UI refactor#13
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Replace hiding/showing of analysis accordions with in-DOM placeholders and collapsed state. Introduces a _PANEL_META class var and per-panel unavailable message + content wrappers so panels remain in the DOM but start collapsed (selected_index=None) and show an inline "not available" note until activated. Update activate/deactivate logic to toggle selected_index and swap placeholders, refresh IR and Energies views when panels are expanded, and read tooltips from _PANEL_META. Also tweak some checkbox descriptions. Tests updated to expect visible-but-collapsed accordions and to verify placeholder/content swapping.
Update Copilot instructions to reflect UI and test changes: add new utility modules (issue_tracker, log_utils, benchmarks) to the file list; change Analysis tab panels to be always present in the DOM with "Not available" placeholders; revise panel metadata to use (panel_name, accordion_attr_name, placeholder) as the single source of truth; simplify panel activation/deactivation semantics (collapse/restore placeholders, never remove from DOM); update developer steps for adding panels. Add critical quality rules: ban include_plotlyjs="cdn" (prefer "require" or inline) and require wrapping .observe() callbacks with _safe_cb to surface exceptions to the Log tab. Update __init__ attributes (unavail placeholders, content boxes, pending button removal) and refresh tests list/baseline to match new behavior. These changes improve offline reliability (Plotly), error visibility in Voilà, and make panel lifecycle explicit for history replay.
Introduce a _safe_cb wrapper to .observe() handlers so exceptions are logged instead of silently dropped, and wire many widget observers through it (trajectory, IR/orb accordions, viz/theme/preset/calc inputs, orbital controls, vibrational controls, slider/frame updates, etc.). Refactor the Analysis panel switcher: remove the button-based switcher UI and per-button logic, simplify _select_ana_panel/_activate/_deactivate behavior to use accordion selected_index and add accordion observers to re-render Plotly charts when shown. Replace several include_plotlyjs='cdn' usages with 'require' to avoid silent failures when offline. Tighten exception handling in pubchem.smiles_to_xyz and check_pubchem_availability (catch Exception instead of bare except). Update tests to match the refactor and add tests/test_code_quality.py to forbid use of include_plotlyjs='cdn' and bare except/pass patterns.
Refresh .github/copilot-instructions.md to match recent code changes: document new QuantUI app build flow (new widgets, _wire_callbacks ordering, _assemble_tabs producing 7 root tabs), update root-tab order and note Help is a floating overlay, and add/rename helper builders (status, theme, welcome, issue widgets). Adjust Analysis panel registry and panel metadata (reorder/availability for frequency panels), tighten thread-safety guidance for Plotly rendering, and update supported methods/bases list. Update test invocation to run tests/ without coverage, bump collected test count and baseline, and add/rename several test modules (issue tracker, visualization, templates, analysis history variants), plus stricter code-quality entry. Revise dependency section into explicit groups with version hints and a new install extras command to reflect runtime and dev extras. Overall: keep the developer-facing instructions consistent with the current implementation and test matrix.
Replace widgets.HTML with widgets.Output for Plotly/matplotlib displays to ensure JS execution and proper display. Add helpers (_set_html_output, _set_plotly_figure_output, _render_plotly_figure, _clear_output_widget) and update code paths to render/clear Output widgets. Make IR control wiring main-thread safe (_wire_ir_controls, _on_ir_mode_changed, _on_ir_fwhm_changed) and queue callbacks where needed. Change IR plot x-axis ordering to low→high (400→4000) and update tests to assert Output.outputs usage and new x-axis orientation.
Introduce a module-level _LAYOUT_TRAITS set and a _layout(...) helper that normalizes legacy/alternate layout kwargs (overflow_y -> overflow, gap -> grid_gap, flex_wrap -> flex_flow) and filters out unsupported traits before constructing widgets.Layout. Replace direct widgets.Layout(...) calls across quantui/app.py with _layout(...) to avoid traitlets warnings/noise and improve compatibility with varied layout argument names. No behavioral changes intended beyond suppressing trait warnings and normalizing inputs.
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This pull request makes significant improvements to the QuantUI documentation and codebase to clarify the app’s architecture, enforce best practices, and enhance test coverage. The changes include a major overhaul of
.github/copilot-instructions.mdto reflect the current UI structure, new developer guidelines, expanded test coverage, and several code quality and UX fixes.Documentation and Architecture Updates:
Updated the
.github/copilot-instructions.mdto reflect the new app structure, including a detailed breakdown of the UI widget hierarchy, tab order, and analysis panel management. The documentation now emphasizes always-visible analysis panels, improved placeholder handling, and the introduction of new widgets like the status panel and issue tracker. [1] [2] [3] [4] [5] [6] [7] [8]Added new developer guidelines, including rules for widget updates in threads, mandatory use of
_safe_cbfor.observe()callbacks, and requirements for pre-commit/test runs before handoff. [1] [2]Testing and Coverage Improvements:
Expanded the test suite from ~700 to ~875 tests, with new tests for issue tracking, notebook interactions, analysis panel history replay, IR plotting, and static code quality (e.g., banning CDN Plotly.js usage). [1] [2]
Updated test expectations for IR accordion widgets to match the new always-visible, collapsed-by-default behavior.
Analysis Panel and UI Behavior:
Refactored the analysis panel registry and panel activation logic to ensure all panels are always present in the DOM, with unavailable panels showing a placeholder message instead of being hidden. The
_PANEL_METAstructure is now the single source of truth for panel metadata. [1] [2] [3] [4]Updated the ordering and activation logic for frequency calculation panels in
_PANEL_REGISTRY, ensuring correct display order and default selection.Code Quality and UX Fixes:
Changed the IR plot x-axis range in
ir_plot.pyto match the user-facing convention (low to high wavenumber).Replaced bare
except:withexcept Exception:inpubchem.pyfor safer error handling and to pass static analysis checks. [1] [2]Dependency Management:
These changes bring the documentation, tests, and codebase into alignment with the current and planned QuantUI architecture, improve reliability and maintainability, and enforce best practices for future development.