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openproblems-bio / openproblems

Formalizing and benchmarking open problems in single-cell genomics
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Add pymde to dimensionality reduction #767

Closed scottgigante-immunai closed 1 year ago

scottgigante-immunai commented 1 year ago

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scottgigante-immunai commented 1 year ago

Ah. We haven't been doing that for any of the other tasks -- is it something we want to continue with DR?

lazappi commented 1 year ago

Ah. We haven't been doing that for any of the other tasks -- is it something we want to continue with DR?

🤷🏻 It could be useful but you should also be able to see what methods are implemented from the website. I'm not particularly attached to it, I think it was in the template I was given so I tried to keep it up to date. Either we keep updating it or remove it, having it half done is probably the worst option.

scottgigante-immunai commented 1 year ago

@LuckyMD thoughts? I moved it to the API section because it wasn't in the other tasks and it made the website very long. I think I'm inclined to let people go to the bibliography if they want details?

LuckyMD commented 1 year ago

Hmm.. it looks like a lot of effort went into that README that we're mostly not using on the website. I wouldn't make it the norm for other tasks, but I would probably keep it here given how much is already there... seems a waste to remove, no?

scottgigante-immunai commented 1 year ago

I agree it seems like a waste to remove, but it could also be a waste to maintain something we don't want or need.

lazappi commented 1 year ago

I agree it seems like a waste to remove, but it could also be a waste to maintain something we don't want or need.

That's what I was thinking. If we don't have it for the other tasks and there's no use for it going forward it should probably be removed to avoid maintaining it (although it did take me a while to write it all in the first place).

LuckyMD commented 1 year ago

fair enough. I hope you could use it for the supplementary materials @lazappi.

scottgigante-immunai commented 1 year ago

I'm going to go ahead and merge this one, and we can remove the method descriptions from the API in a separate PR.

codecov[bot] commented 1 year ago

Codecov Report

Base: 94.78% // Head: 94.78% // Decreases project coverage by -0.00% :warning:

Coverage data is based on head (8e97631) compared to base (3d8964a). Patch coverage: 96.38% of modified lines in pull request are covered.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #767 +/- ## ========================================== - Coverage 94.78% 94.78% -0.01% ========================================== Files 155 155 Lines 4163 4273 +110 Branches 215 225 +10 ========================================== + Hits 3946 4050 +104 - Misses 142 147 +5 - Partials 75 76 +1 ``` | Flag | Coverage Δ | | |---|---|---| | unittests | `94.78% <96.38%> (-0.01%)` | :arrow_down: | Flags with carried forward coverage won't be shown. 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