Fix tests (#170)

* Remove unnecessary pytest options

* Update dependency imports

* Add test for get_available_atlases

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Update tests/tests/test_unit/test_plugin/test_register.py

Co-authored-by: Will Graham <[email protected]>

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Will Graham <[email protected]>

brainreg/napari/register.py

@@ -9,8 +9,10 @@
 import napari
 import numpy as np
 from bg_atlasapi import BrainGlobeAtlas
-from brainglobe_napari_io.cellfinder.reader_dir import load_registration
-from brainglobe_segmentation.atlas.utils import get_available_atlases
+from bg_atlasapi.list_atlases import descriptors, utils
+from brainglobe_napari_io.workflows.wholebrain_cell_reader_dir import (
+    load_registration,
+)
 from fancylog import fancylog
 from magicgui import magicgui
 from napari._qt.qthreading import thread_worker
@@ -32,6 +34,18 @@
 PRE_PROCESSING_ARGS = None
 
 
+def get_available_atlases():
+    """
+    Get the available brainglobe atlases
+    :return: Dict of available atlases (["name":version])
+    """
+    available_atlases = utils.conf_from_url(
+        descriptors.remote_url_base.format("last_versions.conf")
+    )
+    available_atlases = dict(available_atlases["atlases"])
+    return available_atlases
+
+
 def add_registered_image_layers(
     viewer: napari.Viewer, *, registration_directory: pathlib.Path
 ) -> Tuple[napari.layers.Image, napari.layers.Labels]:

pyproject.toml

@@ -85,21 +85,6 @@ include = ["brainreg*"]
 
 [tool.pytest.ini_options]
 addopts = "--cov=brainreg"
-filterwarnings = [
-    "error",
-    # Emitted by scikit-image on import, see https://github.com/scikit-image/scikit-image/issues/6663
-    # This filter should be removed when scikit-image 0.20 is released
-    "ignore:`np.bool8` is a deprecated alias for `np.bool_`",
-    # Emitted by nptyping, see https://github.com/ramonhagenaars/nptyping/issues/102
-    # for upstream issue
-    "ignore:`np.object0` is a deprecated alias for ``np.object0`",
-    "ignore:`np.int0` is a deprecated alias for `np.intp`",
-    "ignore:`np.uint0` is a deprecated alias for `np.uintp`",
-    "ignore:`np.void0` is a deprecated alias for `np.void`",
-    "ignore:`np.bytes0` is a deprecated alias for `np.bytes_`",
-    "ignore:`np.str0` is a deprecated alias for `np.str_`",
-]
-markers = ["slow: marks tests as slow (deselect with '-m \"not slow\"')"]
 
 [tool.black]
 line-length = 79

tests/tests/test_unit/test_plugin/test_register.py

@@ -0,0 +1,20 @@
+from brainreg.napari.register import get_available_atlases
+
+atlas_name = "allen_mouse_50um"
+
+
+def test_get_available_atlases():
+    atlases = get_available_atlases()
+
+    # arbitrary selection of atlases
+    expected_atlases = [
+        "allen_mouse_10um",
+        "allen_mouse_25um",
+        "allen_mouse_50um",
+        "mpin_zfish_1um",
+    ]
+
+    for a in expected_atlases:
+        assert (
+            a in atlases.keys()
+        ), f"{a} is not in the list of expected atlases"