def open_preferences(self):
from kromatography.utils.app_utils import get_preferences
from kromatography.tools.preferences_view import \
RevealChromatographyPreferenceView
prefs = get_preferences()
view = RevealChromatographyPreferenceView(model=prefs)
view.edit_traits(kind="livemodal")
def _job_manager_default(self):
from kromatography.model.factories.job_manager import \
create_start_job_manager
from kromatography.utils.app_utils import get_preferences
preferences = get_preferences()
job_manager = create_start_job_manager(
max_workers=preferences.solver_preferences.executor_num_worker)
return job_manager
def _setup_logging(self):
from kromatography.utils.app_utils import get_preferences, \
initialize_logging
if self.verbose:
verbose = True
else:
preferences = get_preferences()
verbose = preferences.app_preferences.console_logging_level <= 10
self.log_filepath = initialize_logging(verbose=verbose)
def _submit_simulations_as_job(sims):
""" New Generator function for creating sim_workitems but avoiding passing
a complicated HasTraits instance since they are painful to pickle/unpickle.
Parameters
----------
sims : list
List of simulations to submit as a job work item.
"""
from kromatography.solve.api import run_cadet_simulator
from kromatography.utils.app_utils import get_preferences
prefs = get_preferences()
use_slurm = prefs.solver_preferences.use_slurm_scheduler
for sim in sims:
output_file = prepare_simulation_for_run(sim)
yield run_cadet_simulator, (output_file,), {"use_slurm": use_slurm}
def _prepare_exit(self):
""" Do any application-level state saving and clean-up.
"""
from kromatography.utils.app_utils import empty_cadet_input_folder, \
get_preferences
if self.job_manager:
self.job_manager.shutdown()
self.job_manager = None
# Lazily load preferences to give a chance to a user to change that
# parameters after starting:
preferences = get_preferences()
if preferences.solver_preferences.auto_delete_solver_files_on_exit:
empty_cadet_input_folder()
# Remember the recent files
preferences.file_preferences.recent_files = self.recent_files
preferences.to_preference_file()
def param_scans_to_sim_group(group_name,
parameter_scans,
center_sim,
lazy_loading=False,
max_size=None,
group_type=SIM_GROUP_GRID_TYPE,
group_size=-1,
auto_delete_run_sims=False):
""" Returns simulation grid from a list of regular parameter scans.
Parameters
----------
group_name : str
Target group name.
parameter_scans : list(ParameterScanDescription)
List of parameter scan descriptions.
center_sim : Simulation
Center point simulation from which to create all simulations in the
future group.
group_type : str [OPTIONAL]
Type of the future group(s) to be created. Should be one of the values
allowed for the :attr:`simulation_group.SimulationGroup.type`
attribute. Set to a regular grid by default.
lazy_loading : bool (default: False)
Save memory by making the output group of the lazy loading kind.
max_size : None or int [OPTIONAL]
Max size of the group(s) created. If a non-zero value is specified, a
list of simulation group is returned, each with a number of simulation
diffs smaller or equal to max_size.
group_size : int [OPTIONAL]
Size of the resulting group, used only if of Monte-Carlo type. Size is
computed from parameter scan descriptions for the grid type.
auto_delete_run_sims : bool [OPTIONAL, default=False]
Delete CADET files and in memory simulations once they run?
Returns
-------
SimulationGroup or list(SimulationGroup)
SimulationGroup created from the list of parameter scans the group
should explore. If a max_size is provided, returns a list of
SimulationGroup instances collectively scanning the entire parameter
space described by parameter_scans, each with 0 < size <= max_size.
"""
# Override the number of threads per run from preferences in case it has
# changed. Do it on the center sim to avoid having to do it on each
# simulation of the group:
prefs = get_preferences()
target_nthreads = prefs.solver_preferences.cadet_num_threads
if lazy_loading and not isinstance(center_sim, LazyLoadingSimulation):
center_sim = LazyLoadingSimulation.from_simulation(center_sim)
center_sim.solver.nthreads = target_nthreads
else:
# if the nthreads will be overridden, make a copy to avoid modifying
# the source simulation
if center_sim.solver.nthreads != target_nthreads:
center_sim = center_sim.copy()
center_sim.solver.nthreads = target_nthreads
if group_type == SIM_GROUP_GRID_TYPE:
simulation_diffs = sim_diffs_from_grid_parameter_scans(parameter_scans)
elif group_type == SIM_GROUP_MC_TYPE:
simulation_diffs = sim_diffs_from_random_parameter_scans(
parameter_scans, group_size)
else:
msg = "Unsupported group type: {}".format(group_type)
logger.exception(msg)
raise ValueError(msg)
return build_group_or_groups(group_name,
center_sim,
simulation_diffs,
max_size,
group_type=group_type,
auto_delete_run_sims=auto_delete_run_sims)
def _max_recent_files_default(self):
from kromatography.utils.app_utils import get_preferences
preferences = get_preferences()
return preferences.file_preferences.max_recent_files
def _confirm_on_window_close_default(self):
from kromatography.utils.app_utils import get_preferences
prefs = get_preferences()
ui_prefs = prefs.ui_preferences
return ui_prefs.confirm_on_window_close
def _auto_close_empty_windows_on_open_default(self):
from kromatography.utils.app_utils import get_preferences
prefs = get_preferences()
ui_prefs = prefs.ui_preferences
return ui_prefs.auto_close_empty_windows_on_open
def _window_size_default(self):
from kromatography.utils.app_utils import get_preferences
prefs = get_preferences()
ui_prefs = prefs.ui_preferences
return ui_prefs.app_width, ui_prefs.app_height
def _balance_threshold_default(self):
from kromatography.utils.app_utils import get_preferences
prefs = get_preferences()
return prefs.file_preferences.exp_importer_mass_threshold
def _get_app_pref_view(self):
return AppPreferencesView(model=self.model.app_preferences)
def _get_ui_prefs_view(self):
return UIPreferencesView(model=self.model.ui_preferences)
def _get_solver_prefs_view(self):
return SolverPreferencesView(model=self.model.solver_preferences)
def _get_file_pref_view(self):
return FilePreferencesView(model=self.model.file_preferences)
def factory_reset(self):
self.model = RevealChromatographyPreferences(
preference_filepath=get_preference_file()
)
def _instructions_default(self):
return "Most preferences will take effect as soon as the preferences" \
" are saved. No need to restart the application unless " \
"specified."
if __name__ == '__main__':
from kromatography.utils.app_utils import get_preferences
prefs = get_preferences()
view = RevealChromatographyPreferenceView(model=prefs)
view.configure_traits()
def test_get_local_preferences(self):
reset_preferences(target_file=join(HERE, "preferences.yaml"))
prefs = get_preferences(fileloc=HERE)
assert_has_traits_almost_equal(prefs,
RevealChromatographyPreferences())
def test_get_default_preferences(self):
prefs = get_preferences()
self.assertIsInstance(prefs, RevealChromatographyPreferences)
self.assertEqual(prefs.version, CUR_VERSION)
def _nthreads_default(self):
from kromatography.utils.app_utils import get_preferences
prefs = get_preferences()
return prefs.solver_preferences.cadet_num_threads
def _slurm_binary_default(self):
from kromatography.utils.app_utils import get_preferences
prefs = get_preferences()
return prefs.solver_preferences.slurm_binary
def setUp(self):
self.prefs = get_preferences()