How to use latest pyodide kernel

[kp992]

Hi,
I am using the template to run some of the lectures and the version of pandas is 1.5.3. I would like to upgrade pyodide to the latest version. How can I do that?

[Tom-van-Woudenberg]

@DianaBanta ?

[rlanzafame]

Hi @kp992 could you provide a link to the page where you are trying to do this so we can see better if we can help?
To be honest, most of us at TeachBooks use the sphinx-thebe extension "as-is" and adapt the packages that are imported and used by Pyodide, rather than changing Pyodide itself. You should be able to specify the pandas version without changing pyodide, for example with micropip, but it's hard to tell without an example for your use case. Here is the relevant micropip page:
https://micropip.pyodide.org/en/stable/project/usage.html

[kp992]

https://kp992.github.io/intro-wasm-demo/main/inflation_history.html - I am trying to install pandas 2.1.4 using

%pip install "pandas==2.1.4"

which throws

ValueError: Can't find a pure Python 3 wheel for 'pandas==2.1.4'.
See: https://pyodide.org/en/stable/usage/faq.html#why-can-t-micropip-find-a-pure-python-wheel-for-a-package
You can use `await micropip.install(..., keep_going=True)` to get a list of all packages with missing wheels.

[rlanzafame]

OK, I see. The issue is that our TeachBooks template uses a custom version of the sphinx thebe package, which works by loading a few key *.whl files in the _build/html/_static/pypi subdirectory of the built book, one of which is pyodide-kernel version 0.2.0.
When running this in the interactive page:

await micropip.install("pandas")
micropip.list()

I can see that pyodide-kernel is 0.2.0 and micropip is 0.5.0. I don't know how to see what wheels micropip uses for Pandas as the repo structure in 0.5.0 is very different than the current version 0.9.0, but i suspect that this is why pandas higher than 1.5.3 can be loaded.

We are in the process of setting up an improved (and public facing) sphinx extension for Thebe, it will be at github.com/TeachBooks/TeachBooks-Sphinx-Thebe, and you can already see how the wheel files are set up in the source code in ./src/teachbooks_sphinx_thebe/_thebe_static/pypi.

I tried messing with unloading and reloading micropip to try and get 0.9.0 in the pyodide runtime environment, but that is beyond my abilities i think. So i see a couple ways forward:

1. Wait until we get our new teachbooks-sphinx-thebe package ready and then we can look at changing pyodide versions. this will be done by @DianaBanta in the coming weeks/months
2. if you are willing to experiment with the pyodide wheel files yourself and set up thebe-lite in your book repo locally you can look at this repository which still contains an old and unused subdirectory thebe_lite. this is how we used to use the interactive python feature before we set it up as a sphinx extension. I believe commit 78bb6c8 is the one which changed this behavior, and this is the state of the files that illustrates the last stable setup in this configuration.

complete package list from list() above:

Name               | Version | Source
------------------ | ------- | -----------------------------------------------------------------------------------------
packaging          | 23.1    | pyodide
micropip           | 0.5.0   | pyodide
piplite            | 0.2.0   | https://kp992.github.io/intro-wasm-demo/main//_static/pypi/piplite-0.2.0-py3-none-any.whl
ipykernel          | 6.9.2   | pypi
traitlets          | 5.14.3  | pypi
comm               | 0.2.2   | pypi
pyodide-kernel     | 0.2.0   | pypi
matplotlib-inline  | 0.1.7   | pypi
wcwidth            | 0.2.13  | pypi
prompt_toolkit     | 3.0.50  | pypi
ptyprocess         | 0.7.0   | pypi
pexpect            | 4.9.0   | pypi
asttokens          | 3.0.0   | pypi
executing          | 2.2.0   | pypi
pure_eval          | 0.2.3   | pypi
stack-data         | 0.6.3   | pypi
ipython            | 8.21.0  | pypi
decorator          | 5.1.1   | pyodide
parso              | 0.8.3   | pyodide
Pygments           | 2.16.1  | pyodide
jedi               | 0.19.0  | pyodide
widgetsnbextension | 4.0.13  | pypi
jupyterlab_widgets | 3.0.13  | pypi
ipywidgets         | 8.1.5   | pypi
six                | 1.16.0  | pyodide
python-dateutil    | 2.8.2   | pyodide
pytz               | 2023.3  | pyodide
numpy              | 1.25.2  | pyodide
pandas             | 1.5.3   | pyodide
sqlite3            | 1.0.0   | pyodide