Merge branch 'master' into tor/state-transition-related

Author: torfjelde

.JuliaFormatter.toml

@@ -0,0 +1 @@
+style="blue"

.github/workflows/CI.yml

@@ -13,7 +13,7 @@ jobs:
     strategy:
       matrix:
         version:
-          - '1.0'
+          - '1.6'
           - '1'
           - nightly
         os:
@@ -31,7 +31,7 @@ jobs:
             arch: x86
           - os: macOS-latest
             arch: x86
-          - version: '1.0'
+          - version: '1.6'
             num_threads: 2
         include:
           - version: '1'
@@ -45,16 +45,9 @@ jobs:
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      - uses: actions/cache@v1
-        env:
-          cache-name: cache-artifacts
+      - uses: julia-actions/cache@v1
         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 }}-
+          cache-packages: "false" # caching Conda.jl causes precompilation error
       - uses: julia-actions/julia-buildpkg@latest
       - uses: julia-actions/julia-runtest@latest
         env:

.github/workflows/CompatHelper.yml

@@ -3,16 +3,35 @@ on:
   schedule:
     - cron: 0 0 * * *
   workflow_dispatch:
+permissions:
+  contents: write
+  pull-requests: write
 jobs:
   CompatHelper:
     runs-on: ubuntu-latest
     steps:
+      - name: Check if Julia is already available in the PATH
+        id: julia_in_path
+        run: which julia
+        continue-on-error: true
+      - name: Install Julia, but only if it is not already available in the PATH
+        uses: julia-actions/setup-julia@v1
+        with:
+          version: '1'
+          arch: ${{ runner.arch }}
+        if: steps.julia_in_path.outcome != 'success'
+      - name: "Add the General registry via Git"
+        run: |
+          import Pkg
+          ENV["JULIA_PKG_SERVER"] = ""
+          Pkg.Registry.add("General")
+        shell: julia --color=yes {0}
       - name: "Install CompatHelper"
         run: |
           import Pkg
           name = "CompatHelper"
           uuid = "aa819f21-2bde-4658-8897-bab36330d9b7"
-          version = "2"
+          version = "3"
           Pkg.add(; name, uuid, version)
         shell: julia --color=yes {0}
       - name: "Run CompatHelper"

.github/workflows/Docs.yml

@@ -12,13 +12,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@latest
+      - uses: julia-actions/setup-julia@v1
         with:
           version: '1'
-      - name: Install dependencies
-        run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
-      - name: Build and deploy
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-docdeploy@v1
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token
           DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key
-        run: julia --project=docs/ docs/make.jl
+          JULIA_DEBUG: Documenter # Print `@debug` statements (https://github.com/JuliaDocs/Documenter.jl/issues/955)

.github/workflows/Format.yml

@@ -0,0 +1,31 @@
+name: Format
+
+on:
+  pull_request:
+
+concurrency:
+  # Skip intermediate builds: always.
+  # Cancel intermediate builds: only if it is a pull request build.
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+
+jobs:
+  format:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: 1
+      - name: Format code
+        run: |
+          using Pkg
+          Pkg.add(; name="JuliaFormatter", uuid="98e50ef6-434e-11e9-1051-2b60c6c9e899")
+          using JuliaFormatter
+          format("."; verbose=true)
+        shell: julia --color=yes {0}
+      - uses: reviewdog/action-suggester@v1
+        if: github.event_name == 'pull_request'
+        with:
+          tool_name: JuliaFormatter
+          fail_on_error: true

.github/workflows/IntegrationTest.yml

@@ -14,6 +14,7 @@ jobs:
       fail-fast: false
       matrix:
         package:
+          - {user: TuringLang, repo: AdvancedHMC.jl}
           - {user: TuringLang, repo: AdvancedMH.jl}
           - {user: TuringLang, repo: EllipticalSliceSampling.jl}
           - {user: TuringLang, repo: MCMCChains.jl}

.gitignore

@@ -2,4 +2,4 @@
 *.jl.*.cov
 *.jl.mem
 deps/deps.jl
-/Manifest.toml
+Manifest.toml

Project.toml

@@ -3,12 +3,13 @@ uuid = "80f14c24-f653-4e6a-9b94-39d6b0f70001"
 keywords = ["markov chain monte carlo", "probablistic programming"]
 license = "MIT"
 desc = "A lightweight interface for common MCMC methods."
-version = "3.2.1"
+version = "4.5.0"
 
 [deps]
 BangBang = "198e06fe-97b7-11e9-32a5-e1d131e6ad66"
 ConsoleProgressMonitor = "88cd18e8-d9cc-4ea6-8889-5259c0d15c8b"
 Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"
+LogDensityProblems = "6fdf6af0-433a-55f7-b3ed-c6c6e0b8df7c"
 Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
 LoggingExtras = "e6f89c97-d47a-5376-807f-9c37f3926c36"
 ProgressLogging = "33c8b6b6-d38a-422a-b730-caa89a2f386c"
@@ -20,18 +21,19 @@ Transducers = "28d57a85-8fef-5791-bfe6-a80928e7c999"
 [compat]
 BangBang = "0.3.19"
 ConsoleProgressMonitor = "0.1"
-LoggingExtras = "0.4"
+LogDensityProblems = "2"
+LoggingExtras = "0.4, 0.5, 1"
 ProgressLogging = "0.1"
-StatsBase = "0.32, 0.33"
+StatsBase = "0.32, 0.33, 0.34"
 TerminalLoggers = "0.1"
 Transducers = "0.4.30"
-julia = "1"
+julia = "1.6"
 
 [extras]
-Atom = "c52e3926-4ff0-5f6e-af25-54175e0327b1"
+FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b"
 IJulia = "7073ff75-c697-5162-941a-fcdaad2a7d2a"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Atom", "IJulia", "Statistics", "Test"]
+test = ["FillArrays", "IJulia", "Statistics", "Test"]

README.md

@@ -8,3 +8,4 @@ Abstract types and interfaces for Markov chain Monte Carlo methods.
 [![IntegrationTest](https://github.com/TuringLang/AbstractMCMC.jl/workflows/IntegrationTest/badge.svg?branch=master)](https://github.com/TuringLang/AbstractMCMC.jl/actions?query=workflow%3AIntegrationTest+branch%3Amaster)
 [![Codecov](https://codecov.io/gh/TuringLang/AbstractMCMC.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/TuringLang/AbstractMCMC.jl)
 [![Coveralls](https://coveralls.io/repos/github/TuringLang/AbstractMCMC.jl/badge.svg?branch=master)](https://coveralls.io/github/TuringLang/AbstractMCMC.jl?branch=master)
+[![Code Style: Blue](https://img.shields.io/badge/code%20style-blue-4495d1.svg)](https://github.com/invenia/BlueStyle)