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‎.dockerignore‎

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wandb/
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outputs/
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tensorflow_datasets/
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*.zip

‎.github/workflows/pre-commit.yml‎

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name: pre-commit
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on:
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pull_request:
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push:
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branches: [main]
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jobs:
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pre-commit:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ["3.8"]
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steps:
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- name: Checkout repository
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uses: actions/checkout@v3
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- name: Set up Python ${{ matrix.python-version }}
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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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check-latest: true
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- name: Install Wily
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run: pip install wily
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- name: Build cache and diff
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run: wily build .
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- name: Run pre-commit
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uses: pre-commit/[email protected]

‎.github/workflows/unit-test.yml‎

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name: unit-test
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on:
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pull_request:
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push:
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branches: [main]
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jobs:
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build:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ["3.8"]
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steps:
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- name: Checkout repository
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uses: actions/checkout@v3
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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with:
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check-latest: true
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python-version: ${{ matrix.python-version }}
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cache: "pip"
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cache-dependency-path: |
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docker/environment.yml
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docker/environment_mac_m1.yml
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docker/Dockerfile
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docker/requirements.txt
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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 tensorflow-cpu==2.11.0
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pip install jax==0.4.1
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pip install jaxlib==0.4.1
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pip install -r docker/requirements.txt
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pip install -e .
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- name: Test with pytest
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run: |
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pytest tests/unit

‎.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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pip-wheel-metadata/
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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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# 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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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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.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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# pycharm
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.idea/
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# Mac
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.DS_Store
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# notebook
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*.ipynb
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notebooks/
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# hydra outputs
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outputs/
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# wandb outputs
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wandb/

‎.isort.cfg‎

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[settings]
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known_third_party = SimpleITK,absl,chex,haiku,hydra,jax,jraph,numpy,ogb,omegaconf,optax,pandas,pytest,ray,rdkit,setuptools,tensorflow,tensorflow_datasets,tree,wandb
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multi_line_output = 3
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include_trailing_comma = True
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force_grid_wrap = 0
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use_parentheses = True
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line_length = 80

‎.pre-commit-config.yaml‎

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default_language_version:
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python: python3
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repos:
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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-ast
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- id: check-byte-order-marker
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- id: check-builtin-literals
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- id: check-case-conflict
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- id: check-docstring-first
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- id: check-merge-conflict
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- id: check-symlinks
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- id: check-toml
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- id: check-yaml
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- id: debug-statements
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- id: destroyed-symlinks
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- id: end-of-file-fixer
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- id: fix-byte-order-marker
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- id: mixed-line-ending
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- id: file-contents-sorter
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files: "docker/requirements.txt"
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- id: trailing-whitespace
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- repo: https://github.com/PyCQA/isort
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rev: 5.12.0
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hooks:
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- id: isort
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- repo: https://github.com/psf/black
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rev: 23.1.0
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hooks:
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- id: black
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args:
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- --line-length=80
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- repo: https://github.com/pre-commit/mirrors-mypy
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rev: v1.1.1
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hooks:
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- id: mypy
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args:
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[
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--strict-equality,
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--disallow-untyped-calls,
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--disallow-untyped-defs,
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--disallow-incomplete-defs,
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--check-untyped-defs,
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--disallow-untyped-decorators,
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--warn-redundant-casts,
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--warn-unused-ignores,
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--no-warn-no-return,
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--warn-unreachable,
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]
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- repo: https://github.com/pre-commit/mirrors-prettier
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rev: v3.0.0-alpha.6
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hooks:
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- id: prettier
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args:
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- --print-width=80
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- --prose-wrap=always
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- --tab-width=2
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- repo: https://github.com/charliermarsh/ruff-pre-commit
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rev: "v0.0.254"
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hooks:
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- id: ruff
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- repo: https://github.com/pre-commit/mirrors-pylint
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rev: v3.0.0a5
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hooks:
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- id: pylint
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- repo: https://github.com/asottile/pyupgrade
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rev: v3.3.1
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hooks:
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- id: pyupgrade
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args:
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- --py36-plus
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- --py37-plus
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- --py38-plus
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- repo: https://github.com/pycqa/pydocstyle
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rev: 6.3.0
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hooks:
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- id: pydocstyle
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args:
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- --convention=google
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- repo: local
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hooks:
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- id: wily
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name: wily
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entry: wily diff
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verbose: false
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language: python
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additional_dependencies: [wily]

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