Model test

[kewh5868]

Here’s a copyable PR comment/body:

## Summary

This PR packages the current SAXSShell feature work into a staged commit series while keeping generated project artifacts out of version control.

## What Changed

- Added `.gitignore` coverage for generated CsPbI3 SAXS fit exports, zip bundles, and generated reports.
- Added a new UV-Vis pseudo-Voigt fitting tool with CLI entry point, Qt UI, Monte Carlo uncertainty support, exports, and tests.
- Added APS detector stitching utilities, a standalone stitching tool, real APS fixture data, and regression tests.
- Added shared structure-distribution caching and browser support, then wired bondanalysis through it with coordination-number analysis and a multi-project batch queue.
- Improved MD trajectory and cluster extraction workflows with frame timestep inference/manual fallback, restart duplicate handling, solvation-shell export behavior, and batch queue ergonomics.
- Streamlined project queue setup for PDF, representative finder, and xyz2pdb workflows, including progress dialogs, bounded consoles, and richer xyz2pdb reference-bond controls.
- Expanded SAXS Prefit and DREAM workflows with active fit q-ranges, DREAM backend batch run sets, posterior filtering/reporting improvements, stoichiometry compensation, dielectric/formal-charge helpers, and legacy/model template updates.
- Updated SAXS user-guide documentation for the new Prefit, DREAM, solvent, stoichiometry, and template behavior.

## Commit Structure

1. `chore: ignore generated SAXS outputs`
2. `feat(uvvis): add pseudo-Voigt fitting tool`
3. `feat(saxs): add APS detector stitching tool`
4. `feat(bondanalysis): cache structure distributions`
5. `feat(cluster): improve trajectory extraction batching`
6. `feat(batch): streamline project queue setup`
7. `feat(saxs): expand Prefit and DREAM workflows`
8. `docs(saxs): document updated Prefit and DREAM models`

## Validation

- All commits passed the local pre-commit flow:
  - end-of-file fixer
  - trailing whitespace
  - case/merge conflict checks
  - TOML/YAML checks where applicable
  - Black
  - flake8
  - isort
  - codespell
  - prettier
  - docformatter
- Confirmed the working tree is clean after the commit series.
- Confirmed generated artifacts are ignored:
  - `docs/reports/`
  - `tests/CsPbI3_SAXS_fit/`
  - `tests/CsPbI3_SAXS_fit.zip`
- Removed the accidental Windows-path export folder from the checkout.

## Test Notes

A broad touched-area pytest run was started across 883 tests covering the new and modified modules. It passed through the APS, UV-Vis, structure-distribution, bondanalysis, cluster, MD trajectory, PDF, representative finder, xyz2pdb, fullrmc, CLI, lazy import, stoichiometry, template-installation, DREAM runtime, and model-report sections before being stopped during the long SAXS UI tail.

Known caveat: several failures appeared in `tests/test_saxs_prefit.py` and `tests/test_saxs_ui.py` before the run was interrupted, but the full failure traceback summary was not collected.

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[chatgpt-codex-connector]

Resolve custom run-file paths against project directory

When --run-file is provided as a relative path, _resolve_run_file calls Path(run_file).expanduser().resolve(), which resolves against the current working directory instead of project_dir. In practice, running clusterdynamics run /path/to/project --run-file my_run.json from another directory will look for /current/dir/my_run.json (or load the wrong file) rather than /path/to/project/my_run.json, even though this subcommand is defined around a project folder. This makes relative run-file paths unreliable for normal CLI usage outside the project root.

Useful? React with 👍 / 👎.

[kewh5868]

Summary

This PR updates model-test after merging the latest main changes from Rmcsetup (#124) and resolves the overlapping workflow conflicts.

Key additions include:

• Ignored generated/local artifacts, including tests/CsPbI3_SAXS_fit/, tests/CsPbI3_SAXS_fit.zip, reports, and local-only workspace output.
• Added the UV-vis pseudo-Voigt fitting tool.
• Added the APS SAXS detector stitching tool.
• Added structure-distribution caching for bond/angle analysis consumers.
• Improved MD trajectory extraction batching, including restart duplicate handling and frame timestep controls.
• Streamlined batch/project queue setup across MD trajectory, cluster, XYZ-to-PDB, representative finder, and PDF workflows.
• Expanded SAXS Prefit and DREAM workflows, including updated scaled-solvent MonoSQ templates, charged MonoSQ metadata, concentration/charge helpers, DREAM batching, and documentation.
• Updated SAXS model documentation for the new Prefit/DREAM model conventions.

Merge Conflict Resolution

Merged origin/main into model-test and resolved conflicts across docs, SAXS templates/UI, MD trajectory workflow/UI, cluster presets/UI, representative finder workflow/UI, XYZ-to-PDB queue UI, PDF Debyer queue UI, and related tests.

Resolution notes:

• Kept model-test behavior where it extended the incoming main implementation.
• Preserved the newer PDF batch queue frame-inspection UI from main.
• Re-applied the safer saved-project loading behavior from model-test so loading many PDF projects shows progress and does not auto-inspect large saved frame folders.
• Confirmed no conflict markers remain.

Validation

Passed:

• rg conflict-marker scan
• python -m json.tool on conflicted JSON files
• python -m compileall on resolved Python modules
• git diff --check
• Pre-commit hooks during merge commit:
  • black
  • flake8
  • isort
  • codespell
  • prettier
  • docformatter
  • merge-conflict check

Partial:

• Focused pytest run was started for touched conflict areas and reached tests/test_saxs_ui.py.
• The run was stopped to avoid another long hang; failure markers appeared in tests/test_saxs_ui.py before termination and were not investigated in this merge-resolution pass.