DeepRank / pdb2sql

Fast and versatile biomolecular structure PDB file parser using SQL queries
https://pdb2sql.readthedocs.io
Apache License 2.0
24 stars 12 forks source link

Installation: unused dependencies in setup.py #21

Closed JoaoRodrigues closed 4 years ago

JoaoRodrigues commented 4 years ago

Installing pdb2sql from pip downloads a number of third-party modules but not all seem necessary. For example, cython and matplotlib are never used anywhere on the codebase and add quite a bit of space/time to the installation process.

Also, the dependencies listed on the requirements.txt file are not synced with those on setup.py. I know these serve different purposes but it would be better if they matched. If you want to have a 'development' requirements file, then I'd name it requirements-dev.txt and add extra dependencies there.

Linking to the review at JOSS: https://github.com/openjournals/joss-reviews/issues/2077