chore: Update rust CI #215
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WalkthroughThe pull request introduces several modifications to the GitHub Actions workflow for Rust, aimed at streamlining the continuous integration (CI) process. Key changes include updating the toolchain installation method, simplifying linting and testing commands, and enhancing job dependencies. The workflow now directly invokes tools like Changes
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Actionable comments posted: 2
🧹 Outside diff range and nitpick comments (1)
.github/workflows/rust.yml (1)
Line range hint
91-95: Consider optimizing environment variable configurationThe environment variables are duplicated between fast and full test runs. Consider moving common environment variables to the job level.
Here's a suggested refactor:
Testing: needs: [Formatting, Linting] runs-on: ubuntu-latest + env: + TEST_UTA_DATABASE_URL: postgres://uta_admin:[email protected]/uta + TEST_UTA_DATABASE_SCHEMA: uta_20210129 + TEST_SEQREPO_CACHE_MODE: read + TEST_SEQREPO_CACHE_PATH: tests/data/seqrepo_cache.fasta strategy: matrix: include: - label: fast - label: full # ... rest of the job configuration ... steps: - name: Run cargo-llvm-cov with fast tests run: cargo llvm-cov --lcov --output-path lcov.info -- --test-threads 1 - env: - TEST_UTA_DATABASE_URL: postgres://uta_admin:[email protected]/uta - TEST_UTA_DATABASE_SCHEMA: uta_20210129 - TEST_SEQREPO_CACHE_MODE: read - TEST_SEQREPO_CACHE_PATH: tests/data/seqrepo_cache.fasta if: ${{ matrix.label == 'fast' }} - name: Run cargo-test with full tests run: "cargo test --release -- --include-ignored" - env: - TEST_UTA_DATABASE_URL: postgres://uta_admin:[email protected]/uta - TEST_UTA_DATABASE_SCHEMA: uta_20210129 - TEST_SEQREPO_CACHE_MODE: read - TEST_SEQREPO_CACHE_PATH: tests/data/seqrepo_cache.fasta if: ${{ matrix.label == 'full' }}Also applies to: 100-104
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📒 Files selected for processing (1)
.github/workflows/rust.yml(4 hunks)
🧰 Additional context used
🪛 actionlint (1.7.4)
.github/workflows/rust.yml
20-20: unexpected key "components" for "step" section. expected one of "continue-on-error", "env", "id", "if", "name", "run", "shell", "timeout-minutes", "uses", "with", "working-directory"
(syntax-check)
35-35: unexpected key "components" for "step" section. expected one of "continue-on-error", "env", "id", "if", "name", "run", "shell", "timeout-minutes", "uses", "with", "working-directory"
(syntax-check)
🔇 Additional comments (3)
.github/workflows/rust.yml (3)
41-41: Good improvement in job dependencies
Adding explicit dependencies on Formatting and Linting jobs ensures that tests only run after code quality checks pass, which is more efficient.
38-38: Consider removing --no-deps flag from clippy
The --no-deps flag prevents clippy from checking how your code interacts with dependencies, which might miss potential issues in dependency usage patterns.
Let's check if there are any dependency-related lints that might be important:
✅ Verification successful
Keep the --no-deps flag in clippy
Based on the codebase analysis, the dependencies are primarily used for standard functionality and well-maintained crates like:
- Standard library components (std)
- Well-maintained crates (nom, thiserror, serde, etc.)
- Established bioinformatics libraries (bio, seqrepo)
The current usage patterns don't show complex interactions with dependencies that would benefit significantly from clippy's dependency checks. The --no-deps flag helps maintain faster CI runs while still catching important issues in the project's own code.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Search for external dependency usage that might benefit from clippy checks
rg -l "use\s+[a-zA-Z_]+::" --type rust
Length of output: 545
Script:
#!/bin/bash
# Let's check the actual dependency usage patterns to assess potential clippy checks
rg "use\s+[a-zA-Z_]+::" --type rust -A 2
Length of output: 21585
89-90: Verify coverage configuration and test separation
The switch to cargo-llvm-cov is a good improvement as it's more maintained and integrated with LLVM. However, we should ensure:
- Coverage is only collected for relevant code paths
- The separation between fast and full tests is appropriate
Let's check the test organization:
Consider documenting the criteria for fast vs. full tests in the repository's README or CONTRIBUTING guide to help maintainers properly categorize new tests.
Also applies to: 99-99
✅ Verification successful
Test organization is well-structured with appropriate separation
The codebase shows a clear organization of tests with proper separation:
- Only one test is marked as
#[ignore](insrc/mapper/variant.rs), which is a full database test (dnah11_db_snp_full) - Tests are properly organized in test modules with
#[cfg(test)] - The README clearly documents test execution modes:
- Fast tests run by default with
cargo test - Full tests (including ignored ones) require
--include-ignoredflag - Database tests have proper configuration via environment variables
- Fast tests run by default with
The current coverage configuration with cargo llvm-cov running fast tests is appropriate as it:
- Focuses on the core functionality without long-running database tests
- Maintains CI performance while providing meaningful coverage data
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check test attributes to verify fast vs full test separation
rg -B 2 -A 2 "#\[ignore\]" --type rust
# Check if we have any long-running tests that should be marked as ignored
rg -l "test\s+fn\s+" --type rust | xargs rg "tokio::time::sleep|thread::sleep"
Length of output: 315
Script:
#!/bin/bash
# Let's check the test organization more comprehensively
# Find all test functions and their attributes
rg -B 2 "fn\s+\w+(_test|test_\w+|\w+_tests?)\b" --type rust
# Look for any test configuration or test utilities
fd -e rs | xargs rg "mod\s+tests?\b|#\[cfg\(test\)\]" -B 1 -A 3
# Check if there are any test-related constants or configurations
rg "const.*TEST|TEST.*const" --type rust
# Look for any test documentation
fd "README|CONTRIBUTING" | xargs rg -i "test"
Length of output: 5911
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Actionable comments posted: 1
📜 Review details
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📒 Files selected for processing (1)
.github/workflows/rust.yml(4 hunks)
🔇 Additional comments (4)
.github/workflows/rust.yml (4)
19-24: LGTM! Formatting job changes look good
The toolchain installation is properly configured and the formatting check is appropriately simplified.
43-43: LGTM! Good job adding job dependencies
Adding explicit dependencies on Formatting and Linting jobs ensures proper workflow sequencing.
85-87: Verify coverage configuration after switching to llvm-cov
The switch from tarpaulin to llvm-cov looks good, but let's verify the coverage configuration is complete.
Consider adding a coverage configuration file (e.g., codecov.yml) to:
- Set coverage targets
- Configure coverage thresholds
- Specify paths to include/exclude
Also applies to: 91-101
✅ Verification successful
Let me check the actual coverage configuration in the rust.yml file to see how llvm-cov is being used.
Let me check the content of the codecov.yml file to verify if it has proper configuration.
Coverage configuration is properly set up with llvm-cov
The switch from tarpaulin to llvm-cov is complete and well-configured:
- Proper llvm-cov setup in rust.yml with lcov output format
- Codecov integration is configured correctly
- codecov.yml exists with appropriate settings:
- Coverage range set to 70-90%
- Patch status disabled
- Pull request comments configured for diff and files
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check if we have any existing coverage configuration that needs to be updated
echo "Checking for coverage-related configuration files..."
fd -g '*coverage*' -g '*codecov*' -g '*.lcov*'
# Check if there are any coverage-related CI configurations in other workflows
echo "Checking for coverage-related CI configurations..."
rg -l 'coverage|tarpaulin|llvm-cov' .github/workflows/
Length of output: 509
Script:
#!/bin/bash
# Check the coverage configuration in rust.yml
echo "Checking rust.yml for coverage configuration..."
cat .github/workflows/rust.yml
# Also check for any codecov configuration in the root
echo -e "\nChecking for codecov.yml in root..."
ls -la codecov.yml 2>/dev/null || echo "No codecov.yml found"
Length of output: 3327
Script:
#!/bin/bash
# Check the content of codecov.yml
echo "Checking codecov.yml configuration..."
cat codecov.yml
Length of output: 928
Line range hint 1-115: Verify workflow triggers and environment consistency
The overall workflow structure looks good, but let's verify the configuration is complete.
Consider adding:
- A rust-toolchain.toml file to ensure consistent toolchain configuration across local and CI environments
- Documentation in the README about the CI workflow and required components
| uses: dtolnay/rust-toolchain@stable | ||
| with: | ||
| toolchain: stable | ||
| override: true | ||
| components: clippy | ||
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| - name: Lint with clippy | ||
| uses: actions-rs/clippy-check@v1 | ||
| with: | ||
| token: ${{ secrets.GITHUB_TOKEN }} | ||
| run: cargo clippy --no-deps # --all-targets --all-features |
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💡 Codebase verification
🛠️ Refactor suggestion
Restore comprehensive clippy checks for better coverage
The codebase has multiple components that justify using --all-targets --all-features:
- A benchmark target (
translate_cds) - Extensive test dependencies indicating significant test code
- Multiple source modules that could have conditional compilation
-run: cargo clippy --no-deps # --all-targets --all-features
+run: cargo clippy --no-deps --all-targets --all-features🔗 Analysis chain
Consider restoring comprehensive clippy checks
The simplified clippy command removes --all-targets --all-features flags (as seen in the comment). This might reduce the scope of linting coverage.
Let's check if these flags are important for your codebase:
Consider restoring these flags for comprehensive checking:
-run: cargo clippy --no-deps # --all-targets --all-features
+run: cargo clippy --no-deps --all-targets --all-featuresThe previous output showed we have benches, lib, and multiple source files. Let's examine the Cargo.toml to understand the project structure and features better, and specifically look for test files to determine if --all-targets would be beneficial.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check for different target types and features in the project
echo "Checking for different targets (lib, bin, examples, tests)..."
fd -e rs -t f . src/ examples/ tests/ benches/ 2>/dev/null
echo "Checking for feature definitions..."
rg '^\[features\]' -A 5 Cargo.toml
Length of output: 852
Script:
#!/bin/bash
# Let's check the Cargo.toml for targets and dependencies
echo "Checking Cargo.toml for targets and dependencies..."
cat Cargo.toml
# Let's also check for test files specifically
echo -e "\nChecking for test files..."
fd -t f -g '*test*.rs' .
Length of output: 1329
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #215 +/- ##
==========================================
+ Coverage 86.18% 92.20% +6.01%
==========================================
Files 18 18
Lines 7166 11440 +4274
==========================================
+ Hits 6176 10548 +4372
+ Misses 990 892 -98 |
Update actions used in the rust CI, switch from tarpaulin to cargo-llvm-cov
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