Updated CI and tests. Ambiguities left in Aqua

.github/workflows/CompatHelper.yml

@@ -1,16 +1,43 @@
-name: CompatHelper
 on:
   schedule:
     - cron: 0 0 * * *
   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()
+      - 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}
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
-        run: julia -e 'using CompatHelper; CompatHelper.main()'

.github/workflows/SpellCheck.yml

@@ -0,0 +1,13 @@
+name: Spell Check
+
+on: [pull_request]
+
+jobs:
+  typos-check:
+    name: Spell Check with Typos
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Actions Repository
+        uses: actions/checkout@v4
+      - name: Check spelling
+        uses: crate-ci/[email protected]

.github/workflows/TagBot.yml

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

.github/workflows/ci.yml

@@ -1,46 +1,81 @@
 name: CI
 on:
+  pull_request:
+    branches:
+      - main
+      - dev
+    paths-ignore:
+      - "docs/**"
   push:
     branches:
       - main
-    tags: '*'
-  pull_request:
-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/') }}
+    paths-ignore:
+      - "docs/**"
 jobs:
+  formatter:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        julia-version: [1]
+        julia-arch: [x86]
+        os: [ubuntu-latest]
+    steps:
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: ${{ matrix.julia-version }}
+
+      - uses: actions/checkout@v4
+      - name: Install JuliaFormatter and format
+        # This will use the latest version by default but you can set the version like so:
+        #
+        # julia  -e 'using Pkg; Pkg.add(PackageSpec(name="JuliaFormatter", version="0.13.0"))'
+        run: |
+          julia  -e 'using Pkg; Pkg.add(PackageSpec(name="JuliaFormatter", version="1.0.50"))'
+          julia  -e 'using JuliaFormatter; format(".", verbose=true)'
+      - name: Format check
+        run: |
+          julia -e '
+          out = Cmd(`git diff`) |> read |> String
+          if out == ""
+              exit(0)
+          else
+              @error "Some files have not been formatted !!!"
+              write(stdout, out)
+              exit(1)
+          end'
   test:
     name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         version:
-          - "1.10"
-          - 'nightly'
+          - "1.8"
+          - "1" # automatically expands to the latest stable 1.x release of Julia
+          - nightly
         os:
           - ubuntu-latest
-          - macOS-latest
-          - windows-latest
         arch:
           - x64
           - x86
-        threads:
-          - "2"
-        exclude:
+        include:
+          # test macOS and Windows with latest Julia only
           - os: macOS-latest
-            arch: x86
+            arch: x64
+            version: 1
+          - os: windows-latest
+            arch: x64
+            version: 1
           - os: windows-latest
             arch: x86
+            version: 1
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v1
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      - uses: actions/cache@v1
+      - uses: actions/cache@v4
         env:
           cache-name: cache-artifacts
         with:
@@ -52,31 +87,30 @@ jobs:
             ${{ runner.os }}-
       - 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@v1
+      - uses: codecov/codecov-action@v4
         with:
           file: lcov.info
-  docs:
-    name: Documentation
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-      - uses: julia-actions/setup-julia@v1
-        with:
-          version: "1"
-      - run: |
-          julia --project=docs -e '
-            using Pkg
-            Pkg.develop(PackageSpec(path=pwd()))
-            Pkg.instantiate()'
-      - run: |
-          julia --project=docs -e '
-            using Documenter: doctest
-            using CompositionalNetworks
-            doctest(CompositionalNetworks)'
-      - run: julia --project=docs docs/make.jl
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
+  # docs:
+  #   name: Documentation
+  #   runs-on: ubuntu-latest
+  #   steps:
+  #     - uses: actions/checkout@v4
+  #     - uses: julia-actions/setup-julia@v1
+  #       with:
+  #         version: "1"
+  #     - run: |
+  #         julia --project=docs -e '
+  #           using Pkg
+  #           Pkg.develop(PackageSpec(path=pwd()))
+  #           Pkg.instantiate()'
+  #     - run: |
+  #         julia --project=docs -e '
+  #           using Documenter: DocMeta, doctest
+  #           using CompositionalNetworks
+  #           DocMeta.setdocmeta!(CompositionalNetworks, :DocTestSetup, :(using CompositionalNetworks); recursive=true)
+  #           doctest(CompositionalNetworks)'
+  #     - run: julia --project=docs docs/make.jl
+  #       env:
+  #         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  #         DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/register.yml

@@ -0,0 +1,16 @@
+name: Register Package
+on:
+  workflow_dispatch:
+    inputs:
+      version:
+        description: Version to register or component to bump
+        required: true
+jobs:
+  register:
+    runs-on: ubuntu-latest
+    permissions:
+        contents: write
+    steps:
+      - uses: julia-actions/RegisterAction@latest
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}

Project.toml

@@ -1,7 +1,7 @@
 name = "CompositionalNetworks"
 uuid = "4b67e4b5-442d-4ef5-b760-3f5df3a57537"
 authors = ["Jean-François Baffier"]
-version = "0.5.5"
+version = "0.5.6"
 
 [deps]
 ConstraintCommons = "e37357d9-0691-492f-a822-e5ea6a920954"
@@ -21,16 +21,21 @@ ConstraintCommons = "0.2"
 ConstraintDomains = "0.3"
 Dictionaries = "0.4"
 Distances = "0.10"
-JuliaFormatter = "0.22, 1"
+JuliaFormatter = "1"
 OrderedCollections = "1"
+Random = "1"
 TestItemRunner = "0.2"
 TestItems = "0.1"
 ThreadSafeDicts = "0.1"
 Unrolled = "0.1"
 julia = "1.8"
 
 [extras]
+Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
+Evolutionary = "86b6b26d-c046-49b6-aa0b-5f0f74682bd6"
+Memoization = "6fafb56a-5788-4b4e-91ca-c0cea6611c73"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+ThreadPools = "b189fb0b-2eb5-4ed4-bc0c-d34c51242431"
 
 [targets]
-test = ["Test"]
+test = ["Aqua", "Evolutionary", "Memoization", "Test", "ThreadPools"]