setup.py

# -*- coding: utf-8 -*-
from setuptools import setup

# Unsure why, but if not updated, the old version seems lost and cause errors on Colab
import yeastcells.setup
yeastcells.setup.pip_install('-U', 'pyyaml>=5.1')

setup(
      name='yeastcells',
      version=__import__('yeastcells').__version__,

      description='Computer vision based yeast cell synthetic data creation and network training, and detection and tracking pipeline.',
      long_description='Yeast cell detection using a deep convolutional network trained on synthetic data to detect, segment, and track cells. Current state allows segmentation of cells, clustering over time to determine which are the same cell, finding cell boudnaries, plotting segmented and tracked cells in figures and animations, and outputting masks and their area, position, and pixel intensity.',
      
      url='https://github.com/ymzayek/yeastcells-detection-maskrcnn/',

      author='Herbert Kruitbosch, Yasmin Mzayek',
      author_email='H.T.Kruitbosch@rug.nl, y.mzayek@rug.nl',
      classifiers=[
        'Development Status :: 4 - Beta',
        'Programming Language :: Python :: 3',
        'Programming Language :: Python :: 3.7',
      ],
      keywords='yeast cell detection, microscopy images, tif, tiff, mask R-CNN, deep learning, image segmentation, tracking, computer vision, DBSCAN',
      
      packages=['yeastcells'],
      install_requires=[
#         "pyyaml>=5.4.1",
        "download",
        'scikit-image>=0.17.2',
        'scikit-learn>=1.2.2', # some threadpoolctl issues at 0.24
        'opencv-python>=4.4.0.46',
        'opencv-contrib-python>=4.4.0.46',
        'numpy>=1.19.1',
        'scipy>=1.5.2',
        'Shapely>=1.7.0',
        'tqdm>=4.51.0',
        'imgaug>=0.4.0',
        'pandas>=1.1.4',
        "torch",
        "torchvision",
      ],
      zip_safe=True,
)


try:
   import yeastcells.setup
   yeastcells.setup.setup_colab()
except Exception as error:
   import warnings
   warnings.warn(
     "Tried to install detectron2, but it failed. This was only tested on Google Colab. "
     "Ensure proper installation of detectron2 as per these instructions:\n"
     "https://github.com/facebookresearch/detectron2/blob/master/INSTALL.md"
   )
   raise