Add --deps-only flag to separate dependency fetching from source builds

[sbryngelson]

Summary

• Adds --deps-only CLI flag to ./mfc.sh build that only fetches and builds dependencies (FFTW, HDF5, etc.) without building MFC source targets
• Already-configured dependencies are skipped during regular builds, preventing network access in the source build step
• Frontier and Frontier AMD CI now fetch deps on login nodes (internet access) and build source on compute nodes (no network needed)

Test plan

• Verify ./mfc.sh build --deps-only -j 8 builds only dependency targets
• Verify regular ./mfc.sh build -j 8 skips already-configured deps
• Verify Frontier CI: deps fetched on login node, source built + tested on compute node
• Verify Frontier AMD CI: same pattern via symlinked build.sh
• Verify Phoenix CI is unaffected (no login-node build step)
• Verify bench.yml Frontier/Frontier AMD jobs work with updated build_script args

[coderabbitai]

📝 Walkthrough

Walkthrough

This pull request refactors the CI/CD build workflows to separate dependency fetching from source building. Changes include removing the bench argument from Frontier build commands in the benchmarking workflow, updating workflow step labels from "Setup & Build" to "Fetch Dependencies" and "Test" to "Build & Test", removing conditional build-directory checks to enable unconditional builds, simplifying the Frontier build script to only fetch dependencies without the run_bench parameter, and adding a new --deps-only flag to the Python build CLI command that resolves and builds only dependencies without building MFC targets. The toolchain's build module now includes early-exit logic for already-configured dependencies and a dedicated control flow for the deps_only mode.

🚥 Pre-merge checks | ✅ 1 | ❌ 2

❌ Failed checks (1 warning, 1 inconclusive)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 0.00% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.
Description check	❓ Inconclusive	The PR description covers the main changes, motivation, and test plan, but is missing key required template sections like Type of change and Checklist items.	Complete the required template sections: specify Type of change (refactor, new feature, etc.), check the Checklist boxes for tests/documentation updates, and provide explicit testing details for unchecked items.

✅ Passed checks (1 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title accurately summarizes the main change: adding a --deps-only flag to separate dependency fetching from source builds, which is the core feature across all modified files.

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 47.42%. Comparing base (6120810) to head (2f1835a).
⚠️ Report is 4 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1336      +/-   ##
==========================================
+ Coverage   45.01%   47.42%   +2.41%     
==========================================
  Files          70       70              
  Lines       20562    19202    -1360     
  Branches     1962     1634     -328     
==========================================
- Hits         9255     9106     -149     
+ Misses      10179     9229     -950     
+ Partials     1128      867     -261     

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[github-actions]

Claude Code Review

Incremental review from: 407974b
Head SHA: e836a1b

New findings since last Claude review:

• Stale .out files in checkout subdirectories not cleaned (.github/workflows/bench.yml): The new cleanup step uses rm -f *.out (non-recursive, current directory only), but clean: false is added to both checkout steps which write into pr/ and master/ subdirectories. Any .out files generated inside those subdirectories during a previous benchmark run will survive the cleanup step and persist into the next run. If benchmark scripts produce .out files relative to the checkout path (e.g., pr/*.out, master/*.out), those stale outputs could contaminate subsequent benchmark comparisons. Consider using rm -f pr/*.out master/*.out or a recursive form such as find . -name '*.out' -delete to match where outputs actually land.