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mgalardini / pyseer

SEER, reimplemented in python 🐍🔮
http://pyseer.readthedocs.io
Apache License 2.0
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Add >= version constraints to setup.py? #102

Closed tseemann closed 4 years ago

tseemann commented 4 years ago

No version constraints:

https://github.com/mgalardini/pyseer/blob/master/setup.py#L66-L76

But docs specify them?

python 3+ (3.6.6) numpy (1.15.2) scipy (1.1.0) pandas (0.23.4) scikit-learn (0.20.0) statsmodels (0.9.0) pysam (0.15.1) glmnet_python (commit 946b65c) DendroPy (4.4.0)

tseemann commented 4 years ago

Also missing things like pybedtools.

image :-)

mgalardini commented 4 years ago

Those are the versions we used in development and testing, a better indication would be the conda recipe

tseemann commented 4 years ago

Conda recipe doesn't specify versions either. Except for statsmodels And it's only 1.3.1 not 1.3.3

tseemann commented 4 years ago

Will you test on python 3.7 ? It's been out for 1.5 years now. 3.8 is imminent.

mgalardini commented 4 years ago

Yeah, that indicates that realistically there are no restrictions on the versions used. The conda recipe might not have been updated in the pyseer repo but it should be the right one in the bioconda-recipes repo

mgalardini commented 4 years ago

Sure, it's just a matter of editing the .tavis.yml file

tseemann commented 4 years ago

Oh i thought you linked to the bioconda one.

has a pysam thing: https://github.com/bioconda/bioconda-recipes/blob/master/recipes/pyseer/meta.yaml