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Initial implementation of the crystal structure visualization - #186

Merged

AndrewSazonov merged 160 commits into

developfrom

crysview-structure-visualization

Jun 1, 2026

Merged

Initial implementation of the crystal structure visualization#186
AndrewSazonov merged 160 commits into
developfrom
crysview-structure-visualization

Commits on May 30, 2026
- Add crysview-structure-visualization ADR suggestion
  AndrewSazonov
  committed
  cfef893
- Add crysview-structure-visualization implementation plan
  AndrewSazonov
  committed
  95bacb4
- Add crysview viewer and styling enums
  AndrewSazonov
  committed
  9ae8c80
- Add renderer-neutral structure scene model
  AndrewSazonov
  committed
  890122e
- Add orthogonalization and ADP eigendecomposition helpers
  AndrewSazonov
  committed
  17ed15f
- Add extended element database for radii and colours
  AndrewSazonov
  committed
  777f0fc
- Add structure scene builder
  AndrewSazonov
  committed
  a959553
- Add ASCII structure renderer
  AndrewSazonov
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  df333e8
- Add Viewer facade and factory with ASCII engine
  AndrewSazonov
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  fe1e196
- Add style category for structure view styling
  AndrewSazonov
  committed
  b2211b7
- Use six scalar descriptors for the view range
  AndrewSazonov
  committed
  a1abc2b
- Add switchable view category for renderer selection
  AndrewSazonov
  committed
  78484a3
- Wire project.view and project.style with CIF persistence
  AndrewSazonov
  committed
  62d2faf
- Add per-structure geom bond-cutoff category
  AndrewSazonov
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  c39bf8f
- Align single-crystal scatter axes and style in HTML and PDF
  AndrewSazonov
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  85e9e60
- Add structure() and show_structure_options() display surface
  AndrewSazonov
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  f86f169
- Add tests for single-crystal scatter range, ticks, and diagonal
  AndrewSazonov
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  956fc0b
- Vendor pinned Three.js assets
  AndrewSazonov
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  2986038
- Add Three.js structure renderer
  AndrewSazonov
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  e6824a3
- Embed structure figure in HTML report under html_offline
  AndrewSazonov
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  acd43cb
- Document structure view in tutorials and reference
  AndrewSazonov
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  dbcf55f
- Reach Phase 1 review gate
  AndrewSazonov
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  9135f31
- Resync tutorial notebooks with sources
  AndrewSazonov
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  506ce79
- Default structure view engine to environment-aware auto
  AndrewSazonov
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  87e11f8
- Document auto default for structure view engine
  AndrewSazonov
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  6b7ec70
- Fix single-crystal tick rounding and lighten markers and bars
  AndrewSazonov
  committed
  c797089
- Test single-crystal tick step rounding and marker stroke
  AndrewSazonov
  committed
  e21ff4b
- Remove unimplemented Structure.show() superseded by display.structure()
  AndrewSazonov
  committed
  a2a90cc
- Wrap Three.js import map in required imports key
  AndrewSazonov
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  3eb4ce9
- Add import-map regression guard to Phase 2 test plan
  AndrewSazonov
  committed
  00f7c3d
- Force light theme for structure view in HTML reports
  AndrewSazonov
  committed
  f00287a
- Match structure-view modebar and layout to reference demo
  AndrewSazonov
  committed
  d52c094
- Add atom_scale and per-axis axis lengths to structure scene
  AndrewSazonov
  committed
  fb922ea
- Thicken axes, tighten zoom, add PNG download and mixed-site legend
  AndrewSazonov
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  5a4cd3b
- Document atom_scale style option
  AndrewSazonov
  committed
  11b3df0
- Rename rendering selectors to rendering_plot/structure/table
  AndrewSazonov
  committed
  74066b3
- Fall back to identity symmetry for unlisted space groups
  AndrewSazonov
  committed
  3c9f7f7
- Update ADRs to renamed rendering_plot/table selectors
  AndrewSazonov
  committed
  6ef90ee
- Reconcile crysview ADR/plan prose with renamed selectors
  AndrewSazonov
  committed
  0383c01
- Square-root compress atom ball sizes and lower default scale
  AndrewSazonov
  committed
  d23b95f
- Halve bond cylinder radius for ball-and-stick balance
  AndrewSazonov
  committed
  77b6651
- Lower default bond increment to 0.25 A for cleaner bonding
  AndrewSazonov
  committed
  ad0be68
- Default to a trimetric c-axis-up structure view
  AndrewSazonov
  committed
  87b93e9
- Note near-neighbour auto-bonding as a future improvement
  AndrewSazonov
  committed
  c691e72
- Prune bonds to first coordination shell
  AndrewSazonov
  committed
  632b416
- Reduce default zoom ~20% and left-align legend text
  AndrewSazonov
  committed
  1567d05
- Document first-shell bond prune in ADR, plan, and issues
  AndrewSazonov
  committed
  f1250c2
- Write rendering_structure and style sections to project.cif
  AndrewSazonov
  committed
  1bf985b
- Add TikZ structure figure to TeX/PDF reports
  AndrewSazonov
  committed
  266c013
- Document TikZ structure figure in ADR and user guide
  AndrewSazonov
  committed
  d0273b7
- Clip TikZ bonds to atom surfaces for correct occlusion
  AndrewSazonov
  committed
  b4be38c
- Depth-segment cell edges and overlay axis triad in TikZ figure
  AndrewSazonov
  committed
  8983916
- Use depth-occluded axes in TeX structure figure
  AndrewSazonov
  committed
  2aa24aa
- Replace TikZ structure figures with raster PNG
  AndrewSazonov
  committed
  42113e7
- Merge atom_shape and radius_model into atom_view setting
  AndrewSazonov
  committed
  f31996d
- Render true ADP ellipsoids in the raster figure
  AndrewSazonov
  committed
  313e6a1
- Demonstrate ADP atom view in ed-14 tutorial
  AndrewSazonov
  committed
  6414deb
- Add colour-scheme selector to the structure view
  AndrewSazonov
  committed
  37223a4
- Render atoms by ADP shape with relative-proportion wedges
  AndrewSazonov
  committed
  0bac3cb
- Fix anisotropic ADP orientation and reciprocal c-axis
  AndrewSazonov
  committed
  61f5270
- Speed up structure-view zoom; stack the hint in three rows
  AndrewSazonov
  committed
  e4c42bb
- Add specular highlights to the raster structure figure
  AndrewSazonov
  committed
  217d133
- Add HTML specular, bond recolour and asymmetric-unit toggle
  AndrewSazonov
  committed
  71986d3
- Drop atomic radius, improve rendering consistency
  AndrewSazonov
  committed
  956c9c2
Commits on May 31, 2026
- Fix structure-view distortion at off-axis camera angles
  AndrewSazonov
  committed
  8c0f01a
- Default view: longest axis horizontal, second-longest up
  AndrewSazonov
  committed
  66e187a
- Rebuild axis arrows at a constant on-screen size
  AndrewSazonov
  committed
  19f53f7
- Hide a/b/c axis labels with the axes toggle
  AndrewSazonov
  committed
  f37c392
- Note crysview Phase 2 coverage and superseded prose
  AndrewSazonov
  committed
  9898d3a
- Add value-selector-discovery ADR suggestion
  AndrewSazonov
  committed
  1692ac0
- Add structure-view-settings implementation plan
  AndrewSazonov
  committed
  b360e59
- Add EnumDescriptor with show_supported listing
  AndrewSazonov
  committed
  a24643f
- Classify enumerated selectors for discovery
  AndrewSazonov
  committed
  65c7e17
- Add default and description to value-selector enums
  AndrewSazonov
  committed
  c84f7dd
- Use EnumDescriptor for experiment_type axes
  AndrewSazonov
  committed
  d779c9e
- Use EnumDescriptor for atom_sites adp_type
  AndrewSazonov
  committed
  4a483a0
- Use EnumDescriptor for verbosity selector
  AndrewSazonov
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  983a12f
- Use EnumDescriptor for fit_result result_kind
  AndrewSazonov
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  65e1798
- Use EnumDescriptor for fit_parameter_correlations source_kind
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  9d95c7a
- Use EnumDescriptor for extinction model selector
  AndrewSazonov
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  195f648
- Add structure_view content/region category
  AndrewSazonov
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  cf11738
- Add structure_style appearance category
  AndrewSazonov
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  1b22804
- Read structure view and style from new categories
  AndrewSazonov
  committed
  7344a28
- Remove the old style and rendering_structure surfaces
  AndrewSazonov
  committed
  9006b8d
- Move model.md structure styling to structure_style
  AndrewSazonov
  committed
  e24a425
- Show occupancy split as a vertical camera-facing pie
  AndrewSazonov
  committed
  c164ec5
- Update crysview ADR for the structure-view category split
  AndrewSazonov
  committed
  44abff4
- Reach Phase 1 review gate
  AndrewSazonov
  committed
  4aa3494
- Reopen Phase 1 gate pending tutorial migration
  AndrewSazonov
  committed
  827edd2
- Migrate tutorials to structure_style and regenerate notebooks
  AndrewSazonov
  committed
  6fb2df3
- Reach Phase 1 review gate
  AndrewSazonov
  committed
  1be8564
- Apply pixi run fix auto-fixes
  AndrewSazonov
  committed
  6ff808d
- Pin Logger to WARN in rendering_plot invalid-type test
  AndrewSazonov
  committed
  ad954e9
- Regenerate drifted tutorial notebooks
  AndrewSazonov
  committed
  1b5f2bd
- Ignore vendored structure renderers
  AndrewSazonov
  committed
  8dc4aa1
- Reorder tutorial rendering and fix jupytext metadata
  AndrewSazonov
  committed
  6d081c8
- Reduce report margin to 2cm
  AndrewSazonov
  committed
  1533398
- Call theme_colors by keyword in Three.js renderer
  AndrewSazonov
  committed
  2844cb0
- Refactor and annotate structure display modules for lint
  AndrewSazonov
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  2b971e6
- Annotate project view categories and config for lint
  AndrewSazonov
  committed
  ce85302
- Add unit tests for structure display and view categories
  AndrewSazonov
  committed
  19575fc
- Repoint stale tests to renamed and split categories
  AndrewSazonov
  committed
  2f63ef9
- Reflow docs and regenerate package structure
  AndrewSazonov
  committed
  374fab1
- Update ed-17 tutorial to demonstrate structure_style
  AndrewSazonov
  committed
  eb9f3d5
- Add structure view to remaining tutorials
  AndrewSazonov
  committed
  02d6026
- Frame the raster structure image with a container border
  AndrewSazonov
  committed
  8a7345b
- Flatten report headings and widen the structure figure
  AndrewSazonov
  committed
  b8f7515
- Frame structure figure within half page height, full width
  AndrewSazonov
  committed
  818831f
- Document report figure layout in summary-rendering ADR
  AndrewSazonov
  committed
  a565ee6
- Refresh structures before display scene building
  AndrewSazonov
  committed
  67a9996
- Clean up implemented ADR and plan docs
  AndrewSazonov
  committed
  85ab48f
- Change default atom view to covalent
  AndrewSazonov
  committed
  06af172
- Document clean report CIF metadata policy
  AndrewSazonov
  committed
  ee521a0
- Simplify CIF block naming in reports
  AndrewSazonov
  committed
  1f84489
- Polish structure view dark mode and labels toggle
  AndrewSazonov
  committed
  65eaaad
- Refine structure view controls and report axes
  AndrewSazonov
  committed
  7109297
- Clean report CIF metadata and block references
  AndrewSazonov
  committed
  38cda33
- Keep report datablock names unique
  AndrewSazonov
  committed
  e54709f
- Apply pixi run fix auto-fixes
  AndrewSazonov
  committed
  32f7512
- Add tutorial benchmarks
  AndrewSazonov
  committed
  b8b933f
- Finalize Python-CIF category correspondence ADR
  AndrewSazonov
  committed
  52053fb
- Refresh user guide docs for current API
  AndrewSazonov
  committed
  73cf65f
- Add documentation CI ADR suggestion
  AndrewSazonov
  committed
  437a061
- Contain structure view overlays in docs
  AndrewSazonov
  committed
  cff815e
- Format refreshed user guide docs
  AndrewSazonov
  committed
  52904d1
- Render pretty units in fit parameter tables
  AndrewSazonov
  committed
  1b8ffc1
- Sync Plotly and structure themes in docs
  AndrewSazonov
  committed
  eada32f
- Remove redundant line in tutorial docs
  AndrewSazonov
  committed
  cf0a5ed
- Normalize structure toolbar select sizing
  AndrewSazonov
  committed
  46abd05
- Use unified dark plot background
  AndrewSazonov
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  6eaea1e
- Use transparent plot backgrounds
  AndrewSazonov
  committed
  521b9a3
Commits on Jun 1, 2026
- Clarify structure-view settings ADR coverage
  AndrewSazonov
  committed
  92d5b12
- Centralize display theme styling
  AndrewSazonov
  committed
  dd794fb
- Add DisplayThemeColors class
  AndrewSazonov
  committed
  ea888b5
- Clean up Python-CIF ADR review artifacts
  AndrewSazonov
  committed
  a9720a1
- Reset zoom on view reset
  AndrewSazonov
  committed
  2de28dc
- Remove implemented plan records
  AndrewSazonov
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  4996044
- Add responsive resizing for Plotly plots
  AndrewSazonov
  committed
  d6c6408
- Remove unused reason column and standardize titles
  AndrewSazonov
  committed
  89cb84c
- Add Python-CIF correspondence implementation plan
  AndrewSazonov
  committed
  53cf2a5
- Promote Python-CIF correspondence ADR
  AndrewSazonov
  committed
  58d13bd
- Reach Python-CIF correspondence Phase 1 review gate
  AndrewSazonov
  committed
  d06051f
- Make Plotly backgrounds transparent
  AndrewSazonov
  committed
  f0e83f0
- Apply pixi run fix auto-fixes
  AndrewSazonov
  committed
  8648442
- Sync tutorials index.json with index.md and add ed-23 to ed-26
  AndrewSazonov
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  2a0b221
- Add optional width parameter to table rendering
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  8a72a23
- Show plain tutorial title in Jupyter
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  07ae7d2
- Specify instrument and data type in tutorials
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  010f3c9
- Consume Pandas table width argument
  AndrewSazonov
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  b3f8b25
- Add table rendering follow-ups to open issues
  AndrewSazonov
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  82092cb
- Make Plotly modebar background transparent in both themes
  AndrewSazonov
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  e8e10b0
- Tweak axis frame and grid colors
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  committed
  312f42e
- Size correlation matrix cells to 16 label characters
  AndrewSazonov
  committed
  826f5bd
- Merge atoms and asymmetric-unit into a cycle button
  AndrewSazonov
  committed
  013bbc0
- Refine theme legend, grid, and frame colors
  AndrewSazonov
  committed
  1ccf02a
- Sync Plotly theme to annotations, shapes, heatmaps
  AndrewSazonov
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  e5a053e
- Sort notebook cell_metadata_filter to avoid diff churn
  AndrewSazonov
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  2e2d036
- Use display units in parameter tables
  AndrewSazonov
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  7293164
- Adjust Three.js structure overlay styling
  AndrewSazonov
  committed
  54e2248
- Keep structure-view secondary axis upright
  AndrewSazonov
  committed
  cc47350

Commits

Commits on May 30, 2026

Commits on May 31, 2026

Commits on Jun 1, 2026