Migration to Tractables (#138)

* update project toml for julia 1.10

* migration to tractables

* compat helper

* tagbot

* ci update

* fix compat

* update toml

* ChowLiuTrees = "0.2"

* bump version

Author: khosravipasha

.github/workflows/ci.yml

@@ -1,34 +1,56 @@
-name: Unit Tests 
-
-# Controls when the action will run. Triggers the workflow on push or pull request
-# events but only for the master branch
-on: 
-  pull_request:
+name: Unit Tests
+on:
   push:
+    branches: [master]
+    tags: ["*"]
+  pull_request:
   workflow_dispatch:
-
-
+permissions:
+  actions: write
+  contents: read
 env:
   DATADEPS_ALWAYS_ACCEPT: 1
   JIVE_PROCS: 1
-
 jobs:
-  build:
-    runs-on: ubuntu-20.04
-
+  test:
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - '1.6'
+          - '1'
+          - 'nightly'
+        os:
+          - ubuntu-latest
+        arch:
+          - x64
     steps:
-      
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@latest
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
         with:
-          version: 1.7
-
-      # Runs a single command using the runners shell
-      - name: Unit Tests
-        run: |
-          julia --project --check-bounds=yes --depwarn=yes -e 'import Pkg; Pkg.test(; coverage=true)'
-      
-      - name: Codecov Upload
-        run: |
-          julia -e 'using Pkg; Pkg.add("Coverage"); using Coverage; Codecov.submit(process_folder());'
-
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: julia-actions/cache@v1
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v2
+        with:
+          file: lcov.info
+  docs:
+    name: Documentation
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/julia-buildpkg@latest
+      - run: |
+          sudo apt-get -qq update
+          sudo apt install -y pdf2svg texlive-latex-base texlive-binaries texlive-pictures texlive-latex-extra texlive-luatex    
+          luatex -v
+          pdflatex -v
+      - uses: julia-actions/julia-docdeploy@latest
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/compathelper.yml

@@ -2,20 +2,23 @@ name: CompatHelper
 on:
   schedule:
     - cron: '0 0 */7 * *'
-  
   workflow_dispatch:
-  
+
+permissions:
+  contents: write
+  pull-requests: write
+
 jobs:
   CompatHelper:
     runs-on: ubuntu-latest
-    
+
     steps:
       - name: Pkg.add("CompatHelper")
         run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
-        
+    
       - name: CompatHelper.main()
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
-        
+
         run: julia -e 'using CompatHelper; CompatHelper.main()'

.github/workflows/tagbot.yml

@@ -1,9 +1,12 @@
 name: TagBot
 on:
-  issue_comment:  # THIS BIT IS NEW
+  issue_comment:
     types:
       - created
   workflow_dispatch:
+    inputs:
+      lookback:
+        default: 3
 permissions:
   actions: read
   checks: read

Project.toml

@@ -1,7 +1,7 @@
 name = "ProbabilisticCircuits"
 uuid = "2396afbe-23d7-11ea-1e05-f1aa98e17a44"
 authors = ["Guy Van den Broeck <[email protected]>"]
-version = "0.4.1"
+version = "0.5.0"
 
 [deps]
 CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
@@ -16,8 +16,8 @@ SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
 TikzGraphs = "b4f28e30-c73f-5eaf-a395-8a9db949a742"
 
 [compat]
-CUDA = "3.8.1, 4"
-ChowLiuTrees = "0.1.1"
+CUDA = "3.8.1, 4, 5"
+ChowLiuTrees = "0.2"
 CodecZlib = "0.7"
 DirectedAcyclicGraphs = "0.1.3, 0.2"
 Graphs = "1"
@@ -26,3 +26,5 @@ MetaGraphs = "0.7"
 SpecialFunctions = "2.1"
 TikzGraphs = "1.3"
 julia = "1.6"
+Random = "1"
+

README.md

@@ -4,9 +4,9 @@
 
 # Probabilistic<wbr>Circuits<wbr>.jl
 
-[![Unit Tests](https://github.com/Juice-jl/ProbabilisticCircuits.jl/workflows/Unit%20Tests/badge.svg)](https://github.com/Juice-jl/ProbabilisticCircuits.jl/actions?query=workflow%3A%22Unit+Tests%22+branch%3Amaster)  [![codecov](https://codecov.io/gh/Juice-jl/ProbabilisticCircuits.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/Juice-jl/ProbabilisticCircuits.jl) [![](https://img.shields.io/badge/docs-stable-green.svg)](https://juice-jl.github.io/ProbabilisticCircuits.jl/stable) [![](https://img.shields.io/badge/docs-dev-blue.svg)](https://juice-jl.github.io/ProbabilisticCircuits.jl/dev)
+[![Unit Tests](https://github.com/Tractables/ProbabilisticCircuits.jl/workflows/Unit%20Tests/badge.svg)](https://github.com/Tractables/ProbabilisticCircuits.jl/actions?query=workflow%3A%22Unit+Tests%22+branch%3Amaster)  [![codecov](https://codecov.io/gh/Tractables/ProbabilisticCircuits.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/Tractables/ProbabilisticCircuits.jl) [![](https://img.shields.io/badge/docs-stable-green.svg)](https://Tractables.github.io/ProbabilisticCircuits.jl/stable) [![](https://img.shields.io/badge/docs-dev-blue.svg)](https://Tractables.github.io/ProbabilisticCircuits.jl/dev)
 
-This package provides functionalities for learning/constructing probabilistic circuits and using them to compute various probabilistic queries. It is part of the [Juice package](https://github.com/Juice-jl) (Julia Circuit Empanada).
+This package provides functionalities for learning/constructing probabilistic circuits and using them to compute various probabilistic queries. It is part of the [Juice package](https://github.com/Tractables) (Julia Circuit Empanada).
 
 ## Testing
 

README_DEV.md

@@ -6,14 +6,14 @@ Follow these instructions to install and use ProbabilisticCircuits.jl as a devel
 
 Install the Julia package in development mode by running
 
-    julia -e 'using Pkg; Pkg.develop(PackageSpec(url="https://github.com/Juice-jl/ProbabilisticCircuits.jl.git"))'
+    julia -e 'using Pkg; Pkg.develop(PackageSpec(url="https://github.com/Tractables/ProbabilisticCircuits.jl.git"))'
 
 By default this will install the package at `~/.julia/dev` and allow you to change the code there. See the [Pkg manual](https://julialang.github.io/Pkg.jl/v1/managing-packages/#Developing-packages-1) for more details. One can adjust the development directory using environment variables or simply create a symbolic link to/from your favorite development directory.
 
 
 Depending on your usecase you might also want to have `LogicCircuits.jl` in develop mode, in that case run the following to do both:
 
-    julia -e 'using Pkg; Pkg.develop([PackageSpec(url="https://github.com/Juice-jl/LogicCircuits.jl.git"),PackageSpec(url="https://github.com/Juice-jl/ProbabilisticCircuits.jl.git")])'
+    julia -e 'using Pkg; Pkg.develop([PackageSpec(url="https://github.com/Tractables/LogicCircuits.jl.git"),PackageSpec(url="https://github.com/Tractables/ProbabilisticCircuits.jl.git")])'
 
 
 ## Testing
@@ -57,8 +57,8 @@ The example is for Circuit Model Zoo, but should work for others:
 
 1. Push new updates to [UCLA-StarAI/Circuit-Model-Zoo](https://github.com/UCLA-StarAI/Circuit-Model-Zoo)
 2. Do a [new zoo release](https://github.com/UCLA-StarAI/Circuit-Model-Zoo/releases).
-3. Update the `LogicCircuits.jl`'s `Artifact.toml` file with new git tag and hash. Example commit can be found [here](https://github.com/Juice-jl/LogicCircuits.jl/commit/1cd3fda02fa7bd82d1fa02898ee404edce0d7b14).
-4. Do the same for `ProbabilisticCircuits.jl`'s `Artifact.toml` file. Example commit [here](https://github.com/Juice-jl/ProbabilisticCircuits.jl/commit/da7d3678b5f2254e60229632f74cc619505e2b2d).
+3. Update the `LogicCircuits.jl`'s `Artifact.toml` file with new git tag and hash. Example commit can be found [here](https://github.com/Tractables/LogicCircuits.jl/commit/1cd3fda02fa7bd82d1fa02898ee404edce0d7b14).
+4. Do the same for `ProbabilisticCircuits.jl`'s `Artifact.toml` file. Example commit [here](https://github.com/Tractables/ProbabilisticCircuits.jl/commit/da7d3678b5f2254e60229632f74cc619505e2b2d).
 5. Note that for each Artifact.toml, 2 things need to change: `git-tree-sha1` and `sha256`.
 6. Update the `const zoo_version = "/Circuit-Model-Zoo-0.1.4"` inside LogicCircuits.jl to the new zoo version. No changes needed in ProbabilisticCircuits since it uses the same constant.
 

docs/Readme.md

@@ -29,4 +29,4 @@ For more information about pretty URLs, check out  [the documentation](https://j
 
 ## Setting Up LaTeX
 
-Some of plotting tools we use need LaTeX to be installed. Follow the instructions from [TikzPictures.jl](https://github.com/JuliaTeX/TikzPictures.jl) to see what packages are needed. Or you can check the [ci.yml](https://github.com/Juice-jl/ProbabilisticCircuits.jl/blob/master/.github/workflows/ci.yml) which builds our documentation on github actions. If you ran into any issues might be due to old version of TexLive.
+Some of plotting tools we use need LaTeX to be installed. Follow the instructions from [TikzPictures.jl](https://github.com/JuliaTeX/TikzPictures.jl) to see what packages are needed. Or you can check the [ci.yml](https://github.com/Tractables/ProbabilisticCircuits.jl/blob/master/.github/workflows/ci.yml) which builds our documentation on github actions. If you ran into any issues might be due to old version of TexLive.

docs/make.jl

@@ -68,7 +68,7 @@ else
    Documenter.HTML(
         # Use clean URLs, unless built as a "local" build
         prettyurls = !("local" in ARGS),
-        canonical = "https://juice-jl.github.io/ProbabilisticCircuits.jl/stable/",
+        canonical = "https://Tractables.github.io/ProbabilisticCircuits.jl/stable/",
         assets = ["assets/favicon.ico"],
         analytics = "UA-136089579-2",
         highlights = ["yaml"],
@@ -94,7 +94,7 @@ makedocs(
 # for more information.
 deploydocs(
     target = "build",
-    repo = "github.com/Juice-jl/ProbabilisticCircuits.jl.git",
+    repo = "github.com/Tractables/ProbabilisticCircuits.jl.git",
     branch = "gh-pages",
     devbranch = "master",
     devurl = "dev",

docs/src/README.jl

@@ -6,9 +6,9 @@
 
 # # Probabilistic<wbr>Circuits<wbr>.jl
 
-# [![Unit Tests](https://github.com/Juice-jl/ProbabilisticCircuits.jl/workflows/Unit%20Tests/badge.svg)](https://github.com/Juice-jl/ProbabilisticCircuits.jl/actions?query=workflow%3A%22Unit+Tests%22+branch%3Amaster)  [![codecov](https://codecov.io/gh/Juice-jl/ProbabilisticCircuits.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/Juice-jl/ProbabilisticCircuits.jl) [![](https://img.shields.io/badge/docs-stable-green.svg)](https://juice-jl.github.io/ProbabilisticCircuits.jl/stable) [![](https://img.shields.io/badge/docs-dev-blue.svg)](https://juice-jl.github.io/ProbabilisticCircuits.jl/dev)
+# [![Unit Tests](https://github.com/Tractables/ProbabilisticCircuits.jl/workflows/Unit%20Tests/badge.svg)](https://github.com/Tractables/ProbabilisticCircuits.jl/actions?query=workflow%3A%22Unit+Tests%22+branch%3Amaster)  [![codecov](https://codecov.io/gh/Tractables/ProbabilisticCircuits.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/Tractables/ProbabilisticCircuits.jl) [![](https://img.shields.io/badge/docs-stable-green.svg)](https://Tractables.github.io/ProbabilisticCircuits.jl/stable) [![](https://img.shields.io/badge/docs-dev-blue.svg)](https://Tractables.github.io/ProbabilisticCircuits.jl/dev)
 
-# This package provides functionalities for learning/constructing probabilistic circuits and using them to compute various probabilistic queries. It is part of the [Juice package](https://github.com/Juice-jl) (Julia Circuit Empanada).
+# This package provides functionalities for learning/constructing probabilistic circuits and using them to compute various probabilistic queries. It is part of the [Juice package](https://github.com/Tractables) (Julia Circuit Empanada).
 
 # ## Testing
 

docs/src/installation.md

@@ -21,7 +21,7 @@ julia -e 'using Pkg; Pkg.add("ProbabilisticCircuits")'
 You can also install the package with the latest commits on master branch.
 
 ```bash
-julia -e 'using Pkg; Pkg.add([PackageSpec(url="https://github.com/Juice-jl/ProbabilisticCircuits.jl.git")])'
+julia -e 'using Pkg; Pkg.add([PackageSpec(url="https://github.com/Tractables/ProbabilisticCircuits.jl.git")])'
 ```
 #### From Package mode
 !!! note

docs/src/usage.jl

@@ -33,7 +33,7 @@ exp(circuit(true, true, true) - circuit(missing, true, true)) # Pr(rain=1|rainbo
 assignments, log_prob = MAP(circuit, [missing, missing, missing]; batch_size=1)
 print("The MAP assignment of the circuit is (rain=$(assignments[1]), rainbow=$(assignments[2]), wet=$(assignments[3])), with probability $(exp(log_prob)).")
 
-# Besides the above examples, ProbabilisticCircuits.jl provides functionalities for a wide variety of queries, which are detailed in [this manual](https://juice-jl.github.io/ProbabilisticCircuits.jl/stable/manual/queries/).
+# Besides the above examples, ProbabilisticCircuits.jl provides functionalities for a wide variety of queries, which are detailed in [this manual](https://Tractables.github.io/ProbabilisticCircuits.jl/stable/manual/queries/).
 
 # ### Building complex circuit structures