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MacOS Installation Issues #34

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rmarable opened this issue Oct 31, 2023 · 3 comments
Closed

MacOS Installation Issues #34

rmarable opened this issue Oct 31, 2023 · 3 comments

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@rmarable
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Greetings,

We are running into issues installing biomage-utils on a M2 Mac running Ventura (macOS 13.6 - 22G120 with kernel version 22.6.0) and Python-3.11.6 managed by Homebrew.

Here is the output from a failed attempt. Please advise if there is any additional data we can provide.


❯ make install
==> Cleaning up...
    [✓]

==> Creating virtual environment...
    [✓]

==> Installing utility and dependencies...
Requirement already satisfied: pip in ./venv/lib/python3.11/site-packages (23.2.1)
Collecting pip
  Obtaining dependency information for pip from https://files.pythonhosted.org/packages/47/6a/453160888fab7c6a432a6e25f8afe6256d0d9f2cbd25971021da6491d899/pip-23.3.1-py3-none-any.whl.metadata
  Using cached pip-23.3.1-py3-none-any.whl.metadata (3.5 kB)
Using cached pip-23.3.1-py3-none-any.whl (2.1 MB)
Installing collected packages: pip
  Attempting uninstall: pip
    Found existing installation: pip 23.2.1
    Uninstalling pip-23.2.1:
      Successfully uninstalled pip-23.2.1
Successfully installed pip-23.3.1
Obtaining file:///Users/rmarable/src/scicomp/biomage/biomage-utils
  Installing build dependencies ... done
  Checking if build backend supports build_editable ... done
  Getting requirements to build editable ... done
  Preparing editable metadata (pyproject.toml) ... done
Collecting anybase32==1.1.0 (from biomage-utils==0.0.1)
  Using cached anybase32-1.1.0.zip (3.4 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting blessed==1.19.1 (from biomage-utils==0.0.1)
  Using cached blessed-1.19.1-py2.py3-none-any.whl (58 kB)
Collecting boto3==1.17.93 (from biomage-utils==0.0.1)
  Using cached boto3-1.17.93-py2.py3-none-any.whl (131 kB)
Collecting botocore==1.20.93 (from biomage-utils==0.0.1)
  Using cached botocore-1.20.93-py2.py3-none-any.whl (7.6 MB)
Collecting biomage-programmatic-interface==0.0.39 (from biomage-utils==0.0.1)
  Using cached biomage_programmatic_interface-0.0.39-py3-none-any.whl (9.3 kB)
Collecting backoff==2.2.1 (from biomage-utils==0.0.1)
  Using cached backoff-2.2.1-py3-none-any.whl (15 kB)
Collecting certifi==2021.10.8 (from biomage-utils==0.0.1)
  Using cached certifi-2021.10.8-py2.py3-none-any.whl (149 kB)
Collecting cffi==1.15.0 (from biomage-utils==0.0.1)
  Using cached cffi-1.15.0.tar.gz (484 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting cfn-flip==1.2.3 (from biomage-utils==0.0.1)
  Using cached cfn_flip-1.2.3.tar.gz (10 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting chardet==4.0.0 (from biomage-utils==0.0.1)
  Using cached chardet-4.0.0-py2.py3-none-any.whl (178 kB)
Collecting click==8.0.1 (from biomage-utils==0.0.1)
  Using cached click-8.0.1-py3-none-any.whl (97 kB)
Collecting deepdiff==5.5.0 (from biomage-utils==0.0.1)
  Using cached deepdiff-5.5.0-py3-none-any.whl (66 kB)
Collecting Deprecated==1.2.13 (from biomage-utils==0.0.1)
  Using cached Deprecated-1.2.13-py2.py3-none-any.whl (9.6 kB)
Collecting idna==2.10 (from biomage-utils==0.0.1)
  Using cached idna-2.10-py2.py3-none-any.whl (58 kB)
Collecting inquirer==2.10.1 (from biomage-utils==0.0.1)
  Using cached inquirer-2.10.1-py3-none-any.whl (17 kB)
Collecting jmespath==0.10.0 (from biomage-utils==0.0.1)
  Using cached jmespath-0.10.0-py2.py3-none-any.whl (24 kB)
Collecting numpy==1.22.0 (from biomage-utils==0.0.1)
  Using cached numpy-1.22.0.zip (11.3 MB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting ordered-set==4.0.2 (from biomage-utils==0.0.1)
  Using cached ordered-set-4.0.2.tar.gz (10 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting pandas==1.3.4 (from biomage-utils==0.0.1)
  Using cached pandas-1.3.4.tar.gz (4.7 MB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting prompt-tool-kit==1.0.14 (from biomage-utils==0.0.1)
  Using cached prompt_tool_kit-1.0.14-py3-none-any.whl (242 kB)
Collecting prompt-toolkit==1.0.14 (from biomage-utils==0.0.1)
  Using cached prompt_toolkit-1.0.14-py3-none-any.whl (248 kB)
Collecting pycparser==2.21 (from biomage-utils==0.0.1)
  Using cached pycparser-2.21-py2.py3-none-any.whl (118 kB)
Collecting PyGithub==1.55 (from biomage-utils==0.0.1)
  Using cached PyGithub-1.55-py3-none-any.whl (291 kB)
Collecting Pygments==2.11.1 (from biomage-utils==0.0.1)
  Using cached Pygments-2.11.1-py3-none-any.whl (1.1 MB)
Collecting PyJWT==2.3.0 (from biomage-utils==0.0.1)
  Using cached PyJWT-2.3.0-py3-none-any.whl (16 kB)
Collecting PyNaCl==1.4.0 (from biomage-utils==0.0.1)
  Using cached PyNaCl-1.4.0.tar.gz (3.4 MB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting python-dateutil==2.8.2 (from biomage-utils==0.0.1)
  Using cached python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
Collecting python-editor==1.0.4 (from biomage-utils==0.0.1)
  Using cached python_editor-1.0.4-py3-none-any.whl (4.9 kB)
Collecting pytz==2021.3 (from biomage-utils==0.0.1)
  Using cached pytz-2021.3-py2.py3-none-any.whl (503 kB)
Collecting random-name==0.1.1 (from biomage-utils==0.0.1)
  Using cached random_name-0.1.1.tar.gz (4.7 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting readchar==4.0.3 (from biomage-utils==0.0.1)
  Using cached readchar-4.0.3-py3-none-any.whl (8.4 kB)
Collecting regex==2021.11.10 (from biomage-utils==0.0.1)
  Using cached regex-2021.11.10.tar.gz (702 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting requests==2.25.1 (from biomage-utils==0.0.1)
  Using cached requests-2.25.1-py2.py3-none-any.whl (61 kB)
Collecting ruamel.yaml==0.17.21 (from biomage-utils==0.0.1)
  Using cached ruamel.yaml-0.17.21-py3-none-any.whl (109 kB)
Collecting ruamel.yaml.clib==0.2.7 (from biomage-utils==0.0.1)
  Using cached ruamel.yaml.clib-0.2.7-cp311-cp311-macosx_13_0_arm64.whl.metadata (2.2 kB)
Collecting s3transfer==0.4.2 (from biomage-utils==0.0.1)
  Using cached s3transfer-0.4.2-py2.py3-none-any.whl (79 kB)
Collecting six==1.16.0 (from biomage-utils==0.0.1)
  Using cached six-1.16.0-py2.py3-none-any.whl (11 kB)
Collecting tabulate==0.9.0 (from biomage-utils==0.0.1)
  Using cached tabulate-0.9.0-py3-none-any.whl (35 kB)
Collecting urllib3==1.26.7 (from biomage-utils==0.0.1)
  Using cached urllib3-1.26.7-py2.py3-none-any.whl (138 kB)
Collecting wcwidth==0.2.5 (from biomage-utils==0.0.1)
  Using cached wcwidth-0.2.5-py2.py3-none-any.whl (30 kB)
Collecting wrapt==1.13.3 (from biomage-utils==0.0.1)
  Using cached wrapt-1.13.3.tar.gz (48 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... error
  error: subprocess-exited-with-error

  × Preparing metadata (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [85 lines of output]
      Traceback (most recent call last):
        File "/private/var/folders/qg/kdkb1cv92k9dyx577psp88bw0000gn/T/pip-build-env-ynuh3zzh/overlay/lib/python3.11/site-packages/setuptools/config/expand.py", line 81, in __getattr__
          return next(
                 ^^^^^
        File "/private/var/folders/qg/kdkb1cv92k9dyx577psp88bw0000gn/T/pip-build-env-ynuh3zzh/overlay/lib/python3.11/site-packages/setuptools/config/expand.py", line 82, in <genexpr>
          ast.literal_eval(value)
        File "/opt/homebrew/Cellar/[email protected]/3.11.6/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ast.py", line 110, in literal_eval
          return _convert(node_or_string)
                 ^^^^^^^^^^^^^^^^^^^^^^^^
        File "/opt/homebrew/Cellar/[email protected]/3.11.6/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ast.py", line 109, in _convert
          return _convert_signed_num(node)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/opt/homebrew/Cellar/[email protected]/3.11.6/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ast.py", line 83, in _convert_signed_num
          return _convert_num(node)
                 ^^^^^^^^^^^^^^^^^^
        File "/opt/homebrew/Cellar/[email protected]/3.11.6/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ast.py", line 74, in _convert_num
          _raise_malformed_node(node)
        File "/opt/homebrew/Cellar/[email protected]/3.11.6/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ast.py", line 71, in _raise_malformed_node
          raise ValueError(msg + f': {node!r}')
      ValueError: malformed node or string on line 2: <ast.Call object at 0x1010de620>

      The above exception was the direct cause of the following exception:

      Traceback (most recent call last):
        File "/private/var/folders/qg/kdkb1cv92k9dyx577psp88bw0000gn/T/pip-build-env-ynuh3zzh/overlay/lib/python3.11/site-packages/setuptools/config/expand.py", line 193, in read_attr
          return getattr(StaticModule(module_name, spec), attr_name)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/private/var/folders/qg/kdkb1cv92k9dyx577psp88bw0000gn/T/pip-build-env-ynuh3zzh/overlay/lib/python3.11/site-packages/setuptools/config/expand.py", line 87, in __getattr__
          raise AttributeError(f"{self.name} has no attribute {attr}") from e
      AttributeError: wrapt has no attribute __version__

      During handling of the above exception, another exception occurred:

      Traceback (most recent call last):
        File "/Users/rmarable/src/scicomp/biomage/biomage-utils/venv/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
          main()
        File "/Users/rmarable/src/scicomp/biomage/biomage-utils/venv/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/rmarable/src/scicomp/biomage/biomage-utils/venv/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 149, in prepare_metadata_for_build_wheel
          return hook(metadata_directory, config_settings)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/private/var/folders/qg/kdkb1cv92k9dyx577psp88bw0000gn/T/pip-build-env-ynuh3zzh/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 396, in prepare_metadata_for_build_wheel
          self.run_setup()
        File "/private/var/folders/qg/kdkb1cv92k9dyx577psp88bw0000gn/T/pip-build-env-ynuh3zzh/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 507, in run_setup
          super(_BuildMetaLegacyBackend, self).run_setup(setup_script=setup_script)
        File "/private/var/folders/qg/kdkb1cv92k9dyx577psp88bw0000gn/T/pip-build-env-ynuh3zzh/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 341, in run_setup
          exec(code, locals())
        File "<string>", line 41, in <module>
        File "/private/var/folders/qg/kdkb1cv92k9dyx577psp88bw0000gn/T/pip-build-env-ynuh3zzh/overlay/lib/python3.11/site-packages/setuptools/__init__.py", line 103, in setup
          return distutils.core.setup(**attrs)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/private/var/folders/qg/kdkb1cv92k9dyx577psp88bw0000gn/T/pip-build-env-ynuh3zzh/overlay/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 159, in setup
          dist.parse_config_files()
        File "/private/var/folders/qg/kdkb1cv92k9dyx577psp88bw0000gn/T/pip-build-env-ynuh3zzh/overlay/lib/python3.11/site-packages/setuptools/dist.py", line 649, in parse_config_files
          setupcfg.parse_configuration(
        File "/private/var/folders/qg/kdkb1cv92k9dyx577psp88bw0000gn/T/pip-build-env-ynuh3zzh/overlay/lib/python3.11/site-packages/setuptools/config/setupcfg.py", line 189, in parse_configuration
          meta.parse()
        File "/private/var/folders/qg/kdkb1cv92k9dyx577psp88bw0000gn/T/pip-build-env-ynuh3zzh/overlay/lib/python3.11/site-packages/setuptools/config/setupcfg.py", line 500, in parse
          section_parser_method(section_options)
        File "/private/var/folders/qg/kdkb1cv92k9dyx577psp88bw0000gn/T/pip-build-env-ynuh3zzh/overlay/lib/python3.11/site-packages/setuptools/config/setupcfg.py", line 475, in parse_section
          self[name] = value
          ~~~~^^^^^^
        File "/private/var/folders/qg/kdkb1cv92k9dyx577psp88bw0000gn/T/pip-build-env-ynuh3zzh/overlay/lib/python3.11/site-packages/setuptools/config/setupcfg.py", line 293, in __setitem__
          parsed = self.parsers.get(option_name, lambda x: x)(value)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/private/var/folders/qg/kdkb1cv92k9dyx577psp88bw0000gn/T/pip-build-env-ynuh3zzh/overlay/lib/python3.11/site-packages/setuptools/config/setupcfg.py", line 606, in _parse_version
          return expand.version(self._parse_attr(value, self.package_dir, self.root_dir))
                                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/private/var/folders/qg/kdkb1cv92k9dyx577psp88bw0000gn/T/pip-build-env-ynuh3zzh/overlay/lib/python3.11/site-packages/setuptools/config/setupcfg.py", line 417, in _parse_attr
          return expand.read_attr(attr_desc, package_dir, root_dir)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/private/var/folders/qg/kdkb1cv92k9dyx577psp88bw0000gn/T/pip-build-env-ynuh3zzh/overlay/lib/python3.11/site-packages/setuptools/config/expand.py", line 196, in read_attr
          module = _load_spec(spec, module_name)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/private/var/folders/qg/kdkb1cv92k9dyx577psp88bw0000gn/T/pip-build-env-ynuh3zzh/overlay/lib/python3.11/site-packages/setuptools/config/expand.py", line 216, in _load_spec
          spec.loader.exec_module(module)  # type: ignore
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "<frozen importlib._bootstrap_external>", line 940, in exec_module
        File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed
        File "/private/var/folders/qg/kdkb1cv92k9dyx577psp88bw0000gn/T/pip-install-rxli4ixa/wrapt_1e7c9461e64f4d57816b0b1eb20a71d9/src/wrapt/__init__.py", line 10, in <module>
          from .decorators import (adapter_factory, AdapterFactory, decorator,
        File "/private/var/folders/qg/kdkb1cv92k9dyx577psp88bw0000gn/T/pip-install-rxli4ixa/wrapt_1e7c9461e64f4d57816b0b1eb20a71d9/src/wrapt/decorators.py", line 34, in <module>
          from inspect import ismethod, isclass, formatargspec
      ImportError: cannot import name 'formatargspec' from 'inspect' (/opt/homebrew/Cellar/[email protected]/3.11.6/Frameworks/Python.framework/Versions/3.11/lib/python3.11/inspect.py)
      [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.
make: *** [install] Error 1
@gerbeldo
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gerbeldo commented Oct 31, 2023 •
edited
Loading

The issue might be the python version. If I remember correctly, python 3.9.xx should work. I do not have access to an Apple Silicon mac to test though, sorry.

@gerbeldo
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The issue is the wrapt package. The version we have locked can't be installed in python 3.11. Using a venv with 3.9 should solve it.

@rmarable
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rmarable commented Nov 21, 2023 •
edited
Loading

Hi German,

Thanks, using a venv with 3.9 worked as expected.

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@rmarable @gerbeldo