Cython version requirements (are varying for different Python releases)

[tillea]

Hi,
Debian intends to migrate to Python 3.12. In a bug report some incompatibility with this Python version was stated. It would be great if you could make pysam compatible with the latest Python version.
Kind regards, Andreas.

[jmarshall]

The linked build log indicates that a version of Cython that is not compatible with Python 3.12 has been used.

[jmarshall]

Pysam's Cython requirement was bumped to >=0.29.12 when Python 3.8 was new, because that version was the first to adjust to some CPython 3.8 API changes:

0.29.12 (2019-07-07)
* Fix compile error in CPython 3.8b2 regarding the PyCode_New() signature.

For Python 3.10 onwards, in fact you need at least 0.29.24:

0.29.24 (2021-07-14)
* The tracing code was adapted to work with CPython 3.10.

And for Python 3.12, you need at least 3.0:

3.0.0 (2023-07-17)
* cython/cython#5450, not explicitly mentioned in CHANGES.rst (and tracing still doesn't actually work in 3.12)

(The linked full build log shows that Debian have tried to use Cython 0.29.36-1ubuntu2 with Python 3.12.)

So it's probably time we bumped our Cython requirements, or listed them per-version as something like (modulo syntax):

Cython>=0.29.12,<4
Cython>=0.29.24 ; python_version >= "3.10"
Cython>=3.0.0 ; python_version >= "3.12"

Or this can be simplified as we drop older Python versions in a similar time frame.

Many of these excess requirements are due to tracing, because pysam uses # cython: profile=True in its .pyx files even though probably vanishingly few of our users are actually using tracing. I have been meaning to remove that for a while, or at least make it configurable (and default to off) in setup() instead of hard-coding it via Cython directives. Without tracing, our Cython version requirements could also be greatly simplified.

Nonetheless, IMHO it's rapidly become foolish to use anything earlier than Cython 3 anyway.

[tillea]

Debian bug was closed with fixed with cython 3.0.5 Thanks a lot for your patience, Andreas.