Repository Layout

The package now uses a standard src/ layout:

celltraj/
  pyproject.toml
  README.rst
  src/
    celltraj/
      __init__.py
      trajectory.py
      features.py
      imageprep.py
      model.py
      spatial.py
      translate.py
      utilities.py
  docs/
    source/
    make_docs.sh
    publish_to_cancerdynamics.py
  tests/
  tutorials/

Important cleanup decisions:

  • Package modules should import siblings through the package namespace or relative imports, not by adding celltraj/celltraj to sys.path.

  • Generated docs live in docs/build/html/ and are ignored by Git in this repository.

  • Public docs are copied into cancerdynamics-website/public/docs/celltraj/.

  • Legacy generated HTML and root-level docs artifacts are no longer committed to this package repo.

  • sphinx.ext.viewcode is not enabled for public docs. API pages expose docstrings and signatures, not browsable source code.