[CI] Run python examples from scons

.github/workflows/main.yml

@@ -278,3 +278,87 @@ jobs:
         shell: cmd
       - name: Test Cantera
         run: scons test
+
+  # Running of Python examples separated due to significant run time.
+  # Installation restrictions exist on systems with older numpy versions.
+  python-examples-ubuntu:
+    name: Python Examples on Ubuntu with Python 3.8
+    runs-on: ubuntu-latest
+    timeout-minutes: 90
+    steps:
+    - uses: actions/checkout@v2
+      name: Checkout the repository
+      with:
+        submodules: recursive
+    - name: Setup python
+      uses: actions/setup-python@v1
+      with:
+        python-version: '3.8'
+        architecture: x64
+    - name: Install Apt dependencies
+      run: sudo apt-get install libboost-dev gfortran
+    - 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 matplotlib scipy
+    - name: Build Cantera
+      run: python3 `which scons` build -j2
+    - name: Test Cantera
+      run: python3 `which scons` test
+    - name: Run Python examples
+      run: python3 `which scons` check-examples
+
+  python-examples-windows:
+    name: Python Examples on Windows with Python 3.8
+    runs-on: windows-latest
+    timeout-minutes: 90
+    steps:
+    - uses: actions/checkout@v2
+      name: Checkout the repository
+      with:
+        submodules: recursive
+    - name: Set Up Python
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.8
+        architecture: 'x64'
+    - name: Install Python dependencies
+      run: |
+        python -m pip install -U pip setuptools
+        python -m pip install scons pypiwin32 numpy ruamel.yaml cython h5py matplotlib scipy
+    - name: Build Cantera
+      run: |
+        scons build -j2 boost_inc_dir=%BOOST_ROOT_1_69_0% debug=n VERBOSE=y python_package=full ^
+        msvc_version=14.2 f90_interface=n
+      shell: cmd
+    - name: Test Cantera
+      run: scons test
+    - name: Run Python examples
+      run: scons check-examples
+
+  python-examples-macos:
+    name: Python Examples on macOS with Python 3.8
+    runs-on: macos-latest
+    timeout-minutes: 90
+    steps:
+    - uses: actions/checkout@v2
+      name: Checkout the repository
+      with:
+        submodules: recursive
+    - name: Setup Python
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.8
+        architecture: x64
+    - name: Install Brew dependencies
+      run: brew install boost libomp
+    - 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 matplotlib scipy
+    - name: Build Cantera
+      run: python3 `which scons` build -j2
+    - name: Test Cantera
+      run: python3 `which scons` test
+    - name: Run Python examples
+      run: python3 `which scons` check-examples

SConstruct

@@ -30,6 +30,8 @@ Basic usage:
 
     'scons samples' - Compile the C++ and Fortran samples.
 
+    'scons check-examples' - Run all Python examples
+
     'scons msi' - Build a Windows installer (.msi) for Cantera.
 
     'scons sphinx' - Build the Sphinx documentation
@@ -46,7 +48,8 @@ if not COMMAND_LINE_TARGETS:
     sys.exit(0)
 
 valid_commands = ('build','clean','install','uninstall',
-                  'help','msi','samples','sphinx','doxygen','dump')
+                  'help','msi','samples','sphinx','doxygen','dump',
+                  'check-examples')
 
 for command in COMMAND_LINE_TARGETS:
     if command not in valid_commands and not command.startswith('test'):
@@ -1567,6 +1570,7 @@ env['build_targets'] = buildTargets
 libraryTargets = [] # objects that go in the Cantera library
 installTargets = []
 sampleTargets = []
+checkTargets = []
 
 def build(targets):
     """ Wrapper to add target to list of build targets """
@@ -1579,6 +1583,11 @@ def buildSample(*args, **kwargs):
     sampleTargets.extend(targets)
     return targets
 
+def checkExample(targets):
+    """ Wrapper to add target to list of sample checks """
+    checkTargets.extend(targets)
+    return targets
+
 def install(*args, **kwargs):
     """ Wrapper to add target to list of install targets """
     if not addInstallActions:
@@ -1671,7 +1680,7 @@ if not env['renamed_shared_libraries']:
     env['cantera_shared_libs'] = linkLibs
 
 # Add targets from the SConscript files in the various subdirectories
-Export('env', 'build', 'libraryTargets', 'install', 'buildSample')
+Export('env', 'build', 'libraryTargets', 'install', 'buildSample', 'checkExample')
 
 # ext needs to come before src so that libraryTargets is fully populated
 VariantDir('build/ext', 'ext', duplicate=0)
@@ -1704,6 +1713,7 @@ if env['doxygen_docs'] or env['sphinx_docs']:
 VariantDir('build/samples', 'samples', duplicate=0)
 sampledir_excludes = ['\\.o$', '^~$', '\\.in', 'SConscript']
 SConscript('build/samples/cxx/SConscript')
+SConscript('build/samples/python/SConscript')
 
 # Install C++ samples
 install(env.RecursiveInstall, '$inst_sampledir/cxx',
@@ -1721,6 +1731,7 @@ if env['f90_interface'] == 'y':
 
 ### Meta-targets ###
 build_samples = Alias('samples', sampleTargets)
+check_samples = Alias('check-examples', checkTargets)
 
 def postBuildMessage(target, source, env):
     print("*******************************************************")
@@ -1781,15 +1792,18 @@ def postInstallMessage(target, source, env):
         """.format(**env_dict))
 
     if os.name != 'nt':
+        env['setup_cantera'] = pjoin(env['ct_bindir'], 'setup_cantera')
+        env['setup_cantera_csh'] = pjoin(env['ct_bindir'], 'setup_cantera.csh')
         install_message += textwrap.dedent("""
+
             Setup scripts to configure the environment for Cantera are at:
 
-              setup script (bash)         {ct_bindir!s}/setup_cantera
-              setup script (csh/tcsh)     {ct_bindir!s}/setup_cantera.csh
+              setup script (bash)         {setup_cantera!s}
+              setup script (csh/tcsh)     {setup_cantera_csh!s}
 
             It is recommended that you run the script for your shell by typing:
 
-              source {ct_bindir!s}/setup_cantera
+              source {setup_cantera!s}
 
             before using Cantera, or else include its contents in your shell login script.
         """.format(**env_dict))

interfaces/cython/SConscript

@@ -83,14 +83,13 @@ localenv.Depends(ext, localenv['cantera_staticlib'])
 
 for f in (mglob(localenv, 'cantera', 'py') +
           mglob(localenv, 'cantera/test', 'py') +
-          mglob(localenv, 'cantera/examples/tutorial', 'py') +
-          mglob(localenv, 'cantera/examples/equilibrium', 'py') +
           mglob(localenv, 'cantera/examples/kinetics', 'py') +
-          mglob(localenv, 'cantera/examples/transport', 'py') +
-          mglob(localenv, 'cantera/examples/reactors', 'py') +
+          mglob(localenv, 'cantera/examples/multiphase', 'py') +
           mglob(localenv, 'cantera/examples/onedim', 'py') +
+          mglob(localenv, 'cantera/examples/reactors', 'py') +
           mglob(localenv, 'cantera/examples/surface_chemistry', 'py') +
-          mglob(localenv, 'cantera/examples/misc', 'py')):
+          mglob(localenv, 'cantera/examples/thermo', 'py') +
+          mglob(localenv, 'cantera/examples/transport', 'py')):
     localenv.Depends(mod, f)
 
 # Determine installation path and install the Python module

interfaces/cython/cantera/examples/thermo/sound_speed.py

@@ -8,7 +8,7 @@
 import math
 
 
-def equilSoundSpeeds(gas, rtol=1.0e-6, maxiter=5000):
+def equilSoundSpeeds(gas, rtol=1.0e-6, max_iter=5000):
     """
     Returns a tuple containing the equilibrium and frozen sound speeds for a
     gas with an equilibrium composition.  The gas is first set to an
@@ -17,7 +17,7 @@ def equilSoundSpeeds(gas, rtol=1.0e-6, maxiter=5000):
     """
 
     # set the gas to equilibrium at its current T and P
-    gas.equilibrate('TP', rtol=rtol, maxiter=maxiter)
+    gas.equilibrate('TP', rtol=rtol, max_iter=max_iter)
 
     # save properties
     s0 = gas.s
@@ -35,7 +35,7 @@ def equilSoundSpeeds(gas, rtol=1.0e-6, maxiter=5000):
     afrozen = math.sqrt((p1 - p0)/(gas.density - r0))
 
     # now equilibrate the gas holding S and P constant
-    gas.equilibrate('SP', rtol=rtol, maxiter=maxiter)
+    gas.equilibrate('SP', rtol=rtol, max_iter=max_iter)
 
     # equilibrium sound speed
     aequil = math.sqrt((p1 - p0)/(gas.density - r0))

samples/python/SConscript

@@ -0,0 +1,56 @@
+from buildutils import *
+
+Import('env', 'checkExample')
+
+localenv = env.Clone()
+localenv.PrependENVPath('LD_LIBRARY_PATH', Dir('#build/lib').abspath)
+localenv.PrependENVPath('PYTHONPATH', Dir('#build/python').abspath)
+localenv['ENV']['CANTERA_DATA'] = (Dir('#build/data').abspath)
+localenv['ENV']['MPLBACKEND'] = 'Agg'
+if localenv['OS'] == 'Windows':
+    localenv['ENV']['HOMEPATH'] = os.environ['HOMEPATH']
+
+subdirs = [
+    'kinetics',
+    'multiphase',
+    'onedim',
+    'reactors',
+    'surface_chemistry',
+    'thermo',
+    'transport',
+]
+
+broken = [
+    'extract_submechanism.py', # issue #821
+    'diffusion_flame_extinction.py', # issue #872
+    'catalytic_combustion.py', # issue #873
+    'piston.py', # issue #875
+    'surf_pfr.py', # issue #877
+    'ion_burner_flame.py', # poor convergence
+]
+
+dependencies=(env['python_module'] + env['python_extension'])
+
+warning_filters = [r'-W error::DeprecationWarning:']
+if localenv['OS'] == 'Windows':
+    # add exception as pywintypes imports a deprecated module;
+    # text containing whitespaces needs to be enclosed by double quotes
+    warning_filters.append(r'-W ignore:"the imp module is deprecated":')
+
+if localenv['python_package'] == 'full':
+
+    for subdir in subdirs:
+        sub = Dir('#build/python/cantera/examples/{}'.format(subdir)).abspath
+        sample_files = mglob(localenv, sub, 'py')
+        for f in sample_files:
+            if f.name in broken:
+                print("Skipping broken Python example '{}'".format(f.name))
+                continue
+            target = localenv.Command("${SOURCE.name.replace('.py', '.run')}", f,
+                                      "cd {} && ${{python_cmd}} {} "
+                                      "${{SOURCE.name}}".format(sub,
+                                      " ".join(warning_filters)))
+            localenv.Install(target)
+            for dep in dependencies:
+                localenv.Depends(target, dep)
+            checkExample(target)