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Florian Sestak
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Commit train code
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‎.env.example

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# example of file for storing private and user specific environment variables, like keys or system paths
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# rename it to ".env" (excluded from version control by default)
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# .env is loaded by train.py automatically
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# hydra allows you to reference variables in .yaml configs with special syntax: ${oc.env:MY_VAR}
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MY_VAR="/home/user/my/system/path"
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CONDA_ENV="pyt25" # path to conda environment, relevant for training on cluster with slurm (e.g. configs/meluxina.yaml)
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SLURM_ACCOUNT="my_account" # account for slurm, relevant for training on cluster with slurm (e.g. configs/meluxina.yaml)
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WANDB_BASE_URL=""
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WANDB_ENTITY=""
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WANDB_BASE_URL=https://api.wandb.ai
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WANDB_IGNORE_GLOBS=*.log # We ignore to upload the log files to wandb, this fills up the space fast.

‎.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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.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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### VisualStudioCode
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.vscode/*
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!.vscode/settings.json
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!.vscode/tasks.json
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!.vscode/launch.json
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!.vscode/extensions.json
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*.code-workspace
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**/.vscode
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# JetBrains
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.idea/
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# Data & Models
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*.h5
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*.tar
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*.tar.gz
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# Lightning-Hydra-Template
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configs/local/default.yaml
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/data/
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/logs/
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.env
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# Aim logging
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.aim
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wandb/*
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/data/*
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/data
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exports/*
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/exports
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hpc_ckpts/*
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/hpc_ckpts
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ckpts/*
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/ckpts
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lightning_logs/*

‎.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: v5.0.0
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hooks:
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# list of supported hooks: https://pre-commit.com/hooks.html
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- id: trailing-whitespace
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- id: end-of-file-fixer
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- id: check-docstring-first
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- id: check-yaml
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- id: debug-statements
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- id: detect-private-key
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- id: check-executables-have-shebangs
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- id: check-toml
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- id: check-case-conflict
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- id: check-added-large-files
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# python code formatting
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- repo: https://github.com/psf/black
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rev: 24.10.0
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hooks:
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- id: black
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args: [--line-length, "99"]
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# python import sorting
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- repo: https://github.com/PyCQA/isort
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rev: 5.13.2
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hooks:
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- id: isort
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args: ["--profile", "black", "--filter-files"]
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# python upgrading syntax to newer version
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- repo: https://github.com/asottile/pyupgrade
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rev: v3.19.0
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hooks:
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- id: pyupgrade
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args: [--py38-plus]
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# python docstring formatting
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- repo: https://github.com/PyCQA/docformatter
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rev: v1.7.4
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hooks:
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- id: docformatter
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args:
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[
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--in-place,
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--wrap-summaries=99,
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--wrap-descriptions=99,
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--style=sphinx,
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--black,
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]
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language: python
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types: [python]
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# python docstring coverage checking
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- repo: https://github.com/econchick/interrogate
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rev: 1.7.0 # or master if you're bold
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hooks:
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- id: interrogate
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args:
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[
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--verbose,
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--fail-under=80,
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--ignore-init-module,
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--ignore-init-method,
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--ignore-module,
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--ignore-nested-functions,
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-vv,
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]
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# python check (PEP8), programming errors and code complexity
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- repo: https://github.com/PyCQA/flake8
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rev: 7.1.1
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hooks:
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- id: flake8
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args:
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[
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"--extend-ignore",
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"E203,E402,E501,F401,E731,F841,RST2,RST301",
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"--exclude",
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"logs/*,data/*",
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]
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additional_dependencies: [flake8-rst-docstrings==0.3.0]
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# python security linter
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# - repo: https://github.com/PyCQA/bandit
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# rev: "1.7.10"
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# hooks:
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# - id: bandit
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# args: ["-s", "B101"]
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# yaml formatting
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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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types: [yaml]
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exclude: "environment.yaml"
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# shell scripts linter
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- repo: https://github.com/shellcheck-py/shellcheck-py
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rev: v0.10.0.1
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hooks:
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- id: shellcheck
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# md formatting
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- repo: https://github.com/executablebooks/mdformat
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rev: 0.7.18
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hooks:
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- id: mdformat
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args: ["--number"]
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additional_dependencies:
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- mdformat-gfm
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- mdformat-tables
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- mdformat_frontmatter
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# - mdformat-toc
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# - mdformat-black
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# word spelling linter
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- repo: https://github.com/codespell-project/codespell
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rev: v2.3.0
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hooks:
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- id: codespell
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args:
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- --skip=logs/**,data/**,*.ipynb
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- --ignore-words-list=OT,ot
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# jupyter notebook cell output clearing
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- repo: https://github.com/kynan/nbstripout
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rev: 0.7.1
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hooks:
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- id: nbstripout
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# jupyter notebook linting
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- repo: https://github.com/nbQA-dev/nbQA
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rev: 1.8.7
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hooks:
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- id: nbqa-black
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args: ["--line-length=99"]
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- id: nbqa-isort
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args: ["--profile=black"]
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- id: nbqa-flake8
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args:
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[
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"--extend-ignore=E203,E402,E501,E731,F401,F841",
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"--exclude=logs/*,data/*",
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]
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# - repo: https://github.com/PyCQA/autoflake
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# rev: v2.3.1
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# hooks:
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# - id: autoflake
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# mypy
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# - repo: https://github.com/pre-commit/mirrors-mypy
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# rev: v1.6.1
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# hooks:
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# - id: mypy
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# remove unused imports and variables
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- repo: https://github.com/PyCQA/autoflake
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rev: v2.3.1
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hooks:
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- id: autoflake
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args:
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[
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"--in-place",
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"--remove-all-unused-imports",
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"--ignore-init-module-imports",
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]

‎.project-root

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# this file is required for inferring the project root directory
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# do not delete

‎Makefile

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help: ## Show help
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@grep -E '^[.a-zA-Z_-]+:.*?## .*$$' $(MAKEFILE_LIST) | awk 'BEGIN {FS = ":.*?## "}; {printf "\033[36m%-30s\033[0m %s\n", $$1, $$2}'
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clean: ## Clean autogenerated files
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rm -rf dist
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find . -type f -name "*.DS_Store" -ls -delete
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find . | grep -E "(__pycache__|\.pyc|\.pyo)" | xargs rm -rf
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find . | grep -E ".pytest_cache" | xargs rm -rf
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find . | grep -E ".ipynb_checkpoints" | xargs rm -rf
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rm -f .coverage
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clean-logs: ## Clean logs
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rm -rf logs/**
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format: ## Run pre-commit hooks
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pre-commit run -a
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sync: ## Merge changes from main branch to your current branch
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git pull
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git pull origin main
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train: ## Train the model
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python src/train.py

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