wpbonelli

@camille12225 `develop` has moved a lot and linting has switched to [`ruff`](https://github.com/astral-sh/ruff) since this was opened, in case you need to again it can be done with `ruff check .`...

A few more considerations. Example models are currently defined directly as input files. Is this the right way for programmatic access to models? If so, which models to bundle and...

An example models module would also simplify flopy and mf6 autotests, by removing the need for custom fixtures to fetch/prepare models for testing. There has been some effort to standardize...

While it seems like this is resolved (or at least worked around) I guess this can stay open as a case study for the next major version @langevin-usgs @laat0003? We...

probably not necessary given the PRT examples in the modflow6-examples repo

Feel free to reopen if needed @RyanConway91

After thinking on this more > The move to update flopy packages in CI was misguided — we want to test the codebase as it exists in version control. the...

I think MF6 class generation could be deferred to install time with a [custom setuptools build command](https://setuptools.pypa.io/en/latest/userguide/extension.html#) by extending `setuptools.command.build.SubCommand`. The second paragraph [here](https://setuptools.pypa.io/en/latest/userguide/extension.html#setuptools.command.build.SubCommand.build_lib) makes it sound like this is...

The 4 original models load successfully. There is a different one `mf6_test019_VilhelmsenLGR[_nr]` [failing](https://github.com/MODFLOW-USGS/modflow6/actions/runs/8943511125/job/24568556955?pr=1771#step:14:2394). Also `test014_NWTP3Low_dev` loads but [fails to converge](https://github.com/MODFLOW-USGS/modflow6/actions/runs/8931438827/job/24559106985?pr=1767#step:14:1865)

> My suggestion is to deprecate the .tr property and TemporalReference class (eventually remove flopy/utils/reference.py). This seems reasonable though I'll defer to others with more history on the project. If...