pen-stack 4.5.0__tar.gz → 4.5.1__tar.gz

{pen_stack-4.5.0 → pen_stack-4.5.1}/CHANGELOG.md

@@ -3,6 +3,17 @@
 All notable changes to PEN-STACK are documented here. This file follows
 [Keep a Changelog](https://keepachangelog.com/) and the program's phase structure.
 
+## [4.5.1] - 2026-06-09 - ID-correctness patch: cell-type ontology IDs
+
+### Fixed
+Two of the three new v4.5 Tier-A cell-type ontology IDs in `configs/cell_types.yaml` were wrong (verified via
+EBI-OLS): `EFO:0002322` resolved to the **RPMI8226 myeloma line** (not a T cell) and `EFO:0004146` to an
+**obsolete myopathy term** (not hepatocyte). Corrected to the canonical, non-obsolete Cell Ontology terms:
+**primary_T_cell → `CL:0000084`** (T cell), **hepatocyte → `CL:0000182`** (hepatocyte). iPSC (`EFO:0004905`),
+K562 (`EFO:0002067`), HepG2 (`EFO:0001187`) verified correct, as was the ISPpu10 back-test record (Europe PMC
+**PPR1218813** — "ISPpu10 is a structure-gated bridge RNA recombinase…"). No result/test change (the IDs are
+coverage-card metadata; `cell_types.py` reads coverage, not the ontology id).
+
 ## [4.5.0] - 2026-06-09 - v4.5 release: the Living World-Model (knowledge graph + gated living loop)
 
 v4.5 promotes the flat tables into a queryable knowledge graph that keeps itself current. Workstreams

{pen_stack-4.5.0 → pen_stack-4.5.1}/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: 4.5.0
+version: 4.5.1
 date-released: 2026-06-01
 authors:
   - family-names: "Mahaboob Ali"

{pen_stack-4.5.0 → pen_stack-4.5.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pen-stack
-Version: 4.5.0
+Version: 4.5.1
 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
@@ -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-4.5.0-blue.svg)](CHANGELOG.md)
+[![Version](https://img.shields.io/badge/version-4.5.1-blue.svg)](CHANGELOG.md)
 [![Tests](https://img.shields.io/badge/tests-224%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-4.5.0 → pen_stack-4.5.1}/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-4.5.0-blue.svg)](CHANGELOG.md)
+[![Version](https://img.shields.io/badge/version-4.5.1-blue.svg)](CHANGELOG.md)
 [![Tests](https://img.shields.io/badge/tests-224%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-4.5.0 → pen_stack-4.5.1}/configs/cell_types.yaml

@@ -36,13 +36,13 @@ cell_types:
     note: "iPSC/ESC; broad chromatin but TRIP durability not measured here -> durability OOD-labelled, degraded."
   primary_T_cell:
     tier: A
-    efo: "EFO:0002322"        # CD4+/CD8+ primary T cell (CAR-T relevant)
+    ontology: "CL:0000084"    # T cell (Cell Ontology); CAR-T relevant
     coverage: partial
     tracks: [atac, expression]
     note: "primary T cells (CAR-T context); accessibility + expression only -> histone-dependent safety degraded."
   hepatocyte:
     tier: A
-    efo: "EFO:0004146"        # primary hepatocyte
+    ontology: "CL:0000182"    # hepatocyte (Cell Ontology); in-vivo liver target
     coverage: partial
     tracks: [atac, h3k27ac, expression]
     note: "primary hepatocytes (in-vivo liver target); partial panel -> graceful degradation, scope-flagged."

{pen_stack-4.5.0 → pen_stack-4.5.1}/pen_stack/__init__.py

@@ -1,2 +1,2 @@
 """PEN-STACK v3.0 - open infrastructure for genome writing."""
-__version__ = "4.5.0"
+__version__ = "4.5.1"

{pen_stack-4.5.0 → pen_stack-4.5.1}/pen_stack/graph/build.py

@@ -75,8 +75,8 @@ def build_graph() -> Graph:
     cts = _yaml("configs/cell_types.yaml")["cell_types"]
     for ct, card in cts.items():
         g.add_node(Node(id=f"cell_type:{ct}", type="cell_type", props={
-            "tier": card.get("tier"), "efo": card.get("efo"), "coverage": card.get("coverage"),
-            "tracks": card.get("tracks", []), "note": card.get("note")}))
+            "tier": card.get("tier"), "ontology": card.get("efo") or card.get("ontology"),
+            "coverage": card.get("coverage"), "tracks": card.get("tracks", []), "note": card.get("note")}))
 
     # ---- locus nodes (DOI-validated GSH) -------------------------------------------------------
     gsh = _yaml("configs/gsh_validated_heldout.yaml")["gsh"]

{pen_stack-4.5.0 → pen_stack-4.5.1}/pen_stack.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pen-stack
-Version: 4.5.0
+Version: 4.5.1
 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
@@ -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-4.5.0-blue.svg)](CHANGELOG.md)
+[![Version](https://img.shields.io/badge/version-4.5.1-blue.svg)](CHANGELOG.md)
 [![Tests](https://img.shields.io/badge/tests-224%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-4.5.0 → pen_stack-4.5.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pen-stack"
-version = "4.5.0"
+version = "4.5.1"
 description = "Open infrastructure for genome writing: the Writable Genome atlas, the Writer Atlas, and the Write Planner."
 readme = "README.md"
 requires-python = ">=3.11"