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.pre-commit-config.yaml
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.pre-commit-config.yaml
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# enable pre-commit.ci at https://pre-commit.ci/
# it adds:
# 1. auto fixing pull requests
# 2. auto updating the pre-commit configuration
ci:
autoupdate_schedule: monthly
autofix_commit_msg: "style(pre-commit.ci): auto fixes [...]"
autoupdate_commit_msg: "ci(pre-commit.ci): autoupdate"
repos:
- repo: https://github.com/abravalheri/validate-pyproject
rev: v0.22
hooks:
- id: validate-pyproject
- repo: https://github.com/astral-sh/ruff-pre-commit
rev: v0.7.2
hooks:
- id: ruff
exclude: "^src/careamics/lvae_training/.*|^src/careamics/models/lvae/.*"
args: [--fix, --target-version, py38]
- repo: https://github.com/psf/black
rev: 24.10.0
hooks:
- id: black
- repo: https://github.com/pre-commit/mirrors-mypy
rev: v1.13.0
hooks:
- id: mypy
files: "^src/"
exclude: "^src/careamics/lvae_training/.*|^src/careamics/models/lvae/.*|^src/careamics/config/likelihood_model.py|^src/careamics/losses/loss_factory.py|^src/careamics/losses/lvae/losses.py"
args: ['--config-file', 'mypy.ini']
additional_dependencies:
- numpy
- types-PyYAML
- types-setuptools
# check docstrings
- repo: https://github.com/numpy/numpydoc
rev: v1.8.0
hooks:
- id: numpydoc-validation
exclude: "^src/careamics/lvae_training/.*|^src/careamics/models/lvae/.*|^src/careamics/losses/lvae/.*"
# # jupyter linting and formatting
# - repo: https://github.com/nbQA-dev/nbQA
# rev: 1.8.5
# hooks:
# - id: nbqa-ruff
# args: [--fix]
# - id: nbqa-black
# #- id: nbqa-mypy
# strip out jupyter notebooks
- repo: https://github.com/kynan/nbstripout
rev: 0.8.0
hooks:
- id: nbstripout