Support for Cloud Storage URLs (with universal_pathlib)

[Karl5766]

Ali and I are considering using Google Cloud buckets (with a access url like "gs://path/to/file") to read and write OME_ZARR files in snakemake workflows. We would like something as follows:

from snakebids.core.input_generation import generate_inputs
inputs = generate_inputs(
    'gs://khanlab-lightsheet/data/onuska_lifecanvas/bids',  # instead of a local path, we pass in a string starting with "gs://"
    {'spim': {'filters': {'suffix': 'SPIM', 'subject': 'o21', 'extension': 'ome.zarr'}, 'wildcards': ['subject', 'sample', 'acquisition', 'staining']}}
)
print(inputs)

while both pybids and this repo are currently depending on Python's Path class, Ali's idea is to use universal_pathlib's UPath objects as drop-in replacement for Path. For pybids, We made a fork of pybids which supports UPath and passes the unit tests of the main repository.

For this repo, after further modify the os.path.isabs(path) call in input_generation.py to make sure gs://... is not recognized as a local relative path, the above code seems to work.

Depending on a pybids' fork is going to break dependency for other users of this repo (We are considering a PR to the main branch of pybids for UPath support. Right now, however, it's a fork and it's not finalized), but I think a commit replacing os.path.isabs() with an equivalent expression compatible with cloud storage paths is possible (so we can use a UPath compatible version of pybids in our own project if we need UPath support in snakebids). @pvandyken What do you think?

Edit: I modified input_generation.py's line 726 to use path.absolute() != path to test for relative path which is a workaround but I think there is probably a better way to do it.

[pvandyken]

UPath is a subclass of path, so should be sufficient to change that line to path.is_absolute() (after making sure the path is a pathlib). I would coerce to path immediately in the generate_inputs() function.
generate_inputs() should then be typed with the StrPath fake-imported from typeshed:

from typing import TYPE_CHECKING
if TYPE_CHECKING:
	from _typeshed import StrPath

def generate_inputs(
    root: StrPath,
    ...
):
	if not isinstance(path, Path):
	  path = Path(path)
    ...

This should make the function work with any subtype of Path (e.g. UPath), otherwise for strings etc it will coerce into a path. Then just make sure we don't use any of the old os.path functions anywhere.

Should be easy enough to implement, are you willing? It would additionally need a test testing that both PathLike objects work (e.g. objects with __fspath__() implemented) and subclasses of Path work as expected.

[pvandyken]

Left an issue here #451

[Karl5766]

Yes, let me take a look and make a PR for this one.