Kwant's (development version) setup.py understands the option --configfile to specify an alternative path for "build.conf". Together with pip's --global-option it should be possible to use a custom build.conf also when installing with pip. Something like this:

pip3 --global-option="--configfile=/tmp/buid.conf" install git+https://gitlab.kwant-project.org/kwant/kwant.git

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