Fix #73: Refactor graph problem constructors to take graph as input

[GiggleLiu]

Summary

• Remove new(num_vertices, edges) constructors from all 9 graph problem types that internally construct a SimpleGraph
• Rename from_graph(graph, ...) → new(graph, ...) making the graph topology type explicit in the constructor signature
• Rename auxiliary constructors: from_graph_unweighted → unweighted, from_graph_unit_weights → unit_weights, from_graph_with_k → with_k
• Add WeightElement::IS_UNIT const — is_weighted() is now type-based (returns !W::IS_UNIT) instead of comparing weight values at runtime
• Refactor 8 public helper functions (is_independent_set, is_vertex_cover, is_clique, etc.) to take graph: &G instead of raw (num_vertices, edges), with assert_eq! on size mismatch

Commits

1. MaximumIndependentSet — remove SimpleGraph constructors, rename from_graph → new
2. MVC, MDS, MaxClique, MaximalIS — same pattern
3. KColoring — rename from_graph → new, from_graph_with_k → with_k
4. MaxCut, MaximumMatching, TravelingSalesman — edge-weight types, rename from_graph_unweighted → unweighted, from_graph_unit_weights → unit_weights
5. WeightElement::IS_UNIT — type-based is_weighted() using One marker type
6. Helper functions — is_independent_set, is_vertex_cover, is_clique, is_dominating_set, is_maximal_independent_set, is_matching, is_hamiltonian_cycle, is_valid_coloring now take &impl Graph

Test plan

• make test clippy passes
• cargo test --doc passes (47 doc tests)
• No remaining references to old new(num_vertices, edges) pattern

Closes #73

🤖 Generated with Claude Code

[codecov]

Codecov Report

❌ Patch coverage is 99.35484% with 4 lines in your changes missing coverage. Please review.
✅ Project coverage is 96.38%. Comparing base (529114f) to head (cec8a01).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
src/models/graph/maximum_matching.rs	80.00%	2 Missing ⚠️
src/models/graph/kcoloring.rs	88.88%	1 Missing ⚠️
src/models/graph/traveling_salesman.rs	92.85%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #74      +/-   ##
==========================================
+ Coverage   96.36%   96.38%   +0.01%     
==========================================
  Files         191      190       -1     
  Lines       25494    25306     -188     
==========================================
- Hits        24568    24391     -177     
+ Misses        926      915      -11     

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[Copilot]

Pull request overview

Refactors graph problem constructors to accept an explicit graph instance (making topology types visible at the call site), updates related helpers and call sites, and switches is_weighted() to a type-based check via WeightElement::IS_UNIT.

Changes:

• Removed new(num_vertices, edges) / unweighted(...)-style constructors across graph problems; standardized on new(graph, ...) plus renamed convenience ctors (unit_weights, unweighted, with_k).
• Updated public helper functions (is_independent_set, is_vertex_cover, is_clique, etc.) to accept &impl Graph and assert on length mismatches.
• Added WeightElement::IS_UNIT and migrated is_weighted() to be type-based.

Reviewed changes

Copilot reviewed 83 out of 83 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
tests/suites/reductions.rs	Update reduction tests to construct graphs explicitly and pass weights separately.
tests/suites/integration.rs	Update integration tests to new graph-first constructors and renamed ctors.
src/unit_tests/unitdiskmapping_algorithms/common.rs	Update MIS construction in unitdisk mapping helpers to new signature.
src/unit_tests/trait_consistency.rs	Update trait conformance tests to new constructors and edge-weight APIs.
src/unit_tests/testing/macros.rs	Replace macro-based tests with manual equivalents due to ctor signature changes.
src/unit_tests/solvers/brute_force.rs	Update brute force solver test to new MIS constructor signature.
src/unit_tests/rules/travelingsalesman_ilp.rs	Update TSP rule tests to new new(graph, weights) / unit_weights(graph) APIs.
src/unit_tests/rules/spinglass_maxcut.rs	Update MaxCut instances to separate graph and weights, and renamed unweighted ctor.
src/unit_tests/rules/minimumvertexcover_qubo.rs	Update VC→QUBO rule tests to new VC constructors and helper signatures.
src/unit_tests/rules/minimumvertexcover_minimumsetcovering.rs	Update VC→SC rule tests to new constructors and explicit graphs.
src/unit_tests/rules/minimumvertexcover_maximumindependentset.rs	Update IS↔VC rule tests to new constructors and graph-first pattern.
src/unit_tests/rules/minimumvertexcover_ilp.rs	Update VC→ILP rule tests to new constructors.
src/unit_tests/rules/minimumdominatingset_ilp.rs	Update DS→ILP rule tests to new constructors.
src/unit_tests/rules/maximummatching_maximumsetpacking.rs	Update Matching→SP rule tests to new constructors and unit_weights.
src/unit_tests/rules/maximummatching_ilp.rs	Update Matching→ILP rule tests to new constructors and unit_weights.
src/unit_tests/rules/maximumindependentset_triangular.rs	Update MIS→TriangularSubgraph rule tests to new MIS constructor.
src/unit_tests/rules/maximumindependentset_qubo.rs	Update MIS→QUBO rule tests to new constructors.
src/unit_tests/rules/maximumindependentset_maximumsetpacking.rs	Update MIS→SP rule tests to new constructors.
src/unit_tests/rules/maximumindependentset_ilp.rs	Update MIS→ILP rule tests to new constructors.
src/unit_tests/rules/maximumindependentset_gridgraph.rs	Update MIS gridgraph rule tests to renamed ctor and new signature.
src/unit_tests/rules/maximumclique_ilp.rs	Update Clique→ILP rule tests to new constructors.
src/unit_tests/rules/graph.rs	Update chained reduction tests to new MIS constructor and graph casting ctor rename.
src/unit_tests/rules/coloring_qubo.rs	Update KColoring→QUBO rule tests to new KColoring constructor.
src/unit_tests/rules/coloring_ilp.rs	Update KColoring→ILP rule tests to new KColoring constructor.
src/unit_tests/property.rs	Update property tests to construct graphs explicitly and pass weights.
src/unit_tests/models/set/maximum_set_packing.rs	Update SP relationship test to new MIS constructor.
src/unit_tests/models/graph/traveling_salesman.rs	Update TSP model tests to new constructors and type-based weighted semantics.
src/unit_tests/models/graph/minimum_vertex_cover.rs	Update VC model tests and helper usage to graph-based helper functions.
src/unit_tests/models/graph/minimum_dominating_set.rs	Update DS model tests and helper usage to graph-based helper functions.
src/unit_tests/models/graph/maximum_matching.rs	Update Matching model tests and helper usage to graph-based helper functions.
src/unit_tests/models/graph/maximum_independent_set.rs	Update MIS model tests and helper usage to graph-based helper functions.
src/unit_tests/models/graph/maximum_clique.rs	Update Clique model tests and helper usage to graph-based helper functions.
src/unit_tests/models/graph/maximal_is.rs	Update MaximalIS model tests and helper usage to graph-based helper functions.
src/unit_tests/models/graph/max_cut.rs	Update MaxCut model tests to new constructors and renamed unweighted ctor.
src/unit_tests/models/graph/kcoloring.rs	Update KColoring model tests to new constructor and helper signature behavior.
src/unit_tests/io.rs	Update IO tests to new MIS constructor signature.
src/unit_tests/graph_models.rs	Update aggregated graph model tests to new constructors and helper signatures.
src/types.rs	Add WeightElement::IS_UNIT and implement it for i32, f64, and One.
src/topology/mod.rs	Update rustdoc example to construct SimpleGraph explicitly and pass weights.
src/solvers/ilp/solver.rs	Update ILP solver rustdoc example to new MIS constructor.
src/rules/spinglass_maxcut.rs	Update SG→MaxCut construction to new MaxCut new(graph, weights) signature.
src/rules/sat_minimumdominatingset.rs	Update SAT→DS construction to new DS new(graph, weights) signature.
src/rules/sat_maximumindependentset.rs	Update SAT→MIS construction to new MIS new(graph, weights) signature.
src/rules/sat_coloring.rs	Update SAT coloring builder to new KColoring constructor signature.
src/rules/mod.rs	Update macro docs example to renamed ctor (from_graph → new).
src/rules/minimumvertexcover_maximumindependentset.rs	Update IS↔VC reduction targets to construct graphs explicitly and pass weights.
src/rules/maximumindependentset_triangular.rs	Update MIS→TriangularSubgraph reduction to renamed ctor (new).
src/rules/maximumindependentset_maximumsetpacking.rs	Update SP→MIS reduction to new MIS ctor with explicit SimpleGraph.
src/rules/maximumindependentset_gridgraph.rs	Update MIS gridgraph reductions to renamed ctor (new).
src/rules/maximumindependentset_casts.rs	Update MIS variant casts to renamed ctor (new).
src/rules/kcoloring_casts.rs	Update KColoring variant cast to renamed ctor (with_k).
src/models/graph/traveling_salesman.rs	Remove SimpleGraph-only ctors, rename from_graph → new, rename unit-weight ctor, update helper signature.
src/models/graph/minimum_vertex_cover.rs	Remove SimpleGraph-only ctors, rename from_graph → new, update helper signature and panics.
src/models/graph/minimum_dominating_set.rs	Remove SimpleGraph-only ctors, rename from_graph → new, update helper signature and panics.
src/models/graph/maximum_matching.rs	Remove SimpleGraph-only ctors, rename from_graph → new, rename unit-weight ctor, update helper signature and panics.
src/models/graph/maximum_independent_set.rs	Remove SimpleGraph-only ctors, rename from_graph → new, update helper signature and panics.
src/models/graph/maximum_clique.rs	Remove SimpleGraph-only ctors, rename from_graph → new, update helper signature and panics.
src/models/graph/maximal_is.rs	Remove SimpleGraph-only ctors, rename from_graph → new, update helper signature and panics.
src/models/graph/max_cut.rs	Remove SimpleGraph-only ctors, rename from_graph → new, rename unweighted ctor.
src/models/graph/kcoloring.rs	Remove SimpleGraph-only ctor, rename from_graph → new, rename from_graph_with_k → with_k, update helper signature and panics.
src/lib.rs	Update crate-level rustdoc example to new MIS constructor signature.
src/io.rs	Update IO rustdoc example to new MIS constructor signature.
examples/reduction_travelingsalesman_to_ilp.rs	Update example to new TSP new(graph, weights) signature.
examples/reduction_minimumvertexcover_to_qubo.rs	Update example to new VC constructor signature.
examples/reduction_minimumvertexcover_to_minimumsetcovering.rs	Update example to new VC constructor signature.
examples/reduction_minimumvertexcover_to_maximumindependentset.rs	Update example to new VC constructor signature.
examples/reduction_minimumvertexcover_to_ilp.rs	Update example to new VC constructor signature.
examples/reduction_minimumdominatingset_to_ilp.rs	Update example to new DS constructor signature.
examples/reduction_maximummatching_to_maximumsetpacking.rs	Update example to new Matching unit_weights(graph) signature.
examples/reduction_maximummatching_to_ilp.rs	Update example to new Matching unit_weights(graph) signature.
examples/reduction_maximumindependentset_to_qubo.rs	Update example to new MIS constructor signature.
examples/reduction_maximumindependentset_to_minimumvertexcover.rs	Update example to new MIS constructor signature.
examples/reduction_maximumindependentset_to_maximumsetpacking.rs	Update example to new MIS constructor signature.
examples/reduction_maximumindependentset_to_ilp.rs	Update example to new MIS constructor signature.
examples/reduction_maximumclique_to_ilp.rs	Update example to new Clique constructor signature.
examples/reduction_maxcut_to_spinglass.rs	Update example to new MaxCut unweighted(graph) signature.
examples/reduction_kcoloring_to_qubo.rs	Update example to new KColoring constructor signature.
examples/reduction_kcoloring_to_ilp.rs	Update example to new KColoring constructor signature.
docs/src/getting-started.md	Update getting-started snippet to explicit graph + weights construction.
docs/plans/2026-02-16-graph-constructor-refactoring.md	Add implementation plan documenting the refactor steps and call-site migration.
benches/solver_benchmarks.rs	Update benchmarks to new constructors and separated edge weights.
.github/ISSUE_TEMPLATE/rule.md	Add “Motivation” field to rule issue template.
.github/ISSUE_TEMPLATE/problem.md	Add “Motivation” section to problem issue template.

Comments suppressed due to low confidence (1)

src/models/graph/maximum_clique.rs:186

• is_clique() checks adjacency by calling graph.has_edge(u, v) for every selected pair. For SimpleGraph, has_edge uses petgraph::UnGraph::find_edge, which is not constant-time and can make this O(k^2 * deg) for k selected vertices. To avoid a potential regression, consider building a HashSet (or adjacency bitset) once from graph.edges() and then doing O(1) lookups when validating pairs.

    // Check all pairs of selected vertices are adjacent
    for i in 0..selected_vertices.len() {
        for j in (i + 1)..selected_vertices.len() {
            if !graph.has_edge(selected_vertices[i], selected_vertices[j]) {
                return false;
            }
        }
    }

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[Copilot]

TravelingSalesman::evaluate() now indirectly panics when config.len() != graph.num_edges() because is_valid_hamiltonian_cycle() forwards config into is_hamiltonian_cycle(), which asserts on length. Problem::evaluate should generally return SolutionSize::Invalid for malformed assignments rather than panic; consider adding a length check in is_valid_hamiltonian_cycle() (or in evaluate()) and returning false early before calling the asserting helper.

[Copilot]

is_dominating_set() calls graph.neighbors(v) inside the loop over all vertices; the Graph trait returns Vec<usize>, so this allocates on every iteration (O(V) allocations) and can be noticeably slow on larger graphs. Consider building an adjacency list once from graph.edges() (or caching neighbors) and then checking domination using that structure.