poetry: Can't add scanpy package

• I am on the latest Poetry version.

• I have searched the issues of this repo and believe that this is not a duplicate.

• If an exception occurs when executing a command, I executed it again in debug mode (-vvv option).

• Windows10 , Centos7

• 1.1.13

Issue

Just run poetry add scanpy and you can see the error. It cannot be installed successfully.

Error infos:

Using version ^1.9.1 for scanpy

Updating dependencies
Resolving dependencies... (83.2s)

Writing lock file

Package operations: 31 installs, 1 update, 0 removals

  • Installing numpy (1.23.0)
  • Installing joblib (1.1.0)
  • Installing llvmlite (0.34.0): Failed

  EnvCommandError

  Command ['/share2/pub/sunhj/sunhj/Soft/miniconda3/envs/test/bin/pip', 'install', '--no-deps', '/share2/home/sunhj/.cache/pypoetry/artifacts/9e/1c/c8/439ee74bf8837fa4dae6747de4184a713dd70697520cd1d1500b1141f0/llvmlite-0.34.0.tar.gz'] errored with the following return code 1, and output:
  Processing /share2/home/sunhj/.cache/pypoetry/artifacts/9e/1c/c8/439ee74bf8837fa4dae6747de4184a713dd70697520cd1d1500b1141f0/llvmlite-0.34.0.tar.gz
    Preparing metadata (setup.py): started
    Preparing metadata (setup.py): finished with status 'done'
  Building wheels for collected packages: llvmlite
    Building wheel for llvmlite (setup.py): started
    Building wheel for llvmlite (setup.py): finished with status 'error'
    error: subprocess-exited-with-error

    × python setup.py bdist_wheel did not run successfully.
    │ exit code: 1
    ╰─> [26 lines of output]
        running bdist_wheel
        /share2/pub/sunhj/sunhj/Soft/miniconda3/envs/test/bin/python3.10 /tmp/pip-req-build-rjb_h090/ffi/build.py
        LLVM version... Traceback (most recent call last):
          File "/tmp/pip-req-build-rjb_h090/ffi/build.py", line 105, in main_posix
            out = subprocess.check_output([llvm_config, '--version'])
          File "/share2/pub/sunhj/sunhj/Soft/miniconda3/envs/test/lib/python3.10/subprocess.py", line 420, in check_output
            return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
          File "/share2/pub/sunhj/sunhj/Soft/miniconda3/envs/test/lib/python3.10/subprocess.py", line 501, in run
            with Popen(*popenargs, **kwargs) as process:
          File "/share2/pub/sunhj/sunhj/Soft/miniconda3/envs/test/lib/python3.10/subprocess.py", line 969, in __init__
            self._execute_child(args, executable, preexec_fn, close_fds,
          File "/share2/pub/sunhj/sunhj/Soft/miniconda3/envs/test/lib/python3.10/subprocess.py", line 1845, in _execute_child
            raise child_exception_type(errno_num, err_msg, err_filename)
        FileNotFoundError: [Errno 2] No such file or directory: 'llvm-config'

        During handling of the above exception, another exception occurred:

        Traceback (most recent call last):
          File "/tmp/pip-req-build-rjb_h090/ffi/build.py", line 191, in <module>
            main()
          File "/tmp/pip-req-build-rjb_h090/ffi/build.py", line 181, in main
            main_posix('linux', '.so')
          File "/tmp/pip-req-build-rjb_h090/ffi/build.py", line 107, in main_posix
            raise RuntimeError("%s failed executing, please point LLVM_CONFIG "
        RuntimeError: llvm-config failed executing, please point LLVM_CONFIG to the path for llvm-config
        error: command '/share2/pub/sunhj/sunhj/Soft/miniconda3/envs/test/bin/python3.10' failed with exit code 1
        [end of output]

    note: This error originates from a subprocess, and is likely not a problem with pip.
    ERROR: Failed building wheel for llvmlite
    Running setup.py clean for llvmlite
  Failed to build llvmlite
  Installing collected packages: llvmlite
    Running setup.py install for llvmlite: started
    Running setup.py install for llvmlite: finished with status 'error'
    error: subprocess-exited-with-error

    × Running setup.py install for llvmlite did not run successfully.
    │ exit code: 1
    ╰─> [31 lines of output]
        running install
        /share2/pub/sunhj/sunhj/Soft/miniconda3/envs/test/lib/python3.10/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
          warnings.warn(
        running build
        got version from file /tmp/pip-req-build-rjb_h090/llvmlite/_version.py {'version': '0.34.0', 'full': 'c5889c9e98c6b19d5d85ebdd982d64a03931f8e2'}
        running build_ext
        /share2/pub/sunhj/sunhj/Soft/miniconda3/envs/test/bin/python3.10 /tmp/pip-req-build-rjb_h090/ffi/build.py
        LLVM version... Traceback (most recent call last):
          File "/tmp/pip-req-build-rjb_h090/ffi/build.py", line 105, in main_posix
            out = subprocess.check_output([llvm_config, '--version'])
          File "/share2/pub/sunhj/sunhj/Soft/miniconda3/envs/test/lib/python3.10/subprocess.py", line 420, in check_output
            return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
          File "/share2/pub/sunhj/sunhj/Soft/miniconda3/envs/test/lib/python3.10/subprocess.py", line 501, in run
            with Popen(*popenargs, **kwargs) as process:
          File "/share2/pub/sunhj/sunhj/Soft/miniconda3/envs/test/lib/python3.10/subprocess.py", line 969, in __init__
            self._execute_child(args, executable, preexec_fn, close_fds,
          File "/share2/pub/sunhj/sunhj/Soft/miniconda3/envs/test/lib/python3.10/subprocess.py", line 1845, in _execute_child
            raise child_exception_type(errno_num, err_msg, err_filename)
        FileNotFoundError: [Errno 2] No such file or directory: 'llvm-config'

        During handling of the above exception, another exception occurred:

        Traceback (most recent call last):
          File "/tmp/pip-req-build-rjb_h090/ffi/build.py", line 191, in <module>
            main()
          File "/tmp/pip-req-build-rjb_h090/ffi/build.py", line 181, in main
            main_posix('linux', '.so')
          File "/tmp/pip-req-build-rjb_h090/ffi/build.py", line 107, in main_posix
            raise RuntimeError("%s failed executing, please point LLVM_CONFIG "
        RuntimeError: llvm-config failed executing, please point LLVM_CONFIG to the path for llvm-config
        error: command '/share2/pub/sunhj/sunhj/Soft/miniconda3/envs/test/bin/python3.10' failed with exit code 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.
  ╰─> llvmlite

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


  at /share2/pub/sunhj/sunhj/Soft/miniconda3/envs/test/lib/python3.10/site-packages/poetry/utils/env.py:1195 in _run
      1191│                 output = subprocess.check_output(
      1192│                     cmd, stderr=subprocess.STDOUT, **kwargs
      1193│                 )
      1194│         except CalledProcessError as e:
    → 1195│             raise EnvCommandError(e, input=input_)
      1196│
      1197│         return decode(output)
      1198│
      1199│     def execute(self, bin, *args, **kwargs):

  • Updating packaging (20.9 -> 21.3)
  • Installing scipy (1.6.1): Failed

  EnvCommandError

  Command ['/share2/pub/sunhj/sunhj/Soft/miniconda3/envs/test/bin/pip', 'install', '--no-deps', '/share2/home/sunhj/.cache/pypoetry/artifacts/bc/74/e2/a22451059efb69c32be2d51a7727b1133375122dd7564e8a8e9df4f1cd/scipy-1.6.1.tar.gz'] errored with the following return code 1, and output:
  Processing /share2/home/sunhj/.cache/pypoetry/artifacts/bc/74/e2/a22451059efb69c32be2d51a7727b1133375122dd7564e8a8e9df4f1cd/scipy-1.6.1.tar.gz
    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
    ╰─> [139 lines of output]
        setup.py:461: UserWarning: Unrecognized setuptools command ('dist_info --egg-base /tmp/pip-modern-metadata-irsicazy'), proceeding with generating Cython sources and expanding templates
          warnings.warn("Unrecognized setuptools command ('{}'), proceeding with "
        setup.py:563: DeprecationWarning:

          `numpy.distutils` is deprecated since NumPy 1.23.0, as a result
          of the deprecation of `distutils` itself. It will be removed for
          Python >= 3.12. For older Python versions it will remain present.
          It is recommended to use `setuptools < 60.0` for those Python versions.
          For more details, see:
            https://numpy.org/devdocs/reference/distutils_status_migration.html


          from numpy.distutils.core import setup
        Running from SciPy source directory.
        INFO: lapack_opt_info:
        INFO: lapack_armpl_info:
        INFO: customize UnixCCompiler
        INFO:   libraries armpl_lp64_mp not found in ['/share2/pub/sunhj/sunhj/Soft/miniconda3/envs/test/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib', '/usr/lib/']
        INFO:   NOT AVAILABLE
        INFO:
        INFO: lapack_mkl_info:
        INFO:   libraries mkl_rt not found in ['/share2/pub/sunhj/sunhj/Soft/miniconda3/envs/test/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib', '/usr/lib/']
        INFO:   NOT AVAILABLE
        INFO:
        INFO: openblas_lapack_info:
        INFO:   libraries openblas not found in ['/share2/pub/sunhj/sunhj/Soft/miniconda3/envs/test/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib', '/usr/lib/']
        INFO:   NOT AVAILABLE
        INFO:
        INFO: openblas_clapack_info:
        INFO:   libraries openblas,lapack not found in ['/share2/pub/sunhj/sunhj/Soft/miniconda3/envs/test/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib', '/usr/lib/']
        INFO:   NOT AVAILABLE
        INFO:
        INFO: flame_info:
        INFO:   libraries flame not found in ['/share2/pub/sunhj/sunhj/Soft/miniconda3/envs/test/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib', '/usr/lib/']
        INFO:   NOT AVAILABLE
        INFO:
        INFO: accelerate_info:
        INFO:   NOT AVAILABLE
        INFO:
        INFO: atlas_3_10_threads_info:
        INFO: Setting PTATLAS=ATLAS
        INFO:   libraries tatlas,tatlas not found in /share2/pub/sunhj/sunhj/Soft/miniconda3/envs/test/lib
        INFO:   libraries tatlas,tatlas not found in /usr/local/lib64
        INFO:   libraries tatlas,tatlas not found in /usr/local/lib
        INFO:   libraries tatlas,tatlas not found in /usr/lib64/sse2
        INFO:   libraries tatlas,tatlas not found in /usr/lib64
        INFO:   libraries tatlas,tatlas not found in /usr/lib/sse2
        INFO:   libraries tatlas,tatlas not found in /usr/lib
        INFO:   libraries tatlas,tatlas not found in /usr/lib/sse2
        INFO:   libraries tatlas,tatlas not found in /usr/lib/
        INFO: <class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
        INFO:   NOT AVAILABLE
        INFO:
        INFO: atlas_3_10_info:
        INFO:   libraries satlas,satlas not found in /share2/pub/sunhj/sunhj/Soft/miniconda3/envs/test/lib
        INFO:   libraries satlas,satlas not found in /usr/local/lib64
        INFO:   libraries satlas,satlas not found in /usr/local/lib
        INFO:   libraries satlas,satlas not found in /usr/lib64/sse2
        INFO:   libraries satlas,satlas not found in /usr/lib64
        INFO:   libraries satlas,satlas not found in /usr/lib/sse2
        INFO:   libraries satlas,satlas not found in /usr/lib
        INFO:   libraries satlas,satlas not found in /usr/lib/sse2
        INFO:   libraries satlas,satlas not found in /usr/lib/
        INFO: <class 'numpy.distutils.system_info.atlas_3_10_info'>
        INFO:   NOT AVAILABLE
        INFO:
        INFO: atlas_threads_info:
        INFO: Setting PTATLAS=ATLAS
        INFO:   libraries ptf77blas,ptcblas,atlas not found in /share2/pub/sunhj/sunhj/Soft/miniconda3/envs/test/lib
        INFO:   libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib64
        INFO:   libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
        INFO:   libraries ptf77blas,ptcblas,atlas not found in /usr/lib64/sse2
        INFO:   libraries ptf77blas,ptcblas,atlas not found in /usr/lib64
        INFO:   libraries ptf77blas,ptcblas,atlas not found in /usr/lib/sse2
        INFO:   libraries ptf77blas,ptcblas,atlas not found in /usr/lib
        INFO:   libraries ptf77blas,ptcblas,atlas not found in /usr/lib/sse2
        INFO:   libraries ptf77blas,ptcblas,atlas not found in /usr/lib/
        INFO: <class 'numpy.distutils.system_info.atlas_threads_info'>
        INFO:   NOT AVAILABLE
        INFO:
        INFO: atlas_info:
        INFO:   libraries f77blas,cblas,atlas not found in /share2/pub/sunhj/sunhj/Soft/miniconda3/envs/test/lib
        INFO:   libraries f77blas,cblas,atlas not found in /usr/local/lib64
        INFO:   libraries f77blas,cblas,atlas not found in /usr/local/lib
        INFO:   libraries f77blas,cblas,atlas not found in /usr/lib64/sse2
        INFO:   libraries f77blas,cblas,atlas not found in /usr/lib64
        INFO:   libraries f77blas,cblas,atlas not found in /usr/lib/sse2
        INFO:   libraries f77blas,cblas,atlas not found in /usr/lib
        INFO:   libraries f77blas,cblas,atlas not found in /usr/lib/sse2
        INFO:   libraries f77blas,cblas,atlas not found in /usr/lib/
        INFO: <class 'numpy.distutils.system_info.atlas_info'>
        INFO:   NOT AVAILABLE
        INFO:
        INFO: lapack_info:
        INFO:   libraries lapack not found in ['/share2/pub/sunhj/sunhj/Soft/miniconda3/envs/test/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib', '/usr/lib/']
        INFO:   NOT AVAILABLE
        INFO:
        /tmp/pip-build-env-s872i3d3/overlay/lib/python3.10/site-packages/numpy/distutils/system_info.py:1902: UserWarning:
            Lapack (http://www.netlib.org/lapack/) libraries not found.
            Directories to search for the libraries can be specified in the
            numpy/distutils/site.cfg file (section [lapack]) or by setting
            the LAPACK environment variable.
          return getattr(self, '_calc_info_{}'.format(name))()
        INFO: lapack_src_info:
        INFO:   NOT AVAILABLE
        INFO:
        /tmp/pip-build-env-s872i3d3/overlay/lib/python3.10/site-packages/numpy/distutils/system_info.py:1902: UserWarning:
            Lapack (http://www.netlib.org/lapack/) sources not found.
            Directories to search for the sources can be specified in the
            numpy/distutils/site.cfg file (section [lapack_src]) or by setting
            the LAPACK_SRC environment variable.
          return getattr(self, '_calc_info_{}'.format(name))()
        INFO:   NOT AVAILABLE
        INFO:
        Traceback (most recent call last):
          File "/share2/pub/sunhj/sunhj/Soft/miniconda3/envs/test/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 363, in <module>
            main()
          File "/share2/pub/sunhj/sunhj/Soft/miniconda3/envs/test/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 345, in main
            json_out['return_val'] = hook(**hook_input['kwargs'])
          File "/share2/pub/sunhj/sunhj/Soft/miniconda3/envs/test/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 164, in prepare_metadata_for_build_wheel
            return hook(metadata_directory, config_settings)
          File "/tmp/pip-build-env-s872i3d3/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 161, in prepare_metadata_for_build_wheel
            self.run_setup()
          File "/tmp/pip-build-env-s872i3d3/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 253, in run_setup
            super(_BuildMetaLegacyBackend,
          File "/tmp/pip-build-env-s872i3d3/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 145, in run_setup
            exec(compile(code, __file__, 'exec'), locals())
          File "setup.py", line 588, in <module>
            setup_package()
          File "setup.py", line 584, in setup_package
            setup(**metadata)
          File "/tmp/pip-build-env-s872i3d3/overlay/lib/python3.10/site-packages/numpy/distutils/core.py", line 135, in setup
            config = configuration()
          File "setup.py", line 499, in configuration
            raise NotFoundError(msg)
        numpy.distutils.system_info.NotFoundError: No BLAS/LAPACK libraries found.
        To build Scipy from sources, BLAS & LAPACK libraries need to be installed.
        See site.cfg.example in the Scipy source directory and
        https://docs.scipy.org/doc/scipy/reference/building/index.html for details.
        [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.


  at /share2/pub/sunhj/sunhj/Soft/miniconda3/envs/test/lib/python3.10/site-packages/poetry/utils/env.py:1195 in _run
      1191│                 output = subprocess.check_output(
      1192│                     cmd, stderr=subprocess.STDOUT, **kwargs
      1193│                 )
      1194│         except CalledProcessError as e:
    → 1195│             raise EnvCommandError(e, input=input_)
      1196│
      1197│         return decode(output)
      1198│
      1199│     def execute(self, bin, *args, **kwargs):

  • Installing threadpoolctl (3.1.0)
  • Installing tomli (2.0.1)
  • Installing typing-extensions (4.2.0)

Failed to add packages, reverting the pyproject.toml file to its original content.