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mariomulansky / PySpike

Python implementation of spike distance metrics
http://mariomulansky.github.io/PySpike
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Build fails with Python 3.12 (Cython < 3) #73

Closed sanjayankur31 closed 4 weeks ago

sanjayankur31 commented 11 months ago

Given https://github.com/mariomulansky/PySpike/issues/70, I tried to build 0.8.0 with Cython < 3, but it looks like some changes are required to make pyspike support python 3.12. This is the build error we get:

O_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     17 | #warning "Using deprecated NumPy API, disable it with " \
        |  ^~~~~~~
  pyspike/cython/cython_add.c: In function ‘__pyx_memview_slice’:
  pyspike/cython/cython_add.c:14378:3: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations]
  14378 |   if (unlikely(!Py_OptimizeFlag)) {
        |   ^~
  In file included from /usr/include/python3.12/Python.h:48,
                   from pyspike/cython/cython_add.c:6:
  /usr/include/python3.12/cpython/pydebug.h:13:37: note: declared here
     13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag;
        |                                     ^~~~~~~~~~~~~~~
  gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-x86_64-cpython-312/pyspike/cython/cython_add.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-312/pyspike/cython/cython_add.cpython-312-x86_64-linux-gnu.so
  building 'pyspike.cython.cython_get_tau' extension
  gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/python3.12 -c pyspike/cython/cython_get_tau.c -o build/temp.linux-x86_64-cpython-312/pyspike/cython/cython_get_tau.o
  pyspike/cython/cython_get_tau.c: In function ‘__pyx_f_7pyspike_6cython_14cython_get_tau_get_tau’:
  pyspike/cython/cython_get_tau.c:2335:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   2335 |   __pyx_t_3 = ((__pyx_v_i < (__pyx_t_2 - 1)) != 0);
        |                           ^
  pyspike/cython/cython_get_tau.c:2392:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   2392 |   __pyx_t_3 = ((__pyx_v_j < (__pyx_t_2 - 1)) != 0);
        |                           ^
  pyspike/cython/cython_get_tau.c: In function ‘__pyx_memview_slice’:
  pyspike/cython/cython_get_tau.c:10064:3: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations]
  10064 |   if (unlikely(!Py_OptimizeFlag)) {
        |   ^~
  In file included from /usr/include/python3.12/Python.h:48,
                   from pyspike/cython/cython_get_tau.c:6:
  /usr/include/python3.12/cpython/pydebug.h:13:37: note: declared here
     13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag;
        |                                     ^~~~~~~~~~~~~~~
  gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-x86_64-cpython-312/pyspike/cython/cython_get_tau.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-312/pyspike/cython/cython_get_tau.cpython-312-x86_64-linux-gnu.so
  building 'pyspike.cython.cython_profiles' extension
  gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/python3.12 -c pyspike/cython/cython_profiles.c -o build/temp.linux-x86_64-cpython-312/pyspike/cython/cython_profiles.o
  In file included from /usr/lib64/python3.12/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
                   from /usr/lib64/python3.12/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                   from /usr/lib64/python3.12/site-packages/numpy/core/include/numpy/arrayobject.h:5,
                   from pyspike/cython/cython_profiles.c:750:
  /usr/lib64/python3.12/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     17 | #warning "Using deprecated NumPy API, disable it with " \
        |  ^~~~~~~
  pyspike/cython/cython_profiles.c: In function ‘__pyx_pf_7pyspike_6cython_15cython_profiles_2spike_profile_cython’:
  pyspike/cython/cython_profiles.c:4291:3: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations]
   4291 |   if (unlikely(!Py_OptimizeFlag)) {
        |   ^~
  In file included from /usr/include/python3.12/Python.h:48,
                   from pyspike/cython/cython_profiles.c:6:
  /usr/include/python3.12/cpython/pydebug.h:13:37: note: declared here
     13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag;
        |                                     ^~~~~~~~~~~~~~~
  pyspike/cython/cython_profiles.c:4307:3: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations]
   4307 |   if (unlikely(!Py_OptimizeFlag)) {
        |   ^~
  /usr/include/python3.12/cpython/pydebug.h:13:37: note: declared here
     13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag;
        |                                     ^~~~~~~~~~~~~~~
  pyspike/cython/cython_profiles.c: In function ‘__pyx_memview_slice’:
  pyspike/cython/cython_profiles.c:15712:3: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations]
  15712 |   if (unlikely(!Py_OptimizeFlag)) {
        |   ^~
  /usr/include/python3.12/cpython/pydebug.h:13:37: note: declared here
     13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag;
        |                                     ^~~~~~~~~~~~~~~
  gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-x86_64-cpython-312/pyspike/cython/cython_profiles.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-312/pyspike/cython/cython_profiles.cpython-312-x86_64-linux-gnu.so
  building 'pyspike.cython.cython_distances' extension
  gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/python3.12 -c pyspike/cython/cython_distances.c -o build/temp.linux-x86_64-cpython-312/pyspike/cython/cython_distances.o
  In file included from /usr/lib64/python3.12/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
                   from /usr/lib64/python3.12/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                   from /usr/lib64/python3.12/site-packages/numpy/core/include/numpy/arrayobject.h:5,
                   from pyspike/cython/cython_distances.c:750:
  /usr/lib64/python3.12/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     17 | #warning "Using deprecated NumPy API, disable it with " \
        |  ^~~~~~~
  pyspike/cython/cython_distances.c: In function ‘__pyx_pf_7pyspike_6cython_16cython_distances_2spike_distance_cython’:
  pyspike/cython/cython_distances.c:4142:3: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations]
   4142 |   if (unlikely(!Py_OptimizeFlag)) {
        |   ^~
  In file included from /usr/include/python3.12/Python.h:48,
                   from pyspike/cython/cython_distances.c:6:
  /usr/include/python3.12/cpython/pydebug.h:13:37: note: declared here
     13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag;
        |                                     ^~~~~~~~~~~~~~~
  pyspike/cython/cython_distances.c:4158:3: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations]
   4158 |   if (unlikely(!Py_OptimizeFlag)) {
        |   ^~
  /usr/include/python3.12/cpython/pydebug.h:13:37: note: declared here
     13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag;
        |                                     ^~~~~~~~~~~~~~~
  pyspike/cython/cython_distances.c: In function ‘__pyx_memview_slice’:
  pyspike/cython/cython_distances.c:15866:3: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations]
  15866 |   if (unlikely(!Py_OptimizeFlag)) {
        |   ^~
  /usr/include/python3.12/cpython/pydebug.h:13:37: note: declared here
     13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag;
        |                                     ^~~~~~~~~~~~~~~
  gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-x86_64-cpython-312/pyspike/cython/cython_distances.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-312/pyspike/cython/cython_distances.cpython-312-x86_64-linux-gnu.so
  building 'pyspike.cython.cython_directionality' extension
  gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/python3.12 -c pyspike/cython/cython_directionality.c -o build/temp.linux-x86_64-cpython-312/pyspike/cython/cython_directionality.o
  In file included from /usr/lib64/python3.12/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
                   from /usr/lib64/python3.12/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                   from /usr/lib64/python3.12/site-packages/numpy/core/include/numpy/arrayobject.h:5,
                   from pyspike/cython/cython_directionality.c:750:
  /usr/lib64/python3.12/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     17 | #warning "Using deprecated NumPy API, disable it with " \
        |  ^~~~~~~
  pyspike/cython/cython_directionality.c: In function ‘__pyx_memview_slice’:
  pyspike/cython/cython_directionality.c:13656:3: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations]
  13656 |   if (unlikely(!Py_OptimizeFlag)) {
        |   ^~
  In file included from /usr/include/python3.12/Python.h:48,
                   from pyspike/cython/cython_directionality.c:6:
  /usr/include/python3.12/cpython/pydebug.h:13:37: note: declared here
     13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag;
        |                                     ^~~~~~~~~~~~~~~
  gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-x86_64-cpython-312/pyspike/cython/cython_directionality.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-312/pyspike/cython/cython_directionality.cpython-312-x86_64-linux-gnu.so
  building 'pyspike.cython.cython_simulated_annealing' extension
  gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/lib64/python3.12/site-packages/numpy/core/include -I/usr/include/python3.12 -c pyspike/cython/cython_simulated_annealing.c -o build/temp.linux-x86_64-cpython-312/pyspike/cython/cython_simulated_annealing.o
  In file included from /usr/lib64/python3.12/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
                   from /usr/lib64/python3.12/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                   from /usr/lib64/python3.12/site-packages/numpy/core/include/numpy/arrayobject.h:5,
                   from pyspike/cython/cython_simulated_annealing.c:746:
  /usr/lib64/python3.12/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     17 | #warning "Using deprecated NumPy API, disable it with " \
        |  ^~~~~~~
  pyspike/cython/cython_simulated_annealing.c: In function ‘__pyx_pf_7pyspike_6cython_26cython_simulated_annealing_sim_ann_cython’:
  pyspike/cython/cython_simulated_annealing.c:2786:3: warning: ‘ma_version_tag’ is deprecated [-Wdeprecated-declarations]
   2786 |   __Pyx_GetModuleGlobalName(__pyx_t_3, __pyx_n_s_np); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 47, __pyx_L1_error)
        |   ^~~~~~~~~~~~~~~~~~~~~~~~~
  In file included from /usr/include/python3.12/dictobject.h:90,
                   from /usr/include/python3.12/Python.h:61,
                   from pyspike/cython/cython_simulated_annealing.c:6:
  /usr/include/python3.12/cpython/dictobject.h:22:34: note: declared here
     22 |     Py_DEPRECATED(3.12) uint64_t ma_version_tag;
        |                                  ^~~~~~~~~~~~~~
  pyspike/cython/cython_simulated_annealing.c:2791:3: warning: ‘ma_version_tag’ is deprecated [-Wdeprecated-declarations]
   2791 |   __Pyx_GetModuleGlobalName(__pyx_t_5, __pyx_n_s_np); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 47, __pyx_L1_error)
        |   ^~~~~~~~~~~~~~~~~~~~~~~~~
  /usr/include/python3.12/cpython/dictobject.h:22:34: note: declared here
     22 |     Py_DEPRECATED(3.12) uint64_t ma_version_tag;
        |                                  ^~~~~~~~~~~~~~
  pyspike/cython/cython_simulated_annealing.c:2872:3: warning: ‘ma_version_tag’ is deprecated [-Wdeprecated-declarations]
   2872 |   __Pyx_GetModuleGlobalName(__pyx_t_4, __pyx_n_s_np); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 48, __pyx_L1_error)
        |   ^~~~~~~~~~~~~~~~~~~~~~~~~
  /usr/include/python3.12/cpython/dictobject.h:22:34: note: declared here
     22 |     Py_DEPRECATED(3.12) uint64_t ma_version_tag;
        |                                  ^~~~~~~~~~~~~~
  pyspike/cython/cython_simulated_annealing.c: In function ‘__pyx_pf___pyx_MemviewEnum___reduce_cython__’:
  pyspike/cython/cython_simulated_annealing.c:6376:5: warning: ‘ma_version_tag’ is deprecated [-Wdeprecated-declarations]
   6376 |     __Pyx_GetModuleGlobalName(__pyx_t_4, __pyx_n_s_pyx_unpickle_Enum); if (unlikely(!__pyx_t_4)) __PYX_ERR(2, 13, __pyx_L1_error)
        |     ^~~~~~~~~~~~~~~~~~~~~~~~~
  /usr/include/python3.12/cpython/dictobject.h:22:34: note: declared here
     22 |     Py_DEPRECATED(3.12) uint64_t ma_version_tag;
        |                                  ^~~~~~~~~~~~~~
  pyspike/cython/cython_simulated_annealing.c:6422:5: warning: ‘ma_version_tag’ is deprecated [-Wdeprecated-declarations]
   6422 |     __Pyx_GetModuleGlobalName(__pyx_t_5, __pyx_n_s_pyx_unpickle_Enum); if (unlikely(!__pyx_t_5)) __PYX_ERR(2, 15, __pyx_L1_error)
        |     ^~~~~~~~~~~~~~~~~~~~~~~~~
  /usr/include/python3.12/cpython/dictobject.h:22:34: note: declared here
     22 |     Py_DEPRECATED(3.12) uint64_t ma_version_tag;
        |                                  ^~~~~~~~~~~~~~
  pyspike/cython/cython_simulated_annealing.c: In function ‘__pyx_memview_slice’:
  pyspike/cython/cython_simulated_annealing.c:11559:3: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations]
  11559 |   if (unlikely(!Py_OptimizeFlag)) {
        |   ^~
  In file included from /usr/include/python3.12/Python.h:48:
  /usr/include/python3.12/cpython/pydebug.h:13:37: note: declared here
     13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag;
        |                                     ^~~~~~~~~~~~~~~
  pyspike/cython/cython_simulated_annealing.c: In function ‘__Pyx_get_tp_dict_version’:
  pyspike/cython/cython_simulated_annealing.c:19262:5: warning: ‘ma_version_tag’ is deprecated [-Wdeprecated-declarations]
  19262 |     return likely(dict) ? __PYX_GET_DICT_VERSION(dict) : 0;
        |     ^~~~~~
  /usr/include/python3.12/cpython/dictobject.h:22:34: note: declared here
     22 |     Py_DEPRECATED(3.12) uint64_t ma_version_tag;
        |                                  ^~~~~~~~~~~~~~
  pyspike/cython/cython_simulated_annealing.c: In function ‘__Pyx_get_object_dict_version’:
  pyspike/cython/cython_simulated_annealing.c:19274:5: warning: ‘ma_version_tag’ is deprecated [-Wdeprecated-declarations]
  19274 |     return (dictptr && *dictptr) ? __PYX_GET_DICT_VERSION(*dictptr) : 0;
        |     ^~~~~~
  /usr/include/python3.12/cpython/dictobject.h:22:34: note: declared here
     22 |     Py_DEPRECATED(3.12) uint64_t ma_version_tag;
        |                                  ^~~~~~~~~~~~~~
  pyspike/cython/cython_simulated_annealing.c: In function ‘__Pyx_object_dict_version_matches’:
  pyspike/cython/cython_simulated_annealing.c:19278:5: warning: ‘ma_version_tag’ is deprecated [-Wdeprecated-declarations]
  19278 |     if (unlikely(!dict) || unlikely(tp_dict_version != __PYX_GET_DICT_VERSION(dict)))
        |     ^~
  /usr/include/python3.12/cpython/dictobject.h:22:34: note: declared here
     22 |     Py_DEPRECATED(3.12) uint64_t ma_version_tag;
        |                                  ^~~~~~~~~~~~~~
  pyspike/cython/cython_simulated_annealing.c: In function ‘__Pyx__GetModuleGlobalName’:
  pyspike/cython/cython_simulated_annealing.c:19295:5: warning: ‘ma_version_tag’ is deprecated [-Wdeprecated-declarations]
  19295 |     __PYX_UPDATE_DICT_CACHE(__pyx_d, result, *dict_cached_value, *dict_version)
        |     ^~~~~~~~~~~~~~~~~~~~~~~
  /usr/include/python3.12/cpython/dictobject.h:22:34: note: declared here
     22 |     Py_DEPRECATED(3.12) uint64_t ma_version_tag;
        |                                  ^~~~~~~~~~~~~~
  pyspike/cython/cython_simulated_annealing.c: In function ‘__Pyx_Raise’:
  pyspike/cython/cython_simulated_annealing.c:20026:34: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’
  20026 |         PyObject* tmp_tb = tstate->curexc_traceback;
        |                                  ^~
  pyspike/cython/cython_simulated_annealing.c:20029:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’
  20029 |             tstate->curexc_traceback = tb;
        |                   ^~
  pyspike/cython/cython_simulated_annealing.c: In function ‘__Pyx_PyUnicode_Equals’:
  pyspike/cython/cython_simulated_annealing.c:557:51: error: implicit declaration of function ‘_PyUnicode_Ready’; did you mean ‘PyUnicode_READY’? [-Werror=implicit-function-declaration]
    557 |                                               0 : _PyUnicode_Ready((PyObject *)(op)))
        |                                                   ^~~~~~~~~~~~~~~~
  pyspike/cython/cython_simulated_annealing.c:946:43: note: in definition of macro ‘unlikely’
    946 |   #define unlikely(x) __builtin_expect(!!(x), 0)
        |                                           ^
  pyspike/cython/cython_simulated_annealing.c:20143:22: note: in expansion of macro ‘__Pyx_PyUnicode_READY’
  20143 |         if (unlikely(__Pyx_PyUnicode_READY(s1) < 0) || unlikely(__Pyx_PyUnicode_READY(s2) < 0))
        |                      ^~~~~~~~~~~~~~~~~~~~~
  pyspike/cython/cython_simulated_annealing.c: In function ‘__Pyx_PyInt_AddObjC’:
  pyspike/cython/cython_simulated_annealing.c:20642:51: error: ‘PyLongObject’ {aka ‘struct _longobject’} has no member named ‘ob_digit’
  20642 |         const digit* digits = ((PyLongObject*)op1)->ob_digit;
        |                                                   ^~
  pyspike/cython/cython_simulated_annealing.c: In function ‘__Pyx_CLineForTraceback’:
  pyspike/cython/cython_simulated_annealing.c:21049:9: warning: ‘ma_version_tag’ is deprecated [-Wdeprecated-declarations]
  21049 |         __PYX_PY_DICT_LOOKUP_IF_MODIFIED(
        |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  /usr/include/python3.12/cpython/dictobject.h:22:34: note: declared here
     22 |     Py_DEPRECATED(3.12) uint64_t ma_version_tag;
        |                                  ^~~~~~~~~~~~~~
  pyspike/cython/cython_simulated_annealing.c:21049:9: warning: ‘ma_version_tag’ is deprecated [-Wdeprecated-declarations]
  21049 |         __PYX_PY_DICT_LOOKUP_IF_MODIFIED(
        |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  /usr/include/python3.12/cpython/dictobject.h:22:34: note: declared here
     22 |     Py_DEPRECATED(3.12) uint64_t ma_version_tag;
        |                                  ^~~~~~~~~~~~~~
  pyspike/cython/cython_simulated_annealing.c: In function ‘__Pyx_PyInt_As_long’:
  pyspike/cython/cython_simulated_annealing.c:22623:53: error: ‘PyLongObject’ {aka ‘struct _longobject’} has no member named ‘ob_digit’
  22623 |             const digit* digits = ((PyLongObject*)x)->ob_digit;
        |                                                     ^~
  pyspike/cython/cython_simulated_annealing.c:22678:53: error: ‘PyLongObject’ {aka ‘struct _longobject’} has no member named ‘ob_digit’
  22678 |             const digit* digits = ((PyLongObject*)x)->ob_digit;
        |                                                     ^~
  pyspike/cython/cython_simulated_annealing.c: In function ‘__Pyx_PyInt_As_int’:
  pyspike/cython/cython_simulated_annealing.c:22819:53: error: ‘PyLongObject’ {aka ‘struct _longobject’} has no member named ‘ob_digit’
  22819 |             const digit* digits = ((PyLongObject*)x)->ob_digit;
        |                                                     ^~
  pyspike/cython/cython_simulated_annealing.c:22874:53: error: ‘PyLongObject’ {aka ‘struct _longobject’} has no member named ‘ob_digit’
  22874 |             const digit* digits = ((PyLongObject*)x)->ob_digit;
        |                                                     ^~
  pyspike/cython/cython_simulated_annealing.c: In function ‘__Pyx_PyInt_As_char’:
  pyspike/cython/cython_simulated_annealing.c:23053:53: error: ‘PyLongObject’ {aka ‘struct _longobject’} has no member named ‘ob_digit’
  23053 |             const digit* digits = ((PyLongObject*)x)->ob_digit;
        |                                                     ^~
  pyspike/cython/cython_simulated_annealing.c:23108:53: error: ‘PyLongObject’ {aka ‘struct _longobject’} has no member named ‘ob_digit’
  23108 |             const digit* digits = ((PyLongObject*)x)->ob_digit;
        |                                                     ^~
  pyspike/cython/cython_simulated_annealing.c: In function ‘__Pyx_PyIndex_AsSsize_t’:
  pyspike/cython/cython_simulated_annealing.c:23459:45: error: ‘PyLongObject’ {aka ‘struct _longobject’} has no member named ‘ob_digit’
  23459 |     const digit* digits = ((PyLongObject*)b)->ob_digit;
        |                                             ^~
  cc1: some warnings being treated as errors
  error: command '/usr/bin/gcc' failed with exit code 1
  error: subprocess-exited-with-error

  × Building wheel for pyspike (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> See above for output.

  note: This error originates from a subprocess, and is likely not a problem with pip.
  full command: /usr/bin/python3 /usr/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py build_wheel /builddir/build/BUILD/PySpike-0.8.0/.pyproject-builddir/tmphottif77
  cwd: /builddir/build/BUILD/PySpike-0.8.0
  Building wheel for pyspike (pyproject.toml): finished with status 'error'
  ERROR: Failed building wheel for pyspike
Failed to build pyspike
ERROR: Failed to build one or more wheels

I think a few of these are using cpython internals which have changed in 3.12. I see there's some discussion about this here, but I don't know what the fix is at the moment:

https://github.com/cython/cython/issues/5238

I think the issue has been fixed in Cython 3, so a fix would be to update pyspike to work with that?

https://cython.readthedocs.io/en/latest/src/userguide/migrating_to_cy30.html

thomaskreuz commented 4 months ago

Sorry for the late reply.

We addressed #70 with PR #75. Could you please let us know if this is now resolved as well or if you still get the same error message. Thanks a lot!

thomaskreuz commented 4 months ago

Does this mean we can close the issue?

Thanks!

sanjayankur31 commented 4 weeks ago

Yes, we're carrying the patch and that fixes our builds.