Run poetry install failed with the dependency error of pyyaml 5.4.1

[alienzj]

Describe the bug

Run poetry install failed when construct the development environment for MegaQC

To Reproduce

Steps to reproduce the behavior:

1. git clone https://github.com/ewels/MegaQC
2. cd MegaQC
3. poetry install

Error:

Installing dependencies from lock file

Package operations: 24 installs, 0 updates, 0 removals

  • Installing pyyaml (5.4.1)

  EnvCommandError

  Command ['/home/jiezhu/.cache/pypoetry/virtualenvs/megaqc-NrxhcUWU-py3.10/bin/pip', 'install', '--no-deps', 'file:///home/jiezhu/.cache/pypoetry/artifacts/b6/23/45/f5dfdd6e8ba0f620504858ddeb20b47f50b03d0c4b18f873f6575d2e78/PyYAML-5.4.1.tar.gz'] errored with the following return code 1, and output:
  Processing /home/jiezhu/.cache/pypoetry/artifacts/b6/23/45/f5dfdd6e8ba0f620504858ddeb20b47f50b03d0c4b18f873f6575d2e78/PyYAML-5.4.1.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 'error'
    error: subprocess-exited-with-error

    × Getting requirements to build wheel did not run successfully.
    │ exit code: 1
    ╰─> [62 lines of output]
        /tmp/pip-build-env-uvlssdzr/overlay/lib/python3.10/site-packages/setuptools/config/setupcfg.py:293: _DeprecatedConfig: Deprecated config in `setup.cfg`
        !!

                ********************************************************************************
                The license_file parameter is deprecated, use license_files instead.

                By 2023-Oct-30, you need to update your project and remove deprecated calls
                or your builds will no longer be supported.

                See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
                ********************************************************************************

        !!
          parsed = self.parsers.get(option_name, lambda x: x)(value)
        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/jiezhu/.cache/pypoetry/virtualenvs/megaqc-NrxhcUWU-py3.10/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
            main()
          File "/home/jiezhu/.cache/pypoetry/virtualenvs/megaqc-NrxhcUWU-py3.10/lib/python3.10/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/jiezhu/.cache/pypoetry/virtualenvs/megaqc-NrxhcUWU-py3.10/lib/python3.10/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-uvlssdzr/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 341, in get_requires_for_build_wheel
            return self._get_build_requires(config_settings, requirements=['wheel'])
          File "/tmp/pip-build-env-uvlssdzr/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 323, in _get_build_requires
            self.run_setup()
          File "/tmp/pip-build-env-uvlssdzr/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 338, in run_setup
            exec(code, locals())
          File "<string>", line 271, in <module>
          File "/tmp/pip-build-env-uvlssdzr/overlay/lib/python3.10/site-packages/setuptools/__init__.py", line 107, in setup
            return distutils.core.setup(**attrs)
          File "/tmp/pip-build-env-uvlssdzr/overlay/lib/python3.10/site-packages/setuptools/_distutils/core.py", line 185, in setup
            return run_commands(dist)
          File "/tmp/pip-build-env-uvlssdzr/overlay/lib/python3.10/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
            dist.run_commands()
          File "/tmp/pip-build-env-uvlssdzr/overlay/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands
            self.run_command(cmd)
          File "/tmp/pip-build-env-uvlssdzr/overlay/lib/python3.10/site-packages/setuptools/dist.py", line 1234, in run_command
            super().run_command(command)
          File "/tmp/pip-build-env-uvlssdzr/overlay/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
            cmd_obj.run()
          File "/tmp/pip-build-env-uvlssdzr/overlay/lib/python3.10/site-packages/setuptools/command/egg_info.py", line 314, in run
            self.find_sources()
          File "/tmp/pip-build-env-uvlssdzr/overlay/lib/python3.10/site-packages/setuptools/command/egg_info.py", line 322, in find_sources
            mm.run()
          File "/tmp/pip-build-env-uvlssdzr/overlay/lib/python3.10/site-packages/setuptools/command/egg_info.py", line 551, in run
            self.add_defaults()
          File "/tmp/pip-build-env-uvlssdzr/overlay/lib/python3.10/site-packages/setuptools/command/egg_info.py", line 589, in add_defaults
            sdist.add_defaults(self)
          File "/tmp/pip-build-env-uvlssdzr/overlay/lib/python3.10/site-packages/setuptools/command/sdist.py", line 104, in add_defaults
            super().add_defaults()
          File "/tmp/pip-build-env-uvlssdzr/overlay/lib/python3.10/site-packages/setuptools/_distutils/command/sdist.py", line 251, in add_defaults
            self._add_defaults_ext()
          File "/tmp/pip-build-env-uvlssdzr/overlay/lib/python3.10/site-packages/setuptools/_distutils/command/sdist.py", line 336, 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-uvlssdzr/overlay/lib/python3.10/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.

  [notice] A new release of pip is available: 23.1 -> 23.2.1
  [notice] To update, run: pip install --upgrade pip

  at ~/.conda/envs/bioenv3.10/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):

Expected behavior poetry install successfully.

System [please complete the following information, if relevant to the issue]:

• OS: e.g. [Ubuntu 20.04.5 LTS]
• Python: [Python 3.10.8]
• Node: [v10.19.0]
• MegaQC: [commit: cf073f0d79ba30b5cf99cd5159b66018b9d9b9c6]

Additional context

[fgvieira]

Same when using pip, but it seems to be related to pyyaml (see yaml/pyyaml#601).

The second workaround here worked for me.