pen-stack 4.0.0__tar.gz → 4.0.2__tar.gz

{pen_stack-4.0.0 → pen_stack-4.0.2}/CHANGELOG.md

@@ -3,6 +3,40 @@
 All notable changes to PEN-STACK are documented here. This file follows
 [Keep a Changelog](https://keepachangelog.com/) and the program's phase structure.
 
+## [4.0.2] - 2026-06-09 - citation-correctness patch: full-repo DOI audit
+
+### Fixed
+A full sweep of all 56 DOIs in the repo (verified via Crossref + doi.org) found six incorrect or
+non-existent citations — all now corrected to verified, topically-correct references:
+- `configs/gsh_validated_heldout.yaml` H11 locus: `10.1371/journal.pone.0113481` (resolved to an unrelated
+  cardiology paper) → **`10.1093/nar/gkt1290`** (Zhu et al. 2014, *DICE*, NAR 42:e34 — the paper that
+  characterized human H11 on chr22q12.2 between DRG1 and EIF4ENIF1).
+- `configs/delivery_vehicles.yaml` + `configs/rules/{delivery,payload}.yaml`: `10.1089/hum.2017.084`
+  (non-existent), `10.1089/hum.2009.213` (non-existent), `10.1038/sj.gt.3302529` (unrelated erratum) →
+  **`10.1128/JVI.79.15.9933-9944.2005`** (Grieger & Samulski, AAV packaging capacity),
+  **`10.1128/JVI.72.2.926-933.1998`** (multiply-deleted adenovirus vectors), **`10.1038/nbt1101-1067`**
+  (Wade-Martins, HSV-1 amplicon large-capacity).
+- `pen_stack/validate/bench_writetype_tasks.py` provenance: `10.1038/s41586-023-06756-4` (diabetes program)
+  and `10.1126/science.abm1123` (freshwater fish) → **`10.1016/j.cell.2022.03.045`** and
+  **`10.1128/JVI.79.15.9933-9944.2005`**.
+
+The remaining 50 DOIs resolve correctly; three legacy DOIs in `mech/pfam_whitelist.yaml` (Rice 1995 Cell,
+Kholodii 1997 Res Microbiol, Prudhomme 2002 J Bacteriol) carry full author/year/journal references and are
+real classic papers whose pre-modern DOIs do not resolve at doi.org — left unchanged (a registration artifact,
+not an error).
+
+## [4.0.1] - 2026-06-09 - data-correctness patch: writer-verification panel verified against Perry 2025
+
+### Fixed
+- **WS-WV frozen panel is now verbatim from the measured Perry 2025 ISCro4 DMS.** The offline-fallback panel
+  in `atlas/writer_verify.py` previously used *illustrative* Z-scores (2.6/2.1/1.7) and invented control
+  variants (G15D/P88R/L120E), and `_CORE_RESIDUES` used illustrative arginines. Replaced with the REAL values
+  from `science.adz0276` Table S3: the top-3 enhancers **N322P (Z 0.754), H50K (0.742), R278M (0.709)**, real
+  near-neutral variants (V21R, S312Q, G286T), the most-deleterious variants (R132E −5.40, R137E −5.12,
+  R195D −4.98), and the documented catalytic residues **D11/E60/D102/D105/S241** ("Residue Groups" sheet). The
+  real-DMS path (on the VM/Drive) was already correct; only the offline fallback constants were illustrative.
+  Added `test_ws_wv.py::test_frozen_panel_matches_real_perry_dms_table_s3` to guard against drift.
+
 ## [4.0.0] - 2026-06-09 - v4.0 release: the Oracle Mesh (on top of the foundation models) + writer verification
 
 A major bump: the substrate now *composes* the biomolecular foundation models under one contract and verifies

{pen_stack-4.0.0 → pen_stack-4.0.2}/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: 4.0.0
+version: 4.0.2
 date-released: 2026-06-01
 authors:
   - family-names: "Mahaboob Ali"

{pen_stack-4.0.0 → pen_stack-4.0.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pen-stack
-Version: 4.0.0
+Version: 4.0.2
 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
@@ -89,7 +89,7 @@ and durably write new DNA, **which enzyme** can write it there, and **how** to d
 [![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-4.0.0-blue.svg)](CHANGELOG.md)
+[![Version](https://img.shields.io/badge/version-4.0.2-blue.svg)](CHANGELOG.md)
 [![Tests](https://img.shields.io/badge/tests-208%20passing-success.svg)](tests/)
 [![Lint: ruff](https://img.shields.io/badge/lint-ruff-purple.svg)](https://github.com/astral-sh/ruff)
 [![Runtime: Docker](https://img.shields.io/badge/runtime-docker-2496ED.svg)](docker/)

{pen_stack-4.0.0 → pen_stack-4.0.2}/README.md

@@ -14,7 +14,7 @@ and durably write new DNA, **which enzyme** can write it there, and **how** to d
 [![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-4.0.0-blue.svg)](CHANGELOG.md)
+[![Version](https://img.shields.io/badge/version-4.0.2-blue.svg)](CHANGELOG.md)
 [![Tests](https://img.shields.io/badge/tests-208%20passing-success.svg)](tests/)
 [![Lint: ruff](https://img.shields.io/badge/lint-ruff-purple.svg)](https://github.com/astral-sh/ruff)
 [![Runtime: Docker](https://img.shields.io/badge/runtime-docker-2496ED.svg)](docker/)

{pen_stack-4.0.0 → pen_stack-4.0.2}/configs/delivery_vehicles.yaml

@@ -29,7 +29,7 @@ vehicles:
     in_vivo: true
     compatible_cargo_form: [DNA]
     constraint_key: AAV
-    dois: ["10.1089/hum.2017.084"]
+    dois: ["10.1128/JVI.79.15.9933-9944.2005"]   # Grieger & Samulski 2005, AAV packaging capacity
 
   lentivirus:
     cargo_capacity_bp: 8000
@@ -53,7 +53,7 @@ vehicles:
     in_vivo: true
     compatible_cargo_form: [DNA]
     constraint_key: plasmid
-    dois: ["10.1089/hum.2009.213"]
+    dois: ["10.1128/JVI.72.2.926-933.1998"]   # multiply-deleted (gutless-class) adenovirus vectors
 
   hsv_amplicon:
     cargo_capacity_bp: 100000     # >100 kb
@@ -65,7 +65,7 @@ vehicles:
     in_vivo: true
     compatible_cargo_form: [DNA]
     constraint_key: plasmid
-    dois: ["10.1038/sj.gt.3302529"]
+    dois: ["10.1038/nbt1101-1067"]   # Wade-Martins 2001, HSV-1 amplicon (iBAC) large genomic-DNA transfer
 
   lnp_mrna:
     cargo_capacity_bp: 15000      # large RNA payload (mRNA encoding the writer/RNP)

{pen_stack-4.0.0 → pen_stack-4.0.2}/configs/gsh_validated_heldout.yaml

@@ -20,7 +20,7 @@ gsh:
   - {name: CLYBL,    tier: validated, anchor_gene: CLYBL,    doi: "10.1371/journal.pone.0116032"}  # Cerbini 2015
   - {name: CCR5,     tier: validated, anchor_gene: CCR5,     doi: "10.1038/nbt1353"}          # Lombardo 2007
   - {name: hRosa26,  tier: validated, anchor_gene: THUMPD3,  doi: "10.1038/nbt1362"}          # Irion 2007
-  - {name: H11,      tier: validated, anchor_gene: EIF4ENIF1, doi: "10.1371/journal.pone.0113481"}  # H11/HIPP11
+  - {name: H11,      tier: validated, anchor_gene: EIF4ENIF1, doi: "10.1093/nar/gkt1290"}  # H11/HIPP11 (Zhu 2014, DICE; hH11 on chr22q12.2 between DRG1 and EIF4ENIF1)
   # --- tier 1 (cont.): functionally validated in Lin et al. 2024 (eLife 79592), precise hg38 spans ---
   - {name: Pansio-1, tier: validated, anchor_coord: {chrom: chr1,  start: 113339961, end: 113340514}, anchor_gene_note: HIPK1, doi: "10.7554/eLife.79592"}
   - {name: Olonne-18, tier: validated, anchor_coord: {chrom: chr18, start: 56534775,  end: 56536439},  anchor_gene_note: TXNL1, doi: "10.7554/eLife.79592"}

{pen_stack-4.0.0 → pen_stack-4.0.2}/configs/rules/delivery.yaml

@@ -26,7 +26,7 @@ rules:
     mechanism: "vehicle-specific construct hazards (lentiviral internal poly(A), AAV inverted-repeat/homopolymer, recombinogenic direct repeats, GC extremes) lower titre/yield"
     evaluator: delivery_sequence_constraints
     param: {}
-    provenance: { doi: ["10.1089/hum.2017.084"], note: "v3.2 MC2 delivery_constraints scan" }
+    provenance: { doi: ["10.1128/JVI.79.15.9933-9944.2005"], note: "AAV genome/sequence constraints; v3.2 MC2 delivery_constraints scan (labelled heuristic, per-check sources in configs/delivery_constraints.yaml)" }
     test_ref: "tests/unit/test_ws_r.py::test_delivery_controls"
     scope: "labeled heuristic, directional; not a titre predictor"
   - id: delivery.aav_packaging_margin

{pen_stack-4.0.0 → pen_stack-4.0.2}/configs/rules/payload.yaml

@@ -17,6 +17,6 @@ rules:
     mechanism: "an AAV cargo above a single capsid (~4.7 kb) requires split/dual AAV, which drops efficiency sharply"
     evaluator: split_aav_penalty
     param: { single_aav_cap_bp: 4700 }
-    provenance: { doi: ["10.1089/hum.2017.084"], note: "dual-AAV split efficiency" }
+    provenance: { doi: ["10.1128/JVI.79.15.9933-9944.2005"], note: "AAV packaging capacity (~4.7 kb); oversize cargo needs split/dual AAV" }
     test_ref: "tests/unit/test_ws_r.py::test_payload_controls"
     scope: "directional efficiency flag, not a titre prediction"

{pen_stack-4.0.0 → pen_stack-4.0.2}/pen_stack/__init__.py

@@ -1,2 +1,2 @@
 """PEN-STACK v3.0 - open infrastructure for genome writing."""
-__version__ = "4.0.0"
+__version__ = "4.0.2"

{pen_stack-4.0.0 → pen_stack-4.0.2}/pen_stack/atlas/writer_verify.py

@@ -21,16 +21,20 @@ from __future__ import annotations
 import math
 from dataclasses import dataclass
 
-# Known ISCro4 enhancers (Perry 2025 DMS) + documented-neutral/worse controls — a FROZEN retrospective panel
-# (relative activity Z-score wrt WT; positive = enhancing). Used only when the full Perry DMS is absent.
+# A FROZEN retrospective panel of REAL values from the Perry 2025 ISCro4 deep mutational scan
+# (science.adz0276 Table S3, sheet "L2FC_Relative_Z-Scores", column Z_Score_wrt_WT) — the three top-ranked
+# enhancers, three near-neutral variants, and the three most-deleterious variants, copied verbatim from the
+# measured table. Used only when the full Perry DMS is absent (offline/CI); never fabricated.
 _FROZEN_DMS_Z = {
-    "N322P": 2.6, "H50K": 2.1, "R278M": 1.7,            # published enhancers
-    "K12A": 0.1, "S40T": -0.2, "V90I": 0.0,             # ~neutral
-    "G15D": -2.4, "P88R": -1.9, "L120E": -1.5,          # deleterious / worse
+    "N322P": 0.754, "H50K": 0.742, "R278M": 0.709,      # top-3 enhancers (measured Z, ranks 1-3)
+    "V21R": -0.000, "S312Q": -0.001, "G286T": -0.001,   # near-neutral (|Z| ~ 0)
+    "R132E": -5.400, "R137E": -5.115, "R195D": -4.984,  # most-deleterious (measured worst by Z)
 }
 KNOWN_ISCRO4_ENHANCERS = ["N322P", "H50K", "R278M"]
-# minimal conserved core residues a plausible ISCro4-family candidate should retain (active-site heuristic)
-_CORE_RESIDUES = {49: "R", 277: "R"}                     # 0-based; illustrative conserved arginines
+_WORSE_CONTROLS = ["R132E", "R137E", "R195D"]            # measured-worst variants (Perry Table S3)
+# the catalytic residues a plausible ISCro4-family candidate must retain (Perry Table S3, sheet
+# "Residue Groups", Catalytic_Residues == "Catalytic"): D11, E60, D102, D105, S241 (1-based) -> 0-based below
+_CORE_RESIDUES = {10: "D", 59: "E", 101: "D", 104: "D", 240: "S"}
 
 
 def _sigmoid(x: float) -> float:
@@ -91,9 +95,8 @@ def blind_recovery(top_k: int = 5) -> dict:
     ranked = sorted(scores, key=scores.get, reverse=True)
     top = ranked[:top_k]
     recovered = {e: (e in top) for e in KNOWN_ISCRO4_ENHANCERS}
-    worse = ["G15D", "P88R", "L120E"]
     enh_min = min(scores[e] for e in KNOWN_ISCRO4_ENHANCERS)
-    worse_max = max(scores[w] for w in worse)
+    worse_max = max(scores[w] for w in _WORSE_CONTROLS)
     return {"available": True, "model": "frozen_retrospective_panel", "n": len(_FROZEN_DMS_Z), "top_k": top_k,
             "top": top, "recovered": recovered, "all_enhancers_recovered": all(recovered.values()),
             "enhancers_outrank_worse": bool(enh_min > worse_max),

{pen_stack-4.0.0 → pen_stack-4.0.2}/pen_stack/validate/bench_writetype_tasks.py

@@ -53,7 +53,7 @@ PANEL = [
 
 # documented mechanisms behind the legality labels (provenance, not circular)
 PROVENANCE = {
-    "doi": ["10.1038/s41586-023-06756-4", "10.1126/science.abm1123", "10.1038/s41587-020-0561-9"],
+    "doi": ["10.1016/j.cell.2022.03.045", "10.1128/JVI.79.15.9933-9944.2005", "10.1038/s41587-020-0561-9"],
     "note": "RNP/DNA cargo-form compatibility (delivery) + AAV ~4.7 kb packaging limit (payload) are the "
             "documented physical facts; routing per write type follows the v3.3 write-type taxonomy.",
 }

{pen_stack-4.0.0 → pen_stack-4.0.2}/pen_stack.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pen-stack
-Version: 4.0.0
+Version: 4.0.2
 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
@@ -89,7 +89,7 @@ and durably write new DNA, **which enzyme** can write it there, and **how** to d
 [![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-4.0.0-blue.svg)](CHANGELOG.md)
+[![Version](https://img.shields.io/badge/version-4.0.2-blue.svg)](CHANGELOG.md)
 [![Tests](https://img.shields.io/badge/tests-208%20passing-success.svg)](tests/)
 [![Lint: ruff](https://img.shields.io/badge/lint-ruff-purple.svg)](https://github.com/astral-sh/ruff)
 [![Runtime: Docker](https://img.shields.io/badge/runtime-docker-2496ED.svg)](docker/)

{pen_stack-4.0.0 → pen_stack-4.0.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pen-stack"
-version = "4.0.0"
+version = "4.0.2"
 description = "Open infrastructure for genome writing: the Writable Genome atlas, the Writer Atlas, and the Write Planner."
 readme = "README.md"
 requires-python = ">=3.11"