Add regression tests for C++ sample programs

.github/workflows/main.yml

@@ -42,8 +42,6 @@ jobs:
       run: python3 `which scons` build -j2
     - name: Test Cantera
       run: python3 `which scons` test
-    - name: Build Samples
-      run: python3 `which scons` samples
 
   macos-multiple-pythons:
     name: macOS with Python ${{ matrix.python-version }}
@@ -72,8 +70,6 @@ jobs:
       run: python3 `which scons` build -j2
     - name: Test Cantera
       run: python3 `which scons` test
-    - name: Build Samples
-      run: python3 `which scons` samples
 
   # Coverage is its own job because macOS builds of the samples
   # use Homebrew gfortran which is not compatible for coverage
@@ -176,8 +172,6 @@ jobs:
         run: scons build python_cmd=/usr/bin/python3 blas_lapack_libs=lapack,blas -j2
       - name: Test Cantera
         run: scons test
-      - name: Build Samples
-        run: scons samples
 
   multiple-sundials:
     name: Sundials ${{ matrix.sundials-ver }}
@@ -212,9 +206,6 @@ jobs:
       - name: Test Cantera
         run: scons test
         shell: bash -l {0}
-      - name: Build Samples
-        run: scons samples
-        shell: bash -l {0}
 
   cython-latest:
     name: Test pre-release version of Cython
@@ -241,8 +232,6 @@ jobs:
       run: python3 `which scons` build blas_lapack_libs=lapack,blas python_package='full' -j2
     - name: Test Cantera
       run: python3 `which scons` test
-    - name: Build Samples
-      run: python3 `which scons` samples
 
   windows:
     name: ${{ matrix.os }}, MSVC ${{ matrix.vs-toolset }}, Python ${{ matrix.python-version }}
@@ -289,5 +278,3 @@ jobs:
         shell: cmd
       - name: Test Cantera
         run: scons test
-      - name: Build Samples
-        run: scons samples

SConstruct

@@ -79,7 +79,9 @@ if 'clean' in COMMAND_LINE_TARGETS:
     removeDirectory('interfaces/cython/Cantera.egg-info')
     removeDirectory('interfaces/python_minimal/Cantera_minimal.egg-info')
     for name in os.listdir('interfaces/cython/cantera/data/'):
-        if name != '__init__.py':
+        if os.path.isdir('interfaces/cython/cantera/data/' + name):
+            removeDirectory('interfaces/cython/cantera/data/' + name)
+        elif name != '__init__.py':
             removeFile('interfaces/cython/cantera/data/' + name)
     removeDirectory('interfaces/cython/cantera/test/data/test_subdir')
     for name in os.listdir('interfaces/cython/cantera/test/data/'):
@@ -1614,14 +1616,22 @@ for xml in mglob(env, 'data/inputs', 'xml'):
 for yaml in mglob(env, "data", "yaml"):
     dest = pjoin("build", "data", yaml.name)
     build(env.Command(dest, yaml.path, Copy("$TARGET", "$SOURCE")))
+for subdir in os.listdir('data'):
+    if os.path.isdir(pjoin('data', subdir)):
+        for yaml in mglob(env, pjoin("data", subdir), "yaml"):
+            dest = pjoin("build", "data", subdir, yaml.name)
+            if not os.path.exists(pjoin("build", "data", subdir)):
+                os.makedirs(pjoin("build", "data", subdir))
+            build(env.Command(dest, yaml.path, Copy("$TARGET", "$SOURCE")))
+
 
 if addInstallActions:
     # Put headers in place
     headerBase = 'include/cantera'
     install(env.RecursiveInstall, '$inst_incdir', 'include/cantera')
 
     # Data files
-    install('$inst_datadir', mglob(env, 'build/data', 'cti', 'xml', 'yaml'))
+    install(env.RecursiveInstall, '$inst_datadir', 'build/data')
 
 
 ### List of libraries needed to link to Cantera ###

data/air.yaml

@@ -16,7 +16,7 @@ phases:
   species: [O, O2, N, NO, NO2, N2O, N2, AR]
   kinetics: gas
   transport: mixture-averaged
-  state: {T: 300.0, P: 1 atm}
+  state: {T: 300.0, P: 1 atm, X: {O2: 0.21, N2: 0.78, AR: 0.01}}
 
 species:
 - name: O

include/cantera/oneD/Boundary1D.h

@@ -97,6 +97,21 @@ class Boundary1D : public Domain1D
 };
 
 
+/*!
+ * Renamed base class for boundaries between one-dimensional spatial domains.
+ * @deprecated To be removed after Cantera 2.5.
+ */
+class Bdry1D : public Boundary1D
+{
+public:
+    Bdry1D() : Boundary1D() {
+        warn_deprecated("Bdry1D::Bdry1D()",
+                        "To be removed after Cantera 2.5. "
+                        "Class renamed to Boundary1D.");
+    }
+};
+
+
 /**
  * An inlet.
  * @ingroup onedim

include/cantera/oneD/Inlet1D.h

@@ -14,23 +14,4 @@
 
 #include "Boundary1D.h"
 
-namespace Cantera
-{
-
-/*!
- * Renamed base class for boundaries between one-dimensional spatial domains.
- * @deprecated To be removed after Cantera 2.5.
- */
-class Bdry1D : public Boundary1D
-{
-public:
-    Bdry1D() : Boundary1D() {
-        warn_deprecated("Bdry1D::Bdry1D()",
-                        "To be removed after Cantera 2.5. "
-                        "Class renamed to Boundary1D.");
-    }
-};
-
-}
-
 #endif

include/cantera/onedim.h

@@ -14,7 +14,6 @@
 #include "oneD/Sim1D.h"
 #include "oneD/Domain1D.h"
 #include "oneD/Boundary1D.h"
-#include "oneD/Inlet1D.h"
 #include "oneD/StFlow.h"
 
 #endif

include/cantera/transport/TransportFactory.h

@@ -61,8 +61,11 @@ class TransportFactory : public Factory<Transport>
      *  @param thermo    ThermoPhase object
      *  @param log_level log level
      *  @param ndim      Number of dimensions for fluxes
+     *
+     * @deprecated The `ndim` parameter is unused and will be removed after
+     *     Cantera 2.5.
      */
-    virtual Transport* newTransport(const std::string& model, thermo_t* thermo, int log_level=0, int ndim=1);
+    virtual Transport* newTransport(const std::string& model, thermo_t* thermo, int log_level=0, int ndim=-99);
 
     //! Build a new transport manager using the default transport manager
     //! in the phase description and return a base class pointer to it
@@ -93,8 +96,9 @@ class TransportFactory : public Factory<Transport>
     std::map<std::string, bool> m_CK_mode;
 };
 
+//! @copydoc TransportFactory::newTransport(const std::string&, thermo_t*, int, int)
 Transport* newTransportMgr(const std::string& transportModel = "",
-                           thermo_t* thermo = 0, int loglevel = 0, int ndim=1);
+                           thermo_t* thermo = 0, int loglevel = 0, int ndim=-99);
 
 //!  Create a new transport manager instance.
 /*!

interfaces/cython/.gitignore

@@ -1,17 +1,7 @@
 cantera/*.cpp
 cantera/*.c
-cantera/data/*.cti
-cantera/data/*.xml
-cantera/data/*.yaml
-cantera/data/*.yml
-cantera/test/data/*.cti
-cantera/test/data/*.xml
-cantera/test/data/*.inp
-cantera/test/data/*.dat
-cantera/test/data/*.csv
-cantera/test/data/*.yaml
-cantera/test/data/*.yml
-cantera/test/data/test_subdir
+cantera/data
+cantera/test/data
 setup.py
 scripts/ctml_writer.py
 scripts/ctml_writer

interfaces/cython/setup.py.in

@@ -93,7 +93,7 @@ setup(
         'Topic :: Scientific/Engineering :: Chemistry',
     ],
     package_data = {
-        'cantera.data': ['*.*'],
+        'cantera.data': ['*.*', '*/*.*'],
         'cantera.test.data': ['*.*', '*/*.*'],
         'cantera.examples': ['*/*.*'],
         'cantera': ["@py_extension@", '*.pxd'],

samples/cxx/LiC6_electrode/LiC6_electrode.cpp

@@ -9,15 +9,15 @@ void calc_potentials()
     suppress_deprecation_warnings();
     double Tk = 273.15 + 25.0;
 
-    std::string filename = "LiC6_electrodebulk.yaml";
+    std::string filename = "sample-data/LiC6_electrodebulk.yaml";
     std::string phasename = "LiC6_and_Vacancies";
     std::unique_ptr<ThermoPhase> electrodebulk(newPhase(filename,phasename));
     std::string intercalatingSpeciesName("Li(C6)");
     size_t intercalatingSpeciesIdx = electrodebulk->speciesIndex(intercalatingSpeciesName);
     size_t nsp_tot = electrodebulk->nSpecies();
 
-    std::ofstream fout("potentials_output.dat", std::ofstream::out);
-    fout << "x[LiC6] ChemPotential[LiC6] ChemPotential[C6] Uref ActCoeff[LiC6] ActCoeff[C6] dlnActCoeffdx[LiC6] dlnActCoeffdx[C6]" << std::endl;
+    std::ofstream fout("LiC6_electrode_output.csv", std::ofstream::out);
+    fout << "x[LiC6], ChemPotential[LiC6], ChemPotential[C6], Uref ActCoeff[LiC6], ActCoeff[C6], dlnActCoeffdx[LiC6], dlnActCoeffdx[C6]" << std::endl;
 
     vector_fp spvals(nsp_tot);
     vector_fp actCoeff(nsp_tot);
@@ -54,7 +54,7 @@ void calc_potentials()
         electrodebulk->getdlnActCoeffdlnX_diag(dlnActCoeffdlnX_diag.data());
         electrodebulk->getActivityCoefficients(actCoeff.data());
 
-        fout << fmt::format("{} {} {} {} {} {} {} {}\n",
+        fout << fmt::format("{}, {}, {}, {}, {}, {}, {}, {}\n",
             xv[0], spvals[0], spvals[1], Uref, actCoeff[0],
             actCoeff[1], dlnActCoeffdlnX_diag[0], dlnActCoeffdlnX_diag[1]);
     }