Can I use h5py with pyscript?

davidasamy · July 7, 2022, 5:46pm

It appears that h5py was added in this pull request to Pyodide but not included in the Pyodide version 0.20.0 which py-script uses currently. Is it possible I can use a Pyodide version that includes the support for h5py with Pyscript?

Thanks.

neil · July 8, 2022, 11:13am

With the timing of the PR you link to, it isn’t part of 0.20.0, it came a few days after the release date of Pyodide 0.20.0.

However I believe there is a way that might be worth testing in case it works for you, based on the fairly recent announcement about PyScript versioning here:

I think that if you switch your code to point to this version: https://pyscript.net/unstable/pyscript.js (and the associated css etc) then it should pick up the latest Pyodide, because looking in master here, they are pointing to the Pyodide 0.20.1 alpha 2 which includes the change you’re after.

If the above doesn’t work then you could try cloning the repo and building/ serving it locally to see if that way pulls in the later Pyodide but i have a feeling the unstable version method above will work.

neil · July 8, 2022, 2:32pm

Actually this seems like it doesn’t work

I did a minimal test and it can’t do the import . I’m under the weather today, so I’ll have to investigate a bit more fully over the weekend when I’m more “with it” than i am now!

Edit: Still need to check this but i believe my earlier assumption about how the version of Pyodide used gets updated was wrong above. Rather than it being set in the packages.json file, there appears to be a flexible way to pick the runtime as per the field “src” here:

github.com

pyscript/pyscript/blob/main/docs/tutorials/getting-started.md#the-py-config-tag

# Getting started with PyScript

This page will guide you through getting started with PyScript.

## Development setup

PyScript does not require any development environment other
than a web browser (we recommend using [Chrome](https://www.google.com/chrome/)) and a text editor, even though using your [IDE](https://en.wikipedia.org/wiki/Integrated_development_environment) of choice might be convenient.

If you're using [VSCode](https://code.visualstudio.com/), the
[Live Server extension](https://marketplace.visualstudio.com/items?itemName=ritwickdey.LiveServer)
can be used to reload the page as you edit the HTML file.

## Trying before installing

If you're new to programming and know nothing about HTML or just want to try some of PyScript features, we recommend using the [REPL](https://en.wikipedia.org/wiki/Read%E2%80%93eval%E2%80%93print_loop) element in the [PyScript REPL example](https://pyscript.net/examples/repl.html) instead so you can have a programming experience in a REPL that doesn't require any setup. This REPL can be used to have an interactive experience using Python directly.

 Alternatively, you can also use an online editor like W3School's [TryIt Editor](https://www.w3schools.com/html/tryit.asp?filename=tryhtml_default_default) and just plug the code below into it, as shown in the [example](https://docs.pyscript.net/latest/concepts/what-is-pyscript.html#example) page and click the run button.

```html

This file has been truncated. show original

So if you want to have a go, by all means try it with the 0.20 alpha 2 runtime and report back, otherwise I’ll have a shot myself sometime tomorrow/Sunday I hope

davidasamy · July 8, 2022, 5:50pm

Hi Neil,

Thank you for reply, I hope you will recover soon .

I will try your suggested solution, however I’m not even sure if the h5py PR was included in the alpha version.

David

davidasamy · July 8, 2022, 6:38pm

It appears that it was included in the alpha release however the h5py package in pyodide is broken unfortunately.

talmopereira · July 20, 2022, 6:59pm

Hi all – any luck with this in newer releases? @neil