Merge branch 'Cantera:main' into feature/one-dim-sens

Cantera · Jan 12, 2025 · 121a2c5 · 121a2c5
2 parents 6c5fbd9 + 2e0d8ac
commit 121a2c5
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Showing 99 changed files with 302 additions and 1,643 deletions.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -41,14 +41,14 @@ jobs:
       - name: Install Apt dependencies
         run: |
           sudo apt update
-          sudo apt install libboost-dev gfortran libopenmpi-dev libblas-dev \
-            liblapack-dev libhdf5-dev
+          sudo apt install libboost-dev gfortran libopenmpi-dev libopenblas-openmp-dev \
+            libhdf5-dev
           gcc --version
       - name: Upgrade pip
         run: python3 -m pip install -U pip setuptools wheel
       - name: Install Python dependencies
         run: |
-          python3 -m pip install ruamel.yaml scons==3.1.2
+          python3 -m pip install ruamel.yaml scons==4.0.1 packaging
       - name: Build Cantera
         run: |
           python3 `which scons` build env_vars=all -j4 debug=n --debug=time \
@@ -66,23 +66,25 @@ jobs:
     timeout-minutes: 60
     strategy:
       matrix:
-        python-version: ['3.8', '3.10', '3.11', '3.12', '3.13']
-        os: ['ubuntu-20.04', 'ubuntu-22.04']
+        python-version: ['3.10', '3.11', '3.12', '3.13']
+        os: ['ubuntu-24.04']
         numpy: ['']
         cython: ['']
         include:
           # Keep some test cases with NumPy 1.x until we drop support
         - python-version: '3.12'
-          os: 'ubuntu-24.04'
+          os: 'ubuntu-22.04'
           numpy: "'<2.0'"
           # Keep some test cases with older Cython versions
         - python-version: '3.10'
-          os: 'ubuntu-24.04'
+          os: 'ubuntu-22.04'
           cython: "==0.29.31" # minimum supported version
         - python-version: '3.11'
-          os: 'ubuntu-24.04'
+          os: 'ubuntu-22.04'
           cython: "==3.0.8" # System version for Ubuntu 24.04
-
+        - python-version: '3.13'
+          os: 'ubuntu-22.04'
+          numpy: "'<2.2'"
       fail-fast: false
     steps:
     - uses: actions/checkout@v4
@@ -97,14 +99,14 @@ jobs:
     - name: Install Apt dependencies
       run: |
         sudo apt update
-        sudo apt install libboost-dev gfortran libopenmpi-dev libblas-dev \
-          liblapack-dev libhdf5-dev libfmt-dev
+        sudo apt install libboost-dev gfortran libopenmpi-dev libopenblas-openmp-dev \
+          libhdf5-dev libfmt-dev
         gcc --version
     - name: Upgrade pip
       run: python3 -m pip install -U pip setuptools wheel
     - name: Install Python dependencies
       run: |
-        python3 -m pip install ruamel.yaml scons==3.1.2 numpy${{ matrix.numpy }} \
+        python3 -m pip install ruamel.yaml scons==4.0.1 numpy${{ matrix.numpy }} \
           cython${{ matrix.cython }} pandas pytest \
           pytest-github-actions-annotate-failures pytest-xdist pint graphviz
     - name: Build Cantera
@@ -138,7 +140,7 @@ jobs:
         if-no-files-found: error
 
   clang-compiler:
-    name: LLVM/Clang with Python 3.8
+    name: LLVM/Clang with Python 3.13
     runs-on: ubuntu-22.04
     timeout-minutes: 60
     steps:
@@ -149,12 +151,13 @@ jobs:
     - name: Setup Python
       uses: actions/setup-python@v5
       with:
-        python-version: 3.8
+        python-version: '3.13'
         architecture: x64
     - name: Install Apt dependencies
       run: |
         sudo apt update
-        sudo apt install libboost-dev gfortran libomp-dev libomp5 libopenblas-dev libhdf5-dev
+        sudo apt install libboost-dev gfortran libomp-dev libomp5 \
+          libopenblas-openmp-dev  libhdf5-dev
     - name: Upgrade pip
       run: python3 -m pip install -U pip setuptools wheel
     - name: Install Python dependencies
@@ -185,7 +188,7 @@ jobs:
         python-version: ['3.12', '3.13']
         include:
           - macos-version: 'macos-13'
-            python-version: '3.8'
+            python-version: '3.11'
           - macos-version: 'macos-14'
             python-version: '3.10'
             extra-build-args: cxx_flags='-std=c++20'
@@ -257,7 +260,8 @@ jobs:
     - name: Install Apt dependencies
       run: |
         sudo apt update
-        sudo apt install libboost-dev gfortran liblapack-dev libblas-dev libsundials-dev libhdf5-dev
+        sudo apt install libboost-dev gfortran libopenblas-openmp-dev libsundials-dev \
+          libhdf5-dev
         gcc --version
     - name: Upgrade pip
       run: python3 -m pip install -U pip setuptools wheel
@@ -269,7 +273,7 @@ jobs:
     - name: Setup .NET Core SDK
       uses: actions/setup-dotnet@v4
       with:
-        dotnet-version: '6.x'
+        dotnet-version: '8.x'
     - name: Build Cantera
       run: |
         python3 `which scons` build blas_lapack_libs=lapack,blas coverage=y \
@@ -347,7 +351,7 @@ jobs:
         run: |
           sudo apt update
           sudo apt install libboost-dev graphviz texlive-bibtex-extra \
-            libblas-dev liblapack-dev libhdf5-dev libfmt-dev libsundials-dev
+            libopenblas-openmp-dev libhdf5-dev libfmt-dev libsundials-dev
       - name: Upgrade pip
         run: pip install -U pip setuptools wheel
       - name: Install Python dependencies
@@ -434,7 +438,7 @@ jobs:
 
           git checkout --track origin/${BRANCH}
           mkdir -p ${GIT_DEST}
-          tar -zxf ../build/doc/docs.tar.gz -C ${GIT_DEST}
+          tar -zxf ../build/doc/docs.tar.gz --strip-components=1 -C ${GIT_DEST}
           git add .
           git commit -m "Update for Cantera ${GIT_DEST} - Cantera/cantera@${REPO_SHA}"
           git show --stat HEAD
@@ -460,33 +464,34 @@ jobs:
       matrix:
         # Keep some test cases with NumPy 1.x until we explicitly drop support
         include:
-        - os: "ubuntu-20.04"
-          python-version: "3.8"
-          numpy: ""
         - os: "ubuntu-22.04"
-          python-version: "3.8"
+          python-version: "3.10"
           numpy: ""
-        - os: "ubuntu-20.04"
+          libhdf5: "libhdf5-103"
+        - os: "ubuntu-24.04"
           python-version: "3.10"
           numpy: "==1.21.6"
-        - os: "ubuntu-22.04"
-          python-version: "3.10"
-          numpy: ""
+          libhdf5: "libhdf5-103-1t64"
         - os: "ubuntu-22.04"
           python-version: "3.11"
           numpy: "==1.23.5"
-        - os: "ubuntu-20.04"
+          libhdf5: "libhdf5-103"
+        - os: "ubuntu-24.04"
           python-version: "3.11"
           numpy: ""
+          libhdf5: "libhdf5-103-1t64"
         - os: "ubuntu-22.04"
           python-version: "3.12"
           numpy: "==1.26.4"
-        - os: "ubuntu-20.04"
+          libhdf5: "libhdf5-103"
+        - os: "ubuntu-24.04"
           python-version: "3.12"
           numpy: ""
+          libhdf5: "libhdf5-103-1t64"
         - os: "ubuntu-22.04"
           python-version: "3.13"
           numpy: ""
+          libhdf5: "libhdf5-103"
       fail-fast: false
     steps:
       # We're not building Cantera here, we only need the checkout for the samples
@@ -501,7 +506,7 @@ jobs:
       - name: Install Apt dependencies
         run: |
           sudo apt update
-          sudo apt install graphviz libhdf5-103 libfmt-dev
+          sudo apt install graphviz ${{ matrix.libhdf5 }} libfmt-dev libopenblas0-openmp
       - name: Download the wheel artifact
         uses: actions/download-artifact@v4
         with:
@@ -554,17 +559,13 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 60
     env:
-      PYTHON_VERSION: 3.8
+      PYTHON_VERSION: '3.13'
     defaults:
       run:
         shell: bash -l {0}
     strategy:
       matrix:
         include:
-        - sundials-ver: 3
-          fmt-ver: 6.1.2
-        - sundials-ver: 4
-          fmt-ver: 8.1
         - sundials-ver: 5.8
           fmt-ver: 9.1
         - sundials-ver: 6.4.1
@@ -629,14 +630,14 @@ jobs:
     strategy:
       matrix:
         include:
-        - python-version: '3.8'
+        - python-version: '3.13'
           fmt-ver: '10'
         - python-version: '3.10'
           fmt-ver: '8.1'
         - python-version: '3.11'
           fmt-ver: '9.1'
         - python-version: '3.12'
-          fmt-ver: '7.1'
+          fmt-ver: '10.0'
         - python-version: '3.13'
           fmt-ver: '11.0'
           extra-build-args: cxx_flags='/EHsc /std:c++20 /utf-8'
@@ -714,7 +715,7 @@ jobs:
     strategy:
       matrix:
         vs-toolset: ['14.2']
-        python-version: ["3.8", "3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
       fail-fast: false
     steps:
       - uses: actions/checkout@v4
@@ -760,7 +761,7 @@ jobs:
 
   # Adapted from https://www.scivision.dev/intel-oneapi-github-actions/
   linux-intel-oneapi:
-    name: intel-oneAPI on Ubuntu, Python 3.8
+    name: intel-oneAPI on Ubuntu, Python 3.12
     runs-on: ubuntu-latest
     timeout-minutes: 60
     env:
@@ -787,7 +788,7 @@ jobs:
     - name: Setup Python
       uses: actions/setup-python@v5
       with:
-        python-version: 3.8
+        python-version: '3.12'
         architecture: x64
     - name: Upgrade pip
       run: python3 -m pip install -U pip setuptools wheel
@@ -912,12 +913,12 @@ jobs:
     - name: Install Apt dependencies (Ubuntu)
       run: |
         sudo apt update
-        sudo apt install libhdf5-dev libfmt-dev
+        sudo apt install libhdf5-dev libfmt-dev libopenblas0-openmp
       if: matrix.os == 'ubuntu-22.04'
     - name: Setup .NET Core SDK
       uses: actions/setup-dotnet@v4
       with:
-        dotnet-version: '6.x'
+        dotnet-version: '8.x'
     - name: Download the Cantera shared library (.so)
       uses: actions/download-artifact@v4
       with:

diff --git a/README.rst b/README.rst
@@ -92,7 +92,7 @@ possible.
 Development Site
 ================
 
-The current development version is 3.1.0. The current stable version is
+The current development version is 3.2.0a1. The current stable version is
 3.1.0. The `latest Cantera source code <https://github.com/Cantera/cantera>`_,
 the `issue tracker <https://github.com/Cantera/cantera/issues>`_ for bugs and
 enhancement requests, `downloads of Cantera releases and binary installers