Fix unoptimized wheels

[marcelm]

setuptools starting from version 75.7.0 changed how CFLAGS work: They no longer are added to the CFLAGS Python was compiled with, but replace them.

With this change, our CFLAGS of -g0 -DNDEBUG get used directly and the wheels are compiled without proper optimizations because -O2 is missing.

Within cibuildwheel, the Python compiler options that we "lose" by this change are:

-fno-strict-overflow -Wsign-compare -DNDEBUG -g -O3 -Wall

Of these, we really only require -O3 and -DNDEBUG, so the easiest fix should be to just add -O3 to the CFLAGS that we provide.

Found by @rhpvorderman in marcelm/cutadapt#843

[rhpvorderman]

I checked all of the included pythons:

./cpython-3.11.12/bin/python
-Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall
./cpython-3.13.3/bin/python
-fno-strict-overflow -Wsign-compare -DNDEBUG -g -O3 -Wall
./cpython-3.10.17/bin/python
-Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall
./cpython-3.12.10/bin/python
-fno-strict-overflow -Wsign-compare -DNDEBUG -g -O3 -Wall
./cpython-3.14.0b1-nogil/bin/python
-fno-strict-overflow -Wsign-compare -DNDEBUG -g -O3 -Wall
./cpython-3.8.20/bin/python
-Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall
./cpython-3.13.3-nogil/bin/python
-fno-strict-overflow -Wsign-compare -DNDEBUG -g -O3 -Wall
./pp311-pypy311_pp73/bin/python
-DNDEBUG -O2
./cpython-3.14.0b1/bin/python
-fno-strict-overflow -Wsign-compare -DNDEBUG -g -O3 -Wall
./pp310-pypy310_pp73/bin/python
-DNDEBUG -O2
./cpython-3.9.22/bin/python
-Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall
./pipx/venvs/uv/bin/python
-fno-strict-overflow -Wsign-compare -DNDEBUG -g -O3 -Wall
./pipx/venvs/patchelf/bin/python
-fno-strict-overflow -Wsign-compare -DNDEBUG -g -O3 -Wall
./pipx/venvs/swig/lib/python3.12/site-packages/swig/data/share/swig/4.3.1/python
bash: ./pipx/venvs/swig/lib/python3.12/site-packages/swig/data/share/swig/4.3.1/python: Is a directory
./pipx/venvs/swig/bin/python
-fno-strict-overflow -Wsign-compare -DNDEBUG -g -O3 -Wall
./pipx/venvs/auditwheel/bin/python
-fno-strict-overflow -Wsign-compare -DNDEBUG -g -O3 -Wall
./pipx/venvs/cmake/bin/python
-fno-strict-overflow -Wsign-compare -DNDEBUG -g -O3 -Wall
./pipx/shared/bin/python
-fno-strict-overflow -Wsign-compare -DNDEBUG -g -O3 -Wall
./tools/bin/python
-fno-strict-overflow -Wsign-compare -DNDEBUG -g -O3 -Wall

Some of them allso use -fwrapv (guaranteeing that signed integers always wrap) but I don't think that is very relevant for our use cases. (In fact, I would set -fstrict-overflow, signed overflows are undefined, so they don't happen).

[marcelm]

Agreed, and thanks for checking! So ok to merge?

[rhpvorderman]

Yes! And thanks for looking at the CFLAGS. I will update sequali again. For now 1.0.1 with the "big wheels" is fine, but next release I want to make sure that the debug information is gone.

I will have the shakespearian dialogue with myself "To -O3 or not -O3" and decide whether I shall use -O3 or -O2 by default. O3 has better autovectorization, but is sometimes too greedy. I think I will go that route as greedy algorithms are usually quite favourable for our data (150 bp strings at least).