Merge branch 'main' into predict

.github/workflows/CompatHelper.yml

@@ -12,5 +12,5 @@ jobs:
       - name: CompatHelper.main()
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }} # for triggering CI
+          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
         run: julia -e 'using CompatHelper; CompatHelper.main(; subdirs=["", "test"])'

.github/workflows/Docs.yml

@@ -0,0 +1,38 @@
+name: Documentation
+
+on:
+  push:
+    branches:
+      - main
+    tags: '*'
+  pull_request:
+    branches:
+      - main
+
+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/') }}
+
+permissions:
+  contents: write
+  pull-requests: read
+  statuses: write
+
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: '1'
+      - name: Install dependencies
+        run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
+      - name: Build and deploy
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key
+          JULIA_DEBUG: Documenter # Print `@debug` statements (https://github.com/JuliaDocs/Documenter.jl/issues/955)
+        run: julia --project=docs/ docs/make.jl

.github/workflows/DocsNav.yml

@@ -0,0 +1,49 @@
+name: Add Navbar
+
+on:
+  page_build:  # Triggers the workflow on push events to gh-pages branch
+  workflow_dispatch:  # Allows manual triggering
+  schedule:
+    - cron: '0 0 * * 0'  # Runs every week on Sunday at midnight (UTC)
+
+jobs:
+  add-navbar:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - name: Checkout gh-pages
+        uses: actions/checkout@v4
+        with:
+          ref: gh-pages
+          fetch-depth: 0
+
+      - name: Download insert_navbar.sh
+        run: |
+          curl -O https://raw.githubusercontent.com/TuringLang/turinglang.github.io/main/assets/scripts/insert_navbar.sh
+          chmod +x insert_navbar.sh
+
+      - name: Update Navbar
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          git config user.name github-actions[bot]
+          git config user.email github-actions[bot]@users.noreply.github.com
+
+          # Define the URL of the navbar to be used
+          NAVBAR_URL="https://raw.githubusercontent.com/TuringLang/turinglang.github.io/main/assets/scripts/TuringNavbar.html"
+         
+          # Update all HTML files in the current directory (gh-pages root)
+          ./insert_navbar.sh . $NAVBAR_URL
+         
+          # Remove the insert_navbar.sh file
+          rm insert_navbar.sh
+         
+          # Check if there are any changes
+          if [[ -n $(git status -s) ]]; then
+            git add .
+            git commit -m "Added navbar and removed insert_navbar.sh"
+            git push "https://${GITHUB_ACTOR}:${GITHUB_TOKEN}@github.com/${GITHUB_REPOSITORY}.git" gh-pages
+          else
+            echo "No changes to commit"
+          fi

.github/workflows/TagBot.yml

@@ -12,3 +12,4 @@ jobs:
       - uses: JuliaRegistries/TagBot@v1
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
+          ssh: ${{ secrets.DOCUMENTER_KEY }}

.gitignore

@@ -24,4 +24,6 @@ docs/site/
 Manifest.toml
 
 # vs code environment
-.vscode
+.vscode
+
+.DS_Store

Project.toml

@@ -3,21 +3,22 @@ uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf"
 keywords = ["probablistic programming"]
 license = "MIT"
 desc = "Common interfaces for probabilistic programming"
-version = "0.7"
+version = "0.9.0"
 
 [deps]
 AbstractMCMC = "80f14c24-f653-4e6a-9b94-39d6b0f70001"
+Accessors = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697"
 DensityInterface = "b429d917-457f-4dbc-8f4c-0cc954292b1d"
+JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
-Setfield = "efcf1570-3423-57d1-acb7-fd33fddbac46"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 
 [compat]
 AbstractMCMC = "2, 3, 4, 5"
+Accessors = "0.1"
 DensityInterface = "0.4"
-Setfield = "0.8.2, 1"
-StatsBase = "0.32, 0.33"
+JSON = "0.19 - 0.21"
 Random = "1.6"
-SparseArrays = "1.6"
+StatsBase = "0.32, 0.33"
 julia = "~1.6.6, 1.7.3"

docs/Project.toml

@@ -0,0 +1,2 @@
+[deps]
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"

docs/make.jl

@@ -0,0 +1,18 @@
+using Documenter
+using AbstractPPL
+
+# Doctest setup
+DocMeta.setdocmeta!(AbstractPPL, :DocTestSetup, :(using AbstractPPL); recursive=true)
+
+makedocs(;
+    sitename="AbstractPPL",
+    modules=[AbstractPPL],
+    pages=[
+        "Home" => "index.md",
+        "API" => "api.md",
+    ],
+    checkdocs=:exports,
+    doctest=false,
+)
+
+deploydocs(; repo="github.com/TuringLang/AbstractPPL.jl.git", push_preview=true)

docs/src/api.md

@@ -0,0 +1,41 @@
+# API
+
+## VarNames
+
+```@docs
+VarName
+getsym
+getoptic
+inspace
+subsumes
+subsumedby
+vsym
+@varname
+@vsym
+```
+
+## VarName serialisation
+
+```@docs
+index_to_dict
+dict_to_index
+varname_to_string
+string_to_varname
+```
+
+## Abstract model functions
+
+```@docs
+AbstractProbabilisticProgram
+condition
+decondition
+logdensityof
+AbstractContext
+evaluate!!
+```
+
+## Abstract traces
+
+```@docs
+AbstractModelTrace
+```

docs/src/index.md

@@ -0,0 +1,3 @@
+# AbstractPPL.jl
+
+A lightweight package containing interfaces and associated APIs for modelling languages for probabilistic programming.

src/AbstractPPL.jl

@@ -3,14 +3,18 @@ module AbstractPPL
 # VarName
 export VarName,
     getsym,
-    getlens,
+    getoptic,
     inspace,
     subsumes,
     subsumedby,
     varname,
     vsym,
     @varname,
-    @vsym
+    @vsym,
+    index_to_dict,
+    dict_to_index,
+    varname_to_string,
+    string_to_varname
 
 
 # Abstract model functions