aignostics 0.2.16__tar.gz → 0.2.22__tar.gz

{aignostics-0.2.16 → aignostics-0.2.22}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aignostics
-Version: 0.2.16
+Version: 0.2.22
 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/
@@ -49,22 +49,23 @@ Classifier: Programming Language :: Python :: 3.13
 Classifier: Typing :: Typed
 Requires-Python: <4.0,>=3.11
 Requires-Dist: appdirs>=1.4.4
-Requires-Dist: boto3>=1.38.22
+Requires-Dist: boto3>=1.38.27
 Requires-Dist: click
-Requires-Dist: dicom-validator>=0.6.2
-Requires-Dist: dicomweb-client[gcp]>=0.59.3
+Requires-Dist: dicom-validator>=0.7.1
+Requires-Dist: dicomweb-client[gcp]>=0.59.2
 Requires-Dist: duckdb<=1.2.1,>=0.10.0
 Requires-Dist: fastapi[all,standard]>=0.115.12
-Requires-Dist: google-cloud-storage>=3.1.0
+Requires-Dist: google-cloud-storage>=2.12.0
 Requires-Dist: google-crc32c>=1.7.1
 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>=4.23.0
-Requires-Dist: logfire[system-metrics]>=3.16.0
-Requires-Dist: nicegui[native]>=2.17.0
+Requires-Dist: jsonschema>=4.24.0
+Requires-Dist: logfire[system-metrics]>=3.16.1
+Requires-Dist: nicegui[native]>=2.18.0
 Requires-Dist: openslide-bin>=4.0.0.8
 Requires-Dist: openslide-python>=1.4.2
 Requires-Dist: opentelemetry-instrumentation-fastapi>=0.53b0
@@ -97,7 +98,7 @@ 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>=0.15.4
+Requires-Dist: typer>=0.16.0
 Requires-Dist: uptime>=3.0.1
 Requires-Dist: urllib3>=2.2.3
 Requires-Dist: wsidicom>=0.27.1
@@ -105,7 +106,7 @@ 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>=0.13.11; extra == 'marimo'
+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
@@ -195,6 +196,11 @@ The Launchpad is available for Mac OS X, Windows, and Linux, and can be installe
 4. Follow the intuitive graphical interface to analyze public datasets or your own whole slide images 
    with [Atlas H&E-TME](https://www.aignostics.com/products/he-tme-profiling-product) and other computational pathology applications.
 
+> [!Note]
+> The Launchpad features a growing ecosystem of extensions that seamlessly integrate with standard digital pathology tools. To use the Launchpad with all available extensions, run `uvx --with aignostics[qupath,marimo] aignostics launchpad`. Currently available extensions are:
+> 1. **QuPath extension**: View your application results in [QuPath](https://qupath.github.io/) with a single click. The Launchpad creates QuPath projects on-the-fly.
+> 2. **Marimo extension**: Analyze your application results using [Marimo](https://marimo.io/) notebooks embedded in the Launchpad. You don't have to leave the Launchpad to do real data science.
+
 ### CLI: Manage datasets and application runs from your terminal
 
 The Python SDK includes the **Aignostics CLI**, a Command-Line Interface that allows you to

{aignostics-0.2.16 → aignostics-0.2.22}/README.md

@@ -79,6 +79,11 @@ The Launchpad is available for Mac OS X, Windows, and Linux, and can be installe
 4. Follow the intuitive graphical interface to analyze public datasets or your own whole slide images 
    with [Atlas H&E-TME](https://www.aignostics.com/products/he-tme-profiling-product) and other computational pathology applications.
 
+> [!Note]
+> The Launchpad features a growing ecosystem of extensions that seamlessly integrate with standard digital pathology tools. To use the Launchpad with all available extensions, run `uvx --with aignostics[qupath,marimo] aignostics launchpad`. Currently available extensions are:
+> 1. **QuPath extension**: View your application results in [QuPath](https://qupath.github.io/) with a single click. The Launchpad creates QuPath projects on-the-fly.
+> 2. **Marimo extension**: Analyze your application results using [Marimo](https://marimo.io/) notebooks embedded in the Launchpad. You don't have to leave the Launchpad to do real data science.
+
 ### CLI: Manage datasets and application runs from your terminal
 
 The Python SDK includes the **Aignostics CLI**, a Command-Line Interface that allows you to

{aignostics-0.2.16 → aignostics-0.2.22}/examples/notebook.py

@@ -2,7 +2,7 @@
 # requires-python = ">=3.13"
 # dependencies = [
 #     "marimo",
-#     "aignostics==0.2.16",
+#     "aignostics==0.2.22",
 # ]
 # ///
 

{aignostics-0.2.16 → aignostics-0.2.22}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "aignostics"
-version = "0.2.16"
+version = "0.2.22"
 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]>=3.16.0",
-    "nicegui[native]>=2.17.0",
+    "logfire[system-metrics]>=3.16.1",
+    "nicegui[native]>=2.18.0",
     "opentelemetry-instrumentation-fastapi>=0.53b0",
     "opentelemetry-instrumentation-httpx>=0.53b0",
     "opentelemetry-instrumentation-jinja2>=0.53b0",
@@ -89,20 +89,20 @@ dependencies = [
     "pydantic-settings>=2.9.1",
     "pywin32>=310 ; sys_platform == 'win32'",
     "sentry-sdk>=2.29.1",
-    "typer>=0.15.4",
+    "typer>=0.16.0",
     "uptime>=3.0.1",
     # Custom
     "appdirs>=1.4.4",
-    "boto3>=1.38.22",
-    "dicom-validator>=0.6.2",
-    "dicomweb-client[gcp]>=0.59.3",
-    "google-cloud-storage>=3.1.0",
+    "boto3>=1.38.27",
+    "dicom-validator>=0.7.1",
+    "dicomweb-client[gcp]>=0.59.2",
+    "google-cloud-storage>=2.12.0",
     "google-crc32c>=1.7.1",
     "highdicom>=0.25.1",
     "httpx>=0.28.1",
     "humanize>=4.12.3",
     "jsf>=0.11.2",
-    "jsonschema>=4.23.0",
+    "jsonschema>=4.24.0",
     "openslide-bin>=4.0.0.8",
     "openslide-python>=1.4.2",
     "pyjwt[crypto]>=2.10.1",
@@ -130,13 +130,14 @@ dependencies = [
     "s5cmd",
     "sphinx-click",
     "tqdm",
+    "ijson>=3.4.0",
 ]
 
 [project.optional-dependencies]
 jupyter = ["jupyter>=1.1.1"]
 marimo = [
     "cloudpathlib>=0.21.1",
-    "marimo>=0.13.11",
+    "marimo>=0.13.15",
     "matplotlib>=3.10.3",
     "shapely>=2.1.0",
 ]
@@ -151,25 +152,25 @@ dev = [
     "furo>=2024.8.6",
     "git-cliff>=2.8.0",
     "matplotlib>=3.10.1",
-    "mypy>=1.5.0",
+    "mypy>=1.16.0",
     "nox[uv]>=2025.5.1",
     "pip-audit>=2.9.0",
     "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-asyncio>=0.26.0",
+    "pytest-asyncio>=1.0.0",
     "pytest-cov>=6.1.1",
-    "pytest-docker>=3.2.1",
+    "pytest-docker>=3.2.2",
     "pytest-env>=1.1.5",
     "pytest-md-report>=0.7.0",
-    "pytest-regressions>=2.7.0",
+    "pytest-regressions>=2.8.0",
     "pytest-selenium>=4.1.0",
     "pytest-subprocess>=1.5.3",
     "pytest-timeout>=2.4.0",
     "pytest-watcher>=0.4.3",
-    "pytest-xdist[psutil]>=3.6.1",
-    "ruff>=0.11.10",
+    "pytest-xdist[psutil]>=3.7.0",
+    "ruff>=0.11.12",
     "scalene>=1.5.51",
     "sphinx>=8.2.3",
     "sphinx-autobuild>=2024.10.3",
@@ -344,7 +345,6 @@ omit = [
     "*/_notebook.py",
     "*/_pydicom_handler.py",
     "*/_openslide_handler.py",
-    "*/qupath/*",
 ]
 branch = true
 parallel = true
@@ -355,7 +355,7 @@ source = ["src/"]
 
 
 [tool.bumpversion]
-current_version = "0.2.16"
+current_version = "0.2.22"
 parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
 serialize = ["{major}.{minor}.{patch}"]
 search = "{current_version}"

{aignostics-0.2.16 → aignostics-0.2.22}/src/aignostics/application/__init__.py

@@ -12,7 +12,7 @@ from importlib.util import find_spec
 
 # advertise PageBuilder to enable auto-discovery
 if find_spec("nicegui"):
-    from ._gui import PageBuilder
+    from ._gui._page_builder import PageBuilder
 
     __all__ += [
         "PageBuilder",

{aignostics-0.2.16 → aignostics-0.2.22}/src/aignostics/application/_cli.py

@@ -6,24 +6,10 @@ from pathlib import Path
 from typing import Annotated
 
 import typer
-from rich.console import Group
-from rich.live import Live
-from rich.panel import Panel
-from rich.progress import (
-    BarColumn,
-    FileSizeColumn,
-    Progress,
-    TaskID,
-    TaskProgressColumn,
-    TextColumn,
-    TimeElapsedColumn,
-    TimeRemainingColumn,
-    TotalFileSizeColumn,
-    TransferSpeedColumn,
-)
 
 from aignostics.bucket import Service as BucketService
 from aignostics.platform import NotFoundException
+from aignostics.system import Service as SystemService
 from aignostics.utils import console, get_logger
 
 from ._service import DownloadProgress, DownloadProgressState, Service
@@ -370,6 +356,17 @@ def run_upload(
     2. Uploads the files referenced in the CSV file to the Aignostics platform.
     3. Incrementally updates the CSV file with upload progress and the signed URLs for the uploaded files.
     """
+    from rich.progress import (  # noqa: PLC0415
+        BarColumn,
+        FileSizeColumn,
+        Progress,
+        TaskProgressColumn,
+        TextColumn,
+        TimeRemainingColumn,
+        TotalFileSizeColumn,
+        TransferSpeedColumn,
+    )
+
     metadata_dict = read_metadata_csv_to_dict(metadata_csv_file=metadata_csv_file)
     if not metadata_dict:
         sys.exit(2)
@@ -542,7 +539,7 @@ def run_cancel(
 
 
 @result_app.command("download")
-def result_download(
+def result_download(  # noqa: PLR0913, PLR0917
     run_id: Annotated[str, typer.Argument(..., help="Id of the run to download results for")],
     destination_directory: Annotated[
         Path,
@@ -555,7 +552,7 @@ def result_download(
             readable=True,
             resolve_path=True,
         ),
-    ],
+    ] = SystemService.get_user_data_directory("results"),  # noqa: B008
     create_subdirectory_for_run: Annotated[
         bool,
         typer.Option(
@@ -574,20 +571,46 @@ def result_download(
             help="Wait for run completion and download results incrementally",
         ),
     ] = True,
+    qupath_project: Annotated[
+        bool,
+        typer.Option(
+            help="Create a QuPath project referencing input slides and results. \n"
+            "The QuPath project will be created in a subfolder of the destination directory. \n"
+            "This option requires the QuPath extension for Launchpad: "
+            'start the Launchpad with `uvx --with "aignostics[qupath]" aignostics ...` \n'
+            "This options requires installation of the QuPath application: "
+            'Run uvx --with "aignostics[qupath]" aignostics qupath install'
+        ),
+    ] = False,
 ) -> None:
     """Download results of a run."""
     logger.debug(
         "Downloading results for run with ID '%s' to '%s' with options: "
-        "create_subdirectory_for_run=%s, create_subdirectory_per_item=%s, wait_for_completion=%s",
+        "create_subdirectory_for_run=%s, create_subdirectory_per_item=%s, wait_for_completion=%s, qupath_project=%r",
         run_id,
         destination_directory,
         create_subdirectory_for_run,
         create_subdirectory_per_item,
         wait_for_completion,
+        qupath_project,
+    )
+    from rich.console import Group  # noqa: PLC0415
+    from rich.live import Live  # noqa: PLC0415
+    from rich.panel import Panel  # noqa: PLC0415
+    from rich.progress import (  # noqa: PLC0415
+        BarColumn,
+        FileSizeColumn,
+        Progress,
+        TaskID,
+        TaskProgressColumn,
+        TextColumn,
+        TimeElapsedColumn,
+        TimeRemainingColumn,
+        TotalFileSizeColumn,
+        TransferSpeedColumn,
     )
 
     try:
-        progress: DownloadProgress = DownloadProgress()
         download_tasks: dict[str, TaskID] = {}
 
         main_download_progress_ui = Progress(
@@ -612,15 +635,13 @@ def result_download(
         panel = Panel(
             Group(main_download_progress_ui, artifact_download_progress_ui),
             title=f"Run {run_id}",
-            subtitle=progress.status,
+            subtitle="",
             highlight=True,
         )
         with Live(panel):
-            main_task = main_download_progress_ui.add_task(
-                description=progress.status, total=None, extra_description=""
-            )
+            main_task = main_download_progress_ui.add_task(description="", total=None, extra_description="")
 
-            def update_progress() -> None:
+            def update_progress(progress: DownloadProgress) -> None:
                 """Update progress bar for file downloads."""
                 if progress.run:
                     panel.title = f"Run {progress.run.application_run_id} of {progress.run.application_version_id}"
@@ -669,12 +690,12 @@ def result_download(
                     )
 
             destination_directory = Service().application_run_download(
-                progress=progress,
                 run_id=run_id,
                 destination_directory=destination_directory,
                 create_subdirectory_for_run=create_subdirectory_for_run,
                 create_subdirectory_per_item=create_subdirectory_per_item,
                 wait_for_completion=wait_for_completion,
+                qupath_project=qupath_project,
                 download_progress_callable=update_progress,
             )
 

aignostics-0.2.22/src/aignostics/application/_gui/_frame.py

@@ -0,0 +1,164 @@
+from typing import Any
+
+from nicegui import app, background_tasks, context, ui  # noq
+from nicegui import run as nicegui_run
+
+from aignostics.gui import frame
+from aignostics.utils import get_logger
+
+from .._service import Service  # noqa: TID252
+from ._utils import application_id_to_icon, run_status_to_icon_and_color
+
+logger = get_logger(__name__)
+
+BORDERED_SEPARATOR = "bordered separator"
+RUNS_LIMIT = 500
+STORAGE_TAB_RUNS_COMPLETED_ONLY = "runs_completed_only"
+
+
+async def _frame(  # noqa: C901, PLR0913, PLR0915, PLR0917
+    navigation_title: str,
+    navigation_icon: str | None = None,
+    navigation_icon_color: str | None = None,
+    navigation_icon_tooltip: str | None = None,
+    left_sidebar: bool = False,
+    args: dict[str, Any] | None = None,
+) -> None:
+    if args is None:
+        args = {}
+    service = Service()
+    with frame(  # noqa: PLR1702
+        navigation_title=navigation_title,
+        navigation_icon=navigation_icon,
+        navigation_icon_color=navigation_icon_color,
+        navigation_icon_tooltip=navigation_icon_tooltip,
+        left_sidebar=left_sidebar,
+    ):
+        try:
+            with ui.list().props(BORDERED_SEPARATOR).classes("full-width"):
+                ui.item_label("Applications").props("header")
+                ui.separator()
+                for application in service.applications():
+                    with (
+                        ui.item(
+                            on_click=lambda app_id=application.application_id: ui.navigate.to(f"/application/{app_id}")
+                        )
+                        .mark(f"SIDEBAR_APPLICATION:{application.application_id}")
+                        .props("clickable")
+                    ):
+                        with (
+                            ui.item_section().props("avatar"),
+                            ui.icon(application_id_to_icon(application.application_id), color="primary"),
+                        ):
+                            ui.tooltip(application.application_id)
+                        with ui.item_section():
+                            ui.label(f"{application.name}").tailwind.font_weight(
+                                "bold"
+                                if context.client.page.path == "/application/{application_id}"
+                                and args
+                                and args.get("application_id") == application.application_id
+                                else "normal"
+                            )
+        except Exception as e:  # noqa: BLE001
+            ui.label(f"Failed to list applications: {e!s}").mark("LABEL_ERROR")
+
+        async def application_runs_load_and_render(runs_column: ui.column, completed_only: bool = False) -> None:
+            with runs_column:
+                try:
+                    runs = await nicegui_run.io_bound(
+                        Service.application_runs_static, limit=RUNS_LIMIT, completed_only=completed_only
+                    )
+                    if runs is None:
+                        message = "nicegui_run.io_bound(Service.application_runs_static) returned None"  # type: ignore[unreachable]
+                        logger.error(message)
+                        raise RuntimeError(message)  # noqa: TRY301
+                    runs_column.clear()
+                    for index, run_data in enumerate(runs):
+                        with (
+                            ui.item(
+                                on_click=lambda run_id=run_data["application_run_id"]: ui.navigate.to(
+                                    f"/application/run/{run_id}"
+                                )
+                            )
+                            .props("clickable")
+                            .classes("w-full")
+                            .mark(f"SIDEBAR_RUN_ITEM:{index}")
+                        ):
+                            with ui.item_section().props("avatar"):
+                                icon, color = run_status_to_icon_and_color(run_data["status"])
+                                with ui.icon(icon, color=color):
+                                    ui.tooltip(
+                                        f"Run {run_data['application_run_id']}, "
+                                        f"status {run_data['status'].value.upper()}"
+                                    )
+                            with ui.item_section():
+                                ui.label(f"{run_data['application_version_id']}").tailwind.font_weight(
+                                    "bold"
+                                    if context.client.page.path == "/application/run/{application_run_id}"
+                                    and args
+                                    and args.get("application_run_id") == run_data["application_run_id"]
+                                    else "normal"
+                                )
+                                ui.label(
+                                    f"triggered on {run_data['triggered_at'].astimezone().strftime('%m-%d %H:%M')}"
+                                )
+                    if not runs:
+                        with ui.item():
+                            with ui.item_section().props("avatar"):
+                                ui.icon("info")
+                            with ui.item_section():
+                                ui.label("You did not yet create a run.")
+                except Exception:
+                    runs_column.clear()
+                    with ui.item():
+                        with ui.item_section().props("avatar"):
+                            ui.icon("error")
+                        with ui.item_section():
+                            ui.label("Failed to load application runs.")
+                    logger.exception("Failed to load application runs")
+
+        @ui.refreshable
+        async def _runs_list() -> None:
+            with ui.column().classes("full-width justify-center") as runs_column:
+                with ui.row().classes("w-full justify-center"):
+                    ui.spinner(size="lg").classes("m-5")
+                await ui.context.client.connected()
+                background_tasks.create_lazy(
+                    coroutine=application_runs_load_and_render(
+                        runs_column=runs_column,
+                        completed_only=app.storage.tab.get(STORAGE_TAB_RUNS_COMPLETED_ONLY, False),
+                    ),
+                    name="_runs_list",
+                )
+
+        class RunFilterButton(ui.icon):
+            def __init__(self, *args, **kwargs) -> None:  # type: ignore[no-untyped-def]
+                super().__init__(*args, **kwargs)
+                self._state = app.storage.tab.get(STORAGE_TAB_RUNS_COMPLETED_ONLY, False)
+                self.on("click", self.toggle)
+
+            def toggle(self) -> None:
+                self._state = not self._state
+                app.storage.tab[STORAGE_TAB_RUNS_COMPLETED_ONLY] = self._state
+                self.update()
+                _runs_list.refresh()
+
+            def update(self) -> None:
+                self.props(f"color={'positive' if self._state else 'grey'}")
+                super().update()
+
+            def is_active(self) -> bool:
+                return bool(self._state)
+
+        try:
+            with ui.list().props(BORDERED_SEPARATOR).classes("full-width"):
+                with ui.row(align_items="center").classes("justify-center"):
+                    ui.item_label("Runs").props("header")
+                    ui.space()
+                    await ui.context.client.connected()
+                    with RunFilterButton("done_all", size="sm").classes("mr-3").mark("BUTTON_RUNS_FILTER_COMPLETED"):
+                        ui.tooltip("Show completed runs only")
+                ui.separator()
+                await _runs_list()
+        except Exception as e:  # noqa: BLE001
+            ui.label(f"Failed to list application runs: {e!s}").mark("LABEL_ERROR")