CODEWITHSUNDEEP
pythonjupyter-notebookjupyterpytest
president
president

Reputation: 523

Running Jupyter notebook test in pytest. OSError

I have a python test, which should run Jupyter notebook file and check it for errors. When I run it, it returns an error: OSError: [Errno 8] Exec format error: './file.ipynb'

Does anyone know how to fix this?

What I've found in similar questions doesn't seem to be my case.

My code is below:

import os
import subprocess
import tempfile

import nbformat


def _notebook_run(path):
    """Execute a notebook via nbconvert and collect output.
       :returns (parsed nb object, execution errors)
    """
    dirname, __ = os.path.split(path)
    os.chdir(dirname)
    with tempfile.NamedTemporaryFile(suffix=".ipynb") as fout:
        args = [path, fout.name, "nbconvert", "--to", "notebook", "--execute",
          "--ExecutePreprocessor.timeout=60",
          "--output"]
        subprocess.check_call(args)

        fout.seek(0)
        nb = nbformat.read(fout, nbformat.current_nbformat)

    errors = [output for cell in nb.cells if "outputs" in cell
                     for output in cell["outputs"]\
                     if output.output_type == "error"]

    return nb, errors

def test_ipynb():
    nb, errors = _notebook_run('./file.ipynb')
    assert errors == []

Upvotes: 4

Views: 1207

Answers (1)

hoefling
hoefling

Reputation: 66231

Your args are wrong. What you are essentially calling is

$ ./file.ipynb tempfile.ipynb nbconvert --to notebook \
    --execute --ExecutePrerocessor.timeout=60 --output

This doesn't work because file.ipynb is not an executable. You need to invoke jupyter instead:

$ jupyter nbconvert ./file.ipynb --output tempfile.ipynb --to notebook \
    --execute --ExecutePrerocessor.timeout=60

Translated to Python args, this would be for example:

import shutil

...

jupyter_exec = shutil.which('jupyter')
if jupyter_exec is not None:
    args = [jupyter_exec, "nbconvert", path, 
            "--output", fout.name, 
            "--to", "notebook", 
            "--execute", "--ExecutePreprocessor.timeout=60"]
    subprocess.check_call(args)
else:
    # jupyter not installed or not found in PATH

Upvotes: 4

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