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Detect Wyckoff positions automatically from coordinates - #189

Merged

AndrewSazonov merged 55 commits into

developfrom

wyckoff-letter-detection

Jun 3, 2026

Merged

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

Commits on Jun 2, 2026
- Add space-group-database canonical-templates phase
  AndrewSazonov
  committed
  4620fa8
- Refine canonical-templates phase to re-source from cryspy
  AndrewSazonov
  committed
  74c410d
Commits on Jun 3, 2026
- Refine canonical-templates CT1 to fix generator and re-run
  AndrewSazonov
  committed
  940529e
- Settle canonical-templates phase on cctbx-free post-process
  AndrewSazonov
  committed
  7c9f5d7
- Canonicalize space-group coords_xyz templates
  AndrewSazonov
  committed
  4811507
- Assert canonical coords_xyz in packaged DB check
  AndrewSazonov
  committed
  1a2a9e6
- Record canonical coords_xyz invariant and provenance
  AndrewSazonov
  committed
  c4c7a7d
- Reach canonical-templates Phase 1 review gate
  AndrewSazonov
  committed
  62fd107
- Keep pattern-plot top and bottom panels at fixed height
  AndrewSazonov
  committed
  176e6e6
- Test fixed pattern-plot panel heights across row layouts
  AndrewSazonov
  committed
  7675de2
- Inline composite row-height max() and trim docstring
  AndrewSazonov
  committed
  bb817a5
- Keep TeX report panels fixed when rows are hidden
  AndrewSazonov
  committed
  bec2f5e
- Store full canonical Wyckoff orbits via exact check
  AndrewSazonov
  committed
  da7cb4c
- Document two-stage canonical rebuild as invariant step
  AndrewSazonov
  committed
  238cc34
- Build full Wyckoff orbits from cryspy primitive and centering
  AndrewSazonov
  committed
  c27c23e
- Fix plan references to obsolete generator coords source
  AndrewSazonov
  committed
  dcbd901
- Validate canonical coords_xyz and coupled constraints
  AndrewSazonov
  committed
  92c4112
- Note plotting-module docstring fix for Phase 2 review
  AndrewSazonov
  committed
  3053cca
- Mark Phase 2 verification complete
  AndrewSazonov
  committed
  f7948c9
- Assert R-3m special positions stay on-site after fit
  AndrewSazonov
  committed
  833df9a
- Confirm wyckoff letter detection ADR gate
  AndrewSazonov
  committed
  d4cb540
- Add Wyckoff orbit detection to crystallography module
  AndrewSazonov
  committed
  16896f3
- Record free-param-solving Wyckoff snap decision for P1.6
  AndrewSazonov
  committed
  abed076
- Add derived space group Wyckoff category
  AndrewSazonov
  committed
  01ca0da
- Wire derived Wyckoff table into Structure
  AndrewSazonov
  committed
  31d1278
- Add read-only multiplicity to AtomSite
  AndrewSazonov
  committed
  1bb7aea
- Derive allowed Wyckoff letters from the space group
  AndrewSazonov
  committed
  0f1db8e
- Add Wyckoff coordinate snap helper to crystallography module
  AndrewSazonov
  committed
  138c44d
- Detect and track Wyckoff letters in the update flow
  AndrewSazonov
  committed
  838d789
- Read multiplicity from the model in the cryspy calculator
  AndrewSazonov
  committed
  582e12d
- Serialize Wyckoff multiplicity and report Wyckoff table
  AndrewSazonov
  committed
  2819bb6
- Promote wyckoff-letter-detection ADR and close issue #51
  AndrewSazonov
  committed
  3dcf0fa
- Reach Phase 1 review gate
  AndrewSazonov
  committed
  8dd072c
- Preserve explicit Wyckoff letter until a later edit
  AndrewSazonov
  committed
  7cdb2d2
- Build space-group Wyckoff id from multiplicity and letter
  AndrewSazonov
  committed
  f97f583
- Rebuild Wyckoff index and parent links on replace
  AndrewSazonov
  committed
  55a0656
- Reject item assignment and deletion on Wyckoff collection
  AndrewSazonov
  committed
  68fb0d9
- Resolve None-coord-code groups in Wyckoff constraint helper
  AndrewSazonov
  committed
  32371a8
- Sync top-level plan status with completed Phase 1
  AndrewSazonov
  committed
  91dd4d6
- Raise ValueError for Wyckoff read-only mutation per ADR
  AndrewSazonov
  committed
  34d99f1
- Remove wyckoff_letter from tutorial examples
  AndrewSazonov
  committed
  7abbffe
- Apply pixi run fix auto-fixes
  AndrewSazonov
  committed
  25b212b
- Resolve ruff lint findings in Wyckoff Phase 1 code
  AndrewSazonov
  committed
  7c901df
- Update tests for Wyckoff detection behavior changes
  AndrewSazonov
  committed
  b170d0d
- Add tests for derived space_group_wyckoff category
  AndrewSazonov
  committed
  7265ece
- Add detection and lookup tests for Wyckoff crystallography
  AndrewSazonov
  committed
  daded80
- Assert canonical Wyckoff representative templates in data
  AndrewSazonov
  committed
  e59fb8f
- Add atom-site Wyckoff detection behavior tests
  AndrewSazonov
  committed
  bd83195
- Add tutorial-corpus Wyckoff detection regression
  AndrewSazonov
  committed
  692f170
- Satisfy pydoclint and ruff for Wyckoff Phase 2 tests
  AndrewSazonov
  committed
  821e673
- Fix ed-13 Si to the 8a diamond position
  AndrewSazonov
  committed
  ddcd720
- Regenerate tutorial notebooks after Wyckoff letter removal
  AndrewSazonov
  committed
  74f9354
- Restore tutorial-corpus coverage with explicit ground-truth table
  AndrewSazonov
  committed
  04a6721
- Match Fd-3m corpus ground truth to corrected ed-13 Si site
  AndrewSazonov
  committed
  70c32c7
- Mark Phase 2 verification complete in plan
  AndrewSazonov
  committed
  38b3c1c

Commits

Commits on Jun 2, 2026

Commits on Jun 3, 2026