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CHANGELOG.md

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Change Log

v0.x.x Unreleased

New features

Maintenance and fixes

Deprecation

Documentation

v0.9.0 (2020 June 23)

New features

  • loo-pit plot. The kde is computed over the data interval (this could be shorter than [0, 1]). The HDI is computed analitically (#1215)
  • Added html_repr of InferenceData objects for jupyter notebooks. (#1217)
  • Added support for PyJAGS via the function from_pyjags. (#1219 and #1245)
  • from_pymc3 can now retrieve coords and dims from model context (#1228, #1240 and #1249)
  • plot_trace now supports multiple aesthetics to identify chain and variable shape and support matplotlib aliases (#1253)
  • plot_hdi can now take already computed HDI values (#1241)

Maintenance and fixes

  • Include data from MultiObservedRV to observed_data when using from_pymc3 (#1098)
  • Added a note on plot_pair when trying to use plot_kde on InferenceData objects. (#1218)
  • Added log_likelihood argument to from_pyro and a warning if log likelihood cannot be obtained (#1227)
  • Skip tests on matplotlib animations if ffmpeg is not installed (#1227)
  • Fix hpd bug where arguments were being ignored (#1236)
  • Remove false positive warning in plot_hdi and fixed matplotlib axes generation (#1241)
  • Change the default zorder of scatter points from 0 to 0.6 in plot_pair (#1246)
  • Update get_bins for numpy 1.19 compatibility (#1256)
  • Fixes to rug, divergences arguments in plot_trace (#1253)

Deprecation

  • Using from_pymc3 without a model context available now raises a FutureWarning and will be deprecated in a future version (#1227)
  • In plot_trace, chain_prop and compact_prop as tuples will now raise a FutureWarning (#1253)
  • hdi with 2d data raises a FutureWarning (#1241)

Documentation

  • A section has been added to the documentation at InferenceDataCookbook.ipynb illustrating the use of ArviZ in conjunction with PyJAGS. (#1219 and #1245)
  • Fixed inconsistent capitalization in plot_hdi docstring (#1221)
  • Fixed and extended InferenceData.map docs (#1255)

v0.8.3 (2020 May 28)

Maintenance and fixes

  • Restructured internals of from_pymc3 to handle old pymc3 releases and sliced traces and to provide useful warnings (#1211)

v0.8.2 (2020 May 25)

Maintenance and fixes

  • Fixed bug in from_pymc3 for sliced pymc3.MultiTrace input (#1209)

v0.8.1 (2020 May 24)

Maintenance and fixes

  • Fixed bug in from_pymc3 when used with PyMC3<3.9 (#1203)
  • Fixed enforcement of rcParam plot.max_subplots in plot_trace and plot_pair (#1205)
  • Removed extra subplot row and column in in plot_pair with marginal=True (#1205)
  • Added latest PyMC3 release to CI in addition to using GitHub master (#1207)

Documentation

  • Use dev as version indicator in online documentation (#1204)

v0.8.0 (2020 May 23)

New features

  • Stats and plotting functions that provide var_names arg can now filter parameters based on partial naming (filter="like") or regular expressions (filter="regex") (see #1154).
  • Add true_values argument for plot_pair. It allows for a scatter plot showing the true values of the variables #1140
  • Allow xarray.Dataarray input for plots.(#1120)
  • Revamped the hpd function to make it work with mutidimensional arrays, InferenceData and xarray objects (#1117)
  • Skip test for optional/extra dependencies when not installed (#1113)
  • Add option to display rank plots instead of trace (#1134)
  • Add out-of-sample groups (predictions and predictions_constant_data) to from_dict (#1125)
  • Add out-of-sample groups (predictions and predictions_constant_data) and constant_data group to pyro and numpyro translation (#1090, #1125)
  • Add num_chains and pred_dims arguments to from_pyro and from_numpyro (#1090, #1125)
  • Integrate jointplot into pairplot, add point-estimate and overlay of plot kinds (#1079)
  • New grayscale style. This also add two new cmaps cet_grey_r and cet_grey_r. These are perceptually uniform gray scale cmaps from colorcet (linear_grey_10_95_c0) (#1164)
  • Add warmup groups to InferenceData objects, initial support for PyStan (#1126) and PyMC3 (#1171)
  • hdi_prob will not plot hdi if argument hide is passed. Previously credible_interval would omit HPD if None was passed (#1176)
  • Add stats.ic_pointwise rcParam (#1173)
  • Add var_name argument to information criterion calculation: compare, loo and waic (#1173)

Maintenance and fixes

  • Fixed plot_pair functionality for two variables with bokeh backend (#1179)
  • Changed diagonal argument for marginals and fixed point_estimate_marker_kwargs in plot_pair (#1167)
  • Fixed behaviour of credible_interval=None in plot_posterior (#1115)
  • Fixed hist kind of plot_dist with multidimensional input (#1115)
  • Fixed TypeError in transform argument of plot_density and plot_forest when InferenceData is a list or tuple (#1121)
  • Fixed overlaid pairplots issue (#1135)
  • Update Docker building steps (#1127)
  • Updated benchmarks and moved to asv_benchmarks/benchmarks (#1142)
  • Moved _fast_kde, _fast_kde_2d, get_bins and _sturges_formula to numeric_utils and get_coords to utils (#1142)
  • Rank plot: rename axes argument to ax (#1144)
  • Added a warning specifying log scale is now the default in compare/loo/waic functions (#1150).
  • Fixed bug in plot_posterior with rcParam "plot.matplotlib.show" = True (#1151)
  • Set fill_last argument of plot_kde to False by default (#1158)
  • plot_ppc animation: improve docs and error handling (#1162)
  • Fix import error when wrapped function docstring is empty (#1192)
  • Fix passing axes to plot_density with several datasets (#1198)

Deprecation

  • hpd function deprecated in favor of hdi. credible_interval argument replaced by hdi_probthroughout with exception of plot_loo_pit (#1176)
  • plot_hpd function deprecated in favor of plot_hdi. (#1190)

Documentation

  • Add classifier to setup.py including Matplotlib framework (#1133)
  • Image thumbs generation updated to be Bokeh 2 compatible (#1116)
  • Add new examples for plot_pair (#1110)
  • Add examples for psislw and r2_score (#1129)
  • Add more examples on 2D kde customization (#1158)
  • Make docs compatible with sphinx3 and configure intersphinx for better references (#1184)
  • Extend the developer guide and add it to the website (#1184)

v0.7.0 (2020 Mar 2)

New features

  • Add out-of-sample predictions (predictions and predictions_constant_data groups) to pymc3, pystan, cmdstan and cmdstanpy translations (#983, #1032 and #1064)
  • Started adding pointwise log likelihood storage support (#794, #1044 and #1064)
  • Add out-of-sample predictions (predictions and predictions_constant_data groups) to pymc3 and pystan translations (#983 and #1032)
  • Started adding pointwise log likelihood storage support (#794, #1044)
  • Violinplot: rug-plot option (#997)
  • Integrated rcParams plot.point_estimate (#994), stats.ic_scale (#993) and stats.credible_interval (#1017)
  • Added group argument to plot_ppc (#1008), plot_pair (#1009) and plot_joint (#1012)
  • Added transform argument to plot_trace, plot_forest, plot_pair, plot_posterior, plot_rank, plot_parallel, plot_violin,plot_density, plot_joint (#1036)
  • Add skipna argument to hpd and summary (#1035)
  • Added transform argument to plot_trace, plot_forest, plot_pair, plot_posterior, plot_rank, plot_parallel, plot_violin,plot_density, plot_joint (#1036)
  • Add marker functionality to bokeh_plot_elpd (#1040)
  • Add ridgeplot_quantiles argument to plot_forest (#1047)
  • Added the functionality interactive legends for bokeh plots of densityplot, energyplot and essplot (#1024)
  • New defaults for cross validation: loo (old: waic) and log -scale (old: deviance -scale) (#1067)
  • Experimental Feature: Added arviz.wrappers module to allow ArviZ to refit the models if necessary (#771)
  • Experimental Feature: Added reloo function to ArviZ (#771)
  • Added new helper function matplotlib_kwarg_dealiaser (#1073)
  • ArviZ version to InferenceData attributes. (#1086)
  • Add log_likelihood argument to from_pymc3 (#1082)
  • Integrated rcParams for plot.bokeh.layout and plot.backend. (#1089)
  • Add automatic legends in plot_trace with compact=True (matplotlib only) (#1070)
  • Updated hover information for plot_pair with bokeh backend (#1074)

Maintenance and fixes

  • Fixed bug in density and posterior plot bin computation (#1049)
  • Fixed bug in density plot ax argument (#1049)
  • Fixed bug in extracting prior samples for cmdstanpy (#979)
  • Fix erroneous warning in traceplot (#989)
  • Correct bfmi denominator (#991)
  • Removed parallel from jit full (#996)
  • Rename flat_inference_data_to_dict (#1003)
  • Violinplot: fix histogram (#997)
  • Convert all instances of SyntaxWarning to UserWarning (#1016)
  • Fix point_estimate in plot_posterior (#1038)
  • Fix interpolation hpd_plot (#1039)
  • Fix io_pymc3.py to handle models with potentials (#1043)
  • Fix several inconsistencies between schema and from_pymc3 implementation in groups prior, prior_predictive and observed_data (#1045)
  • Stabilize covariance matrix for plot_kde_2d (#1075)
  • Removed extra dim in prior data in from_pyro (#1071)
  • Moved CI and docs (build & deploy) to Azure Pipelines and started using codecov (#1080)
  • Fixed bug in densityplot when variables differ between models (#1096)

Deprecation

  • from_pymc3 now requires PyMC3>=3.8

Documentation

  • Updated InferenceData schema specification (log_likelihood, predictions and predictions_constant_data groups)
  • Clarify the usage of plot_joint (#1001)
  • Added the API link of function to examples (#1013)
  • Updated PyStan_schema_example to include example of out-of-sample prediction (#1032)
  • Added example for concat method (#1037)

v0.6.1 (2019 Dec 28)

New features

  • Update for pair_plot divergences can be selected
  • Default tools follow global (ArviZ) defaults
  • Add interactive legend for a plot, if only two variables are used in pairplot

Maintenance and fixes

  • Change packaging import from absolute to relative format, explicitly importing version function

v0.6.0 (2019 Dec 24)

New features

  • Initial bokeh support.
  • ArviZ.jl a Julia interface to ArviZ (@sethaxen )

Maintenance and fixes

  • Fully support numpyro (@fehiepsi )
  • log_likelihood and observed data from pyro
  • improve rcparams
  • fix az.concat functionality (@anzelpwj )

Documentation

  • distplot docstring plotting example (@jscarbor )

v0.5.1 (2019 Sep 16)

Maintenance and fixes

  • Comment dev requirements in setup.py

v0.5.0 (2019 Sep 15)

New features

v0.4.1 (2019 Jun 9)

New features

  • Reorder stats columns (#695)
  • Plot Forest reports ess and rhat by default(#685)
  • Add pointwise elpd (#678)

Maintenance and fixes

  • Fix io_pymc3 bug (#693)
  • Fix io_pymc3 warning (#686)
  • Fix 0 size bug with pystan (#677)

v0.4.0 (2019 May 20)

New features

  • Add plot_dist (#592)
  • New rhat and ess (#623)
  • Add plot_hpd (#611)
  • Add plot_rank (#625)

Deprecation

  • Remove load_data and save_data (#625)

v0.3.3 (2019 Feb 23)

New features

  • Plot ppc supports multiple chains (#526)
  • Plot titles now wrap (#441)
  • plot_density uses a grid (#379)
  • emcee reader support (#550)
  • Animations in plot_ppc (#546)
  • Optional dictionary for stat_funcs in summary (#583)
  • Can exclude variables in selections with negated variable names (#574)

Maintenance and fixes

  • Order maintained with xarray_var_iter (#557)
  • Testing very improved (multiple)
  • Fix nan handling in effective sample size (#573)
  • Fix kde scaling (#582)
  • xticks for discrete variables (#586)
  • Empty InferenceData saves consistent with netcdf (#577)
  • Removes numpy pinning (#594)

Documentation

  • JOSS and Zenodo badges (#537)
  • Gitter badge (#548)
  • Docs for combining InferenceData (#590)

v0.3.2 (2019 Jan 15)

New features

  • Support PyStan3 (#464)
  • Add some more information to the inference data of tfp (#447)
  • Use Split R-hat (#477)
  • Normalize from_xyz functions (#490)
  • KDE: Display quantiles (#479)
  • Add multiple rope support to plot_forest (#448)
  • Numba jit compilation to speed up some methods (#515)
  • Add from_dict for easier creation of az.InferenceData objects (#524)
  • Add stable logsumexp (#522)

Maintenance and fixes

  • Fix for from_pyro with multiple chains (#463)
  • Check __version__ for attr (#466)
  • And exception to plot compare (#461)
  • Add Docker Testing to travisCI (#473)
  • fix jointplot warning (#478)
  • Fix tensorflow import bug (#489)
  • Rename N_effective to S_effective (#505)

Documentation

  • Add docs to plot compare (#461)
  • Add InferenceData tutorial in header (#502)
  • Added figure to InferenceData tutorial (#510)

v0.3.1 (2018 Dec 18)

Maintenance and fixes

  • Fix installation problem with release 0.3.0

v0.3.0 (2018 Dec 14)

  • First Beta Release