Merge branch 'master' into sunxd/predict_using_fix

.github/dependabot.yml

@@ -0,0 +1,6 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "monthly"

.github/workflows/CI.yml

@@ -10,13 +10,18 @@ on:
   merge_group:
     types: [checks_requested]
 
+# needed to allow julia-actions/cache to delete old caches that it has created
+permissions:
+  actions: write
+  contents: read
+
 jobs:
   test:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         version:
-          - '1.6' # minimum supported version
+          - 'min' # minimum supported version
           - '1' # current stable version
         os:
           - ubuntu-latest
@@ -39,31 +44,31 @@ jobs:
             arch: x64
             num_threads: 2
     steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@v1
+      - uses: actions/checkout@v4
+
+      - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      - uses: actions/cache@v1
-        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 }}-
-      - uses: julia-actions/julia-buildpkg@latest
-      - uses: julia-actions/julia-runtest@latest
+
+      - uses: julia-actions/cache@v2
+
+      - uses: julia-actions/julia-buildpkg@v1
+
+      - uses: julia-actions/julia-runtest@v1
         env:
           GROUP: All
           JULIA_NUM_THREADS: ${{ matrix.num_threads }}
+
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v1
+
+      - uses: codecov/codecov-action@v4
         with:
           file: lcov.info
-      - uses: coverallsapp/github-action@master
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: true
+
+      - uses: coverallsapp/github-action@v2
         with:
           github-token: ${{ secrets.GITHUB_TOKEN }}
           path-to-lcov: lcov.info

.github/workflows/Docs.yml

@@ -21,8 +21,8 @@ jobs:
   docs:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@latest
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
         with:
           version: '1'
       - name: Install dependencies

.github/workflows/DocsPreviewCleanup.yml

@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout gh-pages branch
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           ref: gh-pages
       - name: Delete preview and history + push changes

.github/workflows/Format.yml

@@ -20,8 +20,8 @@ jobs:
   format:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@latest
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
         with:
           version: 1
       - name: Format code

.github/workflows/IntegrationTest.yml

@@ -21,14 +21,14 @@ jobs:
           - {user: TuringLang, repo: Turing.jl}
 
     steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@v1
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
         with:
           version: 1
           arch: x64
-      - uses: julia-actions/julia-buildpkg@latest
+      - uses: julia-actions/julia-buildpkg@v1
       - name: Clone Downstream
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           repository: ${{ matrix.package.user }}/${{ matrix.package.repo }}
           path: downstream

.github/workflows/JuliaPre.yml

@@ -0,0 +1,29 @@
+name: JuliaPre
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+# needed to allow julia-actions/cache to delete old caches that it has created
+permissions:
+  actions: write
+  contents: read
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: 'pre' # pre-release
+          arch: x64
+      - uses: julia-actions/cache@v2
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
+        env:
+          GROUP: DynamicPPL

Project.toml

@@ -1,6 +1,6 @@
 name = "DynamicPPL"
 uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8"
-version = "0.29"
+version = "0.30.2"
 
 [deps]
 ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b"
@@ -43,16 +43,16 @@ DynamicPPLZygoteRulesExt = ["ZygoteRules"]
 [compat]
 ADTypes = "1"
 AbstractMCMC = "5"
-AbstractPPL = "0.8.4"
+AbstractPPL = "0.8.4, 0.9"
 Accessors = "0.1"
 BangBang = "0.4.1"
-Bijectors = "0.13.9"
+Bijectors = "0.13.18"
 ChainRulesCore = "1"
 Compat = "4"
 ConstructionBase = "1.5.4"
 Distributions = "0.25"
 DocStringExtensions = "0.9"
-EnzymeCore = "0.6, 0.7"
+EnzymeCore = "0.6 - 0.8"
 ForwardDiff = "0.10"
 LinearAlgebra = "1.6"
 LogDensityProblems = "2"
@@ -65,12 +65,12 @@ Requires = "1"
 ReverseDiff = "1"
 Test = "1.6"
 ZygoteRules = "0.2"
-julia = "1.6"
+julia = "~1.6.6, 1.7.3"
 
 [extras]
 ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
 EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869"
-MCMCChains = "c7f686f2-ff18-58e9-bc7b-31028e88f75d"
-ZygoteRules = "700de1a5-db45-46bc-99cf-38207098b444"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
+MCMCChains = "c7f686f2-ff18-58e9-bc7b-31028e88f75d"
 ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
+ZygoteRules = "700de1a5-db45-46bc-99cf-38207098b444"

README.md

@@ -3,12 +3,12 @@
 [![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://turinglang.github.io/DynamicPPL.jl/stable)
 [![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://turinglang.github.io/DynamicPPL.jl/dev)
 [![CI](https://github.com/TuringLang/DynamicPPL.jl/workflows/CI/badge.svg?branch=master)](https://github.com/TuringLang/DynamicPPL.jl/actions?query=workflow%3ACI+branch%3Amaster)
-[![JuliaNightly](https://github.com/TuringLang/DynamicPPL.jl/workflows/JuliaNightly/badge.svg?branch=master)](https://github.com/TuringLang/DynamicPPL.jl/actions?query=workflow%3AJuliaNightly+branch%3Amaster)
+[![JuliaPre](https://github.com/TuringLang/DynamicPPL.jl/workflows/JuliaPre/badge.svg?branch=master)](https://github.com/TuringLang/DynamicPPL.jl/actions?query=workflow%3AJuliaPre+branch%3Amaster)
 [![IntegrationTest](https://github.com/TuringLang/DynamicPPL.jl/workflows/IntegrationTest/badge.svg?branch=master)](https://github.com/TuringLang/DynamicPPL.jl/actions?query=workflow%3AIntegrationTest+branch%3Amaster)
 [![Coverage Status](https://coveralls.io/repos/github/TuringLang/DynamicPPL.jl/badge.svg?branch=master)](https://coveralls.io/github/TuringLang/DynamicPPL.jl?branch=master)
 [![Codecov](https://codecov.io/gh/TuringLang/DynamicPPL.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/TuringLang/DynamicPPL.jl)
 [![Code Style: Blue](https://img.shields.io/badge/code%20style-blue-4495d1.svg)](https://github.com/invenia/BlueStyle)
-[![ColPrac: Contributor's Guide on Collaborative Practices for Community Packages](https://img.shields.io/badge/ColPrac-Contributor%27s%20Guide-blueviolet)](https://colprac.sciml.ai/)
+[![ColPrac: Contributor's Guide on Collaborative Practices for Community Packages](https://img.shields.io/badge/ColPrac-Contributor%27s%20Guide-blueviolet)](https://docs.sciml.ai/ColPrac/stable/)
 
 *A domain-specific language and backend for probabilistic programming, used by [Turing.jl](https://github.com/TuringLang/Turing.jl).*
 
@@ -20,24 +20,15 @@ DynamicPPL is the part of Turing.jl that deals with defining, running, and manip
   - A rich contextual dispatch system allowing for tailored behaviour during model execution.
   - A user-friendly syntax for probabilistic queries.
 
-Information on how to use the DynamicPPL frontend to build Bayesian models can be found on the [Turing website](https://turing.ml/). Tutorials explaining how to use the backend can be found [alongside the documentation](https://turinglang.github.io/DynamicPPL.jl/stable/). More information can be found in our paper [DynamicPPL: Stan-like Speed for Dynamic Probabilistic Models](https://arxiv.org/pdf/2002.02702.pdf).
+Information on how to use the DynamicPPL frontend to build Bayesian models can be found on the [Turing website](https://turinglang.org/). Tutorials explaining how to use the backend can be found [alongside the documentation](https://turinglang.github.io/DynamicPPL.jl/stable/). More information can be found in our paper [DynamicPPL: Stan-like Speed for Dynamic Probabilistic Models](https://arxiv.org/pdf/2002.02702.pdf).
 
 ## Do you want to contribute?
 
 If you feel you have some relevant skills and are interested in contributing, please get in touch! You can find us in the #turing channel on the [Julia Slack](https://julialang.org/slack/) or [Discourse](discourse.julialang.org). If you're having any problems, please open a Github issue, even if the problem seems small (like help figuring out an error message). Every issue you open helps us improve the library!
 
 ### Contributor's Guide
 
-This project follows the [![ColPrac: Contributor's Guide on Collaborative Practices for Community Packages](https://img.shields.io/badge/ColPrac-Contributor%27s%20Guide-blueviolet)](https://colprac.sciml.ai/), apart from the following slight variation:
-
-  - The master branch contains the most recent release at any point in time. All non-breaking changes (bug fixes etc.) are merged directly into master and a new patch version is released immediately.
-  - A separate dev branch contains all breaking changes, and is merged into master when a minor version release happens.
-
-For instance, suppose we are currently on version 0.13.5.
-
-  - If someone produces a bug fix, it is merged directly into master and bumps the version to 0.13.6. This change is also merged into dev so that it remains up-to-date with master.
-  - If someone is working on a new feature that is not breaking (performance-related, fancy new syntax that is backwards-compatible etc.), the same happens.
-  - New breaking changes are merged into dev until a release is ready to go, at which point dev is merged into master and version 0.14 is released.
+This project follows the [![ColPrac: Contributor's Guide on Collaborative Practices for Community Packages](https://img.shields.io/badge/ColPrac-Contributor%27s%20Guide-blueviolet)](https://docs.sciml.ai/ColPrac/stable/).
 
 ### Merge Queue
 

docs/make.jl

@@ -22,8 +22,7 @@ makedocs(;
     pages=[
         "Home" => "index.md",
         "API" => "api.md",
-        "Tutorials" => ["tutorials/prob-interface.md"],
-        "Internals" => ["internals/transformations.md"],
+        "Internals" => ["internals/varinfo.md", "internals/transformations.md"],
     ],
     checkdocs=:exports,
     doctest=false,

docs/src/api.md

@@ -124,10 +124,14 @@ Return values of the model function for a collection of samples can be obtained
 generated_quantities
 ```
 
-For a chain of samples, one can compute the pointwise log-likelihoods of each observed random variable with [`pointwise_loglikelihoods`](@ref).
+For a chain of samples, one can compute the pointwise log-likelihoods of each observed random variable with [`pointwise_loglikelihoods`](@ref). Similarly, the log-densities of the priors using
+[`pointwise_prior_logdensities`](@ref) or both, i.e. all variables, using
+[`pointwise_logdensities`](@ref).
 
 ```@docs
+pointwise_logdensities
 pointwise_loglikelihoods
+pointwise_prior_logdensities
 ```
 
 For converting a chain into a format that can more easily be fed into a `Model` again, for example using `condition`, you can use [`value_iterator_from_chain`](@ref).
@@ -290,10 +294,19 @@ resetlogp!!
 ```@docs
 keys
 getindex
-DynamicPPL.getindex_internal
 push!!
 empty!!
 isempty
+DynamicPPL.getindex_internal
+DynamicPPL.setindex_internal!
+DynamicPPL.update_internal!
+DynamicPPL.insert_internal!
+DynamicPPL.length_internal
+DynamicPPL.reset!
+DynamicPPL.update!
+DynamicPPL.insert!
+DynamicPPL.loosen_types!!
+DynamicPPL.tighten_types
 ```
 
 ```@docs