After updating to h5py 3.1.0 fancy indexing in loompy seems to be broken.
Downgrading to 2.10.0 solves the issue, alternatively a workaround is given in this thread where they suggest converting boolean arrays to indices.
This might be solved in later versions of h5py, but maybe it would be good to require h5py < 3.1.0 as an installation requirement for the time being.
Traceback (most recent call last):
File "/home/camiel/cytograph-dev/cytograph/plotting/TF_heatmap.py", line 29, in TF_heatmap
hm.plot(ds, dsagg, out_file=out_file)
File "/home/camiel/cytograph-dev/cytograph/plotting/heatmap.py", line 31, in plot
data = np.log(ds[layer][self.genes, :] + 1)
File "/home/camiel/anaconda3/envs/chromo/lib/python3.7/site-packages/loompy/loom_layer.py", line 88, in __getitem__
return self.ds._file['/matrix'].__getitem__(slice)
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File "/home/camiel/anaconda3/envs/chromo/lib/python3.7/site-packages/h5py/_hl/dataset.py", line 777, in __getitem__
selection = sel.select(self.shape, args, dataset=self)
File "/home/camiel/anaconda3/envs/chromo/lib/python3.7/site-packages/h5py/_hl/selections.py", line 82, in select
return selector.make_selection(args)
File "h5py/_selector.pyx", line 272, in h5py._selector.Selector.make_selection
File "h5py/_selector.pyx", line 183, in h5py._selector.Selector.apply_args
TypeError: Indexing arrays must have integer dtypes
winni2k
commented
3 years ago
After updating to h5py 3.1.0 fancy indexing in loompy seems to be broken. Downgrading to 2.10.0 solves the issue, alternatively a workaround is given in this thread where they suggest converting boolean arrays to indices. This might be solved in later versions of h5py, but maybe it would be good to require h5py < 3.1.0 as an installation requirement for the time being.