pypi version

[Pantelispanka]

Will there ever be a pypi package for the module ? If you are planning for that i can offer some help! Thanks!

[peastman]

I hope so! We first need PyPI packages for OpenMM, which PDBFixer depends on. We're investigating that right now: openmm/openmm#3796. If you want to help, that would be fantastic.

[minhuanli]

Hi, I want to do a quick follow up on this issue.

Why don't we make PDBFixer a PyPI package alone? The main OpenMM module seems tricky because of the cuda stuff, but you could assume people have already installed the OpenMM before they need PDBFixer? Just save people from downloading the whole repo before installation.

[peastman]

What would be the use case for that? If you've already installed OpenMM with conda, what's the benefit of installing PDBFixer with pip instead of conda?

[minhuanli]

I am not sure if I take it correctly. Do you mean PDBFixer itself can be installed by conda? I didn't see that in the installation tutorials

[minhuanli]

One common case for me is that, I have installed OpenMM according to the official document:

conda install -c conda-forge openmm cudatoolkit=xx.x

Then I realize that I also need PDBfixer to preprocess PDB files.

It would be great if I could simply do pip install PDBFixer instead of git clone the whole repo and run pip install .

[peastman]

Correct. This will install it, including all dependencies.

conda install -c conda-forge pdbfixer

We should add that to the README.

[minhuanli]

Got it! That makes much more sense now. Yes, should add this to the README. Thank you for the clarification.

[peastman]

The updated instructions are in #265.

[recursingfeynman]

If pdbfixer were on pypi it would be convenient to install it along with dependencies via poetry. Poetry can also handle dependencies like conda, but unlike it it shows better performance

[k9cdt]

Now that OpenMM has been available on PyPI since May 10, 2024, I think it’s a good time to bring this issue up again.

Uploading pdbfixer to PyPI would really help those of us using it as a dependency in our own projects. Currently, any package on PyPI can’t depend on something that isn’t also on PyPI (which I get, even though it’s a bit limiting).

PEP 725 is still a draft, so it looks like we’ll have to wait before GitHub repositories can be used as dependencies.

[peastman]

The current PyPI builds for OpenMM are just a proof of concept and shouldn't be relied on. I'm hoping in the future we'll have proper builds that are fully tested and supported. We have a ways to go before that can happen though.

[kiyoon]

@peastman I've been using the pypi builds of OpenMM and it's been working solidly. When can I expect to see Pdbfixer as well? I guess this repository is pure python and does not require build steps, so it should be easy to upload it as a proof of concept too, right?

[peastman]

Once OpenMM 8.2 is released and we've confirmed the pip packages work correctly, PDBFixer will be one of the next ones to do.