Fix build issues - macOS rpath, wheel paths, missing pytest

.github/workflows/main.yml

@@ -202,7 +202,7 @@ jobs:
         run: python3 -m pip install -U pip setuptools wheel
       - name: Install Python dependencies
         run: |
-          python3 -m pip install ruamel.yaml scons numpy cython sphinx\<4.0 \
+          python3 -m pip install ruamel.yaml scons numpy cython sphinx\<4.0 jinja2\<3.1.0 \
           sphinxcontrib-katex sphinxcontrib-matlabdomain sphinxcontrib-doxylink
       - name: Build Cantera with documentation
         run: python3 `which scons` build -j2 doxygen_docs=y sphinx_docs=y debug=n optimize=n use_pch=n
@@ -492,7 +492,7 @@ jobs:
           architecture: x64
       - name: Install Python dependencies
         run: |
-          python -m pip install -U pip 'setuptools>=43.0.0' wheel
+          python -m pip install -U pip setuptools wheel
           python -m pip install scons pypiwin32 numpy ruamel.yaml cython h5py pandas pytest pytest-github-actions-annotate-failures
       - name: Restore Boost cache
         uses: actions/cache@v2

SConstruct

@@ -1612,6 +1612,19 @@ if env['python_package'] != 'none':
                 f"Building the full Python package for Python {python_version}")
             env["python_package"] = "full"
 
+if env["python_package"] == "full" and env["OS"] == "Darwin":
+    # We need to know the macOS deployment target in advance to be able to determine
+    # the name of the wheel file for the Python module. If this is not specified by the
+    # MACOSX_DEPLOYMENT_TARGET environment variable, get the value from the Python
+    # installation and use that.
+    if not env["ENV"].get("MACOSX_DEPLOYMENT_TARGET", False):
+        info = get_command_output(
+            env["python_cmd"],
+            "-c",
+            "import sysconfig; print(sysconfig.get_platform())"
+        )
+        env["ENV"]["MACOSX_DEPLOYMENT_TARGET"] = info.split("-")[1]
+
 # Matlab Toolbox settings
 if env["matlab_path"] != "" and env["matlab_toolbox"] == "default":
     env["matlab_toolbox"] = "y"
@@ -1805,9 +1818,14 @@ configh['SOLARIS'] = 1 if env['OS'] == 'Solaris' else None
 configh['DARWIN'] = 1 if env['OS'] == 'Darwin' else None
 
 if env['OS'] == 'Solaris' or env['HAS_CLANG']:
-    configh['NEEDS_GENERIC_TEMPL_STATIC_DECL'] = 1
     env["RPATHPREFIX"] = "-Wl,-rpath,"
 
+if env["OS"] == "Darwin" and env["use_rpath_linkage"] and not env.subst("$__RPATH"):
+    # SCons doesn't want to specify RPATH on macOS, so circumvent that behavior by
+    # specifying this directly as part of LINKFLAGS
+    env.Append(LINKFLAGS=[env.subst(f'$RPATHPREFIX{x}$RPATHSUFFIX')
+                          for x in env['RPATH']])
+
 configh['CT_SUNDIALS_VERSION'] = env['sundials_version'].replace('.','')
 
 if env.get('has_sundials_lapack') and env['use_lapack']:
@@ -1888,13 +1906,16 @@ env.Prepend(CPPPATH=[],
 
 # preprocess input files (cti -> xml)
 convertedInputFiles = set()
+convertEnv = env.Clone()
+convertEnv["ENV"]["CT_NO_XML_WARNINGS"] = "1"
 for cti in multi_glob(env, 'data/inputs', 'cti'):
-    build(env.Command('build/data/%s' % cti.name, cti.path,
-                      Copy('$TARGET', '$SOURCE')))
+    build(convertEnv.Command('build/data/%s' % cti.name, cti.path,
+                             Copy('$TARGET', '$SOURCE')))
     outName = os.path.splitext(cti.name)[0] + '.xml'
     convertedInputFiles.add(outName)
-    build(env.Command('build/data/%s' % outName, cti.path,
-                      '$python_cmd_esc interfaces/cython/cantera/ctml_writer.py $SOURCE $TARGET'))
+    build(convertEnv.Command(
+        'build/data/%s' % outName, cti.path,
+        '$python_cmd_esc interfaces/cython/cantera/ctml_writer.py $SOURCE $TARGET'))
 
 # Copy XML input files which are not present as cti:
 for xml in multi_glob(env, 'data/inputs', 'xml'):
@@ -1923,12 +1944,6 @@ if addInstallActions:
     install(env.RecursiveInstall, '$inst_datadir', 'build/data')
 
 
-### List of libraries needed to link to Cantera ###
-linkLibs = ['cantera']
-
-### List of shared libraries needed to link applications to Cantera
-linkSharedLibs = ['cantera_shared']
-
 if env['system_sundials'] == 'y':
     env['sundials_libs'] = ['sundials_cvodes', 'sundials_ida', 'sundials_nvecserial']
     if env['use_lapack'] and sundials_ver >= parse_version('3.0'):
@@ -1941,27 +1956,27 @@ if env['system_sundials'] == 'y':
 else:
     env['sundials_libs'] = []
 
-linkLibs.extend(env['sundials_libs'])
-linkSharedLibs.extend(env['sundials_libs'])
+# External libraries to link to
+env["external_libs"] = []
+env["external_libs"].extend(env["sundials_libs"])
+
+if env["system_fmt"]:
+    env["external_libs"].append("fmt")
 
-if env['system_fmt']:
-    linkLibs.append('fmt')
-    linkSharedLibs.append('fmt')
+if env["system_yamlcpp"]:
+    env["external_libs"].append("yaml-cpp")
 
-if env['system_yamlcpp']:
-    linkLibs.append('yaml-cpp')
-    linkSharedLibs.append('yaml-cpp')
+if env["blas_lapack_libs"]:
+    env["external_libs"].extend(env["blas_lapack_libs"])
 
-#  Add LAPACK and BLAS to the link line
-if env['blas_lapack_libs']:
-    linkLibs.extend(env['blas_lapack_libs'])
-    linkSharedLibs.extend(env['blas_lapack_libs'])
+# List of static libraries needed to link to Cantera
+env["cantera_libs"] = ["cantera"] + env["external_libs"]
 
-# Store the list of needed static link libraries in the environment
-env['cantera_libs'] = linkLibs
-env['cantera_shared_libs'] = linkSharedLibs
-if not env['renamed_shared_libraries']:
-    env['cantera_shared_libs'] = linkLibs
+# List of shared libraries needed to link to Cantera
+if env["renamed_shared_libraries"]:
+    env["cantera_shared_libs"] = ["cantera_shared"] + env["external_libs"]
+else:
+    env["cantera_shared_libs"] = ["cantera"] + env["external_libs"]
 
 # Add targets from the SConscript files in the various subdirectories
 Export('env', 'build', 'libraryTargets', 'install', 'buildSample')

include/cantera/base/config.h.in

@@ -59,20 +59,6 @@ typedef int ftnlen;       // Fortran hidden string length type
 // with a native compiler
 {SOLARIS!s}
 
-//---------- C++ Compiler Variations ------------------------------
-
-// This define is needed to account for the variability for how
-// static variables in templated classes are defined. Right now
-// this is only turned on for the SunPro compiler on Solaris.
-// in that system , you need to declare the static storage variable.
-// with the following line in the include file
-//
-//    template<class M> Cabinet<M>* Cabinet<M>::s_storage;
-//
-// Note, on other systems that declaration is treated as a definition
-// and this leads to multiple defines at link time
-{NEEDS_GENERIC_TEMPL_STATIC_DECL!s}
-
 //-------------- Optional Cantera Capabilities ----------------------
 
 //    Enable Sundials to use an external BLAS/LAPACK library if it was

include/cantera/kinetics/MultiRate.h

@@ -33,13 +33,13 @@ class MultiRate final : public MultiRateBase
         return m_rxn_rates.at(0).second.type();
     }
 
-    virtual void add(const size_t rxn_index, ReactionRate& rate) override {
+    virtual void add(size_t rxn_index, ReactionRate& rate) override {
         m_indices[rxn_index] = m_rxn_rates.size();
         m_rxn_rates.emplace_back(rxn_index, dynamic_cast<RateType&>(rate));
         m_shared.invalidateCache();
     }
 
-    virtual bool replace(const size_t rxn_index, ReactionRate& rate) override {
+    virtual bool replace(size_t rxn_index, ReactionRate& rate) override {
         if (!m_rxn_rates.size()) {
             throw CanteraError("MultiRate::replace",
                  "Invalid operation: cannot replace rate object "

interfaces/cython/SConscript

@@ -102,10 +102,11 @@ ext = localenv.LoadableModule(f"cantera/_cantera{module_ext}",
                               obj, LIBPREFIX="", SHLIBSUFFIX=module_ext,
                               SHLIBPREFIX="", LIBSUFFIXES=[module_ext])
 
-build_cmd = ("$python_cmd_esc -m pip wheel --no-build-isolation --no-deps "
+build_cmd = ("$python_cmd_esc -m pip wheel -v --no-build-isolation --no-deps "
              "--wheel-dir=build/python/dist build/python")
+plat = info['plat'].replace('-', '_').replace('.', '_')
 wheel_name = (f"Cantera-{env['cantera_version']}-cp{py_version_nodot}"
-              f"-cp{py_version_nodot}-{info['plat'].replace('-', '_')}.whl")
+              f"-cp{py_version_nodot}-{plat}.whl")
 mod = build(localenv.Command(f"#build/python/dist/{wheel_name}", "setup.cfg",
                              build_cmd))
 env['python_module'] = mod

interfaces/cython/cantera/ctml_writer.py

@@ -30,6 +30,7 @@
 
 import sys
 import re
+import os
 
 # Python 2/3 compatibility
 try:
@@ -2761,10 +2762,11 @@ def convert(filename=None, outName=None, text=None):
 def main():
     if len(sys.argv) not in (2,3):
         raise ValueError('Incorrect number of command line arguments.')
-    print("WARNING: The CTI and XML input file formats are deprecated and will be\n"
-          "removed in Cantera 3.0. Use 'cti2yaml.py' to convert CTI input files to\n"
-          "the YAML format. See https://cantera.org/tutorials/legacy2yaml.html for\n"
-          "more information.")
+    if os.environ.get("CT_NO_XML_WARNINGS") != "1":
+        print("WARNING: The CTI and XML input file formats are deprecated and will be\n"
+              "removed in Cantera 3.0. Use 'cti2yaml.py' to convert CTI input files\n"
+              "to the YAML format. See https://cantera.org/tutorials/legacy2yaml.html\n"
+              "for more information.")
 
     convert(*sys.argv[1:])
 

interfaces/cython/setup.py

@@ -1,5 +1,10 @@
-from setuptools import setup, Extension
+from setuptools import setup
+from setuptools.dist import Distribution
 
-extension = Extension("cantera._cantera", sources=[])
+class BinaryDistribution(Distribution):
+    def has_ext_modules(self):
+        return True
 
-setup(ext_modules=[extension])
+setup(
+    distclass=BinaryDistribution,
+)

src/SConscript

@@ -78,15 +78,8 @@ localenv.Depends(lib, localenv['config_h_target'])
 install('$inst_libdir', lib)
 env['cantera_staticlib'] = lib
 
-if (localenv['system_sundials'] == 'y'):
-    localenv.Append(LIBS=localenv['sundials_libs'],
-                    LIBPATH=localenv['sundials_libdir'])
-if localenv['blas_lapack_libs']:
-    localenv.Append(LIBS=localenv['blas_lapack_libs'],
-                    LIBPATH=localenv['blas_lapack_dir'])
-
-if localenv['system_yamlcpp']:
-    localenv.Append(LIBS=['yaml-cpp'])
+localenv.Append(LIBS=localenv['external_libs'],
+                LIBPATH=localenv['sundials_libdir'] + localenv['blas_lapack_dir'])
 
 # Build the Cantera shared library
 if localenv['layout'] != 'debian':

src/clib/Cabinet.h

@@ -205,13 +205,4 @@ class Cabinet
     std::vector<M*> m_table;
 };
 
-//! Declaration stating that the storage for the static member
-//! of each instantiated template will exist
-/*!
- *   The actual storage will be allocated in .cpp files
- */
-#ifdef NEEDS_GENERIC_TEMPL_STATIC_DECL
-template<class M, bool canDelete> Cabinet<M, canDelete>* Cabinet<M, canDelete>::s_storage;
-#endif
-
 #endif

src/clib/ct.cpp

@@ -36,6 +36,7 @@ typedef Cabinet<XML_Node, false> XmlCabinet;
 template<> ThermoCabinet* ThermoCabinet::s_storage = 0;
 template<> KineticsCabinet* KineticsCabinet::s_storage = 0;
 template<> TransportCabinet* TransportCabinet::s_storage = 0;
+template<> XmlCabinet* XmlCabinet::s_storage; // defined in ctxml.cpp
 
 /**
  * Exported functions.

src/clib/ctmultiphase.cpp

@@ -17,7 +17,10 @@ using namespace std;
 using namespace Cantera;
 
 typedef Cabinet<MultiPhase> mixCabinet;
+typedef Cabinet<ThermoPhase> ThermoCabinet;
+
 template<> mixCabinet* mixCabinet::s_storage = 0;
+template<> ThermoCabinet* ThermoCabinet::s_storage; // defined in ct.cpp
 
 extern "C" {
 
@@ -54,7 +57,7 @@ extern "C" {
     int mix_addPhase(int i, int j, double moles)
     {
         try {
-            mixCabinet::item(i).addPhase(&Cabinet<ThermoPhase>::item(j), moles);
+            mixCabinet::item(i).addPhase(&ThermoCabinet::item(j), moles);
             return 0;
         } catch (...) {
             return handleAllExceptions(-1, ERR);

src/clib/ctonedim.cpp

@@ -29,6 +29,9 @@ template<> DomainCabinet* DomainCabinet::s_storage = 0;
 typedef Cabinet<ThermoPhase> ThermoCabinet;
 typedef Cabinet<Kinetics> KineticsCabinet;
 typedef Cabinet<Transport> TransportCabinet;
+template<> ThermoCabinet* ThermoCabinet::s_storage; // defined in ct.cpp
+template<> KineticsCabinet* KineticsCabinet::s_storage; // defined in ct.cpp
+template<> TransportCabinet* TransportCabinet::s_storage; // defined in ct.cpp
 
 extern "C" {
 

src/clib/ctreactor.cpp

@@ -32,6 +32,9 @@ template<> NetworkCabinet* NetworkCabinet::s_storage = 0;
 template<> FlowDeviceCabinet* FlowDeviceCabinet::s_storage = 0;
 template<> WallCabinet* WallCabinet::s_storage = 0;
 template<> ReactorSurfaceCabinet* ReactorSurfaceCabinet::s_storage = 0;
+template<> FuncCabinet* FuncCabinet::s_storage; // defined in ctfunc.cpp
+template<> ThermoCabinet* ThermoCabinet::s_storage; // defined in ct.cpp
+template<> KineticsCabinet* KineticsCabinet::s_storage; // defined in ct.cpp
 
 extern "C" {
 

src/clib/ctrpath.cpp

@@ -23,6 +23,7 @@ template<> DiagramCabinet* DiagramCabinet::s_storage = 0;
 template<> BuilderCabinet* BuilderCabinet::s_storage = 0;
 
 typedef Cabinet<Kinetics> KineticsCabinet;
+template<> KineticsCabinet* KineticsCabinet::s_storage; // defined in ct.cpp
 
 extern "C" {
 

src/clib/ctsurf.cpp

@@ -17,6 +17,8 @@ using namespace std;
 using namespace Cantera;
 
 typedef Cabinet<ThermoPhase> ThermoCabinet;
+template<> ThermoCabinet* ThermoCabinet::s_storage; // defined in ct.cpp
+
 
 extern "C" {
 

test/SConscript

@@ -157,6 +157,12 @@ def addPythonTest(testname, subdir, script, interpreter,
             # Test was successful
             with open(target[0].path, 'w') as passed_file:
                 passed_file.write(time.asctime()+'\n')
+        elif code == 21:  # Special error code from runCythonTests.py for pytest errors
+            msg = (f"{testname}: Test suite requires the Python package 'pytest',"
+                " which can be installed using pip or conda"
+            )
+            test_results.failed[msg] = 100
+            return
         elif env["fast_fail_tests"]:
             sys.exit(1)
 

test/python/runCythonTests.py

@@ -28,19 +28,16 @@
 try:
     import pytest
 except ImportError:
-    pytest = None
-import cantera
-import cantera.test
-
-
-if __name__ == "__main__":
-    if pytest is None:
         print("\n* ERROR: The Cantera Python test suite requires "
             "the Python package 'pytest'.")
         print("* ERROR: Use pip or conda to install 'pytest', "
             "which will enable this feature.")
-        sys.exit(1)
+        sys.exit(21)  # test/SConscript has special handling for this error code
 
+import cantera
+import cantera.test
+
+if __name__ == "__main__":
     print("\n* INFO: using Cantera module found at this location:")
     print(f"*       '{cantera.__file__}'")
     print(f"* INFO: Cantera version: {cantera.__version__}")