无法从 Ubuntu Focal (Python 3.8.10) 中的源安装 Scipy（找不到 `./scipy/_lib/highs/CMakeLists.txt`）

Question

我目前正在尝试从源代码安装 SciPy，但我一直运行遇到问题。我正在按照 https://scipy.github.io/devdocs/building/linux.html.

上的说明进行操作

我做了什么：

克隆了 github 存储库。
已使用 sudo apt-get install gcc g++ gfortran python3-dev libopenblas-dev liblapack-dev 下载依赖项。

什么不起作用：

python3 setup.py build 和 python3 setup.py install 都不起作用，有或没有 sudo。此外，通过键入 pip3 install . 尝试使用 pip 安装它也不起作用。

问题似乎与找不到名为 ./scipy/_lib/highs/CMakeLists.txt 的文件有关。这个文件应该是自动生成的吗？

pip3 install . 的控制台输出：

Processing /mnt/data/Code/Python scripts/scipy
  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 'error'

  error: subprocess-exited-with-error
  
  × Preparing metadata (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [178 lines of output]
      scipy/linalg/_generate_pyx.py: all files up-to-date
      scipy/special/_generate_pyx.py: all files up-to-date
      Running scipy/linalg/_generate_pyx.py
      Running scipy/special/_generate_pyx.py
      Running scipy/stats/_generate_pyx.py
      scipy/cluster/_hierarchy.pyx has not changed
      scipy/cluster/_optimal_leaf_ordering.pyx has not changed
      scipy/linalg/_solve_toeplitz.pyx has not changed
      scipy/linalg/_cythonized_array_utils.pyx has not changed
      scipy/linalg/_decomp_update.pyx.in has not changed
      scipy/ndimage/src/_cytest.pyx has not changed
      scipy/ndimage/src/_ni_label.pyx has not changed
      scipy/optimize/_bglu_dense.pyx has not changed
      scipy/optimize/_group_columns.pyx has not changed
      scipy/optimize/cython_optimize/_zeros.pyx.in has not changed
      scipy/optimize/_lsq/givens_elimination.pyx has not changed
      scipy/optimize/tnc/_moduleTNC.pyx has not changed
      scipy/optimize/_highs/cython/src/_highs_constants.pyx has not changed
      scipy/optimize/_highs/cython/src/_highs_wrapper.pyx has not changed
      scipy/optimize/_trlib/_trlib.pyx has not changed
      scipy/signal/_max_len_seq_inner.pyx has not changed
      scipy/signal/_peak_finding_utils.pyx has not changed
      scipy/signal/_sosfilt.pyx has not changed
      scipy/signal/_spectral.pyx has not changed
      scipy/signal/_upfirdn_apply.pyx has not changed
      scipy/sparse/_csparsetools.pyx.in has not changed
      scipy/sparse/csgraph/_flow.pyx has not changed
      scipy/sparse/csgraph/_matching.pyx has not changed
      scipy/sparse/csgraph/_min_spanning_tree.pyx has not changed
      scipy/sparse/csgraph/_reordering.pyx has not changed
      scipy/fftpack/convolve.pyx has not changed
      scipy/sparse/csgraph/_tools.pyx has not changed
      scipy/interpolate/_bspl.pyx has not changed
      scipy/spatial/_ckdtree.pyx has not changed
      scipy/io/matlab/_mio5_utils.pyx has not changed
      scipy/spatial/_qhull.pyx has not changed
      scipy/spatial/_voronoi.pyx has not changed
      scipy/spatial/transform/_rotation.pyx has not changed
      scipy/special/cython_special.pyx has not changed
      scipy/special/_ellip_harm_2.pyx has not changed
      scipy/special/_test_round.pyx has not changed
      scipy/special/_ufuncs.pyx has not changed
      scipy/interpolate/interpnd.pyx has not changed
      scipy/sparse/csgraph/_traversal.pyx has not changed
      scipy/stats/_qmc_cy.pyx has not changed
      scipy/stats/_sobol.pyx has not changed
      scipy/stats/_stats.pyx has not changed
      scipy/io/matlab/_streams.pyx has not changed
      scipy/linalg/cython_blas.pyx has not changed
      scipy/stats/_unuran/unuran_wrapper.pyx has not changed
      scipy/stats/_boost/src/beta_ufunc.pyx has not changed
      scipy/stats/_boost/src/binom_ufunc.pyx has not changed
      scipy/stats/_boost/src/hypergeom_ufunc.pyx has not changed
      scipy/special/_ufuncs_cxx.pyx has not changed
      scipy/_lib/messagestream.pyx has not changed
      scipy/_lib/_ccallback_c.pyx has not changed
      scipy/spatial/_hausdorff.pyx has not changed
      scipy/_lib/_test_deprecation_def.pyx has not changed
      scipy/stats/_biasedurn.pyx has not changed
      scipy/stats/_levy_stable/levyst.pyx has not changed
      scipy/linalg/cython_lapack.pyx has not changed
      scipy/linalg/_matfuncs_sqrtm_triu.pyx has not changed
      scipy/cluster/_vq.pyx has not changed
      scipy/sparse/csgraph/_shortest_path.pyx has not changed
      scipy/stats/_boost/src/nbinom_ufunc.pyx has not changed
      scipy/special/_comb.pyx has not changed
      scipy/interpolate/_ppoly.pyx has not changed
      scipy/_lib/_test_deprecation_call.pyx has not changed
      scipy/io/matlab/_mio_utils.pyx has not changed
      Cythonizing sources
      lapack_opt_info:
      lapack_mkl_info:
      customize UnixCCompiler
        libraries mkl_rt not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
        NOT AVAILABLE
      
      openblas_lapack_info:
      C compiler: x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC
      
      creating /tmp/tmpxeu9x3zd/tmp
      creating /tmp/tmpxeu9x3zd/tmp/tmpxeu9x3zd
      compile options: '-c'
      x86_64-linux-gnu-gcc: /tmp/tmpxeu9x3zd/source.c
      x86_64-linux-gnu-gcc -pthread /tmp/tmpxeu9x3zd/tmp/tmpxeu9x3zd/source.o -L/usr/lib/x86_64-linux-gnu -lopenblas -o /tmp/tmpxeu9x3zd/a.out
        FOUND:
          libraries = ['openblas', 'openblas']
          library_dirs = ['/usr/lib/x86_64-linux-gnu']
          language = c
          define_macros = [('HAVE_CBLAS', None)]
      
        FOUND:
          libraries = ['openblas', 'openblas']
          library_dirs = ['/usr/lib/x86_64-linux-gnu']
          language = c
          define_macros = [('HAVE_CBLAS', None)]
      
      blas_opt_info:
      blas_mkl_info:
        libraries mkl_rt not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
        NOT AVAILABLE
      
      blis_info:
        libraries blis not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
        NOT AVAILABLE
      
      openblas_info:
      C compiler: x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC
      
      creating /tmp/tmph3qne29w/tmp
      creating /tmp/tmph3qne29w/tmp/tmph3qne29w
      compile options: '-c'
      x86_64-linux-gnu-gcc: /tmp/tmph3qne29w/source.c
      x86_64-linux-gnu-gcc -pthread /tmp/tmph3qne29w/tmp/tmph3qne29w/source.o -L/usr/lib/x86_64-linux-gnu -lopenblas -o /tmp/tmph3qne29w/a.out
        FOUND:
          libraries = ['openblas', 'openblas']
          library_dirs = ['/usr/lib/x86_64-linux-gnu']
          language = c
          define_macros = [('HAVE_CBLAS', None)]
      
        FOUND:
          libraries = ['openblas', 'openblas']
          library_dirs = ['/usr/lib/x86_64-linux-gnu']
          language = c
          define_macros = [('HAVE_CBLAS', None)]
      
      setup.py:390: UserWarning: Unrecognized setuptools command ('dist_info --egg-base /tmp/pip-modern-metadata-qr6r8y4e'), proceeding with generating Cython sources and expanding templates
        warnings.warn("Unrecognized setuptools command ('{}'), proceeding with "
      Running from SciPy source directory.
      /usr/local/lib/python3.8/dist-packages/numpy/distutils/system_info.py:933: UserWarning: Specified path /usr/local/include/python3.8 is invalid.
        return self.get_paths(self.section, key)
      Traceback (most recent call last):
        File "/usr/local/lib/python3.8/dist-packages/pip/_vendor/pep517/in_process/_in_process.py", line 363, in <module>
          main()
        File "/usr/local/lib/python3.8/dist-packages/pip/_vendor/pep517/in_process/_in_process.py", line 345, in main
          json_out['return_val'] = hook(**hook_input['kwargs'])
        File "/usr/local/lib/python3.8/dist-packages/pip/_vendor/pep517/in_process/_in_process.py", line 164, in prepare_metadata_for_build_wheel
          return hook(metadata_directory, config_settings)
        File "/usr/local/lib/python3.8/dist-packages/setuptools/build_meta.py", line 188, in prepare_metadata_for_build_wheel
          self.run_setup()
        File "/usr/local/lib/python3.8/dist-packages/setuptools/build_meta.py", line 281, in run_setup
          super(_BuildMetaLegacyBackend,
        File "/usr/local/lib/python3.8/dist-packages/setuptools/build_meta.py", line 174, in run_setup
          exec(compile(code, __file__, 'exec'), locals())
        File "setup.py", line 532, in <module>
          setup_package()
        File "setup.py", line 528, in setup_package
          setup(**metadata)
        File "/usr/local/lib/python3.8/dist-packages/numpy/distutils/core.py", line 135, in setup
          config = configuration()
        File "setup.py", line 438, in configuration
          config.add_subpackage('scipy')
        File "/usr/local/lib/python3.8/dist-packages/numpy/distutils/misc_util.py", line 1014, in add_subpackage
          config_list = self.get_subpackage(subpackage_name, subpackage_path,
        File "/usr/local/lib/python3.8/dist-packages/numpy/distutils/misc_util.py", line 980, in get_subpackage
          config = self._get_configuration_from_setup_py(
        File "/usr/local/lib/python3.8/dist-packages/numpy/distutils/misc_util.py", line 922, in _get_configuration_from_setup_py
          config = setup_module.configuration(*args)
        File "/mnt/data/Code/Python scripts/scipy/scipy/setup.py", line 18, in configuration
          config.add_subpackage('optimize')
        File "/usr/local/lib/python3.8/dist-packages/numpy/distutils/misc_util.py", line 1014, in add_subpackage
          config_list = self.get_subpackage(subpackage_name, subpackage_path,
        File "/usr/local/lib/python3.8/dist-packages/numpy/distutils/misc_util.py", line 980, in get_subpackage
          config = self._get_configuration_from_setup_py(
        File "/usr/local/lib/python3.8/dist-packages/numpy/distutils/misc_util.py", line 922, in _get_configuration_from_setup_py
          config = setup_module.configuration(*args)
        File "/mnt/data/Code/Python scripts/scipy/scipy/optimize/setup.py", line 130, in configuration
          config.add_subpackage('_highs')
        File "/usr/local/lib/python3.8/dist-packages/numpy/distutils/misc_util.py", line 1014, in add_subpackage
          config_list = self.get_subpackage(subpackage_name, subpackage_path,
        File "/usr/local/lib/python3.8/dist-packages/numpy/distutils/misc_util.py", line 980, in get_subpackage
          config = self._get_configuration_from_setup_py(
        File "/usr/local/lib/python3.8/dist-packages/numpy/distutils/misc_util.py", line 922, in _get_configuration_from_setup_py
          config = setup_module.configuration(*args)
        File "/mnt/data/Code/Python scripts/scipy/scipy/optimize/_highs/setup.py", line 63, in configuration
          _major_dot_minor = _get_version(
        File "/mnt/data/Code/Python scripts/scipy/scipy/optimize/_highs/setup.py", line 50, in _get_version
          with open(CMakeLists, 'r', encoding='utf-8') as f:
      FileNotFoundError: [Errno 2] No such file or directory: '/mnt/data/Code/Python scripts/scipy/scipy/_lib/highs/CMakeLists.txt'
      [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.
╰─> See above for output.

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

Answer 1

如您所见，on git 文件夹 highs 包含在那里，但作为一个子模块，您在克隆 repo 时可能没有下载它。

转到回购主目录运行

git submodule init
git submodule update

然后确认指定的文件夹存在并被填充

无法从 Ubuntu Focal (Python 3.8.10) 中的源安装 Scipy（找不到 `./scipy/_lib/highs/CMakeLists.txt`）

Can't install Scipy from source in Ubuntu Focal (Python 3.8.10) (can't find `./scipy/_lib/highs/CMakeLists.txt`)

python

pip

cmake

scipy