Add code coverage analysis to CI workflow

[krystophny]

User description

Summary

• Adds comprehensive code coverage analysis to the CI workflow
• Implements coverage reporting similar to fortfront's setup
• Provides visibility into test coverage for better quality assurance

Changes

• New test-with-coverage job: Dedicated job for Ubuntu/GCC-12 with coverage instrumentation
• Coverage generation: Uses lcov to capture coverage data with branch coverage enabled
• GitHub integration: Converts coverage to Cobertura XML for GitHub Actions compatibility
• Coverage reporting: Uses insightsengineering/coverage-action for detailed reports
• PR checks: Creates coverage/project and coverage/patch checks with 50% thresholds
• Artifact storage: Uploads coverage reports for review and historical tracking

Additional fixes

• Fixed line truncation error in fluff_diagnostics XML formatting

Test plan

• CI workflow runs successfully on this PR
• Coverage report is generated and visible in PR comments
• Coverage checks appear in the PR status
• Artifacts are uploaded correctly

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PR Type

Enhancement, Tests

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Description

• Add comprehensive code coverage analysis to CI workflow

• Implement coverage reporting with GitHub integration

• Fix XML formatting line truncation error

• Create coverage checks with 50% thresholds

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Diagram Walkthrough

flowchart LR
  A["Test with Coverage Job"] --> B["Generate LCOV Data"]
  B --> C["Convert to Cobertura XML"]
  C --> D["Coverage Action Report"]
  D --> E["GitHub Coverage Checks"]
  E --> F["Upload Coverage Artifacts"]

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File Walkthrough

	Relevant files
Enhancement	ci.yml Add comprehensive coverage analysis workflow                          .github/workflows/ci.yml Add new test-with-coverage job with Ubuntu/GCC-12 Implement LCOV coverage generation with branch coverage Add Cobertura XML conversion for GitHub Actions compatibility Create coverage checks for project and patch thresholds (50%) Upload coverage artifacts and integrate with existing workflow dependencies +180/-3
Bug fix	fluff_diagnostics.f90 Fix XML format string line truncation                                        src/fluff_diagnostics/fluff_diagnostics.f90 Fix line truncation error in XML formatting Split long format string across multiple lines with continuation characters Maintain same functionality with improved readability +7/-3

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[qodo-code-review]

CI Feedback 🧐

(Feedback updated until commit 4a3fae4)

A test triggered by this PR failed. Here is an AI-generated analysis of the failure:

Action: Test Suite (windows-latest, 11)

Failed stage: Set up job [❌]

Failure summary: The action failed because it uses a deprecated version of actions/upload-artifact: v3. GitHub has deprecated v3 of the artifact actions and automatically fails requests that use this version.

Relevant error logs: 1: ##[group]Runner Image Provisioner 2: Hosted Compute Agent ... 15: Image Release: https://github.com/actions/runner-images/releases/tag/win22%2F20250727.1 16: ##[endgroup] 17: ##[group]GITHUB_TOKEN Permissions 18: Actions: read 19: Checks: write 20: Contents: write 21: Issues: write 22: Metadata: read 23: Pages: write 24: PullRequests: write 25: ##[endgroup] 26: Secret source: Actions 27: Prepare workflow directory 28: Prepare all required actions 29: Getting action download info 30: ##[error]This request has been automatically failed because it uses a deprecated version of `actions/upload-artifact: v3`. Learn more: https://github.blog/changelog/2024-04-16-deprecation-notice-v3-of-the-artifact-actions/

[qodo-code-review]

PR Reviewer Guide 🔍

Here are some key observations to aid the review process:

⏱️ Estimated effort to review: 4 🔵🔵🔵🔵⚪

🧪 No relevant tests

🔒 No security concerns identified

⚡ Recommended focus areas for review Incorrect Logic The patch coverage calculation simply reuses project coverage instead of calculating actual patch-specific coverage. This makes the patch coverage check meaningless as it will always match project coverage. const patchCoverage = projectCoverage; Resource Usage The hardcoded OMP_NUM_THREADS=24 may not be appropriate for all GitHub Actions runners and could cause resource contention or inefficient resource usage. OMP_NUM_THREADS=24 fpm test --profile debug --flag '-cpp -fprofile-arcs -ftest-coverage -g' Error Handling The coverage report step uses continue-on-error but subsequent steps depend on the cobertura.xml file it generates, which could lead to failures in coverage checks if the report generation fails. continue-on-error: true with:

[qodo-code-review]

PR Code Suggestions ✨

Explore these optional code suggestions:

Category	Suggestion	Impact
Possible issue	Fix incorrect patch coverage calculation The patch coverage is incorrectly set to the same value as project coverage. This defeats the purpose of having separate coverage checks for the entire project versus just the changed lines in the PR. .github/workflows/ci.yml [122] -const patchCoverage = projectCoverage; +// Calculate actual patch coverage from diff +const patchCoverage = calculatePatchCoverage(xml, context); Apply / Chat Suggestion importance[1-10]: 9 __ Why: The suggestion correctly identifies a significant bug where patchCoverage is incorrectly assigned the value of projectCoverage, making the patch coverage check useless and misleading.	High
General	Use dynamic thread count detection The hardcoded OMP_NUM_THREADS=24 may not be appropriate for all runner environments and could cause resource contention or inefficient execution on machines with fewer cores. .github/workflows/ci.yml [65] -OMP_NUM_THREADS=24 fpm test --profile debug --flag '-cpp -fprofile-arcs -ftest-coverage -g' +OMP_NUM_THREADS=$(nproc) fpm test --profile debug --flag '-cpp -fprofile-arcs -ftest-coverage -g' Apply / Chat Suggestion importance[1-10]: 6 __ Why: The suggestion correctly points out that hardcoding OMP_NUM_THREADS is not ideal and proposes a more robust solution using nproc to dynamically set the thread count based on the runner's available cores.	Low
	Add debugging output for failures The script exits with code 1 on failure but the step doesn't have continue-on-error: false explicitly set. Consider adding error handling or making the failure behavior more explicit. .github/workflows/ci.yml [89-92] if [ ! -f "cobertura.xml" ]; then echo "Failed to generate cobertura.xml" + ls -la exit 1 fi Apply / Chat Suggestion importance[1-10]: 3 __ Why: The suggestion proposes adding a debugging command (ls -la) which can be helpful, but it's a minor improvement to an already functional error-checking block.	Low
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[krystophny]

Superseded by PR #4 which includes all coverage analysis work plus complete AST rule implementations