pyproject.toml

[tool.poetry]
name = "gaia"
version = "0.0.0"
description = "Template repository for a python project"
authors = ["Yifei Yu"]
readme = "README.md"
packages = [
    { include = "gaia", from = "src" }
]
include = [
    { path = "src/gaia/conf_default", format = "sdist" },
    { path = "notebooks", format = "sdist" }
]

[tool.poetry.dependencies]
python = "~3.11"
pydantic = "^2.9.2"
pandas = "^2.2.3"

[tool.poetry.group.dev.dependencies]
isort = "^5.13.2"
pytest = "^8.3.3"
mypy = "^1.11.2"
flake8 = "^7.1.1"
coverage = {extras = ["toml"], version = "^7.6.1"}
black = "^24.8.0"
yamllint = "^1.35.1"
semgrep = "^1.90.0"
ipykernel = "^6.29.5"
nbformat = "^5.10.4"
ruff = "^0.6.8"
shellcheck-py = "^0.10.0.1"
python-dotenv = "^1.0.1"

[build-system]
requires = ["poetry-core>=1.0.0"]
build-backend = "poetry.core.masonry.api"

[tool.black]
line-length = 88
force-exclude = '''
.*/setup\.py$
'''

[tool.isort]
profile = "black"
line_length = 88
src_paths = ["src", "tests"]
extend_skip = ["setup.py"]

[tool.pytest.ini_options]
log_cli = true
log_cli_level = "DEBUG"
log_cli_format = "%(asctime)s [%(levelname)8s] %(message)s (%(filename)s:%(lineno)s)"
log_cli_date_format = "%Y-%m-%d %H:%M:%S"
addopts = "--junitxml=test_report.xml"
testpaths = "tests"

[tool.mypy]
files = "src"
mypy_path = "src"
exclude = [
    ".venv"
]
namespace_packages = true
explicit_package_bases = true
disallow_untyped_defs = true
disallow_any_unimported = true
no_implicit_optional = true
check_untyped_defs = true
warn_return_any = true
warn_unused_ignores = true
show_error_codes = true

[[tool.mypy.overrides]]
module = []
ignore_missing_imports = true
warn_return_any = false

[tool.coverage.paths]
source = ["src", "*/site-packages"]

[tool.coverage.run]
branch = true
source = ["src"]

[tool.coverage.report]
show_missing = true
skip_covered = true
fail_under = 50
exclude_lines = [
    # Have to re-enable the standard pragma
    "pragma: no cover",

    # Don't complain about missing debug-only code:
    "def __repr__",
    '''if self\.debug''',

    # Don't complain if tests don't hit defensive assertion code:
    "raise AssertionError",
    "raise NotImplementedError",

    # Don't complain if non-runnable code isn't run:
    "if 0:",
    "if __name__ == .__main__.:",

    # Don't complain about abstract methods, they aren't run:
    '''@(abc\.)?abstractmethod''',
]

[tool.coverage.html]
directory = "htmlcov"

[tool.coverage.xml]
output = "coverage.xml"

[tool.ruff]
# Exclude a variety of commonly ignored directories.
exclude = [
    ".bzr",
    ".direnv",
    ".eggs",
    ".git",
    ".git-rewrite",
    ".hg",
    ".ipynb_checkpoints",
    ".mypy_cache",
    ".nox",
    ".pants.d",
    ".pyenv",
    ".pytest_cache",
    ".pytype",
    ".ruff_cache",
    ".svn",
    ".tox",
    ".venv",
    ".vscode",
    "__pypackages__",
    "_build",
    "buck-out",
    "build",
    "dist",
    "node_modules",
    "site-packages",
    "venv",
]

# Same as Black.
line-length = 88
indent-width = 4

# Assume Python 3.8
target-version = "py38"

[tool.ruff.lint]
# Enable Pyflakes (`F`) and a subset of the pycodestyle (`E`)  codes by default.
# Unlike Flake8, Ruff doesn't enable pycodestyle warnings (`W`) or
# McCabe complexity (`C901`) by default.
select = ["E4", "E7", "E9", "F"]
ignore = []

# Allow fix for all enabled rules (when `--fix`) is provided.
fixable = ["ALL"]
unfixable = []

# Allow unused variables when underscore-prefixed.
dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"

[tool.ruff.format]
# Like Black, use double quotes for strings.
quote-style = "double"

# Like Black, indent with spaces, rather than tabs.
indent-style = "space"

# Like Black, respect magic trailing commas.
skip-magic-trailing-comma = false

# Like Black, automatically detect the appropriate line ending.
line-ending = "auto"

# Enable auto-formatting of code examples in docstrings. Markdown,
# reStructuredText code/literal blocks and doctests are all supported.
#
# This is currently disabled by default, but it is planned for this
# to be opt-out in the future.
docstring-code-format = false

# Set the line length limit used when formatting code snippets in
# docstrings.
#
# This only has an effect when the `docstring-code-format` setting is
# enabled.
docstring-code-line-length = "dynamic"