chore: Bump pip and pyjwt

[aig-hannes]

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[sonarqubecloud]

Quality Gate passed

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[codecov]

❌ 2 Tests Failed:

Tests completed	Failed	Passed	Skipped
879	2	877	15

View the top 2 failed test(s) by shortest run time

tests.aignostics.application.gui_test::test_gui_run_download

Stack Traces | 46.7s run time

user = <nicegui.testing.user.User object at 0x7f0cc5f535c0>
runner = <typer.testing.CliRunner object at 0x7f0cc5f51e00>
tmp_path = PosixPath('.../pytest-of-runner/pytest-21/test_gui_run_download1')
silent_logging = None
record_property = <function record_property.<locals>.append_property at 0x7f0cf41ec040>

    @pytest.mark.e2e
    @pytest.mark.long_running
    @pytest.mark.flaky(retries=1, delay=5)
    @pytest.mark.timeout(timeout=60 * 10)
    @pytest.mark.sequential  # Helps on Linux with image analysis step otherwise timing out
    async def test_gui_run_download(  # noqa: PLR0914, PLR0915
        user: User, runner: CliRunner, tmp_path: Path, silent_logging: None, record_property
    ) -> None:
        """Test that the user can download a run result via the GUI."""
        record_property("tested-item-id", "SPEC-APPLICATION-SERVICE, SPEC-GUI-SERVICE")
        with patch(
            "aignostics.application._gui._page_application_run_describe.get_user_data_directory",
            return_value=tmp_path,
        ):
            # Find run
            runs = Service().application_runs(
                application_id=HETA_APPLICATION_ID,
                application_version=HETA_APPLICATION_VERSION,
                external_id=SPOT_0_GS_URL,
                tags=["scheduled"],
                has_output=True,
                limit=1,
            )
            if not runs:
                message = f"No matching runs found for application {HETA_APPLICATION_ID} ({HETA_APPLICATION_VERSION}). "
                message += "This test requires the scheduled test test_application_runs_heta_version passing first."
                pytest.skip(message)
    
            run_id = runs[0].run_id
    
            # Explore run
            run = Service().application_run(run_id).details()
            print(
                f"Found existing run: {run.run_id}\n"
                f"application: {run.application_id} ({run.version_number})\n"
                f"status: {run.state}, output: {run.output}\n"
                f"submitted at: {run.submitted_at}, terminated at: {run.terminated_at}\n"
                f"statistics: {run.statistics!r}\n",
                f"custom_metadata: {run.custom_metadata!r}\n",
            )
            # Step 1: Go to latest completed run
            await user.open(f"/application/run/{run.run_id}")
            await user.should_see(f"Run {run.run_id}", retries=100)
            await user.should_see(
                f"Run of {run.application_id} ({run.version_number})",
                retries=100,
            )
    
            # Step 2: Open Result Download dialog
            await user.should_see(marker="BUTTON_DOWNLOAD_RUN", retries=100)
            user.find(marker="BUTTON_DOWNLOAD_RUN").click()
    
            # Step 3: Check download button is initially disabled, then select Data folder
            download_run_button: ui.button = user.find(marker="DIALOG_BUTTON_DOWNLOAD_RUN").elements.pop()
            assert not download_run_button.enabled, "Download button should be disabled before selecting target"
            await user.should_see(marker="BUTTON_DOWNLOAD_DESTINATION_DATA", retries=100)
            user.find(marker="BUTTON_DOWNLOAD_DESTINATION_DATA").click()
            await assert_notified(user, "Using Launchpad results directory")
    
            # Step 4: Trigger Download - wait for button to be enabled
            download_run_button = user.find(marker="DIALOG_BUTTON_DOWNLOAD_RUN").elements.pop()
            assert download_run_button.enabled, "Download button should be enabled after selecting target"
            user.find(marker="DIALOG_BUTTON_DOWNLOAD_RUN").click()
            await assert_notified(user, "Downloading ...")
    
            # Check: Download completed
            await assert_notified(user, "Download completed.", 60 * 4)
            print_directory_structure(tmp_path, "downloaded_run")
    
            # Check for directory layout as expected
            run_dir = tmp_path / run.run_id
            assert run_dir.is_dir(), f"Expected run directory {run_dir} not found"
    
            subdirs = [d for d in run_dir.iterdir() if d.is_dir()]
            assert len(subdirs) == 2, f"Expected two subdirectories in {run_dir}, but found {len(subdirs)}"
    
            input_dir = run_dir / "input"
            assert input_dir.is_dir(), f"Expected input directory {input_dir} not found"
    
            results_dir = run_dir / SPOT_0_FILENAME.replace(".tiff", "")
            assert results_dir.is_dir(), f"Expected run results directory {results_dir} not found"
    
            # Check for input file having been downloaded
            input_file = input_dir / SPOT_0_FILENAME
            assert input_file.exists(), f"Expected input file {input_file} not found"
            assert input_file.stat().st_size == SPOT_0_FILESIZE, (
                f"Expected input file size {SPOT_0_FILESIZE}, but got {input_file.stat().st_size}"
            )
    
            # Check for files in the results directory
            files_in_results_dir = list(results_dir.glob("*"))
            expected_count = len(SPOT_0_EXPECTED_RESULT_FILES)
>           assert len(files_in_results_dir) == expected_count, (
                f"Expected {expected_count} files in {results_dir}, but found {len(files_in_results_dir)}: "
                f"{[f.name for f in files_in_results_dir]}"
            )
E           AssertionError: Expected 12 files in .../pytest-of-runner/pytest-21/test_gui_run_download1/b197ab65-0be1-488c-ad2e-68ab1b6b2603/8fafc17d-a5cc-4e9d-a982-030b1486ca88, but found 14: ['cell_classification_geojson_polygons.json', 'cell_classification_parquet_polygons.parquet', 'tissue_qc_csv_class_information.csv', 'readout_generation_slide_readouts.csv', 'tissue_segmentation_segmentation_map_image.tiff', 'tissue_segmentation_geojson_polygons.json', 'readout_generation_cell_readouts.csv', 'tissue_segmentation_csv_class_information.csv', 'tissue_qc_geojson_polygons.json', 'tissue_qc_parquet_polygons.parquet', 'tissue_segmentation_parquet_polygons.parquet', 'cell_detection_parquet_centers.parquet', 'cell_detection_parquet_polygons.parquet', 'tissue_qc_segmentation_map_image.tiff']
E           assert 14 == 12
E            +  where 14 = len([PosixPath('.../pytest-of-runner/pytest-21/test_gui_run_download1/b197ab65-0be1-488c-ad2e-68ab1b6b2603/8fafc17d-a5cc-4e9d-a982-030b1486ca88/cell_classification_geojson_polygons.json'), PosixPath('.../pytest-of-runner/pytest-21/test_gui_run_download1/b197ab65-0be1-488c-ad2e-68ab1b6b2603/8fafc17d-a5cc-4e9d-a982-030b1486ca88/cell_classification_parquet_polygons.parquet'), PosixPath('.../pytest-of-runner/pytest-21/test_gui_run_download1/b197ab65-0be1-488c-ad2e-68ab1b6b2603/8fafc17d-a5cc-4e9d-a982-030b1486ca88/tissue_qc_csv_class_information.csv'), PosixPath('.../pytest-of-runner/pytest-21/test_gui_run_download1/b197ab65-0be1-488c-ad2e-68ab1b6b2603/8fafc17d-a5cc-4e9d-a982-030b1486ca88/readout_generation_slide_readouts.csv'), PosixPath('.../pytest-of-runner/pytest-21/test_gui_run_download1/b197ab65-0be1-488c-ad2e-68ab1b6b2603/8fafc17d-a5cc-4e9d-a982-030b1486ca88/tissue_segmentation_segmentation_map_image.tiff'), PosixPath('.../pytest-of-runner/pytest-21/test_gui_run_download1/b197ab65-0be1-488c-ad2e-68ab1b6b2603/8fafc17d-a5cc-4e9d-a982-030b1486ca88/tissue_segmentation_geojson_polygons.json'), ...])

.../aignostics/application/gui_test.py:445: AssertionError

tests.aignostics.qupath.gui_test::test_gui_run_qupath_install_to_inspect

Stack Traces | 63.7s run time

user = <nicegui.testing.user.User object at 0x7f0cd6ce2140>
runner = <typer.testing.CliRunner object at 0x7f0cc4d0c670>
tmp_path = PosixPath('.../pytest-of-runner/pytest-21/test_gui_run_qupath_install_to0')
silent_logging = None, qupath_teardown = None, qupath_save_restore = None
record_property = <function record_property.<locals>.append_property at 0x7f0cd6ed5f30>

    @pytest.mark.e2e
    @pytest.mark.long_running
    @pytest.mark.skipif(
        (platform.system() == "Linux" and platform.machine() in {"aarch64", "arm64"}),
        reason="QuPath is not supported on ARM64 Linux",
    )
    @pytest.mark.timeout(timeout=60 * 15)
    @pytest.mark.sequential
    async def test_gui_run_qupath_install_to_inspect(  # noqa: C901, PLR0912, PLR0913, PLR0914, PLR0915, PLR0917
        user: User,
        runner: CliRunner,
        tmp_path: Path,
        silent_logging: None,
        qupath_teardown: None,
        qupath_save_restore: None,
        record_property,
    ) -> None:
        """Test installing QuPath, downloading run results, creating QuPath project from it, and inspecting results."""
        record_property("tested-item-id", "TC-QUPATH-01, SPEC-GUI-SERVICE")
    
        # Find run
        runs = Service().application_runs(
            application_id=HETA_APPLICATION_ID,
            application_version=HETA_APPLICATION_VERSION,
            external_id=SPOT_0_GS_URL,
            tags=["scheduled"],
            has_output=True,
            limit=1,
        )
        if not runs:
            message = f"No matching runs found for application {HETA_APPLICATION_ID} ({HETA_APPLICATION_VERSION}). "
            message += "This test requires the scheduled test test_application_runs_heta_version passing first."
            pytest.skip(message)
    
        run_id = runs[0].run_id
    
        # Explore run
        run = Service().application_run(run_id).details()
        print(
            f"Found existing run: {run.run_id}\n"
            f"application: {run.application_id} ({run.version_number})\n"
            f"status: {run.state}, output: {run.output}\n"
            f"submitted at: {run.submitted_at}, terminated at: {run.terminated_at}\n"
            f"statistics: {run.statistics!r}\n",
            f"custom_metadata: {run.custom_metadata!r}\n",
        )
    
        # Explore results
        results = list(Service().application_run(run_id).results())
        assert results, f"No results found for run {run_id}"
        for item in results:
            print(
                f"Found item: {item.item_id}, status: {item.state}, output: {item.output}, "
                f"external_id: {item.external_id}\n"
                f"custom_metadata: {item.custom_metadata!r}\n",
            )
    
        with patch(
            "aignostics.application._gui._page_application_run_describe.get_user_data_directory", return_value=tmp_path
        ):
            # Step 1: (Re)Install QuPath
            result = runner.invoke(cli, ["qupath", "install"])
            output = normalize_output(result.output, strip_ansi=True)
            assert f"QuPath v{QUPATH_VERSION} installed successfully" in output, (
                f"Expected 'QuPath v{QUPATH_VERSION} installed successfully' in output.\nOutput: {output}"
            )
            assert result.exit_code == 0
    
            # Step 2: Go to latest completed run via GUI
            await user.open(f"/application/run/{run.run_id}")
            await user.should_see(f"Run {run.run_id}")
            await user.should_see(f"Run of {HETA_APPLICATION_ID} ({HETA_APPLICATION_VERSION})")
    
            # Step 3: Open Result Download dialog
            await user.should_see(marker="BUTTON_OPEN_QUPATH", retries=100)
            user.find(marker="BUTTON_OPEN_QUPATH").click()
    
            # Step 4: Select Data destination
            await user.should_see(marker="BUTTON_DOWNLOAD_DESTINATION_DATA")
            download_destination_data_button: ui.button = user.find(
                marker="BUTTON_DOWNLOAD_DESTINATION_DATA"
            ).elements.pop()
            assert download_destination_data_button.enabled, "Download destination button should be enabled"
            user.find(marker="BUTTON_DOWNLOAD_DESTINATION_DATA").click()
            await assert_notified(user, "Using Launchpad results directory", 30)
    
            # Step 5: Trigger Download
            await user.should_see(marker="DIALOG_BUTTON_DOWNLOAD_RUN")
            download_run_button: ui.button = user.find(marker="DIALOG_BUTTON_DOWNLOAD_RUN").elements.pop()
            assert download_run_button.enabled, "Download button should be enabled before downloading"
            user.find(marker="DIALOG_BUTTON_DOWNLOAD_RUN").click()
            await assert_notified(user, "Downloading ...", 30)
    
            # Step 6: Check download completes, QuPath project created, and QuPath launched
            await assert_notified(user, "Download and QuPath project creation completed.", 60 * 5)
            print_directory_structure(tmp_path, "execute")
    
            # Check for directory layout as expected
            run_dir = tmp_path / run.run_id
            assert run_dir.is_dir(), f"Expected run directory {run_dir} not found"
    
            subdirs = [d for d in run_dir.iterdir() if d.is_dir()]
            assert len(subdirs) == 3, f"Expected three subdirectories in {run_dir}, but found {len(subdirs)}"
    
            input_dir = run_dir / "input"
            assert input_dir.is_dir(), f"Expected input directory {input_dir} not found"
    
            results_dir = run_dir / SPOT_0_FILENAME.replace(".tiff", "")
            assert results_dir.is_dir(), f"Expected run results directory {results_dir} not found"
    
            qupath_dir = run_dir / "qupath"
            assert qupath_dir.is_dir(), f"Expected QuPath directory {qupath_dir} not found"
    
            # Check for input file having been downloaded
            input_file = input_dir / SPOT_0_FILENAME
            assert input_file.exists(), f"Expected input file {input_file} not found"
            assert input_file.stat().st_size == SPOT_0_FILESIZE, (
                f"Expected input file size {SPOT_0_FILESIZE}, but got {input_file.stat().st_size}"
            )
    
            # Check for files in the results directory
            files_in_results_dir = list(results_dir.glob("*"))
            expected_count = len(SPOT_0_EXPECTED_RESULT_FILES)
>           assert len(files_in_results_dir) == expected_count, (
                f"Expected {expected_count} files in {results_dir}, but found {len(files_in_results_dir)}: "
                f"{[f.name for f in files_in_results_dir]}"
            )
E           AssertionError: Expected 12 files in .../pytest-of-runner/pytest-21/test_gui_run_qupath_install_to0/b197ab65-0be1-488c-ad2e-68ab1b6b2603/8fafc17d-a5cc-4e9d-a982-030b1486ca88, but found 14: ['cell_classification_geojson_polygons.json', 'cell_classification_parquet_polygons.parquet', 'tissue_qc_csv_class_information.csv', 'readout_generation_slide_readouts.csv', 'tissue_segmentation_segmentation_map_image.tiff', 'tissue_segmentation_geojson_polygons.json', 'readout_generation_cell_readouts.csv', 'tissue_segmentation_csv_class_information.csv', 'tissue_qc_geojson_polygons.json', 'tissue_qc_parquet_polygons.parquet', 'tissue_segmentation_parquet_polygons.parquet', 'cell_detection_parquet_centers.parquet', 'cell_detection_parquet_polygons.parquet', 'tissue_qc_segmentation_map_image.tiff']
E           assert 14 == 12
E            +  where 14 = len([PosixPath('.../pytest-of-runner/pytest-21/test_gui_run_qupath_install_to0/b197ab65-0be1-488c-ad2e-68ab1b6b2603/8fafc17d-a5cc-4e9d-a982-030b1486ca88/cell_classification_geojson_polygons.json'), PosixPath('.../pytest-of-runner/pytest-21/test_gui_run_qupath_install_to0/b197ab65-0be1-488c-ad2e-68ab1b6b2603/8fafc17d-a5cc-4e9d-a982-030b1486ca88/cell_classification_parquet_polygons.parquet'), PosixPath('.../pytest-of-runner/pytest-21/test_gui_run_qupath_install_to0/b197ab65-0be1-488c-ad2e-68ab1b6b2603/8fafc17d-a5cc-4e9d-a982-030b1486ca88/tissue_qc_csv_class_information.csv'), PosixPath('.../pytest-of-runner/pytest-21/test_gui_run_qupath_install_to0/b197ab65-0be1-488c-ad2e-68ab1b6b2603/8fafc17d-a5cc-4e9d-a982-030b1486ca88/readout_generation_slide_readouts.csv'), PosixPath('.../pytest-of-runner/pytest-21/test_gui_run_qupath_install_to0/b197ab65-0be1-488c-ad2e-68ab1b6b2603/8fafc17d-a5cc-4e9d-a982-030b1486ca88/tissue_segmentation_segmentation_map_image.tiff'), PosixPath('.../pytest-of-runner/pytest-21/test_gui_run_qupath_install_to0/b197ab65-0be1-488c-ad2e-68ab1b6b2603/8fafc17d-a5cc-4e9d-a982-030b1486ca88/tissue_segmentation_geojson_polygons.json'), ...])

.../aignostics/qupath/gui_test.py:261: AssertionError

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[aig-hannes]

Failing tests are unrelated