Merge branch 'main' into remove-bokeh-deprecation-warnings

.azure-pipelines/azure-pipelines-external.yml

@@ -88,6 +88,9 @@ jobs:
       if [ "$(pymc3.version)" = "github" ]; then
           # Pip installation is failing for some reason. This is the same thing
           git clone https://github.com/pymc-devs/pymc3
+          cd pymc3
+          git checkout v3
+          cd ..
           pip install $PWD/pymc3
           # python -m pip --no-cache-dir --log log.txt install git+https://github.com/pymc-devs/pymc3
           # cat log.txt

.pylintrc

@@ -73,7 +73,8 @@ disable=missing-docstring,
         not-an-iterable,
         no-member,
         #TODO: Remove this once todos are done
-        fixme
+        fixme,
+        consider-using-with
 
 
 # Enable the message, report, category or checker with the given id(s). You can

CHANGELOG.md

@@ -12,8 +12,11 @@
 * Add more helpful error message for HDF5 problems reading `InferenceData` from NetCDF ([1637](https://github.com/arviz-devs/arviz/pull/1637))
 * Added `data.log_likelihood`, `stats.ic_compare_method` and `plot.density_kind` to `rcParams` ([1611](https://github.com/arviz-devs/arviz/pull/1611))
 * Improve error messages in `stats.compare()`, and `var_name` parameter. ([1616](https://github.com/arviz-devs/arviz/pull/1616))
+* Added ability to plot HDI contours to `plot_kde` with the new `hdi_probs` parameter. ([1665](https://github.com/arviz-devs/arviz/pull/1665))
+* Add dtype parsing and setting in all Stan converters ([1632](https://github.com/arviz-devs/arviz/pull/1632))
 
 ### Maintenance and fixes
+* Fix conversion for numpyro models with ImproperUniform latent sites ([1713](https://github.com/arviz-devs/arviz/pull/1713))
 * Fixed conversion of Pyro output fit using GPUs ([1659](https://github.com/arviz-devs/arviz/pull/1659))
 * Enforced using coordinate values as default labels ([1201](https://github.com/arviz-devs/arviz/pull/1201))
 * Integrate `index_origin` with all the library ([1201](https://github.com/arviz-devs/arviz/pull/1201))
@@ -32,17 +35,23 @@
 * Added type checking to raise an error whenever `InferenceData` object is passed using `io_pymc3`'s `trace` argument ([1629](https://github.com/arviz-devs/arviz/pull/1629))
 * Fix `xlabels` in `plot_elpd` ([1601](https://github.com/arviz-devs/arviz/pull/1601))
 * Renamed `sample` dim to `__sample__` when stacking `chain` and `draw` to avoid dimension collision ([1647](https://github.com/arviz-devs/arviz/pull/1647))
+* Removed the `circular` argument in `plot_dist` in favor of `is_circular` ([1681](https://github.com/arviz-devs/arviz/pull/1681))
+* Fix `legend` argument in `plot_separation` ([1701](https://github.com/arviz-devs/arviz/pull/1701))
+* Removed testing dependency on http download for radon dataset ([1717](https://github.com/arviz-devs/arviz/pull/1717))
+* Fixed plot_kde to take labels with kwargs. ([1710](https://github.com/arviz-devs/arviz/pull/1710))
 * Fix Bokeh deprecation warnings ([1657](https://github.com/arviz-devs/arviz/pull/1657))
 
 ### Deprecation
 * Deprecated `index_origin` and `order` arguments in `az.summary` ([1201](https://github.com/arviz-devs/arviz/pull/1201))
 
 ### Documentation
+* Language improvements of the first third of the "Label guide" ([1699](https://github.com/arviz-devs/arviz/pull/1699))
 * Added "Label guide" page and API section for `arviz.labels` module ([1201](https://github.com/arviz-devs/arviz/pull/1201) and [1635](https://github.com/arviz-devs/arviz/pull/1635))
 * Add "Installation guide" page to the documentation ([1551](https://github.com/arviz-devs/arviz/pull/1551))
 * Improve documentation on experimental `SamplingWrapper` classes ([1582](https://github.com/arviz-devs/arviz/pull/1582))
 * Added example to `plot_hdi` using Inference Data ([1615](https://github.com/arviz-devs/arviz/pull/1615))
 * Removed `geweke` diagnostic from `numba` user guide ([1653](https://github.com/arviz-devs/arviz/pull/1653))
+* Restructured the documentation sections to improve community and about us information ([1587](https://github.com/arviz-devs/arviz/pull/1587))
 
 ## v0.11.2 (2021 Feb 21)
 ### New features
@@ -167,7 +176,7 @@
 
 ## 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](https://github.com/arviz-devs/arviz/pull/1215))
+* loo-pit plot. The kde is computed over the data interval (this could be shorter than [0, 1]). The HDI is computed analytically ([1215](https://github.com/arviz-devs/arviz/pull/1215))
 * Added `html_repr` of InferenceData objects for jupyter notebooks. ([1217](https://github.com/arviz-devs/arviz/pull/1217))
 * Added support for PyJAGS via the function `from_pyjags`. ([1219](https://github.com/arviz-devs/arviz/pull/1219) and [1245](https://github.com/arviz-devs/arviz/pull/1245))
 * `from_pymc3` can now retrieve `coords` and `dims` from model context ([1228](https://github.com/arviz-devs/arviz/pull/1228), [1240](https://github.com/arviz-devs/arviz/pull/1240) and [1249](https://github.com/arviz-devs/arviz/pull/1249))