update: Fixes to allow compatability with newer numpy & pandas

[pettyalex]

Hello,

I cloned MetaXcan and tried to get it running on a modern Mac, and ran into a couple of problems that seem really easy to fix, so I took a shot at fixing them.

Scipy <1.3 is too old to work on Python 3.9 on an Apple Silicon Mac, but all the tests pass with a much newer scipy so I removed the maximum version requirement.

Numpy 1.20 removed numpy.str and numpy.object, but those were just references to str and object so I updated those.

pandas.to_numeric() is removing support for errors='ignore'. It still works as of pandas 2.2.1, but is covered in warnings. If exceptions aren't preferred, maybe we could check if the first value in the column is numeric before attempting to convert?
https://pandas.pydata.org/docs/reference/api/pandas.to_numeric.html

I also added sqlalchemy as an extra requirement if installing to run tests. Would you be interested in moving to pyproject.toml instead of setup.py? I'd be glad to do so: https://packaging.python.org/en/latest/guides/modernize-setup-py-project/

All of these changes together make the project installable with pip install on a modern system, and all the tests pass.

For reference, after removing the scipy max version requirement, these are the package versions I got from a pip install . on python 3.9.16 on MacOS 14:

appdirs==1.4.4
bgen-reader==4.0.8
cachetools==5.3.3
cbgen==1.0.4
certifi==2024.2.2
cffi==1.16.0
charset-normalizer==3.3.2
click==8.1.7
cloudpickle==3.0.0
coloredlogs==15.0.1
cyvcf2==0.30.28
dask==2024.2.1
exceptiongroup==1.2.0
fsspec==2024.2.0
h5py==3.10.0
h5py-cache==1.0
humanfriendly==10.0
idna==3.6
importlib_metadata==7.0.2
iniconfig==2.0.0
locket==1.0.0
MetaXcan==0.7.5
numpy==1.26.4
packaging==23.2
pandas==2.2.1
partd==1.4.1
patsy==0.5.6
platformdirs==4.2.0
pluggy==1.4.0
pooch==1.8.1
pycparser==2.21
pytest==8.1.1
python-dateutil==2.9.0.post0
pytz==2024.1
PyYAML==6.0.1
requests==2.31.0
scipy==1.12.0
six==1.16.0
SQLAlchemy==2.0.28
statsmodels==0.14.1
texttable==1.7.0
tomli==2.0.1
toolz==0.12.1
tqdm==4.66.2
typing_extensions==4.10.0
tzdata==2024.1
urllib3==2.2.1
xarray==2024.2.0
zipp==3.17.0

[Heroico]

Thanks, this looks good.
@hakyim I recommend this update is merged, however it requires some testing on your end to verify no workflow currently in use breaks.