Fix a couple of tests

scirpy/get/__init__.py

@@ -82,7 +82,12 @@ def _airr_col(
     # when saving anndata
     result = np.full(idx.shape, fill_value=None, dtype=object)
 
-    result[mask] = airr_data[np.where(mask)[0], airr_variable, idx[mask].astype(int)]
+    # to_numpy would be faster, but it doesn't work with strings (as this would create an object dtype
+    # which is not allowed as per the awkward documentation)
+    # Currently the performance hit doesn't seem to be a deal breaker, can maybe revisit this in the future.
+    # It is anyway not very efficient to create a result array with an object dtype.
+    _ak_slice = airr_data[np.where(mask)[0], airr_variable, idx[mask].astype(int)]
+    result[mask] = ak.to_list(_ak_slice)
     return result
 
 

scirpy/tests/test_tools.py

@@ -333,7 +333,7 @@ def test_group_abundance():
         ],
         columns=["cell_id", "group", "clone_id"],
     ).set_index("cell_id")
-    adata = AnnData(obs=obs)
+    adata = _make_adata(obs)
 
     # Check counts
     res = ir.tl.group_abundance(
@@ -377,6 +377,7 @@ def test_group_abundance():
 
 def test_spectratype(adata_tra):
     # Check numbers
+    adata_tra.obs["IR_VJ_1_junction_aa"] = ir.get.airr(adata_tra, "junction_aa", "VJ_1")
     res1 = ir.tl.spectratype(
         adata_tra,
         groupby="IR_VJ_1_junction_aa",

scirpy/tests/test_util.py

@@ -17,9 +17,11 @@
 import igraph as ig
 import numpy as np
 import pandas as pd
+import scirpy as ir
 import numpy.testing as npt
 import pytest
 import scipy.sparse
+from typing import cast
 from .fixtures import adata_tra
 
 import warnings
@@ -204,9 +206,10 @@ def test_layout_components(arrange_boxes, component_layout):
 
 def test_translate_dna_to_protein(adata_tra):
     for nt, aa in zip(
-        adata_tra.obs["IR_VJ_1_junction"], adata_tra.obs["IR_VJ_1_junction_aa"]
+        ir.get.airr(adata_tra, "junction", "VJ_1"),
+        ir.get.airr(adata_tra, "junction_aa", "VJ_1"),
     ):
-        assert _translate_dna_to_protein(nt) == aa
+        assert _translate_dna_to_protein(cast(str, nt)) == aa
 
 
 @pytest.mark.parametrize(