def initialize(self, fname=None, dir='.'):
"""Initialize the model.
Parameters
----------
fname : str
Name of initialization file.
dir : str
Path to folder in which to run initialization.
"""
# if len(args) == 0:
# args = (self.setup(case=kwds.pop('case', 'default')), )
# if bmi_call(self.bmi.initialize, *args) == 0:
# self._initialized = True
self._initdir = os.path.abspath(dir)
with cd(self.initdir, create=False):
if bmi_call(self.bmi.initialize, fname or '') == 0:
self._initialized = True
for grid_id in self._grid_ids():
self._grid[grid_id] = dataset_from_bmi_grid(self, grid_id)
for name in set(self.output_var_names + self.input_var_names):
self._var[name] = DataValues(self, name)
def conda_build(recipes, dir='.', batch_mode=False, which_conda=None):
conda = which_conda or which('conda')
env = {
'PATH':
os.pathsep.join([
'/usr/bin',
'/bin',
'/usr/sbin',
'/etc',
'/usr/lib',
]),
}
files_to_upload = []
with cd(dir):
with homebrew_hidden(prompt=not batch_mode):
with setenv(env, verbose=True):
status('pwd: {dir}'.format(dir=dir))
system([conda, 'clean', '--all'])
for recipe in recipes:
try:
system([
conda, 'build', '-c', 'conda-forge', '-c',
'csdms/channel/dev', recipe
])
except CalledProcessError:
break
else:
files_to_upload.append(
conda_build_output(recipe, which_conda=conda))
return files_to_upload
def run_notebook(notebook):
with cd(os.path.dirname(notebook) or '.'):
script = convert_notebook(os.path.basename(notebook))
_, script_file = tempfile.mkstemp(prefix='.', suffix='.py', dir='.')
with open(script_file, 'wb') as fp:
fp.write(script)
try:
subprocess.check_call(['ipython', script_file])
except Exception:
raise
finally:
os.remove(script_file)
def update_until(self, then, method=None, units=None):
with cd(self.initdir):
then = self.time_from(then, units)
if hasattr(self.bmi, "update_until"):
try:
self.bmi.update_until(then)
except NotImplementedError:
pass
self.reset()
while self.get_current_time() < then:
if self.get_current_time() + self.get_time_step() > then:
self.add_data()
self.update()
if self.get_current_time() > then:
self.add_data()
def update_until(self, then, method=None, units=None):
with cd(self.initdir):
then = self.time_from(then, units)
if hasattr(self.bmi, "update_until"):
try:
self.bmi.update_until(then)
except NotImplementedError:
pass
self.reset()
while self.time < then:
if self.time + self.time_step > then:
self.add_data()
self.update()
if self.time > then:
self.add_data()
def initialize(self, fname=None, dir="."): # pylint: disable=redefined-builtin
"""Initialize the model.
Parameters
----------
fname : str
Name of initialization file.
dir : str
Path to folder in which to run initialization.
"""
self._initdir = os.path.abspath(dir)
with cd(self.initdir, create=False):
self.bmi.initialize(fname or "")
self._initialized = True
for grid_id in self._grid_ids():
self._grid[grid_id] = dataset_from_bmi_grid(self, grid_id)
for name in set(self.output_var_names + self.input_var_names):
self._var[name] = DataValues(self, name)
def conda_build(recipes, dir='.', batch_mode=False, which_conda=None):
conda = which_conda or which('conda')
env = {
'PATH': os.pathsep.join(['/usr/bin', '/bin', '/usr/sbin', '/etc',
'/usr/lib', ]), }
files_to_upload = []
with cd(dir):
with homebrew_hidden(prompt=not batch_mode):
with setenv(env, verbose=True):
status('pwd: {dir}'.format(dir=dir))
system([conda, 'clean', '--all'])
for recipe in recipes:
try:
system([conda, 'build', '-c', 'conda-forge',
'-c', 'csdms/channel/dev', recipe])
except CalledProcessError:
break
else:
files_to_upload.append(
conda_build_output(recipe, which_conda=conda))
return files_to_upload
def setup(self, *args, **kwds):
"""Set up a simulation.
Parameters
----------
path : str, optional
Path to a folder to set up the simulation. If not given,
use a temporary folder.
Returns
-------
str
Path to the folder that contains the set up simulation.
"""
if len(args) == 0:
dir_ = tempfile.mkdtemp()
else:
dir_ = args[0]
self._parameters.update(kwds)
FileSystemLoader(self.datadir).stage_all(dir_, **self._parameters)
config = self._meta.run["config_file"]
if config["contents"] and not config["path"]:
config["path"] = dir_
if config["path"]:
with cd(dir_):
config_file = FileTemplate.write(
config["contents"], config["path"], **self._parameters
)
else:
config_file = None
return config_file, os.path.abspath(dir_)
def setup(self, *args, **kwds):
"""Set up a simulation.
Parameters
----------
path : str, optional
Path to a folder to set up the simulation. If not given,
use a temporary folder.
Returns
-------
str
Path to the folder that contains the set up simulation.
"""
if len(args) == 0:
dir_ = tempfile.mkdtemp()
else:
dir_ = args[0]
self._parameters.update(kwds)
FileSystemLoader(self.datadir).stage_all(dir_, **self._parameters)
config = self._meta.run["config_file"]
if config["contents"] and not config["path"]:
config["path"] = dir_
if config["path"]:
with cd(dir_):
config_file = FileTemplate.write(
config["contents"], config["path"], **self._parameters
)
else:
config_file = None
return config_file, os.path.abspath(dir_)
def run(self):
with cd('pymt_{{cookiecutter.plugin_name}}/lib'):
build_interoperability()
_build_ext.run(self)
def finalize(self):
with cd(self.initdir):
self._initialized = False
return self.bmi.finalize()
def update(self):
with cd(self.initdir):
return self.bmi.update()
def finalize(self):
with cd(self.initdir):
return bmi_call(self.bmi.finalize)
def update(self):
with cd(self.initdir):
return bmi_call(self.bmi.update)
