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brianhie / scanorama

Panoramic stitching of single cell data
http://scanorama.csail.mit.edu
MIT License
261 stars 49 forks source link

Fix overly broad conversion of warnings to errors #137

Closed Wainberg closed 1 year ago

Wainberg commented 1 year ago

This avoids the following warning being converted to an error with recent versions of scikit-learn:

Traceback (most recent call last): File "", line 1, in File "site-packages/scanpy/external/pp/_scanorama_integrate.py", line 121, in scanorama_integrate integrated = scanorama.assemble( File "site-packages/scanorama/scanorama.py", line 933, in assemble bias = transform(curr_ds, curr_ref, ds_ind, ref_ind, sigma=sigma, File "site-packages/scanorama/scanorama.py", line 762, in transform avg_bias = batch_bias(curr_ds, match_ds, bias, sigma=sigma, File "site-packages/scanorama/scanorama.py", line 723, in batch_bias weights = rbf_kernel(curr_ds, match_ds, gamma=0.5*sigma) File "site-packages/sklearn/metrics/pairwise.py", line 1294, in rbf_kernel X, Y = check_pairwise_arrays(X, Y) File "site-packages/sklearn/metrics/pairwise.py", line 155, in check_pairwise_arrays X = check_array( File "site-packages/sklearn/utils/validation.py", line 727, in check_array warnings.warn( FutureWarning: np.matrix usage is deprecated in 1.0 and will raise a TypeError in 1.2. Please convert to a numpy array with np.asarray. For more information see: https://numpy.org/doc/stable/reference/generated/numpy.matrix.html

brianhie commented 1 year ago

@Wainberg thanks so much for the PR!