CompatHelper: bump compat for PosteriorStats in [weakdeps] to 0.3, (keep existing compat) (#100)

* CompatHelper: bump compat for PosteriorStats in [weakdeps] to 0.3, (keep existing compat)

* Drop support for older PosteriorStats versions

* Update/unify hdi/ci implementations

* Update PosteriorStats tests

* Add local InferenceObjects to docs sources

* Fix typos in docstrings

* Update doctests

* Build docs with larger terminal width

* Run formatter

* Remove outdated version checks

* Only use larger terminal width on extension doctests

* Increment patch number

* Revert "Only use larger terminal width on extension doctests"

This reverts commit 8da4fa9.

* Don't run extension doctests twice

These already seem to be picked up by the main docs build

* Remove accidentally-introduced div char

* Only use SummaryStats' public API

---------

Co-authored-by: CompatHelper Julia <[email protected]>
Co-authored-by: Seth Axen <[email protected]>

Author: 3 people

Project.toml

@@ -1,7 +1,7 @@
 name = "InferenceObjects"
 uuid = "b5cf5a8d-e756-4ee3-b014-01d49d192c00"
 authors = ["Seth Axen <[email protected]> and contributors"]
-version = "0.4.12"
+version = "0.4.13"
 
 [deps]
 ANSIColoredPrinters = "a4c015fc-c6ff-483c-b24f-f7ea428134e9"
@@ -32,7 +32,7 @@ MLJBase = "1"
 NCDatasets = "0.12.6, 0.13, 0.14"
 OffsetArrays = "1"
 OrderedCollections = "1.6"
-PosteriorStats = "0.1.1, 0.2"
+PosteriorStats = "0.3"
 Random = "1"
 StatsBase = "0.33.7, 0.34"
 Tables = "1.11.0"

docs/Project.toml

@@ -8,6 +8,9 @@ NCDatasets = "85f8d34a-cbdd-5861-8df4-14fed0d494ab"
 PosteriorStats = "7f36be82-ad55-44ba-a5c0-b8b5480d7aa5"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 
+[sources]
+InferenceObjects = {path = ".."}
+
 [compat]
 Documenter = "1"
 DocumenterInterLinks = "1"

docs/make.jl

@@ -29,34 +29,37 @@ doctestfilters = [
     r"\s+\"created_at\" => .*",  # ignore timestamps in doctests
 ]
 
-makedocs(;
-    modules=[
-        InferenceObjects,
-        Base.get_extension(InferenceObjects, :InferenceObjectsMCMCDiagnosticToolsExt),
-        Base.get_extension(InferenceObjects, :InferenceObjectsPosteriorStatsExt),
-    ],
-    authors="Seth Axen <[email protected]> and contributors",
-    repo=Remotes.GitHub("arviz-devs", "InferenceObjects.jl"),
-    sitename="InferenceObjects.jl",
-    format=Documenter.HTML(;
-        prettyurls=get(ENV, "CI", "false") == "true",
-        canonical="https://arviz-devs.github.io/InferenceObjects.jl",
-        edit_link="main",
-        assets=String[],
-    ),
-    pages=[
-        "Home" => "index.md",
-        "Dataset" => "dataset.md",
-        "InferenceData" => "inference_data.md",
-        "Extensions" => [
-            "MCMCDiagnosticTools" => "extensions/mcmcdiagnostictools.md",
-            "PosteriorStats" => "extensions/posteriorstats.md",
+# Increase the terminal width from 80 to 100 chars to avoid column truncation
+withenv("COLUMNS" => 100) do
+    makedocs(;
+        modules=[
+            InferenceObjects,
+            Base.get_extension(InferenceObjects, :InferenceObjectsMCMCDiagnosticToolsExt),
+            Base.get_extension(InferenceObjects, :InferenceObjectsPosteriorStatsExt),
         ],
-    ],
-    doctestfilters=doctestfilters,
-    warnonly=:missing_docs,
-    plugins=[links],
-)
+        authors="Seth Axen <[email protected]> and contributors",
+        repo=Remotes.GitHub("arviz-devs", "InferenceObjects.jl"),
+        sitename="InferenceObjects.jl",
+        format=Documenter.HTML(;
+            prettyurls=get(ENV, "CI", "false") == "true",
+            canonical="https://arviz-devs.github.io/InferenceObjects.jl",
+            edit_link="main",
+            assets=String[],
+        ),
+        pages=[
+            "Home" => "index.md",
+            "Dataset" => "dataset.md",
+            "InferenceData" => "inference_data.md",
+            "Extensions" => [
+                "MCMCDiagnosticTools" => "extensions/mcmcdiagnostictools.md",
+                "PosteriorStats" => "extensions/posteriorstats.md",
+            ],
+        ],
+        doctestfilters=doctestfilters,
+        warnonly=:missing_docs,
+        plugins=[links],
+    )
+end
 
 # run doctests on extensions
 function get_extension(mod::Module, name::Symbol)
@@ -67,16 +70,6 @@ function get_extension(mod::Module, name::Symbol)
     end
 end
 
-using MCMCDiagnosticTools: MCMCDiagnosticTools
-using PosteriorStats: PosteriorStats
-for extended_pkg in (MCMCDiagnosticTools, PosteriorStats)
-    extension_name = Symbol("InferenceObjects", extended_pkg, "Ext")
-    @info "Running doctests for extension $(extension_name)"
-    mod = get_extension(InferenceObjects, extension_name)
-    DocMeta.setdocmeta!(mod, :DocTestSetup, :(using $(Symbol(extended_pkg))))
-    doctest(mod; manual=false)
-end
-
 deploydocs(;
     repo="github.com/arviz-devs/InferenceObjects.jl", devbranch="main", push_preview=true
 )

ext/InferenceObjectsPosteriorStatsExt/InferenceObjectsPosteriorStatsExt.jl

@@ -6,13 +6,15 @@ using InferenceObjects: InferenceObjects
 using PosteriorStats: PosteriorStats
 using StatsBase: StatsBase
 
-import PosteriorStats: hdi, loo, loo_pit, r2_score, summarize, waic
+import PosteriorStats: eti, hdi, loo, loo_pit, r2_score, summarize, waic
 import StatsBase: summarystats
 
-export hdi, loo, loo_pit, r2_score, summarize, waic, summarystats
+export eti, hdi, loo, loo_pit, r2_score, summarize, waic, summarystats
+
+maplayers = isdefined(DimensionalData, :maplayers) ? DimensionalData.maplayers : map
 
 include("utils.jl")
-include("hdi.jl")
+include("ci.jl")
 include("loo.jl")
 include("waic.jl")
 include("loo_pit.jl")

ext/InferenceObjectsPosteriorStatsExt/ci.jl

@@ -0,0 +1,27 @@
+
+for (ci_fun, ci_desc) in
+    (:eti => "equal-tailed interval (ETI)", :hdi => "highest density interval (HDI)")
+    @eval begin
+        # this pattern ensures that the type is completely specified at compile time
+        @doc """
+            $($ci_fun)(data::InferenceData; kwargs...) -> Dataset
+            $($ci_fun)(data::Dataset; kwargs...) -> Dataset
+
+        Calculate the $($ci_desc) for each parameter in the data.
+
+        For more details and a description of the `kwargs`, see
+        [`PosteriorStats.$($ci_fun)`](@extref).
+        """
+        function PosteriorStats.$(ci_fun)(data::InferenceObjects.InferenceData; kwargs...)
+            return PosteriorStats.$(ci_fun)(data.posterior; kwargs...)
+        end
+        function PosteriorStats.$(ci_fun)(data::InferenceObjects.Dataset; kwargs...)
+            ds = maplayers(data) do var
+                return _as_dimarray(
+                    PosteriorStats.$(ci_fun)(_params_array(var); kwargs...), var
+                )
+            end
+            return DimensionalData.rebuild(ds; metadata=DimensionalData.NoMetadata())
+        end
+    end
+end

ext/InferenceObjectsPosteriorStatsExt/hdi.jl

@@ -19,8 +19,8 @@ julia> idata = load_example_data("centered_eight");
 
 julia> loo(idata)
 PSISLOOResult with estimates
- elpd  elpd_mcse    p  p_mcse
-  -31        1.4  0.9    0.33
+ elpd  se_elpd    p  se_p
+  -31      1.4  0.9  0.33
 
 and PSISResult with 500 draws, 4 chains, and 8 parameters
 Pareto shape (k) diagnostic values:

ext/InferenceObjectsPosteriorStatsExt/loo.jl

@@ -13,12 +13,12 @@ function StatsBase.summarystats(data::InferenceObjects.Dataset; kwargs...)
 end
 
 @doc """
-    summarize(data::InferenceData, group=:posterior, stats_funs...; kwargs...)
+    summarize(data::InferenceData, stats_funs...; group=:posterior, kwargs...)
     summarize(data::Dataset, stats_funs...; kwargs...)
 
 Compute summary statistics for the data using the provided functions.
 
-For verbose variable labels, provide `compat_labels=false`. For details on `stats_funs` and
+For verbose variable labels, provide `compact_labels=false`. For details on `stats_funs` and
 `kwargs`, see [`PosteriorStats.summarize`](@extref).
 
 # Examples
@@ -33,18 +33,17 @@ julia> data = load_example_data("centered_eight");
 
 julia> summarize(data)
 SummaryStats
-                          mean  std  hdi_3%  hdi_97%  mcse_mean  mcse_std  ess ⋯
- mu                        4.2  3.3  -1.61     10.3        0.21     0.088      ⋯
- theta[Choate]             6.4  5.9  -3.68     17.9        0.25     0.20       ⋯
- theta[Deerfield]          5.0  4.9  -4.98     13.4        0.21     0.15       ⋯
- theta[Phillips Andover]   3.4  5.4  -7.54     12.9        0.23     0.17       ⋯
- theta[Phillips Exeter]    4.8  5.2  -5.11     14.1        0.21     0.21       ⋯
- theta[Hotchkiss]          3.5  4.8  -6.12     12.0        0.25     0.15       ⋯
- theta[Lawrenceville]      3.7  5.2  -6.50     12.7        0.22     0.21       ⋯
- theta[St. Paul's]         6.5  5.2  -2.67     16.9        0.22     0.15       ⋯
- theta[Mt. Hermon]         4.8  5.7  -5.97     15.4        0.24     0.23       ⋯
- tau                       4.3  3.0   0.715     9.41       0.22     0.14       ⋯
-                                                               3 columns omitted
+                          mean  std  eti94          ess_tail  ess_bulk  rhat  mcse_mean  mcse_std
+ mu                        4.2  3.3  -2.11 .. 9.90       622       241  1.03       0.21     0.088
+ theta[Choate]             6.4  5.9  -3.05 .. 19.1       937       572  1.01       0.25     0.20
+ theta[Deerfield]          5.0  4.9  -4.49 .. 14.2      1214       532  1.01       0.21     0.15
+ theta[Phillips Andover]   3.4  5.4  -8.17 .. 12.7      1017       511  1.01       0.23     0.17
+ theta[Phillips Exeter]    4.8  5.2  -4.84 .. 14.5       911       572  1.01       0.21     0.21
+ theta[Hotchkiss]          3.5  4.8  -6.11 .. 12.0       789       347  1.02       0.25     0.15
+ theta[Lawrenceville]      3.7  5.2  -6.62 .. 12.6       957       506  1.01       0.22     0.21
+ theta[St. Paul's]         6.5  5.2  -2.38 .. 18.3      1031       528  1.01       0.22     0.15
+ theta[Mt. Hermon]         4.8  5.7  -5.52 .. 16.0      1045       538  1.01       0.24     0.23
+ tau                       4.3  3.0   1.06 .. 11.5       214       128  1.03       0.22     0.14
 ```
 
 Compute the mean, standard deviation, median, and median absolute deviation of the `theta`

ext/InferenceObjectsPosteriorStatsExt/summarize.jl

@@ -159,8 +159,17 @@ function observations_and_predictions(
     end
 end
 
+# reshape to (ndraws, nchains, nparams...) and drop the dimensions
+function _params_array(data)
+    sample_dims = Dimensions.dims(data, InferenceObjects.DEFAULT_SAMPLE_DIMS)
+    param_dims = Dimensions.otherdims(data, sample_dims)
+    dims_combined = Dimensions.combinedims((sample_dims..., param_dims...))
+    Dimensions.dimsmatch(Dimensions.dims(data), dims_combined) && return data
+    return PermutedDimsArray(data, dims_combined)
+end
+
 _as_dimarray(x::DimensionalData.AbstractDimArray, ::DimensionalData.AbstractDimArray) = x
-function _as_dimarray(x::Union{Real,Missing}, arr::DimensionalData.AbstractDimArray)
+function _as_dimarray(x, arr::DimensionalData.AbstractDimArray)
     return Dimensions.rebuild(arr, fill(x), ())
 end
 

ext/InferenceObjectsPosteriorStatsExt/utils.jl

@@ -19,8 +19,8 @@ julia> idata = load_example_data("centered_eight");
 
 julia> waic(idata)
 WAICResult with estimates
- elpd  elpd_mcse    p  p_mcse
-  -31        1.4  0.9    0.32
+ elpd  se_elpd    p  se_p
+  -31      1.4  0.9  0.32
 ```
 """
 function PosteriorStats.waic(