TJU-CMC-Org / MINTmap

This is the code repository, to download MINTmap for basic usage please visit our website at
https://cm.jefferson.edu/MINTmap/
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MINTmap v2.0 alpha installation #7

Open cavelandiah opened 1 week ago

cavelandiah commented 1 week ago

Hi there,

Following the installation instructions from the README.md file for the v2.0-alpha release, it’s currently not possible to install MINTmap. After creating the conda environment and executing:

pip install dist/MINTmap-2.0a0-py3-none-any.whl

there appears to be an issue with the pip wheel:

Processing ./dist/MINTmap-2.0a0-py3-none-any.whl
Collecting Jinja2<3.0.0,>=2.11.2 (from MINTmap==2.0a0)
  Downloading Jinja2-2.11.3-py2.py3-none-any.whl.metadata (3.5 kB)
Collecting PyYAML<6.0.0,>=5.3.1 (from MINTmap==2.0a0)
  Downloading PyYAML-5.4.1.tar.gz (175 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... error
  error: subprocess-exited-with-error

  × Getting requirements to build wheel did not run successfully.
  │ exit code: 1
  ╰─> [65 lines of output]
      running egg_info
      writing lib3/PyYAML.egg-info/PKG-INFO
      writing dependency_links to lib3/PyYAML.egg-info/dependency_links.txt
      writing top-level names to lib3/PyYAML.egg-info/top_level.txt
      Traceback (most recent call last):
        File "/home/userx/anaconda3/envs/snowflake/lib/python3.13/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
          main()
          ~~~~^^
        File "/home/userx/anaconda3/envs/snowflake/lib/python3.13/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
          json_out['return_val'] = hook(**hook_input['kwargs'])
                                   ~~~~^^^^^^^^^^^^^^^^^^^^^^^^
        File "/home/userx/anaconda3/envs/snowflake/lib/python3.13/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 118, in get_requires_for_build_wheel
          return hook(config_settings)
        File "/tmp/pip-build-env-c_mxxpfc/overlay/lib/python3.13/site-packages/setuptools/build_meta.py", line 334, in get_requires_for_build_wheel
          return self._get_build_requires(config_settings, requirements=[])
                 ~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/tmp/pip-build-env-c_mxxpfc/overlay/lib/python3.13/site-packages/setuptools/build_meta.py", line 304, in _get_build_requires
          self.run_setup()
          ~~~~~~~~~~~~~~^^
        File "/tmp/pip-build-env-c_mxxpfc/overlay/lib/python3.13/site-packages/setuptools/build_meta.py", line 320, in run_setup
          exec(code, locals())
          ~~~~^^^^^^^^^^^^^^^^
        File "<string>", line 271, in <module>
        File "/tmp/pip-build-env-c_mxxpfc/overlay/lib/python3.13/site-packages/setuptools/__init__.py", line 117, in setup
          return distutils.core.setup(**attrs)
                 ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
        File "/tmp/pip-build-env-c_mxxpfc/overlay/lib/python3.13/site-packages/setuptools/_distutils/core.py", line 183, in setup
          return run_commands(dist)
        File "/tmp/pip-build-env-c_mxxpfc/overlay/lib/python3.13/site-packages/setuptools/_distutils/core.py", line 199, in run_commands
          dist.run_commands()
          ~~~~~~~~~~~~~~~~~^^
        File "/tmp/pip-build-env-c_mxxpfc/overlay/lib/python3.13/site-packages/setuptools/_distutils/dist.py", line 954, in run_commands
          self.run_command(cmd)
          ~~~~~~~~~~~~~~~~^^^^^
        File "/tmp/pip-build-env-c_mxxpfc/overlay/lib/python3.13/site-packages/setuptools/dist.py", line 994, in run_command
          super().run_command(command)
          ~~~~~~~~~~~~~~~~~~~^^^^^^^^^
        File "/tmp/pip-build-env-c_mxxpfc/overlay/lib/python3.13/site-packages/setuptools/_distutils/dist.py", line 973, in run_command
          cmd_obj.run()
          ~~~~~~~~~~~^^
        File "/tmp/pip-build-env-c_mxxpfc/overlay/lib/python3.13/site-packages/setuptools/command/egg_info.py", line 312, in run
          self.find_sources()
          ~~~~~~~~~~~~~~~~~^^
        File "/tmp/pip-build-env-c_mxxpfc/overlay/lib/python3.13/site-packages/setuptools/command/egg_info.py", line 320, in find_sources
          mm.run()
          ~~~~~~^^
        File "/tmp/pip-build-env-c_mxxpfc/overlay/lib/python3.13/site-packages/setuptools/command/egg_info.py", line 543, in run
          self.add_defaults()
          ~~~~~~~~~~~~~~~~~^^
        File "/tmp/pip-build-env-c_mxxpfc/overlay/lib/python3.13/site-packages/setuptools/command/egg_info.py", line 581, in add_defaults
          sdist.add_defaults(self)
          ~~~~~~~~~~~~~~~~~~^^^^^^
        File "/tmp/pip-build-env-c_mxxpfc/overlay/lib/python3.13/site-packages/setuptools/command/sdist.py", line 109, in add_defaults
          super().add_defaults()
          ~~~~~~~~~~~~~~~~~~~~^^
        File "/tmp/pip-build-env-c_mxxpfc/overlay/lib/python3.13/site-packages/setuptools/_distutils/command/sdist.py", line 238, in add_defaults
          self._add_defaults_ext()
          ~~~~~~~~~~~~~~~~~~~~~~^^
        File "/tmp/pip-build-env-c_mxxpfc/overlay/lib/python3.13/site-packages/setuptools/_distutils/command/sdist.py", line 323, in _add_defaults_ext
          self.filelist.extend(build_ext.get_source_files())
                               ~~~~~~~~~~~~~~~~~~~~~~~~~~^^
        File "<string>", line 201, in get_source_files
        File "/tmp/pip-build-env-c_mxxpfc/overlay/lib/python3.13/site-packages/setuptools/_distutils/cmd.py", line 107, in __getattr__
          raise AttributeError(attr)
      AttributeError: cython_sources
      [end of output]

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

× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> See above for output.

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

Do I miss something? Thanks in advance for your help.

phillipeloher commented 1 week ago

Hello, We have seen something like that before. Do you mind trying to revert PyYAML to version 5.3.1 and then reinstall the WHL? If that helps, we will try to fix shortly.