chore(deps): bump nicegui to 3.4.0 (was 3.3.1) and urllib3 to 2.6.1 (…

[helmut-hoffer-von-ankershoffen]

…was 2.6.0)

[codecov]

❌ 1 Tests Failed:

Tests completed	Failed	Passed	Skipped
464	1	463	3

View the top 1 failed test(s) by shortest run time

::tests.aignostics.application.cli_test

Stack Traces | 0s run time

Using pytest.skip outside of a test will skip the entire module. If that's your intention, pass `allow_module_level=True`. If you want to skip a specific test or an entire class, use the @pytest.mark.skip or @pytest.mark.skipif decorators.

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[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

[github-actions]

Claude finished @helmut-hoffer-von-ankershoffen's task —— View job

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Analysis Complete: PR #326 and Test Failure Investigation

I've completed my analysis of this dependency update PR and the associated test failure.

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Executive Summary

PR #326 Dependency Updates: ✅ Safe and appropriate
Test Failure: ❌ Pre-existing bug - NOT caused by this PR
CI/CD Process: ⚠️ Critical issue - PR merged with failing tests

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Detailed Analysis

✅ Dependency Updates Are Safe

Changes in this PR:

• nicegui: 3.3.1 → 3.4.0 (minor version bump)
• urllib3: 2.6.0 → 2.6.1 (patch version bump)

Both are standard maintenance updates with no breaking changes. The updates themselves are not the cause of the test failure.

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❌ Pre-existing Syntax Error in Test File

Location: tests/aignostics/application/cli_test.py:1029

Current (BROKEN):

1029:    # Step 5: Remove the random numberresult.output)
1030:    assert "random" in metadata_with_random, "Random field should be present in metadata"
1031:    assert metadata_with_random["random"] == random_value, f"Random value should be {random_value}"
1032:
1033:    # Step 5: Remove the random number
1034:    del updated_metadata["random"]

Issue Analysis:

1. Line 1029 has corrupted syntax: comment + code fragment concatenated
2. Lines 1030-1031 are duplicate assertions from earlier in the same test (around line 1010-1012)
3. Line 1033 is the correct comment
4. This suggests a bad merge or copy-paste error

Root Cause: Git history shows this error existed in commit 0ac77c4 (before PR #326). This PR only touched pyproject.toml and uv.lock.

Why pytest fails:

Using pytest.skip outside of a test will skip the entire module.

This error occurs because the syntax error on line 1029 causes pytest to fail during module import/collection, before any tests run.

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🚨 Critical: Why Was This PR Merged?

Per repository standards (CLAUDE.md lines 27-31):

If you write code yourself, it is a strict requirement to validate your work on completion before you call it done:

• Linting must pass.
• The unit, integration and e2e test suites must pass.
• Auditing must pass.

Medical Device Software Context:
This SDK is FDA/MDR regulated computational pathology software. Test failures are blocking issues - not warnings.

Codecov Report clearly showed:

• ❌ 1 Test Failed
• Module: tests.aignostics.application.cli_test

Process Failure: This PR should have been blocked from merging.

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Recommended Actions

1️⃣ IMMEDIATE: Fix the Syntax Error (Critical Priority)

Required changes to tests/aignostics/application/cli_test.py:

- 1029:    # Step 5: Remove the random numberresult.output)
- 1030:    assert "random" in metadata_with_random, "Random field should be present in metadata"
- 1031:    assert metadata_with_random["random"] == random_value, f"Random value should be {random_value}"
- 1032:
  1033:    # Step 5: Remove the random number

Replace with:

1029:    # Step 5: Remove the random number

Justification: The two assertions on lines 1030-1031 are duplicates - they already appear correctly earlier in the function after the metadata update (around lines 1010-1012). These are remnants from the corruption and should be removed.

2️⃣ Enhance Pre-commit Hooks

Add Python syntax validation:

# .pre-commit-config.yaml
repos:
  - repo: local
    hooks:
      - id: python-syntax-check
        name: Python syntax check
        entry: python -m py_compile
        language: system
        types: [python]
        pass_filenames: true

3️⃣ Strengthen CI/CD

Add early syntax validation in CI:

# .github/workflows/_test.yml
- name: Validate Python syntax
  run: |
    echo "Checking Python syntax in test files..."
    find tests -name "*.py" -print0 | xargs -0 -n1 python -m py_compile
    echo "✓ All test files have valid syntax"

GitHub Branch Protection:

• Require all CI checks to pass before merge
• Review why this PR bypassed the failing test requirement

4️⃣ Code Review Process

Add to PR review checklist:

• All CI checks are green (no failing tests)
• For dependency updates: Verify test suite runs successfully
• For medical device software: Zero tolerance for test failures

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Test Marker Verification ✅

Per CLAUDE.md requirements, I verified the failing test has proper markers:

@pytest.mark.e2e
@pytest.mark.timeout(timeout=120)
@pytest.mark.skipif(...)
@pytest.mark.sequential
def test_cli_run_dump_and_update_item_custom_metadata(runner: CliRunner) -> None:

Markers are correct. The test would run in CI if not for the syntax error preventing module import.

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Verification Commands

To verify the fix works:

# 1. Check syntax is valid
python -m py_compile tests/aignostics/application/cli_test.py

# 2. Run the specific test
uv run pytest tests/aignostics/application/cli_test.py::test_cli_run_dump_and_update_item_custom_metadata -v

# 3. Run all tests in the module
uv run pytest tests/aignostics/application/cli_test.py -v

# 4. Verify linting passes
make lint

# 5. Run full test suite
make test

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Offer to Create Fix PR

I can create a fix PR immediately with:

Branch name: fix/cli-test-syntax-error-line-1029

Changes:

1. Fix corrupted line 1029 in cli_test.py
2. Remove duplicate assertions (lines 1030-1031)
3. Add Python syntax check to pre-commit hooks
4. Add CI syntax validation step

PR Labels:

• bug (syntax error)
• priority:critical (blocking test execution)
• skip:test_long_running (fix doesn't need long-running tests)

Would you like me to create this fix PR now?

Reply with "yes" or "create the fix" and I'll implement the solution immediately.

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Conclusion

For PR #326 (This PR - Already Merged)

✅ Dependency updates are safe and appropriate
✅ No issues with nicegui 3.4.0 or urllib3 2.6.1
❌ Should not have merged with failing tests

For the Codebase

❌ Critical syntax error exists (pre-existing, not from this PR)
⚠️ CI/CD process needs strengthening for medical device compliance
✅ Test markers and structure are correct

Next Steps: Fix the syntax error immediately and strengthen merge controls to prevent similar issues in regulated software.

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