pen-stack 5.13.0__tar.gz → 6.0.0__tar.gz

{pen_stack-5.13.0 → pen_stack-6.0.0}/CHANGELOG.md

@@ -3,6 +3,26 @@
 All notable changes to PEN-STACK are documented here. This file follows
 [Keep a Changelog](https://keepachangelog.com/) and the program's phase structure.
 
+## [6.0.0] - 2026-06-11 - 1.0 — First Stable (the graduation)
+
+**The Closed-Loop arc is complete (7/7), and PEN-STACK graduates to "1.0 — First Stable."** The public API
+exercised across every surface — verify, safety, generative design, twin, experiment design, build interface,
+closed loop, co-scientist, and the Genome-Writing Challenge — is documented and **frozen** with a deprecation
+policy. "First Stable" is **earned, not declared**: it is cut only after the closed loop is demonstrated (v5.12),
+the benchmark is public (v5.13), and the integration surface ships.
+
+### Changed
+- **`Development Status :: 5 - Production/Stable`** (was Beta). Version **6.0.0** (MAJOR).
+- The public API is documented + frozen with a deprecation policy: **`docs/STABILITY.md`** (semver from 6.0.0;
+  deprecations warn ≥1 MINOR before removal in a MAJOR; the `OracleResult`/`Verdict`/`SafetyVerdict`/immune-profile
+  contracts and invariants — incl. `collapsed_score is None` and the no-fabrication guard — are stable across 6.x).
+- The Genome-Writing Challenge is **public**.
+
+### Notes
+- "1.0 — First Stable" is a commitment to **API stability**, **not** a claim of solving genetic engineering. The
+  unknown funnel remains — made legible (scope flags, known-unknowns, honest baselines, no fabrication), not
+  hidden. The high version numbers of the program's fast youth finally meet a real stability commitment.
+
 ## [5.13.0] - 2026-06-11 - v5.13 release: The Standard (Genome-Writing Challenge + Co-Scientist II)
 
 **Closed-Loop arc, Cycle 7 of 7.** Make PEN-STACK the field's reference — an open, recurring, held-out benchmark

{pen_stack-5.13.0 → pen_stack-6.0.0}/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: 5.13.0
+version: 6.0.0
 date-released: 2026-06-11
 authors:
   - family-names: "Mahaboob Ali"

{pen_stack-5.13.0 → pen_stack-6.0.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pen-stack
-Version: 5.13.0
+Version: 6.0.0
 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
@@ -11,7 +11,7 @@ Project-URL: Changelog, https://github.com/ahmedanees-m/pen-stack/blob/main/CHAN
 Project-URL: Issues, https://github.com/ahmedanees-m/pen-stack/issues
 Project-URL: Benchmark, https://github.com/ahmedanees-m/pen-stack/tree/main/benchmarks/genome_writing_bench
 Keywords: genome-writing,genome-editing,bridge-recombinase,safe-harbor,writable-genome,writer-atlas,write-planner,bioinformatics
-Classifier: Development Status :: 4 - Beta
+Classifier: Development Status :: 5 - Production/Stable
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
@@ -90,8 +90,9 @@ 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-5.13.0-blue.svg)](CHANGELOG.md)
-[![Tests](https://img.shields.io/badge/tests-353%20passing-success.svg)](tests/)
+[![Version](https://img.shields.io/badge/version-6.0.0-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-354%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/)
 [![Validation: pre-registered](https://img.shields.io/badge/validation-pre--registered-critical.svg)](prereg/)
@@ -134,6 +135,19 @@ Two questions gate every genome-writing project, and before PEN-STACK no resourc
 Everything is built on bulk-downloadable public data, runs on a single GPU, and is validated **blind** against
 a pre-registered, honest baseline before release.
 
+## 🎓 v6.0.0 — "1.0 — First Stable"
+
+The **Closed-Loop arc is complete (7/7)** and PEN-STACK has graduated to **1.0 — First Stable**. The public API
+exercised across every surface — `verify`, `safety`, generative `design`, the `twin`, `active` experiment design,
+the `build` interface, the closed `loop`, the `co_scientist`, and the **Genome-Writing Challenge** — is documented
+and **frozen** with a deprecation policy ([`docs/STABILITY.md`](docs/STABILITY.md)). `Development Status ::
+5 - Production/Stable`. "First Stable" is **earned, not declared** — cut only after the closed loop was
+demonstrated (v5.12) and the benchmark went public (v5.13).
+
+> "1.0 — First Stable" is a commitment to **API stability**, not a claim of solving genetic engineering. The
+> unknown funnel remains — made legible (scope flags, known-unknowns, honest baselines, no fabrication), not
+> hidden.
+
 ## What is new in v5.13 — The Standard (Genome-Writing Challenge + Co-Scientist II)
 
 v5.13 (**Closed-Loop arc, Cycle 7 of 7**) makes PEN-STACK the field's reference and its most useful face: the

{pen_stack-5.13.0 → pen_stack-6.0.0}/README.md

@@ -15,8 +15,9 @@ 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-5.13.0-blue.svg)](CHANGELOG.md)
-[![Tests](https://img.shields.io/badge/tests-353%20passing-success.svg)](tests/)
+[![Version](https://img.shields.io/badge/version-6.0.0-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-354%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/)
 [![Validation: pre-registered](https://img.shields.io/badge/validation-pre--registered-critical.svg)](prereg/)
@@ -59,6 +60,19 @@ Two questions gate every genome-writing project, and before PEN-STACK no resourc
 Everything is built on bulk-downloadable public data, runs on a single GPU, and is validated **blind** against
 a pre-registered, honest baseline before release.
 
+## 🎓 v6.0.0 — "1.0 — First Stable"
+
+The **Closed-Loop arc is complete (7/7)** and PEN-STACK has graduated to **1.0 — First Stable**. The public API
+exercised across every surface — `verify`, `safety`, generative `design`, the `twin`, `active` experiment design,
+the `build` interface, the closed `loop`, the `co_scientist`, and the **Genome-Writing Challenge** — is documented
+and **frozen** with a deprecation policy ([`docs/STABILITY.md`](docs/STABILITY.md)). `Development Status ::
+5 - Production/Stable`. "First Stable" is **earned, not declared** — cut only after the closed loop was
+demonstrated (v5.12) and the benchmark went public (v5.13).
+
+> "1.0 — First Stable" is a commitment to **API stability**, not a claim of solving genetic engineering. The
+> unknown funnel remains — made legible (scope flags, known-unknowns, honest baselines, no fabrication), not
+> hidden.
+
 ## What is new in v5.13 — The Standard (Genome-Writing Challenge + Co-Scientist II)
 
 v5.13 (**Closed-Loop arc, Cycle 7 of 7**) makes PEN-STACK the field's reference and its most useful face: the

pen_stack-6.0.0/docs/STABILITY.md

@@ -0,0 +1,51 @@
+# API stability & deprecation policy (v6.0.0 — "1.0 — First Stable")
+
+At **v6.0.0**, PEN-STACK graduates to **1.0 — First Stable**: the public API exercised across all surfaces is
+documented and frozen, with a deprecation policy. "First Stable" is **earned, not declared** — it is cut only
+after the closed loop is demonstrated (v5.12), the benchmark is public (v5.13), and the integration surface ships.
+
+> "1.0 — First Stable" is a commitment to **API stability**, not a claim of solving genetic engineering. The
+> unknown funnel remains — made legible (scope flags, known-unknowns, honest baselines), not hidden.
+
+## Versioning
+
+PEN-STACK follows **semantic versioning** from 6.0.0:
+
+- **MAJOR** (`x.0.0`) — backward-incompatible changes to the public API (below).
+- **MINOR** (`6.x.0`) — backward-compatible additions.
+- **PATCH** (`6.0.x`) — backward-compatible fixes.
+
+## The public API (frozen at 1.0)
+
+These are the supported entry points. Their **signatures and return-shape keys** are stable across 6.x:
+
+| Surface | Entry point |
+|---|---|
+| Verify a write | `pen_stack.verify.verify(design, question=None, *, actor=…) -> Verdict` (legal · safety · immune_profile · confidence · scope) |
+| Safety gate | `pen_stack.safety.safety_gate(design, *, actor=…) -> SafetyVerdict` |
+| Generative design | `pen_stack.design.generate_designs(...)`, `pen_stack.design.pareto_front(...)` |
+| Digital twin | `pen_stack.twin.predict_outcome(design, cell_state)`, `pen_stack.twin.calibrate_outcome(...)` |
+| Experiment design | `pen_stack.active.select_batch(...)`, `pen_stack.active.expected_information_gain(...)` |
+| Build interface | `pen_stack.build.export_protocol(...)`, `pen_stack.build.ingest_result(...)`, `pen_stack.build.run_simulated(...)` |
+| Closed loop | `pen_stack.loop.run_loop(goal, cell_state, …)` |
+| Co-scientist | `pen_stack.agent.co_scientist.co_scientist_session(goal, cell_state)` |
+| Challenge | `benchmarks.genome_writing_challenge.harness.evaluate(submission, round_id)` |
+| CLI / MCP | `pen-stack` / `pen-bridge` console scripts; `pen_stack.agent.mcp_server` |
+
+Internal helpers (underscore-prefixed names, modules under `pen_stack/*/_*`, the `data/`/`wgenome/` training
+pipelines) are **not** part of the public API and may change in any release.
+
+## Deprecation policy
+
+- A public API element is deprecated by a **`DeprecationWarning`** and a CHANGELOG note **at least one MINOR
+  release** before removal.
+- Removal happens only in a **MAJOR** release.
+- The `OracleResult` / `Verdict` / `SafetyVerdict` / immune-profile **contracts** (field names + invariants such as
+  `collapsed_score is None` and the no-fabrication guard) are stable across 6.x.
+
+## What stability does NOT promise
+
+- Model **numbers** may change as oracles / data are updated (they are version-pinned + provenanced; results are
+  reproducible *given a pinned version*, not constant forever).
+- **Scope** stays honest: out-of-scope questions are deferred, known-unknowns declared, baselines reported — at
+  1.0 and beyond.

{pen_stack-5.13.0 → pen_stack-6.0.0}/pen_stack/__init__.py

@@ -1,2 +1,2 @@
 """PEN-STACK v3.0 - open infrastructure for genome writing."""
-__version__ = "5.13.0"
+__version__ = "6.0.0"

{pen_stack-5.13.0 → pen_stack-6.0.0}/pen_stack.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pen-stack
-Version: 5.13.0
+Version: 6.0.0
 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
@@ -11,7 +11,7 @@ Project-URL: Changelog, https://github.com/ahmedanees-m/pen-stack/blob/main/CHAN
 Project-URL: Issues, https://github.com/ahmedanees-m/pen-stack/issues
 Project-URL: Benchmark, https://github.com/ahmedanees-m/pen-stack/tree/main/benchmarks/genome_writing_bench
 Keywords: genome-writing,genome-editing,bridge-recombinase,safe-harbor,writable-genome,writer-atlas,write-planner,bioinformatics
-Classifier: Development Status :: 4 - Beta
+Classifier: Development Status :: 5 - Production/Stable
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
@@ -90,8 +90,9 @@ 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-5.13.0-blue.svg)](CHANGELOG.md)
-[![Tests](https://img.shields.io/badge/tests-353%20passing-success.svg)](tests/)
+[![Version](https://img.shields.io/badge/version-6.0.0-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-354%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/)
 [![Validation: pre-registered](https://img.shields.io/badge/validation-pre--registered-critical.svg)](prereg/)
@@ -134,6 +135,19 @@ Two questions gate every genome-writing project, and before PEN-STACK no resourc
 Everything is built on bulk-downloadable public data, runs on a single GPU, and is validated **blind** against
 a pre-registered, honest baseline before release.
 
+## 🎓 v6.0.0 — "1.0 — First Stable"
+
+The **Closed-Loop arc is complete (7/7)** and PEN-STACK has graduated to **1.0 — First Stable**. The public API
+exercised across every surface — `verify`, `safety`, generative `design`, the `twin`, `active` experiment design,
+the `build` interface, the closed `loop`, the `co_scientist`, and the **Genome-Writing Challenge** — is documented
+and **frozen** with a deprecation policy ([`docs/STABILITY.md`](docs/STABILITY.md)). `Development Status ::
+5 - Production/Stable`. "First Stable" is **earned, not declared** — cut only after the closed loop was
+demonstrated (v5.12) and the benchmark went public (v5.13).
+
+> "1.0 — First Stable" is a commitment to **API stability**, not a claim of solving genetic engineering. The
+> unknown funnel remains — made legible (scope flags, known-unknowns, honest baselines, no fabrication), not
+> hidden.
+
 ## What is new in v5.13 — The Standard (Genome-Writing Challenge + Co-Scientist II)
 
 v5.13 (**Closed-Loop arc, Cycle 7 of 7**) makes PEN-STACK the field's reference and its most useful face: the

{pen_stack-5.13.0 → pen_stack-6.0.0}/pen_stack.egg-info/SOURCES.txt

@@ -55,6 +55,7 @@ docs/INFRA.md
 docs/MCP.md
 docs/RELEASING.md
 docs/REPRO.md
+docs/STABILITY.md
 docs/agent.md
 docs/alphagenome_feasibility.md
 docs/autonomy.md

{pen_stack-5.13.0 → pen_stack-6.0.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pen-stack"
-version = "5.13.0"
+version = "6.0.0"
 description = "Open infrastructure for genome writing: the Writable Genome atlas, the Writer Atlas, and the Write Planner."
 readme = "README.md"
 requires-python = ">=3.11"
@@ -15,7 +15,7 @@ keywords = [
   "writable-genome", "writer-atlas", "write-planner", "bioinformatics",
 ]
 classifiers = [
-  "Development Status :: 4 - Beta",
+  "Development Status :: 5 - Production/Stable",
   "Programming Language :: Python :: 3",
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",