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pepkit / looper

A job submitter for Portable Encapsulated Projects
http://looper.databio.org
BSD 2-Clause "Simplified" License
20 stars 7 forks source link

Replaced SAMPLE_NAME_ATTR with sample_table_index where seen #365

Closed ayobi closed 1 year ago

ayobi commented 1 year ago

Made changes across 5 files. All passed pytests.

Was unable to update one in conductor.py with the function def _get_yaml_path: https://github.com/pepkit/looper/blob/df535be2a0bd7257ee37148cb601d688ec557909/looper/conductor.py#L54-L63

Correct me if I'm wrong but this else sets up for the default YAML location so it would be fine resolving into that namespace 'sample.[SAMPLE_NAME_ATTR]' where sample_name is the default right? Trying to use Project.sample_table_index causes key errors when running through pytest that seem unavoidable.

vreuter commented 1 year ago

Thanks @ayobi . @nsheff can confirm, but indeed I think it makes sense to keep the SAMPLE_NAME_ATTR in the place you've noted in your description above.