Replace pandas.df.append with safe_concat

cellfinder/analyse/analyse.py

@@ -16,7 +16,7 @@
 import tifffile
 from bg_atlasapi import BrainGlobeAtlas
 from brainglobe_utils.general.system import ensure_directory_exists
-from brainglobe_utils.pandas.misc import sanitise_df
+from brainglobe_utils.pandas.misc import safe_pandas_concat, sanitise_df
 
 from cellfinder.export.export import export_points
 
@@ -155,13 +155,16 @@
                 ]
             )
             if n_points:
-                point_numbers = point_numbers.append(
-                    {
-                        "structure_name": structure,
-                        "hemisphere": hemisphere,
-                        "cell_count": n_points,
-                    },
-                    ignore_index=True,
+                point_numbers = safe_pandas_concat(
+                    point_numbers,
+                    pd.DataFrame(
+                        data=[[structure, hemisphere, n_points]],
+                        columns=[
+                            "structure_name",
+                            "hemisphere",
+                            "cell_count",
+                        ],
+                    ),
                 )
     sorted_point_numbers = point_numbers.sort_values(
         by=["cell_count"], ascending=False

tests/data/analyse/region_totals_regression_pandas1_5_3.csv

@@ -0,0 +1,5 @@
+structure_name,left_cell_count,right_cell_count,total_cells,left_volume_mm3,right_volume_mm3,total_volume_mm3,left_cells_per_mm3,right_cells_per_mm3
+Anterodorsal nucleus,1.0,0.0,1.0,0.083,0.075,0.158,12.048192771084336,0.0
+"Paraventricular hypothalamic nucleus, descending division",0.0,1.0,1.0,0.075,0.065,0.14,0.0,15.384615384615383
+Lateral terminal nucleus of the accessory optic tract,0.0,0.0,0.0,0.01,0.009,0.019,0.0,0.0
+Interstitial nucleus of Cajal,0.0,0.0,0.0,0.049,0.047,0.096,0.0,0.0

tests/data/analyse/volumes.csv

@@ -0,0 +1,5 @@
+structure_name,left_volume_mm3,right_volume_mm3,total_volume_mm3
+"Paraventricular hypothalamic nucleus, descending division",0.075,0.065,0.14
+Anterodorsal nucleus,0.083,0.075,0.158
+Lateral terminal nucleus of the accessory optic tract,0.01,0.009000000000000001,0.019000000000000003
+Interstitial nucleus of Cajal,0.049,0.047,0.096

tests/tests/test_unit/test_analyse.py

@@ -0,0 +1,54 @@
+import filecmp
+import os
+from pathlib import Path
+
+import pytest
+
+from cellfinder.analyse.analyse import Point, get_region_totals
+
+
+@pytest.fixture
+def points():
+    p1 = Point(
+        raw_coordinate=[1.0, 1.0, 1.0],
+        atlas_coordinate=[1.0, 1.0, 1.0],
+        structure="Paraventricular hypothalamic nucleus, descending division",
+        structure_id=56,
+        hemisphere="right",
+    )
+    p2 = Point(
+        raw_coordinate=[2.0, 2.0, 2.0],
+        atlas_coordinate=[2.0, 2.0, 2.0],
+        structure="Anterodorsal nucleus",
+        structure_id=57,
+        hemisphere="left",
+    )
+    return [p1, p2]
+
+
+@pytest.fixture
+def structures_with_points():
+    return [
+        "Paraventricular hypothalamic nucleus, descending division",
+        "Anterodorsal nucleus",
+    ]
+
+
+def test_get_region_totals(tmp_path, points, structures_with_points):
+    """Regression test for get_region_totals for pandas 1.5.3 -> 2.1.3+.
+    pd.Dataframe.append was deprecated and remove in this time."""
+    OUTPUT_DATA_LOC = (
+        Path(os.path.dirname(os.path.abspath(__file__))) / "../../data/analyse"
+    ).resolve()
+
+    volumes_path = OUTPUT_DATA_LOC / "volumes.csv"
+    expected_output = (
+        OUTPUT_DATA_LOC / "region_totals_regression_pandas1_5_3.csv"
+    )
+
+    output_path = Path(tmp_path / "tmp_region_totals.csv")
+    get_region_totals(
+        points, structures_with_points, volumes_path, output_path
+    )
+    assert output_path.exists()
+    assert filecmp.cmp(output_path, expected_output)

tests/tests/test_unit/test_tools/test_system.py

@@ -14,12 +14,12 @@
 
 def test_get_subdirectories():
     subdirs = system.get_subdirectories(data_dir)
-    assert len(subdirs) == 9
+    assert len(subdirs) == 10
     assert Path(data_dir / "cells") in subdirs
     assert Path(data_dir / "brain") in subdirs
 
     subdir_names = system.get_subdirectories(data_dir, names_only=True)
-    assert len(subdir_names) == 9
+    assert len(subdir_names) == 10
     assert "cells" in subdir_names
     assert "brain" in subdir_names
 

tox.ini

@@ -14,7 +14,7 @@ INPUT_COREDEV =
     true: coredev
 
 [testenv]
-commands = pytest -v --cov=./ --cov-report=xml
+commands = pytest {toxinidir} -v --cov=./ --cov-report=xml
 deps =
     pytest-cov
     pytest