refactor(clustering)!: use new DbscanCluster type instead of isize #233
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Actionable comments posted: 0
🧹 Nitpick comments (5)
crates/augurs-clustering/src/lib.rs (3)
42-47: Improve panic message in increment method.The panic message "cluster ID overflow" could be more descriptive to help with debugging.
- Self::Cluster(id) => *id = id.checked_add(1).expect("cluster ID overflow"), + Self::Cluster(id) => *id = id.checked_add(1).expect("maximum cluster ID (4,294,967,295) reached"),
50-60: Document test-only PartialEq implementation.Add documentation to explain why this implementation exists and its test-only purpose.
// Simplify tests by allowing comparisons with i32. +// This implementation allows direct comparison with legacy test vectors that use i32, +// where -1 represents noise and positive numbers represent cluster IDs. #[cfg(test)] impl PartialEq<i32> for DbscanCluster {
209-238: Consider using a more maintainable format for large test vectors.The large test vector could be more maintainable if stored in a separate test data file or formatted using a more readable pattern.
Consider one of these approaches:
- Move the vector to a separate test data file (preferred)
- Use a more compact format with line breaks at logical boundaries
- Generate the vector programmatically if it follows a pattern
Example of approach 2:
let expected = vec![ // Cluster 1 (main cluster) &[1; 34][..], // Cluster 2 &[2; 3][..], // Back to cluster 1 &[1; 456][..], // Mixed section 3, -1, 3, -1, 3, // Remaining cluster 1 &[1; 283][..], ].concat();examples/clustering/examples/dbscan_clustering.rs (1)
57-66: Enhance example documentation for the new cluster type.While the example correctly demonstrates the usage, it would be more helpful to add comments explaining the new cluster type representation.
println!("Clusters: {:?}", clusters); assert_eq!( clusters, vec![ + // Cluster ID 1 (using NonZeroU32 internally) DbscanCluster::Cluster(1.try_into().unwrap()), DbscanCluster::Cluster(1.try_into().unwrap()), + // Cluster ID 2 DbscanCluster::Cluster(2.try_into().unwrap()), DbscanCluster::Cluster(2.try_into().unwrap()), + // Points not belonging to any cluster DbscanCluster::Noise, ] );crates/augurs-clustering/README.md (1)
35-44: Enhance example readability and coverage.While the example correctly demonstrates the new
DbscanClustertype, consider these improvements:
- Add an example of noise points to demonstrate both variants of
DbscanCluster- Consider extracting the
try_into().unwrap()into a helper function or const to reduce repetition- Add a comment explaining why
NonZeroU32is used for cluster IDsExample improvement:
// Cluster IDs use NonZeroU32 for memory optimization let cluster1: NonZeroU32 = 1.try_into().unwrap(); let cluster2: NonZeroU32 = 2.try_into().unwrap(); assert_eq!( clusters, vec![ DbscanCluster::Cluster(cluster1), DbscanCluster::Cluster(cluster1), DbscanCluster::Cluster(cluster1), DbscanCluster::Cluster(cluster2), DbscanCluster::Cluster(cluster2), ], ); // Example with noise points let clusters_with_noise = DbscanClusterer::new(0.1, 3).fit(&distance_matrix); assert!(clusters_with_noise.iter().any(|c| matches!(c, DbscanCluster::Noise)));
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crates/augurs-clustering/README.md(2 hunks)crates/augurs-clustering/src/lib.rs(7 hunks)crates/augurs/tests/integration.rs(2 hunks)crates/pyaugurs/src/clustering.rs(1 hunks)examples/clustering/examples/dbscan_clustering.rs(2 hunks)
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🔇 Additional comments (4)
crates/pyaugurs/src/clustering.rs (1)
85-94: LGTM! Clean Python binding implementation.The conversion to
i32is appropriate for Python/numpy compatibility, and the implementation correctly maps the newDbscanClustertype.crates/augurs/tests/integration.rs (1)
21-23: LGTM! Well-structured test adaptation.The
convert_clustershelper function provides a clean way to adapt the tests to the new type system while maintaining readability.crates/augurs-clustering/README.md (2)
11-11: LGTM! Import statement updated to reflect new type.The addition of
DbscanClusterto the imports clearly shows users the available types and aligns with the new type system.
35-44: Verify example correctness with the actual implementation.Let's ensure the example matches the actual implementation and test cases.
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Actionable comments posted: 0
🧹 Nitpick comments (1)
crates/augurs-clustering/src/lib.rs (1)
209-238: Consider moving the large test vector to a separate file.The large test vector makes the test file harder to maintain. Consider moving it to a separate test data file, similar to how
dist.csvis handled.- let expected = vec![ - 1, 1, 1, 1, /* ... many lines ... */ 1, 1, 1, 1, - ]; + let expected: Vec<i32> = include_str!("../data/expected_clusters.txt") + .split(',') + .map(|s| s.trim().parse().unwrap()) + .collect();
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crates/augurs-clustering/README.md(2 hunks)crates/augurs-clustering/src/lib.rs(7 hunks)crates/augurs/tests/integration.rs(2 hunks)crates/pyaugurs/src/clustering.rs(1 hunks)examples/clustering/examples/dbscan_clustering.rs(2 hunks)js/augurs-clustering-js/src/lib.rs(1 hunks)
🚧 Files skipped from review as they are similar to previous changes (2)
- crates/augurs/tests/integration.rs
- crates/pyaugurs/src/clustering.rs
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🔇 Additional comments (6)
crates/augurs-clustering/src/lib.rs (3)
7-48: Well-designed type implementation!The
DbscanClusterenum withNonZeroU32leverages niche optimization, reducing the enum size. The implementation includes comprehensive helper methods and proper documentation.
50-60: Good test helper implementation!The
PartialEq<i32>implementation is appropriately scoped to tests and handles all cases correctly.
Line range hint
98-146: Verify all callers handle the new return type.The implementation correctly uses the new
DbscanClustertype. Let's verify that all callers are updated to handle the new return type.✅ Verification successful
All callers properly handle the new DbscanCluster type
The change is safe as backward compatibility is maintained through:
- PartialEq implementation allowing direct comparisons with integers
- Proper conversion methods between old and new representations
- Tests and examples showing correct usage of both styles
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Find all direct callers of the fit method to verify they handle the new return type # Search for direct calls to fit rg -p "\.fit\(&.*\)" --type rust # Search for any remaining isize type annotations that might need updating rg -p ": Vec<isize>" --type rustLength of output: 2819
Script:
#!/bin/bash # Search for usage patterns of the fit return value rg -p "let .* = .*\.fit\(&.*\)" -A 3 --type rust # Search for any pattern matching or type annotations related to clusters ast-grep --pattern 'match $_ { DbscanCluster::$$ => $$$ }'Length of output: 4510
Script:
#!/bin/bash # Find DbscanCluster type definition ast-grep --pattern 'enum DbscanCluster { $$$ }' # Find convert_clusters implementation ast-grep --pattern 'fn convert_clusters($_) -> $$ { $$$ }' # Find any direct comparisons with Vec<isize> rg "assert_eq.*vec!\[-" --type rustLength of output: 651
Script:
#!/bin/bash # Find the file containing DbscanCluster definition and its usage rg -p "DbscanCluster" --type rust -A 5 # Look for any conversion functions between DbscanCluster and isize rg -p "impl.*DbscanCluster" --type rust -A 10Length of output: 8138
crates/augurs-clustering/README.md (1)
11-11: Documentation accurately reflects the API changes!The README example clearly demonstrates the usage of the new
DbscanClustertype.Also applies to: 35-44
examples/clustering/examples/dbscan_clustering.rs (1)
55-66: Example correctly demonstrates the new API!The example has been properly updated to use
DbscanClusterand includes helpful debug output.js/augurs-clustering-js/src/lib.rs (1)
47-53: Clean JS binding implementation!The binding properly converts
DbscanClustertoi32for JS compatibility while maintaining the same semantics.
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Add a new `DbscanCluster` type to represent the cluster labels, which can be either a cluster ID or a special value indicating noise. The `Cluster` variant is now a `NonZeroU32` instead of an `isize`. We could use a `u32` but using a `NonZeroU32` allows us to make use of the niche optimizations that `NonZeroU32` provides and halves the size of the type. Questionable whether it's worth it though? Closes #229.
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@coderabbitai I'd be interested to hear your thoughts on whether this more explicitly typed approach is a worthwhile tradeoff. IMO it's slightly more typing for users, but more self-explanatory - there's no implicit assumption that |
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Tip For best results, initiate chat on the files or code changes. @sd2k I agree that this is a worthwhile tradeoff. The explicit typing with
While it requires slightly more typing from users, the improved clarity and removal of implicit assumptions (like ✏️ Learnings added
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Add a new
DbscanClustertype to represent the cluster labels, whichcan be either a cluster ID or a special value indicating noise. The
Clustervariant is now aNonZeroU32instead of anisize.We could use a
u32but using aNonZeroU32allows us to make useof the niche optimizations that
NonZeroU32provides and halves thesize of the type. Questionable whether it's worth it though?
Closes #229.
Summary by CodeRabbit
New Features
DbscanClusterenum to provide a more structured representation of clustering results.Bug Fixes
Refactor
DbscanClustertype across multiple components.