def run_tardis(
config,
atom_data=None,
packet_source=None,
simulation_callbacks=[],
virtual_packet_logging=False,
):
"""
This function is one of the core functions to run TARDIS from a given
config object.
It will return a model object containing
Parameters
----------
config : str or dict or tardis.io.config_reader.Configuration
filename of configuration yaml file or dictionary or TARDIS Configuration object
atom_data : str or tardis.atomic.AtomData
if atom_data is a string it is interpreted as a path to a file storing
the atomic data. Atomic data to use for this TARDIS simulation. If set to None, the
atomic data will be loaded according to keywords set in the configuration
[default=None]
virtual_packet_logging : bool
option to enable virtual packet logging
[default=False]
Returns
-------
Simulation
"""
from tardis.io.config_reader import Configuration
from tardis.io.atom_data.base import AtomData
from tardis.simulation import Simulation
if atom_data is not None:
try:
atom_data = AtomData.from_hdf(atom_data)
except TypeError:
atom_data = atom_data
if isinstance(config, Configuration):
tardis_config = config
else:
try:
tardis_config = Configuration.from_yaml(config)
except TypeError:
tardis_config = Configuration.from_config_dict(config)
simulation = Simulation.from_config(
tardis_config,
packet_source=packet_source,
atom_data=atom_data,
virtual_packet_logging=virtual_packet_logging,
)
for cb in simulation_callbacks:
simulation.add_callback(*cb)
simulation.run()
return simulation
def atomic_dataset(atomic_data_fname):
atomic_data = AtomData.from_hdf(atomic_data_fname)
if atomic_data.md5 != DEFAULT_ATOM_DATA_UUID:
pytest.skip('Need default Kurucz atomic dataset (md5="{}"'.format(
DEFAULT_ATOM_DATA_UUID))
else:
return atomic_data
def atomic_dataset(atomic_data_fname):
atomic_data = AtomData.from_hdf(atomic_data_fname)
if atomic_data.md5 != DEFAULT_ATOM_DATA_UUID:
pytest.skip(
'Need default Kurucz atomic dataset (md5="{}"'.format(
DEFAULT_ATOM_DATA_UUID))
else:
return atomic_data
def run_tardis(config,
atom_data=None,
packet_source=None,
simulation_callbacks=[]):
"""
This function is one of the core functions to run TARDIS from a given
config object.
It will return a model object containing
Parameters
----------
config: ~str or ~dict
filename of configuration yaml file or dictionary
atom_data: ~str or ~tardis.atomic.AtomData
if atom_data is a string it is interpreted as a path to a file storing
the atomic data. Atomic data to use for this TARDIS simulation. If set to None, the
atomic data will be loaded according to keywords set in the configuration
[default=None]
"""
from tardis.io.config_reader import Configuration
from tardis.io.atom_data.base import AtomData
from tardis.simulation import Simulation
if atom_data is not None:
try:
atom_data = AtomData.from_hdf(atom_data)
except TypeError:
atom_data = atom_data
try:
tardis_config = Configuration.from_yaml(config)
except TypeError:
tardis_config = Configuration.from_config_dict(config)
simulation = Simulation.from_config(tardis_config,
packet_source=packet_source,
atom_data=atom_data)
for cb in simulation_callbacks:
simulation.add_callback(*cb)
simulation.run()
return simulation
def run_tardis(config, atom_data=None, simulation_callbacks=[]):
"""
This function is one of the core functions to run TARDIS from a given
config object.
It will return a model object containing
Parameters
----------
config: ~str or ~dict
filename of configuration yaml file or dictionary
atom_data: ~str or ~tardis.atomic.AtomData
if atom_data is a string it is interpreted as a path to a file storing
the atomic data. Atomic data to use for this TARDIS simulation. If set to None, the
atomic data will be loaded according to keywords set in the configuration
[default=None]
"""
from tardis.io.config_reader import Configuration
from tardis.io.atom_data.base import AtomData
from tardis.simulation import Simulation
if atom_data is not None:
try:
atom_data = AtomData.from_hdf(atom_data)
except TypeError:
atom_data = atom_data
try:
tardis_config = Configuration.from_yaml(config)
except TypeError:
tardis_config = Configuration.from_config_dict(config)
simulation = Simulation.from_config(tardis_config, atom_data=atom_data)
for cb in simulation_callbacks:
simulation.add_callback(cb)
simulation.run()
return simulation
def setup(self, request, reference, data_path, pytestconfig):
"""
This method does initial setup of creating configuration and performing
a single run of integration test.
"""
# Get capture manager
capmanager = pytestconfig.pluginmanager.getplugin('capturemanager')
# The last component in dirpath can be extracted as name of setup.
self.name = data_path['setup_name']
self.config_file = os.path.join(data_path['config_dirpath'], "config.yml")
# A quick hack to use atom data per setup. Atom data is ingested from
# local HDF or downloaded and cached from a url, depending on data_path
# keys.
atom_data_name = yaml.load(
open(self.config_file), Loader=yaml.CLoader)['atom_data']
# Get the path to HDF file:
atom_data_filepath = os.path.join(
data_path['atom_data_path'], atom_data_name
)
# Load atom data file separately, pass it for forming tardis config.
self.atom_data = AtomData.from_hdf(atom_data_filepath)
# Check whether the atom data file in current run and the atom data
# file used in obtaining the reference data are same.
# TODO: hard coded UUID for kurucz atom data file, generalize it later.
# kurucz_data_file_uuid1 = "5ca3035ca8b311e3bb684437e69d75d7"
# assert self.atom_data.uuid1 == kurucz_data_file_uuid1
# Create a Configuration through yaml file and atom data.
tardis_config = Configuration.from_yaml(self.config_file)
# Check whether current run is with less packets.
if request.config.getoption("--less-packets"):
less_packets = request.config.integration_tests_config['less_packets']
tardis_config['montecarlo']['no_of_packets'] = (
less_packets['no_of_packets']
)
tardis_config['montecarlo']['last_no_of_packets'] = (
less_packets['last_no_of_packets']
)
# We now do a run with prepared config and get the simulation object.
self.result = Simulation.from_config(tardis_config,
atom_data=self.atom_data)
capmanager.suspend_global_capture(True)
# If current test run is just for collecting reference data, store the
# output model to HDF file, save it at specified path. Skip all tests.
# Else simply perform the run and move further for performing
# assertions.
self.result.run()
if request.config.getoption("--generate-reference"):
ref_data_path = os.path.join(
data_path['reference_path'], "{0}.h5".format(self.name)
)
if os.path.exists(ref_data_path):
pytest.skip(
'Reference data {0} does exist and tests will not '
'proceed generating new data'.format(ref_data_path))
self.result.to_hdf(file_path=ref_data_path)
pytest.skip("Reference data saved at {0}".format(
data_path['reference_path']
))
capmanager.resume_global_capture()
# Get the reference data through the fixture.
self.reference = reference
def run_tardis(
config,
atom_data=None,
packet_source=None,
simulation_callbacks=[],
virtual_packet_logging=False,
show_cplots=True,
log_level=None,
specific_log_level=None,
**kwargs,
):
"""
Run TARDIS from a given config object.
It will return a model object containing the TARDIS Simulation.
Parameters
----------
config : str or dict or tardis.io.config_reader.Configuration
filename of configuration yaml file or dictionary or TARDIS Configuration object
atom_data : str or tardis.atomic.AtomData, optional
If atom_data is a string it is interpreted as a path to a file storing
the atomic data. Atomic data to use for this TARDIS simulation. If set to None (i.e. default),
the atomic data will be loaded according to keywords set in the configuration
packet_source : class, optional
A custom packet source class or a child class of `tardis.montecarlo.packet_source`
used to override the TARDIS `BasePacketSource` class.
simulation_callbacks : list of lists, default: `[]`, optional
Set of callbacks to call at the end of every iteration of the Simulation.
The format of the lists should look like:
[[callback1, callback_arg1], [callback2, callback_arg2], ...],
where the callback function signature should look like:
callback_function(simulation, extra_arg1, ...)
virtual_packet_logging : bool, default: False, optional
Option to enable virtual packet logging.
log_level : {'NOTSET', 'DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL'}, default: None, optional
Set the level of the TARDIS logger (follows native python logging framework log levels).
Use this parameter to override the `log_level` specified in the configuration file.
The default value `None` means that the `log_level` specified in the configuration file will be used.
specific_log_level : bool, default: None, optional
Allows to set specific logging levels, overriding the value in the configuration file.
If True, only show the log messages from a particular log level, set by `log_level`.
If False, the logger shows log messages belonging to the level set and all levels above it in severity.
The default value None means that the `specific_log_level` specified in the configuration file will be used.
show_cplots : bool, default: True, optional
Option to enable tardis convergence plots.
**kwargs : dict, optional
Optional keyword arguments including those
supported by :obj:`tardis.visualization.tools.convergence_plot.ConvergencePlots`.
Returns
-------
tardis.simulation.Simulation
Notes
-----
Please see the `logging tutorial <https://tardis-sn.github.io/tardis/io/optional/logging_configuration.html>`_ to know more about `log_level` and `specific` options.
"""
from tardis.io.logger.logger import logging_state
from tardis.io.config_reader import Configuration
from tardis.io.atom_data.base import AtomData
from tardis.simulation import Simulation
if isinstance(config, Configuration):
tardis_config = config
else:
try:
tardis_config = Configuration.from_yaml(config)
except TypeError:
logger.debug(
"TARDIS Config not available via YAML. Reading through TARDIS Config Dictionary"
)
tardis_config = Configuration.from_config_dict(config)
if not isinstance(show_cplots, bool):
raise TypeError("Expected bool in show_cplots argument")
logging_state(log_level, tardis_config, specific_log_level)
if atom_data is not None:
try:
atom_data = AtomData.from_hdf(atom_data)
except TypeError:
logger.debug(
"Atom Data Cannot be Read from HDF. Setting to Default Atom Data"
)
atom_data = atom_data
simulation = Simulation.from_config(
tardis_config,
packet_source=packet_source,
atom_data=atom_data,
virtual_packet_logging=virtual_packet_logging,
show_cplots=show_cplots,
**kwargs,
)
for cb in simulation_callbacks:
simulation.add_callback(*cb)
simulation.run()
return simulation
def setup(self, request, reference, data_path, pytestconfig):
"""
This method does initial setup of creating configuration and performing
a single run of integration test.
"""
# Get capture manager
capmanager = pytestconfig.pluginmanager.getplugin('capturemanager')
# The last component in dirpath can be extracted as name of setup.
self.name = data_path['setup_name']
self.config_file = os.path.join(data_path['config_dirpath'], "config.yml")
# A quick hack to use atom data per setup. Atom data is ingested from
# local HDF or downloaded and cached from a url, depending on data_path
# keys.
atom_data_name = yaml.load(open(self.config_file))['atom_data']
# Get the path to HDF file:
atom_data_filepath = os.path.join(
data_path['atom_data_path'], atom_data_name
)
# Load atom data file separately, pass it for forming tardis config.
self.atom_data = AtomData.from_hdf(atom_data_filepath)
# Check whether the atom data file in current run and the atom data
# file used in obtaining the reference data are same.
# TODO: hard coded UUID for kurucz atom data file, generalize it later.
# kurucz_data_file_uuid1 = "5ca3035ca8b311e3bb684437e69d75d7"
# assert self.atom_data.uuid1 == kurucz_data_file_uuid1
# Create a Configuration through yaml file and atom data.
tardis_config = Configuration.from_yaml(self.config_file)
# Check whether current run is with less packets.
if request.config.getoption("--less-packets"):
less_packets = request.config.integration_tests_config['less_packets']
tardis_config['montecarlo']['no_of_packets'] = (
less_packets['no_of_packets']
)
tardis_config['montecarlo']['last_no_of_packets'] = (
less_packets['last_no_of_packets']
)
# We now do a run with prepared config and get the simulation object.
self.result = Simulation.from_config(tardis_config,
atom_data=self.atom_data)
capmanager.suspendcapture(True)
# If current test run is just for collecting reference data, store the
# output model to HDF file, save it at specified path. Skip all tests.
# Else simply perform the run and move further for performing
# assertions.
self.result.run()
if request.config.getoption("--generate-reference"):
ref_data_path = os.path.join(
data_path['reference_path'], "{0}.h5".format(self.name)
)
if os.path.exists(ref_data_path):
pytest.skip(
'Reference data {0} does exist and tests will not '
'proceed generating new data'.format(ref_data_path))
self.result.to_hdf(file_path=ref_data_path)
pytest.skip("Reference data saved at {0}".format(
data_path['reference_path']
))
capmanager.resumecapture()
# Get the reference data through the fixture.
self.reference = reference