X arrays can only be sparse

single-cell-data / SOMA

A flexible and extensible API for annotated 2D matrix data stored in multiple underlying formats.

MIT License

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X arrays can only be sparse #45

Closed johnkerl closed 1 year ago

johnkerl commented 2 years ago

From recent conversation with @bkmartinjr I believe X arrays will always be sparse.

If I am correct, this should be updated at https://github.com/single-cell-data/SOMA/blob/main/abstract_specification.md#somaexperiment--somameasurement.

cc @thetorpedodog and @gspowley.

bkmartinjr commented 2 years ago

Hi @johnkerl - I apologize for adding noise to the system, but after reviewing my notes, I concluded that we decided to allow both dense & sparse. Sparse is far more common for transcriptomic data, but there are use cases for both.

The prose spec is correct (checked it). The only bug I saw is image/diagram, which I will fix. I will leave this bug assigned to me until that is done. Thanks for following up on this!

johnkerl commented 1 year ago

X arrays can now be sparse or dense. See also #106 which did related work.