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pyproject.toml
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pyproject.toml
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[build-system]
requires = ["pdm-pep517>=1.0.0", "numpy>=1.23.5"]
build-backend = "pdm.pep517.api"
[project]
name = "cyto-dl"
version = "0.4.2"
description = """\
Collection of representation learning models, techniques, callbacks, utils, \
used to create latent variable models of cell shape, morphology and \
intracellular organization.\
"""
readme = "README.md"
authors = [
{ name = "Benji Morris", email = "[email protected]" },
{ name = "Guilherme Pires", email = "[email protected]" },
{ name = "Ritvik Vasan", email = "[email protected]" },
]
dependencies = [
"hydra-core~=1.3.0",
"hydra-colorlog>=1.2",
"hydra-optuna-sweeper>=1.2",
"torch~=2.0.0",
"numpy>=1.23",
"matplotlib>=3.7",
"pandas>=1.5",
"fire>=0.5",
"mlflow>=2.1",
"omegaconf>=2.3",
"pyarrow>=10.0",
"pyrootutils>=1.0",
"PyYAML>=6.0",
"scikit-learn>=1.2",
"universal-pathlib>=0.0",
"ome-zarr>=0.6",
"anndata>=0.8",
"monai>=1.2",
"timm>=0.9.7",
"tqdm>=4.64",
"lightning>=2.0",
"einops>=0.6.1",
"edt>=2.3.1",
"astropy>=5.2",
"rich",
"boto3",
"bioio>=1.0.1",
"bioio-czi",
"bioio-ome-tiff",
"bioio-tifffile",
"tifffile>=2024.0.0",
"online-stats>=2023",
"positional-encodings>=6.0.3",
]
requires-python = ">=3.9,<3.11"
[project.optional-dependencies]
equiv = [
"lie_learn==0.0.1.post1",
"escnn~=1.0.7",
"py3nj==0.1.2",
"e3nn~=0.5.1"
]
spharm = [
"vtk~=9.2",
"aicscytoparam~=0.1",
"pyshtools==4.10.3",
]
s3 = [
"boto3>=1.23.5,<1.24.5",
"s3fs~=2023.1"
]
torchserve = [
"torchserve>=0.8.0",
"gorilla>=0.4.0",
]
pcloud = [
"pyntcloud>=0.3.1",
"aicsshparam>=0.1.7",
"torch-geometric>=2.3.1",
"point-cloud-utils>=0.29.6",
"geomloss>=0.2.6",
"Ninja>=1.11.1",
"torchio>=0.19.1",
]
all = [
"cyto-dl[equiv,spharm,s3,torchserve,pcloud]",
]
test = [
"cyto-dl",
"pytest~=7.2",
"pytest-cov[toml]~=4.0",
]
docs = [
"cyto-dl",
"furo<=2023.3.23",
"m2r2<=0.3.3.post2",
"sphinx<=6.1.3",
]
[project.urls]
Homepage = "https://github.com/AllenCellModeling/cyto-dl"
[tool.pdm.build]
includes = ["cyto_dl", "README.md", "LICENSE", "**/*.yaml" ]
excludes = ["**/*.pyc", "**/__pycache__"]
[tool.flake8]
ignore = [
"E203",
"E402",
"W291",
"W503",
]
max-line-length = 88
[tool.pytest.ini_options]
addopts = [
"--color=yes",
"--durations=0",
"--strict-markers",
"--doctest-modules",
]
filterwarnings = [
"ignore::DeprecationWarning",
"ignore::UserWarning",
]
log_cli = "True"
markers = [
"slow: slow tests",
]
minversion = "6.0"
testpaths = "tests/"
[tool.coverage.report]
exclude_lines = [
"pragma: nocover",
"raise NotImplementedError",
"raise NotImplementedError()",
"if __name__ == .__main__.:",
]
# https://pypi.org/project/bumpver
[tool.bumpver]
current_version = "0.4.2"
version_pattern = "MAJOR.MINOR.PATCH[.PYTAGNUM]"
commit_message = "Bump version {old_version} -> {new_version}"
commit = true
tag = false # no longer useful to tag here, must happen in create_publish_pr.yaml
push = false
[tool.bumpver.file_patterns]
"pyproject.toml" = ['current_version = "{version}"', 'version = "{version}"']
"version.toml" = ['version = "{version}"']
"cyto_dl/__init__.py" = ['__version__ = "{version}"']