CodingThrust
diff --git a/‎Cargo.toml‎
Lines changed: 2 additions & 2 deletions b/‎Cargo.toml‎
Lines changed: 2 additions & 2 deletions
diff --git a/‎Makefile‎
Lines changed: 45 additions & 14 deletions b/‎Makefile‎
Lines changed: 45 additions & 14 deletions
diff --git a/‎benches/solver_benchmarks.rs‎
Lines changed: 1 addition & 0 deletions b/‎benches/solver_benchmarks.rs‎
Lines changed: 1 addition & 0 deletions
diff --git a/‎docs/paper/compare_mapping.typ‎
Lines changed: 249 additions & 0 deletions b/‎docs/paper/compare_mapping.typ‎
Lines changed: 249 additions & 0 deletions
@@ -9,7 +9,7 @@ keywords = ["np-hard", "optimization", "reduction", "sat", "graph"]
 categories = ["algorithms", "science"]
 
 [features]
-default = []
+default = ["ilp"]
 ilp = ["good_lp"]
 
 [dependencies]
@@ -22,9 +22,9 @@ num-traits = "0.2"
 good_lp = { version = "1.8", default-features = false, features = ["highs"], optional = true }
 inventory = "0.3"
 ordered-float = "5.0"
+rand = "0.8"
 
 [dev-dependencies]
-rand = "0.8"
 proptest = "1.0"
 criterion = "0.5"
 
 
@@ -1,29 +1,31 @@
 # Makefile for problemreductions
 
-.PHONY: help build test fmt clippy doc mdbook paper clean coverage
+.PHONY: help build test fmt clippy doc mdbook paper clean coverage rust-export compare
 
 # Default target
 help:
 	@echo "Available targets:"
-	@echo "  build      - Build the project"
-	@echo "  test       - Run all tests"
-	@echo "  fmt        - Format code with rustfmt"
-	@echo "  fmt-check  - Check code formatting"
-	@echo "  clippy     - Run clippy lints"
-	@echo "  doc        - Build mdBook documentation"
-	@echo "  mdbook     - Build and serve mdBook (with live reload)"
-	@echo "  paper      - Build Typst paper (requires typst)"
-	@echo "  coverage   - Generate coverage report (requires cargo-llvm-cov)"
-	@echo "  clean      - Clean build artifacts"
-	@echo "  check      - Quick check (fmt + clippy + test)"
+	@echo "  build        - Build the project"
+	@echo "  test         - Run all tests"
+	@echo "  fmt          - Format code with rustfmt"
+	@echo "  fmt-check    - Check code formatting"
+	@echo "  clippy       - Run clippy lints"
+	@echo "  doc          - Build mdBook documentation"
+	@echo "  mdbook       - Build and serve mdBook (with live reload)"
+	@echo "  paper        - Build Typst paper (requires typst)"
+	@echo "  coverage     - Generate coverage report (requires cargo-llvm-cov)"
+	@echo "  clean        - Clean build artifacts"
+	@echo "  check        - Quick check (fmt + clippy + test)"
+	@echo "  rust-export  - Generate Rust mapping JSON exports"
+	@echo "  compare      - Generate and compare Rust mapping exports"
 
 # Build the project
 build:
 	cargo build --all-features
 
-# Run all tests
+# Run all tests (including ignored tests)
 test:
-	cargo test --all-features
+	cargo test --all-features -- --include-ignored
 
 # Format code
 fmt:
@@ -62,3 +64,32 @@ clean:
 # Quick check before commit
 check: fmt-check clippy test
 	@echo "✅ All checks passed!"
+
+# Generate Rust mapping JSON exports for all graphs and modes
+GRAPHS := diamond bull house petersen
+MODES := unweighted weighted triangular
+rust-export:
+	@for graph in $(GRAPHS); do \
+		for mode in $(MODES); do \
+			echo "Exporting $$graph ($$mode)..."; \
+			cargo run --example export_mapping_stages -- $$graph $$mode; \
+		done; \
+	done
+
+# Generate Rust exports and show comparison
+compare: rust-export
+	@echo ""
+	@echo "=== Julia vs Rust Comparison ==="
+	@for graph in $(GRAPHS); do \
+		echo ""; \
+		echo "=== $$graph ==="; \
+		echo "-- unweighted --"; \
+		echo "Julia: $$(jq '{nodes: .num_grid_nodes, overhead: .mis_overhead, tape: .num_tape_entries}' tests/julia/$${graph}_unweighted_trace.json)"; \
+		echo "Rust:  $$(jq '{nodes: .stages[3].num_nodes, overhead: .total_overhead, tape: ((.crossing_tape | length) + (.simplifier_tape | length))}' tests/julia/$${graph}_rust_unweighted.json)"; \
+		echo "-- weighted --"; \
+		echo "Julia: $$(jq '{nodes: .num_grid_nodes, overhead: .mis_overhead, tape: .num_tape_entries}' tests/julia/$${graph}_weighted_trace.json)"; \
+		echo "Rust:  $$(jq '{nodes: .stages[3].num_nodes, overhead: .total_overhead, tape: ((.crossing_tape | length) + (.simplifier_tape | length))}' tests/julia/$${graph}_rust_weighted.json)"; \
+		echo "-- triangular --"; \
+		echo "Julia: $$(jq '{nodes: .num_grid_nodes, overhead: .mis_overhead, tape: .num_tape_entries}' tests/julia/$${graph}_triangular_trace.json)"; \
+		echo "Rust:  $$(jq '{nodes: .stages[3].num_nodes, overhead: .total_overhead, tape: ((.crossing_tape | length) + (.simplifier_tape | length))}' tests/julia/$${graph}_rust_triangular.json)"; \
+	done
@@ -88,6 +88,7 @@ fn bench_satisfiability(c: &mut Criterion) {
 }
 
 /// Benchmark SpinGlass on varying sizes.
+#[allow(clippy::manual_is_multiple_of)] // Type inference issues with is_multiple_of
 fn bench_spin_glass(c: &mut Criterion) {
     let mut group = c.benchmark_group("SpinGlass");
 
 
@@ -0,0 +1,249 @@
+#import "@preview/cetz:0.3.2"
+
+// Load JSON data for different modes
+// Paths relative to this document (docs/paper/)
+#let load_julia_unweighted(name) = json("../../tests/julia/" + name + "_unweighted_trace.json")
+#let load_julia_weighted(name) = json("../../tests/julia/" + name + "_weighted_trace.json")
+#let load_julia_triangular(name) = json("../../tests/julia/" + name + "_triangular_trace.json")
+#let load_rust_square(name) = json("../../tests/julia/" + name + "_rust_unweighted.json")
+#let load_rust_triangular(name) = json("../../tests/julia/" + name + "_rust_triangular.json")
+
+// Color scheme
+#let julia_color = rgb("#2196F3")  // Blue
+#let rust_color = rgb("#FF5722")   // Orange
+#let both_color = rgb("#4CAF50")   // Green
+
+// Create position key for comparison
+#let pos_key(r, c) = str(r) + "," + str(c)
+
+// Convert Julia 1-indexed nodes to 0-indexed (Rust is already 0-indexed)
+// Preserves state field if present (O=Occupied, D=Doubled, C=Connected)
+#let julia_to_0indexed(nodes) = nodes.map(n => (
+  row: n.row - 1,
+  col: n.col - 1,
+  weight: if "weight" in n { n.weight } else { 1 },
+  state: if "state" in n { n.state } else { "O" }
+))
+
+// Extract copyline nodes from Julia copy_lines (convert to 0-indexed)
+#let julia_copylines_to_nodes(copy_lines) = {
+  let nodes = ()
+  for cl in copy_lines {
+    for loc in cl.locations {
+      nodes.push((
+        row: loc.row - 1,
+        col: loc.col - 1,
+        weight: if "weight" in loc { loc.weight } else { 1 }
+      ))
+    }
+  }
+  nodes
+}
+
+// Color for connected cells
+#let connected_color = rgb("#E91E63")  // Pink/Magenta for Connected
+
+// Draw grid with nodes - all positions are 0-indexed
+// triangular: if true, offset odd rows by 0.5 for triangular lattice
+// Shows Connected cells (state="C") with a different color (ring)
+#let draw_grid(nodes, grid_size, title, node_color: black, unit: 4pt, triangular: false) = {
+  let rows = grid_size.at(0)
+  let cols = grid_size.at(1)
+  let occupied = nodes.map(n => pos_key(n.row, n.col))
+
+  // Helper to compute x position with optional triangular offset
+  let get_x(r, c) = {
+    if triangular and calc.rem(r, 2) == 1 { c + 1.0 }  // odd rows offset by 0.5
+    else { c + 0.5 }
+  }
+
+  cetz.canvas(length: unit, {
+    import cetz.draw: *
+    content((cols / 2, rows + 2), text(size: 7pt, weight: "bold", title))
+
+    // Draw empty grid sites as small dots
+    for r in range(0, rows) {
+      for c in range(0, cols) {
+        let key = pos_key(r, c)
+        if not occupied.contains(key) {
+          let y = rows - r - 0.5
+          let x = get_x(r, c)
+          circle((x, y), radius: 0.08, fill: luma(200), stroke: none)
+        }
+      }
+    }
+
+    // Draw filled nodes - Connected cells shown with different color
+    for node in nodes {
+      let r = node.row
+      let c = node.col
+      let w = if "weight" in node { node.weight } else { 1 }
+      let s = if "state" in node { node.state } else { "O" }
+      let y = rows - r - 0.5
+      let x = get_x(r, c)
+      let radius = if w == 1 { 0.25 } else if w == 2 { 0.35 } else { 0.45 }
+      // Connected cells shown with ring (stroke) instead of fill
+      if s == "C" {
+        circle((x, y), radius: radius, fill: none, stroke: 1.5pt + connected_color)
+      } else {
+        circle((x, y), radius: radius, fill: node_color, stroke: none)
+      }
+    }
+  })
+}
+
+// Compare two node sets
+#let compare_nodes(julia_nodes, rust_nodes) = {
+  let julia_keys = julia_nodes.map(n => pos_key(n.row, n.col))
+  let rust_keys = rust_nodes.map(n => pos_key(n.row, n.col))
+  let both = ()
+  let julia_only = ()
+  let rust_only = ()
+
+  for n in julia_nodes {
+    let key = pos_key(n.row, n.col)
+    if rust_keys.contains(key) { both.push((n.row, n.col)) }
+    else { julia_only.push((n.row, n.col)) }
+  }
+  for n in rust_nodes {
+    let key = pos_key(n.row, n.col)
+    if not julia_keys.contains(key) { rust_only.push((n.row, n.col)) }
+  }
+  (both: both, julia_only: julia_only, rust_only: rust_only)
+}
+
+// Draw comparison grid
+#let draw_comparison(julia_nodes, rust_nodes, grid_size, title, unit: 4pt, triangular: false) = {
+  let rows = grid_size.at(0)
+  let cols = grid_size.at(1)
+  let cmp = compare_nodes(julia_nodes, rust_nodes)
+  let all_occupied = cmp.both + cmp.julia_only + cmp.rust_only
+  let occupied_keys = all_occupied.map(((r, c)) => pos_key(r, c))
+
+  let get_x(r, c) = {
+    if triangular and calc.rem(r, 2) == 1 { c + 1.0 }
+    else { c + 0.5 }
+  }
+
+  cetz.canvas(length: unit, {
+    import cetz.draw: *
+    content((cols / 2, rows + 3), text(size: 7pt, weight: "bold", title))
+    content((cols / 2, rows + 1.5), text(size: 5pt)[
+      #box(fill: both_color, width: 4pt, height: 4pt) #cmp.both.len()
+      #box(fill: julia_color, width: 4pt, height: 4pt) #cmp.julia_only.len()
+      #box(fill: rust_color, width: 4pt, height: 4pt) #cmp.rust_only.len()
+    ])
+
+    for r in range(0, rows) {
+      for c in range(0, cols) {
+        let key = pos_key(r, c)
+        if not occupied_keys.contains(key) {
+          let y = rows - r - 0.5
+          let x = get_x(r, c)
+          circle((x, y), radius: 0.08, fill: luma(200), stroke: none)
+        }
+      }
+    }
+
+    for (r, c) in cmp.both {
+      circle((get_x(r, c), rows - r - 0.5), radius: 0.35, fill: both_color, stroke: none)
+    }
+    for (r, c) in cmp.julia_only {
+      circle((get_x(r, c), rows - r - 0.5), radius: 0.35, fill: julia_color, stroke: none)
+    }
+    for (r, c) in cmp.rust_only {
+      circle((get_x(r, c), rows - r - 0.5), radius: 0.35, fill: rust_color, stroke: none)
+    }
+  })
+}
+
+// Compare a single mode
+// triangular: if true, use triangular lattice visualization (offset odd rows)
+#let compare_mode(name, mode, julia, rust, triangular: false) = {
+  let grid_size = julia.grid_size
+  // Use grid_nodes_copylines_only if available (has state: O, D, C), else fall back to copy_lines
+  let julia_copylines = if "grid_nodes_copylines_only" in julia {
+    julia_to_0indexed(julia.grid_nodes_copylines_only)
+  } else {
+    julia_copylines_to_nodes(julia.copy_lines)
+  }
+  let julia_before_simp = julia_to_0indexed(julia.at("grid_nodes_before_simplifiers", default: julia.grid_nodes))
+  let julia_final = julia_to_0indexed(julia.grid_nodes)
+  // Rust stages: 0=copylines only, 1=with connections, 2=after crossing, 3=after simplifiers
+  let rust_stage1 = rust.stages.at(1).grid_nodes  // with connections (matches Julia copylines_only)
+  let rust_stage2 = rust.stages.at(2).grid_nodes  // after crossing gadgets
+  let rust_stage3 = rust.stages.at(3).grid_nodes  // after simplifiers
+
+  [
+    = #name - #mode
+
+    == Overview
+    #table(
+      columns: 3,
+      stroke: 0.5pt,
+      [*Metric*], [*Julia*], [*Rust*],
+      [Vertices], [#julia.num_vertices], [#rust.num_vertices],
+      [Grid], [#grid_size.at(0)×#grid_size.at(1)], [#rust.stages.at(0).grid_size.at(0)×#rust.stages.at(0).grid_size.at(1)],
+      [Final Nodes], [#julia.num_grid_nodes], [#rust.stages.at(3).num_nodes],
+      [Before Simpl], [#julia.num_grid_nodes_before_simplifiers], [#rust.stages.at(2).num_nodes],
+      [Overhead], [#julia.mis_overhead], [#rust.total_overhead],
+      [Tape], [#julia.tape.len()], [#(rust.crossing_tape.len() + rust.simplifier_tape.len())],
+    )
+
+    == Copylines with Connections
+    #grid(
+      columns: 3,
+      gutter: 0.3em,
+      draw_grid(julia_copylines, grid_size, "Julia", node_color: julia_color, triangular: triangular),
+      draw_grid(rust_stage1, grid_size, "Rust", node_color: rust_color, triangular: triangular),
+      draw_comparison(julia_copylines, rust_stage1, grid_size, "Diff", triangular: triangular),
+    )
+
+    == After Crossing Gadgets
+    #grid(
+      columns: 3,
+      gutter: 0.3em,
+      draw_grid(julia_before_simp, grid_size, "Julia", node_color: julia_color, triangular: triangular),
+      draw_grid(rust_stage2, grid_size, "Rust", node_color: rust_color, triangular: triangular),
+      draw_comparison(julia_before_simp, rust_stage2, grid_size, "Diff", triangular: triangular),
+    )
+
+    == Final
+    #grid(
+      columns: 3,
+      gutter: 0.3em,
+      draw_grid(julia_final, grid_size, "Julia", node_color: julia_color, triangular: triangular),
+      draw_grid(rust_stage3, grid_size, "Rust", node_color: rust_color, triangular: triangular),
+      draw_comparison(julia_final, rust_stage3, grid_size, "Diff", triangular: triangular),
+    )
+
+    #pagebreak()
+  ]
+}
+
+// Compare all 3 modes for a graph
+#let compare_graph(name) = {
+  let julia_uw = load_julia_unweighted(name)
+  let julia_w = load_julia_weighted(name)
+  let julia_tri = load_julia_triangular(name)
+  let rust_sq = load_rust_square(name)
+  let rust_tri = load_rust_triangular(name)
+
+  [
+    #compare_mode(name, "UnWeighted (Square)", julia_uw, rust_sq)
+    #compare_mode(name, "Weighted (Square)", julia_w, rust_sq)
+    #compare_mode(name, "Triangular Weighted", julia_tri, rust_tri, triangular: true)
+  ]
+}
+
+// Document setup
+#set page(margin: 0.6cm, paper: "a4")
+#set text(size: 6pt)
+
+#align(center, text(size: 12pt, weight: "bold")[Julia vs Rust Mapping Comparison])
+#v(0.3em)
+
+#compare_graph("diamond")
+#compare_graph("bull")
+#compare_graph("house")
+#compare_graph("petersen")
Original file line number	Diff line number	Diff line change
`@@ -88,6 +88,7 @@ fn bench_satisfiability(c: &mut Criterion) {`
`88`	`88`	`}`
`89`	`89`
`90`	`90`	`/// Benchmark SpinGlass on varying sizes.`
	`91`	`+#[allow(clippy::manual_is_multiple_of)] // Type inference issues with is_multiple_of`
`91`	`92`	`fn bench_spin_glass(c: &mut Criterion) {`
`92`	`93`	`let mut group = c.benchmark_group("SpinGlass");`
`93`	`94`