refactor + linting + updating dependencies

Cargo.toml

@@ -21,24 +21,23 @@ keywords = ["scientific", "quantum", "QEC"]
 categories = ["science", "simulation"]
 
 [workspace.dependencies]
+rand = "0.9"
+rand_chacha = "0.9"
+rand_xoshiro = "0.7"
+uuid = { version = "1", features = ["v4"] }
 pyo3 = "0.23"
-rand = "0.8"
 rayon = "1"
-rand_chacha = "0.3"
-rand_xoshiro = "0.6"
 clap = { version = "4", features = ["derive"] }
 log = "0.4"
 env_logger = "0.11"
 memmap2 = "0.9"
-uuid = { version = "1", features = ["v4"] }
 serde = { version = "1", features = ["derive"] }
 os_pipe = "1"
-lazy_static = "1.5.0"
-parking_lot = "0.12.3"
-serde_json = "1.0.137"
+lazy_static = "1"
+parking_lot = "0.12"
+serde_json = "1"
 num-complex = "0.4"
 num-traits = "0.2"
-tempfile = "3"
 criterion = "0.5"
 
 pecos-core = { version = "0.1.1", path = "crates/pecos-core" }
@@ -56,13 +55,14 @@ lto = "fat"
 
 [workspace.lints.clippy]
 # For more details see: https://doc.rust-lang.org/clippy/lints.html
-suspicious = "warn"
-complexity = "warn"
-perf = "warn"
-style = "warn"
-pedantic = "warn"
+suspicious = { level = "warn", priority = -1 }
+complexity = { level = "warn", priority = -1 }
+perf = { level = "warn", priority = -1 }
+style = { level = "warn", priority = -1 }
+pedantic = { level = "warn", priority = -1 }
 # restriction = "warn"
-cargo = "warn"
+cargo = { level = "warn", priority = -1 }
+multiple-crate-versions = "allow" # TODO: remove when possible
 
 [workspace.metadata.commands]
 test-py = ["./scripts/setup-env.sh", "cargo", "test", "-p", "pecos-python"]

Makefile

@@ -24,24 +24,24 @@ installreqs: ## Install Python project requirements to root .venv
 # ---------------------------------
 .PHONY: build
 build: installreqs ## Compile and install for development
-	cd python/pecos-rslib/ && uv run maturin develop --uv
-	cd python/quantum-pecos && uv pip install -e .[all]
+	@unset CONDA_PREFIX && cd python/pecos-rslib/ && uv run maturin develop --uv
+	@unset CONDA_PREFIX && cd python/quantum-pecos && uv pip install -e .[all]
 
 .PHONY: build-basic
 build-basic: installreqs ## Compile and install for development but do not include install extras
-	cd python/pecos-rslib/ && uv run maturin develop --uv
-	cd python/quantum-pecos && uv pip install -e .
+	@unset CONDA_PREFIX && cd python/pecos-rslib/ && uv run maturin develop --uv
+	@unset CONDA_PREFIX && cd python/quantum-pecos && uv pip install -e .
 
 .PHONY: build-release
 build-release: installreqs ## Build a faster version of binaries
-	cd python/pecos-rslib/ && uv run maturin develop --uv --release
-	cd python/quantum-pecos && uv pip install -e .[all]
+	@unset CONDA_PREFIX && cd python/pecos-rslib/ && uv run maturin develop --uv --release
+	@unset CONDA_PREFIX && cd python/quantum-pecos && uv pip install -e .[all]
 
 .PHONY: build-native
 build-native: installreqs ## Build a faster version of binaries with native CPU optimization
-	cd python/pecos-rslib/ && RUSTFLAGS='-C target-cpu=native' \
+	@unset CONDA_PREFIX && cd python/pecos-rslib/ && RUSTFLAGS='-C target-cpu=native' \
 	&& uv run maturin develop --uv --release
-	cd python/quantum-pecos && uv pip install -e .[all]
+	@unset CONDA_PREFIX && cd python/quantum-pecos && uv pip install -e .[all]
 
 # Documentation
 # -------------
@@ -79,14 +79,15 @@ rstest:  ## Run Rust tests
 .PHONY: pytest
 pytest:  ## Run tests on the Python package (not including optional dependencies). ASSUMES: previous build command
 	uv run pytest ./python/tests/ -m "not optional_dependency"
+	uv run pytest ./python/pecos-rslib/tests/
 
 .PHONY: pytest-dep
 pytest-dep: ## Run tests on the Python package only for optional dependencies. ASSUMES: previous build command
 	uv run pytest ./python/tests/ -m optional_dependency
 
 .PHONY: pytest-all
-pytest-all:  ## Run all tests on the Python package ASSUMES: previous build command
-	uv run pytest ./python/tests/
+pytest-all:  pytest ## Run all tests on the Python package ASSUMES: previous build command
+	uv run pytest ./python/tests/ -m "optional_dependency"
 
 # .PHONY: pytest-doc
 # pydoctest:  ## Run doctests with pytest. ASSUMES: A build command was ran previously. ASSUMES: previous build command
@@ -103,13 +104,13 @@ test: rstest pytest-all ## Run all tests. ASSUMES: previous build command
 clean:  ## Clean up caches and build artifacts
 	@rm -rf *.egg-info
 	@rm -rf dist
-	@rm -rf **/build/
+	@find . -type d -name "build" -exec rm -rf {} +
 	@rm -rf python/docs/_build
-	@rm -rf **/.pytest_cache/
-	@rm -rf **/.ipynb_checkpoints
+	@find . -type d -name ".pytest_cache" -exec rm -rf {} +
+	@find . -type d -name ".ipynb_checkpoints" -exec rm -rf {} +
 	@rm -rf .ruff_cache/
-	@rm -rf **/.hypothesis/
-	@rm -rf **/junit/
+	@find . -type d -name ".hypothesis" -exec rm -rf {} +
+	@find . -type d -name "junit" -exec rm -rf {} +
 	@cargo clean
 
 .PHONY: pip-install-uv

crates/benchmarks/Cargo.toml

@@ -13,7 +13,6 @@ publish = false
 [dev-dependencies]
 criterion = { workspace = true }
 pecos = { workspace = true }
-pecos-core = { workspace = true }
 
 [[bench]]
 name = "benchmarks"

crates/pecos-cli/src/main.rs

@@ -68,6 +68,7 @@ fn detect_program_type(path: &Path) -> Result<ProgramType, Box<dyn Error>> {
     }
 }
 
+#[allow(clippy::upper_case_acronyms)]
 enum ProgramType {
     QIR,
     PHIR,

crates/pecos-core/Cargo.toml

@@ -16,7 +16,6 @@ rand_chacha = { workspace = true }
 rand_xoshiro = { workspace = true }
 num-traits = { workspace = true }
 num-complex = { workspace = true }
-log = { workspace = true }
 serde = { workspace = true, features = ["derive"] }
 
 [lints]

crates/pecos-core/src/angle.rs

@@ -975,9 +975,9 @@ mod tests {
 
     #[test]
     fn test_randomized_values_u32_to_u64() {
-        let mut rng = rand::thread_rng();
+        let mut rng = rand::rng();
         for _ in 0..1000 {
-            let random_u32: u32 = rng.gen();
+            let random_u32: u32 = rng.random();
             let angle_u32 = Angle::<u32>::new(random_u32);
             let converted: Angle<u64> = angle_u32.into();
             let back: Angle<u32> = converted.try_into().expect("Lossless conversion failed");
@@ -987,9 +987,9 @@ mod tests {
 
     #[test]
     fn test_randomized_values_u64_to_u32() {
-        let mut rng = rand::thread_rng();
+        let mut rng = rand::rng();
         for _ in 0..1000 {
-            let random_u64: u64 = rng.gen();
+            let random_u64: u64 = rng.random();
             let angle_u64 = Angle::<u64>::new(random_u64);
             let result: Result<Angle<u32>, _> = angle_u64.try_into();
             if u32::try_from(random_u64).is_ok() {
@@ -1314,28 +1314,28 @@ mod tests {
 
     #[test]
     fn test_randomized_conversions() {
-        let mut rng = rand::thread_rng();
+        let mut rng = rand::rng();
 
         for _ in 0..1000 {
-            let val_u8: u8 = rng.gen();
+            let val_u8: u8 = rng.random();
             let angle = Angle::<u8>::new(val_u8);
             let up: Angle<u16> = angle.into();
             let down: Angle<u8> = up.try_into().expect("Lossless downscaling failed");
             assert_eq!(angle, down);
 
-            let val_u16: u16 = rng.gen();
+            let val_u16: u16 = rng.random();
             let angle = Angle::<u16>::new(val_u16);
             let up: Angle<u32> = angle.into();
             let down: Angle<u16> = up.try_into().expect("Lossless downscaling failed");
             assert_eq!(angle, down);
 
-            let val_u32: u32 = rng.gen();
+            let val_u32: u32 = rng.random();
             let angle = Angle::<u32>::new(val_u32);
             let up: Angle<u64> = angle.into();
             let down: Angle<u32> = up.try_into().expect("Lossless downscaling failed");
             assert_eq!(angle, down);
 
-            let val_u64: u64 = rng.gen();
+            let val_u64: u64 = rng.random();
             let angle = Angle::<u64>::new(val_u64);
             let up: Angle<u128> = angle.into();
             let down: Angle<u64> = up.try_into().expect("Lossless downscaling failed");

crates/pecos-core/src/sims_rngs.rs

@@ -13,6 +13,5 @@
 pub mod chacha_rng;
 pub mod choices;
 pub mod cyclic_rng;
-// pub mod mock_rng;
 pub mod sim_rng;
 pub mod xoshiro_rng;