Installing SloppyCell

[rjpbonnal]

Dear SloppyCell developers, do you have a working procedure to install SloppyCell, preferably using conda?

Bests, R

[thelahunginjeet]

I've got a lecacy python 2.7 environment for this purpose, but there's no way I used to conda to install. Very likely just distutils (did it so long ago I can't really remember). Sorry I can't be more help.

KB

[RyanGutenkunst]

Hi Kevin,

FYI: Bryan Daniels got SloppyCell ported to Python 3.x, if you ever need it: https://github.com/GutenkunstLab/SloppyCell .

Best, Ryan

On Oct 2, 2023, at 10:41 AM, Kevin Brown @.***> wrote:

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I've got a lecacy python 2.7 environment for this purpose, but there's no way I used to conda to install. Very likely just distutils (did it so long ago I can't really remember). Sorry I can't be more help.

KB

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[thelahunginjeet]

Thanks Ryan - glad to know it didn't just die.

[sbalasbas3]

I am also having trouble with installing SloppyCell.

These are what I have in my own local Anaconda environment:

Python version: 3.12.7 | packaged by Anaconda, Inc. | (main, Oct 4 2024, 13:17:27) [MSC v.1929 64 bit (AMD64)] NumPy version: 2.1.3 SciPy version: 1.14.1 Matplotlib version: 3.9.2

And when I try to install SloppyCell, I get the following error indicating the necessity to have numpy.distutils. I do not know how to resolve this:

  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'error'
Note: you may need to restart the kernel to use updated packages.
  error: subprocess-exited-with-error

  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [6 lines of output]
      Traceback (most recent call last):
        File "<string>", line 2, in <module>
        File "<pip-setuptools-caller>", line 34, in <module>
        File "C:\users\sbalasbasiii\downloads\sloppycell-master\sloppycell-master\setup.py", line 2, in <module>
          import numpy.distutils.core as core
      ModuleNotFoundError: No module named 'numpy.distutils'
      [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.

Would you recommend downgrading to a previous version of either numpy or Python? I also get problems when doing that.

[RyanGutenkunst]

numpy.distutils has been deprecated: https://numpy.org/devdocs/reference/distutils_status_migration.html . From that page, it seems like your best bet is to downgrade to at least Python 3.11. Unfortunately, my group does not have the bandwidth to migrate SloppyCell to a more modern build system. Maybe @bcdaniels does?