EDIT: As of 2021-08-06, this solution seems to work for scipy 1.7.0 (native, not through rosetta):
brew install openblas
pip install cython pybind11 pythran numpy
OPENBLAS=$(brew --prefix openblas) CFLAGS="-falign-functions=8 ${CFLAGS}" pip install --no-use-pep517 scipy==1.7.0
Hi there, I did not find any other issues related to this on here. I'm having some issues installing scipy on my M1 Macbook Air.
khuynh@kmba:~ $ python3 --version
Python 3.9.1
OPENBLAS="$(brew --prefix openblas)" MACOSX_DEPLOYMENT_TARGET=11.1 python3 -m pip install numpy --no-use-pep517
python3 -m pip install matplotlib pandas
python3 -m pip install scipy
khuynh@kmba:~ $ python3 -m pip install scipy
Collecting scipy
Using cached scipy-1.6.0.tar.gz (27.3 MB)
Installing build dependencies ... error
ERROR: Command errored out with exit status 1:
command: /opt/homebrew/opt/python@3.9/bin/python3.9 /opt/homebrew/lib/python3.9/site-packages/pip install --ignore-installed --no-user --prefix /private/var/folders/jc/hrnrv7f1059b2dx2kvsf4wk80000gn/T/pip-build-env-lm96mgjq/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- wheel 'setuptools<=51.0.0' 'Cython>=0.29.18' 'numpy==1.16.5; python_version=='"'"'3.7'"'"'' 'numpy==1.17.3; python_version=='"'"'3.8'"'"'' 'numpy==1.19.3; python_version=='"'"'3.9'"'"'' 'numpy; python_version>='"'"'3.10'"'"'' 'pybind11>=2.4.3'
cwd: None
Complete output (226 lines):
Ignoring numpy: markers 'python_version == "3.7"' don't match your environment
Ignoring numpy: markers 'python_version == "3.8"' don't match your environment
Ignoring numpy: markers 'python_version >= "3.10"' don't match your environment
Collecting numpy==1.19.3
Using cached numpy-1.19.3.zip (7.3 MB)
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 wheel metadata: started
Preparing wheel metadata: finished with status 'error'
ERROR: Command errored out with exit status 1:
command: /opt/homebrew/opt/python@3.9/bin/python3.9 /opt/homebrew/lib/python3.9/site-packages/pip/_vendor/pep517/_in_process.py prepare_metadata_for_build_wheel /var/folders/jc/hrnrv7f1059b2dx2kvsf4wk80000gn/T/tmpbdr967n3
cwd: /private/var/folders/jc/hrnrv7f1059b2dx2kvsf4wk80000gn/T/pip-install-rxxkdkwc/numpy_f22187e5fa894f3cab417c6a812e04c1
Complete output (209 lines):
Running from numpy source directory.
setup.py:480: UserWarning: Unrecognized setuptools command, proceeding with generating Cython sources and expanding templates
run_build = parse_setuppy_commands()
Processing numpy/random/_bounded_integers.pxd.in
Processing numpy/random/_philox.pyx
Processing numpy/random/_bounded_integers.pyx.in
Processing numpy/random/_sfc64.pyx
Processing numpy/random/_mt19937.pyx
Processing numpy/random/bit_generator.pyx
Processing numpy/random/mtrand.pyx
Processing numpy/random/_generator.pyx
Processing numpy/random/_pcg64.pyx
Processing numpy/random/_common.pyx
Cythonizing sources
blas_opt_info:
blas_mkl_info:
customize UnixCCompiler
libraries mkl_rt not found in ['/opt/homebrew/Cellar/python@3.9/3.9.1_5/Frameworks/Python.framework/Versions/3.9/lib', '/usr/local/lib', '/usr/lib']
NOT AVAILABLE
blis_info:
libraries blis not found in ['/opt/homebrew/Cellar/python@3.9/3.9.1_5/Frameworks/Python.framework/Versions/3.9/lib', '/usr/local/lib', '/usr/lib']
NOT AVAILABLE
openblas_info:
libraries openblas not found in ['/opt/homebrew/Cellar/python@3.9/3.9.1_5/Frameworks/Python.framework/Versions/3.9/lib', '/usr/local/lib', '/usr/lib']
NOT AVAILABLE
atlas_3_10_blas_threads_info:
Setting PTATLAS=ATLAS
libraries tatlas not found in ['/opt/homebrew/Cellar/python@3.9/3.9.1_5/Frameworks/Python.framework/Versions/3.9/lib', '/usr/local/lib', '/usr/lib']
NOT AVAILABLE
atlas_3_10_blas_info:
libraries satlas not found in ['/opt/homebrew/Cellar/python@3.9/3.9.1_5/Frameworks/Python.framework/Versions/3.9/lib', '/usr/local/lib', '/usr/lib']
NOT AVAILABLE
atlas_blas_threads_info:
Setting PTATLAS=ATLAS
libraries ptf77blas,ptcblas,atlas not found in ['/opt/homebrew/Cellar/python@3.9/3.9.1_5/Frameworks/Python.framework/Versions/3.9/lib', '/usr/local/lib', '/usr/lib']
NOT AVAILABLE
atlas_blas_info:
libraries f77blas,cblas,atlas not found in ['/opt/homebrew/Cellar/python@3.9/3.9.1_5/Frameworks/Python.framework/Versions/3.9/lib', '/usr/local/lib', '/usr/lib']
NOT AVAILABLE
accelerate_info:
libraries accelerate not found in ['/opt/homebrew/Cellar/python@3.9/3.9.1_5/Frameworks/Python.framework/Versions/3.9/lib', '/usr/local/lib', '/usr/lib']
Library accelerate was not found. Ignoring
libraries veclib not found in ['/opt/homebrew/Cellar/python@3.9/3.9.1_5/Frameworks/Python.framework/Versions/3.9/lib', '/usr/local/lib', '/usr/lib']
Library veclib was not found. Ignoring
FOUND:
extra_compile_args = ['-faltivec', '-I/System/Library/Frameworks/vecLib.framework/Headers']
extra_link_args = ['-Wl,-framework', '-Wl,Accelerate']
define_macros = [('NO_ATLAS_INFO', 3), ('HAVE_CBLAS', None)]
FOUND:
extra_compile_args = ['-faltivec', '-I/System/Library/Frameworks/vecLib.framework/Headers']
extra_link_args = ['-Wl,-framework', '-Wl,Accelerate']
define_macros = [('NO_ATLAS_INFO', 3), ('HAVE_CBLAS', None)]
non-existing path in 'numpy/distutils': 'site.cfg'
lapack_opt_info:
lapack_mkl_info:
libraries mkl_rt not found in ['/opt/homebrew/Cellar/python@3.9/3.9.1_5/Frameworks/Python.framework/Versions/3.9/lib', '/usr/local/lib', '/usr/lib']
NOT AVAILABLE
openblas_lapack_info:
libraries openblas not found in ['/opt/homebrew/Cellar/python@3.9/3.9.1_5/Frameworks/Python.framework/Versions/3.9/lib', '/usr/local/lib', '/usr/lib']
NOT AVAILABLE
openblas_clapack_info:
libraries openblas,lapack not found in ['/opt/homebrew/Cellar/python@3.9/3.9.1_5/Frameworks/Python.framework/Versions/3.9/lib', '/usr/local/lib', '/usr/lib']
NOT AVAILABLE
flame_info:
libraries flame not found in ['/opt/homebrew/Cellar/python@3.9/3.9.1_5/Frameworks/Python.framework/Versions/3.9/lib', '/usr/local/lib', '/usr/lib']
NOT AVAILABLE
atlas_3_10_threads_info:
Setting PTATLAS=ATLAS
libraries lapack_atlas not found in /opt/homebrew/Cellar/python@3.9/3.9.1_5/Frameworks/Python.framework/Versions/3.9/lib
libraries tatlas,tatlas not found in /opt/homebrew/Cellar/python@3.9/3.9.1_5/Frameworks/Python.framework/Versions/3.9/lib
libraries lapack_atlas not found in /usr/local/lib
libraries tatlas,tatlas not found in /usr/local/lib
libraries lapack_atlas not found in /usr/lib
libraries tatlas,tatlas not found in /usr/lib
<class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
NOT AVAILABLE
atlas_3_10_info:
libraries lapack_atlas not found in /opt/homebrew/Cellar/python@3.9/3.9.1_5/Frameworks/Python.framework/Versions/3.9/lib
libraries satlas,satlas not found in /opt/homebrew/Cellar/python@3.9/3.9.1_5/Frameworks/Python.framework/Versions/3.9/lib
libraries lapack_atlas not found in /usr/local/lib
libraries satlas,satlas not found in /usr/local/lib
libraries lapack_atlas not found in /usr/lib
libraries satlas,satlas not found in /usr/lib
<class 'numpy.distutils.system_info.atlas_3_10_info'>
NOT AVAILABLE
atlas_threads_info:
Setting PTATLAS=ATLAS
libraries lapack_atlas not found in /opt/homebrew/Cellar/python@3.9/3.9.1_5/Frameworks/Python.framework/Versions/3.9/lib
libraries ptf77blas,ptcblas,atlas not found in /opt/homebrew/Cellar/python@3.9/3.9.1_5/Frameworks/Python.framework/Versions/3.9/lib
libraries lapack_atlas not found in /usr/local/lib
libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
libraries lapack_atlas not found in /usr/lib
libraries ptf77blas,ptcblas,atlas not found in /usr/lib
<class 'numpy.distutils.system_info.atlas_threads_info'>
NOT AVAILABLE
atlas_info:
libraries lapack_atlas not found in /opt/homebrew/Cellar/python@3.9/3.9.1_5/Frameworks/Python.framework/Versions/3.9/lib
libraries f77blas,cblas,atlas not found in /opt/homebrew/Cellar/python@3.9/3.9.1_5/Frameworks/Python.framework/Versions/3.9/lib
libraries lapack_atlas not found in /usr/local/lib
libraries f77blas,cblas,atlas not found in /usr/local/lib
libraries lapack_atlas not found in /usr/lib
libraries f77blas,cblas,atlas not found in /usr/lib
<class 'numpy.distutils.system_info.atlas_info'>
NOT AVAILABLE
FOUND:
extra_compile_args = ['-faltivec', '-I/System/Library/Frameworks/vecLib.framework/Headers']
extra_link_args = ['-Wl,-framework', '-Wl,Accelerate']
define_macros = [('NO_ATLAS_INFO', 3), ('HAVE_CBLAS', None)]
/opt/homebrew/Cellar/python@3.9/3.9.1_5/Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/dist.py:274: UserWarning: Unknown distribution option: 'define_macros'
warnings.warn(msg)
running dist_info
running build_src
build_src
building py_modules sources
creating build
creating build/src.macosx-11-arm64-3.9
creating build/src.macosx-11-arm64-3.9/numpy
creating build/src.macosx-11-arm64-3.9/numpy/distutils
building library "npymath" sources
Traceback (most recent call last):
File "/opt/homebrew/lib/python3.9/site-packages/pip/_vendor/pep517/_in_process.py", line 280, in <module>
main()
File "/opt/homebrew/lib/python3.9/site-packages/pip/_vendor/pep517/_in_process.py", line 263, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
File "/opt/homebrew/lib/python3.9/site-packages/pip/_vendor/pep517/_in_process.py", line 133, in prepare_metadata_for_build_wheel
return hook(metadata_directory, config_settings)
File "/private/var/folders/jc/hrnrv7f1059b2dx2kvsf4wk80000gn/T/pip-build-env-u2e50a1f/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 157, in prepare_metadata_for_build_wheel
self.run_setup()
File "/private/var/folders/jc/hrnrv7f1059b2dx2kvsf4wk80000gn/T/pip-build-env-u2e50a1f/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 248, in run_setup
super(_BuildMetaLegacyBackend,
File "/private/var/folders/jc/hrnrv7f1059b2dx2kvsf4wk80000gn/T/pip-build-env-u2e50a1f/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 142, in run_setup
exec(compile(code, __file__, 'exec'), locals())
File "setup.py", line 508, in <module>
setup_package()
File "setup.py", line 500, in setup_package
setup(**metadata)
File "/private/var/folders/jc/hrnrv7f1059b2dx2kvsf4wk80000gn/T/pip-install-rxxkdkwc/numpy_f22187e5fa894f3cab417c6a812e04c1/numpy/distutils/core.py", line 169, in setup
return old_setup(**new_attr)
File "/private/var/folders/jc/hrnrv7f1059b2dx2kvsf4wk80000gn/T/pip-build-env-u2e50a1f/overlay/lib/python3.9/site-packages/setuptools/__init__.py", line 165, in setup
return distutils.core.setup(**attrs)
File "/opt/homebrew/Cellar/python@3.9/3.9.1_5/Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/core.py", line 148, in setup
dist.run_commands()
File "/opt/homebrew/Cellar/python@3.9/3.9.1_5/Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/dist.py", line 966, in run_commands
self.run_command(cmd)
File "/opt/homebrew/Cellar/python@3.9/3.9.1_5/Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/private/var/folders/jc/hrnrv7f1059b2dx2kvsf4wk80000gn/T/pip-build-env-u2e50a1f/overlay/lib/python3.9/site-packages/setuptools/command/dist_info.py", line 31, in run
egg_info.run()
File "/private/var/folders/jc/hrnrv7f1059b2dx2kvsf4wk80000gn/T/pip-install-rxxkdkwc/numpy_f22187e5fa894f3cab417c6a812e04c1/numpy/distutils/command/egg_info.py", line 24, in run
self.run_command("build_src")
File "/opt/homebrew/Cellar/python@3.9/3.9.1_5/Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/opt/homebrew/Cellar/python@3.9/3.9.1_5/Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/private/var/folders/jc/hrnrv7f1059b2dx2kvsf4wk80000gn/T/pip-install-rxxkdkwc/numpy_f22187e5fa894f3cab417c6a812e04c1/numpy/distutils/command/build_src.py", line 144, in run
self.build_sources()
File "/private/var/folders/jc/hrnrv7f1059b2dx2kvsf4wk80000gn/T/pip-install-rxxkdkwc/numpy_f22187e5fa894f3cab417c6a812e04c1/numpy/distutils/command/build_src.py", line 155, in build_sources
self.build_library_sources(*libname_info)
File "/private/var/folders/jc/hrnrv7f1059b2dx2kvsf4wk80000gn/T/pip-install-rxxkdkwc/numpy_f22187e5fa894f3cab417c6a812e04c1/numpy/distutils/command/build_src.py", line 288, in build_library_sources
sources = self.generate_sources(sources, (lib_name, build_info))
File "/private/var/folders/jc/hrnrv7f1059b2dx2kvsf4wk80000gn/T/pip-install-rxxkdkwc/numpy_f22187e5fa894f3cab417c6a812e04c1/numpy/distutils/command/build_src.py", line 378, in generate_sources
source = func(extension, build_dir)
File "numpy/core/setup.py", line 658, in get_mathlib_info
st = config_cmd.try_link('int main(void) { return 0;}')
File "/opt/homebrew/Cellar/python@3.9/3.9.1_5/Frameworks/Python.framework/Versions/3.9/lib/python3.9/distutils/command/config.py", line 241, in try_link
self._check_compiler()
File "/private/var/folders/jc/hrnrv7f1059b2dx2kvsf4wk80000gn/T/pip-install-rxxkdkwc/numpy_f22187e5fa894f3cab417c6a812e04c1/numpy/distutils/command/config.py", line 80, in _check_compiler
self.fcompiler = new_fcompiler(compiler=self.fcompiler,
File "/private/var/folders/jc/hrnrv7f1059b2dx2kvsf4wk80000gn/T/pip-install-rxxkdkwc/numpy_f22187e5fa894f3cab417c6a812e04c1/numpy/distutils/fcompiler/__init__.py", line 880, in new_fcompiler
compiler = get_default_fcompiler(plat, requiref90=requiref90,
File "/private/var/folders/jc/hrnrv7f1059b2dx2kvsf4wk80000gn/T/pip-install-rxxkdkwc/numpy_f22187e5fa894f3cab417c6a812e04c1/numpy/distutils/fcompiler/__init__.py", line 851, in get_default_fcompiler
compiler_type = _find_existing_fcompiler(matching_compiler_types,
File "/private/var/folders/jc/hrnrv7f1059b2dx2kvsf4wk80000gn/T/pip-install-rxxkdkwc/numpy_f22187e5fa894f3cab417c6a812e04c1/numpy/distutils/fcompiler/__init__.py", line 802, in _find_existing_fcompiler
c.customize(dist)
File "/private/var/folders/jc/hrnrv7f1059b2dx2kvsf4wk80000gn/T/pip-install-rxxkdkwc/numpy_f22187e5fa894f3cab417c6a812e04c1/numpy/distutils/fcompiler/__init__.py", line 526, in customize
linker_so_flags = self.flag_vars.linker_so
File "/private/var/folders/jc/hrnrv7f1059b2dx2kvsf4wk80000gn/T/pip-install-rxxkdkwc/numpy_f22187e5fa894f3cab417c6a812e04c1/numpy/distutils/fcompiler/environment.py", line 37, in __getattr__
return self._get_var(name, conf_desc)
File "/private/var/folders/jc/hrnrv7f1059b2dx2kvsf4wk80000gn/T/pip-install-rxxkdkwc/numpy_f22187e5fa894f3cab417c6a812e04c1/numpy/distutils/fcompiler/environment.py", line 53, in _get_var
var = self._hook_handler(name, hook)
File "/private/var/folders/jc/hrnrv7f1059b2dx2kvsf4wk80000gn/T/pip-install-rxxkdkwc/numpy_f22187e5fa894f3cab417c6a812e04c1/numpy/distutils/fcompiler/__init__.py", line 705, in _environment_hook
return hook()
File "/private/var/folders/jc/hrnrv7f1059b2dx2kvsf4wk80000gn/T/pip-install-rxxkdkwc/numpy_f22187e5fa894f3cab417c6a812e04c1/numpy/distutils/fcompiler/gnu.py", line 346, in get_flags_linker_so
flags = GnuFCompiler.get_flags_linker_so(self)
File "/private/var/folders/jc/hrnrv7f1059b2dx2kvsf4wk80000gn/T/pip-install-rxxkdkwc/numpy_f22187e5fa894f3cab417c6a812e04c1/numpy/distutils/fcompiler/gnu.py", line 136, in get_flags_linker_so
os.environ['MACOSX_DEPLOYMENT_TARGET'] = target
File "/opt/homebrew/Cellar/python@3.9/3.9.1_5/Frameworks/Python.framework/Versions/3.9/lib/python3.9/os.py", line 684, in __setitem__
value = self.encodevalue(value)
File "/opt/homebrew/Cellar/python@3.9/3.9.1_5/Frameworks/Python.framework/Versions/3.9/lib/python3.9/os.py", line 756, in encode
raise TypeError("str expected, not %s" % type(value).__name__)
TypeError: str expected, not int
----------------------------------------
ERROR: Command errored out with exit status 1: /opt/homebrew/opt/python@3.9/bin/python3.9 /opt/homebrew/lib/python3.9/site-packages/pip/_vendor/pep517/_in_process.py prepare_metadata_for_build_wheel /var/folders/jc/hrnrv7f1059b2dx2kvsf4wk80000gn/T/tmpbdr967n3 Check the logs for full command output.
----------------------------------------
ERROR: Command errored out with exit status 1: /opt/homebrew/opt/python@3.9/bin/python3.9 /opt/homebrew/lib/python3.9/site-packages/pip install --ignore-installed --no-user --prefix /private/var/folders/jc/hrnrv7f1059b2dx2kvsf4wk80000gn/T/pip-build-env-lm96mgjq/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- wheel 'setuptools<=51.0.0' 'Cython>=0.29.18' 'numpy==1.16.5; python_version=='"'"'3.7'"'"'' 'numpy==1.17.3; python_version=='"'"'3.8'"'"'' 'numpy==1.19.3; python_version=='"'"'3.9'"'"'' 'numpy; python_version>='"'"'3.10'"'"'' 'pybind11>=2.4.3' Check the logs for full command output.
>>> import sys, numpy; print(numpy.__version__, sys.version_info)
1.19.5 sys.version_info(major=3, minor=9, micro=1, releaselevel='final', serial=0)
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