ci: update registry auth and improve adaptive worker scaling

Refactor the release workflow to use a structured container object with authenticated pulls for macOS ARM64 builds. Replace single-worker activation with dynamic upfront provisioning based on node and worker counts. Implement an absolute efficiency gain threshold for scaling checks and add early termination to improve adaptive scaling stability. Bump obikmer crate version to 1.1.27.

.gitea/workflows/ci.yml

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

.gitea/workflows/release.yml

@@ -13,7 +13,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
         with:
-          fetch-tags: true
+          fetch-depth: 0
 
       - name: Create Gitea release
         id: create
@@ -86,21 +86,17 @@ 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:
@@ -112,7 +108,7 @@ jobs:
           restore-keys: macos-arm64-cargo-
 
       - name: Build macOS binary
-        run: cargo zigbuild --release --target aarch64-apple-darwin --no-default-features
+        run: cargo build --release --target aarch64-apple-darwin --no-default-features
 
       - name: Prepare and upload artifact
         env:

Makefile

@@ -92,6 +92,7 @@ release: bump-version
 	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); \
+	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); \
-	git tag -a "v$$new_version" -m "$$notes" "$$git_hash" && \
+	tag_msg="$${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 = "1.1.18"
+version = "1.1.27"
 dependencies = [
  "clap",
  "csv",

src/obikindex/src/numa.rs

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

src/obikmer/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "obikmer"
-version = "1.1.18"
+version = "1.1.27"
 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"]