sh 2.0.0 breaks Isca installation

[sit23]

Description

I've just tried to do a fresh install of Isca on maths2 (one of our newer linux servers here in Exeter), and it's installed the sh package at version 2.0.0. When I try and run the Held Suarez test case, I get the following error:

python held_suarez_test_case.py 
Traceback (most recent call last):
  File "/emmy-noether/home/sit204/Isca/src/extra/python/isca/helpers.py", line 69, in git_run_in_directory
    git_test = codedir_git.log('-1', '--format="%H"').stdout
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'str' object has no attribute 'stdout'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/emmy-noether/home/sit204/Isca/exp/test_cases/held_suarez/held_suarez_test_case.py", line 10, in <module>
    cb = DryCodeBase.from_directory(GFDL_BASE)
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/emmy-noether/home/sit204/Isca/src/extra/python/isca/codebase.py", line 35, in from_directory
    return cls(directory=directory, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/emmy-noether/home/sit204/Isca/src/extra/python/isca/codebase.py", line 398, in __init__
    super(GreyCodeBase, self).__init__(*args, **kwargs)
  File "/emmy-noether/home/sit204/Isca/src/extra/python/isca/codebase.py", line 86, in __init__
    self.git = git_run_in_directory(GFDL_BASE, self.codedir)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/emmy-noether/home/sit204/Isca/src/extra/python/isca/helpers.py", line 73, in git_run_in_directory
    git_test = codedir_git.log('-1', '--format="%H"').stdout
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'str' object has no attribute 'stdout'

Upon closer inspection, it seems that sh 2.0.0 has changed its behaviour, such that the output of functions like codedir_git.log('-1', '--format="%H"') returns a str type, where previously it returned something of type sh.RunningCommand. The former does not have an stdout attr, but sh.RunningCommand does. This will need to be updated such that newer versions of sh can be accommodated.

[AndrewILWilliams]

Aha! I was just about to raise an issue because I'm also having a lot of problem with sh upon reinstalling Isca. Is there a simple fix for this?

Cheers, Andrew

[AndrewILWilliams]

I can get past it if I force sh==1.9 in the requirements.txt, but I'm not sure if that's correct because I still can't get it to run...potentially a different issue though

[sit23]

The fix I used was just to install an older version of sh. I haven't gotten round to doing the fix for sh 2.0.0.