From ca2fc14af071b86750fbd6a0c6f07c07edaca609 Mon Sep 17 00:00:00 2001
From: Claude <noreply@anthropic.com>
Date: Thu, 21 May 2026 15:18:23 +0000
Subject: [PATCH 1/3] refactor(substrate): graduate 5 modules from hpc/ to
 crate root
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Content-Transfer-Encoding: 8bit

Continues the substrate-graduation thread documented in #192's wrap-up
and extended in #193's simd_caps lift. Five more modules move from
`crate::hpc::*` (the rustynum migration staging area) to crate root
where they sit alongside `simd.rs`, `simd_runtime/`, `simd_caps`, and
the W1a polyfill surface they're supposed to compose with.

| Module | Reason |
|---|---|
| `bitwise`        | Pure SIMD primitives (popcount, hamming over byte slices); already uses `crate::simd::U64x8` polyfill internally; already re-exported via `simd.rs:512`. |
| `heel_f64x8`     | All-F64x8 polyfill consumer (dot, cosine, sum-sq, weighted-hamming); already re-exported via `simd.rs:563`. |
| `distance`       | Spatial 3D + slice-shape L1/L2/L∞ (PR-X10 A6); the linalg/mod.rs hard-boundary comment now points here at root. |
| `byte_scan`      | Pure SIMD utility (needle search, delimiter find). |
| `spatial_hash`   | Pure SIMD utility (bucketing, candidate gather). |

# Why these five, why now

All five satisfied the low-hanging-fruit criteria from #193's wrap-up
discussion:
  1. No internal `hpc/` dependencies (only `super::simd_caps` which
     still resolves correctly because `simd_caps` is itself at crate
     root post-#192).
  2. Already polyfill-clean — no raw-intrinsic refactor needed before
     the move.
  3. Already partially exposed via `crate::simd::*` re-exports.

The next graduation tier (`fingerprint`, `dn_tree`, `ogit_bridge`,
`splat3d`) needs a polyfill audit before it can move, and
`fingerprint` in particular is gated on the W1a-#5 POPCOUNT-U64
primitive landing (so its bit ops can route through `U64xN.popcnt()`
instead of raw `u64.count_ones()`).

# Back-compat preserved end-to-end

Every cross-repo consumer using `ndarray::hpc::{bitwise, heel_f64x8,
distance, byte_scan, spatial_hash}::*` continues to compile
unmodified. The `src/hpc/mod.rs` declarations change from
`pub mod X;` to `pub use crate::X;` — Rust re-exports modules just
like other items, so `crate::hpc::X::*` resolves through to the same
items as `crate::X::*`. Internal `super::simd_caps::simd_caps()`
calls inside the moved files continue to work because `super::` at
crate root resolves to `crate::*` which has `simd_caps` (graduated
in #192).

# Changes

- `git mv` five files from `src/hpc/` to `src/`.
- `src/lib.rs` gains five `#[cfg(feature = "std")] pub mod X;`
  declarations next to the existing `simd_caps` block, each with a
  one-liner docstring naming the graduation source and the
  substrate-tier reason for the move.
- `src/hpc/mod.rs` replaces five `pub mod X;` with `pub use crate::X;`
  (back-compat re-exports).
- `src/hpc/linalg/mod.rs` updates the hard-boundary comment from
  "No distance metrics — those live in `crate::hpc::distance`" to
  point at `crate::distance` (the new canonical path) with a
  parenthetical noting the back-compat re-export.
- The `bitwise.rs` declaration in `src/hpc/mod.rs` is now a comment
  instead of being interleaved with `pub mod hdc`/`pub mod projection`
  to make the graduation status visible at a glance.

# Verification

- `cargo build -p ndarray --lib` — clean
- `cargo build -p ndarray --lib --no-default-features` — clean
  (the new `#[cfg(feature = "std")]` gates match the existing
  `simd_caps` pattern; nostd targets see no change)
- `cargo test -p ndarray --lib bitwise:: distance:: heel_f64x8::
  byte_scan:: spatial_hash::` — all 119 tests on the five graduated
  modules pass at the new path (test names now `bitwise::tests::*`
  rather than `hpc::bitwise::tests::*`)
- `cargo test -p ndarray --lib --features "pillar,ogit_bridge,
  runtime-dispatch" hpc::` — 2167 passed, 0 failed, 28 ignored
- `cargo fmt --all --check` — clean
- `cargo clippy --features "pillar,ogit_bridge,runtime-dispatch"
  --lib -- -D warnings` — clean

# Next graduation candidates (deferred)

- `hpc::fingerprint` — needs W1a-#5 POPCOUNT-U64 to land first so
  bit ops can route through `U64xN.popcnt()` instead of raw
  `u64.count_ones()`. Cognitive-shader-foundation explicitly names
  `Fingerprint<N>` as a MUST-be-in-`ndarray::simd::*` type.
- `hpc::dn_tree` (bitwise core) — same polyfill-audit dependency.
  The cognitive DNTree/DNConfig/TraversalHit state stays in
  `hpc/` after the split.
- `hpc::ogit_bridge` — pure logic, no SIMD, can move once the
  fingerprint + dn_tree audits are out of the way (avoids three
  partial graduations in flight at once).
- `hpc::splat3d` — already mostly polyfill-clean; pure path
  rewrite. Defer because it's a larger consumer surface than
  the five in this PR.
---
 src/{hpc => }/bitwise.rs      |  0
 src/{hpc => }/byte_scan.rs    |  0
 src/{hpc => }/distance.rs     |  0
 src/{hpc => }/heel_f64x8.rs   |  0
 src/hpc/linalg/mod.rs         |  3 ++-
 src/hpc/mod.rs                | 16 +++++++++-------
 src/lib.rs                    | 29 +++++++++++++++++++++++++++++
 src/{hpc => }/spatial_hash.rs |  0
 8 files changed, 40 insertions(+), 8 deletions(-)
 rename src/{hpc => }/bitwise.rs (100%)
 rename src/{hpc => }/byte_scan.rs (100%)
 rename src/{hpc => }/distance.rs (100%)
 rename src/{hpc => }/heel_f64x8.rs (100%)
 rename src/{hpc => }/spatial_hash.rs (100%)

diff --git a/src/hpc/bitwise.rs b/src/bitwise.rs
similarity index 100%
rename from src/hpc/bitwise.rs
rename to src/bitwise.rs
diff --git a/src/hpc/byte_scan.rs b/src/byte_scan.rs
similarity index 100%
rename from src/hpc/byte_scan.rs
rename to src/byte_scan.rs
diff --git a/src/hpc/distance.rs b/src/distance.rs
similarity index 100%
rename from src/hpc/distance.rs
rename to src/distance.rs
diff --git a/src/hpc/heel_f64x8.rs b/src/heel_f64x8.rs
similarity index 100%
rename from src/hpc/heel_f64x8.rs
rename to src/heel_f64x8.rs
diff --git a/src/hpc/linalg/mod.rs b/src/hpc/linalg/mod.rs
index 58608f40..a2963c94 100644
--- a/src/hpc/linalg/mod.rs
+++ b/src/hpc/linalg/mod.rs
@@ -40,7 +40,8 @@
 //!
 //! - **No SIMD primitives** — use `crate::simd::{F32x16, …}` directly.
 //! - **No `#[target_feature]` annotations** — those live in `simd_avx512.rs`.
-//! - **No distance metrics** — those live in `crate::hpc::distance`.
+//! - **No distance metrics** — those live in `crate::distance` (graduated
+//!   from `crate::hpc::distance`; back-compat re-export in `crate::hpc::*`).
 
 mod matrix;
 pub use matrix::{Mat2, Mat3, Mat4, MatN, Spd2, Spd3};
diff --git a/src/hpc/mod.rs b/src/hpc/mod.rs
index ff7981fc..5e0022a5 100644
--- a/src/hpc/mod.rs
+++ b/src/hpc/mod.rs
@@ -27,7 +27,8 @@ pub mod reductions;
 pub mod statistics;
 pub mod activations;
 pub mod hdc;
-pub mod bitwise;
+// Bitwise SIMD primitives — graduated to crate root. Back-compat re-export.
+pub use crate::bitwise;
 pub mod projection;
 pub mod cogrecord;
 pub mod graph;
@@ -56,8 +57,8 @@ pub mod soa;
 pub mod node;
 #[allow(missing_docs)]
 pub mod cascade;
-#[allow(missing_docs)]
-pub mod heel_f64x8;
+// HEEL F64x8 distance kernels — graduated to crate root. Back-compat re-export.
+pub use crate::heel_f64x8;
 // AMX is an x86_64-only ISA (Intel Sapphire Rapids+); both modules use
 // `asm!` with `rcx`/`rax` register names that don't exist on other
 // architectures (rejected at parse time on s390x / aarch64 / wasm32).
@@ -169,10 +170,11 @@ pub mod parallel_search;
 // ZeckF64 progressive edge encoding + batch/top-k
 pub mod zeck;
 
-// SIMD-accelerated spatial / byte-scan / hash utilities
-pub mod distance;
-pub mod byte_scan;
-pub mod spatial_hash;
+// SIMD-accelerated spatial / byte-scan / hash utilities — graduated to crate root.
+// Back-compat re-exports for existing `use ndarray::hpc::{distance,byte_scan,spatial_hash}::*`.
+pub use crate::byte_scan;
+pub use crate::distance;
+pub use crate::spatial_hash;
 
 // Variable-width palette index codec (Minecraft-style bit packing)
 #[allow(missing_docs)]
diff --git a/src/lib.rs b/src/lib.rs
index 5b5851fd..e6c33e7c 100644
--- a/src/lib.rs
+++ b/src/lib.rs
@@ -272,6 +272,35 @@ pub mod simd_amx;
 #[cfg(feature = "std")]
 pub mod simd_caps;
 
+/// Bitwise SIMD primitives — popcount, Hamming distance over byte slices.
+/// Graduated from `crate::hpc::bitwise::*` (substrate-tier; uses
+/// `crate::simd::U64x8` polyfill internally). Back-compat re-export in
+/// `crate::hpc::*` preserves existing import paths.
+#[cfg(feature = "std")]
+pub mod bitwise;
+
+/// F64x8 HEEL distance kernels — 8-plane weighted Hamming, f64 SIMD
+/// dot / cosine / sum-of-squares. Graduated from `crate::hpc::heel_f64x8::*`.
+#[cfg(feature = "std")]
+pub mod heel_f64x8;
+
+/// Batch distance computations — spatial 3D-point queries +
+/// slice-shape L1 / L2 / L∞ (PR-X10 A6). Graduated from
+/// `crate::hpc::distance::*`.
+#[cfg(feature = "std")]
+pub mod distance;
+
+/// SIMD-accelerated byte-scan utilities — needle search, delimiter
+/// finding, parallel byte comparison. Graduated from
+/// `crate::hpc::byte_scan::*`.
+#[cfg(feature = "std")]
+pub mod byte_scan;
+
+/// SIMD-accelerated spatial hash — bucketing, candidate gather, hash
+/// collision detection. Graduated from `crate::hpc::spatial_hash::*`.
+#[cfg(feature = "std")]
+pub mod spatial_hash;
+
 #[cfg(feature = "std")]
 #[allow(clippy::all, missing_docs, dead_code, unused_variables, unused_imports)]
 pub mod simd_neon;
diff --git a/src/hpc/spatial_hash.rs b/src/spatial_hash.rs
similarity index 100%
rename from src/hpc/spatial_hash.rs
rename to src/spatial_hash.rs

From 417131bc36e75cf097788fc6199e94e4bd2fca83 Mon Sep 17 00:00:00 2001
From: Claude <noreply@anthropic.com>
Date: Thu, 21 May 2026 15:28:23 +0000
Subject: [PATCH 2/3] fix(lints+docs): clippy clean on graduated modules +
 rustdoc examples
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Content-Transfer-Encoding: 8bit

Two CI / review-feedback fixes on PR #194:

1) Clippy (`-D warnings`, --features rayon / approx,serde,rayon):
   10 errors surfaced because the graduated modules are no longer
   under hpc/mod.rs's `#![allow(clippy::all, ...)]` umbrella.
   Fixed each at the canonical Rust idiom rather than re-applying
   the umbrella — graduated modules hold to the higher standard:

   - `bitwise.rs:110,155` — `acc = acc + (x + y);` →
     `acc += x + y;` (assign_op_pattern; bare without parens).
   - `distance.rs:99` — `for j in i..n { points[j] }` →
     `for p in &points[i..n] { p[0]..p[2] }` (needless_range_loop).
   - `byte_scan.rs:38,71` — `for j in i..n { if haystack[j] == needle
     { result.push(j); }}` → `for (offset, &byte) in haystack[i..n]
     .iter().enumerate() { if byte == needle { result.push(i + offset);
     }}` (needless_range_loop with index preservation).
   - `byte_scan.rs:101,129` — same pattern but counting via
     `total += 1`; switched to `for &byte in &haystack[i..n]`
     (no index needed at all).
   - `spatial_hash.rs:334` — `for lane in 0..8 { d2_arr[lane] }` →
     `for (lane, &d2_lane) in d2_arr.iter().enumerate()`.
   - `spatial_hash.rs:342` — `for i in (chunks*8)..candidates.len()
     { candidates[i] }` → `let tail_start = chunks * 8;
     for (offset, &cand) in candidates[tail_start..].iter()
     .enumerate() { result.push((tail_start + offset, d2)) }`.

2) CodeRabbit + CLAUDE.md hard rule ("All public APIs need ///
   doc comments with examples"):
   Added `# Example` rustdoc blocks to each of the five new
   `pub mod` declarations in `src/lib.rs`. Each example uses
   only the actual public API of the target module (verified by
   running the doctests):

   - `bitwise` — popcount + hamming over [0xFF; 16]/[0x00; 16]
   - `heel_f64x8` — cosine_f64_simd + dot_f64_simd over [1.0; 32]
   - `distance` — l1/l2/linf_f64_simd over pythagorean (3,0)/(0,4)
   - `byte_scan` — byte_find_all over a 23-char fixture
   - `spatial_hash` — SpatialHash::new + insert + len

All five doctests pass under `cargo test --doc`. `cargo clippy
--features rayon --lib -- -D warnings` and `cargo clippy
--features approx,serde,rayon -- -D warnings` both green.
---
 src/bitwise.rs      |  4 ++--
 src/byte_scan.rs    | 20 +++++++++---------
 src/distance.rs     | 10 ++++-----
 src/lib.rs          | 50 +++++++++++++++++++++++++++++++++++++++++++++
 src/spatial_hash.rs | 13 ++++++------
 5 files changed, 74 insertions(+), 23 deletions(-)

diff --git a/src/bitwise.rs b/src/bitwise.rs
index 870314e8..0d849dde 100644
--- a/src/bitwise.rs
+++ b/src/bitwise.rs
@@ -107,7 +107,7 @@ unsafe fn hamming_avx512bw(a: &[u8], b: &[u8]) -> u64 {
         let hi = xor.shr_epi16(4) & low_mask;
         let popcnt_lo = lookup.shuffle_bytes(lo);
         let popcnt_hi = lookup.shuffle_bytes(hi);
-        acc = acc + (popcnt_lo + popcnt_hi);
+        acc += popcnt_lo + popcnt_hi;
 
         i += 64;
         inner_count += 1;
@@ -152,7 +152,7 @@ unsafe fn popcount_avx512bw(a: &[u8]) -> u64 {
         let hi = va.shr_epi16(4) & low_mask;
         let popcnt_lo = lookup.shuffle_bytes(lo);
         let popcnt_hi = lookup.shuffle_bytes(hi);
-        acc = acc + (popcnt_lo + popcnt_hi);
+        acc += popcnt_lo + popcnt_hi;
 
         i += 64;
         inner_count += 1;
diff --git a/src/byte_scan.rs b/src/byte_scan.rs
index 4f692cc6..6667bf74 100644
--- a/src/byte_scan.rs
+++ b/src/byte_scan.rs
@@ -35,9 +35,9 @@ pub(crate) mod simd_impl {
             i += 32;
         }
         // Scalar tail
-        for j in i..n {
-            if haystack[j] == needle {
-                result.push(j);
+        for (offset, &byte) in haystack[i..n].iter().enumerate() {
+            if byte == needle {
+                result.push(i + offset);
             }
         }
         result
@@ -68,9 +68,9 @@ pub(crate) mod simd_impl {
             i += 64;
         }
         // Scalar tail
-        for j in i..n {
-            if haystack[j] == needle {
-                result.push(j);
+        for (offset, &byte) in haystack[i..n].iter().enumerate() {
+            if byte == needle {
+                result.push(i + offset);
             }
         }
         result
@@ -98,8 +98,8 @@ pub(crate) mod simd_impl {
             }
             i += 32;
         }
-        for j in i..n {
-            if haystack[j] == needle {
+        for &byte in &haystack[i..n] {
+            if byte == needle {
                 total += 1;
             }
         }
@@ -126,8 +126,8 @@ pub(crate) mod simd_impl {
             total += mask.count_ones() as usize;
             i += 64;
         }
-        for j in i..n {
-            if haystack[j] == needle {
+        for &byte in &haystack[i..n] {
+            if byte == needle {
                 total += 1;
             }
         }
diff --git a/src/distance.rs b/src/distance.rs
index 79f4229e..d85e3242 100644
--- a/src/distance.rs
+++ b/src/distance.rs
@@ -96,10 +96,10 @@ pub(crate) mod simd_impl {
         }
 
         // Scalar tail
-        for j in i..n {
-            let dx = query[0] - points[j][0];
-            let dy = query[1] - points[j][1];
-            let dz = query[2] - points[j][2];
+        for p in &points[i..n] {
+            let dx = query[0] - p[0];
+            let dy = query[1] - p[1];
+            let dz = query[2] - p[2];
             out.push(dx * dx + dy * dy + dz * dz);
         }
     }
@@ -211,7 +211,7 @@ pub fn l1_f64_simd(a: &[f64], b: &[f64]) -> f64 {
     for i in 0..chunks {
         let va = F64x8::from_slice(&a[i * 8..]);
         let vb = F64x8::from_slice(&b[i * 8..]);
-        acc = acc + (va - vb).abs();
+        acc += (va - vb).abs();
     }
     let mut sum = acc.reduce_sum();
     let offset = chunks * 8;
diff --git a/src/lib.rs b/src/lib.rs
index e6c33e7c..70d56b9e 100644
--- a/src/lib.rs
+++ b/src/lib.rs
@@ -276,28 +276,78 @@ pub mod simd_caps;
 /// Graduated from `crate::hpc::bitwise::*` (substrate-tier; uses
 /// `crate::simd::U64x8` polyfill internally). Back-compat re-export in
 /// `crate::hpc::*` preserves existing import paths.
+///
+/// # Example
+///
+/// ```
+/// use ndarray::bitwise::{hamming_distance_raw, popcount_raw};
+/// let a = [0xFFu8; 16];
+/// let b = [0x00u8; 16];
+/// assert_eq!(hamming_distance_raw(&a, &b), 128);
+/// assert_eq!(popcount_raw(&a), 128);
+/// ```
 #[cfg(feature = "std")]
 pub mod bitwise;
 
 /// F64x8 HEEL distance kernels — 8-plane weighted Hamming, f64 SIMD
 /// dot / cosine / sum-of-squares. Graduated from `crate::hpc::heel_f64x8::*`.
+///
+/// # Example
+///
+/// ```
+/// use ndarray::heel_f64x8::{cosine_f64_simd, dot_f64_simd};
+/// let a = vec![1.0_f64; 32];
+/// let b = vec![1.0_f64; 32];
+/// assert!((cosine_f64_simd(&a, &b) - 1.0).abs() < 1e-10);
+/// assert!((dot_f64_simd(&a, &b) - 32.0).abs() < 1e-10);
+/// ```
 #[cfg(feature = "std")]
 pub mod heel_f64x8;
 
 /// Batch distance computations — spatial 3D-point queries +
 /// slice-shape L1 / L2 / L∞ (PR-X10 A6). Graduated from
 /// `crate::hpc::distance::*`.
+///
+/// # Example
+///
+/// ```
+/// use ndarray::distance::{l1_f64_simd, l2_f64_simd, linf_f64_simd};
+/// let a = vec![3.0_f64, 0.0];
+/// let b = vec![0.0_f64, 4.0];
+/// assert!((l1_f64_simd(&a, &b) - 7.0).abs() < 1e-12);
+/// assert!((l2_f64_simd(&a, &b) - 5.0).abs() < 1e-12);
+/// assert!((linf_f64_simd(&a, &b) - 4.0).abs() < 1e-12);
+/// ```
 #[cfg(feature = "std")]
 pub mod distance;
 
 /// SIMD-accelerated byte-scan utilities — needle search, delimiter
 /// finding, parallel byte comparison. Graduated from
 /// `crate::hpc::byte_scan::*`.
+///
+/// # Example
+///
+/// ```
+/// use ndarray::byte_scan::byte_find_all;
+/// let haystack = b"hello world, hello rust";
+/// let hits = byte_find_all(haystack, b'l');
+/// assert_eq!(hits, vec![2, 3, 9, 15, 16]);
+/// ```
 #[cfg(feature = "std")]
 pub mod byte_scan;
 
 /// SIMD-accelerated spatial hash — bucketing, candidate gather, hash
 /// collision detection. Graduated from `crate::hpc::spatial_hash::*`.
+///
+/// # Example
+///
+/// ```
+/// use ndarray::spatial_hash::SpatialHash;
+/// let mut grid = SpatialHash::new(1.0);
+/// grid.insert(0, 0.0, 0.0, 0.0);
+/// grid.insert(1, 10.0, 10.0, 10.0);
+/// assert_eq!(grid.len(), 2);
+/// ```
 #[cfg(feature = "std")]
 pub mod spatial_hash;
 
diff --git a/src/spatial_hash.rs b/src/spatial_hash.rs
index ae4303a2..84a4f117 100644
--- a/src/spatial_hash.rs
+++ b/src/spatial_hash.rs
@@ -331,18 +331,19 @@ pub(crate) unsafe fn batch_sq_dist_avx2(query: [f32; 3], candidates: &[[f32; 3]]
 
         // Compare: d2 <= radius_sq (scalar array comparison — no F32x8 cmp polyfill)
         let d2_arr = d2.to_array();
-        for lane in 0..8 {
-            if d2_arr[lane] <= radius_sq {
-                result.push((base + lane, d2_arr[lane]));
+        for (lane, &d2_lane) in d2_arr.iter().enumerate() {
+            if d2_lane <= radius_sq {
+                result.push((base + lane, d2_lane));
             }
         }
     }
 
     // Scalar tail
-    for i in (chunks * 8)..candidates.len() {
-        let d2 = sq_dist_f32(query, candidates[i]);
+    let tail_start = chunks * 8;
+    for (offset, &cand) in candidates[tail_start..].iter().enumerate() {
+        let d2 = sq_dist_f32(query, cand);
         if d2 <= radius_sq {
-            result.push((i, d2));
+            result.push((tail_start + offset, d2));
         }
     }
 

From 17d0eae2915a31402dc2971e333e55d810b90446 Mon Sep 17 00:00:00 2001
From: Claude <noreply@anthropic.com>
Date: Thu, 21 May 2026 18:02:13 +0000
Subject: [PATCH 3/3] refactor(substrate): graduate 4 more modules from hpc/ to
 crate root
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Continues the substrate-graduation thread from #192 (simd_caps),
#193 (clippy/doc cleanup), and #194 (bitwise/heel_f64x8/distance/
byte_scan/spatial_hash). Same low-hanging-fruit criteria — no
internal hpc/ deps, polyfill-clean, single-line back-compat shim
keeps every existing import resolving.

| Module          | Reason                                                         |
|---|---|
| `aabb`          | SIMD AABB intersection/expansion/distance; only deps are       |
|                 | `crate::simd::F32x16` + `super::simd_caps` (graduated #192).   |
| `nibble`        | 4-bit packed nibble batch ops; only dep is `crate::simd::U8x64`.|
| `palette_codec` | Variable-width palette index codec (1-8 bit packing); zero deps.|
| `property_mask` | AVX-512 VPTERNLOGD bitset queries on block state bits;         |
|                 | only dep is `crate::simd::U64x8`.                              |

# Why these four, why now

All four satisfy the criteria from #194's wrap-up:
  1. No internal `hpc/` dependencies — only `crate::simd::*`
     (polyfill surface) and `super::simd_caps` (which is itself
     at crate root post-#192).
  2. Polyfill-clean — no raw-intrinsic refactor required.
  3. Single in-tree downstream caller (`hpc::framebuffer` uses
     `palette_codec`) → the `pub use crate::palette_codec;`
     back-compat shim keeps that resolution working zero-touch.

# Mechanical changes

- `git mv src/hpc/{aabb,nibble,palette_codec,property_mask}.rs src/`
- `src/lib.rs`: added four `pub mod` declarations under
  `#[cfg(feature = "std")]`, each with a `# Example` rustdoc block
  per CLAUDE.md "all public APIs need doc comments with examples".
- `src/hpc/mod.rs`: replaced the four `pub mod` declarations with
  `pub use crate::{aabb, nibble, palette_codec, property_mask};`
  back-compat re-exports. `crate::hpc::aabb::*` and friends keep
  resolving for every existing call site, identical to how
  `crate::hpc::bitwise::*` works post-#194.

# Clippy / lint cleanup

17 clippy errors surfaced under `-D warnings` once the modules
left the `hpc/mod.rs` `#![allow(clippy::all, ...)]` umbrella.
Fixed each at the canonical Rust idiom (the #194 cleanup pattern,
417131bc), no umbrella re-application:

- **manual_div_ceil (6 sites)** — `(n + d - 1) / d` → `n.div_ceil(d)`
  in `nibble.rs` (x2), `palette_codec.rs` (x3), `property_mask.rs`.
- **needless_range_loop (10 sites)** — `for i in start..vec.len()`
  rewrites to `for x in &vec[start..]` (when index unused) or
  `for (i, &x) in iter().enumerate().skip(start)` (when index used).
  Sites: `aabb.rs` x4, `nibble.rs` x3, `palette_codec.rs` x1,
  `property_mask.rs` x2.
- **missing_docs (4 sites)** — added field doc comments on
  `pub struct Aabb { min, max }` and `pub struct Ray { origin,
  inv_dir }`. Previously masked by the `hpc/mod.rs` umbrella's
  `#![allow(missing_docs)]`.

# Doctest correction

Initial `# Example` in `src/lib.rs` for `palette_codec` asserted
`bits_for_palette_size(1) == 1` per the module's own docstring
table, but the impl returns 0 for `palette_size <= 1` (trivial-
palette special case). Changed assertion to use `bits_for_palette_
size(2) == 1` — exercises the same code path with input the impl
actually handles per spec.

# Verification

```
cargo check --lib                                          green
cargo clippy --lib -- -D warnings                          green
cargo clippy --lib --features rayon -- -D warnings         green
cargo clippy --features approx,serde,rayon -- -D warnings  green
cargo test --doc (15 graduated-module doctests)            pass
cargo test --lib (104 unit tests across 4 modules)         pass
```

# What's next

`hpc/` inventory: ~55 → ~51 modules at the staging path. Next-batch
candidates per the same criteria need a deps audit before move:
`framebuffer` (uses `palette_codec` shim, otherwise crate-root),
`ocr_simd`/`ocr_felt`, `audio`. Filed in AGENT_LOG entry for the
follow-up pass.

https://claude.ai/code/session_01HbqooFZHAjaUtFEzhA1R2u
---
 .claude/board/AGENT_LOG.md     | 54 +++++++++++++++++++++++++++++++
 src/{hpc => }/aabb.rs          | 19 ++++++-----
 src/hpc/mod.rs                 | 20 ++++++------
 src/lib.rs                     | 58 ++++++++++++++++++++++++++++++++++
 src/{hpc => }/nibble.rs        | 24 +++++++-------
 src/{hpc => }/palette_codec.rs | 11 +++----
 src/{hpc => }/property_mask.rs |  9 +++---
 7 files changed, 153 insertions(+), 42 deletions(-)
 rename src/{hpc => }/aabb.rs (97%)
 rename src/{hpc => }/nibble.rs (96%)
 rename src/{hpc => }/palette_codec.rs (98%)
 rename src/{hpc => }/property_mask.rs (99%)

diff --git a/.claude/board/AGENT_LOG.md b/.claude/board/AGENT_LOG.md
index b6948deb..cf9133a9 100644
--- a/.claude/board/AGENT_LOG.md
+++ b/.claude/board/AGENT_LOG.md
@@ -28,6 +28,60 @@
 ## Entries (append below; newest first)
 
 
+## 2026-05-21T16:00 — substrate-graduation batch 3 (opus 4.7)
+
+**Branch:** `claude/continue-ndarray-x0Oaw`
+**Continues:** PR #194 batch of 5 (`bitwise`/`heel_f64x8`/`distance`/`byte_scan`/`spatial_hash`) + #193 (`simd_caps`).
+**Verdict:** SHIP — `cargo check`, `cargo clippy --features approx,serde,rayon -- -D warnings`, doctest suite (15 graduated-module doctests pass), and unit tests (104 lib tests pass) all green.
+
+**Modules graduated (4):**
+
+| Module | Old path | New path | Internal hpc/ deps? |
+|---|---|---|---|
+| `aabb`           | `src/hpc/aabb.rs`           | `src/aabb.rs`           | None — only `super::simd_caps` (now resolves via crate root) |
+| `nibble`         | `src/hpc/nibble.rs`         | `src/nibble.rs`         | None — only `super::simd_caps` |
+| `palette_codec`  | `src/hpc/palette_codec.rs`  | `src/palette_codec.rs`  | None — pure logic |
+| `property_mask`  | `src/hpc/property_mask.rs`  | `src/property_mask.rs`  | None — only `super::simd_caps` |
+
+**Why these four, why now (criteria carried over from #194 wrap-up):**
+1. No internal `hpc/` dependencies. All four only reach into `crate::simd::*` (the polyfill surface) and `super::simd_caps` (itself at crate root post-#192).
+2. Already polyfill-clean — no raw-intrinsic refactor required before the move.
+3. Single in-tree downstream caller (`hpc::framebuffer` imports `palette_codec`) → the `pub use crate::palette_codec;` back-compat shim in `hpc/mod.rs` keeps that resolution working zero-touch.
+
+**Changes:**
+- `git mv src/hpc/{aabb,nibble,palette_codec,property_mask}.rs src/`
+- Added `pub mod {aabb, nibble, palette_codec, property_mask};` to `src/lib.rs` (with `# Example` rustdoc blocks per CLAUDE.md hard rule "all public APIs need /// doc comments with examples").
+- Replaced the four `pub mod` declarations in `src/hpc/mod.rs` with `pub use crate::{aabb, nibble, palette_codec, property_mask};` back-compat re-exports.
+
+**Lint follow-ups (graduated modules lose the `#![allow(clippy::all, …)]` umbrella that `hpc/mod.rs` carries):**
+
+17 clippy errors surfaced under `-D warnings`. All fixed at the canonical Rust idiom rather than re-applying the umbrella, per the #194 cleanup precedent (417131bc):
+
+- **`manual_div_ceil` (6 sites)**: `(n + d - 1) / d` → `n.div_ceil(d)` in `nibble.rs` (×2), `palette_codec.rs` (×3), `property_mask.rs` (×1).
+- **`needless_range_loop` (10 sites)**: `for i in start..vec.len() { vec[i] }` → `for x in &vec[start..]` or `for (i, &x) in iter().enumerate()` depending on whether the index is used. Sites in `aabb.rs` (×4), `nibble.rs` (×3), `palette_codec.rs` (×1), `property_mask.rs` (×2).
+- **`missing_docs` (4 sites)**: Added field doc comments on `pub struct Aabb { min, max }` and `pub struct Ray { origin, inv_dir }` — these were previously caught by the `hpc/mod.rs` umbrella's `#![allow(missing_docs)]`.
+
+**Doctest fix:** Initial `bits_for_palette_size(1) → 1` in the `lib.rs` `# Example` block was wrong — the actual impl returns 0 for `palette_size <= 1` (trivial-palette special case; the bits/indices table in `palette_codec.rs`'s module docstring overpromises). Changed example to `bits_for_palette_size(2) → 1`.
+
+**Verification:**
+
+```
+cargo check --lib                                              → clean
+cargo clippy --lib -- -D warnings                              → clean
+cargo clippy --lib --features rayon -- -D warnings             → clean
+cargo clippy --features approx,serde,rayon -- -D warnings      → clean
+cargo test --doc (filtered: graduated modules)                 → 15 doctests pass
+cargo test --lib aabb::tests nibble::tests palette_codec::tests property_mask::tests → 104 unit tests pass
+```
+
+**No back-compat break:** every existing `use ndarray::hpc::{aabb, nibble, palette_codec, property_mask}::*` continues to resolve via the `pub use crate::*` shims in `hpc/mod.rs`. Verified via `cargo check` of the full workspace — `framebuffer.rs:29` (the one in-tree downstream consumer of `palette_codec`) compiles unchanged.
+
+**Remaining hpc/ inventory after this batch:** ~55 → ~51 modules at crate root path `crate::hpc::*`. Next-batch candidates (still low-hanging by the same criteria) — to be audited in a separate pass before move: `framebuffer` (depends on `palette_codec` shim, otherwise pure crate-root), `ocr_simd`/`ocr_felt` (need dep audit), `audio` (depends on `crate::simd`).
+
+**Commit:** TBD (pending push).
+
+---
+
 ## 2026-05-13T00:00 — agent #3 polyfill-ops (sonnet)
 
 **File:** `src/simd_ops.rs` (288 lines)
diff --git a/src/hpc/aabb.rs b/src/aabb.rs
similarity index 97%
rename from src/hpc/aabb.rs
rename to src/aabb.rs
index 43770fe8..180dbf1a 100644
--- a/src/hpc/aabb.rs
+++ b/src/aabb.rs
@@ -17,7 +17,9 @@
 #[derive(Debug, Clone, Copy, PartialEq)]
 #[repr(C)]
 pub struct Aabb {
+    /// Minimum corner of the bounding box (x, y, z).
     pub min: [f32; 3],
+    /// Maximum corner of the bounding box (x, y, z).
     pub max: [f32; 3],
 }
 
@@ -97,7 +99,10 @@ impl Aabb {
 #[derive(Debug, Clone, Copy, PartialEq)]
 #[repr(C)]
 pub struct Ray {
+    /// Ray origin point (x, y, z).
     pub origin: [f32; 3],
+    /// Per-axis reciprocal of the ray direction (1 / dx, 1 / dy, 1 / dz);
+    /// `inf` is valid (encodes a zero-component direction, slab test skips it).
     pub inv_dir: [f32; 3],
 }
 
@@ -122,8 +127,7 @@ impl Ray {
 #[inline]
 fn sq_dist_point_aabb(point: [f32; 3], aabb: &Aabb) -> f32 {
     let mut dist_sq = 0.0f32;
-    for axis in 0..3 {
-        let v = point[axis];
+    for (axis, &v) in point.iter().enumerate() {
         if v < aabb.min[axis] {
             let d = aabb.min[axis] - v;
             dist_sq += d * d;
@@ -230,8 +234,8 @@ unsafe fn aabb_intersect_batch_avx512(query: &Aabb, candidates: &[Aabb]) -> Vec<
     }
 
     // Scalar tail
-    for i in (chunks * 16)..candidates.len() {
-        result.push(query.intersects(&candidates[i]));
+    for cand in &candidates[chunks * 16..] {
+        result.push(query.intersects(cand));
     }
 
     result
@@ -403,16 +407,15 @@ unsafe fn ray_aabb_slab_test_avx512(ray: &Ray, aabbs: &[Aabb]) -> (Vec<bool>, Ve
         let t_enter_clamped = t_enter.simd_max(zero);
         let t_arr = t_enter_clamped.to_array();
 
-        for i in 0..16 {
+        for (i, &t) in t_arr.iter().enumerate() {
             let hit = (hit_mask >> i) & 1 != 0;
             hits.push(hit);
-            t_values.push(if hit { t_arr[i] } else { f32::MAX });
+            t_values.push(if hit { t } else { f32::MAX });
         }
     }
 
     // Scalar tail for remainder
-    for i in (chunks * 16)..aabbs.len() {
-        let aabb = &aabbs[i];
+    for aabb in &aabbs[chunks * 16..] {
         let mut t_enter = f32::NEG_INFINITY;
         let mut t_exit = f32::INFINITY;
 
diff --git a/src/hpc/mod.rs b/src/hpc/mod.rs
index 5e0022a5..3e195b8b 100644
--- a/src/hpc/mod.rs
+++ b/src/hpc/mod.rs
@@ -176,17 +176,15 @@ pub use crate::byte_scan;
 pub use crate::distance;
 pub use crate::spatial_hash;
 
-// Variable-width palette index codec (Minecraft-style bit packing)
-#[allow(missing_docs)]
-pub mod palette_codec;
-
-// SIMD-accelerated HPC modules (block properties, nibble light data, AABB collision)
-#[allow(missing_docs)]
-pub mod property_mask;
-#[allow(missing_docs)]
-pub mod nibble;
-#[allow(missing_docs)]
-pub mod aabb;
+// Variable-width palette index codec — graduated to crate root.
+// Back-compat re-export for existing `use ndarray::hpc::palette_codec::*`.
+pub use crate::palette_codec;
+
+// SIMD-accelerated HPC modules (block properties, nibble light data, AABB
+// collision) — all three graduated to crate root. Back-compat re-exports.
+pub use crate::aabb;
+pub use crate::nibble;
+pub use crate::property_mask;
 
 // Holographic phase-space operations (ported from rustynum-holo)
 #[allow(missing_docs)]
diff --git a/src/lib.rs b/src/lib.rs
index 70d56b9e..c19d6fc7 100644
--- a/src/lib.rs
+++ b/src/lib.rs
@@ -351,6 +351,64 @@ pub mod byte_scan;
 #[cfg(feature = "std")]
 pub mod spatial_hash;
 
+/// Axis-aligned bounding box batch operations — SIMD-accelerated
+/// intersection, expansion, distance queries. Graduated from
+/// `crate::hpc::aabb::*`.
+///
+/// # Example
+///
+/// ```
+/// use ndarray::aabb::Aabb;
+/// let a = Aabb::new([0.0, 0.0, 0.0], [1.0, 1.0, 1.0]);
+/// let b = Aabb::new([0.5, 0.5, 0.5], [1.5, 1.5, 1.5]);
+/// assert!(a.intersects(&b));
+/// ```
+#[cfg(feature = "std")]
+pub mod aabb;
+
+/// Nibble batch operations for 4-bit packed data (light levels, palettes).
+/// Graduated from `crate::hpc::nibble::*`.
+///
+/// # Example
+///
+/// ```
+/// use ndarray::nibble::nibble_unpack;
+/// let unpacked = nibble_unpack(&[0x3A], 2);
+/// assert_eq!(unpacked, vec![0xA, 0x3]);
+/// ```
+#[cfg(feature = "std")]
+pub mod nibble;
+
+/// Variable-width palette index codec (Minecraft-style bit packing).
+/// Packs/unpacks palette indices (0–255) into 1–8 bit widths.
+/// Graduated from `crate::hpc::palette_codec::*`.
+///
+/// # Example
+///
+/// ```
+/// use ndarray::palette_codec::bits_for_palette_size;
+/// assert_eq!(bits_for_palette_size(2), 1);
+/// assert_eq!(bits_for_palette_size(16), 4);
+/// assert_eq!(bits_for_palette_size(256), 8);
+/// ```
+#[cfg(feature = "std")]
+pub mod palette_codec;
+
+/// Block property mask — compiled bitset queries on block state bits.
+/// AVX-512 VPTERNLOGD tests 3 conditions in 1 cycle. Graduated from
+/// `crate::hpc::property_mask::*`.
+///
+/// # Example
+///
+/// ```
+/// use ndarray::property_mask::PropertyMask;
+/// let mask = PropertyMask::new().require_bit(0).forbid_bit(3);
+/// assert!(mask.test(0b0000_0001));    // bit 0 set, bit 3 clear → match
+/// assert!(!mask.test(0b0000_1001));   // bit 3 set → no match
+/// ```
+#[cfg(feature = "std")]
+pub mod property_mask;
+
 #[cfg(feature = "std")]
 #[allow(clippy::all, missing_docs, dead_code, unused_variables, unused_imports)]
 pub mod simd_neon;
diff --git a/src/hpc/nibble.rs b/src/nibble.rs
similarity index 96%
rename from src/hpc/nibble.rs
rename to src/nibble.rs
index 05659f95..560c7c72 100644
--- a/src/hpc/nibble.rs
+++ b/src/nibble.rs
@@ -21,7 +21,7 @@
 /// assert_eq!(nibble_unpack(packed, 2), vec![0xA, 0x3]);
 /// ```
 pub fn nibble_unpack(packed: &[u8], count: usize) -> Vec<u8> {
-    assert!(packed.len() >= (count + 1) / 2, "packed buffer too small");
+    assert!(packed.len() >= count.div_ceil(2), "packed buffer too small");
 
     let mut out = Vec::with_capacity(count);
 
@@ -105,7 +105,7 @@ pub(crate) unsafe fn nibble_unpack_avx2(packed: &[u8], count: usize, out: &mut V
 /// assert_eq!(packed, vec![0x3A]);
 /// ```
 pub fn nibble_pack(values: &[u8]) -> Vec<u8> {
-    let out_len = (values.len() + 1) / 2;
+    let out_len = values.len().div_ceil(2);
     let mut out = vec![0u8; out_len];
 
     for (i, &v) in values.iter().enumerate() {
@@ -175,10 +175,10 @@ unsafe fn nibble_sub_clamp_avx2(packed: &mut [u8], delta: u8) {
         let mut data = [0u8; 32];
         data.copy_from_slice(&packed[offset..offset + 32]);
 
-        for j in 0..32 {
-            let lo = (data[j] & 0x0F).saturating_sub(delta);
-            let hi = ((data[j] >> 4) & 0x0F).saturating_sub(delta);
-            data[j] = lo | (hi << 4);
+        for byte in &mut data {
+            let lo = (*byte & 0x0F).saturating_sub(delta);
+            let hi = ((*byte >> 4) & 0x0F).saturating_sub(delta);
+            *byte = lo | (hi << 4);
         }
 
         packed[offset..offset + 32].copy_from_slice(&data);
@@ -263,9 +263,9 @@ pub(crate) unsafe fn nibble_above_threshold_avx2(packed: &[u8], threshold: u8) -
         let base_byte = c * 32;
         let chunk = &packed[base_byte..base_byte + 32];
 
-        for j in 0..32 {
-            let lo = chunk[j] & 0x0F;
-            let hi = (chunk[j] >> 4) & 0x0F;
+        for (j, &b) in chunk.iter().enumerate() {
+            let lo = b & 0x0F;
+            let hi = (b >> 4) & 0x0F;
             if lo > threshold {
                 result.push((base_byte + j) * 2);
             }
@@ -277,9 +277,9 @@ pub(crate) unsafe fn nibble_above_threshold_avx2(packed: &[u8], threshold: u8) -
 
     // Scalar tail
     let tail_start = chunks * 32;
-    for byte_idx in tail_start..packed.len() {
-        let lo = packed[byte_idx] & 0x0F;
-        let hi = packed[byte_idx] >> 4;
+    for (byte_idx, &b) in packed.iter().enumerate().skip(tail_start) {
+        let lo = b & 0x0F;
+        let hi = b >> 4;
         if lo > threshold {
             result.push(byte_idx * 2);
         }
diff --git a/src/hpc/palette_codec.rs b/src/palette_codec.rs
similarity index 98%
rename from src/hpc/palette_codec.rs
rename to src/palette_codec.rs
index 9dc4d8a5..7447a76f 100644
--- a/src/hpc/palette_codec.rs
+++ b/src/palette_codec.rs
@@ -56,7 +56,7 @@ pub fn pack_indices(indices: &[u8], bits_per_index: usize) -> Vec<u64> {
     assert!(bits_per_index > 0 && bits_per_index <= 8, "bits_per_index must be 1..=8");
 
     let indices_per_word = 64 / bits_per_index;
-    let n_words = (indices.len() + indices_per_word - 1) / indices_per_word;
+    let n_words = indices.len().div_ceil(indices_per_word);
     let mut packed = vec![0u64; n_words];
     let mask = (1u64 << bits_per_index) - 1;
 
@@ -110,7 +110,7 @@ pub fn pack_indices_bytes(indices: &[u8], bits_per_index: usize) -> Vec<u8> {
 ///
 /// Inverse of [`pack_indices_bytes`].
 pub fn unpack_indices_bytes(packed: &[u8], bits_per_index: usize, count: usize) -> Vec<u8> {
-    let n_words = (packed.len() + 7) / 8;
+    let n_words = packed.len().div_ceil(8);
     let mut words = Vec::with_capacity(n_words);
     for chunk in packed.chunks(8) {
         let mut buf = [0u8; 8];
@@ -145,7 +145,7 @@ pub fn transcode(packed: &[u64], old_bits: usize, new_bits: usize, count: usize)
 
     let old_per_word = 64 / old_bits;
     let new_per_word = 64 / new_bits;
-    let n_new_words = (count + new_per_word - 1) / new_per_word;
+    let n_new_words = count.div_ceil(new_per_word);
     let old_mask = (1u64 << old_bits) - 1;
     let new_mask = (1u64 << new_bits) - 1;
 
@@ -309,8 +309,7 @@ unsafe fn unpack_generic_avx512(packed: &[u64], bits_per_index: usize, count: us
     let mut result = Vec::with_capacity(count);
     let mut emitted = 0usize;
 
-    for word_idx in 0..packed.len() {
-        let word = packed[word_idx];
+    for &word in packed {
         for slot in 0..indices_per_word {
             if emitted >= count {
                 return result;
@@ -336,7 +335,7 @@ unsafe fn unpack_generic_avx512(packed: &[u64], bits_per_index: usize, count: us
 unsafe fn pack_generic_avx512(indices: &[u8], bits_per_index: usize) -> Vec<u64> {
     assert!(bits_per_index > 0 && bits_per_index <= 8);
     let indices_per_word = 64 / bits_per_index;
-    let n_words = (indices.len() + indices_per_word - 1) / indices_per_word;
+    let n_words = indices.len().div_ceil(indices_per_word);
     let mask = (1u64 << bits_per_index) - 1;
     let mut packed = vec![0u64; n_words];
 
diff --git a/src/hpc/property_mask.rs b/src/property_mask.rs
similarity index 99%
rename from src/hpc/property_mask.rs
rename to src/property_mask.rs
index f16f6dab..063b709e 100644
--- a/src/hpc/property_mask.rs
+++ b/src/property_mask.rs
@@ -90,7 +90,7 @@ impl PropertyMask {
     /// The returned vector has `ceil(states.len() / 64)` entries.
     pub fn test_section(&self, states: &[u64]) -> Vec<u64> {
         let n = states.len();
-        let result_len = (n + 63) / 64;
+        let result_len = n.div_ceil(64);
         let mut result = vec![0u64; result_len];
 
         #[cfg(target_arch = "x86_64")]
@@ -233,8 +233,8 @@ impl PropertyMask {
         }
 
         // Scalar tail
-        for i in (chunks * 8)..states.len() {
-            if self.test(states[i]) {
+        for &state in &states[chunks * 8..] {
+            if self.test(state) {
                 total += 1;
             }
         }
@@ -376,8 +376,7 @@ unsafe fn count_section_multi_avx512(masks: &[PropertyMask], states: &[u64]) ->
     }
 
     // Scalar tail
-    for i in (chunks * 8)..states.len() {
-        let state = states[i];
+    for &state in &states[chunks * 8..] {
         for (m_idx, mask) in masks.iter().enumerate() {
             if mask.test(state) {
                 counts[m_idx] += 1;