Updating multiple dependencies (#445)

.github/dependabot.yml

@@ -16,6 +16,9 @@ updates:
       grpc-deps:
         patterns:
           - "io.grpc*"
+      junit:
+        patterns:
+          - "org.junit*"
   - package-ecosystem: pip
     directory: /biomedicus_client/
     schedule:

biomedicus_client/pyproject.toml

@@ -38,7 +38,7 @@ classifiers = [
 ]
 dependencies = [
     "mtap>=1.4.3",
-    "tqdm==4.66.5",
+    "tqdm==4.67.1",
     "pyyaml==6.0.2"
 ]
 dynamic = ["version"]

java/build.gradle

@@ -67,7 +67,7 @@ repositories {
 }
 
 dependencies {
-    implementation group: 'org.jetbrains', name: 'annotations', version: '26.0.0'
+    implementation group: 'org.jetbrains', name: 'annotations', version: '26.0.1'
 
     implementation group: 'edu.umn.nlpie', name: 'mtap', version: '1.4.+'
 
@@ -87,9 +87,9 @@ dependencies {
     runtimeOnly group: 'org.apache.logging.log4j', name: 'log4j-slf4j2-impl', version: '2.24.1'
     runtimeOnly group: 'org.apache.logging.log4j', name: 'log4j-core', version: '2.24.1'
 
-    testImplementation group: 'org.junit.jupiter', name: 'junit-jupiter-api', version: '5.11.2'
-    testImplementation group: 'org.mockito', name: 'mockito-core', version: '5.14.1'
-    testRuntimeOnly group: 'org.junit.jupiter', name: 'junit-jupiter-engine', version: '5.11.2'
+    testImplementation group: 'org.junit.jupiter', name: 'junit-jupiter-api', version: '5.11.4'
+    testImplementation group: 'org.mockito', name: 'mockito-core', version: '5.15.2'
+    testRuntimeOnly group: 'org.junit.jupiter', name: 'junit-jupiter-engine', version: '5.11.4'
 }
 
 test {

pyproject.toml

@@ -38,19 +38,19 @@ classifiers = [
 dependencies = [
     "biomedicus_client>=3.4.3",  # We get mtap and tqdm transitively from the client
     "numpy==2.0.2",
-    "regex==2024.9.11",
-    "torch==2.4.1",
+    "regex==2024.11.6",
+    "torch==2.5.1",
     "requests==2.32.3",
-    "watchdog==5.0.3",
+    "watchdog==6.0.0",
 ]
 dynamic = ["version"]
 
 [project.optional-dependencies]
 test = [
-    "pytest==8.3.3"
+    "pytest==8.3.4"
 ]
 stanza = [
-    "stanza==1.9.2",
+    "stanza==1.10.1",
 ]
 
 [project.scripts]

python/tests/concepts/test_concepts.py

@@ -1,6 +1,6 @@
-from importlib.resources import files
 from mtap import Pipeline, RemoteProcessor, events_client
 from mtap.serialization import JsonSerializer
+from pathlib import Path
 
 
 def test_duplicate_concepts(events_service, concepts_service):
@@ -9,7 +9,7 @@ def test_duplicate_concepts(events_service, concepts_service):
         events_address=events_service
     )
     with events_client(events_service) as client:
-        with files().joinpath('concepts_test.json').open('r') as f:
+        with Path(__file__).parent.joinpath('concepts_test.json').open('r') as f:
             event = JsonSerializer.file_to_event(f, client)
         with event:
             doc = event.documents['plaintext']