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forlilab / Meeko

Interface for AutoDock, molecule parameterization
https://meeko.readthedocs.io/
GNU Lesser General Public License v2.1
204 stars 49 forks source link

Prep v0.6.0 #226

Closed diogomart closed 2 weeks ago

diogomart commented 2 weeks ago

Updated version strings to v0.6.0 Moved scripts to meeko/cli, per conda-forge requirements and already implemented in v0.5.1 Removed script mk_get_openff_epsilon_sigma.py

rwxayheee commented 2 weeks ago

Would you want to put dependencies in setup.py install_requires=, or do you prefer them to stay in installation guide? I'm fine with either way The template making function introduces a new dependency (gemmi)

diogomart commented 2 weeks ago

I'm including as you suggest unless @nbruciaferri objects due to conflicts with conda. Advantage of including is that a local pip install from source pip install . will automatically fetch the dependencies from PyPI. Numpy is already included, we are missing rdkit, scipy, and gemmi. Not including prody because it brings biopython, and pyparsing, and downgrades numpy, and it is possible that users have a more complex environment situation if they are installing from source. Users can always manually install prody. Also making pandas an optional dependency, only used to convert interaction analysis to a dataframe. This function is not used by ringtail.

rwxayheee commented 2 weeks ago

Thanks! Ringtail also needs pandas although there's no explicit install_requires= in setup.py. I'm completely fine either way

diogomart commented 2 weeks ago

I think a pip installation from PyPI should install dependencies. At least that's what I'm seeing for popular packages. For example, pip install scipy installs numpy. And pandas and matplotlib install a bunch of stuff. The issue for ringtail might be that chemicalite is not on PyPI, only on conda-forge, but @maylinnp might drop that dependency in the future. https://github.com/forlilab/Ringtail/issues/58

nbruciaferri commented 2 weeks ago

As long as we already checked that the packages in the install_requires= are working and available I'm fine with it.