forked from gem-pasteur/macsyfinder
/
setup.py
771 lines (642 loc) · 30.1 KB
/
setup.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
################################################################################
# MacSyFinder - Detection of macromolecular systems in protein datasets #
# using systems modelling and similarity search. #
# Authors: Sophie Abby, Bertrand Néron #
# Copyright © 2014 Institut Pasteur (Paris) and CNRS. #
# See the COPYRIGHT file for details #
# #
# MacsyFinder is distributed under the terms of the GNU General Public License #
# (GPLv3). See the COPYING file for details. #
################################################################################
import time
import sys
import os
from ConfigParser import SafeConfigParser, NoSectionError, NoOptionError
try:
import warnings
except ImportError:
warnings = None
from distutils import log, dir_util
from distutils.core import setup
from distutils.core import Command
from distutils.dist import Distribution
from distutils.command.build import build
from distutils.command.install import install
from distutils.command.install_data import install_data as _install_data
from distutils.command.build_scripts import build_scripts as _build_scripts
from distutils.command.install_scripts import install_scripts as _install_scripts
from distutils.command.sdist import sdist
from distutils.errors import DistutilsFileError, DistutilsOptionError, DistutilsPlatformError
from distutils.versionpredicate import VersionPredicate
from distutils.util import subst_vars as distutils_subst_vars
from distutils.util import get_platform, change_root, convert_path
class check_and_build( build ):
def run(self):
chk = True
for req in require_python:
chk &= self.check_python(req)
for req in require_packages:
chk &= self.check_package(req)
if not chk:
sys.exit(1)
build.run(self)
log.info( """
Unit tests are available. It is _highly_ recommended to run tests now.
to run test, run 'python setup.py test -vv'""")
def check_python(self, req):
chk = VersionPredicate(req)
ver = '.'.join([str(v) for v in sys.version_info[:2]])
if not chk.satisfied_by(ver):
log.error("Invalid python version, expected %s" % req)
return False
return True
def check_package(self, req):
chk = VersionPredicate(req)
try:
mod = __import__(chk.name)
except:
log.error("Missing mandatory %s python module" % chk.name)
return False
for v in [ '__version__', 'version' ]:
ver = getattr(mod, v, None)
break
try:
if ver and not chk.satisfied_by(ver):
log.error("Invalid module version, expected %s" % req)
return False
except:
pass
return True
class build_scripts(_build_scripts):
def finalize_options(self):
_build_scripts.finalize_options(self)
self.scripts = self.distribution.scripts
self.viewer = self.distribution.viewer
def run(self):
self.mkpath(self.build_dir)
must_clean = []
for _file in self.distribution.viewer:
#if the link already exists (build already ran don't try to create it
if not os.path.exists(_file):
macsyview_src = os.path.join('macsyview', _file)
if os.path.exists(macsyview_src):
os.symlink(os.path.abspath(os.path.join('macsyview', _file)), _file)
must_clean.append(_file)
self.scripts += self.viewer
else:
log.warn("macsyview not found")
_build_scripts.run(self)
for _link in must_clean:
os.unlink(_link)
class test(Command):
description = "run the unit tests against the build library"
user_options = [('verbosity' , 'v' , 'verbosity of outputs (cumulative option ex -vv)', 1),
('build-base=', 'b', "base build directory (default: 'build.build-base')"),
('build-lib=', None, "build directory for all modules (default: 'build.build-lib')"),
('plat-name=', 'p', "platform name to build for, if supported (default: %s)" % get_platform()),
]
help_options = []
def initialize_options(self):
self.verbosity = None
self.build_base = 'build'
self.build_lib = None
self.build_purelib = None
self.build_platlib = None
self.plat_name = None
self.skip_build = 0
self.warn_dir = 1
def finalize_options(self):
#if self.build_lib is None:
# self.build_lib = os.path.join(self.build_base, 'lib' )
if self.verbosity is None:
self.verbosity = 0
else:
self.verbosity = int(self.verbosity)
if self.plat_name is None:
self.plat_name = get_platform()
else:
# plat-name only supported for windows (other platforms are
# supported via ./configure flags, if at all). Avoid misleading
# other platforms.
if os.name != 'nt':
raise DistutilsOptionError(
"--plat-name only supported on Windows (try "
"using './configure --help' on your platform)")
plat_specifier = ".%s-%s" % (self.plat_name, sys.version[0:3])
# Make it so Python 2.x and Python 2.x with --with-pydebug don't
# share the same build directories. Doing so confuses the build
# process for C modules
if hasattr(sys, 'gettotalrefcount'):
plat_specifier += '-pydebug'
# 'build_purelib' and 'build_platlib' just default to 'lib' and
# 'lib.<plat>' under the base build directory. We only use one of
# them for a given distribution, though --
if self.build_purelib is None:
self.build_purelib = os.path.join(self.build_base, 'lib')
if self.build_platlib is None:
self.build_platlib = os.path.join(self.build_base,
'lib' + plat_specifier)
# 'build_lib' is the actual directory that we will use for this
# particular module distribution -- if user didn't supply it, pick
# one of 'build_purelib' or 'build_platlib'.
if self.build_lib is None:
if os.path.exists(self.build_purelib):
self.build_lib = self.build_purelib
elif os.path.exists(self.build_platlib):
self.build_lib = self.build_platlib
def run(self):
"""
"""
if not self.skip_build:
self.run_command('build')
# If we built for any other platform, we can't install.
build_plat = self.distribution.get_command_obj('build').plat_name
# check warn_dir - it is a clue that the 'install' is happening
# internally, and not to sys.path, so we don't check the platform
# matches what we are running.
if self.warn_dir and build_plat != get_platform():
raise DistutilsPlatformError("Can't test when "
"cross-compiling")
from test import main
if self.build_lib is None:
if os.path.exists(self.build_purelib):
self.build_lib = self.build_purelib
elif os.path.exists(self.build_platlib):
self.build_lib = self.build_platlib
log.info("running test")
os.environ['MACSY_HOME'] = os.path.dirname(os.path.abspath(__file__))
test_res = main.run(self.build_lib, [], verbosity = self.verbosity)
kind_of_skipped = {}
for test in test_res.skipped:
kind_of_skipped[test[1]] = True
for skip_reason in kind_of_skipped.keys():
if skip_reason == "neither makeblast nor formatdb found in PATH":
msg = """
#####################################################################
neither makeblast nor formatdb found in PATH
You'll have to provide the full path of
makeblastdb or formatdb in config file or command line to run macsyfinder
#####################################################################"""
elif skip_reason == "hmmsearch not found in PATH":
msg = """
########################################################
hmmsearch not found in PATH
You'll have to provide the full path of
hmmsearch in config file or command line to run macsyfinder
########################################################"""
else:
msg = skip_reason
log.warn( msg )
if not test_res.wasSuccessful():
sys.exit("some tests fails. Run python setup.py test -vv to have more details")
class install_macsyfinder(install):
#I use record to store all installed files and reuse this record file for uninstall
#so this option is not available anymore for the users
for i, opt in enumerate(install.user_options):
if opt[0] == 'record=':
install.user_options.pop(i)
def initialize_options(self):
install.initialize_options(self)
def finalize_options(self):
install.finalize_options(self)
self.record = self.distribution.uninstall_files
with open(self.distribution.uninstall_prefix, "w") as _f:
_f.write("[install]\n")
_f.write('install_scripts = {}\n'.format(os.path.normpath(self.install_scripts)))
_f.write('install_lib = {}\n'.format(os.path.normpath(self.install_lib)))
def run(self):
inst = self.distribution.command_options.get('install')
vars_2_subst = {'PREFIX': inst.get('prefix', ''),
'PREFIXCONF' : os.path.join(get_install_conf_dir(inst), 'macsyfinder'),
'PREFIXDATA' : os.path.join(get_install_data_dir(inst), 'macsyfinder'),
'PREFIXDOC' : os.path.join(get_install_doc_dir(inst), 'macsyfinder'),
}
for _file in self.distribution.fix_prefix:
input_file = os.path.join(self.build_lib, _file)
output_file = input_file + '.tmp'
subst_vars(input_file, output_file, vars_2_subst)
os.unlink(input_file)
self.move_file(output_file, input_file)
install.run(self)
class install_data(_install_data):
user_options = [
('install-dir=', 'd',
"base directory for installing data files "
"(default: installation base dir)"),
('root=', None,
"install everything relative to this alternate root directory"),
('force', 'f', "force installation (overwrite existing files)"),
]
boolean_options = ['force']
def finalize_options(self):
inst = self.distribution.command_options.get('install')
self.install_dir = get_install_data_dir(inst)
self.set_undefined_options('install',
('root', 'root'),
('force', 'force'),
)
self.prefix_data = self.install_dir
self.files_2_install = self.distribution.data_files
with open(self.distribution.uninstall_prefix, "a") as _f:
_f.write('install_data = {}\n'.format(self.install_dir))
def run(self):
self.mkpath(self.install_dir)
for f in self.files_2_install:
if isinstance(f, str):
if not os.path.exists(f):
log.warn("WARNING the document {} cannot be found, installation skipped".format(f))
# it's a simple file, so copy it
f = convert_path(f)
if self.warn_dir:
self.warn("setup script did not provide a directory for "
"'%s' -- installing right in '%s'" %
(f, self.install_dir))
(out, _) = self.copy_file(f, self.install_dir)
self.outfiles.append(out)
else:
# it's a tuple with path to install to and a list of path
dir = convert_path(f[0])
if not os.path.isabs(dir):
dir = os.path.join(self.install_dir, dir)
elif self.root:
dir = change_root(self.root, dir)
self.mkpath(dir)
if f[1] == []:
# If there are no files listed, the user must be
# trying to create an empty directory, so add the
# directory to the list of output files.
self.outfiles.append(dir)
else:
# Copy files, adding them to the list of output files.
for data in f[1]:
data = convert_path(data)#return name that will work on the native filesystem
if not os.path.exists(data):
log.warn("WARNING the document {} cannot be found, installation skipped".format(data))
continue
if os.path.isdir(data):
out = self.copy_tree(data, dir)
self.outfiles.extend(out)
else:
(out, _) = self.copy_file(data, dir)
self.outfiles.append(out)
class install_doc(install_data):
install.sub_commands += [('install_doc', lambda self: not self.no_doc)]
description = "installation directory for documentation files"
setattr(install, 'install_doc', None)
setattr(install, 'no_doc', None)
install.user_options.append(('install-doc=', None, description))
install.user_options.append(('no-doc', None, 'do not install documentation'))
user_options = [
('install-doc=', 'd', "base directory for installing documentation files " "(default: installation base dir share/doc)"),
('root=', None, "install everything relative to this alternate root directory"),
('force', 'f', "force installation (overwrite existing files)"),
('no-doc', None, 'do not install documentation')
]
boolean_options = ['force']
def initialize_options(self):
install_data.initialize_options(self)
self.install_doc = None
self.no_doc = None
self.files_2_install = self.distribution.doc_files
def finalize_options(self):
inst = self.distribution.command_options.get('install')
self.install_dir = get_install_doc_dir(inst)
self.set_undefined_options('install',
('root', 'root'),
('force', 'force'),
)
self.prefix_data = self.install_dir
self.no_doc = inst.get('no_doc', ('command line', False))[1]
with open(self.distribution.uninstall_prefix, "a") as _f:
_f.write('install_doc = {}\n'.format(self.install_dir))
def run(self):
install_data.run(self)
class install_conf(install_data):
install.sub_commands += [('install_conf', lambda self:True)]
description = "installation directory for configuration files"
setattr(install, 'install_conf', None)
install.user_options.append(('install-conf=', None, description))
user_options = [
('install-conf=', 'd',
"base directory for installing configuration files "
"(default: installation base dir etc)"),
('root=', None,
"install everything relative to this alternate root directory"),
('force', 'f', "force installation (overwrite existing files)"),
]
boolean_options = ['force']
def initialize_options(self):
install_data.initialize_options(self)
self.conf_files = self.distribution.conf_files
def finalize_options(self):
inst = self.distribution.command_options.get('install')
self.install_dir = get_install_conf_dir(inst)
self.set_undefined_options('install',
('root', 'root'),
('force', 'force'),
)
with open(self.distribution.uninstall_prefix, "a") as _f:
_f.write('install_conf = {}\n'.format(self.install_dir))
def run(self):
self.mkpath(self.install_dir)
inst = self.distribution.command_options.get('install')
vars_2_subst = {'PREFIX': inst['prefix'][1] if 'prefix' in inst else '',
'PREFIXCONF' : os.path.join(get_install_conf_dir(inst), 'macsyfinder'),
'PREFIXDATA' : os.path.join(get_install_data_dir(inst), 'macsyfinder'),
'PREFIXDOC' : os.path.join(get_install_doc_dir(inst), 'macsyfinder')
}
for f in self.conf_files:
if isinstance(f, str):
# it's a simple file, so copy it
f = convert_path(f)
if self.warn_dir:
self.warn("setup script did not provide a directory for "
"'%s' -- installing right in '%s'" %
(f, self.install_dir))
dest = os.path.join(self.install_dir, f +".new" )
(out, _) = self.copy_file(f, self.install_dir)
self.outfiles.append(out)
else:
# it's a tuple with path to install to and a list of files
_dir = convert_path(f[0])
if not os.path.isabs(_dir):
_dir = os.path.join(self.install_dir, _dir)
elif self.root:
_dir = change_root(self.root, _dir)
self.mkpath(_dir)
if f[1] == []:
# If there are no files listed, the user must be
# trying to create an empty directory, so add the
# directory to the list of output files.
self.outfiles.append(_dir)
else:
# Copy files, adding them to the list of output files.
for conf in f[1]:
conf = convert_path(conf)
dest = os.path.join(_dir,os.path.basename(conf) + ".new" )
(out, _) = self.copy_file(conf, dest)
if conf in self.distribution.fix_conf:
input_file = out
output_file = input_file + '.tmp'
subst_vars(input_file, output_file, vars_2_subst)
if os.path.exists(input_file):
os.unlink(input_file)
self.move_file(output_file, input_file)
self.outfiles.append(input_file)
class install_viewer(_install_scripts):
install.sub_commands += [('install_viewer', lambda self: not self.no_viewer)]
description = 'Install MacSyView, MacSyView allow to view graphically results of MacSyFinder (need a web browser to work).'
setattr(install, 'no_viewer', None)
install.user_options.append(('no-viewer', None, 'do not install MacSyView'))
user_options = [ ('no-viewer', None, )]
def initialize_options(self):
_install_scripts.initialize_options(self)
self.no_viewer = False
def finalize_options(self):
_install_scripts.finalize_options(self)
inst = self.distribution.command_options.get('install')
self.no_viewer = inst.get('no_viewer', ('command line', False))[1]
def run(self):
def subst(src_file, dest_file, local_vars):
with open(src_file , 'r') as f_in:
with open(dest_file, 'w') as f_out:
for line in f_in:
for var in local_vars:
new_line = line.replace('$'+var, local_vars[var])
f_out.write(new_line)
inst = self.distribution.command_options.get('install')
vars_2_subst = {'MACSYVIEW' :os.path.join(get_install_data_dir(inst), 'macsyfinder', 'macsyview', 'app', 'index.html')}
for _file in self.distribution.fix_viewer:
input_file = os.path.join(self.build_dir, _file)
output_file = input_file + '.tmp'
subst(input_file, output_file, vars_2_subst)
os.unlink(input_file)
self.move_file(output_file, input_file)
_install_scripts.run(self)
class Uninstall(Command):
description = "remove installed files"
user_options = []
def initialize_options (self):
self.install_scripts = None
self.install_lib = None
self.install_data = None
self.install_doc = None
self.install_conf = None
def finalize_options(self):
self.parser = SafeConfigParser()
if not os.path.exists(self.distribution.uninstall_prefix):
raise DistutilsFileError( "Cannot unistall macsyfinder.\n{}: No such file".format(self.distribution.uninstall_prefix))
used_files = self.parser.read(self.distribution.uninstall_prefix)
for attr in [ attr for attr in vars(self) if attr.startswith('install_')]:
try:
value = self.parser.get('install', attr)
except(NoSectionError, NoOptionError):
continue
setattr(self, attr, value)
def run(self):
prefixes = []
for attr in [ attr for attr in vars(self) if attr.startswith('install_')]:
prefixes.append( getattr(self, attr))
print "prefixes = ", prefixes
def clean_tree(_dir):
find_prefix = False
for prefix in prefixes:
print "== ", prefix, ".find(",_dir,") = ",prefix.find(_dir)
if prefix.find(_dir) != -1:
find_prefix = True
return prefix
print "find_prefix =",prefix
if find_prefix:
return
try:
if not self.dry_run:
os.rmdir(_dir)
log.info("remove dir {}".format(_dir))
except OSError as err:
if err.errno == os.errno.ENOTEMPTY:
return
else:
self.warn(err)
return
clean_tree(os.path.dirname(_dir))
try:
with open(self.distribution.uninstall_files) as record_file:
for path in record_file:
path = os.path.normpath(path.strip())
try:
if not self.dry_run:
os.unlink(path)
log.info("remove file {}".format(path))
except Exception, err:
pass
_dir = os.path.dirname(path)
clean_tree(_dir)
except IOError, err:
msg = "Cannot unistall macsyfinder.\n"
if err.errno == os.errno.ENOENT:
msg += "Cannot access \"{}\": No such file".format(self.distribution.uninstall_files)
elif err.errno == os.errno.EACCES:
msg += "Cannot access \"{}\": Permission denied".format(self.distribution.uninstall_files)
else:
msg += str(err)
raise DistutilsFileError(msg)
###################################
# #
# creation of source distribution #
# #
###################################
class sdist_macsy(sdist):
user_options = [('macsyview-dir=', None, 'The location of the macsyview project')] + sdist.user_options
def initialize_options(self):
sdist.initialize_options(self)
self.macsyview_dir = None
self.macsyview_link_name = None
def run(self):
inst = self.distribution.command_options.get('sdist')
self.macsyview_link_name = 'macsyview'
if not inst.has_key('macsyview_dir'):
self.must_clean = False
if not os.path.exists(self.macsyview_link_name):
sys.exit('Missing mandatory macsyview-dir to specify the location of macsyview project')
else:
self.set_up()
sdist.run(self)
self.clean_up()
def update_mktemplate(self):
with open('MANIFEST.in', 'a') as f:
f.write('recursive-include {0} *\n'.format(os.path.join(self.macsyview_link_name, 'app')))
def set_up(self):
if os.path.exists( self.macsyview_link_name ):
if os.path.realpath(self.macsyview_link_name) == os.path.realpath(self.macsyview_dir):
self.must_clean = False
return
else:
raise RuntimeError( "there already exist a 'macsyview' path in %s and is different than %s"%( os.getcwd(), self.macsyview_dir) )
os.symlink( self.macsyview_dir , self.macsyview_link_name )
self.must_clean = True
def clean_up(self):
if self.must_clean:
os.unlink( self.macsyview_link_name )
# def build_macsyview(self):
# from subprocess import Popen, PIPE
# process_ = Popen(
# command,
# shell = True ,
# stdout= sys.stdout,
# stdin = None ,
# stderr = sys.stderr,
# cwd = self.niaid_home_dir
# )
# process_.wait()
# if process_.returncode != 0:
# raise RuntimeError
class UsageDistribution(Distribution):
def __init__(self, attrs = None):
#It's important to define opotions before to call __init__
#otherwise AttributeError: UsageDistribution instance has no attribute 'conf_files'
self.conf_files = None
self.doc_files = None
self.viewer = None
self.fix_prefix = None
self.fix_conf = None
self.fix_viewer = None
self.uninstall_prefix = os.path.join(os.path.dirname(__file__), "uninstall.cfg")
self.uninstall_files = os.path.join(os.path.dirname(__file__), "uninstall_files")
Distribution.__init__(self, attrs = attrs)
self.common_usage = """\
Common commands: (see '--help-commands' for more)
setup.py build will build the package underneath 'build/'
setup.py test will run the tests on the newly build library
setup.py install will install the package
setup.py uninstall will unistall every installed files
"""
def get_install_data_dir(inst):
if 'VIRTUAL_ENV' in os.environ:
inst['prefix'] = ('environment', os.environ['VIRTUAL_ENV'])
if 'install_data' in inst:
install_dir = inst['install_data'][1]
elif 'prefix' in inst:
install_dir = os.path.join(inst['prefix'][1], 'share')
else:
install_dir = os.path.join('/', 'usr', 'share')
return install_dir
def get_install_conf_dir(inst):
if 'VIRTUAL_ENV' in os.environ:
inst['prefix'] = ('environment', os.environ['VIRTUAL_ENV'])
if 'install_conf' in inst:
install_dir = inst['install_conf'][1]
elif 'prefix' in inst:
install_dir = os.path.join(inst['prefix'][1], 'etc')
else:
install_dir = '/etc'
return install_dir
def get_install_doc_dir(inst):
if 'VIRTUAL_ENV' in os.environ:
inst['prefix'] = ('environment', os.environ['VIRTUAL_ENV'])
if 'install_doc' in inst:
install_dir = inst['install_doc'][1]
elif 'prefix' in inst:
install_dir = os.path.join(inst['prefix'][1], 'share', 'doc' )
else:
install_dir = os.path.join('/', 'usr', 'share', 'doc')
return install_dir
def subst_vars(src, dst, vars):
try:
src_file = open(src, "r")
except os.error, err:
raise DistutilsFileError, "could not open '%s': %s" % (src, err)
try:
dest_file = open(dst, "w")
except os.error, err:
raise DistutilsFileError, "could not create '%s': %s" % (dst, err)
with src_file:
with dest_file:
for line in src_file:
new_line = distutils_subst_vars(line, vars)
dest_file.write(new_line)
require_python = [ 'python (>=2.7, <3.0)' ]
require_packages = []
setup(name = 'macsyfinder',
version = time.strftime("1.0.1"),
description = """MacSyFinder: Detection of macromolecular systems
in protein datasets using systems modelling and similarity search""",
author = "Sophie Abby, Bertrand Néron",
author_email = "sabby@pasteur.fr, bneron@pasteur.fr",
classifiers = [
'Operating System :: POSIX' ,
'Programming Language :: Python' ,
'Topic :: Bioinformatics' ,
] ,
packages = ['macsypy'],
scripts = [ 'bin/macsyfinder'] ,
viewer = ['bin/macsyview'],
#(dataprefix +'where to put the data in the install, [where to find the data in the tar ball]
data_files = [('macsyfinder/DEF', ['data/DEF/']),
('macsyfinder/profiles', ['data/profiles/']),
('macsyfinder/sequence_data', ['data/sequence_data/']),
('macsyfinder/macsyview/app', ['macsyview/app/'])
],
conf_files = [('macsyfinder', ['etc/macsyfinder.conf'])],
doc_files = [('macsyfinder/html', ['doc/_build/html/']),
('macsyfinder/pdf', ['doc/_build/latex/Macsyfinder.pdf']),
],
#file where some variable must be fix by install_conf
fix_conf = ['etc/macsyfinder.conf'],
#file where some variable must be fix by macsyfinder_install
fix_prefix = ['macsypy/config.py', 'macsypy/registries.py' ],
fix_viewer = ['macsyview'],
cmdclass= { 'build' : check_and_build ,
'build_scripts' : build_scripts,
'test': test,
'install' : install_macsyfinder,
'install_viewer' : install_viewer,
'install_data' : install_data,
'install_conf' : install_conf,
'install_doc' : install_doc,
'uninstall' : Uninstall,
'sdist': sdist_macsy,
},
distclass = UsageDistribution
)