Cannot run preprocessing. NameError: name 'calculate_protein_embeddings' is not defined about prosmith HOT 5 CLOSED

Thanks for your reply.
I solved this by uncommenting the "#from protein_embeddings import *" from the preprecessing.py

A few more things could be helpful.

1. protein_embedding.py has some unwanted indent that caused error.
2. Some packages are missing in the readme. e.g esm. Could you release a requirements.txt or a poetry.lock file for user to install all the required packages?

Thank you,
Yang

from prosmith.

Also having big reproducibility issues right now. This might help you for the first steps:
You need to make the package installable that local imports are recognized. You can do this by writing a setup.py file with this minimal content:

from setuptools import setup, find_packages

setup(
    name="prosmith",
    description="Prosmith",
    package_dir={'': 'code'},
    packages=find_packages(where='code'),
    classifiers=[
        "Programming Language :: Python :: 3",
        "License :: OSI Approved :: MIT License",
        "Operating System :: OS Independent",
    ],
)

then you can install the project with pip install .
make sure you create the setup.py where readme.md is and call pip install . from there...

from prosmith.

I had all the mentioned issues as well but was too hesitated to open a PR, too:/

from prosmith.

Sorry for my late response, I was very busy during the last weeks.
@fmoorhof thanks for fixing the issues! I merged your pull request.

from prosmith.

Thank you Both!

from prosmith.