Migration to Tractables

.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-latest
-
+  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: 1.6
-
-      # 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 +1,25 @@
 name: TagBot
 on:
-  issue_comment:  # THIS BIT IS NEW
+  issue_comment:
     types:
       - created
   workflow_dispatch:
+    inputs:
+      lookback:
+        default: 3
+permissions:
+  actions: read
+  checks: read
+  contents: write
+  deployments: read
+  issues: read
+  discussions: read
+  packages: read
+  pages: read
+  pull-requests: read
+  repository-projects: read
+  security-events: read
+  statuses: read
 jobs:
   TagBot:
     if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'

Project.toml

@@ -1,7 +1,7 @@
 name = "LogicCircuits"
 uuid = "a7847b3b-b7f1-4dd5-83c3-60e0aa0f8599"
 authors = ["Guy Van den Broeck <[email protected]>"]
-version = "0.3.3"
+version = "0.4.0"
 
 [deps]
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
@@ -23,10 +23,10 @@ TikzGraphs = "b4f28e30-c73f-5eaf-a395-8a9db949a742"
 
 [compat]
 CSV = "0.7, 0.8, 0.9, 0.10"
-CUDA = "3"
+CUDA = "3, 5"
 CodecZlib = "0.7"
 DataFrames = "1.1, 1.2"
-DirectedAcyclicGraphs = "0.1.2"
+DirectedAcyclicGraphs = "0.2"
 Graphs = "1.4"
 Lerche = "0.5"
 LoopVectorization = "0.12"
@@ -35,3 +35,8 @@ StatsFuns = "0.9"
 Tables = "1"
 TikzGraphs = "1.3"
 julia = "1.6"
+LazyArtifacts = "1"
+Statistics = "1"
+Random = "1"
+Pkg = "1"
+

README.md

@@ -4,11 +4,11 @@
 
 # Logic<wbr>Circuits<wbr>.jl
 
-[![Unit Tests](https://github.com/Juice-jl/LogicCircuits.jl/workflows/Unit%20Tests/badge.svg)](https://github.com/Juice-jl/LogicCircuits.jl/actions?query=workflow%3A%22Unit+Tests%22+branch%3Amaster) [![codecov](https://codecov.io/gh/Juice-jl/LogicCircuits.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/Juice-jl/LogicCircuits.jl) [![](https://img.shields.io/badge/docs-stable-green.svg)](https://juice-jl.github.io/LogicCircuits.jl/stable) [![](https://img.shields.io/badge/docs-dev-blue.svg)](https://juice-jl.github.io/LogicCircuits.jl/dev)
+[![Unit Tests](https://github.com/Tractables/LogicCircuits.jl/workflows/Unit%20Tests/badge.svg)](https://github.com/Tractables/LogicCircuits.jl/actions?query=workflow%3A%22Unit+Tests%22+branch%3Amaster) [![codecov](https://codecov.io/gh/Tractables/LogicCircuits.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/Tractables/LogicCircuits.jl) [![](https://img.shields.io/badge/docs-stable-green.svg)](https://Tractables.github.io/LogicCircuits.jl/stable) [![](https://img.shields.io/badge/docs-dev-blue.svg)](https://Tractables.github.io/LogicCircuits.jl/dev)
 
-This package provides basic functionality for doing logical reasoning using logical circuits. It has the stand-alone functionality illustrated below, and it serves as the logical foundations for other [Juice packages](https://github.com/Juice-jl) (Julia Circuit Empanada).
+This package provides basic functionality for doing logical reasoning using logical circuits. It has the stand-alone functionality illustrated below, and it serves as the logical foundations for other [Juice packages](https://github.com/Tractables) (Julia Circuit Empanada).
 
-## Quick Tutorial [![Open Notebook](https://raw.githubusercontent.com/jupyter/design/master/logos/Badges/nbviewer_badge.svg)](https://nbviewer.jupyter.org/github/Juice-jl/LogicCircuits.jl/blob/gh-pages/dev/generated/usage.ipynb)
+## Quick Tutorial [![Open Notebook](https://raw.githubusercontent.com/jupyter/design/master/logos/Badges/nbviewer_badge.svg)](https://nbviewer.jupyter.org/github/Tractables/LogicCircuits.jl/blob/gh-pages/dev/generated/usage.ipynb)
 
 Assuming that the LogicCircuits Julia package has been installed with `julia -e 'using Pkg; Pkg.add("LogicCircuits")'`, we can start using it as follows.
 
@@ -43,7 +43,7 @@ circuit(true, true, true) # sun is true, rain is true, rainbow is true
 true
 ````
 
-The purpose of this package, however, is to enable more interesting inference scenarios. This is possible by ensuring that the circuit has certain [properties](https://juice-jl.github.io/LogicCircuits.jl/dev/manual/properties/), such as *decomposability*, *determinism*, and more.
+The purpose of this package, however, is to enable more interesting inference scenarios. This is possible by ensuring that the circuit has certain [properties](https://Tractables.github.io/LogicCircuits.jl/dev/manual/properties/), such as *decomposability*, *determinism*, and more.
 Our current circuit happens to already be decomposable and deterministic by construction:
 
 ````julia
@@ -109,7 +109,7 @@ Incorporating these constraints has increased the size of our circuit.
 plot(circuit; simplify=true)
 ```
 
-<img src="https://juice-jl.github.io/LogicCircuits.jl/dev/generated/example-circuit.svg" alt="Example Logic Circuit">
+<img src="https://Tractables.github.io/LogicCircuits.jl/dev/generated/example-circuit.svg" alt="Example Logic Circuit">
 
 Crucially, the circuit is still decomposable and deterministic.
 
@@ -176,11 +176,11 @@ circuit = compile(manager, zoo_cnf("iscas89/s208.1.scan.cnf")) # CNF has 285 cla
  * Algorithms that transform circuits in non-trivial ways (split, clone, smooth, condition, etc.), verify and enforce structural properties.
  * Functionality to load and save circuits in various file formats
 
-Please see [![](https://img.shields.io/badge/docs-stable-green.svg)](https://juice-jl.github.io/LogicCircuits.jl/stable) or [![](https://img.shields.io/badge/docs-dev-blue.svg)](https://juice-jl.github.io/LogicCircuits.jl/dev) for further details.
+Please see [![](https://img.shields.io/badge/docs-stable-green.svg)](https://Tractables.github.io/LogicCircuits.jl/stable) or [![](https://img.shields.io/badge/docs-dev-blue.svg)](https://Tractables.github.io/LogicCircuits.jl/dev) for further details.
 
 ## Development
 
-If you are interested in modifying the package please see the [development readme](https://juice-jl.github.io/LogicCircuits.jl/dev/development/).
+If you are interested in modifying the package please see the [development readme](https://Tractables.github.io/LogicCircuits.jl/dev/development/).
 
 ## Acknowledgements
 

docs/make.jl

@@ -75,7 +75,7 @@ pages = [
 
 format = Documenter.HTML(
     prettyurls = !("local" in ARGS),
-    canonical = "https://juice-jl.github.io/LogicCircuits.jl/stable/",
+    canonical = "https://Tractables.github.io/LogicCircuits.jl/stable/",
     assets = ["assets/favicon.ico"],
     analytics = "UA-136089579-2",
     highlights = ["yaml"],
@@ -103,7 +103,7 @@ makedocs(
 # for more information.
 deploydocs(
     target = "build",
-    repo = "github.com/Juice-jl/LogicCircuits.jl.git",
+    repo = "github.com/Tractables/LogicCircuits.jl.git",
     branch = "gh-pages",
     devbranch = "master",
     devurl = "dev",

docs/src/README.jl

@@ -6,17 +6,17 @@
 
 # # Logic<wbr>Circuits<wbr>.jl
 
-# [![Unit Tests](https://github.com/Juice-jl/LogicCircuits.jl/workflows/Unit%20Tests/badge.svg)](https://github.com/Juice-jl/LogicCircuits.jl/actions?query=workflow%3A%22Unit+Tests%22+branch%3Amaster) [![codecov](https://codecov.io/gh/Juice-jl/LogicCircuits.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/Juice-jl/LogicCircuits.jl) [![](https://img.shields.io/badge/docs-stable-green.svg)](https://juice-jl.github.io/LogicCircuits.jl/stable) [![](https://img.shields.io/badge/docs-dev-blue.svg)](https://juice-jl.github.io/LogicCircuits.jl/dev)
+# [![Unit Tests](https://github.com/Tractables/LogicCircuits.jl/workflows/Unit%20Tests/badge.svg)](https://github.com/Tractables/LogicCircuits.jl/actions?query=workflow%3A%22Unit+Tests%22+branch%3Amaster) [![codecov](https://codecov.io/gh/Tractables/LogicCircuits.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/Tractables/LogicCircuits.jl) [![](https://img.shields.io/badge/docs-stable-green.svg)](https://Tractables.github.io/LogicCircuits.jl/stable) [![](https://img.shields.io/badge/docs-dev-blue.svg)](https://Tractables.github.io/LogicCircuits.jl/dev)
 
-# This package provides basic functionality for doing logical reasoning using logical circuits. It has the stand-alone functionality illustrated below, and it serves as the logical foundations for other [Juice packages](https://github.com/Juice-jl) (Julia Circuit Empanada).
+# This package provides basic functionality for doing logical reasoning using logical circuits. It has the stand-alone functionality illustrated below, and it serves as the logical foundations for other [Juice packages](https://github.com/Tractables) (Julia Circuit Empanada).
 
 include("usage.jl")
 
-# Please see [![](https://img.shields.io/badge/docs-stable-green.svg)](https://juice-jl.github.io/LogicCircuits.jl/stable) or [![](https://img.shields.io/badge/docs-dev-blue.svg)](https://juice-jl.github.io/LogicCircuits.jl/dev) for further details.
+# Please see [![](https://img.shields.io/badge/docs-stable-green.svg)](https://Tractables.github.io/LogicCircuits.jl/stable) or [![](https://img.shields.io/badge/docs-dev-blue.svg)](https://Tractables.github.io/LogicCircuits.jl/dev) for further details.
 
 # ## Development
 
-# If you are interested in modifying the package please see the [development readme](https://juice-jl.github.io/LogicCircuits.jl/dev/development/).
+# If you are interested in modifying the package please see the [development readme](https://Tractables.github.io/LogicCircuits.jl/dev/development/).
 
 # ## Acknowledgements
 

docs/src/development.md

@@ -6,7 +6,7 @@ Follow these instructions to install and use LogicCircuits.jl as a developer of
 
 Install the Julia package in development mode by running
 
-    julia -e 'using Pkg; Pkg.develop(PackageSpec(url="https://github.com/Juice-jl/LogicCircuits.jl.git"))'
+    julia -e 'using Pkg; Pkg.develop(PackageSpec(url="https://github.com/Tractables/LogicCircuits.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.
 
@@ -71,8 +71,8 @@ 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/src/installation.md

@@ -21,7 +21,7 @@ julia -e 'using Pkg; Pkg.add("LogicCircuits")'
 To install the package with the latest commits on master branch, run:
 
 ```bash
-julia -e 'using Pkg; Pkg.add(PackageSpec(url="https://github.com/Juice-jl/LogicCircuits.jl.git"))'
+julia -e 'using Pkg; Pkg.add(PackageSpec(url="https://github.com/Tractables/LogicCircuits.jl.git"))'
 ```
 
 #### From Julia Pkg REPL

docs/src/usage.jl

@@ -1,8 +1,8 @@
 
-#!plot # ## Quick Tutorial [![Open Notebook](https://raw.githubusercontent.com/jupyter/design/master/logos/Badges/nbviewer_badge.svg)](https://nbviewer.jupyter.org/github/Juice-jl/LogicCircuits.jl/blob/gh-pages/dev/generated/usage.ipynb)
+#!plot # ## Quick Tutorial [![Open Notebook](https://raw.githubusercontent.com/jupyter/design/master/logos/Badges/nbviewer_badge.svg)](https://nbviewer.jupyter.org/github/Tractables/LogicCircuits.jl/blob/gh-pages/dev/generated/usage.ipynb)
 
 #plot # ### Quick Tutorial
-#plot # [![Open Notebook](https://raw.githubusercontent.com/jupyter/design/master/logos/Badges/nbviewer_badge.svg)](https://nbviewer.jupyter.org/github/Juice-jl/LogicCircuits.jl/blob/gh-pages/dev/generated/usage.ipynb)
+#plot # [![Open Notebook](https://raw.githubusercontent.com/jupyter/design/master/logos/Badges/nbviewer_badge.svg)](https://nbviewer.jupyter.org/github/Tractables/LogicCircuits.jl/blob/gh-pages/dev/generated/usage.ipynb)
 
 # Assuming that the LogicCircuits Julia package has been installed with `julia -e 'using Pkg; Pkg.add("LogicCircuits")'`, we can start using it as follows.
 
@@ -23,7 +23,7 @@ circuit(true, true, true) # sun is true, rain is true, rainbow is true
 
 #src TODO: specific for ipython, visualize circuit using plot(circuit)?
 
-# The purpose of this package, however, is to enable more interesting inference scenarios. This is possible by ensuring that the circuit has certain [properties](https://juice-jl.github.io/LogicCircuits.jl/dev/manual/properties/), such as *decomposability*, *determinism*, and more.
+# The purpose of this package, however, is to enable more interesting inference scenarios. This is possible by ensuring that the circuit has certain [properties](https://Tractables.github.io/LogicCircuits.jl/dev/manual/properties/), such as *decomposability*, *determinism*, and more.
 # Our current circuit happens to already be decomposable and deterministic by construction:
 isdecomposable(circuit) && isdeterministic(circuit)
 @test true == isdecomposable(circuit) && isdeterministic(circuit) #jl
@@ -66,7 +66,7 @@ circuit &= (¬(rain ∨ snow) ⇐ ¬cloud); # no rain or snow without clouds
 #!plot # plot(circuit; simplify=true)
 #!plot # ```
 
-#!plot # <img src="https://juice-jl.github.io/LogicCircuits.jl/dev/generated/example-circuit.svg" alt="Example Logic Circuit">
+#!plot # <img src="https://Tractables.github.io/LogicCircuits.jl/dev/generated/example-circuit.svg" alt="Example Logic Circuit">
 
 # Crucially, the circuit is still decomposable and deterministic.
 isdecomposable(circuit) && isdeterministic(circuit)

test/aqua_test.jl

@@ -5,5 +5,6 @@ using Test
 @testset "Aqua tests" begin
     Aqua.test_all(LogicCircuits, 
                     ambiguities = false,
-                    unbound_args= false)
+                    unbound_args= false,
+                    piracies = false)
 end

test/transformations_test.jl

@@ -31,7 +31,7 @@ end
     @test prob_equiv(slc, sstructplc, 3)
 
     # Case when not all literals appear in the LC. See:
-    # https://github.com/Juice-jl/ProbabilisticCircuits.jl/issues/80
+    # https://github.com/Tractables/ProbabilisticCircuits.jl/issues/80
     cnf = IOBuffer(b"""c Encodes the following: ϕ = (1 ∨ ¬2) ∧ (3 ∨ ¬4) ∧ (1 ∨ ¬4)
                     p cnf 4 3
                     1 -2 0