ci: update macOS ARM64 build workflow and bump obikmer version

Replace manual Zig/cargo-zigbuild setup with a pre-configured Docker container (`joseluisq/rust-linux-darwin-builder`). Use explicit Clang cross-compilers for native macOS ARM64 compilation. Bump the `obikmer` package version to 1.1.25.

.gitea/workflows/ci.yml

@@ -1,9 +1,8 @@
 name: CI
 
 on:
-  push:
-    branches: ['main']
   pull_request:
+    branches: ['main']
 
 jobs:
   build:

.gitea/workflows/release.yml

@@ -6,7 +6,32 @@ on:
       - "v*"
 
 jobs:
-  build-linux-static:
+  create-release:
+    runs-on: ubuntu-latest
+    outputs:
+      release_id: ${{ steps.create.outputs.release_id }}
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Create Gitea release
+        id: create
+        env:
+          GITEA_TOKEN: ${{ secrets.GITEATOKEN }}
+          TAG: ${{ github.ref_name }}
+        run: |
+          sudo apt-get update -qq && sudo apt-get install -y -qq jq
+          body=$(git for-each-ref --format='%(contents)' "refs/tags/$TAG")
+          release_id=$(curl -s -X POST \
+            "${{ github.server_url }}/api/v1/repos/${{ github.repository }}/releases" \
+            -H "Authorization: token $GITEA_TOKEN" \
+            -H "Content-Type: application/json" \
+            -d "{\"tag_name\":\"$TAG\",\"name\":\"$TAG\",\"body\":$(echo "$body" | jq -Rs .)}" | jq -r '.id')
+          echo "release_id=$release_id" >> $GITHUB_OUTPUT
+
+  build-linux-x86_64:
+    needs: create-release
     runs-on: ubuntu-latest
     defaults:
       run:
@@ -45,23 +70,59 @@ jobs:
           PKG_CONFIG_ALLOW_CROSS: "1"
         run: cargo zigbuild --release --target x86_64-unknown-linux-musl
 
-      - name: Prepare artifact
+      - name: Prepare and upload artifact
+        env:
+          GITEA_TOKEN: ${{ secrets.GITEATOKEN }}
+          RELEASE_ID: ${{ needs.create-release.outputs.release_id }}
         run: |
           mkdir -p /tmp/dist
           cp target/x86_64-unknown-linux-musl/release/obikmer /tmp/dist/obikmer-linux-x86_64
           strip /tmp/dist/obikmer-linux-x86_64
-
-      - name: Create Gitea release and upload binary
-        env:
-          GITEA_TOKEN: ${{ secrets.GITEATOKEN }}
-          TAG: ${{ github.ref_name }}
-        run: |
-          release_id=$(curl -s -X POST \
-            "${{ github.server_url }}/api/v1/repos/${{ github.repository }}/releases" \
-            -H "Authorization: token $GITEA_TOKEN" \
-            -H "Content-Type: application/json" \
-            -d "{\"tag_name\":\"$TAG\",\"name\":\"$TAG\"}" | jq -r '.id')
           curl -s -X POST \
-            "${{ github.server_url }}/api/v1/repos/${{ github.repository }}/releases/$release_id/assets" \
+            "${{ github.server_url }}/api/v1/repos/${{ github.repository }}/releases/$RELEASE_ID/assets" \
             -H "Authorization: token $GITEA_TOKEN" \
             -F "attachment=@/tmp/dist/obikmer-linux-x86_64"
+
+  build-macos-arm64:
+    needs: create-release
+    runs-on: ubuntu-latest
+    container: joseluisq/rust-linux-darwin-builder:latest
+    defaults:
+      run:
+        working-directory: src
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Add target and install jq
+        run: |
+          rustup target add aarch64-apple-darwin
+          apt-get update -qq && apt-get install -y -qq jq
+
+      - name: Cache cargo registry
+        uses: actions/cache@v4
+        with:
+          path: |
+            ~/.cargo/registry
+            ~/.cargo/git
+            src/target
+          key: macos-arm64-cargo-${{ hashFiles('src/Cargo.lock') }}
+          restore-keys: macos-arm64-cargo-
+
+      - name: Build macOS binary
+        env:
+          CC: aarch64-apple-darwin22.4-clang
+          CXX: aarch64-apple-darwin22.4-clang++
+          CARGO_TARGET_AARCH64_APPLE_DARWIN_LINKER: aarch64-apple-darwin22.4-clang
+        run: cargo build --release --target aarch64-apple-darwin
+
+      - name: Prepare and upload artifact
+        env:
+          GITEA_TOKEN: ${{ secrets.GITEATOKEN }}
+          RELEASE_ID: ${{ needs.create-release.outputs.release_id }}
+        run: |
+          mkdir -p /tmp/dist
+          cp target/aarch64-apple-darwin/release/obikmer /tmp/dist/obikmer-macos-arm64
+          curl -s -X POST \
+            "${{ github.server_url }}/api/v1/repos/${{ github.repository }}/releases/$RELEASE_ID/assets" \
+            -H "Authorization: token $GITEA_TOKEN" \
+            -F "attachment=@/tmp/dist/obikmer-macos-arm64"

Makefile

@@ -90,5 +90,9 @@ release: bump-version
 	@jj git push --change @
 	@new_version=$$(grep '^version = ' $(CARGO_TOML) | head -n 1 | sed 's/version = "\(.*\)"/\1/'); \
 	git_hash=$$(jj log -r @ --no-graph -T 'commit_id'); \
-	git tag "v$$new_version" "$$git_hash" && \
+	commits=$$(jj log -r 'latest(tags())..@' --no-graph -T 'description ++ "\n"' 2>/dev/null || \
+	           jj log --no-graph -T 'description ++ "\n"' --limit 30); \
+	notes=$$(printf 'Write concise markdown release notes for obikmer (a Rust kmer genomics tool). Be technical and direct. Base them strictly on these commit messages:\n\n%s' "$$commits" | aichat 2>/dev/null); \
+	tag_msg="$${notes:-Release v$$new_version}"; \
+	git tag -a "v$$new_version" -m "$$tag_msg" "$$git_hash" && \
 	git push origin "v$$new_version"

src/Cargo.lock

@@ -1704,7 +1704,7 @@ dependencies = [
 
 [[package]]
 name = "obikmer"
-version = "1.1.15"
+version = "1.1.25"
 dependencies = [
  "clap",
  "csv",

src/obikindex/Cargo.toml

@@ -17,4 +17,8 @@ serde            = { version = "1", features = ["derive"] }
 serde_json       = "1"
 indicatif        = "0.17"
 tracing          = "0.1.44"
-hwlocality       = { version = "1.0.0-alpha.11", features = ["vendored"] }
+hwlocality       = { version = "1.0.0-alpha.11", features = ["vendored"], optional = true }
+
+[features]
+default = ["numa"]
+numa    = ["hwlocality"]

src/obikindex/src/numa.rs

@@ -12,9 +12,13 @@ use std::sync::Arc;
 use std::time::{Duration, Instant};
 
 use crossbeam_channel::unbounded;
+#[cfg(feature = "numa")]
 use hwlocality::Topology;
+#[cfg(feature = "numa")]
 use hwlocality::cpu::binding::CpuBindingFlags;
+#[cfg(feature = "numa")]
 use hwlocality::cpu::cpuset::CpuSet;
+#[cfg(feature = "numa")]
 use hwlocality::object::types::ObjectType;
 use obisys::CpuSample;
 use tracing::debug;
@@ -40,6 +44,7 @@ impl NumaSetup {
 
 /// Detect NUMA topology and build per-node Rayon pools.
 /// Always succeeds: falls back to a single synthetic UMA node on failure.
+#[cfg(feature = "numa")]
 pub fn build() -> NumaSetup {
     if let Ok(topology) = Topology::new() {
         let nodes: Vec<Vec<usize>> = topology
@@ -81,8 +86,21 @@ pub fn build() -> NumaSetup {
     }
 }
 
+#[cfg(not(feature = "numa"))]
+pub fn build() -> NumaSetup {
+    let n_cores = std::thread::available_parallelism()
+        .map(|n| n.get())
+        .unwrap_or(1);
+    debug!("UMA: single synthetic node, {} core(s)", n_cores);
+    NumaSetup {
+        pools:         vec![None],
+        cpus_per_node: vec![(0..n_cores).collect()],
+    }
+}
+
 /// Bind the calling thread to `cpu_indices` using hwloc.
 /// Silently returns on any error so the thread still runs, just unbound.
+#[cfg(feature = "numa")]
 pub fn pin_current_thread(cpu_indices: &[usize]) {
     let Ok(topology) = Topology::new() else { return };
     let mut cpuset = CpuSet::new();
@@ -92,8 +110,12 @@ pub fn pin_current_thread(cpu_indices: &[usize]) {
     let _ = topology.bind_cpu(&cpuset, CpuBindingFlags::THREAD);
 }
 
+#[cfg(not(feature = "numa"))]
+pub fn pin_current_thread(_cpu_indices: &[usize]) {}
+
 // ── Internal helpers ──────────────────────────────────────────────────────────
 
+#[cfg(feature = "numa")]
 fn build_pool(cpus: &[usize]) -> Option<rayon::ThreadPool> {
     let cpus = cpus.to_vec();
     rayon::ThreadPoolBuilder::new()

src/obikmer/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "obikmer"
-version = "1.1.15"
+version = "1.1.25"
 edition = "2024"
 
 [[bin]]
@@ -18,7 +18,7 @@ obikrope      = { path = "../obikrope" }
 obikpartitionner = { path = "../obikpartitionner" }
 obisys        = { path = "../obisys" }
 obiskio       = { path = "../obiskio" }
-obikindex     = { path = "../obikindex" }
+obikindex     = { path = "../obikindex", default-features = false }
 obitaxonomy   = { path = "../obitaxonomy" }
 obilayeredmap = { path = "../obilayeredmap" }
 clap          = { version = "4", features = ["derive"] }
@@ -33,4 +33,6 @@ tracing-subscriber = { version = "0.3", features = ["fmt", "env-filter"] }
 pprof = { version = "0.13", features = ["prost-codec"], optional = true }
 
 [features]
+default   = ["numa"]
+numa      = ["obikindex/numa"]
 profiling = ["dep:pprof"]