feature-skip-preprocess-on-restart

[danieljvickers]

I have deleted valuable restart data one-to-many times because I forget to call -t simulation on restart. This PR makes the adjustment that pre_process must be explicitly called on restart. This still allows one to restart cases with preprocess if they desire to modify patches, but prevents the deletion of all data from the directory because one forgets to set a target.

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Acknowledgement

• I confirm this PR meets the above expectations and reflects my own understanding and real-world context.

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PR template credit: junegunn

[github-actions]

Claude Code Review

Head SHA: 2835916

Files changed:

• 4
• docs/documentation/case.md
• toolchain/mfc/args.py
• toolchain/mfc/lint_docs.py
• toolchain/mfc/run/run.py

Findings:

• args["targets_explicit"] = any(tok in ("-t", "--targets") for tok in cli_argv) (toolchain/mfc/args.py:92) only matches tokens that are exactly -t or --targets. It misses argparse's other valid forms for the same flag: --targets=simulation (equals syntax), an unambiguous abbreviation like --target (argparse allow_abbrev is on by default), or an attached short form like -tsimulation. If a user runs a restart with ./mfc.sh run case.py --targets=pre_process simulation (or any of these other forms) and t_step_start > 0, targets_explicit is computed as False, so run() (toolchain/mfc/run/run.py:164-166) silently drops pre_process from the target list even though the user explicitly requested it — the opposite of the intended "only auto-skip when the user didn't ask for it" behavior, and it happens silently (just a yellow console note, easy to miss), regenerating stale/no pre_process output instead of what was explicitly asked for.

[sbryngelson]

lol. check ai comments when you have a chance

[Copilot]

Pull request overview

Prevents default preprocessing from overwriting restart data.

Changes:

• Detects explicitly requested run targets.
• Skips preprocessing for restart runs by default.
• Documents the behavior and updates documentation linting.

Reviewed changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 2 comments.

File	Description
toolchain/mfc/run/run.py	Adds restart-aware preprocessing exclusion.
toolchain/mfc/args.py	Records explicit target selection.
toolchain/mfc/lint_docs.py	Allows the documented target name.
docs/documentation/case.md	Documents restart behavior.

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 61.67%. Comparing base (e2f0e26) to head (c3a27fe).
⚠️ Report is 1 commits behind head on master.

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #1761   +/-   ##
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  Coverage   61.67%   61.67%           
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  Files          84       84           
  Lines       21619    21619           
  Branches     3196     3196           
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  Hits        13334    13334           
  Misses       6093     6093           
  Partials     2192     2192           

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