Contributing

Contributions are welcome, and they are greatly appreciated! The development of this package takes place on GitHub. Issues, bugs, and feature requests should be reported there. Code and documentation can be improved by submitting a pull request. Please add documentation and tests for any new code.

The package can be set up (ideally in a fresh virtual environment) for local development with the following:

$ git clone https://github.com/epfl-lts2/pygsp.git
$ cd pygsp
$ make install

The make install command (which runs uv sync --all-extras) ensures that all dependencies required for development (to run the test suite and build the documentation) are installed. Only graph-tool will be missing: install it manually as it cannot be installed by uv.

You can improve or add functionality in the pygsp folder, along with corresponding unit tests in pygsp/tests/test_*.py (with reasonable coverage). If you have a nice example to demonstrate the use of the introduced functionality, please consider adding a tutorial in doc/tutorials or a short example in examples.

Update README.rst and CHANGELOG.rst if applicable.

After making any change, please check the style, run the tests, and build the documentation with the following (enforced by GitHub Actions):

$ make lint
$ make test
$ make doc

Check the generated coverage report at htmlcov/index.html to make sure the tests reasonably cover the changes you’ve introduced.

To iterate faster, you can partially run the test suite, at various degrees of granularity, as follows:

$ python -m pytest pygsp/tests/test_docstrings.py
$ python -m pytest pygsp/tests/test_graphs.py::TestGraphs
$ python -m pytest pygsp/tests/test_graphs.py::test_save_load

Making a release

  1. Update the version number and release date in setup.py, pygsp/__init__.py and CHANGELOG.rst.

  2. Create a git tag with git tag -a v0.5.0 -m "PyGSP v0.5.0".

  3. Push the tag to GitHub with git push github v0.5.0. The tag should now appear in the releases and tags tab.

  4. Create a release on GitHub and select the created tag. A DOI should then be issued by Zenodo.

  5. Go on Zenodo and fix the metadata if necessary.

  6. Build the distribution with make dist and check that the dist/PyGSP-0.5.0.tar.gz source archive contains all required files. The binary wheel should be found as dist/PyGSP-0.5.0-py2.py3-none-any.whl.

  7. Test the upload and installation process:

    $ uv publish --publish-url https://test.pypi.org/legacy/ dist/*
$ pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple pygsp

    Log in as the LTS2 user.

  8. Build and upload the distribution to the real PyPI with make release.

  9. Update the conda feedstock (at least the version number and sha256 in recipe/meta.yaml) by sending a PR to conda-forge.

Repository organization

LICENSE.txt         Project license
*.rst               Important documentation
Makefile            Targets for make
setup.py            Meta information about package (published on PyPI)
.gitignore          Files ignored by the git revision control system
.github/workflows/  Defines testing on GitHub Actions continuous integration

pygsp/              Contains the modules (the actual toolbox implementation)
 __init.py__        Load modules at package import
 *.py               One file per module

pygsp/tests/        Contains the test suites (will be distributed to end user)
 __init.py__        Load modules at package import
 test_*.py          One test suite per module
 test_docstrings.py Test the examples in the docstrings (reference doc)
 test_tutorials.py  Test the tutorials in doc/tutorials
 test_all.py        Launch all the tests (docstrings, tutorials, modules)

doc/                Package documentation
 conf.py            Sphinx configuration
 index.rst          Documentation entry page
 *.rst              Include doc files from root directory

doc/reference/      Reference documentation
 index.rst          Reference entry page
 *.rst              Only directives, the actual doc is alongside the code

doc/tutorials/
 index.rst          Tutorials entry page
 *.rst              One file per tutorial