chore: use dependency groups (PEP 735)

[mwtoews]

Use dependency groups, which is a standard Python feature introduced in PEP 735 to group a list of project dependencies, usually for internal development. This is preferred instead of creating optional dependencies, which is a user-facing option to install package extras.

Note that uv sync will include the "dev" group by default.

[wpbonelli]

Thanks @mwtoews, is compatibility with older versions of pip not sufficient reason to have both dependency-groups and optional-dependencies? It's a bit of a pain to keep them in sync but we already do so in devtools. The main motivation there is not pip compatibility, it's that the groups are user-facing, not just internal. But I wonder if it's worth supporting older pip for a while, since PEP 735 support came only last year.

[mwtoews]

I don't think that duplication of lists of dependencies for both dependency-groups and optional-dependencies is necessary for pip compatibility for a few reasons:

• These groups (test, lint, and docs) are only useful for developers, and most developers should normally use recent pip versions that support --group, usually in virtual environments.
• These changes don't impact users with older versions of pip. For example pip install --dry-run modflowapi[nonexisting] would just show "warning: The package modflowapi==0.2.0 does not have an extra named nonexisting", but will still install the package.
• Furthermore, I haven't seen any other modern Python project duplicate lists of dependencies, except for modflow-devtools (which confused me initially).

[wpbonelli]

Is it atypical for projects to have both internal and user-facing groups? What do you suggest doing for e.g. devtools and flopy?

[mwtoews]

I think extras are pretty useful user-facing options, but they are limited to pip-users (conda just introduced a similar concept via CEP 44 implemented in rattler). But I consider dependency groups (test, lint, docs, etc.) to be internal/developer features, and they are not published in the metadata to PyPI, e.g. flopy==3.10.0 shows on the side-bar:

whereas I'd expect the only user-facing extras to be optional and codegen.

I'll look into a PR to implement this for flopy.