update tests, mostly related to expecting names as strings and the re…

…levant stringlist, namedlist classes from biocutils

tests/test_aggregate_across_cells.py

@@ -8,7 +8,7 @@ def test_aggregate_across_cells_simple():
     x = numpy.round(numpy.random.rand(1000, 8) * 5)
     y = scranpy.aggregate_across_cells(x, groups)
 
-    assert y.col_data.column("factor_1") == ["A", "B", "C", "D"]
+    assert list(y.col_data.column("factor_1")) == ["A", "B", "C", "D"]
     assert list(y.col_data.column("counts")) == [3, 2, 2, 1]
 
     obs_a = y.assay("sums")[:, 0]
@@ -27,7 +27,7 @@ def test_aggregate_across_cells_combinations():
     y = scranpy.aggregate_across_cells(x, {"group": groups, "batch": batches})
 
     assert y.col_data.column("group") == ["A", "A", "B", "B"]
-    assert y.col_data.column("batch") == [1, 2, 1, 2]
+    assert y.col_data.column("batch") == ["1", "2", "1", "2"]
     assert list(y.col_data.column("counts")) == [2, 2, 2, 2]
 
     obs_a = y.assay("sums")[:, 1]
@@ -41,10 +41,10 @@ def test_aggregate_across_cells_combinations():
     # Try out different input types.
     y2 = scranpy.aggregate_across_cells(x, (groups, batches))
     assert y2.col_data.column("factor_1") == ["A", "A", "B", "B"]
-    assert y2.col_data.column("factor_2") == [1, 2, 1, 2]
+    assert y2.col_data.column("factor_2") == ["1", "2", "1", "2"]
     assert (y2.assay("sums") == y.assay("sums")).all()
 
     y2 = scranpy.aggregate_across_cells(x, BiocFrame({"g": groups, "b": batches}))
     assert y2.col_data.column("g") == ["A", "A", "B", "B"]
-    assert y2.col_data.column("b") == [1, 2, 1, 2]
+    assert y2.col_data.column("b") == ["1", "2", "1", "2"]
     assert (y2.assay("detected") == y.assay("detected")).all()

tests/test_analyze.py

@@ -136,4 +136,4 @@ def test_analyze_summarizedexperiment(mock_data):
     sce.alternative_experiments = { "adt": adt_se }
     out = analyze_sce(sce, adt_exp = "adt", assay_type="counts")
     assert out.gene_variances.row_names == se.row_names
-    assert out.adt_markers[0].row_names == adt_se.row_names
+    assert out.adt_markers["0"].row_names == adt_se.row_names

tests/test_score_markers.py

@@ -18,29 +18,29 @@ def test_score_markers(mock_data):
     res = score_markers(out, grouping=grouping)
 
     assert res is not None
-    assert "means" in res[1].columns
-    assert isinstance(res[1].column("delta_detected"), BiocFrame)
+    assert "means" in res["1"].columns
+    assert isinstance(res["1"].column("delta_detected"), BiocFrame)
 
     # Works when blocks are supplied.
     resb = score_markers(
         out, grouping=grouping, options=ScoreMarkersOptions(block=mock_data.block)
     )
     assert resb is not None
-    assert "detected" in resb[1].columns
-    assert isinstance(resb[1].column("lfc"), BiocFrame)
+    assert "detected" in resb["1"].columns
+    assert isinstance(resb["1"].column("lfc"), BiocFrame)
 
     # Same results in parallel.
     resp = score_markers(
         out, grouping=grouping, options=ScoreMarkersOptions(num_threads=3)
     )
-    assert (res[0].column("means") == resp[0].column("means")).all()
+    assert (res["0"].column("means") == resp["0"].column("means")).all()
     assert (
-        res[1].column("cohen").column("mean") == resp[1].column("cohen").column("mean")
+        res["1"].column("cohen").column("mean") == resp["1"].column("cohen").column("mean")
     ).all()
     assert (
-        res[2].column("auc").column("min_rank")
-        == resp[2].column("auc").column("min_rank")
+        res["2"].column("auc").column("min_rank")
+        == resp["2"].column("auc").column("min_rank")
     ).all()
     assert (
-        res[3].column("lfc").column("min") == resp[3].column("lfc").column("min")
+        res["3"].column("lfc").column("min") == resp["3"].column("lfc").column("min")
     ).all()

tests/test_suggest_adt_qc_filters.py

@@ -78,6 +78,8 @@ def test_suggest_adt_qc_filters_custom(mock_data):
     assert list(filters_custom.column("detected")) == [4, 5, 6]
     assert list(filters_custom.column("subset_totals").column("foo")) == [7, 8, 9]
 
+    print("HEREEEEE")
+
     # Now with some blocks, out of order.
     filters_custom = suggest_adt_qc_filters(
         result,
@@ -93,6 +95,8 @@ def test_suggest_adt_qc_filters_custom(mock_data):
         ),
     )
 
+    print("filters_custom", filters_custom)
+
     assert filters_custom.shape[0] == 3
     assert list(filters_custom.column("detected")) == [6, 5, 4]
     assert list(filters_custom.column("subset_totals").column("foo")) == [9, 8, 7]