fastlmm/bed-reader

Required packages not in setup.py

Closed this issue · 2 comments

eric-czech commented

Hey @CarlKCarlK, I see only numpy is in the setup.py dependency list:

bed-reader/setup.py

Line 149 in a775a57

install_requires = ["numpy>=1.11.3"]

But the requirements.txt has several others:

bed-reader/requirements.txt

Lines 1 to 5 in a775a57

numpy
pandas
dataclass
pywin32; sys_platform == "win32"
pooch

pooch being missing is currently breaking the sgkit-plink build with:

ImportError while importing test module '/home/runner/work/sgkit-plink/sgkit-plink/sgkit_plink/tests/test_pysnptools.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/opt/hostedtoolcache/Python/3.8.5/x64/lib/python3.8/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
sgkit_plink/__init__.py:1: in <module>
    from .pysnptools import read_plink  # noqa: F401
sgkit_plink/pysnptools.py:8: in <module>
    from bed_reader import open_bed
/opt/hostedtoolcache/Python/3.8.5/x64/lib/python3.8/site-packages/bed_reader/__init__.py:2: in <module>
    from bed_reader._sample_data import sample_file, tmp_path
/opt/hostedtoolcache/Python/3.8.5/x64/lib/python3.8/site-packages/bed_reader/_sample_data.py:7: in <module>
    import pooch
E   ModuleNotFoundError: No module named 'pooch'

I'm guessing _sample_data.py isn't critical for downstream usage so is it possible to only import that when a function in that module is called instead?

CarlKCarlK commented