Convert to pyproject.toml and update CI

[kroq-gar78]

All package dev and production dependencies have been consolidated into pyproject.toml . setup.py did not specify all the required packages, so it could not be pip install'd without errors.

CI now also runs tests on Python 3.13.

Note that I saw a defaults.cfg mentioned in setup.py , but I'm not actually familiar with this repo, so I'm assuming it's not used anywhere.

[Copilot]

Pull Request Overview

This PR migrates the project from legacy setup.py and requirements.txt files to a modern pyproject.toml-based configuration, aligning with PEP 517/518 standards. The migration includes updates to CI/CD workflows, removal of Travis CI configuration, and modernization of the build and installation process.

• Migration from setup.py to pyproject.toml for project configuration
• Updated GitHub Actions workflows to use pyproject.toml and Python 3.9-3.13
• Removed legacy files (setup.py, requirements.txt, test_requirements.txt, .travis.yml)

Reviewed Changes

Copilot reviewed 8 out of 9 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
pyproject.toml	New project configuration file with build system, dependencies, and dependency groups
setup.py	Removed legacy setup script
requirements.txt	Removed in favor of pyproject.toml dependencies
test_requirements.txt	Removed in favor of pyproject.toml test dependency group
.travis.yml	Removed legacy Travis CI configuration
.github/workflows/run_tests.yml	Updated to use pyproject.toml, Python 3.9-3.13, and new installation method
.github/workflows/build_docs.yml	Updated to use pyproject.toml and Python 3.13
.github/workflows/publish_to_pypi.yml	Updated to use modern python -m build instead of setup.py
README.rst	Updated installation instructions to remove setup.py reference

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[Copilot]

The requires-python constraint specifies Python >=3.6, but the CI workflow tests against Python 3.9-3.13 only (line 14 of run_tests.yml). This mismatch could lead to compatibility issues. Consider updating requires-python to >=3.9 to match the tested versions, or expand CI testing to include Python 3.6-3.8 if older versions need to be supported.

Suggested change

	requires-python = ">=3.6"
	requires-python = ">=3.9"

[kroq-gar78]

This change will break compatibility with Python <= 3.8. If you make this change and then try to install the package in a 3.8 env, it will error.

[Copilot]

The --group flag is not a valid pip option. For PEP 735 dependency groups defined in pyproject.toml, you should use pip install -e .[test] with the optional dependency syntax, or consider using a tool like uv that supports the --group flag. Alternatively, install the dependencies separately: pip install -e . && pip install pytest pytest-cov codecov scikit-image.

Suggested change

	pip install -e . --group test
	pip install -e .[test]

[Copilot]

The --group flag is not a valid pip option. For PEP 735 dependency groups defined in pyproject.toml, you should use pip install -e .[docs] with the optional dependency syntax, or consider using a tool like uv that supports the --group flag. Alternatively, install the dependencies separately: pip install -e . --no-build-isolation && pip install numpydoc ipython Sphinx sphinx-gallery sphinx-rtd-theme sphinx-bootstrap-theme.

Suggested change

	pip install -e . --group docs --no-build-isolation
	pip install -e .[docs] --no-build-isolation

[Copilot]

The [dependency-groups] table is part of PEP 735, which is a recent addition to Python packaging standards. Standard pip doesn't support this yet. Consider using [project.optional-dependencies] instead for broader compatibility, which would allow installing groups with pip install -e .[test] or pip install -e .[docs]. This approach is more widely supported and compatible with standard pip.

[kroq-gar78]

Interestingly Copilot is out of date by 6 months. Pip 25.1 (rel. April 2025) supports dependency groups: https://discuss.python.org/t/announcement-pip-25-1-release/89702

[anwarnunez]

Thanks for the PR @kroq-gar78 !

It looks good to me. I'm happy to merge this in as-is.
w.r.t. Python 3.8: I'm ok either way. I'm for ignoring the Copilot suggestion and keeping 3.8 support unless others think otherwise.

@mvdoc : Are you good with these changes, too?

[mvdoc]

+1 let's merge

…

On Thu, Nov 6, 2025 at 3:41 AM Anwar Nunez-Elizalde < ***@***.***> wrote: *anwarnunez* left a comment (gallantlab/pymoten#47) <#47 (comment)> Thanks for the PR @kroq-gar78 <https://github.com/kroq-gar78> ! It looks good to me. I'm happy to merge this in as-is. w.r.t. Python 3.8: I'm ok either way. I'm for ignoring the Copilot suggestion and keeping 3.8 support unless others think otherwise. @mvdoc <https://github.com/mvdoc> : Are you good with these changes, too? — Reply to this email directly, view it on GitHub <#47 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABO5TGVVIZGRU7TMPT2DRL333MXU5AVCNFSM6AAAAACKCDNYRKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTIOJWG43TCNBZHE> . You are receiving this because you were mentioned.Message ID: ***@***.***>

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