refactor: make hwlocality optional and streamline release workflow

Extracts release creation into a dedicated `create-release` job that outputs a shared `release_id`, allowing downstream build jobs to upload binaries directly and ensuring atomic initialization. Introduces a `numa` feature flag for `obikindex` to make `hwlocality` optional, providing graceful fallbacks like a synthetic UMA node when disabled. Also bumps `obikmer` to 1.1.16.

.gitea/workflows/ci.yml

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

.gitea/workflows/release.yml

@@ -11,10 +11,6 @@ jobs:
     outputs:
       release_id: ${{ steps.create.outputs.release_id }}
     steps:
-      - uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
-
       - name: Create Gitea release
         id: create
         env:
@@ -22,12 +18,11 @@ jobs:
           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 "$body" | jq -Rs .)}" | jq -r '.id')
+            -d "{\"tag_name\":\"$TAG\",\"name\":\"$TAG\"}" | jq -r '.id')
           echo "release_id=$release_id" >> $GITHUB_OUTPUT
 
   build-linux-x86_64:
@@ -86,17 +81,21 @@ jobs:
   build-macos-arm64:
     needs: create-release
     runs-on: ubuntu-latest
-    container:
-      image: registry.metabarcoding.org/cibuilder/rustcrossosx:latest
-      credentials:
-        username: ${{ github.actor }}
-        password: ${{ secrets.REGISTRYTOKEN }}
     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:
@@ -108,7 +107,7 @@ jobs:
           restore-keys: macos-arm64-cargo-
 
       - name: Build macOS binary
-        run: cargo build --release --target aarch64-apple-darwin --no-default-features
+        run: cargo zigbuild --release --target aarch64-apple-darwin --no-default-features
 
       - name: Prepare and upload artifact
         env:

Makefile

@@ -90,9 +90,5 @@ release: bump-version
 	@jj git push --change @
 	@new_version=$$(grep '^version = ' $(CARGO_TOML) | head -n 1 | sed 's/version = "\(.*\)"/\1/'); \
 	git_hash=$$(jj log -r @ --no-graph -T 'commit_id'); \
-	commits=$$(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" "$$git_hash" && \
+	git tag "v$$new_version" "$$git_hash" && \
 	git push origin "v$$new_version"

src/Cargo.lock

@@ -1704,7 +1704,7 @@ dependencies = [
 
 [[package]]
 name = "obikmer"
-version = "1.1.27"
+version = "1.1.16"
 dependencies = [
  "clap",
  "csv",

src/obikindex/src/numa.rs

@@ -287,9 +287,8 @@ impl PartitionRunner {
             drop(event_tx);
 
             // ── Controller ────────────────────────────────────────────────────
-            let initial_workers = n_nodes.min(max_workers).min(n_total);
-            for _ in 0..initial_workers { activate_tx.send(()).ok(); }
-            let mut n_active              = initial_workers;
+            activate_tx.send(()).ok();
+            let mut n_active              = 1usize;
             let mut cpu_sample            = CpuSample::now();
             let mut eff_at_last_spawn     = 0.0f64; // 0 = no previous spawn to evaluate
             let mut completed             = 0usize;
@@ -362,13 +361,13 @@ fn maybe_activate(
     // Going from k-1 → k workers, the minimum acceptable speedup is (k-1+0.2)/(k-1).
     // For the very first extra worker (n_active == 1, no previous spawn), skip this
     // check: eff_at_last_spawn == 0 acts as the sentinel.
-    let last_spawn_was_beneficial = if *eff_at_last_spawn < 1e-9 || eff < 1e-9 {
-        true  // first additional worker, or measurement too short: no prior data to evaluate
+    let last_spawn_was_beneficial = if *eff_at_last_spawn < 1e-9 {
+        true  // first additional worker: no prior data to evaluate
     } else {
-        let k_new = *n_active as f64;  // worker count after the last spawn
-        let min_gain = 0.2 / k_new;
-        let actual_gain = (eff - *eff_at_last_spawn) / eff;
-        actual_gain >= min_gain
+        let k_before   = (*n_active - 1) as f64;
+        let min_speedup = (k_before + 0.2) / k_before;
+        let actual_speedup = eff / *eff_at_last_spawn;
+        actual_speedup >= min_speedup
     };
 
     if last_spawn_was_beneficial {

src/obikmer/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "obikmer"
-version = "1.1.27"
+version = "1.1.16"
 edition = "2024"
 
 [[bin]]
@@ -18,7 +18,7 @@ obikrope      = { path = "../obikrope" }
 obikpartitionner = { path = "../obikpartitionner" }
 obisys        = { path = "../obisys" }
 obiskio       = { path = "../obiskio" }
-obikindex     = { path = "../obikindex", default-features = false }
+obikindex     = { path = "../obikindex" }
 obitaxonomy   = { path = "../obitaxonomy" }
 obilayeredmap = { path = "../obilayeredmap" }
 clap          = { version = "4", features = ["derive"] }
@@ -33,6 +33,4 @@ 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"]