pen-stack 6.4.2__tar.gz → 6.4.3__tar.gz

{pen_stack-6.4.2 → pen_stack-6.4.3}/CHANGELOG.md

@@ -3,6 +3,14 @@
 All notable changes to PEN-STACK are documented here. This file follows
 [Keep a Changelog](https://keepachangelog.com/) and the program's phase structure.
 
+## [6.4.3] - 2026-06-12 - Chat vehicle-parse fix (AAVS1 no longer hijacks the vehicle)
+
+**PATCH.** `web/tools.py::parse_goal` matched the delivery vehicle by substring, so the safe-harbour nickname
+**AAVS1** (which contains "aav") wrongly selected the **AAV** vehicle even when the user said *lentivirus* or
+*LNP* — producing the wrong immune profile (e.g. genotoxicity 1.0 instead of lentivirus's 0.481). Fix: strip the
+safe-harbour nicknames (AAVS1/H11/HIPP11/ROSA26) from the vehicle-search text before matching, so the user's
+stated vehicle wins. Explicit "AAV" still selects AAV. New test locks all three cases.
+
 ## [6.4.2] - 2026-06-12 - Co-Scientist chat: real writer recommendations + self-explanatory values
 
 **PATCH — fixes a stale/confusing chat experience reported from the live app.** Three problems, three fixes:

{pen_stack-6.4.2 → pen_stack-6.4.3}/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: 6.4.2
+version: 6.4.3
 date-released: 2026-06-12
 authors:
   - family-names: "Mahaboob Ali"

{pen_stack-6.4.2 → pen_stack-6.4.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pen-stack
-Version: 6.4.2
+Version: 6.4.3
 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-6.4.2-blue.svg)](CHANGELOG.md)
+[![Version](https://img.shields.io/badge/version-6.4.3-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-6.4.2 → pen_stack-6.4.3}/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-6.4.2-blue.svg)](CHANGELOG.md)
+[![Version](https://img.shields.io/badge/version-6.4.3-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-6.4.2 → pen_stack-6.4.3}/pen_stack/__init__.py

@@ -1,2 +1,2 @@
 """PEN-STACK v3.0 - open infrastructure for genome writing."""
-__version__ = "6.4.2"
+__version__ = "6.4.3"

{pen_stack-6.4.2 → pen_stack-6.4.3}/pen_stack/web/tools.py

@@ -28,6 +28,9 @@ _BP_RE = re.compile(r"(\d{3,6})\s*bp", re.I)
 # uppercase tokens that look like a gene but are not one (jargon / vehicle / form abbreviations)
 _GENE_STOP = {"DNA", "RNA", "MRNA", "AAV", "LNP", "HSV", "CAR", "RNP", "PCR", "WT", "KO", "KI", "ITR",
               "ORF", "UTR", "CDS", "GFP", "ID", "QC", "VG", "MOI", "HLA", "MHC", "CRISPR", "CAS", "TF"}
+# safe-harbour locus nicknames whose text collides with a vehicle keyword (AAVS1 ⊃ "aav") — stripped before
+# vehicle matching so the user's stated vehicle (e.g. lentivirus) is not overridden by the locus name.
+_SAFE_HARBOUR_RE = re.compile(r"\b(aavs1|h11|hipp11|rosa26)\b", re.I)
 
 
 def _first(text: str, table: dict, default):
@@ -59,9 +62,13 @@ def parse_goal(message: str) -> dict:
         cargo = int(m.group(1))
     genes = [g for g in _GENE_RE.findall(message) if g not in _GENE_STOP]
     gene = genes[0] if genes else "AAVS1"
+    # Vehicle matching is substring-based (so "lentivir" catches "lentiviral"); but the safe-harbour nickname
+    # "AAVS1" contains "aav", which would wrongly match the AAV vehicle even when the user said lentivirus/LNP.
+    # Strip those nicknames from the vehicle-search text first so the stated vehicle wins.
+    veh_text = _SAFE_HARBOUR_RE.sub(" ", message.lower())
     return {"write_type": "insertion", "gene": gene, "chrom": _resolve_chrom(gene) or "chr19",
             "edit_intent": _first(message, _INTENTS, "safe_harbour_insertion"),
-            "delivery_vehicle": _first(message, _VEHICLES, "AAV_single"), "cargo_bp": cargo,
+            "delivery_vehicle": _first(veh_text, _VEHICLES, "AAV_single"), "cargo_bp": cargo,
             "cell_type": _first(message, _CELLS, "k562"),
             # the user's plain-language goal IS the cargo-function description the Guardian must screen — so a
             # message like "express a ricin toxin" is biosecurity-screened, not silently passed as benign.

{pen_stack-6.4.2 → pen_stack-6.4.3}/pen_stack.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pen-stack
-Version: 6.4.2
+Version: 6.4.3
 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-6.4.2-blue.svg)](CHANGELOG.md)
+[![Version](https://img.shields.io/badge/version-6.4.3-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-6.4.2 → pen_stack-6.4.3}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pen-stack"
-version = "6.4.2"
+version = "6.4.3"
 description = "Open infrastructure for genome writing: the Writable Genome atlas, the Writer Atlas, and the Write Planner."
 readme = "README.md"
 requires-python = ">=3.11"