pen-stack 6.3.0__tar.gz → 6.3.1__tar.gz

{pen_stack-6.3.0 → pen_stack-6.3.1}/CHANGELOG.md

@@ -3,6 +3,30 @@
 All notable changes to PEN-STACK are documented here. This file follows
 [Keep a Changelog](https://keepachangelog.com/) and the program's phase structure.
 
+## [6.3.1] - 2026-06-12 - v6.3.1: router fix — general "how does it work" no longer misrouted to the meta lane
+
+**Patch (routing correctness).** Found by a rigorous full-stack test pass (every oracle + every endpoint + the 4
+chat lanes + general/biological-intelligence questions). PATCH release on the stable 6.x API.
+
+### Fixed
+- **Router meta-lane over-capture.** A general-biology question phrased "…and how does **it** work / cut DNA?"
+  (e.g. *"what is CRISPR-Cas9 and how does it cut DNA?"*) matched the meta pattern `how (do|does) (you|it|this|pen)`
+  and was answered from PEN-STACK capability facts instead of general knowledge. Narrowed the bare-pronoun meta
+  trigger to `how (do|does) (you|pen)` so a general "how does it …" routes to the **general** lane (labelled,
+  with an engine pointer); pen-stack-scoped "how do you compute X" stays **meta** (the verb-qualified pattern is
+  unchanged). Regression cases added to `tests/unit/test_ws_chat.py::test_router_classifies_the_four_lanes`.
+
+### Verified (rigorous v6.3 test pass)
+- **Oracle mesh (42/42, engine-direct):** ViennaRNA computes a real MFE fold (−38.3 kcal/mol); AlphaGenome /
+  Evo2 / vcell (Arc-STATE) / AF3·Boltz·Chai·Protenix / RFdiffusion·ProteinMPNN·ESM3 either compute or **honestly
+  defer with the OOD gate + provenance intact** — never fabricate; the generative-candidate `as_claim()` guard
+  raises. Computed immune layers reproduce orderings FROM DATA: genotoxicity LV 0.481 < gammaretro 0.177
+  (LMO2/SCID-X1), capsid AAV 0.28 > Ad 0.18, CpG O/E rich > poor, seroprevalence AAV 0.55 / Ad5 0.35, anti-PEG
+  0.515; full `verify()` clears a clean design, rejects a 7 kb single-AAV (alt lentivirus legal), refuses ricin,
+  rejects an RNP-over-AAV, and flags multiplex translocation risk 0.95.
+- **App surface (live, LLM on):** every endpoint 200 + grounded shape; the 4 chat lanes route correctly with the
+  grounding guard clean on the grounded lanes (0 ungrounded numbers, Nemotron backend).
+
 ## [6.3.0] - 2026-06-12 - v6.3.0: The Hybrid Co-Scientist (grounded engine + general intelligence)
 
 **The chat gains general + biological intelligence WITHOUT loosening the no-fabrication core.** A 4-lane router

{pen_stack-6.3.0 → pen_stack-6.3.1}/CITATION.cff

@@ -1,7 +1,7 @@
 cff-version: 1.2.0
 message: "If you use PEN-STACK, please cite it as below."
 title: "PEN-STACK: open infrastructure for genome writing"
-version: 6.3.0
+version: 6.3.1
 date-released: 2026-06-11
 authors:
   - family-names: "Mahaboob Ali"

{pen_stack-6.3.0 → pen_stack-6.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pen-stack
-Version: 6.3.0
+Version: 6.3.1
 Summary: Open infrastructure for genome writing: the Writable Genome atlas, the Writer Atlas, and the Write Planner.
 Author-email: Anees Ahmed Mahaboob Ali <ahmedaneesm@gmail.com>
 License: MIT
@@ -90,7 +90,7 @@ every design against rule-grounded mechanism, reports calibrated confidence, cit
 [![codecov](https://codecov.io/gh/ahmedanees-m/pen-stack/branch/main/graph/badge.svg)](https://codecov.io/gh/ahmedanees-m/pen-stack)
 [![License: MIT](https://img.shields.io/badge/License-MIT-informational.svg)](LICENSE)
 [![Python 3.11+](https://img.shields.io/badge/python-3.11%2B-blue.svg)](https://www.python.org/)
-[![Version](https://img.shields.io/badge/version-6.3.0-blue.svg)](CHANGELOG.md)
+[![Version](https://img.shields.io/badge/version-6.3.1-blue.svg)](CHANGELOG.md)
 [![Status](https://img.shields.io/badge/status-1.0%20First%20Stable-success.svg)](docs/STABILITY.md)
 [![Tests](https://img.shields.io/badge/tests-378%20passing-success.svg)](tests/)
 [![Lint: ruff](https://img.shields.io/badge/lint-ruff-purple.svg)](https://github.com/astral-sh/ruff)

{pen_stack-6.3.0 → pen_stack-6.3.1}/README.md

@@ -15,7 +15,7 @@ every design against rule-grounded mechanism, reports calibrated confidence, cit
 [![codecov](https://codecov.io/gh/ahmedanees-m/pen-stack/branch/main/graph/badge.svg)](https://codecov.io/gh/ahmedanees-m/pen-stack)
 [![License: MIT](https://img.shields.io/badge/License-MIT-informational.svg)](LICENSE)
 [![Python 3.11+](https://img.shields.io/badge/python-3.11%2B-blue.svg)](https://www.python.org/)
-[![Version](https://img.shields.io/badge/version-6.3.0-blue.svg)](CHANGELOG.md)
+[![Version](https://img.shields.io/badge/version-6.3.1-blue.svg)](CHANGELOG.md)
 [![Status](https://img.shields.io/badge/status-1.0%20First%20Stable-success.svg)](docs/STABILITY.md)
 [![Tests](https://img.shields.io/badge/tests-378%20passing-success.svg)](tests/)
 [![Lint: ruff](https://img.shields.io/badge/lint-ruff-purple.svg)](https://github.com/astral-sh/ruff)

{pen_stack-6.3.0 → pen_stack-6.3.1}/pen_stack/__init__.py

@@ -1,2 +1,2 @@
 """PEN-STACK v3.0 - open infrastructure for genome writing."""
-__version__ = "6.3.0"
+__version__ = "6.3.1"

{pen_stack-6.3.0 → pen_stack-6.3.1}/pen_stack/web/router.py

@@ -30,7 +30,7 @@ _EXPLAIN = re.compile(r"\b(what (do|does|is) (that|these|those|this|the)\b|what
                       r"explain (that|this|the)|interpret|what does (it|that) mean|"
                       r"reference range|what range|is that (good|bad|high|low|safe)|how do i read)\b", re.I)
 
-_META = re.compile(r"\b(pen[\s-]?stack|how (do|does) (you|it|this|pen)|how is .* (computed|calculated|derived|scored)|"
+_META = re.compile(r"\b(pen[\s-]?stack|how (do|does) (you|pen)|how is .* (computed|calculated|derived|scored)|"
                    r"how many (enzyme|writer|vector|vehicle|axe|model|system|locus|loci|gene|cell|oracle)\w*|"
                    r"how accurate|accuracy|how reliable|validated|what (can|do) you (do|cover|offer|support)|"
                    r"your (coverage|capabilit|method|model|data|engine)|how (does|is) immunogenicity|"

{pen_stack-6.3.0 → pen_stack-6.3.1}/pen_stack.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pen-stack
-Version: 6.3.0
+Version: 6.3.1
 Summary: Open infrastructure for genome writing: the Writable Genome atlas, the Writer Atlas, and the Write Planner.
 Author-email: Anees Ahmed Mahaboob Ali <ahmedaneesm@gmail.com>
 License: MIT
@@ -90,7 +90,7 @@ every design against rule-grounded mechanism, reports calibrated confidence, cit
 [![codecov](https://codecov.io/gh/ahmedanees-m/pen-stack/branch/main/graph/badge.svg)](https://codecov.io/gh/ahmedanees-m/pen-stack)
 [![License: MIT](https://img.shields.io/badge/License-MIT-informational.svg)](LICENSE)
 [![Python 3.11+](https://img.shields.io/badge/python-3.11%2B-blue.svg)](https://www.python.org/)
-[![Version](https://img.shields.io/badge/version-6.3.0-blue.svg)](CHANGELOG.md)
+[![Version](https://img.shields.io/badge/version-6.3.1-blue.svg)](CHANGELOG.md)
 [![Status](https://img.shields.io/badge/status-1.0%20First%20Stable-success.svg)](docs/STABILITY.md)
 [![Tests](https://img.shields.io/badge/tests-378%20passing-success.svg)](tests/)
 [![Lint: ruff](https://img.shields.io/badge/lint-ruff-purple.svg)](https://github.com/astral-sh/ruff)

{pen_stack-6.3.0 → pen_stack-6.3.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pen-stack"
-version = "6.3.0"
+version = "6.3.1"
 description = "Open infrastructure for genome writing: the Writable Genome atlas, the Writer Atlas, and the Write Planner."
 readme = "README.md"
 requires-python = ">=3.11"