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setup.py
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setup.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""The setup script."""
from setuptools import find_packages, setup
with open("README.md") as readme_file:
readme = readme_file.read()
test_requirements = [
"codecov",
"black",
"flake8",
"pytest",
"pytest-cov",
"pytest-raises",
]
setup_requirements = ["pytest-runner"]
dev_requirements = [
"bumpversion>=0.5.3",
"coverage>=5.0a4",
"flake8>=3.7.7",
"ipython>=7.5.0",
"m2r>=0.2.1",
"pre-commit>=1.20.0",
"pytest>=4.3.0",
"pytest-cov==2.6.1",
"pytest-raises>=0.10",
"pytest-runner>=4.4",
"Sphinx>=2.0.0b1",
"sphinx_rtd_theme>=0.1.2",
"tox>=3.5.2",
"twine>=1.13.0",
"wheel>=0.33.1",
]
interactive_requirements = [
"altair",
"altair-data-server",
"jupyterlab",
"matplotlib>=3.1.2",
]
requirements = [
"aicsimageio>=3.0.2",
"anndata>=0.6.22",
"fire>=0.2.1",
"imageio>=2.6.1",
"numpy>=1.17.2",
"quilt3distribute>=0.1.2",
"pandas>=0.25.1",
"pingouin>=0.3.0",
"python-dateutil==2.8.0",
"scikit-image>=0.16.1",
"scikit-learn>=0.21.3",
"tqdm>=4.36.1",
]
extra_requirements = {
"test": test_requirements,
"setup": setup_requirements,
"dev": dev_requirements,
"interactive": interactive_requirements,
"all": [
*requirements,
*test_requirements,
*setup_requirements,
*dev_requirements,
*interactive_requirements,
],
}
setup(
author="Rory Donovan-Maiye",
author_email="rorydm@alleninstitute.org",
classifiers=[
"Development Status :: 2 - Pre-Alpha",
"Intended Audience :: Developers",
"License :: Allen Institute Software License",
"Natural Language :: English",
"Programming Language :: Python :: 3.6",
"Programming Language :: Python :: 3.7",
],
description="data ingestion, processing, and analysis for cardio/FISH project",
entry_points={
"console_scripts": [
"download_2D_segs=fish_morphology_code.bin.download_quilt_data:main_segs",
"download_2D_contrasted=fish_morphology_code.bin.download_quilt_data:main_contrasted",
"download_2D_features=fish_morphology_code.bin.download_quilt_data:main_features",
"download_2D_nonstructure_features=fish_morphology_code.bin.download_quilt_data:main_nonstructure_features",
"download_ML_struct_scores=fish_morphology_code.bin.download_quilt_data:main_MLstruct",
"download_scrnaseq=fish_morphology_code.bin.download_quilt_data:main_scrnaseq",
"download_scrnaseq_raw=fish_morphology_code.bin.download_quilt_data:main_scrnaseq_raw",
"download_nonstructure_2D_segs=fish_morphology_code.bin.download_quilt_data:main_nonstructure_segs",
"contrast_and_segment=fish_morphology_code.bin.stretch:main",
"make_cellprofiler_image_set=fish_morphology_code.bin.make_cellprofiler_image_set:main_make_imageset",
"add_fovid_to_structure=fish_morphology_code.bin.add_fovid_to_structure:main",
"find_border_cells=fish_morphology_code.bin.find_border_cells:main_flag_border_cells",
"merge_cellprofiler_output_nonstructure=fish_morphology_code.bin.merge_cellprofiler_output_nonstructure:main",
"merge_cellprofiler_output_structure=fish_morphology_code.bin.merge_cellprofiler_output_structure:main",
"correct_napari_segs=fish_morphology_code.bin.correct_napari_segs:main_napari_correct",
]
},
install_requires=requirements,
license="Allen Institute Software License",
long_description=readme,
long_description_content_type="text/markdown",
include_package_data=True,
keywords="fish_morphology_code",
name="fish_morphology_code",
packages=find_packages(),
python_requires=">=3.6",
setup_requires=setup_requirements,
test_suite="fish_morphology_code/tests",
tests_require=test_requirements,
extras_require=extra_requirements,
url="https://github.com/AllenCellModeling/fish_morphology_code",
# Do not edit this string manually, always use bumpversion
# Details in CONTRIBUTING.rst
version="0.1.0",
zip_safe=False,
)