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Can't install Cellcano in M1 Mac #6

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nleroy917 opened this issue Jun 19, 2023 · 2 comments · May be fixed by #7
Closed

Can't install Cellcano in M1 Mac #6

nleroy917 opened this issue Jun 19, 2023 · 2 comments · May be fixed by #7

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@nleroy917
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Hi! Thanks for providing this package. I really appreciate the clear documentation.

I had an issue installing Cellcano:
I can't seem to install Cellcano in a fresh virtual environment with python on my M1 MacBook. I first tried to install using the instructions in the documentation:

pip install Cellcano

This gives a really long, and odd stack trace:

pip install Cellcano
Collecting Cellcano
  Using cached Cellcano-1.0.4.tar.gz (15 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
INFO: pip is looking at multiple versions of cellcano to determine which version is compatible with other requirements. This could take a while.
  Using cached Cellcano-1.0.3.tar.gz (15 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
  Using cached Cellcano-1.0.2.tar.gz (15 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
  Using cached Cellcano-1.0.1.tar.gz (15 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
  Using cached Cellcano-1.0.0.tar.gz (15 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
  ╰─> [17 lines of output]
      Traceback (most recent call last):
        File "/Users/nathanleroy/sandbox/cellcano-test/venv/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
          main()
        File "/Users/nathanleroy/sandbox/cellcano-test/venv/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 "/Users/nathanleroy/sandbox/cellcano-test/venv/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 "/private/var/folders/_w/yrr0qqbd52gc6jj0fnqyk8640000gn/T/pip-build-env-fhqejdy_/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 "/private/var/folders/_w/yrr0qqbd52gc6jj0fnqyk8640000gn/T/pip-build-env-fhqejdy_/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 323, in _get_build_requires
          self.run_setup()
        File "/private/var/folders/_w/yrr0qqbd52gc6jj0fnqyk8640000gn/T/pip-build-env-fhqejdy_/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 487, in run_setup
          super(_BuildMetaLegacyBackend,
        File "/private/var/folders/_w/yrr0qqbd52gc6jj0fnqyk8640000gn/T/pip-build-env-fhqejdy_/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 338, in run_setup
          exec(code, locals())
        File "<string>", line 4, in <module>
      FileNotFoundError: [Errno 2] No such file or directory: 'DESCRIPTION'
      [end of output]

It seemed to be getting stuck looking through PyPi versions... so I then cloned the repository and tried to install from source:

git clone https://github.com/marvinquiet/Cellcano.git
cd Cellcano
pip install .

This got me further but gave me a weird FileNotFoundError for the rpy2 dependency:

FileNotFoundError: [Errno 2] No such file or directory: '/private/var/folders/_w/yrr0qqbd52gc6jj0fnqyk8640000gn/T/pip-install-5_qkniwu/rpy2_6697f4de8fe84bab886138ed845b2719/requirements.txt'

Finally, I just manually removed all pinned dependencies from setup.py and specified the tensorflow-macos requirement instead of tensorflow, and then everything was installed nicely. I haven't tested it fully, but I thought I'd open the issue to let you know there might be install issues on an M1.
@marvinquiet
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Owner

Hi Nathan @nleroy917,

I feel really grateful that you have helped me test this on M1. I will update the documentation about this. Please let me know if you encounter any other problems. I do not have an M1 but I will try my best to help.

Sincerely,
Wenjing

@nleroy917
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Thanks! Everything worked great once I messed with the dependencies a bit. It was super easy using the reference data you provided - pipelines like this are very much needed!!!

For reference, these are the reqs I went with:

 install_requires=[
        'tensorflow',
        'six',
        'anndata',
        'scanpy',
        'numpy',
        'h5py',
        'keras',
        'rpy2'
]

I just removed any pinned dependencies.

@lujiaying lujiaying linked a pull request Jun 28, 2023 that will close this issue
setup.py fix for M1 installation #7
Open
@nleroy917 nleroy917 mentioned this issue Nov 16, 2023
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setup.py fix for M1 installation nleroy917/Cellcano
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@marvinquiet @nleroy917