pip install --no-binary h5py 'firedrake[check]' fails on MacOS

[postmortes]

Running on an Apple M3 MacBook Air, Sequoia 15.4.1 and following the installation instructions from https://www.firedrakeproject.org/install.html#installing-firedrake-using-pip

Python version is 3.12.0, also tried with 3.13.0

Got most of the way there, updated everything on the system, and then fell at what feels like the final hurdle. The output from the commmand is below (sorry about the length). There's a complaint about Cython, and that now seems to be the real problem.

UPDATE: originally I noted that there were issues with libsupermesh and libspatialindex -- this turned out to be anaconda "lying" to me. Despite it having been instructed to update itself, it hadn't, and was using an old version with old files from an Intel-CPU machine. Uninstalling and reinstalling solved that problem, but the Cython issue remains and is preventing the creation of the petsc4py wheel.

---

(venv-firedrake) MacBook-Air:~ beelzebub$ pip install --no-binary h5py 'firedrake[check]'
Collecting firedrake[check]
Using cached firedrake-2025.4.0.post0.tar.gz (894 kB)
Installing build dependencies ... error
error: subprocess-exited-with-error

× pip subprocess to install build dependencies did not run successfully.
│ exit code: 1
╰─> [78 lines of output]
Ignoring mpi4py: markers 'python_version < "3.13"' don't match your environment
Collecting Cython>=3.0
Using cached cython-3.1.0-cp313-cp313-macosx_11_0_arm64.whl.metadata (30 kB)
Collecting libsupermesh
Using cached libsupermesh-2025.3.0-cp313-cp313-macosx_15_0_arm64.whl
Collecting mpi4py>3
Using cached mpi4py-4.0.3-cp313-cp313-macosx_15_0_arm64.whl
Collecting numpy
Using cached numpy-2.2.5-cp313-cp313-macosx_14_0_arm64.whl.metadata (62 kB)
Collecting pkgconfig
Using cached pkgconfig-1.5.5-py3-none-any.whl.metadata (4.0 kB)
Collecting pybind11
Using cached pybind11-2.13.6-py3-none-any.whl.metadata (9.5 kB)
Collecting setuptools>61.2
Using cached setuptools-80.4.0-py3-none-any.whl.metadata (6.5 kB)
Collecting petsc4py==3.23.0
Using cached petsc4py-3.23.0.tar.gz (437 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 rtree>=1.2
Using cached rtree-1.4.0-py3-none-macosx_11_0_arm64.whl.metadata (2.1 kB)
Using cached cython-3.1.0-cp313-cp313-macosx_11_0_arm64.whl (2.8 MB)
Using cached numpy-2.2.5-cp313-cp313-macosx_14_0_arm64.whl (5.1 MB)
Using cached pkgconfig-1.5.5-py3-none-any.whl (6.7 kB)
Using cached pybind11-2.13.6-py3-none-any.whl (243 kB)
Using cached setuptools-80.4.0-py3-none-any.whl (1.2 MB)
Using cached rtree-1.4.0-py3-none-macosx_11_0_arm64.whl (439 kB)
Building wheels for collected packages: petsc4py
Building wheel for petsc4py (pyproject.toml): started
Building wheel for petsc4py (pyproject.toml): finished with status 'error'
error: subprocess-exited-with-error

    × Building wheel for petsc4py (pyproject.toml) did not run successfully.
    │ exit code: 1
    ╰─> [33 lines of output]
        running bdist_wheel
        running build
        running build_src
        using Cython 3.1.0
        cythonizing 'petsc4py/PETSc.pyx' -> 'petsc4py/PETSc.c'
        warning: petsc4py/PETSc/petscis.pxi:198:4: '__getsegcount__' relates to the old Python 2 buffer protocol and is no longer used.
        warning: petsc4py/PETSc/petscis.pxi:203:4: '__getreadbuffer__' relates to the old Python 2 buffer protocol and is no longer used.
        warning: petsc4py/PETSc/petscvec.pxi:588:4: '__getsegcount__' relates to the old Python 2 buffer protocol and is no longer used.
        warning: petsc4py/PETSc/petscvec.pxi:593:4: '__getreadbuffer__' relates to the old Python 2 buffer protocol and is no longer used.
        warning: petsc4py/PETSc/petscvec.pxi:598:4: '__getwritebuffer__' relates to the old Python 2 buffer protocol and is no longer used.
  
        Error compiling Cython file:
        ------------------------------------------------------------
        ...
  
            @classmethod
            def Print(
                cls,
                *args: Any,
                sep: str = ' ',
                           ^
        ------------------------------------------------------------
  
        petsc4py/PETSc/Sys.pyx:159:19: Compiler crash in ExpressionWriter
  
  
        Compiler crash traceback from this point on:
          File "Cython/Compiler/Visitor.py", line 174, in Cython.Compiler.Visitor.TreeVisitor._visit
          File "/private/var/folders/c5/4hqcgj397bdb_8zffwl7ytfh0000gn/T/pip-install-gnpy1b5f/petsc4py_75d15752d5be4b24b6f0c9ffac360ce1/conf/cyautodoc.py", line 28, in visit_UnicodeNode
            self.emit_string(node, '')
            ^^^^^^^^^^^^^^^^
        AttributeError: 'ExpressionWriter' object has no attribute 'emit_string'
        error: Cython failure: 'petsc4py/PETSc.pyx' -> 'petsc4py/PETSc.c'
        [end of output]
  
    note: This error originates from a subprocess, and is likely not a problem with pip.
    ERROR: Failed building wheel for petsc4py
  Failed to build petsc4py
  ERROR: Failed to build installable wheels for some pyproject.toml based projects (petsc4py)
  [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.

[connorjward]

This is a known issue. We have just rebuilt the documentation with a temporary workaround (setting PIP_CONSTRAINT).

[postmortes]

Awesome! That's done the trick, and firedrake has successfully built now, thank-you!