chore: enhance testing CI/CD #117
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WalkthroughThis pull request updates the testing configuration and workflow across the project. In the CI/CD workflow, the Changes
Sequence Diagram(s)sequenceDiagram
participant Dev as Developer
participant CI as CI/CD Pipeline
participant Executor as Test Executor
participant Summary as JUnit Summary Step
participant Uploader as Coverage Uploader
Dev->>CI: Push commit with changes
CI->>Executor: Start Unit-Tests job
Executor->>Executor: Run tests with "pixi run -e ${{ matrix.env }} test -s -vv"
Executor->>Summary: Always execute test-summary step
Summary-->>CI: Produce JUnit test report
CI->>Uploader: Conditionally upload coverage report
Uploader-->>CI: Coverage artifact processed
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Actionable comments posted: 0
🧹 Nitpick comments (2)
config/pytest.ini (1)
63-69: Consider adding more specific warning filters.While the current warning filters are good, consider being more specific about which DeprecationWarnings to ignore.
filterwarnings = - ignore::DeprecationWarning + ignore::DeprecationWarning:pytest.* + ignore::DeprecationWarning:_pytest.* # Add specific warning messages to ignore here ignore::UserWarning:pydicom.*.github/workflows/ci-cd.yml (1)
44-50: Fix trailing spaces in YAML.Remove trailing spaces to maintain consistent formatting.
- name: JUnit Test Summary id: pytest-summary uses: test-summary/action@v2 - with: + with: paths: .cache/test-results/**/*.xml show: "fail,skip" if: always()🧰 Tools
🪛 YAMLlint (1.35.1)
[error] 47-47: trailing spaces
(trailing-spaces)
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⛔ Files ignored due to path filters (1)
pixi.lockis excluded by!**/*.lock
📒 Files selected for processing (4)
.github/workflows/ci-cd.yml(2 hunks)config/pytest.ini(1 hunks)pyproject.toml(1 hunks)tests/test_feature_extraction.py(1 hunks)
🧰 Additional context used
🪛 YAMLlint (1.35.1)
.github/workflows/ci-cd.yml
[error] 43-43: trailing spaces
(trailing-spaces)
[error] 47-47: trailing spaces
(trailing-spaces)
⏰ Context from checks skipped due to timeout of 90000ms (8)
- GitHub Check: Unit-Tests (windows-latest, py312)
- GitHub Check: Unit-Tests (windows-latest, py311)
- GitHub Check: Unit-Tests (windows-latest, py310)
- GitHub Check: Unit-Tests (macos-14, py312)
- GitHub Check: Unit-Tests (macos-14, py311)
- GitHub Check: Unit-Tests (macos-14, py310)
- GitHub Check: Unit-Tests (macos-latest, py311)
- GitHub Check: Unit-Tests (macos-latest, py310)
🔇 Additional comments (7)
tests/test_feature_extraction.py (2)
47-57: LGTM! Improved fixture management with module scope and safer cleanup.The changes enhance test reliability by:
- Using module scope to reduce fixture setup/teardown overhead
- Adding existence check before cleanup to prevent errors during parallel test execution
58-68: LGTM! Consistent fixture improvements applied.The same improvements have been correctly applied to the lung4DMetadataPath fixture.
config/pytest.ini (3)
1-11: LGTM! Well-structured basic configuration.The configuration properly sets:
- Minimum pytest version for compatibility
- Cache directory for test artifacts
- Progress-style console output for better visibility
12-45: LGTM! Comprehensive test execution configuration.The addopts section effectively configures:
- Detailed test output with --showlocals
- Coverage reporting in multiple formats
- Parallel test execution with load grouping
- JUnit XML reporting for CI integration
51-61: LGTM! Clear test discovery patterns.Well-defined patterns for:
- Test paths
- Excluded directories
- Test file naming conventions
pyproject.toml (1)
76-78: LGTM! Simplified test execution configuration.Test command now properly uses the centralized pytest.ini configuration, making it easier to maintain and modify test settings.
.github/workflows/ci-cd.yml (1)
32-34: LGTM! Enhanced test execution visibility.Added verbosity flags (-s -vv) to improve test output in CI logs.
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #117 +/- ##
===========================================
+ Coverage 48.12% 83.39% +35.26%
===========================================
Files 34 34
Lines 1492 1734 +242
===========================================
+ Hits 718 1446 +728
+ Misses 774 288 -486 ☔ View full report in Codecov by Sentry. |
copied over the pytest config from med-imagetools
can easily view errors in gha during pytest without going into the action logs
small fix to the fixtures that delete temporary paths and are used by multiple tests (can cause errors during parallel runs)
also cleanups for each PRs gha caches
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