Merge dea8432 into dfd353d

.pylintrc

@@ -67,7 +67,11 @@ disable=missing-docstring,
         import-outside-toplevel,
         no-else-continue,
         unnecessary-comprehension,
-        unsubscriptable-object
+        unsubscriptable-object,
+        cyclic-import,
+
+        #TODO: Remove this once todos are done
+        fixme
 
 
 # Enable the message, report, category or checker with the given id(s). You can

arviz/data/io_numpyro.py

@@ -1,3 +1,4 @@
+# pylint: disable=cyclic-import
 """NumPyro-specific conversion code."""
 import logging
 import numpy as np

arviz/data/io_pyro.py

@@ -1,3 +1,4 @@
+# pylint: disable=cyclic-import
 """Pyro-specific conversion code."""
 import logging
 import numpy as np

arviz/plots/autocorrplot.py

@@ -1,14 +1,14 @@
 """Autocorrelation plot of data."""
 import numpy as np
 
-from .backends import check_bokeh_version
 from ..data import convert_to_dataset
 from .plot_utils import (
     _scale_fig_size,
     default_grid,
     xarray_var_iter,
     _create_axes_grid,
     filter_plotters_list,
+    get_plotting_method,
 )
 from ..utils import _var_names
 
@@ -136,17 +136,14 @@ def plot_autocorr(
     )
 
     if backend == "bokeh":
-        check_bokeh_version()
-        from .backends.bokeh.bokeh_autocorrplot import _plot_autocorr
 
         autocorr_plot_args.pop("xt_labelsize")
         autocorr_plot_args.pop("titlesize")
         autocorr_plot_args["line_width"] = autocorr_plot_args.pop("linewidth")
         autocorr_plot_args["show"] = show
-        axes = _plot_autocorr(**autocorr_plot_args)  # pylint: disable=unexpected-keyword-arg
-    else:
-        from .backends.matplotlib.mpl_autocorrplot import _plot_autocorr
 
-        axes = _plot_autocorr(**autocorr_plot_args)
+    # TODO: Add backend kwargs
+    method = get_plotting_method("plot_autocorr", "autocorrplot", backend)
+    axes = method(**autocorr_plot_args)
 
     return axes

arviz/plots/backends/__init__.py

@@ -1,2 +1 @@
 """ArviZ plotting backends."""
-from .bokeh import *

arviz/plots/backends/bokeh/__init__.py

@@ -1,7 +1,32 @@
-# pylint: disable=no-member,invalid-name,redefined-outer-name
+# pylint: disable=no-member,invalid-name,redefined-outer-name, wrong-import-position
 """Bokeh Plotting Backend."""
 import packaging
 
+# Set plot generic bokeh keyword arg defaults if none provided
+BACKEND_KWARG_DEFAULTS = {"show": True}
+
+from .autocorrplot import plot_autocorr
+from .compareplot import plot_compare
+from .densityplot import plot_density
+from .distplot import plot_dist
+from .elpdplot import plot_elpd
+from .energyplot import plot_energy
+from .essplot import plot_ess
+from .forestplot import plot_forest
+from .hpdplot import plot_hpd
+from .jointplot import plot_joint
+from .kdeplot import plot_kde
+from .khatplot import plot_khat
+from .loopitplot import plot_loo_pit
+from .mcseplot import plot_mcse
+from .pairplot import plot_pair
+from .parallelplot import plot_parallel
+from .ppcplot import plot_ppc
+from .posteriorplot import plot_posterior
+from .rankplot import plot_rank
+from .traceplot import plot_trace
+from .violinplot import plot_violin
+
 
 def output_notebook(*args, **kwargs):
     """Wrap bokeh.plotting.output_notebook."""

arviz/plots/backends/bokeh/bokeh_autocorrplot.py → arviz/plots/backends/bokeh/autocorrplot.py

@@ -1,16 +1,17 @@
 """Bokeh Autocorrplot."""
-import numpy as np
 import bokeh.plotting as bkp
-from bokeh.models.annotations import Title
+import numpy as np
 from bokeh.layouts import gridplot
+from bokeh.models.annotations import Title
 
-from ....stats import autocorr
 from ...plot_utils import make_label
+from ....stats import autocorr
 
 
-def _plot_autocorr(
+def plot_autocorr(
     axes, plotters, max_lag, line_width, combined=False, show=True,
 ):
+    """Bokeh autocorrelation plot."""
     for (var_name, selection, x), ax_ in zip(plotters, axes.flatten()):
         x_prime = x
         if combined:

arviz/plots/backends/bokeh/bokeh_compareplot.py → arviz/plots/backends/bokeh/compareplot.py

@@ -5,7 +5,7 @@
 from ....rcparams import rcParams
 
 
-def _compareplot(
+def plot_compare(
     ax,
     comp_df,
     figsize,
@@ -20,7 +20,7 @@ def _compareplot(
     step,
     show,
 ):
-
+    """Bokeh compareplot."""
     if ax is None:
         tools = rcParams["plot.bokeh.tools"]
         output_backend = rcParams["plot.bokeh.output_backend"]

arviz/plots/backends/bokeh/bokeh_densityplot.py → arviz/plots/backends/bokeh/densityplot.py

@@ -1,16 +1,16 @@
 """Bokeh Densityplot."""
 import bokeh.plotting as bkp
-from bokeh.models.annotations import Title
-from bokeh.layouts import gridplot
 import numpy as np
+from bokeh.layouts import gridplot
+from bokeh.models.annotations import Title
 
-from ....stats import hpd
 from ...kdeplot import _fast_kde
 from ...plot_utils import make_label
+from ....stats import hpd
 from ....stats.stats_utils import histogram
 
 
-def _plot_density(
+def plot_density(
     ax,
     all_labels,
     to_plot,
@@ -26,6 +26,7 @@ def _plot_density(
     data_labels,
     show,
 ):
+    """Bokeh density plot."""
     axis_map = {label: ax_ for label, ax_ in zip(all_labels, ax.flatten())}
     if data_labels is None:
         data_labels = {}

arviz/plots/backends/bokeh/bokeh_distplot.py → arviz/plots/backends/bokeh/distplot.py

@@ -2,12 +2,13 @@
 import bokeh.plotting as bkp
 import numpy as np
 
+from . import BACKEND_KWARG_DEFAULTS
 from ...kdeplot import plot_kde
 from ...plot_utils import get_bins
 from ....rcparams import rcParams
 
 
-def _plot_dist_bokeh(
+def plot_dist(
     values,
     values2=None,
     color="C0",
@@ -28,8 +29,14 @@ def _plot_dist_bokeh(
     pcolormesh_kwargs=None,
     hist_kwargs=None,
     ax=None,
-    show=True,
+    backend_kwargs=None,
+    **kwargs  # pylint: disable=unused-argument
 ):
+    """Bokeh distplot."""
+    if backend_kwargs is None:
+        backend_kwargs = {}
+
+    backend_kwargs = {**BACKEND_KWARG_DEFAULTS, **backend_kwargs}
 
     if ax is None:
         tools = rcParams["plot.bokeh.tools"]
@@ -75,12 +82,14 @@ def _plot_dist_bokeh(
             pcolormesh_kwargs=pcolormesh_kwargs,
             ax=ax,
             backend="bokeh",
+            # TODO: Revisit this when I refactor backend args for kde
             show=False,
         )
     else:
         raise TypeError('Invalid "kind":{}. Select from {{"auto","kde","hist"}}'.format(kind))
 
-    if show:
+    # TODO: Temporary setting just to make sure tests work. This needs to be removed
+    if backend_kwargs["show"] is True:
         bkp.show(ax, toolbar_location="above")
     return ax
 

arviz/plots/backends/bokeh/bokeh_elpdplot.py → arviz/plots/backends/bokeh/elpdplot.py

@@ -2,16 +2,15 @@
 import warnings
 
 import bokeh.plotting as bkp
-from bokeh.models.annotations import Title
-from bokeh.layouts import gridplot
 import numpy as np
-
+from bokeh.layouts import gridplot
+from bokeh.models.annotations import Title
 
 from ...plot_utils import _scale_fig_size
 from ....rcparams import rcParams
 
 
-def _plot_elpd(
+def plot_elpd(
     ax,
     models,
     pointwise_data,
@@ -26,6 +25,7 @@ def _plot_elpd(
     threshold,
     show,
 ):
+    """Bokeh elpd plot."""
     if numvars == 2:
         (figsize, _, _, _, _, markersize) = _scale_fig_size(
             figsize, textsize, numvars - 1, numvars - 1

arviz/plots/backends/bokeh/bokeh_energyplot.py → arviz/plots/backends/bokeh/energyplot.py

@@ -2,15 +2,16 @@
 import bokeh.plotting as bkp
 from bokeh.models import Label
 
+from .distplot import _histplot_bokeh_op
 from ...kdeplot import plot_kde
-from .bokeh_distplot import _histplot_bokeh_op
 from ....rcparams import rcParams
 from ....stats import bfmi as e_bfmi
 
 
-def _plot_energy(
+def plot_energy(
     ax, series, energy, kind, bfmi, figsize, line_width, fill_kwargs, plot_kwargs, bw, legend, show,
 ):
+    """Bokeh energy plot."""
     if ax is None:
         tools = rcParams["plot.bokeh.tools"]
         output_backend = rcParams["plot.bokeh.output_backend"]

arviz/plots/backends/bokeh/bokeh_essplot.py → arviz/plots/backends/bokeh/essplot.py

@@ -1,23 +1,19 @@
 # pylint: disable=all
 """Bokeh ESS plots."""
 import bokeh.plotting as bkp
+import numpy as np
+from bokeh.layouts import gridplot
 from bokeh.models import Dash, Span, ColumnDataSource
 from bokeh.models.annotations import Title
-from bokeh.layouts import gridplot
-import numpy as np
 from scipy.stats import rankdata
 
-
 from ...plot_utils import (
     make_label,
     _create_axes_grid,
-    get_coords,
-    filter_plotters_list,
 )
-from ....rcparams import rcParams
 
 
-def _plot_ess(
+def plot_ess(
     ax,
     plotters,
     xdata,
@@ -51,6 +47,7 @@ def _plot_ess(
     hline_kwargs,
     show,
 ):
+    """Bokeh essplot."""
     if ax is None:
         _, ax = _create_axes_grid(
             len(plotters),

arviz/plots/backends/bokeh/bokeh_forestplot.py → arviz/plots/backends/bokeh/forestplot.py

@@ -3,16 +3,16 @@
 from collections import defaultdict, OrderedDict
 from itertools import cycle, tee
 
-import numpy as np
 import bokeh.plotting as bkp
+import matplotlib.pyplot as plt
+import numpy as np
+from bokeh.layouts import gridplot
 from bokeh.models import Band, ColumnDataSource
 from bokeh.models.annotations import Title
 from bokeh.models.tickers import FixedTicker
-from bokeh.layouts import gridplot
-import matplotlib.pyplot as plt
 
-from ...plot_utils import _scale_fig_size, xarray_var_iter, make_label, get_bins
 from ...kdeplot import _fast_kde
+from ...plot_utils import _scale_fig_size, xarray_var_iter, make_label, get_bins
 from ....rcparams import rcParams
 from ....stats import hpd
 from ....stats.diagnostics import _ess, _rhat
@@ -27,7 +27,7 @@ def pairwise(iterable):
     return zip(first, second)
 
 
-def _plot_forest(
+def plot_forest(
     ax,
     datasets,
     var_names,
@@ -51,6 +51,7 @@ def _plot_forest(
     r_hat,
     show,
 ):
+    """Bokeh forest plot."""
     plot_handler = PlotHandler(
         datasets, var_names=var_names, model_names=model_names, combined=combined, colors=colors
     )

arviz/plots/backends/bokeh/bokeh_hpdplot.py → arviz/plots/backends/bokeh/hpdplot.py

@@ -2,13 +2,14 @@
 from itertools import cycle
 
 import bokeh.plotting as bkp
-from matplotlib.pyplot import rcParams as mpl_rcParams
 import numpy as np
+from matplotlib.pyplot import rcParams as mpl_rcParams
 
 from ....rcparams import rcParams
 
 
-def _plot_hpdplot(ax, x_data, y_data, plot_kwargs, fill_kwargs, show):
+def plot_hpd(ax, x_data, y_data, plot_kwargs, fill_kwargs, show):
+    """Bokeh hpd plot."""
     if ax is None:
         tools = rcParams["plot.bokeh.tools"]
         output_backend = rcParams["plot.bokeh.output_backend"]

arviz/plots/backends/bokeh/bokeh_jointplot.py → arviz/plots/backends/bokeh/jointplot.py

@@ -1,15 +1,15 @@
 """Bokeh jointplot."""
 import bokeh.plotting as bkp
-from bokeh.layouts import gridplot
 import numpy as np
+from bokeh.layouts import gridplot
 
 from ...distplot import plot_dist
 from ...kdeplot import plot_kde
 from ...plot_utils import make_label
 from ....rcparams import rcParams
 
 
-def _plot_joint(
+def plot_joint(
     ax,
     figsize,
     plotters,
@@ -22,6 +22,7 @@ def _plot_joint(
     marginal_kwargs,
     show,
 ):
+    """Bokeh joint plot."""
     if ax is None:
         tools = rcParams["plot.bokeh.tools"]
         output_backend = rcParams["plot.bokeh.output_backend"]
@@ -92,7 +93,7 @@ def _plot_joint(
             rotated=rotate,
             ax=ax_,
             backend="bokeh",
-            show=False,
+            backend_kwargs={"show": False},
             **marginal_kwargs
         )