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 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 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 citation_script():
warn_deprecation()
print(
create_banner(
"\nThis command will be deprecated soon. Use `cobaya-bib` instead.\n"
))
bib_script()
def gui_script():
warn_deprecation()
try:
app = QApplication(sys.argv)
except NameError:
# TODO: fix this long logger setup
from cobaya.log import logger_setup, LoggedError
logger_setup(0, None)
raise LoggedError(
"cosmo_generator", "PySide2 is not installed! "
"Check Cobaya's documentation for the cosmo_generator "
"('Basic cosmology runs').")
clip = app.clipboard()
window = MainWindow()
window.clipboard = clip
sys.exit(app.exec_())
def citation_script():
warn_deprecation()
from cobaya.mpi import am_single_or_primary_process
if am_single_or_primary_process():
warn_deprecation()
# 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 run_script(args=None):
"""Shell script wrapper for :func:`run.run` (including :func:`post.post`)"""
warn_deprecation()
import argparse
# kwargs for flags that should be True|None, instead of True|False
# (needed in order not to mistakenly override input file inside the run() function
trueNone_kwargs = {"action": "store_true", "default": None}
parser = argparse.ArgumentParser(
prog="cobaya run", description="Cobaya's run script.")
parser.add_argument("input_file", 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", metavar="/packages/path", default=None,
help="Path where external packages were installed.")
parser.add_argument("-" + "o", "--" + "output",
action="store", metavar="/some/path", default=None,
help="Path and prefix for the text output.")
parser.add_argument("-" + "d", "--" + "debug",
help="Produce verbose debug output.", **trueNone_kwargs)
continuation = parser.add_mutually_exclusive_group(required=False)
continuation.add_argument("-" + "r", "--" + "resume",
help=("Resume an existing chain if it has similar info "
"(fails otherwise)."), **trueNone_kwargs)
continuation.add_argument("-" + "f", "--" + "force",
help=("Overwrites previous output, if it exists "
"(use with care!)"), **trueNone_kwargs)
parser.add_argument("--%s" % "test",
help="Initialize model and sampler, and exit.", **trueNone_kwargs)
parser.add_argument("-M", "--minimize",
help=("Replaces the sampler in the input and runs a minimization "
"process (incompatible with post-processing)."),
**trueNone_kwargs)
parser.add_argument("--version", action="version", version=get_version())
parser.add_argument("--no-mpi",
help=("disable MPI when mpi4py installed but MPI does "
"not actually work"),
**trueNone_kwargs)
arguments = parser.parse_args(args)
info = arguments.input_file
del arguments.input_file
run(info, **arguments.__dict__)
def create_image_script():
warn_deprecation()
logger_setup()
parser = argparse.ArgumentParser(
prog="cobaya create-image",
description=(
"Cobaya's tool for preparing Docker (for Shifter) and Singularity images."))
parser.add_argument("files", action="store", nargs="+", metavar="input_file.yaml",
help="One or more input files.")
parser.add_argument("-v", "--mpi-version", action="store", default=None,
metavar="X.Y(.Z)", dest="version", help="Version of the MPI lib.")
group_type = parser.add_mutually_exclusive_group(required=True)
group_type.add_argument("-d", "--docker", action="store_const", const="docker",
help="Create a Docker image (for Shifter).", dest="type")
group_type.add_argument("-s", "--singularity", action="store_const", dest="type",
const="singularity", help="Create a Singularity image.")
arguments = parser.parse_args()
if arguments.type == "docker":
create_docker_image(arguments.files, MPI_version=arguments.version)
elif arguments.type == "singularity":
create_singularity_image(arguments.files, MPI_version=arguments.version)
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"
]
})
def run():
warn_deprecation()
Opts = batchjob_args.batchArgs(
'Submit jobs to run chains or importance sample',
notExist=True,
notall=True,
converge=True)
jobqueue.addArguments(Opts.parser, combinedJobs=True)
Opts.parser.add_argument('--subitems',
action='store_true',
help='include sub-grid items')
Opts.parser.add_argument('--not_queued', action='store_true')
Opts.parser.add_argument('--minimize',
action='store_true',
help='Run minimization jobs')
Opts.parser.add_argument('--importance_minimize',
action='store_true',
help=('Run minimization jobs for chains '
'that are importance sampled'))
Opts.parser.add_argument('--minimize_failed',
action='store_true',
help='run where minimization previously failed')
Opts.parser.add_argument(
'--checkpoint_run',
nargs='?',
default=None,
const=0,
type=float,
help=('run if stopped and not finished; if optional value '
'given then only run chains with convergence worse than '
'the given value'))
Opts.parser.add_argument(
'--importance_ready',
action='store_true',
help='where parent chain has converged and stopped')
Opts.parser.add_argument(
'--importance_changed',
action='store_true',
help=('run importance jobs where the parent chain has '
'changed since last run'))
Opts.parser.add_argument(
'--parent_converge',
type=float,
default=0,
help='minimum R-1 convergence for importance job parent')
Opts.parser.add_argument(
'--parent_stopped',
action='store_true',
help='only run if parent chain is not still running')
(batch, args) = Opts.parseForBatch()
if args.not_queued:
print('Getting queued names...')
queued = jobqueue.queue_job_names(args.batchPath)
def notQueued(name):
for job in queued:
if name in job:
# print 'Already running:', name
return False
return True
variant = ''
if args.importance_minimize:
variant = '_minimize'
if args.importance is None:
args.importance = []
if args.minimize:
args.noimportance = True
variant = '_minimize'
if args.importance is None:
if args.importance_changed or args.importance_ready:
args.importance = []
else:
args.noimportance = True
isMinimize = args.importance_minimize or args.minimize
if args.combine_one_job_name:
print('Combining multiple (hopefully fast) into single job script: ' +
args.combine_one_job_name)
global iniFiles
iniFiles = []
jobqueue.checkArguments(**args.__dict__)
def jobName():
s = "-".join(
[os.path.splitext(os.path.basename(ini))[0] for ini in iniFiles])
if len(iniFiles) < 2 or len(s) < 70:
return s
base = os.path.basename(iniFiles[0])
if len(base) > 70:
base = base[:70]
return base + '__' + hashlib.md5(s).hexdigest()[:16]
def submitJob(ini):
global iniFiles
if not args.dryrun:
print('Submitting...' + ini)
else:
print('... ' + ini)
iniFiles.append(ini)
if args.combine_one_job_name:
return
if len(iniFiles) >= args.runs_per_job:
if args.runs_per_job > 1:
print('--> jobName: ', jobName())
jobqueue.submitJob(jobName(), iniFiles, **args.__dict__)
iniFiles = []
for jobItem in Opts.filteredBatchItems(wantSubItems=args.subitems):
if ((not args.notexist or isMinimize and not jobItem.chainMinimumExists()
or not isMinimize and not jobItem.chainExists()) and (
not args.minimize_failed or not jobItem.chainMinimumConverged())
and (isMinimize or args.notall is None or not jobItem.allChainExists(args.notall))) \
and (not isMinimize or getattr(jobItem, 'want_minimize', True)):
if not args.parent_converge or not jobItem.isImportanceJob or jobItem.parent.hasConvergeBetterThan(
args.parent_converge):
if args.converge == 0 or not jobItem.hasConvergeBetterThan(
args.converge, returnNotExist=True):
if args.checkpoint_run is None or jobItem.wantCheckpointContinue(
args.checkpoint_run) and jobItem.notRunning():
if (not jobItem.isImportanceJob or isMinimize
or (args.importance_ready
and jobItem.parent.chainFinished()
or not args.importance_ready
and jobItem.parent.chainExists()) and
(not args.importance_changed
or jobItem.parentChanged()) and
(not args.parent_stopped
or jobItem.parent.notRunning())):
if not args.not_queued or notQueued(jobItem.name):
submitJob(jobItem.iniFile(variant))
if len(iniFiles) > 0:
if args.runs_per_job > 1: print('--> jobName: ', jobName())
jobqueue.submitJob(args.combine_one_job_name or jobName(),
iniFiles,
sequential=args.combine_one_job_name is not None,
**args.__dict__)
def doc_script():
from cobaya.mpi import am_single_or_primary_process
if not am_single_or_primary_process():
return
warn_deprecation()
# Parse arguments
import argparse
parser = argparse.ArgumentParser(
description="Prints defaults for Cobaya's internal modules.")
parser.add_argument("module",
action="store",
nargs="?",
default="",
metavar="module_name",
help="The module whose defaults are 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="module_kind",
help=("Kind of module whose defaults are requested: " +
", ".join(['%s' % kind for kind in _kinds]) + ". " +
"Use only when module name is not unique (it would fail)."))
parser.add_argument("-p",
"--python",
action="store_true",
default=False,
help="Request Python instead of YAML.")
expand_flag, expand_flag_ishort = "expand", 1
parser.add_argument("-" + expand_flag[expand_flag_ishort],
"--" + expand_flag,
action="store_true",
default=False,
help="Expand YAML defaults.")
arguments = parser.parse_args()
# Remove plurals (= name of src subfolders), for user-friendliness
if arguments.module.lower() in subfolders.values():
arguments.module = next(k for k in subfolders
if arguments.module == subfolders[k])
# Kind given, list all
if not arguments.module:
msg = "Available modules: (some may need external code/data)"
print(msg + "\n" + "-" * len(msg))
for kind in _kinds:
print("%s:" % kind)
print(_indent + ("\n" + _indent).join(get_available_modules(kind)))
return
# Kind given: list all modules of that kind
if arguments.module.lower() in _kinds:
print("%s:" % arguments.module.lower())
print(_indent +
("\n" +
_indent).join(get_available_modules(arguments.module.lower())))
return
# Otherwise, check if it's a unique module name
try:
if arguments.kind:
arguments.kind = arguments.kind[0].lower()
to_print = get_default_info(arguments.module,
arguments.kind,
return_yaml=not arguments.python,
yaml_expand_defaults=arguments.expand,
fail_if_not_found=True)
if arguments.python:
print(import_odict + pformat(to_print))
else:
print(to_print)
if "!defaults" in to_print:
print("# This file contains defaults. "
"To populate them, use the flag --%s (or -%s)." %
(expand_flag, expand_flag[expand_flag_ishort]))
except:
if not arguments.kind:
print("Specify its kind with '--%s [module_kind]'." % kind_opt)
return 1
return
def run_script(args=None):
warn_deprecation()
import argparse
parser = argparse.ArgumentParser(prog="cobaya run",
description="Cobaya's run script.")
parser.add_argument("input_file",
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",
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",
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("-" + "o",
"--" + "output",
action="store",
metavar="/some/path",
default=None,
help="Path and prefix for the text output.")
parser.add_argument("-" + "d",
"--" + "debug",
action="store_true",
help="Produce verbose debug output.")
continuation = parser.add_mutually_exclusive_group(required=False)
continuation.add_argument(
"-" + "r",
"--" + "resume",
action="store_true",
help="Resume an existing chain if it has similar info "
"(fails otherwise).")
continuation.add_argument("-" + "f",
"--" + "force",
action="store_true",
help="Overwrites previous output, if it exists "
"(use with care!)")
parser.add_argument("--%s" % "test",
action="store_true",
help="Initialize model and sampler, and exit.")
parser.add_argument("--version", action="version", version=get_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(args)
# MARKED FOR DEPRECATION IN v3.0
if arguments.modules is not None:
logger_setup()
logger = get_logger("run")
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) is None:
setattr(arguments, packages_path_arg, arguments.modules)
del arguments.modules
# END OF DEPRECATION BLOCK
info = arguments.input_file
del arguments.input_file
run(info, **arguments.__dict__)
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 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 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 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 make_grid_script():
warn_deprecation()
args = getArgs()
args.interactive = True
makeGrid(**args.__dict__)
def doc_script():
from cobaya.mpi import is_main_process
if not is_main_process():
return
warn_deprecation()
# Parse arguments
import argparse
parser = argparse.ArgumentParser(
description="Prints defaults for Cobaya's components.")
parser.add_argument("component",
action="store",
nargs="?",
default="",
metavar="component_name",
help="The component whose defaults are 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=("Kind of component whose defaults are requested: " +
", ".join(['%s' % kind for kind in kinds]) + ". " +
"Use only when component name is not unique (it would fail)."))
parser.add_argument("-p",
"--python",
action="store_true",
default=False,
help="Request Python instead of YAML.")
expand_flag, expand_flag_ishort = "expand", 1
parser.add_argument("-" + expand_flag[expand_flag_ishort],
"--" + expand_flag,
action="store_true",
default=False,
help="Expand YAML defaults.")
arguments = parser.parse_args()
# Remove plurals (= name of src subfolders), for user-friendliness
if arguments.component.lower() in subfolders.values():
arguments.component = next(k for k in subfolders
if arguments.component == subfolders[k])
# Kind given, list all
if not arguments.component:
msg = "Available components: (some may need external code/data)"
print(msg + "\n" + "-" * len(msg))
for kind in kinds:
print("%s:" % kind)
print(_indent +
("\n" +
_indent).join(get_available_internal_class_names(kind)))
return
# Kind given: list all components of that kind
if arguments.component.lower() in kinds:
print("%s:" % arguments.component.lower())
print(_indent + ("\n" + _indent).join(
get_available_internal_class_names(arguments.component.lower())))
return
# Otherwise, check if it's a unique component name
try:
if arguments.kind:
arguments.kind = arguments.kind[0].lower()
if arguments.kind not in kinds:
print("Kind %r not recognized. Try one of %r" %
(arguments.kind, tuple(kinds)))
raise ValueError
else:
arguments.kind = get_kind(arguments.component)
to_print = get_default_info(arguments.component,
arguments.kind,
return_yaml=not arguments.python,
yaml_expand_defaults=arguments.expand)
if arguments.python:
print(pformat({arguments.kind: {arguments.component: to_print}}))
else:
print(arguments.kind + ":\n" + _indent + arguments.component +
":\n" + 2 * _indent +
("\n" + 2 * _indent).join(to_print.split("\n")))
if "!defaults" in to_print:
print("# This file contains defaults. "
"To populate them, use the flag --%s (or -%s)." %
(expand_flag, expand_flag[expand_flag_ishort]))
except Exception:
if isinstance(Exception, LoggedError.__class__):
pass
else:
if not arguments.kind:
print("Specify its kind with '--%s [component_kind]'." %
kind_opt)
return 1
return
def doc_script(args=None):
"""Command line script for the documentation."""
warn_deprecation()
logger_setup()
logger = get_logger("doc")
# Parse arguments
import argparse
parser = argparse.ArgumentParser(
prog="cobaya doc",
description="Prints defaults for Cobaya's components.")
parser.add_argument(
"component",
action="store",
nargs="?",
default="",
metavar="component_name",
help=("The component whose defaults are requested. "
"Pass a component kind (sampler, theory, likelihood) to "
"list all available (internal) ones, pass nothing to list "
"all available (internal) components of all kinds."))
parser.add_argument("-p",
"--python",
action="store_true",
default=False,
help="Request Python instead of YAML.")
expand_flag, expand_flag_ishort = "expand", 1
parser.add_argument("-" + expand_flag[expand_flag_ishort],
"--" + expand_flag,
action="store_true",
default=False,
help="Expand YAML defaults.")
arguments = parser.parse_args(args)
# Nothing passed: list all
if not arguments.component:
msg = "Available components: (some may need external code/data)"
print(msg + "\n" + "-" * len(msg))
for kind in kinds:
print("%s:" % kind)
print(_indent +
("\n" +
_indent).join(get_available_internal_class_names(kind)))
return
# A kind passed (plural or singular): list all of that kind
if arguments.component.lower() in subfolders.values():
arguments.component = next(k for k in subfolders
if arguments.component == subfolders[k])
if arguments.component.lower() in kinds:
print("%s:" % arguments.component.lower())
print(_indent + ("\n" + _indent).join(
get_available_internal_class_names(arguments.component.lower())))
return
# Otherwise, try to identify the component
try:
cls = get_component_class(arguments.component, logger=logger)
except ComponentNotFoundError:
suggestions = similar_internal_class_names(arguments.component)
logger.error(
f"Could not identify component '{arguments.component}'. "
f"Did you mean any of the following? {suggestions} (mind capitalization!)"
)
return 1
to_print = get_default_info(cls,
return_yaml=not arguments.python,
yaml_expand_defaults=arguments.expand)
if arguments.python:
print(pformat({cls.get_kind(): {arguments.component: to_print}}))
else:
print(cls.get_kind() + ":\n" + _indent + arguments.component + ":\n" +
2 * _indent + ("\n" + 2 * _indent).join(to_print.split("\n")))
if "!defaults" in to_print:
print("# This file contains defaults. "
"To populate them, use the flag --%s (or -%s)." %
(expand_flag, expand_flag[expand_flag_ishort]))
def install_script():
from cobaya.mpi import am_single_or_primary_process
if am_single_or_primary_process():
warn_deprecation()
# 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 simply 'polychord', 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]
elif arguments.files == ["polychord"]:
infos = [{"sampler": {"polychord": None}}]
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"]
})
