Add Python 3.10 to the CI runners

.github/workflows/main.yml

@@ -20,7 +20,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: [ '3.6', '3.7', '3.8', '3.9' ]
+        python-version: [ '3.6', '3.9', '3.10' ]
         os: ['ubuntu-18.04', 'ubuntu-20.04']
       fail-fast: false
     steps:
@@ -36,7 +36,7 @@ jobs:
     - name: Install Apt dependencies
       run: |
         sudo apt update
-        sudo apt install libboost-dev gfortran
+        sudo apt install libboost-dev gfortran libopenmpi-dev
     - name: Upgrade pip
       run: python3 -m pip install -U pip setuptools wheel
     - name: Install Python dependencies
@@ -47,15 +47,43 @@ jobs:
     - name: Test Cantera
       run:
         python3 `which scons` test show_long_tests=yes verbose_tests=yes --debug=time
-      env:
-        GITHUB_ACTIONS: "true"
+
+  clang-compiler:
+    name: LLVM/Clang with Python 3.8
+    runs-on: ubuntu-20.04
+    steps:
+    - uses: actions/checkout@v2
+      name: Checkout the repository
+      with:
+        submodules: recursive
+    - name: Setup Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.8
+        architecture: x64
+    - name: Install Apt dependencies
+      run: |
+        sudo apt update
+        sudo apt install libboost-dev gfortran libomp-dev libomp5
+    - name: Upgrade pip
+      run: python3 -m pip install -U pip setuptools wheel
+    - name: Install Python dependencies
+      run: python3 -m pip install ruamel.yaml scons numpy cython h5py pandas pytest
+        pytest-github-actions-annotate-failures
+    - name: Build Cantera
+      run: python3 `which scons` build env_vars=all
+        CXX=clang++-12 CC=clang-12 f90_interface=n extra_lib_dirs=/usr/lib/llvm/lib
+        -j2 debug=n --debug=time
+    - name: Test Cantera
+      run:
+        python3 `which scons` test show_long_tests=yes verbose_tests=yes --debug=time
 
   macos-multiple-pythons:
     name: macOS with Python ${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: [ '3.7', '3.8', '3.9' ]
+        python-version: [ '3.7', '3.9', '3.10' ]
         os: ['macos-10.15']
       fail-fast: false
     steps:
@@ -88,8 +116,6 @@ jobs:
     - name: Test Cantera
       run:
         python3 `which scons` test show_long_tests=yes verbose_tests=yes --debug=time
-      env:
-        GITHUB_ACTIONS: "true"
 
   # Coverage is its own job because macOS builds of the samples
   # use Homebrew gfortran which is not compatible for coverage
@@ -116,20 +142,33 @@ jobs:
       run: python3 -m pip install -U pip setuptools wheel
     - name: Install Python dependencies
       run: python3 -m pip install ruamel.yaml scons numpy cython h5py pandas scipy pytest
-        pytest-github-actions-annotate-failures
+        pytest-github-actions-annotate-failures gcovr
     - name: Build Cantera
       run: |
         python3 `which scons` build blas_lapack_libs=lapack,blas coverage=y \
-        optimize=n skip_slow_tests=y no_optimize_flags=-DNDEBUG env_vars=all -j2 --debug=time
+        optimize=n skip_slow_tests=y no_optimize_flags='-DNDEBUG -O0' \
+        FORTRANFLAGS='-O0' env_vars=all -j2 --debug=time
     - name: Test Cantera
       run:
         python3 `which scons` test show_long_tests=yes verbose_tests=yes --debug=time
-      env:
-        GITHUB_ACTIONS: "true"
+    - name: Process coverage files
+      run: |
+        gcovr --root . --exclude-unreachable-branches --exclude-throw-branches \
+        --exclude-directories '\.sconf_temp' --exclude-directories 'build/ext$' \
+        --exclude '.*ext.*' --exclude '(.+/)?_cantera\.cpp$' --exclude '^test.*' \
+        --xml coverage.xml --html-details htmlcoverage.html --txt
+    - name: Archive code coverage results
+      uses: actions/upload-artifact@v2
+      with:
+        name: code-coverage-report
+        path: htmlcoverage*
+        retention-days: 5
     - name: Upload Coverage to Codecov
-      run: bash <(curl -s https://codecov.io/bash)
-      env:
-        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+      uses: codecov/codecov-action@v2
+      with:
+        verbose: true
+        files: ./coverage.xml
+        fail_ci_if_error: true
 
   docs:
     name: Build docs
@@ -176,6 +215,7 @@ jobs:
         uses: actions/upload-artifact@v2
         with:
           path: build/docs.tar.gz
+          name: docs
           retention-days: 2
       # The known_hosts key is generated with `ssh-keygen -F cantera.org` from a
       # machine that has previously logged in to cantera.org and trusts
@@ -203,7 +243,7 @@ jobs:
     runs-on: ubuntu-18.04
     strategy:
       matrix:
-        python-version: ['3.6', '3.7', '3.8', '3.9']
+        python-version: ['3.6', '3.9', '3.10']
       fail-fast: false
     steps:
       - uses: actions/checkout@v2
@@ -238,6 +278,8 @@ jobs:
         uses: actions/upload-artifact@v2
         with:
           path: results.txt
+          retention-days: 2
+          name: example-results
         # Run this step if the job was successful or failed, but not if it was cancelled
         # Using always() would run this step if the job was cancelled as well.
         if: failure() || success()
@@ -250,7 +292,7 @@ jobs:
         shell: bash -l {0}
     strategy:
       matrix:
-        sundials-ver: [ 2, 3, 4, 5.7 ]
+        sundials-ver: [ 2, 3, 4, 5.8 ]
       fail-fast: false
     steps:
       - uses: actions/checkout@v2
@@ -315,7 +357,7 @@ jobs:
       matrix:
         os: ['windows-2019']
         vs-toolset: ['14.0', '14.2']
-        python-version: [ '3.6', '3.7', '3.8', '3.9' ]
+        python-version: [ '3.6', '3.9', '3.10' ]
         # Must use windows-2016 image because it installs VS2017 (MSVC 14.1)
         # Scons cannot find MSVC 14.1 when VS2019 is installed
         include:
@@ -370,8 +412,6 @@ jobs:
         shell: cmd
       - name: Test Cantera
         run: scons test show_long_tests=yes verbose_tests=yes --debug=time
-        env:
-          GITHUB_ACTIONS: "true"
 
   # Adapted from https://www.scivision.dev/intel-oneapi-github-actions/
   linux-intel-oneapi:

SConstruct

@@ -540,7 +540,7 @@ config_options = [
            scripts).""",
         {
             "cl": "/openmp",
-            "icc": "openmp",
+            "icc": "-qopenmp",
             "icx": "-qopenmp",
             "apple-clang": "-Xpreprocessor -fopenmp",
             "default": "-fopenmp",
@@ -1177,7 +1177,17 @@ else:
     env['cxx_stdlib'] = []
 
 env['HAS_CLANG'] = conf.CheckDeclaration('__clang__', '', 'C++')
-env['HAS_OPENMP'] = conf.CheckLibWithHeader("omp", "omp.h", language="C++")
+if not env["using_apple_clang"]:
+    # This checks for these three libraries in order and stops when it finds the
+    # first success. Intel = iomp5, LLVM/clang = omp, GCC = gomp. Since gomp is
+    # likely to be installed on the system even if other compilers are installed
+    # or in use, it needs to go last in the check.
+    env['HAS_OPENMP'] = conf.CheckLibWithHeader(
+        ["iomp5", "omp", "gomp"], "omp.h", language="C++"
+    )
+else:
+    env["HAS_OPENMP"] = False
+    logger.info("Not checking for OpenMP support due to using XCode compiler.")
 
 boost_version_source = get_expression_value(['<boost/version.hpp>'], 'BOOST_LIB_VERSION')
 retcode, boost_lib_version = conf.TryRun(boost_version_source, '.cpp')

ext/SConscript

@@ -167,12 +167,12 @@ def generate_license(target, source, env):
 
 
 localenv["license_files"] = license_files
-license = build(localenv.Command("LICENSE.txt", license_files.values(),
+license = build(localenv.Command("LICENSE.txt", list(license_files.values()),
                                  generate_license))
 env["license_target"] = license
 install('$inst_docdir', license)
 
 if env['OS'] == 'Windows':
     # RTF version is required for Windows installer
-    build(localenv.Command("LICENSE.rtf", license_files.values(),
+    build(localenv.Command("LICENSE.rtf", list(license_files.values()),
                            generate_license))