Can't install dev version on python3.12

[jlaehne]

When upgrading my development conda environment to python3.12 or python3.13, I can't install rosettasciio any more with pip install -e . and it seems to be caused by the cython parsing of the bruker plugin. Here is the relevant part of the error message:

...
      rsciio/bruker/unbcf_fast.c: In function '__pyx_pf_6rsciio_6bruker_10unbcf_fast_parse_to_numpy':
      rsciio/bruker/unbcf_fast.c:7318:3: warning: 'ma_version_tag' is deprecated [-Wdeprecated-declarations]
       7318 |   __Pyx_GetModuleGlobalName(__pyx_t_2, __pyx_n_s_np); if (unlikely(!__pyx_t_2)) __PYX_ERR(1, 319, __pyx_L1_error)
            |   ^~~~~~~~~~~~~~~~~~~~~~~~~
      In file included from /home/me/.conda/envs/hyperspy-dev/include/python3.12/dictobject.h:90,
                       from /home/me/.conda/envs/hyperspy-dev/include/python3.12/Python.h:64,
                       from rsciio/bruker/unbcf_fast.c:19:
      /home/me/.conda/envs/hyperspy-dev/include/python3.12/cpython/dictobject.h:22:34: note: declared here
         22 |     Py_DEPRECATED(3.12) uint64_t ma_version_tag;
            |                                  ^~~~~~~~~~~~~~
      rsciio/bruker/unbcf_fast.c:7367:3: warning: 'ma_version_tag' is deprecated [-Wdeprecated-declarations]
       7367 |   __Pyx_GetModuleGlobalName(__pyx_t_1, __pyx_n_s_np); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 321, __pyx_L1_error)
            |   ^~~~~~~~~~~~~~~~~~~~~~~~~
      /home/me/.conda/envs/hyperspy-dev/include/python3.12/cpython/dictobject.h:22:34: note: declared here
         22 |     Py_DEPRECATED(3.12) uint64_t ma_version_tag;
            |                                  ^~~~~~~~~~~~~~
      rsciio/bruker/unbcf_fast.c:7423:3: warning: 'ma_version_tag' is deprecated [-Wdeprecated-declarations]
       7423 |   __Pyx_GetModuleGlobalName(__pyx_t_1, __pyx_n_s_np); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 324, __pyx_L1_error)
            |   ^~~~~~~~~~~~~~~~~~~~~~~~~
      /home/me/.conda/envs/hyperspy-dev/include/python3.12/cpython/dictobject.h:22:34: note: declared here
         22 |     Py_DEPRECATED(3.12) uint64_t ma_version_tag;
            |                                  ^~~~~~~~~~~~~~
      rsciio/bruker/unbcf_fast.c:7479:3: warning: 'ma_version_tag' is deprecated [-Wdeprecated-declarations]
       7479 |   __Pyx_GetModuleGlobalName(__pyx_t_1, __pyx_n_s_np); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 327, __pyx_L1_error)
            |   ^~~~~~~~~~~~~~~~~~~~~~~~~
      /home/me/.conda/envs/hyperspy-dev/include/python3.12/cpython/dictobject.h:22:34: note: declared here
         22 |     Py_DEPRECATED(3.12) uint64_t ma_version_tag;
            |                                  ^~~~~~~~~~~~~~
      rsciio/bruker/unbcf_fast.c: In function '__pyx_pf___pyx_MemviewEnum___reduce_cython__':
      rsciio/bruker/unbcf_fast.c:9726:5: warning: 'ma_version_tag' is deprecated [-Wdeprecated-declarations]
       9726 |     __Pyx_GetModuleGlobalName(__pyx_t_4, __pyx_n_s_pyx_unpickle_Enum); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 13, __pyx_L1_error)
            |     ^~~~~~~~~~~~~~~~~~~~~~~~~
      /home/me/.conda/envs/hyperspy-dev/include/python3.12/cpython/dictobject.h:22:34: note: declared here
         22 |     Py_DEPRECATED(3.12) uint64_t ma_version_tag;
            |                                  ^~~~~~~~~~~~~~
      rsciio/bruker/unbcf_fast.c:9772:5: warning: 'ma_version_tag' is deprecated [-Wdeprecated-declarations]
       9772 |     __Pyx_GetModuleGlobalName(__pyx_t_5, __pyx_n_s_pyx_unpickle_Enum); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 15, __pyx_L1_error)
            |     ^~~~~~~~~~~~~~~~~~~~~~~~~
      /home/me/.conda/envs/hyperspy-dev/include/python3.12/cpython/dictobject.h:22:34: note: declared here
         22 |     Py_DEPRECATED(3.12) uint64_t ma_version_tag;
            |                                  ^~~~~~~~~~~~~~
      rsciio/bruker/unbcf_fast.c: In function '__pyx_memview_slice':
      rsciio/bruker/unbcf_fast.c:14909:3: warning: 'Py_OptimizeFlag' is deprecated [-Wdeprecated-declarations]
      14909 |   if (unlikely(!Py_OptimizeFlag)) {
            |   ^~
      In file included from /home/me/.conda/envs/hyperspy-dev/include/python3.12/Python.h:48:
      /home/me/.conda/envs/hyperspy-dev/include/python3.12/cpython/pydebug.h:13:37: note: declared here
         13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag;
            |                                     ^~~~~~~~~~~~~~~
      rsciio/bruker/unbcf_fast.c: In function '__pyx_pymod_exec_unbcf_fast':
      rsciio/bruker/unbcf_fast.c:22375:3: warning: 'ma_version_tag' is deprecated [-Wdeprecated-declarations]
      22375 |   __Pyx_GetModuleGlobalName(__pyx_t_1, __pyx_n_s_sys); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 6, __pyx_L1_error)
            |   ^~~~~~~~~~~~~~~~~~~~~~~~~
      /home/me/.conda/envs/hyperspy-dev/include/python3.12/cpython/dictobject.h:22:34: note: declared here
         22 |     Py_DEPRECATED(3.12) uint64_t ma_version_tag;
            |                                  ^~~~~~~~~~~~~~
      rsciio/bruker/unbcf_fast.c: In function '__Pyx_Raise':
      rsciio/bruker/unbcf_fast.c:23089:34: error: 'PyThreadState' {aka 'struct _ts'} has no member named 'curexc_traceback'
      23089 |         PyObject* tmp_tb = tstate->curexc_traceback;
            |                                  ^~
      rsciio/bruker/unbcf_fast.c:23092:19: error: 'PyThreadState' {aka 'struct _ts'} has no member named 'curexc_traceback'
      23092 |             tstate->curexc_traceback = tb;
            |                   ^~
      rsciio/bruker/unbcf_fast.c: In function '__Pyx_get_tp_dict_version':
      rsciio/bruker/unbcf_fast.c:23575:5: warning: 'ma_version_tag' is deprecated [-Wdeprecated-declarations]
      23575 |     return likely(dict) ? __PYX_GET_DICT_VERSION(dict) : 0;
            |     ^~~~~~
      /home/me/.conda/envs/hyperspy-dev/include/python3.12/cpython/dictobject.h:22:34: note: declared here
         22 |     Py_DEPRECATED(3.12) uint64_t ma_version_tag;
            |                                  ^~~~~~~~~~~~~~
      rsciio/bruker/unbcf_fast.c: In function '__Pyx_get_object_dict_version':
      rsciio/bruker/unbcf_fast.c:23587:5: warning: 'ma_version_tag' is deprecated [-Wdeprecated-declarations]
      23587 |     return (dictptr && *dictptr) ? __PYX_GET_DICT_VERSION(*dictptr) : 0;
            |     ^~~~~~
      /home/me/.conda/envs/hyperspy-dev/include/python3.12/cpython/dictobject.h:22:34: note: declared here
         22 |     Py_DEPRECATED(3.12) uint64_t ma_version_tag;
            |                                  ^~~~~~~~~~~~~~
      rsciio/bruker/unbcf_fast.c: In function '__Pyx_object_dict_version_matches':
      rsciio/bruker/unbcf_fast.c:23591:5: warning: 'ma_version_tag' is deprecated [-Wdeprecated-declarations]
      23591 |     if (unlikely(!dict) || unlikely(tp_dict_version != __PYX_GET_DICT_VERSION(dict)))
            |     ^~
      /home/me/.conda/envs/hyperspy-dev/include/python3.12/cpython/dictobject.h:22:34: note: declared here
         22 |     Py_DEPRECATED(3.12) uint64_t ma_version_tag;
            |                                  ^~~~~~~~~~~~~~
      rsciio/bruker/unbcf_fast.c: In function '__Pyx__GetModuleGlobalName':
      rsciio/bruker/unbcf_fast.c:23608:5: warning: 'ma_version_tag' is deprecated [-Wdeprecated-declarations]
      23608 |     __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version)
            |     ^~~~~~~~~~~~~~~~~~~~~~~
      /home/me/.conda/envs/hyperspy-dev/include/python3.12/cpython/dictobject.h:22:34: note: declared here
         22 |     Py_DEPRECATED(3.12) uint64_t ma_version_tag;
            |                                  ^~~~~~~~~~~~~~
      rsciio/bruker/unbcf_fast.c: In function '__Pyx_PyUnicode_Equals':
      rsciio/bruker/unbcf_fast.c:570:51: error: implicit declaration of function '_PyUnicode_Ready'; did you mean 'PyUnicode_READY'? [-Wimplicit-function-declaration]
        570 |                                               0 : _PyUnicode_Ready((PyObject *)(op)))
            |                                                   ^~~~~~~~~~~~~~~~
      rsciio/bruker/unbcf_fast.c:951:43: note: in definition of macro 'unlikely'
        951 |   #define unlikely(x) __builtin_expect(!!(x), 0)
            |                                           ^
      rsciio/bruker/unbcf_fast.c:23896:22: note: in expansion of macro '__Pyx_PyUnicode_READY'
      23896 |         if (unlikely(__Pyx_PyUnicode_READY(s1) < 0) || unlikely(__Pyx_PyUnicode_READY(s2) < 0))
            |                      ^~~~~~~~~~~~~~~~~~~~~
      rsciio/bruker/unbcf_fast.c: In function '__Pyx_Import':
      rsciio/bruker/unbcf_fast.c:24299:21: warning: the comparison will always evaluate as 'true' for the pointer operand in '(char *)"rsciio.bruker.unbcf_fast" + 6' must not be NULL [-Waddress]
      24299 |             if ((1) && (strchr(__Pyx_MODULE_NAME, '.'))) {
            |                     ^~
      rsciio/bruker/unbcf_fast.c: In function '__Pyx_PyInt_AddObjC':
      rsciio/bruker/unbcf_fast.c:24458:51: error: 'PyLongObject' {aka 'struct _longobject'} has no member named 'ob_digit'
      24458 |         const digit* digits = ((PyLongObject*)op1)->ob_digit;
            |                                                   ^~
      rsciio/bruker/unbcf_fast.c: In function '__Pyx_CLineForTraceback':
      rsciio/bruker/unbcf_fast.c:24812:9: warning: 'ma_version_tag' is deprecated [-Wdeprecated-declarations]
      24812 |         __PYX_PY_DICT_LOOKUP_IF_MODIFIED(
            |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      /home/me/.conda/envs/hyperspy-dev/include/python3.12/cpython/dictobject.h:22:34: note: declared here
         22 |     Py_DEPRECATED(3.12) uint64_t ma_version_tag;
            |                                  ^~~~~~~~~~~~~~
      rsciio/bruker/unbcf_fast.c:24812:9: warning: 'ma_version_tag' is deprecated [-Wdeprecated-declarations]
      24812 |         __PYX_PY_DICT_LOOKUP_IF_MODIFIED(
            |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      /home/me/.conda/envs/hyperspy-dev/include/python3.12/cpython/dictobject.h:22:34: note: declared here
         22 |     Py_DEPRECATED(3.12) uint64_t ma_version_tag;
            |                                  ^~~~~~~~~~~~~~
      rsciio/bruker/unbcf_fast.c: In function '__Pyx_PyInt_As_int':
      rsciio/bruker/unbcf_fast.c:26039:53: error: 'PyLongObject' {aka 'struct _longobject'} has no member named 'ob_digit'
      26039 |             const digit* digits = ((PyLongObject*)x)->ob_digit;
            |                                                     ^~
      rsciio/bruker/unbcf_fast.c:26094:53: error: 'PyLongObject' {aka 'struct _longobject'} has no member named 'ob_digit'
      26094 |             const digit* digits = ((PyLongObject*)x)->ob_digit;
            |                                                     ^~
      rsciio/bruker/unbcf_fast.c: In function '__Pyx_PyInt_As_uint32_t':
      rsciio/bruker/unbcf_fast.c:26235:53: error: 'PyLongObject' {aka 'struct _longobject'} has no member named 'ob_digit'
      26235 |             const digit* digits = ((PyLongObject*)x)->ob_digit;
            |                                                     ^~
      rsciio/bruker/unbcf_fast.c:26290:53: error: 'PyLongObject' {aka 'struct _longobject'} has no member named 'ob_digit'
      26290 |             const digit* digits = ((PyLongObject*)x)->ob_digit;
            |                                                     ^~
      rsciio/bruker/unbcf_fast.c: In function '__Pyx_PyInt_As_uint64_t':
      rsciio/bruker/unbcf_fast.c:26431:53: error: 'PyLongObject' {aka 'struct _longobject'} has no member named 'ob_digit'
      26431 |             const digit* digits = ((PyLongObject*)x)->ob_digit;
            |                                                     ^~
      rsciio/bruker/unbcf_fast.c:26486:53: error: 'PyLongObject' {aka 'struct _longobject'} has no member named 'ob_digit'
      26486 |             const digit* digits = ((PyLongObject*)x)->ob_digit;
            |                                                     ^~
      rsciio/bruker/unbcf_fast.c: In function '__Pyx_PyInt_As_uint16_t':
      rsciio/bruker/unbcf_fast.c:26703:53: error: 'PyLongObject' {aka 'struct _longobject'} has no member named 'ob_digit'
      26703 |             const digit* digits = ((PyLongObject*)x)->ob_digit;
            |                                                     ^~
      rsciio/bruker/unbcf_fast.c:26758:53: error: 'PyLongObject' {aka 'struct _longobject'} has no member named 'ob_digit'
      26758 |             const digit* digits = ((PyLongObject*)x)->ob_digit;
            |                                                     ^~
      rsciio/bruker/unbcf_fast.c: In function '__Pyx_PyInt_As_long':
      rsciio/bruker/unbcf_fast.c:26975:53: error: 'PyLongObject' {aka 'struct _longobject'} has no member named 'ob_digit'
      26975 |             const digit* digits = ((PyLongObject*)x)->ob_digit;
            |                                                     ^~
      rsciio/bruker/unbcf_fast.c:27030:53: error: 'PyLongObject' {aka 'struct _longobject'} has no member named 'ob_digit'
      27030 |             const digit* digits = ((PyLongObject*)x)->ob_digit;
            |                                                     ^~
      rsciio/bruker/unbcf_fast.c: In function '__Pyx_PyInt_As_char':
      rsciio/bruker/unbcf_fast.c:27209:53: error: 'PyLongObject' {aka 'struct _longobject'} has no member named 'ob_digit'
      27209 |             const digit* digits = ((PyLongObject*)x)->ob_digit;
            |                                                     ^~
      rsciio/bruker/unbcf_fast.c:27264:53: error: 'PyLongObject' {aka 'struct _longobject'} has no member named 'ob_digit'
      27264 |             const digit* digits = ((PyLongObject*)x)->ob_digit;
            |                                                     ^~
      rsciio/bruker/unbcf_fast.c: In function '__Pyx_PyIndex_AsSsize_t':
      rsciio/bruker/unbcf_fast.c:27615:45: error: 'PyLongObject' {aka 'struct _longobject'} has no member named 'ob_digit'
      27615 |     const digit* digits = ((PyLongObject*)b)->ob_digit;
            |                                             ^~
      Traceback (most recent call last):
        File "/tmp/pip-build-env-qdqyn5m7/overlay/lib/python3.12/site-packages/setuptools/_distutils/spawn.py", line 70, in spawn
          subprocess.check_call(cmd, env=_inject_macos_ver(env))
        File "/home/me/.conda/envs/hyperspy-dev/lib/python3.12/subprocess.py", line 413, in check_call
          raise CalledProcessError(retcode, cmd)
      subprocess.CalledProcessError: Command '['/home/me/.conda/envs/hyperspy-dev/bin/gcc', '-pthread', '-B', '/home/me/.conda/envs/hyperspy-dev/compiler_compat', '-fno-strict-overflow', '-DNDEBUG', '-O2', '-Wall', '-fPIC', '-O2', '-isystem', '/home/me/.conda/envs/hyperspy-dev/include', '-fPIC', '-O2', '-isystem', '/home/me/.conda/envs/hyperspy-dev/include', '-fPIC', '-I/home/me/.conda/envs/hyperspy-dev/include/python3.12', '-c', 'rsciio/bruker/unbcf_fast.c', '-o', '/tmp/tmpmotbr_54.build-temp/rsciio/bruker/unbcf_fast.o']' returned non-zero exit status 1.
....
      error: command '/home/me/.conda/envs/hyperspy-dev/bin/gcc' failed with exit code 1

...

[ericpre]

This is surprising, because python 3.12 has been used for a while now (on CI, packaging, user install or dev install). python 3.13 is more recent but it seems to work fine on CI and when testing locally.

They must be something in your local install. Maybe try to figure out if your are using a C compiler or some dependencies that are not supported? Use CI as baseline to know what works?
Alternatively, it could be a "corrupted" install, something in setting path, activating python environment.