aignostics 0.2.19__tar.gz → 0.2.22__tar.gz

{aignostics-0.2.19 → aignostics-0.2.22}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aignostics
-Version: 0.2.19
+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

{aignostics-0.2.19 → aignostics-0.2.22}/examples/notebook.py

@@ -2,7 +2,7 @@
 # requires-python = ">=3.13"
 # dependencies = [
 #     "marimo",
-#     "aignostics==0.2.19",
+#     "aignostics==0.2.22",
 # ]
 # ///
 

{aignostics-0.2.19 → aignostics-0.2.22}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "aignostics"
-version = "0.2.19"
+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",
@@ -354,7 +355,7 @@ source = ["src/"]
 
 
 [tool.bumpversion]
-current_version = "0.2.19"
+current_version = "0.2.22"
 parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
 serialize = ["{major}.{minor}.{patch}"]
 search = "{current_version}"

{aignostics-0.2.19 → 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-0.2.19 → 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")