fix(tests): resolve linter issues and update source code

- Fix linter issues in application module
- Fix linter issues in qupath module
- Update service implementations for consistency
- Resolve merge conflicts from main branch integration
- Skip tests requiring Google Cloud credentials in local environment
- Fix pre-commit configuration errors
- Ensure code passes all static analysis checks

[skip:test:long-running]

Author: muhabalwan-aginx

ATTRIBUTIONS.md

@@ -506,7 +506,7 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 ```
 
-## aignostics (0.2.190) - MIT License
+## aignostics (0.2.192) - MIT License
 
 🔬 Python SDK providing access to the Aignostics Platform. Includes Aignostics Launchpad (Desktop Application), Aignostics CLI (Command-Line Interface), example notebooks, and Aignostics Client Library.
 
@@ -3659,7 +3659,7 @@ SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 ```
 
-## boto3 (1.40.47) - Apache Software License
+## boto3 (1.40.50) - Apache Software License
 
 The AWS SDK for Python
 
@@ -3857,7 +3857,7 @@ Copyright 2013-2017 Amazon.com, Inc. or its affiliates. All Rights Reserved.
 
 ```
 
-## botocore (1.40.47) - Apache Software License
+## botocore (1.40.50) - Apache Software License
 
 Low-level, data-driven core of boto 3.
 
@@ -7585,7 +7585,7 @@ SOFTWARE.
 
 ```
 
-## fastapi (0.118.2) - MIT License
+## fastapi (0.119.0) - MIT License
 
 FastAPI framework, high performance, easy to learn, fast to code, ready for production
 
@@ -9312,7 +9312,7 @@ Google Cloud API client core library
 
 ```
 
-## google-cloud-storage (3.4.0) - Apache Software License
+## google-cloud-storage (3.4.1) - Apache Software License
 
 Google Cloud Storage API client library
 
@@ -10576,7 +10576,7 @@ THE SOFTWARE.
 
 ```
 
-## ijson (3.4.0) - UNKNOWN
+## ijson (3.4.0.post0) - UNKNOWN
 
 Iterative JSON parser with standard Python iterator interfaces
 
@@ -12635,7 +12635,7 @@ license-expression is a comprehensive utility library to parse, compare, simplif
 
 ```
 
-## logfire (4.12.0) - UNKNOWN
+## logfire (4.13.0) - UNKNOWN
 
 The best Python observability tool! 🪵🔥
 
@@ -12969,7 +12969,7 @@ THE SOFTWARE.
 
 ```
 
-## matplotlib (3.10.6) - Python Software Foundation License
+## matplotlib (3.10.7) - Python Software Foundation License
 
 Python plotting package
 
@@ -13884,7 +13884,7 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 ```
 
-## nicegui (3.0.3) - MIT License
+## nicegui (3.0.4) - MIT License
 
 Create web-based user interfaces with Python. The nice way.
 
@@ -23772,7 +23772,7 @@ A tool for scanning Python environments for known vulnerabilities
 
 ```
 
-## platformdirs (4.4.0) - MIT License
+## platformdirs (4.5.0) - MIT License
 
 A small Python package for determining appropriate platform-specific dirs, e.g. a `user data dir`.
 
@@ -24683,43 +24683,6 @@ Proxy Implementation
 * URL: http://github.com/jtushman/proxy_tools
 * Author(s): Jonathan Tushman
 
-## pscript (0.7.7) - BSD License
-
-Python to JavaScript compiler.
-
-* URL: http://pscript.readthedocs.io
-* Author(s): Almar Klein and contributors
-
-### License Text
-
-```
-Copyright (c) 2015-2020, PScript developers
-All rights reserved.
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
-
-* Redistributions of source code must retain the above copyright notice, this
-  list of conditions and the following disclaimer.
-
-* Redistributions in binary form must reproduce the above copyright notice,
-  this list of conditions and the following disclaimer in the documentation
-  and/or other materials provided with the distribution.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-
-```
-
 ## psutil (7.1.0) - BSD-3-Clause
 
 Cross-platform lib for process and system monitoring.
@@ -26614,7 +26577,7 @@ SOFTWARE.
 
 ```
 
-## pytest-env (1.1.5) - MIT License
+## pytest-env (1.2.0) - MIT License
 
 pytest plugin that allows you to add environment variables.
 
@@ -29629,7 +29592,7 @@ SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 ```
 
-## sentry-sdk (2.40.0) - BSD License
+## sentry-sdk (2.41.0) - BSD License
 
 Python client for Sentry (https://sentry.io)
 
@@ -30701,7 +30664,7 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 ```
 
-## swagger-plugin-for-sphinx (5.1.3) - UNKNOWN
+## swagger-plugin-for-sphinx (5.2.0) - UNKNOWN
 
 Sphinx plugin which renders a OpenAPI specification with Swagger
 
@@ -31352,7 +31315,7 @@ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 THE SOFTWARE.
 ```
 
-## tomli (2.2.1) - MIT License
+## tomli (2.3.0) - UNKNOWN
 
 A lil' TOML parser
 
@@ -33728,40 +33691,6 @@ Copyright (C) 2016-present the uvloop authors and contributors.
 
 ```
 
-## vbuild (0.8.2) - MIT License
-
-A simple module to extract html/script/style from a vuejs '.vue' file (can minimize/es2015 compliant js) ... just py2 or py3, NO nodejs !
-
-* URL: https://github.com/manatlan/vbuild
-* Author(s): manatlan
-
-### License Text
-
-```
-MIT License
-
-Copyright (c) 2018 manatlan
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
-
-```
-
 ## virtualenv (20.34.0) - MIT License
 
 Virtual Python Environment builder

pyproject.toml

@@ -561,12 +561,3 @@ ignore_tags = "rc"
 topo_order = false
 # sort the commits inside sections by oldest/newest order
 sort_commits = "newest"
-
-
-# set max number of arguments for pylint
-# https://pylint.pycqa.org/en/latest/user_guide/run.html#cmdline-options
-# pylint will raise an error if the number of arguments exceeds this value
-# this is to avoid pylint errors in the CI pipeline
-# and to allow for more flexible code structure
-[tool.ruff.lint.pylint]
-max-args = 6

tests/aignostics/application/cli_test.py

@@ -18,7 +18,7 @@
 
 @pytest.mark.e2e
 @pytest.mark.timeout(timeout=60)
-def test_cli_application_list(runner: CliRunner, record_property) -> None:
+def test_cli_application_list_non_verbose(runner: CliRunner, record_property) -> None:
     """Check application list command runs successfully."""
     record_property("tested-item-id", "SPEC-APPLICATION-SERVICE")
     result = runner.invoke(cli, ["application", "list"])
@@ -191,7 +191,7 @@ def test_cli_run_submit_fails_on_missing_url(runner: CliRunner, tmp_path: Path,
 @pytest.mark.e2e
 @pytest.mark.long_running
 @pytest.mark.timeout(timeout=60 * 10)
-def test_cli_run_submit_and_describe_and_cancel_and_download(  # noqa: PLR0915
+def test_cli_run_submit_and_describe_and_cancel_and_download_and_delete(  # noqa: PLR0915
     runner: CliRunner, tmp_path: Path, record_property
 ) -> None:
     """Check run submit command runs successfully."""
@@ -387,7 +387,7 @@ def test_cli_run_result_download_uuid_not_found(runner: CliRunner, tmp_path: Pat
 
 @pytest.mark.e2e
 @pytest.mark.timeout(timeout=60)
-def test_cli_run_result_delete(runner: CliRunner, record_property) -> None:
+def test_cli_run_result_delete_not_found(runner: CliRunner, record_property) -> None:
     """Check run result delete command runs successfully."""
     result = runner.invoke(cli, ["application", "run", "result", "delete", "00000000000000000000000000000000"])
     assert "Run with ID '00000000000000000000000000000000' not found." in normalize_output(result.stdout)

tests/aignostics/application/gui_test.py

@@ -53,7 +53,7 @@ async def test_gui_index(user: User, record_property) -> None:
         ),
     ],
 )
-async def test_gui_home_to_application(
+async def test_gui_home_to_application(  # noqa: PLR0913, PLR0917
     user: User, application_id: str, application_name: str, expected_text: str, silent_logging: None, record_property
 ) -> None:
     """Test that the user sees the specific application page with expected content."""

tests/aignostics/dataset/gui_test.py

@@ -23,7 +23,7 @@ async def test_gui_idc_shows(user: User) -> None:
 @pytest.mark.long_running
 @pytest.mark.flaky(retries=1, delay=5, only_on=[AssertionError])
 @pytest.mark.timeout(timeout=60 * 5)
-async def test_gui_idc_downloads(user: User, tmp_path, silent_logging, record_property) -> None:
+async def test_gui_idc_downloads(user: User, tmp_path: Path, silent_logging: bool, record_property) -> None:
     """Test that the user can download a dataset to a temporary directory."""
     record_property("tested-item-id", "TC-DATASET-GUI-01")
     # Mock get_user_data_directory to return the tmpdir for this test

tests/aignostics/platform/settings_test.py

@@ -195,16 +195,70 @@ def test_authentication_settings_with_env_vars(record_property, mock_env_vars, r
     assert settings1.client_id_device.get_secret_value() == "test-client-id-device"
 
 
-# TODO(Helmut): fixme
-@pytest.mark.skip(reason="Broken feature")
-@pytest.mark.unit
-def test_custom_env_file_location(record_property, mock_env_vars) -> None:
-    """Test custom env file location."""
+def test_custom_env_file_location(reset_cached_settings, record_property) -> None:
+    """Test custom env file location.
+
+    This test verifies that a custom env file can be specified via the AIGNOSTICS_ENV_FILE
+    environment variable and that Settings will load from that file. The test uses a context
+    manager to ensure proper cleanup of the temporary env file.
+
+    Note: This test uses health_timeout instead of client_id_device because in CI environments,
+    the AIGNOSTICS_CLIENT_ID_DEVICE environment variable takes precedence over env file values
+    (as per pydantic-settings priority). The health_timeout field is less likely to be set
+    in CI environments.
+    """
+    import sys
+    import tempfile
+    from contextlib import contextmanager
+
     record_property("tested-item-id", "SPEC-PLATFORM-SERVICE")
-    custom_env_file = "/home/dummy/test_env_file"
-    with mock.patch.dict(os.environ, {f"{__project_name__.upper()}_ENV_FILE": custom_env_file}):
-        settings = Settings.model_config
-        assert custom_env_file in settings["env_file"]
+
+    settings_module = "aignostics.platform._settings"
+
+    @contextmanager
+    def temp_env_file(content: str):  # type: ignore[misc]
+        """Context manager for creating a temporary env file that's cleaned up automatically.
+
+        Args:
+            content: The content to write to the temporary env file.
+
+        Yields:
+            str: The path to the temporary env file.
+        """
+        with tempfile.NamedTemporaryFile(mode="w", suffix=".env", delete=False, encoding="utf-8") as f:
+            f.write(content)
+            temp_path = f.name
+        try:
+            yield temp_path
+        finally:
+            Path(temp_path).unlink(missing_ok=True)
+
+    # Create a temporary env file with test settings
+    with temp_env_file("AIGNOSTICS_HEALTH_TIMEOUT=42.5\n") as custom_env_file:
+        # Set the custom env file location BEFORE importing Settings
+        # This requires reimporting the module to pick up the new env var
+        # Clear ALL AIGNOSTICS_ environment variables to ensure clean state
+        env_patch = {k: v for k, v in os.environ.items() if not k.startswith(f"{__project_name__.upper()}_")}
+
+        # Now set only the variables we want for this test
+        env_patch[f"{__project_name__.upper()}_ENV_FILE"] = custom_env_file
+
+        try:
+            with mock.patch.dict(os.environ, env_patch, clear=True):
+                # Remove the module from sys.modules to force reimport
+                if settings_module in sys.modules:
+                    del sys.modules[settings_module]
+
+                # Now import Settings fresh - it should read from the custom env file
+                from aignostics.platform._settings import Settings
+
+                assert custom_env_file in Settings.model_config["env_file"]
+                test_settings = Settings()
+                assert test_settings.health_timeout == pytest.approx(42.5)
+        finally:
+            # Restore the original module state by deleting it so it gets reimported fresh next time
+            if settings_module in sys.modules:
+                del sys.modules[settings_module]
 
 
 @pytest.mark.unit

tests/aignostics/qupath/gui_test.py

@@ -76,8 +76,6 @@ async def test_gui_qupath_install_and_launch(
     user: User, runner: CliRunner, silent_logging: None, qupath_teardown
 ) -> None:
     """Test that the user can install and launch QuPath via the GUI."""
-    pytest.skip("Skip interim - TODO (Helmut)")
-
     result = runner.invoke(cli, ["qupath", "uninstall"])
     assert result.exit_code in {0, 2}, f"Uninstall command failed with exit code {result.exit_code}"
     was_installed = not result.exit_code

tests/aignostics/system/gui_test.py

@@ -21,6 +21,7 @@ async def test_gui_system_alive(user: User) -> None:
 
 
 @pytest.mark.e2e
+@pytest.mark.flaky(retries=2, delay=5, only_on=[AssertionError])
 @pytest.mark.timeout(timeout=60 * 3)
 @pytest.mark.sequential
 async def test_gui_system_switch_right(user: User, silent_logging, record_property) -> None:

tests/aignostics/utils/gui_test.py

@@ -133,16 +133,16 @@ def test_gui_run_custom_params(
 @pytest.mark.unit
 @mock.patch("aignostics.utils._gui.__is_running_in_container__", True)
 @mock.patch("nicegui.ui.run")
-def test_gui_run_in_container_with_native(mock_ui: mock.MagicMock, record_property) -> None:
+def test_gui_run_in_container_with_native(mock_ui_run: mock.MagicMock, record_property) -> None:
     """Test that gui_run raises ValueError when running native in container.
 
     Args:
-        mock_ui: Mock for nicegui UI run
+        mock_ui_run: Mock for nicegui UI run
         nicegui_reset_globals: Fixture to reset NiceGUI globals
         record_property: pytest record_property fixture
     """
     record_property("tested-item-id", "SPEC-UTILS-SERVICE")
     with pytest.raises(ValueError) as excinfo:
         gui_run(native=True)
     assert "Native GUI cannot be run in a container" in str(excinfo.value)
-    mock_ui.assert_not_called()
+    mock_ui_run.assert_not_called()