Clique Table Generation

[akifcorduk]

This PR implements the first part of the paper from the paper: Preprocessing and Cutting Planes with Conflict Graphs.
This part contains only the preprocessing parts and clique cuts will follow in a separate PR:

• Clique detection by converting constraints into sorted knapsack constraints. This allows fast clique detection.
• Additional cliques in the same constraint by utilizing sorting structures.
• Clique extension/merging across the conflict graph.
• Clique covering and problem modification.

The data structures and query functions are implemented and will be used as a basis for clique cuts and usage in heuristics.

Benchmark results: no impact on benchmarks as this is just the first part, improvements will come from clique cuts.

Summary by CodeRabbit

• New Features

  • Automatic clique detection and injection into MIP presolve to improve preprocessing.
  • Host-to-solver constraint sync allowing external problem updates to be applied before solving.

• Improvements

  • Presolve now respects a time cap to bound preprocessing work.
  • Improved constraint handling and propagation during solution setup.
  • Local search initialization refined for more reliable first-run behavior.

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📝 Walkthrough

Walkthrough

Adds a clique-based presolve subsystem and integrates it into the MIP pipeline, extends CSR sparse-matrix API, exposes a new problem setter for host-derived constraints, adjusts build files, and updates presolve/solver/local-search flows and comments.

Changes

Cohort / File(s)	Summary
Build Configuration cpp/CMakeLists.txt, cpp/src/mip/CMakeLists.txt	Updated solve_MIP include directories (PRIVATE src, PUBLIC BUILD_INTERFACE include) and added clique_table.cu to non-LP build list.
Clique Infrastructure cpp/src/mip/presolve/conflict_graph/clique_table.cuh, cpp/src/mip/presolve/conflict_graph/clique_table.cu	New templated clique table/types and extensive algorithms for extracting, extending, pruning, and inserting cliques from knapsack-like constraints; explicit instantiations for float/double.
Sparse Matrix API cpp/src/dual_simplex/sparse_matrix.hpp, cpp/src/dual_simplex/sparse_matrix.cpp	Added csr_matrix_t::get_constraint_range() and insert_row() overloads; added CSC→CSR scatter helper; fixed comment typo and updated copyright year.
Presolve / Diversity Integration cpp/src/mip/diversity/diversity_manager.cu	Hooked initial-clique finding into run_presolve: construct host_problem, compute initial cliques, update host constraints via set_constraints_from_host_user_problem, reorder/gate bounds updates and trivial presolve.
Probing Cache / Comments cpp/src/mip/presolve/probing_cache.cu, cpp/src/mip/presolve/probing_cache.cuh	Added unordered_set include; added explanatory comments about probing cache behavior (no API/behavioral changes).
Problem Representation cpp/src/mip/problem/problem.cuh, cpp/src/mip/problem/problem.cu	Added problem_t::set_constraints_from_host_user_problem(...) to populate device CSR, rhs, bounds, range handling, names, and variable types from a host user_problem; resize_constraints now preserves/initializes prev_dual elements. (Note: duplicate definition observed in cu file.)
Solver Integration cpp/src/mip/solver.cu	Introduced presolve time cap (min(10% remaining, 60s)) and call to context.problem_ptr->set_constraints_from_host_user_problem(branch_and_bound_problem) before branch-and-bound setup.
Local Search Initialization cpp/src/mip/local_search/local_search.cu	On first run, initialize in_fj.cstr_weights to constraint count and fill with 1.0.

Estimated code review effort

🎯 5 (Critical) | ⏱️ ~120 minutes

🚥 Pre-merge checks | ✅ 2 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 0.00% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (2 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title 'Clique Table Generation' directly and specifically describes the main feature being added: clique table data structures and generation functionality.
Description check	✅ Passed	The pull request description clearly relates to the changeset by explaining the implementation of clique detection, extension, and preprocessing based on a specific paper.

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✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment

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[rg20]

@akifcorduk is this still relevant?

[akifcorduk]

/merge