def __load(self):
"""
Explicitly load CASM project into memory.
"""
if self._ptr is None:
self._api = API()
if self.verbose:
streamptr = self._api.stdout()
else:
streamptr = self._api.nullstream()
if self.verbose:
errstreamptr = self._api.stderr()
else:
errstreamptr = self._api.nullstream()
self._ptr = self._api.primclex_new(self.path, streamptr, streamptr, errstreamptr)
def __load(self):
"""
Explicitly load CASM project into memory.
"""
if self._ptr is None:
self._api = API()
if self.verbose:
streamptr = self._api.stdout()
else:
streamptr = self._api.nullstream()
if self.verbose:
errstreamptr = self._api.stderr()
else:
errstreamptr = self._api.nullstream()
self._ptr = self._api.primclex_new(self.path, streamptr, streamptr, errstreamptr)
class Project(object):
"""The Project class contains information about a CASM project
Attributes
----------
path: str
Path to project root directory
name: str
Project name
settings: casm.project.ProjectSettings instance
Contains project settings
dir: casm.project.DirectoryStructure instance
Provides file and directory locations within the project
prim: casm.project.Prim instance
Represents the primitive crystal structure
composition_axes: casm.project.CompositionAxes
Currently selected composition axes
all_composition_axes: dict(str:casm.project.CompositionAxes)
Dict containing name:CompositionAxes pairs, including both standard and
custom composition axes
casm_exe: str
The casm CLI executable to use when necessary
verbose: bool
How much to print to stdout
"""
def __init__(self, path=None, casm_exe=None, verbose=True):
"""
Construct a CASM Project representation.
Arguments
----------
path: str, optional, default=None
Path to project root directory. Default=None uses project containing
current working directory
casm_exe: str, optional, default=None
CASM executable to use for command line interface. Default
uses $CASM if it exists in the environment, else "casm".
verbose: bool, optional, default=True
How much to print to stdout
"""
# will hold a ctypes.c_void_p when loading CASM project into memory
self._ptr = None
# will keep a casm.API instance
self._api = None
# set path to this CASM project
if project_path(path) is None:
if path is None:
raise Exception("No CASM project found using " + os.getcwd())
else:
raise Exception("No CASM project found using " + path)
# set executable name
if casm_exe is None:
if "CASM" in os.environ:
casm_exe = os.environ["CASM"]
else:
casm_exe = "casm"
self.path = project_path(path)
self.__refresh()
self.casm_exe = casm_exe
self.verbose = verbose
self.all_composition_axes = {}
if os.path.exists(self.dir.composition_axes()):
with open(self.dir.composition_axes(), 'r') as f:
data = json.load(f)
if "standard_axes" in data:
for key, val in data["standard_axes"].iteritems():
self.all_composition_axes[key] = CompositionAxes(
key, val)
if "custom_axes" in data:
for key, val in data["custom_axes"].iteritems():
self.all_composition_axes[key] = CompositionAxes(
key, val)
self.composition_axes = self.all_composition_axes[
data["current_axes"]]
def __del__(self):
self.__unload()
def __load(self):
"""
Explicitly load CASM project into memory.
"""
if self._ptr is None:
self._api = API()
if self.verbose:
streamptr = self._api.stdout()
else:
streamptr = self._api.nullstream()
if self.verbose:
errstreamptr = self._api.stderr()
else:
errstreamptr = self._api.nullstream()
self._ptr = self._api.primclex_new(self.path, streamptr, streamptr,
errstreamptr)
def __unload(self):
"""
Explicitly unload CASM project from memory.
"""
if self._ptr is not None:
self._api.primclex_delete(self._ptr)
self._ptr = None
def __refresh(self):
"""
Reload self.settings and self.dir
Use this after adding or modifying files in the CASM project but no
special call to refresh PrimClex properties is required
"""
self.dir = DirectoryStructure(self.path)
self.settings = ProjectSettings(self.path)
self._prim = None
@property
def prim(self):
if self._prim is None:
self._prim = Prim(self)
return self._prim
@property
def name(self):
return self.settings.data['name']
def refresh(self,
read_settings=False,
read_composition=False,
read_chem_ref=False,
read_configs=False,
clear_clex=False):
"""
Refresh PrimClex properties to reflect changes to CASM project files.
"""
if read_settings:
self.dir = DirectoryStructure(self.path)
self.settings = ProjectSettings(self.path)
if self._ptr is not None:
self._api.primclex_refresh(self.data(), read_settings,
read_composition, read_chem_ref,
read_configs, clear_clex)
def data(self):
"""
Returns a 'ctypes.c_void_p' that points to a CASM project. (PrimClex)
"""
self.__load()
return self._ptr
def command(self, args):
"""
Execute a command via the c api.
Args:
args: A string containing the command to be executed. Ex: "select --set-on -o /abspath/to/my_selection"
Returns:
(stdout, stderr, returncode): The result of running the command via the command line iterface
"""
return self._command_via_capi(args)
def _command_via_capi(self, args):
"""
Execute a command via the c api.
Args:
args: A string containing the command to be executed. Ex: "select --set-on -o /abspath/to/my_selection"
Returns:
(stdout, stderr, returncode): The result of running the command via the command line iterface
"""
# this also ensures self._api is not None
data = self.data()
# construct stringstream objects to capture stdout, debug, stderr
ss = self._api.ostringstream_new()
ss_debug = self._api.ostringstream_new()
ss_err = self._api.ostringstream_new()
res = self._api(args, self.data(), self.path, ss, ss_debug, ss_err)
# copy strings and delete stringstreams
stdout = self._api.ostringstream_to_str(ss)
self._api.ostringstream_delete(ss)
self._api.ostringstream_delete(ss_debug)
stderr = self._api.ostringstream_to_str(ss_err)
self._api.ostringstream_delete(ss_err)
self.__refresh()
return (stdout, stderr, res)
class Project(object):
"""The Project class contains information about a CASM project
Attributes
----------
path: str
Path to project root directory
settings: casm.project.ProjectSettings instance
Contains project settings
dir: casm.project.DirectoryStructure instance
Provides file and directory locations within the project
casm_exe: str
The casm CLI executable to use when necessary
verbose: bool
How much to print to stdout
"""
def __init__(self, path=None, casm_exe=None, verbose=True):
"""
Construct a CASM Project representation.
Arguments
----------
path: str, optional, default=None
Path to project root directory. Default=None uses project containing
current working directory
casm_exe: str, optional, default=None
CASM executable to use for command line interface. Default
uses $CASM if it exists in the environment, else "casm".
verbose: bool, optional, default=True
How much to print to stdout
"""
# will hold a ctypes.c_void_p when loading CASM project into memory
self._ptr = None
# will keep a casm.API instance
self._api = None
# set path to this CASM project
if project_path(path) is None:
if path is None:
raise Exception("No CASM project found using " + os.getcwd())
else:
raise Exception("No CASM project found using " + path)
# set executable name
if casm_exe is None:
if "CASM" in os.environ:
casm_exe = os.environ["CASM"]
else:
casm_exe = "casm"
self.path = project_path(path)
self.__refresh()
self.casm_exe = casm_exe
self.verbose = verbose
def __del__(self):
self.__unload()
def __load(self):
"""
Explicitly load CASM project into memory.
"""
if self._ptr is None:
self._api = API()
if self.verbose:
streamptr = self._api.stdout()
else:
streamptr = self._api.nullstream()
if self.verbose:
errstreamptr = self._api.stderr()
else:
errstreamptr = self._api.nullstream()
self._ptr = self._api.primclex_new(self.path, streamptr, streamptr, errstreamptr)
def __unload(self):
"""
Explicitly unload CASM project from memory.
"""
if self._ptr is not None:
self._api.primclex_delete(self._ptr)
self._ptr = None
def __refresh(self):
"""
Reload self.settings and self.dir
Use this after adding or modifying files in the CASM project but no
special call to refresh PrimClex properties is required
"""
self.dir = DirectoryStructure(self.path)
self.settings = ProjectSettings(self.path)
def refresh(
self, read_settings=False, read_composition=False, read_chem_ref=False, read_configs=False, clear_clex=False
):
"""
Refresh PrimClex properties to reflect changes to CASM project files.
"""
if read_settings:
self.dir = DirectoryStructure(self.path)
self.settings = ProjectSettings(self.path)
if self._ptr is not None:
self._api.primclex_refresh(
self.data(), read_settings, read_composition, read_chem_ref, read_configs, clear_clex
)
def data(self):
"""
Returns a 'ctypes.c_void_p' that points to a CASM project. (PrimClex)
"""
self.__load()
return self._ptr
def command(self, args):
"""
Execute a command via the c api.
Args:
args: A string containing the command to be executed. Ex: "select --set-on -o /abspath/to/my_selection"
Returns:
(stdout, stderr, returncode): The result of running the command via the command line iterface
"""
return self._command_via_capi(args)
def _command_via_capi(self, args):
"""
Execute a command via the c api.
Args:
args: A string containing the command to be executed. Ex: "select --set-on -o /abspath/to/my_selection"
Returns:
(stdout, stderr, returncode): The result of running the command via the command line iterface
"""
# this also ensures self._api is not None
data = self.data()
# construct stringstream objects to capture stdout, debug, stderr
ss = self._api.ostringstream_new()
ss_debug = self._api.ostringstream_new()
ss_err = self._api.ostringstream_new()
res = self._api(args, self.data(), self.path, ss, ss_debug, ss_err)
# copy strings and delete stringstreams
stdout = self._api.ostringstream_to_str(ss)
self._api.ostringstream_delete(ss)
self._api.ostringstream_delete(ss_debug)
stderr = self._api.ostringstream_to_str(ss_err)
self._api.ostringstream_delete(ss_err)
self.__refresh()
return (stdout, stderr, res)