[SCons] Make Eigen available to Cantera

Check for a system copy of Eigen, and if that is not found, install
Eigen's headers with the Cantera headers. Add the header 'eigen_dense.h'
to provide a single header to include from other locations.

SConstruct

@@ -407,6 +407,11 @@ config_options = [
         'sphinx_cmd',
         """Command to use for building the Sphinx documentation.""",
         'sphinx-build', PathVariable.PathAccept),
+    EnumVariable(
+        'system_eigen',
+        """Select whether to use Eigen from a system installation ('y'), from
+           a git submodule ('n'), or to decide automatically ('default').""",
+        'default', ('default', 'y', 'n')),
     EnumVariable(
         'system_sundials',
         """Select whether to use Sundials from a system installation ('y'), from
@@ -771,6 +776,30 @@ if env['system_googletest'] in ('n', 'default'):
                          'Try manually checking out the submodule with:\n\n'
                          '    git submodule update --init --recursive ext/googletest\n')
 
+# Check for Eigen and checkout submodule if needed
+if env['system_eigen'] in ('y', 'default'):
+    if conf.CheckCXXHeader('Eigen/Dense', '<>'):
+        env['system_eigen'] = True
+    elif env['system_eigen'] == 'y':
+        config_error('Expected system installation of Eigen, but it '
+                     'could not be found.')
+
+if env['system_eigen'] in ('n', 'default'):
+    env['system_eigen'] = False
+    if not os.path.exists('ext/eigen/Eigen/Dense'):
+        if not os.path.exists('.git'):
+            config_error('Eigen is missing. Install Eigen in ext/eigen.')
+
+        try:
+            code = subprocess.call(['git','submodule','update','--init',
+                                    '--recursive','ext/eigen'])
+        except Exception:
+            code = -1
+        if code:
+            config_error('Eigen not found and submodule checkout failed.\n'
+                         'Try manually checking out the submodule with:\n\n'
+                         '    git submodule update --init --recursive ext/eigen\n')
+
 
 def get_expression_value(includes, expression):
     s = ['#include ' + i for i in includes]
@@ -1222,6 +1251,7 @@ cdefine('LAPACK_FTN_TRAILING_UNDERSCORE', 'lapack_ftn_trailing_underscore')
 cdefine('FTN_TRAILING_UNDERSCORE', 'lapack_ftn_trailing_underscore')
 cdefine('LAPACK_NAMES_LOWERCASE', 'lapack_names', 'lower')
 configh['CT_USE_LAPACK'] = 0 if env['BUILD_BLAS_LAPACK'] else 1
+cdefine('CT_USE_SYSTEM_EIGEN', env['system_eigen'])
 
 config_h = env.Command('include/cantera/base/config.h',
                        'include/cantera/base/config.h.in',

ext/SConscript

@@ -111,6 +111,10 @@ if env['system_sundials'] == 'n':
             [f for f in mglob(localenv, 'sundials/src/'+subdir, 'c')
             if '_klu' not in f.name and '_superlumt' not in f.name]))
 
+if not env['system_eigen']:
+    build(localenv.Command('#include/cantera/ext/Eigen', '#ext/eigen/Eigen',
+                           Copy('$TARGET', '$SOURCE')))
+
 # Google Test: Used internally for Cantera unit tests.
 if not env['system_googletest']:
     localenv = prep_gtest(env)

include/cantera/base/config.h.in

@@ -42,6 +42,8 @@ typedef int ftnlen;       // Fortran hidden string length type
 %(LAPACK_FTN_TRAILING_UNDERSCORE)s
 %(CT_USE_LAPACK)s
 
+%(CT_USE_SYSTEM_EIGEN)s
+
 //--------- operating system --------------------------------------
 
 // The configure script defines this if the operating system is Mac

include/cantera/numerics/eigen_dense.h

@@ -0,0 +1,6 @@
+#include "cantera/base/ct_defs.h"
+#if CT_USE_SYSTEM_EIGEN
+#include <Eigen/Dense>
+#else
+#include "cantera/ext/Eigen/Dense"
+#endif