CHANGELOG.md

Change Log

v0.x.x Unreleased

New features

• Added to_zarr and from_zarr methods to InferenceData (1518)
• Added confidence interval band to auto-correlation plot (1535)

Maintenance and fixes

• Updated from_cmdstanpy, from_cmdstan, from_numpyro and from_pymc3 converters to follow schema convention (1550, 1541, 1525 and 1555)
• Fix calculation of mode as point estimate (1552)
• Remove variable name from legend in posterior predictive plot (1559)
• Added significant digits formatter to round rope values (1569)
• Updated from_cmdstan. csv reader, dtype problem fixed and dtype kwarg added for manual dtype casting (1565)

Deprecation

• Removed Geweke diagnostic (1545)
• Removed credible_interval and include_circ arguments (1548)

Documentation

• Added an example for converting dataframe to InferenceData (1556)
• Added example for coords argument in plot_posterior docstring (1566)

v0.11.1 (2021 Feb 2)

Maintenance and fixes

• Fixed ovelapping titles and repeating warnings on circular traceplot (1517)
• Removed repetitive variable names from forest plots of multivariate variables (1527)
• Fixed regression in plot_pair labels that prevented coord names to be shown when necessary (1533)

Documentation

• Use tabs in ArviZ example gallery (1521)

v0.11.0 (2021 Dec 17)

New features

• Added to_dataframe method to InferenceData (1395)
• Added __getitem__ magic to InferenceData (1395)
• Added group argument to summary (1408)
• Add ref_line, bar, vlines and marker_vlines kwargs to plot_rank (1419)
• Add observed argument to (un)plot observed data in plot_ppc (1422)
• Add support for named dims and coordinates with multivariate observations (1429)
• Add support for discrete variables in rank plots (1433) and loo_pit (1500)
• Add skipna argument to plot_posterior (1432)
• Make stacking the default method to compute weights in compare (1438)
• Add copy() method to InferenceData class. (1501).

Maintenance and fixes

• prevent wrapping group names in InferenceData repr_html (1407)
• Updated CmdStanPy interface (1409)
• Remove left out warning about default IC scale in compare (1412)
• Fixed a typo found in an error message raised in distplot.py (1414)
• Fix typo in loo_pit extraction of log likelihood (1418)
• Have from_pystan store attrs as strings to allow netCDF storage (1417)
• Remove ticks and spines in plot_violin (1426 )
• Use circular KDE function and fix tick labels in circular plot_trace (1428)
• Fix pair_plot for mixed discrete and continuous variables (1434)
• Fix in-sample deviance in plot_compare (1435)
• Fix computation of weights in compare (1438)
• Avoid repeated warning in summary (1442)
• Fix hdi failure with boolean array (1444)
• Automatically get the current axes instance for plt_kde, plot_dist and plot_hdi (1452)
• Add grid argument to manually specify the number of rows and columns (1459)
• Switch to compact=True by default in our plots (1468)
• plot_elpd, avoid modifying the input dict (1477)
• Do not plot divergences in plot_trace when kind=rank_vlines or kind=rank_bars (1476)
• Allow ignoring observed argument of pymc3.DensityDist in from_pymc3 (1495)
• Make from_pymc3 compatible with theano-pymc 1.1.0 (1495)
• Improve typing hints (1491, (1492, (1493, (1494 and (1497)

Deprecation

• plot_khat deprecate annotate argument in favor of threshold. The new argument accepts floats (1478)

Documentation

• Reorganize documentation and change sphinx theme (1406)
• Switch to MyST and MyST-NB for markdown/notebook parsing in docs (1406)
• Incorporated input_core_dims in hdi and plot_hdi docstrings (1410)
• Add documentation pages about experimental SamplingWrappers usage (1373)
• Show example titles in gallery page (1484)
• Add sample_stats naming convention to the InferenceData schema (1063)
• Extend api documentation about InferenceData methods (1338)

Experimental

• Modified SamplingWrapper base API (1373)

v0.10.0 (2020 Sep 24)

New features

• Added InferenceData dataset containing circular variables (1265)
• Added is_circular argument to plot_dist and plot_kde allowing for a circular histogram (Matplotlib, Bokeh) or 1D KDE plot (Matplotlib). (1266)
• Added to_dict method for InferenceData object (1223)
• Added circ_var_names argument to plot_trace allowing for circular traceplot (Matplotlib) (1336)
• Ridgeplot is hdi aware. By default displays truncated densities at the specified hdi_prop level (1348)
• Added plot_separation (1359)
• Extended methods from xr.Dataset to InferenceData (1254)
• Add extend and add_groups to InferenceData (1300 and 1386)
• Added __iter__ method (.items) for InferenceData (1356)
• Add support for discrete variables in plot_bpv (#1379)

Maintenance and fixes

• Automatic conversion of list/tuple to numpy array in distplot (1277)
• plot_posterior fix overlap of hdi and rope (1263)
• plot_dist bins argument error fixed (1306)
• Improve handling of circular variables in az.summary (1313)
• Removed change of default warning in ELPDData string representation (1321)
• Update radon example dataset to current InferenceData schema specification (1320)
• Update from_cmdstan functionality and add warmup groups (1330 and 1351)
• Restructure plotting code to be compatible with mpl>=3.3 (1312 and 1352)
• Replaced _fast_kde() with kde() which now also supports circular variables via the argument circular (1284).
• Increased from_pystan attrs information content (1353)
• Allow plot_trace to return and accept axes (1361)
• Update diagnostics to be on par with posterior package (1366)
• Use method="average" in scipy.stats.rankdata (1380)
• Add more plot_parallel examples (1380)
• Bump minimum xarray version to 0.16.1 (1389
• Fix multi rope for plot_forest (1390)
• Bump minimum xarray version to 0.16.1 (1389)
• from_dict will now store warmup groups even with the main group missing (1386)
• increase robustness for repr_html handling (1392)

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)
• plot_bpv. A new plot for Bayesian p-values (1222)

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 default branch (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

• Add from_numpyro Integration (811)
• Numba Google Summer of Code additions (https://ban-zee.github.io/jekyll/update/2019/08/19/Submission.html)
• Model checking, Inference Data, and Convergence assessments (https://github.com/OriolAbril/gsoc2019/blob/master/final_work_submission.md)

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