pyproject.toml

[build-system]
requires = ["setuptools>=68", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "beiwe-forest"
version = "1.0.1beta"
description = "Forest is a library for analyzing smartphone-based high-throughput digital phenotyping data"
authors = [
    {name = "Jukka-Pekka Onnela"},
    {name = "Josh Barback"},
    {name = "Zachary Clement"},
    {name = "Hassan Dawood"},
    {name = "Georgios Efstathiadis"},
    {name = "Patrick Emedom-Nnamdi"},
    {name = "Ceyhun Olcan"},
    {name = "Emily J. Huang"},
    {name = "Marta Karas"},
    {name = "Gang Liu"},
    {name = "Nellie Ponarul"},
    {name = "Marcin Straczkiewicz"},
    {name = "Ilya Sytchev"},
    {name = "Anna Beukenhorst"},
]

maintainers = [
    {name = "Onnela Lab", email = "onnela.lab@gmail.com"},
    {name = "Eli Jones", email = "biblicabeebli@gmail.com"},
]
readme = "README.md"
license = {text = "BSD-3-Clause"}
requires-python = ">=3.12, <3.15"
dependencies = [
    "audioread",
    "holidays",
    "numpy",
    "openrouteservice",
    "pandas",
    "pyproj",
    "python-dateutil",
    "tzdata",
    "ratelimit",
    "requests",
    "scipy",
    "shapely",
    "soundfile",
    "ssqueezepy",
    "timezonefinder",
    "zstandard",
]
keywords = ["digital phenotyping", "smartphone", "statistics", "accelerometer", "GPS"]
classifiers = [
    "Development Status :: 4 - Beta",
    "Environment :: Console",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: BSD License",
    "Natural Language :: English",
    "Operating System :: MacOS :: MacOS X",
    "Operating System :: Microsoft :: Windows",
    "Operating System :: POSIX :: Linux",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.12",
    "Topic :: Scientific/Engineering :: Information Analysis",
]

[project.urls]
Documentation = "https://forest.beiwe.org"
Homepage = "https://forest.beiwe.org"
Issues = "https://github.com/onnela-lab/forest/issues"
Source = "https://github.com/onnela-lab/forest"

[project.optional-dependencies]
dev = [
    "build",
    "cffconvert",
    "ruff",
    "flake8",
    "flake8-pytest-style",
    "flake8-pyproject",
    "mypy",
    "pandas-stubs",
    "pytest",
    "pytest-mock",
    "pytest-xdist",
    "twine",
    "types-python-dateutil",
    "types-requests",
    "types-setuptools",
]


[tool.setuptools.package-data]
"forest.poplar.raw" = ["noncode/*.csv", "noncode/*.json"]

#
## Type checker config
#

[tool.mypy]
mypy_path = "src"
packages = ["forest"]
python_version = "3.12"


[[tool.mypy.overrides]]
# remember to run mypy --install-types
module = [
    "audioread",
    "audioread.*",
    "openrouteservice",
    "openrouteservice.*",
    "scipy.*",
    "soundfile",
    "ssqueezepy",
]
ignore_missing_imports = true

#
## Pytest config
#

[tool.pytest.ini_options]
# addopts = "--import-mode=importlib"  # this does not seem to be necessary anymore

testpaths = ["tests"]

#
## Linting and type checking tools
#

## Ruff
[tool.ruff]
line-length = 100  # target a 100 character line length
indent-width = 4


[tool.ruff.lint.pycodestyle]
max-line-length = 105  # only go above 100 when it makes the code clearer.


[tool.ruff.format]
indent-style = "space"  # use spaces for indentation
line-ending = "lf"      # use \n for line endings
skip-magic-trailing-comma = true  # even with this set to true the , is added to imports


[tool.ruff.lint]
future-annotations = true

select = [  # (linting directives to enable)
    "E",       # pycodestyle errors
    "W",       # pycodestyle warnings
    "F",       # pyflakes codes
    "UP",      # pyupgrade codes
    "COM818",  # trailing-comma-on-bare-tuple
    "A",       # flake8-annotations codes
    "SIM",     # code simplification rules - noqa with a reason if you ignore
    "TID",     # "tidy import" checks
    "ARG",     # argument-related checks, unused args, (at least hide them with an _underscore)
    # "I",       # import checks and sorting - cannot get this to match isort
    # "DTZ",     # Timezone checks - can't enable due to datetime handling
]

extend-ignore = [  # (linting directives to ignore)
    "W293",  # blank line contains whitespace
]

exclude = [
    "build",
    ".venv",
    "venv",
    "*.ipynb",
    "private",
]


## Flake8 - not actually used, but IDEs using it need it configured.
[tool.flake8]
line-length = 100
max-line-length = 100

extend-ignore = [
    "W293",  # blank line contains whitespace
]

exclude = [
    "build",
    ".venv",
    "venv",
]


## isort - import formatter - (would use ruff, cannot get identical formatting out of it)
[tool.isort]
combine_as_imports = true
float_to_top = true
honor_noqa = true
line_length = 100
lines_after_imports = 2
multi_line_output = 10  # "HANGING_INDENT_WITH_PARENTHESES"
py_version = 312
remove_redundant_aliases = true
star_first = true
use_parentheses = true

known_third_party = []  # Force these libraries to a special spot in import order (second to bottom)

known_local_folder = []

known_first_party = []  # Force these libraries to a special spot in import order (bottom)