amazon-utac 1.0.0__tar.gz

amazon_utac-1.0.0/.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,35 @@
+---
+name: Bug report
+about: Report something that isn't working as expected
+title: "[BUG] "
+labels: bug
+assignees: ""
+---
+
+## Description
+
+A clear and concise description of the bug.
+
+## Steps to reproduce
+
+1. ...
+2. ...
+3. ...
+
+## Expected behavior
+
+What you expected to happen.
+
+## Actual behavior
+
+What actually happened (include full error messages / tracebacks if any).
+
+## Environment
+
+- Package version: (`pip show <package-name>` or `git describe --tags`)
+- Python version:
+- OS:
+
+## Additional context
+
+Anything else relevant — logs, screenshots, related issues.

amazon_utac-1.0.0/.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,29 @@
+---
+name: Feature request
+about: Suggest a new feature, module, or enhancement
+title: "[FEATURE] "
+labels: enhancement
+assignees: ""
+---
+
+## Summary
+
+A clear and concise description of the feature.
+
+## Motivation
+
+Why is this needed? What problem does it solve, or what new capability
+does it enable within the GenesisAeon ecosystem?
+
+## Proposed approach
+
+How might this be implemented? (Sketches, pseudocode, references to
+related GenesisAeon packages or Diamond Interface methods are welcome.)
+
+## Alternatives considered
+
+Any alternative approaches you've thought about.
+
+## Additional context
+
+Links to relevant papers, prior discussion, or related issues/PRs.

amazon_utac-1.0.0/.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,31 @@
+## Summary
+
+What does this PR do, in one or two sentences?
+
+## Related issue(s)
+
+Closes #...
+
+## Type of change
+
+- [ ] Bug fix
+- [ ] New feature
+- [ ] Breaking change (Diamond Interface or other public API)
+- [ ] Documentation
+- [ ] Tooling / CI / release process
+- [ ] Dependency update
+
+## Checklist
+
+- [ ] Tests added/updated and passing locally (`pytest`)
+- [ ] `CHANGELOG.md` updated under `## [Unreleased]`
+- [ ] Documentation updated (README, docstrings, notebooks if relevant)
+- [ ] If this changes `run_cycle` / `get_crep_state` / `get_utac_state` /
+      `get_phase_events` / `to_zenodo_record`: noted as a breaking change
+      and version bump plan described above
+- [ ] If this touches scientific claims/predictions: sources cited and
+      speculative vs. validated status is clear
+
+## Additional notes
+
+Anything reviewers should know.

amazon_utac-1.0.0/.github/workflows/ci.yml

@@ -0,0 +1,63 @@
+name: CI
+
+on:
+  push:
+    branches: ["main", "master", "claude/**"]
+  pull_request:
+    branches: ["main", "master"]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  lint:
+    name: Lint (ruff + mypy)
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+      - name: Install dev dependencies
+        run: pip install -e ".[dev]"
+      - name: Run ruff
+        run: ruff check src tests
+      - name: Run mypy
+        run: mypy src
+
+  test:
+    name: Tests (Python ${{ matrix.python-version }})
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: pip install -e ".[dev]"
+      - name: Run pytest with coverage
+        run: pytest --cov=src --cov-report=xml
+      - name: Upload coverage
+        if: matrix.python-version == '3.11'
+        uses: codecov/codecov-action@v4
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: coverage.xml
+
+  docs:
+    name: Docs (mkdocs --strict)
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+      - name: Install dev dependencies
+        run: pip install -e ".[dev,docs]"
+      - name: Build docs
+        run: mkdocs build --strict

amazon_utac-1.0.0/.github/workflows/release.yml

@@ -0,0 +1,79 @@
+name: Release
+
+on:
+  push:
+    tags:
+      - "v*.*.*"
+
+permissions:
+  contents: write
+  id-token: write
+
+jobs:
+  build:
+    name: Build distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+      - name: Install build tools
+        run: pip install build
+      - name: Build wheel and sdist
+        run: python -m build
+      - name: Upload artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+  publish-pypi:
+    name: Publish to PyPI
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+  github-release:
+    name: Create GitHub Release
+    needs: publish-pypi
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+      - name: Create GitHub Release
+        uses: softprops/action-gh-release@v2
+        with:
+          files: dist/*
+          generate_release_notes: true
+          draft: false
+          prerelease: ${{ contains(github.ref, 'alpha') || contains(github.ref, 'beta') || contains(github.ref, 'rc') }}
+
+  publish-zenodo:
+    name: Publish to Zenodo
+    needs: github-release
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Upload to Zenodo
+        run: |
+          echo "Zenodo upload triggered for tag ${{ github.ref_name }}"
+          echo "Configure ZENODO_TOKEN secret and zenodraft/action for automatic upload."
+        # Replace with actual zenodo-upload action when token is configured:
+        # uses: zenodraft/action@main
+        # with:
+        #   concept-doi: 10.5281/zenodo.XXXXXXXX  # <- enter your concept DOI
+        #   token: ${{ secrets.ZENODO_TOKEN }}

amazon_utac-1.0.0/.gitignore

@@ -0,0 +1,22 @@
+# Python
+__pycache__/
+*.py[cod]
+*.egg-info/
+.eggs/
+dist/
+build/
+.venv/
+.uv/
+
+# Testing
+.coverage
+htmlcov/
+.pytest_cache/
+
+# Docs
+site/
+
+# Editors
+.vscode/
+.idea/
+*.swp

amazon_utac-1.0.0/.pre-commit-config.yaml

@@ -0,0 +1,17 @@
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.6.0
+    hooks:
+      - id: ruff
+        args: [--fix]
+      - id: ruff-format
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-toml
+      - id: check-merge-conflict
+      - id: debug-statements

amazon_utac-1.0.0/.zenodo.json

@@ -0,0 +1,34 @@
+{
+  "title": "amazon-utac — P19: GenesisAeon Package 19 — Amazon Rainforest Savannisation as a UTAC System",
+  "description": "<p>UTAC dynamical model of the Amazon rainforest savannisation tipping point, calibrated against Lovejoy &amp; Nobre (2019) and Boulton et al. (2022). Reports Γ_Amazon ≈ 0.116 (LOW-CREP, fragile regime).</p><p>Part of the <strong>GenesisAeon</strong> ecosystem (P19, domain: ecology / rainforest savannisation). Within the GenesisAeon CREP Criticality Spectrum, this package's characteristic coupling value is Γ ≈ 0.116.</p><p>See <a href=\"https://github.com/GenesisAeon/amazon-utac\">github.com/GenesisAeon/amazon-utac</a> for source, documentation, and reproducibility notebooks.</p>",
+  "creators": [
+    {
+      "name": "Römer, Johann",
+      "affiliation": "Independent Researcher / MOR Research Collective"
+    }
+  ],
+  "license": "MIT",
+  "upload_type": "software",
+  "access_right": "open",
+  "keywords": [
+    "GenesisAeon",
+    "P19",
+    "ecology",
+    "rainforest savannisation",
+    "UTAC",
+    "CREP",
+    "open science"
+  ],
+  "related_identifiers": [
+    {
+      "identifier": "10.5281/zenodo.19645351",
+      "relation": "isPartOf",
+      "resource_type": "publication-article",
+      "scheme": "doi"
+    }
+  ],
+  "version": "1.0.0",
+  "communities": [
+    { "identifier": "genesisaeon" }
+  ]
+}

amazon_utac-1.0.0/CHANGELOG.md

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+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/).
+
+## [Unreleased]
+
+## [1.0.0] - 2026
+### Added
+- Initial v1.0.0 release as part of the GenesisAeon ecosystem-wide 1.0.0
+  milestone.
+- Standardized release tooling: `.zenodo.json`, `RELEASE_GUIDE.md`,
+  `CONTRIBUTING.md`, issue/PR templates (CI and release workflows already
+  existed in this repo).
+
+### Changed
+- `.zenodo.json` metadata normalized to match the package's actual MIT
+  license and 1.0.0 version, and aligned with the GenesisAeon ecosystem
+  metadata template.

amazon_utac-1.0.0/CITATION.cff

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+cff-version: 1.2.0
+message: >
+  If you use this software in your research, please cite it using the metadata below.
+title: "amazon-utac: Amazon Rainforest Savannisation Threshold UTAC Model"
+abstract: >
+  GenesisAeon Package 19. Models the Amazon rainforest → savanna tipping
+  transition as a UTAC dynamical system with a double-well potential landscape.
+  Implements the CREP tensor (C, R, E, P) calibrated against Lovejoy & Nobre
+  (2019) and Boulton et al. (2022). Central result: Γ_Amazon ≈ 0.116 (LOW-CREP
+  zone). Includes Ethics-Gate Light (Phase H) for responsible scientific output.
+version: "0.1.0"
+date-released: "2026-04-23"
+license: MIT
+repository-code: "https://github.com/GenesisAeon/amazon-utac"
+doi: "10.5281/zenodo.19645351"
+keywords:
+  - amazon
+  - deforestation
+  - tipping point
+  - savannisation
+  - UTAC
+  - CREP
+  - GenesisAeon
+  - forest resilience
+  - critical slowing down
+authors:
+  - name: "MOR Research Collective / GenesisAeon"
+    email: "genesisaeon@example.org"
+references:
+  - type: article
+    title: "Amazon tipping point: Last chance for action"
+    authors:
+      - family-names: Lovejoy
+        given-names: Thomas E.
+      - family-names: Nobre
+        given-names: Carlos A.
+    journal: "Science Advances"
+    volume: 5
+    issue: 12
+    year: 2019
+    doi: "10.1126/sciadv.aba2949"
+  - type: article
+    title: "Pronounced loss of Amazon rainforest resilience since the early 2000s"
+    authors:
+      - family-names: Boulton
+        given-names: Chris A.
+      - family-names: Lenton
+        given-names: Timothy M.
+      - family-names: Boers
+        given-names: Niklas
+    journal: "Nature Climate Change"
+    volume: 12
+    pages: "271-278"
+    year: 2022
+    doi: "10.1038/s41558-022-01287-8"
+  - type: software
+    title: "Boulton et al. 2022 — Resilience dataset"
+    doi: "10.5281/zenodo.5831935"

amazon_utac-1.0.0/CONTRIBUTING.md

@@ -0,0 +1,49 @@
+# Contributing
+
+Thanks for your interest in contributing to this GenesisAeon ecosystem
+package!
+
+## Getting started
+
+1. Fork and clone the repository.
+2. Create a virtual environment: `python -m venv .venv && source .venv/bin/activate`
+   (or `.venv\Scripts\activate` on Windows).
+3. Install in editable mode with dev dependencies:
+   `pip install -e ".[dev]"` (or `.[test]` if `dev` extras don't exist).
+4. Run the test suite: `pytest`.
+
+## Code style
+
+- Format with `ruff format` and lint with `ruff check`.
+- Type-check with `mypy` where the package uses type hints.
+- Keep functions documented with docstrings (Google or NumPy style,
+  whichever this repo already uses).
+
+## Diamond Interface packages
+
+If this package implements the GenesisAeon Diamond Interface
+(`run_cycle`, `get_crep_state`, `get_utac_state`, `get_phase_events`,
+`to_zenodo_record`), any change to these methods' signatures or return
+shapes is a **breaking change** and requires a MAJOR version bump (see
+`RELEASE_GUIDE.md`).
+
+## Pull requests
+
+- One logical change per PR.
+- Add or update tests for any behavioral change.
+- Update `CHANGELOG.md` under an `## [Unreleased]` section.
+- Fill out the PR template (`.github/PULL_REQUEST_TEMPLATE.md`).
+
+## Reporting issues
+
+Please use the issue templates in `.github/ISSUE_TEMPLATE/` — they help us
+triage bug reports vs. feature requests quickly.
+
+## Scientific claims
+
+This is part of a research framework. If your contribution touches any
+scientific model, prediction, or benchmark (e.g. CREP `Γ` values, UTAC
+parameters, falsifiable predictions), please:
+- Cite the source (paper, dataset, or prior GenesisAeon Zenodo record).
+- Clearly mark speculative vs. validated claims, consistent with this
+  repo's existing `DISCLAIMER.md` (if present).

amazon_utac-1.0.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 JohannRömer
+
+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.

amazon_utac-1.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: amazon-utac
+Version: 1.0.0
+Summary: GenesisAeon Package 19: UTAC dynamical model of the Amazon rainforest savannisation tipping point. Bundles the diamond-setup project scaffold CLI.
+Project-URL: Homepage, https://github.com/GenesisAeon/amazon-utac
+Project-URL: Repository, https://github.com/GenesisAeon/amazon-utac
+Project-URL: Documentation, https://genesisaeon.github.io/amazon-utac
+Project-URL: Issues, https://github.com/GenesisAeon/amazon-utac/issues
+Project-URL: Zenodo, https://doi.org/10.5281/zenodo.19645351
+Author: GenesisAeon / MOR Research Collective
+License: MIT
+License-File: LICENSE
+Keywords: amazon,cli,crep,project-generator,scaffold,skeleton,template,tipping-point,utac
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Software Development :: Code Generators
+Requires-Python: >=3.10
+Requires-Dist: numpy>=1.26
+Requires-Dist: pydantic>=2.7
+Requires-Dist: pyyaml>=6.0
+Requires-Dist: rich>=13.7.0
+Requires-Dist: scipy>=1.12
+Requires-Dist: typer>=0.12.0
+Provides-Extra: dev
+Requires-Dist: mypy>=1.10.0; extra == 'dev'
+Requires-Dist: pre-commit>=3.7.0; extra == 'dev'
+Requires-Dist: pytest-cov>=5.0.0; extra == 'dev'
+Requires-Dist: pytest>=8.0.0; extra == 'dev'
+Requires-Dist: ruff>=0.6.0; extra == 'dev'
+Provides-Extra: docs
+Requires-Dist: mkdocs-material>=9.5.0; extra == 'docs'
+Requires-Dist: mkdocs>=1.6.0; extra == 'docs'
+Provides-Extra: notebooks
+Requires-Dist: ipykernel>=6.0; extra == 'notebooks'
+Requires-Dist: jupyter>=1.0; extra == 'notebooks'
+Requires-Dist: matplotlib>=3.8; extra == 'notebooks'
+Description-Content-Type: text/markdown
+
+# amazon-utac
+
+> GenesisAeon Package 19 — Amazon Rainforest Savannisation as UTAC System
+
+<p align="center">
+  <a href="https://doi.org/10.5281/zenodo.19645351"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.19645351.svg" alt="DOI (GenesisAeon Whitepaper)"/></a>
+  <a href="LICENSE"><img src="https://img.shields.io/badge/License-MIT-blue.svg" alt="MIT License"/></a>
+  <a href="https://creativecommons.org/licenses/by/4.0/"><img src="https://img.shields.io/badge/docs-CC%20BY%204.0-lightblue.svg" alt="CC BY 4.0"/></a>
+  <a href="https://github.com/GenesisAeon/genesis-os"><img src="https://img.shields.io/badge/part%20of-genesis--os-blueviolet" alt="Part of genesis-os"/></a>
+  <img src="https://img.shields.io/badge/UTAC-package%2019-orange" alt="Package 19"/>
+</p>
+
+**Amazon rainforest → savanna transition modelled as reversed UTAC system.**
+
+**Key result**: Γ_Amazon ≈ 0.116 (low-CREP, fragile regime).
+
+## Installation
+
+```bash
+pip install amazon-utac
+```
+
+For development (running tests, linting):
+
+```bash
+pip install -e ".[dev]"
+```
+
+## Quickstart
+
+```bash
+amazon-utac run --scenario current-rate
+amazon-utac threshold --deforestation-rate 0.01
+```
+
+## Integration in genesis-os
+
+```python
+from genesis_os import GenesisOS
+os = GenesisOS()
+amazon = os.load_package(19)
+results = amazon.run_cycle(duration_years=80)
+```
+
+## Benchmark
+
+Validated against Lovejoy & Nobre (2019) and Boulton et al. (2022).
+
+## Falsifiable Prediction
+
+With 1 % annual deforestation, tipping threshold crossed in 2038 ± 5 years.
+
+## Role in the GenesisAeon Ecosystem
+
+`amazon-utac` is **GenesisAeon Package 19 (P19)**, in the **ecology /
+rainforest savannisation** domain. It applies the GenesisAeon UTAC
+(Universal Threshold Activation Criticality) framework and CREP tensor to
+model the Amazon forest–savanna tipping point, contributing the
+cross-domain Γ_Amazon ≈ 0.116 data point to the ecosystem-wide CREP
+Criticality Spectrum.
+
+## Citation
+
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.PLACEHOLDER.svg)](https://doi.org/10.5281/zenodo.PLACEHOLDER)
+
+DOI will be assigned automatically on first GitHub Release once
+Zenodo–GitHub integration is enabled for this repo. Until then, please cite
+the GenesisAeon whitepaper DOI above, or `CITATION.cff` in this repository.
+
+## License
+
+Code: MIT • Docs & Data: CC BY 4.0

amazon_utac-1.0.0/README.md

@@ -0,0 +1,72 @@
+# amazon-utac
+
+> GenesisAeon Package 19 — Amazon Rainforest Savannisation as UTAC System
+
+<p align="center">
+  <a href="https://doi.org/10.5281/zenodo.19645351"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.19645351.svg" alt="DOI (GenesisAeon Whitepaper)"/></a>
+  <a href="LICENSE"><img src="https://img.shields.io/badge/License-MIT-blue.svg" alt="MIT License"/></a>
+  <a href="https://creativecommons.org/licenses/by/4.0/"><img src="https://img.shields.io/badge/docs-CC%20BY%204.0-lightblue.svg" alt="CC BY 4.0"/></a>
+  <a href="https://github.com/GenesisAeon/genesis-os"><img src="https://img.shields.io/badge/part%20of-genesis--os-blueviolet" alt="Part of genesis-os"/></a>
+  <img src="https://img.shields.io/badge/UTAC-package%2019-orange" alt="Package 19"/>
+</p>
+
+**Amazon rainforest → savanna transition modelled as reversed UTAC system.**
+
+**Key result**: Γ_Amazon ≈ 0.116 (low-CREP, fragile regime).
+
+## Installation
+
+```bash
+pip install amazon-utac
+```
+
+For development (running tests, linting):
+
+```bash
+pip install -e ".[dev]"
+```
+
+## Quickstart
+
+```bash
+amazon-utac run --scenario current-rate
+amazon-utac threshold --deforestation-rate 0.01
+```
+
+## Integration in genesis-os
+
+```python
+from genesis_os import GenesisOS
+os = GenesisOS()
+amazon = os.load_package(19)
+results = amazon.run_cycle(duration_years=80)
+```
+
+## Benchmark
+
+Validated against Lovejoy & Nobre (2019) and Boulton et al. (2022).
+
+## Falsifiable Prediction
+
+With 1 % annual deforestation, tipping threshold crossed in 2038 ± 5 years.
+
+## Role in the GenesisAeon Ecosystem
+
+`amazon-utac` is **GenesisAeon Package 19 (P19)**, in the **ecology /
+rainforest savannisation** domain. It applies the GenesisAeon UTAC
+(Universal Threshold Activation Criticality) framework and CREP tensor to
+model the Amazon forest–savanna tipping point, contributing the
+cross-domain Γ_Amazon ≈ 0.116 data point to the ecosystem-wide CREP
+Criticality Spectrum.
+
+## Citation
+
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.PLACEHOLDER.svg)](https://doi.org/10.5281/zenodo.PLACEHOLDER)
+
+DOI will be assigned automatically on first GitHub Release once
+Zenodo–GitHub integration is enabled for this repo. Until then, please cite
+the GenesisAeon whitepaper DOI above, or `CITATION.cff` in this repository.
+
+## License
+
+Code: MIT • Docs & Data: CC BY 4.0