Unexpected keyword argument {'n_jobs': 8}

[eriksamuelsson1]

I'm running into an issue when I try to run the function in preparation for integrating my datasets.

I tried the solution listed in issue #49 ( Temporarily switching to scipy=1.8.1), but that did not work.

`Performing cosine normalization...
Starting MNN correct iteration. Reference batch: 0
Step 1 of 1: processing batch 1
Looking for MNNs...

---

TypeError Traceback (most recent call last)
Cell In[12], line 1
----> 1 cdata = sc.external.pp.mnn_correct(data1,data2, svd_dim = 50, batch_key = 'dataset', batch_categories = ['set1','set2',], save_raw = True, var_subset = var_genes)

File ~\Anaconda3\envs\spapros\lib\site-packages\scanpy\external\pp_mnn_correct.py:135, 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)
129 raise ImportError(
130 'Please install the package mnnpy '
131 '(https://github.com/chriscainx/mnnpy). '
132 )
134 n_jobs = settings.n_jobs if n_jobs is None else n_jobs
--> 135 datas, mnn_list, angle_list = mnn_correct(
136 *datas,
137 var_index=var_index,
138 var_subset=var_subset,
139 batch_key=batch_key,
140 index_unique=index_unique,
141 batch_categories=batch_categories,
142 k=k,
143 sigma=sigma,
144 cos_norm_in=cos_norm_in,
145 cos_norm_out=cos_norm_out,
146 svd_dim=svd_dim,
147 var_adj=var_adj,
148 compute_angle=compute_angle,
149 mnn_order=mnn_order,
150 svd_mode=svd_mode,
151 do_concatenate=do_concatenate,
152 save_raw=save_raw,
153 n_jobs=n_jobs,
154 **kwargs,
155 )
156 return datas, mnn_list, angle_list

File ~\Anaconda3\envs\spapros\lib\site-packages\mnnpy\mnn.py:122, 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)
120 if var_subset is not None and set(adata_vars) == set(var_subset):
121 var_subset = None
--> 122 corrected = mnn_correct((adata.X for adata in datas), var_index=adata_vars,
123 var_subset=var_subset, k=k, sigma=sigma, cos_norm_in=cos_norm_in,
124 cos_norm_out=cos_norm_out, svd_dim=svd_dim, var_adj=var_adj,
125 compute_angle=compute_angle, mnn_order=mnn_order,
126 svd_mode=svd_mode, do_concatenate=do_concatenate, **kwargs)
127 print('Packing AnnData object...')
128 if do_concatenate:

File ~\Anaconda3\envs\spapros\lib\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 for MNNs...')
--> 178 mnn_ref, mnn_new = find_mutual_nn(data1=ref_batch_in, data2=new_batch_in, k1=k, k2=k,
179 n_jobs=n_jobs)
180 print(' Computing correction vectors...')
181 correction_in = compute_correction(ref_batch_in, new_batch_in, mnn_ref, mnn_new,
182 new_batch_in, sigma)

File _ckdtree.pyx:783, in scipy.spatial._ckdtree.cKDTree.query()

File _ckdtree.pyx:387, in scipy.spatial._ckdtree.get_num_workers()

TypeError: Unexpected keyword argument {'n_jobs': 8}

`