Prevent crash if folder already exists

[jcohenadad]

When launching multiple sct_run_batch in parallel using run_all with the same output folder, the following error sometimes happens:

Spinal Cord Toolbox (git-master-253936cfc07712c587d9f4cfbbcb760f151172f0)

/home/jcohen/sct/scripts/sct_run_batch.py:241: UserWarning: Using the `-config|-c` flag with additional arguments is discouraged
  warnings.warn(UserWarning('Using the `-config|-c` flag with additional arguments is discouraged'))
configuring
Traceback (most recent call last):
  File "/home/jcohen/sct/scripts/sct_run_batch.py", line 479, in <module>
    main(sys.argv[1:])
  File "/home/jcohen/sct/scripts/sct_run_batch.py", line 300, in main
    os.mkdir(pth)
FileExistsError: [Errno 17] File exists: '/scratch/jcohen/results_csa_t1/results'

This PR fixes the problem by changing: os.mkdir(pth) for os.mkdir(pth, exist_ok=True)

Fixes #2866

[jcohenadad]

oops!

/home/jcohen/sct/scripts/sct_run_batch.py:241: UserWarning: Using the `-config|-c` flag with additional arguments is discouraged
  warnings.warn(UserWarning('Using the `-config|-c` flag with additional arguments is discouraged'))
configuring
Traceback (most recent call last):
  File "/home/jcohen/sct/scripts/sct_run_batch.py", line 481, in <module>
    main(sys.argv[1:])
  File "/home/jcohen/sct/scripts/sct_run_batch.py", line 299, in main
    os.mkdir(pth, exist_ok=True)
TypeError: 'exist_ok' is an invalid keyword argument for this function

ah! https://docs.python.org/3.2/library/os.html#os.makedirs

[PaulBautin]

@jcohenadad, up to now i only tested if the sbatch batch script worked, i am not sure i can configure slurm without connecting to a cluster. But it should work, I'm just wondering if makedirs does not make using exist_ok=True redundant. https://stackoverflow.com/questions/13819496/what-is-different-between-makedirs-and-mkdir-of-os

[jcohenadad]

@jcohenadad, up to now i only tested if the sbatch batch script worked, i am not sure i can configure slurm without connecting to a cluster. But it should work, I'm just wondering if makedirs does not make using exist_ok=True redundant. https://stackoverflow.com/questions/13819496/what-is-different-between-makedirs-and-mkdir-of-os

@PaulBautin i'm not sure what post you are referring to in the URL, but this is the reason i switched for makedirs:

(Can not comment, just add to NPE's answer.)

In Python3, os.makedirs has a default parameter exist_ok=False.
If you set it to True, then os.makedirs will not throw any exception if the leaf exists.
(While os.mkdir doesn't have this parameter.)

Just like this:

os.makedirs('dirA', exist_ok=True)

[PaulBautin]

@jcohenadad you are right. So unless you want a test with another configuration of slurm, it is all good for me.

[jcohenadad]

@jcohenadad you are right. So unless you want a test with another configuration of slurm, it is all good for me.

if it's all good you need to approve the review so i can merge