Fix JavaScript state indexing for vector-ordered matrices

[Copilot]

This PR does several things

• adds a vector size function that is reused by both the python and javascript wrappers
• adds a few apis to the musica state/micm classes which allows us to drop the wrappers in wasm
• Exclusively uses embind (to the best of my ability) to marshal data between javascript/c++
• Allows the javascript solver to use any number of grid cells, regardless of solver type, by abstracing getting/setting data onto the state
  • We may want to think about doing the same thing with Python, though that would mean we would be using the c-interface less. Unsure what tradeoff is best
• refactors the javascript tests to reduce duplication and expand the number of options we test

Fixes #697

[codecov-commenter]

Codecov Report

❌ Patch coverage is 49.18919% with 94 lines in your changes missing coverage. Please review.
✅ Project coverage is 75.80%. Comparing base (24811ee) to head (4457d66).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
src/micm/state.cpp	0.00%	66 Missing ⚠️
javascript/micm/solver.js	73.91%	12 Missing ⚠️
javascript/micm/state.js	83.01%	9 Missing ⚠️
src/micm/micm_c_interface.cpp	0.00%	5 Missing ⚠️
src/micm/micm.cpp	0.00%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #729      +/-   ##
==========================================
- Coverage   76.63%   75.80%   -0.83%     
==========================================
  Files         108      108              
  Lines        7849     7974     +125     
==========================================
+ Hits         6015     6045      +30     
- Misses       1834     1929      +95     

Flag	Coverage Δ
cpp_fortran	68.49% <7.59%> (-1.11%)	⬇️
javascript	92.21% <80.18%> (-1.80%)	⬇️
python	82.75% <ø> (ø)

Flags with carried forward coverage won't be shown. Click here to find out more.

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.
• 📦 JS Bundle Analysis: Save yourself from yourself by tracking and limiting bundle sizes in JS merges.

[Copilot]

Pull request overview

This PR fixes JavaScript state indexing for vector-ordered matrices by refactoring the WASM bindings to exclusively use embind for data marshaling between JavaScript and C++. The implementation adds new APIs to the musica state/micm classes, consolidates the vector size function for reuse across wrappers, and extends support for any number of grid cells regardless of solver type.

Changes:

• Added GetMusicaVectorSize() function in C++ for consistent vector size retrieval across Python and JavaScript
• Implemented new SetConcentrations(), GetConcentrations(), SetRateConstants(), and GetRateConstants() methods on State class that handle vector-ordered matrix indexing
• Refactored JavaScript bindings to use embind exclusively, removing custom wrapper classes (StateWrapper, MICMWrapper)
• Expanded JavaScript tests to cover multiple grid cells (1, 5, 10, 20) and all solver types

Reviewed changes

Copilot reviewed 21 out of 22 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
src/micm/state.cpp	Added new methods for setting/getting concentrations and rate constants with proper vector-ordered indexing
src/micm/micm_c_interface.cpp	Implemented GetMusicaVectorSize() function for determining vector size based on solver type
src/micm/micm.cpp	Added convenience constructor accepting config path directly
python/bindings/micm/micm.cpp	Updated to use shared GetMusicaVectorSize() function
javascript/src/musica_wasm.cpp	Complete rewrite using embind exclusively, removed custom wrapper classes
javascript/src/micm/*.h/cpp	Deleted wrapper files, replaced with direct embind bindings
javascript/micm/*.js	Updated to use new WASM API with proper parameter naming (airDensities)
javascript/tests/**/*.test.js	Refactored tests to reduce duplication and test multiple grid cells/solver types
javascript/CMakeLists.txt	Removed wrapper source files from build
package.json	Added -DMUSICA_ENABLE_TESTS=OFF to prevent building tests during WASM build
include/musica/micm/*.hpp	Added new method declarations and forward declaration to break circular dependency

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[boulderdaze]

The function name could be just GetVectorSize() to be consistent with other functions such as?

size_t GetMaximumNumberOfGridCells(MICM *micm);

[K20shores]

true