Fix AutoDiff_Ext tests for Julia 1.12 compatibility

.buildkite/CUDA_Ext.yml

@@ -4,7 +4,7 @@ steps:
       setup:
         version:
           - "1.10" # oldest
-          #- "1"    # latest
+          - "1"    # latest
     plugins:
       - JuliaCI/julia#v1:
           version: "{{matrix.version}}"
@@ -22,12 +22,3 @@ steps:
       GROUP: "CUDA_Ext"
       SECRET_CODECOV_TOKEN: "ZfhQu/IcRLqNyZ//ZNs5sjBPaV76IHfU5gui52Qn+Rp8tOurukqgScuyDt+3HQ4R0hJYBw1/Nqg6jmBsvWSc9NEUx8kGsUJFHfN3no0+b+PFxA8oJkWc9EpyIsjht5ZIjlsFWR3f0DpPqMEle/QyWOPcal63CChXR8oAoR+Fz1Bh8GkokLlnC8F9Ugp9xBlu401GCbyZhvLTZnNIgK5yy9q8HBJnBg1cPOhI81J6JvYpEmcIofEzFV/qkfpTUPclu43WNoFX2DZPzbxilf3fsAd5/+nRkRfkNML8KiN4mnmjHxPPbuY8F5zC/PS5ybXtDpfvaMQc01WApXCkZk0ZAQ==;U2FsdGVkX1+eDT7dqCME5+Ox5i8GvWRTQbwiP/VYjapThDbxXFDeSSIC6Opmon+M8go22Bun3bat6Fzie65ang=="
     timeout_in_minutes: 60
-    if: | 
-        // Don't run Buildkite if the commit message includes the text [skip ci], [ci skip], or [no ci]
-        // Don't run Buildkite for PR draft
-        // Only run Buildkite when new commits and PR are made to main branch
-        build.message !~ /\[skip ci\]/ &&
-        build.message !~ /\[ci skip\]/ &&
-        build.message !~ /\[no ci\]/   &&
-        !build.pull_request.draft      &&
-        (build.branch =~ /main/ || build.pull_request.base_branch =~ /main/)

.buildkite/pipeline.yml

@@ -1,16 +1,25 @@
 # see: https://github.com/staticfloat/forerunner-buildkite-plugin
 steps:
   - label: ":runner: Dynamically launch pipelines"
+    if: | 
+        // Don't run Buildkite if the commit message includes the text [skip ci], [ci skip], or [no ci]
+        // Don't run Buildkite for PR draft
+        // Only run Buildkite when new commits and PR are made to main branch
+        build.message !~ /\[skip ci\]/ &&
+        build.message !~ /\[ci skip\]/ &&
+        build.message !~ /\[no ci\]/   &&
+        !build.pull_request.draft      &&
+        (build.branch =~ /main/ || build.pull_request.base_branch =~ /main/)
+    agents:
+      queue: "juliagpu"
     plugins:
-      - staticfloat/forerunner:
+      - staticfloat/forerunner: # CUDA.jl tests
           watch:
             - ".buildkite/pipeline.yml"
             - ".buildkite/CUDA_Ext.yml"
             - "src/**"
             - "ext/QuantumToolboxCUDAExt.jl"
             - "test/runtests.jl"
-            - "test/cuda_ext.jl"
+            - "test/ext-test/gpu/**"
             - "Project.toml"
           target: ".buildkite/CUDA_Ext.yml"
-    agents:
-      queue: "juliagpu"

.github/ISSUE_TEMPLATE/bug_report.yaml

@@ -16,13 +16,13 @@ body:
       label: Code to Reproduce the Bug
       description: Please provide a minimal working example. Paste your code directly (It will be automatically formatted, so there's no need for backticks)
       placeholder: "using QuantumToolbox\nprint(qeye(2))"
-      render: shell
+      render: julia
   - type: textarea
     id: bug-output
     attributes:
       label: Code Output
       description: Please paste the relevant output here (automatically formatted)
-      placeholder: "Quantum Object:   type=Operator   dims=[2]   size=(2, 2)   ishermitian=true\n2×2 Diagonal{ComplexF64, Vector{ComplexF64}}:\n 1.0+0.0im      ⋅    \n     ⋅      1.0+0.0im"
+      placeholder: "Quantum Object:   type=Operator()   dims=[2]   size=(2, 2)   ishermitian=true\n2×2 Diagonal{ComplexF64, Vector{ComplexF64}}:\n 1.0+0.0im      ⋅    \n     ⋅      1.0+0.0im"
       render: shell
   - type: textarea
     id: expected-behaviour
@@ -37,7 +37,7 @@ body:
     attributes:
       label: Your Environment
       description: Please use `QuantumToolbox.about()` or `QuantumToolbox.versioninfo()` to get the information about your environment and paste it here (automatically formatted)
-      placeholder: "Julia              Ver. ***\nQuantumToolbox     Ver. ***\nLinearSolve        Ver. ***\nOrdinaryDiffEqCore Ver. ***\nOS       : ***\nWORD_SIZE: ***\nLIBM     : ***\nLLVM     : ***\nBLAS     : ***"
+      placeholder: "Julia              Ver. ***\nQuantumToolbox     Ver. ***\nSciMLOperators     Ver. ***\nLinearSolve        Ver. ***\nOrdinaryDiffEqCore Ver. ***\nOS       : ***\nWORD_SIZE: ***\nLIBM     : ***\nLLVM     : ***\nBLAS     : ***"
       render: shell
     validations:
       required: true

.github/dependabot.yml

@@ -4,4 +4,8 @@ updates:
   - package-ecosystem: "github-actions"
     directory: "/" # Location of package manifests
     schedule:
-      interval: "weekly"
+      interval: "weekly"
+    labels:
+      - "dependencies"
+      - "Skip ChangeLog"
+

.github/pull_request_template.md

@@ -1,18 +1,19 @@
 ## Checklist
 Thank you for contributing to `QuantumToolbox.jl`! Please make sure you have finished the following tasks before opening the PR.
 
-- [ ] Please read [Contributor Covenant Code of Conduct](https://github.com/qutip/QuantumToolbox.jl/blob/main/CODE_OF_CONDUCT.md)
-- [ ] Any code changes were done in a way that does not break public API
-- [ ] Appropriate tests were added.
-- [ ] Any code changes should be formatted by running: `julia -e 'using JuliaFormatter; format(".")'`
-- [ ] All documentation (in `docs/` folder) related to code changes were updated.
+- [ ] Please read [Contributing to Quantum Toolbox in Julia](https://qutip.org/QuantumToolbox.jl/stable/resources/contributing).
+- [ ] Any code changes were done in a way that does not break public API.
+- [ ] Appropriate tests were added and tested locally by running: `make test`.
+- [ ] Any code changes should be `julia` formatted by running: `make format`.
+- [ ] All documents (in `docs/` folder) related to code changes were updated and able to build locally by running: `make docs`.
+- [ ] (If necessary) the `CHANGELOG.md` should be updated (regarding to the code changes) and built by running: `make changelog`.
 
 Request for a review after you have completed all the tasks. If you have not finished them all, you can also open a [Draft Pull Request](https://github.blog/2019-02-14-introducing-draft-pull-requests/) to let the others know this on-going work.
 
 ## Description
 Describe the proposed change here.
 
 ## Related issues or PRs
-Please mention the related issues or PRs here. If the PR fixes an issue, use the keyword close/closes/closed/fix/fixes/fixed/resolve/resolves/resolved followed by the issue id, e.g. fix #1234
+Please mention the related issues or PRs here. If the PR fixes an issue, use the keyword close/closes/closed/fix/fixes/fixed/resolve/resolves/resolved followed by the issue id, e.g. fix #[id]
 
-## Additional context
+## Additional context

.github/workflows/Benchmarks.yml

@@ -34,7 +34,7 @@ jobs:
     runs-on: ubuntu-latest
     if: ${{ !github.event.pull_request.draft }}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - uses: julia-actions/setup-julia@v2
         with:
           version: '1'
@@ -49,6 +49,7 @@ jobs:
             Pkg.instantiate();
             include("runbenchmarks.jl")'
 
+      # this will update benchmarks/data.js in gh-pages branch
       - name: Parse & Upload Benchmark Results
         uses: benchmark-action/github-action-benchmark@v1
         with:

.github/workflows/CI-Julia-nightly.yml

@@ -0,0 +1,61 @@
+name: Runtests (Julia nightly)
+
+on:
+  push:
+    branches:
+      - 'main'
+    paths:
+      - '.github/workflows/CI-Julia-nightly.yml'
+      - 'src/**'
+      - 'ext/**'
+      - 'test/runtests.jl'
+      - 'test/core-test/**'
+      - 'Project.toml'
+  pull_request:
+    branches:
+      - 'main'
+    paths:
+      - '.github/workflows/CI-Julia-nightly.yml'
+      - 'src/**'
+      - 'ext/**'
+      - 'test/runtests.jl'
+      - 'test/core-test/**'
+      - 'Project.toml'
+    types:
+      - opened
+      - reopened
+      - synchronize
+      - ready_for_review
+
+jobs:
+  test:
+    name: ${{ matrix.os }} - ${{ matrix.arch }} ( ${{ matrix.group }} )
+    runs-on: ${{ matrix.os }}
+    permissions: # needed to allow julia-actions/cache to delete old caches that it has created
+      actions: write
+      contents: read
+    if: ${{ !github.event.pull_request.draft }}
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - 'nightly'
+        os:
+          - 'ubuntu-latest'
+        arch:
+          - 'x64'
+        group:
+          - 'Core'
+
+    steps:
+      - uses: actions/checkout@v5
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: julia-actions/cache@v2
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
+        env:
+          GROUP: ${{ matrix.group }}
+          JULIA_NUM_THREADS: auto

.github/workflows/CI.yml

@@ -8,7 +8,9 @@ on:
       - '.github/workflows/CI.yml'
       - 'src/**'
       - 'ext/**'
-      - 'test/**'
+      - 'test/runtests.jl'
+      - 'test/core-test/**'
+      - 'test/ext-test/cpu/**'
       - 'Project.toml'
   pull_request:
     branches:
@@ -17,7 +19,9 @@ on:
       - '.github/workflows/CI.yml'
       - 'src/**'
       - 'ext/**'
-      - 'test/**'
+      - 'test/runtests.jl'
+      - 'test/core-test/**'
+      - 'test/ext-test/cpu/**'
       - 'Project.toml'
     types:
       - opened
@@ -27,8 +31,8 @@ on:
 
 jobs:
   test:
-    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} ( ${{ matrix.group }} )
-    runs-on: ${{ matrix.os }}
+    name: Julia ${{ matrix.version }} - ${{ matrix.node.os }} - ${{ matrix.node.arch }} ( ${{ matrix.group }} )
+    runs-on: ${{ matrix.node.os }}
     permissions: # needed to allow julia-actions/cache to delete old caches that it has created
       actions: write
       contents: read
@@ -39,53 +43,53 @@ jobs:
         # for core tests (latest and oldest supported versions)
         version:
           - '1.10' # oldest
-        #  - '1'    # latest
-        os:
-          - ubuntu-latest
-          - windows-latest
-        arch:
-          - x64
+          - '1'    # latest
+        node:
+          - os: 'ubuntu-latest'
+            arch: 'x64'
+          - os: 'windows-latest'
+            arch: 'x64'
+          - os: 'macOS-latest'
+            arch: 'arm64'
         group:
-          - Core
+          - 'Core'
 
         include:
-          # for core tests on macOS (M-series chip)
-          - version: '1.10'    # oldest
-            os: 'macOS-latest'
-            arch: 'x64'
-            group: 'Core'
-          # - version: '1'       # latest
-          #   os: 'macOS-latest'
-          #   arch: 'arm64'
-          #   group: 'Core'
-
           # for core tests (intermediate versions)
-          # - version: '1.x'
-          #   os: 'ubuntu-latest'
-          #   arch: 'x64'
-          #   group: 'Core'
+          - version: '1.11'
+            node:
+              os: 'ubuntu-latest'
+              arch: 'x64'
+            group: 'Core'
 
-          # for code quality tests
+          # for extension tests
           - version: '1'
-            os: 'ubuntu-latest'
-            arch: 'x64'
-            group: 'Code-Quality'
+            node:
+              os: 'ubuntu-latest'
+              arch: 'x64'
+            group: 'Makie_Ext'
+          - version: '1.11'
+            node:
+              os: 'ubuntu-latest'
+              arch: 'x64'
+            group: 'AutoDiff_Ext'
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
-          arch: ${{ matrix.arch }}
+          arch: ${{ matrix.node.arch }}
       - uses: julia-actions/cache@v2
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
         env:
           GROUP: ${{ matrix.group }}
+          JULIA_NUM_THREADS: auto
       - uses: julia-actions/julia-processcoverage@v1
         with:
           directories: src,ext
-      - uses: codecov/codecov-action@v4
+      - uses: codecov/codecov-action@v5
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
         with:

.github/workflows/ChangeLogCheck.yml

@@ -0,0 +1,39 @@
+# Enforces the update of the file CHANGELOG.md on every pull request
+# Can be skipped with the `Skip ChangeLog` label
+name: ChangeLog Update Check
+on:
+  pull_request:
+    types: [opened, synchronize, reopened, ready_for_review, labeled, unlabeled]
+
+jobs:
+  changelog:
+    runs-on: ubuntu-latest
+    if: ${{ !github.event.pull_request.draft }}
+    steps:
+      # check whether CHANGELOG.md is updated
+      - uses: dangoslen/changelog-enforcer@v3
+        with:
+          skipLabels: 'Skip ChangeLog'
+
+      # check whether the format of CHANGELOG.md is correct
+      - uses: actions/checkout@v5
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: '1'
+      - name: Install and Run Changelog
+        run: |
+          julia -e 'import Pkg; Pkg.add("Changelog")'
+          julia -e 'using Changelog; Changelog.generate(Changelog.CommonMark(), "CHANGELOG.md"; repo = "qutip/QuantumToolbox.jl")'
+
+      - name: CHANGELOG Format Check
+        run: |
+          julia -e '
+            output = Cmd(`git diff --name-only`) |> read |> String
+            if output == ""
+                exit(0)
+            else
+                @error "The format of CHANGELOG.md is not correct !!!"
+                write(stdout, "Please format it by running the following command:\n")
+                write(stdout, "make changelog")
+                exit(1)
+            end'

.github/workflows/CleanPreviewDoc.yml

@@ -0,0 +1,31 @@
+name: Cleanup Preview Documentation
+
+on:
+  pull_request:
+    types: [closed]
+
+permissions:
+    contents: write
+    deployments: write
+
+jobs:
+  cleanup-preview-doc:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout gh-pages branch
+        uses: actions/checkout@v5
+        with:
+          ref: gh-pages
+      - name: Delete preview and history + push changes
+        run: |
+            if [ -d "previews/PR$PRNUM" ]; then
+              git config user.name "Documenter.jl"
+              git config user.email "[email protected]"
+              git rm -rf "previews/PR$PRNUM"
+              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:
+            GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+            PRNUM: ${{ github.event.number }}