Prepare CodonTrace Genesis 0.3.0b1 beta release

Promote CodonTrace Genesis from 0.3.0a2 alpha to 0.3.0b1 beta.
Changes included:
Align package version, runtime version, release labels, citation metadata, and release evidence.
Update README, CLAIMS, BENCHMARKS, REPRODUCIBILITY, publishing docs, and release checklist for public beta wording.
Add Studio boundary policy to keep UI, FastAPI, WebSocket, Tauri, installer, and product CLI code out of the core library.
Add AST-based core boundary guard and release test coverage.
Add Phase 1 Studio execution handoff documents in HTML and Markdown.
Add safe performance planning notes for future live/interactive Studio execution without changing scientific semantics.
Add cross-OS CI smoke matrix for Ubuntu, Windows, and macOS across Python 3.11–3.14.
Keep CodonTrace Genesis dependency-free, library-first, and evidence/replay focused.
This release does not turn the core library into a UI product. CodonTrace Studio remains a separate future consumer application.

Author: Parvaz-Jamei

.github/workflows/ci.yml

@@ -1,6 +1,6 @@
 name: CI
 
-on:
+"on":
   push:
   pull_request:
 
@@ -12,17 +12,18 @@ env:
   PIP_DISABLE_PIP_VERSION_CHECK: "1"
 
 jobs:
-  test:
-    name: Python ${{ matrix.python-version }}
-    runs-on: ubuntu-latest
-    timeout-minutes: 25
+  core-smoke-cross-os:
+    name: Core smoke (${{ matrix.os }}, Python ${{ matrix.python-version }})
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 30
     strategy:
       fail-fast: false
       matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
         python-version: ["3.11", "3.12", "3.13", "3.14"]
     steps:
       - name: Checkout
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
 
       - name: Set up Python
         uses: actions/setup-python@v6
@@ -38,15 +39,8 @@ jobs:
       - name: Compile package, tests, examples, and tools
         run: python -m compileall -q src tests examples tools
 
+      - name: Enforce core boundary with AST import guard
+        run: python tools/check_core_boundary.py
+
       - name: Run release-critical tests
-        run: |
-          python -m pytest \
-            tests/test_export_import.py \
-            tests/test_api_signature.py \
-            tests/test_genesis_causal_mechanism_hardening.py \
-            tests/test_genesis_causal_mechanism_runtime_wiring_integrity.py \
-            tests/test_genesis_integration_public_api_unification.py \
-            tests/test_genesis_integration_runtime_wiring.py \
-            tests/release \
-            tests/genesis_gates \
-            --disable-plugin-autoload
+        run: python -m pytest tests/test_export_import.py tests/test_api_signature.py tests/test_genesis_causal_mechanism_hardening.py tests/test_genesis_causal_mechanism_runtime_wiring_integrity.py tests/test_genesis_integration_public_api_unification.py tests/test_genesis_integration_runtime_wiring.py tests/release tests/genesis_gates --disable-plugin-autoload

.github/workflows/publish-pypi.yml

@@ -1,6 +1,6 @@
 name: Publish to PyPI
 
-on:
+"on":
   release:
     types: [published]
 
@@ -17,7 +17,7 @@ jobs:
     timeout-minutes: 20
     steps:
       - name: Checkout
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
 
       - name: Set up Python
         uses: actions/setup-python@v6
@@ -35,7 +35,7 @@ jobs:
         run: python -m twine check dist/*
 
       - name: Upload artifacts
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         with:
           name: python-distributions
           path: dist/
@@ -49,7 +49,7 @@ jobs:
       contents: read
     steps:
       - name: Download distributions
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v8
         with:
           name: python-distributions
           path: dist/

BENCHMARKS.md

@@ -1,11 +1,11 @@
 # Benchmark Protocols
 
-Version target: `0.3.0a2`  
-Release DOI: `10.5281/zenodo.20337435`  
-License: `AGPL-3.0-or-later`  
-Status: Public alpha research software  
-Primary runner: `examples/collective_joss_evidence_benchmark.py`  
-Primary smoke test: `tests/examples/test_collective_joss_evidence_benchmark_smoke.py`  
+Version target: `0.3.0b1`
+Release DOI: `10.5281/zenodo.20337435`
+License: `AGPL-3.0-or-later`
+Status: Public beta research software
+Primary runner: `examples/collective_joss_evidence_benchmark.py`
+Primary smoke test: `tests/examples/test_collective_joss_evidence_benchmark_smoke.py`
 Reference artifact inspected: `joss_evidence_smoke_20260522_182358.zip`
 
 This document defines the benchmark protocol for CodonTrace Genesis as deterministic, replay/audit-first research software for digital evolution, ALife experiments, causal mechanism auditing, and claim-gated evidence generation.
@@ -73,7 +73,7 @@ JOSS-safe benchmark wording:
 examples/collective_joss_evidence_benchmark.py
 ```
 
-The runner is the user-facing benchmark entry point. It produces CSV/JSON/HTML artifacts and is designed to stay compatible with the public-alpha `0.3.0a2` branch.
+The runner is the user-facing benchmark entry point. It produces CSV/JSON/HTML artifacts and is designed to stay compatible with the public-beta `0.3.0b1` branch.
 
 ### Smoke test
 
@@ -146,10 +146,10 @@ The inspected smoke artifact reports:
 | Field | Value |
 |---|---:|
 | Runner | `collective_joss_evidence_benchmark` |
-| Runner schema | `collective_joss_evidence_benchmark_v1.1.0_public_alpha_a2` |
-| CodonTrace version | `0.3.0a2` |
-| Target public version | `0.3.0a2` |
-| Expected version | `0.3.0a2` |
+| Runner schema | `collective_joss_evidence_benchmark_v1.1.0_public_beta_b1` |
+| CodonTrace version | `0.3.0b1` |
+| Target public version | `0.3.0b1` |
+| Expected version | `0.3.0b1` |
 | Release DOI | `10.5281/zenodo.20337435` |
 | Profile | `smoke` |
 | Seed start | `1` |
@@ -293,32 +293,22 @@ Interpretation:
 
 ---
 
-## 9. Known provenance note
+## 9. Provenance label check
 
-The inspected smoke `summary.json` includes:
+For the `0.3.0b1` beta release, benchmark provenance should report a single aligned release identity:
 
 ```text
-release_artifact_name: codontrace-0.3.0a1-release-bundle.zip
-```
-
-while the run configuration and actual CodonTrace version report:
-
-```text
-codontrace_version: 0.3.0a2
-target_public_version: 0.3.0a2
-expected_version: 0.3.0a2
+release_artifact_name: codontrace-0.3.0b1-release-bundle.zip
+codontrace_version: 0.3.0b1
+target_public_version: 0.3.0b1
+expected_version: 0.3.0b1
 ```
 
 Interpretation:
 
-- This is not a smoke-run failure.
-- The benchmark executed with `0.3.0a2`.
-- The stale `release_artifact_name` should be cleaned before the next formal release so provenance text does not confuse reviewers.
-- Until cleaned, benchmark reports should treat this as a minor provenance-label issue, not as evidence that the run used `0.3.0a1`.
-
-Recommended fix before the next release:
-
-> Update any static release-artifact label or default metadata that still mentions `0.3.0a1`.
+- A benchmark report that claims to target this beta line must not use stale alpha artifact labels.
+- Historical alpha labels may remain only in lineage/history tests and archival notes.
+- Release-facing benchmark outputs should use the runtime package version or `RELEASE_ARTIFACT_NAME` rather than hard-coded legacy strings.
 
 ---
 
@@ -756,7 +746,7 @@ The smoke zip does not need to be uploaded into the repository immediately.
 
 The current smoke benchmark supports:
 
-- runner execution on `0.3.0a2`,
+- runner execution on `0.3.0b1`,
 - generation of structured artifacts,
 - artifact-manifest creation,
 - environment recording,

CHANGELOG.md

@@ -1,5 +1,23 @@
 # Changelog
 
+## 0.3.0b1 — Studio-readiness beta release
+
+### Changed
+
+- Promoted current package identity from `0.3.0a2` alpha to `0.3.0b1` beta.
+- Updated package metadata, runtime `codontrace.__version__`, citation metadata, release evidence, README install pins, and current release artifact identity.
+- Kept historical `added_in`/compatibility provenance fields intact where they describe APIs introduced during the alpha line.
+
+### Added
+
+- Added `docs/STUDIO_PHASE1_EXECUTION_SPEC.html` as the repo-ready Phase 1 Studio execution handoff.
+- Added `docs/STUDIO_BOUNDARY.md` to lock the library/UI boundary before Studio work begins.
+- Added `docs/PERFORMANCE_PHASE1.md` as a safe profiling and optimization plan for live execution without changing scientific semantics.
+
+### Notes
+
+This beta promotion does not make CodonTrace a UI product and does not loosen the claim boundary. The core remains a dependency-free research library; Studio/API/Desktop work belongs in a separate consumer repository.
+
 ## 0.3.0a2 — AGPL metadata correction alpha release
 
 ### Changed

CITATION.cff

@@ -1,15 +1,15 @@
 cff-version: 1.2.0
 message: "If you use CodonTrace Genesis, please cite the versioned software release."
 title: "CodonTrace Genesis"
-version: "0.3.0a2"
+version: "0.3.0b1"
 authors:
   - family-names: "Jamei"
     given-names: "Parvaz"
 license: "AGPL-3.0-or-later"
 repository-code: "https://github.com/Parvaz-Jamei/codontrace-genesis"
 doi: "10.5281/zenodo.20337435"
-date-released: "2026-05-22"
-abstract: "CodonTrace Genesis is a deterministic, library-first research-alpha toolkit for digital-evolution experiments, causal mechanism auditing, capsule-mediated transfer, skill-compression inheritance, role and collective-behavior instrumentation, and replayable evidence artifacts."
+date-released: "2026-06-05"
+abstract: "CodonTrace Genesis is a deterministic, library-first research-beta toolkit for digital-evolution experiments, causal mechanism auditing, capsule-mediated transfer, skill-compression inheritance, role and collective-behavior instrumentation, and replayable evidence artifacts."
 keywords:
   - digital evolution
   - causal mechanism auditing

CLAIMS.md

@@ -1,11 +1,11 @@
 # CodonTrace Genesis Claim Policy
 
-Version target: `0.3.0a2`  
-Release DOI: `10.5281/zenodo.20337435`  
-License: `AGPL-3.0-or-later`  
-Status: Public alpha research software  
-Repository: `https://github.com/Parvaz-Jamei/codontrace-genesis`  
-Package: `codontrace==0.3.0a2`
+Version target: `0.3.0b1`
+Release DOI: `10.5281/zenodo.20337435`
+License: `AGPL-3.0-or-later`
+Status: Public beta research software
+Repository: `https://github.com/Parvaz-Jamei/codontrace-genesis`
+Package: `codontrace==0.3.0b1`
 
 This document defines the strongest claims that CodonTrace Genesis can make today, the claims that require stronger benchmark evidence, and the claims that are explicitly blocked for the current release.
 
@@ -76,12 +76,12 @@ Use instead:
 
 ## 3. Stable software claims allowed now
 
-These claims are allowed for the current public alpha release because they describe implemented software scope, packaging, metadata, and instrumentation intent rather than final scientific discoveries.
+These claims are allowed for the current public beta release because they describe implemented software scope, packaging, metadata, and instrumentation intent rather than final scientific discoveries.
 
 | Area | Allowed claim | Required wording discipline |
 |---|---|---|
-| Research software | CodonTrace Genesis is public alpha research software for digital evolution, causal mechanism auditing, replayable ALife experiments, and evidence-gated AI/evolution studies. | Say “research software” or “research library,” not “proven intelligence system.” |
-| Packaging | CodonTrace Genesis is published as a Python package and can be installed from PyPI as `codontrace==0.3.0a2`. | Tie install claims to the exact version. |
+| Research software | CodonTrace Genesis is public beta research software for digital evolution, causal mechanism auditing, replayable ALife experiments, and evidence-gated AI/evolution studies. | Say “research software” or “research library,” not “proven intelligence system.” |
+| Packaging | CodonTrace Genesis is published as a Python package and can be installed from PyPI as `codontrace==0.3.0b1`. | Tie install claims to the exact version. |
 | Citation | The release has a Zenodo DOI and citation metadata. | Cite the exact DOI/version used. |
 | License | The public release uses `AGPL-3.0-or-later`. | Keep commercial/proprietary exceptions separate from the open license. |
 | Determinism | The library is designed around deterministic experiment specifications, digests, replay records, and artifact manifests. | Do not claim every user experiment is automatically deterministic unless seeds/configs/artifacts are preserved. |
@@ -99,25 +99,25 @@ These claims are allowed for the current public alpha release because they descr
 
 This section records the strongest evidence observed in the currently inspected runner output package. It is useful as development evidence and as a guide for the next public benchmark.
 
-It should **not** be used as a publication-grade claim until the run is repeated on the current public release (`0.3.0a2` or newer), archived with its configuration/artifacts, and reported with enough seeds and controls.
-
-Inspected artifact: `collective_heavy_outputs.zip`  
-Runner: `codontrace_collective_intelligence_heavy_runner`  
-Runner schema: `collective_heavy_runner_v1.2.0_incremental_checkpointing`  
-Observed engine/package version: `0.2.0a25`  
-Profile: `quick`  
-Seed count: `2`  
-Ticks/generations: `8`  
-Population: `6`  
-Workers: `1`  
-Runs planned/completed/failed: `40 / 40 / 0`  
+It should **not** be used as a publication-grade claim until the run is repeated on the current public release (`0.3.0b1` or newer), archived with its configuration/artifacts, and reported with enough seeds and controls.
+
+Inspected artifact: `collective_heavy_outputs.zip`
+Runner: `codontrace_collective_intelligence_heavy_runner`
+Runner schema: `collective_heavy_runner_v1.2.0_incremental_checkpointing`
+Observed engine/package version: `0.2.0a25`
+Profile: `quick`
+Seed count: `2`
+Ticks/generations: `8`
+Population: `6`
+Workers: `1`
+Runs planned/completed/failed: `40 / 40 / 0`
 Unique result digests: `40`
 
 Important provenance warning:
 
-- The inspected output was generated from an older `0.2.0a25` development/release artifact, not the current public `0.3.0a2` PyPI release.
+- The inspected output was generated from an older `0.2.0a25` development/release artifact, not the current public `0.3.0b1` PyPI release.
 - The inspected summary includes a release-identity/provenance warning around the tested zip name.
-- Therefore this snapshot is valid as **development evidence** and **instrumentation evidence**, but not as a final public benchmark for `0.3.0a2`.
+- Therefore this snapshot is valid as **development evidence** and **instrumentation evidence**, but not as a final public benchmark for `0.3.0b1`.
 
 ### 4.1 Evidence categories observed
 
@@ -255,7 +255,7 @@ These require a stronger public benchmark:
 
 ## 7. Explicitly blocked claims for the current release
 
-The following claims must not be made for `0.3.0a2` unless a future paper/benchmark explicitly satisfies the required evidence level.
+The following claims must not be made for `0.3.0b1` unless a future paper/benchmark explicitly satisfies the required evidence level.
 
 - CodonTrace has proven artificial general intelligence.
 - CodonTrace has proven consciousness or subjective experience.
@@ -383,7 +383,7 @@ Suggested citation target:
 
 - Software DOI: `10.5281/zenodo.20337435`
 - Repository: `https://github.com/Parvaz-Jamei/codontrace-genesis`
-- Package: `codontrace==0.3.0a2`
+- Package: `codontrace==0.3.0b1`
 
 ---
 
@@ -412,7 +412,7 @@ This file should be updated whenever a new public benchmark, JOSS paper, arXiv p
 
 Recommended update triggers:
 
-- a benchmark is rerun on `0.3.0a2` or newer,
+- a benchmark is rerun on `0.3.0b1` or newer,
 - a new Zenodo artifact is created,
 - an external user cites or uses the library,
 - a JOSS/arXiv/paper artifact is prepared,

GENESIS_COMPATIBILITY_MATRIX.md

@@ -1,6 +1,6 @@
-# GENESIS Compatibility Matrix — v0.3.0a1 unified-runtime
+# GENESIS Compatibility Matrix — v0.3.0b1 beta unified-runtime
 
-CodonTrace is not yet a proof of artificial life, AGI, consciousness, or open-ended autonomous discovery. It is a GENESIS-aligned research-alpha foundation engine.
+CodonTrace is not yet a proof of artificial life, AGI, consciousness, or open-ended autonomous discovery. It is a GENESIS-aligned research-beta foundation engine.
 
 | GENESIS Concept | Current API | Status | Operational Level | Missing / Limitation | Evidence / Tests | Claim Allowed? |
 |---|---|---:|---|---|---|---|
@@ -46,7 +46,7 @@ CodonTrace is not yet a proof of artificial life, AGI, consciousness, or open-en
 |---|---|---:|---|
 | Causal validation | `codontrace.genesis.causal_validation` | scaffold/implemented | Separates temporal precedence, association, conditional association, intervention, and ground-truth recovery; never claims true causality by graph alone. |
 | ADF macro validation | `adf_runtime`, `adf_validation` | scaffold/implemented | ADF decode and macro expansion are operational; language emergence is not claimed without null models and ablation. |
-| Active QD search loop | `qd_search` | scaffold/implemented | Archive can feed parent selection/emission; still research-alpha, not full OEE proof. |
+| Active QD search loop | `qd_search` | scaffold/implemented | Archive can feed parent selection/emission; still research-beta, not full OEE proof. |
 | Capsule transfer validation | `capsule_validation` | scaffold/implemented | Adoption counters alone are not transfer proof; ON/OFF or before/after effect needed. |
 | Discovery experiment protocol | `discovery_protocol` | scaffold/implemented | D0/shadow/persistence/ablation/multiseed/replay gates downgrade unsupported claims. |
 | Scientific manifest strictness | `validate_scientific_manifest` | scaffold/implemented | Flags missing or placeholder hashes for paper-grade runs. |