[chris-ashe]

This pull request adds comprehensive tracking and visualization of plasma composition by both particle number and mass, including detailed support for impurity species. It introduces new data fields, calculations, output reporting, and plotting functions to provide a clearer and more complete picture of plasma constituents in both the core model and its outputs.

Enhancements to plasma composition tracking and reporting:

• Added new fields to PhysicsData for the mass and number of all major plasma species (deuterons, tritons, helions, alpha particles, electrons) as well as a wide set of impurity ions (e.g., beryllium, carbon, oxygen, etc.), enabling fine-grained tracking of plasma constituents.
• Implemented calculations in DetailedPhysics for the mass and number of each plasma species and impurity, updating these values during model execution.
• Expanded the output routine to report the mass and particle count for each plasma species and impurity, improving the transparency and detail of simulation results.

Visualization improvements:

• Added two new plotting functions, plot_plasma_composition_bar and plot_plasma_mass_composition_bar, to visualize the plasma composition by particle number and mass, respectively, including impurity species. These are now integrated into the summary plotting API and summary page layout.

Checklist

I confirm that I have completed the following checks:

• My changes follow the PROCESS style guide
• I have justified any large differences in the regression tests caused by this pull request in the comments.
• I have added new tests where appropriate for the changes I have made.
• If I have had to change any existing unit or integration tests, I have justified this change in the pull request comments.
• If I have made documentation changes, I have checked they render correctly.
• I have added documentation for my change, if appropriate.

[github-actions]

⚠️ improve_quality_job warning!

Files changed by this PR have introduced 1 more linting errors when compared to main

Please fix these

To check what these are, run hatch run lint:fmt_extra on your branch and on main

[codecov-commenter]

Codecov Report

❌ Patch coverage is 68.32298% with 51 lines in your changes missing coverage. Please review.
✅ Project coverage is 51.46%. Comparing base (d1a7687) to head (d9b73a2).

Files with missing lines	Patch %	Lines
process/core/io/plot/summary/plasma/physics.py	4.54%	42 Missing ⚠️
process/models/physics/physics.py	85.71%	6 Missing ⚠️
process/core/io/plot/summary/api.py	0.00%	3 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #4741      +/-   ##
==========================================
+ Coverage   50.94%   51.46%   +0.52%     
==========================================
  Files         181      181              
  Lines       30406    30559     +153     
==========================================
+ Hits        15490    15728     +238     
+ Misses      14916    14831      -85     

☔ View full report in Codecov by Harness.
📢 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.