from setuptools import setup

from setuptools.command.install import install

import subprocess

import os

PACKAGES=[  'pandas==0.25.0',

            'numpy',

            'dask[dataframe]',

            'distributed',

            'nonechucks',

            'dask-image',

            'opencv-python',

            'scikit-learn',

            'scipy',

            'umap-learn',

            'pysnooper',

            'tifffile',

            'seaborn',

            'scikit-image',

            'openslide-python',

            'Shapely',

            'click==6.7',

            'torch',

            'torchvision',

            'albumentations',

            'GPUtil',

            'beautifulsoup4',

            'plotly',

            'xarray',

            'matplotlib',

            'networkx',

            'shap',

            'pyyaml',

            'torch-encoding',

            'xmltodict',

            #'lightnet',

            'brambox',

            'blosc',

            'numcodecs',

            'zarr',

            'pytorchcv',

            'h5py',

            'timm'

            ]

with open('README.md','r', encoding='utf-8') as f:

      long_description = f.read()

class CustomInstallCommand(install):

    """Custom install setup to help run shell commands (outside shell) before installation"""

    def run(self):

        #for package in PACKAGES:

        #os.system('pip install {}'.format(package))#install.do_egg_install(self)

        self.do_egg_install()#install.run(self)

        subprocess.call('rm -rf apex'.split())

        os.system('git clone https://github.com/NVIDIA/apex')

        #try:

        #os.system('cd apex && pip install -v --no-cache-dir --global-option="--cpp_ext" --global-option="--cuda_ext" ./')

        #except:

        os.system('echo pwd && cd apex && (pip install -v --no-cache-dir --global-option="--cpp_ext" --global-option="--cuda_ext" ./ || pip install -v --no-cache-dir ./)')

        subprocess.call('rm -rf apex'.split())

setup(name='pathflowai',

      version='0.1.1',

      description='A modular approach for preprocessing and deep learning on histopathology images.',

      url='https://github.com/jlevy44/PathFlowAI',

      author='Joshua Levy',

      author_email='joshualevy44@berkeley.edu',

      license='MIT',

      scripts=['bin/install_apex',

               'bin/install_lightnet'],

      #cmdclass={'install': CustomInstallCommand},

      entry_points={

            'console_scripts':['pathflowai-preprocess=pathflowai.cli_preprocessing:preprocessing',

                               'pathflowai-visualize=pathflowai.cli_visualizations:visualize',

                               'pathflowai-monitor=pathflowai.monitor_memory_usage:monitor',

                               'pathflowai-train_model=pathflowai.model_training:train']

      },

      long_description=long_description,

      long_description_content_type='text/markdown',

      packages=['pathflowai'],

      install_requires=PACKAGES)