TLDR; pip install pymol-open-source

The open source version of PyMOL is excellent and it can be installed with mamba from conda forge via mamba install conda-forge::pymol-open-source.

However, until now there was no PyPI package available which means that you could not install PyMOL via pip and you had to specify a PyMOL dependency outside of the convenient python packaging ecosystem. This meant that as a result you could not make your own package installable via pip without telling users to install PyMOL separately. Edit: In March 2025, Martin Urban kindly added wheels for open source PyMOL to PyPI that allow for pip install pymol-open-source-whl. They are up-to-date with the latest released PyMOL version (3.1.0) that does not yet support numpy>=2.

In an attempt to improve the situation, I setup a GitHub project containing a workflow that creates precompiled files using GitHub actions for Linux, Windows, and MacOS that builds on the testing actions in the open source code base. The actions instruct GitHub-hosted runners to download the source code, build the packages, share the files on the releases page, and upload them to PyPI.

Currently, wheel files for the latest alpha version of PyMOL (3.2.0a0) are available which plays nicely with numpy>=2.

The workflow is hacky, especially in comparison to the shiny pymol open source conda forge feedstock, but it works, at least for now. Next up, adding MacOS ARM builds.