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pepkit / looper

A job submitter for Portable Encapsulated Projects
http://looper.databio.org
BSD 2-Clause "Simplified" License
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namespaces output plugin #302

Closed xuebingjie1990 closed 3 years ago

xuebingjie1990 commented 3 years ago

output namespaces into .yaml file #298

xuebingjie1990 commented 3 years ago

You need to change the plugin to accept an input that would indicate where to save the file (see #298), not overwrite sample.yaml

do you think I should create a get_submission_yaml_path or edit the current get_sample_yaml_path to get the output path? because most of the code would be duplicates..

stolarczyk commented 3 years ago

line 79 in conductor.py:

/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/looper/conductor.py:79: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
stolarczyk commented 3 years ago

do you think I should create a get_submission_yaml_path or edit the current get_sample_yaml_path to get the output path? because most of the code would be duplicates..

It's up to you. I'm not sure if this will be duplicated.. we don't need the template rendering part there.

stolarczyk commented 3 years ago
nsheff commented 3 years ago

Is this ready to be merged?

stolarczyk commented 3 years ago

Is this ready to be merged?

I believe @xuebingjie1990 has finished this. I'll work on a unit test for this.