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
packages=find_packages(exclude=['docs', 'tests']),
install_requires=[
'numpy>=1.12.0', 'scipy>=1.0', 'pandas>=1.0.1', 'PyYAML>=5.1',
'requests>=2.18', 'py-bobyqa>=1.2', 'GetDist>=1.1.1',
'fuzzywuzzy>=0.17', 'packaging', 'tqdm'
],
extras_require={
'test': ['pytest', 'pytest-forked', 'flaky', 'mpi4py'],
'gui': ['pyqt5', 'pyside2']
},
package_data={
'cobaya':
list(
chain(*[['%s/*/*.yaml' %
folder, '%s/*/*.bibtex' % folder]
for folder in subfolders.values()]))
},
entry_points={
'console_scripts': [
'cobaya-install=cobaya.install:install_script',
'cobaya-create-image=cobaya.containers:create_image_script',
'cobaya-prepare-data=cobaya.containers:prepare_data_script',
'cobaya-run=cobaya.run:run_script',
'cobaya-doc=cobaya.doc:doc_script',
'cobaya-bib=cobaya.bib:bib_script',
'cobaya-grid-create=cobaya.grid_tools:make_grid_script',
'cobaya-grid-run=cobaya.grid_tools.runbatch:run',
'cobaya-run-job=cobaya.grid_tools.runMPI:run_single',
'cobaya-cosmo-generator=cobaya.cosmo_input:gui_script',
],
},
classifiers=[
'Development Status :: 3 - Alpha',
'Environment :: Console',
'Intended Audience :: Science/Research',
'Topic :: Scientific/Engineering :: Astronomy',
'License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+)',
'Programming Language :: Python :: 2.7',
],
keywords='montecarlo sampling cosmology',
packages=find_packages(exclude=['docs', 'tests']),
install_requires=[
'numpy>=1.12.0', 'scipy >= 0.18', 'pandas>=0.17.1', 'PyYAML>=3.12',
'wget>=3.2', 'imageio>=2.2.0'
],
package_data={
'cobaya': ['%s/*/*.yaml' % folder for folder in subfolders.values()]
},
entry_points={
'console_scripts': [
'cobaya-install=cobaya.install:install_script',
'cobaya-create-image=cobaya.containers:create_image_script',
'cobaya-prepare-data=cobaya.containers:prepare_data_script',
'cobaya-run=cobaya.run:run_script',
'cobaya-citation=cobaya.citation:citation_script',
'cobaya-grid-create=cobaya.grid_tools:MakeGridScript',
'cobaya-grid-run=cobaya.grid_tools.runbatch:run',
'cobaya-cosmo-generator=cobaya.cosmo_input:gui_script',
],
},
)
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]))
