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‎.git_archival.txt

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node: $Format:%H$
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node-date: $Format:%cI$
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describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
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ref-names: $Format:%D$

‎.gitattributes

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.git_archival.txt export-subst

‎.github/CONTRIBUTING.md

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See the [Scientific Python Developer Guide][spc-dev-intro] for a detailed
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description of best practices for developing scientific packages.
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[spc-dev-intro]: https://scientific-python-cookie.readthedocs.io/guide/intro
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# Setting up a development environment manually
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You can set up a development environment by running:
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```bash
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python3 -m venv .venv
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source ./.venv/bin/activate
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pip install -v -e .[dev]
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```
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or just
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```bash
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hatch shell
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```
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# Post setup
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You should prepare pre-commit, which will help you by checking that commits pass
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required checks:
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```bash
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pip install pre-commit # or brew install pre-commit on macOS
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pre-commit install # Will install a pre-commit hook into the git repo
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```
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You can also/alternatively run `pre-commit run` (changes only) or
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`pre-commit run --all-files` to check even without installing the hook.
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This project uses pre-commit for all style checking. Install pre-commit and run:
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```bash
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pre-commit run -a
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```
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to check all files.
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# Testing
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Use pytest to run the unit checks:
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```bash
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pytest
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```
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# Coverage
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Use pytest-cov to generate coverage reports:
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```bash
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pytest --cov=dask-ngs
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```
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# Building docs
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You can build the docs using:
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```bash
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hatch docs
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```

‎.github/dependabot.yml

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version: 2
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updates:
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# Maintain dependencies for GitHub Actions
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- package-ecosystem: "github-actions"
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directory: "/"
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schedule:
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interval: "weekly"

‎.github/workflows/ci.yml

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name: CI
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on:
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workflow_dispatch:
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pull_request:
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push:
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branches:
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- main
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release:
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types:
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- published
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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env:
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FORCE_COLOR: 3
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jobs:
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pre-commit:
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name: Format
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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with:
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fetch-depth: 0
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- uses: actions/setup-python@v4
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with:
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python-version: "3.x"
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- uses: pre-commit/[email protected]
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with:
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extra_args: --hook-stage manual --all-files
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checks:
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name: Check Python ${{ matrix.python-version }} on ${{ matrix.runs-on }}
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runs-on: ${{ matrix.runs-on }}
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needs: [pre-commit]
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strategy:
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fail-fast: false
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matrix:
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python-version: ["3.7", "3.11"]
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runs-on: [ubuntu-latest, macos-latest, windows-latest]
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steps:
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- uses: actions/checkout@v3
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with:
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fetch-depth: 0
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- uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install package
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run: python -m pip install .[test]
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- name: Test package
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run: >-
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python -m pytest -ra --cov --cov-report=xml --cov-report=term
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--durations=20
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- name: Upload coverage report
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uses: codecov/[email protected]
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dist:
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needs: [pre-commit]
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name: Distribution build
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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with:
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fetch-depth: 0
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- name: Build sdist and wheel
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run: pipx run build
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- uses: actions/upload-artifact@v3
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with:
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path: dist
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- name: Check products
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run: pipx run twine check dist/*
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publish:
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needs: [dist]
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name: Publish to PyPI
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environment: pypi
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permissions:
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id-token: write
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runs-on: ubuntu-latest
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if: github.event_name == 'release' && github.event.action == 'published'
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steps:
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- uses: actions/download-artifact@v3
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with:
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name: artifact
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path: dist
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- uses: pypa/gh-action-pypi-publish@release/v1
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if: github.event_name == 'release' && github.event.action == 'published'
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with:
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# Remember to tell (test-)pypi about this repo before publishing
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# Remove this line to publish to PyPI
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repository-url: https://test.pypi.org/legacy/

‎.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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# PEP 582; used by e.g. github.com/David-OConnor/pyflow
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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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# setuptools_scm
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src/*/_version.py
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# ruff
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.ruff_cache/
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# OS specific stuff
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.DS_Store
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.DS_Store?
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._*
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.Spotlight-V100
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.Trashes
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ehthumbs.db
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Thumbs.db
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# Common editor files
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*~
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*.swp

‎.pre-commit-config.yaml

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ci:
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autoupdate_commit_msg: "chore: update pre-commit hooks"
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autofix_commit_msg: "style: pre-commit fixes"
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repos:
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- repo: https://github.com/psf/black
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rev: "23.3.0"
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hooks:
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- id: black-jupyter
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: "v4.4.0"
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hooks:
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- id: check-added-large-files
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- id: check-case-conflict
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- id: check-merge-conflict
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- id: check-symlinks
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- id: check-yaml
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- id: debug-statements
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- id: end-of-file-fixer
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- id: mixed-line-ending
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- id: name-tests-test
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args: ["--pytest-test-first"]
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- id: requirements-txt-fixer
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- id: trailing-whitespace
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- repo: https://github.com/pre-commit/pygrep-hooks
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rev: "v1.10.0"
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hooks:
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- id: rst-backticks
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- id: rst-directive-colons
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- id: rst-inline-touching-normal
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- repo: https://github.com/asottile/blacken-docs
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rev: "1.13.0"
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hooks:
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- id: blacken-docs
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additional_dependencies: [black==23.3.0]
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- repo: https://github.com/charliermarsh/ruff-pre-commit
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rev: "v0.0.264"
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hooks:
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- id: ruff
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args: ["--fix", "--show-fixes"]
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- repo: https://github.com/codespell-project/codespell
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rev: "v2.2.4"
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hooks:
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- id: codespell

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