def __init__(self, configpath):
with open(configpath, 'r') as f:
self.config = yaml.load(f.read())
try:
self.nfsim = NFSim(
os.path.join(self.config['libpath'], 'libnfsim_c.so'))
except OSError:
print("Cannot open libnfsim_c.so. Please check libpath in "
"mcellr.yaml")
sys.exit(0)
def __init__(self, configpath):
self.config = {}
self.config['bionetgen'] = os.path.join(configpath, 'bng2', 'BNG2.pl')
self.config['mcell'] = os.path.join(configpath, 'mcell')
self.config['libpath'] = os.path.join(configpath, 'lib')
self.config['scriptpath'] = configpath
prefix = "lib"
if (sys.platform == 'linux') or (sys.platform == 'linux2'):
extension = "so"
elif (sys.platform == 'darwin'):
extension = "dylib"
elif (sys.platform == 'win32'):
extension = "dll"
else:
raise Exception("Unexpected platform: {0}".format(sys.platform))
libNFsim_path = os.path.join(self.config['libpath'],
'{0}NFsim.{1}'.format(prefix, extension))
libnfsim_c_path = os.path.join(
self.config['libpath'], '{0}nfsim_c.{1}'.format(prefix, extension))
if not os.path.exists(libNFsim_path):
# try the build directory paths
libNFsim_path = os.path.join(
self.config['libpath'], '..', 'nfsim',
'{0}NFsim.{1}'.format(prefix, extension))
if not os.path.exists(libnfsim_c_path):
# try the cygwin variant
libnfsim_c_path = os.path.join(
self.config['libpath'], '..', 'nfsimCInterface',
'{0}nfsim_c.{1}'.format(prefix, extension))
if not os.path.exists(libNFsim_path):
# default to system search using LD_LIBRARY_PATH on Unix or PATH on Windows
libNFsim_path = '{0}NFsim.{1}'.format(prefix, extension)
if not os.path.exists(libnfsim_c_path):
# default to system search
libnfsim_c_path = '{0}nfsim_c.{1}'.format(prefix, extension)
print("Loading libs from " + libNFsim_path + " and " +
libnfsim_c_path + ".")
self.nfsim = NFSim(libnfsim_c_path, libNFsim_path=libNFsim_path)
