modelarchive - The ModelArchive Python package

https://modelarchive.org/

modelarchive collects all Python functionality developed for ModelArchive in a single package - essentially the “Everything ModelArchive” toolkit.

Yes, the name is a bit long, but ma alone felt too short ;) You can conveniently import it as:

import modelarchive as ma

The package is organised into submodules covering different areas of functionality. Currently available:

• modelcif: help with editing ModelCIF files, translating from legacy PDB format and extending existing ModelCIf-formatted files

Installation

From PyPI:

pip install modelarchive-py

From source:

git clone https://git.scicore.unibas.ch/schwede/modelarchive-py
cd modelarchive-py
pip install .

For development, to see code changes immediately effective in your environment and to include development tools, run:

 pip install -e ".[dev]"

Versioning

modelarchive follows Semantic Versioning, so you can safely depend on modelarchive-py>=<MAJOR VERSION>.0.0 to get updates without breaking changes.

Documentation

Documentation is kept up to date here. There is the stable version, pointing to the current release, and there is latest, pointing to the dev branch. Older versions of the documentation are also kept available.

Developing ModelArchive

• consider copying hooks/pre-push to .git/hooks/ for version number checks
• best install the package to get all requirements resolved
• run pytest as python3 -m pytest [-s] (pytest will be installed with [dev])
• for unit test coverage, run python3 -m pytest --cov-report=term-missing --cov=modelarchive [-s]
• in the doc/ subdirectory, run make html to create the documentation
• in the doc/ subdirectory, run make doctest to run Doctests
• updating the package on PyPi happens via our CI/CD pipeline
  • merge dev into main
  • edit CHANGELOG.md
  • push a tag of form <Major>.<Minor>.<Bugfix>
  • runs the release pipeline to create a package on PyPi and a release in GitLab
  • merge main into dev
• updating the Read the Docs page happens via our CI/CD pipeline
  • push to dev to update latest
  • push release tag to update stable