codontrace 0.3.0a1__tar.gz

codontrace-0.3.0a1/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+  pull_request:
+
+permissions:
+  contents: read
+
+env:
+  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: "true"
+  PIP_DISABLE_PIP_VERSION_CHECK: "1"
+
+jobs:
+  test:
+    name: Python ${{ matrix.python-version }}
+    runs-on: ubuntu-latest
+    timeout-minutes: 25
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.11", "3.12", "3.13", "3.14"]
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v5
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+
+      - name: Install test dependencies
+        run: |
+          python -m pip install --upgrade pip setuptools wheel
+          python -m pip install -e . pytest
+
+      - name: Compile package, tests, examples, and tools
+        run: python -m compileall -q src tests examples tools
+
+      - 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

codontrace-0.3.0a1/.github/workflows/publish-pypi.yml

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+name: Publish to PyPI
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+env:
+  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: "true"
+  PIP_DISABLE_PIP_VERSION_CHECK: "1"
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    timeout-minutes: 20
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v5
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.11"
+          cache: pip
+
+      - name: Install build tools
+        run: python -m pip install --upgrade pip build twine
+
+      - name: Build distributions
+        run: python -m build
+
+      - name: Check distributions
+        run: python -m twine check dist/*
+
+      - name: Upload artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-distributions
+          path: dist/
+
+  publish:
+    needs: build
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write
+      contents: read
+    steps:
+      - name: Download distributions
+        uses: actions/download-artifact@v4
+        with:
+          name: python-distributions
+          path: dist/
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

codontrace-0.3.0a1/CHANGELOG.md

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+# Changelog
+
+## 0.3.0a1 — Alpha research release
+
+This release prepares CodonTrace Genesis for public alpha distribution as a deterministic research-software library.
+
+### Added
+
+- Causal mechanism surfaces for capsule ablation, capsule outcome windows, signal-memory-action links, skill-compression ablation, and child-outcome audits.
+- Role, territory, collective-task, role-ablation, heldout-partner, multi-agent contribution, source-reputation, counterfactual-replay, and extended OEE schema surfaces.
+- Runtime-wiring manifest digests for the new causal mechanism policies.
+- Integration audit helpers for public API, replay-policy coverage, evidence consistency, package hygiene, and reference hygiene.
+- CI and PyPI Trusted Publishing workflow templates.
+
+### Changed
+
+- Release identity is aligned to `0.3.0a1`.
+- Public documentation was rewritten for release-facing clarity and claim control.
+
+### Claim policy
+
+This is an alpha research-software release. It exposes deterministic primitives and evidence structures; it does not claim AGI, consciousness, artificial life, benchmark superiority, causal certainty, or autonomous open-ended discovery.

codontrace-0.3.0a1/CITATION.cff

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+cff-version: 1.2.0
+message: "If you use CodonTrace, please cite the versioned software release."
+title: "CodonTrace Genesis"
+version: "0.3.0a1"
+authors:
+  - family-names: "Jamei"
+    given-names: "Parvaz"
+license: "MIT"
+repository-code: "https://github.com/Parvaz-Jamei/codontrace-genesis"
+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."
+keywords:
+  - digital evolution
+  - causal mechanism auditing
+  - semantic genomes
+  - deterministic simulation
+  - quality diversity
+  - open-endedness
+  - research software

codontrace-0.3.0a1/CONTRIBUTING.md

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+# Contributing
+
+## Development setup
+
+```bash
+python -m pip install -e ".[dev]"
+```
+
+## Required checks
+
+```bash
+python -m ruff check .
+python -m ruff format --check .
+python -m mypy src/codontrace examples
+python -m pytest
+python -m build
+python -m twine check dist/*
+```
+
+Keep codontrace compact, testable, research-oriented, PyPI-ready, honest about limitations, and free of scope creep.

codontrace-0.3.0a1/LICENSE

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+MIT License
+
+Copyright (c) 2026 Parvaz Jamei
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

codontrace-0.3.0a1/MANIFEST.in

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+include README.md
+include LICENSE
+include CHANGELOG.md
+include SECURITY.md
+include CONTRIBUTING.md
+include RELEASE_EVIDENCE.md
+include CITATION.cff
+include pyproject.toml
+recursive-include docs *.md
+recursive-include examples *.py
+recursive-include tests *.py
+recursive-include tools *.py
+recursive-include .github/workflows *.yml
+recursive-include .github/workflows *.yaml
+prune artifacts
+prune reports
+prune build
+prune dist
+global-exclude __pycache__
+global-exclude *.py[cod]
+global-exclude .DS_Store
+global-exclude .pytest_cache
+global-exclude .mypy_cache
+global-exclude .ruff_cache
+global-exclude *.html
+global-exclude *.patch