Conda environment build issue

[brunnedu]

Over the last couple days, I suddenly wasn't able to build the conda environment using conda env create -f environment.yml anymore and kept getting the attached error message. After following advice given in yaml/pyyaml#724 (comment) and changing the pyyaml requirement to pyyaml==5.3.1 I was able to build the environment again. Not sure if this is a good permanent fix but I just wanted to raise awareness about this issue.

Error message:

Collecting pyyaml==5.4.1
Using cached PyYAML-5.4.1.tar.gz (175 kB)
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'

Pip subprocess 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-7n51fsjq/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 "/itet-stor/brunnedu/net_scratch/conda_envs/datacomp/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 363, in <module>
      main()
    File "/itet-stor/brunnedu/net_scratch/conda_envs/datacomp/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 "/itet-stor/brunnedu/net_scratch/conda_envs/datacomp/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 130, in get_requires_for_build_wheel
      return hook(config_settings)
    File "/tmp/pip-build-env-7n51fsjq/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 355, in get_requires_for_build_wheel
      return self._get_build_requires(config_settings, requirements=['wheel'])
    File "/tmp/pip-build-env-7n51fsjq/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 325, in _get_build_requires
      self.run_setup()
    File "/tmp/pip-build-env-7n51fsjq/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 341, in run_setup
      exec(code, locals())
    File "<string>", line 271, in <module>
    File "/tmp/pip-build-env-7n51fsjq/overlay/lib/python3.10/site-packages/setuptools/__init__.py", line 103, in setup
      return distutils.core.setup(**attrs)
    File "/tmp/pip-build-env-7n51fsjq/overlay/lib/python3.10/site-packages/setuptools/_distutils/core.py", line 185, in setup
      return run_commands(dist)
    File "/tmp/pip-build-env-7n51fsjq/overlay/lib/python3.10/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
      dist.run_commands()
    File "/tmp/pip-build-env-7n51fsjq/overlay/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands
      self.run_command(cmd)
    File "/tmp/pip-build-env-7n51fsjq/overlay/lib/python3.10/site-packages/setuptools/dist.py", line 989, in run_command
      super().run_command(command)
    File "/tmp/pip-build-env-7n51fsjq/overlay/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
      cmd_obj.run()
    File "/tmp/pip-build-env-7n51fsjq/overlay/lib/python3.10/site-packages/setuptools/command/egg_info.py", line 318, in run
      self.find_sources()
    File "/tmp/pip-build-env-7n51fsjq/overlay/lib/python3.10/site-packages/setuptools/command/egg_info.py", line 326, in find_sources
      mm.run()
    File "/tmp/pip-build-env-7n51fsjq/overlay/lib/python3.10/site-packages/setuptools/command/egg_info.py", line 548, in run
      self.add_defaults()
    File "/tmp/pip-build-env-7n51fsjq/overlay/lib/python3.10/site-packages/setuptools/command/egg_info.py", line 586, in add_defaults
      sdist.add_defaults(self)
    File "/tmp/pip-build-env-7n51fsjq/overlay/lib/python3.10/site-packages/setuptools/command/sdist.py", line 113, in add_defaults
      super().add_defaults()
    File "/tmp/pip-build-env-7n51fsjq/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-7n51fsjq/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-7n51fsjq/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.

failed

CondaEnvException: Pip failed

[gabrielilharco]

Thanks @brunnedu. I'm not able to reproduce this issue on my end, but good to know there's a fix in case others have the same issue

[adv010]

Thanks @brunnedu ! Ran into the same issue on Linux, this was helpful

[vanga]

@gabrielilharco do you think it will be useful to document this in the readme? or change the version to something that works?
I went through the same debugging as the OP where I landed upon that github issue of pyyaml suggesting to use 5.3.1 version.