seqtree 1.3.2__tar.gz → 1.3.3__tar.gz

{seqtree-1.3.2 → seqtree-1.3.3}/.gitignore

@@ -25,6 +25,10 @@ tmp/
 /CLAUDE.md
 /ROADMAP.md
 /SOURCES.md
-/skills/
+/skills/*
+!/skills/seqtree/
 /add_bindings.py
 /add_native.py
+
+# Private retired branches, notes and scratch; never package or publish.
+/attic/

{seqtree-1.3.2 → seqtree-1.3.3}/CHANGELOG.md

@@ -3,6 +3,18 @@
 All notable changes to `seqtree`. Dates are release dates. From 1.0.0 the project follows semantic
 versioning: breaking changes need a **major** bump.
 
+## Unreleased
+
+## 1.3.3
+
+- Cap automatic native CPU budgets at 16 allocated CPUs; preserve larger explicit
+  requests within the allocation and serial inner kernels in sample workers.
+
+- Reject unknown setup flags before creating an environment or installing packages.
+- Keep native bindings in the reviewed nanobind 2.x range.
+- Build documentation from declared extras on master/dev and pull requests;
+  deploy master only, without development builds cancelling release documentation.
+
 ## [1.3.1] — 2026-10-19
 
 ### Changed

{seqtree-1.3.2 → seqtree-1.3.3}/CMakeLists.txt

@@ -7,9 +7,7 @@ set(CMAKE_POSITION_INDEPENDENT_CODE ON)
 if(NOT CMAKE_BUILD_TYPE)
   set(CMAKE_BUILD_TYPE Release)
 endif()
-if(NOT MSVC)
-  set(CMAKE_CXX_FLAGS_RELEASE "-O3")
-endif()  # MSVC Release already uses /O2; -O3 is not a valid MSVC flag
+# Keep CMake/toolchain Release flags, including compiler-specific optimization.
 
 option(SEQTREE_TESTS "Build C++ tests" OFF)
 option(SEQTREE_BENCH "Build C++ benchmarks" OFF)

{seqtree-1.3.2 → seqtree-1.3.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: seqtree
-Version: 1.3.2
+Version: 1.3.3
 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>
@@ -22,8 +22,8 @@ Requires-Dist: biopython>=1.81; extra == "test"
 Provides-Extra: bench
 Requires-Dist: huggingface_hub; extra == "bench"
 Provides-Extra: docs
-Requires-Dist: sphinx; extra == "docs"
-Requires-Dist: pydata-sphinx-theme; extra == "docs"
+Requires-Dist: sphinx>=7; extra == "docs"
+Requires-Dist: pydata-sphinx-theme>=0.15; extra == "docs"
 Provides-Extra: control
 Requires-Dist: huggingface_hub; extra == "control"
 Provides-Extra: pmhc
@@ -36,7 +36,7 @@ Description-Content-Type: text/markdown
 [![Python](https://img.shields.io/pypi/pyversions/seqtree.svg)](https://pypi.org/project/seqtree/)
 [![License](https://img.shields.io/badge/license-GPLv3-green)](LICENSE)
 [![CI](https://github.com/antigenomics/seqtree/actions/workflows/ci.yml/badge.svg)](https://github.com/antigenomics/seqtree/actions/workflows/ci.yml)
-[![Docs](https://github.com/antigenomics/seqtree/actions/workflows/docs.yml/badge.svg?branch=dev)](https://antigenomics.github.io/seqtree/)
+[![Docs](https://github.com/antigenomics/seqtree/actions/workflows/docs.yml/badge.svg?branch=master)](https://antigenomics.github.io/seqtree/)
 
 Fast fuzzy search over biological sequences (amino-acid or nucleotide), as a C++
 core with a minimal Python binding. Build an immutable index once, then search
@@ -64,7 +64,7 @@ for hit in idx.search("CASSLAPGATNEKLFF", p):
     print(hit.ref_id, hit.score, hit.n_subs)
 
 # parallel batch (releases the GIL)
-results = idx.search_batch(queries, p, threads=0)   # 0 = all cores
+results = idx.search_batch(queries, p, threads=0)   # 0 = automatic, up to 16 allocated CPUs
 
 # matrix-weighted budget. Name seqtrie -- engine="auto" always means seqtm.
 # gap_open must follow the matrix: 2 * blosum62.scale() == 28, not the default 1.
@@ -300,3 +300,12 @@ with separate alignment-selection and final scoring coefficients.
 insertion/deletion cap; its default preserves previous behavior. See the
 [API reference](https://antigenomics.github.io/seqtree/api.html) for array contracts
 and tie, count, exclusion and unsupported-value semantics.
+
+## Agent skill
+
+The public [seqtree skill](skills/seqtree/SKILL.md) guides use of the C++20 library
+and Python bindings for sequence search, alignment, distances, and batch operations.
+
+CPU budgets use `threads=0` for automatic parallel work, capped at 16 allocated CPUs.
+Use `1` for serial work or a positive
+count to override the automatic cap within the scheduler/container allocation.

{seqtree-1.3.2 → seqtree-1.3.3}/README.md

@@ -4,7 +4,7 @@
 [![Python](https://img.shields.io/pypi/pyversions/seqtree.svg)](https://pypi.org/project/seqtree/)
 [![License](https://img.shields.io/badge/license-GPLv3-green)](LICENSE)
 [![CI](https://github.com/antigenomics/seqtree/actions/workflows/ci.yml/badge.svg)](https://github.com/antigenomics/seqtree/actions/workflows/ci.yml)
-[![Docs](https://github.com/antigenomics/seqtree/actions/workflows/docs.yml/badge.svg?branch=dev)](https://antigenomics.github.io/seqtree/)
+[![Docs](https://github.com/antigenomics/seqtree/actions/workflows/docs.yml/badge.svg?branch=master)](https://antigenomics.github.io/seqtree/)
 
 Fast fuzzy search over biological sequences (amino-acid or nucleotide), as a C++
 core with a minimal Python binding. Build an immutable index once, then search
@@ -32,7 +32,7 @@ for hit in idx.search("CASSLAPGATNEKLFF", p):
     print(hit.ref_id, hit.score, hit.n_subs)
 
 # parallel batch (releases the GIL)
-results = idx.search_batch(queries, p, threads=0)   # 0 = all cores
+results = idx.search_batch(queries, p, threads=0)   # 0 = automatic, up to 16 allocated CPUs
 
 # matrix-weighted budget. Name seqtrie -- engine="auto" always means seqtm.
 # gap_open must follow the matrix: 2 * blosum62.scale() == 28, not the default 1.
@@ -268,3 +268,12 @@ with separate alignment-selection and final scoring coefficients.
 insertion/deletion cap; its default preserves previous behavior. See the
 [API reference](https://antigenomics.github.io/seqtree/api.html) for array contracts
 and tie, count, exclusion and unsupported-value semantics.
+
+## Agent skill
+
+The public [seqtree skill](skills/seqtree/SKILL.md) guides use of the C++20 library
+and Python bindings for sequence search, alignment, distances, and batch operations.
+
+CPU budgets use `threads=0` for automatic parallel work, capped at 16 allocated CPUs.
+Use `1` for serial work or a positive
+count to override the automatic cap within the scheduler/container allocation.

{seqtree-1.3.2 → seqtree-1.3.3}/include/seqtree/parallel.hpp

@@ -67,7 +67,7 @@ inline unsigned available_cpus() {
 }
 
 // Runs body(i, local) for every i in [0, n), across nt workers pulling contiguous chunks off
-// one atomic cursor. `threads <= 0` means the detected available CPU budget.
+// one atomic cursor. `threads <= 0` selects up to 16 available CPUs; positive counts may exceed that cap.
 //
 // `make_local()` is called once per worker and its result handed to every body() that worker
 // runs -- that is how a Searcher or a scratch buffer gets allocated once per thread rather
@@ -85,7 +85,7 @@ template <class MakeLocal, class Body>
 void parallel_for(size_t n, int threads, MakeLocal make_local, Body body,
                   size_t chunk_min = 1, size_t chunk_max = 1024) {
     const unsigned available = available_cpus();
-    unsigned nt = threads > 0 ? unsigned(threads) : available;
+    unsigned nt = threads > 0 ? unsigned(threads) : std::min(available, 16u);
     if (nt > available || nt >= 1000)
         throw std::invalid_argument("worker count exceeds the available CPU budget; request fewer threads");
     if (n == 0) return;

{seqtree-1.3.2 → seqtree-1.3.3}/pyproject.toml

@@ -1,10 +1,10 @@
 [build-system]
-requires = ["scikit-build-core>=0.12", "nanobind>=2.5"]
+requires = ["scikit-build-core>=0.12", "nanobind>=2.5,<3"]
 build-backend = "scikit_build_core.build"
 
 [project]
 name = "seqtree"
-version = "1.3.2"
+version = "1.3.3"
 description = "Fast fuzzy search over biological sequences (C++ core, Python bindings)"
 readme = "README.md"
 requires-python = ">=3.10"
@@ -26,7 +26,7 @@ dependencies = []
 # seqtree itself has no runtime dependencies and must never import it.
 test = ["pytest>=7.4", "pytest-cov>=4.1", "biopython>=1.81"]
 bench = ["huggingface_hub"]
-docs = ["sphinx", "pydata-sphinx-theme"]
+docs = ["sphinx>=7", "pydata-sphinx-theme>=0.15"]
 control = ["huggingface_hub"]  # only needed to download controls larger than the bundled subset
 pmhc = ["huggingface_hub"]     # only needed to fetch the isalgo/pmhc_data epitope tables
 
@@ -40,6 +40,7 @@ wheel.packages = ["python/seqtree"]
 cmake.build-type = "Release"
 # Keep the sdist lean: ship only what builds the package. Anchor with a leading "/".
 sdist.exclude = [
+    "/attic/",
     "/bench", "/tests", "/docs", "/.github", "/setup.sh", "/build", "/appendix", "/examples",
     # Local agent config: machine-specific absolute paths and unrelated repo names.
     "/.claude", "/CLAUDE.md", "/AGENTS.md", "/ROADMAP.md", "/SOURCES.md", "/skills",

seqtree-1.3.2/RELEASE_AUDIT.md

@@ -1,12 +0,0 @@
-# Release audit — 17 October 2026
-
-The requested generic batch/search APIs are implemented. No new native algorithm is needed for the audited downstream requirements.
-
-- Native batch search and edit histograms; aggregate insertion/deletion caps.
-- Float64 global-alignment target reductions, separate candidate/final scoring semantics, fixed populations under exact exclusion.
-- Grouped geometry, fixed audit partitions, bounded deterministic sparse radius hits and optional-geometry compatibility at the supported nanobind floor.
-- Shared CPU allocation checks; one-thread inline execution and explicit over-budget rejection.
-
-Verification on `0852ff5`: **379 passed, 1 Linux-only platform skip** across `test_batch_threads.py`, `test_alignment_max.py`, `test_edit_histogram.py`, `test_grouped_optional_geometry.py` and `test_grouped_sparse_hits.py`. An additional 280 checks cover grouped populations, withholding, paired lanes, offsets, score bins and partitions. Native budget was two CPUs; numerical libraries used one thread. The committed `examples/01_gapped_search.py` runs and its per-query cutoff/search output was inspected. Sphinx builds with `-W`.
-
-The local `dev` commits `0126e00`, `858056b` and `0852ff5` were three commits ahead of the remote at audit start. They are preserved and included when this audited `dev` is pushed. The changelog now covers these capabilities; public API documentation already describes the alignment reductions. [Issue 18](https://github.com/antigenomics/seqtree/issues/18) tracks integration into the release head and the remaining exact-head cross-platform/wheel gate. Publishing remains the maintainer's action; this audit creates no tag or release. Focused checks do not substitute for complete release CI.