Numpy import issues with ClearMap.compile

[jemajet]

Hi, I'm working on installing from source in a non-conda environment, and I was running into an issue with
running ClearMap.Compile with the TraceCode cythonization step. When cythonizing just that file, I ran into the error of

cythonize -i -a /transfer/ClearMap2/ClearMap/ImageProcessing/Tracing/TraceCode.pyx
running build_ext
building 'ClearMap.ImageProcessing.Tracing.TraceCode' extension
creating /transfer/ClearMap2/tmpbovrp7cy/transfer
creating /transfer/ClearMap2/tmpbovrp7cy//transfer/ClearMap2
creating /transfer/ClearMap2/tmpbovrp7cy/transfer/ClearMap2/ClearMap
creating /transfer/ClearMap2/tmpbovrp7cy/transfer/ClearMap2/ClearMap/ImageProcessing
creating /transfer/ClearMap2/tmpbovrp7cy/transfer/ClearMap2/ClearMap/ImageProcessing/Tracing
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/transfer/ClearMap2/ClearMap/ImageProcessing/Tracing -I/usr/local/include/python3.8 -c /transfer/ClearMap2/ClearMap/ImageProcessing/Tracing/TraceCode.cpp -o /transfer/ClearMap2/tmpbovrp7cy/transfer/ClearMap2/ClearMap/ImageProcessing/Tracing/TraceCode.o
/transfer/ClearMap2/ClearMap/ImageProcessing/Tracing/TraceCode.cpp:785:10: fatal error: numpy/arrayobject.h: No such file or directory
 #include "numpy/arrayobject.h"
          ^~~~~~~~~~~~~~~~~~~~~
compilation terminated.
error: command 'gcc' failed with exit status 1

I was able to work around this by installing from setup.py with the command python setup.py build_ext --inplace, since that script uses np.get_include() to find the numpy path. I'm not sure if this is an issue that needs to change with the installation documentation or within the Compile.py script, otherwise I'd make a pull request with a fix. Happy to help with the fix if needed, but wanted to bring this to your attention.

[crousseau]

@jemajet Indeed, in the future, I'd rather go with the setup script (or the more recent alternative when I get the time to) than using the compile script or compiling by hand