setup.py

#!/usr/bin/env python3
"""
Copyright 2017 Ryan Wick (rrwick@gmail.com)
https://github.com/rrwick/Unicycler

This script builds Unicycler's C++ components and installs it in the user's PATH.
Run `python3 setup.py install` to install Unicycler.

This file is part of Unicycler. Unicycler is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by the Free Software Foundation,
either version 3 of the License, or (at your option) any later version. Unicycler is distributed in
the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
details. You should have received a copy of the GNU General Public License along with Unicycler. If
not, see <http://www.gnu.org/licenses/>.
"""

# Make sure this is being run with Python 3.4 or later.
import sys
if sys.version_info.major != 3 or sys.version_info.minor < 4:
    sys.exit('Error: you must execute setup.py using Python 3.4 or later')

import os
import shutil
import shlex
from distutils.core import Command
import subprocess
import multiprocessing
import fnmatch
import importlib.util
from unicycler.misc import get_ascii_art, get_pilon_jar_path

# Install setuptools if not already present.
if not importlib.util.find_spec("setuptools"):
    import ez_setup
    ez_setup.use_setuptools()

from setuptools import setup
from setuptools.command.install import install

# Make sure we're running from the setup.py directory.
script_dir = os.path.dirname(os.path.realpath(__file__))
if script_dir != os.getcwd():
    os.chdir(script_dir)

# Get the program version from another file.
__version__ = '0.0.0'
exec(open('unicycler/version.py').read())

with open('README.md', 'rb') as readme:
    LONG_DESCRIPTION = readme.read().decode()


def missing_tool(tool_name):
    path = shutil.which(tool_name)
    if path is None and tool_name == 'pilon':
        path = get_pilon_jar_path(None)
    if path is None:
        return [tool_name]
    else:
        return []


def tool_check():
    # Check for required programs.
    tools = ['spades.py', 'java', 'pilon', 'samtools', 'bowtie2', 'bowtie2-build',
             'makeblastdb', 'tblastn']
    missing_tools = []
    for tool in tools:
        missing_tools += missing_tool(tool)
    if missing_tools:
        print('WARNING: some tools required by Unicycler could not be found: ' +
              ', '.join(missing_tools))
        print('You may need to install them to use all Unicycler features.')
        print('')
    else:
        print('All tools required by Unicycler were found.')


class UnicyclerInstall(install):
    """
    The install process copies the C++ shared library to the install location.
    """
    user_options = install.user_options + [
        ('makeargs=', None, 'Arguments to be given to make')
    ]

    def initialize_options(self):
        install.initialize_options(self)
        self.makeargs = None

    if __name__ == '__main__':
        def run(self):
            # Make sure we have permission to write the files.
            if os.path.isdir(self.install_lib) and not os.access(self.install_lib, os.W_OK):
                sys.exit('Error: no write permission for ' + self.install_lib + '  ' +
                         'Perhaps you need to use sudo?')
            if os.path.isdir(self.install_scripts) and not os.access(self.install_scripts, os.W_OK):
                sys.exit('Error: no write permission for ' + self.install_scripts + '  ' +
                         'Perhaps you need to use sudo?')

            # Clean up any previous Unicycler compilation.
            clean_cmd = ['make', 'distclean']
            self.execute(lambda: subprocess.call(clean_cmd), [],
                         'Cleaning previous compilation: ' + ' '.join(clean_cmd))

            # Build Unicycler's C++ code.
            make_cmd = ['make']
            try:
                make_cmd += ['-j', str(min(8, multiprocessing.cpu_count()))]
            except NotImplementedError:
                pass
            if self.makeargs:
                make_cmd += shlex.split(self.makeargs)
            self.execute(lambda: subprocess.call(make_cmd), [],
                         'Compiling Unicycler: ' + ' '.join(make_cmd))
            cpp_code = os.path.join('unicycler', 'cpp_functions.so')
            if not os.path.isfile(cpp_code):
                sys.exit("Error: compilation of Unicycler's C++ component failed")

            install.run(self)

            # Copy non-Python stuff to the installation directory.
            shutil.copyfile(cpp_code, os.path.join(self.install_lib, 'unicycler',
                                                   'cpp_functions.so'))
            gene_data_source_dir = os.path.join('unicycler', 'gene_data')
            gene_data_dest_dir = os.path.join(self.install_lib, 'unicycler', 'gene_data')
            if not os.path.exists(gene_data_dest_dir):
                os.makedirs(gene_data_dest_dir)
            shutil.copyfile(os.path.join(gene_data_source_dir, 'start_genes.fasta'),
                            os.path.join(gene_data_dest_dir, 'start_genes.fasta'))
            shutil.copyfile(os.path.join(gene_data_source_dir, 'lambda_phage.fasta'),
                            os.path.join(gene_data_dest_dir, 'lambda_phage.fasta'))

            # Display a success message!
            print(get_ascii_art())
            print('Unicycler is installed!')
            print('')
            print('Example commands:')
            print('  unicycler --help')
            print('  unicycler --help_all')
            print('  unicycler -1 short_reads_1.fastq.gz -2 short_reads_2.fastq.gz '
                  '-o path/to/output_dir')
            print('  unicycler -1 short_reads_1.fastq.gz -2 short_reads_2.fastq.gz '
                  '-l long_reads.fastq.gz -o path/to/output_dir')
            print('')

            tool_check()


class UnicyclerClean(Command):
    """
    Custom clean command that really cleans up everything, except for:
      - the compiled *.so file needed when running the programs
      - setuptools-*.egg file needed when running this script
    """
    user_options = []

    def initialize_options(self):
        self.cwd = None

    def finalize_options(self):
        self.cwd = os.getcwd()

    def run(self):
        assert os.getcwd() == self.cwd, 'Must be in package root: %s' % self.cwd

        delete_directories = []
        for root, dir_names, filenames in os.walk(self.cwd):
            for dir_name in fnmatch.filter(dir_names, '*.egg-info'):
                delete_directories.append(os.path.join(root, dir_name))
            for dir_name in fnmatch.filter(dir_names, 'build'):
                delete_directories.append(os.path.join(root, dir_name))
            for dir_name in fnmatch.filter(dir_names, '__pycache__'):
                delete_directories.append(os.path.join(root, dir_name))
        for delete_directory in delete_directories:
            print('Deleting directory:', delete_directory)
            shutil.rmtree(delete_directory)

        delete_files = []
        for root, dir_names, filenames in os.walk(self.cwd):
            for filename in fnmatch.filter(filenames, 'setuptools*.zip'):
                delete_files.append(os.path.join(root, filename))
            for filename in fnmatch.filter(filenames, '*.o'):
                delete_files.append(os.path.join(root, filename))
            for filename in fnmatch.filter(filenames, '*.pyc'):
                delete_files.append(os.path.join(root, filename))
        for delete_file in delete_files:
            print('Deleting file:', delete_file)
            os.remove(delete_file)


class UnicyclerToolCheck(Command):
    """
    Custom command to run the tool check for unicycler without having to call install
    """
    user_options = []

    def initialize_options(self):
        pass

    def finalize_options(self):
        pass

    def run(self):
        tool_check()


setup(name='unicycler',
      version=__version__,
      description='bacterial genome assembler for hybrid read sets',
      long_description=LONG_DESCRIPTION,
      url='http://github.com/rrwick/unicycler',
      author='Ryan Wick',
      author_email='rrwick@gmail.com',
      license='GPL',
      packages=['unicycler'],
      entry_points={"console_scripts": ['unicycler = unicycler.unicycler:main',
                                        'unicycler_align = unicycler.unicycler_align:main',
                                        'unicycler_check = unicycler.unicycler_check:main',
                                        'unicycler_polish = unicycler.unicycler_polish:main',
                                        'unicycler_scrub = unicycler.unicycler_scrub:main']},
      zip_safe=False,
      cmdclass={'install': UnicyclerInstall,
                'clean': UnicyclerClean,
                'toolcheck': UnicyclerToolCheck}
      )