Cutfem final changes (3D)

[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. EQUIV. POLY. KERNAL file is/will remain larger that 100kb.
• [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.
• [ ] 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

[codecov[bot]]

Codecov Report

Merging #1219 into master will increase coverage by 0.51%. The diff coverage is 67.65%.

@@            Coverage Diff             @@
##           master    #1219      +/-   ##
==========================================
+ Coverage   51.63%   52.14%   +0.51%     
==========================================
  Files         539      528      -11     
  Lines      102272   109012    +6740     
==========================================
+ Hits        52806    56847    +4041     
- Misses      49466    52165    +2699     

Impacted Files	Coverage Δ
proteus/ADR.py	0.00% <0.00%> (ø)
proteus/NonlinearSolvers.py	33.45% <0.00%> (+0.90%)	:arrow_up:
proteus/Quadrature.py	97.71% <ø> (ø)
proteus/SWFlow/models/GN_sw_p.py	97.22% <ø> (ø)
proteus/SWFlow/models/sw_p.py	94.44% <ø> (-0.16%)	:arrow_down:
proteus/WaveTools.py	0.00% <0.00%> (ø)
proteus/config/centennial.py	0.00% <0.00%> (ø)
proteus/config/copper.py	0.00% <ø> (ø)
proteus/config/jim.py	0.00% <0.00%> (ø)
proteus/config/mustang.py	0.00% <0.00%> (ø)
... and 241 more

---

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[cekees]

@ejtovar at some point the gmsh installed via conda quit install properly on os x, which is why in this PR you see I've added pip install gmsh as a work around. Don't know what's going on, but you it's not an issue with this PR--our nightly build is also failing now as you can see from the "build failing" badge on the README.