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theislab / zellkonverter

Conversion between scRNA-seq objects
https://theislab.github.io/zellkonverter/
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Began adding an R-native writer. #48

Open LTLA opened 3 years ago

LTLA commented 3 years ago

Pretty much as it says. Missing all the sparse bits and pieces for obsp, varp and the sparse layers; this is waiting on grimbough/rhdf5#80. Will need some testing, as usual; I haven't verified that it works with Python, but it does at least work with the R-native reader. (One nice property of the zellkonverter set-up is that we can easily check one implementation against the other.)

Wait for #46 to resolve before we even consider merging this bad boy.

ivirshup commented 3 years ago

Just a heads up on this, I will be making some changes to the on disk format of AnnData for the next release. Most of these changes will just be adding metadata to written elements so we are never inferring how to read them back in. This metadata will include a name of the type and a version for the encoding. See https://github.com/theislab/anndata/pull/554 for details.

In short, maybe hold off on merging this until that's through? These changes should be landing on the development branch on AnnData before the end of June.

LTLA commented 3 years ago

I'm down for that. We're close to the next BioC release and I'd like to spend what time we have left on checking the reader.