pen-stack 4.0.1__tar.gz → 4.0.3__tar.gz

{pen_stack-4.0.1 → pen_stack-4.0.3}/CHANGELOG.md

@@ -3,6 +3,50 @@
 All notable changes to PEN-STACK are documented here. This file follows
 [Keep a Changelog](https://keepachangelog.com/) and the program's phase structure.
 
+## [4.0.3] - 2026-06-09 - ID-correctness patch: UniProt + Pfam + ontology audit
+
+### Fixed
+A whole-repo audit of structured IDs (verified against InterPro, UniProt, EBI-OLS, mygene):
+- **`pen_stack/mech/pfam_whitelist.yaml` (v1.2.1 -> v1.2.2):** the 26 Pfam accessions were all correct, but
+  **13 of 22 `example_uniprot` proteins did not actually contain their claimed domain** (membership checked
+  against each protein's UniProt Pfam cross-references) — including a marine-worm **Histone H3** (PF13586), a
+  mouse **mannosyltransferase** (PF05621/TniB), **I-AniI** (a LAGLIDADG enzyme) mislabelled HNH (PF01844), a
+  **glycine-betaine transporter** and a Tn3 transposase mis-filed as rve, and an **obsolete 404** accession
+  (PF08721) — despite the header claiming a spot-check. All corrected to reviewed/curated proteins whose
+  UniProt entry genuinely carries the domain (e.g. ISCro4 `D2TGM5`, Tn5 `Q46731`, Tn7-TnsA `P13988`, Bxb1
+  integrase `Q9B086`, McrA `P24200`); the audit-status header was corrected to stop over-claiming.
+- **`configs/atlas_families.yaml`** (drives family expansion in `expand.py`): IS621 `A0A0F6B5L8` (a
+  betaine transporter) -> **`A0A2X3M8B0`** (IS621 transposase); phiC31 `Q9T2A6` (a plant NAD(P)H
+  oxidoreductase) -> **`Q9T221`** (phiC31 integrase). The Pfam-query signatures and discovery DOIs were
+  already correct.
+
+### Verified clean
+The 4 EFO cell-type IDs map correctly (EFO:0002067=K562, EFO:0001187=HepG2, EFO:0002784=GM12878,
+EFO:0005483=ES-Bruce4); all GSH gene symbols are valid HGNC symbols; all 26 Pfam accessions resolve with the
+correct domain name.
+
+## [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

{pen_stack-4.0.1 → pen_stack-4.0.3}/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: 4.0.1
+version: 4.0.3
 date-released: 2026-06-01
 authors:
   - family-names: "Mahaboob Ali"

{pen_stack-4.0.1 → pen_stack-4.0.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pen-stack
-Version: 4.0.1
+Version: 4.0.3
 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
@@ -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-4.0.1-blue.svg)](CHANGELOG.md)
+[![Version](https://img.shields.io/badge/version-4.0.3-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-4.0.1 → pen_stack-4.0.3}/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-4.0.1-blue.svg)](CHANGELOG.md)
+[![Version](https://img.shields.io/badge/version-4.0.3-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-4.0.1 → pen_stack-4.0.3}/configs/atlas_families.yaml

@@ -63,7 +63,7 @@ families:
 curated_representatives:
   - representative_system: IS621
     family: bridge_IS110
-    uniprot: A0A0F6B5L8
+    uniprot: A0A2X3M8B0   # IS621 transposase (E. coli); was A0A0F6B5L8 (a glycine-betaine transporter - wrong)
     confidence: measured
     human_cell_activity: "model bridge recombinase; recombination characterised (Durrant 2024)"
     key_dois: ["10.1038/s41586-024-07552-4"]
@@ -75,7 +75,7 @@ curated_representatives:
     key_dois: ["10.64898/2026.03.19.712850"]    # bioRxiv ISPpu10 (Europe PMC PPR1218813; resolved via PEN-MONITOR)
   - representative_system: phiC31
     family: serine_integrase
-    uniprot: Q9T2A6
+    uniprot: Q9T221   # phiC31 integrase (Streptomyces phage phiC31, gene int); was Q9T2A6 (a plant NAD(P)H oxidoreductase - wrong)
     confidence: measured
     human_cell_activity: "large serine integrase; attB x attP; used in human cell landing pads"
     key_dois: ["10.1128/microbiolspec.MDNA3-0046-2014"]

{pen_stack-4.0.1 → pen_stack-4.0.3}/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-4.0.1 → pen_stack-4.0.3}/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-4.0.1 → pen_stack-4.0.3}/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-4.0.1 → pen_stack-4.0.3}/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-4.0.1 → pen_stack-4.0.3}/pen_stack/__init__.py

@@ -1,2 +1,2 @@
 """PEN-STACK v3.0 - open infrastructure for genome writing."""
-__version__ = "4.0.1"
+__version__ = "4.0.3"

{pen_stack-4.0.1 → pen_stack-4.0.3}/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-4.0.1 → pen_stack-4.0.3}/pen_stack.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pen-stack
-Version: 4.0.1
+Version: 4.0.3
 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
@@ -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-4.0.1-blue.svg)](CHANGELOG.md)
+[![Version](https://img.shields.io/badge/version-4.0.3-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-4.0.1 → pen_stack-4.0.3}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pen-stack"
-version = "4.0.1"
+version = "4.0.3"
 description = "Open infrastructure for genome writing: the Writable Genome atlas, the Writer Atlas, and the Write Planner."
 readme = "README.md"
 requires-python = ">=3.11"