def prepare_data_script():
warn_deprecation()
logger_setup()
if "CONTAINED" not in os.environ:
log.error("This command should only be run within a container. "
"Run 'cobaya-install' instead.")
raise HandledException
parser = argparse.ArgumentParser(
description=
"Cobaya's installation tool for the data needed by a container.")
parser.add_argument(
"-f",
"--force",
action="store_true",
default=False,
help="Force re-installation of apparently installed modules.")
arguments = parser.parse_args()
try:
info = load_input(requirements_file_path)
except IOError:
log.error(
"Cannot find the requirements file. This should not be happening.")
raise HandledException
install(info,
path=_modules_path,
force=arguments.force,
**{
_code: False,
_data: True
})
def bib_script():
from cobaya.mpi import is_main_process
if not is_main_process():
return
warn_deprecation()
# Parse arguments and launch
import argparse
parser = argparse.ArgumentParser(
prog="cobaya bib",
description=
"Prints bibliography to be cited for a component or input file.")
parser.add_argument(
"components_or_files",
action="store",
nargs="+",
metavar="component_name or input_file.yaml",
help="Component(s) or input file(s) whose bib info is requested.")
kind_opt, kind_opt_ishort = "kind", 0
parser.add_argument(
"-" + kind_opt[kind_opt_ishort],
"--" + kind_opt,
action="store",
nargs=1,
default=None,
metavar="component_kind",
help=("If component name given, "
"kind of component whose bib is requested: " +
", ".join(['%s' % kind for kind in kinds]) + ". " +
"Use only when component name is not unique (it would fail)."))
arguments = parser.parse_args()
# Case of files
are_yaml = [(os.path.splitext(f)[1] in _yaml_extensions)
for f in arguments.components_or_files]
if all(are_yaml):
infos = [load_input(f) for f in arguments.components_or_files]
print(prettyprint_bib(*get_bib_info(*infos)))
elif not any(are_yaml):
if arguments.kind:
arguments.kind = arguments.kind[0].lower()
for component in arguments.components_or_files:
try:
print(
create_banner(component,
symbol=_default_symbol,
length=_default_length))
print(get_bib_component(component, arguments.kind))
return
except:
if not arguments.kind:
print(
"Specify its kind with '--%s [component_kind]'." %
kind_opt +
"(NB: all requested components must have the same kind, "
"or be requested separately).")
print("")
else:
print("Give either a list of input yaml files, "
"or of component names (not a mix of them).")
return 1
return
def create_docker_image(filenames, MPI_version=None):
log.info("Creating Docker image...")
if not MPI_version:
MPI_version = "3.2"
# log.warning("You have not specified an MPICH version. "
# "It is strongly encouraged to request the one installed in your cluster,"
# " using '--mpi-version X.Y'. Defaulting to MPICH v%s.", MPI_version)
dc = get_docker_client()
modules = yaml_dump(get_modules(*[load_input(f)
for f in filenames])).strip()
echos_reqs = "RUN " + " && \\ \n ".join([
r'echo "%s" >> %s' % (block, requirements_file_path)
for block in modules.split("\n")
])
echos_help = "RUN " + " && \\ \n ".join([
r'echo "%s" >> %s' % (line, help_file_path)
for line in image_help("docker").split("\n")
])
recipe = r"""
FROM cobaya/base_mpich_%s:latest
%s
RUN cobaya-install %s --%s %s --just-code --force ### NEEDS PYTHON UPDATE! --no-progress-bars
%s
CMD ["cat", "%s"]
""" % (MPI_version, echos_reqs, requirements_file_path, _modules_path_arg,
_modules_path, echos_help, help_file_path)
image_name = "cobaya:" + uuid.uuid4().hex[:6]
with StringIO(recipe) as stream:
dc.images.build(fileobj=stream, tag=image_name)
log.info(
"Docker image '%s' created! "
"Do 'docker save %s | gzip > some_name.tar.gz'"
"to save it to the current folder.", image_name, image_name)
def bib_script(args=None):
"""Command line script for the bibliography."""
warn_deprecation()
# Parse arguments and launch
import argparse
parser = argparse.ArgumentParser(
prog="cobaya bib",
description=
("Prints bibliography to be cited for one or more components or input files."
))
parser.add_argument(
"files_or_components",
action="store",
nargs="+",
metavar="input_file.yaml|component_name",
help="Component(s) or input file(s) whose bib info is requested.")
arguments = parser.parse_args(args)
# Configure the logger ASAP
logger_setup()
logger = get_logger("bib")
# Gather requests
infos: List[Union[Dict, str]] = []
for f in arguments.files_or_components:
if os.path.splitext(f)[1].lower() in Extension.yamls:
infos += [load_input(f)]
else: # a single component name, no kind specified
infos += [f]
if not infos:
logger.info(
"Nothing to do. Pass input files or component names as arguments.")
return
print(pretty_repr_bib(*get_bib_info(*infos, logger=logger)))
def citation_script():
from cobaya.mpi import am_single_or_primary_process
if am_single_or_primary_process():
# Configure the logger ASAP
from cobaya.log import logger_setup
logger_setup()
# Parse arguments and launch
import argparse
parser = argparse.ArgumentParser(description="Cobaya's citation tool.")
parser.add_argument("files", action="store", nargs="+", metavar="input_file.yaml",
help="One or more input files.")
from cobaya.input import load_input
infos = [load_input(f) for f in parser.parse_args().files]
print(prettyprint_citation(citation(*infos)))
def citation_script():
from cobaya.mpi import get_mpi_rank
if not get_mpi_rank():
# Configure the logger ASAP
from cobaya.log import logger_setup
logger_setup()
# Parse arguments and launch
import argparse
parser = argparse.ArgumentParser(description="Cobaya's citation tool.")
parser.add_argument("files", action="store", nargs="+", metavar="input_file.yaml",
help="One or more input files.")
from cobaya.input import load_input
infos = [load_input(f) for f in parser.parse_args().files]
citation(*infos)
def create_singularity_image(filenames, MPI_version=None):
log.info("Creating Singularity image...")
if not MPI_version:
MPI_version = "2.1.1"
# log.warning("You have not specified an OpenMPI version. "
# "It is strongly encouraged to request the one installed in your cluster,"
# " using '--mpi-version X.Y.Z'. Defaulting to OpenMPI v%s.", MPI_version)
components = yaml_dump(
get_used_components(*[load_input(f) for f in filenames])).strip()
echos_reqs = "\n " + "\n ".join([""] + [
'echo "%s" >> %s' % (block, requirements_file_path)
for block in components.split("\n")
])
recipe = (
dedent("""
Bootstrap: docker
From: cobaya/base_openmpi_%s:latest\n
%%post\n""" % MPI_version) + dedent(echos_reqs) + dedent("""
export CONTAINED=TRUE
cobaya-install %s --%s %s --just-code --force ### --no-progress-bars
mkdir $COBAYA_PRODUCTS
%%help
%s
""" % (
requirements_file_path,
# TODO: this looks wrong?
packages_path_input,
os.path.join(packages_path_arg, packages_path_input, data_path),
"\n ".join(image_help("singularity").split("\n")[1:]))))
with NamedTemporaryFile(delete=False) as recipe_file:
recipe_file.write(recipe.encode('utf-8'))
recipe_file_name = recipe_file.name
image_name = "cobaya_" + uuid.uuid4().hex[:6] + ".simg"
process_build = Popen(
["singularity", "build", image_name, recipe_file_name],
stdout=PIPE,
stderr=PIPE)
out, err = process_build.communicate()
if process_build.returncode:
log.info(out)
log.info(err)
raise LoggedError(log,
"Image creation failed! See error message above.")
log.info("Singularity image '%s' created!", image_name)
def install_script():
from cobaya.mpi import am_single_or_primary_process
if not am_single_or_primary_process():
# Configure the logger ASAP
logger_setup()
log = logging.getLogger(__name__.split(".")[-1])
# Parse arguments
import argparse
parser = argparse.ArgumentParser(
description="Cobaya's installation tool for external modules.")
parser.add_argument(
"files",
action="store",
nargs="+",
metavar="input_file.yaml",
help="One or more input files "
"(or 'cosmo' for a basic collection of cosmological modules)")
parser.add_argument(
"-" + _modules_path_arg[0],
"--" + _modules_path_arg,
action="store",
nargs=1,
required=True,
metavar="/install/path",
help="Desired path where to install external modules.")
parser.add_argument(
"-f",
"--force",
action="store_true",
default=False,
help="Force re-installation of apparently installed modules.")
parser.add_argument(
"--no-progress-bars",
action="store_true",
default=False,
help="No progress bars shown. Shorter logs (used in Travis).")
group_just = parser.add_mutually_exclusive_group(required=False)
group_just.add_argument("-C",
"--just-code",
action="store_false",
default=True,
help="Install code of the modules.",
dest=_data)
group_just.add_argument("-D",
"--just-data",
action="store_false",
default=True,
help="Install data of the modules.",
dest=_code)
arguments = parser.parse_args()
if arguments.files == ["cosmo"]:
log.info(
"Installing cosmological modules (input files will be ignored")
from cobaya.cosmo_input import install_basic
infos = [install_basic]
else:
from cobaya.input import load_input
infos = [load_input(f) for f in arguments.files]
# Launch installer
install(*infos,
path=getattr(arguments, _modules_path_arg)[0],
**{
arg: getattr(arguments, arg)
for arg in ["force", _code, _data, "no_progress_bars"]
})
def install_script():
set_mpi_disabled(True)
warn_deprecation()
# Parse arguments
import argparse
parser = argparse.ArgumentParser(
description="Cobaya's installation tool for external packages.")
parser.add_argument(
"files_or_components",
action="store",
nargs="+",
metavar="input_file.yaml|component_name",
help="One or more input files or component names "
"(or simply 'cosmo' to install all the requisites for basic"
" cosmological runs)")
parser.add_argument(
"-" + _packages_path_arg[0],
"--" + _packages_path_arg_posix,
action="store",
nargs=1,
required=False,
metavar="/packages/path",
default=[None],
help="Desired path where to install external packages. "
"Optional if one has been set globally or as an env variable"
" (run with '--show_%s' to check)." % _packages_path_arg_posix)
# 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!
output_show_packages_path = resolve_packages_path()
if output_show_packages_path and os.environ.get(_packages_path_env):
output_show_packages_path += " (from env variable %r)" % _packages_path_env
elif output_show_packages_path:
output_show_packages_path += " (from config file)"
else:
output_show_packages_path = "(Not currently set.)"
parser.add_argument(
"--show-" + _packages_path_arg_posix,
action="version",
version=output_show_packages_path,
help="Prints default external packages installation folder "
"and exits.")
parser.add_argument(
"-" + _force[0],
"--" + _force,
action="store_true",
default=False,
help="Force re-installation of apparently installed packages.")
parser.add_argument(
"--skip",
action="store",
nargs="*",
metavar="keyword",
help="Keywords of components that will be skipped during "
"installation.")
parser.add_argument(
"--no-progress-bars",
action="store_true",
default=False,
help="No progress bars shown. Shorter logs (used in Travis).")
parser.add_argument("--just-check",
action="store_true",
default=False,
help="Just check whether components are installed.")
parser.add_argument(
"--no-set-global",
action="store_true",
default=False,
help="Do not store the installation path for later runs.")
group_just = parser.add_mutually_exclusive_group(required=False)
group_just.add_argument("-C",
"--just-code",
action="store_false",
default=True,
help="Install code of the components.",
dest=_data)
group_just.add_argument("-D",
"--just-data",
action="store_false",
default=True,
help="Install data of the components.",
dest=_code)
arguments = parser.parse_args()
# Configure the logger ASAP
logger_setup()
logger = logging.getLogger(__name__.split(".")[-1])
# Gather requests
infos = []
for f in arguments.files_or_components:
if f.lower() == "cosmo":
logger.info("Installing basic cosmological packages.")
from cobaya.cosmo_input import install_basic
infos += [install_basic]
elif f.lower() == "cosmo-tests":
logger.info("Installing *tested* cosmological packages.")
from cobaya.cosmo_input import install_tests
infos += [install_tests]
elif os.path.splitext(f)[1].lower() in _yaml_extensions:
from cobaya.input import load_input
infos += [load_input(f)]
else:
try:
kind = get_kind(f)
infos += [{kind: {f: None}}]
except Exception:
logger.warning("Could not identify component %r. Skipping.", f)
if not infos:
logger.info("Nothing to install.")
return
# MARKED FOR DEPRECATION IN v3.0
if getattr(arguments, modules) != [None]:
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))
# END OF DEPRECATION BLOCK
# Launch installer
install(*infos,
path=getattr(arguments, _packages_path_arg)[0],
**{
arg: getattr(arguments, arg)
for arg in [
"force", _code, _data, "no_progress_bars", "just_check",
"no_set_global", "skip"
]
})
def post(info, sample=None):
logger_setup(info.get(_debug), info.get(_debug_file))
log = logging.getLogger(__name__.split(".")[-1])
try:
info_post = info[_post]
except KeyError:
log.error("No 'post' block given. Nothing to do!")
raise HandledException
if get_mpi_rank():
log.warning(
"Post-processing is not yet MPI-able. Doing nothing for rank > 1 processes."
)
return
# 1. Load existing sample
output_in = Output(output_prefix=info.get(_output_prefix), resume=True)
info_in = load_input(output_in.file_full) if output_in else deepcopy(info)
dummy_model_in = DummyModel(info_in[_params], info_in[_likelihood],
info_in.get(_prior, None),
info_in.get(_theory, None))
if output_in:
i = 0
while True:
try:
collection = Collection(dummy_model_in,
output_in,
name="%d" % (1 + i),
load=True,
onload_skip=info_post.get("skip", 0),
onload_thin=info_post.get("thin", 1))
if i == 0:
collection_in = collection
else:
collection_in._append(collection)
i += 1
except IOError:
break
elif sample:
if isinstance(sample, Collection):
sample = [sample]
collection_in = deepcopy(sample[0])
for s in sample[1:]:
try:
collection_in._append(s)
except:
log.error("Failed to load some of the input samples.")
raise HandledException
i = len(sample)
else:
log.error(
"Not output from where to load from or input collections given.")
raise HandledException
log.info("Loaded %d chain%s. Will process %d samples.", i,
"s" if i - 1 else "", collection_in.n())
if collection_in.n() <= 1:
log.error(
"Not enough samples for post-processing. Try using a larger sample, "
"or skipping or thinning less.")
raise HandledException
# 2. Compare old and new info: determine what to do
add = info_post.get("add", {})
remove = info_post.get("remove", {})
# Add a dummy 'one' likelihood, to absorb unused parameters
if not add.get(_likelihood):
add[_likelihood] = odict()
add[_likelihood].update({"one": None})
# Expand the "add" info
add = get_full_info(add)
# 2.1 Adding/removing derived parameters and changes in priors of sampled parameters
out = {_params: deepcopy(info_in[_params])}
for p in remove.get(_params, {}):
pinfo = info_in[_params].get(p)
if pinfo is None or not is_derived_param(pinfo):
log.error(
"You tried to remove parameter '%s', which is not a derived paramter. "
"Only derived parameters can be removed during post-processing.",
p)
raise HandledException
out[_params].pop(p)
mlprior_names_add = []
for p, pinfo in add.get(_params, {}).items():
pinfo_in = info_in[_params].get(p)
if is_sampled_param(pinfo):
if not is_sampled_param(pinfo_in):
# No added sampled parameters (de-marginalisation not implemented)
if pinfo_in is None:
log.error(
"You added a new sampled parameter %r (maybe accidentaly "
"by adding a new likelihood that depends on it). "
"Adding new sampled parameters is not possible. Try fixing "
"it to some value.", p)
raise HandledException
else:
log.error(
"You tried to change the prior of parameter '%s', "
"but it was not a sampled parameter. "
"To change that prior, you need to define as an external one.",
p)
raise HandledException
if mlprior_names_add[:1] != _prior_1d_name:
mlprior_names_add = (
[_minuslogprior + _separator + _prior_1d_name] +
mlprior_names_add)
elif is_derived_param(pinfo):
if p in out[_params]:
log.error(
"You tried to add derived parameter '%s', which is already "
"present. To force its recomputation, 'remove' it too.", p)
raise HandledException
elif is_fixed_param(pinfo):
# Only one possibility left "fixed" parameter that was not present before:
# input of new likelihood, or just an argument for dynamical derived (dropped)
if ((p in info_in[_params] and pinfo[_p_value] !=
(pinfo_in or {}).get(_p_value, None))):
log.error(
"You tried to add a fixed parameter '%s: %r' that was already present"
" but had a different value or was not fixed. This is not allowed. "
"The old info of the parameter was '%s: %r'", p,
dict(pinfo), p, dict(pinfo_in))
raise HandledException
else:
log.error("This should not happen. Contact the developers.")
raise HandledException
out[_params][p] = pinfo
# For the likelihood only, turn the rest of *derived* parameters into constants,
# so that the likelihoods do not try to compute them)
# But be careful to exclude *input* params that have a "derived: True" value
# (which in "full info" turns into "derived: 'lambda [x]: [x]'")
out_params_like = deepcopy(out[_params])
for p, pinfo in out_params_like.items():
if ((is_derived_param(pinfo) and not (_p_value in pinfo)
and p not in add.get(_params, {}))):
out_params_like[p] = {_p_value: np.nan, _p_drop: True}
parameterization_like = Parameterization(out_params_like,
ignore_unused_sampled=True)
# 2.2 Manage adding/removing priors and likelihoods
warn_remove = False
for level in [_prior, _likelihood]:
out[level] = getattr(dummy_model_in, level)
if level == _prior:
out[level].remove(_prior_1d_name)
for pdf in info_post.get("remove", {}).get(level, []) or []:
try:
out[level].remove(pdf)
warn_remove = True
except ValueError:
log.error(
"Trying to remove %s '%s', but it is not present. "
"Existing ones: %r", level, pdf, out[level])
raise HandledException
if warn_remove:
log.warning("You are removing a prior or likelihood pdf. "
"Notice that if the resulting posterior is much wider "
"than the original one, or displaced enough, "
"it is probably safer to explore it directly.")
if _prior in add:
mlprior_names_add += [
_minuslogprior + _separator + name for name in add[_prior]
]
out[_prior] += list(add[_prior])
prior_recompute_1d = (mlprior_names_add[:1] == [
_minuslogprior + _separator + _prior_1d_name
])
# Don't initialise the theory code if not adding/recomputing theory,
# theory-derived params or likelihoods
recompute_theory = info_in.get(_theory) and not (list(
add[_likelihood]) == ["one"] and not any([
is_derived_param(pinfo) for pinfo in add.get(_params, {}).values()
]))
if recompute_theory:
# Inherit from the original chain (needs input|output_params, renames, etc
theory = list(info_in[_theory].keys())[0]
info_theory_out = odict([[
theory,
recursive_update(deepcopy(info_in[_theory][theory]),
add.get(_theory, {theory: {}})[theory])
]])
else:
info_theory_out = None
chi2_names_add = [
_chi2 + _separator + name for name in add[_likelihood]
if name is not "one"
]
out[_likelihood] += [l for l in add[_likelihood] if l is not "one"]
if recompute_theory:
log.warn(
"You are recomputing the theory, but in the current version this does "
"not force recomputation of any likelihood or derived parameter, "
"unless explicitly removed+added.")
for level in [_prior, _likelihood]:
for i, x_i in enumerate(out[level]):
if x_i in list(out[level])[i + 1:]:
log.error(
"You have added %s '%s', which was already present. If you "
"want to force its recomputation, you must also 'remove' it.",
level, x_i)
raise HandledException
# 3. Create output collection
if "suffix" not in info_post:
log.error("You need to provide a 'suffix' for your chains.")
raise HandledException
# Use default prefix if it exists. If it does not, produce no output by default.
# {post: {output: None}} suppresses output, and if it's a string, updates it.
out_prefix = info_post.get(_output_prefix, info.get(_output_prefix))
if out_prefix not in [None, False]:
out_prefix += "_" + _post + "_" + info_post["suffix"]
output_out = Output(output_prefix=out_prefix,
force_output=info.get(_force))
info_out = deepcopy(info)
info_out[_post] = info_post
# Updated with input info and extended (full) add info
info_out.update(info_in)
info_out[_post]["add"] = add
dummy_model_out = DummyModel(out[_params],
out[_likelihood],
info_prior=out[_prior])
if recompute_theory:
theory = list(info_theory_out.keys())[0]
if _input_params not in info_theory_out[theory]:
log.error(
"You appear to be post-processing a chain generated with an older "
"version of Cobaya. For post-processing to work, please edit the "
"'[root]__full.info' file of the original chain to add, inside the "
"theory code block, the list of its input parameters. E.g.\n----\n"
"theory:\n %s:\n input_params: [param1, param2, ...]\n"
"----\nIf you get strange errors later, it is likely that you did not "
"specify the correct set of theory parameters.\n"
"The full set of input parameters are %s.", theory,
list(dummy_model_out.parameterization.input_params()))
raise HandledException
prior_add = Prior(dummy_model_out.parameterization, add.get(_prior))
likelihood_add = Likelihood(add[_likelihood],
parameterization_like,
info_theory=info_theory_out,
modules=info.get(_path_install))
# Remove auxiliary "one" before dumping -- 'add' *is* info_out[_post]["add"]
add[_likelihood].pop("one")
if likelihood_add.theory:
# Make sure that theory.needs is called at least once, for adjustments
likelihood_add.theory.needs()
collection_out = Collection(dummy_model_out, output_out, name="1")
output_out.dump_info({}, info_out)
# 4. Main loop!
log.info("Running post-processing...")
last_percent = 0
for i, point in enumerate(collection_in.data.itertuples()):
log.debug("Point: %r", point)
sampled = [
getattr(point, param)
for param in dummy_model_in.parameterization.sampled_params()
]
derived = odict(
[[param, getattr(point, param, None)]
for param in dummy_model_out.parameterization.derived_params()])
inputs = odict([[
param,
getattr(
point, param,
dummy_model_in.parameterization.constant_params().get(
param,
dummy_model_out.parameterization.constant_params().get(
param, None)))
] for param in dummy_model_out.parameterization.input_params()])
# Solve inputs that depend on a function and were not saved
# (we don't use the Parameterization_to_input method in case there are references
# to functions that cannot be loaded at the moment)
for p, value in inputs.items():
if value is None:
func = dummy_model_out.parameterization._input_funcs[p]
args = dummy_model_out.parameterization._input_args[p]
inputs[p] = func(*[getattr(point, arg) for arg in args])
# Add/remove priors
priors_add = prior_add.logps(sampled)
if not prior_recompute_1d:
priors_add = priors_add[1:]
logpriors_add = odict(zip(mlprior_names_add, priors_add))
logpriors_new = [
logpriors_add.get(name, -getattr(point, name, 0))
for name in collection_out.minuslogprior_names
]
if log.getEffectiveLevel() <= logging.DEBUG:
log.debug("New set of priors: %r",
dict(zip(dummy_model_out.prior, logpriors_new)))
if -np.inf in logpriors_new:
continue
# Add/remove likelihoods
output_like = []
if likelihood_add:
# Notice "one" (last in likelihood_add) is ignored: not in chi2_names
loglikes_add = odict(
zip(chi2_names_add,
likelihood_add.logps(inputs, _derived=output_like)))
output_like = dict(zip(likelihood_add.output_params, output_like))
else:
loglikes_add = dict()
loglikes_new = [
loglikes_add.get(name, -0.5 * getattr(point, name, 0))
for name in collection_out.chi2_names
]
if log.getEffectiveLevel() <= logging.DEBUG:
log.debug("New set of likelihoods: %r",
dict(zip(dummy_model_out.likelihood, loglikes_new)))
if output_like:
log.debug("New set of likelihood-derived parameters: %r",
output_like)
if -np.inf in loglikes_new:
continue
# Add/remove derived parameters and change priors of sampled parameters
for p in add[_params]:
if p in dummy_model_out.parameterization._directly_output:
derived[p] = output_like[p]
elif p in dummy_model_out.parameterization._derived_funcs:
func = dummy_model_out.parameterization._derived_funcs[p]
args = dummy_model_out.parameterization._derived_args[p]
derived[p] = func(*[
getattr(point, arg, output_like.get(arg, None))
for arg in args
])
if log.getEffectiveLevel() <= logging.DEBUG:
log.debug(
"New derived parameters: %r",
dict([[
p, derived[p]
] for p in dummy_model_out.parameterization.derived_params()
if p in add[_params]]))
# Save to the collection (keep old weight for now)
collection_out.add(sampled,
derived=derived.values(),
weight=getattr(point, _weight),
logpriors=logpriors_new,
loglikes=loglikes_new)
# Display progress
percent = np.round(i / collection_in.n() * 100)
if percent != last_percent and not percent % 5:
last_percent = percent
progress_bar(log, percent, " (%d/%d)" % (i, collection_in.n()))
if not collection_out.data.last_valid_index():
log.error(
"No elements in the final sample. Possible causes: "
"added a prior or likelihood valued zero over the full sampled domain, "
"or the computation of the theory failed everywhere, etc.")
raise HandledException
# Reweight -- account for large dynamic range!
# Prefer to rescale +inf to finite, and ignore final points with -inf.
# Remove -inf's (0-weight), and correct indices
difflogmax = max(collection_in[_minuslogpost] -
collection_out[_minuslogpost])
collection_out.data[_weight] *= np.exp(collection_in[_minuslogpost] -
collection_out[_minuslogpost] -
difflogmax)
collection_out.data = (
collection_out.data[collection_out.data.weight > 0].reset_index(
drop=True))
collection_out._n = collection_out.data.last_valid_index() + 1
# Write!
collection_out._out_update()
log.info("Finished! Final number of samples: %d", collection_out.n())
return info_out, {"sample": collection_out}
def install_script(args=None):
set_mpi_disabled()
warn_deprecation()
# Parse arguments
import argparse
parser = argparse.ArgumentParser(
prog="cobaya install",
description="Cobaya's installation tool for external packages.")
parser.add_argument(
"files_or_components",
action="store",
nargs="+",
metavar="input_file.yaml|component_name",
help="One or more input files or component names "
"(or simply 'cosmo' to install all the requisites for basic"
" cosmological runs)")
parser.add_argument(
"-" + packages_path_arg[0],
"--" + packages_path_arg_posix,
action="store",
required=False,
metavar="/packages/path",
default=None,
help="Desired path where to install external packages. "
"Optional if one has been set globally or as an env variable"
" (run with '--show_%s' to check)." % packages_path_arg_posix)
# MARKED FOR DEPRECATION IN v3.0
modules = "modules"
parser.add_argument("-" + modules[0],
"--" + modules,
action="store",
required=False,
metavar="/packages/path",
default=None,
help="Deprecated! Use %s instead." %
packages_path_arg_posix)
# END OF DEPRECATION BLOCK -- CONTINUES BELOW!
output_show_packages_path = resolve_packages_path()
if output_show_packages_path and os.environ.get(packages_path_env):
output_show_packages_path += " (from env variable %r)" % packages_path_env
elif output_show_packages_path:
output_show_packages_path += " (from config file)"
else:
output_show_packages_path = "(Not currently set.)"
parser.add_argument(
"--show-" + packages_path_arg_posix,
action="version",
version=output_show_packages_path,
help="Prints default external packages installation folder "
"and exits.")
parser.add_argument(
"-" + "f",
"--" + "force",
action="store_true",
default=False,
help="Force re-installation of apparently installed packages.")
parser.add_argument(
"--skip",
action="store",
nargs="*",
metavar="keyword",
help="Keywords of components that will be skipped during "
"installation.")
parser.add_argument(
"--no-progress-bars",
action="store_true",
default=False,
help="No progress bars shown. Shorter logs (used in Travis).")
parser.add_argument("--%s" % "test",
action="store_true",
default=False,
help="Just check whether components are installed.")
# MARKED FOR DEPRECATION IN v3.0
parser.add_argument("--just-check",
action="store_true",
default=False,
help="Just check whether components are installed.")
# END OF DEPRECATION BLOCK -- CONTINUES BELOW!
parser.add_argument(
"--no-set-global",
action="store_true",
default=False,
help="Do not store the installation path for later runs.")
parser.add_argument(
"--skip-global",
action="store_true",
default=False,
help="Skip installation of already-available Python modules.")
parser.add_argument("-" + "d",
"--" + "debug",
action="store_true",
help="Produce verbose debug output.")
group_just = parser.add_mutually_exclusive_group(required=False)
group_just.add_argument("-C",
"--just-code",
action="store_false",
default=True,
help="Install code of the components.",
dest=data_path)
group_just.add_argument("-D",
"--just-data",
action="store_false",
default=True,
help="Install data of the components.",
dest=code_path)
arguments = parser.parse_args(args)
# Configure the logger ASAP
logger_setup()
logger = get_logger("install")
# Gather requests
infos: List[InputDict] = []
for f in arguments.files_or_components:
if f.lower() == "cosmo":
logger.info("Installing basic cosmological packages.")
from cobaya.cosmo_input import install_basic
infos += [install_basic]
elif f.lower() == "cosmo-tests":
logger.info("Installing *tested* cosmological packages.")
from cobaya.cosmo_input import install_tests
infos += [install_tests]
elif os.path.splitext(f)[1].lower() in Extension.yamls:
from cobaya.input import load_input
infos += [load_input(f)]
else:
try:
kind = get_kind(f)
infos += [{kind: {f: None}}]
except Exception:
logger.warning("Could not identify component %r. Skipping.", f)
if not infos:
logger.info("Nothing to install.")
return
# List of deprecation warnings, to be printed *after* installation
deprecation_warnings = []
# MARKED FOR DEPRECATION IN v3.0
if getattr(arguments, modules) is not None:
raise LoggedError(
logger, "-m/--modules has been deprecated in favor of "
"-%s/--%s", packages_path_arg[0], packages_path_arg_posix)
# END OF DEPRECATION BLOCK
# MARKED FOR DEPRECATION IN v3.0
if arguments.just_check is True:
raise LoggedError(logger,
"--just-check has been deprecated in favor of --%s",
"test")
# END OF DEPRECATION BLOCK
# Launch installer
install(*infos,
path=getattr(arguments, packages_path_arg),
**{
arg: getattr(arguments, arg)
for arg in [
"force", code_path, data_path, "no_progress_bars", "test",
"no_set_global", "skip", "skip_global", "debug"
]
})
# MARKED FOR DEPRECATION IN v3.0
for warning_msg in deprecation_warnings:
logger.warning(warning_msg)
def install_script():
from cobaya.mpi import get_mpi_rank
if not get_mpi_rank():
# Configure the logger ASAP
logger_setup()
log = logging.getLogger(__name__.split(".")[-1])
# Parse arguments
import argparse
parser = argparse.ArgumentParser(
description="Cobaya's installation tool for external modules.")
parser.add_argument("files",
action="store",
nargs="+",
metavar="input_file.yaml",
help="One or more input files.")
parser.add_argument(
"-p",
"--path",
action="store",
nargs=1,
required=True,
metavar="/install/path",
help="Desired path where to install external modules.")
parser.add_argument(
"-f",
"--force",
action="store_true",
default=False,
help="Force re-installation of apparently installed modules.")
parser.add_argument(
"--no-progress-bars",
action="store_true",
default=False,
help="No progress bars shown. Shorter logs (used in Travis).")
group_just = parser.add_mutually_exclusive_group(required=False)
group_just.add_argument("-c",
"--just-code",
action="store_false",
default=True,
help="Install code of the modules.",
dest=_data)
group_just.add_argument("-d",
"--just-data",
action="store_false",
default=True,
help="Install data of the modules.",
dest=_code)
arguments = parser.parse_args()
from cobaya.input import load_input
try:
infos = [load_input(f) for f in arguments.files]
except HandledException:
log.error("Maybe you meant to pass an installation path? "
"In that case, use '--path=/path/to/modules'.")
raise HandledException
# Launch installer
install(*infos,
path=arguments.path[0],
**{
arg: getattr(arguments, arg)
for arg in ["force", _code, _data, "no_progress_bars"]
})
def install_script(args=None):
"""Command line script for the installer."""
set_mpi_disabled()
warn_deprecation()
# Parse arguments
import argparse
parser = argparse.ArgumentParser(
prog="cobaya install",
description="Cobaya's installation tool for external packages.")
parser.add_argument(
"files_or_components",
action="store",
nargs="+",
metavar="input_file.yaml|component_name",
help="One or more input files or component names "
"(or simply 'cosmo' to install all the requisites for basic"
" cosmological runs)")
parser.add_argument(
"-" + packages_path_arg[0],
"--" + packages_path_arg_posix,
action="store",
required=False,
metavar="/packages/path",
default=None,
help="Desired path where to install external packages. "
"Optional if one has been set globally or as an env variable"
" (run with '--show_%s' to check)." % packages_path_arg_posix)
output_show_packages_path = resolve_packages_path()
if output_show_packages_path and os.environ.get(packages_path_env):
output_show_packages_path += " (from env variable %r)" % packages_path_env
elif output_show_packages_path:
output_show_packages_path += " (from config file)"
else:
output_show_packages_path = "(Not currently set.)"
parser.add_argument(
"--show-" + packages_path_arg_posix,
action="version",
version=output_show_packages_path,
help="Prints default external packages installation folder "
"and exits.")
parser.add_argument(
"-" + "f",
"--" + "force",
action="store_true",
default=False,
help="Force re-installation of apparently installed packages.")
parser.add_argument("--%s" % "test",
action="store_true",
default=False,
help="Just check whether components are installed.")
parser.add_argument("--upgrade",
action="store_true",
default=False,
help="Force upgrade of obsolete components.")
parser.add_argument("--skip",
action="store",
nargs="*",
metavar="keyword",
help=("Keywords of components that will be "
"skipped during installation."))
parser.add_argument(
"--skip-global",
action="store_true",
default=False,
help="Skip installation of already-available Python modules.")
parser.add_argument("-" + "d",
"--" + "debug",
action="store_true",
help="Produce verbose debug output.")
group_just = parser.add_mutually_exclusive_group(required=False)
group_just.add_argument("-C",
"--just-code",
action="store_false",
default=True,
help="Install code of the components.",
dest=data_path)
group_just.add_argument("-D",
"--just-data",
action="store_false",
default=True,
help="Install data of the components.",
dest=code_path)
parser.add_argument(
"--no-progress-bars",
action="store_true",
default=False,
help=("No progress bars shown; use when output is saved into a "
"text file (e.g. when running on a cluster)."))
parser.add_argument(
"--no-set-global",
action="store_true",
default=False,
help="Do not store the installation path for later runs.")
arguments = parser.parse_args(args)
# Configure the logger ASAP
logger_setup(arguments.debug)
logger = get_logger("install")
# Gather requests
infos: List[Union[InputDict, str]] = []
for f in arguments.files_or_components:
if f.lower() == "cosmo":
logger.info("Installing basic cosmological packages.")
from cobaya.cosmo_input import install_basic
infos += [install_basic]
elif f.lower() == "cosmo-tests":
logger.info("Installing *tested* cosmological packages.")
from cobaya.cosmo_input import install_tests
infos += [install_tests]
elif os.path.splitext(f)[1].lower() in Extension.yamls:
from cobaya.input import load_input
infos += [load_input(f)]
else: # a single component name, no kind specified
infos += [f]
# Launch installer
install(*infos,
path=getattr(arguments, packages_path_arg),
logger=logger,
**{
arg: getattr(arguments, arg)
for arg in [
"force", code_path, data_path, "no_progress_bars", "test",
"no_set_global", "skip", "skip_global", "debug", "upgrade"
]
})
