Jammy2211/autolens_workspace

autlens PyYAML issue

Closed this issue · 5 comments

skcajs commented

Hi, I'm having trouble trying to install autolens on my mac (OS ventura 13.4), I'm installing via conda.

Python versions 3.11

When doing pip install autolens...

I get this error:

`

Collecting PyYAML==5.4.1 (from autoconf==2023.7.5.2->autolens)
Using cached 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
╰─> [68 lines of output]
/private/var/folders/wn/sgq3s3995f376l6s7qtqsnqw0000gn/T/pip-build-env-tgni6t47/overlay/lib/python3.11/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 "/Users/sam/anaconda3/envs/autolens/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
      main()
    File "/Users/sam/anaconda3/envs/autolens/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
      json_out['return_val'] = hook(**hook_input['kwargs'])
                               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/Users/sam/anaconda3/envs/autolens/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 118, in get_requires_for_build_wheel
      return hook(config_settings)
             ^^^^^^^^^^^^^^^^^^^^^
    File "/private/var/folders/wn/sgq3s3995f376l6s7qtqsnqw0000gn/T/pip-build-env-tgni6t47/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 355, in get_requires_for_build_wheel
      return self._get_build_requires(config_settings, requirements=['wheel'])
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/private/var/folders/wn/sgq3s3995f376l6s7qtqsnqw0000gn/T/pip-build-env-tgni6t47/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 325, in _get_build_requires
      self.run_setup()
    File "/private/var/folders/wn/sgq3s3995f376l6s7qtqsnqw0000gn/T/pip-build-env-tgni6t47/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 341, in run_setup
      exec(code, locals())
    File "<string>", line 271, in <module>
    File "/private/var/folders/wn/sgq3s3995f376l6s7qtqsnqw0000gn/T/pip-build-env-tgni6t47/overlay/lib/python3.11/site-packages/setuptools/__init__.py", line 107, in setup
      return distutils.core.setup(**attrs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/private/var/folders/wn/sgq3s3995f376l6s7qtqsnqw0000gn/T/pip-build-env-tgni6t47/overlay/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 185, in setup
      return run_commands(dist)
             ^^^^^^^^^^^^^^^^^^
    File "/private/var/folders/wn/sgq3s3995f376l6s7qtqsnqw0000gn/T/pip-build-env-tgni6t47/overlay/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
      dist.run_commands()
    File "/private/var/folders/wn/sgq3s3995f376l6s7qtqsnqw0000gn/T/pip-build-env-tgni6t47/overlay/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands
      self.run_command(cmd)
    File "/private/var/folders/wn/sgq3s3995f376l6s7qtqsnqw0000gn/T/pip-build-env-tgni6t47/overlay/lib/python3.11/site-packages/setuptools/dist.py", line 1233, in run_command
      super().run_command(command)
    File "/private/var/folders/wn/sgq3s3995f376l6s7qtqsnqw0000gn/T/pip-build-env-tgni6t47/overlay/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
      cmd_obj.run()
    File "/private/var/folders/wn/sgq3s3995f376l6s7qtqsnqw0000gn/T/pip-build-env-tgni6t47/overlay/lib/python3.11/site-packages/setuptools/command/egg_info.py", line 319, in run
      self.find_sources()
    File "/private/var/folders/wn/sgq3s3995f376l6s7qtqsnqw0000gn/T/pip-build-env-tgni6t47/overlay/lib/python3.11/site-packages/setuptools/command/egg_info.py", line 327, in find_sources
      mm.run()
    File "/private/var/folders/wn/sgq3s3995f376l6s7qtqsnqw0000gn/T/pip-build-env-tgni6t47/overlay/lib/python3.11/site-packages/setuptools/command/egg_info.py", line 549, in run
      self.add_defaults()
    File "/private/var/folders/wn/sgq3s3995f376l6s7qtqsnqw0000gn/T/pip-build-env-tgni6t47/overlay/lib/python3.11/site-packages/setuptools/command/egg_info.py", line 587, in add_defaults
      sdist.add_defaults(self)
    File "/private/var/folders/wn/sgq3s3995f376l6s7qtqsnqw0000gn/T/pip-build-env-tgni6t47/overlay/lib/python3.11/site-packages/setuptools/command/sdist.py", line 113, in add_defaults
      super().add_defaults()
    File "/private/var/folders/wn/sgq3s3995f376l6s7qtqsnqw0000gn/T/pip-build-env-tgni6t47/overlay/lib/python3.11/site-packages/setuptools/_distutils/command/sdist.py", line 251, in add_defaults
      self._add_defaults_ext()
    File "/private/var/folders/wn/sgq3s3995f376l6s7qtqsnqw0000gn/T/pip-build-env-tgni6t47/overlay/lib/python3.11/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 "/private/var/folders/wn/sgq3s3995f376l6s7qtqsnqw0000gn/T/pip-build-env-tgni6t47/overlay/lib/python3.11/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.
`

I think this is a problem with PyYAML version 5.4.1. It seems widely documented issue and they suggest using 5.3...

I suspect, as also stated in the issue below, PyYAML needs to be version 6 to be compatible with Python 3.10 and 3.11.

yaml/pyyaml#724

rhayes777 commented
skcajs commented

Hi Rhyes777,

I've created a new conda environment with python version 3.9 and 3.10, and both produce the same error.
The specific python version I'm using now is Python 3.10.12

rhayes777 commented
skcajs commented

Unfortunately I think it forces 5.4.1 as per this line "Collecting PyYAML==5.4.1".

Will build from source for now. :)

rhayes777 commented
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