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locks; strict;
comment	@# @;


1.6
date	2025.04.15.16.10.42;	author adam;	state Exp;
branches;
next	1.5;
commitid	z7l68MNvTBwciaRF;

1.5
date	2024.08.05.20.42.07;	author adam;	state Exp;
branches;
next	1.4;
commitid	9ASQCSMoEFvqVFkF;

1.4
date	2022.02.10.14.21.59;	author adam;	state Exp;
branches;
next	1.3;
commitid	6MqrECbqVO4rY4sD;

1.3
date	2020.07.01.16.03.59;	author adam;	state Exp;
branches;
next	1.2;
commitid	DDaJYKRl9nhxtoeC;

1.2
date	2020.02.16.03.02.15;	author minskim;	state Exp;
branches;
next	1.1;
commitid	QolK2d7vccbwwQWB;

1.1
date	2019.11.25.04.08.33;	author minskim;	state Exp;
branches;
next	;
commitid	A3Hv6sXeVZJFybMB;


desc
@@


1.6
log
@py-arviz: updated to 0.21.0

v0.21.0 (2025 Mar 06)

New features

Maintenance and fixes
- Make `arviz.data.generate_dims_coords` handle `dims` and `default_dims` consistently
- Only emit a warning for custom groups in `InferenceData` when explicitly requested
- Splits Bayes Factor computation out from `az.plot_bf` into `az.bayes_factor`
- Update `method="sd"` of `mcse` to not use normality assumption
- Add exception in `az.plot_hdi` for `x` of type `str`

Documentation
- Add example of ECDF comparison plot to gallery
- Change Twitter to X, including the icon
- Update Bokeh link in Installation.rst
- Add missing periods to the ArviZ community page
- Fix missing docstring

v0.20.0 (2024 Sep 28)

New features
- Add optimized simultaneous ECDF confidence bands
- Add support for setting groups with `idata[group]`

Maintenance and fixes
- Make `dm-tree` and optional dependency
- Fix bug in `psislw` modifying input inplace
- Fix behaviour of two dimensional KDE plot with recent matplotlib releases
- Make defaults in `plot_compare` more intuitive

Documentation
- Added extensions of virtual environments in [.gitignore](https://github.com/arviz-devs/arviz/blob/main/.gitignore)
- Fixed the issue in the [Contribution References Documentation](https://python.arviz.org/en/latest/contributing/index.html)
- Improve docstrings for `loo` and `waic`
@
text
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@


1.5
log
@py-arviz: updated to 0.19.0

v0.19.0 (2024 Jul 19)

New features
-  Use revised Pareto k threshold
-   Added arguments `ci_prob`, `eval_points`, `rvs`, and `random_state` to `plot_ecdf`
-   Deprecated rcParam `stats.hdi_prob` and replaced with `stats.ci_prob`
- Expose features from [arviz-base](https://arviz-base.readthedocs.io), [arviz-stats](https://arviz-stats.readthedocs.io) and [arviz-plots](https://arviz-plots.readthedocs.io) as `arviz.preview`
 submodule

Maintenance and fixes
- Ensure support with numpy 2.0
- Update testing strategy to include an environment without optional dependencies and
 an environment with [scientific python nightlies](https://anaconda.org/scientific-python-nightly-wheels)
- Address bokeh related deprecations

- Fix legend overwriting issue in `plot_trace`

Deprecation
-  Support for arrays and DataArrays in plot_khat has been deprecated. Only ELPDdata will be supported in the future
-  Removed arguments `values2`, `fpr`, `pointwise`, and `pit` in `plot_ecdf`

v0.18.0 (2024 Apr 4)

New features
- Add new example data `rugby_field` and update `rugby` example data
- Support for `pytree`s and robust to nested dictionaries.
- Add `.close` method to `InferenceData`


Maintenance and fixes
- Fix deprecation warnings in multiple dependencies

Deprecation

- Removed arguments `values2`, `fpr`, `pointwise`, `npoints`, and `pit` in `plot_ecdf`
@
text
@d1 1
a1 2
@@comment $NetBSD: PLIST,v 1.4 2022/02/10 14:21:59 adam Exp $
${PYSITELIB}/${WHEEL_INFODIR}/LICENSE
d5 1
@


1.4
log
@py-arviz: updated to 0.11.4

v0.11.4 (2021 Oct 3)
Maintenance and fixes
* Fix standard deviation code in density utils by replacing it with `np.std`.

v0.11.3 (2021 Oct 1)
New features
* Added `labeller` argument to enable label customization in plots and summary
* Added `arviz.labels` module with classes and utilities
* Added probability estimate within ROPE in `plot_posterior`
* Added `rope_color` and `ref_val_color` arguments to `plot_posterior`
* Improved retrieving or pointwise log likelihood in `from_cmdstanpy`, `from_cmdstan` and `from_pystan`
* Added interactive legend to bokeh `forestplot`
* Added interactive legend to bokeh `ppcplot`
* Add more helpful error message for HDF5 problems reading `InferenceData` from NetCDF
* Added `data.log_likelihood`, `stats.ic_compare_method` and `plot.density_kind` to `rcParams`
* Improve error messages in `stats.compare()`, and `var_name` parameter.
* Added ability to plot HDI contours to `plot_kde` with the new `hdi_probs` parameter.
* Add dtype parsing and setting in all Stan converters
* Add option to specify colors for each element in ppc_plot

Maintenance and fixes
* Fix conversion for numpyro models with ImproperUniform latent sites
* Fixed conversion of Pyro output fit using GPUs
* Enforced using coordinate values as default labels
* Integrate `index_origin` with all the library
* Fix pareto k threshold typo in reloo function
* Preserve shape from Stan code in `from_cmdstanpy`
* Updated `from_pystan` converters to follow schema convention
* Used generator instead of list wherever possible
* Correctly use chain index when constructing PyMC3 `DefaultTrace` in `from_pymc3`
* Fix bugs in CmdStanPyConverter
* Fix `c` argument in `plot_khat`
* Fix `ax` argument in `plot_elpd`
* Remove warning in `stats.py` compare function
* Fix `ess/rhat` plots in `plot_forest`
* Fix `from_numpyro` crash when importing model with `thinning=x` for `x > 1`
* Upload updated mypy.ini in ci if mypy copilot fails
* Added type checking to raise an error whenever `InferenceData` object is passed using `io_pymc3`'s `trace` argument
* Fix `xlabels` in `plot_elpd`
* Renamed `sample` dim to `__sample__` when stacking `chain` and `draw` to avoid dimension collision
* Removed the `circular` argument in `plot_dist` in favor of `is_circular`
* Fix `legend` argument in `plot_separation`
* Removed testing dependency on http download for radon dataset
* Fixed plot_kde to take labels with kwargs.
* Fixed xarray related tests.
* Fix Bokeh deprecation warnings
* Fix credible inteval percentage in legend in `plot_loo_pit`
* Arguments `filter_vars` and `filter_groups` now raise `ValueError` if illegal arguments are passed
* Remove constrained_layout from arviz rcparams
* Fix plot_elpd for a single outlier

Deprecation
* Deprecated `index_origin` and `order` arguments in `az.summary`

Documentation
* Language improvements of the first third of the "Label guide"
* Added "Label guide" page and API section for `arviz.labels` module
* Add "Installation guide" page to the documentation
* Improve documentation on experimental `SamplingWrapper` classes
* Added example to `plot_hdi` using Inference Data
* Removed `geweke` diagnostic from `numba` user guide
* Restructured the documentation sections to improve community and about us information

v0.11.2 (2021 Feb 21)
New features
* Added `to_zarr` and `from_zarr` methods to InferenceData
* Added confidence interval band to auto-correlation plot

Maintenance and fixes
* Updated CmdStanPy converter form compatibility with versions >=0.9.68
* Updated `from_cmdstanpy`, `from_cmdstan`, `from_numpyro` and `from_pymc3` converters to follow schema convention
* Fix calculation of mode as point estimate
* Remove variable name from legend in posterior predictive plot
* Added significant digits formatter to round rope values
* Updated `from_cmdstan`. csv reader, dtype problem fixed and dtype kwarg added for manual dtype casting

Deprecation
* Removed Geweke diagnostic
* Removed credible_interval and include_circ arguments

Documentation
* Added an example for converting dataframe to InferenceData
* Added example for `coords` argument in `plot_posterior` docstring

v0.11.1 (2021 Feb 2)
Maintenance and fixes
* Fixed ovelapping titles and repeating warnings on circular traceplot
* Removed repetitive variable names from forest plots of multivariate variables
* Fixed regression in `plot_pair` labels that prevented coord names to be shown when necessary

Documentation
* Use tabs in ArviZ example gallery

v0.11.0 (2021 Dec 17)
New features
* Added `to_dataframe` method to InferenceData
* Added `__getitem__` magic to InferenceData
* Added group argument to summary
* Add `ref_line`, `bar`, `vlines` and `marker_vlines` kwargs to `plot_rank`
* Add observed argument to (un)plot observed data in `plot_ppc`
* Add support for named dims and coordinates with multivariate observations
* Add support for discrete variables in rank plots
  `loo_pit`
* Add `skipna` argument to `plot_posterior`
* Make stacking the default method to compute weights in `compare`
* Add `copy()` method to `InferenceData` class.

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

Deprecation
* `plot_khat` deprecate `annotate` argument in favor of `threshold`. The new argument accepts floats

Documentation
* Reorganize documentation and change sphinx theme
* Switch to [MyST](https://myst-parser.readthedocs.io/en/latest/) and [MyST-NB](https://myst-nb.readthedocs.io/en/latest/index.html)
  for markdown/notebook parsing in docs
* Incorporated `input_core_dims` in `hdi` and `plot_hdi` docstrings
* Add documentation pages about experimental `SamplingWrapper`s usage
* Show example titles in gallery page
* Add `sample_stats` naming convention to the InferenceData schema
* Extend api documentation about `InferenceData` methods

Experimental
* Modified `SamplingWrapper` base API

v0.10.0 (2020 Sep 24)
New features
* Added InferenceData dataset containing circular variables
* Added `is_circular` argument to `plot_dist` and `plot_kde` allowing for a circular histogram (Matplotlib, Bokeh) or 1D KDE plot (Matplotlib).
* Added `to_dict` method for InferenceData object
* Added `circ_var_names` argument to `plot_trace` allowing for circular traceplot (Matplotlib)
* Ridgeplot is hdi aware. By default displays truncated densities at the specified `hdi_prop` level
* Added `plot_separation`
* Extended methods from `xr.Dataset` to `InferenceData`
* Add `extend` and `add_groups` to `InferenceData`
* Added `__iter__` method (`.items`) for InferenceData
* Add support for discrete variables in `plot_bpv`

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


1.3
log
@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
@
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@


1.2
log
@math/py-arviz: Update to 0.6.1

Highlights:

- Initial bokeh support.
- Fully support numpyro
- log_likelihood and observed data from pyro
- ArviZ.jl
- improve rcparams
- fix az.concat functionality
- distplot docstring plotting example
@
text
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@


1.1
log
@math/py-arviz: Import version 0.5.1

ArviZ (pronounced "AR-vees") is a Python package for exploratory
analysis of Bayesian models. Includes functions for posterior
analysis, model checking, comparison and diagnostics.
@
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@