Merge pull request 'ci: update registry auth and improve adaptive worker scaling' (#51) from push-qlpywtroutvx into main

Reviewed-on: #51

.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:

src/Cargo.lock

@@ -1704,7 +1704,7 @@ dependencies = [
 
 [[package]]
 name = "obikmer"
-version = "1.1.19"
+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 mut n_active              = 1usize;
+            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;
             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 {
-        true  // first additional worker: no prior data to evaluate
+    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
     } else {
-        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
+        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
     };
 
     if last_spawn_was_beneficial {

src/obikmer/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "obikmer"
-version = "1.1.19"
+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"]