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claassenlab / MORESCA

This repository provides a template and some resources on standardized scRNA-seq analysis using Python.
GNU Affero General Public License v3.0
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Relaxation of package requirements #7

Open mbruhns opened 1 year ago

mbruhns commented 1 year ago

Since we're fairly restrictive regarding the compatible Python version (>=3.10), the required package versions should be as lenient as possible. This is especially important since users should be able to use this tool and pipe the output directly into another tool that is not considered in our pipeline.

Do you know of any best practices on how to relax the requirements while enabling stable builds?

Baschdl commented 1 year ago

One idea would be to specify versions with >=, build the package with Github actions triggered by commits (by new versions of external packages would be nicer but it's not immediately clear to me how to do that) and then make the version requirements more restrictive once something fails. Would require us to have 100% test coverage, at least on a very rudimentary level (every line of code should be at least somehow executed), such that we really see those failures.

mbruhns commented 1 year ago

Yehaa, tests! I hoped there would be a different solution 😅

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Baschdl commented 1 year ago

Should be pretty simple integration tests: run the pipeline with the cross product of all possible method configurations. Do we have a place where all possible options for the configuration is tracked?

mbruhns commented 1 year ago

True, but I was hoping for a tool that does this version matching for us automatically.