chore: update obikmer to 1.1.24

Bumps the obikmer version in Cargo.toml from 1.1.21 to 1.1.24 and updates Cargo.lock to align with the upstream patch release (1.1.23). This ensures consistent dependency resolution across builds.

.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 +70,60 @@ 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 $GITEA_TOKEN" \
             -F "attachment=@/tmp/dist/obikmer-linux-x86_64"
+
+  build-macos-arm64:
+    needs: create-release
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: src
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install Rust + zigbuild
+        run: |
+          curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y --default-toolchain stable
+          echo "$HOME/.cargo/bin" >> $GITHUB_PATH
+          sudo apt-get update -qq && sudo apt-get install -y -qq jq
+          pip install ziglang --quiet --break-system-packages
+          $HOME/.cargo/bin/cargo install cargo-zigbuild
+          $HOME/.cargo/bin/rustup target add aarch64-apple-darwin
+
+      - name: Cache cargo registry
+        uses: actions/cache@v4
+        with:
+          path: |
+            ~/.cargo/registry
+            ~/.cargo/git
+            src/target
+          key: macos-arm64-cargo-${{ hashFiles('src/Cargo.lock') }}
+          restore-keys: macos-arm64-cargo-
+
+      - name: Build macOS binary
+        env:
+          MACOSX_DEPLOYMENT_TARGET: "11.0"
+        run: cargo zigbuild --release --target aarch64-apple-darwin11.0 --no-default-features
+
+      - 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 = "1.1.24"
 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 = "1.1.24"
 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"]