffraction-lib:wyckoff-letter-detectionCopy head branch name to clipboard

Jun 3, 2026

Conversation Commits55 (55)Checks Files changed

Merged

Detect Wyckoff positions automatically from coordinates#189
AndrewSazonov merged 55 commits into
developfrom
wyckoff-letter-detection

Commits

Commits on Jun 2, 2026

Add space-group-database canonical-templates phase
AndrewSazonov
committed
Refine canonical-templates phase to re-source from cryspy
AndrewSazonov
committed

Commits on Jun 3, 2026

Refine canonical-templates CT1 to fix generator and re-run
AndrewSazonov
committed
Settle canonical-templates phase on cctbx-free post-process
AndrewSazonov
committed
Canonicalize space-group coords_xyz templates
AndrewSazonov
committed
Assert canonical coords_xyz in packaged DB check
AndrewSazonov
committed
Record canonical coords_xyz invariant and provenance
AndrewSazonov
committed
Reach canonical-templates Phase 1 review gate
AndrewSazonov
committed
Keep pattern-plot top and bottom panels at fixed height
AndrewSazonov
committed
Test fixed pattern-plot panel heights across row layouts
AndrewSazonov
committed
Inline composite row-height max() and trim docstring
AndrewSazonov
committed
Keep TeX report panels fixed when rows are hidden
AndrewSazonov
committed
Store full canonical Wyckoff orbits via exact check
AndrewSazonov
committed
Document two-stage canonical rebuild as invariant step
AndrewSazonov
committed
Build full Wyckoff orbits from cryspy primitive and centering
AndrewSazonov
committed
Fix plan references to obsolete generator coords source
AndrewSazonov
committed
Validate canonical coords_xyz and coupled constraints
AndrewSazonov
committed
Note plotting-module docstring fix for Phase 2 review
AndrewSazonov
committed
Mark Phase 2 verification complete
AndrewSazonov
committed
Assert R-3m special positions stay on-site after fit
AndrewSazonov
committed
Confirm wyckoff letter detection ADR gate
AndrewSazonov
committed
Add Wyckoff orbit detection to crystallography module
AndrewSazonov
committed
Record free-param-solving Wyckoff snap decision for P1.6
AndrewSazonov
committed
Add derived space group Wyckoff category
AndrewSazonov
committed
Wire derived Wyckoff table into Structure
AndrewSazonov
committed
Add read-only multiplicity to AtomSite
AndrewSazonov
committed
Derive allowed Wyckoff letters from the space group
AndrewSazonov
committed
Add Wyckoff coordinate snap helper to crystallography module
AndrewSazonov
committed
Detect and track Wyckoff letters in the update flow
AndrewSazonov
committed
Read multiplicity from the model in the cryspy calculator
AndrewSazonov
committed
Serialize Wyckoff multiplicity and report Wyckoff table
AndrewSazonov
committed
Promote wyckoff-letter-detection ADR and close issue #51
AndrewSazonov
committed
Reach Phase 1 review gate
AndrewSazonov
committed
Preserve explicit Wyckoff letter until a later edit
AndrewSazonov
committed
Build space-group Wyckoff id from multiplicity and letter
AndrewSazonov
committed
Rebuild Wyckoff index and parent links on replace
AndrewSazonov
committed
Reject item assignment and deletion on Wyckoff collection
AndrewSazonov
committed
Resolve None-coord-code groups in Wyckoff constraint helper
AndrewSazonov
committed
Sync top-level plan status with completed Phase 1
AndrewSazonov
committed
Raise ValueError for Wyckoff read-only mutation per ADR
AndrewSazonov
committed
Remove wyckoff_letter from tutorial examples
AndrewSazonov
committed
Apply pixi run fix auto-fixes
AndrewSazonov
committed
Resolve ruff lint findings in Wyckoff Phase 1 code
AndrewSazonov
committed
Update tests for Wyckoff detection behavior changes
AndrewSazonov
committed
Add tests for derived space_group_wyckoff category
AndrewSazonov
committed
Add detection and lookup tests for Wyckoff crystallography
AndrewSazonov
committed
Assert canonical Wyckoff representative templates in data
AndrewSazonov
committed
Add atom-site Wyckoff detection behavior tests
AndrewSazonov
committed
Add tutorial-corpus Wyckoff detection regression
AndrewSazonov
committed
Satisfy pydoclint and ruff for Wyckoff Phase 2 tests
AndrewSazonov
committed
Fix ed-13 Si to the 8a diamond position
AndrewSazonov
committed
Regenerate tutorial notebooks after Wyckoff letter removal
AndrewSazonov
committed
Restore tutorial-corpus coverage with explicit ground-truth table
AndrewSazonov
committed
Match Fd-3m corpus ground truth to corrected ed-13 Si site
AndrewSazonov
committed
Mark Phase 2 verification complete in plan
AndrewSazonov
committed

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