fix: resolve test race conditions, add logging, and fix CI deadlock

Re-enables the `numa` feature in CI workflows to prevent container/cgroup deadlocks while preserving validation correctness. Fixes concurrent test race conditions by replacing thread-local parameter storage with process-wide atomics and mutex locks. Integrates `tracing-subscriber` for structured logging and adds thread-ID tracking to debug worker lifecycles. Additionally bumps the crate version, updates `.gitignore`, documents experimental evolutionary distance pipelines, and refactors hardcoded test constants.

src/obikindex/Cargo.toml

@@ -24,6 +24,7 @@ hwlocality       = { version = "1.0.0-alpha.11", features = ["vendored"], option
 [dev-dependencies]
 obiread  = { path = "../obiread" }
 tempfile = "3"
+tracing-subscriber = { version = "0.3", features = ["fmt", "env-filter"] }
 
 [features]
 default = ["numa"]

src/obikindex/src/numa.rs

@@ -295,20 +295,27 @@ impl PartitionRunner {
                     let pool = node.pool.clone();
 
                     s.spawn(move || {
+                        let tid = std::thread::current().id();
+                        debug!(?tid, "PartitionRunner worker: waiting on activation");
                         if arx.recv().is_err() {
+                            debug!(?tid, "PartitionRunner worker: activation channel closed, exiting");
                             return;
                         }
+                        debug!(?tid, "PartitionRunner worker: activated");
                         if !cpu_ids.is_empty() {
                             pin_current_thread(cpu_ids);
                         }
                         for i in &prx {
+                            debug!(?tid, partition = i, "PartitionRunner worker: picked partition");
                             let t = Instant::now();
                             let r = match &pool {
                                 Some(p) => p.install(|| f(i)),
                                 None => f(i),
                             };
+                            debug!(?tid, partition = i, "PartitionRunner worker: partition done");
                             etx.send(WorkerEvent::Completed(i, r, t.elapsed())).ok();
                         }
+                        debug!(?tid, "PartitionRunner worker: no more partitions, exiting");
                     });
                 }
             }
@@ -319,13 +326,18 @@ impl PartitionRunner {
             // ── Controller ────────────────────────────────────────────────────
             let mut activation = NodeActivation::new(&activate_txs, &node_caps, max_workers);
             activation.activate_initial(INITIAL_DIVISOR, n_total);
+            debug!(n_total, activated = activation.total(), "PartitionRunner controller: initial activation");
 
             let mut cpu_sample = CpuSample::now();
             let mut io_sample = IoSample::now();
             let mut completed = 0usize;
 
             while completed < n_total {
-                let Ok(event) = event_rx.recv() else { break };
+                debug!(completed, n_total, "PartitionRunner controller: waiting for an event");
+                let Ok(event) = event_rx.recv() else {
+                    debug!("PartitionRunner controller: event channel closed, stopping");
+                    break;
+                };
                 match event {
                     WorkerEvent::Completed(i, r, dur) => {
                         match r {

src/obikindex/src/siblings.rs

@@ -976,7 +976,23 @@ mod tests {
     /// the same primitives `obikmer`'s `scatter` step uses (minus the
     /// multi-file `obipipeline` wrapper — a single sequence needs none of
     /// that): normalise -> build superkmers -> route -> write.
+    /// `cargo test` doesn't install a `tracing` subscriber the way `obikmer`'s
+    /// CLI does, so `debug!`/etc. are silent no-ops by default — including the
+    /// `PartitionRunner` instrumentation that would matter most for
+    /// re-diagnosing a hang here. `try_init` is idempotent across concurrently
+    /// running tests (later calls just find a subscriber already installed).
+    fn init_tracing() {
+        let _ = tracing_subscriber::fmt()
+            .with_env_filter(
+                tracing_subscriber::EnvFilter::try_from_default_env()
+                    .unwrap_or_else(|_| tracing_subscriber::EnvFilter::new("info")),
+            )
+            .with_writer(std::io::stderr)
+            .try_init();
+    }
+
     fn build_single_genome_index(dir: &Path, label: &str, seq: &[u8]) -> KmerIndex {
+        init_tracing();
         let fasta_path = dir.join(format!("{label}.fasta"));
         let mut f = std::fs::File::create(&fasta_path).unwrap();
         writeln!(f, ">{label}").unwrap();