Add line to a bunch of files and run the files

editfiles.py

#!/usr/bin/env python
import pathlib
import subprocess

# Get the list of files we want to modify
p=pathlib.Path('mom6')
filelist=list(p.glob('**/sync_output_to_gdata.sh'))

# Loop on the files
for f in filelist:
  # Add the line
  with f.open('a') as fo:
      # I've added an 'echo' for testing but feel free to remove it
      fo.write('echo rsync --ignore-existing --exclude ".nc." -vrltoD --safe-links restart*0 ${GDATADIR}\n')
  # Make sure file is executable
  f.chmod(0o700)
  
  # Execute script
  subprocess.run(str(f))

Also, you need to change the definition of p at the start to be an absolute path:
p=pathlib.Path('/short/v45/nc3060/mom6')
or whatever path you need.

I guess you don't need the absolute path at the start, but it is much safer to use one.

@aidanheerdegen,

subprocess.run(str(f))

gives error

    subprocess.run(str(f))
  File "/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.07/lib/python3.6/subprocess.py", line 403, in run
    with Popen(*popenargs, **kwargs) as process:
  File "/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.07/lib/python3.6/subprocess.py", line 709, in __init__
    restore_signals, start_new_session)
  File "/g/data3/hh5/public/apps/miniconda3/envs/analysis3-19.07/lib/python3.6/subprocess.py", line 1344, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'layer4/layer4_tau1e-1_manyshortridges/sync_output_to_gdata.sh': 'layer4/layer4_tau1e-1_manyshortridges/sync_output_to_gdata.sh'

This did the job

subprocess.run('./sync_output_to_gdata.sh')

Have you tried simply replacing subprocess.run(str(f)) in the initial gist with subprocess.run(str(f), cwd=str(f.parent)) ?
Just thinking this might not work as f will have the path in as well. Try:
subprocess.run(str(f.name),cwd=str(f.parent))

thanks @ccarouge