Relax Dependencies + Add Dependency Groups

[Grochocinski]

Linked Issue (Required)

Fixes #188

The Fix

Relaxed Core Dependency Requirements

Dependency Name	Old Minimum	New Minimum	Reasoning
numpy	2.3.4	2.0.0	Breaking changes between v1.X and v2.X
cvxpy	1.7.3	1.6.0	Oldest version compatible with numpy v2
matplotlib	3.10.7	3.9.0	Oldest version compatible with numpy v2
pandas	2.3.3	2.2.2	Oldest version compatible with numpy v2
scipy	1.16.3	1.13.0	Oldest version compatible with numpy v2
pydantic	2.12.3	2.2.0	Oldest version compatible with numpy v2 that didn't raise serialized value warnings
boltons	25.0.0	0.6.3	Oldest version with typeutils
joblib	1.5.2	1.0.0	Oldest stable version
seaborn	0.13.2	0.13.0	density_norm has a different name in prior versions

The process for establishing the new minimums was performed by pinning a package to a specific version and advancing/regressing the pinned version until warnings/errors were raised while running the regression test suite or until tests in the suite failed. Plotting packages were tested manually via notebooks and the GUI since the regression test suite does not utilize any plots. The pinning and version adjustment was repeated for each package with the environment being rebuilt after each adjustment to ensure any inter-dependency requirements were satisfied.

Removed Unused Core pillow Dependency

It was not used anywhere in the current codebase.

Relaxed Optional Dependency Versions

This followed the same process as the relaxing of the core dependencies.

Added Additional Optional Dependency Groups

• build: additional packages required for building the simoptlib package
  • setuptools>=61.0: the build-system currently used to build the package, version constraint matches existing minimum (see top of pyproject.toml)
• testing: additional packages required to run the included testing suite
  • pyyaml>=6.0: expected results are stored in .yaml files which cannot be opened without a yaml library of some sort. v6.0.3 is the newest version, so v6.0 was selected as the minimum since it works and is quite old (>4 years) so users should easily be able to resolve a compatible version
  • pytest and pytest-xdist were moved from the dev group to the testing group

Changed project.optional-dependencies to dependency-groups

project.optional-dependencies is meant for user-facing optional dependencies while dependency-groups is meant for dev-facing optional dependencies. Since none of the dependency groups are useful to end-users who are dealing solely with the published package, the dependency groups should be listed under dependency-groups instead.

Pinned dev Dependency Versions

ruff and ty were both pinned to their latest versions so that they would not unexpectedly update and cause GitHub actions to error unexpectedly. Additionally, jupytext was pinned since jupytext writes its version in each <notebook>.py's metadata header, so pinning it to a specific version like 1.17.3 (the version used to create the files) prevents repeated unnecessary updates to the metadata header.

Additional Notes

I'm marking this as a bug fix (and thus merging to main) since the current high dependency requirements can result in unsolvable dependencies for any downstream packages.

Verification

• ruff check passes on my code
• ty check passes on my code
• The bug is reproducible on the master branch.
• The bug is NO LONGER reproducible on this branch.
• All tests in the tests directory are passing.

[Grochocinski]

please Squash and merge after reviewing

[Grochocinski]

needed to force-push after rebasing off of master to avoid pushing unrelated commits to master

[cenwangumass]

Will reconsider this if there are concrete user report