Add test for napari reader

btrack/napari/reader.py

@@ -57,7 +57,7 @@ def reader_function(path: PathLike) -> List[LayerDataTuple]:
         to layer_type=="image" if not provided
     """
     # handle both a string and a list of strings
-    paths = [path] if isinstance(path, str) else path
+    paths = [path] if not isinstance(path, list) else path
 
     # store the layers to be generated
     layers = []
@@ -66,6 +66,7 @@ def reader_function(path: PathLike) -> List[LayerDataTuple]:
         with HDF5FileHandler(_path, "r") as hdf:
 
             # get the segmentation if there is one
+            import pdb; pdb.set_trace()
             if "segmentation" in hdf._hdf:
                 segmentation = hdf.segmentation
                 layers.append((segmentation, {}, "labels"))

tests/conftest.py

@@ -22,6 +22,8 @@ def test_objects():
 def hdf5_file_path(tmp_path, test_objects) -> Path:
     """
     Create and save a btrack HDF5 file, and return the path.
+
+    Note that this only saves segmentation results, not tracking results.
     """
     fn = Path(tmp_path) / "test.h5"
 

tests/napari/test_reader.py

@@ -4,6 +4,13 @@
 napari_reader = pytest.importorskip("btrack.napari.reader")
 
 
-def test_get_reader_pass():
-    reader = napari_reader.get_reader("fake.file")
+def test_reader(hdf5_file_path):
+    reader = napari_reader.get_reader(hdf5_file_path)
     assert reader is not None
+
+    tracks = reader(hdf5_file_path)
+    assert isinstance(tracks, list)
+    # TODO: update the HDF file so that it has some tracks that can be read.
+    # For now this just checks that the reader can read an emtpy HDF5 file
+    # with no tracks in it
+    assert len(tracks) == 0