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|
import distutils.sysconfig
import os
from defaults import *
import atexit
Export('codePath')
config_file = 'build_config.py'
gcv = distutils.sysconfig.get_config_var
vars = Variables(['.variables.cache', config_file], ARGUMENTS)
vars.Add(PathVariable('PREFIX',
'Install directory',
defaultPrefix,
PathVariable.PathAccept))
vars.Add('URL', "Sets the url of pdb2pqr's web interface.", defaultURL)
vars.Add('OPAL', 'Sets the url of a pdb2pqr opal service.', '')
vars.Add('APBS_OPAL', 'Sets the url of a apbs opal service.', '')
vars.Add(PathVariable('APBS',
'Location of the APBS binary if installed',
'',
PathVariable.PathAccept))
vars.Add('MAX_ATOMS', 'Sets the maximum number of atoms in a protein for non-Opal job submission. '
'Only affects web tools', 10000, None, int)
vars.Add(BoolVariable('BUILD_PDB2PKA',
'Set to False to skip building ligand and pdb2pka support. Requires numpy.',
True))
vars.Add(BoolVariable('REBUILD_SWIG',
'Set to True to rebuild the swig bindings. Requires swig on the the user path.',
False))
vars.Add(BoolVariable('DEBUG',
'Set to True to compiled components with debug headers.',
False))
vars.Add('EXTRA_CXXFLAGS', 'Set to add extra CXX flags to the build.', '')
vars.Add('EXTRA_LINKFLAGS', 'Set to add extra link flags to the build.', '')
#TODO: setup rebuilding of docs.
# THIS SHOULD BE A TARGET!
#AddOption('--rebuild-docs',
# dest='docs',
# action='store_true',
# default=False,
# help='Rebuild pydocs.')
#Windows: make sure we use correct target arch.
target_arch='x86_64'
import platform
arch = platform.architecture()
bit_str = arch[0]
if bit_str == '32bit':
target_arch='x86'
if os.name == 'nt':
tool_chain = ['default', 'mssdk']
else:
tool_chain = ['default']
tool_chain.append('swig')
env = Environment(variables=vars,
MSVC_VERSION='9.0',
TARGET_ARCH=target_arch,
MSSDK_VERSION='6.0A',
tools=tool_chain,
SWIGFLAGS=['-python', '-c++'],
SHLIBPREFIX="",
SHLIBSUFFIX=gcv('SO'),
LDMODULESUFFIX=gcv('SO'))
python_lib = 'python' + gcv('VERSION')
env.Append(LIBS=[python_lib])
#To get swig to work on windows.
#env.Append(ENV={'PATH' : os.environ['PATH']})
if os.name == 'nt' and 'icc' not in tool_chain:
env.Append(CXXFLAGS = ['/EHsc'])
if env['DEBUG']:
if os.name == 'nt' and 'icc' not in tool_chain:
env.Append(CXXFLAGS = ['/DEBUG'])
else:
env.MergeFlags('-g')
if env['EXTRA_CXXFLAGS']:
env.Append(CXXFLAGS = [env['EXTRA_CXXFLAGS']])
if env['EXTRA_LINKFLAGS']:
env.Append(LINKFLAGS = [env['EXTRA_LINKFLAGS']])
if 'LDFLAGS' in os.environ:
env.Append(LINKFLAGS = os.environ['LDFLAGS'])
if os.name == 'nt':
#Check to see if we are running in a virtualenv
if hasattr(sys, 'real_prefix'):
python_root = sys.real_prefix
else:
python_root = sys.prefix
python_include = os.path.join(python_root, 'include')
python_libs = os.path.join(python_root, 'libs')
env.Append(LIBPATH=[python_libs])
else:
env.Append(LIBPATH=[gcv('LIBDIR')])
Export('env')
prefix = env['PREFIX']
prefix = prefix.replace('\\', '/')
if not prefix.endswith('/'):
prefix+='/'
env['PREFIX'] = prefix
Help(vars.GenerateHelpText(env))
vars.Save('.variables.cache', env)
#Not the optimal way to do this...
#Should figure out how to do it with a delete command
Clean('pdb2pqr.py', '.variables.cache')
url = env['URL']
#Not sure if this is needed.
if url is not None:
if not url.endswith('/'):
url += '/'
submitAction = url+'pdb2pqr.cgi'
else:
url = defaultURL
#Can it always just be this?
submitAction = 'pdb2pqr.cgi'
maxatomsStr = str(env['MAX_ATOMS'])
replacementDict = {'@WHICHPYTHON@':pythonBin,
'@INSTALLDIR@':prefix,
'@MAXATOMS@':maxatomsStr,
'@website@':url,
'@srcpath@':codePath,
'@PDB2PQR_VERSION@':productVersion,
'@action@':submitAction,
'@APBS_LOCATION@':env['APBS'],
'@APBS_OPAL_URL@':env['APBS_OPAL'],
'@PDB2PQR_OPAL_URL@':env['OPAL']}
#If any replacement strings change recompile those files.
#As the product version can be based on the time this may
# rebuild string replacement files after less than one minute between builds
settingsValues = env.Value(replacementDict)
#We have a separate dict for server.html.in as we need to use regex
#Regex does not play nice with some possible user strings
#Set up regex to alternately clear tags or wipe sections
if env['OPAL'] == '':
#Not using opal for pdb2pqr.
print "not using opal", env['OPAL']
withOpalRegex = r'@WITHOPAL@.*?@WITHOPAL@'
withoutOpalRegex = '@WITHOUTOPAL@'
else:
#Using opal for pdb2pqr.
print "using opal", env['OPAL']
withOpalRegex = '@WITHOPAL@'
withoutOpalRegex = r'@WITHOUTOPAL@.*?@WITHOUTOPAL@'
serverHtmlDict = {'@website@':url,
'@PDB2PQR_VERSION@':productVersion,
'@MAXATOMS@':maxatomsStr,
'@action@':submitAction,
withOpalRegex:'',
withoutOpalRegex:''}
chmodAction = Chmod('$TARGET', 0755)
serverHtmlCopySub = CopySub('$TARGET', '$SOURCE', serverHtmlDict, useRegex=True)
normalCopySub = CopySub('$TARGET', '$SOURCE', replacementDict, useRegex=False)
subFiles = [('pdb2pqr.py', 'pdb2pqr.py.in', True),
('apbs_cgi.cgi', 'apbs_cgi.py', True),
('visualize.cgi', 'visualize.py', True),
('querystatus.cgi', 'querystatus.py', True),
('src/aconf.py', 'src/aconf.py.in', False),
('html/server.html', 'html/server.html.in', False)]
compile_targets = []
for target, source, chmod in subFiles:
actions = [normalCopySub] if target != 'html/server.html' else [serverHtmlCopySub]
if chmod:
actions.append(chmodAction)
result = env.Command(target, source, actions)
compile_targets.append(result)
if target == 'pdb2pqr.py':
pdb2pqr = result
Export('pdb2pqr')
Default(result)
Depends(result, settingsValues)
Default(env.Command('pdb2pqr.cgi', 'pdb2pqr.py', Copy('$TARGET', '$SOURCE')))
#Check to see why we can't build pdb2pka.
numpy_error = False
if env['BUILD_PDB2PKA']:
try:
import numpy
except ImportError:
print 'WARNING: PDB2PKA build skipped, numpy not installed. Ligand support will not be available.'
numpy_error = True
if not numpy_error:
import distutils
env.Append(CPPPATH=[distutils.sysconfig.get_python_inc(), numpy.get_include()])
alg_srcs = ['pdb2pka/substruct/Algorithms.cpp']
algorithms_pyc = env.LoadableModule('pdb2pka/substruct/Algorithms', ['pdb2pka/substruct/Algorithms.cpp'])
Default(algorithms_pyc)
Alias('algorithms', algorithms_pyc)
compile_targets.append(algorithms_pyc)
if os.name == 'nt':
alg_msvs_env = env.Clone(MSVSBUILDCOM='cd .. && '+pythonBin+' scons/scons.py algorithms DEBUG=True',
MSVSCLEANCOM='cd .. && '+pythonBin+' scons/scons.py -c algorithms',
MSVSREBUILDCOM='cd .. && '+pythonBin+' scons/scons.py -c algorithms && '+pythonBin+' scons/scons.py algorithms DEBUG=True')
algorithms_project = alg_msvs_env.MSVSProject(target = 'msvs/Algorithms' + env['MSVSPROJECTSUFFIX'],
auto_build_solution=0,
srcs = ['../pdb2pka/substruct/Algorithms.cpp'],
buildtarget = algorithms_pyc[0],
variant = 'Debug|x64')
Alias('msvs', algorithms_project)
pmc_srcs = ['pdb2pka/pMC_mult.cpp', 'pdb2pka/pMC_mult_wrap.cpp']
if env['REBUILD_SWIG']:
pmc_pyc = env.LoadableModule('pdb2pka/_pMC_mult', ['pdb2pka/pMC_mult.cpp', 'pdb2pka/pMC_mult.i'])
build_swig = ' REBUILD_SWIG=True'
else:
pmc_pyc = env.LoadableModule('pdb2pka/_pMC_mult', ['pdb2pka/pMC_mult.cpp', 'pdb2pka/pMC_mult_wrap.cpp'])
build_swig = ' '
Default(pmc_pyc)
Alias('pmc_mult', pmc_pyc)
compile_targets.append(pmc_pyc)
if os.name == 'nt':
pmc_msvs_env = env.Clone(MSVSBUILDCOM='cd .. && '+pythonBin+' scons/scons.py pmc_mult DEBUG=True'+build_swig,
MSVSCLEANCOM='cd .. && '+pythonBin+' scons/scons.py -c pmc_mult',
MSVSREBUILDCOM='cd .. && '+pythonBin+' scons/scons.py -c pmc_mult && '+pythonBin+' scons/scons.py pmc_mult DEBUG=True'+build_swig)
pmc_mult_project = pmc_msvs_env.MSVSProject(target = 'msvs/pMC_mult' + env['MSVSPROJECTSUFFIX'],
auto_build_solution=0,
srcs = ['../pdb2pka/pMC_mult.cpp', '../pdb2pka/pMC_mult_wrap.cpp'],
incs = ['../pdb2pka/pMC_mult.h'],
resources = ['../pdb2pka/pMC_mult.i'],
buildtarget = pmc_pyc[0],
variant = 'Debug|x64')
Alias('msvs', pmc_mult_project)
pdb2pqr_sln = env.MSVSSolution(target = 'msvs/pdb2pqr' + env['MSVSSOLUTIONSUFFIX'],
projects = [pmc_mult_project, algorithms_project],
variant = 'Debug|x64')
Alias('msvs', pdb2pqr_sln)
SConscript('tests/SConscript')
SConscript('SConscript-install.py', exports='env compile_targets')
SConscript('SConscript-error.py')
def print_default_message(target_list):
target_list = map(str, target_list)
if any('test' in x for x in target_list):
return
if GetOption("clean"):
return
if not GetOption("help"):
print
print 'TARGETS:', target_list
print
print '========================'
print 'Configuration Parameters'
print '========================'
print
print 'Version:', productVersion
print 'Install directory:', env['PREFIX']
if numpy_error:
print
print 'WARNING: PDB2PKA build skipped, numpy not installed. Ligand support will not be available.'
print
else:
print 'pdb2pka and ligand support:', env['BUILD_PDB2PKA']
print 'Path to the website directory:', url
if env['OPAL'] == '':
print 'PDB2PQR jobs run via the web interface will be forked on the server.'
else:
print 'PDB2PQR jobs run via the web interface will be run via opal at', env['OPAL']
else:
print
print 'Run "python scons/scons.py" to build pdb2pqr.'
print
print 'The preferred way to configure the build is by editing the file', config_file
print
print 'Run scons with the python that you intend to use with pdb2pqr.'
print 'For example: "/opt/bin/python scons/scons.py" will setup pdb2pqr to be run with /opt/bin/python'
if 'install' not in target_list:
print
print 'Run "python scons/scons.py install" to install pdb2pqr in', env['PREFIX']
print
print 'Run "python scons/scons.py basic-test" for a basic functionality test'
print 'Run "python scons/scons.py advanced-test" for a single test of ligand and PROPKA support. Requires numpy and PDB2PKA support compiled.'
print 'Run "python scons/scons.py complete-test" for a complete test of all functionality EXCEPT PDB2PKA. Requires numpy and PDB2PKA support compiled.'
print 'Run "python scons/scons.py pdb2pka-test" for a test of PDB2PKA functionality.'
print ' Requires numpy, PDB2PKA support compiled AND the APBS python libraries compiled and installed in the pdb2pka directory.'
print
print 'To setup a web service create a symbolic link to', env['PREFIX'], 'that enables you to view', env['URL'],'after running "scons/scons.py install"'
print
print 'Run "python scons/scons.py msvs" to build Visual Studio projects for the Algorithms and pMC_mult modules.'
print 'VS project generation is not well supported in scons. Resulting projects should build using NMAKE but cannot be used for debugging.'
print 'The resulting projects will need to modified to use VS natively to compile the code or debug.'
if 'install' in target_list:
print
print 'pdb2pqr installed in', env['PREFIX']
atexit.register(print_default_message, BUILD_TARGETS)
|
