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Cluster ml saxs#43

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kewh5868 merged 4 commits into
mainfrom
cluster-ml-saxs
Mar 31, 2026
Merged

Cluster ml saxs#43
kewh5868 merged 4 commits into
mainfrom
cluster-ml-saxs

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@kewh5868 kewh5868 commented Mar 31, 2026

Summary

This PR bundles a broad set of application, workflow, UI, and documentation updates across the SAXSShell codebase.

Major additions

  • Added a new Blender-based structure rendering tool with an interactive preview UI
  • Added a new PDF calculation workflow and UI
  • Expanded SAXS workflows, project tooling, UI behavior, and regression coverage
  • Expanded cluster dynamics ML workflow, plotting, reporting, and UI support
  • Refreshed documentation, MkDocs navigation, and site assets

Blender renderer updates

  • Added the new blenderxyz workflow and desktop UI
  • Added support for both XYZ and PDB inputs
  • Added interactive preview controls for rotate, pan, zoom, and reset view
  • Added synced orientation editing so the viewer, row values, and render values stay aligned
  • Added per-orientation controls in the table for lighting, aesthetic style, render quality, and legend output
  • Added orientation duplication and custom orientation editing
  • Added progress reporting during Blender renders
  • Added transparent PNG output and brighter lighting controls
  • Added optional .blend output alongside rendered PNGs
  • Added atom legend export support
  • Added VESTA-style bond threshold editing for loaded structures
  • Added more non-photorealistic/cartoon-like aesthetic presets
  • Improved render framing so the full molecule stays in view
  • Improved output naming to include style/quality metadata
  • Added the orientation probe helper used to validate preview/render consistency

PDF calculation updates

  • Added the pdf.debyer workflow package
  • Added a Qt UI for PDF calculation and workflow execution
  • Added package wiring and test coverage for PDF setup flows

SAXS / application updates

  • Expanded Debye, DREAM, prefit, stoichiometry, and project manager functionality
  • Improved SAXS UI tabs and main window integration
  • Promoted the legacy poly LMA HS template into the active template set
  • Added and updated regression tests covering CLI, UI, and workflow behavior

Cluster dynamics ML updates

  • Expanded dataset and workflow support
  • Improved the ML UI and plotting behavior
  • Improved cluster dynamics reporting integration
  • Added broader regression coverage for cluster dynamics ML features

Documentation updates

  • Refreshed installation, quickstart, project setup, and overview docs
  • Added user guides for cluster dynamics ML and PDF calculation
  • Updated GUI, template, preloaded model, and SAXS prefit documentation
  • Added site icon assets and updated MkDocs navigation

Validation

  • Pre-commit hooks passed during commit creation, including formatting, linting, import sorting, and docs formatting checks

Closes #14
Closes #20
Closes #31
Closes #33
Closes #35
Closes #36

kewh5868 added 4 commits March 31, 2026 17:31
@kewh5868
feat: expand cluster dynamics ML workflow tooling
58c71f8 
Add broader cluster dynamics ML support across data loading, workflow orchestration, UI interactions, plotting, and reporting.\n\nHighlights:\n- extend the ML workflow and dataset utilities to cover the new training and analysis paths\n- enrich the cluster dynamics ML window and plot panel behavior for more complete interactive use\n- tighten cluster dynamics reporting and main-window integration\n- add regression coverage for the expanded cluster dynamics ML feature set
@kewh5868
feat: broaden SAXS workflows and project tooling
d56318a 
Expand the SAXS stack across debye profiles, DREAM runtime behavior, prefit workflow logic, project management, and the desktop UI.\n\nHighlights:\n- add richer profile and stoichiometry utilities used by downstream analysis flows\n- strengthen DREAM settings, distributions, runtime handling, and result management\n- improve prefit geometry and workflow support for more complete setup paths\n- extend project manager capabilities, prior plotting, and top-level application integration\n- refresh the SAXS UI tabs and add broader regression coverage for CLI and UI behavior\n- promote the legacy poly LMA HS template into the active template set
@kewh5868
feat: add PDF calculation and Blender rendering tools
3f4bb0c 
Introduce two substantial user-facing toolchains: a PDF calculation workflow and a Blender-based structure rendering application.\n\nHighlights:\n- add the debyer PDF package, workflow, and Qt UI wiring\n- add the Blender renderer package, CLI, workflow layer, shared render settings, and interactive main window\n- register the new blenderxyz console entrypoint in project metadata\n- add the orientation probe helper script used to compare viewer and Blender orientations\n- cover the new PDF and Blender functionality with dedicated tests and package exports
@kewh5868
docs: refresh guides and site assets
9c15b94 
Update the top-level docs and MkDocs content to cover the newly expanded workflows, tools, and user interface areas.\n\nHighlights:\n- refresh installation, quickstart, project setup, and overview pages\n- add dedicated user guides for cluster dynamics ML and PDF calculation workflows\n- update GUI, template, preloaded model, and SAXS prefit documentation\n- add site icon assets and wire the documentation navigation to the new pages
@kewh5868 kewh5868 merged commit e9462f5 into main Mar 31, 2026
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