Add python and scipy installation checks to tutorial notebooks  #155

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1. jvlatzko commented on Feb 21, 2023

   

   jvlatzko

   on Feb 21, 2023

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   FWIW, I cannot reproduce the problem, it works fine for me, same JAX, same jaxopt.
   Are you somehow calling scipy directly, differnet than the tutorial?
2. Richardjmorton commented on Feb 21, 2023

   

   Richardjmorton

   on Feb 21, 2023

   Last edited by Richardjmorton

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   No. As I mention, I also just opened the notebook on colab and get the same result.

   It works fine if I change the solver, e.g., jaxopt.BFGS
3. jvlatzko commented on Feb 21, 2023

   

   jvlatzko

   on Feb 21, 2023

   Last edited by jvlatzko

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   Can reproduce:
   Run in Colab:

   jax.__version__
0.3.25

   Also,

   print(jax.scipy)
<module 'jax.scipy' from '/usr/local/lib/python3.8/dist-packages/jax/scipy/__init__.py'>

   On my machine,

   print(jax.scipy)
<module 'jax.scipy' from '/home/vincent/.cache/pypoetry/virtualenvs/tinygpenv-7oompMSj-py3.10/lib/python3.10/site-packages/jax/scipy/__init__.py'>

   (Yes, I set up a new env for this).

   What is your scipy stack?
4. Richardjmorton commented on Feb 22, 2023

   

   Richardjmorton

   on Feb 22, 2023

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   Hi, turns out my jupyter kernel was picking the conda base environment, rather than the virtual env. This meant that it was using python 3.8, scipy1.7 as default.

   Not sure why... anyway, looks like the issue is probably due to scipy version.

   Thanks for the help!
5. Richardjmorton

   closed this as completedon Feb 22, 2023
6. Richardjmorton

   reopened this on Feb 22, 2023
7. Richardjmorton commented on Feb 22, 2023

   

   Richardjmorton

   on Feb 22, 2023

   Last edited by Richardjmorton

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   Sorry to close/reopen, thought it might be relevant to add something to the tutroial notebooks to install the correct python/scipy version for using on colab.

   Changed the issue title to reflect this... feel free to finese if it's not descriptive enough.

   I can also fix and open a pull request if desired.
8. Richardjmorton

   changed the title [-]Issue running Fitting a mean function[/-] [+]Add python and scipy installation checks to notebooks [/+] on Feb 22, 2023
9. Richardjmorton

   changed the title [-]Add python and scipy installation checks to notebooks [/-] [+]Add python and scipy installation checks to tutorial notebooks [/+] on Feb 22, 2023
10. dfm commented on Feb 23, 2023

    

    dfm

    on Feb 23, 2023

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    Thanks! Yeah - this looks to be an incompatibility between jaxopt and older versions of scipy. It would be ideal if jaxopt bounded their required version of scipy (1.0.0 is not sufficient :D), but it's probably easier for us to just update scipy in all the notebooks that use jaxopt. If you'd be willing to open a PR that does something like replacing

    try:
        import jaxopt
    except ImportError:
        %pip install -q jaxopt

    with

    try:
        import jaxopt
    except ImportError:
        %pip install -q -U jaxopt scipy

    in the notebooks. I'm not too fussed about documenting this here since it's really a jaxopt issue, rather than a tinygp one, but if you feel strongly that it should be, feel free to include some comments on that too!

    Thanks!