MUSE-OS 1.0.2__tar.gz

MUSE_OS-1.0.2/.bumpversion.cfg

@@ -0,0 +1,8 @@
+[bumpversion]
+current_version = 1.0.2
+commit = True
+tag = True
+
+[bumpversion:file:src/muse/__init__.py]
+
+[bumpversion:file:docs/conf.py]

MUSE_OS-1.0.2/.dockerignore

@@ -0,0 +1,15 @@
+*
+!README.m
+!docs
+!setup.py
+!setup.cfg
+!tests/
+!src/muse/
+!docs/bibliography.bib
+!docs/bibliography.rst
+!docs/conf.py
+!docs/developer_guide
+!docs/index,rs
+!docs/installation.rst
+!docs/user_gide/
+!docs/model/

MUSE_OS-1.0.2/.editorconfig

@@ -0,0 +1,12 @@
+# EditorConfig is awesome: http://EditorConfig.org
+
+# top-most EditorConfig file
+root = true
+
+[*.py]
+indent_style = space
+indent_size = 4
+tab_width = 4
+charset = utf-8
+max_line_length=88
+insert_final_newline = true

MUSE_OS-1.0.2/.flake8

@@ -0,0 +1,11 @@
+[flake8]
+max-line-length = 88
+exclude = 
+	.tox,
+	.git,
+    .venv,
+    venv,
+	build,
+	__pycache__,
+extend-ignore =
+	E203,W503

MUSE_OS-1.0.2/.github/PULL_REQUEST_TEMPLATE.md

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+# Description
+
+*Please include a summary of the change and which issue is fixed (if any). Please also
+include relevant motivation and context. List any dependencies that are required for
+this change.*
+
+Fixes # (issue)
+
+## Type of change
+
+Please add a line in the relevant section of
+[CHANGELOG.md](https://github.com/SGIModel/StarMuse/blob/development/CHANGELOG.md) to
+document the change (include PR #) - note reverse order of PR #s.
+
+- [ ] New feature (non-breaking change which adds functionality)
+- [ ] Optimization (non-breaking, back-end change that speeds up the code)
+- [ ] Bug fix (non-breaking change which fixes an issue)
+- [ ] Breaking change (whatever its nature)
+
+## Key checklist
+
+- [ ] All tests pass: `$ python -m pytest`
+- [ ] The documentation builds and looks OK: `$ python -m sphinx -b html docs docs/build`
+
+## Further checks
+
+- [ ] Code is commented, particularly in hard-to-understand areas
+- [ ] Tests added that prove fix is effective or that feature works

MUSE_OS-1.0.2/.github/dependabot.yml

@@ -0,0 +1,11 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"

MUSE_OS-1.0.2/.github/workflows/broken-link-check.yml

@@ -0,0 +1,21 @@
+on:
+  schedule:
+    - cron: 0 0 1 * * # run monthly
+  repository_dispatch: # run manually
+    types: [check-link]
+  push:
+    branches: [main, develop]
+  pull_request:
+      types: [opened, synchronize, reopened]
+
+name: Broken Link Check
+jobs:
+  check:
+    name: Broken Link Check
+    runs-on: ubuntu-latest
+    steps:
+      - name: Broken Link Check
+        uses: ruzickap/action-my-broken-link-checker@v2
+        with:
+          url: https://muse-os.readthedocs.io/en/latest/
+          cmd_params: '--timeout=20 --buffer-size=8192 --max-connections=3 --color=always --skip-tls-verification --header="User-Agent:curl/7.54.0"'  # muffet parameters

MUSE_OS-1.0.2/.github/workflows/ci.yml

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+name: QA, tests and publishing
+
+on:
+    pull_request:
+        types: [opened, synchronize, reopened]
+    push:
+      branches: [main, develop]
+      tags:
+        - '*'
+jobs:
+  # Checks the style using the pre-commit hooks
+  qa:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: pre-commit/action@v3.0.0
+
+  # Only then, normal testing proceeds
+  unit-tests:
+    needs: qa
+    runs-on: ${{ matrix.os }}
+
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.8", "3.9"]
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip==22.1.2
+        pip install -U setuptools==62.6.0 wheel xlrd==1.2.0
+        pip install -e .[all]
+
+    # The unit tests, with coverage under linux
+    - name: Unit tests (linux)
+      if: (runner.os == 'Linux')
+      run: |
+        pip install pytest-cov
+        pytest -m "not regression" --junitxml=junit/pytest.xml \
+            --cov=muse \
+            --cov-branch \
+            --cov-report=xml:coverage/coverage.xml
+
+    - name: Unit tests (not linux)
+      if: (runner.os != 'Linux')
+      run: pytest -m "not regression"
+
+  regression-tests:
+    needs: qa
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.8", "3.9"]
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip==22.1.2
+          pip install -U setuptools==62.6.0 wheel xlrd==1.2.0
+          pip install -e .[all]
+
+      # The regression tests (with non coverage)
+      - name: Regression tests
+        run: pytest -m "regression"
+
+  # If all tests pass, we try to build a wheel
+  build-wheel:
+    # needs: [regression-tests, unit-tests]
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Build sdist
+        run: |
+          python -m pip install --upgrade build
+          python -m build
+
+      - uses: actions/upload-artifact@v3
+        with:
+          path: dist/MUSE*
+
+  # And if we are pushing a tag, then we try to publish it
+  publish-TestPyPI:
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+    needs: build-wheel
+    name: Publish MUSE to TestPyPI
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write 
+
+    steps:
+
+      - name: Download sdist artifact
+        uses: actions/download-artifact@v3
+        with:
+          name: artifact
+          path: dist
+
+      - name: Display structure of downloaded files
+        run: ls -R dist
+
+      - name: Publish package distributions to TestPyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+          skip-existing: true
+
+  publish-PyPI:
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+    needs: publish-TestPyPI
+    name: Publish MUSE to PyPI
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write 
+
+    steps:
+
+      - name: Download sdist artifact
+        uses: actions/download-artifact@v3
+        with:
+          name: artifact
+          path: dist
+
+      - name: Display structure of downloaded files
+        run: ls -R dist
+
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

MUSE_OS-1.0.2/.github/workflows/documentation.yml

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+name: "Build and publish documentation"
+on:
+    pull_request:
+        types: [opened, synchronize, reopened]
+    push:
+        branches: ["main"]
+
+jobs:
+  html_docs:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: ammaraskar/sphinx-action@master
+      with:
+        docs-folder: "docs/"
+        pre-build-command: |
+            apt update -y 
+            apt install -y pandoc
+            python -m pip install -e .
+            python -m pip install --upgrade -r docs/requirements.txt
+        build-command: sphinx-build -n -b html . ../build/html
+    - uses: actions/upload-artifact@v3
+      with:
+        name: DocumentationHTML
+        path: build/html/
+    - name: Deploy
+      uses: peaceiris/actions-gh-pages@v3
+      if: github.ref == 'refs/heads/master'
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: ./build/html
+
+  pdf_docs:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: ammaraskar/sphinx-action@master
+      with:
+        docs-folder: "docs/"
+        pre-build-command: |
+            apt update -y 
+            apt install -y pandoc
+            python -m pip install -e .
+            python -m pip install --upgrade -r docs/requirements.txt
+        build-command: sphinx-build -n -b latex . ../build/latex
+    - name: build latex
+      run: |
+        sudo apt update -y 
+        sudo apt install -y latexmk texlive-latex-recommended \
+                texlive-latex-extra texlive-fonts-recommended
+        sudo chown -R $(whoami) build
+        cd build/latex
+        latexmk -interaction=nonstopmode -pdf muse
+    - uses: actions/upload-artifact@v3
+      with:
+        name: DocumentationPDF
+        path: build/latex/muse.pdf

MUSE_OS-1.0.2/.github/workflows/pre-commit_autoupdate.yml

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+name: Pre-commit auto-update
+
+on:
+  schedule:
+    - cron: "0 0 * * 1"  # midnight every Monday
+
+jobs:
+  auto-update:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+      - uses: browniebroke/pre-commit-autoupdate-action@main
+      - uses: peter-evans/create-pull-request@v5
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          branch: update/pre-commit-hooks
+          title: Update pre-commit hooks
+          commit-message: "chore: update pre-commit hooks"
+          body: Update versions of pre-commit hooks to latest version.

MUSE_OS-1.0.2/.github/workflows/remove_old_artifacts.yml

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+name: Remove old artifacts
+
+on:
+  schedule:
+    - cron: '0 0 1 * *'
+
+jobs:
+  remove-old-artifacts:
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+
+    steps:
+    - name: Remove old artifacts
+      uses: c-hive/gha-remove-artifacts@v1
+      with:
+        age: '15 days'
+        skip-tags: true
+        skip-recent: 5

MUSE_OS-1.0.2/.gitignore

@@ -0,0 +1,169 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+docs/_static/
+docs/_sources/
+docs/_modules/
+docs/_images/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+/Results/
+/FileLog.txt
+/Power/Data/MusePower/Data/
+/MUSEGlobalSettings.csv/
+src/StarMUSE.egg-info/
+/Industry/
+/Agriculture/
+/Transport/
+/Commercial/
+/Power/
+/Refinery/
+/Residential/
+/Sequestration/
+/Supply/
+/ReferenceMaterial&Data/
+junit/
+.benchmarks/
+other/
+JUnits.xml
+.DS_Store
+docs/developer_guide/tutorial/*.md
+docs/developer_guide/tutorial/Results
+docs/developer_guide/tutorial/model/
+docs/developer_guide/tutorial/mynewfunctions.py
+.vim/
+.tool-versions
+.local/
+.envrc
+shell.nix
+
+
+.vscode/*
+!.vscode/settings.json
+!.vscode/launch.json
+!.vscode/extension.json
+!.vscode/tasks.json
+
+model/
+
+*.html

MUSE_OS-1.0.2/.pre-commit-config.yaml

@@ -0,0 +1,30 @@
+# default_language_version:
+#   python: python3.8
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: check-merge-conflict
+      - id: debug-statements
+  - repo: https://github.com/timothycrosley/isort
+    rev: "5.12.0"
+    hooks:
+      - id: isort
+        additional_dependencies: [toml]
+  - repo: https://github.com/psf/black
+    rev: "23.3.0"
+    hooks:
+      - id: black
+  - repo: https://github.com/PyCQA/flake8
+    rev: 6.0.0
+    hooks:
+      - id: flake8
+  # - repo: https://github.com/pre-commit/mirrors-mypy
+  #   rev: "v0.910-1"
+  #   hooks:
+  #     - id: mypy
+  - repo: https://github.com/igorshubovych/markdownlint-cli
+    rev: v0.34.0
+    hooks:
+      - id: markdownlint
+        args: ["--disable", "MD013"]

MUSE_OS-1.0.2/.readthedocs.yaml

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+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.9"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: docs/conf.py
+
+# If using Sphinx, optionally build your docs in additional formats such as PDF
+# formats:
+#    - pdf
+
+# Optionally declare the Python requirements required to build your docs
+python:
+   install:
+   - method: pip
+     path: .
+     extra_requirements:
+         - doc

MUSE_OS-1.0.2/.vscode/extensions.json

@@ -0,0 +1,14 @@
+{
+	// See https://go.microsoft.com/fwlink/?LinkId=827846 to learn about workspace recommendations.
+	// Extension identifier format: ${publisher}.${name}. Example: vscode.csharp
+	// List of extensions which should be recommended for users of this workspace.
+	"recommendations": [
+		"bungcip.better-toml",
+		"janisdd.vscode-edit-csv",
+		"github.vscode-pull-request-github",
+		"ms-python.python",
+		"mechatroner.rainbow-csv"
+	],
+	// List of extensions recommended by VS Code that should not be recommended for users of this workspace.
+	"unwantedRecommendations": []
+}

MUSE_OS-1.0.2/.vscode/launch.json

@@ -0,0 +1,56 @@
+{
+    // Use IntelliSense to learn about possible attributes.
+    // Hover to view descriptions of existing attributes.
+    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "Model: default",
+            "type": "python",
+            "request": "launch",
+            "module": "muse",
+            "args": [
+                "--model",
+                "default"
+            ]
+        },
+        {
+            "name": "Model: multiple-agents",
+            "type": "python",
+            "request": "launch",
+            "module": "muse",
+            "args": [
+                "--model",
+                "multiple-agents"
+            ]
+        },
+        {
+            "name": "model/settings.toml",
+            "type": "python",
+            "request": "launch",
+            "module": "muse",
+            "args": [
+                "model/settings.toml",
+            ]
+        },
+        {
+            "name": "Model: minimum-service",
+            "type": "python",
+            "request": "launch",
+            "module": "muse",
+            "args": [
+                "--model",
+                "minimum-service"
+            ]
+        },
+        {
+            "name": "No retro",
+            "type": "python",
+            "request": "launch",
+            "module": "muse",
+            "args": [
+                "/Users/dalonsoa/Documents/Projects/scratch/MUSE/run/example/default_sara/settings.toml",
+            ]
+        },
+    ]
+}

MUSE_OS-1.0.2/.vscode/settings.json

@@ -0,0 +1,11 @@
+{
+    "python.linting.pylintEnabled": false,
+    "python.linting.flake8Enabled": true,
+    "python.linting.enabled": true,
+    "editor.formatOnSave": true,
+    "python.formatting.provider": "black",
+    "python.linting.mypyEnabled": true,
+    "python.testing.pytestEnabled": true,
+    "restructuredtext.confPath": "${workspaceFolder}/docs",
+    "python.pythonPath": "/opt/anaconda3/envs/muse/bin/python",
+}