[PR-75] Use mkmf in a backwards-compatible manner

[Copilot]

Describe your changes

mkmf PR 75 makes mkmf a proper conda package, moving executables from bin/ → mkmf/bin/ within the repo and installing templates to $CONDA_PREFIX/share/mkmf/templates/. These changes ensure fre-cli works with both the old and new mkmf structures.

fre/make/make_helpers.py

• get_mktemplate_path() now checks $CONDA_PREFIX/share/mkmf/templates/<name> as a fallback when a bare template filename isn't found in the submodule path (fre/mkmf/templates/)

# submodule path checked first (priority); conda package path is the fallback
if Path(submodule_path).exists():
    template_path = submodule_path
else:
    conda_prefix = os.environ.get("CONDA_PREFIX")
    if conda_prefix:
        conda_path = conda_prefix + "/share/mkmf/templates/" + mk_template
        if Path(conda_path).exists():
            template_path = conda_path

fre/make/gfdlfremake/buildDocker.py

• mkmf clone-and-copy Dockerfile step now checks for new PR 75 structure (mkmf/mkmf/bin/) before falling back to old structure (mkmf/bin/)

meta.yaml

• Build script loops over executables, trying fre/mkmf/mkmf/bin/ first, then fre/mkmf/bin/, with a warning if neither exists (mkmf may be a separate conda dependency)
• Copies fre/mkmf/templates/* to $PREFIX/share/mkmf/templates/ during conda build, mirroring what mkmf PR 75 does in the standalone mkmf package and making fre-cli self-contained for template resolution

docs/setup.rst

• Fixed incorrect PATH (${PWD}/mkmf/bin → ${PWD}/fre/mkmf/bin) and added the PR 75 path so both submodule structures work: ${PWD}/fre/mkmf/bin:${PWD}/fre/mkmf/mkmf/bin

fre/make/tests/test_make_helpers.py

• Added test_mktemplate_name_conda_prefix: uses monkeypatch to verify the conda prefix fallback resolves templates correctly

Issue ticket number and link (if applicable)

Checklist before requesting a review

• I ran my code
• I tried to make my code readable
• I tried to comment my code
• I wrote a new test, if applicable
• I wrote new instructions/documentation, if applicable
• I ran pytest and inspected it's output
• I ran pylint and attempted to implement some of it's feedback
• No print statements; all user-facing info uses logging module

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[codecov]

Codecov Report

❌ Patch coverage is 90.90909% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 84.11%. Comparing base (9a0d45f) to head (31c794a).

Files with missing lines	Patch %	Lines
fre/make/make_helpers.py	90.90%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #774      +/-   ##
==========================================
+ Coverage   84.10%   84.11%   +0.01%     
==========================================
  Files          70       70              
  Lines        4780     4790      +10     
==========================================
+ Hits         4020     4029       +9     
- Misses        760      761       +1     

Flag	Coverage Δ
unittests	84.11% <90.90%> (+0.01%)	⬆️

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Files with missing lines	Coverage Δ
fre/make/gfdlfremake/buildDocker.py	90.98% <ø> (ø)
fre/make/make_helpers.py	95.83% <90.90%> (-4.17%)	⬇️

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[ilaflott]

@copilot NOAA-GFDL/mkmf PR 75 was updated- iterate

[Copilot]

@copilot NOAA-GFDL/mkmf PR 75 was updated- iterate

Updated to align with the latest mkmf PR 75 (commit a8620434). The key new addition in PR 75 is that templates are now installed to $PREFIX/share/mkmf/templates/ in the mkmf conda package. I've updated fre-cli's meta.yaml to mirror this: fre/mkmf/templates/* is now copied to $PREFIX/share/mkmf/templates/ during fre-cli's conda build, making fre-cli self-contained (commit 31c794a). The make_helpers.py conda prefix fallback already handles this location correctly.