fix(deps): adapt lint and tests to ruff 0.16 and typer 0.27

Lock file maintenance bumped ruff (0.15->0.16) and typer (0.26->0.27),
breaking CI:

- ruff 0.16 stabilizes PLR0917 (too-many-positional-arguments) into the
  ALL selection; append PLR0917 to the existing per-site noqa on the 34
  affected functions (PLR0913 stays, it is an independent rule).
- ruff 0.16 formats Python code blocks embedded in Markdown; reformat the
  snippet in tests/CLAUDE.md accordingly.
- typer 0.27 renders the missing-argument metavar as the parameter name
  ('run_id') instead of upper-case ('RUN_ID'); update the assertion in
  test_cli_run_result_delete_fails_on_no_arg.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

Author: olivermeyer

src/aignostics/application/_cli.py

@@ -427,7 +427,7 @@ def application_describe(  # noqa: C901, PLR0912
 
 
 @run_app.command(name="execute")
-def run_execute(  # noqa: PLR0913
+def run_execute(  # noqa: PLR0913, PLR0917
     application_id: Annotated[
         str,
         typer.Argument(help="Id of application version to execute."),
@@ -641,7 +641,7 @@ def run_prepare(
 
 
 @run_app.command(name="upload")
-def run_upload(  # noqa: PLR0913
+def run_upload(  # noqa: PLR0913, PLR0917
     application_id: Annotated[
         str,
         typer.Argument(help="Id of the application to upload data for. "),
@@ -754,7 +754,7 @@ def update_progress(bytes_uploaded: int, source: Path, platform_bucket_url: str)
 
 
 @run_app.command("submit")
-def run_submit(  # noqa: PLR0913
+def run_submit(  # noqa: PLR0913, PLR0917
     application_id: Annotated[
         str,
         typer.Argument(help="Id of the application to submit run for."),
@@ -889,7 +889,7 @@ def run_submit(  # noqa: PLR0913
 
 
 @run_app.command("list")
-def run_list(  # noqa: PLR0913
+def run_list(  # noqa: PLR0913, PLR0917
     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[
@@ -1642,7 +1642,7 @@ def run_share_token_revoke(
 
 
 @result_app.command("download")
-def result_download(  # noqa: C901, PLR0913, PLR0915
+def result_download(  # noqa: C901, PLR0913, PLR0915, PLR0917
     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
+def download_available_items(  # noqa: PLR0913, PLR0917
     progress: DownloadProgress,
     application_run: Run,
     destination_directory: Path,
@@ -223,7 +223,7 @@ def download_available_items(  # noqa: PLR0913
             downloaded_items.add(item.external_id)
 
 
-def download_item_artifact(  # noqa: PLR0913
+def download_item_artifact(  # noqa: PLR0913, PLR0917
     progress: DownloadProgress,
     run: Run,
     artifact: Any,  # noqa: ANN401
@@ -285,7 +285,7 @@ def download_item_artifact(  # noqa: PLR0913
     )
 
 
-def download_file_with_progress(  # noqa: PLR0913
+def download_file_with_progress(  # noqa: PLR0913, PLR0917
     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
+async def _frame(  # noqa: C901, PLR0913, PLR0915, PLR0917
     navigation_title: str,
     navigation_icon: str | None = None,
     navigation_icon_color: str | None = None,

src/aignostics/application/_service.py

@@ -320,7 +320,7 @@ def _apply_mappings_to_entry(entry: dict[str, Any], mappings: list[str]) -> None
                 Service._process_key_value_pair(entry, key_value, external_id)
 
     @staticmethod
-    def generate_metadata_from_source_directory(  # noqa: PLR0913
+    def generate_metadata_from_source_directory(  # noqa: PLR0913, PLR0917
         source_directory: Path,
         application_id: str,
         application_version: str | None = None,
@@ -432,7 +432,7 @@ def generate_metadata_from_source_directory(  # noqa: PLR0913
             raise RuntimeError(message) from e
 
     @staticmethod
-    def application_run_upload(  # noqa: PLR0913
+    def application_run_upload(  # noqa: PLR0913, PLR0917
         application_id: str,
         metadata: list[dict[str, Any]],
         application_version: str | None = None,
@@ -501,7 +501,7 @@ def application_run_upload(  # noqa: PLR0913
                 open(source_file_path, "rb") as f,
             ):
 
-                def read_in_chunks(  # noqa: PLR0913
+                def read_in_chunks(  # noqa: PLR0913, PLR0917
                     external_id: str,
                     file_size: int,
                     upload_progress_queue: Any | None = None,  # noqa: ANN401
@@ -535,7 +535,7 @@ def read_in_chunks(  # noqa: PLR0913
         return True
 
     @staticmethod
-    def application_runs_static(  # noqa: PLR0913
+    def application_runs_static(  # noqa: PLR0913, PLR0917
         application_id: str | None = None,
         application_version: str | None = None,
         external_id: str | None = None,
@@ -606,7 +606,7 @@ def application_runs_static(  # noqa: PLR0913
             )
         ]
 
-    def application_runs(  # noqa: C901, PLR0912, PLR0913, PLR0915
+    def application_runs(  # noqa: C901, PLR0912, PLR0913, PLR0915, PLR0917
         self,
         application_id: str | None = None,
         application_version: str | None = None,
@@ -828,7 +828,7 @@ def application_run(self, run_id: str, share_token: str | None = None) -> Run:
             logger.exception(message)
             raise RuntimeError(message) from e
 
-    def application_run_submit_from_metadata(  # noqa: PLR0913
+    def application_run_submit_from_metadata(  # noqa: PLR0913, PLR0917
         self,
         application_id: str,
         metadata: list[dict[str, Any]],
@@ -996,7 +996,7 @@ def application_run_submit_from_metadata(  # noqa: PLR0913
             logger.exception(message)
             raise RuntimeError(message) from e
 
-    def application_run_submit(  # noqa: PLR0913, PLR0912, C901, PLR0915
+    def application_run_submit(  # noqa: PLR0913, PLR0912, C901, PLR0915, PLR0917
         self,
         application_id: str,
         items: list[InputItem],
@@ -1629,7 +1629,7 @@ def application_run_revoke_share_token(self, run_id: str, share_token_id: str) -
             raise NotFoundException(message)
 
     @staticmethod
-    def application_run_download_static(  # noqa: PLR0913
+    def application_run_download_static(  # noqa: PLR0913, PLR0917
         run_id: str,
         destination_directory: Path,
         create_subdirectory_for_run: bool = True,
@@ -1674,7 +1674,7 @@ def application_run_download_static(  # noqa: PLR0913
             download_progress_queue,
         )
 
-    def application_run_download(  # noqa: C901, PLR0912, PLR0913, PLR0915
+    def application_run_download(  # noqa: C901, PLR0912, PLR0913, PLR0915, PLR0917
         self,
         run_id: str,
         destination_directory: Path,

src/aignostics/platform/resources/applications.py

@@ -515,7 +515,7 @@ def _prepare_document_request(
         return endpoint_url, token_provider, ssl_verify, proxy
 
     # Private helper; splitting params would require a thin DTO.
-    def _stream_document(  # noqa: PLR0913
+    def _stream_document(  # noqa: PLR0913, PLR0917
         self,
         url: str,
         write_chunk: t.Callable[[bytes], object],

src/aignostics/platform/resources/runs.py

@@ -909,7 +909,7 @@ def __call__(self, run_id: str) -> Run:
         """
         return Run(self._api, run_id)
 
-    def submit(  # noqa: PLR0913
+    def submit(  # noqa: PLR0913, PLR0917
         self,
         application_id: str,
         items: list[ItemCreationRequest],
@@ -983,7 +983,7 @@ def submit(  # noqa: PLR0913
         operation_cache_clear()  # Clear all caches since we added a new run
         return Run(self._api, str(res.run_id))
 
-    def list(  # noqa: PLR0913
+    def list(  # noqa: PLR0913, PLR0917
         self,
         application_id: str | None = None,
         application_version: str | None = None,
@@ -1031,7 +1031,7 @@ def list(  # noqa: PLR0913
             )
         )
 
-    def list_data(  # noqa: PLR0913
+    def list_data(  # noqa: PLR0913, PLR0917
         self,
         application_id: str | None = None,
         application_version: str | None = None,

src/aignostics/qupath/_service.py

@@ -428,7 +428,7 @@ def get_installation_path() -> Path:
         return Path(platformdirs.user_data_dir(__project_name__)).resolve()
 
     @staticmethod
-    def _download_qupath(  # noqa: C901, PLR0912, PLR0913, PLR0915
+    def _download_qupath(  # noqa: C901, PLR0912, PLR0913, PLR0915, PLR0917
         version: str,
         path: Path,
         platform_system: str | None = None,
@@ -759,7 +759,7 @@ def _extract_qupath(  # noqa: C901, PLR0912, PLR0915
         raise RuntimeError(message)
 
     @staticmethod
-    def install_qupath(  # noqa: PLR0913
+    def install_qupath(  # noqa: PLR0913, PLR0917
         version: str = QUPATH_VERSION,
         path: Path | None = None,
         reinstall: bool = True,

src/aignostics/utils/_gui.py

@@ -30,7 +30,7 @@ def gui_register_pages() -> None:
         page_builder.register_pages()
 
 
-def gui_run(  # noqa: PLR0913
+def gui_run(  # noqa: PLR0913, PLR0917
     native: bool = True,
     show: bool = False,
     host: str | None = None,

tests/CLAUDE.md

@@ -80,9 +80,10 @@ The decorator intercepts `nocache` and does not pass it to the wrapped function.
 @cached_operation(ttl=60)
 def f() -> int: ...
 
-f()                 # populates cache
-f()                 # cache hit, f not re-run
-f(nocache=True)     # re-runs f, refreshes cache
+
+f()  # populates cache
+f()  # cache hit, f not re-run
+f(nocache=True)  # re-runs f, refreshes cache
 ```
 
 See `nocache_test.py` for the full decorator / client / edge-case coverage.

tests/aignostics/application/cli_test.py

@@ -1307,7 +1307,7 @@ def test_cli_run_result_delete_fails_on_no_arg(runner: CliRunner, record_propert
     """Check run result delete command runs successfully."""
     record_property("tested-item-id", "SPEC-APPLICATION-SERVICE")
     result = runner.invoke(cli, ["application", "run", "result", "delete"])
-    assert "Missing argument 'RUN_ID'." in normalize_output(result.stderr)
+    assert "Missing argument 'run_id'." in normalize_output(result.stderr)
     assert result.exit_code == 2