Update CHILI intercomparion data and scripts to match spec exactly

[nichollsh]

Description

I have re-run the CHILI intercomparison simulations with PROTEUS. This means that CHILI uses the latest version of the code.

• Updated PROTEUS and ran simulations again (separate PR in CHILI repo will merge these)
• Set escape efficiency=30% to match other codes, enabling more valid comparisons
• Re-order CHILI output CSV files to match the required specification
• Add missing columns to CHILI output files (e.g. viscosity, mixing ratio profiles

Checklist

• I have followed the contributing guidelines
• My code follows the style guidelines of this project
• I have performed a self-review of my code
• My changes generate no new warnings or errors
• I have checked that the tests still pass on my computer
• I have updated the docs, as appropriate
• I have added tests for these changes, as appropriate
• I have checked that all dependencies have been updated, as required

Relevant people

@timlichtenberg @MarijnJ0 @EmmaPostolec

[Copilot]

Pull request overview

This PR updates the CHILI intercomparison helper scripts and associated configs to regenerate CHILI-formatted outputs from the latest PROTEUS runs, including updated scalar/profile CSV content and intercomparison-specific runtime settings.

Changes:

• Update tools/chili_postproc.py to produce CHILI-spec scalar + profile CSVs (new columns, revised ordering, profile extraction via read_ncdf_profile, viscosity extraction from SPIDER JSONs).
• Update CHILI intercomparison configs to match agreed protocol settings (notably escape efficiency and time-stepping/output cadence), and enable SLURM for the CHILI grid config.
• Adjust PROTEUS internals: add combine_edges option to read_ncdf_profile, and update the adaptive timestep minimum-relative term.

Reviewed changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
tools/chili_postproc.py	Reworks CHILI CSV generation (scalars + tau profiles), adds new columns (e.g., viscosity) and switches profile reading to read_ncdf_profile.
tools/chili_generate.py	Changes default output path generation to write under scratch/ and appends per-planet directories.
src/proteus/interior/timestep.py	Adjusts minimum timestep computation by removing a * 0.01 factor in the relative minimum term.
src/proteus/atmos_clim/common.py	Extends read_ncdf_profile with a combine_edges option and updates docstring/type annotation.
input/chili/intercomp/_base.toml	Updates CHILI intercomparison runtime parameters and sets escape efficiency to 0.3.
input/chili/intercomp/_base.grid.toml	Enables SLURM for the intercomparison grid runs.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 69.12%. Comparing base (ee834f0) to head (98c8172).
⚠️ Report is 2 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #659      +/-   ##
==========================================
+ Coverage   69.03%   69.12%   +0.09%     
==========================================
  Files          98       98              
  Lines       10114    10123       +9     
  Branches     1400     1401       +1     
==========================================
+ Hits         6982     6998      +16     
+ Misses       2792     2791       -1     
+ Partials      340      334       -6     

Flag	Coverage Δ
unit-tests	56.31% <100.00%> (+0.09%)	⬆️

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[timlichtenberg]

Great!