Got more tests to pass.

src/singler/_utils.py

@@ -8,12 +8,6 @@
 import warnings
 
 
-def _factorize(x: Sequence) -> Tuple[list, numpy.ndarray]:
-    f = biocutils.Factor.from_sequence(x, sort_levels=False)
-    print(f)
-    return f.levels, numpy.array(f.codes, dtype=numpy.uint32)
-
-
 def _create_map(x: Sequence) -> dict:
     mapping = {}
     for i, val in enumerate(x):

src/singler/annotate_integrated.py

@@ -1,6 +1,7 @@
 from typing import Any, Optional, Sequence, Tuple, Union
 
 import biocframe
+import warnings
 
 from ._utils import _clean_matrix, _restrict_features
 from .train_single import train_single
@@ -132,6 +133,15 @@ def annotate_integrated(
     all_ref_labels = []
     all_ref_features = []
     for r in range(nrefs):
+        curref_labels = ref_labels[r]
+        if isinstance(curref_labels, str):
+            warnings.warn(
+                "setting 'ref_labels' to a column name of the column data is deprecated",
+                category=DeprecationWarning
+            )
+            curref_labels = ref_data[r].get_column_data().column(curref_labels)
+        all_ref_labels.append(curref_labels)
+
         curref_data, curref_features = _clean_matrix(
             ref_data[r],
             ref_features[r],
@@ -161,7 +171,7 @@ def annotate_integrated(
     for r in range(nrefs):
         curbuilt = train_single(
             ref_data=all_ref_data[r],
-            ref_labels=ref_labels[r],
+            ref_labels=all_ref_labels[r],
             ref_features=all_ref_features[r],
             test_features=test_features,
             **train_single_args,

src/singler/annotate_single.py

@@ -91,6 +91,13 @@ def annotate_single(
         A :py:class:`~biocframe.BiocFrame.BiocFrame` of labelling results, see
         :py:func:`~singler.classify_single.classify_single` for details.
     """
+    if isinstance(ref_labels, str):
+        warnings.warn(
+            "setting 'ref_labels' to a column name of the column data is deprecated",
+            category=DeprecationWarning
+        )
+        ref_labels = ref_data.get_column_data().column(ref_labels)
+
     test_data, test_features = _clean_matrix(
         test_data,
         test_features,

src/singler/train_single.py

@@ -8,7 +8,7 @@
 import warnings
 
 from . import lib_singler as lib
-from ._utils import _clean_matrix, _factorize, _restrict_features, _stable_intersect
+from ._utils import _clean_matrix, _restrict_features, _stable_intersect
 from .get_classic_markers import get_classic_markers
 
 
@@ -176,6 +176,12 @@ def train_single(
         The pre-built reference, ready for use in downstream methods like
         :py:meth:`~singler.classify_single_reference.classify_single`.
     """
+    if isinstance(ref_labels, str):
+        warnings.warn(
+            "setting 'ref_labels' to a column name of the column data is deprecated",
+            category=DeprecationWarning
+        )
+        ref_labels = ref_data.get_column_data().column(ref_labels)
 
     ref_data, ref_features = _clean_matrix(
         ref_data,
@@ -196,13 +202,13 @@ def train_single(
             ref_features = biocutils.subset_sequence(ref_features, keep)
             ref_data = delayedarray.DelayedArray(ref_data)[keep,:]
 
-    if isinstance(ref_labels, str):
-        warnings.warn(
-            "setting 'labels' to a column name of the column data is deprecated",
-            category=DeprecationWarning
-        )
-        ref_labels = ref_data.get_column_data().column(ref_labels)
-    unique_labels, label_idx = _factorize(ref_labels)
+    for f in ref_labels:
+        if f is None:
+            raise ValueError("entries of 'ref_labels' cannot be missing")
+    if not isinstance(ref_labels, biocutils.Factor): # TODO: move over to biocutils so coercion can no-op.
+        ref_labels = biocutils.Factor.from_sequence(ref_labels, sort_levels=False) # TODO: add a dtype= option.
+    unique_labels = ref_labels.levels
+    label_idx = ref_labels.codes.astype(dtype=numpy.uint32, copy=False)
 
     markers = _identify_genes(
         ref_data=ref_data, 

tests/test_integrated_with_celldex.py

@@ -16,19 +16,17 @@ def test_with_minimal_args():
     )
     immune_cell_ref = celldex.fetch_reference("dice", "2024-02-26", realize_assays=True)
 
-    with pytest.raises(Exception):
-        singler.annotate_integrated(
-            test_data=sce.assays["counts"],
-            ref_data_list=(blueprint_ref, immune_cell_ref),
-            ref_labels_list="label.main",
-            num_threads=6,
-        )
-
     single, integrated = singler.annotate_integrated(
         test_data=sce,
-        ref_data_list=(blueprint_ref, immune_cell_ref),
-        ref_labels_list="label.main",
-        num_threads=6,
+        ref_data=(
+            blueprint_ref,
+            immune_cell_ref
+        ),
+        ref_labels=[
+            blueprint_ref.get_column_data().column("label.main"),
+            immune_cell_ref.get_column_data().column("label.main")
+        ],
+        num_threads=2
     )
     assert len(single) == 2
     assert isinstance(integrated, BiocFrame)
@@ -43,14 +41,21 @@ def test_with_all_supplied():
     immune_cell_ref = celldex.fetch_reference("dice", "2024-02-26", realize_assays=True)
 
     single, integrated = singler.annotate_integrated(
-        test_data=sce,
+        test_data=sce.assays["counts"],
         test_features=sce.get_row_names(),
-        ref_data_list=(blueprint_ref, immune_cell_ref),
-        ref_labels_list=[
-            x.get_column_data().column("label.main")
-            for x in (blueprint_ref, immune_cell_ref)
+        ref_data=(
+            blueprint_ref,
+            immune_cell_ref
+        ),
+        ref_labels=[
+            blueprint_ref.get_column_data().column("label.main"),
+            immune_cell_ref.get_column_data().column("label.main")
+        ],
+        ref_features=[
+            blueprint_ref.get_row_names(),
+            immune_cell_ref.get_row_names()
         ],
-        ref_features_list=[x.get_row_names() for x in (blueprint_ref, immune_cell_ref)],
+        num_threads=2
     )
 
     assert len(single) == 2
@@ -67,8 +72,9 @@ def test_with_colname():
 
     single, integrated = singler.annotate_integrated(
         test_data=sce,
-        ref_data_list=(blueprint_ref, immune_cell_ref),
-        ref_labels_list="label.main",
+        ref_data=(blueprint_ref, immune_cell_ref),
+        ref_labels=["label.main"] * 2,
+        num_threads=2
     )
 
     assert len(single) == 2

tests/test_single_with_celldex.py

@@ -4,21 +4,12 @@
 import scrnaseq
 import pandas as pd
 import scipy
-import pytest
 from biocframe import BiocFrame
 
 def test_with_minimal_args():
     sce = scrnaseq.fetch_dataset("zeisel-brain-2015", "2023-12-14", realize_assays=True)
-
     immgen_ref = celldex.fetch_reference("immgen", "2024-02-26", realize_assays=True)
 
-    with pytest.raises(Exception):
-        matches = singler.annotate_single(
-            test_data=sce.assays["counts"],
-            ref_data=immgen_ref,
-            ref_labels=immgen_ref.get_column_data().column("label.main"),
-        )
-
     matches = singler.annotate_single(
         test_data=sce,
         ref_data=immgen_ref,
@@ -32,11 +23,10 @@ def test_with_minimal_args():
 
 def test_with_all_supplied():
     sce = scrnaseq.fetch_dataset("zeisel-brain-2015", "2023-12-14", realize_assays=True)
-
     immgen_ref = celldex.fetch_reference("immgen", "2024-02-26", realize_assays=True)
 
     matches = singler.annotate_single(
-        test_data=sce,
+        test_data=sce.assays["counts"],
         test_features=sce.get_row_names(),
         ref_data=immgen_ref,
         ref_labels=immgen_ref.get_column_data().column("label.main"),
@@ -50,7 +40,6 @@ def test_with_all_supplied():
 
 def test_with_colname():
     sce = scrnaseq.fetch_dataset("zeisel-brain-2015", "2023-12-14", realize_assays=True)
-
     immgen_ref = celldex.fetch_reference("immgen", "2024-02-26", realize_assays=True)
 
     matches = singler.annotate_single(

tests/test_train_integrated.py

@@ -30,7 +30,7 @@ def test_train_integrated():
         test_features,
         ref_prebuilt=[built1, built2],
         ref_names=["FOO", "BAR"],
-        num_threads=3,
+        num_threads=2,
     )
 
     assert pintegrated.reference_names == ["FOO", "BAR"]

tests/test_utils.py

@@ -1,5 +1,4 @@
 from singler._utils import (
-    _factorize,
     _stable_intersect,
     _stable_union,
     _clean_matrix,
@@ -8,17 +7,6 @@
 import summarizedexperiment
 
 
-def test_factorize():
-    lev, ind = _factorize([1, 3, 5, 5, 3, 1])
-    assert list(lev) == ["1", "3", "5"]
-    assert (ind == [0, 1, 2, 2, 1, 0]).all()
-
-    # Preserves the order.
-    lev, ind = _factorize(["C", "D", "A", "B", "C", "A"])
-    assert list(lev) == ["C", "D", "A", "B"]
-    assert (ind == [0, 1, 2, 3, 0, 2]).all()
-
-
 def test_intersect():
     # Preserves the order in the first argument.
     out = _stable_intersect(["B", "C", "A", "D", "E"], ["A", "C", "E"])