Update CI setup and GitHub organization references

.github/workflows/ci.yml

@@ -1,32 +1,51 @@
-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: [main]
+    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: 1.6
-
-      # Runs a single command using the runners shell
-      - name: Unit Tests
-        run: |
-          julia --project -e 'using Pkg; Pkg.instantiate(); Pkg.build();'
-          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
+      - uses: julia-actions/julia-docdeploy@latest
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/compathelper.yml

@@ -2,20 +2,18 @@ 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'

README.md

@@ -1,9 +1,9 @@
 # DirectedAcyclicGraphs.jl
 
-[![Unit Tests](https://github.com/Juice-jl/DirectedAcyclicGraphs.jl/workflows/Unit%20Tests/badge.svg)](https://github.com/Juice-jl/DirectedAcyclicGraphs.jl/actions?query=workflow%3A%22Unit+Tests%22+branch%3Amain)  [![codecov](https://codecov.io/gh/Juice-jl/DirectedAcyclicGraphs.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/Juice-jl/DirectedAcyclicGraphs.jl) [![](https://img.shields.io/badge/docs-dev-blue.svg)](https://juice-jl.github.io/DirectedAcyclicGraphs.jl/dev/)
+[![Unit Tests](https://github.com/Tractables/DirectedAcyclicGraphs.jl/workflows/Unit%20Tests/badge.svg)](https://github.com/Tractables/DirectedAcyclicGraphs.jl/actions?query=workflow%3A%22Unit+Tests%22+branch%3Amain)  [![codecov](https://codecov.io/gh/Tractables/DirectedAcyclicGraphs.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/Tractables/DirectedAcyclicGraphs.jl) [![](https://img.shields.io/badge/docs-dev-blue.svg)](https://Tractables.github.io/DirectedAcyclicGraphs.jl/dev/)
 
 This package provides basic infrastructure to work with [Directed Acyclic Graphs](https://en.wikipedia.org/wiki/Directed_acyclic_graph) (DAGs) in Julia.
-It forms the foundation for packages such as [LogicCircuits](https://github.com/Juice-jl/LogicCircuits.jl) and [ProbabilisticCircuits](https://github.com/Juice-jl/ProbabilisticCircuits.jl), which define custom DAGs that represent logical or probabilistic computation graphs. 
+It forms the foundation for packages such as [LogicCircuits](https://github.com/Tractables/LogicCircuits.jl) and [ProbabilisticCircuits](https://github.com/Tractables/ProbabilisticCircuits.jl), which define custom DAGs that represent logical or probabilistic computation graphs.
 
 Functionality includes:
  * applying `foreach` over the nodes of the DAG in topological or reverse topological order, linearize the DAG
@@ -15,4 +15,4 @@ Functionality includes:
  * arrange the DAG nodes in feedforward layers
  * collecting various statistics about the types of nodes and their in/out-degree
 
-For example usage, please see the unit tests for [DAGs](https://github.com/Juice-jl/DirectedAcyclicGraphs.jl/blob/main/test/dags_test.jl) and the special case of [trees](https://github.com/Juice-jl/DirectedAcyclicGraphs.jl/blob/main/test/trees_test.jl), or the source code of the dependent packages. A brief description of functions can be found in the [![](https://img.shields.io/badge/docs-dev-blue.svg)](https://juice-jl.github.io/DirectedAcyclicGraphs.jl/dev/).
+For example usage, please see the unit tests for [DAGs](https://github.com/Tractables/DirectedAcyclicGraphs.jl/blob/main/test/dags_test.jl) and the special case of [trees](https://github.com/Tractables/DirectedAcyclicGraphs.jl/blob/main/test/trees_test.jl), or the source code of the dependent packages. A brief description of functions can be found in the [![](https://img.shields.io/badge/docs-dev-blue.svg)](https://Tractables.github.io/DirectedAcyclicGraphs.jl/dev/).

docs/make.jl

@@ -14,7 +14,7 @@ pages = [
 
 format = Documenter.HTML(
     prettyurls = !("local" in ARGS),
-    canonical = "https://juice-jl.github.io/DirectedAcyclicGraphs.jl/stable/",
+    canonical = "https://tractables.github.io/DirectedAcyclicGraphs.jl/stable/",
     assets = ["assets/favicon.ico"],
     analytics = "UA-136089579-2",
     highlights = ["yaml"],
@@ -39,7 +39,7 @@ makedocs(
 # for more information.
 deploydocs(
     target = "build",
-    repo = "github.com/Juice-jl/DirectedAcyclicGraphs.jl.git",
+    repo = "github.com/Tractables/DirectedAcyclicGraphs.jl.git",
     branch = "gh-pages",
     devbranch = "main",
     devurl = "dev",

docs/src/installation.md

@@ -17,7 +17,7 @@ julia -e 'using Pkg; Pkg.add("DirectedAcyclicGraphs")'
 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/DirectedAcyclicGraphs.jl.git"))'
+julia -e 'using Pkg; Pkg.add(PackageSpec(url="https://github.com/Tractables/DirectedAcyclicGraphs.jl.git"))'
 ```
 
 #### From Julia Pkg REPL