Update dependencies

.github/dependabot.yml

@@ -0,0 +1,7 @@
+# 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

@@ -1,21 +1,45 @@
 name: CompatHelper
-
 on:
   schedule:
-    - cron: '00 00 * * *'
-  push:
-    branches:
-      - actions/trigger/CompatHelper
+    - 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@v2
+        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()'
-
+          # COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }}

.github/workflows/DocPreviewCleanup.yml

@@ -0,0 +1,33 @@
+name: Doc Preview Cleanup
+
+on:
+  pull_request:
+    types: [closed]
+
+# Ensure that only one "Doc Preview Cleanup" workflow is force pushing at a time
+concurrency:
+  group: doc-preview-cleanup
+  cancel-in-progress: false
+
+jobs:
+  doc-preview-cleanup:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - name: Checkout gh-pages branch
+        uses: actions/checkout@v4
+        with:
+          ref: gh-pages
+      - name: Delete preview and history + push changes
+        run: |
+          if [ -d "${preview_dir}" ]; then
+              git config user.name "Documenter.jl"
+              git config user.email "[email protected]"
+              git rm -rf "${preview_dir}"
+              git commit -m "delete preview"
+              git branch gh-pages-new $(echo "delete history" | git commit-tree HEAD^{tree})
+              git push --force origin gh-pages-new:gh-pages
+          fi
+        env:
+          preview_dir: previews/PR${{ github.event.number }}

.github/workflows/TagBot.yml

@@ -4,6 +4,11 @@ on:
     types:
       - created
   workflow_dispatch:
+    inputs:
+      lookback:
+        default: 3
+permissions:
+  contents: write
 jobs:
   TagBot:
     if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'

.github/workflows/ci.yml

@@ -5,10 +5,17 @@ on:
     branches:
       - main
       - dev
+      - 'releases/**'
     tags: '*'
   pull_request:
   release:
 
+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/') }}
+
 jobs:
   test:
     name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
@@ -18,64 +25,53 @@ jobs:
       fail-fast: false
       matrix:
         version:
+          - '1.10'
           - '1'
+          - 'pre'
         os:
           - ubuntu-latest
-          - macOS-latest
-          - windows-latest
         arch:
           - x64
-          - x86
-        exclude:
-          # 32-bit Julia binaries are not available on macOS
-          - os: macOS-latest
-            arch: x86
-          - os: windows-latest
+        include:
+          - version: 1
+            os: ubuntu-latest
             arch: x86
+          - version: 1
+            os: macOS-latest
+            arch: x64
+          - version: 1
+            os: windows-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: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      - name: Cache artifacts
-        uses: actions/cache@v2
-        env:
-          cache-name: cache-artifacts
+      - uses: julia-actions/cache@v2
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
         with:
-          path: ~/.julia/artifacts
-          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
-          restore-keys: |
-            ${{ runner.os }}-test-${{ env.cache-name }}-
-            ${{ runner.os }}-test-
-            ${{ runner.os }}-
-      - uses: julia-actions/julia-buildpkg@latest
-      - uses: julia-actions/julia-runtest@latest
+          coverage: ${{ matrix.version == '1' && matrix.os == 'ubuntu-latest' && matrix.arch == 'x64' }}
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v1
+        if: matrix.version == '1' && matrix.os == 'ubuntu-latest' && matrix.arch == 'x64'
+      - uses: codecov/codecov-action@v4
+        if: matrix.version == '1' && matrix.os == 'ubuntu-latest' && matrix.arch == 'x64'
         with:
+          fail_ci_if_error: true
+          token: ${{ secrets.CODECOV_TOKEN }}
           file: lcov.info
   docs:
     name: Documentation
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@latest
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
         with:
           version: '1'
-      - name: Cache artifacts
-        uses: actions/cache@v2
-        env:
-          cache-name: cache-artifacts
-        with:
-          path: ~/.julia/artifacts
-          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/docs/Project.toml') }}
-          restore-keys: |
-            ${{ runner.os }}-test-${{ env.cache-name }}-
-            ${{ runner.os }}-test-
-            ${{ runner.os }}-
-      - uses: julia-actions/julia-buildpkg@latest
-      - uses: julia-actions/julia-docdeploy@latest
+      - uses: julia-actions/cache@v2
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-docdeploy@v1
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           # Needed due to https://github.com/JuliaDocs/Documenter.jl/issues/1177

Project.toml

@@ -1,6 +1,6 @@
 name = "MGVI"
 uuid = "fdae7790-d271-4276-880d-f72bbddf129c"
-version = "0.3.1"
+version = "0.3.2"
 
 [deps]
 AutoDiffOperators = "6e1301d5-4f4d-4fb5-9679-7191e22f0e0e"
@@ -38,8 +38,8 @@ LineSearches = "7"
 LinearMaps = "3"
 Optim = "1"
 PDMats = "0.11.5"
-Parameters = "0.12"
+Parameters = "0.12, 0.13"
 PositiveFactorizations = "0.2"
 StaticArrays = "0.12, 1.0"
 ValueShapes = "0.9, 0.10, 0.11"
-julia = "1.5"
+julia = "1.10"

docs/Project.toml

@@ -19,4 +19,4 @@ ValueShapes = "136a8f8c-c49b-4edb-8b98-f3d64d48be8f"
 Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
 
 [compat]
-Documenter = "~0.24"
+Documenter = "1"

docs/make.jl

@@ -16,8 +16,8 @@ GENERATED_DOCS = joinpath(GENERATED, "docs")
 
 EXECUTE_MD = true
 
-mkdir(GENERATED)
-cp(SRC, GENERATED_SRC)
+mkpath(GENERATED)
+cp(SRC, GENERATED_SRC, force = true)
 
 function dir_replace(content)
     content = replace(content, "@__DIR__" => '"' * GENERATED_SRC * '"')
@@ -56,14 +56,12 @@ makedocs(
         "LICENSE" => "LICENSE.md",
     ],
     doctest = ("fixdoctests" in ARGS) ? :fix : true,
-    linkcheck = ("linkcheck" in ARGS),
-    strict = !("nonstrict" in ARGS),
+    linkcheck = !("nonstrict" in ARGS),
+    warnonly = ("nonstrict" in ARGS),
 )
 
 deploydocs(
-    root = GENERATED,
-    target = "docs",
     repo = "github.com/bat/MGVI.jl.git",
     forcepush = true,
-    push_preview = true
+    push_preview = true,
 )