conda run -n can fail if a conda environment is already active

[samsrabin]

Brief summary of bug

For tests that invoke cmds_to_setup_conda(), manually calling the script invoking that function (e.g., case.build for FSURDATMODIFYCTSM) could fail if doing so with a conda environment already activated. The problem is that

conda run -n ctsm_pylib ...

seems to not actually use ctsm_pylib if, for instance, the conda base environment is active.

Note that this is a different issue (and gives a different sort of error) from #2111.

General bug information

CTSM version you are using: ctsm5.1.dev133

Does this bug cause significantly incorrect results in the model's science? No

Configurations affected: FSURDATMODIFYCTSM and RXCROPMATURITY tests.

Important details of your setup / configuration so we can reproduce the bug

Calling case.build for an FSURDATMODIFYCTSM test fails for me if I've previously done conda activate base.

Important output or errors that show the problem

In TestStatus.log, something like:

subprocess.CalledProcessError: Command '. /glade/scratch/afoster/tests_0814-163644ch/FSURDATMODIFYCTSM_D_Mmpi-serial_Ld1.5x5_amazon.I2000Clm50SpRs.cheyenne_intel.C.0814-163644ch_int/.env_mach_specific.sh;  conda run -n ctsm_pylib python3 /glade/work/afoster/CTSM/tools/modify_input_files/fsurdat_modifier /glade/scratch/afoster/tests_0814-163644ch/FSURDATMODIFYCTSM_D_Mmpi-serial_Ld1.5x5_amazon.I2000Clm50SpRs.cheyenne_intel.C.0814-163644ch_int/modify_fsurdat.cfg' returned non-zero exit status 1.

And in fsurdat_modifier.log, something like:

Traceback (most recent call last):
  File "/glade/u/home/samrabin/ctsm_standardize-time-metadata/tools/modify_input_files/fsurdat_modifier", line 15, in <module>
    from ctsm.modify_input_files.fsurdat_modifier import main
  File "/glade/u/home/samrabin/ctsm_standardize-time-metadata/tools/modify_input_files/../../python/ctsm/modify_input_files/fsurdat_modifier.py", line 20, in <module>
    from ctsm.modify_input_files.modify_fsurdat import ModifyFsurdat
  File "/glade/u/home/samrabin/ctsm_standardize-time-metadata/tools/modify_input_files/../../python/ctsm/modify_input_files/modify_fsurdat.py", line 12, in <module>
    import numpy as np
ModuleNotFoundError: No module named 'numpy'

ERROR conda.cli.main_run:execute(47): `conda run python3 /glade/u/home/samrabin/ctsm_standardize-time-metadata/tools/modify_input_files/fsurdat_modifier /glade/scratch/samrabin/tests_0815-121457ch/FSURDATMODIFYCTSM_D_Mmpi-serial_Ld1.5x5_amazon.I2000Clm50SpRs.cheyenne_intel.0815-121457ch/modify_fsurdat.cfg` failed. (See above for error)

(The missing module could be something other than numpy.)

[ekluzek]

@samsrabin thanks for adding this issue and figuring out how to fix it!

This is important to fix for me since I normally use python via a conda environment. And there seems to be python issues if you try to run the standard python scripts without a current version of python (such as run_sys_tests and create_test, etc.).