Archive creation does not support pathlib paths

When feeding paths into the HetMat archiving functions, it would be very helpful if pathlib paths were supported inputs, as opposed to just strings.

all_paths_1 = hetmat.metagraph.extract_all_metapaths(1)
paths_1 = []
for path in all_paths_1:
    path = pathlib.Path(f'path-counts/dwpc-0.5/{path}.sparse.npz')
    if path.exists():
        paths_1.append(path)

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-31-49cc11dbbf57> in <module>()
      1 hetmech.hetmat.archive.create_archive_by_globs(
----> 2     'dwpc-0.5-len-2.zip', '.', include_globs=paths_2)

~/Documents/hetmech/hetmech/hetmat/archive.py in create_archive_by_globs(destination_path, root_directory, include_globs, exclude_globs, include_paths, **kwargs)
     35     source_paths = set()
     36     for glob in include_globs:
---> 37         source_paths |= set(root_directory.glob(glob))
     38     for glob in exclude_globs:
     39         source_paths -= set(root_directory.glob(glob))

~/.conda/envs/hetmech/lib/python3.6/pathlib.py in glob(self, pattern)
   1072             raise ValueError("Unacceptable pattern: {!r}".format(pattern))
   1073         pattern = self._flavour.casefold(pattern)
-> 1074         drv, root, pattern_parts = self._flavour.parse_parts((pattern,))
   1075         if drv or root:
   1076             raise NotImplementedError("Non-relative patterns are unsupported")

~/.conda/envs/hetmech/lib/python3.6/pathlib.py in parse_parts(self, parts)
     60             if altsep:
     61                 part = part.replace(altsep, sep)
---> 62             drv, root, rel = self.splitroot(part)
     63             if sep in rel:
     64                 for x in reversed(rel.split(sep)):

~/.conda/envs/hetmech/lib/python3.6/pathlib.py in splitroot(self, part, sep)
    281 
    282     def splitroot(self, part, sep=sep):
--> 283         if part and part[0] == sep:
    284             stripped_part = part.lstrip(sep)
    285             # According to POSIX path resolution:

TypeError: 'PosixPath' object does not support indexing

Whereas simply changing the append to be a string works correctly.

all_paths_1 = hetmat.metagraph.extract_all_metapaths(1)
paths_1 = []
for path in all_paths_1:
    path = pathlib.Path(f'path-counts/dwpc-0.5/{path}.sparse.npz')
    if path.exists():
        paths_1.append(str(path))

greenelab / connectivity-search-analyses

Archive creation does not support pathlib paths #126