docs: replace Rust code with JSON schema tables in paper

[GiggleLiu]

Summary

• Replace render-struct (Rust code blocks) with render-schema function that renders Field/Type/Description tables from problem_schemas.json — more useful for users who want to interop with this package
• Classify reduction references as "Reduces to:" / "Reduces from:" instead of flat "Implemented reductions:" lists
• Remove all Rust code blocks and See #link(...) lines from the paper, keeping mathematical examples

Test plan

• make paper compiles successfully
• make test passes
• make clippy clean
• PDF visually verified — schema tables render correctly

🤖 Generated with Claude Code

[codecov]

Codecov Report

❌ Patch coverage is 99.85591% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 97.37%. Comparing base (d6e82e3) to head (36e66c4).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
src/rules/unitdiskmapping/pathdecomposition.rs	83.33%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #38      +/-   ##
==========================================
+ Coverage   97.30%   97.37%   +0.07%     
==========================================
  Files         176      176              
  Lines       26080    26217     +137     
==========================================
+ Hits        25378    25530     +152     
+ Misses        702      687      -15     

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[Copilot]

Pull request overview

This PR updates the crate’s public-facing problem naming and documentation/examples to use explicit optimization-direction names (e.g., MaximumIndependentSet, MinimumVertexCover) and enhances exported reduction metadata (notably overhead formulas) for documentation/visualization.

Changes:

• Renames several core problem types and updates all corresponding reductions, tests, examples, and docs to match the new names.
• Extends reduction-graph JSON export to include per-edge overhead formulas (and updates the docs UI to display them).
• Adds PathDecompositionMethod::Auto and switches unit-disk mapping defaults to automatic method selection; improves polynomial formatting/printing utilities.

Reviewed changes

Copilot reviewed 121 out of 124 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
tests/suites/integration.rs	Updates integration tests to renamed problem types.
tests/suites/examples.rs	Updates example list names to match renamed examples.
tests/data/qubo/minimumvertexcover_to_qubo.json	Adds/updates QUBO ground-truth fixture for MVC→QUBO.
tests/data/qubo/maximumsetpacking_to_qubo.json	Adds/updates QUBO ground-truth fixture for MSP→QUBO.
tests/data/qubo/maximumindependentset_to_qubo.json	Adds/updates QUBO ground-truth fixture for MIS→QUBO.
src/unit_tests/variant.rs	Updates variant tests to renamed problem types.
src/unit_tests/unitdiskmapping_algorithms/common.rs	Updates unit-disk mapping test utilities to renamed MIS type.
src/unit_tests/trait_consistency.rs	Updates trait consistency tests for renamed problems and energy modes.
src/unit_tests/testing/macros.rs	Updates macro tests to renamed problem types.
src/unit_tests/rules/sat_minimumdominatingset.rs	Updates SAT→MDS reduction unit tests for renamed type.
src/unit_tests/rules/sat_maximumindependentset.rs	Updates SAT→MIS reduction unit tests for renamed type.
src/unit_tests/rules/registry.rs	Updates reduction registry test expectations for renamed problems.
src/unit_tests/rules/minimumvertexcover_qubo.rs	Updates MVC→QUBO reduction tests for renamed MVC type.
src/unit_tests/rules/minimumvertexcover_minimumsetcovering.rs	Updates MVC→MSC reduction tests for renamed types.
src/unit_tests/rules/minimumvertexcover_maximumindependentset.rs	Updates MIS↔MVC reduction tests for renamed types.
src/unit_tests/rules/minimumvertexcover_ilp.rs	Updates MVC→ILP reduction tests for renamed MVC type.
src/unit_tests/rules/minimumsetcovering_ilp.rs	Updates MSC→ILP reduction tests for renamed MSC type.
src/unit_tests/rules/minimumdominatingset_ilp.rs	Updates MDS→ILP reduction tests for renamed MDS type.
src/unit_tests/rules/maximumsetpacking_qubo.rs	Updates MSP→QUBO reduction tests for renamed MSP type.
src/unit_tests/rules/maximumsetpacking_ilp.rs	Updates MSP→ILP reduction tests for renamed MSP type.
src/unit_tests/rules/maximummatching_ilp.rs	Updates MaximumMatching→ILP tests for renamed matching type.
src/unit_tests/rules/maximumindependentset_qubo.rs	Updates MIS→QUBO reduction tests for renamed MIS type.
src/unit_tests/rules/maximumindependentset_maximumsetpacking.rs	Updates MIS↔MSP reduction tests for renamed types.
src/unit_tests/rules/maximumindependentset_ilp.rs	Updates MIS→ILP reduction tests for renamed MIS type.
src/unit_tests/registry/schema.rs	Updates schema registry tests for renamed problems.
src/unit_tests/registry/category.rs	Updates category registry tests for renamed subcategory variants.
src/unit_tests/reduction_graph.rs	Updates reduction graph tests for renamed nodes and edges.
src/unit_tests/property.rs	Updates property-based tests for renamed MIS/MVC types.
src/unit_tests/io.rs	Updates IO tests for renamed MIS type (serde roundtrips).
src/unit_tests/export.rs	Updates export tests that reference renamed problem names.
src/types.rs	Minor rustdoc formatting tweak.
src/traits.rs	Updates rustdoc examples to reflect renamed problems.
src/topology/mod.rs	Updates module-level rustdoc example to renamed MIS type.
src/testing/mod.rs	Updates docs/examples for testing macros to renamed types.
src/testing/macros.rs	Updates rustdoc examples for macros to renamed types.
src/solvers/ilp/solver.rs	Updates solver rustdoc example to renamed MIS type.
src/rules/unitdiskmapping/triangular/mod.rs	Switches default triangular mapping to PathDecompositionMethod::Auto.
src/rules/unitdiskmapping/triangular/mapping.rs	Switches default weighted triangular mapping to Auto and updates docs.
src/rules/unitdiskmapping/triangular/gadgets.rs	Minor comment change in triangular gadget implementation area.
src/rules/unitdiskmapping/pathdecomposition.rs	Adds Auto method and selection logic (≤30 exact, otherwise greedy).
src/rules/unitdiskmapping/ksg/mapping.rs	Switches KSG mapping defaults to Auto and updates docs.
src/rules/unitdiskmapping/alpha_tensor.rs	Minor rustdoc formatting tweak.
src/rules/sat_minimumdominatingset.rs	Renames SAT→DominatingSet reduction to SAT→MinimumDominatingSet; updates overhead.
src/rules/sat_maximumindependentset.rs	Renames SAT→IndependentSet reduction to SAT→MaximumIndependentSet; updates overhead.
src/rules/sat_ksat.rs	Updates overhead metadata to incorporate literal-count terms.
src/rules/sat_coloring.rs	Updates BoolVar import path and overhead formula.
src/rules/registry.rs	Updates rustdoc examples to renamed problem names.
src/rules/mod.rs	Renames and re-exports rule modules to match renamed problems.
src/rules/minimumvertexcover_qubo.rs	Renames VC→QUBO rule to MVC→QUBO and updates tests path.
src/rules/minimumvertexcover_minimumsetcovering.rs	Renames VC→SC rule to MVC→MSC and updates tests path.
src/rules/minimumvertexcover_maximumindependentset.rs	Renames IS↔VC rule to MIS↔MVC and updates tests path.
src/rules/minimumvertexcover_ilp.rs	Renames VC→ILP rule to MVC→ILP and updates tests path.
src/rules/minimumsetcovering_ilp.rs	Renames SC→ILP rule to MSC→ILP and updates tests path.
src/rules/minimumdominatingset_ilp.rs	Renames DS→ILP rule to MDS→ILP and updates tests path.
src/rules/maximumsetpacking_qubo.rs	Renames SP→QUBO rule to MSP→QUBO and updates tests path.
src/rules/maximumsetpacking_ilp.rs	Renames SP→ILP rule to MSP→ILP and updates tests path.
src/rules/maximummatching_maximumsetpacking.rs	Renames Matching→SetPacking rule to MaximumMatching→MaximumSetPacking.
src/rules/maximummatching_ilp.rs	Renames Matching→ILP rule to MaximumMatching→ILP and updates tests path.
src/rules/maximumindependentset_qubo.rs	Renames IS→QUBO rule to MIS→QUBO and updates tests path.
src/rules/maximumindependentset_maximumsetpacking.rs	Renames IS↔SP rule to MIS↔MSP and updates tests path.
src/rules/maximumindependentset_ilp.rs	Renames IS→ILP rule to MIS→ILP and updates tests path.
src/rules/maximumclique_ilp.rs	Renames Clique→ILP rule to MaximumClique→ILP and updates tests path.
src/rules/graph.rs	Adds overhead serialization to reduction graph JSON; updates naming/doc path mappings.
src/rules/factoring_circuit.rs	Updates overhead polynomial formula to use two-bit-size product.
src/rules/coloring_qubo.rs	Fixes/updates overhead polynomial for coloring→QUBO variable count.
src/rules/coloring_ilp.rs	Simplifies overhead definitions using poly! macro.
src/rules/circuit_spinglass.rs	Escapes brackets in rustdoc so they render correctly.
src/registry/schema.rs	Updates rustdoc example name for problem schema entries.
src/registry/info.rs	Improves rustdoc formatting for type-name examples.
src/registry/category.rs	Renames subcategory enum variants and updates documentation text.
src/polynomial.rs	Adds Display impls and extends poly! to support variable products.
src/models/set/mod.rs	Renames set modules/types to Minimum/Maximum variants and updates re-exports.
src/models/set/minimum_set_covering.rs	Renames SetCovering→MinimumSetCovering and updates schema registration/tests.
src/models/set/maximum_set_packing.rs	Renames SetPacking→MaximumSetPacking and updates schema registration/tests.
src/models/satisfiability/sat.rs	Adds num_literals() and includes it in problem_size().
src/models/mod.rs	Updates model re-exports and docs for renamed problems.
src/models/graph/mod.rs	Renames graph modules/types to Minimum/Maximum variants and updates re-exports.
src/models/graph/minimum_vertex_cover.rs	Renames VertexCovering→MinimumVertexCover and updates schema registration/tests.
src/models/graph/minimum_dominating_set.rs	Renames DominatingSet→MinimumDominatingSet and updates schema registration/tests.
src/models/graph/maximum_matching.rs	Renames Matching→MaximumMatching and updates schema registration/tests.
src/models/graph/maximum_independent_set.rs	Renames IndependentSet→MaximumIndependentSet and updates schema registration/tests.
src/models/graph/maximum_clique.rs	Renames Clique→MaximumClique and updates schema registration/tests.
src/lib.rs	Updates crate docs and prelude exports to renamed problems.
src/io.rs	Updates rustdoc examples for IO APIs to renamed problems.
src/export.rs	Updates export struct rustdoc to reflect renamed problem naming.
scripts/generate_qubo_tests.py	Renames generated fixture filenames to match renamed problems.
examples/reduction_sat_to_minimumdominatingset.rs	Updates SAT→MDS example naming and exported filenames.
examples/reduction_sat_to_maximumindependentset.rs	Updates SAT→MIS example naming and exported filenames.
examples/reduction_minimumvertexcover_to_qubo.rs	Updates MVC→QUBO example naming and exported filenames.
examples/reduction_minimumvertexcover_to_minimumsetcovering.rs	Updates MVC→MSC example naming and exported filenames.
examples/reduction_minimumvertexcover_to_maximumindependentset.rs	Updates MVC→MIS example naming and exported filenames.
examples/reduction_minimumvertexcover_to_ilp.rs	Updates MVC→ILP example naming and exported filenames.
examples/reduction_minimumsetcovering_to_ilp.rs	Updates MSC→ILP example naming and exported filenames.
examples/reduction_minimumdominatingset_to_ilp.rs	Updates MDS→ILP example naming and exported filenames.
examples/reduction_maximumsetpacking_to_qubo.rs	Updates MSP→QUBO example naming and exported filenames.
examples/reduction_maximumsetpacking_to_ilp.rs	Updates MSP→ILP example naming and exported filenames.
examples/reduction_maximummatching_to_maximumsetpacking.rs	Updates MaximumMatching→MSP example naming and exported filenames.
examples/reduction_maximummatching_to_ilp.rs	Updates MaximumMatching→ILP example naming and exported filenames.
examples/reduction_maximumindependentset_to_qubo.rs	Updates MIS→QUBO example naming and exported filenames.
examples/reduction_maximumindependentset_to_minimumvertexcover.rs	Updates MIS→MVC example naming and exported filenames.
examples/reduction_maximumindependentset_to_maximumsetpacking.rs	Updates MIS→MSP example naming and exported filenames.
examples/reduction_maximumindependentset_to_ilp.rs	Updates MIS→ILP example naming and exported filenames.
examples/reduction_maximumclique_to_ilp.rs	Updates MaximumClique→ILP example naming and exported filenames.
docs/src/io.md	Updates docs snippets to renamed problem types.
docs/src/introduction.md	Updates reduction graph UI to show overhead and updates example naming.
docs/src/getting-started.md	Updates getting-started snippets to renamed problem types.
benches/solver_benchmarks.rs	Updates benchmark group names and problem types to renamed variants.

Comments suppressed due to low confidence (8)

src/models/graph/maximum_matching.rs:5

• Doc comment repeats "Maximum" ("Maximum MaximumMatching"), which reads like a typo and is inconsistent with the type name. Update the module docs and the struct docs to consistently use "MaximumMatching" (or "Maximum Matching").
  examples/reduction_sat_to_maximumindependentset.rs:15
• The output paths in the header comment are inconsistent: this example writes using the name "sat_to_mis", so the result file should be sat_to_mis.result.json (not sat_to_is.result.json).
  examples/reduction_maximumindependentset_to_maximumsetpacking.rs:15
• Header comment still references the old result filename (is_to_setpacking.result.json), but this example writes under the name mis_to_msp (see write_example("mis_to_msp", ...)). Update the documented result path to docs/paper/examples/mis_to_msp.result.json for consistency.
  examples/reduction_maximumindependentset_to_minimumvertexcover.rs:14
• The documented result filename (is_to_vc.result.json) doesn’t match the example name mis_to_mvc used in write_example. Update the header comment to reference docs/paper/examples/mis_to_mvc.result.json.
  src/rules/maximummatching_ilp.rs:4
• Docstring has a duplicated word: "Maximum MaximumMatching". This should read "MaximumMatching" (or "Maximum Matching") to avoid confusing users and rustdoc search results.
  scripts/generate_qubo_tests.py:65
• The JSON metadata here still uses old problem names (e.g., "problem": "VertexCovering") even though the file/test name is minimumvertexcover_to_qubo. Even if tests ignore this field today, it makes the dataset self-inconsistent and harder to reuse; consider updating these strings to the new Problem::NAME values (e.g., MinimumVertexCover, MaximumIndependentSet, MaximumSetPacking).

    save_test("minimumvertexcover_to_qubo", {
        "problem": "VertexCovering",
        "source": {"num_vertices": n_nodes, "edges": edges, "penalty": penalty},
        "qubo_matrix": Q.tolist(),
        "qubo_num_vars": int(Q.shape[0]),
        "qubo_optimal": qubo_result,
    }, outdir)

src/models/graph/maximum_matching.rs:28

• The struct-level doc comment also contains the duplicated term "Maximum MaximumMatching". Update this header to "The MaximumMatching problem" (or "Maximum Matching") for consistency.
  examples/reduction_minimumvertexcover_to_maximumindependentset.rs:15
• The header comment lists vc_to_is.result.json, but this example writes under mvc_to_mis (see write_example("mvc_to_mis", ...)). Update the documented result filename to docs/paper/examples/mvc_to_mis.result.json.

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[Copilot]

GraphSubcategory::MaximumMatching looks like an accidental rename of the generic "matching" subcategory. Since name() still returns "matching", keeping the variant as Matching would avoid a breaking public API change and better reflect the category concept.

[Copilot]

StringSubcategory::MaximumMatching reads like a problem-specific rename rather than a generic category label. If this was meant to remain the string-matching subcategory, consider keeping the variant name Matching to avoid breaking the public API.

[Copilot]

Comment header looks like an accidental search/replace: it says "Pattern MaximumMatching..." but the section is about general pattern matching for gadgets. Rename it back to "Pattern Matching and Application Functions" to avoid confusion.