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 e64f153.

* Mark correct test as broken

Project.toml

@@ -1,7 +1,7 @@
 name = "ArviZ"
 uuid = "131c737c-5715-5e2e-ad31-c244f01c1dc7"
 authors = ["Seth Axen <[email protected]>"]
-version = "0.6.6"
+version = "0.6.7"
 
 [deps]
 Conda = "8f4d0f93-b110-5947-807f-2305c1781a2d"

docs/src/api/data.md

@@ -25,7 +25,7 @@ to_netcdf
 
 ```@docs
 concat
-extract_dataset
+extract
 ```
 
 ## Example data

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()

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

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]

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