Merge upstreabgm main#10
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Co-authored-by: Keith White <91701813+kewh5868@users.noreply.github.com>
* feat(plotting): add reusable plot editor controls Add shared plotting helpers for Igor-style labels, editable line plots, heatmaps, and stacked histograms. Wire the heatmap editor into cluster dynamics views and vectorize bond/angle measurements used by representative-style plotting workflows. * feat(fullrmc): expand Packmol solvent setup workflow Add Packmol Docker linking, solvent-shell analysis/building, free-solvent allocation, structure-mode aware Packmol setup, and constraints preview/open helpers. Update the fullrmc UI and tests around the integrated RMC setup flow. * feat(representativefinder): add project-backed CLI and UI Introduce the representativefinder package, console entry point, run-file workflow, Qt setup/analyzer windows, and representative persistence helpers. Add tests and a performance harness while keeping generated benchmark outputs ignored. * feat(viewer): allow structure background color edits Add a structure-viewer background color control, preserve the selected background across redraws, and cover the behavior in the viewer tests. * feat(saxs): add representative and FFT Born workflows Add representative-structure component sources, template metadata capabilities, persisted plot editor state, and 1D/3D Born component workflow integration. Introduce the 3D FFT Born backend/UI and expand project, prefit, electron-density, and SAXS UI tests. * docs: document expanded SAXS and fullrmc workflows Refresh the docs landing pages, install/setup guides, and user-guide navigation for representative structures, 1D/3D Born workflows, Packmol Docker linking, and updated SAXS/fullrmc terminology. * ci: pin docformatter hook to Python 3.12 Run the docformatter hook with Python 3.12 so its untokenize dependency does not build under Python 3.14, where the package setup fails while reading AST constants. * fix(mdtrajectory): preserve restart frame identity Handle CP2K restart-overlap frames by using source i-index metadata and skipping earlier duplicate source frames by default. Add an opt-in duplicate export mode, stricter XYZ filename/header validation, and a validate-export CLI command to catch mismatched exports. * fix(cluster): defer smart shell union finalization Finalize smart solvation shell runs only when they close, preserving deferred unions across contiguous frame runs and resumes. Add coverage for linear scaling over contiguous runs and for resumed exports that must rebuild deferred shell unions correctly. * feat(ui): add periodic table selector Add a reusable Qt periodic-table widget and element picker dialog for workflows that need single-atom component selection. * feat(fullrmc): support supplemental Packmol components Extend FullRMC setup to plan supplemental solute and solvent components, track generated Packmol inputs, and expose the workflow in the Qt setup interface with CLI coverage. * feat(clusterdynamicsml): add run files and lifetime plots Add project-scoped run configuration files and batch-run CLI support for cluster dynamics ML, plus lifetime distribution plotting and tests. * feat(batch): add project run files and queue tools Add saved run configurations, run-file setup UIs, CLI batch execution, and batch queue windows for the core project workflows, with coverage for cluster extraction, cluster dynamics, MD trajectory export, representative selection, and XYZ to PDB conversion. * feat(pdf): expand Debyer workflow and batch queue Add PDF batch queue execution, richer partial/experimental analysis controls, R(r) coordination fitting support, and tests for the expanded Debyer workflow. * feat(saxs): add charged hard-sphere model templates Add the Hayter-MSA charged MonoSQ template and a model-scale solvent template, with metadata, documentation, and regression coverage for the solution-scattering conventions. * feat(app): add workflow launchers and data overlay Wire batch queues and run-file setup tools into the SAXS main window, keep project-writing tool windows single-instance, and add an experimental data overlay viewer with UI coverage. * feat(xyz2pdb): add DMSO MD reference Add the DMSO molecular-dynamics residue reference JSON and PDB template to the XYZ to PDB reference library. * docs: update workflow and platform guidance Update GitHub-facing READMEs and user docs for macOS/Linux versus Windows setup guidance, batch/run-file workflows, and the expanded analysis tools. * fix(saxs): honor deprecated template metadata Allow templates in the active template directory to be hidden by deprecated metadata, and update installer test fixtures to use current archived template locations with finite DREAM validation output.
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