py-arviz: updated to 0.9.0

v0.9.0:

Highlights
loo-pit KDE and HDI were improved
html_repr of InferenceData objects for jupyter notebooks
Support for PyJAGS
from_pymc3 automatically retrieves coords and dims from model context
plot_trace now supports multiple aesthetics to identify chain and variable shape and supports matplotlib aliases
plot_hdi can now take already computed HDI values

Deprecations
from_pymc3 without a model context available raises aFutureWarning and will be deprecated in a future version
In plot_trace, chain_prop and compact_prop as tuples will now raise a FutureWarning
hdi with 2d data raises a FutureWarning

3 files changed, 120 insertions, 77 deletions

diff --git a/math/py-arviz/Makefile b/math/py-arviz/Makefile
index f92838dadd7..5b17fcfe4b1 100644
--- a/math/py-arviz/Makefile
+++ b/math/py-arviz/Makefile
@@ -1,8 +1,8 @@
-# $NetBSD: Makefile,v 1.3 2020/02/16 03:02:15 minskim Exp $
+# $NetBSD: Makefile,v 1.4 2020/07/01 16:03:59 adam Exp $
 
-DISTNAME=	arviz-0.6.1
+DISTNAME=	arviz-0.9.0
 PKGNAME=	${PYPKGPREFIX}-${DISTNAME}
-CATEGORIES=	math
+CATEGORIES=	math python
 MASTER_SITES=	${MASTER_SITE_PYPI:=a/arviz/}
 
 MAINTAINER=	minskim@NetBSD.org
@@ -18,9 +18,9 @@ DEPENDS+=	${PYPKGPREFIX}-pandas>=0.23:../../math/py-pandas
 DEPENDS+=	${PYPKGPREFIX}-scipy>=0.19:../../math/py-scipy
 DEPENDS+=	${PYPKGPREFIX}-xarray>=0.11:../../math/py-xarray
 
-PYTHON_VERSIONS_INCOMPATIBLE=	27
-
 USE_LANGUAGES=	# none
 
+PYTHON_VERSIONS_INCOMPATIBLE=	27
+
 .include "../../lang/python/egg.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/math/py-arviz/PLIST b/math/py-arviz/PLIST
index 6af0de18d5f..9502f250647 100644
--- a/math/py-arviz/PLIST
+++ b/math/py-arviz/PLIST
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.2 2020/02/16 03:02:15 minskim Exp $
+@comment $NetBSD: PLIST,v 1.3 2020/07/01 16:03:59 adam Exp $
 ${PYSITELIB}/${EGG_INFODIR}/PKG-INFO
 ${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt
 ${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt
@@ -42,6 +42,9 @@ ${PYSITELIB}/arviz/data/io_netcdf.pyo
 ${PYSITELIB}/arviz/data/io_numpyro.py
 ${PYSITELIB}/arviz/data/io_numpyro.pyc
 ${PYSITELIB}/arviz/data/io_numpyro.pyo
+${PYSITELIB}/arviz/data/io_pyjags.py
+${PYSITELIB}/arviz/data/io_pyjags.pyc
+${PYSITELIB}/arviz/data/io_pyjags.pyo
 ${PYSITELIB}/arviz/data/io_pymc3.py
 ${PYSITELIB}/arviz/data/io_pymc3.pyc
 ${PYSITELIB}/arviz/data/io_pymc3.pyo
@@ -54,6 +57,9 @@ ${PYSITELIB}/arviz/data/io_pystan.pyo
 ${PYSITELIB}/arviz/data/io_tfp.py
 ${PYSITELIB}/arviz/data/io_tfp.pyc
 ${PYSITELIB}/arviz/data/io_tfp.pyo
+${PYSITELIB}/arviz/numeric_utils.py
+${PYSITELIB}/arviz/numeric_utils.pyc
+${PYSITELIB}/arviz/numeric_utils.pyo
 ${PYSITELIB}/arviz/plots/__init__.py
 ${PYSITELIB}/arviz/plots/__init__.pyc
 ${PYSITELIB}/arviz/plots/__init__.pyo
@@ -75,6 +81,9 @@ ${PYSITELIB}/arviz/plots/backends/bokeh/compareplot.pyo
 ${PYSITELIB}/arviz/plots/backends/bokeh/densityplot.py
 ${PYSITELIB}/arviz/plots/backends/bokeh/densityplot.pyc
 ${PYSITELIB}/arviz/plots/backends/bokeh/densityplot.pyo
+${PYSITELIB}/arviz/plots/backends/bokeh/distcomparisonplot.py
+${PYSITELIB}/arviz/plots/backends/bokeh/distcomparisonplot.pyc
+${PYSITELIB}/arviz/plots/backends/bokeh/distcomparisonplot.pyo
 ${PYSITELIB}/arviz/plots/backends/bokeh/distplot.py
 ${PYSITELIB}/arviz/plots/backends/bokeh/distplot.pyc
 ${PYSITELIB}/arviz/plots/backends/bokeh/distplot.pyo
@@ -90,9 +99,9 @@ ${PYSITELIB}/arviz/plots/backends/bokeh/essplot.pyo
 ${PYSITELIB}/arviz/plots/backends/bokeh/forestplot.py
 ${PYSITELIB}/arviz/plots/backends/bokeh/forestplot.pyc
 ${PYSITELIB}/arviz/plots/backends/bokeh/forestplot.pyo
-${PYSITELIB}/arviz/plots/backends/bokeh/hpdplot.py
-${PYSITELIB}/arviz/plots/backends/bokeh/hpdplot.pyc
-${PYSITELIB}/arviz/plots/backends/bokeh/hpdplot.pyo
+${PYSITELIB}/arviz/plots/backends/bokeh/hdiplot.py
+${PYSITELIB}/arviz/plots/backends/bokeh/hdiplot.pyc
+${PYSITELIB}/arviz/plots/backends/bokeh/hdiplot.pyo
 ${PYSITELIB}/arviz/plots/backends/bokeh/jointplot.py
 ${PYSITELIB}/arviz/plots/backends/bokeh/jointplot.pyc
 ${PYSITELIB}/arviz/plots/backends/bokeh/jointplot.pyo
@@ -141,6 +150,9 @@ ${PYSITELIB}/arviz/plots/backends/matplotlib/compareplot.pyo
 ${PYSITELIB}/arviz/plots/backends/matplotlib/densityplot.py
 ${PYSITELIB}/arviz/plots/backends/matplotlib/densityplot.pyc
 ${PYSITELIB}/arviz/plots/backends/matplotlib/densityplot.pyo
+${PYSITELIB}/arviz/plots/backends/matplotlib/distcomparisonplot.py
+${PYSITELIB}/arviz/plots/backends/matplotlib/distcomparisonplot.pyc
+${PYSITELIB}/arviz/plots/backends/matplotlib/distcomparisonplot.pyo
 ${PYSITELIB}/arviz/plots/backends/matplotlib/distplot.py
 ${PYSITELIB}/arviz/plots/backends/matplotlib/distplot.pyc
 ${PYSITELIB}/arviz/plots/backends/matplotlib/distplot.pyo
@@ -156,9 +168,9 @@ ${PYSITELIB}/arviz/plots/backends/matplotlib/essplot.pyo
 ${PYSITELIB}/arviz/plots/backends/matplotlib/forestplot.py
 ${PYSITELIB}/arviz/plots/backends/matplotlib/forestplot.pyc
 ${PYSITELIB}/arviz/plots/backends/matplotlib/forestplot.pyo
-${PYSITELIB}/arviz/plots/backends/matplotlib/hpdplot.py
-${PYSITELIB}/arviz/plots/backends/matplotlib/hpdplot.pyc
-${PYSITELIB}/arviz/plots/backends/matplotlib/hpdplot.pyo
+${PYSITELIB}/arviz/plots/backends/matplotlib/hdiplot.py
+${PYSITELIB}/arviz/plots/backends/matplotlib/hdiplot.pyc
+${PYSITELIB}/arviz/plots/backends/matplotlib/hdiplot.pyo
 ${PYSITELIB}/arviz/plots/backends/matplotlib/jointplot.py
 ${PYSITELIB}/arviz/plots/backends/matplotlib/jointplot.pyc
 ${PYSITELIB}/arviz/plots/backends/matplotlib/jointplot.pyo
@@ -201,6 +213,9 @@ ${PYSITELIB}/arviz/plots/compareplot.pyo
 ${PYSITELIB}/arviz/plots/densityplot.py
 ${PYSITELIB}/arviz/plots/densityplot.pyc
 ${PYSITELIB}/arviz/plots/densityplot.pyo
+${PYSITELIB}/arviz/plots/distcomparisonplot.py
+${PYSITELIB}/arviz/plots/distcomparisonplot.pyc
+${PYSITELIB}/arviz/plots/distcomparisonplot.pyo
 ${PYSITELIB}/arviz/plots/distplot.py
 ${PYSITELIB}/arviz/plots/distplot.pyc
 ${PYSITELIB}/arviz/plots/distplot.pyo
@@ -216,9 +231,9 @@ ${PYSITELIB}/arviz/plots/essplot.pyo
 ${PYSITELIB}/arviz/plots/forestplot.py
 ${PYSITELIB}/arviz/plots/forestplot.pyc
 ${PYSITELIB}/arviz/plots/forestplot.pyo
-${PYSITELIB}/arviz/plots/hpdplot.py
-${PYSITELIB}/arviz/plots/hpdplot.pyc
-${PYSITELIB}/arviz/plots/hpdplot.pyo
+${PYSITELIB}/arviz/plots/hdiplot.py
+${PYSITELIB}/arviz/plots/hdiplot.pyc
+${PYSITELIB}/arviz/plots/hdiplot.pyo
 ${PYSITELIB}/arviz/plots/jointplot.py
 ${PYSITELIB}/arviz/plots/jointplot.pyc
 ${PYSITELIB}/arviz/plots/jointplot.pyo
@@ -254,6 +269,7 @@ ${PYSITELIB}/arviz/plots/rankplot.pyc
 ${PYSITELIB}/arviz/plots/rankplot.pyo
 ${PYSITELIB}/arviz/plots/styles/arviz-colors.mplstyle
 ${PYSITELIB}/arviz/plots/styles/arviz-darkgrid.mplstyle
+${PYSITELIB}/arviz/plots/styles/arviz-grayscale.mplstyle
 ${PYSITELIB}/arviz/plots/styles/arviz-white.mplstyle
 ${PYSITELIB}/arviz/plots/styles/arviz-whitegrid.mplstyle
 ${PYSITELIB}/arviz/plots/traceplot.py
@@ -274,75 +290,102 @@ ${PYSITELIB}/arviz/stats/diagnostics.pyo
 ${PYSITELIB}/arviz/stats/stats.py
 ${PYSITELIB}/arviz/stats/stats.pyc
 ${PYSITELIB}/arviz/stats/stats.pyo
+${PYSITELIB}/arviz/stats/stats_refitting.py
+${PYSITELIB}/arviz/stats/stats_refitting.pyc
+${PYSITELIB}/arviz/stats/stats_refitting.pyo
 ${PYSITELIB}/arviz/stats/stats_utils.py
 ${PYSITELIB}/arviz/stats/stats_utils.pyc
 ${PYSITELIB}/arviz/stats/stats_utils.pyo
 ${PYSITELIB}/arviz/tests/__init__.py
 ${PYSITELIB}/arviz/tests/__init__.pyc
 ${PYSITELIB}/arviz/tests/__init__.pyo
+${PYSITELIB}/arviz/tests/base_tests/__init__.py
+${PYSITELIB}/arviz/tests/base_tests/__init__.pyc
+${PYSITELIB}/arviz/tests/base_tests/__init__.pyo
+${PYSITELIB}/arviz/tests/base_tests/test_data.py
+${PYSITELIB}/arviz/tests/base_tests/test_data.pyc
+${PYSITELIB}/arviz/tests/base_tests/test_data.pyo
+${PYSITELIB}/arviz/tests/base_tests/test_diagnostics.py
+${PYSITELIB}/arviz/tests/base_tests/test_diagnostics.pyc
+${PYSITELIB}/arviz/tests/base_tests/test_diagnostics.pyo
+${PYSITELIB}/arviz/tests/base_tests/test_diagnostics_numba.py
+${PYSITELIB}/arviz/tests/base_tests/test_diagnostics_numba.pyc
+${PYSITELIB}/arviz/tests/base_tests/test_diagnostics_numba.pyo
+${PYSITELIB}/arviz/tests/base_tests/test_helpers.py
+${PYSITELIB}/arviz/tests/base_tests/test_helpers.pyc
+${PYSITELIB}/arviz/tests/base_tests/test_helpers.pyo
+${PYSITELIB}/arviz/tests/base_tests/test_plot_utils.py
+${PYSITELIB}/arviz/tests/base_tests/test_plot_utils.pyc
+${PYSITELIB}/arviz/tests/base_tests/test_plot_utils.pyo
+${PYSITELIB}/arviz/tests/base_tests/test_plots_bokeh.py
+${PYSITELIB}/arviz/tests/base_tests/test_plots_bokeh.pyc
+${PYSITELIB}/arviz/tests/base_tests/test_plots_bokeh.pyo
+${PYSITELIB}/arviz/tests/base_tests/test_plots_matplotlib.py
+${PYSITELIB}/arviz/tests/base_tests/test_plots_matplotlib.pyc
+${PYSITELIB}/arviz/tests/base_tests/test_plots_matplotlib.pyo
+${PYSITELIB}/arviz/tests/base_tests/test_rcparams.py
+${PYSITELIB}/arviz/tests/base_tests/test_rcparams.pyc
+${PYSITELIB}/arviz/tests/base_tests/test_rcparams.pyo
+${PYSITELIB}/arviz/tests/base_tests/test_stats.py
+${PYSITELIB}/arviz/tests/base_tests/test_stats.pyc
+${PYSITELIB}/arviz/tests/base_tests/test_stats.pyo
+${PYSITELIB}/arviz/tests/base_tests/test_stats_numba.py
+${PYSITELIB}/arviz/tests/base_tests/test_stats_numba.pyc
+${PYSITELIB}/arviz/tests/base_tests/test_stats_numba.pyo
+${PYSITELIB}/arviz/tests/base_tests/test_stats_utils.py
+${PYSITELIB}/arviz/tests/base_tests/test_stats_utils.pyc
+${PYSITELIB}/arviz/tests/base_tests/test_stats_utils.pyo
+${PYSITELIB}/arviz/tests/base_tests/test_utils.py
+${PYSITELIB}/arviz/tests/base_tests/test_utils.pyc
+${PYSITELIB}/arviz/tests/base_tests/test_utils.pyo
+${PYSITELIB}/arviz/tests/base_tests/test_utils_numba.py
+${PYSITELIB}/arviz/tests/base_tests/test_utils_numba.pyc
+${PYSITELIB}/arviz/tests/base_tests/test_utils_numba.pyo
 ${PYSITELIB}/arviz/tests/conftest.py
 ${PYSITELIB}/arviz/tests/conftest.pyc
 ${PYSITELIB}/arviz/tests/conftest.pyo
+${PYSITELIB}/arviz/tests/external_tests/__init__.py
+${PYSITELIB}/arviz/tests/external_tests/__init__.pyc
+${PYSITELIB}/arviz/tests/external_tests/__init__.pyo
+${PYSITELIB}/arviz/tests/external_tests/test_data_cmdstan.py
+${PYSITELIB}/arviz/tests/external_tests/test_data_cmdstan.pyc
+${PYSITELIB}/arviz/tests/external_tests/test_data_cmdstan.pyo
+${PYSITELIB}/arviz/tests/external_tests/test_data_cmdstanpy.py
+${PYSITELIB}/arviz/tests/external_tests/test_data_cmdstanpy.pyc
+${PYSITELIB}/arviz/tests/external_tests/test_data_cmdstanpy.pyo
+${PYSITELIB}/arviz/tests/external_tests/test_data_emcee.py
+${PYSITELIB}/arviz/tests/external_tests/test_data_emcee.pyc
+${PYSITELIB}/arviz/tests/external_tests/test_data_emcee.pyo
+${PYSITELIB}/arviz/tests/external_tests/test_data_numpyro.py
+${PYSITELIB}/arviz/tests/external_tests/test_data_numpyro.pyc
+${PYSITELIB}/arviz/tests/external_tests/test_data_numpyro.pyo
+${PYSITELIB}/arviz/tests/external_tests/test_data_pyjags.py
+${PYSITELIB}/arviz/tests/external_tests/test_data_pyjags.pyc
+${PYSITELIB}/arviz/tests/external_tests/test_data_pyjags.pyo
+${PYSITELIB}/arviz/tests/external_tests/test_data_pymc.py
+${PYSITELIB}/arviz/tests/external_tests/test_data_pymc.pyc
+${PYSITELIB}/arviz/tests/external_tests/test_data_pymc.pyo
+${PYSITELIB}/arviz/tests/external_tests/test_data_pyro.py
+${PYSITELIB}/arviz/tests/external_tests/test_data_pyro.pyc
+${PYSITELIB}/arviz/tests/external_tests/test_data_pyro.pyo
+${PYSITELIB}/arviz/tests/external_tests/test_data_pystan.py
+${PYSITELIB}/arviz/tests/external_tests/test_data_pystan.pyc
+${PYSITELIB}/arviz/tests/external_tests/test_data_pystan.pyo
+${PYSITELIB}/arviz/tests/external_tests/test_data_tfp.py
+${PYSITELIB}/arviz/tests/external_tests/test_data_tfp.pyc
+${PYSITELIB}/arviz/tests/external_tests/test_data_tfp.pyo
 ${PYSITELIB}/arviz/tests/helpers.py
 ${PYSITELIB}/arviz/tests/helpers.pyc
 ${PYSITELIB}/arviz/tests/helpers.pyo
-${PYSITELIB}/arviz/tests/test_data.py
-${PYSITELIB}/arviz/tests/test_data.pyc
-${PYSITELIB}/arviz/tests/test_data.pyo
-${PYSITELIB}/arviz/tests/test_data_cmdstan.py
-${PYSITELIB}/arviz/tests/test_data_cmdstan.pyc
-${PYSITELIB}/arviz/tests/test_data_cmdstan.pyo
-${PYSITELIB}/arviz/tests/test_data_cmdstanpy.py
-${PYSITELIB}/arviz/tests/test_data_cmdstanpy.pyc
-${PYSITELIB}/arviz/tests/test_data_cmdstanpy.pyo
-${PYSITELIB}/arviz/tests/test_data_emcee.py
-${PYSITELIB}/arviz/tests/test_data_emcee.pyc
-${PYSITELIB}/arviz/tests/test_data_emcee.pyo
-${PYSITELIB}/arviz/tests/test_data_numpyro.py
-${PYSITELIB}/arviz/tests/test_data_numpyro.pyc
-${PYSITELIB}/arviz/tests/test_data_numpyro.pyo
-${PYSITELIB}/arviz/tests/test_data_pymc.py
-${PYSITELIB}/arviz/tests/test_data_pymc.pyc
-${PYSITELIB}/arviz/tests/test_data_pymc.pyo
-${PYSITELIB}/arviz/tests/test_data_pyro.py
-${PYSITELIB}/arviz/tests/test_data_pyro.pyc
-${PYSITELIB}/arviz/tests/test_data_pyro.pyo
-${PYSITELIB}/arviz/tests/test_data_pystan.py
-${PYSITELIB}/arviz/tests/test_data_pystan.pyc
-${PYSITELIB}/arviz/tests/test_data_pystan.pyo
-${PYSITELIB}/arviz/tests/test_data_tfp.py
-${PYSITELIB}/arviz/tests/test_data_tfp.pyc
-${PYSITELIB}/arviz/tests/test_data_tfp.pyo
-${PYSITELIB}/arviz/tests/test_diagnostics.py
-${PYSITELIB}/arviz/tests/test_diagnostics.pyc
-${PYSITELIB}/arviz/tests/test_diagnostics.pyo
-${PYSITELIB}/arviz/tests/test_plot_utils.py
-${PYSITELIB}/arviz/tests/test_plot_utils.pyc
-${PYSITELIB}/arviz/tests/test_plot_utils.pyo
-${PYSITELIB}/arviz/tests/test_plots_bokeh.py
-${PYSITELIB}/arviz/tests/test_plots_bokeh.pyc
-${PYSITELIB}/arviz/tests/test_plots_bokeh.pyo
-${PYSITELIB}/arviz/tests/test_plots_matplotlib.py
-${PYSITELIB}/arviz/tests/test_plots_matplotlib.pyc
-${PYSITELIB}/arviz/tests/test_plots_matplotlib.pyo
-${PYSITELIB}/arviz/tests/test_rcparams.py
-${PYSITELIB}/arviz/tests/test_rcparams.pyc
-${PYSITELIB}/arviz/tests/test_rcparams.pyo
-${PYSITELIB}/arviz/tests/test_stats.py
-${PYSITELIB}/arviz/tests/test_stats.pyc
-${PYSITELIB}/arviz/tests/test_stats.pyo
-${PYSITELIB}/arviz/tests/test_stats_utils.py
-${PYSITELIB}/arviz/tests/test_stats_utils.pyc
-${PYSITELIB}/arviz/tests/test_stats_utils.pyo
-${PYSITELIB}/arviz/tests/test_utils.py
-${PYSITELIB}/arviz/tests/test_utils.pyc
-${PYSITELIB}/arviz/tests/test_utils.pyo
 ${PYSITELIB}/arviz/utils.py
 ${PYSITELIB}/arviz/utils.pyc
 ${PYSITELIB}/arviz/utils.pyo
-${PYSITELIB}/benchmarks/__init__.py
-${PYSITELIB}/benchmarks/__init__.pyc
-${PYSITELIB}/benchmarks/__init__.pyo
-${PYSITELIB}/benchmarks/benchmarks.py
-${PYSITELIB}/benchmarks/benchmarks.pyc
-${PYSITELIB}/benchmarks/benchmarks.pyo
+${PYSITELIB}/arviz/wrappers/__init__.py
+${PYSITELIB}/arviz/wrappers/__init__.pyc
+${PYSITELIB}/arviz/wrappers/__init__.pyo
+${PYSITELIB}/arviz/wrappers/base.py
+${PYSITELIB}/arviz/wrappers/base.pyc
+${PYSITELIB}/arviz/wrappers/base.pyo
+${PYSITELIB}/arviz/wrappers/wrap_pystan.py
+${PYSITELIB}/arviz/wrappers/wrap_pystan.pyc
+${PYSITELIB}/arviz/wrappers/wrap_pystan.pyo
diff --git a/math/py-arviz/distinfo b/math/py-arviz/distinfo
index cbccbe8f5e6..60649ae912d 100644
--- a/math/py-arviz/distinfo
+++ b/math/py-arviz/distinfo
@@ -1,6 +1,6 @@
-$NetBSD: distinfo,v 1.2 2020/02/16 03:02:15 minskim Exp $
+$NetBSD: distinfo,v 1.3 2020/07/01 16:03:59 adam Exp $
 
-SHA1 (arviz-0.6.1.tar.gz) = b97d3e8552b652ca0687c000c8fe695730149870
-RMD160 (arviz-0.6.1.tar.gz) = fae4cc2ba4b07766cb93d648a4d07a6c83540e61
-SHA512 (arviz-0.6.1.tar.gz) = af13aea66ec2fe7ee62168d9ec7d72e221b658bbdfe44e13f7c8ddaab5d48792fe059d15be1806d61eaf4d223659a6e4adec1786396db60fa26dec7fedcbf436
-Size (arviz-0.6.1.tar.gz) = 1363493 bytes
+SHA1 (arviz-0.9.0.tar.gz) = 01268d658953ef91018c9a0fcd75d6e17577d212
+RMD160 (arviz-0.9.0.tar.gz) = 37af60260a8682c83f174b6eae1a3cc98e049599
+SHA512 (arviz-0.9.0.tar.gz) = 70bf850e2ca2e15c18f5cdf738a2021fc4281ffcef1e04121bc241d912180a5b26cff69342b950ec2321183aa93460ee4dfbaab9ad6d0481be499e6ffd12a5ac
+Size (arviz-0.9.0.tar.gz) = 1435491 bytes