Use the Eigen library with cppyy

I've been successfully using cppyy for automatic python bindings for a C++ project I'm working on. I recently included the Eigen library, but I'm having trouble using this together with cppyy. Does anyone have any experience doing this, or know how I should do this?

I have the following structure for the repo (only relevant parts shown):

.
├── CMakeLists.txt
├── build
├── external
   ── eigen
├── include
   ── all .hpp files
├── src
   ── all .cpp files
├── python
   ── qmc.py

Here the external/eigen is a copy of the Eigen GitHub repo. The qmc.py file is where the cppyy magic happens, and it looks like this (before trying to add Eigen, this works just fine)

import cppyy
import tempfile
import os
import glob

try:
    current_dir = os.path.dirname(__file__)
except NameError:
    current_dir = os.getcwd()
source_dir = os.path.dirname(current_dir)
install_dir = os.path.join(source_dir, 'build')
include_dir = os.path.join(source_dir, 'include')
eigen_dir = os.path.join(source_dir, 'external', 'eigen')
print(current_dir, source_dir, include_dir, install_dir)

def cmake_run(build_type='Release', c_compiler='gcc', cxx_compiler='g++'):
    os.environ['CC'] = c_compiler
    os.environ['CXX'] = cxx_compiler
    os.system('cd {} && cmake {} -DCMAKE_BUILD_TYPE={}'.format(install_dir, source_dir, build_type))

def load_library():
    os.system('cd {} && make engine'.format(install_dir))
    libraries = glob.glob(os.path.join(install_dir, 'libengine.*'))
    print('Found libraries: {}'.format(libraries))
    library = libraries[0]
    cppyy.load_library(library)
    for header in glob.glob(os.path.join(include_dir, '*.hpp')):
        print('Loading {}'.format(header))
        cppyy.include(header)

The build part works, but as soon as I try to load any header that uses Eigen, I get an error. I've tried just about everything I can think of (include needed headers manually one by one, copying the entire library into the build dir etc.) but regardless of what I do the same type of errors pop up. Something like

In file included from 
/path/to/repo/projects/include/myheader.hpp:3:10: fatal error: 'Eigen/Dense' file not found
#include <Eigen/Dense>
         ^~~~~~~~~~~~~

Any help with what to change here would be much appreciated!

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