Implement a simple atlas manager widget

brainrender_napari/__init__.py

@@ -1,4 +1,4 @@
 __version__ = "0.0.1"
 
 
-__all__ = "BrainrenderWidget"
+__all__ = "BrainrenderViewerWidget, BrainrenderManagerWidget"

brainrender_napari/brainrender_manager_widget.py

@@ -0,0 +1,54 @@
+"""
+A napari widget to download and update atlases.
+
+Available atlases are shown in a table view using the Qt model/view framework
+[Qt Model/View framework](https://doc.qt.io/qt-6/model-view-programming.html)
+"""
+
+from brainglobe_utils.qtpy.logo import header_widget
+from napari.viewer import Viewer
+from qtpy.QtWidgets import (
+    QGroupBox,
+    QVBoxLayout,
+    QWidget,
+)
+
+from brainrender_napari.widgets.atlas_manager_view import AtlasManagerView
+
+
+class BrainrenderManagerWidget(QWidget):
+    """The purpose of this class is
+    * to hold atlas visualisation widgets for napari
+    * coordinate between these widgets and napari
+    """
+
+    def __init__(self, napari_viewer: Viewer):
+        """Instantiates the atlas viewer widget
+        and sets up coordinating connections"""
+        super().__init__()
+
+        self._viewer = napari_viewer
+        self.setLayout(QVBoxLayout())
+        self.layout().addWidget(
+            header_widget(
+                "brainrender",
+                "Atlas management",
+                tutorial_file_name="manage-atlas-napari.html",
+                citation_doi="https://doi.org/10.7554/eLife.65751",
+                github_repo_name="brainrender-napari",
+                help_text="For help, hover the cursor over the "
+                "atlases/regions.",
+            )
+        )
+
+        # create widgets
+        self.atlas_manager_view = AtlasManagerView(parent=self)
+
+        # add widgets to the layout as group boxes
+        self.atlas_manager_group = QGroupBox("Atlas Manager")
+        self.atlas_manager_group.setToolTip(
+            "Double-click on row to download/update an atlas"
+        )
+        self.atlas_manager_group.setLayout(QVBoxLayout())
+        self.atlas_manager_group.layout().addWidget(self.atlas_manager_view)
+        self.layout().addWidget(self.atlas_manager_group)

brainrender_napari/brainrender_widget.py → brainrender_napari/brainrender_viewer_widget.py

@@ -26,7 +26,7 @@
 from brainrender_napari.widgets.structure_view import StructureView
 
 
-class BrainrenderWidget(QWidget):
+class BrainrenderViewerWidget(QWidget):
     """The purpose of this class is
     * to hold atlas visualisation widgets for napari
     * coordinate between these widgets and napari

brainrender_napari/napari.yaml

@@ -2,9 +2,14 @@ name: brainrender-napari
 display_name: brainrender
 contributions:
   commands:
-    - id: brainrender-napari.make_brainrender_widget
-      python_name: brainrender_napari.brainrender_widget:BrainrenderWidget
-      title: Make Brainrender Napari
+    - id: brainrender-napari.make_brainrender_viewer_widget
+      python_name: brainrender_napari.brainrender_viewer_widget:BrainrenderViewerWidget
+      title: Make Brainrender Napari Viewer
+    - id: brainrender-napari.make_brainrender_manager_widget
+      python_name: brainrender_napari.brainrender_manager_widget:BrainrenderManagerWidget
+      title: Make Brainrender Napari Manager
   widgets:
-    - command: brainrender-napari.make_brainrender_widget
+    - command: brainrender-napari.make_brainrender_viewer_widget
       display_name: Brainrender
+    - command: brainrender-napari.make_brainrender_manager_widget
+      display_name: Manage atlas versions

tests/test_integration/test_brainrender_manager_widget.py

@@ -0,0 +1,32 @@
+"""These tests should just check that the subwidget signal and napari
+are connected as expected. Lower level tests should happen in the tests
+for the widget themselves."""
+
+import pytest
+
+from brainrender_napari.brainrender_manager_widget import (
+    BrainrenderManagerWidget,
+)
+
+
+@pytest.fixture
+def manager_widget(make_napari_viewer) -> BrainrenderManagerWidget:
+    """Fixture to expose the atlas viewer widget to tests.
+
+    Simultaneously acts as a smoke test that the widget
+    can be instantiated without crashing."""
+    viewer = make_napari_viewer()
+    return BrainrenderManagerWidget(viewer)
+
+
+def test_atlas_manager_view_tooltip(manager_widget):
+    for expected_keyword in [
+        "double-click",
+        "download/update",
+        "row",
+        "atlas",
+    ]:
+        assert (
+            expected_keyword
+            in manager_widget.atlas_manager_group.toolTip().lower()
+        )

tests/test_integration/test_brainrender_widget.py → tests/test_integration/test_brainrender_viewer_widget.py

@@ -4,17 +4,19 @@
 
 import pytest
 
-from brainrender_napari.brainrender_widget import BrainrenderWidget
+from brainrender_napari.brainrender_viewer_widget import (
+    BrainrenderViewerWidget,
+)
 
 
 @pytest.fixture
-def brainrender_widget(make_napari_viewer) -> BrainrenderWidget:
+def viewer_widget(make_napari_viewer) -> BrainrenderViewerWidget:
     """Fixture to expose the atlas viewer widget to tests.
 
     Simultaneously acts as a smoke test that the widget
     can be instantiated without crashing."""
     viewer = make_napari_viewer()
-    return BrainrenderWidget(viewer)
+    return BrainrenderViewerWidget(viewer)
 
 
 @pytest.mark.parametrize(
@@ -25,12 +27,12 @@ def brainrender_widget(make_napari_viewer) -> BrainrenderWidget:
     ],
 )
 def test_checkbox_visibility(
-    brainrender_widget, mocker, expected_visibility, atlas
+    viewer_widget, mocker, expected_visibility, atlas
 ):
     checkbox_visibility_mock = mocker.patch(
-        "brainrender_napari.brainrender_widget.QCheckBox.setVisible"
+        "brainrender_napari.brainrender_viewer_widget.QCheckBox.setVisible"
     )
-    brainrender_widget._on_atlas_selection_changed(atlas)
+    viewer_widget._on_atlas_selection_changed(atlas)
     checkbox_visibility_mock.assert_called_once_with(expected_visibility)
 
 
@@ -43,82 +45,78 @@ def test_checkbox_visibility(
     ],
 )
 def test_double_click_on_locally_available_atlas_row(
-    brainrender_widget, mocker, qtbot, expected_atlas_name
+    viewer_widget, mocker, qtbot, expected_atlas_name
 ):
     """Check for a few local low-res atlases that double-clicking them
     on the atlas viewer view calls the expected atlas representation function.
     """
     add_atlas_to_viewer_mock = mocker.patch(
-        "brainrender_napari.brainrender_widget"
+        "brainrender_napari.brainrender_viewer_widget"
         ".NapariAtlasRepresentation.add_to_viewer"
     )
-    with qtbot.waitSignal(
-        brainrender_widget.atlas_viewer_view.add_atlas_requested
-    ):
-        brainrender_widget.atlas_viewer_view.add_atlas_requested.emit(
+    with qtbot.waitSignal(viewer_widget.atlas_viewer_view.add_atlas_requested):
+        viewer_widget.atlas_viewer_view.add_atlas_requested.emit(
             expected_atlas_name
         )
     add_atlas_to_viewer_mock.assert_called_once()
 
 
-def test_structure_row_double_clicked(brainrender_widget, mocker):
+def test_structure_row_double_clicked(viewer_widget, mocker):
     """Checks that when the structure view widgets emit "VS" and
     the allen_mouse_100um atlas is selected, the NapariAtlasRepresentation
     function is called in the expected way.
     """
     add_structure_to_viewer_mock = mocker.patch(
-        "brainrender_napari.brainrender_widget"
+        "brainrender_napari.brainrender_viewer_widget"
         ".NapariAtlasRepresentation.add_structure_to_viewer"
     )
-    brainrender_widget.atlas_viewer_view.selectRow(
+    viewer_widget.atlas_viewer_view.selectRow(
         4
     )  # allen_mouse_100um is in row 4
 
-    brainrender_widget.structure_view.add_structure_requested.emit("VS")
+    viewer_widget.structure_view.add_structure_requested.emit("VS")
     add_structure_to_viewer_mock.assert_called_once_with("VS")
 
 
-def test_add_additional_reference_selected(brainrender_widget, mocker):
+def test_add_additional_reference_selected(viewer_widget, mocker):
     """Checks that when the atlas viewer view requests an additional
     reference, the NapariAtlasRepresentation function is called in
     the expected way."""
     add_additional_reference_mock = mocker.patch(
-        "brainrender_napari.brainrender_widget"
+        "brainrender_napari.brainrender_viewer_widget"
         ".NapariAtlasRepresentation.add_additional_reference"
     )
-    brainrender_widget.atlas_viewer_view.selectRow(
-        5
-    )  # mpin_zfish_1um is in row 5
+    viewer_widget.atlas_viewer_view.selectRow(5)  # mpin_zfish_1um is in row 5
     assert (
-        brainrender_widget.atlas_viewer_view.selected_atlas_name()
+        viewer_widget.atlas_viewer_view.selected_atlas_name()
         == "mpin_zfish_1um"
     )
     additional_reference_name = "GAD1b"
-    brainrender_widget.atlas_viewer_view.additional_reference_requested.emit(
+    viewer_widget.atlas_viewer_view.additional_reference_requested.emit(
         additional_reference_name
     )
     add_additional_reference_mock.assert_called_once_with(
         additional_reference_name
     )
 
 
-def test_show_structures_checkbox(brainrender_widget, mocker):
+def test_show_structures_checkbox(viewer_widget, mocker):
     structure_view_refresh_mock = mocker.patch(
-        "brainrender_napari.brainrender_widget.StructureView.refresh"
+        "brainrender_napari.brainrender_viewer_widget.StructureView.refresh"
     )
-    brainrender_widget.atlas_viewer_view.selectRow(
+    viewer_widget.atlas_viewer_view.selectRow(
         0
     )  # example_mouse_100um is in row 0
     structure_view_refresh_mock.assert_called_with(
         "example_mouse_100um", False
     )
 
-    brainrender_widget.show_structure_names.click()
+    viewer_widget.show_structure_names.click()
     assert structure_view_refresh_mock.call_count == 2
     structure_view_refresh_mock.assert_called_with("example_mouse_100um", True)
 
 
-def test_structure_view_tooltip(brainrender_widget):
+def test_structure_view_tooltip(viewer_widget):
     for expected_keyword in [
         "double-click",
         "atlas region",
@@ -131,11 +129,11 @@ def test_structure_view_tooltip(brainrender_widget):
     ]:
         assert (
             expected_keyword
-            in brainrender_widget.structure_tree_group.toolTip().lower()
+            in viewer_widget.structure_tree_group.toolTip().lower()
         )
 
 
-def test_atlas_viewer_view_tooltip(brainrender_widget):
+def test_atlas_viewer_view_tooltip(viewer_widget):
     for expected_keyword in [
         "double-click",
         "add",
@@ -146,5 +144,5 @@ def test_atlas_viewer_view_tooltip(brainrender_widget):
     ]:
         assert (
             expected_keyword
-            in brainrender_widget.atlas_viewer_group.toolTip().lower()
+            in viewer_widget.atlas_viewer_group.toolTip().lower()
         )