metadata-generation-failed while installing Scipy

Question

I have been trying to install Scipy and I got an error called metadata-generation-failed, and I came over to stackoverflow looking for a solution but non of them worked for me. Neither updating pip, nor using commands such as --use-deprecated=legacy-resolver nor --use-deprecated=backtrack-on-build-failures. I ran out of ideas, if somebody can help I would appreciate. Code is right below:

`

Collecting scipy
  Using cached scipy-1.9.3.tar.gz (42.1 MB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Installing backend dependencies ... done
  Preparing metadata (pyproject.toml) ... error
  error: subprocess-exited-with-error
  
  × Preparing metadata (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [75 lines of output]
      The Meson build system
      Version: 0.64.1
      Source dir: /private/var/folders/sy/vl408hcx0d11wftbc8rshy9r0000gn/T/pip-install-6luprtwk/scipy
      Build dir: /private/var/folders/sy/vl408hcx0d11wftbc8rshy9r0000gn/T/pip-install-6luprtwk/scipy/.mesonpy-be8nnvg4/build
      Build type: native build
      Project name: SciPy
      Project version: 1.9.3
      C compiler for the host machine: cc (clang 12.0.5 "Apple clang version 12.0.5 (clang-1205.0.22.11)")
      C linker for the host machine: cc ld64 650.9
      C++ compiler for the host machine: c++ (clang 12.0.5 "Apple clang version 12.0.5 (clang-1205.0.22.11)")
      C++ linker for the host machine: c++ ld64 650.9
      Host machine cpu family: aarch64
      Host machine cpu: aarch64
      Compiler for C supports arguments -Wno-unused-but-set-variable: NO
      Compiler for C supports arguments -Wno-unused-but-set-variable: NO (cached)
      Compiler for C supports arguments -Wno-unused-function: YES
      Compiler for C supports arguments -Wno-conversion: YES
      Compiler for C supports arguments -Wno-misleading-indentation: YES
      Compiler for C supports arguments -Wno-incompatible-pointer-types: YES
      Library m found: YES
      
      ../../meson.build:57:0: ERROR: Unknown compiler(s): [['gfortran'], ['flang'], ['nvfortran'], ['pgfortran'], ['ifort'], ['ifx'], ['g95']]
      The following exception(s) were encountered:
      Running `gfortran --version` gave "[Errno 2] No such file or directory: 'gfortran'"
      Running `gfortran -V` gave "[Errno 2] No such file or directory: 'gfortran'"
      Running `flang --version` gave "[Errno 2] No such file or directory: 'flang'"
      Running `flang -V` gave "[Errno 2] No such file or directory: 'flang'"
      Running `nvfortran --version` gave "[Errno 2] No such file or directory: 'nvfortran'"
      Running `nvfortran -V` gave "[Errno 2] No such file or directory: 'nvfortran'"
      Running `pgfortran --version` gave "[Errno 2] No such file or directory: 'pgfortran'"
      Running `pgfortran -V` gave "[Errno 2] No such file or directory: 'pgfortran'"
      Running `ifort --version` gave "[Errno 2] No such file or directory: 'ifort'"
      Running `ifort -V` gave "[Errno 2] No such file or directory: 'ifort'"
      Running `ifx --version` gave "[Errno 2] No such file or directory: 'ifx'"
      Running `ifx -V` gave "[Errno 2] No such file or directory: 'ifx'"
      Running `g95 --version` gave "[Errno 2] No such file or directory: 'g95'"
      Running `g95 -V` gave "[Errno 2] No such file or directory: 'g95'"
      
      A full log can be found at /private/var/folders/sy/vl408hcx0d11wftbc8rshy9r0000gn/T/pip-install-6luprtwk/scipy/.mesonpy-be8nnvg4/build/meson-logs/meson-log.txt
      + meson setup --prefix=/Library/Frameworks/Python.framework/Versions/3.10 /private/var/folders/sy/vl408hcx0d11wftbc8rshy9r0000gn/T/pip-install-6luprtwk/scipy /private/var/folders/sy/vl408hcx0d11wftbc8rshy9r0000gn/T/pip-install-6luprtwk/scipy/.mesonpy-be8nnvg4/build --native-file=/private/var/folders/sy/vl408hcx0d11wftbc8rshy9r0000gn/T/pip-install-6luprtwk/scipy/.mesonpy-native-file.ini -Ddebug=false -Doptimization=2
      Traceback (most recent call last):
        File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 144, in prepare_metadata_for_build_wheel
          hook = backend.prepare_metadata_for_build_wheel
      AttributeError: module 'mesonpy' has no attribute 'prepare_metadata_for_build_wheel'
      
      During handling of the above exception, another exception occurred:
      
      Traceback (most recent call last):
        File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 351, in <module>
          main()
        File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 333, in main
          json_out['return_val'] = hook(**hook_input['kwargs'])
        File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 148, in prepare_metadata_for_build_wheel
          whl_basename = backend.build_wheel(metadata_directory, config_settings)
        File "/private/var/folders/sy/vl408hcx0d11wftbc8rshy9r0000gn/T/pip-build-env-5s9erroi/overlay/lib/python3.10/site-packages/mesonpy/__init__.py", line 1060, in build_wheel
          with _project(config_settings) as project:
        File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/contextlib.py", line 135, in __enter__
          return next(self.gen)
        File "/private/var/folders/sy/vl408hcx0d11wftbc8rshy9r0000gn/T/pip-build-env-5s9erroi/overlay/lib/python3.10/site-packages/mesonpy/__init__.py", line 975, in _project
          with Project.with_temp_working_dir(
        File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/contextlib.py", line 135, in __enter__
          return next(self.gen)
        File "/private/var/folders/sy/vl408hcx0d11wftbc8rshy9r0000gn/T/pip-build-env-5s9erroi/overlay/lib/python3.10/site-packages/mesonpy/__init__.py", line 750, in with_temp_working_dir
          yield cls(source_dir, tmpdir, build_dir, meson_args)
        File "/private/var/folders/sy/vl408hcx0d11wftbc8rshy9r0000gn/T/pip-build-env-5s9erroi/overlay/lib/python3.10/site-packages/mesonpy/__init__.py", line 632, in __init__
          self._configure(reconfigure=bool(build_dir) and not native_file_mismatch)
        File "/private/var/folders/sy/vl408hcx0d11wftbc8rshy9r0000gn/T/pip-build-env-5s9erroi/overlay/lib/python3.10/site-packages/mesonpy/__init__.py", line 680, in _configure
          self._meson('setup', *setup_args)
        File "/private/var/folders/sy/vl408hcx0d11wftbc8rshy9r0000gn/T/pip-build-env-5s9erroi/overlay/lib/python3.10/site-packages/mesonpy/__init__.py", line 657, in _meson
          return self._proc('meson', *args)
        File "/private/var/folders/sy/vl408hcx0d11wftbc8rshy9r0000gn/T/pip-build-env-5s9erroi/overlay/lib/python3.10/site-packages/mesonpy/__init__.py", line 652, in _proc
          subprocess.check_call(list(args), env=self._env)
        File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/subprocess.py", line 369, in check_call
          raise CalledProcessError(retcode, cmd)
      subprocess.CalledProcessError: Command '['meson', 'setup', '--prefix=/Library/Frameworks/Python.framework/Versions/3.10', '/private/var/folders/sy/vl408hcx0d11wftbc8rshy9r0000gn/T/pip-install-6luprtwk/scipy', '/private/var/folders/sy/vl408hcx0d11wftbc8rshy9r0000gn/T/pip-install-6luprtwk/scipy/.mesonpy-be8nnvg4/build', '--native-file=/private/var/folders/sy/vl408hcx0d11wftbc8rshy9r0000gn/T/pip-install-6luprtwk/scipy/.mesonpy-native-file.ini', '-Ddebug=false', '-Doptimization=2']' returned non-zero exit status 1.
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> scipy

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.

`

I tried using commands such as --use-deprecated=legacy-resolver and --use-deprecated=backtrack-on-build-failures that I found in several cases on this page, expecting to solve my issue and finally get to install the library, but non of them worked, and I always end up with the same result:

`

  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> scipy

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.

`

Answer 1

Are you trying to install scipy on macOS 11. If so, then we don't support scipy on that version of macOS. For M1 wheels you need to be on macOS 12 or later. I think Intel is ok on macOS 11. If you are trying to install scipy from source you need to install various packages for installation, the absence of gfortran is what's giving this error.