Fixing the Selene->PECOS integration to handle dynamic programs

Cargo.toml

@@ -98,6 +98,9 @@ rand_core = "0.9"
 rand_xoshiro = "0.7"
 rapidhash = { version = "4", features = ["rng"] }
 
+# Concurrency
+crossbeam-channel = "0.5"
+
 # Windows workaround: Disable zstd-sys legacy feature to avoid MSVC ICE
 # MSVC 14.43 has an internal compiler error (C1001) when compiling zstd_v06.c
 # The legacy feature compiles old zstd formats (v0.1-v0.7) that PECOS doesn't need
@@ -117,8 +120,7 @@ pecos-qec = { version = "0.1.1", path = "crates/pecos-qec" }
 pecos-rng = { version = "0.1.1", path = "crates/pecos-rng" }
 pecos-qis-ffi = { version = "0.1.1", path = "crates/pecos-qis-ffi" }
 pecos-qis-ffi-types = { version = "0.1.1", path = "crates/pecos-qis-ffi-types" }
-pecos-qis-selene = { version = "0.1.1", path = "crates/pecos-qis-selene" }
-pecos-qis-core = { version = "0.1.1", path = "crates/pecos-qis-core" }
+pecos-qis = { version = "0.1.1", path = "crates/pecos-qis" }
 pecos-hugr-qis = { version = "0.1.1", path = "crates/pecos-hugr-qis" }
 pecos-hugr = { version = "0.1.1", path = "crates/pecos-hugr" }
 pecos-llvm = { version = "0.1.1", path = "crates/pecos-llvm" }

crates/benchmarks/Cargo.toml

@@ -9,7 +9,8 @@ license.workspace = true
 keywords.workspace = true
 categories.workspace = true
 publish = false
-readme = "../../README.md"
+description = "Performance benchmarks for PECOS (internal)"
+readme = "README.md"
 
 [dev-dependencies]
 criterion.workspace = true

crates/pecos-build/Cargo.toml

@@ -3,7 +3,7 @@ name = "pecos-build"
 version.workspace = true
 edition.workspace = true
 description = "PECOS build utilities - dependency management, LLVM setup, and build script helpers"
-readme.workspace = true
+readme = "README.md"
 authors.workspace = true
 homepage.workspace = true
 repository.workspace = true

crates/pecos-build/README.md

@@ -0,0 +1,37 @@
+# pecos-build
+
+Build utilities and dependency management for PECOS.
+
+## Purpose
+
+Used by build scripts (`build.rs`) to manage external dependencies. Handles downloading, caching, and locating libraries.
+
+## Key Features
+
+- **LLVM 14 management**: Install, configure, and find LLVM 14
+- **Dependency downloads**: QuEST, Qulacs, Stim, Eigen, etc.
+- **Tool finding**: `find_tool("llvm-as")`, `find_llvm_14()`
+- **Manifest parsing**: Load `pecos.toml` for dependency versions
+
+## PECOS Home Directory
+
+All dependencies managed under `~/.pecos/`:
+
+```
+~/.pecos/
+├── cache/   # Downloaded archives
+├── deps/    # Extracted source trees
+├── llvm/    # LLVM installation
+└── tmp/     # Temporary files
+```
+
+## Usage
+
+```rust
+// In build.rs
+use pecos_build::{ensure_dep_ready, Manifest, find_tool};
+
+let manifest = Manifest::find_and_load_validated()?;
+let quest_path = ensure_dep_ready("quest", &manifest)?;
+let llvm_as = find_tool("llvm-as");
+```

crates/pecos-chromobius/Cargo.toml

@@ -2,14 +2,14 @@
 name = "pecos-chromobius"
 version.workspace = true
 edition.workspace = true
-readme.workspace = true
+readme = "README.md"
 authors.workspace = true
 homepage.workspace = true
 repository.workspace = true
 license.workspace = true
 keywords.workspace = true
 categories.workspace = true
-description = "Chromobius decoder wrapper for PECOS"
+description = "Chromobius color code decoder for PECOS"
 
 [dependencies]
 pecos-decoder-core.workspace = true

crates/pecos-chromobius/README.md

@@ -0,0 +1,19 @@
+# pecos-chromobius
+
+Chromobius color code decoder for PECOS.
+
+## Purpose
+
+Wraps the Chromobius decoder for color code quantum error correction. Uses Mobius matching for efficient syndrome decoding.
+
+## Key Types
+
+- `ChromobiusDecoder` - Main decoder interface
+- `ChromobiusConfig` - Decoder configuration
+
+## Acknowledgements
+
+This crate wraps [Chromobius](https://github.com/quantumlib/chromobius), a color code decoder developed by Craig Gidney and Cody Jones at Google Quantum AI.
+
+**Paper:**
+- Gidney, C. & Jones, C. (2023). "New circuits and an open source decoder for the color code." [arXiv:2312.08813](https://arxiv.org/abs/2312.08813)

crates/pecos-core/Cargo.toml

@@ -8,8 +8,8 @@ repository.workspace = true
 license.workspace = true
 keywords.workspace = true
 categories.workspace = true
-description = "Provides core definitions and functions for PECOS simulations."
-readme = "../../README.md"
+description = "Core types and utilities for PECOS"
+readme = "README.md"
 
 [dependencies]
 bitvec.workspace = true

crates/pecos-core/README.md

@@ -1,5 +1,18 @@
 # pecos-core
 
-`pecos-core` is an **internal crate** to provide core functionality.
+Core types and utilities for PECOS.
 
-This is not intended for external use.
+## Purpose
+
+Provides fundamental types used across the PECOS ecosystem.
+
+## Key Types
+
+- `QubitId` - Qubit identifier
+- `Gate` - Gate representation
+- `Pauli`, `PauliString` - Pauli operators
+- `Bit`, `BitSet`, `BitVec` - Bit manipulation
+- `Angle` - Angle representations
+- `Phase`, `Sign` - Phase utilities
+
+This is an internal crate. Most users should use the `pecos` meta-crate.

crates/pecos-decoder-core/Cargo.toml

@@ -2,7 +2,7 @@
 name = "pecos-decoder-core"
 version.workspace = true
 edition.workspace = true
-readme.workspace = true
+readme = "README.md"
 authors.workspace = true
 homepage.workspace = true
 repository.workspace = true

crates/pecos-decoder-core/README.md

@@ -0,0 +1,20 @@
+# pecos-decoder-core
+
+Core decoder traits and types for PECOS.
+
+## Purpose
+
+Defines the fundamental decoder traits used across all decoder implementations. Separated from `pecos-decoders` to avoid circular dependencies.
+
+## Key Traits
+
+- `Decoder` - Core trait all decoders implement
+- `BatchDecoder` - Batch decoding interface
+- `CssDecoder` - CSS code specific decoding
+- `SoftDecoder` - Soft information (LLR) decoding
+
+## Additional Types
+
+- `DecoderError` - Unified error types
+- `DecodingResultTrait` - Result trait
+- `CheckMatrixConfig` - Matrix configuration

crates/pecos-decoders/Cargo.toml

@@ -2,14 +2,14 @@
 name = "pecos-decoders"
 version.workspace = true
 edition.workspace = true
-readme.workspace = true
+readme = "README.md"
 authors.workspace = true
 homepage.workspace = true
 repository.workspace = true
 license.workspace = true
 keywords.workspace = true
 categories.workspace = true
-description = "Unified decoder library for PECOS - meta crate"
+description = "Unified decoder meta-crate for PECOS"
 
 [dependencies]
 pecos-decoder-core.workspace = true

crates/pecos-decoders/README.md

@@ -0,0 +1,26 @@
+# pecos-decoders
+
+Unified decoder meta-crate for PECOS.
+
+## Purpose
+
+Provides a unified interface to all PECOS decoders through feature-gated re-exports.
+
+## Features
+
+Enable the appropriate features to include specific decoder families:
+
+- `ldpc` - LDPC decoders (BP-OSD, BP-LSD, Union-Find, etc.)
+- `fusion-blossom` - Fusion Blossom MWPM decoder
+- `pymatching` - PyMatching MWPM decoder
+- `tesseract` - Tesseract search-based decoder
+- `chromobius` - Chromobius color code decoder
+- `all` - Enable all decoders
+
+## Key Types
+
+Re-exports from `pecos-decoder-core`:
+- `Decoder` trait - Interface for QEC decoders
+- `BatchDecoder` trait - Batch decoding interface
+- `CssDecoder` trait - CSS code specific decoding
+- `SoftDecoder` trait - Soft information decoding

crates/pecos-engines/Cargo.toml

@@ -2,14 +2,14 @@
 name = "pecos-engines"
 version.workspace = true
 edition.workspace = true
-readme.workspace = true
+readme = "README.md"
 authors.workspace = true
 homepage.workspace = true
 repository.workspace = true
 license.workspace = true
 keywords.workspace = true
 categories.workspace = true
-description = "Provides simulator engines for PECOS simulations."
+description = "Simulation engine infrastructure for PECOS"
 
 [lib]
 crate-type = ["rlib"]