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pnpnpn / dna2vec

dna2vec: Consistent vector representations of variable-length k-mers
MIT License
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Fix requirements.txt for python3 dependency installation #16

Open kclejeune opened 4 years ago

kclejeune commented 4 years ago

The existing version of requirements.txt fails when trying to build packages with wheels. I manually installed packages and then used pip freeze to create new versions.

kclejeune commented 4 years ago

The biopython==1.76 and many other libraries are not needed.

Could you list the specific libraries you’re referring to? They may not be direct requirements for your codebase but if it shows up in pip freeze then it’s important to include as a dependency to avoid version incompatibilities.

kclejeune commented 4 years ago

I'd like to reiterate emphasize the importance of these "unnecessary" libraries - they are not dependencies of your codebase, but they are necessary in order to reproduce a working environment if dependencies are updated in the future.

pnpnpn commented 4 years ago

I'd like to reiterate emphasize the importance of these "unnecessary" libraries - they are not dependencies of your codebase, but they are necessary in order to reproduce a working environment if dependencies are updated in the future.

That makes sense. I noticed that this is using latest version of gensim. Does it work with the current code? I think there has been significant change to the gensim API since gensim==0.13.2.

kclejeune commented 4 years ago

I'd like to reiterate emphasize the importance of these "unnecessary" libraries - they are not dependencies of your codebase, but they are necessary in order to reproduce a working environment if dependencies are updated in the future.

That makes sense. I noticed that this is using latest version of gensim. Does it work with the current code? I think there has been significant change to the gensim API since gensim==0.13.2.

These dependencies work with all proposed changes on #15. I'll check if it works with the existing codebase and get back to you.