Can't pip install scipy on M1

Question

I can't "pip instal scipy" on my m1 mac, I get an error:

Collecting scipy
  Using cached scipy-1.7.3.tar.gz (36.1 MB)
  Installing build dependencies ... error
  error: subprocess-exited-with-error
  
  × pip subprocess to install build dependencies did not run successfully.
  │ exit code: 1
  ╰─> [3280 lines of output]
      Looking in indexes: https://pypi.org/simple, https://pypi.dev.project.com/pypi/, https://pypi.dev.project.com/pypi/
      Ignoring numpy: markers 'python_version == "3.7" and platform_machine == "aarch64"' don't match your environment
      Ignoring numpy: markers 'python_version == "3.8" and platform_machine == "aarch64"' don't match your environment
      Ignoring numpy: markers 'python_version == "3.8" and (platform_machine != "arm64" or platform_system != "Darwin") and platform_python_implementation != "PyPy"' don't match your environment
      Ignoring numpy: markers 'python_version == "3.9" and (platform_machine != "arm64" or platform_system != "Darwin") and platform_python_implementation != "PyPy"' don't match your environment
      Ignoring numpy: markers 'python_version == "3.10" and platform_python_implementation != "PyPy"' don't match your environment
      Ignoring numpy: markers 'python_version == "3.7" and platform_python_implementation == "PyPy"' don't match your environment
      Ignoring numpy: markers 'python_version == "3.8" and platform_python_implementation == "PyPy"' don't match your environment
      Ignoring numpy: markers 'python_version == "3.9" and platform_python_implementation == "PyPy"' don't match your environment
      Ignoring numpy: markers 'python_version == "3.10" and platform_python_implementation == "PyPy"' don't match your environment
      Collecting wheel<0.38.0
        Using cached wheel-0.37.1-py2.py3-none-any.whl (35 kB)
      Collecting setuptools<58.0.0
        Using cached setuptools-57.5.0-py3-none-any.whl (819 kB)
      Collecting Cython<3.0,>=0.29.18
        Using cached Cython-0.29.28-py2.py3-none-any.whl (983 kB)
      Collecting pybind11<2.8.0,>=2.4.3
        Using cached pybind11-2.7.1-py2.py3-none-any.whl (200 kB)
      Collecting pythran<0.10.0,>=0.9.12
        Using cached pythran-0.9.12.post1-py3-none-any.whl (4.3 MB)
      Collecting numpy==1.16.5
        Using cached numpy-1.16.5.zip (5.1 MB)
        Preparing metadata (setup.py): started
        Preparing metadata (setup.py): finished with status 'done'
      Collecting ply>=3.4
        Using cached ply-3.11-py2.py3-none-any.whl (49 kB)
      Collecting gast~=0.5.0
        Using cached gast-0.5.3-py3-none-any.whl (19 kB)
      Collecting beniget~=0.4.0
        Using cached beniget-0.4.1-py3-none-any.whl (9.4 kB)
      Building wheels for collected packages: numpy
        Building wheel for numpy (setup.py): started
        Building wheel for numpy (setup.py): finished with status 'error'
        error: subprocess-exited-with-error
      
        × python setup.py bdist_wheel did not run successfully.
        │ exit code: 1
        ╰─> [2943 lines of output]
            Running from numpy source directory.
            blas_opt_info:
            blas_mkl_info:
            customize UnixCCompiler
              libraries mkl_rt not found in ['/Users/danieljohnson/Documents/code/project/venv/lib', '/usr/local/lib', '/usr/lib']
              NOT AVAILABLE
      
            blis_info:
            customize UnixCCompiler
              libraries blis not found in ['/Users/danieljohnson/Documents/code/project/venv/lib', '/usr/local/lib', '/usr/lib']
              NOT AVAILABLE
      
            openblas_info:
            customize UnixCCompiler
            customize UnixCCompiler
              libraries openblas not found in ['/Users/danieljohnson/Documents/code/project/venv/lib', '/usr/local/lib', '/usr/lib']
              NOT AVAILABLE

... the end of the error is:

error: Command "clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -I/Users/danieljohnson/Documents/code/project/venv/lib/python3.7/site-packages/numpy/core/include -DNPY_INTERNAL_BUILD=1 -DHAVE_NPY_CONFIG_H=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE=1 -D_LARGEFILE64_SOURCE=1 -Inumpy/core/include -Ibuild/src.macosx-12.3-arm64-3.7/numpy/core/include/numpy -Inumpy/core/src/common -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/Users/danieljohnson/Documents/code/project/venv/include -I/Users/danieljohnson/.pyenv/versions/3.7.13/include/python3.7m -Ibuild/src.macosx-12.3-arm64-3.7/numpy/core/src/common -Ibuild/src.macosx-12.3-arm64-3.7/numpy/core/src/npymath -Ibuild/src.macosx-12.3-arm64-3.7/numpy/core/src/common -Ibuild/src.macosx-12.3-arm64-3.7/numpy/core/src/npymath -c build/src.macosx-12.3-arm64-3.7/numpy/core/src/multiarray/_multiarray_tests.c -o build/temp.macosx-12.3-arm64-3.7/build/src.macosx-12.3-arm64-3.7/numpy/core/src/multiarray/_multiarray_tests.o -MMD -MF build/temp.macosx-12.3-arm64-3.7/build/src.macosx-12.3-arm64-3.7/numpy/core/src/multiarray/_multiarray_tests.o.d" failed with exit status 1
            [end of output]
      
        note: This error originates from a subprocess, and is likely not a problem with pip.
      error: legacy-install-failure
      
      × Encountered error while trying to install package.
      ╰─> numpy
      
      note: This is an issue with the package mentioned above, not pip.
      hint: See above for output from the failure.
      [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.

I've tried pip and pip3 uninstalling numpy, using older versions, installing scypi with --no-deps.

I can import numpy in a python console.

A "pip show numpy" displays:

Name: numpy
Version: 1.21.6
Summary: NumPy is the fundamental package for array computing with Python.
Home-page: https://www.numpy.org
Author: Travis E. Oliphant et al.
Author-email: 
License: BSD
Location: /Users/danieljohnson/Documents/code/project/venv/lib/python3.7/site-packages
Requires: 
Required-by: pandas

I'm not sure what to try. I think it either has something to do with the m1 architecture or the install not being able to find numpy for some reason.

Answer 1

I would suggest you to use conda for managing your Python resources on your Mac M1 machine, unless you have a specific reason to stick with pip or pip3.

Below are the key steps that might help you to quickly install scipy package:

1. Install miniconda on your Mac: please follow step 1 to 6 on this page under the title Installing on MacOS. Don't worry about subpoint, Anaconda Installer for MacOS, in step 1 on the link attached above.

2. Create a new environment for your work purpose. It's recommended to not install packages in base environment of conda, and that's why I am suggesting for creating new environment. Please follow the sections, Managing conda and Managing environments, on this page.

3. Set conda-forge as conda's highest priority channel. This means conda will always check if Python packages you want to install are available via conda-forge or not. To do this, please type following lines of code in the terminal:

   conda config --add channels conda-forge 
   conda config --set channel_priority strict 
   

   You can read about conda-forge here.

4. Finally, type conda install scipy in the terminal by activating your non-base conda environment. This should install scipy along with its dependencies with your permission on your machine.