Build issue on MacOs app 10.5 for installation of surface_dynamics package

[farbulu94]

I have successfully installed SageMath 10.5 using a disk image as mentioned here.
However, when trying to install this version of the package surface_dynamics via sage -pip install surface_dynamics, I encountered an error.
Any help would be greatly appreciated!

System Information

• MacBook Pro 2017, Intel Core 5, macOS Big Sur Version 11.6.2
• Xcode version 13.2
• Clang version: Apple clang version 13.0.0 (clang-1300.0.29.30) Target: x86_64-apple-darwin20.6.0 Thread model: posix InstalledDir: /Library/Developer/CommandLineTools/usr/bin

The full command error is

sage -pip install surface_dynamics
Collecting surface_dynamics
  Using cached surface_dynamics-0.7.0.tar.gz (8.4 MB)
  Installing build dependencies ... error
  error: subprocess-exited-with-error
  
  × pip subprocess to install build dependencies did not run successfully.
  │ exit code: 1
  ╰─> [105 lines of output]
      Collecting setuptools>=42
        Using cached setuptools-75.8.0-py3-none-any.whl.metadata (6.7 kB)
      Collecting wheel
        Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
      Collecting Cython
        Using cached Cython-3.0.12-cp312-cp312-macosx_10_9_x86_64.whl.metadata (3.5 kB)
      Collecting numpy
        Using cached numpy-2.2.3-cp312-cp312-macosx_10_13_x86_64.whl.metadata (62 kB)
      Collecting cypari2
        Using cached cypari2-2.2.1.tar.gz (127 kB)
        Installing build dependencies: started
        Installing build dependencies: finished with status 'done'
        Getting requirements to build wheel: started
        Getting requirements to build wheel: finished with status 'done'
        Preparing metadata (pyproject.toml): started
        Preparing metadata (pyproject.toml): finished with status 'done'
      Collecting cysignals>=1.11.3 (from cypari2)
        Using cached cysignals-1.12.3-cp312-cp312-macosx_10_9_x86_64.whl.metadata (12 kB)
      Using cached setuptools-75.8.0-py3-none-any.whl (1.2 MB)
      Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
      Using cached Cython-3.0.12-cp312-cp312-macosx_10_9_x86_64.whl (3.3 MB)
      Using cached numpy-2.2.3-cp312-cp312-macosx_10_13_x86_64.whl (20.9 MB)
      Using cached cysignals-1.12.3-cp312-cp312-macosx_10_9_x86_64.whl (221 kB)
      Building wheels for collected packages: cypari2
        Building wheel for cypari2 (pyproject.toml): started
        Building wheel for cypari2 (pyproject.toml): finished with status 'error'
        error: subprocess-exited-with-error
      
        × Building wheel for cypari2 (pyproject.toml) did not run successfully.
        │ exit code: 1
        ╰─> [68 lines of output]
            running bdist_wheel
            running build
            running build_py
            creating build/lib.macosx-10.12-x86_64-cpython-312/cypari2
            copying cypari2/__init__.py -> build/lib.macosx-10.12-x86_64-cpython-312/cypari2
            running egg_info
            writing cypari2.egg-info/PKG-INFO
            writing dependency_links to cypari2.egg-info/dependency_links.txt
            writing requirements to cypari2.egg-info/requires.txt
            writing top-level names to cypari2.egg-info/top_level.txt
            reading manifest file 'cypari2.egg-info/SOURCES.txt'
            reading manifest template 'MANIFEST.in'
            warning: no previously-included files matching '*.c' found anywhere in distribution
            warning: no previously-included files matching '.gitignore' found anywhere in distribution
            warning: no previously-included files matching 'readthedocs*' found anywhere in distribution
            warning: no previously-included files matching '.install-pari.sh' found anywhere in distribution
            no previously-included directories found matching '.github'
            no previously-included directories found matching 'dist'
            adding license file 'LICENSE'
            writing manifest file 'cypari2.egg-info/SOURCES.txt'
            copying cypari2/closure.pxd -> build/lib.macosx-10.12-x86_64-cpython-312/cypari2
            copying cypari2/closure.pyx -> build/lib.macosx-10.12-x86_64-cpython-312/cypari2
            copying cypari2/convert.pxd -> build/lib.macosx-10.12-x86_64-cpython-312/cypari2
            copying cypari2/convert.pyx -> build/lib.macosx-10.12-x86_64-cpython-312/cypari2
            copying cypari2/custom_block.pyx -> build/lib.macosx-10.12-x86_64-cpython-312/cypari2
            copying cypari2/cypari.h -> build/lib.macosx-10.12-x86_64-cpython-312/cypari2
            copying cypari2/gen.pxd -> build/lib.macosx-10.12-x86_64-cpython-312/cypari2
            copying cypari2/gen.pyx -> build/lib.macosx-10.12-x86_64-cpython-312/cypari2
            copying cypari2/handle_error.pxd -> build/lib.macosx-10.12-x86_64-cpython-312/cypari2
            copying cypari2/handle_error.pyx -> build/lib.macosx-10.12-x86_64-cpython-312/cypari2
            copying cypari2/pari_instance.pxd -> build/lib.macosx-10.12-x86_64-cpython-312/cypari2
            copying cypari2/pari_instance.pyx -> build/lib.macosx-10.12-x86_64-cpython-312/cypari2
            copying cypari2/paridecl.pxd -> build/lib.macosx-10.12-x86_64-cpython-312/cypari2
            copying cypari2/paripriv.pxd -> build/lib.macosx-10.12-x86_64-cpython-312/cypari2
            copying cypari2/pycore_long.h -> build/lib.macosx-10.12-x86_64-cpython-312/cypari2
            copying cypari2/pycore_long.pxd -> build/lib.macosx-10.12-x86_64-cpython-312/cypari2
            copying cypari2/stack.pxd -> build/lib.macosx-10.12-x86_64-cpython-312/cypari2
            copying cypari2/stack.pyx -> build/lib.macosx-10.12-x86_64-cpython-312/cypari2
            copying cypari2/string_utils.pxd -> build/lib.macosx-10.12-x86_64-cpython-312/cypari2
            copying cypari2/string_utils.pyx -> build/lib.macosx-10.12-x86_64-cpython-312/cypari2
            copying cypari2/types.pxd -> build/lib.macosx-10.12-x86_64-cpython-312/cypari2
            copying cypari2/auto_paridecl.pxd -> build/lib.macosx-10.12-x86_64-cpython-312/cypari2
            running build_ext
            warning: cypari2/pari_instance.pyx:559:8: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
            warning: cypari2/pari_instance.pyx:1391:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
            Compiling cypari2/closure.pyx because it changed.
            Compiling cypari2/convert.pyx because it changed.
            Compiling cypari2/custom_block.pyx because it changed.
            Compiling cypari2/gen.pyx because it changed.
            Compiling cypari2/handle_error.pyx because it changed.
            Compiling cypari2/pari_instance.pyx because it changed.
            Compiling cypari2/stack.pyx because it changed.
            Compiling cypari2/string_utils.pyx because it changed.
            [1/8] Cythonizing cypari2/closure.pyx
            [2/8] Cythonizing cypari2/convert.pyx
            [3/8] Cythonizing cypari2/custom_block.pyx
            [4/8] Cythonizing cypari2/gen.pyx
            [5/8] Cythonizing cypari2/handle_error.pyx
            [6/8] Cythonizing cypari2/pari_instance.pyx
            [7/8] Cythonizing cypari2/stack.pyx
            [8/8] Cythonizing cypari2/string_utils.pyx
            building 'cypari2.closure' extension
            creating build/temp.macosx-10.12-x86_64-cpython-312/cypari2
            gcc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -g -O3 -Wall -Wno-unused -O2 -mmacosx-version-min=10.12 -mno-avx2 -mno-bmi2 -Icypari2 -I/private/var/folders/00/tlkkn7td1x523hnnlpc_cbj80000gn/T/pip-build-env-e_3k0chf/overlay/lib/python3.12/site-packages/cysignals -I/private/var/tmp/sage-10.5-current/local/include -I/private/var/tmp/sage-10.5-current/local/var/lib/sage/venv-python3.12.5/include/python3.12 -c cypari2/closure.c -o build/temp.macosx-10.12-x86_64-cpython-312/cypari2/closure.o
            gcc -bundle -undefined dynamic_lookup -L/private/var/tmp/sage-10.5-current/local/lib -L/private/var/tmp/sage-10.5-current/local/lib -ld_classic -Wl,-platform_version,macos,10.12,11.3 -L/private/var/tmp/sage-10.5-current/local/lib -L/private/var/tmp/sage-10.5-current/local/var/lib/sage/venv-python3.12.5/lib -L/private/var/tmp/sage-10.5-current/local/lib -L/private/var/tmp/sage-10.5-current/local/lib -ld_classic -Wl,-platform_version,macos,10.12,11.3 build/temp.macosx-10.12-x86_64-cpython-312/cypari2/closure.o -L/private/var/tmp/sage-10.5-current/local/lib -L/private/var/tmp/sage-10.5-current/local/lib64 -L/private/var/tmp/sage-10.5-current/local/var/lib/sage/venv-python3.12.5/lib -lgmp -lpari -o build/lib.macosx-10.12-x86_64-cpython-312/cypari2/closure.cpython-312-darwin.so
            ld: library not found for -ld_classic
            clang: error: linker command failed with exit code 1 (use -v to see invocation)
            error: command '/usr/bin/gcc' failed with exit code 1
            [end of output]
      
        note: This error originates from a subprocess, and is likely not a problem with pip.
        ERROR: Failed building wheel for cypari2
      Failed to build cypari2
      ERROR: Failed to build installable wheels for some pyproject.toml based projects (cypari2)
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× pip subprocess to install build dependencies 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.

Using the flags CC=clang, CXX=clang++ does not solve the problem.

This is Issue #115 for surface_dynamics.
After discussing with @videlec, we decided to try to install the package without installing the build dependency of cypari2.
For this I cloned the package via git clone https://github.com/flatsurf/surface-dynamics and replaced the second line
requires = ["setuptools>=42", "wheel", "Cython", "numpy", "cypari2"] in the file pyproject.toml by the line
requires = ["setuptools>=42", "wheel", "Cython", "numpy"], then installed the package via sage -pip install surface-dynamics/.
After this I no longer received an error for cypari2, however the command cimport did not find the .pxd files and also I received the warning pplpy not installed. Will not compile iet_family from setup.py, even though ppl and pplpy are installed.

The full command error at this point is is

sage -pip install surface-dynamics/
Processing ./surface-dynamics
  Installing build dependencies ... done
  Getting requirements to build wheel ... error
  error: subprocess-exited-with-error
  
  × Getting requirements to build wheel did not run successfully.
  │ exit code: 1
  ╰─> [332 lines of output]
      Warning: pplpy not installed. Will not compile iet_family.
      
      Error compiling Cython file:
      ------------------------------------------------------------
      ...
      # Otherwise we end up with the strange error
      #     sage: from .origami import Origami
      #     Traceback (most recent call last):
      #     ...
      #     AttributeError: 'module' object has no attribute 'ModuleElementWithMutability'
      cimport sage.structure.element
              ^
      ------------------------------------------------------------
      
      surface_dynamics/flat_surfaces/origamis/origami_dense.pyx:41:8: 'sage/structure/element.pxd' not found
      
      Error compiling Cython file:
      ------------------------------------------------------------
      ...
      #     Traceback (most recent call last):
      #     ...
      #     AttributeError: 'module' object has no attribute 'ModuleElementWithMutability'
      cimport sage.structure.element
      
      from sage.rings.integer cimport Integer, smallInteger
      ^
      ------------------------------------------------------------
      
      surface_dynamics/flat_surfaces/origamis/origami_dense.pyx:43:0: 'sage/rings/integer.pxd' not found
      
      Error compiling Cython file:
      ------------------------------------------------------------
      ...
      #     Traceback (most recent call last):
      #     ...
      #     AttributeError: 'module' object has no attribute 'ModuleElementWithMutability'
      cimport sage.structure.element
      
      from sage.rings.integer cimport Integer, smallInteger
      ^
      ------------------------------------------------------------
      
      surface_dynamics/flat_surfaces/origamis/origami_dense.pyx:43:0: 'sage/rings/integer/Integer.pxd' not found
      
      Error compiling Cython file:
      ------------------------------------------------------------
      ...
      #     Traceback (most recent call last):
      #     ...
      #     AttributeError: 'module' object has no attribute 'ModuleElementWithMutability'
      cimport sage.structure.element
      
      from sage.rings.integer cimport Integer, smallInteger
      ^
      ------------------------------------------------------------
      
      surface_dynamics/flat_surfaces/origamis/origami_dense.pyx:43:0: 'sage/rings/integer/smallInteger.pxd' not found
      
      Error compiling Cython file:
      ------------------------------------------------------------
      ...
              sage: lattice(sum(((m * b2).rows() for m in matrices), []))
              (2, 1, 1)
              sage: lattice(sum(((m * b3).rows() for m in matrices), []))
              (2, 1, 3)
          """
          cdef Integer zero = smallInteger(0)
               ^
      ------------------------------------------------------------
      
      surface_dynamics/flat_surfaces/origamis/origami_dense.pyx:163:9: 'Integer' is not a type identifier
      
      Error compiling Cython file:
      ------------------------------------------------------------
      ...
              (2, 1, 1)
              sage: lattice(sum(((m * b3).rows() for m in matrices), []))
              (2, 1, 3)
          """
          cdef Integer zero = smallInteger(0)
          cdef Integer one = smallInteger(1)
               ^
      ------------------------------------------------------------
      
      surface_dynamics/flat_surfaces/origamis/origami_dense.pyx:164:9: 'Integer' is not a type identifier
      
      Error compiling Cython file:
      ------------------------------------------------------------
      ...
              sage: lattice(sum(((m * b3).rows() for m in matrices), []))
              (2, 1, 3)
          """
          cdef Integer zero = smallInteger(0)
          cdef Integer one = smallInteger(1)
          cdef Integer a, m
               ^
      ------------------------------------------------------------
      
      surface_dynamics/flat_surfaces/origamis/origami_dense.pyx:165:9: 'Integer' is not a type identifier
      
      Error compiling Cython file:
      ------------------------------------------------------------
      ...
              sage: lattice(sum(((m * b2).rows() for m in matrices), []))
              (2, 1, 1)
              sage: lattice(sum(((m * b3).rows() for m in matrices), []))
              (2, 1, 3)
          """
          cdef Integer zero = smallInteger(0)
                              ^
      ------------------------------------------------------------
      
      surface_dynamics/flat_surfaces/origamis/origami_dense.pyx:163:24: 'smallInteger' is not a constant, variable or function identifier
      
      Error compiling Cython file:
      ------------------------------------------------------------
      ...
              (2, 1, 1)
              sage: lattice(sum(((m * b3).rows() for m in matrices), []))
              (2, 1, 3)
          """
          cdef Integer zero = smallInteger(0)
          cdef Integer one = smallInteger(1)
                             ^
      ------------------------------------------------------------
      
      surface_dynamics/flat_surfaces/origamis/origami_dense.pyx:164:23: 'smallInteger' is not a constant, variable or function identifier
      
      Error compiling Cython file:
      ------------------------------------------------------------
      ...
          # Clean the list w of vectors and remove the (0, 0) entries,
          # at the same time looking for vectors of the form (a, 0).
          a = zero
          i = 0
          while i < len(w):
              if not isinstance(w[i][0], Integer) or not isinstance(w[i][1], Integer):
                                         ^
      ------------------------------------------------------------
      
      surface_dynamics/flat_surfaces/origamis/origami_dense.pyx:179:35: 'Integer' is not a constant, variable or function identifier
      
      Error compiling Cython file:
      ------------------------------------------------------------
      ...
          # Clean the list w of vectors and remove the (0, 0) entries,
          # at the same time looking for vectors of the form (a, 0).
          a = zero
          i = 0
          while i < len(w):
              if not isinstance(w[i][0], Integer) or not isinstance(w[i][1], Integer):
                                                                             ^
      ------------------------------------------------------------
      
      surface_dynamics/flat_surfaces/origamis/origami_dense.pyx:179:71: 'Integer' is not a constant, variable or function identifier
      
      Error compiling Cython file:
      ------------------------------------------------------------
      ...
          # at the same time looking for vectors of the form (a, 0).
          a = zero
          i = 0
          while i < len(w):
              if not isinstance(w[i][0], Integer) or not isinstance(w[i][1], Integer):
                  w[i] = (Integer(w[i][0]), Integer(w[i][1]))
                          ^
      ------------------------------------------------------------
      
      surface_dynamics/flat_surfaces/origamis/origami_dense.pyx:180:20: 'Integer' is not a constant, variable or function identifier
      
      Error compiling Cython file:
      ------------------------------------------------------------
      ...
          # at the same time looking for vectors of the form (a, 0).
          a = zero
          i = 0
          while i < len(w):
              if not isinstance(w[i][0], Integer) or not isinstance(w[i][1], Integer):
                  w[i] = (Integer(w[i][0]), Integer(w[i][1]))
                                            ^
      ------------------------------------------------------------
      
      surface_dynamics/flat_surfaces/origamis/origami_dense.pyx:180:38: 'Integer' is not a constant, variable or function identifier
      
      Error compiling Cython file:
      ------------------------------------------------------------
      ...
                  h = 1
                  i = u[i]
                  while seen[i] == 0:
                      i = u[i]
                      h += 1
                  wh[j] = (smallInteger(w), smallInteger(h))
                           ^
      ------------------------------------------------------------
      
      surface_dynamics/flat_surfaces/origamis/origami_dense.pyx:844:21: 'smallInteger' is not a constant, variable or function identifier
      
      Error compiling Cython file:
      ------------------------------------------------------------
      ...
                  h = 1
                  i = u[i]
                  while seen[i] == 0:
                      i = u[i]
                      h += 1
                  wh[j] = (smallInteger(w), smallInteger(h))
                                            ^
      ------------------------------------------------------------
      
      surface_dynamics/flat_surfaces/origamis/origami_dense.pyx:844:38: 'smallInteger' is not a constant, variable or function identifier
      
      Error compiling Cython file:
      ------------------------------------------------------------
      ...
                      k = 1
                      while br_sg[u[j]] == 0:
                          i_to_tr[j] = k
                          j = r[j]
                          k += 1
                      periods.append((smallInteger(k), smallInteger(0)))
                                      ^
      ------------------------------------------------------------
      
      surface_dynamics/flat_surfaces/origamis/origami_dense.pyx:912:32: 'smallInteger' is not a constant, variable or function identifier
      
      Error compiling Cython file:
      ------------------------------------------------------------
      ...
                      k = 1
                      while br_sg[u[j]] == 0:
                          i_to_tr[j] = k
                          j = r[j]
                          k += 1
                      periods.append((smallInteger(k), smallInteger(0)))
                                                       ^
      ------------------------------------------------------------
      
      surface_dynamics/flat_surfaces/origamis/origami_dense.pyx:912:49: 'smallInteger' is not a constant, variable or function identifier
      
      Error compiling Cython file:
      ------------------------------------------------------------
      ...
                      j = i
                      k = 1
                      while i_to_tr[j] == -1:
                          j = u[j]
                          k += 1
                      periods.append((smallInteger(-i_to_tr[j]), k))
                                      ^
      ------------------------------------------------------------
      
      surface_dynamics/flat_surfaces/origamis/origami_dense.pyx:922:32: 'smallInteger' is not a constant, variable or function identifier
      
      Error compiling Cython file:
      ------------------------------------------------------------
      ...
      
                  sage: o = Origami('(1)(2)(3)', '(1,2,3)')
                  sage: o.is_reduced()
                  False
              """
              return self.lattice_of_periods() == (smallInteger(1), smallInteger(0), smallInteger(1))
                                                   ^
      ------------------------------------------------------------
      
      surface_dynamics/flat_surfaces/origamis/origami_dense.pyx:1043:45: 'smallInteger' is not a constant, variable or function identifier
      
      Error compiling Cython file:
      ------------------------------------------------------------
      ...
      
                  sage: o = Origami('(1)(2)(3)', '(1,2,3)')
                  sage: o.is_reduced()
                  False
              """
              return self.lattice_of_periods() == (smallInteger(1), smallInteger(0), smallInteger(1))
                                                                    ^
      ------------------------------------------------------------
      
      surface_dynamics/flat_surfaces/origamis/origami_dense.pyx:1043:62: 'smallInteger' is not a constant, variable or function identifier
      
      Error compiling Cython file:
      ------------------------------------------------------------
      ...
      
                  sage: o = Origami('(1)(2)(3)', '(1,2,3)')
                  sage: o.is_reduced()
                  False
              """
              return self.lattice_of_periods() == (smallInteger(1), smallInteger(0), smallInteger(1))
                                                                                     ^
      ------------------------------------------------------------
      
      surface_dynamics/flat_surfaces/origamis/origami_dense.pyx:1043:79: 'smallInteger' is not a constant, variable or function identifier
      
      Error compiling Cython file:
      ------------------------------------------------------------
      ...
              d = {}
              for b in blocks:
                  orbit = G.Orbit(b, libgap.OnSets)
                  action = G.Action(orbit, libgap.OnSets)
                  rr, uu = libgap.GeneratorsOfGroup(action)
                  d[frozenset(map(Integer, b))] = origami_from_gap_permutations(rr, uu)
                                  ^
      ------------------------------------------------------------
      
      surface_dynamics/flat_surfaces/origamis/origami_dense.pyx:2613:28: 'Integer' is not a constant, variable or function identifier
      [1/3] Cythonizing surface_dynamics/flat_surfaces/origamis/origami_dense.pyx
      Traceback (most recent call last):
        File "/Users/fial/Library/SageMath-10-5/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 389, in <module>
          main()
        File "/Users/fial/Library/SageMath-10-5/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 373, in main
          json_out["return_val"] = hook(**hook_input["kwargs"])
                                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/Users/fial/Library/SageMath-10-5/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 143, in get_requires_for_build_wheel
          return hook(config_settings)
                 ^^^^^^^^^^^^^^^^^^^^^
        File "/private/var/folders/00/tlkkn7td1x523hnnlpc_cbj80000gn/T/pip-build-env-tl92kt8q/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 334, in get_requires_for_build_wheel
          return self._get_build_requires(config_settings, requirements=[])
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/private/var/folders/00/tlkkn7td1x523hnnlpc_cbj80000gn/T/pip-build-env-tl92kt8q/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 304, in _get_build_requires
          self.run_setup()
        File "/private/var/folders/00/tlkkn7td1x523hnnlpc_cbj80000gn/T/pip-build-env-tl92kt8q/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 320, in run_setup
          exec(code, locals())
        File "<string>", line 85, in <module>
        File "/private/var/folders/00/tlkkn7td1x523hnnlpc_cbj80000gn/T/pip-build-env-tl92kt8q/overlay/lib/python3.12/site-packages/Cython/Build/Dependencies.py", line 1154, in cythonize
          cythonize_one(*args)
        File "/private/var/folders/00/tlkkn7td1x523hnnlpc_cbj80000gn/T/pip-build-env-tl92kt8q/overlay/lib/python3.12/site-packages/Cython/Build/Dependencies.py", line 1321, in cythonize_one
          raise CompileError(None, pyx_file)
      Cython.Compiler.Errors.CompileError: surface_dynamics/flat_surfaces/origamis/origami_dense.pyx
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× Getting requirements to build wheel 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.

Finally, I decided to deactivate all compiled modules in surface_dynamics, that is, I replaced all the content in setup.py by the lines
from setuptools import setup setup()
and modified some .py files of the package to make it work, after this I could finally use some of the features of surface_dynamics.

[culler]

There should be no reason to rebuild any of the depencies, like cypari2, which are already installed in Sage_macOS.

Apparently you had downloaded the source code for the surface_dynamics package. I would
expect that running
sage -python -m pip install .
in the source directory would work to install the package. Alternatively cd to the source directory, start sage and run
%pip install .
at the sage prompt.

`

[NathanDunfield]

It looks like the build process the Cython modules of surface_dynamics is not finding certain Sage .pxd files it needs:

 surface_dynamics/*/origami_dense.pyx:43:0: 'sage/rings/integer.pxd' not found

The files are there, for example:

/var/tmp/sage-10.5-current/local/var/lib/sage/venv-python3.12.5/lib/python3.12/site-packages/sage/rings/integer.pxd

which is the expected location:

sage: sage.__path__
_NamespacePath(['/private/var/tmp/sage-10.5-current/local/var/lib/sage/venv-python3.12.5/lib/python3.12/site-packages/sage'])

[videlec]

I am confused by why the pip machinery tries to install or reinstall cypari2. It is listed as a build dependency in surface_dynamics pyproject.toml file

[build-system]
requires = ["setuptools>=42", "wheel", "Cython", "numpy", "cypari2"]
build-backend = "setuptools.build_meta"

Maybe the pip install command should be run with the --no-build-isolation option? Could the same build isolation be responsible for the failure to find sage .pxd files?

[culler]

@videlec - I think you found it!

When I ran
sage -python -m pip install --no-build-isolation .
from the surface-dynamics-0.7.0 directory the package built and installed without errors.

I do not know the cause of this yet. But I found that if I use sage -python -m venv to construct a venv then I am not able to load cypari2 from that venv.

I believe that using build-isolation means making a venv and doing the package build from the venv. If cypari2 cannot be loaded from such a venv it would explain why pip tries to build it. It also probably means that many other things will not be found, such as .pxd files.

[farbulu94]

There should be no reason to rebuild any of the depencies, like cypari2, which are already installed in Sage_macOS.

Apparently you had downloaded the source code for the surface_dynamics package. I would expect that running sage -python -m pip install . in the source directory would work to install the package. Alternatively cd to the source directory, start sage and run %pip install . at the sage prompt.

`

This finishes in essentially the same error

Building wheels for collected packages: cypari2
        Building wheel for cypari2 (pyproject.toml): started
        Building wheel for cypari2 (pyproject.toml): finished with status 'error'
        error: subprocess-exited-with-error
      
        × Building wheel for cypari2 (pyproject.toml) did not run successfully.

[NathanDunfield]

I believe that using build-isolation means making a venv and doing the package build from the venv. If cypari2 cannot be loaded from such a venv it would explain why pip tries to build it. It also probably means that many other things will not be found, such as .pxd files.

Yes, that's correct.

[culler]

One other thing that I noticed is that every directory in the Sage_macOS site-packages directory has the quarantine xattr set and those cannot be removed even by the root user. That is probably something that happens when you install a notarized app on macOS. This msy or may not be relevant to this problem, but I suspect it is.

I don't know for cereain why the venv does not work, but I have suspicions. I suspect that Apple's gatekeeper notices that the python executable in the venv is a symlink to the python executable in the notarized app and, because of that, denies permission to dynamically load any .so or .dylib files. When python says that cypari2 is not found it propbably means that cypari2 can not be loaded.

[NathanDunfield]

I don't know for cerain why the venv does not work, but I have suspicions. I suspect that Apple's gatekeeper notices that the python executable in the venv is a symlink to the python executable in the notarized app and, because of that, denies permission to dynamically load any .so or .dylib files. When python says that cypari2 is not found it propbably means that cypari2 can not be loaded.

I think this is not the issue. When you do pip install with the default level of build isolation, it creates a new venv and installs the packages listed in build-system.requires fresh off PyPI, even if some version of the package is available locally. Since cypari2 does not have binary wheels on PyPI, it's fetching the source and trying to build it and then failing for whatever reason.

[NathanDunfield]

Also, if one creates a venv which includes the "system site-packages" then cypari2 is available just fine:

$ sage -python -m venv --system-site-packages test_venv
$ test_venv/bin/python
Python 3.12.5 (main, Nov 27 2024, 22:50:56) [Clang 16.0.0 (clang-1600.0.26.4)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import cypari2
>>>

[culler]

I think I know the mechanism for the gatekeeper behavior.

When I notarize the app I have to explicitly give it an entitlement which allows it to load dynamic libraries without verifying the signature on the library (and requiring that the library has a matching signature or something like that). That entitlement is stored in the notarization certificate which is saved in the app bundle when the notarization is "stapled" (and available over the internet by querying Apple's notarization server).

But the venv python is not contained in any app bundle. So when you run the signed python executable from the venv, the gatekeeper looks for entitlements in its containing bundle, which does not exist, and therefore the gatekeeper denies permission to dynamically load anything. I notice that when I use the venv I am able to load modules from the lib-dynloads directory but I am not able to load anything in site-packages. So my explanation above is not complete, but I think it is approximately correct.

[culler]

Also, if one creates a venv which includes the "system site-packages" then cypari2 is available just fine:

WOW!

I think that means that my explanation is all wrong. The only difference between those two venvs is whether pvenv.cfg sets include-system-site-packages to true or false. So this is not a gatekeeper issue at all, and python is not lying. The difference is just whether python is allowed to look for site-packages outside of the venv. Of course it won't find cypari2 inside of the venv.

Frankly, that is a big relief for me!