Fix #215

scverse · Apr 7, 2021 · 801e359 · 801e359
1 parent a732450
commit 801e359
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Showing 2 changed files with 6 additions and 3 deletions.
diff --git a/scirpy/_tools/_clonotypes.py b/scirpy/_tools/_clonotypes.py
@@ -306,6 +306,7 @@ def define_clonotype_clusters(
         adata.obs[key_added] = clonotype_cluster_series
         adata.obs[key_added + "_size"] = clonotype_cluster_size_series
         adata.uns[key_added] = clonotype_distance_res
+        logging.info(f'Stored clonal assignments in `adata.obs["{key_added}"]`.')
     else:
         return (
             clonotype_cluster_series,

diff --git a/scirpy/ir_dist/_clonotype_neighbors.py b/scirpy/ir_dist/_clonotype_neighbors.py
@@ -1,7 +1,6 @@
 from multiprocessing import cpu_count
-from typing import Union, Sequence, Tuple, Dict
+from typing import Union, Sequence
 from anndata import AnnData
-from tqdm.contrib import tmap
 from scanpy import logging
 from .._compat import Literal
 import numpy as np
@@ -219,7 +218,10 @@ def compute_distances(self) -> sp.csr_matrix:
         # only use multiprocessing for sufficiently large datasets
         # for small datasets the overhead is too large for a benefit
         if self.n_jobs == 1 or n_clonotypes <= 2 * self.chunksize:
-            dist_rows = tqdm(self._dist_for_clonotype(i) for i in range(n_clonotypes))
+            dist_rows = tqdm(
+                (self._dist_for_clonotype(i) for i in range(n_clonotypes)),
+                total=n_clonotypes,
+            )
         else:
             logging.info(
                 "NB: Computation happens in chunks. The progressbar only advances "