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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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remove `pipeline. sample_yaml_path` key? #307

Closed stolarczyk closed 3 years ago

stolarczyk commented 3 years ago

before we implemented the pre-submission hooks system the sample yaml path could be changed with pipeline. sample_yaml_path key. Now we want to take advantage of the new pipeline.var_templates section. Therefore, I've decided to make the looper.write_sample_yaml plugin parameterizable with pipeline.var_templates.sample_yaml_path but kept the old way (with lower priority) for backwards compatibility. But this release will make big changes in the way we save sample yamls etc, so maybe we should completely switch to the new system?

Originally posted by @stolarczyk in https://github.com/pepkit/looper/pull/292#issuecomment-700898909

nsheff commented 3 years ago

by completely switch, the only thing that means is drop backwards compatibility?

nsheff commented 3 years ago

For things like this that are actually being used I'm generally in favor of keeping backwards compatibility, at least for awhile. it can be deprecated and warned. but you've already implemented it -- what's the advantage of dropping backwards compatibility? it just has potential to frustrate users.

stolarczyk commented 3 years ago

what's the advantage of dropping backwards compatibility?

making things simpler.

I thought we might eliminate the old way since backwards compatibility is already broken since the sample yaml creation will need to be explicitly defined as a pre-submission hook. So current users will need to edit piface anyway to get the sample YAML file. But I don't have strong feelings about keeping it until next major release..

nsheff commented 3 years ago

ok good point. that's fine with me in that case since it's already broken.