apallath / prog_practices_demo

Repository accompanying the Patel Group tutorial on good programming practices.

Programming Practices Demo

This GitHub repository accompanies my July 2021 tutorial on 'Good Programming Practices' for new members of the Patel Group.

By using an example Python program to calculate the radius of gyration of a small polymer and a relatively large protein, this repository (and the accompanying slides) cover the following topics:

Modular programming (functions, classes, and objects)

• Modularity using functions:

  • examples/rg_functions/

• Object-oriented programming:

  • analysis_demo/gmx_analysis.py
  • examples/rg/

Testing

tests/unit/test_rgyr.py and tests/unit/test_selection_parsers.py demonstrate unit testing. tests/integration/test_poly.py and tests/integration/test_protein.py demonstrate the use of 'gold master' integration tests.

Documentation

Scripts to generate documentation from analysis_demo's docstrings are in docsource/. GitHub pages documentation is hosted from the docs/ folder.

Continuous integration

See GitHub Actions for this repository.