refactor(docs): mf6 classes and codegen templates

[mwtoews]

This makes base mf6 classes and in the jinja codegen template docstrings more consistent, among other changes detailed here:

• Move primary class initialization documentation from "init" to "class" (since the default for Sphinx's autoclass_content is 'class', thus class docs are rendered preferentially over init docs). Keep a short docstring for init, which does not get rendered by Spinx, but satisfies (e.g.) D107.
• Consistent case and punctuation for parameter descriptions; add defaults or tag as optional.
• Mirror parameter descriptions in base .py class and in .jinga templates, checking they also match function signatures.
• Adjust function calls to use more keyword parameters than positional to guard against API changes.
• Move static functions out of Filters (in flopy.mf6.utils.codegen.filters), since it wasn't used as an OOP class; only minor changes to the filter functions were required (e.g. renaming variables to distinguish them from functions with the same name).
• Mark TODO for a Dfn bug with "items" in the "children" filter (issue not raised yet, but will be described soon)
• Adjust generate_classes command to allow --no-verbose to turn off verbose (default remains with --verbose on).

[codecov]

Codecov Report

❌ Patch coverage is 0% with 301 lines in your changes missing coverage. Please review.
✅ Project coverage is 72.5%. Comparing base (556c088) to head (dab7c4a).
⚠️ Report is 41 commits behind head on develop.

Files with missing lines	Patch %	Lines
flopy/mf6/utils/codegen/filters.py	0.0%	276 Missing ⚠️
flopy/mf6/utils/codegen/__init__.py	0.0%	24 Missing ⚠️
flopy/mf6/utils/generate_classes.py	0.0%	1 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #2593      +/-   ##
===========================================
+ Coverage     55.5%    72.5%   +16.9%     
===========================================
  Files          644      667      +23     
  Lines       124135   128669    +4534     
===========================================
+ Hits         68947    93307   +24360     
+ Misses       55188    35362   -19826     

Files with missing lines	Coverage Δ
flopy/mf6/mfmodel.py	57.0% <ø> (-23.9%)	⬇️
flopy/mf6/mfpackage.py	68.4% <ø> (-13.2%)	⬇️
flopy/mf6/mfsimbase.py	62.2% <ø> (-13.2%)	⬇️
flopy/mf6/utils/generate_classes.py	17.5% <0.0%> (ø)
flopy/mf6/utils/codegen/__init__.py	0.0% <0.0%> (ø)
flopy/mf6/utils/codegen/filters.py	0.0% <0.0%> (ø)

... and 545 files with indirect coverage changes

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[wpbonelli]

thanks for this!

CI failure is unrelated, it's a particle tracking thing. should be fixed soon enough.

Mark TODO for a Dfn bug with "items" in the "children" filter (issue not raised yet, but will be described soon)

yeah, this code generation stuff is now consuming a new TOML format for DFNs which is still not really hammered out yet. but its coming from devtools. we froze the version recently to avoid churn. you may want to raise the issue on devtools, unless it's also relevant here?

[mwtoews]

I'm only partway narrowing down the issue, but the issue is connected to recent dfn additions to modflow6 that trace to devtools that break code generation from flopy. So it's a bit all over the place.

[wpbonelli]

recent dfn additions to modflow6 that trace to devtools

I just meant to warn you that any DFN oddities you see here may not be changes to dfns in modflow6, rather more likely related to our monkeying around in devtools.

So it's a bit all over the place.

Yes. Things to be kept in sync across several repos. Painful, but temporary