Merge branch 'master' into loglogistic_distribution

Author: devmotion

.github/workflows/CI.yml

@@ -2,12 +2,12 @@ name: CI
 
 on:
   pull_request:
-    branches:
-      - master
   push:
     branches:
       - master
     tags: '*'
+  workflow_dispatch:
+  merge_group:
 
 concurrency:
   # Skip intermediate builds: always.
@@ -17,38 +17,26 @@ concurrency:
 
 jobs:
   test:
-    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ github.event_name }}
     runs-on: ${{ matrix.os }}
-    continue-on-error: ${{ matrix.version == 'nightly' }}
     strategy:
       fail-fast: false
       matrix:
         version:
-          - '1.3'
+          - 'min'
           - '1'
-          - 'nightly'
+          - pre
         os:
           - ubuntu-latest
           - macos-latest
           - windows-latest
-        arch:
-          - x64
     steps:
-      - uses: actions/checkout@v3
-      - uses: julia-actions/setup-julia@v1
+      - uses: actions/checkout@v5
+      - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
-          arch: ${{ matrix.arch }}
-      - uses: actions/cache@v3
-        env:
-          cache-name: cache-artifacts
-        with:
-          path: ~/.julia/artifacts
-          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
-          restore-keys: |
-            ${{ runner.os }}-test-${{ env.cache-name }}-
-            ${{ runner.os }}-test-
-            ${{ runner.os }}-
+          show-versioninfo: true
+      - uses: julia-actions/cache@v2
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
       - run: |
@@ -57,17 +45,20 @@ jobs:
             Pkg.instantiate()'
       - run: julia --project=perf perf/samplers.jl
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v3
+      - uses: codecov/codecov-action@v5
         with:
+          token: ${{ secrets.CODECOV_TOKEN }} # required
+          fail_ci_if_error: true
           files: lcov.info
   docs:
     name: Documentation
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - uses: julia-actions/setup-julia@v1
+      - uses: actions/checkout@v5
+      - uses: julia-actions/setup-julia@v2
         with:
           version: '1'
+          show-versioninfo: true
       - run: |
           julia --project=docs -e '
             using Pkg

.github/workflows/DocPreviewCleanup.yml

@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout gh-pages branch
-        uses: actions/checkout@v3
+        uses: actions/checkout@v5
         with:
           ref: gh-pages
       - name: Delete preview and history + push changes

.github/workflows/IntegrationTest.yml

@@ -31,14 +31,14 @@ jobs:
           #- {user: TuringLang, repo: DistributionsAD.jl, group: ForwardDiff} takes > 1 hour
 
     steps:
-      - uses: actions/checkout@v3
-      - uses: julia-actions/setup-julia@v1
+      - uses: actions/checkout@v5
+      - uses: julia-actions/setup-julia@v2
         with:
           version: 1
           arch: x64
       - uses: julia-actions/julia-buildpkg@latest
       - name: Clone Downstream
-        uses: actions/checkout@v3
+        uses: actions/checkout@v5
         with:
           repository: ${{ matrix.package.user }}/${{ matrix.package.repo }}
           path: downstream

Project.toml

@@ -1,9 +1,10 @@
 name = "Distributions"
 uuid = "31c24e10-a181-5473-b8eb-7969acd0382f"
 authors = ["JuliaStats"]
-version = "0.25.100"
+version = "0.25.122"
 
 [deps]
+AliasTables = "66dad0bd-aa9a-41b7-9441-69ab47430ed8"
 ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
 DensityInterface = "b429d917-457f-4dbc-8f4c-0cc954292b1d"
 FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b"
@@ -22,24 +23,44 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 [weakdeps]
 ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
 DensityInterface = "b429d917-457f-4dbc-8f4c-0cc954292b1d"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [extensions]
 DistributionsChainRulesCoreExt = "ChainRulesCore"
 DistributionsDensityInterfaceExt = "DensityInterface"
+DistributionsTestExt = "Test"
 
 [compat]
+AliasTables = "1"
+Aqua = "0.8.9"
+Calculus = "0.5"
 ChainRulesCore = "1"
+ChainRulesTestUtils = "1"
 DensityInterface = "0.4"
+Distributed = "<0.0.1, 1"
 FillArrays = "0.9, 0.10, 0.11, 0.12, 0.13, 1"
-PDMats = "0.10, 0.11"
+FiniteDifferences = "0.12"
+ForwardDiff = "0.10, 1"
+JSON = "0.21"
+LinearAlgebra = "<0.0.1, 1"
+OffsetArrays = "1"
+PDMats = "0.11.35"
+Printf = "<0.0.1, 1"
 QuadGK = "2"
+Random = "<0.0.1, 1"
+SparseArrays = "<0.0.1, 1"
 SpecialFunctions = "1.2, 2"
+StableRNGs = "1"
+StaticArrays = "1"
+Statistics = "1"
 StatsAPI = "1.6"
 StatsBase = "0.32, 0.33, 0.34"
 StatsFuns = "0.9.15, 1"
-julia = "1.3"
+Test = "<0.0.1, 1"
+julia = "1.10"
 
 [extras]
+Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 Calculus = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9"
 ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
 ChainRulesTestUtils = "cdddcdb0-9152-4a09-a978-84456f9df70a"
@@ -55,4 +76,4 @@ StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["StableRNGs", "Calculus", "ChainRulesCore", "ChainRulesTestUtils", "DensityInterface", "Distributed", "FiniteDifferences", "ForwardDiff", "JSON", "SparseArrays", "StaticArrays", "Test", "OffsetArrays"]
+test = ["Aqua", "StableRNGs", "Calculus", "ChainRulesCore", "ChainRulesTestUtils", "DensityInterface", "Distributed", "FiniteDifferences", "ForwardDiff", "JSON", "SparseArrays", "StaticArrays", "Test", "OffsetArrays"]

README.md

@@ -4,6 +4,7 @@ Distributions.jl
 [![Build Status](https://github.com/JuliaStats/Distributions.jl/workflows/CI/badge.svg)](https://github.com/JuliaStats/Distributions.jl/actions)
 [![](https://zenodo.org/badge/DOI/10.5281/zenodo.2647458.svg)](https://zenodo.org/record/2647458)
 [![Coverage Status](https://coveralls.io/repos/JuliaStats/Distributions.jl/badge.svg?branch=master)](https://coveralls.io/r/JuliaStats/Distributions.jl?branch=master)
+[![Aqua QA](https://raw.githubusercontent.com/JuliaTesting/Aqua.jl/master/badge.svg)](https://github.com/JuliaTesting/Aqua.jl)
 
 [![](https://img.shields.io/badge/docs-latest-blue.svg)](https://JuliaStats.github.io/Distributions.jl/latest/)
 [![](https://img.shields.io/badge/docs-stable-blue.svg)](https://JuliaStats.github.io/Distributions.jl/stable/)

docs/Project.toml

@@ -4,5 +4,5 @@ Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 GR = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71"
 
 [compat]
-Documenter = "0.26, 0.27"
-GR = "0.72.1"
+Documenter = "1"
+GR = "0.72.1, 0.73"

docs/make.jl

@@ -1,10 +1,11 @@
 using Documenter, Distributions
 import Random: AbstractRNG, rand!
 
-makedocs(
+makedocs(;
     sitename = "Distributions.jl",
     modules  = [Distributions],
-    format   = Documenter.HTML(; prettyurls = get(ENV, "CI", nothing) == "true"),
+    format   = Documenter.HTML(; prettyurls = get(ENV, "CI", nothing) == "true",
+                                 assets = ["assets/favicon.ico"]),
     pages    = [
         "index.md",
         "starting.md",
@@ -17,16 +18,18 @@ makedocs(
         "reshape.md",
         "cholesky.md",
         "mixture.md",
+        "product.md",
         "order_statistics.md",
         "convolution.md",
         "fit.md",
         "extends.md",
         "density_interface.md",
-    ]
+    ],
+    warnonly = true,
 )
 
 deploydocs(;
     repo = "github.com/JuliaStats/Distributions.jl.git",
     versions = ["stable" => "v^", "v#.#", "dev" => "master"],
-    push_preview=true,
+    push_preview = true,
 )

docs/src/assets/favicon.ico

@@ -27,6 +27,8 @@ The function `fit_mle` is for maximum likelihood estimation.
 ### Synopsis
 
 ```@docs
+fit(D, x)
+fit(D, x, w)
 fit_mle(D, x)
 fit_mle(D, x, w)
 ```

docs/src/fit.md

@@ -21,6 +21,7 @@ size(::MultivariateDistribution)
 eltype(::Type{MultivariateDistribution})
 mean(::MultivariateDistribution)
 var(::MultivariateDistribution)
+std(::MultivariateDistribution)
 cov(::MultivariateDistribution)
 cor(::MultivariateDistribution)
 entropy(::MultivariateDistribution)
@@ -55,9 +56,9 @@ Multinomial
 Distributions.AbstractMvNormal
 MvNormal
 MvNormalCanon
+MvLogitNormal
 MvLogNormal
 Dirichlet
-Product
 ```
 
 ## Addition Methods
@@ -104,15 +105,6 @@ params{D<:Distributions.AbstractMvLogNormal}(::Type{D},m::AbstractVector,S::Abst
 Distributions._logpdf(d::MultivariateDistribution, x::AbstractArray)
 ```
 
-## Product distributions
-
-```@docs
-Distributions.product_distribution
-```
-
-Using `product_distribution` is advised to construct product distributions. 
-For some distributions, it constructs a special multivariate type.
-
 ## Index
 
 ```@index