aignostics 0.2.52__tar.gz → 0.2.58__tar.gz

{aignostics-0.2.52 → aignostics-0.2.58}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aignostics
-Version: 0.2.52
+Version: 0.2.58
 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/
@@ -49,8 +49,8 @@ Classifier: Programming Language :: Python :: 3.13
 Classifier: Typing :: Typed
 Requires-Python: <4.0,>=3.11
 Requires-Dist: appdirs>=1.4.4
-Requires-Dist: boto3>=1.38.33
-Requires-Dist: click
+Requires-Dist: auth0-python>=4.10.0
+Requires-Dist: boto3>=1.38.36
 Requires-Dist: dicom-validator>=0.7.1
 Requires-Dist: dicomweb-client[gcp]>=0.59.2
 Requires-Dist: duckdb<=1.4.0,>=0.10.0
@@ -61,10 +61,11 @@ Requires-Dist: highdicom>=0.25.1
 Requires-Dist: httpx>=0.28.1
 Requires-Dist: humanize>=4.12.3
 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]>=3.17.0
-Requires-Dist: nicegui[native]>=2.19.0
+Requires-Dist: logfire[system-metrics]>=3.19.0
+Requires-Dist: nicegui[native]>=2.20.0
 Requires-Dist: openslide-bin>=4.0.0.8
 Requires-Dist: openslide-python>=1.4.2
 Requires-Dist: opentelemetry-instrumentation-fastapi>=0.53b0
@@ -75,27 +76,22 @@ Requires-Dist: opentelemetry-instrumentation-sqlite3>=0.53b0
 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: packaging>=25.0
 Requires-Dist: pandas<=2.3.0
-Requires-Dist: platformdirs
-Requires-Dist: psutil
+Requires-Dist: platformdirs>=4.3.8
 Requires-Dist: psutil>=7.0.0
-Requires-Dist: pyarrow
+Requires-Dist: pyarrow>=20.0.0
 Requires-Dist: pydantic-settings>=2.9.1
 Requires-Dist: pyjwt[crypto]>=2.10.1
 Requires-Dist: python-dateutil>=2.9.0.post0
 Requires-Dist: pywin32>=310; sys_platform == 'win32'
 Requires-Dist: pyyaml>=6.0
-Requires-Dist: requests
 Requires-Dist: requests-oauthlib>=2.0.0
 Requires-Dist: requests>=2.32.3
-Requires-Dist: s5cmd
 Requires-Dist: s5cmd>=0.2.0
-Requires-Dist: sentry-sdk>=2.29.1
+Requires-Dist: sentry-sdk>=2.30.0
 Requires-Dist: shapely>=2.1.1
 Requires-Dist: show-in-file-manager>=1.1.5
-Requires-Dist: sphinx-click
-Requires-Dist: tqdm
 Requires-Dist: tqdm>=4.67.1
 Requires-Dist: typer>=0.16.0
 Requires-Dist: uptime>=3.0.1
@@ -109,7 +105,6 @@ Requires-Dist: marimo>=0.13.15; extra == 'marimo'
 Requires-Dist: matplotlib>=3.10.3; extra == 'marimo'
 Requires-Dist: shapely>=2.1.0; extra == 'marimo'
 Provides-Extra: qupath
-Requires-Dist: ijson>=3.4.0; extra == 'qupath'
 Description-Content-Type: text/markdown
 
 

{aignostics-0.2.52 → aignostics-0.2.58}/examples/notebook.py

@@ -2,7 +2,7 @@
 # requires-python = ">=3.13"
 # dependencies = [
 #     "marimo",
-#     "aignostics==0.2.52",
+#     "aignostics==0.2.58",
 # ]
 # ///
 

{aignostics-0.2.52 → aignostics-0.2.58}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "aignostics"
-version = "0.2.52"
+version = "0.2.58"
 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]>=3.17.0",
-    "nicegui[native]>=2.19.0",
+    "logfire[system-metrics]>=3.19.0",
+    "nicegui[native]>=2.20.0",
     "opentelemetry-instrumentation-fastapi>=0.53b0",
     "opentelemetry-instrumentation-httpx>=0.53b0",
     "opentelemetry-instrumentation-jinja2>=0.53b0",
@@ -88,48 +88,44 @@ dependencies = [
     "psutil>=7.0.0",
     "pydantic-settings>=2.9.1",
     "pywin32>=310 ; sys_platform == 'win32'",
-    "sentry-sdk>=2.29.1",
+    "sentry-sdk>=2.30.0",
     "typer>=0.16.0",
     "uptime>=3.0.1",
     # Custom
     "appdirs>=1.4.4",
-    "boto3>=1.38.33",
+    "auth0-python>=4.10.0",
+    "boto3>=1.38.36",
     "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-crc32c>=1.7.1",
     "highdicom>=0.25.1",
     "httpx>=0.28.1",
     "humanize>=4.12.3",
+    "idc-index-data==21.0.0",
+    "ijson>=3.4.0",
     "jsf>=0.11.2",
     "jsonschema>=4.24.0",
     "openslide-bin>=4.0.0.8",
     "openslide-python>=1.4.2",
+    "packaging>=25.0",
+    "pandas<=2.3.0",
+    "platformdirs>=4.3.8",
+    "psutil>=7.0.0",
+    "pyarrow>=20.0.0",
     "pyjwt[crypto]>=2.10.1",
     "python-dateutil>=2.9.0.post0",
+    # "pywebview[qt6]>=5.4; sys_platform == 'linux'",
     "pyyaml>=6.0",
     "requests>=2.32.3",
     "requests-oauthlib>=2.0.0",
     "s5cmd>=0.2.0",
+    "shapely>=2.1.1",
     "show-in-file-manager>=1.1.5",
     "tqdm>=4.67.1",
     "urllib3>=2.2.3",
-    "shapely>=2.1.1",
     "wsidicom>=0.27.1",
-    # "pywebview[qt6]>=5.4; sys_platform == 'linux'",
-    # idc-index
-    "click",
-    'duckdb>=0.10.0,<=1.4.0',
-    "idc-index-data==21.0.0",
-    "packaging",
-    "pandas<=2.3.0",
-    "platformdirs",
-    "psutil",
-    "pyarrow",
-    "requests",
-    "s5cmd",
-    "sphinx-click",
-    "tqdm",
 ]
 
 [project.optional-dependencies]
@@ -140,7 +136,7 @@ marimo = [
     "matplotlib>=3.10.3",
     "shapely>=2.1.0",
 ]
-qupath = ["ijson>=3.4.0"]
+qupath = [] # Making this a default extra
 [dependency-groups]
 dev = [
     "autodoc-pydantic>=2.2.0",
@@ -175,6 +171,7 @@ dev = [
     "scalene>=1.5.51",
     "sphinx>=8.2.3",
     "sphinx-autobuild>=2024.10.3",
+    "sphinx-click>=6.0.0",
     "sphinx-copybutton>=0.5.2",
     "sphinx-inline-tabs>=2023.4.21",
     "sphinx-mdinclude>=0.6.2",
@@ -355,7 +352,7 @@ source = ["src/"]
 
 
 [tool.bumpversion]
-current_version = "0.2.52"
+current_version = "0.2.58"
 parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
 serialize = ["{major}.{minor}.{patch}"]
 search = "{current_version}"

{aignostics-0.2.52 → aignostics-0.2.58}/src/aignostics/application/_cli.py

@@ -281,10 +281,11 @@ def run_execute(  # noqa: PLR0913, PLR0917
         list[str],
         typer.Argument(
             help="Mapping to use for amending metadata CSV file. "
-            "Each mapping is of the form '<regexp>:<key>:<value>,<key>:<value>,...'. "
+            "Each mapping is of the form '<regexp>:<key>:<value>,<key>:<value>,...'."
             "The regular expression is matched against the reference attribute of the entry. "
             "The key/value pairs are applied to the entry if the pattern matches. "
-            "You can use the mapping option multiple times to set values for multiple files. ",
+            "You can use the mapping option multiple times to set values for multiple files. "
+            'Example: ".*:staining_method:H&E,tissue:LIVER,disease:LIVER_CANCER"',
         ),
     ],
     create_subdirectory_for_run: Annotated[

{aignostics-0.2.52 → aignostics-0.2.58}/src/aignostics/application/_gui/_page_builder.py

@@ -8,16 +8,16 @@ from aignostics.utils import BasePageBuilder
 class PageBuilder(BasePageBuilder):
     @staticmethod
     def register_pages() -> None:
-        from nicegui import app, ui  # noq  # noqa: PLC0415
+        from nicegui import Client, app, ui  # noq  # noqa: PLC0415
 
         app.add_static_files("/application_assets", Path(__file__).parent / "assets")
 
         @ui.page("/")
-        async def page_index() -> None:
+        async def page_index(client: Client) -> None:
             """Index page of application module, serving as the homepage of Aignostics Launchpad."""
             from ._page_index import _page_index  # noqa: PLC0415
 
-            await _page_index()
+            await _page_index(client)
 
         @ui.page("/application/{application_id}")
         async def page_application_describe(application_id: str) -> None:

aignostics-0.2.58/src/aignostics/application/_gui/_page_index.py

@@ -0,0 +1,73 @@
+"""GUI of application module including homepage of Aignostics Launchpad."""
+
+from importlib.util import find_spec
+
+from nicegui import Client, app, ui  # noq
+
+from aignostics.utils import get_logger
+
+from ._frame import _frame
+
+logger = get_logger(__name__)
+
+
+async def _page_index(client: Client) -> None:
+    """Homepage of Applications."""
+    client.content.classes(remove="nicegui-content")
+    client.content.classes(add="pl-5 pt-5")
+
+    await _frame("Analyze your Whole Slide Images with AI", left_sidebar=True)
+
+    with ui.row().classes("p-4 pt-2 pr-0"), ui.column():
+        await ui.context.client.connected()
+        ui.label("Welcome to the Aignostics Launchpad").bind_text_from(
+            app.storage.tab,
+            "user_info",
+            lambda user_info: (
+                f"Welcome {user_info.profile.given_name if user_info.profile else ''} to the Aignostics Launchpad"
+            ),
+        ).classes("text-4xl mb-2")
+        ui.label(
+            "Using the Launchpad, you can run Aignostics Atlas applications on your whole slide images, "
+            "monitor progress, and download results for analysis."
+        ).classes("text-2xl")
+        with ui.row().classes("w-full h-screen flex"):
+            with ui.column().classes("flex-1 pr-0"):
+                ui.label("Have your slides ready to go?").classes("text-xl")
+                ui.label(
+                    "Select the relevant application from the left sidebar to upload your images to get started."
+                ).classes("text")
+                ui.label("Looking to test with public data first?").classes("text-xl")
+                ui.label(
+                    'Open ☰ menu and click "Download Datasets" to select a dataset '
+                    "from Image Data Commons by the National Cancer Institute to test with."
+                ).classes("text")
+                ui.label("Already submitted your slides?").classes("text-xl")
+                ui.label(
+                    "Select your run on the left to monitor progress, cancel while pending, or download results."
+                ).classes("text")
+
+                if find_spec("ijson"):
+                    from aignostics.qupath import Service as QuPathService  # noqa: PLC0415
+
+                    ui.label("Visualize results in QuPath Microscopy Viewer?").classes("text-xl")
+                    if QuPathService.is_installed():
+                        ui.label('Select a completed run and click "QuPath" to visualize results.').classes("text")
+                    else:
+                        ui.label(
+                            "To visualize results with one click the QuPath application must be installed. "
+                            'Select "QuPath extension" in the ☰ menu to install.'
+                        ).classes("text")
+
+                if find_spec("marimo"):
+                    ui.label("Analyze results in Python Notebooks?").classes("text-xl")
+                    ui.label('On completed runs click "Marimo" to directly open the notebook.').classes("text")
+
+            with (
+                ui.carousel(animated=True, arrows=True, navigation=True)
+                .classes("flex-1 h-full m-0 p-0 self-end bg-[#423D6B] ")
+                .props("infinite autoplay=1000 control-color=transparent")
+            ):
+                for i in range(1, 5):  # Loop from 1 to 4
+                    with ui.carousel_slide().classes("p-0 m-0"):
+                        ui.image(f"/application_assets/home-card-{i}.png").classes("w-full h-auto object-contain")

{aignostics-0.2.52 → aignostics-0.2.58}/src/aignostics/application/_service.py

@@ -32,6 +32,9 @@ from aignostics.platform import (
     NotFoundException,
     OutputArtifactElement,
 )
+from aignostics.platform import (
+    Service as PlatformService,
+)
 from aignostics.utils import UNHIDE_SENSITIVE_INFO, BaseService, Health, get_logger, sanitize_path_component
 from aignostics.wsi import Service as WSIService
 
@@ -47,7 +50,6 @@ if has_qupath_extra:
 
 logger = get_logger(__name__)
 
-
 APPLICATION_RUN_DOWNLOAD_SLEEP_SECONDS = 5
 APPLICATION_RUN_FILE_READ_CHUNK_SIZE = 1024 * 1024 * 1024  # 1GB
 APPLICATION_RUN_DOWNLOAD_CHUNK_SIZE = 1024 * 1024  # 1MB
@@ -150,6 +152,7 @@ class Service(BaseService):
 
     _settings: Settings
     _client: Client | None = None
+    _platform_service: PlatformService | None = None
 
     def __init__(self) -> None:
         """Initialize service."""
@@ -192,6 +195,22 @@ class Service(BaseService):
             logger.debug("Reusing platform client.")
         return self._client
 
+    def _get_platform_service(self) -> PlatformService:
+        """Get the platform service.
+
+        Returns:
+            PlatformService: The platform service.
+
+        Raises:
+            Exception: If the client cannot be created.
+        """
+        if self._platform_service is None:
+            logger.debug("Creating platform service.")
+            self._platform_service = PlatformService()
+        else:
+            logger.debug("Reusing platform service.")
+        return self._platform_service
+
     def applications(self) -> list[Application]:
         """Get a list of all applications.
 

{aignostics-0.2.52 → aignostics-0.2.58}/src/aignostics/cli.py

@@ -66,6 +66,7 @@ if __name__ == "__main__":  # pragma: no cover
     try:
         cli()
     except Exception as e:  # noqa: BLE001
-        logger.critical("Fatal error occurred: %s", e)
-        console.print(f"Fatal error occurred: {e}", style="error")
+        message = f"An error occurred while running the CLI: {e!s}"
+        logger.critical(message)
+        console.print(message, style="error")
         sys.exit(1)

{aignostics-0.2.52 → aignostics-0.2.58}/src/aignostics/constants.py

@@ -5,7 +5,7 @@ from pathlib import Path
 
 # Configuration required by oe-python-template
 API_VERSIONS: dict[str, str] = {"v1": "1.0.0"}
-MODULES_TO_INSTRUMENT: list[str] = ["aignostics.platform", "aignostics.application"]
+MODULES_TO_INSTRUMENT: list[str] = ["aignostics.qupath"]
 NOTEBOOK_DEFAULT = Path(__file__).parent / "notebook" / "_notebook.py"
 
 # Project specific configuration

{aignostics-0.2.52 → aignostics-0.2.58}/src/aignostics/gui/_frame.py

@@ -1,11 +1,15 @@
 """Layout including sidebar and menu."""
 
 import contextlib
+import platform
 from collections.abc import Generator
 from contextlib import contextmanager
 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
 
 from ._theme import theme
@@ -13,6 +17,7 @@ from ._theme import theme
 FLAT_COLOR_WHITE = "flat color=white"
 
 HEALTH_UPDATE_INTERVAL = 30
+USERINFO_UPDATE_INTERVAL = 60
 
 
 @contextmanager
@@ -35,14 +40,61 @@ def frame(  # noqa: C901, PLR0915
     Yields:
         Generator[Any, Any, Any]: The context manager for the page frame.
     """
-    from nicegui import app, background_tasks, context, run, ui  # noqa: PLC0415
+    from nicegui import background_tasks, context, run  # noqa: PLC0415
 
+    from aignostics.platform import Service as PlatformService  # noqa: PLC0415
+    from aignostics.platform import UserInfo  # noqa: PLC0415
     from aignostics.system import Service as SystemService  # noqa: PLC0415
 
     theme()
 
+    user_info: UserInfo | None = None
     launchpad_healthy: bool | None = None
 
+    @ui.refreshable
+    def _user_info_ui() -> None:
+        spinner = ui.spinner().props("flat color=purple-400")
+        if user_info and user_info.profile:
+            spinner.set_visibility(False)
+            icon = "img:" + user_info.profile.picture if user_info.profile.picture else "account_circle"
+            with (
+                ui.dropdown_button(icon=icon)
+                .style("width: 30px; height: 30px; border-radius: 50%")
+                .classes("mr-3")
+                .props(FLAT_COLOR_WHITE),
+                ui.card(),
+            ):
+                ui.label(f"{user_info.profile.name} ({user_info.profile.email})")
+                ui.label(f"{user_info.role.capitalize()} at {user_info.org_name or user_info.org_id}")
+                ui.label(f"Authentication valid for {naturaldelta(user_info.token.expires_in)}")
+                ui.separator()
+                with ui.row().classes("items-center justify-between"):
+                    ui.button("Re-authenticate now", icon="switch_account", on_click=_user_info_ui_relogin).props(
+                        add="style=fab-mini"
+                    )
+
+    async def _user_info_ui_load() -> None:
+        nonlocal user_info
+        with contextlib.suppress(Exception):
+            user_info = await run.cpu_bound(PlatformService.get_user_info)
+        await ui.context.client.connected()
+        app.storage.tab["user_info"] = user_info
+        _user_info_ui.refresh()
+
+    ui.timer(interval=USERINFO_UPDATE_INTERVAL, callback=_user_info_ui_load, immediate=True)
+
+    async def _user_info_ui_relogin() -> None:
+        """Relogin to the platform."""
+        nonlocal user_info
+        user_info = None
+        await ui.context.client.connected()
+        app.storage.tab["user_info"] = user_info
+        _user_info_ui.refresh()
+        with contextlib.suppress(Exception):
+            user_info = await run.cpu_bound(PlatformService.get_user_info, relogin=True)
+            app.storage.tab["user_info"] = user_info
+        _user_info_ui.refresh()
+
     @ui.refreshable
     def health_icon() -> None:
         if launchpad_healthy:
@@ -123,12 +175,12 @@ def frame(  # noqa: C901, PLR0915
             icon="dark_mode",
         ).set_visibility(False)
 
-        ui.button(icon="folder_special", on_click=lambda _: open_user_data_directory()).props("flat color=purple-400")
-        ui.tooltip("Open data directory of Launchpad")
+        _user_info_ui()
 
-        with ui.link(target="https://aignostics.readthedocs.org/", new_tab=True):
-            ui.button(icon="local_library").props(FLAT_COLOR_WHITE)
-            ui.tooltip("Open manual")
+        with ui.button(icon="folder_special", on_click=lambda _: open_user_data_directory()).props(
+            "flat color=purple-400"
+        ):
+            ui.tooltip("Open data directory of Launchpad")
 
         with ui.button(on_click=lambda _: right_drawer.toggle(), icon="menu").props(FLAT_COLOR_WHITE):
             ui.tooltip("Open menu")
@@ -140,7 +192,7 @@ def frame(  # noqa: C901, PLR0915
         yield
 
     # Populate the right_drawer we created earlier
-    with right_drawer, ui.column(align_items="stretch").classes("h-full"):
+    with right_drawer, ui.column(align_items="stretch").classes("h-full"):  # noqa: PLR1702
         with ui.list():
             with ui.item(on_click=lambda _: ui.navigate.to("/")).props("clickable"):
                 with ui.item_section().props("avatar"):
@@ -158,14 +210,15 @@ def frame(  # noqa: C901, PLR0915
                     )
         ui.space()
         with ui.list():
-            if find_spec("ijson"):
-                with ui.item(on_click=lambda _: ui.navigate.to("/qupath")).props("clickable"):
-                    with ui.item_section().props("avatar"):
-                        ui.icon("visibility", color="primary")
-                    with ui.item_section():
-                        ui.label("QuPath Extension").tailwind.font_weight(
-                            "bold" if context.client.page.path == "/qupath" else "normal"
-                        )
+            if find_spec("ijson"):  # noqa: SIM102
+                if not (platform.system() == "Linux" and platform.machine() == "aarch64"):
+                    with ui.item(on_click=lambda _: ui.navigate.to("/qupath")).props("clickable"):
+                        with ui.item_section().props("avatar"):
+                            ui.icon("visibility", color="primary")
+                        with ui.item_section():
+                            ui.label("QuPath Extension").tailwind.font_weight(
+                                "bold" if context.client.page.path == "/qupath" else "normal"
+                            )
             if find_spec("marimo"):
                 with ui.item(on_click=lambda _: ui.navigate.to("/notebook")).props("clickable"):
                     with ui.item_section().props("avatar"):

{aignostics-0.2.52 → aignostics-0.2.58}/src/aignostics/platform/__init__.py

@@ -18,6 +18,7 @@ from aignx.codegen.models import OutputArtifactReadResponse as OutputArtifactDat
 from aignx.codegen.models import OutputArtifactResultReadResponse as OutputArtifactElement
 from aignx.codegen.models import RunReadResponse as ApplicationRunData
 
+from ._cli import cli
 from ._client import Client
 from ._constants import (
     API_ROOT_DEV,
@@ -43,7 +44,7 @@ from ._constants import (
     TOKEN_URL_STAGING,
 )
 from ._messages import AUTHENTICATION_FAILED, NOT_YET_IMPLEMENTED, UNKNOWN_ENDPOINT_URL
-from ._service import Service
+from ._service import Service, TokenInfo, UserInfo
 from ._settings import Settings, settings
 from ._utils import calculate_file_crc32c, download_file, generate_signed_url, mime_type_to_file_ending
 from .resources.runs import LIST_APPLICATION_RUNS_MAX_PAGE_SIZE, LIST_APPLICATION_RUNS_MIN_PAGE_SIZE, ApplicationRun
@@ -94,7 +95,10 @@ __all__ = [
     "OutputArtifactElement",
     "Service",
     "Settings",
+    "TokenInfo",
+    "UserInfo",
     "calculate_file_crc32c",
+    "cli",
     "download_file",
     "generate_signed_url",
     "mime_type_to_file_ending",