Google Colab: sleap and scipy issues

[ajuavinett]

Bug description

Colab cannot install sleap, this appears to be an issue with scipy, which will also not install in a Colab environment.

Expected behaviour

After running the following in Colab...

!pip uninstall -y opencv-python opencv-contrib-python
!pip install "sleap[pypi]>=1.3.3"

... I expected sleap to be installed and usable! :) Similarly, after running !pip install scipy==1.9.0 (or other versions) I expect scipy to be installed.

Actual behaviour

After trying sleap install, I receive the following message (after other dependencies successfully install as needed):

Collecting scipy<=1.9.0,>=1.4.1 (from sleap[pypi]>=1.3.3)
  Using cached scipy-1.9.0.tar.gz (42.0 MB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Installing backend dependencies ... done
  error: subprocess-exited-with-error
  
  × Preparing metadata (pyproject.toml) 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.
  Preparing metadata (pyproject.toml) ... error
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.

After trying scipy install, I receive a similar message.

Your personal set up

This is in Colab, which currently ships with Python 3.11.11.

How to reproduce

Run

!pip uninstall -y opencv-python opencv-contrib-python
!pip install "sleap[pypi]>=1.3.3"

or

!pip uninstall -y opencv-python opencv-contrib-python
!pip install "sleap[pypi]>=1.4.1"

or

!pip install scipy==1.9.0

in a new Colab notebook.

[gitttt-1234]

Hi @ajuavinett!

Colab recently updated their python to 3.11 which requires scipy > 1.9. However, for our package we use python 3.7.12 which supports scipy <= 1.9 (we pinned the version to resolve dependency conflicts). We could get past the scipy dependency however, there would again be a conflict with tensorflow with the latest python version. You could try creating a virtual env in colab with python v3.7.12 (it's a bit tricky but might work)

Thanks,

Divya

[ajuavinett]

Thank you! Okay, so I was able to install a virtual environment for Python 3.7 in Colab using the following:

# Install venv if it's not already installed
!sudo apt-get update -y
!sudo apt-get install python3.7-venv 

# Create a virtual environment named 'my_sleap_env'
!python3.7 -m venv my_sleap_env 

# Activate the virtual environment
!source my_sleap_env/bin/activate 

# Install sleap
!pip install sleap[pypi]==1.4.1

This works for getting past issue with scipy and many other packages install just fine. However, now I'm receiving a error: legacy-install-failure with python-rapidjson. I'm wondering if you could think of any way around this?