pyproject.toml

[build-system]
build-backend = "poetry_dynamic_versioning.backend"
requires = [ "poetry-core>=1.7", "poetry-dynamic-versioning>=1.1" ]

[tool.poetry]
name = "pycytominer"
# This version is a placeholder updated during build by poetry-dynamic-versioning
version = "0.0.0"
description = "Python package for processing image-based profiling data"
authors = [
  "Erik Serrano",
  "Niranj Chandrasekaran",
  "Dave Bunten",
  "Kenneth I. Brewer",
  "Jenna Tomkinson",
  "Roshan Kern",
  "Michael Bornholdt",
  "Stephen Fleming",
  "Ruifan Pei",
  "John Arevalo",
  "Hillary Tsang",
  "Vincent Rubinetti",
  "Erin Weisbart",
  "Charlotte Bunne",
  "Alexandr A. Kalinin",
  "Rebecca Senft",
  "Stephen J. Taylor",
  "Nasim Jamali",
  "Adeniyi Adeboye",
  "Allen Goodman",
  "Juan Caicedo",
  "Anne E. Carpenter",
  "Beth A. Cimini",
  "Shantanu Singh",
  "Gregory P. Way",
]
maintainers = [
  "Gregory P. Way <gregory.way@cuanschutz.edu>",
  "Dave Bunten <dave.bunten@cuanschutz.edu>",
  "Kenneth I. Brewer <ken@kenbrewer.com>",
]
license = "BSD-3-Clause"
readme = "README.md"
homepage = "https://pycytominer.readthedocs.io/"
repository = "https://github.com/cytomining/pycytominer"
include = [ { path = "poetry.lock", format = "sdist" } ]

[tool.poetry.dependencies]
python = ">=3.9,<3.13"
numpy = ">=1.16.5"
scipy = ">=1.5"
pandas = ">=1.2.0"
scikit-learn = ">=0.21.2"
sqlalchemy = ">=1.3.6,<3"
pyarrow = ">=8.0.0"

# Extra dependencies for cell_locations 
fsspec = { version = ">=2023.1.0", optional = true }
s3fs = { version = ">=2023.4.0", optional = true }
boto3 = { version = ">=1.26.79", optional = true }
fire = { version = ">=0.5.0", optional = true }

# Extra dependencies for collate
cytominer-database = { version = "0.3.4", optional = true }

[tool.poetry.extras]
cell-locations = [ "fsspec", "s3fs", "boto3", "fire" ]
collate = [ "cytominer-database" ]

[tool.poetry.group.dev]
optional = true

[tool.poetry.group.dev.dependencies]
pytest = ">=5.0.1"
codecov = ">=2.1.12"
pytest-cov = "^4.1.0"
pre-commit = ">=3.3.2"
commitizen = "^3.12.0"
ruff = ">=0.3.4,<0.8.0"
mypy = "^1.11.2"
types-openpyxl = "^3.1.5.20240918"
pandas-stubs = [
  { version = "<2.2.2.240909", python = "<3.10" },
  { version = "^2.2.2.240909", python = ">=3.10" },
]
types-sqlalchemy = "^1.4.53.38"

[tool.poetry.group.docs]
optional = true

[tool.poetry.group.docs.dependencies]
mkdocs = "*"
sphinx = ">=7.1,<7.5"
sphinx-autobuild = ">=2021.3.14,<2025.0.0"
sphinx-autoapi = "^3.0.0"
ipython = "^8.12"
groundwork-sphinx-theme = "^1.1.1"
sphinx-copybutton = "^0.5.2"
nbsphinx = "^0.9.3"
m2r2 = "^0.3.3.post2"
furo = "^2023.9.10"
mock = "^5.1.0"
autodoc = "^0.5.0"
dunamai = "^1.19.0"

[tool.poetry-dynamic-versioning]
enable = true
style = "pep440"
vcs = "git"

[tool.poetry-dynamic-versioning.substitution]
files = [ "pycytominer/__about__.py" ]

[tool.setuptools_scm]
# Avoids warnings about missing section
# see: https://setuptools-scm.readthedocs.io/en/latest/usage/
root = "."

[tool.ruff]
target-version = "py39"
line-length = 88
fix = true

format.preview = true
lint.select = [
  # flake8-builtins
  "A",
  # flake8-comprehensions
  "C4",
  # pycodestyle
  "E",
  # pyflakes
  "F",
  # isort
  "I",
  # pygrep-hooks
  "PGH",
  # ruff
  "RUF",
  # flake8-bandit
  "S",
  # flake8-simplify
  "SIM",
  # flake8-debugger
  "T10",
  # pyupgrade
  "UP",
  "W",
  # flake8-2020
  "YTT",
  # The following checks are disabled, but we are working towards enabling them in the future.
  # flake8-bugbear
  # "B",
  # mccabe
  # "C90",
  # tryceratops
  # "TRY",
]
lint.ignore = [
  # LineTooLong
  "E501",
  # DoNotAssignLambda
  "E731",
]
# Ignore `E402` and `F401` (unusued imports) in all `__init__.py` files
lint.per-file-ignores."__init__.py" = [ "E402", "F401" ]
lint.per-file-ignores."pycytominer/cyto_utils/*" = [
  # I (isort) is ignored due to circular dependencies in the cyto_utils module
  "I",
  # S608 (raw sql operations) is ignored because it is a common pattern in the cyto_utils module
  "S608",
]
# Ignore assert statements in tests
lint.per-file-ignores."tests/*" = [ "S101" ]

[tool.pytest.ini_options]
testpaths = "tests"
filterwarnings = [
  "ignore::DeprecationWarning:pycytominer.*",
]

[tool.mypy]
exclude = [
  # ignore notebook-based walkthroughs
  "walkthroughs",
  # ignore tests dir
  "tests",
]

[[tool.mypy.overrides]]
# ignore missing import errors for the following
# packages which do not have standard type stubs
# or experience issues with imported types.
module = [
  "sklearn.*",
  "scipy.*",
  "cytominer_database.*",
  "fire.*",
  "boto3.*",
  "botocore.*",
]
ignore_missing_imports = true

[tool.commitizen]
# This version is used for changelog tracking and is updated using `cz bump`
version = "1.2.1"
name = "cz_conventional_commits"
tag_format = "v$version"
version_scheme = "pep440"
version_provider = "commitizen"
update_changelog_on_bump = true
template = "dev_tools/commitizen/CHANGELOG.md.j2"
version_files = [
  "CITATION.cff",
]