Increase test coverage for widgets (#8)

This adds some basic tests to cover the sub-widgets that make up the
main data portal widget.

Note that coverage likely doesn't cover lines that are run via QThreads,
which explains some of the uncovered lines:
nedbat/coveragepy#582 (comment)

This also removes the preview widget, which isn't being actively used,
and ignores coverage of test code itself.

setup.cfg

@@ -55,11 +55,15 @@ napari.manifest =
 [options.extras_require]
 testing =
     tox
-    pytest  # https://docs.pytest.org/en/latest/contents.html
-    pytest-cov  # https://pytest-cov.readthedocs.io/en/latest/
-    pytest-qt  # https://pytest-qt.readthedocs.io/en/latest/
+    pytest
+    pytest-cov
+    pytest-mock
+    pytest-qt
     napari
     pyqt5
 
 [options.package_data]
 * = *.yaml
+
+[coverage:run]
+omit = **/_tests/**

src/napari_cryoet_data_portal/_listing_widget.py

@@ -30,7 +30,7 @@ def __init__(self, parent: Optional[QWidget] = None) -> None:
         self.filter = QLineEdit()
         self.filter.setPlaceholderText("Filter datasets and tomograms")
         self.filter.setClearButtonEnabled(True)
-        self._progress = ProgressWidget(
+        self._progress: ProgressWidget = ProgressWidget(
             work=self._loadDatasets,
             yieldCallback=self._onDatasetLoaded,
         )

src/napari_cryoet_data_portal/_metadata_widget.py

@@ -24,7 +24,7 @@ def __init__(self, parent: Optional[QWidget] = None) -> None:
         self._main = QSearchableTreeWidget()
         self._main.layout().setContentsMargins(0, 0, 0, 0)
         self._main.filter.setPlaceholderText("Filter metadata")
-        self._progress = ProgressWidget(
+        self._progress: ProgressWidget = ProgressWidget(
             work=self._loadMetadata,
             returnCallback=self._onMetadataLoaded,
         )

src/napari_cryoet_data_portal/_open_widget.py

@@ -70,7 +70,7 @@ def __init__(
             self.resolution.addItem(res.name, res)
         self.resolution.setCurrentText(LOW_RESOLUTION.name)
         self.resolution_label.setBuddy(self.resolution)
-        self._progress = ProgressWidget(
+        self._progress: ProgressWidget = ProgressWidget(
             work=self._loadTomogram,
             yieldCallback=self._onLayerLoaded,
         )

src/napari_cryoet_data_portal/_progress_widget.py

@@ -1,5 +1,6 @@
 from typing import Callable, Generator, Generic, Optional, TypeVar, Union
 
+from qtpy.QtCore import Signal
 from qtpy.QtWidgets import (
     QHBoxLayout,
     QLabel,
@@ -24,20 +25,22 @@
 class ProgressWidget(QWidget, Generic[YieldType, SendType, ReturnType]):
     """Shows progress and handles cancellation of a task."""
 
+    finished = Signal()
+
     def __init__(
         self,
         *,
         work: WorkType,
-        yieldCallback: YieldCallback = None,
-        returnCallback: ReturnCallback = None,
+        yieldCallback: Optional[YieldCallback] = None,
+        returnCallback: Optional[ReturnCallback] = None,
         parent: Optional[QWidget] = None,
     ) -> None:
         super().__init__(parent)
 
         self._worker: Optional[TaskWorker] = None
         self._work: WorkType = work
-        self._yieldCallback: YieldCallback = yieldCallback
-        self._returnCallback: ReturnCallback = returnCallback
+        self._yieldCallback: Optional[YieldCallback] = yieldCallback
+        self._returnCallback: Optional[ReturnCallback] = returnCallback
 
         self._last_id: Optional[int] = None
 
@@ -101,6 +104,7 @@ def _onWorkerFinished(self, task_id: int) -> None:
         if self._last_id == task_id:
             self._worker = None
             self._setLoaded()
+        self.finished.emit()
 
     def _isTaskCancelled(self, task_id: int) -> bool:
         if self._worker is None:

src/napari_cryoet_data_portal/_tests/_mocks.py

@@ -0,0 +1,168 @@
+from typing import Any, Dict, Tuple
+
+import numpy as np
+
+from napari_cryoet_data_portal._model import Dataset, Tomogram
+
+
+MOCK_S3_URI = 's3://mock-portal'
+
+
+def mock_dataset(
+    *,
+    name: str,
+    tomograms: Tuple[Tomogram, ...],
+) -> Dataset:
+    path = f"{MOCK_S3_URI}/{name}"
+    return Dataset(
+        name=name,
+        path=path,
+        tomograms=tomograms,
+    )
+
+
+def mock_tomogram(
+        *,
+        dataset_name: str,
+        tomogram_name: str,
+        voxel_spacing: str,
+        annotation_names: Tuple[str, ...]
+) -> Tomogram:
+    path = f"{MOCK_S3_URI}/{dataset_name}/{tomogram_name}"
+    tomogram_path = f"{path}/Tomograms/VoxelSpacing{voxel_spacing}"
+    image_path = f"{tomogram_path}/CanonicalTomogram/{tomogram_name}.zarr"
+    annotations_path = f"{tomogram_path}/Annotations"
+    annotations_paths = tuple(
+        f"{annotations_path}/{name}.json"
+        for name in annotation_names
+    )
+    return Tomogram(
+        name=tomogram_name,
+        path=path,
+        tomogram_path=tomogram_path,
+        image_path=image_path,
+        annotation_paths=annotations_paths,
+    )
+
+
+MOCK_TOMOGRAM_TS_026 = mock_tomogram(
+    dataset_name="10000",
+    tomogram_name="TS_026",
+    voxel_spacing="13.48",
+    annotation_names=("ribosome", "fatty-acid-synthase"),
+)
+
+MOCK_TOMOGRAM_TS_026_METADATA = {
+    'run_name': 'TS_026',
+    'voxel_spacing': 13.48,
+    'size': {
+        'z': 8,
+        'y': 8,
+        'x': 8,
+    }
+}
+
+MOCK_TOMOGRAM_TS_026_IMAGE_DATA = [
+    np.zeros((8, 8, 8)),
+    np.zeros((4, 4, 4)),
+    np.zeros((2, 2, 2)),
+]
+
+MOCK_TOMOGRAM_TS_026_IMAGE_ATTRS = {
+    'name': 'TS_026',
+    'scale': (1, 1, 1),
+}
+
+MOCK_TOMOGRAM_TS_026_RIBOSOME_DATA = [[0, 0, 0], [2, 2, 2]]
+MOCK_TOMOGRAM_TS_026_RIBOSOME_ATTRS = {'name': 'ribosome'}
+
+MOCK_TOMOGRAM_TS_026_FAS_DATA = [[1, 1, 1], [3, 3, 3]]
+MOCK_TOMOGRAM_TS_026_FAS_ATTRS = {'name': 'fatty acid synthase'}
+
+MOCK_TOMOGRAM_TS_027 = mock_tomogram(
+    dataset_name="10000",
+    tomogram_name="TS_027",
+    voxel_spacing="13.48",
+    annotation_names=("ribosome", "fatty-acid-synthase"),
+)
+
+MOCK_DATASET_10000 = mock_dataset(
+    name="10000",
+    tomograms=(MOCK_TOMOGRAM_TS_026, MOCK_TOMOGRAM_TS_027),
+)
+
+MOCK_DATASET_10000_METADATA = {
+    'dataset_title': 'mock dataset',
+    'authors': [
+        {
+            'name': 'mock author',
+            'ORCID': "0000-1111-2222-3333",
+        }
+    ],
+    'organism': {
+        'name': 'mock organism',
+    }
+}
+
+MOCK_TOMOGRAM_POS_128 = mock_tomogram(
+    dataset_name="10004",
+    tomogram_name="Position_128_2",
+    voxel_spacing="7.56",
+    annotation_names=("ribosome"),
+)
+
+MOCK_TOMOGRAM_POS_129 = mock_tomogram(
+    dataset_name="10004",
+    tomogram_name="Position_129_2",
+    voxel_spacing="7.56",
+    annotation_names=("ribosome"),
+)
+
+MOCK_DATASET_10004 = mock_dataset(
+    name="10004",
+    tomograms=(MOCK_TOMOGRAM_POS_128, MOCK_TOMOGRAM_POS_129),
+)
+
+MOCK_DATASETS = (MOCK_DATASET_10000, MOCK_DATASET_10004)
+
+
+def mock_path_exists(path: str) -> bool:
+    return path == MOCK_S3_URI
+
+
+def mock_list_dir(path: str) -> Tuple[str, ...]:
+    if path == f'{MOCK_S3_URI}':
+        return tuple(ds.name for ds in MOCK_DATASETS)
+    for ds in MOCK_DATASETS:
+        if ds.path == path:
+            return tuple(tomo.name for tomo in ds.tomograms)
+        for tomo in ds.tomograms:
+            anno_path = f"{tomo.tomogram_path}/Annotations"
+            if path == anno_path:
+                return tuple(
+                    p.split('/')[-1]
+                    for p in tomo.annotation_paths
+                )
+    raise ValueError(f"Mock path not supported: {path}")
+
+
+def mock_read_json(path: str) -> Dict[str, Any]:
+    if path == MOCK_DATASET_10000.metadata_path:
+        return MOCK_DATASET_10000_METADATA
+    if path == MOCK_TOMOGRAM_TS_026.tomogram_metadata_path:
+        return MOCK_TOMOGRAM_TS_026_METADATA
+    raise ValueError(f'Mock path not supported: {path}')
+
+
+def mock_read_tomogram_ome_zarr(path: str) -> Dict[str, Any]:
+    if path == MOCK_TOMOGRAM_TS_026.image_path:
+        return MOCK_TOMOGRAM_TS_026_IMAGE_DATA, MOCK_TOMOGRAM_TS_026_IMAGE_ATTRS, "image"
+    raise ValueError(f'Mock path not supported: {path}')
+
+
+def mock_read_points_annotations_json(path: str) -> Dict[str, Any]:
+    if path == MOCK_TOMOGRAM_TS_026.annotation_paths[0]:
+        return MOCK_TOMOGRAM_TS_026_RIBOSOME_DATA, MOCK_TOMOGRAM_TS_026_RIBOSOME_ATTRS, "points"
+    if path == MOCK_TOMOGRAM_TS_026.annotation_paths[1]:
+        return MOCK_TOMOGRAM_TS_026_FAS_DATA, MOCK_TOMOGRAM_TS_026_FAS_ATTRS, "points"
+    raise ValueError(f'Mock path not supported: {path}')