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cfef893
Add crysview-structure-visualization ADR suggestion
AndrewSazonov May 30, 2026
95bacb4
Add crysview-structure-visualization implementation plan
AndrewSazonov May 30, 2026
9ae8c80
Add crysview viewer and styling enums
AndrewSazonov May 30, 2026
890122e
Add renderer-neutral structure scene model
AndrewSazonov May 30, 2026
17ed15f
Add orthogonalization and ADP eigendecomposition helpers
AndrewSazonov May 30, 2026
777f0fc
Add extended element database for radii and colours
AndrewSazonov May 30, 2026
a959553
Add structure scene builder
AndrewSazonov May 30, 2026
df333e8
Add ASCII structure renderer
AndrewSazonov May 30, 2026
fe1e196
Add Viewer facade and factory with ASCII engine
AndrewSazonov May 30, 2026
b2211b7
Add style category for structure view styling
AndrewSazonov May 30, 2026
a1abc2b
Use six scalar descriptors for the view range
AndrewSazonov May 30, 2026
78484a3
Add switchable view category for renderer selection
AndrewSazonov May 30, 2026
62d2faf
Wire project.view and project.style with CIF persistence
AndrewSazonov May 30, 2026
c39bf8f
Add per-structure geom bond-cutoff category
AndrewSazonov May 30, 2026
85e9e60
Align single-crystal scatter axes and style in HTML and PDF
AndrewSazonov May 30, 2026
f86f169
Add structure() and show_structure_options() display surface
AndrewSazonov May 30, 2026
956fc0b
Add tests for single-crystal scatter range, ticks, and diagonal
AndrewSazonov May 30, 2026
2986038
Vendor pinned Three.js assets
AndrewSazonov May 30, 2026
e6824a3
Add Three.js structure renderer
AndrewSazonov May 30, 2026
acd43cb
Embed structure figure in HTML report under html_offline
AndrewSazonov May 30, 2026
dbcf55f
Document structure view in tutorials and reference
AndrewSazonov May 30, 2026
9135f31
Reach Phase 1 review gate
AndrewSazonov May 30, 2026
506ce79
Resync tutorial notebooks with sources
AndrewSazonov May 30, 2026
87e11f8
Default structure view engine to environment-aware auto
AndrewSazonov May 30, 2026
6b7ec70
Document auto default for structure view engine
AndrewSazonov May 30, 2026
c797089
Fix single-crystal tick rounding and lighten markers and bars
AndrewSazonov May 30, 2026
e21ff4b
Test single-crystal tick step rounding and marker stroke
AndrewSazonov May 30, 2026
a2a90cc
Remove unimplemented Structure.show() superseded by display.structure()
AndrewSazonov May 30, 2026
3eb4ce9
Wrap Three.js import map in required imports key
AndrewSazonov May 30, 2026
00f7c3d
Add import-map regression guard to Phase 2 test plan
AndrewSazonov May 30, 2026
f00287a
Force light theme for structure view in HTML reports
AndrewSazonov May 30, 2026
d52c094
Match structure-view modebar and layout to reference demo
AndrewSazonov May 30, 2026
fb922ea
Add atom_scale and per-axis axis lengths to structure scene
AndrewSazonov May 30, 2026
5a4cd3b
Thicken axes, tighten zoom, add PNG download and mixed-site legend
AndrewSazonov May 30, 2026
11b3df0
Document atom_scale style option
AndrewSazonov May 30, 2026
74066b3
Rename rendering selectors to rendering_plot/structure/table
AndrewSazonov May 30, 2026
3c9f7f7
Fall back to identity symmetry for unlisted space groups
AndrewSazonov May 30, 2026
6ef90ee
Update ADRs to renamed rendering_plot/table selectors
AndrewSazonov May 30, 2026
0383c01
Reconcile crysview ADR/plan prose with renamed selectors
AndrewSazonov May 30, 2026
d23b95f
Square-root compress atom ball sizes and lower default scale
AndrewSazonov May 30, 2026
77b6651
Halve bond cylinder radius for ball-and-stick balance
AndrewSazonov May 30, 2026
ad0be68
Lower default bond increment to 0.25 A for cleaner bonding
AndrewSazonov May 30, 2026
87b93e9
Default to a trimetric c-axis-up structure view
AndrewSazonov May 30, 2026
c691e72
Note near-neighbour auto-bonding as a future improvement
AndrewSazonov May 30, 2026
632b416
Prune bonds to first coordination shell
AndrewSazonov May 30, 2026
1567d05
Reduce default zoom ~20% and left-align legend text
AndrewSazonov May 30, 2026
f1250c2
Document first-shell bond prune in ADR, plan, and issues
AndrewSazonov May 30, 2026
1bf985b
Write rendering_structure and style sections to project.cif
AndrewSazonov May 30, 2026
266c013
Add TikZ structure figure to TeX/PDF reports
AndrewSazonov May 30, 2026
d0273b7
Document TikZ structure figure in ADR and user guide
AndrewSazonov May 30, 2026
b4be38c
Clip TikZ bonds to atom surfaces for correct occlusion
AndrewSazonov May 30, 2026
8983916
Depth-segment cell edges and overlay axis triad in TikZ figure
AndrewSazonov May 30, 2026
2aa24aa
Use depth-occluded axes in TeX structure figure
AndrewSazonov May 30, 2026
42113e7
Replace TikZ structure figures with raster PNG
AndrewSazonov May 30, 2026
f31996d
Merge atom_shape and radius_model into atom_view setting
AndrewSazonov May 30, 2026
313e6a1
Render true ADP ellipsoids in the raster figure
AndrewSazonov May 30, 2026
6414deb
Demonstrate ADP atom view in ed-14 tutorial
AndrewSazonov May 30, 2026
37223a4
Add colour-scheme selector to the structure view
AndrewSazonov May 30, 2026
0bac3cb
Render atoms by ADP shape with relative-proportion wedges
AndrewSazonov May 30, 2026
61f5270
Fix anisotropic ADP orientation and reciprocal c-axis
AndrewSazonov May 30, 2026
e4c42bb
Speed up structure-view zoom; stack the hint in three rows
AndrewSazonov May 30, 2026
217d133
Add specular highlights to the raster structure figure
AndrewSazonov May 30, 2026
71986d3
Add HTML specular, bond recolour and asymmetric-unit toggle
AndrewSazonov May 30, 2026
956c9c2
Drop atomic radius, improve rendering consistency
AndrewSazonov May 30, 2026
8c0f01a
Fix structure-view distortion at off-axis camera angles
AndrewSazonov May 31, 2026
66e187a
Default view: longest axis horizontal, second-longest up
AndrewSazonov May 31, 2026
19f53f7
Rebuild axis arrows at a constant on-screen size
AndrewSazonov May 31, 2026
f37c392
Hide a/b/c axis labels with the axes toggle
AndrewSazonov May 31, 2026
9898d3a
Note crysview Phase 2 coverage and superseded prose
AndrewSazonov May 31, 2026
1692ac0
Add value-selector-discovery ADR suggestion
AndrewSazonov May 31, 2026
b360e59
Add structure-view-settings implementation plan
AndrewSazonov May 31, 2026
a24643f
Add EnumDescriptor with show_supported listing
AndrewSazonov May 31, 2026
65c7e17
Classify enumerated selectors for discovery
AndrewSazonov May 31, 2026
c84f7dd
Add default and description to value-selector enums
AndrewSazonov May 31, 2026
d779c9e
Use EnumDescriptor for experiment_type axes
AndrewSazonov May 31, 2026
4a483a0
Use EnumDescriptor for atom_sites adp_type
AndrewSazonov May 31, 2026
983a12f
Use EnumDescriptor for verbosity selector
AndrewSazonov May 31, 2026
65e1798
Use EnumDescriptor for fit_result result_kind
AndrewSazonov May 31, 2026
9d95c7a
Use EnumDescriptor for fit_parameter_correlations source_kind
AndrewSazonov May 31, 2026
195f648
Use EnumDescriptor for extinction model selector
AndrewSazonov May 31, 2026
cf11738
Add structure_view content/region category
AndrewSazonov May 31, 2026
1b22804
Add structure_style appearance category
AndrewSazonov May 31, 2026
7344a28
Read structure view and style from new categories
AndrewSazonov May 31, 2026
9006b8d
Remove the old style and rendering_structure surfaces
AndrewSazonov May 31, 2026
e24a425
Move model.md structure styling to structure_style
AndrewSazonov May 31, 2026
c164ec5
Show occupancy split as a vertical camera-facing pie
AndrewSazonov May 31, 2026
44abff4
Update crysview ADR for the structure-view category split
AndrewSazonov May 31, 2026
4aa3494
Reach Phase 1 review gate
AndrewSazonov May 31, 2026
827edd2
Reopen Phase 1 gate pending tutorial migration
AndrewSazonov May 31, 2026
6fb2df3
Migrate tutorials to structure_style and regenerate notebooks
AndrewSazonov May 31, 2026
1be8564
Reach Phase 1 review gate
AndrewSazonov May 31, 2026
6ff808d
Apply pixi run fix auto-fixes
AndrewSazonov May 31, 2026
ad954e9
Pin Logger to WARN in rendering_plot invalid-type test
AndrewSazonov May 31, 2026
1b5f2bd
Regenerate drifted tutorial notebooks
AndrewSazonov May 31, 2026
8dc4aa1
Ignore vendored structure renderers
AndrewSazonov May 31, 2026
6d081c8
Reorder tutorial rendering and fix jupytext metadata
AndrewSazonov May 31, 2026
1533398
Reduce report margin to 2cm
AndrewSazonov May 31, 2026
2844cb0
Call theme_colors by keyword in Three.js renderer
AndrewSazonov May 31, 2026
2b971e6
Refactor and annotate structure display modules for lint
AndrewSazonov May 31, 2026
ce85302
Annotate project view categories and config for lint
AndrewSazonov May 31, 2026
19575fc
Add unit tests for structure display and view categories
AndrewSazonov May 31, 2026
2f63ef9
Repoint stale tests to renamed and split categories
AndrewSazonov May 31, 2026
374fab1
Reflow docs and regenerate package structure
AndrewSazonov May 31, 2026
eb9f3d5
Update ed-17 tutorial to demonstrate structure_style
AndrewSazonov May 31, 2026
02d6026
Add structure view to remaining tutorials
AndrewSazonov May 31, 2026
8a7345b
Frame the raster structure image with a container border
AndrewSazonov May 31, 2026
b8f7515
Flatten report headings and widen the structure figure
AndrewSazonov May 31, 2026
818831f
Frame structure figure within half page height, full width
AndrewSazonov May 31, 2026
a565ee6
Document report figure layout in summary-rendering ADR
AndrewSazonov May 31, 2026
67a9996
Refresh structures before display scene building
AndrewSazonov May 31, 2026
85ab48f
Clean up implemented ADR and plan docs
AndrewSazonov May 31, 2026
06af172
Change default atom view to covalent
AndrewSazonov May 31, 2026
ee521a0
Document clean report CIF metadata policy
AndrewSazonov May 31, 2026
1f84489
Simplify CIF block naming in reports
AndrewSazonov May 31, 2026
65eaaad
Polish structure view dark mode and labels toggle
AndrewSazonov May 31, 2026
7109297
Refine structure view controls and report axes
AndrewSazonov May 31, 2026
38cda33
Clean report CIF metadata and block references
AndrewSazonov May 31, 2026
e54709f
Keep report datablock names unique
AndrewSazonov May 31, 2026
32f7512
Apply pixi run fix auto-fixes
AndrewSazonov May 31, 2026
b8b933f
Add tutorial benchmarks
AndrewSazonov May 31, 2026
52053fb
Finalize Python-CIF category correspondence ADR
AndrewSazonov May 31, 2026
73cf65f
Refresh user guide docs for current API
AndrewSazonov May 31, 2026
437a061
Add documentation CI ADR suggestion
AndrewSazonov May 31, 2026
cff815e
Contain structure view overlays in docs
AndrewSazonov May 31, 2026
52904d1
Format refreshed user guide docs
AndrewSazonov May 31, 2026
1b8ffc1
Render pretty units in fit parameter tables
AndrewSazonov May 31, 2026
eada32f
Sync Plotly and structure themes in docs
AndrewSazonov May 31, 2026
cf0a5ed
Remove redundant line in tutorial docs
AndrewSazonov May 31, 2026
46abd05
Normalize structure toolbar select sizing
AndrewSazonov May 31, 2026
6eaea1e
Use unified dark plot background
AndrewSazonov May 31, 2026
521b9a3
Use transparent plot backgrounds
AndrewSazonov May 31, 2026
92d5b12
Clarify structure-view settings ADR coverage
AndrewSazonov Jun 1, 2026
dd794fb
Centralize display theme styling
AndrewSazonov Jun 1, 2026
ea888b5
Add DisplayThemeColors class
AndrewSazonov Jun 1, 2026
a9720a1
Clean up Python-CIF ADR review artifacts
AndrewSazonov Jun 1, 2026
2de28dc
Reset zoom on view reset
AndrewSazonov Jun 1, 2026
4996044
Remove implemented plan records
AndrewSazonov Jun 1, 2026
d6c6408
Add responsive resizing for Plotly plots
AndrewSazonov Jun 1, 2026
89cb84c
Remove unused reason column and standardize titles
AndrewSazonov Jun 1, 2026
53cf2a5
Add Python-CIF correspondence implementation plan
AndrewSazonov Jun 1, 2026
58d13bd
Promote Python-CIF correspondence ADR
AndrewSazonov Jun 1, 2026
d06051f
Reach Python-CIF correspondence Phase 1 review gate
AndrewSazonov Jun 1, 2026
f0e83f0
Make Plotly backgrounds transparent
AndrewSazonov Jun 1, 2026
8648442
Apply pixi run fix auto-fixes
AndrewSazonov Jun 1, 2026
2a0b221
Sync tutorials index.json with index.md and add ed-23 to ed-26
AndrewSazonov Jun 1, 2026
8a72a23
Add optional width parameter to table rendering
AndrewSazonov Jun 1, 2026
07ae7d2
Show plain tutorial title in Jupyter
AndrewSazonov Jun 1, 2026
010f3c9
Specify instrument and data type in tutorials
AndrewSazonov Jun 1, 2026
b3f8b25
Consume Pandas table width argument
AndrewSazonov Jun 1, 2026
82092cb
Add table rendering follow-ups to open issues
AndrewSazonov Jun 1, 2026
e8e10b0
Make Plotly modebar background transparent in both themes
AndrewSazonov Jun 1, 2026
312f42e
Tweak axis frame and grid colors
AndrewSazonov Jun 1, 2026
826f5bd
Size correlation matrix cells to 16 label characters
AndrewSazonov Jun 1, 2026
013bbc0
Merge atoms and asymmetric-unit into a cycle button
AndrewSazonov Jun 1, 2026
1ccf02a
Refine theme legend, grid, and frame colors
AndrewSazonov Jun 1, 2026
e5a053e
Sync Plotly theme to annotations, shapes, heatmaps
AndrewSazonov Jun 1, 2026
2e2d036
Sort notebook cell_metadata_filter to avoid diff churn
AndrewSazonov Jun 1, 2026
7293164
Use display units in parameter tables
AndrewSazonov Jun 1, 2026
54e2248
Adjust Three.js structure overlay styling
AndrewSazonov Jun 1, 2026
cc47350
Keep structure-view secondary axis upright
AndrewSazonov Jun 1, 2026
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1 change: 1 addition & 0 deletions .prettierignore
Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,7 @@ docs/docs/assets/
node_modules

# Vendored snapshots
src/easydiffraction/display/structure/renderers/vendor/
src/easydiffraction/report/templates/html/vendor/
src/easydiffraction/report/templates/tex/styles/
src/easydiffraction/utils/_vendored/jupyter_dark_detect/
Expand Down
12 changes: 12 additions & 0 deletions THIRD_PARTY_LICENSES.md
Original file line number Diff line number Diff line change
Expand Up @@ -11,3 +11,15 @@ The vendored report LaTeX style files are documented in

The vendored report HTML assets are documented in
`src/easydiffraction/report/templates/html/vendor/LICENSES.md`.

## Structure-View Three.js

The vendored Three.js assets for the crysview structure view (MIT) are
documented in
`src/easydiffraction/display/structure/renderers/vendor/threejs/LICENSES.md`.

## Structure-View Element Data

The bundled per-element radii and colour palettes (with per-source
provenance) are documented in
`src/easydiffraction/display/structure/assets/LICENSES.md`.
10 changes: 5 additions & 5 deletions docs/dev/adrs/accepted/category-owner-sections.md
Original file line number Diff line number Diff line change
Expand Up @@ -85,13 +85,13 @@ Its current children are:
The public API stays flat and user-facing:

- `project.info`
- `project.chart`
- `project.table`
- `project.rendering_plot`
- `project.rendering_table`

Saved `project.cif` remains a section file without a `data_` header. It
serializes the `_project.*` metadata category plus the `_chart.*` and
`_table.*` configuration categories without pretending that the project
config is a real datablock.
serializes the `_project.*` metadata category plus the
`_rendering_plot.*` and `_rendering_table.*` configuration categories
without pretending that the project config is a real datablock.

### 4. CIF serialization is split by responsibility

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745 changes: 745 additions & 0 deletions docs/dev/adrs/accepted/crysview-structure-visualization.md

Large diffs are not rendered by default.

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