Fix compatibility with Jupyter notebooks

[dosumis]

Running Jupyter notebooks with cas requires rolling back the jsonschema library version to 4.18. Presumably we can include Jupyter as a dependency and Poetry will deal with this issue?

[ubyndr]

Hi @dosumis,

Can you share details of your environment please?

• Are you using a virtual environment (venv) to run Jupyter?
• What is the Python version you are using?
• Can you confirm you are using the venv as your kernel?

Also, could you try the following steps from scratch and see if they work?

1. Validate your Python version:
   Run one of the following commands:

   python --version

   python3 --version

   python3.10 --version

2. Create a fresh venv:
   Pick a version higher than 3.10.* and use it to create a fresh virtual environment:

   python3.10 -m venv venv

3. Activate the venv:

   source venv/bin/activate

4. Verify the Python version within the venv:
   (I had an alias for python that was mapped to 3.9.* in my environment, so better safe than sorry.)

   python --version

   It should display Python 3.10.*

5. Install Jupyter Notebook within the venv:

   python -m pip install notebook

6. Run Jupyter Notebook:

   python -m jupyter notebook

7. Check the Kernel Source:
   Open the notebook you have been working on and check the upper right-hand corner for the kernel source—it should show "venv".

   

8. Verify the Python version within the Notebook:
   In a notebook cell, run:

   !python --version

9. Install the required dependencies:
   Previously, you might have been using:

   import sys
   !{sys.executable} -m pip install pandas
   !{sys.executable} -m pip install anndata
   !{sys.executable} -m pip install --upgrade cas-tools

   which uses the Python from outside of the venv. Instead, use:

   !pip install pandas
   !pip install anndata
   !pip install --upgrade cas-tools

   This should install cas-tools without any issues.

Could you please follow these steps and let me know if it worked? Thank you.

cc @hkir-dev