mnnpy

mnnpy copied to clipboard

mnn_correct gives several Numba warnings and IndexError

2

Dear Chris, I posted this to the SCANPY Github repo but they directed me to you. Any ideas what could be causing this [error](https://github.com/theislab/scanpy/issues/1167#issue-601302612) Thanks

auesro

Remove the numba acceleration part in utils code so it can work well now.

HelloWorldLTY

I'm just the messenger on this one, all credit to @mbargull who sorted this when I was trying to create an mnnpy Bioconda recipe- see https://github.com/bioconda/bioconda-recipes/pull/23893. The Bioconda package now...

pinin4fjords

Current verbosity is hard-coded with `print` statements (e.g. https://github.com/chriscainx/mnnpy/blob/master/mnnpy/mnn.py#L168). Using `logging` and including a `verbose` keyword argument would allow users to turn these off if desired.

scottgigante

NumbaDeprecationWarning

1

/Users/cahanlab/anaconda3/envs/pyEnv2/lib/python3.6/site-packages/numba/object_mode_passes.py:188: NumbaDeprecationWarning: Fall-back from the nopython compilation path to the object mode compilation path has been detected, this is deprecated behaviour. For more information visit http://numba.pydata.org/numba-doc/latest/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit File "../../../../anaconda3/envs/pyEnv2/lib/python3.6/site-packages/mnnpy/utils.py", line 107:...

jayypaul

scottgigante

Hi, thanks for your great package. It worked well when I used it a while ago on a Mac. Now, I just wanted to re-run my code on Windows 10...

sichra

These two samples should integrate highly but they unfortunately don't. Keep getting NumbaPendingDeprecationWarnings when I try to run mnn_correct.. : Fall-back from the nopython compilation path to the object mode...

jayypaul

This would resolve an installation issue that I had with mnnpy on my MacOS Catalina system a few days ago. I'm positive that these lines would save users a lot...

tamjazad

I'm trying to apply mnn on my data, basically following the README of this project, but ```python corrected = mnnpy.mnn_correct(*tn5_data_list, batch_categories=batches) Traceback (most recent call last): File "", line 1,...

dawe