mnnpy

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Hi I'm using sc.external.pp.mnn_correct to correct three batches with in total 13383 obs and 6214 vars in jupyterlab. I'm using: scanpy==1.7.2 anndata==0.8.0 umap==0.5.2 numpy==1.21.5 scipy==1.8.0 pandas==1.4.1 scikit-learn==1.0.2 statsmodels==0.13.2 python-igraph==0.9.9 with...

brainfo

Taking len of `None` when passing matrices instead of anndata

1

The default value of `var_index` is `None`, but the first thing you do with it if the data is not `AnnData` is take the `len`. https://github.com/chriscainx/mnnpy/blob/master/mnnpy/mnn.py#L148 ``` >>> import numpy...

scottgigante

scipy cKDTree: `n_jobs` has been renamed `workers`

1

``` File ~/.conda/envs/py39/lib/python3.9/site-packages/mnnpy/mnn.py:178, in mnn_correct(var_index, var_subset, batch_key, index_unique, batch_categories, k, sigma, cos_norm_in, cos_norm_out, svd_dim, var_adj, compute_angle, mnn_order, svd_mode, do_concatenate, save_raw, n_jobs, *datas, **kwargs) 176 new_batch_out = out_batches[target] 177 print(' Looking...

alexlenail

Unexpected keyword argument {'n_jobs': 20}

1

I keep getting this error and i ' m not sure what is the problem . Appriciated your helps . Package was installed. `--------------------------------------------------------------------------- TypeError Traceback (most recent call last)...

DRSEI

`scipy.spatial.cKDTree` replaced `n_jobs` with `workers` in 1.6.0 and [removed `n_jobs` in 1.9.0](https://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.cKDTree.query.html). This currently causes an error in [openproblems](https://github.com/openproblems-bio/openproblems/runs/7655839315?check_suite_focus=true#step:12:991)

scottgigante-immunai

Illegal instruction (core dumped)

1

Hii, I am trying to run `mnn_correct` but it is throwing `Illegal instruction (core dumped)` error. Without any additional information. I am getting this error while calling `adjust_shift_variance` function. Any...

nitinnarwade

I'm trying to use mnnpy through scanpy, but I seem to have hit an installation error. When I run `pip install mnnpy` in the command line, I get the following...

sfhill

arrays used as indices must be of integer (or boolean) type

12

Hi mnnpy, I am getting an error using mnnpy.mnn_correct and wondering if you could please comment on my error. I have the latest version of numba and llvmlite. Here is...

aheravi

to merge after fix_for_numba_jit. ability to choose different ks for each, can really improve the algorithm's ability to perform mnn when we have very diffferent dataset sizes. like 10 to...

jkobject

When importing mnnpy version 0.1.9.5 with python 3.8.8, it failed with error `[1] 1768057 illegal hardware instruction (core dumped) python` but python 3.8.8 can import 0.1.9.3

brainfo