cluster.py fails if paths have no directory spec

[justinrporter]

$ python ~/projects/enspara/enspara/apps/cluster.py \
  --trajectories trajectory-*.xtc \
  --topology fs-peptide.pdb \
  --algorithm khybrid \
  --cluster-number 20 \
  --subsample 10 \
  --atoms '(name N or name C or name CA)' \
  --distances fs-khybrid-clusters0020-distances.h5 \
  --center-features fs-khybrid-clusters0020-centers.pickle \
  --assignments fs-khybrid-clusters0020-assignments.h5
[clustering blah blah]
05-01-2020 11:00:57 __main__ INFO    Clustered 28000 frames into 20 clusters in 2.8169675880053546 seconds.
05-01-2020 11:00:57 __main__ INFO    --center-indices not provided, not writing center indices to file.
05-01-2020 11:00:57 __main__ INFO    Wrote center indices in 0.00 sec.
05-01-2020 11:00:57 __main__ INFO    Saving cluster centers at
Traceback (most recent call last):
  File "/Users/jrporter/projects/enspara/enspara/apps/cluster.py", line 514, in <module>
    sys.exit(main(sys.argv))
  File "/Users/jrporter/projects/enspara/enspara/apps/cluster.py", line 502, in main
    write_centers(result, args)
  File "/Users/jrporter/projects/enspara/enspara/apps/cluster.py", line 422, in write_centers
    os.makedirs(outdir)
  File "/Users/jrporter/.envs/enspara/bin/../lib/python3.6/os.py", line 220, in makedirs
    mkdir(name, mode)
FileNotFoundError: [Errno 2] No such file or directory: ''

Problem goes away if you specify e.g. --distances ./fs-khybrid-clusters0020-distances.h5 (with the ./).

[roblaine]

Hi @justinrporter,

Testing on my own linux machine using the same command that you were, I found that the behaviour could be replicated by specifying the arg to the center-features flag without a relative path.
Eg, --center-features fs-khybrid-clusters0020-centers.pickle causes the error, but --center-features ./fs-khybrid-clusters0020-centers.pickle, and --center-features $(pwd)/fs-khybrid-clusters0020-centers.pickle did not.

I can open a PR with a fix regardless, its only a couple of lines long if you want to take a look.

[justinrporter]

Thanks for the comment! Yes, I think that the cluster.py should work equally well with and without a path, and so I would welcome a PR fixing this!

[roblaine]

Just opened a PR for the issue I identified, but unsure if its the same as what this issue is about, or if it needs to be its own issue.

I wasn't able to reproduce the error you were seeing when you supplied the --distances flag with a relative path and no leading ./, so not really sure if I can help there, but hopefully what I've written is helpful.