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pyproject.toml
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pyproject.toml
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[tool.poetry]
name = "astrocast"
version = "0.4.2"
description = "Package to analyze calcium fluorescence events in astrocytes"
authors = ["Jan Philipp Reising <jan.reising@ki.se>", "Ana Cristina González"]
[tool.poetry.dependencies]
python = ">=3.9,<3.11"
h5py = "^3.9.0"
hdbscan = "^0.8.33"
matplotlib = "^3.8.0"
multiprocess = "^0.70.15"
networkx = "^3.1"
pandas = "^2.1.0"
powerlaw = "^1.5"
pynwb = "^2.5.0"
deprecated = "^1.2.14"
deprecation = "^2.1.0"
peakutils = "^1.3.4"
holoviews = "^1.17.1"
pointpats = "^2.3.0"
psutil = "^5.9.5"
scipy = "^1.11"
seaborn = "^0.12.2"
humanize = "^4.8.0"
pyyaml = "^6.0.1"
prettytable = "^3.9.0"
colorama = "^0.4.6"
shiny = "^0.5.1"
pyinform = "^0.2.0"
opencv-python = "^4.8.0.76"
scikit-image = "^0.21.0"
scikit-learn = "^1.3.0"
tqdm = "^4.66.1"
tiledb = "^0.23.0"
tifffile = "^2023.8.30"
xxhash = "^3.3.0"
numpy = "*"
xarray = "^2023.8.0"
colorcet = "^3.0.1"
dask = "^2023.9.2"
czifile = "^2019.7.2"
awkward = "^2.4.2"
dask-image = "^2023.8.1"
fastcluster = "^1.2.6"
torch = "2.0.0"
jnormcorre = "^0.0.7"
dtaidistance = "^2.3.10"
tsfresh = "^0.20.1"
tslearn = "^0.6.2"
umap-learn = [
{ version = "*", platform = 'windows' },
{ version = "*", platform = 'linux' }
]
keras = "*"
datashader = "^0.15.2"
llvmlite = "~0.39"
gdown = "^4.7.1"
climage = "^0.2.0"
simple-slurm = "^0.2.6"
pydantic = { version = "^1", optional = true }
jupyterlab = "^4.0.8"
ipywidgets = "^8.1.1"
napari = { version = "^0.4.14", extras = ["all"], optional = true }
napari-plot = { version = "^0.1.5", optional = true }
napari-time-series-plotter = { version = "*", optional = true }
pytest-cov = { version = "^4.1.0", optional = true }
pytest-xdist = { version = "^3.3.1", optional = true }
pytest-rerunfailures = { version = "*", optional = true }
pytest = { extras = ["testing"], version = "^7.4.3", optional = true }
sphinx = { version = "^7.2.6", optional = true }
sphinx-rtd-theme = { version = "^1.3.0", optional = true }
sphinx-autodoc-typehints = { version = "^1.25.2", optional = true }
tensorflow = "*"
tensorflow-io-gcs-filesystem = { version = "0.31.0", platform = "windows" }
pyqt5-qt5 = { version = "5.15.2", optional = true }
build = "0.10.0"
[tool.poetry.scripts]
astrocast = 'astrocast.cli_interfaces:cli'
[tool.poetry.extras]
video_player = ["napari", "pyqt5-qt5", "napari-plot", "napari-time-series-plotter", "pydantic"]
testing = ["pytest", "pytest-cov", "pytest-xdist", "pytest-rerunfailures"]
doc = ["sphinx", "sphinx-rtd-theme", "sphinx-autodoc-typehints"]
all = ["pytest-rerunfailures", "pyqt5-qt5", "napari", "napari-plot", "napari-time-series-plotter", "pydantic", "pytest", "pytest-cov", "pytest-xdist", "sphinx", "sphinx-rtd-theme", "sphinx-autodoc-typehints"]
[tool.pytest.ini_options]
markers = [
"tensorflow: marks tests as using tensorflow (deselect with '-m \"not tensorflow\"')",
"vis: marks tests as visualization tests (deselect with '-m \"not vis\"')",
]
[build-system]
requires = ["poetry-core"]
build-backend = "poetry.core.masonry.api"