Fix Apple Silicon install: update build deps, guard volesti intrinsics, fix setup.py flags

[Mohit-Lakra]

Fixes #124
This PR removes the blockers I described above:

• [build-system] now depends on setuptools and numpy>=1.23.5,<2, so Poetry can fetch a wheel that exists on Python
  3.11. The lockfile is updated so sparseqr points to commit 535df76 (v1.4.1), which builds on arm64.
• volesti/external/PackedCSparse/FloatArray.h only includes <immintrin.h> when the compiler actually defines SSE/AVX
  macros, and the .template qualifiers in volesti/include/sampling/mmcs.hpp and parallel_mmcs.hpp are removed so clang
  accepts the code.
• setup.py sets -std=c++17 via CXXFLAGS instead of feeding it to the C compiler, keeping the lp_solve C sources on
  legal flags.

To reproduce the working setup on macOS 14.6 (M2), you need Homebrew’s GLPK/GMP/SWIG for swiglpk. Then:

one-time: install native deps

brew install glpk gmp swig

use Python 3.11 for the Poetry environment and point swiglpk at Homebrew’s include/lib

env -u CONDA_PREFIX -u CONDA_DEFAULT_ENV -u CONDA_SHLVL -u CONDA_PROMPT_MODIFIER
-u CONDA_EXE -u _CONDA_EXE -u _CONDA_ROOT -u CONDA_PYTHON_EXE -u _CE_CONDA -u _CE_M
GLPK_HEADER_PATH=/opt/homebrew/include
LDFLAGS="-L/opt/homebrew/lib"
CPPFLAGS="-I/opt/homebrew/include"
PATH="$HOME/.local/bin:$PATH"
poetry env use $(which python3.11)

env …same… poetry install
env …same… poetry run python tests/fba.py

Those commands now complete successfully. I also ran the other test scripts in tests/ (full_dimensional.py,
max_ball.py, scaling.py, rounding.py, sampling.py) under the same environment and they pass.

[Mohit-Lakra]

@vissarion, @TolisChal
I identified an issue where the build setup fails on Mac M-series systems, so I’ve submitted a PR to modernize setup.py and the related dependencies. This should fix the installation errors for those users. Happy to get a review when convenient.

[Mohit-Lakra]

Note for Reviewers: I have verified this builds successfully on macOS (M2) locally.

This PR currently focuses on the Python build system (setup.py, poetry). To fully compile the C++ extensions on macOS, a few patches are needed in the volesti submodule (guarding intrinsics for ARM64).

I can submit those C++ fixes as a separate upstream PR to volesti and update the submodule here once merged. Let me know if you prefer that workflow!

[Mohit-Lakra]

Verification Update: Full Success on macOS M2 (Apple Silicon)

I have successfully verified that this build correctly links the C++ backend and performs high-dimensional sampling on macOS ARM64.

The Test: I loaded the E. coli core model via cobra and passed the stoichiometric matrix directly to the dingo C++ engine to bypass file parser inconsistencies.