New update stack2

[cekees]

Mandatory Checklist

Please ensure that the following criteria are met:

• [x] Title of pull request describes the changes/features
• [x] Request at least 2 reviewers
• [x] If new files are being added, the files are no larger than 100kB. Post the file sizes.
• [x] Code coverage did not decrease. If this is a bug fix, a test should cover that bug fix. If a new feature is added, a test should be made to cover that feature.
• [x] New features have appropriate documentation strings (readable by sphinx)
• [x] Contributor has read and agreed with CONTRIBUTING.md and has added themselves to CONTRIBUTORS.md

As a general rule of thumb, try to follow PEP8 guidelines.

Description

This is a major infrastructure update, but it doesn't change any frequently used functionality in Proteus proper. The coverage is going to show up as reduced, but too much non-proteus package code was getting included in the coverage computation. Moving forward we should be able to focus on increasing the coverage on the package itself and further removing unused code and dependencies as well as tests that are being skipped on any platforms.

[codecov[bot]]

Codecov Report

Merging #1246 (ff261e1) into main (64d5e85) will decrease coverage by 5.26%. The diff coverage is 42.85%.

@@            Coverage Diff             @@
##             main    #1246      +/-   ##
==========================================
- Coverage   52.82%   47.55%   -5.27%     
==========================================
  Files         531       90     -441     
  Lines      109802    71766   -38036     
==========================================
- Hits        58004    34130   -23874     
+ Misses      51798    37636   -14162     

Impacted Files	Coverage Δ
proteus/Archiver.py	36.18% <ø> (+4.54%)	:arrow_up:
proteus/__init__.py	26.08% <ø> (ø)
proteus/MeshTools.py	55.83% <36.11%> (+0.55%)	:arrow_up:
proteus/FemTools.py	38.10% <60.00%> (+0.07%)	:arrow_up:
proteus/Quadrature.py	97.71% <100.00%> (+<0.01%)	:arrow_up:
proteus/TwoPhaseFlow/utils/Parameters.py	88.82% <0.00%> (-0.24%)	:arrow_down:
proteus/tests/CLSVOF/with_RANS3PF/clsvof_p.py
proteus/tests/CLSVOF/with_RANS3PF/ls_consrv_n.py
proteus/tests/levelset/vortex2D/vortex2D.py
...eus/tests/levelset/vortex/ls_consrv_vortex_3d_n.py
... and 432 more

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[cekees]

@adimako one thing I found that would be a small job to increased portability and remove dependencies would be to remove the curses.h code in the Fenton library. It's not a big deal if the interactive, text-based selection of Fenton theory parameters is useful (though in the long run it might be easier to reimplement that interface code using python and leave the C++ just for the computations.

[cekees]

@ejtovar LFS is working fine for me on both mac os x and linux. I did have some headaches getting all the files properly out of git and into LFS with the proper gitattributes set. I decided that we're never going to be free of binary and large data files for testing, so I'd rather just consistently use LFS than keep those file types in the repository. If you need to add csv, npy, bin, etc. Just do git lfs track filename before your do git lfs add. Or if you accidently add something, do git rm --cached filename; git commit; before adding it back properly.