[JOSS Review] Document how to run tests

[yunus-kausable]

Hi @djpasseyjr,

this is Yunus, I'm one of the reviewers of your JOSS submission. Super interesting submission, thank you … looking forward to reviewing!

I've started to go through the repository and the paper and will be opening issues in this project for anything that I'd like to bring up; some of these may just be questions or suggestions, for others it may be good to discuss a bit more. Please don't just change things because it's part of the review. It's your project after all.
I hope this process also works for you?

Below, some first small (purely infrastructural) things from trying to run the tests locally.

Let me know if you have any questions, please. Cheers :)

---

Specify custom surd and pyclustering dependencies

You can just add them to the dev options in pyproject.toml :

dev = [
    # ...
    "pydantic",
    "surd @ git+https://github.com/djpasseyjr/surd.git",
    "pyclustering @ git+https://github.com/djpasseyjr/pyclustering"
]

You already have very good error messages, but given that you are using the pyproject.toml anyway I think this would smooth things out. Or was there a particular reason not to do this?

Add a section to the README.md on how to run the tests.

Doesn't need to be a lot, perhaps just:

## Running Tests
1. Follow installation instructions for the cloned repository, see above.
2. Install test dependencies using `pip install -e ".[dev]"`
3. Run tests: `python -m pytest -v tests`

The tests all passed for me, yay 🎉

Also test more recent Python versions automatically

Afais, the GitHub action only tests this with Python 3.9 - 3.11. My local tests ran without problems on 3.13.

Automatically testing on more recent versions would be great, actually, at least up to 3.13. Note that Python 3.9 is EOL by now …

You can also add the following to your pyproject.toml (under [project]) to communicate classifiers to PyPI that show up on the PyPI project page (and in a badge, if you want):

  classifiers = [
      "Programming Language :: Python :: 3",
      "Programming Language :: Python :: 3.9",
      "Programming Language :: Python :: 3.10",
      "Programming Language :: Python :: 3.11",
      "Programming Language :: Python :: 3.12",
      "Programming Language :: Python :: 3.13",
      "License :: OSI Approved :: MIT License",
  ]

  requires-python = ">=3.9"

[djpasseyjr]

@yunus-kausable Thanks for your review. I'm wrapping up paper comments in #9. Anything to add? Be sure to read the shorter version paper.pdf and not the outdated (and misleadingly named) paper_full.pdf

You can also look over my JOSS review PR #4.

[yunus-kausable]

Thanks for flagging #9, @djpasseyjr, and apologies that I haven't continued on my review yet. If it's ok, I'd finalise my comments for the paper until tomorrow evening and add them to #9?

[djpasseyjr]

That sounds great.

[djpasseyjr]

I'm making changes right now, so you'll probably see the version that incorporates feedback from the other reviewer.