ModuleNotFoundError: Command `doctest` not found by nbqa

How do I use nbqa with doctest? I tried nbqa doctest mynb.ipynb and got an error ModuleNotFoundError: Command doctest not found by nbqa I can run doctest if I do nbconvert then python -m doctest mynb.ipynb

% nbqa --version
nbqa 0.3.3
% nbqa doctest mynb.ipynb
Traceback (most recent call last):
  File "/Users/ntaylor/src/nanml-notebook/docs/venv/bin/nbqa", line 8, in <module>
    sys.exit(main())
  File "/Users/ntaylor/src/nanml-notebook/docs/venv/lib/python3.8/site-packages/nbqa/__main__.py", line 531, in main
    output_codes = [
  File "/Users/ntaylor/src/nanml-notebook/docs/venv/lib/python3.8/site-packages/nbqa/__main__.py", line 532, in <listcomp>
    _run_on_one_root_dir(i, cli_args, configs, project_root)
  File "/Users/ntaylor/src/nanml-notebook/docs/venv/lib/python3.8/site-packages/nbqa/__main__.py", line 474, in _run_on_one_root_dir
    out, err, output_code, mutated = _run_command(
  File "/Users/ntaylor/src/nanml-notebook/docs/venv/lib/python3.8/site-packages/nbqa/__main__.py", line 355, in _run_command
    raise ModuleNotFoundError(_get_command_not_found_msg(command))
ModuleNotFoundError: Command `doctest` not found by nbqa.

Please make sure you have it installed in the same Python environment as nbqa. See
e.g. https://realpython.com/python-virtual-environments-a-primer/ for how to set up
a virtual environment in Python.

Since nbqa is installed at /Users/ntaylor/src/nanml-notebook/docs/venv/lib/python3.8/site-packages/nbqa and uses the Python executable found at
/Users/ntaylor/src/nanml-notebook/docs/venv/bin/python, you could fix this issue by running `/Users/ntaylor/src/nanml-notebook/docs/venv/bin/python -m pip install doctest`.

[MarcoGorelli]

I think I have an idea, actually - does your doctest import something it’s not able to find?

The problem is that to detect whether you have the code quality tool you’re running installed or not, we do

    output = subprocess.run(
        [sys.executable, "-m", command, str(arg), *cmd_args],
        stderr=subprocess.PIPE,
        stdout=subprocess.PIPE,
        cwd=tmpdirname,
        env=env,
    )

    mutated = _get_mtimes(arg) != before

    output_code = output.returncode

    out = output.stdout.decode()
    err = output.stderr.decode()

    if "No module named" in err:
        raise ModuleNotFoundError(_get_command_not_found_msg(command))

However, this is buggy, because No module named might be returned by the code quality tool itself! So, we have a bug.

In the short-run, I’d recommend fixing your docstring so that everything you use in it was imported correctly. We’ll make a patch release for this at the weekend - @s-weigand had suggested a better way of checking if packages are installed, and I wish I’d followed his advice immediately now 😳

@all-contributors please add @ntaylor-nanigans for bug

[MarcoGorelli]

closed in #365

@ntaylor-nanigans please try upgrading to version 0.3.4, I’d like to think this is fixed - if there are issues, please do let us know!