setup.py

import os
import sys
from glob import glob
import re
import tarfile
import subprocess
import shutil
import zipfile
import tempfile
import re
import time


VERSION = "0.5"
AUTHOR = "BAQLaVa Development Team"
MAINTAINER = "Jordan Jensen"
MAINTAINER_EMAIL = "jordanjensen@g.harvard.edu"


# check for either of the required versions
# required python versions (3.6+)
required_python_version_major = [3]
required_python_version_minor = [10]

pass_check = False
try:
	for major, minor in zip(required_python_version_major, required_python_version_minor):
		if (sys.version_info[0] == major and sys.version_info[1] >= minor):
			pass_check = True
except (AttributeError, IndexError):
	sys.exit("CRITICAL ERROR: The python version found (version 1) " +
	         "does not match the version required (version " +
	         str(required_python_version_major) + "." +
	         str(required_python_version_minor) + "+)")

if not pass_check:
	sys.exit("CRITICAL ERROR: The python version found (version " +
	         str(sys.version_info[0]) + "." + str(sys.version_info[1]) + ") " +
	         "does not match the version required (version " +
	         str(required_python_version_major) + "." +
	         str(required_python_version_minor) + "+)")

if not pass_check:
	sys.exit("CRITICAL ERROR: The python version found (version " +
	         str(sys.version_info[0]) + "." + str(sys.version_info[1]) + ") " +
	         "does not match the version required (version " +
	         str(required_python_version_major) + "." +
	         str(required_python_version_minor) + "+)")


try:
	import setuptools
except ImportError:
	sys.exit("Please install setuptools.")

# check setuptools version
required_setuptools_version_major = 1
try:
	setuptools_version = setuptools.__version__
	setuptools_version_major = int(setuptools_version.split(".")[0])
	if setuptools_version_major < required_setuptools_version_major:
		sys.exit("CRITICAL ERROR: The setuptools version found (version " +
		         setuptools_version + ") does not match the version required " +
		         "(version " + str(required_setuptools_version_major) + "+)." +
					" Please upgrade your setuptools version.")
except (ValueError, IndexError, NameError):
	sys.exit("CRITICAL ERROR: Unable to call setuptools version. Please upgrade setuptools.")

from setuptools.command.install import install as _install

import distutils

# try to import urllib.request.urlretrieve for python3
try:
	from urllib.request import urlretrieve
except ImportError:
	from urllib import urlretrieve

def byte_to_megabyte(byte):
	"""
	Convert byte value to megabyte
	"""

	return byte / (1024.0 ** 2)


class ReportHook():
	def __init__(self):
		self.start_time = time.time()

	def report(self, blocknum, block_size, total_size):
		"""
		Print download progress message
		"""

		if blocknum == 0:
			self.start_time = time.time()
			if total_size > 0:
				print("Downloading file of size: " + "{:.2f}".format(byte_to_megabyte(total_size)) + " MB\n")
		else:
			total_downloaded = blocknum * block_size
			status = "{:3.2f} MB ".format(byte_to_megabyte(total_downloaded))

			if total_size > 0:
				percent_downloaded = total_downloaded * 100.0 / total_size
				# use carriage return plus sys.stdout to overwrite stdout
				try:
					download_rate = total_downloaded / (time.time() - self.start_time)
					estimated_time = (total_size - total_downloaded) / download_rate
				except ZeroDivisionError:
					download_rate = 0
					estimated_time = 0
				estimated_minutes = int(estimated_time / 60.0)
				estimated_seconds = estimated_time - estimated_minutes * 60.0
				status += "{:3.2f}".format(percent_downloaded) + " %  " + \
				          "{:5.2f}".format(byte_to_megabyte(download_rate)) + " MB/sec " + \
				          "{:2.0f}".format(estimated_minutes) + " min " + \
				          "{:2.0f}".format(estimated_seconds) + " sec "
			status += "        \r"
			sys.stdout.write(status)


def download(url, download_file):
	"""
	Download a file from a url
	"""

	try:
		print("Downloading " + url)
		file, headers = urlretrieve(url, download_file, reporthook=ReportHook().report)
		# print final return to start new line of stdout
		print("\n")
	except EnvironmentError:
		print("WARNING: Unable to download " + url)


def download_unpack_tar(url, download_file_name, folder, software_name):
	"""
	Download the url to the file and decompress into the folder
	"""

	# Check for write permission to the target folder
	if not os.access(folder, os.W_OK):
		print("WARNING: The directory is not writeable: " +
		      folder + " . Please modify the permissions.")

	download_file = os.path.join(folder, download_file_name)

	download(url, download_file)

	error_during_extract = False

	try:
		tarfile_handle = tarfile.open(download_file)
		tarfile_handle.extractall(path=folder)
		tarfile_handle.close()
	except (EnvironmentError, tarfile.ReadError):
		print("WARNING: Unable to extract " + software_name + ".")
		error_during_extract = True

	if not error_during_extract:
		try:
			os.unlink(download_file)
		except EnvironmentError:
			print("WARNING: Unable to remove the temp download: " + download_file)


def download_unpack_zip(url, download_file_name, folder, software_name):
	"""
	Download the url to the file and decompress into the folder
	"""

	# Check for write permission to the target folder
	if not os.access(folder, os.W_OK):
		print("WARNING: The directory is not writeable: " +
		      folder + " . Please modify the permissions.")

	download_file = os.path.join(folder, download_file_name)

	download(url, download_file)

	error_during_extract = False

	try:
		zipfile_handle = zipfile.ZipFile(download_file)
		zipfile_handle.extractall(path=folder)
		zipfile_handle.close()
	except EnvironmentError:
		print("WARNING: Unable to extract " + software_name + ".")
		error_during_extract = True

	if not error_during_extract:
		try:
			os.unlink(download_file)
		except EnvironmentError:
			print("WARNING: Unable to remove the temp download: " + download_file)


setuptools.setup(
	name="baqlava",
	author=AUTHOR,
	author_email=MAINTAINER_EMAIL,
	version=VERSION,
	license="MIT",
	description="BAQLaVa: Bioinformatic Application of Quantification and Labeling of Viral Taxonomy (BAQLaVa).",
	url="https://github.com/biobakery/baqlava",
	keywords=['microbial', 'microbiome', 'bioinformatics', 'microbiology', 'metagenomic', 'baqlava' ,'anadama2'],
	platforms=['Linux', 'MacOS'],
	classifiers=[
		"Programming Language :: Python",
		"Development Status :: 5 - Production/Stable",
		"Environment :: Console",
		"Operating System :: MacOS",
		"Operating System :: Unix",
		"Programming Language :: Python :: 3.6",
		"Topic :: Scientific/Engineering :: Bio-Informatics"
	],
	#install_requires=['anadama2>=0.7.4'],
	packages=setuptools.find_packages(),
	# cmdclass={'install': Install},
	entry_points={
		'console_scripts': [
			'baqlava = baqlava.baqlava:main',
                        'baqlava_join_tables = baqlava.utility_scripts.join_tables:main',
		]},
	package_data={
		'baqlava': [
			'configs/*',
			'utility_files/*',
			'utility_scripts/*',
			'data/nucleotidedb/*',
			'data/proteindb/*',
		]},
	# scripts=['baqlava/baqlava.py'],
	zip_safe=False
)