Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Unclear error message with PEP without looper section #286

Closed
afrendeiro opened this issue Aug 25, 2020 · 1 comment · Fixed by #274
Closed

Unclear error message with PEP without looper section #286

afrendeiro opened this issue Aug 25, 2020 · 1 comment · Fixed by #274
Assignees

Comments

@afrendeiro
Copy link
Contributor

afrendeiro commented Aug 25, 2020

If running looper run with a PEP without a looper section, looper throws an error that is hard to understand:

Traceback (most recent call last):
  File "//home/afr/.local/bin/looper", line 8, in <module>
    sys.exit(main())
  File "/home/afr/.local/lib/python3.8/site-packages/looper/looper.py", line 691, in main
    args = enrich_args_via_cfg(args, aux_parser)
  File "/home/afr/.local/lib/python3.8/site-packages/looper/utils.py", line 213, in enrich_args_via_cfg
    elif dest in cfg_args_all:
TypeError: argument of type 'NoneType' is not iterable

If a looper section is really required in the PEP, then a message stating that is absent should be presented.

@stolarczyk
Copy link
Member

stolarczyk commented Aug 25, 2020

good catch, that's a bug.

The thing is, looper section is not really required -- you can provide the output_dir (and any other looper.X setting using the CLI). So for output_dir one can use --output-dir $HOME. But this is considered experimental, so we specify the looper section as required in the docs: http://looper.databio.org/en/latest/defining-a-project/

In your case none of the options to provide output_dir were used, which needs to be accommodated.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
Development

Successfully merging a pull request may close this issue.

2 participants