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Merge pull request #5 from uwplasma/rj/refactoring
Add documentation and requirements for ESSOS package, as well as GitHub Workflows
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‎.github/workflows/build_test.yml‎

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name: Build and Test
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on:
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push:
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branches: [ main ]
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pull_request:
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branches: [ main ]
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permissions:
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contents: read
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jobs:
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build:
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runs-on: ubuntu-20.04
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strategy:
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matrix:
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python-version: [ '3.9', '3.10', '3.11', '3.12']
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name: Python ${{ matrix.python-version }} Test
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v3
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install ESSOS
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run: |
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python -m pip install --upgrade pip
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pip install .
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install flake8 pytest coverage pytest-cov
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if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
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- name: Lint with flake8
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run: |
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# stop the build if there are Python syntax errors or undefined names
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flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics --exclude=examples_old
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# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
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flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics --exclude=examples_old
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- name: Run tests with coverage
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run: |
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pytest --cov-branch --cov-report=xml --cov=essos
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- name: Upload coverage reports to Codecov
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uses: codecov/codecov-action@v5
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with:
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token: ${{ secrets.CODECOV_TOKEN }}
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slug: uwplasma/ESSOS

‎.github/workflows/pypi_publish.yml‎

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name: Upload Python Package
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on:
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push:
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tags:
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- '**'
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release:
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types:
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- created
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permissions:
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contents: read
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jobs:
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release-build:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- uses: actions/setup-python@v5
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with:
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python-version: "3.x"
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- name: Install build tools
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run: |
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python -m pip install --upgrade pip
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python -m pip install build setuptools_scm
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- name: Update version dynamically
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run: |
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# Use setuptools_scm to manage versioning dynamically
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echo "__version__ = '$(python -m setuptools_scm)'" > essos/version.py
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- name: Build distributions
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run: python -m build
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- name: Upload distributions as artifacts
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uses: actions/upload-artifact@v4
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with:
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name: release-dists
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path: dist/
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create-tag:
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runs-on: ubuntu-latest
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needs:
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- release-build
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steps:
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- uses: actions/checkout@v4
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- name: Install setuptools_scm
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run: |
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python -m pip install setuptools_scm
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pypi-publish:
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runs-on: ubuntu-latest
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needs:
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- create-tag
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permissions:
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id-token: write
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steps:
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- name: Retrieve release distributions
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uses: actions/download-artifact@v4
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with:
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name: release-dists
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path: dist/
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- name: Publish distributions to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1

‎.gitignore‎

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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]
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*$py.class
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# C extensions
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*.so
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# Distribution / packaging
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.Python
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build/
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develop-eggs/
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dist/
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downloads/
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eggs/
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.eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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wheels/
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share/python-wheels/
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*.egg-info/
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.installed.cfg
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*.egg
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MANIFEST
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# PyInstaller
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# Usually these files are written by a python script from a template
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# before PyInstaller builds the exe, so as to inject date/other infos into it.
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*.manifest
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*.spec
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.nox/
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.coverage
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.coverage.*
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.cache
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nosetests.xml
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coverage.xml
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*.cover
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*.py,cover
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.hypothesis/
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.pytest_cache/
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cover/
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# Translations
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*.mo
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*.pot
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# Django stuff:
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*.log
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local_settings.py
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db.sqlite3
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db.sqlite3-journal
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# Flask stuff:
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instance/
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.webassets-cache
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# Scrapy stuff:
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.scrapy
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# Sphinx documentation
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docs/_build/
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# PyBuilder
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.pybuilder/
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target/
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# Jupyter Notebook
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.ipynb_checkpoints
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# IPython
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profile_default/
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ipython_config.py
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# pyenv
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# For a library or package, you might want to ignore these files since the code is
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# intended to run in multiple environments; otherwise, check them in:
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# .python-version
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# pipenv
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# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
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# However, in case of collaboration, if having platform-specific dependencies or dependencies
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# having no cross-platform support, pipenv may install dependencies that don't work, or not
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# install all needed dependencies.
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#Pipfile.lock
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# poetry
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# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
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# This is especially recommended for binary packages to ensure reproducibility, and is more
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# commonly ignored for libraries.
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# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
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#poetry.lock
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# pdm
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# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
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#pdm.lock
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# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
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# in version control.
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# https://pdm.fming.dev/latest/usage/project/#working-with-version-control
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.pdm.toml
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.pdm-python
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.pdm-build/
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# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
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__pypackages__/
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# Celery stuff
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celerybeat-schedule
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celerybeat.pid
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# SageMath parsed files
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*.sage.py
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# Environments
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.env
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.venv
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env/
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venv/
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ENV/
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env.bak/
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venv.bak/
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# Spyder project settings
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.spyderproject
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.spyproject
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# Rope project settings
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.ropeproject
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# mkdocs documentation
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/site
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# mypy
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.mypy_cache/
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.dmypy.json
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dmypy.json
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# Pyre type checker
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.pyre/
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# pytype static type analyzer
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.pytype/
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# Cython debug symbols
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cython_debug/
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# PyCharm
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# JetBrains specific template is maintained in a separate JetBrains.gitignore that can
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# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
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# and can be added to the global gitignore or merged into this file. For a more nuclear
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# option (not recommended) you can uncomment the following to ignore the entire idea folder.
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#.idea/
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.DS_Store
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*.cpython-3*
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*.pdf
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.DS_Store
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examples/output/
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*/output
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output/*
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tests/comparisons_SIMSOPT/output/*
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essos/version.py
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*.json
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*.png
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*.vtu
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*.vts

‎.readthedocs.yaml‎

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# Required
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version: 2
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# Set the OS, Python version, and other tools you might need
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build:
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os: ubuntu-24.04
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tools:
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python: "3.13"
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# Build documentation in the "docs/" directory with Sphinx
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sphinx:
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configuration: docs/conf.py
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python:
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install:
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- requirements: docs/requirements.txt

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