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bacpop / PopPUNK

PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)
https://www.bacpop.org/poppunk
Apache License 2.0
87 stars 17 forks source link

Update and align installation requirements with requirements file. #242

Open ccoulombe opened 1 year ago

ccoulombe commented 1 year ago

Update pp-sketchlib and scikit-learn requirements according to the requirements.txt file

ccoulombe commented 1 year ago

More to it, if the requirements for building and installing are different, it can be useful to have two requirements file: requirements.txt and requirements-dev.txt where the dev one use the installation reqs:

-r requirements.txt
Cython>=0.26.1
...

Plus, from the setup.py one can then use the installation requirements file to read the list of reqs to use in the setup.py. 

with open('requirements.txt') as reqs:
  install_reqs = map(str.strip, reqs.readlines())

 ...

 setup(
 install_requires =  install_reqs
 )

This avoids maintaining multiple list of requirements that can diverge one of the others.

johnlees commented 1 year ago

I think this is something to look at again when we get back to a PyPI version. For now I am going to remove the file entirely