arviz 0.16.1__py3-none-any.whl → 0.17.1__py3-none-any.whl

arviz/__init__.py

@@ -1,6 +1,6 @@
 # pylint: disable=wildcard-import,invalid-name,wrong-import-position
 """ArviZ is a library for exploratory analysis of Bayesian models."""
-__version__ = "0.16.1"
+__version__ = "0.17.1"
 
 import logging
 import os

arviz/data/inference_data.py

@@ -1,5 +1,6 @@
 # pylint: disable=too-many-lines,too-many-public-methods
 """Data structure for using netcdf groups with xarray."""
+import os
 import re
 import sys
 import uuid
@@ -23,14 +24,13 @@ from typing import (
     Union,
     overload,
 )
-import os
 
 import numpy as np
 import xarray as xr
 from packaging import version
 
 from ..rcparams import rcParams
-from ..utils import HtmlTemplate, _subset_list, either_dict_or_kwargs
+from ..utils import HtmlTemplate, _subset_list, _var_names, either_dict_or_kwargs
 from .base import _extend_xr_method, _make_json_serializable, dict_to_dataset
 
 if sys.version_info[:2] >= (3, 9):
@@ -56,6 +56,7 @@ SUPPORTED_GROUPS = [
     "posterior_predictive",
     "predictions",
     "log_likelihood",
+    "log_prior",
     "sample_stats",
     "prior",
     "prior_predictive",
@@ -63,6 +64,8 @@ SUPPORTED_GROUPS = [
     "observed_data",
     "constant_data",
     "predictions_constant_data",
+    "unconstrained_posterior",
+    "unconstrained_prior",
 ]
 
 WARMUP_TAG = "warmup_"
@@ -73,6 +76,7 @@ SUPPORTED_GROUPS_WARMUP = [
     f"{WARMUP_TAG}predictions",
     f"{WARMUP_TAG}sample_stats",
     f"{WARMUP_TAG}log_likelihood",
+    f"{WARMUP_TAG}log_prior",
 ]
 
 SUPPORTED_GROUPS_ALL = SUPPORTED_GROUPS + SUPPORTED_GROUPS_WARMUP
@@ -236,6 +240,10 @@ class InferenceData(Mapping[str, xr.Dataset]):
             self._groups_warmup.remove(group)
         object.__delattr__(self, group)
 
+    def __delitem__(self, key: str) -> None:
+        """Delete an item from the InferenceData object using del idata[key]."""
+        self.__delattr__(key)
+
     @property
     def _groups_all(self) -> List[str]:
         return self._groups + self._groups_warmup
@@ -246,8 +254,7 @@ class InferenceData(Mapping[str, xr.Dataset]):
 
     def __iter__(self) -> Iterator[str]:
         """Iterate over groups in InferenceData object."""
-        for group in self._groups_all:
-            yield group
+        yield from self._groups_all
 
     def __contains__(self, key: object) -> bool:
         """Return True if the named item is present, and False otherwise."""
@@ -620,6 +627,8 @@ class InferenceData(Mapping[str, xr.Dataset]):
         self,
         groups=None,
         filter_groups=None,
+        var_names=None,
+        filter_vars=None,
         include_coords=True,
         include_index=True,
         index_origin=None,
@@ -635,6 +644,7 @@ class InferenceData(Mapping[str, xr.Dataset]):
         skipped implicitly.
 
         Raises TypeError if no valid groups are found.
+        Raises ValueError if no data are selected.
 
         Parameters
         ----------
@@ -646,6 +656,15 @@ class InferenceData(Mapping[str, xr.Dataset]):
             If "like", interpret groups as substrings of the real group or metagroup names.
             If "regex", interpret groups as regular expressions on the real group or
             metagroup names. A la `pandas.filter`.
+        var_names : str or list of str, optional
+            Variables to be extracted. Prefix the variables by `~` when you want to exclude them.
+        filter_vars: {None, "like", "regex"}, optional
+            If `None` (default), interpret var_names as the real variables names. If "like",
+            interpret var_names as substrings of the real variables names. If "regex",
+            interpret var_names as regular expressions on the real variables names. A la
+            `pandas.filter`.
+            Like with plotting, sometimes it's easier to subset saying what to exclude
+            instead of what to include
         include_coords: bool
             Add coordinate values to column name (tuple).
         include_index: bool
@@ -677,6 +696,11 @@ class InferenceData(Mapping[str, xr.Dataset]):
         dfs = {}
         for group in group_names:
             dataset = self[group]
+            group_var_names = _var_names(var_names, dataset, filter_vars, "ignore")
+            if (group_var_names is not None) and not group_var_names:
+                continue
+            if group_var_names is not None:
+                dataset = dataset[[var_name for var_name in group_var_names if var_name in dataset]]
             df = None
             coords_to_idx = {
                 name: dict(map(reversed, enumerate(dataset.coords[name].values, index_origin)))
@@ -712,8 +736,11 @@ class InferenceData(Mapping[str, xr.Dataset]):
                     df = dataframe
                     continue
                 df = df.join(dataframe, how="outer")
-            df = df.reset_index()
-            dfs[group] = df
+            if df is not None:
+                df = df.reset_index()
+                dfs[group] = df
+        if not dfs:
+            raise ValueError("No data selected for the dataframe.")
         if len(dfs) > 1:
             for group, df in dfs.items():
                 df.columns = [
@@ -1466,7 +1493,7 @@ class InferenceData(Mapping[str, xr.Dataset]):
 
             import numpy as np
             rng = np.random.default_rng(73)
-            ary = rng.normal(size=(post.dims["chain"], post.dims["draw"], obs.dims["match"]))
+            ary = rng.normal(size=(post.sizes["chain"], post.sizes["draw"], obs.sizes["match"]))
             idata.add_groups(
                 log_likelihood={"home_points": ary},
                 dims={"home_points": ["match"]},

arviz/data/io_beanmachine.py

@@ -18,7 +18,7 @@ class BMConverter:
         self.coords = coords
         self.dims = dims
 
-        import beanmachine.ppl as bm
+        import beanmachine.ppl as bm  # pylint: disable=import-error
 
         self.beanm = bm
 
@@ -99,6 +99,11 @@ def from_beanmachine(
         Map of dimensions to coordinates
     dims : dict of {str : list of str}
         Map variable names to their coordinates
+
+    Warnings
+    --------
+    `beanmachine` is no longer under active development, and therefore, it
+    is not possible to test this converter in ArviZ's CI.
     """
     return BMConverter(
         sampler=sampler,