Unable to recompile with `fre make all`

[uramirez8707]

I am seeing some odd behavior with fre make that I assume relates to the --force-checkout changes. 

You can reproduce this behavior with the am5.yaml

module load fre/2026.01.alpha2
fre make all -y am5.yaml -p ncrc5.intel25 -t prod-openmp --execute

After the first make call, if I run the same fre make command again (e.g. I made some changes to the source code and need to recompile. I get an error:

OSError: [Errno 
Error executing checkout script: /gpfs/f5/gfdl_f/scratch/Uriel.Ramirez/am5/am5f11d12r0_canopy_test_me/am5f11d12r0_compile/src/checkout.sh.] 
Try removing test folder: /gpfs/f5/gfdl_f/scratch/Uriel.Ramirez/am5/am5f11d12r0_canopy_test_me

[singhd789]

@uramirez8707 After changing the source code, did you use --force-checkout when running the command again? At the moment, it should be removing and re-creating the src directory. 🤔

[uramirez8707]

This is without --force-checkout

[singhd789]

This is without --force-checkout

Ah ok yeah, that makes sense then. So is the issue here that you changed the source code but none of the information in the compile.yaml should change? (i.e. the checkout script would look the same?)

If it already exists and has been run, I think this error is the behavior we should see (though it could use a better error message). You would want to use --force-checkout to re-do the checkout and update the source code.

If it hasn't been run yet, I think there should just be a message that the checkout script was previously created.

[singhd789]

To-do: add more documentation for this use case in #792