BiocPy/GenomicRanges

Add missing dependency on joblib

mmokrejs opened this issue · 2 comments

mmokrejs commented

Following your example from README.md I get:

>>> subject = genomicranges.read_ucsc(genome="hg38")
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/foo/genomicranges/lib/python3.11/site-packages/genomicranges/io/ucsc.py", line 61, in read_ucsc
    data = parse_gtf(path, compressed=compressed)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/foo/genomicranges/lib/python3.11/site-packages/genomicranges/io/gtf.py", line 58, in parse_gtf
    from joblib import Parallel, delayed
ModuleNotFoundError: No module named 'joblib'
>>>
jkanche commented

The package specified additional requirements that installs these optional packages.

pip install genomicranges[optional]

I'll add this to the documentation. Thank you for raising this issue.

mmokrejs commented

The package specified additional requirements that installs these optional packages.

pip install genomicranges[optional]

Maybe I missed that, I just did pip install genomicranges per my shell history. I thought it will install all deps but this [optional] is fine with me.

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