Move fixtures into conftest.py (#331)

* Move `fixture`s into `conftest.py`

* Just import `btrack`

* Move `Container`

* Fix tests

* Rename writer

* Use `qtpy`

tests/conftest.py

@@ -2,7 +2,9 @@
 from typing import Union
 
 import numpy as np
+import numpy.typing as npt
 import pytest
+from qtpy import QtWidgets
 
 import btrack
 
@@ -14,6 +16,16 @@
 )
 
 
+def _write_h5_file(file_path: os.PathLike, test_objects) -> os.PathLike:
+    """
+    Write a h5 file with test objects and return path.
+    """
+    with btrack.io.HDF5FileHandler(file_path, "w") as h:
+        h.write_objects(test_objects)
+
+    return file_path
+
+
 @pytest.fixture
 def test_objects():
     """
@@ -31,24 +43,14 @@ def test_real_objects():
     return btrack.io.import_CSV(TEST_DATA_PATH / "test_data.csv")
 
 
-def write_h5_file(file_path: os.PathLike, test_objects) -> os.PathLike:
-    """
-    Write a h5 file with test objects and return path.
-    """
-    with btrack.io.HDF5FileHandler(file_path, "w") as h:
-        h.write_objects(test_objects)
-
-    return file_path
-
-
 @pytest.fixture
 def hdf5_file_path(tmp_path, test_objects) -> os.PathLike:
     """
     Create and save a btrack HDF5 file, and return the path.
 
     Note that this only saves segmentation results, not tracking results.
     """
-    return write_h5_file(tmp_path / "test.h5", test_objects)
+    return _write_h5_file(tmp_path / "test.h5", test_objects)
 
 
 @pytest.fixture(params=["single", "list"])
@@ -61,11 +63,11 @@ def hdf5_file_path_or_paths(
     Note that this only saves segmentation results, not tracking results.
     """
     if request.param == "single":
-        return write_h5_file(tmp_path / "test.h5", test_objects)
+        return _write_h5_file(tmp_path / "test.h5", test_objects)
     elif request.param == "list":
         return [
-            write_h5_file(tmp_path / "test1.h5", test_objects),
-            write_h5_file(tmp_path / "test2.h5", test_objects),
+            _write_h5_file(tmp_path / "test1.h5", test_objects),
+            _write_h5_file(tmp_path / "test2.h5", test_objects),
         ]
     else:
         raise ValueError("Invalid requests.param, must be one of 'single' or 'list'")
@@ -85,3 +87,25 @@ def default_rng():
     Create a default PRNG to use for tests.
     """
     return np.random.default_rng(seed=RANDOM_SEED)
+
+
+@pytest.fixture
+def track_widget(make_napari_viewer) -> QtWidgets.QWidget:
+    """Provides an instance of the track widget to test"""
+    make_napari_viewer()  # make sure there is a viewer available
+    return btrack.napari.main.create_btrack_widget()
+
+
+@pytest.fixture
+def simplistic_tracker_outputs() -> (
+    tuple[npt.NDArray, dict[str, npt.NDArray], dict[int, list]]
+):
+    """Provides simplistic return values of a btrack run.
+    They have the correct types and dimensions, but contain zeros.
+    Useful for mocking the tracker.
+    """
+    n, d = 10, 3
+    data = np.zeros((n, d + 1))
+    properties = {"some_property": np.zeros(n)}
+    graph = {0: [0]}
+    return data, properties, graph

tests/napari/test_dock_widget.py

@@ -3,10 +3,7 @@
 import json
 from unittest.mock import patch
 
-import numpy as np
-import numpy.typing as npt
 import pytest
-from qtpy import QtWidgets
 
 import napari
 
@@ -32,13 +29,6 @@ def test_add_widget(make_napari_viewer):
     assert len(list(viewer.window._dock_widgets)) == num_dw + 1
 
 
-@pytest.fixture
-def track_widget(make_napari_viewer) -> QtWidgets.QWidget:
-    """Provides an instance of the track widget to test"""
-    make_napari_viewer()  # make sure there is a viewer available
-    return btrack.napari.main.create_btrack_widget()
-
-
 @pytest.mark.parametrize(
     "config",
     [btrack.datasets.cell_config(), btrack.datasets.particle_config()],
@@ -123,22 +113,6 @@ def test_reset_button(track_widget):
     assert new_relax == original_relax
 
 
-@pytest.fixture
-def simplistic_tracker_outputs() -> (
-    tuple[npt.NDArray, dict[str, npt.NDArray], dict[int, list]]
-):
-    """Provides simplistic return values of a btrack run.
-
-    They have the correct types and dimensions, but contain zeros.
-    Useful for mocking the tracker.
-    """
-    n, d = 10, 3
-    data = np.zeros((n, d + 1))
-    properties = {"some_property": np.zeros(n)}
-    graph = {0: [0]}
-    return data, properties, graph
-
-
 def test_run_button(track_widget, simplistic_tracker_outputs):
     """Tests that clicking the run button calls run_tracker,
     and that the napari viewer has an additional tracks layer after running.