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‎.github/CODEOWNERS‎

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* @clintval

‎.github/workflows/python_package.yml‎

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name: Code checks
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on: [push]
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env:
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POETRY_VERSION: 1.8.2
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jobs:
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Tests:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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PYTHON_VERSION: ["3.11", "3.12"]
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python ${{ matrix.PYTHON_VERSION }}
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.PYTHON_VERSION }}
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- name: Get full Python version
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id: full-python-version
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shell: bash
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run: echo "version=$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")" >> $GITHUB_OUTPUT
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- name: Install poetry
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run: |
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python -m pip install --upgrade pipx
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pipx install poetry==${{env.POETRY_VERSION}}
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- name: Set up cache
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uses: actions/cache@v4
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id: cache
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with:
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path: .venv
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key: venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('**/poetry.lock') }}
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- name: Ensure cache is healthy
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if: steps.cache.outputs.cache-hit == 'true'
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shell: bash
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run: poetry run pip --version >/dev/null 2>&1 || rm -rf .venv
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- name: Install the library
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run: poetry install -v
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- name: Install the task runner poethepoet
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run: poetry self add 'poethepoet[poetry_plugin]'
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- name: Test the library
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run: poetry task check-all
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‎.gitignore‎

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.vscode/
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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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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/#use-with-ide
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.pdm.toml
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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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venv/
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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/

‎CONTRIBUTING.md‎

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# Development and Testing
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## Primary Development Commands
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To check and resolve linting issues in the codebase, run:
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```console
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poetry run ruff check --fix
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```
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To check and resolve formatting issues in the codebase, run:
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```console
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poetry run ruff format
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```
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To check the unit tests in the codebase, run:
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```console
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poetry run pytest
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```
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To check the typing in the codebase, run:
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```console
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poetry run mypy
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```
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To generate a code coverage report after testing locally, run:
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```console
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poetry run coverage html
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```
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To check the lock file is up to date:
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```console
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poetry check --lock
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```
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## Shortcut Task Commands
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To be able to run shortcut task commands, first install the Poetry plugin [`poethepoet`](https://poethepoet.natn.io/index.html):
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```console
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poetry self add 'poethepoet[poetry_plugin]'
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```
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> [!NOTE]
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> Upon the release of Poetry [v2.0.0](https://github.com/orgs/python-poetry/discussions/9793#discussioncomment-11043205), Poetry will automatically support bootstrap installation of [project-specific plugins](https://github.com/python-poetry/poetry/pull/9547) and installation of the task runner will become automatic for this project.
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> The `pyproject.toml` syntax will be:
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>
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> ```toml
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> [tool.poetry]
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> requires-poetry = ">=2.0"
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>
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> [tool.poetry.requires-plugins]
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> poethepoet = ">=0.29"
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> ```
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###### For Running Individual Checks
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```console
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poetry task check-lock
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poetry task check-format
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poetry task check-lint
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poetry task check-tests
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poetry task check-typing
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```
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###### For Running All Checks
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```console
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poetry task check-all
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```
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###### For Running Individual Fixes
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```console
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poetry task fix-format
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poetry task fix-lint
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```
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###### For Running All Fixes
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```console
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poetry task fix-all
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```
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###### For Running All Fixes and Checks
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```console
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poetry task fix-and-check-all
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```

‎LICENSE‎

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MIT License
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Copyright © 2024 Fulcrum Genomics LLC
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.

‎README.md‎

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# seshatio
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[![CI](https://github.com/clintval/seshatio/actions/workflows/python_package.yml/badge.svg?branch=main)](https://github.com/clintval/seshatio/actions/workflows/python_package.yml?query=branch%3Amain)
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[![Python Versions](https://img.shields.io/badge/python-3.11_|_3.12-blue)](https://github.com/clintval/seshatio)
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[![MyPy Checked](http://www.mypy-lang.org/static/mypy_badge.svg)](http://mypy-lang.org/)
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[![Poetry](https://img.shields.io/endpoint?url=https://python-poetry.org/badge/v0.json)](https://python-poetry.org/)
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[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://docs.astral.sh/ruff/)
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A toTools for programatically annotating VCFs with the Seshat TP53 database.
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## Recommended Installation
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Install the Python package and dependency management tool [`poetry`](https://python-poetry.org/docs/#installation) using official documentation.
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You must have Python 3.11 or greater available on your system path, which could be managed by [`mamba`](https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html), [`pyenv`](https://github.com/pyenv/pyenv), or another package manager.
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Finally, install the dependencies of the project with:
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```console
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poetry install
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```
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To check successful installation, run:
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```console
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poetry run seshatio hello --name Fulcrum
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```
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## Installing into a Mamba Environment
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Install the Python package and dependency management tool [`poetry`](https://python-poetry.org/docs/#installation) and the environment manager [`mamba`](https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html) using official documentation.
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Create and activate a virtual environment with Python 3.11 or greater:
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```console
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mamba create -n seshatio python=3.11
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mamba activate seshatio
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```
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Then, because Poetry will auto-detect an activated environment, install the project with:
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```console
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poetry install
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```
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To check successful installation, run:
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```console
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seshatio hello --name Fulcrum
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```
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## Development and Testing
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See the [contributing guide](./CONTRIBUTING.md) for more information.

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