Issue1663 #1680
Issue1663 #1680
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Cool! Does this mean I can use stringIO to get the PDB string /without saving to temp, as I was doing) when geom.save_pdb? |
I don't think so - see https://stackoverflow.com/questions/44381249/treat-a-string-as-a-file-in-python |
| 'you supplied %s' % type(filename)) | ||
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| topology = _parse_topology(top) | ||
| atom_indices = cast_indices(atom_indices) | ||
| with DTRTrajectoryFile(filename) as f: | ||
| with DTRTrajectoryFile(str(filename)) as f: |
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Is this conversion with str() correct? What if the path is a Bytes and the filename is not valid utf-8?
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You are right - I should be using os.fspath(filename) not assuming a cast to str will work. However in testing this it seems that the current mdtraj release doesn't support bytes as paths anyway:
traj = 'frame0.pdb'
import mdtraj as mdt
t = mdt.load(traj)
with open(bytes(traj, encoding='utf-8')) as f:
... data = f.read()
...t = mdt.load(bytes(traj, encoding='utf-8'))
Traceback (most recent call last):
File "", line 1, in
File "/Users/pazcal/miniconda3/envs/py37/lib/python3.7/site-packages/mdtraj-1.9.6-py3.7-macosx-10.9-x86_64.egg/mdtraj/core/trajectory.py", line 378, in load
extensions = [_get_extension(f) for f in filename_or_filenames]
File "/Users/pazcal/miniconda3/envs/py37/lib/python3.7/site-packages/mdtraj-1.9.6-py3.7-macosx-10.9-x86_64.egg/mdtraj/core/trajectory.py", line 378, in
extensions = [_get_extension(f) for f in filename_or_filenames]
File "/Users/pazcal/miniconda3/envs/py37/lib/python3.7/site-packages/mdtraj-1.9.6-py3.7-macosx-10.9-x86_64.egg/mdtraj/core/trajectory.py", line 202, in _get_extension
(base, extension) = os.path.splitext(filename)
File "/Users/pazcal/miniconda3/envs/py37/lib/python3.7/posixpath.py", line 122, in splitext
p = os.fspath(p)
TypeError: expected str, bytes or os.PathLike object, not int
Does this count as a separate issue/bug?
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If you make this PR use fspath, at least we’re not adding to the problem, right?
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Have I broken something or is the problem elsewhere? |
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Something was just flakey. I re-ran the build, it worked, and I hit the green merge button. |
Hi. 'Path-like' objects should now be supported as arguments to all trajectory and topology I/O methods. New tests check ability to read from, and write to, Paths in all formats. Docstrings have been edited as required.