Repository File Structure

The PyMedPhys repository has the following general structure:

pymedphys/
|   README.rst
|   LICENSE
|   CHANGELOG.md
|   pyproject.toml
|   ...
|
|-- lib/pymedphys/
|   | -- docs/
|
|-- ...

PyMedPhys contains a series of top-level files. These include:

README.rst:

A text file containing general information on the PyMedPhys repository with links to important sections. On the PyMedPhys GitHub page, README.rst determines the text you see below the file structure.

LICENSE:

A text file that contains a full copy of the license used by PyMedPhys.

CHANGELOG.md:

A text file containing release notes for the PyMedPhys source code library. CHANGELOG.md determines the text presented on the Release Notes page.

pyproject.toml:

Package metadata, supported Python versions, dependencies, extras, and tool configuration. Hatchling is the build backend; uv manages the development environment.

uv.lock:

The resolved dependencies used by uv and CI. Commit lockfile changes together with the generated dependency files.

.github/workflows/:

GitHub Actions workflows; see the workflow guide.

.readthedocs.yml:

The ReadTheDocs build configuration for the published documentation.

requirements*.txt:

Exported dependency files. Regenerate these with uv run pymedphys dev propagate after changing dependencies; do not edit them by hand.

You’ll quickly note from a cursory look through PyMedPhys that there are actually many more top-level files. Most of these help configure specific tasks, such as installation & automated testing. They are probably less critical to understand in detail in order to comprehend PyMedPhys’ structure, so we’ll disregard them for now in the interest of brevity.

(Most of) the rest of PyMedPhys is arranged in the following directories:

lib/pymedphys/:

The main PyMedPhys package.

lib/pymedphys/docs/:

Contains most of PyMedPhys’ documentation. The files within docs/ make up the text you are reading right now! A documentation generator called Sphinx converts the files in docs/ into human-readable format. The same tool also pulls the docstrings from PyMedPhys’ source code and displays them in the documentation pages.