pyproject.toml

# https://peps.python.org/pep-0517/
[build-system]
requires = ["hatchling", "hatch-vcs"]
build-backend = "hatchling.build"

# https://hatch.pypa.io/latest/config/metadata/
[tool.hatch.version]
source = "vcs"

# [tool.hatch.metadata]
# allow-direct-references = true

# https://peps.python.org/pep-0621/
[project]
name = "cali"
description = "A GUI to visualize, segment and analyze calcium imaging data."
readme = "README.md"
requires-python = ">=3.11"
license = { text = "BSD 3-Clause License" }
authors = [
    { email = "federico.gasparoli@gmail.com", name = "Federico Gasparoli" },
]
classifiers = [
    "Development Status :: 3 - Alpha",
    "License :: OSI Approved :: BSD License",
    "Natural Language :: English",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Typing :: Typed",
]
dynamic = ["version"]
dependencies = [
    "oasis-deconv==0.2.0", # Build from source to avoid broken prebuilt wheels
    "numba",
    "pymmcore-widgets >=0.8.0",
    "pymmcore-plus >=0.16.0",
    "qtpy",
    "vispy",
    "zarr==2.*",
    "tifffile",
    "tqdm",
    "pyyaml",
    "cmap",
    "pyconify",
    "rich",
    "ndv[vispy]==0.0.4",
    "scikit-image",
    "scipy<1.17",  # oasis incompatible with scipy>=1.17 (toeplitz batch change)
    "scikit-learn",
    "PyQt6",
    "pyqtgraph",
    "tensorstore >=0.1.67,!=0.1.72",
    "pydantic<2.11.0",
    "pandas",
    "superqt[iconify]",
    "sqlmodel>=0.0.27",
]

[project.optional-dependencies]
# Cellpose is optional - choose the version that fits your Python version
cp3 = ["cellpose>=3.0.0,<4.0.0"]
cp4 = ["cellpose>=4.0.0"]

[tool.uv]
conflicts = [
    [
      { extra = "cp3" },
      { extra = "cp4" },
    ],
]

[dependency-groups]
test = ["pytest>=6.0", "pytest-cov", "pytest-qt"]
dev = [
    "black",
    "ipython",
    "mypy",
    "pre-commit",
    "pytest-cov",
    "pytest",
    "rich",
    "ruff",
    "pytest-xdist>=3.8.0",
]

[project.urls]
homepage = "https://github.com/fdrgsp/cali"
repository = "https://github.com/fdrgsp/cali"

[project.scripts]
cali = "cali.__main__:main"

[tool.uv.sources]
cali = { workspace = true }

[tool.hatch.build.targets.wheel]
only-include = ["src"]
sources = ["src"]

# https://docs.astral.sh/ruff/configuration/
[tool.ruff]
line-length = 88
target-version = "py39"
src = ["src", "tests"]
fix = true
unsafe-fixes = true
exclude = ["_dev/**"]


# https://docs.astral.sh/ruff/rules
[tool.ruff.lint]
pydocstyle = { convention = "numpy" }
select = [
    "E",    # style errors
    "W",    # style warnings
    "F",    # flakes
    "D",    # pydocstyle
    "D417", # Missing argument descriptions in Docstrings
    "I",    # isort
    "UP",   # pyupgrade
    "C4",   # flake8-comprehensions
    "B",    # flake8-bugbear
    "A001", # flake8-builtins
    "ANN",  # flake8-annotations
    "RUF",  # ruff-specific rules
    "TC",   # flake8-type-checking
    "TID",  # flake8-tidy-imports
]
ignore = [
    "ANN401", # allow the use of Any type
    "D401",   # First line should be in imperative mood (remove to opt in)
]

[tool.ruff.lint.per-file-ignores]
"tests/*.py" = ["D", "S"]

[tool.ruff.format]
docstring-code-format = true

# https://docs.pytest.org/en/6.2.x/customize.html
[tool.pytest.ini_options]
minversion = "6.0"
testpaths = ["tests"]
filterwarnings = [
    "error",
    "ignore:Failing to pass a value:DeprecationWarning",
    "ignore:Could not find cvxpy.*:UserWarning",
    "ignore:nperseg.*is greater than signal length:UserWarning",
    "ignore::FutureWarning",
    "ignore:Conversion of an array with ndim > 0 to a scalar:DeprecationWarning",
    "ignore:'count' is passed as positional argument:DeprecationWarning:vispy",
    "ignore:Sparse invariant checks are implicitly disabled.*:UserWarning",
]

# https://mypy.readthedocs.io/en/stable/config_file.html
[tool.mypy]
files = "src/**/"
strict = true
disallow_any_generics = false
disallow_subclassing_any = false
show_error_codes = true
pretty = true
plugins = ["pydantic.mypy"]
exclude = ".*\\.ipynb$"

# Ignore missing imports for large packages not available in pre-commit
[[tool.mypy.overrides]]
module = [
    "pymmcore_plus.*",
    "pymmcore_widgets.*",
]
ignore_missing_imports = true

# https://coverage.readthedocs.io/en/6.4/config.html
[tool.coverage.report]
exclude_lines = [
    "pragma: no cover",
    "if TYPE_CHECKING:",
    "@overload",
    "except ImportError",
    "raise AssertionError",
    "if __name__ == .__main__.:",
    "raise NotImplementedError",
    "\\.\\.\\.",
]
omit = ["*/_model_graph.py"]
show_missing = true

[tool.coverage.run]
source = ["cali"]

# https://github.com/mgedmin/check-manifest#configuration
[tool.check-manifest]
ignore = [
    ".pre-commit-config.yaml",
    ".ruff_cache/**/*",
    "tests/**/*",
    "_dev/**/*",
]

[tool.typos.files]
extend-exclude = ["*.ipynb"]

[tool.typos.default] 
extend-ignore-identifiers-re = ["(?i)nd2?.*", "(?i)ome", "(?i)fovs?", "sems", "selectin", "pn", "id"]