Files

Anto01 a3f18dc377 chore: Project cleanup and Canvas UX improvements (Phase 7-9)

## Cleanup (v0.5.0)
- Delete 102+ orphaned MCP session temp files
- Remove build artifacts (htmlcov, dist, __pycache__)
- Archive superseded plan docs (RALPH_LOOP V2/V3, CANVAS V3, etc.)
- Move debug/analysis scripts from tests/ to tools/analysis/
- Archive redundant NX journals to archive/nx_journals/
- Archive monolithic PROTOCOL.md to docs/archive/
- Update .gitignore with missing patterns
- Clean old study files (optimization_log_old.txt, run_optimization_old.py)

## Canvas UX (Phases 7-9)
- Phase 7: Resizable panels with localStorage persistence
  - Left sidebar: 200-400px, Right panel: 280-600px
  - New useResizablePanel hook and ResizeHandle component
- Phase 8: Enable all palette items
  - All 8 node types now draggable
  - Singleton logic for model/solver/algorithm/surrogate
- Phase 9: Solver configuration
  - Add SolverEngine type (nxnastran, mscnastran, python, etc.)
  - Add NastranSolutionType (SOL101-SOL200)
  - Engine/solution dropdowns in config panel
  - Python script path support

## Documentation
- Update CHANGELOG.md with recent versions
- Update docs/00_INDEX.md
- Create examples/README.md
- Add docs/plans/CANVAS_UX_IMPROVEMENTS.md

2026-01-24 15:17:34 -05:00

deprecated/result_extractors

refactor: Major reorganization of optimization_engine module structure

2025-12-29 12:30:59 -05:00

nx_journals

chore: Project cleanup and Canvas UX improvements (Phase 7-9)

2026-01-24 15:17:34 -05:00

scripts

refactor: Major reorganization of optimization_engine module structure

2025-12-29 12:30:59 -05:00

test_scripts

refactor: Reorganize code structure and create tests directory

2026-01-07 09:01:37 -05:00

README.md

feat: Add TrialManager and DashboardDB for unified trial management

2025-12-28 12:20:19 -05:00

README.md

Atomizer Archive

This directory contains deprecated/replaced code that is kept for reference and potential rollback.

Structure

archive/
├── extractors/           # Deprecated physics extractors
│   └── zernike_legacy/   # Pre-OPD Zernike extractors
└── README.md

Archive Policy

When replacing functionality:

Move the old file to the appropriate archive subdirectory
Add a header comment noting the archive date and replacement
Update this README with the change

Archived Items

extractors/zernike_legacy/ (2024-12-28)

Replaced by: extract_zernike_opd.py (ZernikeOPDExtractor)

Reason: The OPD method provides more accurate wavefront error calculations by:

Using optical path difference (OPD) directly instead of surface displacement
Proper handling of relative subcase comparisons
Better numerical stability for high-order Zernike modes

Archived files:

File	Original Class	Description
`extract_zernike.py`	`ZernikeExtractor`	Original displacement-based Zernike
`extract_zernike_surface.py`	`ZernikeSurfaceExtractor`	Surface-normal projection variant
`extract_zernike_figure.py`	`ZernikeFigureExtractor`	Figure error variant

To restore: Copy files back to optimization_engine/extractors/ and update __init__.py