Missing documentation

[PelzKo]

Somehow I am not able to find any documentation:

• The examples on the website seem to be outdated as it expects the package to be called pdbx
• If I run initdocs.sh after cloning the repository, I get this configuration error
  Configuration error: config directory doesn't contain a conf.py file (/home/konstantin/Programming/py-mmcif/docs-sphinx/source) make: *** [Makefile:20: html] Error 2
• If I delete the folder docs-sphinx, I get this extension error
  Extension error: Could not import extension sphinxcontrib.napoleon (exception: cannot import name 'Callable' from 'collections' (/home/user/miniforge3/envs/alphafold_stuff/lib/python3.13/collections/__init__.py)) make: *** [Makefile:20: html] Error 2
• There is no available prebuilt documentation

Could you please guide me in a direction so I can find documentation and use the package?

[piehld]

Hi @PelzKo, thanks for reaching out and reporting this to us. That page does appear to be quite old and likely outdated, so we will review and try to update that as soon as possible.

In the meantime, I can point you to some minimal examples and documentation:

• If you are interested in simply importing, exporting, and working with mmCIF data in Python, we coincidentally held a webinar yesterday about this in which we demonstrated this Jupyter notebook. (*You can easily open that up and run through it by clicking on the "Open in Colab" badge at the top of the notebook.)
  • This notebook mainly makes use of another RCSB PDB Python package, rcsb.utils.io, which basically provides a simplified wrapper for the py-mmcif package here, along with some other useful tooling (e.g., working with JSON, pickle, and list files)
• If you are interested in primarily using the py-mmcif package here, I can refer you to the following:
  • Installation instructions are provided in the README here
  • Example package usage for basic I/O purposes: https://github.com/rcsb/py-mmcif/blob/master/mmcif/tests/testIoAdapterPy.py
  • Example package usage for working with Data Categories: https://github.com/rcsb/py-mmcif/blob/master/mmcif/tests/testDataCategory.py
  • Additional example usage can be found in the other test files under: https://github.com/rcsb/py-mmcif/tree/master/mmcif/tests

Also, if you can share what you are interested in doing in particular, I could try to provide you with some specific examples and guidance for your use case, so please let us know.

Last, in case you aren't totally fluent in mmCIF terminology, here's a screenshot highlighting some of the common terms (i.e., "Data Container," "Category," "Attributes," ...):