changes for Cobaya 2.0 compatibility

getdist/chains.py

@@ -40,7 +40,8 @@ def slice_or_none(x, start=None, end=None):
     return getattr(x, "__getitem__", lambda _: None)(slice(start, end))
 
 
-def chainFiles(root, chain_indices=None, ext='.txt', first_chain=0, last_chain=-1, chain_exclude=None):
+def chainFiles(root, chain_indices=None, ext='.txt', separator="_",
+               first_chain=0, last_chain=-1, chain_exclude=None):
     """
     Creates a list of file names for samples given a root name and optional filters
 
@@ -59,8 +60,8 @@ def chainFiles(root, chain_indices=None, ext='.txt', first_chain=0, last_chain=-
         fname = root
         if index > 0:
             # deal with just-folder prefix
-            if not root.endswith("/"):
-                fname += '_'
+            if not root.endswith((os.sep, "/")):
+                fname += separator
             fname += str(index)
         if not fname.endswith(ext): fname += ext
         if index > first_chain and not os.path.exists(fname) or 0 < last_chain < index: break
@@ -849,17 +850,22 @@ def __init__(self, root=None, jobItem=None, paramNamesFile=None, names=None, lab
         :param kwargs: extra options for :class:`~.chains.WeightedSamples`'s constructor
 
         """
+        from getdist.cobaya_interface import get_sampler_type, _separator_files
+
         self.chains = None
         WeightedSamples.__init__(self, **kwargs)
         self.jobItem = jobItem
         self.ignore_lines = float(kwargs.get('ignore_rows', 0))
         self.root = root
         if not paramNamesFile and root:
-            mid = ('' if root.endswith("/") else "__")
-            if os.path.exists(root + '.paramnames'):
-                paramNamesFile = root + '.paramnames'
-            elif os.path.exists(root + mid + 'full.yaml'):
-                paramNamesFile = root + mid + 'full.yaml'
+            mid = not root.endswith((os.sep, "/"))
+            endings = ['.paramnames', ('__' if mid else '') + 'full.yaml',
+                       (_separator_files if mid else '') + 'updated.yaml']
+            try:
+                paramNamesFile = next(
+                    root + ending for ending in endings if os.path.exists(root + ending))
+            except StopIteration:
+                paramNamesFile = None
         self.setParamNames(paramNamesFile or names)
         if labels is not None:
             self.paramNames.setLabels(labels)
@@ -871,7 +877,6 @@ def __init__(self, root=None, jobItem=None, paramNamesFile=None, names=None, lab
                 raise ValueError("Unknown sampler type %s" % sampler)
             self.sampler = sampler.lower()
         elif isinstance(paramNamesFile, six.string_types) and paramNamesFile.endswith("yaml"):
-            from getdist.yaml_format_tools import get_sampler_type
             self.sampler = get_sampler_type(paramNamesFile)
         else:
             self.sampler = "mcmc"

getdist/yaml_format_tools.py → getdist/cobaya_interface.py

@@ -1,13 +1,12 @@
-# JT 2017-18
+# JT 2017-19
 
 from __future__ import division
 from importlib import import_module
 from six import string_types
 from copy import deepcopy
-import re
 from collections import OrderedDict as odict
 import numpy as np
-import yaml
+
 
 # Conventions
 _prior = "prior"
@@ -21,6 +20,7 @@
 _p_derived = "derived"
 _p_renames = "renames"
 _separator = "__"
+_separator_files = "."
 _minuslogprior = "minuslogprior"
 _prior_1d_name = "0"
 _chi2 = "chi2"
@@ -29,78 +29,6 @@
 _post = "post"
 
 
-# Exceptions
-class InputSyntaxError(Exception):
-    """Syntax error in YAML input."""
-
-
-# Better loader for YAML
-# 1. Matches 1e2 as 100 (no need for dot, or sign after e),
-#    from http://stackoverflow.com/a/30462009
-# 2. Wrapper to load mappings as OrderedDict (for likelihoods and params),
-#    from http://stackoverflow.com/a/21912744
-def yaml_load(text_stream, Loader=yaml.Loader, object_pairs_hook=odict, file_name=None):
-    class OrderedLoader(Loader):
-        pass
-
-    def construct_mapping(loader, node):
-        loader.flatten_mapping(node)
-        return object_pairs_hook(loader.construct_pairs(node))
-
-    OrderedLoader.add_constructor(
-        yaml.resolver.BaseResolver.DEFAULT_MAPPING_TAG, construct_mapping)
-    OrderedLoader.add_implicit_resolver(
-        u'tag:yaml.org,2002:float',
-        re.compile(u'''^(?:
-            [-+]?(?:[0-9][0-9_]*)\\.[0-9_]*(?:[eE][-+]?[0-9]+)?
-            |[-+]?(?:[0-9][0-9_]*)(?:[eE][-+]?[0-9]+)
-            |\\.[0-9_]+(?:[eE][-+][0-9]+)?
-            |[-+]?[0-9][0-9_]*(?::[0-5]?[0-9])+\\.[0-9_]*
-            |[-+]?\\.(?:inf|Inf|INF)
-            |\\.(?:nan|NaN|NAN))$''', re.X),
-        list(u'-+0123456789.'))
-
-    # Ignore python objects
-    def dummy_object_loader(loader, suffix, node):
-        return None
-
-    OrderedLoader.add_multi_constructor(
-        u'tag:yaml.org,2002:python/name:', dummy_object_loader)
-    try:
-        return yaml.load(text_stream, OrderedLoader)
-    # Redefining the general exception to give more user-friendly information
-    except yaml.YAMLError as exception:
-        errstr = "Error in your input file " + ("'" + file_name + "'" if file_name else "")
-        if hasattr(exception, "problem_mark"):
-            line = 1 + exception.problem_mark.line
-            column = 1 + exception.problem_mark.column
-            signal = " --> "
-            signal_right = "    <---- "
-            sep = "|"
-            context = 4
-            lines = text_stream.split("\n")
-            pre = ((("\n" + " " * len(signal) + sep).join(
-                [""] + lines[max(line - 1 - context, 0):line - 1]))) + "\n"
-            errorline = (signal + sep + lines[line - 1] +
-                         signal_right + "column %s" % column)
-            post = ((("\n" + " " * len(signal) + sep).join(
-                [""] + lines[line + 1 - 1:min(line + 1 + context - 1, len(lines))]))) + "\n"
-            raise InputSyntaxError(
-                errstr + " at line %d, column %d." % (line, column) +
-                pre + errorline + post +
-                "Maybe inconsistent indentation, '=' instead of ':', "
-                "no space after ':', or a missing ':' on an empty group?")
-        else:
-            raise InputSyntaxError(errstr)
-
-
-def yaml_load_file(input_file):
-    """Wrapper to load a yaml file."""
-    with open(input_file, "r") as f:
-        lines = "".join(f.readlines())
-    return yaml_load(lines, file_name=input_file)
-
-
 def get_info_params(info):
     """
     Extracts parameter info from the new yaml format.
@@ -207,7 +135,8 @@ def expand_info_param(info_param):
 
 def get_sampler_type(filename_or_info):
     if isinstance(filename_or_info, string_types):
+        from getdist.yaml_tools import yaml_load_file
         filename_or_info = yaml_load_file(filename_or_info)
     default_sampler_for_chain_type = "mcmc"
     sampler = list(filename_or_info.get(_sampler, [default_sampler_for_chain_type]))[0]
-    return {"mcmc": "mcmc", "polychord": "nested"}[sampler]
+    return {"mcmc": "mcmc", "polychord": "nested", "minimize": "minimize"}[sampler]

getdist/gui/mainwindow.py

@@ -1006,8 +1006,8 @@ def _updateComboBoxRootname(self, listOfRoots):
         self.comboBoxRootname.clear()
         self.listRoots.show()
         self.pushButtonRemove.show()
-        baseRoots = [(os.path.basename(root) if not root.endswith("/")
-                      else os.path.basename(root[:-1]) + "/")
+        baseRoots = [(os.path.basename(root) if not root.endswith((os.sep, "/"))
+                      else os.path.basename(root[:-1]) + os.sep)
                      for root in listOfRoots]
         self.comboBoxRootname.addItems(baseRoots)
         if len(baseRoots) > 1:
@@ -1039,8 +1039,8 @@ def newRootItem(self, root):
             else:
                 path = self.rootdirname
             # new style, if the prefix is just a folder
-            if root[-1] == "/":
-                path = "/".join(path.split("/")[:-1])
+            if root[-1] in (os.sep, "/"):
+                path = os.sep.join(path.replace("/", os.sep).split(os.sep)[:-1])
             info = plots.RootInfo(root, path, self.batch)
             plotter.sampleAnalyser.addRoot(info)
 

getdist/mcsamples.py

@@ -66,16 +66,22 @@ def loadMCSamples(file_root, ini=None, jobItem=None, no_cache=False, settings={}
     if settings and dist_settings: raise ValueError('Use settings or dist_settings')
     if dist_settings: settings = dist_settings
     files = chainFiles(file_root)
+    if not files:  # try new Cobaya format
+        files = chainFiles(file_root, separator='.')
     path, name = os.path.split(file_root)
     path = getdist.cache_dir or path
     if not os.path.exists(path): os.mkdir(path)
     cachefile = os.path.join(path, name) + '.py_mcsamples'
     samples = MCSamples(file_root, jobItem=jobItem, ini=ini, settings=settings)
     if os.path.isfile(file_root + '.paramnames'):
         allfiles = files + [file_root + '.ranges', file_root + '.paramnames', file_root + '.properties.ini']
-    else:  # new format (txt+yaml)
-        mid = "" if file_root.endswith("/") else "__"
-        allfiles = files + [file_root + mid + ending for ending in ['input.yaml', 'full.yaml']]
+    else:  # Cobaya
+        folder = os.path.dirname(file_root)
+        prefix = os.path.basename(file_root)
+        allfiles = files + [
+            os.path.join(folder, f) for f in os.listdir(folder) if (
+                    f.startswith(prefix) and
+                    any([f.lower().endswith(end) for end in ['updated.yaml', 'full.yaml']]))]
     if not no_cache and os.path.exists(cachefile) and lastModified(allfiles) < os.path.getmtime(cachefile):
         try:
             with open(cachefile, 'rb') as inp:
@@ -95,12 +101,18 @@ def loadMCSamples(file_root, ini=None, jobItem=None, no_cache=False, settings={}
     return samples
 
 
-def loadCobayaSamples(info, collections, name_tag=None,
-                      ignore_rows=0, ini=None, settings={}):
+def loadCobayaSamples(*args, **kwargs):
+    logging.warning("'loadCobayaSamples' will be deprecated in the future. "
+                    "Use 'MCSamplesFromCobaya' instead.")
+    return MCSamplesFromCobaya(*args, **kwargs)
+
+
+def MCSamplesFromCobaya(info, collections, name_tag=None,
+                        ignore_rows=0, ini=None, settings={}):
     """
-    Loads a set of samples from Cobaya's output.
+    Creates a set of samples from Cobaya's output.
     Parameter names, ranges and labels are taken from the "info" dictionary
-    (always use the "full", updated one generated by `cobaya.run`).
+    (always use the "updated" one generated by `cobaya.run`).
 
     For a description of the various analysis settings and default values see
     `analysis_defaults.ini <http://getdist.readthedocs.org/en/latest/analysis_settings.html>`_.
@@ -114,6 +126,10 @@ def loadCobayaSamples(info, collections, name_tag=None,
     :param settings: dictionary of analysis settings to override defaults
     :return: The :class:`MCSamples` instance
     """
+    from getdist.cobaya_interface import _p_label, _p_renames, _weight, _minuslogpost
+    from getdist.cobaya_interface import get_info_params, get_range, is_derived_param
+    from getdist.cobaya_interface import get_sampler_type, _post
+
     if not hasattr(info, "keys"):
         raise TypeError("Cannot regonise arguments. Are you sure you are calling "
                         "with (info, collections, ...) in that order?")
@@ -127,9 +143,6 @@ def loadCobayaSamples(info, collections, name_tag=None,
             "The second argument does not appear to be a (list of) samples `Collection`.")
     if not all([list(c.data) == columns for c in collections[1:]]):
         raise ValueError("The given collections don't have the same columns.")
-    from getdist.yaml_format_tools import _p_label, _p_renames, _weight, _minuslogpost
-    from getdist.yaml_format_tools import get_info_params, get_range, is_derived_param
-    from getdist.yaml_format_tools import get_sampler_type, _post
     # Check consistency with info
     info_params = get_info_params(info)
     # ####################################################################################
@@ -139,8 +152,8 @@ def loadCobayaSamples(info, collections, name_tag=None,
     thin = info.get(_post, {}).get("thin", 1)
     # Maybe warn if trying to ignore rows twice?
     if ignore_rows != 0 and skip != 0:
-        logging.warn("You are asking for rows to be ignored (%r), but some (%r) were "
-                     "already ignored in the original chain.", ignore_rows, skip)
+        logging.warning("You are asking for rows to be ignored (%r), but some (%r) were "
+                        "already ignored in the original chain.", ignore_rows, skip)
     # Should we warn about thin too?
     # Most importantly: do we want to save somewhere the fact that we have *already*
     #                   thinned/skipped?
@@ -182,7 +195,8 @@ class MCSamples(Chains):
     """
     The main high-level class for a collection of parameter samples.
 
-    Derives from :class:`.chains.Chains`, adding high-level functions including Kernel Density estimates, parameter ranges and custom settings.
+    Derives from :class:`.chains.Chains`, adding high-level functions including
+    Kernel Density estimates, parameter ranges and custom settings.
     """
 
     def __init__(self, root=None, jobItem=None, ini=None, settings=None, ranges=None,
@@ -2083,10 +2097,15 @@ def _setLikeStats(self):
 
     def _readRanges(self):
         if self.root:
+            from getdist.cobaya_interface import _separator_files
             ranges_file_classic = self.root + '.ranges'
-            ranges_file_new = (
-                    self.root + ('' if self.root.endswith('/') else '__') + 'full.yaml')
-            for ranges_file in [ranges_file_classic, ranges_file_new]:
+            ranges_file_cobaya_old = (
+                    self.root + ('' if self.root.endswith((os.sep, "/")) else '__') + 'full.yaml')
+            ranges_file_cobaya = (
+                    self.root + (
+                '' if self.root.endswith((os.sep, "/")) else _separator_files) + 'updated.yaml')
+            for ranges_file in [
+                ranges_file_classic, ranges_file_cobaya_old, ranges_file_cobaya]:
                 if os.path.isfile(ranges_file):
                     self.ranges = ParamBounds(ranges_file)
                     return
@@ -2553,9 +2572,9 @@ def GetChainRootFiles(rootdir):
     """
     pattern = os.path.join(rootdir, '*.paramnames')
     files = [os.path.splitext(f)[0] for f in glob.glob(pattern)]
-    ending = 'full.yaml'
-    pattern = os.path.join(rootdir, "*" + ending)
-    files += [f[:-len(ending)].rstrip("_") for f in glob.glob(pattern)]
+    for ending in ['full.yaml', 'updated.yaml']:
+        pattern = os.path.join(rootdir, "*" + ending)
+        files += [f[:-len(ending)].rstrip("_.") for f in glob.glob(pattern)]
     files.sort()
     return files
 

getdist/paramnames.py

@@ -378,10 +378,9 @@ def loadFromFile(self, fileName):
             with open(fileName) as f:
                 self.names = [ParamInfo(line) for line in [s.strip() for s in f] if line != '']
         elif extension.lower() in ('.yaml', '.yml'):
-            from getdist.yaml_format_tools import yaml_load_file, get_info_params
-            from getdist.yaml_format_tools import is_sampled_param, is_derived_param
-            from getdist.yaml_format_tools import _p_label, _p_renames
-
+            from getdist.yaml_tools import yaml_load_file
+            from getdist.cobaya_interface import get_info_params, is_sampled_param
+            from getdist.cobaya_interface import is_derived_param, _p_label, _p_renames
             info_params = get_info_params(yaml_load_file(fileName))
             # first sampled, then derived
             self.names = [ParamInfo(name=param, label=(info or {}).get(_p_label, param),

getdist/parampriors.py

@@ -31,8 +31,8 @@ def loadFromFile(self, fileName):
                     if len(strings) == 3:
                         self.setRange(strings[0], strings[1:])
         elif extension in ('.yaml', '.yml'):
-            from getdist.yaml_format_tools import yaml_load_file, get_info_params
-            from getdist.yaml_format_tools import get_range, is_fixed_param
+            from getdist.cobaya_interface import get_range, is_fixed_param, get_info_params
+            from getdist.yaml_tools import yaml_load_file
             info_params = get_info_params(yaml_load_file(fileName))
             for p, info in info_params.items():
                 if not is_fixed_param(info):

getdist/plots.py

@@ -14,6 +14,7 @@
 from paramgrid import gridconfig, batchjob
 import getdist
 from getdist import MCSamples, loadMCSamples, ParamNames, ParamInfo, IniFile
+from getdist.chains import chainFiles
 from getdist.paramnames import escapeLatex, makeList, mergeRenames
 from getdist.parampriors import ParamBounds
 from getdist.densities import Density1D, Density2D
@@ -446,8 +447,8 @@ def samplesForRoot(self, root, file_root=None, cache=True, settings=None):
         if isinstance(root, MCSamples): return root
         if os.path.isabs(root):
             # deal with just-folder prefix
-            if root.endswith("/"):
-                root = os.path.basename(root[:-1]) + "/"
+            if root.endswith((os.sep, "/")):
+                root = os.path.basename(root[:-1]) + os.sep
             else:
                 root = os.path.basename(root)
         if root in self.mcsamples and cache: return self.mcsamples[root]
@@ -457,6 +458,7 @@ def samplesForRoot(self, root, file_root=None, cache=True, settings=None):
         else:
             dist_settings = {}
         if not file_root:
+            from getdist.cobaya_interface import _separator_files
             for chain_dir in self.chain_dirs:
                 if hasattr(chain_dir, "resolveRoot"):
                     jobItem = chain_dir.resolveRoot(root)
@@ -468,7 +470,8 @@ def samplesForRoot(self, root, file_root=None, cache=True, settings=None):
                         break
                 else:
                     name = os.path.join(chain_dir, root)
-                    if os.path.exists(name + '_1.txt') or os.path.exists(name + '.txt'):
+                    if any([chainFiles(name, separator=sep)
+                            for sep in ['_', _separator_files]]):
                         file_root = name
                         break
         if not file_root:
@@ -1944,7 +1947,7 @@ def triangle_plot(self, roots, params=None, legend_labels=None, plot_3d_with_par
         :param title_limit:if not None, a maginalized limit (1,2..) to print as the title of the first root on the diagonal 1D plots
         :param upper_kwargs: dict for same-named arguments for use when making upper-triangle 2D plots (contour_colors, etc). Set show_1d=False to not add to the diagonal.
         :param diag1d_kwargs: list of dict for arguments when making 1D plots on grid diagonal
-        :param markers: optional dict giving marker values indexed by parameter, or a list of marker values for each parameter plotted  
+        :param markers: optional dict giving marker values indexed by parameter, or a list of marker values for each parameter plotted
         :param param_limits: a dictionary holding a mapping from parameter names to axis limits for that parameter
         :param kwargs: optional keyword arguments for :func:`~GetDistPlotter.plot_2d` or :func:`~GetDistPlotter.plot_3d` (lower triangle only)