aignostics 0.2.34__tar.gz → 0.2.37__tar.gz

{aignostics-0.2.34 → aignostics-0.2.37}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aignostics
-Version: 0.2.34
+Version: 0.2.37
 Summary: 🔬 Python SDK providing access to the Aignostics Platform. Includes Aignostics Launchpad (Desktop Application), Aignostics CLI (Command-Line Interface), example notebooks, and Aignostics Client Library.
 Project-URL: Homepage, https://aignostics.readthedocs.io/en/latest/
 Project-URL: Documentation, https://aignostics.readthedocs.io/en/latest/
@@ -49,7 +49,7 @@ Classifier: Programming Language :: Python :: 3.13
 Classifier: Typing :: Typed
 Requires-Python: <4.0,>=3.11
 Requires-Dist: appdirs>=1.4.4
-Requires-Dist: boto3>=1.38.27
+Requires-Dist: boto3>=1.38.30
 Requires-Dist: click
 Requires-Dist: dicom-validator>=0.7.1
 Requires-Dist: dicomweb-client[gcp]>=0.59.2
@@ -64,8 +64,8 @@ Requires-Dist: idc-index-data==21.0.0
 Requires-Dist: ijson>=3.4.0
 Requires-Dist: jsf>=0.11.2
 Requires-Dist: jsonschema>=4.24.0
-Requires-Dist: logfire[system-metrics]>=3.16.1
-Requires-Dist: nicegui[native]>=2.18.0
+Requires-Dist: logfire[system-metrics]>=3.17.0
+Requires-Dist: nicegui[native]>=2.19.0
 Requires-Dist: openslide-bin>=4.0.0.8
 Requires-Dist: openslide-python>=1.4.2
 Requires-Dist: opentelemetry-instrumentation-fastapi>=0.53b0
@@ -77,7 +77,7 @@ Requires-Dist: opentelemetry-instrumentation-tornado>=0.53b0
 Requires-Dist: opentelemetry-instrumentation-urllib3>=0.53b0
 Requires-Dist: opentelemetry-instrumentation-urllib>=0.53b0
 Requires-Dist: packaging
-Requires-Dist: pandas<=2.2.4
+Requires-Dist: pandas<=2.3.0
 Requires-Dist: platformdirs
 Requires-Dist: psutil
 Requires-Dist: psutil>=7.0.0

{aignostics-0.2.34 → aignostics-0.2.37}/examples/notebook.py

@@ -2,7 +2,7 @@
 # requires-python = ">=3.13"
 # dependencies = [
 #     "marimo",
-#     "aignostics==0.2.34",
+#     "aignostics==0.2.37",
 # ]
 # ///
 

{aignostics-0.2.34 → aignostics-0.2.37}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "aignostics"
-version = "0.2.34"
+version = "0.2.37"
 description = "🔬 Python SDK providing access to the Aignostics Platform. Includes Aignostics Launchpad (Desktop Application), Aignostics CLI (Command-Line Interface), example notebooks, and Aignostics Client Library."
 readme = "README.md"
 authors = [
@@ -75,8 +75,8 @@ requires-python = ">=3.11, <4.0"
 dependencies = [
     # From Template
     "fastapi[standard,all]>=0.115.12",
-    "logfire[system-metrics]>=3.16.1",
-    "nicegui[native]>=2.18.0",
+    "logfire[system-metrics]>=3.17.0",
+    "nicegui[native]>=2.19.0",
     "opentelemetry-instrumentation-fastapi>=0.53b0",
     "opentelemetry-instrumentation-httpx>=0.53b0",
     "opentelemetry-instrumentation-jinja2>=0.53b0",
@@ -93,7 +93,7 @@ dependencies = [
     "uptime>=3.0.1",
     # Custom
     "appdirs>=1.4.4",
-    "boto3>=1.38.27",
+    "boto3>=1.38.30",
     "dicom-validator>=0.7.1",
     "dicomweb-client[gcp]>=0.59.2",
     "google-cloud-storage>=2.12.0",
@@ -122,7 +122,7 @@ dependencies = [
     'duckdb>=0.10.0,<=1.2.1',
     "idc-index-data==21.0.0",
     "packaging",
-    "pandas<=2.2.4",
+    "pandas<=2.3.0",
     "platformdirs",
     "psutil",
     "pyarrow",
@@ -150,7 +150,7 @@ dev = [
     "detect-secrets>=1.5.0",
     "enum-tools>=0.13.0",
     "furo>=2024.8.6",
-    "git-cliff>=2.8.0",
+    "git-cliff>=2.9.1",
     "matplotlib>=3.10.1",
     "mypy>=1.16.0",
     "nox[uv]>=2025.5.1",
@@ -158,7 +158,7 @@ dev = [
     "pip-licenses @ git+https://github.com/neXenio/pip-licenses.git@master", # https://github.com/raimon49/pip-licenses/pull/224
     "pre-commit>=4.1.0",
     "pyright>=1.1.401",
-    "pytest>=8.3.5",
+    "pytest>=8.4.0",
     "pytest-asyncio>=1.0.0",
     "pytest-cov>=6.1.1",
     "pytest-docker>=3.2.2",
@@ -184,7 +184,7 @@ dev = [
     "swagger-plugin-for-sphinx>=5.1.0",
     "tomli>=2.1.0",
     "types-pyyaml>=6.0.12.20250516",
-    "types-requests>=2.32.0.20250515",
+    "types-requests>=2.32.0.20250602",
     "watchdog>=6.0.0",
 ]
 
@@ -216,6 +216,7 @@ override-dependencies = [ # https://github.com/astral-sh/uv/issues/4422
     "h11>=0.16.0",                      # CVE-2025-47287
     "rfc3987; sys_platform == 'never'", # GPLv3
     "tornado>=6.5.0",                   # CVE-2025-47287
+    "jupyter-core>=5.8.1",              # CVE-2025-30167
 ]
 
 [tool.ruff]
@@ -355,7 +356,7 @@ source = ["src/"]
 
 
 [tool.bumpversion]
-current_version = "0.2.34"
+current_version = "0.2.37"
 parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
 serialize = ["{major}.{minor}.{patch}"]
 search = "{current_version}"

{aignostics-0.2.34 → aignostics-0.2.37}/src/aignostics/bucket/_service.py

@@ -28,13 +28,13 @@ class Service(BaseService):
         """Initialize service."""
         super().__init__(Settings)
 
-    def info(self) -> dict[str, Any]:  # noqa: PLR6301
+    def info(self) -> dict[str, Any]:
         """Determine info of this service.
 
         Returns:
             dict[str,Any]: The info of this service.
         """
-        return {}
+        return {"settings": self._settings.model_dump()}
 
     def health(self) -> Health:  # noqa: PLR6301
         """Determine health of this service.
@@ -97,7 +97,7 @@ class Service(BaseService):
         url = self._get_s3_client().generate_presigned_url(
             ClientMethod="put_object",
             Params={"Bucket": self._settings.name if bucket_name is None else bucket_name, "Key": object_key},
-            ExpiresIn=3600,
+            ExpiresIn=self._settings.upload_signed_url_expiration_seconds,
         )
         return cast("str", url)
 
@@ -163,7 +163,7 @@ class Service(BaseService):
         url = self._get_s3_client().generate_presigned_url(
             ClientMethod="get_object",
             Params={"Bucket": self._settings.name if bucket_name is None else bucket_name, "Key": object_key},
-            ExpiresIn=3600,
+            ExpiresIn=self._settings.download_signed_url_expiration_seconds,
         )
         return cast("str", url)
 

aignostics-0.2.37/src/aignostics/bucket/_settings.py

@@ -0,0 +1,86 @@
+"""Settings of the bucket module."""
+
+from enum import StrEnum
+from typing import Annotated
+
+from pydantic import Field, PlainSerializer, SecretStr
+from pydantic_settings import SettingsConfigDict
+
+from ..utils import OpaqueSettings, __env_file__, __project_name__  # noqa: TID252
+
+
+class BucketProtocol(StrEnum):
+    GS = "gs"
+    S3 = "s3"
+
+
+class Settings(OpaqueSettings):
+    """Settings."""
+
+    model_config = SettingsConfigDict(
+        env_prefix=f"{__project_name__.upper()}_BUCKET_",
+        extra="ignore",
+        env_file=__env_file__,
+        env_file_encoding="utf-8",
+    )
+
+    protocol: Annotated[
+        BucketProtocol,
+        Field(
+            description=("Protocol to access the cloud bucket, default is gs"),
+            default="gs",
+        ),
+    ]
+
+    name: Annotated[
+        str,
+        Field(description=("Name of the cloud bucket")),
+    ]
+
+    region_name: Annotated[
+        str,
+        Field(description=("Region of the cloud bucket"), default="EUROPE-WEST3"),
+    ]
+
+    hmac_access_key_id: Annotated[
+        SecretStr,
+        PlainSerializer(func=OpaqueSettings.serialize_sensitive_info, return_type=str, when_used="always"),
+        Field(description=("HMAC access key ID of the cloud bucket")),
+    ]
+
+    hmac_secret_access_key: Annotated[
+        SecretStr,
+        PlainSerializer(func=OpaqueSettings.serialize_sensitive_info, return_type=str, when_used="always"),
+        Field(description=("HMAC secret access key of the cloud bucket")),
+    ]
+
+    upload_signed_url_expiration_seconds: Annotated[
+        int,
+        Field(
+            description=("Expiration time for signed URLs created and used by the Python SDK to upload to the bucket."),
+            default=2
+            * 60
+            * 60,  # The Python SDK creates the signed upload URLs immediately before uploading, so 2h is sufficient.
+            ge=60,  # Minimum expiration time is 60 seconds, see https://docs.aws.amazon.com/AmazonS3/latest/userguide/using-presigned-url.html
+            le=7
+            * 24
+            * 60
+            * 60,  # Limit to 7 days as this is the max e.g. at AWS, see https://docs.aws.amazon.com/AmazonS3/latest/userguide/using-presigned-url.html
+        ),
+    ]
+
+    download_signed_url_expiration_seconds: Annotated[
+        int,
+        Field(
+            description=(
+                "Expiration time of the signed URLs provided by the Python SDK to the platform on submitting "
+                "application runs."
+            ),
+            default=7 * 24 * 60 * 60,  # The platform queues application runs, so we set a gracious default of 7d.
+            ge=60,  # Minimum expiration time is 60 seconds, see https://docs.aws.amazon.com/AmazonS3/latest/userguide/using-presigned-url.html
+            le=7
+            * 24
+            * 60
+            * 60,  # Limit to 7 days as this is the max e.g. at AWS, see https://docs.aws.amazon.com/AmazonS3/latest/userguide/using-presigned-url.html
+        ),
+    ]

{aignostics-0.2.34 → aignostics-0.2.37}/src/aignostics/qupath/annotate.groovy

@@ -76,4 +76,4 @@ features.each { feature ->
 
 // Add objects to hierarchy
 addObjects(newObjects)
-println("Added " + newObjects.size() + " annotations from GeoJSON")
+println("Added " + newObjects.size() + " annotations from GeoJSON")

{aignostics-0.2.34 → aignostics-0.2.37}/src/aignostics/utils/_settings.py

@@ -34,7 +34,7 @@ class OpaqueSettings(BaseSettings):
     def serialize_sensitive_info(input_value: SecretStr, info: FieldSerializationInfo) -> str | None:
         if not input_value:
             return None
-        if info.context.get(UNHIDE_SENSITIVE_INFO, False):  # type: ignore
+        if info.context and info.context.get(UNHIDE_SENSITIVE_INFO, False):
             return input_value.get_secret_value()
         return str(input_value)
 

aignostics-0.2.34/src/aignostics/bucket/_settings.py

@@ -1,53 +0,0 @@
-"""Settings of the bucket module."""
-
-from enum import StrEnum
-from typing import Annotated
-
-from pydantic import Field, SecretStr
-from pydantic_settings import SettingsConfigDict
-
-from ..utils import OpaqueSettings, __env_file__, __project_name__  # noqa: TID252
-
-
-class BucketProtocol(StrEnum):
-    GS = "gs"
-    S3 = "s3"
-
-
-class Settings(OpaqueSettings):
-    """Settings."""
-
-    model_config = SettingsConfigDict(
-        env_prefix=f"{__project_name__.upper()}_BUCKET_",
-        extra="ignore",
-        env_file=__env_file__,
-        env_file_encoding="utf-8",
-    )
-
-    protocol: Annotated[
-        BucketProtocol,
-        Field(
-            description=("Protocol to access the cloud bucket, default is gs"),
-            default="gs",
-        ),
-    ]
-
-    name: Annotated[
-        str,
-        Field(description=("Name of the cloud bucket")),
-    ]
-
-    region_name: Annotated[
-        str,
-        Field(description=("Region of the cloud bucket"), default="EUROPE-WEST3"),
-    ]
-
-    hmac_access_key_id: Annotated[
-        SecretStr,
-        Field(description=("HMAC access key ID of the cloud bucket")),
-    ]
-
-    hmac_secret_access_key: Annotated[
-        SecretStr,
-        Field(description=("HMAC secret access key of the cloud bucket")),
-    ]