Feat (mfusg): FloPy MODFLOW-USG support (with .bas file example) #1476

[swfwmd]

• Feat(mfusg): add mfusg transport version 2.4.0 support

fixes and updates included with feature:
New Features

• MfUsgBct : Block Centered Transport (BCT)
• MfUsgPcb : Prescribed Concentration Boundary (PCB)
• MfUsgDdf: Density Driven Flow (DDF)
• MfUsgDpf: Dual Porosity Flow (DPF)
• MfUsgDpt: Dual Porosity Transport (DPT)
• MfUsgMdt: Matrix Diffusion Transport (MDT)
• MfUsgRch: Recharge (RCH)
• MfUsgLak: Lake (LAK)

Modified Packages

• MfUsgBcf : Block Centered Flow (BCF)
• MfUsgCln : Connected Linear Network (CLN)
• MfUsgSms : Sparse Matrix Solver (SMS)
• MfUsgWel : Well (WEL)
• ModflowFhb : Flow and Head Boundary (FHB)

See Panday, S., 2024; USG-Transport Version 2.4.0: Transport and Other Enhancements to MODFLOW-USG, GSI Environmental, July 2024 http://www.gsi-net.com/en/software/free-software/USG-Transport.html

[codecov]

Codecov Report

Attention: Patch coverage is 6.27262% with 2331 lines in your changes missing coverage. Please review.

Project coverage is 34.7%. Comparing base (bb9824e) to head (7957756).
Report is 9 commits behind head on develop.

Files with missing lines	Patch %	Lines
flopy/mfusg/mfusgoc.py	2.9%	656 Missing ⚠️
flopy/mfusg/mfusgbct.py	3.6%	421 Missing ⚠️
flopy/mfusg/mfusglak.py	3.4%	394 Missing ⚠️
flopy/mfusg/mfusgrch.py	4.9%	232 Missing ⚠️
flopy/mfusg/mfusgdpt.py	7.9%	186 Missing ⚠️
flopy/mfusg/mfusgmdt.py	10.1%	142 Missing ⚠️
flopy/mfusg/mfusgcln.py	2.2%	87 Missing ⚠️
flopy/mfusg/mfusgdpf.py	20.7%	61 Missing ⚠️
flopy/mfusg/mfusgpcb.py	29.7%	52 Missing ⚠️
flopy/mfusg/mfusgddf.py	21.6%	47 Missing ⚠️
... and 5 more

Additional details and impacted files

@@            Coverage Diff             @@
##           develop   #2378      +/-   ##
==========================================
- Coverage     68.4%   34.7%   -33.7%     
==========================================
  Files          294     301       +7     
  Lines        59390   61927    +2537     
==========================================
- Hits         40652   21525   -19127     
- Misses       18738   40402   +21664     

Files with missing lines	Coverage Δ
flopy/mfusg/__init__.py	100.0% <100.0%> (ø)
flopy/mfusg/mfusgwel.py	11.1% <ø> (-60.4%)	⬇️
flopy/mfusg/mfusgdisu.py	7.4% <0.0%> (-74.8%)	⬇️
flopy/modflow/mffhb.py	5.8% <0.0%> (-48.4%)	⬇️
flopy/mfusg/mfusg.py	14.5% <0.0%> (-51.8%)	⬇️
flopy/mfusg/mfusgsms.py	6.3% <0.0%> (-84.1%)	⬇️
flopy/mfusg/mfusgbcf.py	7.5% <0.0%> (-1.4%)	⬇️
flopy/mfusg/mfusgddf.py	21.6% <21.6%> (ø)
flopy/mfusg/mfusgpcb.py	29.7% <29.7%> (ø)
flopy/mfusg/mfusgdpf.py	20.7% <20.7%> (ø)
... and 7 more

... and 245 files with indirect coverage changes

---- 🚨 Try these New Features:

• Flaky Tests Detection - Detect and resolve failed and flaky tests

[langevin-usgs]

Thanks for this, @swfwmd. Have you thought about some of the other issues raised in #1476? It's still unclear how to test these changes. Maybe @cnicol-gwlogic or @martinvonk have some thoughts?

[swfwmd]

I am working on the test cases and will commit later

[cnicol-gwlogic]

My understanding was a key barrier to flopy tests for usg-transport was this: a git repo with tagged releases and ci testing for usg-transport was needed, so the flopy ci can pull in that executable as needed as usg-transport is developed.

I had a very quick stab at this some time ago based on mf6, but again haven't had the time to finish it. It needs some work, and would need to be brought into pymake etc. Someone pointed out to me last week that pymake downloads usg-transport exe from he gsi site these days, I believe, but I don't think it compiles the code and does not seem to live update versions as usg t releases are made (as far as I noticed in my glancing look).

[martinvonk]

My understanding was a key barrier to flopy tests for usg-transport was this: a git repo with tagged releases and ci testing for usg-transport was needed, so the flopy ci can pull in that executable as needed as usg-transport is developed.

This was also my understanding. And I did not have the time (or fortran experience :)) either to set this up. So if we'd want this, we would have to:

1. Set up and improve the USG-transport repo with tests, releases and all the fancy CI stuff
2. Merge the two FloPy forks that now exist for MODFLOW USG-Transport. For example, my fork has the Richards equation and PFAS transport options. Haven't looked closely at @swfwmd fork yet for it's functionalities.
3. Make tests and example notebooks for the FloPy usage of MODFLOW USG-Transport

[hzhang4]

I will contact Sorab to see if it is possible to set up a git repo for usg-transport.

[jdhughes-usgs]

The gsi version of mfusg is available from https://github.com/MODFLOW-USGS/executables/releases. This could be used to test usg-transport flopy functionality.

[swfwmd]

Added tests and notebooks:

Added test_usg_transport.py
Added example/data/mfusg_transport
with 9 test examples
Ex1_1D
Ex2_Radial
Ex3_Conduit
Ex4_DualDomain
Ex5_Henry
Ex6_Stallman
Ex7_Matrix_Diffusion
Ex8_Lake
Ex9_PFAS

Added example notebooks
mfusg_transport_Ex1_1D.py
mfusg_transport_Ex2_Radial.py
mfusg_transport_Ex3_Conduit.py
mfusg_transport_Ex4_DualDomain.py
mfusg_transport_Ex5_Henry.py
mfusg_transport_Ex6_Stallman_Heat_Transport.py
mfusg_transport_Ex7a_Discrete_Fracture.py
mfusg_transport_Ex7b_SandBox.py
mfusg_transport_Ex7c_ChainDecay.py
mfusg_transport_Ex8_Lake.py
mfusg_transport_Ex9_PFAS.py

Modified test_usg.py