DIG-1434: Update htsget to Python 3.12

[daisieh]

Adding the environment variable as suggested here fixes the issue and now we can update python to 3.12.

[mshadbolt]

I get errors when I try to build uwsgi and pysam

There are a lot of errors but tried to search through logs to find things relevant:
uwsgi:

#9 50.62   Building wheel for uwsgi (setup.py): finished with status 'error'
#9 50.64   error: subprocess-exited-with-error
#9 50.64   
#9 50.64   × python setup.py bdist_wheel did not run successfully.
#9 50.64   │ exit code: 1
#9 50.64   ╰─> [299 lines of output]
#9 50.64       /usr/local/lib/python3.12/site-packages/setuptools/_distutils/dist.py:266: UserWarning: Unknown distribution option: 'descriptions'
#9 50.64         warnings.warn(msg)
#9 50.64       running bdist_wheel
#9 50.64       running build
#9 50.64       running build_py
#9 50.64       creating build
#9 50.64       creating build/lib
#9 50.64       copying uwsgidecorators.py -> build/lib
#9 50.64       /usr/local/lib/python3.12/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
#9 50.64       !!
#9 50.64       
#9 50.64               ********************************************************************************
#9 50.64               Please avoid running ``setup.py`` directly.
#9 50.64               Instead, use pypa/build, pypa/installer or other
#9 50.64               standards-based tools.
#9 50.64       
#9 50.64               See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
#9 50.64               ********************************************************************************
#9 50.64       
#9 50.64       !!
#9 50.64         self.initialize_options()
#9 50.64       installing to build/bdist.linux-aarch64/wheel
#9 50.64       running install
#9 50.64       using profile: buildconf/default.ini
#9 50.64       detected include path: ['/usr/lib/gcc/aarch64-linux-gnu/12/include', '/usr/local/include', '/usr/include/aarch64-linux-gnu', '/usr/include']
#9 50.64       Patching "bin_name" to properly install_scripts dir
...
[thread 2][gcc] core/cache.o
#9 50.64       core/lock.c: In function ‘uwsgi_lock_fast_init’:
#9 50.64       core/lock.c:114:17: warning: ‘pthread_mutexattr_setrobust_np’ is deprecated: pthread_mutexattr_setrobust_np is deprecated, use pthread_mutexattr_setrobust [-Wdeprecated-declarations]
#9 50.64         114 |                 if (pthread_mutexattr_setrobust(&attr, PTHREAD_MUTEX_ROBUST)) {
#9 50.64             |                 ^~
#9 50.64       In file included from /usr/include/features.h:489,
#9 50.64                        from /usr/include/aarch64-linux-gnu/bits/libc-header-start.h:33,
#9 50.64                        from /usr/include/stdio.h:27,
#9 50.64                        from ./uwsgi.h:165,
#9 50.64                        from core/lock.c:1:
#9 50.64       /usr/include/pthread.h:951:12: note: declared here
#9 50.64         951 | extern int __REDIRECT_NTH (pthread_mutexattr_setrobust_np,
#9 50.64             |            ^~~~~~~~~~~~~~
#9 50.64       core/lock.c: In function ‘uwsgi_lock_fast’:
#9 50.64       core/lock.c:176:17: warning: ‘pthread_mutex_consistent_np’ is deprecated: pthread_mutex_consistent_np is deprecated, use pthread_mutex_consistent [-Wdeprecated-declarations]
#9 50.64         176 |                 pthread_mutex_consistent((pthread_mutex_t *) uli->lock_ptr);
#9 50.64             |                 ^~~~~~~~~~~~~~~~~~~~~~~~
#9 50.64       /usr/include/pthread.h:859:12: note: declared here
#9 50.64         859 | extern int __REDIRECT_NTH (pthread_mutex_consistent_np, (pthread_mutex_t *),
#9 50.64             |            ^~~~~~~~~~~~~~
...
 50.64       [thread 2][gcc] plugins/python/wsgi_handlers.o
#9 50.64       plugins/python/python_plugin.c:138:9: warning: ‘Py_NoSiteFlag’ is deprecated [-Wdeprecated-declarations]
#9 50.64         138 |         {"no-site", no_argument, 0, "do not import site module", uwsgi_opt_true, &Py_NoSiteFlag, 0},
#9 50.64             |         ^
#9 50.64       In file included from /usr/local/include/python3.12/Python.h:48,
#9 50.64                        from plugins/python/uwsgi_python.h:4,
#9 50.64                        from plugins/python/python_plugin.c:1:
#9 50.64       /usr/local/include/python3.12/cpython/pydebug.h:14:37: note: declared here
#9 50.64          14 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_NoSiteFlag;
#9 50.64             |                                     ^~~~~~~~~~~~~
#9 50.64       plugins/python/python_plugin.c: In function ‘uwsgi_python_init’:
#9 50.64       plugins/python/python_plugin.c:239:17: warning: ‘Py_SetPythonHome’ is deprecated [-Wdeprecated-declarations]
#9 50.64         239 |                 Py_SetPythonHome(wpyhome);
#9 50.64             |                 ^~~~~~~~~~~~~~~~
#9 50.64       In file included from /usr/local/include/python3.12/Python.h:94:
#9 50.64       /usr/local/include/python3.12/pylifecycle.h:40:38: note: declared here
#9 50.64          40 | Py_DEPRECATED(3.11) PyAPI_FUNC(void) Py_SetPythonHome(const wchar_t *);
#9 50.64             |                                      ^~~~~~~~~~~~~~~~
#9 50.64       plugins/python/python_plugin.c:263:9: warning: ‘Py_SetProgramName’ is deprecated [-Wdeprecated-declarations]
#9 50.64         263 |         Py_SetProgramName(pname);
#9 50.64             |         ^~~~~~~~~~~~~~~~~
#9 50.64       /usr/local/include/python3.12/pylifecycle.h:37:38: note: declared here
#9 50.64          37 | Py_DEPRECATED(3.11) PyAPI_FUNC(void) Py_SetProgramName(const wchar_t *);
#9 50.64             |                                      ^~~~~~~~~~~~~~~~~
#9 50.64       plugins/python/python_plugin.c:269:9: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations]
#9 50.64         269 |         Py_OptimizeFlag = up.optimize;
#9 50.64             |         ^~~~~~~~~~~~~~~
#9 50.64       /usr/local/include/python3.12/cpython/pydebug.h:13:37: note: declared here
#9 50.64          13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag;
#9 50.64             |                                     ^~~~~~~~~~~~~~~
#9 50.64       plugins/python/python_plugin.c: In function ‘uwsgi_python_pre_uwsgi_fork’:
#9 50.64       plugins/python/python_plugin.c:1327:17: error: too few arguments to function ‘_PyImport_AcquireLock’
#9 50.64        1327 |                 _PyImport_AcquireLock();
#9 50.64             |                 ^~~~~~~~~~~~~~~~~~~~~
#9 50.64       In file included from /usr/local/include/python3.12/import.h:91,
#9 50.64                        from /usr/local/include/python3.12/Python.h:99:
#9 50.64       /usr/local/include/python3.12/cpython/import.h:13:18: note: declared here
#9 50.64          13 | PyAPI_FUNC(void) _PyImport_AcquireLock(PyInterpreterState *interp);
#9 50.64             |                  ^~~~~~~~~~~~~~~~~~~~~
#9 50.64       plugins/python/python_plugin.c: In function ‘uwsgi_python_post_uwsgi_fork’:
#9 50.64       plugins/python/python_plugin.c:1339:25: error: too few arguments to function ‘_PyImport_ReleaseLock’
#9 50.64        1339 |                         _PyImport_ReleaseLock();
#9 50.64             |                         ^~~~~~~~~~~~~~~~~~~~~
#9 50.64       /usr/local/include/python3.12/cpython/import.h:14:17: note: declared here
#9 50.64          14 | PyAPI_FUNC(int) _PyImport_ReleaseLock(PyInterpreterState *interp);
#9 50.64             |                 ^~~~~~~~~~~~~~~~~~~~~
#9 50.64       plugins/python/python_plugin.c: In function ‘uwsgi_python_suspend’:
#9 50.64       plugins/python/python_plugin.c:1596:78: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘recursion_remaining’; did you mean ‘c_recursion_remaining’?
#9 50.64        1596 |                 up.current_recursion_remaining[wsgi_req->async_id] = tstate->recursion_remaining;
#9 50.64             |                                                                              ^~~~~~~~~~~~~~~~~~~
#9 50.64             |                                                                              c_recursion_remaining
#9 50.64       plugins/python/python_plugin.c:1605:63: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘recursion_remaining’; did you mean ‘c_recursion_remaining’?
#9 50.64        1605 |                 up.current_main_recursion_remaining = tstate->recursion_remaining;
#9 50.64             |                                                               ^~~~~~~~~~~~~~~~~~~
#9 50.64             |                                                               c_recursion_remaining
#9 50.64       plugins/python/python_plugin.c: In function ‘uwsgi_python_resume’:
#9 50.64       plugins/python/python_plugin.c:1839:25: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘recursion_remaining’; did you mean ‘c_recursion_remaining’?
#9 50.64        1839 |                 tstate->recursion_remaining = up.current_recursion_remaining[wsgi_req->async_id];
#9 50.64             |                         ^~~~~~~~~~~~~~~~~~~
#9 50.64             |                         c_recursion_remaining
#9 50.64       plugins/python/python_plugin.c:1848:25: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘recursion_remaining’; did you mean ‘c_recursion_remaining’?
#9 50.64        1848 |                 tstate->recursion_remaining = up.current_main_recursion_remaining;
#9 50.64             |                         ^~~~~~~~~~~~~~~~~~~
#9 50.64             |                         c_recursion_remaining
#9 50.64       plugins/python/pyutils.c: In function ‘init_pyargv’:
#9 50.64       plugins/python/pyutils.c:391:9: warning: ‘PySys_SetArgv’ is deprecated [-Wdeprecated-declarations]
#9 50.64         391 |         PySys_SetArgv(up.argc, up.py_argv);
#9 50.64             |         ^~~~~~~~~~~~~
#9 50.64       In file included from /usr/local/include/python3.12/Python.h:96,
#9 50.64                        from plugins/python/uwsgi_python.h:4,
#9 50.64                        from plugins/python/pyutils.c:1:
#9 50.64       /usr/local/include/python3.12/sysmodule.h:13:38: note: declared here
#9 50.64          13 | Py_DEPRECATED(3.11) PyAPI_FUNC(void) PySys_SetArgv(int, wchar_t **);
#9 50.64             |                                      ^~~~~~~~~~~~~
#9 50.64       [end of output]

Since there were so many errors with uwsgi, I can only see the end of the pysam logs
pysam:

#9 42.02       pysam/libchtslib.c: In function ‘__Pyx_PyInt_As_long’:
#9 42.02       pysam/libchtslib.c:19943:53: error: ‘PyLongObject’ {aka ‘struct _longobject’} has no member named ‘ob_digit’
#9 42.02       19943 |             const digit* digits = ((PyLongObject*)x)->ob_digit;
#9 42.02             |                                                     ^~
#9 42.02       pysam/libchtslib.c:19998:53: error: ‘PyLongObject’ {aka ‘struct _longobject’} has no member named ‘ob_digit’
#9 42.02       19998 |             const digit* digits = ((PyLongObject*)x)->ob_digit;
#9 42.02             |                                                     ^~
#9 42.02       pysam/libchtslib.c: In function ‘__Pyx_PyIndex_AsSsize_t’:
#9 42.02       pysam/libchtslib.c:20503:45: error: ‘PyLongObject’ {aka ‘struct _longobject’} has no member named ‘ob_digit’
#9 42.02       20503 |     const digit* digits = ((PyLongObject*)b)->ob_digit;
#9 42.02             |                                             ^~
#9 42.02       error: command '/usr/bin/gcc' failed with exit code 1
#9 42.02       [end of output]
#9 42.02   
#9 42.02   note: This error originates from a subprocess, and is likely not a problem with pip.
#9 42.03   Running setup.py clean for pysam
#9 42.03   ERROR: Failed building wheel for pysam

seems like maybe a lot of things related to c compiler?

[mshadbolt]

build worked after properly updating and rebuilding