Merge remote-tracking branch 'origin/master' into bug/diffusion

.github/workflows/benchmarks.yml

@@ -20,11 +20,11 @@ jobs:
           sudo apt-get update
           sudo apt-get install -y ninja-build ccache
       - name: Set up cmake
-        uses: jwlawson/actions-setup-cmake@v1.13
+        uses: jwlawson/actions-setup-cmake@v2.0.0
         with:
           cmake-version: 3.22.x
       - name: Clone w/ submodules
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           submodules: recursive
       # figure out vector extensions for ccache key

.github/workflows/build-pip-wheels.yml

@@ -6,24 +6,22 @@ on:
       - ciwheel
     tags:
       - v*
-
   schedule:
-    - cron: '0 2 * * 0' # run at 2 AM every sunday
+    - cron: '0 3 * * 0'
 
 jobs:
   get_timestamp:
     name: Prep pyproject.toml
     runs-on: ubuntu-latest
-
     steps:
       - name: Get Arbor
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           submodules: recursive
       - name: Create unique version in pyproject.toml
         if: startsWith(github.ref, 'refs/tags/v') == false
         run: python3 -c 'import time;f=open("pyproject.toml","r+");c = f.readlines();d=[i.split("#")[0].strip()[:-1]+time.strftime("%Y%m%d%H%I%S")+"\"\n" if i.startswith("version") else i for i in c];f.seek(0);f.writelines(d);f.truncate()'
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
             name: arbver
             path: ${{ github.workspace }}/pyproject.toml
@@ -38,24 +36,26 @@ jobs:
 
     steps:
       - name: Get Arbor
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           submodules: recursive
       - name: Delete pyproject.toml
         run: rm -f pyproject.toml
       - name: Get pyproject.toml
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: arbver
       - name: Check pyproject.toml
         run: cat pyproject.toml
+      - name: Move fast and...
+        run: python3 -m pip config set global.break-system-packages true
       - name: Install cibuildwheel
         run: python3 -m pip install cibuildwheel
       - name: Build wheels
         run: python3 -m cibuildwheel --output-dir dist
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
-          name: dist
+          name: dist-${{ matrix.os }}
           path: dist/*.whl
 
   build_sdist:
@@ -69,13 +69,13 @@ jobs:
       - name: Get packages
         run: python3 -m pip install build
       - name: Get Arbor
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           submodules: recursive
       - name: Delete pyproject.toml
         run: rm -f pyproject.toml
       - name: Get pyproject.toml
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: arbver
       - name: Check pyproject.toml
@@ -90,7 +90,7 @@ jobs:
         run: scripts/run_python_examples.sh
       - name: Test executables
         run: scripts/test_executables.sh
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: dist
           path: dist/*.tar.gz
@@ -100,7 +100,7 @@ jobs:
     runs-on: ubuntu-latest
     needs: [build_binary_wheels, build_sdist]
     steps:
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
           name: dist
       - name: Publish distribution 📦 to Test PyPI
@@ -118,10 +118,10 @@ jobs:
     needs: [build_binary_wheels, build_sdist]
     steps:
       - name: "Clone w/ submodules"
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
-          submodules: "recursive"
+          submodules: recursive
           path: arbor
       - name: Make full tarball
         run: |

.github/workflows/codeql.yml

@@ -0,0 +1,86 @@
+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ "master" ]
+    paths-ignore: 'doc/**'
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ "master" ]
+    paths-ignore: 'doc/**'
+
+jobs:
+  analyze:
+    name: Analyze
+    # Runner size impacts CodeQL analysis time. To learn more, please see:
+    #   - https://gh.io/recommended-hardware-resources-for-running-codeql
+    #   - https://gh.io/supported-runners-and-hardware-resources
+    #   - https://gh.io/using-larger-runners
+    # Consider using larger runners for possible analysis time improvements.
+    runs-on: ${{ (matrix.language == 'swift' && 'macos-latest') || 'ubuntu-latest' }}
+    timeout-minutes: ${{ (matrix.language == 'swift' && 120) || 360 }}
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'cpp', 'python' ]
+        # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby', 'swift' ]
+        # Use only 'java' to analyze code written in Java, Kotlin or both
+        # Use only 'javascript' to analyze code written in JavaScript, TypeScript or both
+        # Learn more about CodeQL language support at https://aka.ms/codeql-docs/language-support
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+      with:
+        submodules: recursive
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v3
+      with:
+        languages: ${{ matrix.language }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+
+        # For more details on CodeQL's query packs, refer to: https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
+        # queries: security-extended,security-and-quality
+
+    - name: Build arbor
+      run: |
+           mkdir build
+           cd build
+           cmake .. -DCMAKE_CXX_COMPILER=g++ -DCMAKE_C_COMPILER=gcc -DARB_WITH_PYTHON=ON -DARB_VECTORIZE=ON -DPython3_EXECUTABLE=`which python` -DARB_WITH_MPI=OFF -DARB_USE_BUNDLED_LIBS=ON -DARB_WITH_ASSERTIONS=ON -DARB_WITH_PROFILING=ON
+           make -j4 tests examples pyarb
+           cd -
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
+
+    #   If the Autobuild fails above, remove it and uncomment the following three lines.
+    #   modify them (or add more) to build your code if your project, please refer to the EXAMPLE below for guidance.
+
+    # - run: |
+    #     echo "Run, Build Application using script"
+    #     ./location_of_script_within_repo/buildscript.sh
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v3
+      with:
+        category: "/language:${{matrix.language}}"

.github/workflows/lint.yml

@@ -11,17 +11,17 @@ jobs:
     strategy:
       fail-fast: false
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: '3.10'
       - name: Get packages
         run: |
           python -m pip install --upgrade pip
           pip install flake8
       - name: Clone w/ submodules
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           submodules: recursive
       - name: Python Formatting

.github/workflows/sanitize.yml

@@ -33,11 +33,11 @@ jobs:
           sudo apt-get update
           sudo apt-get install -y ninja-build ccache
       - name: Set up cmake
-        uses: jwlawson/actions-setup-cmake@v1.13
+        uses: jwlawson/actions-setup-cmake@v2.0.0
         with:
           cmake-version: 3.19.x
       - name: Clone w/ submodules
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           submodules: recursive
       - name: Update pip

.github/workflows/test-docs.yaml

@@ -14,21 +14,21 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-20.04]
-        python-version: [3.8]
+        os: [ubuntu-22.04]
+        python-version: ["3.10"]
     steps:
       - name: Set up cmake
-        uses: jwlawson/actions-setup-cmake@v1.13
+        uses: jwlawson/actions-setup-cmake@v2.0.0
         with:
           cmake-version: ${{ matrix.config.cmake }}
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Update pip and setup venv
         run: python -m pip install --upgrade pip && python -m venv ~/env && . ~/env/bin/activate && echo "PATH=$PATH" >> $GITHUB_ENV
       - name: Clone w/ submodules
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           submodules: recursive
       - name: Install Python packages

.github/workflows/test-matrix.yml

@@ -17,70 +17,70 @@ jobs:
         config:
         - {
             name:  "Linux Min GCC",
-            os:    "ubuntu-20.04",
-            cc:    "gcc-9",
-            cxx:   "g++-9",
-            py:    "3.8",
+            os:    "ubuntu-22.04",
+            cc:    "gcc-12",
+            cxx:   "g++-12",
+            py:    "3.9",
             cmake: "3.19.x",
             mpi:   "ON",
             simd:  "OFF"
           }
         - {
             name:  "Linux Min Clang",
-            os:    "ubuntu-20.04",
-            cc:    "clang-9",
-            cxx:   "clang++-9",
-            py:    "3.8",
+            os:    "ubuntu-22.04",
+            cc:    "clang-12",
+            cxx:   "clang++-12",
+            py:    "3.9",
             cmake: "3.19.x",
             mpi:   "ON",
             simd:  "OFF"
           }
         - {
             name:  "MacOS Min",
-            os:    "macos-11",
+            os:    "macos-12",
             cc:    "clang",
             cxx:   "clang++",
-            py:    "3.8",
+            py:    "3.9",
             cmake: "3.19.x",
             mpi:   "ON",
             simd:  "OFF"
           }
         - {
             name:  "Linux Max GCC",
-            os:    "ubuntu-22.04",
-            cc:    "gcc-12",
-            cxx:   "g++-12",
-            py:    "3.11",
+            os:    "ubuntu-24.04",
+            cc:    "gcc-14",
+            cxx:   "g++-14",
+            py:    "3.12",
             cmake: "3.22.x",
             mpi:   "ON",
             simd:  "OFF"
           }
         - {
             name:  "Linux SIMD",
-            os:    "ubuntu-22.04",
-            cc:    "gcc-12",
-            cxx:   "g++-12",
-            py:    "3.11",
+            os:    "ubuntu-24.04",
+            cc:    "gcc-14",
+            cxx:   "g++-14",
+            py:    "3.12",
             cmake: "3.22.x",
             mpi:   "OFF",
             simd:  "ON"
           }
         - {
             name:  "Linux Max Clang",
-            os:    "ubuntu-22.04",
-            cc:    "clang-14",
-            cxx:   "clang++-14",
-            py:    "3.11",
+            os:    "ubuntu-24.04",
+            cc:    "clang-18",
+            cxx:   "clang++-18",
+            py:    "3.12",
             cmake: "3.22.x",
             mpi:   "ON",
             simd:  "OFF"
           }
         - {
             name:  "MacOS Max",
-            os:    "macos-13",
+            os:    "macos-14",
             cc:    "clang",
             cxx:   "clang++",
-            py:    "3.11",
+            py:    "3.12",
             cmake: "3.22.x",
             mpi:   "ON",
             simd:  "OFF"
@@ -105,19 +105,19 @@ jobs:
         run: |
           brew install openmpi ninja ccache
       - name: Set up cmake
-        uses: jwlawson/actions-setup-cmake@v1.13
+        uses: jwlawson/actions-setup-cmake@v2.0.0
         with:
           cmake-version: ${{ matrix.config.cmake }}
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.config.py }}
       - name: Update pip
         run: python -m pip install --upgrade pip
       - name: Install Python packages
         run:  pip install numpy sphinx svgwrite sphinx-rtd-theme mpi4py pandas seaborn
       - name: Clone w/ submodules
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           submodules: recursive
       # figure out vector extensions for ccache key