Building from source skips Cython compile

[cooperlab]

When building from source using the directions on the front page, the Cython modules are not compiled.

[manthey]

The readme is outdated since we switched to just a pyproject.toml, but, assuming a new enough version of pip and the availability of a c compiler, they should still work. This worked for me in a fresh environment.

Specifically, I did
docker run --rm -t python:3.13-slim bash
To get a pristine environment, then

# get enough to build c programs and install from git
apt-get update; apt-get install -y build-essential git
# Clone our repo
git clone https://github.com/DigitalSlideArchive/HistomicsTK.git
cd HistomicsTK
# find-links to get all our tile sources
pip install -e . --find-links https://girder.github.io/large_image_wheels
# This will fail if cython hasn't compiled modules
python -c 'import histomicstk.features.compute_haralick_features'

What environment were you in and what version of pip was available?

[cooperlab]

This is pip 23.12 and Python 3.10. I'm running in the container nvcr.io/nvidia/tensorflow:23.07-tf2-py3.

It is at least trying to compile now but is quitting when the numpy arrayobject.h header cannot be located. Before, it was happily completing without compiling. We have numpy in the build-system requires so I'm not sure where to go from here.