misc cleanup of CI and agents

.github/workflows/benchmark.yml

@@ -1,8 +1,7 @@
 name: Benchmarks
 on:
   pull_request_target:
-    branches:
-      - master
+    branches: [master, main]
 permissions:
   pull-requests: write
 

.github/workflows/ci.yml

@@ -27,19 +27,14 @@ jobs:
         os:
           - ubuntu-latest
         threads:
-          - '1'
-          - '5'
+          - '2'
         arch:
           - x64
         include:
           - arch: aarch64
             os: macos-latest
             version: '1'
             threads: '1'
-          - arch: x64
-            os: macos-latest
-            version: '1'
-            threads: '1'
           - arch: x64
             os: windows-latest
             version: '1'

AGENTS.md

@@ -0,0 +1,147 @@
+# PBCCompiler.jl
+
+Tools for Pauli Based Computation (PBC), a modality of quantum computation.
+
+## Project Structure
+
+- `src/PBCCompiler.jl` - Main module with circuit operations and compiler infrastructure
+- `src/traversal.jl` - Circuit traversal utilities for gate simplifications
+- `src/affectedqubits.jl` - Query functions for qubit indices affected by operations
+- `src/plotting.jl` - Plotting function stubs (scaffolding for extensions)
+- `ext/PBCCompilerMakieExt/` - Makie extension for circuit visualization
+- `test/` - Test suite using TestItemRunner.jl
+- `benchmark/` - Performance benchmarks using BenchmarkTools.jl
+
+## Dependencies
+
+- **Moshi.jl** - Algebraic data types via `@data` macro
+- **QuantumClifford.jl** - Pauli operators and stabilizer formalism
+
+## Key Concepts
+
+### Circuit Operations (`CircuitOp`)
+Algebraic data type representing quantum circuit operations:
+- `Measurement` - Pauli measurement with classical bit output
+- `Pauli` - Pauli gate application
+- `ExpHalfPiPauli`, `ExpQuatPiPauli`, `ExpEighPiPauli` - Rotation gates (pi/2, pi/4, pi/8)
+- `PrepMagic` - Magic state preparation
+- `PauliConditional` - Pauli gate conditioned on another Pauli
+- `BitConditional` - Operation conditioned on classical bit
+
+### Compilation Pipeline
+The `preprocess_circuit` function transforms circuits through stages:
+1. Remove Pauli conditionals
+2. Commute non-Clifford gates to front
+3. Group non-Clifford operations
+4. Commute measurements to end
+5. Remove non-Clifford gates (introduce magic states)
+6. Remove post-measurement operations
+
+### Runtime
+- `QuantumRuntime` - Abstract type for quantum execution backends
+- `MockRuntime` - Testing runtime where measurements return deterministic results
+- `ComputerState` - Tracks circuit, instruction pointer, and memory state
+
+### Circuit Traversal
+The `traversal` function (`src/traversal.jl`) applies transformations to adjacent pairs of circuit operations:
+```julia
+traversal(circuit, pair_transformation, direction=:right, starting_index=1, end_index=:end)
+```
+- `pair_transformation(op1, op2)` returns:
+  - `(new_op1, new_op2)` tuple to replace the pair
+  - Single operation to combine the pair into one
+  - `nothing` to keep unchanged
+- Supports left-to-right (`:right`) or right-to-left (`:left`) traversal
+- Used for gate commutation, simplification, and compilation passes
+
+**Note on Moshi types**: Use `Moshi.Data.isa_variant(op, CircuitOp.Pauli)` instead of `op isa CircuitOp.Pauli` to check variant types.
+
+### Affected Qubits
+The `affectedqubits` function (`src/affectedqubits.jl`) returns the sorted list of qubit indices affected by an operation or circuit:
+```julia
+affectedqubits(op::CircuitOp.Type) -> Vector{Int}
+affectedqubits(circuit::Circuit) -> Vector{Int}
+```
+
+### Circuit Visualization (Makie Extension)
+When Makie is loaded, the `PBCCompilerMakieExt` extension provides circuit plotting:
+```julia
+using CairoMakie  # or GLMakie
+using PBCCompiler
+
+circuit = Circuit([...])
+circuitplot(circuit)  # Create a plot
+circuitplot!(ax, circuit)  # Add to existing axis
+circuitplot_axis(fig[1,1], circuit)  # Create complete figure panel
+```
+
+**Plot features:**
+- Gates shown as colored rectangles spanning affected qubits
+- Horizontal qubit wire lines
+- Measurement results marked with classical bit index (e.g., "c0")
+- Conditional operations marked with dependency index (e.g., "?c0")
+- PrepMagic gates not visualized (placeholder for future)
+
+**Configurable attributes:**
+- `gatewidth`, `qubitspacing` - Gate dimensions
+- `wirecolor`, `wirelinewidth` - Wire appearance
+- `paulicolor`, `measurementcolor`, etc. - Gate colors by variant
+
+## Development
+
+### Workflow
+1. Always pull latest master: `git pull`
+2. Create feature branches for new work
+3. Commit often at each change
+4. Update CLAUDE.md with new functionality
+5. Run tests before creating PRs
+6. Add benchmarks for new performance-critical functionality
+
+### Docstring Guidelines
+- Docstrings are for **users**, not developers
+- Do not include implementation details (e.g., "uses pattern matching", "implemented via recursion")
+- Focus on: what the function does, its arguments, return values, and usage examples
+- Implementation notes belong in code comments, not docstrings
+
+### Run tests
+```bash
+julia -tauto --project -e 'using Pkg; Pkg.test("PBCCompiler")'
+```
+
+### Benchmarks
+Benchmarks are managed with BenchmarkTools.jl and run in CI via AirspeedVelocity.jl.
+
+Run benchmarks locally:
+```bash
+julia -tauto --project=benchmark -e 'include("benchmark/benchmarks.jl"); run(SUITE)'
+```
+
+**When to add benchmarks:**
+- New compilation passes or transformations
+- New traversal operations
+- Any function that processes circuits at scale
+- Performance-critical code paths
+
+**Benchmark file structure:**
+- Add new benchmarks to `benchmark/benchmarks.jl`
+- Use `evals=1` for functions that modify state in-place
+- Use `setup=` to create fresh data for each evaluation
+- Group related benchmarks using `BenchmarkGroup`
+
+### Julia invocation
+Always use the `-tauto` flag when launching Julia to utilize all available threads, which drastically speeds up compilation times:
+```bash
+julia -tauto --project
+```
+
+### Related source code
+- QuantumClifford.jl source: `../QuantumClifford.jl`
+- QuantumInterface.jl source: `../QuantumInterface.jl`
+
+### Reference paper
+- "Game of Surface Codes" - https://quantum-journal.org/papers/q-2019-03-05-128/pdf/
+
+## Related Packages
+
+- [QuantumClifford.jl](https://github.com/QuantumSavory/QuantumClifford.jl) - Stabilizer formalism
+- [BPGates.jl](https://github.com/QuantumSavory/BPGates.jl) - Bell-preserving gates

CLAUDE.md

@@ -1,147 +1 @@
-# PBCCompiler.jl
-
-Tools for Pauli Based Computation (PBC), a modality of quantum computation.
-
-## Project Structure
-
-- `src/PBCCompiler.jl` - Main module with circuit operations and compiler infrastructure
-- `src/traversal.jl` - Circuit traversal utilities for gate simplifications
-- `src/affectedqubits.jl` - Query functions for qubit indices affected by operations
-- `src/plotting.jl` - Plotting function stubs (scaffolding for extensions)
-- `ext/PBCCompilerMakieExt/` - Makie extension for circuit visualization
-- `test/` - Test suite using TestItemRunner.jl
-- `benchmark/` - Performance benchmarks using BenchmarkTools.jl
-
-## Dependencies
-
-- **Moshi.jl** - Algebraic data types via `@data` macro
-- **QuantumClifford.jl** - Pauli operators and stabilizer formalism
-
-## Key Concepts
-
-### Circuit Operations (`CircuitOp`)
-Algebraic data type representing quantum circuit operations:
-- `Measurement` - Pauli measurement with classical bit output
-- `Pauli` - Pauli gate application
-- `ExpHalfPiPauli`, `ExpQuatPiPauli`, `ExpEighPiPauli` - Rotation gates (pi/2, pi/4, pi/8)
-- `PrepMagic` - Magic state preparation
-- `PauliConditional` - Pauli gate conditioned on another Pauli
-- `BitConditional` - Operation conditioned on classical bit
-
-### Compilation Pipeline
-The `preprocess_circuit` function transforms circuits through stages:
-1. Remove Pauli conditionals
-2. Commute non-Clifford gates to front
-3. Group non-Clifford operations
-4. Commute measurements to end
-5. Remove non-Clifford gates (introduce magic states)
-6. Remove post-measurement operations
-
-### Runtime
-- `QuantumRuntime` - Abstract type for quantum execution backends
-- `MockRuntime` - Testing runtime where measurements return deterministic results
-- `ComputerState` - Tracks circuit, instruction pointer, and memory state
-
-### Circuit Traversal
-The `traversal` function (`src/traversal.jl`) applies transformations to adjacent pairs of circuit operations:
-```julia
-traversal(circuit, pair_transformation, direction=:right, starting_index=1, end_index=:end)
-```
-- `pair_transformation(op1, op2)` returns:
-  - `(new_op1, new_op2)` tuple to replace the pair
-  - Single operation to combine the pair into one
-  - `nothing` to keep unchanged
-- Supports left-to-right (`:right`) or right-to-left (`:left`) traversal
-- Used for gate commutation, simplification, and compilation passes
-
-**Note on Moshi types**: Use `Moshi.Data.isa_variant(op, CircuitOp.Pauli)` instead of `op isa CircuitOp.Pauli` to check variant types.
-
-### Affected Qubits
-The `affectedqubits` function (`src/affectedqubits.jl`) returns the sorted list of qubit indices affected by an operation or circuit:
-```julia
-affectedqubits(op::CircuitOp.Type) -> Vector{Int}
-affectedqubits(circuit::Circuit) -> Vector{Int}
-```
-
-### Circuit Visualization (Makie Extension)
-When Makie is loaded, the `PBCCompilerMakieExt` extension provides circuit plotting:
-```julia
-using CairoMakie  # or GLMakie
-using PBCCompiler
-
-circuit = Circuit([...])
-circuitplot(circuit)  # Create a plot
-circuitplot!(ax, circuit)  # Add to existing axis
-circuitplot_axis(fig[1,1], circuit)  # Create complete figure panel
-```
-
-**Plot features:**
-- Gates shown as colored rectangles spanning affected qubits
-- Horizontal qubit wire lines
-- Measurement results marked with classical bit index (e.g., "c0")
-- Conditional operations marked with dependency index (e.g., "?c0")
-- PrepMagic gates not visualized (placeholder for future)
-
-**Configurable attributes:**
-- `gatewidth`, `qubitspacing` - Gate dimensions
-- `wirecolor`, `wirelinewidth` - Wire appearance
-- `paulicolor`, `measurementcolor`, etc. - Gate colors by variant
-
-## Development
-
-### Workflow
-1. Always pull latest master: `git pull`
-2. Create feature branches for new work
-3. Commit often at each change
-4. Update CLAUDE.md with new functionality
-5. Run tests before creating PRs
-6. Add benchmarks for new performance-critical functionality
-
-### Docstring Guidelines
-- Docstrings are for **users**, not developers
-- Do not include implementation details (e.g., "uses pattern matching", "implemented via recursion")
-- Focus on: what the function does, its arguments, return values, and usage examples
-- Implementation notes belong in code comments, not docstrings
-
-### Run tests
-```bash
-julia -tauto --project -e 'using Pkg; Pkg.test("PBCCompiler")'
-```
-
-### Benchmarks
-Benchmarks are managed with BenchmarkTools.jl and run in CI via AirspeedVelocity.jl.
-
-Run benchmarks locally:
-```bash
-julia -tauto --project=benchmark -e 'include("benchmark/benchmarks.jl"); run(SUITE)'
-```
-
-**When to add benchmarks:**
-- New compilation passes or transformations
-- New traversal operations
-- Any function that processes circuits at scale
-- Performance-critical code paths
-
-**Benchmark file structure:**
-- Add new benchmarks to `benchmark/benchmarks.jl`
-- Use `evals=1` for functions that modify state in-place
-- Use `setup=` to create fresh data for each evaluation
-- Group related benchmarks using `BenchmarkGroup`
-
-### Julia invocation
-Always use the `-tauto` flag when launching Julia to utilize all available threads, which drastically speeds up compilation times:
-```bash
-julia -tauto --project
-```
-
-### Related source code
-- QuantumClifford.jl source: `../QuantumClifford.jl`
-- QuantumInterface.jl source: `../QuantumInterface.jl`
-
-### Reference paper
-- "Game of Surface Codes" - https://quantum-journal.org/papers/q-2019-03-05-128/pdf/
-
-## Related Packages
-
-- [QuantumClifford.jl](https://github.com/QuantumSavory/QuantumClifford.jl) - Stabilizer formalism
-- [BPGates.jl](https://github.com/QuantumSavory/BPGates.jl) - Bell-preserving gates
+@AGENTS.md