Allows for file-like objects to be passed to read_molecule_file

[IAlibay]

Fixes #83

Changes:

• open_file_for_reading: fseek -> seek
• read_molecule_file: adds an extra argument filename which can be used to identify the file type when passing a file-like object.
• A version of the basic tests that passes a file object (:class:_io.TextIOWrapper) instead of the actual file path (this might be excessive / in the wrong place, but I thought I'd add them in anyways as a "proof of concept").

Question:

• Should the extra attribute checks for the file-like objects removed in #40 be added back?

[codecov[bot]]

Codecov Report

Merging #84 into master will increase coverage by 0.16%. The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master      #84      +/-   ##
==========================================
+ Coverage   70.24%   70.41%   +0.16%     
==========================================
  Files          25       25              
  Lines        4137     4140       +3     
==========================================
+ Hits         2906     2915       +9     
+ Misses       1231     1225       -6     

Impacted Files	Coverage Δ
propka/input.py	62.87% <100.00%> (+4.33%)	:arrow_up:

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[orbeckst]

Should the extra attribute checks for the file-like objects removed in #40 be added back?

I don't remember why I added all of them way-back-when – probably related to MDAnalysis.lib.util.isstream. It is possible that I wasn't quite sure what was needed to ultimately make it work. If your streamlined version does the job then I think it's fine. I would make sure the StringIO works.

(I wouldn't bother with streams from the network (via urllib2 or request) although it could be fun :-).)

[IAlibay]

Should the extra attribute checks for the file-like objects removed in #40 be added back?

I don't remember why I added all of them way-back-when – probably related to MDAnalysis.lib.util.isstream. It is possible that I wasn't quite sure what was needed to ultimately make it work. If your streamlined version does the job then I think it's fine. I would make sure the StringIO works.

(I wouldn't bother with streams from the network (via urllib2 or request) although it could be fun :-).)

As it is now, it's probably not the safest way to ensure the object will be read, but it should work for normal use cases.

In some cases e.g. BufferedIOBase derived objects, might not work (i.e. if object.seekable() returns False). Although I'm not really sure of a case where this would be useful / worth handling.

[orbeckst]

Very nice, thank you @IAlibay .

@sobolevnrm / @speleo3 do you want to have a quick look at the PR? (Disclosure: I am biased, I want the feature to work again as soon as possible...)

[speleo3]

Looks pretty good to me, but I have one comment: I think the argument logic of read_molecule_file can be streamlined. Instead of having the filename either in the first or the third argument, and allowing the first argument to be either a path or a stream, I suggest this API:

def read_molecule_file(filename: str, mol_container, stream=None):
    """
    Args:
        filename (str): input file name
        mol_container:  MolecularContainer object
        stream: optional input file handle. If None, then open `filename` as a local file for reading.
    """

What do you think?

[sobolevnrm]

Very nice, thank you @IAlibay .

@sobolevnrm / @speleo3 do you want to have a quick look at the PR? (Disclosure: I am biased, I want the feature to work again as soon as possible...)

I probably won't be able to look at it until tonight. However, I'm confident in the assessment of you and @speleo3. Thanks!

[IAlibay]

Looks pretty good to me, but I have one comment: I think the argument logic of read_molecule_file can be streamlined. Instead of having the filename either in the first or the third argument, and allowing the first argument to be either a path or a stream, I suggest this API:

def read_molecule_file(filename: str, mol_container, stream=None):
    """
    Args:
        filename (str): input file name
        mol_container:  MolecularContainer object
        stream: optional input file handle. If None, then open `filename` as a local file for reading.
    """

What do you think?

That is a lot cleaner :) It makes the try/except block a lot nicer.

[sobolevnrm]

This looks awesome -- thank you, all!