Clean up SuperBuild of mandatory dependencies

CMakeLists.txt

 
 ## Options--what do you want to do
 
-option ( BUILD_SHARED_LIBS         "Shared or static libraries"  OFF ) 
-option ( LEMMA_ENABLE_TESTING      "Turn on unit testing" OFF )
-option ( LEMMA_BUILD_EXAMPLES      "Compile example Lemma applications" OFF )
-option ( LEMMA_USE_OPENMP          "Use OpenMP in Lemma" OFF )
-option ( LEMMA_BUILD_DOCUMENTATION "Build Doxygen man pages" OFF )
+option ( BUILD_SHARED_LIBS          "Shared or static libraries"  OFF ) 
+option ( LEMMA_ENABLE_TESTING       "Turn on unit testing" OFF )
+option ( LEMMA_BUILD_EXAMPLES       "Compile example Lemma applications" OFF )
+option ( LEMMA_USE_OPENMP           "Use OpenMP in Lemma" OFF )
+option ( LEMMA_BUILD_DOCUMENTATION  "Build Doxygen man pages" OFF )
 
 ## Hard Dependencies
 find_package (Eigen3 3.3  NO_MODULE QUIET)   # Matrix/Vector & Math
-find_package (yaml-cpp 0.6 QUIET)           # Serialisation of classes 
+find_package (yaml-cpp 0.6 QUIET)            # Serialisation of classes 
+
+INCLUDE_DIRECTORIES(${YAML_CPP_INCLUDE_DIR})
 
 if (LEMMA_BUILD_DOCUMENTATION)
     find_package(Doxygen REQUIRED)

Modules/FDEM1D/include/AEMSurvey.h

 namespace Lemma {
 
 /**
+  \ingroup FDEM1D
   \brief   Contains pertinant information about an AEM survey
   \details All important details about an AEM survey are stored here, but
            nothing about the underlying earth model.

Modules/FDEM1D/include/AEMSurveyReader.h

 namespace Lemma {
 
     /**
+      \ingroup FDEM1D
       \brief   Reads an ASCII description of an AEM survey
       \details The file format is described as follows.
      */

Modules/FDEM1D/include/DipoleSource.h

 
     // ==========================================================================
     //        Class:  DipoleSource
+    /// \ingroup  FDEM1D
     /// \brief    Dipole sources form the backbone of Lemma.
     /// \details  More complex sources are constructed from a superposition of
     ///           dipoles.

Modules/FDEM1D/include/EMEarth1D.h

 
     // =======================================================================
     //        Class:  EmEarth1D
-    /// \brief  Implimentation of 1D EM solution.
+    /// \ingroup  FDEM1D
+    /// \brief    Implimentation of 1D EM solution.
     /// \details  We've done a lot of different things.
     // =======================================================================
     class EMEarth1D : public LemmaObject {

Modules/FDEM1D/include/FHTAnderson801.h

 
 // ==========================================================================
 //        Class:  FHTAnderson801
-/** \brief   Computes the Hankel transform of orders 0 and 1 using lagged
+/** \ingroup FDEM1D
+    \brief   Computes the Hankel transform of orders 0 and 1 using lagged
              and related convolutions.
     \details A rewrite of work by Anderson who wrote a FORTRAN program
              that he released while working at the USGS:

Modules/FDEM1D/include/FHTKey101.h

 namespace Lemma {
 
     /**
+      \ingroup FDEM1D
       \brief   Impliments the fast Hankel transform as outlines by Key 2011
-      \details This filter uses 51, 101, or 201 filter points and supports both lagged and related
+      \details This filter uses 101 filter points and supports both lagged and related
                 kernel arguments. This algorithm is a port of code carrying the following copyright and
                 restriction:
                 %------------------------------------------------------------------%

Modules/FDEM1D/include/FHTKey201.h

 namespace Lemma {
 
     /**
+      \ingroup FDEM1D
       \brief   Impliments the fast Hankel transform as outlines by Key 2011
       \details This filter uses 51, 101, or 201 filter points and supports both lagged and related
                 kernel arguments. This algorithm is a port of code carrying the following copyright and

Modules/FDEM1D/include/FHTKey51.h

 namespace Lemma {
 
     /**
+      \ingroup FDEM1D
       \brief   Impliments the fast Hankel transform as outlines by Key 2011
       \details This filter uses 51, 101, or 201 filter points and supports both lagged and related
                 kernel arguments. This algorithm is a port of code carrying the following copyright and

Modules/FDEM1D/include/FieldPoints.h

     // =======================================================================
     //        Class:  FieldPoints
     /**
-     *  \brief  Points in the subsurface where 1D EM calculations are made
+     *  \ingroup FEM1D
+     *  \brief   Points in the subsurface where 1D EM calculations are made
      *  \details These are the points where Hankel transform calculations are
      *           made.
-     *  \note In previous versions of Lemma, this class was called ReceiverPoints,
-     *        the functionality remains roughly the same, but the name is more
-     *        appropriate.
+     *  \note    In previous versions of Lemma, this class was called ReceiverPoints,
+     *           the functionality remains roughly the same, but the name is more
+     *           appropriate.
      */
     // =======================================================================
     class FieldPoints : public LemmaObject {

Modules/FDEM1D/include/GQChave.h

 
 	// =======================================================================
 	//        Class:  GQChave
-	/// \brief  Calculates hankel transform using gaussian quadrature.
+    /// \ingroup  FDEM1D
+	/// \brief    Calculates hankel transform using gaussian quadrature.
 	/// \details  Accurate but slow, this is a port of Alan Chave's public domain
     /// fortran code
 	// =======================================================================

Modules/FDEM1D/include/GroundedElectricDipole.h

 namespace Lemma {
 
     /**
+      \ingroup FDEM1D
       \brief   Grounded electric dipole
       \details Used to model an idealised grounded electrid dipole of arbitrary
                polarisation.

Modules/FDEM1D/include/HankelTransform.h

 
         // ===================================================================
         //        Class:  HankelTransform
+        /// \ingroup FDEM1D
         /// \brief   Abstract class for hankel transforms
         /// \details
         // ===================================================================

Modules/FDEM1D/include/KernelEM1DBase.h

     //  Class:  KernelEM1DBase
     /**
       @class
+      \ingroup FDEM1D
       \brief   Pure virtual base class of KernelEm1D
       \details Defines interface for HankelTransform classes
      */

Modules/FDEM1D/include/KernelEM1DManager.h

     //  Class:  KernelEM1DManager
     /**
       @class
-      \brief
-      \details
+      \ingroup FDEM1D
+      \brief   Keeps track of Kernels for EM1D
+      \details This class keeps track of the various types of kernel terms
+               which can be shared between permutations of sources. Care is
+               taken to avoid duplicate calculations
      */
     // ===================================================================
     class KernelEM1DManager : public LemmaObject {

Modules/FDEM1D/include/KernelEM1DReflBase.h

     //  Class:  KernelEM1DReflBase
     /**
       @class
+      \ingroup FDEM1D
       \brief   Abstract class defining EM1DRefl class.
       \details Derived classes are template specialized for optimal performance.
      */

Modules/FDEM1D/include/KernelEM1DReflSpec.h

     //  Class:  KernelEM1DReflSpec
     /**
       @class
+      \ingroup FDEM1D
       \brief   Specialized version of KernelEM1DReflBase
       \details Through use of template specialisations, this KernelEm1D
                class delivers much better performance. This class is internal

Modules/FDEM1D/include/KernelEM1DSpec.h

     //  Class:  KernelEM1DSpec
     /**
       @class
+      \ingroup FDEM1D
       \brief   Optimized version of KernelEm1D
       \details Through use of template specialisations, this KernelEm1D
                class delivers much better performance.

Modules/FDEM1D/include/LayeredEarthEMReader.h

 namespace Lemma {
 
     /**
+      \ingroup FDEM1D
       \brief Reads ASCII representation of LayeredEarth, similiar to UBC format.
       \details Largely superceded by YAML serialisation, this class remains for legacy purposes.
      */

Modules/FDEM1D/include/MagneticDipole.h

 
 /**
   @class
+  \ingroup FDEM1D
   \brief   Magnetic Dipole
   \details Used to model an idealised magnetic dipole of arbitrary
            polarisation.

Modules/FDEM1D/include/PolygonalWireAntenna.h

 
     // ===================================================================
     //        Class:  PolygonalWireAntenna
+    /// \ingroup FDEM1D
     /// \brief   Class representing polygonal wire antennae.
     /// \details For EM calculations, dipoles representing this loop are
     ///    created dynamically, depending on receiver location.

Modules/FDEM1D/include/QWEKey.h

     enum sZeroType{J0, J1, NPI};
 
     /**
-      \brief  Port of Key's quadrature with extrapolation Hankel transform algorithm.
+      \ingroup FDEM1D
+      \brief   Port of Key's quadrature with extrapolation Hankel transform algorithm.
       \details Details of the algorithm can be found in Key2011. This code is a port
                of the published algorithm, which contains the following notice:
         %------------------------------------------------------------------%

Modules/FDEM1D/include/UngroundedElectricDipole.h

 namespace Lemma {
 
     /**
-      \brief  Ungrounded electric dipole
+      \ingroup FDEM1D
+      \brief   Ungrounded electric dipole
       \details Used to model an idealised ungrounded electric dipole. Used primarily in integrating
                 around current sources.
      */

Modules/FDEM1D/include/costransintegrationkernel.h

     //  Class:  CosTransIntegrationKernel
     /**
       @class
+      \ingroup  FDEM1D
       \brief    Integration kernel for testing cosine transform.
       \details  Evaluates cosine at the argument, using lagged convolution.
                 all of these kernels have exact solutions.

Modules/LemmaCore/CMakeLists.txt

 	add_dependencies(lemmacore MATIO)
 endif()
 
+target_link_libraries (lemmacore Eigen3::Eigen)
+target_link_libraries (lemmacore ${YAML_CPP_LIBRARIES}) 
+
 # Linking
 if ( LEMMA_VTK6_SUPPORT OR LEMMA_VTK7_SUPPORT OR LEMMA_VTK8_SUPPORT ) 
 	target_link_libraries(lemmacore ${VTK_LIBRARIES})
 
 # find_package(yaml-cpp) does not seem to properly define library names...
 # a better solution than this is welcome 
-#target_link_libraries(lemmacore ${YAML_CPP_LIBRARIES}) 
+
 #if (WIN32)
 #	target_link_libraries(lemmacore "libyaml-cppmdd") 
 #else()

Modules/LemmaCore/include/lemma.h

   @version  $Id: lemma.h 203 2015-01-09 21:19:04Z tirons $
  **/
 
+//  \image html lemma.png
 /** \mainpage Lemma is an ElectroMagnetics Modelling API
-    \image html lemma.png
 
     \authors Trevor Irons and M. Andrew Kass and others
 
-    Lemma is a recursive acronym that stands for <B>L</B>emma is an
-    <B>E</B>lectro<B>M</B>agnetics <B>M</B>odelling <B>A</B>PI.
-    Lemma is a cross-platform library delivering an expressive API that
-    can be used to easily create versatile programs.
-    We are building a powerful, flexible, expresive framework that allows
-    for the straightforward creation of geophysical EM applications.
-    Lemma is not itself a program, instead it is a collection of building
-    blocks to make applications. We chose this name because:
+    Originally Lemma was intended as a recursive acronym standing for
+    <B>L</B>emma is an <B>E</B>lectro<B>M</B>agnetics <B>M</B>odelling <B>A</B>PI.
+    As the breadth of the project has expanded, the name has remained
+    appropriate in a more liteal sense. Lemma is a flexible cross-platform
+    library delivering an expressive API that can be used to easily create
+    versatile programs. Lemma is not itself a program, instead it is a
+    collection of building blocks to make applications. We retain this name because:
 
     - In mathematics a Lemma is a proven proposition which is used as a
     stepping stone to a larger result rather than as a statement in-and-of
     We feel that this is a partucularily approprate name, as Lemma's
     API can be leveraged create powerful applications such as forward
     modelling and inverting frequency and time-domain
-    surveys of arbitrary survey design, SNMR surveys, CSAMT and more.
+    surveys of arbitrary survey design, sNMR surveys, CSAMT and more.
 
     \section Motivation
     Why another Geophysical EM project? For starters, there
 
     The 1D EM solver was derived (but updated heavily) from a Fortran
     programme written by Ki Ha Lee in 1984. We have communicated with Ki Ha,
-    and he assured us that this code is in the public domian.
+    and he assured us that this code is in the public domain.
 
     A Gaussian quadrature hankel transform originally written by Alan Chave was
     ported to C++. This code is in the public domain, and the source code was