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theislab / zellkonverter

Conversion between scRNA-seq objects
https://theislab.github.io/zellkonverter/
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Turn sparse DelayedArray support back on #50

Open lazappi opened 3 years ago

lazappi commented 3 years ago

Reminder to do this now that https://github.com/grimbough/rhdf5/issues/79 has been fixed.

To do:

lazappi commented 3 years ago

Tried doing this quickly, writing worked ok but it broke reading.

LTLA commented 3 years ago

Will look at this later. I think we need to flip a few flags in h5writeAttributes to properly save it as a UTF-8 string scalar. What was the error?

lazappi commented 3 years ago

I probably should have copied it here but from memory, something along the lines of X is not a valid path.

lazappi commented 1 month ago

Just checked where this is at. If you remove the is_sparse() check in this line:

https://github.com/theislab/zellkonverter/blob/e47c845cf7ae268c1b7088ec140bdf827aac826d/R/write.R#L91

Then writing works fine but reading the output file fails with this error:

Error in py_call_impl(callable, call_args$unnamed, call_args$named) : 
  TypeError: unhashable type: 'list'
Error raised while reading key 'X' of <class 'h5py._hl.group.Group'> from /

And this error on the Python side:

TypeError: unhashable type: 'list'
Error raised while reading key 'X' of <class 'h5py._hl.group.Group'> from /