BUG: cythonizing firedrake/cython/dmcommon.pyx fails with cython 3.0+

[francesco-ballarin]

Describe the bug
Cythonizing firedrake/cython/dmcommon.pyx fails with cython 3.0+

Steps to Reproduce
Upgrade cython to 3.0+ and try to install firedrake

Expected behavior
A successful cythonization

Error message

      [1/1] Cythonizing firedrake/cython/dmcommon.pyx
      warning: firedrake/cython/petschdr.pxi:8:0: 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
      warning: firedrake/cython/petschdr.pxi:160:48: The keyword 'nogil' should appear at the end of the function signature line. Placing it before 'except' or 'noexcept' will be disallowed in a future version of Cython.
      warning: firedrake/cython/dmcommon.pyx:993:42: Buffer unpacking not optimized away.
      warning: firedrake/cython/dmcommon.pyx:993:42: Buffer unpacking not optimized away.
      warning: firedrake/cython/dmcommon.pyx:2265:4: Buffer unpacking not optimized away.
      warning: firedrake/cython/dmcommon.pyx:2265:4: Buffer unpacking not optimized away.
      warning: firedrake/cython/dmcommon.pyx:2657:4: Buffer unpacking not optimized away.
      warning: firedrake/cython/dmcommon.pyx:2657:4: Buffer unpacking not optimized away.
      warning: firedrake/cython/dmcommon.pyx:2658:4: Buffer unpacking not optimized away.
      warning: firedrake/cython/dmcommon.pyx:2658:4: Buffer unpacking not optimized away.
      
      Error compiling Cython file:
      ------------------------------------------------------------
      ...
                      dim1 -= 1
                      break
              else:
                  raise RuntimeError("Found inconsistent fiat_cone and plex_cone")
          assert dim1 == 0
          return (2**dim) * eo + io
                               ^
      ------------------------------------------------------------
      
      firedrake/cython/dmcommon.pyx:989:25: Cannot assign type 'double' to 'PetscInt'
      
      Error compiling Cython file:
      ------------------------------------------------------------
      ...
                      cfacets[k].global_u = v[1]
                      cfacets[k].global_v = v[0]
                  cfacets[k].local_facet = f
                  k += 1
          CHKERR(PetscFree(facet_ranks))
          qsort(cfacets, offsets[0][nranks[0]], sizeof(CommFacet), &CommFacet_cmp)
                                                                   ^
      ------------------------------------------------------------
      
      firedrake/cython/dmcommon.pyx:2374:61: Cannot assign type 'int (*)(void *, void *) except? -1 nogil' to 'int (*)(const void *, const void *) noexcept nogil'. Exception values are incompatible. Suggest adding 'noexcept' to type 'int (void *, void *) except? -1 nogil'.
      
      Error compiling Cython file:
      ------------------------------------------------------------
      ...
              CHKERR(DMGetLabel(dm.dm, "ghost_region", &label))
              get_chart(dm.dm, &pStart, &pEnd)
              for p in range(nleaves):
                  CHKERR(DMLabelSetValue(label, ilocal[p], 1))
              CHKERR(DMLabelCreateIndex(label, pStart, pEnd))
          CHKERR(DMPlexSetAdjacencyUser(dm.dm, DMPlexGetAdjacency_Facet_Support, NULL))
                                               ^
      ------------------------------------------------------------
      
      firedrake/cython/dmcommon.pyx:3154:41: Cannot assign type 'int (PetscDM, PetscInt, PetscInt *, PetscInt *, void *) except? -1 nogil' to 'int (*)(PetscDM, PetscInt, PetscInt *, PetscInt *, void *) noexcept nogil'. Exception values are incompatible. Suggest adding 'noexcept' to type 'int (PetscDM, PetscInt, PetscInt *, PetscInt *, void *) except? -1 nogil'.
      
      Error compiling Cython file:
      ------------------------------------------------------------
      ...
                              for vi in range(nface_vertices):
                                  if cell_closure[cell,v] == face_vertices[vi]:
                                      incident = 1
                                      break
                              if incident == 0:
                                  face_indices[nfaces] += v * 10**(1-fi)
                                              ^
      ------------------------------------------------------------
      
      firedrake/cython/dmcommon.pyx:633:40: Cannot assign type 'double' to 'PetscInt'
      
      Error compiling Cython file:
      ------------------------------------------------------------
      ...
                  if plex_cone_copy[2 * j] == fiat_cone[2 * i] or plex_cone_copy[2 * j + 1] == fiat_cone[2 * i]:
                      if plex_cone_copy[2 * j] == fiat_cone[2 * i] and plex_cone_copy[2 * j + 1] == fiat_cone[2 * i + 1]:
                          # io += (2**(dim - 1 - i)) * 0
                          pass
                      elif plex_cone_copy[2 * j + 1] == fiat_cone[2 * i] and plex_cone_copy[2 * j] == fiat_cone[2 * i + 1]:
                          io += (2**(dim - 1 - i)) * 1
                          ^
      ------------------------------------------------------------
      
      firedrake/cython/dmcommon.pyx:977:20: Cannot assign type 'double' to 'PetscInt'
      Traceback (most recent call last):
        File "<string>", line 2, in <module>
        File "<pip-setuptools-caller>", line 34, in <module>
        File "/tmp/firedrake-src/setup.py", line 68, in <module>
          setup(name='firedrake',
        File "/usr/lib/python3/dist-packages/setuptools/__init__.py", line 108, in setup
          return distutils.core.setup(**attrs)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/usr/lib/python3/dist-packages/setuptools/_distutils/core.py", line 185, in setup
          return run_commands(dist)
                 ^^^^^^^^^^^^^^^^^^
        File "/usr/lib/python3/dist-packages/setuptools/_distutils/core.py", line 201, in run_commands
          dist.run_commands()
        File "/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py", line 969, in run_commands
          self.run_command(cmd)
        File "/usr/lib/python3/dist-packages/setuptools/dist.py", line 1213, in run_command
          super().run_command(command)
        File "/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py", line 988, in run_command
          cmd_obj.run()
        File "/usr/lib/python3/dist-packages/setuptools/command/install.py", line 68, in run
          return orig.install.run(self)
                 ^^^^^^^^^^^^^^^^^^^^^^
        File "/usr/lib/python3/dist-packages/setuptools/_distutils/command/install.py", line 698, in run
          self.run_command('build')
        File "/usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py", line 318, in run_command
          self.distribution.run_command(command)
        File "/usr/lib/python3/dist-packages/setuptools/dist.py", line 1213, in run_command
          super().run_command(command)
        File "/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py", line 988, in run_command
          cmd_obj.run()
        File "/usr/lib/python3/dist-packages/setuptools/_distutils/command/build.py", line 132, in run
          self.run_command(cmd_name)
        File "/usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py", line 318, in run_command
          self.distribution.run_command(command)
        File "/usr/lib/python3/dist-packages/setuptools/dist.py", line 1213, in run_command
          super().run_command(command)
        File "/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py", line 988, in run_command
          cmd_obj.run()
        File "/usr/lib/python3/dist-packages/setuptools/_distutils/command/build_ext.py", line 346, in run
          self.build_extensions()
        File "/usr/lib/python3/dist-packages/setuptools/_distutils/command/build_ext.py", line 468, in build_extensions
          self._build_extensions_serial()
        File "/usr/lib/python3/dist-packages/setuptools/_distutils/command/build_ext.py", line 494, in _build_extensions_serial
          self.build_extension(ext)
        File "/usr/local/lib/python3.11/dist-packages/Cython/Distutils/build_ext.py", line 122, in build_extension
          new_ext = cythonize(
                    ^^^^^^^^^^
        File "/usr/local/lib/python3.11/dist-packages/Cython/Build/Dependencies.py", line 1134, in cythonize
          cythonize_one(*args)
        File "/usr/local/lib/python3.11/dist-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one
          raise CompileError(None, pyx_file)
      Cython.Compiler.Errors.CompileError: firedrake/cython/dmcommon.pyx
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: legacy-install-failure

Environment:

• cython 3.0+

Additional Info
None

[francesco-ballarin]

This is to let you know that Google Colab will upgrade to Cython 3.0+ in the next few days, see
googlecolab/backend-info@bddc676

Once that upgrade is live I can probably try to downgrade to Cython 0.29 in my build environment, but this may come at the risk of breaking the firedrake installation in the runtime environment.

[connorjward]

This is fixed by #3290. Was fairly straightforward.

[francesco-ballarin]

#3546 has fixed this.