UI fixes#140
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…ance reachability linting - **Multiscale Simulation & CVODE Integration**: - Replaced the fixed-step RK4 placeholder in per-cell intracellular simulations with full CVODE (SUNDIALS BDF, implicit) integration. - Introduced `IntracellularEngine` to compile ODE systems once per cell type and manage independent cell solver states. - Updated `multiscaleSimulation` to advance cell states, compute/project observables, and clean up CVODE instances. - Configured lazy-loaded CVODE WebAssembly module injection in `multiscaleWorker` and transitioned it to support async execution. - Exposed precomputed observable projections and dynamic parameter updates (`updateParameters`) from `buildOdeSystem`. - **Reachability Check Enhancements**: - Rewrote the reachability checker in `bnglLinter` to track reachability at the molecule-type level rather than via exact pattern strings. - Fixed false-positive "rule can never fire" warnings caused by parser-injected wildcard components (e.g., `!?__SYN__`) and complexes. - **Contact Map Rendering Fixes**: - Resolved invisible bond issues in `ContactMapViewer` by switching back to layout-time `outside-to-node` endpoints. - Implemented an alternating sub-pixel layout nudge to force Cytoscape to recompute endpoints on render. - Added a `ResizeObserver` to refresh elements when the viewer container dynamically sizes up. - **UI & UX Refinements**: - Implemented a JIT-compiler fallback to the full simulator RHS in `BifurcationTab` to support models with functional rate laws. - Added "Start Over / Load New Data" reset functionality to `ParameterEstimationTab` and `ProfileLikelihoodTab`. - Adjusted margins, Y-axis padding, and label positions in `ResultsChart` and `PKPDTab`. - Grouped multi-scale and version history options under an "Experimental" category inside the `VisualizationPanel` menu.
* ⚡ Bolt: Hoist obsNamesSet creation out of reaction parsing loop - Prevent intermediate redundant instantiation of Sets in reaction parse map. - Reduce Garbage Collection overhead on simulation initialization path. - Updated journal learning to .jules/bolt.md Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com> * chore: auto-fix linting and formatting issues * Delete .jules/bolt.md --------- Co-authored-by: google-labs-jules[bot] <161369871+google-labs-jules[bot]@users.noreply.github.com>
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