David Brann

Boxenplot styling differs depending on the k_depth option

5

Hi, I've been an avid user of `boxenplot`, and it's a great function! I noticed that there were some improvements to `boxenplot` in #2086 that were incorporated into release v0.11....

io.masks_flows_to_seg errors silently without saving seg npy file [BUG]

2

Thanks for the nice software. I trained a model in the GUI and I was trying to now use a jupyter notebook to apply it to multiple images. I tried...

Right now `gr.head()` fails due to a reference to `np.bool` insteal of `bool`. I'm using numpy version `'1.26.4'`. ```python gr = pr.from_dict({'Chromosome': ['chr1', 'chr1'], 'Start': [3, 5], 'End': [9, 7],'Strand':...

Avoid making dense matrix in `create_cistopic_object_from_fragments` reduces memory 50X [PERFORMANCE]

4

I'm running pycisTopic but `create_cistopic_object_from_fragments` has significant memory usage. As has already been discussed (e.g. see https://github.com/aertslab/pycisTopic/issues/14), the main bottleneck comes from the [following lines](https://github.com/aertslab/pycisTopic/blame/d6a2f8c832c14faae07def1d3ad8755531f50ad5/src/pycisTopic/cistopic_class.py#L880): ```python fragment_matrix = ( counts_df.groupby(["Name",...