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pyproject.toml
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pyproject.toml
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[tool.poetry]
name = "looptrace"
version = "0.11.0"
description = "Library and programs for tracing chromatin loops from microscopy images"
authors = [
"Kai Sandvold Beckwith",
"Vince Reuter <[email protected]>",
]
readme = "README.md"
include = ["looptrace/looptrace-assembly*.jar"]
license = "MIT"
repository = "https://github.com/gerlichlab/looptrace"
classifiers = [
"Development Status :: 1 - Planning",
"Programming Language :: Python",
"Programming Language :: Python :: 3.11",
"Typing :: Typed",
]
[tool.poetry.dependencies]
# These are the main runtime dependencies.
python = ">= 3.11, < 3.12"
cellpose = { version = "v2.2.2", optional = true }
dask = "^2023.5.1"
expression = "^5.0.2"
flowdec = { version = "^1.1.0", optional = true }
gertils = { git = "https://github.com/gerlichlab/gertils.git", tag = "v0.5.1" }
hypothesis = { version = "^6.92.1", extras = ["numpy"], optional = true }
joblib = "^1.3.1"
looptrace-loci-vis = { git = "https://github.com/gerlichlab/looptrace-loci-vis", tag = "v0.2.2", optional = true }
looptrace-regionals-vis = { git = "https://github.com/gerlichlab/looptrace-regionals-vis", tag = "v0.3.2", optional = true }
matplotlib = { version = "^3.7.0", optional = true }
more-itertools = { version = "^10.2.0", optional = true }
#napari = { version = "^0.4.19", extras = ["all", "pyqt"], optional = true } # most computers
napari = { version = "^0.4.19", optional = true } # newer Macs (M1, M2)
nd2 = "^0.5.3"
nuclei-vis-napari = { git = "https://github.com/gerlichlab/nuclei-vis-napari", tag = "v0.1.4", optional = true }
numba = { version = "^0.57.0", optional = true }
numcodecs = "^0.11.0"
numpy = ">= 1.24.2, < 1.25"
numpydoc_decorator = "^2.2.1"
pandas = "^1.5.3"
piper = { version = "^0.14.2", optional = true }
pyqt6 = { version = "^6.5.0", optional = true }
pytest = { version = "^7.3.1", optional = true }
pytest-skip-slow = { version = "^0.0.5", optional = true }
pyyaml = "^6.0"
scipy = "^1.10.1"
scikit-image = "^0.20.0"
seaborn = { version = "^0.12.0", optional = true }
spotfishing = { git = "https://github.com/gerlichlab/spotfishing", tag = "v0.3.0" }
tensorflow = { version = "^2.16.1", optional = true }
tqdm = "^4.65.0"
zarr = "2.17.2"
[tool.poetry.extras]
analysis = ["matplotlib", "numba", "seaborn"]
deconvolution = ["flowdec", "tensorflow"]
dev = ["looptrace-loci-vis", "looptrace-regionals-vis", "matplotlib", "nuclei-vis-napari", "numba", "seaborn"]
interactive-visualisation = ["looptrace-loci-vis", "looptrace-regionals-vis", "napari", "nuclei-vis-napari"]
new-mac-napari = ["pyqt6"] # needed for visual support on newer Macs (M1, M2)
nuclei = ["cellpose"]
pipeline = ["cellpose", "piper"]
polymer = ["numba"]
test = ["hypothesis", "more-itertools", "pytest", "pytest-skip-slow"]
[build-system]
requires = ["poetry-core"]
build-backend = "poetry.core.masonry.api"