[DO NOT MERGE] Clique Table and Preprocessing

[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: there is little to no change in benchmarks. This PR is a basis for the clique cuts PR.

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.

[copy-pr-bot]

Auto-sync is disabled for draft pull requests in this repository. Workflows must be run manually.

Contributors can view more details about this message here.

[coderabbitai]

Note

Reviews paused

It looks like this branch is under active development. To avoid overwhelming you with review comments due to an influx of new commits, CodeRabbit has automatically paused this review. You can configure this behavior by changing the reviews.auto_review.auto_pause_after_reviewed_commits setting.

Use the following commands to manage reviews:

• @coderabbitai resume to resume automatic reviews.
• @coderabbitai review to trigger a single review.

Use the checkboxes below for quick actions:

• ▶️ Resume reviews
• 🔍 Trigger review

📝 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 | ✅ 1 | ❌ 2

❌ Failed checks (2 warnings)

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.
Title check	⚠️ Warning	The PR title '[DO NOT MERGE] Clique Table and Preprocessing' uses the '[DO NOT MERGE]' prefix, which is a strong indicator of work-in-progress status and is not appropriate for a production-ready changeset.	Remove '[DO NOT MERGE]' prefix and revise the title to clearly describe the main change, such as 'Add clique table and preprocessing for conflict graph' or similar, once the PR is ready for merge.

✅ Passed checks (1 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.

_{✏️ Tip: You can configure your own custom pre-merge checks in the settings.}

✨ Finishing Touches

🧪 Generate unit tests (beta)

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

---

_{Comment @coderabbitai help to get the list of available commands and usage tips.}

[rg20]

@akifcorduk is this still relevant?