openproblems-bio / openproblems

Formalizing and benchmarking open problems in single-cell genomics
MIT License
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add magic with reverse norm order #797

Closed scottgigante-immunai closed 1 year ago

scottgigante-immunai commented 1 year ago

Reversing the order of sqrt and libnorm inexplicably improves performance. Adding this to MAGIC with explicit naming so users are aware that this is different from defaults.

scottgigante-immunai commented 1 year ago

Tests at https://tower.nf/orgs/openproblems-bio/workspaces/openproblems-bio/watch/MJO29wdT7zRgp

codecov[bot] commented 1 year ago

Codecov Report

Base: 94.78% // Head: 94.92% // Increases project coverage by +0.14% :tada:

Coverage data is based on head (e3db9fa) compared to base (3d8964a). Patch coverage: 99.35% of modified lines in pull request are covered.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #797 +/- ## ========================================== + Coverage 94.78% 94.92% +0.14% ========================================== Files 155 157 +2 Lines 4163 4279 +116 Branches 215 227 +12 ========================================== + Hits 3946 4062 +116 Misses 142 142 Partials 75 75 ``` | Flag | Coverage Δ | | |---|---|---| | unittests | `94.92% <99.35%> (+0.14%)` | :arrow_up: | Flags with carried forward coverage won't be shown. 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scottgigante-immunai commented 1 year ago

Mind converting your review to an approval instead of a comment so I can merge? Thanks!

wes-lewis commented 1 year ago

Tests at https://tower.nf/orgs/openproblems-bio/workspaces/openproblems-bio/watch/MJO29wdT7zRgp

It appears that one of the denoising:Tabula Muris tests failed, but I'm not sure if the error that is shown (137) is a flake. I'm use to looking at github actions rather than NextFlow to gauge whether tests have passed. I'm inclined to merge unless this is seen as a significant issue.

Ed: the overall workflow is passing. Individual jobs failing for 137 is an OOM which is saved by rerunning with more memory.