Jupyter4NFDI GitHub Actions

This repository contains the currently supported Jupyter4NFDI GitHub Actions.

Add a Jupyter4NFDI badge to your GitHub README.md:

[![Jupyter4NFDI approved](https://github.com/_repoowner_/_repotype_/actions/workflows/main.yml/badge.svg)](https://hub.nfdi-jupyter.de/v2/gh/_repoowner_/_repotype_/HEAD)

Clicking on the Badge will launch your repository on Jupyter4NFDI.

Test notebooks

With this simple Action you can check if your repository and all notebooks inside are running on Jupyter4NFDI.

1. Visit https://hub.nfdi-jupyter.de/hub/token , log in and create a token for the GitHub Action.
2. In your GitHub Repo browse to Settings -> Environments -> New Environment -> Name: jupyter4nfdi -> Add environment secret -> Secret Name: JUPYTERHUB_API_TOKEN, Value: token from first step
3. In your GitHub Repo browse to Actions -> "set up a workflow yourself" -> Copy the following text into it and click on "Commit changes" in the top right corner.

name: Runs on Jupyter4NFDI

on:
  workflow_dispatch:
  schedule:
    - cron: "0 7 * * 1"

jobs:
  notebooks:
    runs-on: ubuntu-latest
    environment: jupyter4nfdi
    steps:
      - name: Run notebooks via papermill on JupyterHub
        uses: NFDI-Jupyter/ghactions/.github/actions/notebooks@main
        with:
          repo: ${{ github.repository }}
          ref: ${{ github.ref_name }}
          # notebook_dirs: '["notebooks", "examples"]' # Only check specific folders in your repo
          token: ${{ secrets.JUPYTERHUB_API_TOKEN }}

That's it. Every monday at 7am all notebooks in your repository are executed on Jupyter4NFDI, to verify they're working as expected.

Successful Example

See logs here

========== PAPERMILL LOGS ==========
{
  "exitCode": 0,
  "results": [
    {
      "notebook": "notebooks/index.ipynb",
      "exitCode": 0,
      "stdout": "Input Notebook:  notebooks/index.ipynb\nOutput Notebook: /tmp/tmp7s_dmcxb/index.ipynb\n\nExecuting:   0%|          | 0/9 [00:00<?, ?cell/s]Executing notebook with kernel: python3\n\nExecuting:  11%|\u2588         | 1/9 [00:01<00:11,  1.49s/cell]\nExecuting:  44%|\u2588\u2588\u2588\u2588\u258d     | 4/9 [00:04<00:05,  1.01s/cell]\nExecuting:  89%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2589 | 8/9 [00:04<00:00,  2.30cell/s]\nExecuting: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 9/9 [00:04<00:00,  2.53cell/s]\nExecuting: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 9/9 [00:05<00:00,  1.78cell/s]\n"
    }
  ]
}
===================================
Papermill job completed successfully

Failed Example

See logs here

========== PAPERMILL LOGS ==========
{
  "exitCode": 1,
  "results": [
    {
      "notebook": "/home/jovyan/index.ipynb",
      "exitCode": 1,
      "stdout": ...,
    }
  ]
}
===================================
Papermill job failed (exitCode=1)
Error: Input Notebook:  /home/jovyan/index.ipynb
Output Notebook: /tmp/tmpg1gskghl/index.ipynb
...

ModuleNotFoundError: No module named 'matplotlib'


Error: Process completed with exit code 1.