Fixes and additions for new MODFLOW USG Transport support

[martinvonk]

Fixes #2616.

Do you want a test for this? I could not find a test for the get_angldegx method so I did not make one for this method either. But I could make one (for both) if you guys want.

[codecov]

Codecov Report

❌ Patch coverage is 18.75000% with 13 lines in your changes missing coverage. Please review.
✅ Project coverage is 72.5%. Comparing base (556c088) to head (5bd9e90).
⚠️ Report is 57 commits behind head on develop.

Files with missing lines	Patch %	Lines
flopy/utils/gridgen.py	10.0%	9 Missing ⚠️
flopy/mfusg/mfusglpf.py	33.3%	4 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #2617      +/-   ##
===========================================
+ Coverage     55.5%    72.5%   +17.0%     
===========================================
  Files          644      667      +23     
  Lines       124135   129018    +4883     
===========================================
+ Hits         68947    93623   +24676     
+ Misses       55188    35395   -19793     

Files with missing lines	Coverage Δ
flopy/mfusg/mfusgbas.py	88.3% <ø> (ø)
flopy/mfusg/mfusgbct.py	85.9% <ø> (ø)
flopy/mfusg/mfusglpf.py	74.0% <33.3%> (-6.4%)	⬇️
flopy/utils/gridgen.py	75.7% <10.0%> (-11.3%)	⬇️

... and 552 files with indirect coverage changes

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[wpbonelli]

Presumably @aymanalz had this but it accidentally didn't make it into #2575?

I think if this is exercised by an example notebook there is no need for a test. But we wouldn't turn one down by any means. And I see now the new notebooks are getting skipped in CI tests and omitted from the gallery in RTD, that's why this wasn't caught.

If you like, you can fix that by

• renaming the new notebooks something with "tutorial" or "example" in the name
• adding them to examples.rst or tutorials.rst

I'm also happy to do that separately, either way

[martinvonk]

I opened a nice box of pandora adding the notebooks to the tests :)

I fixed some of the failing notebooks, but some of them still don't run. Maybe @aymanalz can have a look as well as he made the notebooks. Because there are clearly some things missing:

• tutorial07c_ChainDecay.py has 4 species but they are not available in the .con output file. Each species is called with the text keyword argument to concobj = HeadUFile(f"{mf.model_ws}/{mf.name}.con", text=f"conc0{idx + 1}") but it is not found in the file.
• tutorial08_Lake.py has an emtpy file.got for the ModflowGage package:

gages = [[-1, -37, 3]]
files = [f"{mf.name}.got"]
gage = ModflowGage(mf, numgage=1, gage_data=gages, files=files)

[wpbonelli]

Ah, ok. So the notebooks still need some work. Well, thanks for opening the box @martinvonk. I bumped this to the next milestone as 3.9.4 is imminent.

[martinvonk]

Ah, ok. So the notebooks still need some work. Well, thanks for opening the box @martinvonk. I bumped this to the next milestone as 3.9.4 is imminent.

Okay! We could also merge this and fix the other two notebooks later? With this PR at least some of the notebooks work.

[wpbonelli]

@martinvonk that sounds good to me but I'll let @christianlangevin make the call. In any case, you can skip the two failing notebooks for now?