def init_matlab_toolbox(matlab_cobra_path=None):
"""initialize the matlab cobra toolbox, and load its functions
into mlab's namespace (very useful for ipython tab completion)
matlab_cobra_path: the path to the directory containing the MATLAB
cobra installation. Using the default None will attempt to find the
toolbox in the MATLAB path"""
if matlab_cobra_path is None:
matlab_cobra_path, tmp = os.path.split(
cobra.matlab.which('initCobraToolbox'))
if not os.path.isfile(os.path.join(matlab_cobra_path, "initCobraToolbox.m")):
print "initCobraToolbox not found in given path"
return
# store the current directory so we can return to it
curdir = os.path.abspath(os.curdir)
# if the user has a pathdef file, it will not get used by the MATLAB
# engine, so it needs to be called manually
try:
os.chdir(matlab_home)
matlab.path(matlab.pathdef())
except:
pass
os.chdir(matlab_cobra_path)
matlab.initCobraToolbox()
os.chdir(curdir)
# discover MATLAB functions
with warnings.catch_warnings():
warnings.simplefilter("ignore")
os.path.walk(matlab_cobra_path, _probe, None)
os.path.walk(mlab_path, _probe, None)
for function in _useful_matlab_functions:
exec("matlab.%s.__doc__" % function)
def init_matlab_toolbox(matlab_cobra_path=None, discover_functions=True):
"""initialize the matlab cobra toolbox, and load its functions
into mlab's namespace (very useful for ipython tab completion)
matlab_cobra_path: the path to the directory containing the MATLAB
cobra installation. Using the default None will attempt to find the
toolbox in the MATLAB path
discover_functions: Whether mlabwrap should autodiscover all cobra toolbox
functions in matlab. This is convenient for tab completion, but may take
some time."""
# find initCobraToolbox.m
if matlab_cobra_path is None:
matlab_cobra_path = os.path.split(
cobra.matlab.which('initCobraToolbox'))[0]
if matlab_cobra_path == "":
for i in _possible_cobra_locations:
poss_path = os.path.expanduser(i)
if os.path.isfile(poss_path + "/initCobraToolbox.m"):
matlab_cobra_path = poss_path
break
if not os.path.isfile(os.path.join(matlab_cobra_path,
"initCobraToolbox.m")):
print "initCobraToolbox not found in given path"
return
# store the current directory so we can return to it
curdir = os.path.abspath(os.curdir)
os.chdir(matlab_cobra_path)
matlab.initCobraToolbox()
os.chdir(curdir)
# discover MATLAB functions
for matlab_func in ["plot", "figure", "hist", "load", "find"]:
getattr(matlab, matlab_func)
for filename in os.listdir(mlab_path):
getattr(matlab, filename.replace(".m", ""))
if not discover_functions:
return # done now, do not need to find matlab cobra functions
with warnings.catch_warnings():
warnings.simplefilter("ignore")
walker = os.walk(matlab_cobra_path)
# skip docs and external
dirpath, dirnames, filenames = walker.next()
dirnames.pop(dirnames.index("external"))
dirnames.pop(dirnames.index("docs"))
for root, dirs, files in walker:
for filename in files:
if filename.endswith(".m"):
try:
getattr(matlab, filename.replace(".m", ""))
except:
continue