Show progressbar if supported by backend

src/scirpy/ir_dist/metrics.py

@@ -13,7 +13,7 @@
 from scanpy import logging
 from scipy.sparse import coo_matrix, csr_matrix
 
-from scirpy.util import _doc_params, deprecated, tqdm
+from scirpy.util import _doc_params, _parallelize_with_joblib, deprecated
 
 _doc_params_parallel_distance_calculator = """\
 n_jobs
@@ -228,12 +228,8 @@ def calc_dist_mat(
         # precompute blocks as list to have total number of blocks for progressbar
         blocks = list(self._block_iter(seqs, seqs2, block_size=block_size))
 
-        # joblib + tqdm, see https://stackoverflow.com/a/76726101/2340703
-        block_results = tqdm(
-            joblib.Parallel(return_as="generator", n_jobs=self.n_jobs)(
-                joblib.delayed(self._compute_block)(*block) for block in blocks
-            ),
-            total=len(blocks),
+        block_results = _parallelize_with_joblib(
+            (joblib.delayed(self._compute_block)(*block) for block in blocks), total=len(blocks), n_jobs=self.n_jobs
         )
 
         try:

src/scirpy/util/__init__.py

@@ -9,6 +9,7 @@
 import pandas as pd
 import scipy.sparse
 from anndata import AnnData
+from joblib import Parallel
 from mudata import MuData
 from scanpy import logging
 from scipy.sparse import issparse
@@ -561,3 +562,18 @@ def _translate_dna_to_protein(dna_seq: str):
         else:
             protein.append("N")
     return "".join(protein)
+
+
+def _parallelize_with_joblib(delayed_objects, *, total=None, **kwargs):
+    """Wrapper around joblib.Parallel that shows a progressbar if the backend supports it.
+
+    Progressbar solution from https://stackoverflow.com/a/76726101/2340703
+    """
+    try:
+        return tqdm(Parallel(return_as="generator", **kwargs)(delayed_objects), total=total)
+    except ValueError:
+        logging.info(
+            "Backend doesn't support return_as='generator'. No progress bar will be shown. "
+            "Consider setting verbosity in joblib.parallel_config"
+        )
+        return Parallel(return_as="list", **kwargs)(delayed_objects)