New interface for belief propagation decoder

.github/dependabot.yml

@@ -0,0 +1,8 @@
+
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"

.github/workflows/CompatHelper.yml

@@ -1,45 +1,17 @@
 name: CompatHelper
 on:
   schedule:
-    - cron: 0 0 * * *
+    - cron: '00 00 * * *'
   workflow_dispatch:
-permissions:
-  contents: write
-  pull-requests: write
 jobs:
   CompatHelper:
     runs-on: ubuntu-latest
     steps:
-      - name: Check if Julia is already available in the PATH
-        id: julia_in_path
-        run: which julia
-        continue-on-error: true
-      - name: Install Julia, but only if it is not already available in the PATH
-        uses: julia-actions/setup-julia@v1
-        with:
-          version: '1'
-          arch: ${{ runner.arch }}
-        if: steps.julia_in_path.outcome != 'success'
-      - name: "Add the General registry via Git"
-        run: |
-          import Pkg
-          ENV["JULIA_PKG_SERVER"] = ""
-          Pkg.Registry.add("General")
-        shell: julia --color=yes {0}
-      - name: "Install CompatHelper"
-        run: |
-          import Pkg
-          name = "CompatHelper"
-          uuid = "aa819f21-2bde-4658-8897-bab36330d9b7"
-          version = "3"
-          Pkg.add(; name, uuid, version)
-        shell: julia --color=yes {0}
-      - name: "Run CompatHelper"
-        run: |
-          import CompatHelper
-          CompatHelper.main()
-        shell: julia --color=yes {0}
+      - 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 }}
-          # COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }}
+          # COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }}
+        run: julia -e 'using CompatHelper; CompatHelper.main()'

.github/workflows/TagBot.yml

@@ -4,22 +4,6 @@ on:
     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'
@@ -28,4 +12,4 @@ jobs:
       - uses: JuliaRegistries/TagBot@v1
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
-          ssh: ${{ secrets.DOCUMENTER_KEY }}
+          ssh: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/benchmark-comment.yml

@@ -0,0 +1,64 @@
+# To workaroud https://github.com/actions/first-interaction/issues/10 in a secure way,
+# we take the following steps to generate and comment a performance benchmark result:
+# 1. first "performance tracking" workflow will generate the benchmark results in an unprivileged environment triggered on `pull_request` event
+# 2. then this "performance tracking (comment)" workflow will show the result to us as a PR comment in a privileged environment
+# Note that this workflow can only be modifed by getting checked-in to the default branch
+# and thus is secure even though this workflow is granted with write permissions, etc.
+# xref: https://securitylab.github.com/research/github-actions-preventing-pwn-requests/
+
+name: Performance tracking (comment)
+
+on:
+  workflow_run:
+    workflows:
+      - performance tracking
+    types:
+      - completed
+
+jobs:
+  comment:
+    runs-on: ubuntu-latest
+    #runs-on: self-hosted
+    if: >
+      ${{ github.event.workflow_run.event == 'pull_request' &&
+          github.event.workflow_run.conclusion == 'success' }}
+    steps:
+      - uses: actions/checkout@v4
+
+      # restore records from the artifacts
+      - uses: dawidd6/action-download-artifact@v3
+        with:
+          workflow: benchmark.yml
+          name: performance-tracking
+          workflow_conclusion: success
+      - name: output benchmark result
+        id: output-result-markdown
+        run: |
+          echo ::set-output name=body::$(cat ./benchmark-result.artifact)
+      - name: output pull request number
+        id: output-pull-request-number
+        run: |
+          echo ::set-output name=body::$(cat ./pull-request-number.artifact)
+
+      # check if the previous comment exists
+      - name: find comment
+        uses: peter-evans/find-comment@v3
+        id: fc
+        with:
+          issue-number: ${{ steps.output-pull-request-number.outputs.body }}
+          comment-author: 'github-actions[bot]'
+          body-includes: Benchmark Result
+
+      # create/update comment
+      - name: create comment
+        if: ${{ steps.fc.outputs.comment-id == 0 }}
+        uses: peter-evans/create-or-update-comment@v4
+        with:
+          issue-number: ${{ steps.output-pull-request-number.outputs.body }}
+          body: ${{ steps.output-result-markdown.outputs.body }}
+      - name: update comment
+        if: ${{ steps.fc.outputs.comment-id != 0 }}
+        uses: peter-evans/create-or-update-comment@v4
+        with:
+          comment-id: ${{ steps.fc.outputs.comment-id }}
+          body: ${{ steps.output-result-markdown.outputs.body }}

.github/workflows/benchmark.yml

@@ -0,0 +1,57 @@
+name: Performance tracking
+on:
+  pull_request:
+
+env:
+  PYTHON: ~
+
+jobs:
+  performance-tracking:
+    runs-on: ubuntu-latest
+    #runs-on: self-hosted
+    steps:
+      # setup
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: 'nightly'
+      - uses: julia-actions/julia-buildpkg@latest
+      - name: install dependencies
+        run: julia -e 'using Pkg; pkg"add PkgBenchmark [email protected]"'
+
+      # run the benchmark suite
+      - name: run benchmarks
+        run: |
+          julia -e '
+            using BenchmarkCI
+            BenchmarkCI.judge()
+            BenchmarkCI.displayjudgement()
+            '
+
+      # generate and record the benchmark result as markdown
+      - name: generate benchmark result
+        run: |
+          body=$(julia -e '
+          using BenchmarkCI
+
+          let
+              judgement = BenchmarkCI._loadjudge(BenchmarkCI.DEFAULT_WORKSPACE)
+              title = "Benchmark Result"
+              ciresult = BenchmarkCI.CIResult(; judgement, title)
+              BenchmarkCI.printcommentmd(stdout::IO, ciresult)
+          end
+          ')
+          body="${body//'%'/'%25'}"
+          body="${body//$'\n'/'%0A'}"
+          body="${body//$'\r'/'%0D'}"
+          echo $body > ./benchmark-result.artifact
+
+      # record the pull request number
+      - name: record pull request number
+        run: echo ${{ github.event.pull_request.number }} > ./pull-request-number.artifact
+
+      # save as artifacts (performance tracking (comment) workflow will use it)
+      - uses: actions/upload-artifact@v4
+        with:
+          name: performance-tracking
+          path: ./*.artifact

.github/workflows/changelog-enforcer.yml

@@ -0,0 +1,15 @@
+name: "Changelog Enforcer"
+on:
+  pull_request:
+    # The specific activity types are listed here to include "labeled" and "unlabeled"
+    # (which are not included by default for the "pull_request" trigger).
+    # This is needed to allow skipping enforcement of the changelog in PRs with specific labels,
+    # as defined in the (optional) "skipLabels" property.
+    types: [opened, synchronize, reopened, ready_for_review, labeled, unlabeled]
+
+jobs:
+  # Enforces the update of a changelog file on every pull request 
+  changelog:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: dangoslen/changelog-enforcer@v3

.github/workflows/ci-julia-nightly.yml

@@ -0,0 +1,43 @@
+name: CI-nightly
+on:
+  push:
+    branches: [master, main]
+    tags: ["*"]
+  pull_request:
+env:
+  PYTHON: ~
+jobs:
+  test:
+    name: Julia ${{ matrix.version }} - t=${{ matrix.threads }} - jet=${{ matrix.jet }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - os: ubuntu-latest
+            arch: x64
+            version: nightly
+            threads: 2
+            jet: 'false'
+          - os: ubuntu-latest
+            arch: x64
+            version: '1'
+            threads: 2
+            jet: 'true'
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: julia-actions/cache@v1
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
+        env:
+          JULIA_NUM_THREADS: ${{ matrix.threads }}
+          JET_TEST: ${{ matrix.jet }}
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v4
+        with:
+          file: lcov.info
+          token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/ci.yml

@@ -0,0 +1,56 @@
+name: CI
+on:
+  push:
+    branches: [master, main]
+    tags: ["*"]
+  pull_request:
+env:
+  PYTHON: ~
+jobs:
+  test:
+    name: Julia ${{ matrix.version }} - t=${{ matrix.threads }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - '1'
+          - '1.9'
+        os:
+          - ubuntu-latest
+        threads:
+          - '1'
+          - '2'
+        arch:
+          - x64
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: julia-actions/cache@v1
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
+        env:
+          JULIA_NUM_THREADS: ${{ matrix.threads }}
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v4
+        with:
+          file: lcov.info
+          token: ${{ secrets.CODECOV_TOKEN }}
+  docs:
+    name: Documentation
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: '1'
+      - uses: julia-actions/cache@v1
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-docdeploy@v1
+        env:
+          GKSwstype: nul # Fix for Plots with GR backend.
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}