Example #1
0
def test_prior_inherit_differentgiven():
    test_info = deepcopy(test_info_common)
    test_info["prior"] = {"third": "lambda a1: 1"}
    updated_info, _ = run(test_info)
    likname = list(test_info_common["likelihood"])[0]
    default_info = get_default_info(likname, "likelihood")
    default_info["prior"].update(test_info["prior"])
    assert updated_info["prior"] == default_info["prior"]
Example #2
0
def test_prior_inherit_samegiven():
    test_info = deepcopy(test_info_common)
    likname = list(test_info_common["likelihood"])[0]
    default_info = get_default_info(likname, "likelihood")
    name, prior = deepcopy(default_info["prior"]).popitem()
    test_info["prior"] = {name: prior}
    updated_info, _ = run(test_info)
    assert updated_info["prior"] == default_info["prior"]
Example #3
0
def test_prior_inherit_differentgiven():
    test_info = deepcopy(test_info_common)
    test_info[_prior] = {"third": "lambda a1: 1"}
    updated_info, products = run(test_info)
    likname = list(test_info_common[_likelihood].keys())[0]
    default_info = get_default_info(likname, _likelihood)
    default_info[_prior].update(test_info[_prior])
    assert updated_info[_prior] == default_info[_prior]
Example #4
0
def test_prior_inherit_samegiven_differentdefinition():
    test_info = deepcopy(test_info_common)
    likname = list(test_info_common[_likelihood].keys())[0]
    default_info = get_default_info(likname, _likelihood)
    name, prior = deepcopy(default_info[_prior]).popitem()
    test_info[_prior] = {name: "this is not a prior"}
    with pytest.raises(HandledException):
        updated_info, products = run(test_info)
Example #5
0
def test_prior_inherit_samegiven():
    test_info = deepcopy(test_info_common)
    likname = list(test_info_common[_likelihood].keys())[0]
    default_info = get_default_info(likname, _likelihood)
    name, prior = deepcopy(default_info[_prior]).popitem()
    test_info[_prior] = {name: prior}
    updated_info, products = run(test_info)
    assert updated_info[_prior] == default_info[_prior]
Example #6
0
def test_prior_inherit_samegiven_differentdefinition():
    test_info = deepcopy(test_info_common)
    likname = list(test_info_common[kinds.likelihood])[0]
    default_info = get_default_info(likname, kinds.likelihood)
    name, prior = deepcopy(default_info[_prior]).popitem()
    test_info[_prior] = {name: "this is not a prior"}
    with pytest.raises(LoggedError):
        updated_info, products = run(test_info)
Example #7
0
def test_prior_inherit_samegiven_differentdefinition():
    test_info = deepcopy(test_info_common)
    likname = list(test_info_common["likelihood"])[0]
    default_info = get_default_info(likname, "likelihood")
    name, prior = deepcopy(default_info["prior"]).popitem()
    test_info["prior"] = {name: "this is not a prior"}
    with pytest.raises(LoggedError):
        run(test_info)
Example #8
0
def test_run_file(tmpdir):
    input_file = os.path.join(tmpdir, 'pars.yaml')
    root = os.path.join(tmpdir, 'test')
    yaml_dump_file(input_file, dict(test_info_common, output=root))
    run_script([input_file, '--force'])
    likname = list(test_info_common["likelihood"])[0]
    default_info = get_default_info(likname, "likelihood")
    updated_info = yaml_load_file(root + '.updated.yaml')
    assert updated_info["prior"] == default_info["prior"]
Example #9
0
def test_inherit_label_and_bounds():
    test_info = deepcopy(test_info_common)
    likname = list(test_info_common[kinds.likelihood])[0]
    default_info_params = get_default_info(likname, kinds.likelihood)[_params]
    test_info[_params] = deepcopy(default_info_params)
    test_info[_params]["a1"].pop(partag.latex, None)
    # Remove limits, so they are inherited
    test_info = deepcopy(test_info_common)
    test_info[_params] = deepcopy(default_info_params)
    test_info[_params]["b1"].pop("min")
    test_info[_params]["b1"].pop("max")
    updated_info, products = run(test_info)
    assert updated_info[_params]["b1"]["min"] == default_info_params["b1"][
        "min"]
    assert updated_info[_params]["b1"]["max"] == default_info_params["b1"][
        "max"]
Example #10
0
def test_inherit_label_and_bounds():
    test_info = deepcopy(test_info_common)
    likname = list(test_info_common["likelihood"])[0]
    default_info_params = get_default_info(likname, "likelihood")["params"]
    test_info["params"] = deepcopy(default_info_params)
    test_info["params"]["a1"].pop("latex", None)
    # Remove limits, so they are inherited
    test_info = deepcopy(test_info_common)
    test_info["params"] = deepcopy(default_info_params)
    test_info["params"]["b1"].pop("min")
    test_info["params"]["b1"].pop("max")
    updated_info, _ = run(test_info)
    assert updated_info["params"]["b1"]["min"] == default_info_params["b1"][
        "min"]
    assert updated_info["params"]["b1"]["max"] == default_info_params["b1"][
        "max"]
Example #11
0
 def __init__(self, kind, component, parent=None):
     super().__init__()
     self.clipboard = parent.clipboard
     self.setWindowTitle("%s : %s" % (kind, component))
     self.setGeometry(0, 0, 500, 500)
     # noinspection PyArgumentList
     self.move(QApplication.desktop().screenGeometry().center() -
               self.rect().center())
     self.show()
     # Main layout
     self.layout = QVBoxLayout()
     self.setLayout(self.layout)
     self.display_tabs = QTabWidget()
     self.display = {}
     for k in ["yaml", "python", "bibliography"]:
         self.display[k] = QTextEdit()
         self.display[k].setLineWrapMode(QTextEdit.NoWrap)
         self.display[k].setFontFamily("mono")
         self.display[k].setCursorWidth(0)
         self.display[k].setReadOnly(True)
         self.display_tabs.addTab(self.display[k], k)
     self.layout.addWidget(self.display_tabs)
     # Fill text
     defaults_txt = get_default_info(component, kind, return_yaml=True)
     _indent = "  "
     defaults_txt = (kind + ":\n" + _indent + component + ":\n" +
                     2 * _indent +
                     ("\n" + 2 * _indent).join(defaults_txt.split("\n")))
     from cobaya.yaml import yaml_load
     self.display["python"].setText(pformat(yaml_load(defaults_txt)))
     self.display["yaml"].setText(defaults_txt)
     self.display["bibliography"].setText(get_bib_component(
         component, kind))
     # Buttons
     self.buttons = QHBoxLayout()
     self.close_button = QPushButton('Close', self)
     self.copy_button = QPushButton('Copy to clipboard', self)
     self.buttons.addWidget(self.close_button)
     self.buttons.addWidget(self.copy_button)
     self.close_button.released.connect(self.close)
     self.copy_button.released.connect(self.copy_clipb)
     self.layout.addLayout(self.buttons)
Example #12
0
 def __init__(self, kind, module, parent=None):
     super(DefaultsDialog, self).__init__()
     self.clipboard = parent.clipboard
     self.setWindowTitle("%s : %s" % (kind, module))
     self.setGeometry(0, 0, 500, 500)
     self.move(
         QApplication.desktop().screenGeometry().center() - self.rect().center())
     self.show()
     # Main layout
     self.layout = QVBoxLayout()
     self.setLayout(self.layout)
     self.display_tabs = QTabWidget()
     self.display = {}
     for k in ["yaml", "python", "bibliography"]:
         self.display[k] = QTextEdit()
         self.display[k].setLineWrapMode(QTextEdit.NoWrap)
         self.display[k].setFontFamily("mono")
         self.display[k].setCursorWidth(0)
         self.display[k].setReadOnly(True)
         self.display_tabs.addTab(self.display[k], k)
     self.layout.addWidget(self.display_tabs)
     # Fill text
     defaults_txt = get_default_info(
         module, kind, return_yaml=True, fail_if_not_found=True)
     from cobaya.yaml import yaml_load
     self.display["python"].setText(
         "from collections import OrderedDict\n\ninfo = " +
         pformat(yaml_load(defaults_txt)))
     self.display["yaml"].setText(defaults_txt)
     self.display["bibliography"].setText(get_bib_module(module, kind))
     # Buttons
     self.buttons = QHBoxLayout()
     self.close_button = QPushButton('Close', self)
     self.copy_button = QPushButton('Copy to clipboard', self)
     self.buttons.addWidget(self.close_button)
     self.buttons.addWidget(self.copy_button)
     self.close_button.released.connect(self.close)
     self.copy_button.released.connect(self.copy_clipb)
     self.layout.addLayout(self.buttons)
Example #13
0
def test_inherit_label_and_bounds():
    test_info = deepcopy(test_info_common)
    likname = list(test_info_common[_likelihood].keys())[0]
    default_info_params = get_default_info(likname, _likelihood)[_params]
    test_info[_params] = deepcopy(default_info_params)
    test_info[_params]["a1"].pop(_p_label, None)
    # First, change one limit (so no inheritance at all)
    test_info[_params]["b1"].pop("min")
    new_max = 2
    test_info[_params]["b1"]["max"] = new_max
    updated_info, products = run(test_info)
    assert updated_info[_params]["a1"] == default_info_params["a1"]
    assert updated_info[_params]["b1"].get("min") is None
    assert updated_info[_params]["b1"]["max"] == new_max
    # Second, remove limits, so they are inherited
    test_info = deepcopy(test_info_common)
    test_info[_params] = deepcopy(default_info_params)
    test_info[_params]["b1"].pop("min")
    test_info[_params]["b1"].pop("max")
    updated_info, products = run(test_info)
    assert updated_info[_params]["b1"]["min"] == default_info_params["b1"]["min"]
    assert updated_info[_params]["b1"]["max"] == default_info_params["b1"]["max"]
Example #14
0
def get_product_id_and_clik_file(name):
    """Gets the PLA product info from the defaults file."""
    defaults = get_default_info(name, _likelihood)[_likelihood][name]
    return defaults.get("product_id"), defaults.get("clik_file")
Example #15
0
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]))
Example #16
0
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
Example #17
0
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
Example #18
0
def body_of_test(modules,
                 best_fit,
                 info_likelihood,
                 info_theory,
                 ref_chi2,
                 best_fit_derived=None):
    assert modules, "I need a modules folder!"
    info = {
        _path_install: modules,
        _theory: info_theory,
        _likelihood: info_likelihood,
        _sampler: {
            "evaluate": None
        }
    }
    # Add best fit
    info[_params] = merge_params_info(*([yaml_load(baseline_cosmology)] + [
        get_default_info(lik, _likelihood).get(_params, {})
        for lik in info[_likelihood]
    ]))
    for p in best_fit:
        try:
            if _prior in info[_params].get(p, {}):
                info[_params][p]["ref"] = best_fit[p]
        except:  # was fixed or derived
            info[_params][p] = best_fit[p]
    # We'll pop some derived parameters, so copy
    derived = deepcopy(baseline_cosmology_derived)
    best_fit_derived = deepcopy(best_fit_derived)
    if list(info[_theory].keys())[0] == "classy":
        # More stuff that CLASS needs for the Planck model
        info[_params].update(baseline_cosmology_classy_extra)
        # Remove "cosmomc_theta" in favour of "H0" (remove it from derived then!)
        info[_params].pop("cosmomc_theta")
        info[_params].pop("theta")
        info[_params]["H0"] = {
            _prior: {
                "min": 0,
                "max": 100
            },
            _p_ref: best_fit["H0"]
        }
        derived.pop("H0")
        if best_fit_derived is not None:
            best_fit_derived.pop("H0", None)
            # Don't test those that have not been implemented yet
            for p in [
                    "zstar",
                    "rstar",
                    "thetastar",
                    "DAstar",
                    "zdrag",
                    "kd",
                    "thetad",
                    "zeq",
                    "keq",
                    "thetaeq",
                    "thetarseq",
                    # BBN!!!
                    "DH",
                    "Y_p"
            ]:
                derived.pop(p)
                best_fit_derived.pop(p, None)
    else:
        info[_theory]["camb"] = info[_theory]["camb"] or {}
        info[_theory]["camb"].update({"stop_at_error": True})
    # Add derived
    if best_fit_derived is not None:
        info[_params].update(derived)
    updated_info, products = run(info)
    # Check value of likelihoods
    for lik in info[_likelihood]:
        chi2 = products["sample"][_chi2 + separator + lik][0]
        assert abs(chi2 - ref_chi2[lik]) < ref_chi2["tolerance"], (
            "Testing likelihood '%s': | %g - %g | = %g >= %g" %
            (lik, chi2, ref_chi2[lik], abs(chi2 - ref_chi2[lik]),
             ref_chi2["tolerance"]))
    # Check value of derived parameters
    not_tested = []
    not_passed = []
    for p in best_fit_derived or {}:
        if best_fit_derived[p][0] is None or p not in best_fit_derived:
            not_tested += [p]
            continue
        rel = (abs(products["sample"][_derived_pre + p][0] -
                   best_fit_derived[p][0]) / best_fit_derived[p][1])
        if rel > tolerance_derived * (2 if p in ("YHe", "Y_p", "DH", "sigma8",
                                                 "s8omegamp5") else 1):
            not_passed += [(p, rel)]
    print("Derived parameters not tested because not implemented: %r" %
          not_tested)
    assert not not_passed, "Some derived parameters were off: %r" % not_passed
Example #19
0
def create_input(**kwargs):
    get_comments = kwargs.pop("get_comments", False)
    preset = kwargs.pop("preset", None)
    if preset:
        fields = deepcopy(input_database.preset[preset])
        fields.update(kwargs)
        return create_input(get_comments=get_comments, **fields)
    # Need to copy to select theory.
    # Likelihoods always AT THE END!
    # (to check that sampled parameters are not redefined as derived)
    infos = odict()
    kwargs_params = [
        "primordial", "geometry", "hubble", "matter", "neutrinos",
        "dark_energy", "bbn", "reionization"
    ]
    kwargs_likes = ["like_cmb", "like_bao", "like_sn", "like_H0"]
    for k in kwargs_params + kwargs_likes:
        if k not in kwargs:
            infos[k] = odict()
        try:
            infos[k] = deepcopy(
                getattr(input_database, k)[kwargs.get(k,
                                                      input_database._none)])
        except KeyError:
            raise ValueError("Unknown value '%s' for '%s'" %
                             (kwargs.get(k, input_database._none), k))
    theory_requested = kwargs.get(_theory)
    for i, (field, info) in enumerate(infos.items()):
        if not info:
            continue
        error_msg = info.pop(input_database._error_msg, None)
        try:
            info[_theory] = {theory_requested: info[_theory][theory_requested]}
        except KeyError:
            return (
                "There is no preset for\n'%s'" %
                (info.get(input_database._desc, field)) +
                "with theory code '%s'." % theory_requested +
                ("\n--> " + error_msg if error_msg else
                 "\nThis does not mean that you cannot use this model with that "
                 "theory code; just that we have not implemented this yet."))
        # Add non-translatable parameters (in info["theory"][classy|camb][params])
        if _params not in info:
            info[_params] = odict()
        info[_params].update((info[_theory][theory_requested]
                              or odict()).pop(_params, odict()))
        # Remove the *derived* parameters mentioned by the likelihoods that
        # are already *sampled* by some part of the model
        if field.startswith("like_") and _params in info:
            remove_derived = []
            for p in info[_params]:
                if any([(p in info_part[_params])
                        for info_part in list(infos.values())[:i]]):
                    remove_derived += [p]
            for p in remove_derived:
                info[_params].pop(p)
    # Prepare sampler info
    info_sampler = deepcopy(
        input_database.sampler.get(kwargs.get(_sampler), {}))
    if info_sampler:
        sampler_name = list(info_sampler[_sampler])[0]
        info_sampler[_sampler][
            sampler_name] = info_sampler[_sampler][sampler_name] or {}
        # Add recommended options for samplers
        for info in infos.values():
            this_info_sampler = info.pop(_sampler, {})
            if sampler_name in this_info_sampler:
                info_sampler[_sampler][sampler_name].update(
                    this_info_sampler[sampler_name])
    # Reorder, to have the *parameters* shown in the correct order, and *merge*
    all_infos = [info_sampler] + [
        infos[k] for k in kwargs_likes[::-1] + kwargs_params[::-1]
    ]
    comments = [info.pop(input_database._comment, None) for info in all_infos]
    comments = [c for c in comments if c]
    [info.pop(input_database._desc, None) for info in all_infos]
    merged = merge_info(*all_infos)
    # Simplify parameter infos
    for p, info in merged[_params].items():
        merged[_params][p] = reduce_info_param(info)
    # Translate from Planck param names
    planck_to_theo = get_default_info(
        theory_requested, _theory)[_theory][theory_requested][_p_renames]
    if kwargs.get("planck_names", False):
        merged[_theory][
            theory_requested] = merged[_theory][theory_requested] or {}
        merged[_theory][theory_requested]["use_planck_names"] = True
    else:
        merged_params_translated = odict([
            translate(p, info, planck_to_theo)
            for p, info in merged[_params].items()
        ])
        merged[_params] = merged_params_translated
    if get_comments and comments:
        merged[input_database._comment] = comments
    return merged
Example #20
0
def test_prior_inherit_nonegiven():
    updated_info, products = run(test_info_common)
    likname = list(test_info_common[_likelihood].keys())[0]
    default_info = get_default_info(likname, _likelihood)
    assert updated_info[_prior] == default_info[_prior]
Example #21
0
def test_prior_inherit_nonegiven():
    updated_info, _ = run(test_info_common)
    likname = list(test_info_common["likelihood"])[0]
    default_info = get_default_info(likname, "likelihood")
    assert updated_info["prior"] == default_info["prior"]
Example #22
0
from copy import deepcopy
from collections import OrderedDict as odict
from six import string_types
import numpy as np

from cobaya.input import merge_info
from cobaya.conventions import _theory, _params, _p_drop, _p_alias
from cobaya.input import get_default_info
import input_database

planck_to_classy = get_default_info("classy", _theory)[_theory]["classy"]["planck_to_classy"]
planck_to_camb = get_default_info("camb", _theory)[_theory]["camb"]["planck_to_camb"]


def translate(p, info=None, dictionary=None, add_alias=False):
    dictionary = dictionary or {}
    # Ignore if dropped
    if not (info if hasattr(info, "keys") else {}).get(_p_drop, False):
        p_old = p
        p = dictionary.get(p, p)
        if hasattr(info, "keys") and p_old != p:
            pre_aliases = np.atleast_1d(info.get(_p_alias, [])).tolist()
            info.update({_p_alias: pre_aliases + [p_old]})
    # Try to modify lambda parameters too!
    if isinstance(info, string_types):
        if info.startswith("lambda"):
            arguments = info.split(":")[0].split()[1:]
            if not isinstance(arguments, string_types):
                arguments = "".join(arguments)
            arguments = arguments.split(",")
            arguments_t = [translate(pi, dictionary=dictionary)[0] for pi in arguments]