TypeError: __init__() takes from 1 to 2 positional arguments but 4 were given

[ernohanninen]

Hello,

When running this code:

num_trajs = 4
flavor = "k-means"
num_metacells = 300

adata = anndata.read_h5ad("/media/ernohanninen/TOSHIBA/cycletree.h5ad")

cellpath_obj = cp.CellPath(adata = adata, preprocess = True)
cellpath_obj.all_in_one(flavor = flavor, num_metacells = num_metacells, n_neighs = 13, num_trajs = num_trajs, prop_insert = 0.0, seed = 0, mode = "exact")

I get the following error:

Traceback (most recent call last):
File "run_CellPath.py", line 19, in
cellpath_obj.all_in_one(flavor = flavor, num_metacells = num_metacells, n_neighs = 13, num_trajs = num_trajs, prop_insert = 0.0, seed = 0, mode = "exact")
File "/home/ernohanninen/miniconda3/envs/TRAenv/lib/python3.8/site-packages/cellpath/cellpath.py", line 349, in all_in_one
self.meta_cell_construction(flavor = flavor, n_clusters = num_metacells, resolution = resolution, **kwargs)
File "/home/ernohanninen/miniconda3/envs/TRAenv/lib/python3.8/site-packages/cellpath/cellpath.py", line 121, in meta_cell_construction
self.X_clust, self.velo_clust = clust.meta_cells(self.adata, kernel = _kwargs["kernel"],
File "/home/ernohanninen/miniconda3/envs/TRAenv/lib/python3.8/site-packages/cellpath/clustering.py", line 136, in meta_cells
k = KernelRidge(alpha, kernel, gamma)
TypeError: init() takes from 1 to 2 positional arguments but 4 were given

[PeterZZQ]

Hi,

It was a bug due to the update of the sklearn package. I have updated the code on GitHub and also on Pypi. The bug should be fixed now. You can update your cellpath package with pip or directly pull the GitHub repo down to directly install from the source code.

[ernohanninen]

The code is running. Thank you!