Perform cythonize() in build directory instead of source tree

[pramodk]

• previously generates .cpp files in source tree. To have clean builds, move those in build dir
• remove unnecessary includes for some cython extensions

[sonarcloud]

Quality Gate passed

Kudos, no new issues were introduced!

0 New issues
0 Security Hotspots
No data about Coverage
0.0% Duplication on New Code

See analysis details on SonarCloud

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (128c684) 66.30% compared to head (608a74e) 66.30%.

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #2662      +/-   ##
==========================================
- Coverage   66.30%   66.30%   -0.01%     
==========================================
  Files         558      558              
  Lines      108434   108425       -9     
==========================================
- Hits        71899    71892       -7     
+ Misses      36535    36533       -2     

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[bbpbuildbot]

Logfiles from GitLab pipeline #188873 (:white_check_mark:) have been uploaded here!

Status and direct links:

• ✅ mac_m1_cmake_build: [cmake, ON, OFF, OFF, address]
• ✅ spack_setup
• ✅ build:nmodl
• ✅ build:neuron:nmodl:intel:legacy
• ✅ build:neuron:nmodl:intel:shared
• ✅ build:neuron:nmodl:nvhpc:acc:legacy
• ✅ build:neuron:nmodl:nvhpc:acc:shared
• ✅ build:neuron:nmodl:nvhpc:omp:legacy
• ✅ build:neuron:nmodl:nvhpc:omp
• ✅ test:neuron:nmodl:intel:legacy
• ✅ test:neuron:nmodl:intel:shared
• ✅ test:neuron:nmodl:nvhpc:acc:legacy
• ✅ test:neuron:nmodl:nvhpc:acc:shared
• ✅ test:neuron:nmodl:nvhpc:omp:legacy
• ✅ test:neuron:nmodl:nvhpc:omp

[nrnhines]

I like the idea behind this. Why is it a work in progress? Because setup.py is going away?

[JCGoran]

This is a welcome change, but if we want to move away from setup.py in the long run, I think it would be better to make a CMakeLists.txt for both RX3D and MUSIC modules, as then we do not depend on setup.py at all.
For this, we can use the cython CLI command to convert the .pyx files to .cpp ones, after which we can create a shared library using standard CMake tooling.