Upgrade to cryoet-data-portal client v3.0

setup.cfg

@@ -31,7 +31,7 @@ project_urls =
 [options]
 packages = find:
 install_requires =
-    cryoet_data_portal>=2
+    cryoet_data_portal ~= 3.0
     fsspec[http,s3]
     npe2
     numpy

src/napari_cryoet_data_portal/_sample_data.py

@@ -1,13 +1,10 @@
 from typing import List
 
 import numpy as np
-from npe2.types import FullLayerData
 from cryoet_data_portal import Client, Tomogram, TomogramVoxelSpacing
+from npe2.types import FullLayerData
 
-from napari_cryoet_data_portal import (
-    read_annotation,
-    read_tomogram,
-)
+from napari_cryoet_data_portal import read_annotation, read_tomogram
 
 
 def tomogram_10000_ts_026() -> List[FullLayerData]:
@@ -22,20 +19,32 @@ def tomogram_10000_ts_027() -> List[FullLayerData]:
 
 def _read_tomogram_from_10000(name: str) -> List[FullLayerData]:
     client = Client()
-    
+
     tomogram_spacing_url = f"https://files.cryoetdataportal.cziscience.com/10000/{name}/Tomograms/VoxelSpacing13.480/"
-    tomogram_spacing = next(TomogramVoxelSpacing.find(client, [TomogramVoxelSpacing.https_prefix == tomogram_spacing_url]))
+    tomogram_spacing = TomogramVoxelSpacing.find(
+        client, [TomogramVoxelSpacing.https_prefix == tomogram_spacing_url]
+    ).pop()
 
-    tomogram: Tomogram = next(tomogram_spacing.tomograms)
+    tomogram: Tomogram = tomogram_spacing.tomograms.pop()
 
     tomogram_image = read_tomogram(tomogram)
     # Materialize lowest resolution for speed.
     tomogram_image = (np.asarray(tomogram_image[0][-1]), *tomogram_image[1:])
     tomogram_image[1]["scale"] = (4, 4, 4)
 
     annotations = tuple(tomogram_spacing.annotations)
-    ribosome_points = read_annotation(annotations[0], tomogram=tomogram)
-    fatty_acid_points = read_annotation(annotations[1], tomogram=tomogram)
+    ribosome_annotations = [
+        item
+        for item in annotations
+        if item.object_name.lower() == "cytosolic ribosome"
+    ].pop()
+    fas_annotations = [
+        item
+        for item in annotations
+        if item.object_name.lower() == "fatty acid synthase"
+    ].pop()
+    ribosome_points = read_annotation(ribosome_annotations, tomogram=tomogram)
+    fatty_acid_points = read_annotation(fas_annotations, tomogram=tomogram)
 
     return [
         tomogram_image,

src/napari_cryoet_data_portal/_tests/conftest.py

@@ -1,5 +1,4 @@
 import pytest
-
 from cryoet_data_portal import Client, Dataset, Tomogram
 
 
@@ -10,9 +9,15 @@ def client() -> Client:
 
 @pytest.fixture()
 def dataset(client: Client) -> Dataset:
-    return next(Dataset.find(client, [Dataset.id == 10000]))
+    return Dataset.find(client, [Dataset.id == 10000]).pop()
 
 
 @pytest.fixture()
 def tomogram(client: Client) -> Tomogram:
-    return next(Tomogram.find(client, [Tomogram.name == 'TS_026', Tomogram.https_omezarr_dir.like("%13.480%")]))
+    return Tomogram.find(
+        client,
+        [
+            Tomogram.name == "TS_026",
+            Tomogram.https_omezarr_dir.like("%13.480%"),
+        ],
+    ).pop()