fix: Tighten lint expectations and example helpers

crates/fhe-math/benches/ntt.rs

@@ -1,7 +1,4 @@
-// Allow indexing in benchmarks for convenience
-#![allow(clippy::indexing_slicing)]
-#![allow(missing_docs)]
-
+#![expect(missing_docs, reason = "examples/benches/tests omit docs by design")]
 use criterion::{BenchmarkId, Criterion, criterion_group, criterion_main};
 use fhe_math::{ntt::NttOperator, zq::Modulus};
 use rand::rng;

crates/fhe-math/benches/rns.rs

@@ -1,7 +1,4 @@
-// Allow indexing in benchmarks for convenience
-#![allow(clippy::indexing_slicing)]
-#![allow(missing_docs)]
-
+#![expect(missing_docs, reason = "examples/benches/tests omit docs by design")]
 use criterion::{BenchmarkId, Criterion, criterion_group, criterion_main};
 use fhe_math::rns::{RnsContext, RnsScaler, ScalingFactor};
 use num_bigint::BigUint;

crates/fhe-math/benches/rq.rs

@@ -1,7 +1,8 @@
-// Allow indexing in benchmarks for convenience
-#![allow(clippy::indexing_slicing)]
-#![allow(missing_docs)]
-
+#![expect(missing_docs, reason = "examples/benches/tests omit docs by design")]
+#![expect(
+    clippy::indexing_slicing,
+    reason = "performance or example code relies on validated indices"
+)]
 use criterion::measurement::WallTime;
 use criterion::{BenchmarkGroup, BenchmarkId, Criterion, criterion_group, criterion_main};
 use fhe_math::rq::*;

crates/fhe-math/benches/zq.rs

@@ -1,7 +1,8 @@
-// Allow indexing in benchmarks for convenience
-#![allow(clippy::indexing_slicing)]
-#![allow(missing_docs)]
-
+#![expect(missing_docs, reason = "examples/benches/tests omit docs by design")]
+#![expect(
+    clippy::indexing_slicing,
+    reason = "performance or example code relies on validated indices"
+)]
 use criterion::{BenchmarkId, Criterion, criterion_group, criterion_main};
 use fhe_math::zq::Modulus;
 use rand::rng;

crates/fhe-math/src/ntt/native.rs

@@ -1,6 +1,9 @@
-// Allow indexing in this performance-critical NTT implementation.
+// Expect indexing in this performance-critical NTT implementation.
 // The unsafe blocks already indicate this is performance-sensitive code.
-#![allow(clippy::indexing_slicing)]
+#![expect(
+    clippy::indexing_slicing,
+    reason = "performance or example code relies on validated indices"
+)]
 
 use crate::zq::Modulus;
 use itertools::Itertools;

crates/fhe-math/src/proto/mod.rs

@@ -1,6 +1,4 @@
 //! Protobuf for the `fhe-math` crate.
 
-#![allow(missing_docs)]
-
 /// Protobuf for polynomials.
 pub mod rq;

crates/fhe-math/src/proto/rq.rs

@@ -1,6 +1,7 @@
-#![allow(missing_docs)]
-
-#[allow(clippy::derive_partial_eq_without_eq)]
+#[expect(
+    clippy::derive_partial_eq_without_eq,
+    reason = "prost-generated types do not need Eq"
+)]
 #[derive(Clone, PartialEq, ::prost::Message)]
 pub struct Rq {
     #[prost(enumeration = "Representation", tag = "1")]

crates/fhe-math/src/rns/mod.rs

@@ -1,6 +1,9 @@
 #![warn(missing_docs, unused_imports)]
-// Allow indexing in this performance-critical RNS implementation
-#![allow(clippy::indexing_slicing)]
+// Expect indexing in this performance-critical RNS implementation
+#![expect(
+    clippy::indexing_slicing,
+    reason = "performance or example code relies on validated indices"
+)]
 
 //! Residue-Number System operations.
 
@@ -69,7 +72,10 @@ impl RnsContext {
                 product_dig *= &BigUintDig::from(moduli_u64[i]);
             }
 
-            #[allow(clippy::type_complexity)]
+            #[expect(
+                clippy::type_complexity,
+                reason = "complex tuple is produced by multiunzip"
+            )]
             let (moduli, q_tilde, q_tilde_shoup, q_star, garner): (
                 Vec<Modulus>,
                 Vec<u64>,

crates/fhe-math/src/rns/scaler.rs

@@ -1,6 +1,9 @@
 #![warn(missing_docs, unused_imports)]
-// Allow indexing in this performance-critical RNS scaler implementation
-#![allow(clippy::indexing_slicing)]
+// Expect indexing in this performance-critical RNS scaler implementation
+#![expect(
+    clippy::indexing_slicing,
+    reason = "performance or example code relies on validated indices"
+)]
 
 //! RNS scaler inspired from Remark 3.2 of <https://eprint.iacr.org/2021/204.pdf>.
 

crates/fhe-math/src/rq/convert.rs

@@ -434,7 +434,7 @@ impl From<&Poly> for Vec<BigUint> {
 
 #[cfg(test)]
 mod tests {
-    #![allow(clippy::expect_used)]
+    #![expect(clippy::expect_used, reason = "bounds are validated before use")]
 
     use crate::{
         Error as CrateError,

crates/fhe-math/src/rq/mod.rs

@@ -1,7 +1,10 @@
 #![warn(missing_docs, unused_imports)]
-// Allow indexing/slicing in this performance-critical polynomial arithmetic module.
+// Expect indexing/slicing in this performance-critical polynomial arithmetic module.
 // This code heavily uses RNS representation and requires fast array access.
-#![allow(clippy::indexing_slicing)]
+#![expect(
+    clippy::indexing_slicing,
+    reason = "performance or example code relies on validated indices"
+)]
 
 //! Polynomials in R_q\[x\] = (ZZ_q1 x ... x ZZ_qn)\[x\] where the qi's are
 //! prime moduli in zq.

crates/fhe-math/src/rq/ops.rs

@@ -110,7 +110,7 @@ impl Sub<&Poly> for &Poly {
 }
 
 impl MulAssign<&Poly> for Poly {
-    #[allow(clippy::panic)]
+    #[expect(clippy::panic, reason = "panic indicates violated internal invariant")]
     fn mul_assign(&mut self, p: &Poly) {
         assert!(!p.has_lazy_coefficients);
         assert_ne!(

crates/fhe-math/src/zq/mod.rs

@@ -1118,7 +1118,6 @@ mod tests {
         let ntests = 100;
         let mut rng = rand::rng();
 
-        #[allow(clippy::single_element_loop)]
         for p in [4611686018326724609] {
             let q = Modulus::new(p).unwrap();
             assert!(primes::supports_opt(p));

crates/fhe-util/src/lib.rs

@@ -56,7 +56,7 @@ pub fn sample_vec_cbd<R: RngCore + CryptoRng>(
 
 /// Transcodes a vector of u64 of `nbits`-bit numbers into a vector of bytes.
 #[must_use]
-#[allow(clippy::expect_used)]
+#[expect(clippy::expect_used, reason = "bounds are validated before use")]
 pub fn transcode_to_bytes(a: &[u64], nbits: usize) -> Vec<u8> {
     assert!(0 < nbits && nbits <= 64);
 
@@ -96,7 +96,7 @@ pub fn transcode_to_bytes(a: &[u64], nbits: usize) -> Vec<u8> {
 
 /// Transcodes a vector of u8 into a vector of u64 of `nbits`-bit numbers.
 #[must_use]
-#[allow(clippy::expect_used)]
+#[expect(clippy::expect_used, reason = "bounds are validated before use")]
 pub fn transcode_from_bytes(b: &[u8], nbits: usize) -> Vec<u64> {
     assert!(0 < nbits && nbits <= 64);
     let mask = (u64::MAX >> (64 - nbits)) as u128;
@@ -135,7 +135,7 @@ pub fn transcode_from_bytes(b: &[u8], nbits: usize) -> Vec<u64> {
 /// Transcodes a vector of u64 of `input_nbits`-bit numbers into a vector of u64
 /// of `output_nbits`-bit numbers.
 #[must_use]
-#[allow(clippy::expect_used)]
+#[expect(clippy::expect_used, reason = "bounds are validated before use")]
 pub fn transcode_bidirectional(a: &[u64], input_nbits: usize, output_nbits: usize) -> Vec<u64> {
     assert!(0 < input_nbits && input_nbits <= 64);
     assert!(0 < output_nbits && output_nbits <= 64);
@@ -196,8 +196,11 @@ pub fn variance<T: PrimInt>(values: &[T]) -> f64 {
 
 #[cfg(test)]
 mod tests {
-    // Allow indexing in tests for convenience
-    #![allow(clippy::indexing_slicing)]
+    // Expect indexing in tests for convenience
+    #![expect(
+        clippy::indexing_slicing,
+        reason = "performance or example code relies on validated indices"
+    )]
 
     use itertools::Itertools;
     use rand::RngCore;
@@ -291,6 +294,15 @@ mod tests {
         assert_eq!(&decoded[..input.len()], input);
     }
 
+    #[test]
+    fn transcode_empty_roundtrip() {
+        let input: Vec<u64> = Vec::new();
+        let bytes = transcode_to_bytes(&input, 8);
+        assert!(bytes.is_empty());
+        let decoded = transcode_from_bytes(&bytes, 8);
+        assert!(decoded.is_empty());
+    }
+
     #[test]
     fn inv_kats() {
         // KATs for inversion generated in Sage using the following code.

crates/fhe/benches/bfv.rs

@@ -1,6 +1,9 @@
-// Allow indexing in benchmarks for convenience
-#![allow(clippy::indexing_slicing)]
-#![allow(missing_docs)]
+// Expect indexing in benchmarks for convenience
+#![expect(missing_docs, reason = "examples/benches/tests omit docs by design")]
+#![expect(
+    clippy::indexing_slicing,
+    reason = "performance or example code relies on validated indices"
+)]
 
 use criterion::{BenchmarkId, Criterion, criterion_group, criterion_main};
 use fhe::bfv::{

crates/fhe/benches/bfv_optimized_ops.rs

@@ -1,6 +1,5 @@
-// Allow indexing in benchmarks for convenience
-#![allow(clippy::indexing_slicing)]
-#![allow(missing_docs)]
+// Expect indexing in benchmarks for convenience
+#![expect(missing_docs, reason = "examples/benches/tests omit docs by design")]
 
 use criterion::{BenchmarkId, Criterion, criterion_group, criterion_main};
 use fhe::bfv::{BfvParameters, Ciphertext, Encoding, Plaintext, SecretKey, dot_product_scalar};

crates/fhe/benches/bfv_rgsw.rs

@@ -1,6 +1,5 @@
-// Allow indexing in benchmarks for convenience
-#![allow(clippy::indexing_slicing)]
-#![allow(missing_docs)]
+// Expect indexing in benchmarks for convenience
+#![expect(missing_docs, reason = "examples/benches/tests omit docs by design")]
 
 use criterion::{BenchmarkId, Criterion, criterion_group, criterion_main};
 use fhe::bfv::{BfvParameters, Ciphertext, Encoding, Plaintext, RGSWCiphertext, SecretKey};

crates/fhe/examples/bfv_basic.rs

@@ -1,6 +1,9 @@
-// Allow indexing in examples for simplicity
-#![allow(clippy::indexing_slicing)]
-#![allow(missing_docs)]
+// Expect indexing in examples for simplicity
+#![expect(missing_docs, reason = "examples/benches/tests omit docs by design")]
+#![expect(
+    clippy::indexing_slicing,
+    reason = "performance or example code relies on validated indices"
+)]
 
 use std::error::Error;
 

crates/fhe/examples/bfv_ops.rs

@@ -1,6 +1,9 @@
-// Allow indexing in examples for simplicity
-#![allow(clippy::indexing_slicing)]
-#![allow(missing_docs)]
+// Expect indexing in examples for simplicity
+#![expect(missing_docs, reason = "examples/benches/tests omit docs by design")]
+#![expect(
+    clippy::indexing_slicing,
+    reason = "performance or example code relies on validated indices"
+)]
 
 mod util;
 

crates/fhe/examples/mulpir.rs

@@ -1,6 +1,9 @@
-// Allow indexing in examples for simplicity
-#![allow(clippy::indexing_slicing)]
-#![allow(missing_docs)]
+// Expect indexing in examples for simplicity
+#![expect(missing_docs, reason = "examples/benches/tests omit docs by design")]
+#![expect(
+    clippy::indexing_slicing,
+    reason = "performance or example code relies on validated indices"
+)]
 
 // Implementation of MulPIR using the `fhe` crate.
 //

crates/fhe/examples/pir.rs

@@ -1,23 +1,25 @@
-// Allow indexing in examples for simplicity
-#![allow(clippy::indexing_slicing)]
-#![allow(missing_docs)]
+//! CLI configuration for PIR example runs.
+// Expect indexing in examples for simplicity
 
 use clap::Parser;
 
+/// Command-line arguments for configuring a PIR example run.
 #[derive(Parser)]
 pub struct Cli {
     #[arg(
         long,
         help = "The number of elements in the database",
         default_value = "65536"
     )]
+    /// Number of elements in the database.
     pub database_size: usize,
 
     #[arg(
         long,
         help = "The size of each database element",
         default_value = "1024"
     )]
+    /// Size in bytes of each database element.
     pub element_size: usize,
 }
 

crates/fhe/examples/rgsw.rs

@@ -1,6 +1,9 @@
-// Allow indexing in examples for simplicity
-#![allow(clippy::indexing_slicing)]
-#![allow(missing_docs)]
+// Expect indexing in examples for simplicity
+#![expect(missing_docs, reason = "examples/benches/tests omit docs by design")]
+#![expect(
+    clippy::indexing_slicing,
+    reason = "performance or example code relies on validated indices"
+)]
 
 use std::error::Error;
 

crates/fhe/examples/sealpir.rs

@@ -1,6 +1,9 @@
-// Allow indexing in examples for simplicity
-#![allow(clippy::indexing_slicing)]
-#![allow(missing_docs)]
+// Expect indexing in examples for simplicity
+#![expect(missing_docs, reason = "examples/benches/tests omit docs by design")]
+#![expect(
+    clippy::indexing_slicing,
+    reason = "performance or example code relies on validated indices"
+)]
 
 // Implementation of SealPIR using the `fhe` crate.
 //