aignostics 0.2.64__tar.gz → 0.2.68__tar.gz

{aignostics-0.2.64 → aignostics-0.2.68}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aignostics
-Version: 0.2.64
+Version: 0.2.68
 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/
@@ -50,12 +50,12 @@ Classifier: Typing :: Typed
 Requires-Python: <4.0,>=3.11
 Requires-Dist: appdirs>=1.4.4
 Requires-Dist: auth0-python>=4.10.0
-Requires-Dist: boto3>=1.38.38
+Requires-Dist: boto3>=1.38.39
 Requires-Dist: dicom-validator>=0.7.1
 Requires-Dist: dicomweb-client[gcp]>=0.59.2
 Requires-Dist: duckdb<=1.4.0,>=0.10.0
 Requires-Dist: fastapi[all,standard]>=0.115.13
-Requires-Dist: google-cloud-storage>=2.12.0
+Requires-Dist: google-cloud-storage>=3.1.1
 Requires-Dist: google-crc32c>=1.7.1
 Requires-Dist: highdicom>=0.25.1
 Requires-Dist: httpx>=0.28.1
@@ -64,7 +64,7 @@ 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]>=3.21.0
+Requires-Dist: logfire[system-metrics]>=3.21.1
 Requires-Dist: nicegui[native]>=2.20.0
 Requires-Dist: openslide-bin>=4.0.0.8
 Requires-Dist: openslide-python>=1.4.2
@@ -95,13 +95,13 @@ Requires-Dist: show-in-file-manager>=1.1.5
 Requires-Dist: tqdm>=4.67.1
 Requires-Dist: typer>=0.16.0
 Requires-Dist: uptime>=3.0.1
-Requires-Dist: urllib3>=2.2.3
+Requires-Dist: urllib3>=2.5.0
 Requires-Dist: wsidicom>=0.27.1
 Provides-Extra: jupyter
 Requires-Dist: jupyter>=1.1.1; extra == 'jupyter'
 Provides-Extra: marimo
 Requires-Dist: cloudpathlib>=0.21.1; extra == 'marimo'
-Requires-Dist: marimo>=0.13.15; extra == 'marimo'
+Requires-Dist: marimo>=0.14.0; extra == 'marimo'
 Requires-Dist: matplotlib>=3.10.3; extra == 'marimo'
 Requires-Dist: shapely>=2.1.0; extra == 'marimo'
 Provides-Extra: qupath

{aignostics-0.2.64 → aignostics-0.2.68}/examples/notebook.py

@@ -2,7 +2,7 @@
 # requires-python = ">=3.13"
 # dependencies = [
 #     "marimo",
-#     "aignostics==0.2.64",
+#     "aignostics==0.2.68",
 # ]
 # ///
 

{aignostics-0.2.64 → aignostics-0.2.68}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "aignostics"
-version = "0.2.64"
+version = "0.2.68"
 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 = [
@@ -75,7 +75,7 @@ requires-python = ">=3.11, <4.0"
 dependencies = [
     # From Template
     "fastapi[standard,all]>=0.115.13",
-    "logfire[system-metrics]>=3.21.0",
+    "logfire[system-metrics]>=3.21.1",
     "nicegui[native]>=2.20.0",
     "opentelemetry-instrumentation-fastapi>=0.53b0",
     "opentelemetry-instrumentation-httpx>=0.53b0",
@@ -94,11 +94,11 @@ dependencies = [
     # Custom
     "appdirs>=1.4.4",
     "auth0-python>=4.10.0",
-    "boto3>=1.38.38",
+    "boto3>=1.38.39",
     "dicom-validator>=0.7.1",
     "dicomweb-client[gcp]>=0.59.2",
     "duckdb>=0.10.0,<=1.4.0",
-    "google-cloud-storage>=2.12.0",
+    "google-cloud-storage>=3.1.1",
     "google-crc32c>=1.7.1",
     "highdicom>=0.25.1",
     "httpx>=0.28.1",
@@ -124,7 +124,7 @@ dependencies = [
     "shapely>=2.1.1",
     "show-in-file-manager>=1.1.5",
     "tqdm>=4.67.1",
-    "urllib3>=2.2.3",
+    "urllib3>=2.5.0",
     "wsidicom>=0.27.1",
 ]
 
@@ -132,7 +132,7 @@ dependencies = [
 jupyter = ["jupyter>=1.1.1"]
 marimo = [
     "cloudpathlib>=0.21.1",
-    "marimo>=0.13.15",
+    "marimo>=0.14.0",
     "matplotlib>=3.10.3",
     "shapely>=2.1.0",
 ]
@@ -153,10 +153,10 @@ 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",
     "pyinstaller>=6.14.0",
-    "pyright>=1.1.401",
-    "pytest>=8.4.0",
+    "pyright>=1.1.402",
+    "pytest>=8.4.1",
     "pytest-asyncio>=1.0.0",
-    "pytest-cov>=6.1.1",
+    "pytest-cov>=6.2.1",
     "pytest-docker>=3.2.2",
     "pytest-env>=1.1.5",
     "pytest-md-report>=0.7.0",
@@ -167,7 +167,7 @@ dev = [
     "pytest-timeout>=2.4.0",
     "pytest-watcher>=0.4.3",
     "pytest-xdist[psutil]>=3.7.0",
-    "ruff>=0.11.12",
+    "ruff>=0.12.0",
     "scalene>=1.5.51",
     "sphinx>=8.2.3",
     "sphinx-autobuild>=2024.10.3",
@@ -182,7 +182,7 @@ dev = [
     "swagger-plugin-for-sphinx>=5.1.0",
     "tomli>=2.1.0",
     "types-pyyaml>=6.0.12.20250516",
-    "types-requests>=2.32.0.20250602",
+    "types-requests>=2.32.4.20250611",
     "watchdog>=6.0.0",
 ]
 
@@ -215,6 +215,7 @@ override-dependencies = [ # https://github.com/astral-sh/uv/issues/4422
     "h11>=0.16.0",                      # CVE-2025-43859
     "tornado>=6.5.0",                   # CVE-2025-47287
     "jupyter-core>=5.8.1",              # CVE-2025-30167
+    "urllib3>=2.5.0",                   # CVE-2025-50181, CVE-2025-50182
 ]
 
 [tool.ruff]
@@ -352,7 +353,7 @@ source = ["src/"]
 
 
 [tool.bumpversion]
-current_version = "0.2.64"
+current_version = "0.2.68"
 parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
 serialize = ["{major}.{minor}.{patch}"]
 search = "{current_version}"

{aignostics-0.2.64 → aignostics-0.2.68}/src/aignostics/bucket/_gui.py

@@ -299,7 +299,7 @@ class PageBuilder(BasePageBuilder):
                     return
 
                 bucket_form.destination = get_user_data_directory("datasets/idc")
-                bucket_form.destination_label.set_text(f"Download to {bucket_form.destination!s}")
+                bucket_form.destination_label.set_text(f"Will download to {bucket_form.destination!s}")
                 await _update_button_states()
 
             async def _select_destination() -> None:
@@ -323,7 +323,7 @@ class PageBuilder(BasePageBuilder):
                         )
                     else:
                         bucket_form.destination = path
-                        bucket_form.destination_label.set_text(f"Download to {bucket_form.destination!s}")
+                        bucket_form.destination_label.set_text(f"Will download to {bucket_form.destination!s}")
                         bucket_form.destination_open_button.enable()
                         ui.notify(f"You chose directory {bucket_form.destination}.", type="info")
                 else:
@@ -338,29 +338,44 @@ class PageBuilder(BasePageBuilder):
                 show_in_file_manager(str(bucket_form.destination))
 
             with ui.row().classes("w-full gap-4"):
-                bucket_form.download_button = (
-                    ui.button(
-                        "Download",
-                        icon="download",
-                        on_click=_download_selected,
-                    )
-                    .mark("BUTTON_DOWNLOAD_OBJECTS")
-                    .props("color=primary")
-                    .classes("w-1/5")
-                )
-                bucket_form.download_button.disable()
-
-                with ui.button("Data", on_click=_select_data, icon="folder_special", color="purple-400").mark(
-                    "BUTTON_DOWNLOAD_DESTINATION_DATA"
-                ):
-                    ui.tooltip("Use Launchpad datasets directory")
-
-                with ui.button("Custom", on_click=_select_destination, icon="folder").mark(
-                    "BUTTON_DOWNLOAD_DESTINATION"
-                ):
-                    ui.tooltip("Select a custom directory")
+                with ui.column().classes("w-1/2"):
+                    with ui.row().classes("w-full"):
+                        bucket_form.download_button = (
+                            ui.button(
+                                "Download",
+                                icon="download",
+                                on_click=_download_selected,
+                            )
+                            .mark("BUTTON_DOWNLOAD_OBJECTS")
+                            .props("color=primary")
+                        )
+                        bucket_form.download_button.disable()
+
+                        ui.space()
+
+                        with ui.button("Data", on_click=_select_data, icon="folder_special", color="purple-400").mark(
+                            "BUTTON_DOWNLOAD_DESTINATION_DATA"
+                        ):
+                            ui.tooltip("Use Launchpad datasets directory")
+
+                        with ui.button("Custom", on_click=_select_destination, icon="folder").mark(
+                            "BUTTON_DOWNLOAD_DESTINATION"
+                        ):
+                            ui.tooltip("Select a custom directory")
+                    with ui.row(align_items="center").classes("w-full"):
+                        bucket_form.destination_label = ui.label(
+                            MESSAGE_NO_DOWNLOAD_FOLDER_SELECTED
+                            if bucket_form.destination is None
+                            else str(f"Will download to {bucket_form.destination}")
+                        )
+                        ui.space()
+                        bucket_form.destination_open_button = ui.button(
+                            icon="folder_open", on_click=_open_destination, color="secondary"
+                        )
+                        bucket_form.destination_open_button.mark("BUTTON_OPEN_DESTINATION").disable()
 
                 ui.space()
+
                 bucket_form.delete_button = (
                     ui.button(
                         "Delete",
@@ -373,18 +388,6 @@ class PageBuilder(BasePageBuilder):
                 )
                 bucket_form.delete_button.disable()
 
-            with ui.row(align_items="center").classes("w-2/5"):
-                ui.space()
-                bucket_form.destination_label = ui.label(
-                    MESSAGE_NO_DOWNLOAD_FOLDER_SELECTED
-                    if bucket_form.destination is None
-                    else str(f"Download to {bucket_form.destination}")
-                ).classes("max-w-72")
-                bucket_form.destination_open_button = ui.button(
-                    icon="folder_open", on_click=_open_destination, color="secondary"
-                )
-                bucket_form.destination_open_button.mark("BUTTON_OPEN_DESTINATION").disable()
-
             # Progress card for downloads (initially hidden)
             with ui.card().classes("w-full") as progress_card:
                 bucket_form.download_progress_card = progress_card

{aignostics-0.2.64 → aignostics-0.2.68}/src/aignostics/bucket/_service.py

@@ -4,14 +4,15 @@ import hashlib
 import re
 from collections.abc import Callable, Generator
 from pathlib import Path
-from typing import Any, cast
+from typing import TYPE_CHECKING, Any, cast
 
 import humanize
 import requests
-from botocore.client import BaseClient, Config
-from botocore.exceptions import ClientError
 from pydantic import BaseModel, computed_field
 
+if TYPE_CHECKING:
+    from botocore.client import BaseClient
+
 from aignostics.utils import UNHIDE_SENSITIVE_INFO, BaseService, Health, get_logger, get_user_data_directory
 
 from ._settings import Settings
@@ -111,7 +112,7 @@ class Service(BaseService):
             components={},
         )
 
-    def _get_s3_client(self, endpoint_url: str = ENDPOINT_URL_DEFAULT) -> BaseClient:
+    def _get_s3_client(self, endpoint_url: str = ENDPOINT_URL_DEFAULT) -> "BaseClient":
         """Get a Boto3 S3 client instance for cloud bucket on Aignostics Platform.
 
         Args:
@@ -121,6 +122,7 @@ class Service(BaseService):
             BaseClient: A Boto3 S3 client instance.
         """
         from boto3 import Session  # noqa: PLC0415
+        from botocore.client import Config  # noqa: PLC0415
 
         # https://www.kmp.tw/post/accessgcsusepythonboto3/
         session = Session(
@@ -599,6 +601,8 @@ class Service(BaseService):
         Raises:
             ValueError: If any provided regex pattern is invalid.
         """
+        from botocore.exceptions import ClientError  # noqa: PLC0415
+
         matched_objects = self.find(what, what_is_key=what_is_key, detail=False)
         object_keys_to_delete = [obj for obj in matched_objects if isinstance(obj, str)]
 

{aignostics-0.2.64 → aignostics-0.2.68}/src/aignostics/cli.py

@@ -7,14 +7,20 @@ from pathlib import Path
 import typer
 
 from .constants import MODULES_TO_INSTRUMENT, NOTEBOOK_DEFAULT
-from .utils import __is_running_in_container__, __version__, boot, console, get_logger, prepare_cli
+from .utils import (
+    __is_running_in_container__,
+    __version__,
+    boot,
+    console,
+    get_logger,
+    prepare_cli,
+)
 
 boot(MODULES_TO_INSTRUMENT)
 logger = get_logger(__name__)
 
 cli = typer.Typer(
     help="Command Line Interface (CLI) of Aignostics Python SDK providing access to Aignostics Platform.",
-    no_args_is_help=True,
 )
 
 if find_spec("nicegui") and find_spec("webview") and not __is_running_in_container__:
@@ -62,6 +68,7 @@ if find_spec("marimo"):
 
 prepare_cli(cli, f"🔬 Aignostics Python SDK v{__version__} - built with love in Berlin 🐻")
 
+
 if __name__ == "__main__":  # pragma: no cover
     try:
         cli()

{aignostics-0.2.64 → aignostics-0.2.68}/src/aignostics/gui/_frame.py

@@ -8,7 +8,6 @@ from importlib.util import find_spec
 from typing import Any
 
 from humanize import naturaldelta
-from nicegui import app, ui
 
 from aignostics.utils import __version__, open_user_data_directory
 
@@ -42,7 +41,7 @@ def frame(  # noqa: C901, PLR0915
     Yields:
         Generator[Any, Any, Any]: The context manager for the page frame.
     """
-    from nicegui import background_tasks, context, run  # noqa: PLC0415
+    from nicegui import app, background_tasks, context, run, ui  # noqa: PLC0415
 
     from aignostics.platform import Service as PlatformService  # noqa: PLC0415
     from aignostics.platform import UserInfo  # noqa: PLC0415

{aignostics-0.2.64 → aignostics-0.2.68}/src/aignostics/platform/_authentication.py

@@ -18,14 +18,13 @@ from requests_oauthlib import OAuth2Session
 from aignostics.platform._messages import AUTHENTICATION_FAILED, INVALID_REDIRECT_URI
 from aignostics.platform._settings import settings
 
+CALLBACK_PORT_RETRY_COUNT = 10
+CLAIM_ROLE = "https://aignostics-platform-samia/role"
 try:
     import sentry_sdk
 except ImportError:
     sentry_sdk = None  # type: ignore[assignment]
 
-CALLBACK_PORT_RETRY_COUNT = 10
-CLAIM_ROLE = "https://aignostics-platform-samia/role"
-
 
 class AuthenticationResult(BaseModel):
     """Represents the result of an OAuth authentication flow."""

{aignostics-0.2.64 → aignostics-0.2.68}/src/aignostics/utils/_cli.py

@@ -21,7 +21,6 @@ def prepare_cli(cli: typer.Typer, epilog: str) -> None:
             cli.add_typer(_cli)
 
     cli.info.epilog = epilog
-    cli.info.no_args_is_help = True
     if not any(arg.endswith("typer") for arg in Path(sys.argv[0]).parts):
         for command in cli.registered_commands:
             command.epilog = cli.info.epilog
@@ -34,6 +33,17 @@ def prepare_cli(cli: typer.Typer, epilog: str) -> None:
     _no_args_is_help_recursively(cli)
 
 
+def no_args_is_help_workaround(ctx: typer.Context) -> None:
+    """Workaround for Typer bug, see https://github.com/fastapi/typer/pull/1240.
+
+    Raises:
+        typer.Exit: If no subcommand is invoked, prints the help message and exits.
+    """
+    if ctx.invoked_subcommand is None:
+        print(ctx.get_help())
+        raise typer.Exit
+
+
 def _add_epilog_recursively(cli: typer.Typer, epilog: str) -> None:
     """
     Add epilog to all typers in the tree.
@@ -60,9 +70,18 @@ def _no_args_is_help_recursively(cli: typer.Typer) -> None:
     Args:
         cli (typer.Typer): Typer instance
     """
+    # Apply workaround to the main CLI app itself
+    if not hasattr(cli, "no_args_callback_added"):
+        cli.callback(invoke_without_command=True)(no_args_is_help_workaround)
+        cli.no_args_callback_added = True  # type: ignore[attr-defined]
+
+    # Apply workaround to all subcommands recursively
     for group in cli.registered_groups:
         if isinstance(group, typer.models.TyperInfo):
-            group.no_args_is_help = True
             typer_instance = group.typer_instance
             if (typer_instance is not cli) and typer_instance:
+                # Add the callback workaround to each subcommand typer
+                if not hasattr(typer_instance, "no_args_callback_added"):
+                    typer_instance.callback(invoke_without_command=True)(no_args_is_help_workaround)
+                    typer_instance.no_args_callback_added = True  # type: ignore[attr-defined]
                 _no_args_is_help_recursively(typer_instance)

{aignostics-0.2.64 → aignostics-0.2.68}/src/aignostics/wsi/_gui.py

@@ -1,12 +1,15 @@
 """WSI API."""
 
-from pathlib import Path
+from __future__ import annotations
 
-from fastapi import Response
-from fastapi.responses import RedirectResponse
+from pathlib import Path
+from typing import TYPE_CHECKING
 
 from aignostics.utils import BasePageBuilder, get_logger
 
+if TYPE_CHECKING:
+    from fastapi import Response
+
 from ._service import Service
 
 logger = get_logger(__name__)
@@ -29,6 +32,9 @@ class PageBuilder(BasePageBuilder):
             Returns:
                 fastapi.Response: HTTP response containing the thumbnail or fallback image.
             """
+            from fastapi import Response  # noqa: PLC0415
+            from fastapi.responses import RedirectResponse  # noqa: PLC0415
+
             try:
                 return Response(content=Service().get_thumbnail_bytes(Path(source)), media_type="image/png")
             except ValueError:
@@ -48,6 +54,9 @@ class PageBuilder(BasePageBuilder):
             Returns:
                 fastapi.Response: HTTP response containing the converted tiff or fallback image
             """
+            from fastapi import Response  # noqa: PLC0415
+            from fastapi.responses import RedirectResponse  # noqa: PLC0415
+
             try:
                 return Response(content=Service().get_tiff_as_jpg(url), media_type="image/jpeg")
             except ValueError: