setup.py fails to generate .c files

[ldesousa]

I am trying to build and install the programme on Ubuntu 20.04. Try as I might, setuptools does not generate the .c files by itself leading to a build failure. Details in the log below:

$ uname -a
Linux luis-notebook 5.4.0-90-generic #101-Ubuntu SMP Fri Oct 15 20:00:55 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

$ python3 --version
Python 3.8.10

$ git clone [email protected]:ItziModel/itzi.git
Cloning into 'itzi'...
Warning: Permanently added the RSA host key for IP address '140.82.112.3' to the list of known hosts.
Enter passphrase for key '/home/duque004/.ssh/id_rsa':
Enter passphrase for key '/home/duque004/.ssh/id_rsa':
remote: Enumerating objects: 3099, done.
remote: Counting objects: 100% (3099/3099), done.
remote: Compressing objects: 100% (1166/1166), done.
remote: Total 3099 (delta 2027), reused 2971 (delta 1900), pack-reused 0
Receiving objects: 100% (3099/3099), 1.73 MiB | 2.59 MiB/s, done.
Resolving deltas: 100% (2027/2027), done.

$ cd itzi
$ python3 -m venv env
$ source env/bin/activate
$ pip3 install cython numpy
Collecting cython
  Using cached Cython-0.29.24-cp38-cp38-manylinux1_x86_64.whl (1.9 MB)
Collecting numpy
  Using cached numpy-1.21.4-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (15.7 MB)
Installing collected packages: cython, numpy
Successfully installed cython-0.29.24 numpy-1.21.4

$ python setup.py build_ext --inplace
running build_ext
compiler: unix
building 'itzi.flow' extension
creating build
creating build/temp.linux-x86_64-3.8
creating build/temp.linux-x86_64-3.8/itzi
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/duque004/git/itzi/env/lib/python3.8/site-packages/numpy/core/include -I/home/duque004/git/itzi/env/include -I/usr/include/python3.8 -c itzi/flow.c -o build/temp.linux-x86_64-3.8/itzi/flow.o -O3 -w -fopenmp
x86_64-linux-gnu-gcc: error: itzi/flow.c: No such file or directory
x86_64-linux-gnu-gcc: fatal error: no input files
compilation terminated.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1

It is possible to run cython manually to get things going (see below), but that is not so convinient. Am I using setuptools correctly?

$ cython -a itzi/flow.pyx
/home/duque004/git/itzi/env/lib/python3.8/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /home/duque004/git/itzi/itzi/flow.pyx
  tree = Parsing.p_module(s, pxd, full_module_name)

$ cython -a itzi/swmm/swmm_c.pyx
/home/duque004/git/itzi/env/lib/python3.8/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /home/duque004/git/itzi/itzi/swmm/swmm_c.pyx
  tree = Parsing.p_module(s, pxd, full_module_name)

$ python setup.py build_ext --inplace
running build_ext
compiler: unix
building 'itzi.swmm.swmm_c' extension
[...]
copying build/lib.linux-x86_64-3.8/itzi/flow.cpython-38-x86_64-linux-gnu.so -> itzi
copying build/lib.linux-x86_64-3.8/itzi/swmm/swmm_c.cpython-38-x86_64-linux-gnu.so -> itzi/swmm