Merge pull request #1 from brainglobe/fetch-xml-test-data

Add test fixtures for cell matching regression test

tests/tests/conftest.py

@@ -1,9 +1,30 @@
 from pathlib import Path
 
+import pooch
 import pytest
 
 
 @pytest.fixture
 def data_path():
     """Directory storing all test data"""
     return Path(__file__).parent.parent / "data"
+
+
+@pytest.fixture
+def test_data_registry():
+    """
+    Create a test data registry for BrainGlobe.
+
+    Returns:
+        pooch.Pooch: The test data registry object.
+
+    """
+    registry = pooch.create(
+        path=pooch.os_cache("brainglobe_test_data"),
+        base_url="https://gin.g-node.org/BrainGlobe/test-data/raw/master/",
+        registry={
+            "cellfinder/cells-z-1000-1050.xml": None,
+            "cellfinder/other-cells-z-1000-1050.xml": None,
+        },
+    )
+    return registry

tests/tests/test_cells/test_matches.py

@@ -11,6 +11,36 @@
     match_cells,
     match_points,
 )
+from brainglobe_utils.IO.cells import get_cells
+
+
+@pytest.fixture
+def cells_and_other_cells(test_data_registry):
+    """
+    Provides real-life cell coordinates from a CFOS-labelled brain from
+    two different cellfinder versions (pre- and post cellfinder PR #398).
+    Intended to be used for regression testing our cell matching code.
+
+    Parameters
+    ----------
+    test_data_registry : Pooch.pooch
+        The BrainGlobe test data registry.
+
+    Returns
+    -------
+    cell_data : List[Cell]
+        The loaded cell data.
+
+    """
+    cell_data_path = test_data_registry.fetch(
+        "cellfinder/cells-z-1000-1050.xml"
+    )
+    other_cell_data_path = test_data_registry.fetch(
+        "cellfinder/other_cells-z-1000-1050.xml"
+    )
+    cell_data = get_cells(cell_data_path)
+    other_cell_data = get_cells(other_cell_data_path)
+    return cell_data, other_cell_data
 
 
 def as_cell(x: List[float]):
@@ -19,6 +49,13 @@ def as_cell(x: List[float]):
     return cells
 
 
+@pytest.mark.xfail
+def test_cell_matching_regression(cells_and_other_cells):
+    cells, other_cells = cells_and_other_cells
+    # TODO implement cell matching regression test here, then remove xfail
+    assert False
+
+
 @pytest.mark.parametrize("use_scipy", [True, False])
 @pytest.mark.parametrize("pre_match", [True, False])
 def test_cell_matches_equal_size(pre_match, use_scipy):