def get_citation_info(module, kind):
folder = get_folder(module, kind, absolute=True)
filename = os.path.join(folder, module + ".bibtex")
try:
with open(filename, "r") as f:
lines = "".join(f.readlines())
except IOError:
if not os.path.isdir(folder):
lines = "[Module '%s.%s' not known.]" % (kind, module)
else:
lines = "[no citation information found]"
return lines + "\n"
def get_default_info(module, kind):
path_to_defaults = os.path.join(get_folder(module, kind), module + ".yaml")
try:
default_module_info = yaml_load_file(path_to_defaults)
except IOError:
# probably an external module
default_module_info = {kind: {module: {}}}
log.debug("Module %s:%s does not have a defaults file. " % (kind, module) +
"Maybe it is an external module.")
try:
default_module_info[kind][module]
except KeyError:
log.error("The defaults file for '%s' should be structured "
"as %s:%s:{[options]}.", module, kind, module)
raise HandledException
return default_module_info
def is_equal_info(info1, info2, strict=True, print_not_log=False):
"""
Compares two information dictionaries.
Set ``strict=False`` (default: ``True``) to ignore options that would not affect
the statistics of a posterior sample, including order of params/priors/likelihoods.
"""
if print_not_log:
myprint = print
else:
myprint = log.info
myname = inspect.stack()[0][3]
ignore = set([]) if strict else set(
[_debug, _debug_file, _resume, _path_install, _force_reproducible])
ignore_params = (set([]) if strict else set(
[_p_label, _p_renames, _p_ref, _p_proposal, "min", "max"]))
if set(info1).difference(ignore) != set(info2).difference(ignore):
myprint(myname +
": different blocks or options: %r (old) vs %r (new)" %
(set(info1).difference(ignore), set(info2).difference(ignore)))
return False
for block_name in info1:
if block_name in ignore:
continue
block1, block2 = info1[block_name], info2[block_name]
if not hasattr(block1, "keys"):
if block1 != block2:
myprint(myname + ": different option '%s'" % block_name)
return False
if block_name in [_sampler, _theory]:
# Internal order does NOT matter
if set(block1) != set(block2):
myprint(myname + ": different [%s]" % block_name)
return False
# Anything to ignore?
for k in block1:
module_folder = get_folder(k,
block_name,
sep=".",
absolute=False)
try:
ignore_k = getattr(
import_module(module_folder, package=_package),
"ignore_at_resume", {})
except ImportError:
ignore_k = {}
block1k, block2k = deepcopy(block1[k]), deepcopy(block2[k])
if not strict:
for kignore in ignore_k:
try:
block1k.pop(kignore, None)
block2k.pop(kignore, None)
except:
pass
if recursive_odict_to_dict(block1k) != recursive_odict_to_dict(
block2k):
myprint(myname + ": different content of [%s:%s]" %
(block_name, k))
return False
elif block_name in [_params, _likelihood, _prior]:
# Internal order DOES matter, but just up to 1st level
f = list if strict else set
if f(block1) != f(block2):
myprint(
myname +
": different [%s] or different order of them: %r vs %r" %
(block_name, list(block1), list(block2)))
return False
for k in block1:
block1k, block2k = deepcopy(block1[k]), deepcopy(block2[k])
if block_name == _params:
# Unify notation
block1k = expand_info_param(block1k)
block2k = expand_info_param(block2k)
if not strict:
for kignore in ignore_params:
try:
block1k.pop(kignore, None)
block2k.pop(kignore, None)
except:
pass
# Fixed params, it doesn't matter if they are saved as derived
for b in [block1k, block2k]:
if _p_value in b:
b.pop(_p_derived, None)
if (recursive_odict_to_dict(block1k) !=
recursive_odict_to_dict(block2k)):
myprint(myname + ": different content of [%s:%s]" %
(block_name, k))
return False
return True
def install(*infos, **kwargs):
if not log.root.handlers:
logger_setup()
path = kwargs.get("path", ".")
if not path:
# See if we can get one (and only one) from infos
paths = set(
[p for p in [info.get(_path_install) for info in infos] if p])
if len(paths) == 1:
path = paths[0]
else:
print("logging?")
log.error(
"No 'path' argument given and could not extract one (and only one) "
"from the infos.")
raise HandledException
abspath = os.path.abspath(path)
log.info("Installing modules at '%s'\n", abspath)
kwargs_install = {
"force": kwargs.get("force", False),
"no_progress_bars": kwargs.get("no_progress_bars")
}
for what in (_code, _data):
kwargs_install[what] = kwargs.get(what, True)
spath = os.path.join(abspath, what)
if kwargs_install[what] and not os.path.exists(spath):
try:
os.makedirs(spath)
except OSError:
log.error(
"Could not create the desired installation folder '%s'",
spath)
raise HandledException
failed_modules = []
for kind, modules in get_modules(*infos).items():
for module in modules:
print(make_header(kind, module))
module_folder = get_folder(module, kind, sep=".", absolute=False)
try:
imported_module = import_module(module_folder,
package=_package)
except ImportError:
if kind == _likelihood:
info = (next(info for info in infos if module in info.get(
_likelihood, {}))[_likelihood][module]) or {}
if isinstance(info, string_types) or _external in info:
log.warning(
"Module '%s' is a custom likelihood. "
"Nothing to do.\n", module)
flag = False
else:
log.error("Module '%s' not recognized.\n" % module)
failed_modules += ["%s:%s" % (kind, module)]
continue
is_installed = getattr(imported_module, "is_installed", None)
if is_installed is None:
log.info("Built-in module: nothing to do.\n")
continue
if is_installed(path=abspath, **kwargs_install):
log.info("External module already installed.\n")
if kwargs_install["force"]:
log.info("Forcing re-installation, as requested.")
else:
log.info("Doing nothing.\n")
continue
try:
success = imported_module.install(path=abspath,
**kwargs_install)
except:
traceback.print_exception(*sys.exc_info(), file=sys.stdout)
log.error(
"An unknown error occurred. Delete the modules folder and try "
"again. Notify the developers if this error persists.")
success = False
if success:
log.info("Successfully installed!\n")
else:
log.error(
"Installation failed! Look at the error messages above. "
"Solve them and try again, or, if you are unable to solve, "
"install this module manually.")
failed_modules += ["%s:%s" % (kind, module)]
continue
# test installation
if not is_installed(path=abspath, **kwargs_install):
log.error(
"Installation apparently worked, "
"but the subsequent installation test failed! "
"Look at the error messages above. "
"Solve them and try again, or, if you are unable to solve, "
"install this module manually.")
failed_modules += ["%s:%s" % (kind, module)]
if failed_modules:
bullet = "\n - "
log.error(
"The installation (or installation test) of some module(s) has failed: "
"%s\nCheck output of the installer of each module above "
"for precise error info.\n", bullet + bullet.join(failed_modules))
raise HandledException
def install(*infos, **kwargs):
path = kwargs.get("path", ".")
abspath = os.path.abspath(path)
kwargs_install = {
"force": kwargs.get("force", False),
"no_progress_bars": kwargs.get("no_progress_bars")
}
for what in (_code, _data):
kwargs_install[what] = kwargs.get(what, True)
spath = os.path.join(abspath, what)
if kwargs_install[what] and not os.path.exists(spath):
try:
os.makedirs(spath)
except OSError:
log.error(
"Could not create the desired installation folder '%s'",
spath)
raise HandledException
failed_modules = []
for kind, modules in get_modules(*infos).items():
for module in modules:
print(make_header(kind, module))
module_folder = get_folder(module, kind, sep=".", absolute=False)
try:
imported_module = import_module(module_folder, package=package)
except ImportError:
if kind == _likelihood:
log.warn(
"Module '%s' not recognised. Assuming it's a custom "
"likelihood. Nothing to do.\n", module)
else:
log.error("Module '%s' not recognised.\n" % module)
failed_modules += ["%s:%s" % (kind, module)]
continue
is_installed = getattr(imported_module, "is_installed", None)
if is_installed is None:
log.info("Built-in module: nothing to do.\n")
continue
if is_installed(path=abspath, **kwargs_install):
log.info("External module already installed.\n")
if kwargs_install["force"]:
log.info("Forcing re-installation, as requested.")
else:
log.info("Doing nothing.\n")
continue
try:
success = imported_module.install(path=abspath,
**kwargs_install)
except:
traceback.print_exception(*sys.exc_info(), file=sys.stdout)
log.error(
"An unknown error occurred. Delete the modules folder and try "
"again. Notify the developers if this error persists.")
success = False
if success:
log.info("Successfully installed!\n")
else:
log.error(
"Installation failed! Look at the error messages above. "
"Solve them and try again, or, if you are unable to solve, "
"install this module manually.")
failed_modules += ["%s:%s" % (kind, module)]
continue
# test installation
if not is_installed(path=abspath, **kwargs_install):
log.error(
"Installation apparently worked, "
"but the subsequent installation test failed! "
"Look at the error messages above. "
"Solve them and try again, or, if you are unable to solve, "
"install this module manually.")
failed_modules += ["%s:%s" % (kind, module)]
if failed_modules:
log.error(
"The instalation (or installation test) of some module(s) has failed: "
"%r. Check output above.\n", failed_modules)
raise HandledException