chore: Prep branch for HETA 1.3.0 release

[ari-nz]

No description provided.

[sonarqubecloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

[Copilot]

Pull request overview

Prepares the test suite constants for an upcoming HETA (he-tme) 1.3.0 cycle by updating which application version tests target in staging and by normalizing the ordering of expected output artifact metadata used by E2E tests.

Changes:

• Reordered SPOT_0_EXPECTED_RESULT_FILES / SPOT_1_EXPECTED_RESULT_FILES entries (no content changes, ordering only).
• Updated the staging HETA_APPLICATION_VERSION constant to 1.3.0-rc.1.

[codecov]

❌ 3 Tests Failed:

Tests completed	Failed	Passed	Skipped
875	3	872	19

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

tests.aignostics.application.cli_test::test_cli_application_dump_schemata

Stack Traces | 0.825s run time

runner = <typer.testing.CliRunner object at 0x7f550089e8b0>
tmp_path = PosixPath('.../pytest-18/popen-gw0/test_cli_application_dump_sche0')
record_property = <function record_property.<locals>.append_property at 0x7f5500159d20>

    @pytest.mark.e2e
    @pytest.mark.timeout(timeout=60)
    def test_cli_application_dump_schemata(runner: CliRunner, tmp_path: Path, record_property) -> None:
        """Check application dump schemata works as expected."""
        record_property("tested-item-id", "SPEC-APPLICATION-SERVICE")
        result = runner.invoke(
            cli,
            [
                "application",
                "dump-schemata",
                HETA_APPLICATION_ID,
                "--application-version",
                HETA_APPLICATION_VERSION,
                "--destination",
                str(tmp_path),
                "--zip",
            ],
        )
>       assert result.exit_code == 0
E       assert 1 == 0
E        +  where 1 = <Result SystemExit(1)>.exit_code

.../aignostics/application/cli_test.py:240: AssertionError

tests.aignostics.application.gui_test::test_gui_cli_submit_to_run_result_delete

Stack Traces | 5.51s run time

user = <nicegui.testing.user.User object at 0x7f4bfb608050>
runner = <typer.testing.CliRunner object at 0x7f4bf98c1450>
silent_logging = None
record_property = <function record_property.<locals>.append_property at 0x7f4c18499fe0>

    @pytest.mark.e2e
    @pytest.mark.long_running
    @pytest.mark.flaky(retries=2, delay=5, only_on=[AssertionError])
    @pytest.mark.timeout(timeout=60 * 5)
    @pytest.mark.sequential
    async def test_gui_cli_submit_to_run_result_delete(
        user: User,
        runner: CliRunner,
        silent_logging: None,
        record_property,
    ) -> None:
        """Test that the user can submit a run via the CLI up to deleting the run results."""
        record_property("tested-item-id", "SPEC-APPLICATION-SERVICE, SPEC-GUI-SERVICE")
    
        with tempfile.TemporaryDirectory() as tmpdir:
            tmp_path = Path(tmpdir)
            application = Service().application(HETA_APPLICATION_ID)
    
            # Submit run
            csv_content = (
                "external_id;checksum_base64_crc32c;resolution_mpp;width_px;height_px;staining_method;tissue;disease;"
            )
            csv_content += "platform_bucket_url\n"
            csv_content += ";5onqtA==;0.26268186053789266;7447;7196;H&E;LUNG;LUNG_CANCER;gs:.../bucket/test"
            csv_path = tmp_path / "dummy.csv"
            csv_path.write_text(csv_content)
            result = await to_thread(
                runner.invoke,
                cli,
                [
                    "application",
                    "run",
                    "submit",
                    HETA_APPLICATION_ID,
                    str(csv_path),
                    "--application-version",
                    HETA_APPLICATION_VERSION,
                    "--note",
                    "test_gui_cli_submit_to_run_result_delete",
                    "--tags",
                    "test_gui_cli_submit_to_run_result_delete",
                    "--deadline",
                    (datetime.now(tz=UTC) + timedelta(minutes=5)).isoformat(),
                    "--gpu-type",
                    PIPELINE_GPU_TYPE,
                ],
            )
>           assert result.exit_code == 0
E           assert 1 == 0
E            +  where 1 = <Result SystemExit(1)>.exit_code

.../aignostics/application/gui_test.py:130: AssertionError

View the full list of 1 ❄️ flaky test(s)

tests.aignostics.application.cli_test::test_cli_application_list_verbose

Flake rate in main: 8.82% (Passed 31 times, Failed 3 times)

Stack Traces | 1.42s run time

runner = <typer.testing.CliRunner object at 0x7f55009e68b0>
record_property = <function record_property.<locals>.append_property at 0x7f55008483b0>

    @pytest.mark.e2e
    @pytest.mark.scheduled
    @pytest.mark.timeout(timeout=60)
    def test_cli_application_list_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", "--verbose"])
        assert result.exit_code == 0
        assert HETA_APPLICATION_ID in normalize_output(result.output)
>       assert HETA_APPLICATION_VERSION in normalize_output(result.output)
E       assert '1.3.0-rc.1' in 'Available Applications:================================================================================Application ID: he-tmeName: Atlas H&E-TMERegulatory Classes: Available Versions:  - 1.2.0 (2026-05-08 19:02:28.875257+00:00)    Changelog: ## HETA Changelog - Version 1.2.0*Release Date: May 2026*### Features* Added support for `.mrxs` (Mirax) image files* Exposed GeoParquet outputs as user-facing artifacts* Added prostate, pancreatic, and stomach cancer types* Annotated and cleaned up pipeline components### Fixes* Fixed cell assignment in gaps between tissue regions for cell-to-cell statistics* Computed tissue areas from polygons; removed the "No Tissue" category* Fixed rare crash during processing cluster startup when nodes are replaced* Fixed Python dependency and compatibility issues* Fixed security dependency pins and regenerated lock files### Support* Dedicated support channel: <support@aignostics.com>* Extensive documentation available at platform.aignostics.com    Artifacts: 1 input(s), 14 output(s)  - 1.1.1 (2026-04-27 21:24:17.093125+00:00)    Changelog: ## HETA Changelog - Version 1.1.1*Release Date: April 2026*### Bug Fixes & Improvements* Fixed incorrect content ty...tailed Readouts that quantify the analysis results.    This internal variant supports application-specific configuration via ``custom_metadata.application.he-tme-internal``.--------------------------------------------------------------------------------Application ID: test-appName: Test ApplicationRegulatory Classes: demo, RuOAvailable Versions:  - 1.0.0 (2026-04-27 20:44:52.814231+00:00)    Changelog: Release test-app v1.0.0    Artifacts: 1 input(s), 6 output(s)  - 0.99.0 (2025-11-24 16:15:50.072582+00:00)    Changelog:     Artifacts: 2 input(s), 6 output(s)  - 0.0.6 (2025-11-14 17:29:33.275163+00:00)    Changelog: test-app changes that align internal services    Artifacts: 1 input(s), 6 output(s)Description:  This is the test application with two algorithms: TissueQc and Tissue Segmentation--------------------------------------------------------------------------------Application ID: validation-appName: validation-appRegulatory Classes: Available Versions:  - 0.1.0 (2026-01-19 12:38:16.573922+00:00)    Changelog:      Artifacts: 1 input(s), 2 output(s)Description:  This is the validation application--------------------------------------------------------------------------------'
E        +  where 'Available Applications:================================================================================Application ID: he-tmeName: Atlas H&E-TMERegulatory Classes: Available Versions:  - 1.2.0 (2026-05-08 19:02:28.875257+00:00)    Changelog: ## HETA Changelog - Version 1.2.0*Release Date: May 2026*### Features* Added support for `.mrxs` (Mirax) image files* Exposed GeoParquet outputs as user-facing artifacts* Added prostate, pancreatic, and stomach cancer types* Annotated and cleaned up pipeline components### Fixes* Fixed cell assignment in gaps between tissue regions for cell-to-cell statistics* Computed tissue areas from polygons; removed the "No Tissue" category* Fixed rare crash during processing cluster startup when nodes are replaced* Fixed Python dependency and compatibility issues* Fixed security dependency pins and regenerated lock files### Support* Dedicated support channel: <support@aignostics.com>* Extensive documentation available at platform.aignostics.com    Artifacts: 1 input(s), 14 output(s)  - 1.1.1 (2026-04-27 21:24:17.093125+00:00)    Changelog: ## HETA Changelog - Version 1.1.1*Release Date: April 2026*### Bug Fixes & Improvements* Fixed incorrect content ty...tailed Readouts that quantify the analysis results.    This internal variant supports application-specific configuration via ``custom_metadata.application.he-tme-internal``.--------------------------------------------------------------------------------Application ID: test-appName: Test ApplicationRegulatory Classes: demo, RuOAvailable Versions:  - 1.0.0 (2026-04-27 20:44:52.814231+00:00)    Changelog: Release test-app v1.0.0    Artifacts: 1 input(s), 6 output(s)  - 0.99.0 (2025-11-24 16:15:50.072582+00:00)    Changelog:     Artifacts: 2 input(s), 6 output(s)  - 0.0.6 (2025-11-14 17:29:33.275163+00:00)    Changelog: test-app changes that align internal services    Artifacts: 1 input(s), 6 output(s)Description:  This is the test application with two algorithms: TissueQc and Tissue Segmentation--------------------------------------------------------------------------------Application ID: validation-appName: validation-appRegulatory Classes: Available Versions:  - 0.1.0 (2026-01-19 12:38:16.573922+00:00)    Changelog:      Artifacts: 1 input(s), 2 output(s)Description:  This is the validation application--------------------------------------------------------------------------------' = normalize_output('Available Applications:\n================================================================================\nApplication ID: he-tme\nName: Atlas H&E-TME\nRegulatory Classes: \nAvailable Versions:\n  - 1.2.0 (2026-05-08 19:02:28.875257+00:00)\n    Changelog: ## HETA Changelog - Version 1.2.0\n*Release Date: May 2026*\n\n### Features\n\n* Added support for `.mrxs` (Mirax) image files\n* Exposed GeoParquet outputs as user-facing artifacts\n* Added prostate, pancreatic, and stomach cancer types\n* Annotated and cleaned up pipeline components\n\n### Fixes\n\n* Fixed cell assignment in gaps between tissue regions for cell-to-cell statistics\n* Computed tissue areas from polygons; removed the "No Tissue" category\n* Fixed rare crash during processing cluster startup when nodes are replaced\n* Fixed Python dependency and compatibility issues\n* Fixed security dependency pins and regenerated lock files\n\n### Support\n\n* Dedicated support channel: <support@aignostics.com>\n* Extensive documentation available at platform.aignostics.com\n    Artifacts: 1 input(s), 14 output(s)\n  - 1.1.1 (2026-04-27 21:24:17.093125+00:00)\n    Changelog: ## HETA Changelog - Version 1.1.1\n*Release Date: Apr...his internal variant supports application-specific configuration via ``custom_metadata.application.he-tme-internal``.\n--------------------------------------------------------------------------------\nApplication ID: test-app\nName: Test Application\nRegulatory Classes: demo, RuO\nAvailable Versions:\n  - 1.0.0 (2026-04-27 20:44:52.814231+00:00)\n    Changelog: Release test-app v1.0.0\n    Artifacts: 1 input(s), 6 output(s)\n  - 0.99.0 (2025-11-24 16:15:50.072582+00:00)\n    Changelog: \n    Artifacts: 2 input(s), 6 output(s)\n  - 0.0.6 (2025-11-14 17:29:33.275163+00:00)\n    Changelog: test-app changes that align internal services\n    Artifacts: 1 input(s), 6 output(s)\nDescription:\n  This is the test application with two algorithms: TissueQc and Tissue Segmentation\n--------------------------------------------------------------------------------\nApplication ID: validation-app\nName: validation-app\nRegulatory Classes: \nAvailable Versions:\n  - 0.1.0 (2026-01-19 12:38:16.573922+00:00)\n    Changelog:  \n    Artifacts: 1 input(s), 2 output(s)\nDescription:\n  This is the validation application\n--------------------------------------------------------------------------------\n')
E        +    where 'Available Applications:\n================================================================================\nApplication ID: he-tme\nName: Atlas H&E-TME\nRegulatory Classes: \nAvailable Versions:\n  - 1.2.0 (2026-05-08 19:02:28.875257+00:00)\n    Changelog: ## HETA Changelog - Version 1.2.0\n*Release Date: May 2026*\n\n### Features\n\n* Added support for `.mrxs` (Mirax) image files\n* Exposed GeoParquet outputs as user-facing artifacts\n* Added prostate, pancreatic, and stomach cancer types\n* Annotated and cleaned up pipeline components\n\n### Fixes\n\n* Fixed cell assignment in gaps between tissue regions for cell-to-cell statistics\n* Computed tissue areas from polygons; removed the "No Tissue" category\n* Fixed rare crash during processing cluster startup when nodes are replaced\n* Fixed Python dependency and compatibility issues\n* Fixed security dependency pins and regenerated lock files\n\n### Support\n\n* Dedicated support channel: <support@aignostics.com>\n* Extensive documentation available at platform.aignostics.com\n    Artifacts: 1 input(s), 14 output(s)\n  - 1.1.1 (2026-04-27 21:24:17.093125+00:00)\n    Changelog: ## HETA Changelog - Version 1.1.1\n*Release Date: Apr...his internal variant supports application-specific configuration via ``custom_metadata.application.he-tme-internal``.\n--------------------------------------------------------------------------------\nApplication ID: test-app\nName: Test Application\nRegulatory Classes: demo, RuO\nAvailable Versions:\n  - 1.0.0 (2026-04-27 20:44:52.814231+00:00)\n    Changelog: Release test-app v1.0.0\n    Artifacts: 1 input(s), 6 output(s)\n  - 0.99.0 (2025-11-24 16:15:50.072582+00:00)\n    Changelog: \n    Artifacts: 2 input(s), 6 output(s)\n  - 0.0.6 (2025-11-14 17:29:33.275163+00:00)\n    Changelog: test-app changes that align internal services\n    Artifacts: 1 input(s), 6 output(s)\nDescription:\n  This is the test application with two algorithms: TissueQc and Tissue Segmentation\n--------------------------------------------------------------------------------\nApplication ID: validation-app\nName: validation-app\nRegulatory Classes: \nAvailable Versions:\n  - 0.1.0 (2026-01-19 12:38:16.573922+00:00)\n    Changelog:  \n    Artifacts: 1 input(s), 2 output(s)\nDescription:\n  This is the validation application\n--------------------------------------------------------------------------------\n' = <Result okay>.output

.../aignostics/application/cli_test.py:188: AssertionError

To view more test analytics, go to the Test Analytics Dashboard
_{📋 Got 3 mins? Take this short survey to help us improve Test Analytics.}