seqtree 1.0.0__tar.gz → 1.0.1__tar.gz

{seqtree-1.0.0 → seqtree-1.0.1}/CHANGELOG.md

@@ -3,6 +3,14 @@
 All notable changes to `seqtree`. Dates are release dates. From 1.0.0 the project follows semantic
 versioning: breaking changes need a **major** bump.
 
+## [1.0.1] — 2026-10-09
+
+### Fixed
+
+- A one-thread batch executes on the calling thread instead of launching a worker.
+- Worker scratch-allocation exceptions propagate to the caller rather than terminating the process.
+- A partially started worker pool joins its running workers if thread creation fails.
+
 ## [1.0.0] — 2026-09-06
 
 ### Added

{seqtree-1.0.0 → seqtree-1.0.1}/CMakeLists.txt

@@ -65,6 +65,7 @@ if(SEQTREE_TESTS)
     tests/cpp/test_positional.cpp
     tests/cpp/test_kmer_index.cpp
     tests/cpp/test_text_index.cpp
+    tests/cpp/test_parallel.cpp
   )
   target_include_directories(seqtree_tests PRIVATE tests/cpp src)
   target_link_libraries(seqtree_tests PRIVATE seqtree_core)

{seqtree-1.0.0 → seqtree-1.0.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: seqtree
-Version: 1.0.0
+Version: 1.0.1
 Summary: Fast fuzzy search over biological sequences (C++ core, Python bindings)
 Keywords: sequence-search,fuzzy-matching,CDR3,immunology,bioinformatics,trie
 Author-Email: ISALGO laboratory <mikhail.shugay@gmail.com>

{seqtree-1.0.0 → seqtree-1.0.1}/include/seqtree/parallel.hpp

@@ -37,30 +37,38 @@ void parallel_for(size_t n, int threads, MakeLocal make_local, Body body,
                               : std::max(1u, std::thread::hardware_concurrency());
     nt = unsigned(std::min<size_t>(nt, n));  // n >= 1 here, so nt >= 1
 
+    // A serial budget runs on the calling thread; spawning one worker only adds overhead.
+    if (nt == 1) {
+        auto local = make_local();
+        for (size_t i = 0; i < n; ++i) body(i, local);
+        return;
+    }
+
     std::atomic<size_t> next{0};
     const size_t chunk = std::clamp<size_t>(n / (size_t(nt) * 8), chunk_min, chunk_max);
     std::exception_ptr err;
     std::mutex emu;
 
     auto worker = [&] {
-        auto local = make_local();
-        for (;;) {
-            const size_t start = next.fetch_add(chunk);
-            if (start >= n) break;
-            const size_t end = std::min(n, start + chunk);
-            for (size_t i = start; i < end; ++i) {
-                try {
+        // Scratch construction can allocate and throw too. Nothing may escape the entry point.
+        try {
+            auto local = make_local();
+            for (;;) {
+                const size_t start = next.fetch_add(chunk);
+                if (start >= n) break;
+                const size_t end = std::min(n, start + chunk);
+                for (size_t i = start; i < end; ++i) {
                     body(i, local);
-                } catch (...) {
-                    std::lock_guard<std::mutex> lk(emu);
-                    if (!err) err = std::current_exception();
-                    return;
                 }
             }
+        } catch (...) {
+            std::lock_guard<std::mutex> lk(emu);
+            if (!err) err = std::current_exception();
         }
     };
 
-    std::vector<std::thread> pool;
+    // A failed thread launch must also join workers already started before unwinding.
+    std::vector<std::jthread> pool;
     pool.reserve(nt);
     for (unsigned t = 0; t < nt; ++t) pool.emplace_back(worker);
     for (auto& th : pool) th.join();

{seqtree-1.0.0 → seqtree-1.0.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "scikit_build_core.build"
 
 [project]
 name = "seqtree"
-version = "1.0.0"
+version = "1.0.1"
 description = "Fast fuzzy search over biological sequences (C++ core, Python bindings)"
 readme = "README.md"
 requires-python = ">=3.10"