nuc-morph-analysis/pyproject.toml at dev · AllenCell/nuc-morph-analysis · GitHub

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[project]
authors = [
    {name = "Allen Institute for Cell Science", email = "julie.dixon@alleninstitute.org"},
]
classifiers=[
    "Natural Language :: English",
    "Programming Language :: Python :: 3.9",
]
description="Analysis of nuclear growth and shape from colony timelapses"
license = {file = "LICENSE"}
name="nuc_morph_analysis"
readme = "README.md"
requires-python = ">=3.9,<3.12"
urls = {Repository = "https://https://github.com/AllenCell/nuc-morph-analysis"}
version = "1.0.0"
dependencies = [
    "jupyter",
    "ipykernel",
    "ipywidgets",
    "numpy",
    "pandas",
    "tqdm",
    "matplotlib",
    "scikit-image",
    "scikit-learn",
    "seaborn",
    "scipy>=1.10",
    "imageio",
    "bigtree",
    "argparse",
    "aicsimageio>=4.14.0",
    "ipython>=8.18.1",
    "av>=10.0.0",
    "shapely>=2.0.2",
    "fire>=0.5.0",
    "pyarrow>=15.0.0",
    "termcolor>=2.4.0",
    "cvapipe-analysis>=0.2.0",
    "vtk-osmesa>=9.3.0",
    "colorizer-data @ git+https://github.com/allen-cell-animated/colorizer-data.git@v1.4.2",
    "bioio-ome-zarr>=1.0.1",
    "bioio>=1.0.2",
    "bioio-base>=1.0.1",
    "colour-science>=0.4.4",
    "opencv-python-headless>=4.10.0.82",
    "yarl>=1.9.4",
]

[project.optional-dependencies]
internal = [
    "aicsfiles>=5.1.0",
]
[build-system]
requires = ["pdm-backend"]
build-backend = "pdm.backend"

[tool.mypy]
packages = "nuc_morph_analysis"
# Make mypy less strict: ignore these classes of errors
disable_error_code = ["call-overload", "var-annotated"]

[[tool.mypy.overrides]]
# The following dependencies are untyped. mypy should ignore them
module = [
    "aicsfiles",
    "aicsimageio",
    "aicsshparam",
    "colorizer_data.utils",
    "colorizer_data.writer",
    "cvapipe_analysis",
    "cvapipe_analysis.steps.shapemode.shapemode_tools",
    "cvapipe_analysis.tools",
    "fire",
    "matplotlib",
    "matplotlib.collections",
    "matplotlib.colors",
    "matplotlib.cm",
    "matplotlib.patches",
    "matplotlib.pyplot",
    "matplotlib.font_manager",
    "matplotlib.lines",
    "matplotlib.markers",
    "matplotlib.ticker",
    "matplotlib.gridspec",
    "matplotlib.transforms",
    "mpl_toolkits.axes_grid1",
    "mpl_toolkits.axes_grid1.anchored_artists",
    "mpl_toolkits.axes_grid1.axes_divider",
    "mpl_toolkits.mplot3d",
    "seaborn",
    "scipy",
    "scipy.cluster",
    "scipy.ndimage",
    "scipy.optimize",
    "scipy.signal",
    "scipy.spatial",
    "scipy.stats",
    "shapely",
    "skimage",
    "skimage.exposure",
    "skimage.morphology",
    "skimage.registration",
    "skimage.segmentation",
    "skimage.measure",
    "sklearn",
    "sklearn.decomposition",
    "sklearn.linear_model",
    "sklearn.exposure",
    "sklearn.linear_model",
    "sklearn.model_selection",
    "sklearn.pipeline",
    "sklearn.preprocessing",
    "sklearn.transform",
    "vtk",
    "vtk.util",
    "yarl.URL",
]
ignore_missing_imports = true

[[tool.pdm.source]]
name = "prebuilt-vtk"
url = "https://wheels.vtk.org"

[tool.pdm.scripts]
requirements = "pdm export -f requirements --without-hashes -o"

[tool.pdm.dev-dependencies]
dev = [
    "pytest>=7.4.2",
    "mypy>=1.8.0",
    "pandas-stubs>=2.0.1.230501",
    "lxml-stubs>=0.5.1",
    "types-Pillow>=10.2.0.20240213",
    "types-PyYAML>=6.0.12.12",
    "types-Pygments>=2.17.0.20240106",
    "types-Send2Trash>=1.8.2.7",
    "types-colorama>=0.4.15.20240205",
    "types-decorator>=5.1.8.20240106",
    "types-jsonschema>=4.21.0.20240118",
    "types-openpyxl>=3.1.0.20240301",
    "types-psutil>=5.9.5.20240205",
    "types-pycurl>=7.45.2.20240106",
    "types-six>=1.16.21.20240301",
    "types-tqdm>=4.66.0.20240106",
    "opencv-stubs>=0.0.8",
    "types-termcolor>=1.1.6.2",
]