def get_output(*args, **kwargs):
"""
Auxiliary function to retrieve the output driver
(e.g. whether to get the MPI-wrapped one, or a dummy output driver).
"""
if kwargs.get("output_prefix"):
from cobaya.mpi import import_MPI
return import_MPI(".output", "Output")(*args, **kwargs)
else:
return OutputDummy(*args, **kwargs)
def get_Output(*args, **kwargs):
"""
Auxiliary function to retrieve the output driver.
"""
if kwargs.get("output_prefix"):
from cobaya.mpi import import_MPI
Output = import_MPI(".output", "Output")
return Output(*args, **kwargs)
else:
return OutputDummy(*args, **kwargs)
def get_output(*args, **kwargs):
"""
Auxiliary function to retrieve the output driver
(e.g. whether to get the MPI-wrapped one, or a dummy output driver).
"""
# MARKED FOR DEPRECATION IN v3.0
if kwargs.get("output_prefix") is not None:
kwargs["prefix"] = kwargs["output_prefix"]
# END OF DEPRECATION BLOCK
if kwargs.get("prefix"):
from cobaya.mpi import import_MPI
return import_MPI(".output", "Output")(*args, **kwargs)
else:
return OutputDummy(*args, **kwargs)
def run_script():
import os
import argparse
from cobaya.conventions import _path_install, _debug
parser = argparse.ArgumentParser(description="Cobaya's run script.")
parser.add_argument("input_file",
nargs=1,
action="store",
metavar="input_file.yaml",
help="An input file to run.")
parser.add_argument(
"-p",
"--path",
action="store",
nargs="+",
metavar="/some/path",
help="Path where modules were automatically installed.")
parser.add_argument("--" + _debug,
action="store_true",
help="Set this flag for debug output.")
args = parser.parse_args()
if any([(os.path.splitext(f)[0] in ("input", "full"))
for f in args.input_file]):
raise ValueError("'input' and 'full' are reserved file names. "
"Please, use a different one.")
from cobaya.mpi import import_MPI
load_input = import_MPI(".input", "load_input")
info = load_input(args.input_file[0])
# solve path
path_env = os.environ.get("COBAYA_MODULES", None)
path_cmd = (lambda x: x[0] if x else None)(getattr(args, "path"))
path_input = info.get(_path_install)
if path_cmd and path_input:
raise ValueError(
"*CONFLICT* You have specified a modules folder both in the command line "
"('%s') and the input file ('%s'). There should only be one." %
(path_cmd, path_input))
info[_path_install] = path_input or (path_cmd or path_env)
if getattr(args, _debug):
info[_debug] = True
run(info)
def run_script():
warn_deprecation()
import os
import argparse
parser = argparse.ArgumentParser(description="Cobaya's run script.")
parser.add_argument("input_file",
nargs=1,
action="store",
metavar="input_file.yaml",
help="An input file to run.")
parser.add_argument("-" + _packages_path_arg[0],
"--" + _packages_path_arg_posix,
action="store",
nargs=1,
metavar="/packages/path",
default=[None],
help="Path where external packages were installed.")
# MARKED FOR DEPRECATION IN v3.0
modules = "modules"
parser.add_argument("-" + modules[0],
"--" + modules,
action="store",
nargs=1,
required=False,
metavar="/packages/path",
default=[None],
help="To be deprecated! "
"Alias for %s, which should be used instead." %
_packages_path_arg_posix)
# END OF DEPRECATION BLOCK -- CONTINUES BELOW!
parser.add_argument("-" + _output_prefix[0],
"--" + _output_prefix,
action="store",
nargs=1,
metavar="/some/path",
default=[None],
help="Path and prefix for the text output.")
parser.add_argument("-" + _debug[0],
"--" + _debug,
action="store_true",
help="Produce verbose debug output.")
continuation = parser.add_mutually_exclusive_group(required=False)
continuation.add_argument(
"-" + _resume[0],
"--" + _resume,
action="store_true",
help="Resume an existing chain if it has similar info "
"(fails otherwise).")
continuation.add_argument("-" + _force[0],
"--" + _force,
action="store_true",
help="Overwrites previous output, if it exists "
"(use with care!)")
parser.add_argument("--%s" % _test_run,
action="store_true",
help="Initialize model and sampler, and exit.")
parser.add_argument("--version", action="version", version=__version__)
parser.add_argument("--no-mpi",
action='store_true',
help="disable MPI when mpi4py installed but MPI does "
"not actually work")
arguments = parser.parse_args()
if arguments.no_mpi or getattr(arguments, _test_run, False):
set_mpi_disabled()
if any((os.path.splitext(f)[0] in ("input", "updated"))
for f in arguments.input_file):
raise ValueError("'input' and 'updated' are reserved file names. "
"Please, use a different one.")
load_input = import_MPI(".input", "load_input")
given_input = arguments.input_file[0]
if any(given_input.lower().endswith(ext) for ext in _yaml_extensions):
info = load_input(given_input)
output_prefix_cmd = getattr(arguments, _output_prefix)[0]
output_prefix_input = info.get(_output_prefix)
info[_output_prefix] = output_prefix_cmd or output_prefix_input
else:
# Passed an existing output_prefix? Try to find the corresponding *.updated.yaml
updated_file = get_info_path(*split_prefix(given_input),
kind="updated")
try:
info = load_input(updated_file)
except IOError:
raise ValueError(
"Not a valid input file, or non-existent run to resume")
# We need to update the output_prefix to resume the run *where it is*
info[_output_prefix] = given_input
# If input given this way, we obviously want to resume!
info[_resume] = True
# solve packages installation path cmd > env > input
# MARKED FOR DEPRECATION IN v3.0
if getattr(arguments, modules) != [None]:
logger_setup()
logger = logging.getLogger(__name__.split(".")[-1])
logger.warning(
"*DEPRECATION*: -m/--modules will be deprecated in favor of "
"-%s/--%s in the next version. Please, use that one instead.",
_packages_path_arg[0], _packages_path_arg_posix)
# BEHAVIOUR TO BE REPLACED BY ERROR:
if getattr(arguments, _packages_path_arg) == [None]:
setattr(arguments, _packages_path_arg, getattr(arguments, modules))
# BEHAVIOUR TO BE REPLACED BY ERROR:
check_deprecated_modules_path(info)
# END OF DEPRECATION BLOCK
info[_packages_path] = \
getattr(arguments, _packages_path_arg)[0] or info.get(_packages_path)
info[_debug] = getattr(arguments, _debug) or info.get(
_debug, _debug_default)
info[_test_run] = getattr(arguments, _test_run, False)
# If any of resume|force given as cmd args, ignore those in the input file
resume_arg, force_arg = [
getattr(arguments, arg) for arg in [_resume, _force]
]
if any([resume_arg, force_arg]):
info[_resume], info[_force] = resume_arg, force_arg
if _post in info:
post(info)
else:
run(info)
def run_script():
warn_deprecation()
import os
import argparse
parser = argparse.ArgumentParser(description="Cobaya's run script.")
parser.add_argument("input_file",
nargs=1,
action="store",
metavar="input_file.yaml",
help="An input file to run.")
parser.add_argument(
"-" + _modules_path_arg[0],
"--" + _modules_path_arg,
action="store",
nargs=1,
metavar="/some/path",
default=[None],
help="Path where modules were automatically installed.")
parser.add_argument("-" + _output_prefix[0],
"--" + _output_prefix,
action="store",
nargs=1,
metavar="/some/path",
default=[None],
help="Path and prefix for the text output.")
parser.add_argument("-" + _debug[0],
"--" + _debug,
action="store_true",
help="Produce verbose debug output.")
continuation = parser.add_mutually_exclusive_group(required=False)
continuation.add_argument(
"-" + _resume[0],
"--" + _resume,
action="store_true",
help="Resume an existing chain if it has similar info "
"(fails otherwise).")
continuation.add_argument("-" + _force[0],
"--" + _force,
action="store_true",
help="Overwrites previous output, if it exists "
"(use with care!)")
parser.add_argument("--version", action="version", version=__version__)
args = parser.parse_args()
if any([(os.path.splitext(f)[0] in ("input", "updated"))
for f in args.input_file]):
raise ValueError("'input' and 'updated' are reserved file names. "
"Please, use a different one.")
load_input = import_MPI(".input", "load_input")
given_input = args.input_file[0]
if any(given_input.lower().endswith(ext) for ext in _yaml_extensions):
info = load_input(given_input)
output_prefix_cmd = getattr(args, _output_prefix)[0]
output_prefix_input = info.get(_output_prefix)
info[_output_prefix] = output_prefix_cmd or output_prefix_input
else:
# Passed an existing output_prefix? Try to find the corresponding *.updated.yaml
updated_file = (
given_input +
(_separator_files if not given_input.endswith(os.sep) else "") +
_updated_suffix + _yaml_extensions[0])
try:
info = load_input(updated_file)
except IOError:
raise ValueError(
"Not a valid input file, or non-existent sample to resume")
# We need to update the output_prefix to resume the sample *where it is*
info[_output_prefix] = given_input
# If input given this way, we obviously want to resume!
info[_resume] = True
# solve modules installation path cmd > env > input
path_cmd = getattr(args, _modules_path_arg)[0]
path_env = os.environ.get(_modules_path_env, None)
path_input = info.get(_path_install)
info[_path_install] = path_cmd or (path_env or path_input)
info[_debug] = getattr(args, _debug) or info.get(_debug, _debug_default)
info[_resume] = getattr(args, _resume, _resume_default)
info[_force] = getattr(args, _force, False)
if _post in info:
post(info)
else:
run(info)
def run(info):
assert hasattr(info, "items"), (
"The agument of `run` must be a dictionary with the info needed for the run. "
"If you were trying to pass an input file instead, load it first with "
"`cobaya.input.load_input`.")
# Import names
from cobaya.conventions import _likelihood, _prior, _params
from cobaya.conventions import _theory, _sampler, _path_install
from cobaya.conventions import _debug, _debug_file, _output_prefix
# Configure the logger ASAP
from cobaya.log import logger_setup
logger_setup(info.get(_debug), info.get(_debug_file))
# Debug (lazy call)
import logging
if logging.root.getEffectiveLevel() <= logging.DEBUG:
# Don't dump unless we are doing output, just in case something not serializable
# May be fixed in the future if we find a way to serialize external functions
if info.get(_output_prefix):
from cobaya.yaml import yaml_dump
logging.getLogger(__name__.split(".")[-1]).debug(
"Input info (dumped to YAML):\n%s", yaml_dump(info))
# Import general classes
from cobaya.prior import Prior
from cobaya.sampler import get_Sampler as Sampler
# Import the functions and classes that need MPI wrapping
from cobaya.mpi import import_MPI
# Likelihood = import_MPI(".likelihood", "LikelihoodCollection")
from cobaya.likelihood import LikelihoodCollection as Likelihood
# Initialise output, if requiered
do_output = info.get(_output_prefix)
if do_output:
Output = import_MPI(".output", "Output")
output = Output(info)
else:
from cobaya.output import Output_dummy
output = Output_dummy(info)
# Create the full input information, including defaults for each module.
from cobaya.input import get_full_info
full_info = get_full_info(info)
if logging.root.getEffectiveLevel() <= logging.DEBUG:
# Don't dump unless we are doing output, just in case something not serializable
# May be fixed in the future if we find a way to serialize external functions
if info.get(_output_prefix):
logging.getLogger(__name__.split(".")[-1]).debug(
"Updated info (dumped to YAML):\n%s", yaml_dump(full_info))
# We dump the info now, before modules initialization, lest it is accidentaly modified
output.dump_info(info, full_info)
# Set the path of the installed modules, if given
from cobaya.tools import set_path_to_installation
set_path_to_installation(info.get(_path_install))
# Initialise parametrization, likelihoods and prior
from cobaya.parametrization import Parametrization
with Parametrization(full_info[_params]) as par:
with Prior(par, full_info.get(_prior)) as prior:
with Likelihood(full_info[_likelihood], par,
full_info.get(_theory)) as lik:
with Sampler(full_info[_sampler], par, prior, lik,
output) as sampler:
sampler.run()
# For scripted calls
return deepcopy(full_info), sampler.products()
