chore(deps): lock file maintenance

noxfile.py

@@ -171,11 +171,13 @@ def audit(session: nox.Session) -> None:
         "--with-description",
     ]
 
-    pip_licenses_base_args.extend([
-        "--ignore-packages",
-        "aignostics",
-        "pyinstaller",  # https://pyinstaller.org/en/stable/license.html
-    ])
+    pip_licenses_base_args.extend(
+        [
+            "--ignore-packages",
+            "aignostics",
+            "pyinstaller",  # https://pyinstaller.org/en/stable/license.html
+        ]
+    )
 
     # Filter by .license-types-allowed file if it exists
     allowed_licenses = []
@@ -657,7 +659,7 @@ def docs(session: nox.Session) -> None:
 
 @nox.session(python=[PYTHON_VERSION], default=False)
 def docs_pdf(session: nox.Session) -> None:
-    """Setup dev environment post project creation."""  # noqa: DOC501
+    """Setup dev environment post project creation."""
     _setup_venv(session, True)
     try:
         out = session.run("latexmk", "--version", external=True, silent=True)

pyproject.toml

@@ -259,7 +259,7 @@ allow-direct-references = true
 
 [tool.ruff]
 target-version = "py311"
-preview = true
+preview = false
 fix = true
 line-length = 120
 extend-exclude = [
@@ -298,7 +298,8 @@ ignore = [
     "T201",     # Remove `print`
     "INP001",   # Checks for packages that are missing an __init__.py file.
     "BLE001",   # Accept for now TODO(Helmut): Add proper exception handling later
-    "ASYNC240"  # Aiopath broken in Python 3.11 which we want to support
+    "ASYNC240", # Aiopath broken in Python 3.11 which we want to support
+    "PLW0717"   # Allow try-clauses with more than 5 statements
 ]
 
 [tool.ruff.lint.per-file-ignores]

sonar-project.properties

@@ -10,3 +10,15 @@ sonar.python.version=3.11, 3.12, 3.13
 sonar.python.coverage.reportPaths=reports/coverage.xml
 sonar.coverage.exclusions=noxfile.py, template/**, tests/**, examples/**, docs/**, dist/**, dist_vercel/**, dist_native/**, **/third_party/**, codegen/**, **/_notebook.py, **/_pydicom_handler.py, **/_openslide_handler.py
 sonar.exclusions=template/**, examples/**, docs/**, dist/**, dist_vercel/**, dist_native/**, **/third_party/**, codegen/**, **/_notebook.py
+
+# Suppress cognitive complexity findings in complex but intentional functions
+sonar.issue.ignore.multicriteria=e1,e2,e3,e4
+sonar.issue.ignore.multicriteria.e1.ruleKey=python:S3776
+sonar.issue.ignore.multicriteria.e1.resourceKey=src/aignostics/application/_gui/_page_application_run_describe.py
+sonar.issue.ignore.multicriteria.e2.ruleKey=python:S3776
+sonar.issue.ignore.multicriteria.e2.resourceKey=src/aignostics/application/_service.py
+sonar.issue.ignore.multicriteria.e3.ruleKey=python:S3776
+sonar.issue.ignore.multicriteria.e3.resourceKey=src/aignostics/wsi/_pydicom_handler.py
+# Suppress unnecessary async finding in GUI page (async required by NiceGUI framework)
+sonar.issue.ignore.multicriteria.e4.ruleKey=python:S6966
+sonar.issue.ignore.multicriteria.e4.resourceKey=src/aignostics/application/_gui/_page_application_describe.py

src/aignostics.py

@@ -57,7 +57,7 @@
         sys.argv = [module_name, *module_args]
         try:
             if module_name == "marimo":
-                from marimo._cli.cli import main  # noqa: PLC2701
+                from marimo._cli.cli import main
 
                 main(prog_name="marimo")
             else:

src/aignostics/application/_cli.py

@@ -422,7 +422,7 @@ def application_describe(  # noqa: C901, PLR0912
 
 
 @run_app.command(name="execute")
-def run_execute(  # noqa: PLR0913, PLR0917
+def run_execute(  # noqa: PLR0913
     application_id: Annotated[
         str,
         typer.Argument(help="Id of application version to execute."),
@@ -636,7 +636,7 @@ def run_prepare(
 
 
 @run_app.command(name="upload")
-def run_upload(  # noqa: PLR0913, PLR0917
+def run_upload(  # noqa: PLR0913
     application_id: Annotated[
         str,
         typer.Argument(help="Id of the application to upload data for. "),
@@ -749,7 +749,7 @@ def update_progress(bytes_uploaded: int, source: Path, platform_bucket_url: str)
 
 
 @run_app.command("submit")
-def run_submit(  # noqa: PLR0913, PLR0917
+def run_submit(  # noqa: PLR0913
     application_id: Annotated[
         str,
         typer.Argument(help="Id of the application to submit run for."),
@@ -884,7 +884,7 @@ def run_submit(  # noqa: PLR0913, PLR0917
 
 
 @run_app.command("list")
-def run_list(  # noqa: PLR0913, PLR0917
+def run_list(  # noqa: PLR0913
     verbose: Annotated[bool, typer.Option(help="Show application details")] = False,
     limit: Annotated[int | None, typer.Option(help="Maximum number of runs to display")] = None,
     tags: Annotated[
@@ -1517,7 +1517,7 @@ def run_share_token_revoke(
 
 
 @result_app.command("download")
-def result_download(  # noqa: C901, PLR0913, PLR0915, PLR0917
+def result_download(  # noqa: C901, PLR0913, PLR0915
     run_id: Annotated[str, typer.Argument(..., help="Id of the run to download results for")],
     destination_directory: Annotated[
         Path,

src/aignostics/application/_download.py

@@ -146,7 +146,7 @@ def update_progress(
         download_progress_queue.put_nowait(progress)
 
 
-def download_available_items(  # noqa: PLR0913, PLR0917
+def download_available_items(  # noqa: PLR0913
     progress: DownloadProgress,
     application_run: Run,
     destination_directory: Path,
@@ -223,7 +223,7 @@ def download_available_items(  # noqa: PLR0913, PLR0917
             downloaded_items.add(item.external_id)
 
 
-def download_item_artifact(  # noqa: PLR0913, PLR0917
+def download_item_artifact(  # noqa: PLR0913
     progress: DownloadProgress,
     run: Run,
     artifact: Any,  # noqa: ANN401
@@ -285,7 +285,7 @@ def download_item_artifact(  # noqa: PLR0913, PLR0917
     )
 
 
-def download_file_with_progress(  # noqa: PLR0913, PLR0917
+def download_file_with_progress(  # noqa: PLR0913
     progress: DownloadProgress,
     signed_url: str,
     artifact_path: Path,

src/aignostics/application/_gui/_frame.py

@@ -29,7 +29,7 @@ class SearchInput:
 _runs_last_refresh_time: datetime | None = None
 
 
-async def _frame(  # noqa: C901, PLR0913, PLR0915, PLR0917
+async def _frame(  # noqa: C901, PLR0913, PLR0915
     navigation_title: str,
     navigation_icon: str | None = None,
     navigation_icon_color: str | None = None,
@@ -45,7 +45,7 @@ async def _frame(  # noqa: C901, PLR0913, PLR0915, PLR0917
     else:
         search_input.query = ""
 
-    with frame(  # noqa: PLR1702
+    with frame(
         navigation_title=navigation_title,
         navigation_icon=navigation_icon,
         navigation_icon_color=navigation_icon_color,
@@ -58,16 +58,15 @@ async def _frame(  # noqa: C901, PLR0913, PLR0915, PLR0917
             try:
                 applications = await nicegui_run.io_bound(Service.applications_static)
                 if applications is None:
-                    message = (  # type: ignore[unreachable]
+                    message = (
                         "nicegui_run.io_bound(Service.applications_static) returned None, "
                         "likely canceled by application shutdown."
                     )
                     logger.error(message)
                     raise RuntimeError(message)  # noqa: TRY301
                 for application in applications:
                     with (
-                        ui
-                        .item(
+                        ui.item(
                             on_click=lambda app_id=application.application_id: ui.navigate.to(f"/application/{app_id}")
                         )
                         .mark(f"SIDEBAR_APPLICATION:{application.application_id}")
@@ -113,7 +112,7 @@ async def application_runs_load_and_render(  # noqa: C901, PLR0915
                         query=query,
                     )
                     if runs is None:
-                        message = (  # type: ignore[unreachable]
+                        message = (
                             "nicegui_run.io_bound(Service.application_runs_static) returned None, "
                             "likely canceled by shutdown."
                         )
@@ -144,8 +143,7 @@ async def application_runs_load_and_render(  # noqa: C901, PLR0915
                     runs_column.clear()
                     for index, run_data in enumerate(runs) if runs else []:
                         with (
-                            ui
-                            .item(
+                            ui.item(
                                 on_click=lambda run_id=run_data["run_id"]: ui.navigate.to(f"/application/run/{run_id}")
                             )
                             .props("clickable")
@@ -228,8 +226,7 @@ def _on_tag_click(t: str = tag) -> None:
         @ui.refreshable
         async def _runs_list() -> None:
             with (
-                ui
-                .scroll_area()
+                ui.scroll_area()
                 .props('id="runs-list-container"')
                 .classes("w-full")
                 .style("height: calc(100vh - 250px);")