adding various decoders back from previous branch

Cargo.toml

@@ -128,6 +128,24 @@ pecos-decoders = { version = "0.1.1", path = "crates/pecos-decoders" }
 # ldpc decoder wrapper (https://github.com/quantumgizmos/ldpc)
 pecos-ldpc-decoders = { version = "0.1.1", path = "crates/pecos-ldpc-decoders" }
 
+# PyMatching decoder wrapper (https://github.com/oscarhiggott/PyMatching)
+pecos-pymatching = { version = "0.1.1", path = "crates/pecos-pymatching" }
+
+# Tesseract decoder wrapper (https://github.com/quantumlib/tesseract-decoder)
+pecos-tesseract = { version = "0.1.1", path = "crates/pecos-tesseract" }
+
+# Chromobius decoder wrapper (https://github.com/quantumlib/chromobius)
+pecos-chromobius = { version = "0.1.1", path = "crates/pecos-chromobius" }
+
+# Fusion Blossom decoder wrapper (pure Rust MWPM)
+pecos-fusion-blossom = { version = "0.1.1", path = "crates/pecos-fusion-blossom" }
+
+# Fusion Blossom library (pure Rust MWPM decoder)
+fusion-blossom = "0.2"
+
+# petgraph for graph algorithms (used by pymatching)
+petgraph = "0.8"
+
 # QuEST simulator wrapper (https://github.com/quest-kit/QuEST)
 pecos-quest = { version = "0.1.1", path = "crates/pecos-quest" }
 

crates/pecos-build/src/manifest.rs

@@ -608,7 +608,7 @@ mod tests {
         assert_eq!(qulacs_deps.len(), 3); // qulacs, eigen, boost
 
         let ldpc_deps = manifest.get_crate_dependencies("pecos-ldpc-decoders");
-        assert!(ldpc_deps.len() >= 5);
+        assert_eq!(ldpc_deps.len(), 3); // ldpc, stim, boost
     }
 
     #[test]

crates/pecos-chromobius/Cargo.toml

@@ -0,0 +1,31 @@
+[package]
+name = "pecos-chromobius"
+version.workspace = true
+edition.workspace = true
+readme.workspace = true
+authors.workspace = true
+homepage.workspace = true
+repository.workspace = true
+license.workspace = true
+keywords.workspace = true
+categories.workspace = true
+description = "Chromobius decoder wrapper for PECOS"
+
+[dependencies]
+pecos-decoder-core.workspace = true
+ndarray.workspace = true
+thiserror.workspace = true
+cxx.workspace = true
+
+[build-dependencies]
+pecos-build.workspace = true
+cxx-build.workspace = true
+cc.workspace = true
+env_logger.workspace = true
+log.workspace = true
+
+[lib]
+name = "pecos_chromobius"
+
+[lints]
+workspace = true

crates/pecos-chromobius/build.rs

@@ -0,0 +1,13 @@
+//! Build script for pecos-chromobius
+
+mod build_chromobius;
+mod build_stim;
+mod chromobius_patch;
+
+fn main() {
+    // Initialize logger for build script
+    env_logger::init();
+
+    // Build Chromobius (download handled inside build_chromobius)
+    build_chromobius::build().expect("Chromobius build failed");
+}

crates/pecos-chromobius/build_chromobius.rs

@@ -0,0 +1,237 @@
+//! Build script for Chromobius decoder integration
+
+use log::info;
+use pecos_build::{Manifest, Result, ensure_dep_ready, report_cache_config};
+use std::env;
+use std::fs;
+use std::path::{Path, PathBuf};
+
+// Use the shared modules from the parent
+use crate::build_stim;
+use crate::chromobius_patch;
+
+/// Get the build profile from Cargo's environment
+fn get_build_profile() -> String {
+    if let Ok(out_dir) = env::var("OUT_DIR") {
+        let parts: Vec<&str> = out_dir.split(std::path::MAIN_SEPARATOR).collect();
+        if let Some(target_idx) = parts.iter().position(|&p| p == "target")
+            && let Some(profile_name) = parts.get(target_idx + 1)
+        {
+            return match *profile_name {
+                "native" => "native",
+                "release" => "release",
+                "debug" => "debug",
+                _ => {
+                    if env::var("PROFILE").as_deref() == Ok("release") {
+                        "release"
+                    } else {
+                        "debug"
+                    }
+                }
+            }
+            .to_string();
+        }
+    }
+
+    match env::var("PROFILE").as_deref() {
+        Ok("release") => "release".to_string(),
+        _ => "debug".to_string(),
+    }
+}
+
+/// Main build function for Chromobius
+pub fn build() -> Result<()> {
+    println!("cargo:rerun-if-changed=build_chromobius.rs");
+    println!("cargo:rerun-if-changed=src/bridge.rs");
+    println!("cargo:rerun-if-changed=src/bridge.cpp");
+    println!("cargo:rerun-if-changed=include/chromobius_bridge.h");
+    println!("cargo:rerun-if-env-changed=FORCE_REBUILD");
+
+    let out_dir = PathBuf::from(env::var("OUT_DIR")?);
+
+    // Always emit link directives - Cargo will cache these
+    println!("cargo:rustc-link-search=native={}", out_dir.display());
+    println!("cargo:rustc-link-lib=static=chromobius-bridge");
+
+    // Get dependencies (downloads to ~/.pecos/cache/, extracts to ~/.pecos/deps/)
+    let manifest = Manifest::find_and_load_validated()?;
+    let chromobius_dir = ensure_dep_ready("chromobius", &manifest)?;
+    let stim_dir = ensure_dep_ready("stim", &manifest)?;
+    let pymatching_dir = ensure_dep_ready("pymatching", &manifest)?;
+
+    // Apply compatibility patches for newer Stim version
+    chromobius_patch::patch_chromobius_for_newer_stim(&chromobius_dir)?;
+
+    // Generate amalgamated stim.h if needed
+    build_stim::generate_amalgamated_header(&stim_dir)?;
+
+    // Build using cxx
+    build_cxx_bridge(&chromobius_dir, &stim_dir, &pymatching_dir)?;
+
+    Ok(())
+}
+
+fn build_cxx_bridge(chromobius_dir: &Path, stim_dir: &Path, pymatching_dir: &Path) -> Result<()> {
+    let chromobius_src_dir = chromobius_dir.join("src");
+    let stim_src_dir = stim_dir.join("src");
+    let pymatching_src_dir = pymatching_dir.join("src");
+
+    // Find essential source files
+    let chromobius_files = collect_chromobius_sources(&chromobius_src_dir)?;
+    let stim_files = build_stim::collect_stim_sources(&stim_src_dir);
+    let pymatching_files = collect_pymatching_sources(&pymatching_src_dir)?;
+
+    // Build the cxx bridge first to generate headers
+    let mut build = cxx_build::bridge("src/bridge.rs");
+
+    let target = env::var("TARGET").unwrap_or_default();
+
+    // On macOS, explicitly use system clang to ensure SDK paths are correct.
+    if target.contains("darwin") && env::var("CXX").is_err() && env::var("CC").is_err() {
+        build.compiler("/usr/bin/clang++");
+    }
+
+    // Add our bridge implementation
+    build.file("src/bridge.cpp");
+
+    // Add Chromobius core files
+    for file in chromobius_files {
+        build.file(file);
+    }
+
+    // Add PyMatching files
+    for file in pymatching_files {
+        build.file(file);
+    }
+
+    // Configure build
+    build
+        .std("c++20")
+        .include(&chromobius_src_dir)
+        .include(&stim_src_dir)
+        .include(stim_dir) // For amalgamated stim.h
+        .include(&pymatching_src_dir)
+        .include("include")
+        .include("src")
+        .define("CHROMOBIUS_BRIDGE_EXPORTS", None);
+
+    // Report ccache/sccache configuration
+    report_cache_config();
+
+    // Use build profile for optimization settings
+    let profile = get_build_profile();
+    match profile.as_str() {
+        "native" => {
+            build.flag_if_supported("-O3");
+            if env::var("CARGO_CFG_TARGET_ARCH").ok() == env::var("HOST_ARCH").ok() {
+                build.flag_if_supported("-march=native");
+            }
+        }
+        "release" => {
+            build.flag_if_supported("-O3");
+        }
+        _ => {
+            build.flag_if_supported("-O0");
+            build.flag_if_supported("-g");
+        }
+    }
+
+    // Add Stim files to the main build
+    for file in &stim_files {
+        build.file(file);
+    }
+
+    // Platform-specific configurations
+    if cfg!(not(target_env = "msvc")) {
+        build
+            .flag("-fvisibility=hidden")
+            .flag("-fvisibility-inlines-hidden")
+            .flag("-w")
+            .flag_if_supported("-fopenmp")
+            .flag("-fPIC");
+
+        if target.contains("darwin") {
+            build.flag("-stdlib=libc++");
+            build.flag("-L/usr/lib");
+            build.flag("-Wl,-search_paths_first");
+        }
+    } else {
+        build
+            .flag("/W0")
+            .flag("/MD")
+            .flag("/EHsc") // Enable C++ exception handling
+            .flag_if_supported("/permissive-")
+            .flag_if_supported("/Zc:__cplusplus");
+
+        // Force include standard headers that external libraries assume are available
+        // MSVC is stricter than GCC/Clang about transitive includes
+        build.flag("/FI").flag("array"); // For std::array
+        build.flag("/FI").flag("numeric"); // For std::iota (used by PyMatching)
+    }
+
+    build.compile("chromobius-bridge");
+
+    // On macOS, link against the system C++ library
+    if target.contains("darwin") {
+        println!("cargo:rustc-link-search=native=/usr/lib");
+        println!("cargo:rustc-link-lib=c++");
+        println!("cargo:rustc-link-arg=-Wl,-search_paths_first");
+    }
+
+    Ok(())
+}
+
+fn collect_chromobius_sources(chromobius_src_dir: &Path) -> Result<Vec<PathBuf>> {
+    let mut files = Vec::new();
+
+    // Collect all non-test, non-perf, non-pybind .cc files
+    collect_cc_files_filtered(chromobius_src_dir, &mut files)?;
+
+    info!("Found {} Chromobius source files", files.len());
+    Ok(files)
+}
+
+fn collect_pymatching_sources(pymatching_src_dir: &Path) -> Result<Vec<PathBuf>> {
+    let mut files = Vec::new();
+
+    // PyMatching sparse_blossom implementation files
+    let sparse_blossom_dir = pymatching_src_dir.join("pymatching/sparse_blossom");
+    if sparse_blossom_dir.exists() {
+        collect_cc_files_filtered(&sparse_blossom_dir, &mut files)?;
+    }
+
+    info!("Found {} PyMatching source files", files.len());
+    Ok(files)
+}
+
+fn collect_cc_files_filtered(dir: &Path, files: &mut Vec<PathBuf>) -> Result<()> {
+    for entry in fs::read_dir(dir)? {
+        let entry = entry?;
+        let path = entry.path();
+
+        if path.is_dir() {
+            // Skip test directories
+            if let Some(name) = path.file_name().and_then(|n| n.to_str())
+                && (name == "test" || name == "tests")
+            {
+                continue;
+            }
+            collect_cc_files_filtered(&path, files)?;
+        } else if path.extension().and_then(|s| s.to_str()) == Some("cc") {
+            let filename = path.file_name().and_then(|n| n.to_str()).unwrap_or("");
+            // Skip test, perf, pybind, and main files
+            if filename.contains(".test.")
+                || filename.contains(".perf.")
+                || filename.contains(".pybind.")
+                || filename == "main.cc"
+            {
+                continue;
+            }
+            if !files.contains(&path) {
+                files.push(path);
+            }
+        }
+    }
+
+    Ok(())
+}