Installation error: command 'clang' failed with exit status 1

[William Song]

the last part of error message is

seqlearn/_decode/bestfirst.c:600:10: fatal error: 'numpy/arrayobject.h' file not found
#include "numpy/arrayobject.h"
         ^~~~~~~~~~~~~~~~~~~~~
1 error generated.
error: command 'clang' failed with exit status 1
----------------------------------------

ERROR: Command errored out with exit status 1: /usr/local/opt/python/bin/python3.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/4f/zswmtvpn44gfvcz53m_c24400000gn/T/pip-install-6hdkoh2q/seqlearn/setup.py'"'"'; file='"'"'/private/var/folders/4f/zswmtvpn44gfvcz53m_c24400000gn/T/pip-install-6hdkoh2q/seqlearn/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /private/var/folders/4f/zswmtvpn44gfvcz53m_c24400000gn/T/pip-record-gr6jqkyt/install-record.txt --single-version-externally-managed --compile --install-headers /usr/local/include/python3.7m/seqlearn Check the logs for full command output.

[Danielle Madeley]

It looks like retrieving the numpy dir is not working when installing from PyPi (and other places?)

Run this in your terminal and you should be able to install.

export CFLAGS="-I$(python -c 'import numpy; print(numpy.get_include())')"

In general, if you want to improve the ease of installation of this module, setup.py should be extended to include Cython. You can also build a custom extension to include numpy when building e.g. https://stackoverflow.com/a/42163080/4391298