安装tsfresh[matrixprofile]及matrixprofile包失败的技术求助

• 使用最新版tsfresh做特征提取时，弹出警告「WARNING - Dependency not available for matrix_profile, this feature will be disabled!」并触发异常
• 创建Python 3.8版本的conda环境后，执行pip install tsfresh[matrixprofile]时pip无法找到对应包
• 切换执行pip install matrixprofile时出现元数据生成失败错误，更换不同版本的matrixprofile及Python版本后问题仍未解决

错误详情如下：

(tsfresh__py_3.8) alessio@Alessios-MBP Alessio % pip install matrixprofile

Collecting matrixprofile
  Using cached matrixprofile-1.1.10.tar.gz (331 kB)
  Preparing metadata (setup.py) ... error
  error: subprocess-exited-with-error
  
  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [47 lines of output]
      /private/var/folders/s_/wcbhtkn953d2yl21zd8frrsr0000gn/T/pip-install-t8b6g2j3/matrixprofile_a5506b66a087426399cf87c5232c0f73/setup.py:4: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
      !!
      
              ********************************************************************************
              Requirements should be satisfied by a PEP 517 installer.
              If you are using pip, you can try `pip install --use-pep517`.
              ********************************************************************************
      
      !!
        dist.Distribution().fetch_build_eggs(['cython>=0.x', 'numpy>=1.16.2', 'wheel'])
      Traceback (most recent call last):
        File "/Users/alessio/miniforge3/envs/tsfresh__py_3.8/lib/python3.8/site-packages/pkg_resources/_vendor/packaging/requirements.py", line 35, in __init__
          parsed = _parse_requirement(requirement_string)
        File "/Users/alessio/miniforge3/envs/tsfresh__py_3.8/lib/python3.8/site-packages/pkg_resources/_vendor/packaging/_parser.py", line 64, in parse_requirement
          return _parse_requirement(Tokenizer(source, rules=DEFAULT_RULES))
        File "/Users/alessio/miniforge3/envs/tsfresh__py_3.8/lib/python3.8/site-packages/pkg_resources/_vendor/packaging/_parser.py", line 82, in _parse_requirement
          url, specifier, marker = _parse_requirement_details(tokenizer)
        File "/Users/alessio/miniforge3/envs/tsfresh__py_3.8/lib/python3.8/site-packages/pkg_resources/_vendor/packaging/_parser.py", line 126, in _parse_requirement_details
          marker = _parse_requirement_marker(
        File "/Users/alessio/miniforge3/envs/tsfresh__py_3.8/lib/python3.8/site-packages/pkg_resources/_vendor/packaging/_parser.py", line 147, in _parse_requirement_marker
          tokenizer.raise_syntax_error(
        File "/Users/alessio/miniforge3/envs/tsfresh__py_3.8/lib/python3.8/site-packages/pkg_resources/_vendor/packaging/_tokenizer.py", line 165, in raise_syntax_error
          raise ParserSyntaxError(
      pkg_resources.extern.packaging._tokenizer.ParserSyntaxError: Expected end or semicolon (after version specifier)
          cython>=0.x
                ~~~^
      
      The above exception was the direct cause of the following exception:
      
      Traceback (most recent call last):
        File "<string>", line 2, in <module>
        File "<pip-setuptools-caller>", line 34, in <module>
        File "/private/var/folders/s_/wcbhtkn953d2yl21zd8frrsr0000gn/T/pip-install-t8b6g2j3/matrixprofile_a5506b66a087426399cf87c5232c0f73/setup.py", line 4, in <module>
          dist.Distribution().fetch_build_eggs(['cython>=0.x', 'numpy>=1.16.2', 'wheel'])
        File "/Users/alessio/miniforge3/envs/tsfresh__py_3.8/lib/python3.8/site-packages/setuptools/dist.py", line 907, in fetch_build_eggs
          return _fetch_build_eggs(self, requires)
        File "/Users/alessio/miniforge3/envs/tsfresh__py_3.8/lib/python3.8/site-packages/setuptools/installer.py", line 38, in _fetch_build_eggs
          resolved_dists = pkg_resources.working_set.resolve(
        File "/Users/alessio/miniforge3/envs/tsfresh__py_3.8/lib/python3.8/site-packages/pkg_resources/__init__.py", line 806, in resolve
          requirements = list(requirements)[::-1]
        File "/Users/alessio/miniforge3/envs/tsfresh__py_3.8/lib/python3.8/site-packages/pkg_resources/__init__.py", line 3174, in __init__
          super(Requirement, self).__init__(requirement_string)
        File "/Users/alessio/miniforge3/envs/tsfresh__py_3.8/lib/python3.8/site-packages/pkg_resources/_vendor/packaging/requirements.py", line 37, in __init__
          raise InvalidRequirement(str(e)) from e
      pkg_resources.extern.packaging.requirements.InvalidRequirement: Expected end or semicolon (after version specifier)
          cython>=0.x
                ~~~^
      [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.

解决办法 #

1. 手动修复matrixprofile源码依赖 #

错误核心是matrixprofile的setup.py中使用了cython>=0.x这种不符合PEP规范的版本号，导致新版本pip/setuptools无法解析。按以下步骤操作：

• 先安装兼容的基础依赖：

  pip install cython>=0.29.0 numpy>=1.16.2 wheel
  

• 克隆matrixprofile源码：

  git clone https://github.com/matrix-profile-foundation/matrixprofile.git
  

• 进入源码目录，修改setup.py第4行，将'cython>=0.x'替换为'cython>=0.29.0'
• 执行本地安装：

  pip install .
  

2. 禁用tsfresh的matrixprofile特征（无需该功能时使用） #

如果不需要矩阵轮廓相关的特征，可以直接在特征提取时禁用该模块，避免触发异常：

from tsfresh import extract_features

# 提取特征时跳过matrixprofile相关计算
features = extract_features(
    your_data,
    kind_to_fc_parameters={"matrix_profile": None}
)

或者直接安装基础版tsfresh，不安装matrixprofile相关依赖：

pip install tsfresh

3. 尝试通过conda安装兼容版本 #

试试conda仓库中的预编译兼容版本：

conda install -c conda-forge matrixprofile

内容的提问来源于stack exchange，提问作者Alessio Bolpagni