DCPROGS · remislp · Jan 16, 2017 · Jan 16, 2017 · Jan 17, 2017 · Jan 17, 2017
diff --git a/.travis.yml b/.travis.yml
@@ -37,7 +37,7 @@ addons:
 
 env:
   global:
-    - DOLONGDOUBLE="-DDCPROGS_LONG_DOUBLE=OFF"
+    - DOLONGDOUBLE="-DHJCFIT_LONG_DOUBLE=OFF"
     - UPLOADDOCS=false
 matrix:
   include:
@@ -48,7 +48,7 @@ matrix:
       env: UPLOADDOCS=true
     - os: linux
       python: 3.5
-      env: DOLONGDOUBLE="-DDCPROGS_LONG_DOUBLE=ON"
+      env: DOLONGDOUBLE="-DHJCFIT_LONG_DOUBLE=ON"
     - os: osx
       osx_image: xcode7.3
       python: 2.7

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,5 +1,5 @@
 ########################
-#   DCProgs computes missed-events likelihood as described in
+#   HJCFIT computes missed-events likelihood as described in
 #   Hawkes, Jalali and Colquhoun (1990, 1992)
 #
 #   Copyright (C) 2013  University College London
@@ -35,7 +35,7 @@ option(pythonBindings "Enable python bindings."                 on)
 option(compileDocs    "Compile c++11 documentation examples."   on)
 option(openmp         "Enable OpenMP parallelization."          on)
 option(executenotebooks "Execute example Jupyter notebooks."    on)
-CMAKE_DEPENDENT_OPTION(DCPROGS_USE_MPFR "Enable fallback to MPFR Multi precision" ON "UNIX" OFF)
+CMAKE_DEPENDENT_OPTION(HJCFIT_USE_MPFR "Enable fallback to MPFR Multi precision" ON "UNIX" OFF)
 
 set(JUPYTER_KERNEL "" CACHE STRING "Jupyter kernel to run notebooks with defaults to python2 or python3 depending on python version")
 # Provides backwards compatibility and prevents MACOS_RPATH warning
@@ -132,28 +132,28 @@ if(NOT HAS_CXX11_NOEXCEPT)
   set(noexcept TRUE)
 endif()
 
-if(NOT DCPROGS_LONG_DOUBLE)
-  set(DCPROGS_LONG_DOUBLE False CACHE BOOL
+if(NOT HJCFIT_LONG_DOUBLE)
+  set(HJCFIT_LONG_DOUBLE False CACHE BOOL
       "If True, will use long doubles rather than simple doubles.")
-endif(NOT DCPROGS_LONG_DOUBLE)
+endif(NOT HJCFIT_LONG_DOUBLE)
 
-if(NOT DCPROGS_USE_MPFR)
-  set(DCPROGS_USE_MPFR False CACHE BOOL
+if(NOT HJCFIT_USE_MPFR)
+  set(HJCFIT_USE_MPFR False CACHE BOOL
   "If True, will use MPFR arbitrary precision floats as fall back if regular double calculations fail.")
-endif(NOT DCPROGS_USE_MPFR)
+endif(NOT HJCFIT_USE_MPFR)
 
-if(DCPROGS_USE_MPFR)
+if(HJCFIT_USE_MPFR)
   find_or_add_hunter_package(GMP)
   find_or_add_hunter_package(MPFR)
   include_directories(${PROJECT_SOURCE_DIR}/mpfr)
-endif(DCPROGS_USE_MPFR)
+endif(HJCFIT_USE_MPFR)
 configure_file (
- "${PROJECT_SOURCE_DIR}/DCProgsConfig.h.in"
- "${PROJECT_BINARY_DIR}/DCProgsConfig.h"
+ "${PROJECT_SOURCE_DIR}/HJCFITConfig.h.in"
+ "${PROJECT_BINARY_DIR}/HJCFITConfig.h"
 )
 
-# Save all DCPROGS headers in the same place in Windows
-install(FILES ${PROJECT_BINARY_DIR}/DCProgsConfig.h DESTINATION include/dcprogs)
+# Save all HJCFIT headers in the same place in Windows
+install(FILES ${PROJECT_BINARY_DIR}/HJCFITConfig.h DESTINATION include/HJCFIT)
 
 include(${CMAKE_SCRIPTS}/documentation.cmake)
 

diff --git a/DCProgsConfig.h.in → HJCFITConfig.h.in b/DCProgsConfig.h.in → HJCFITConfig.h.in
@@ -1,5 +1,5 @@
 /***********************
-    DCProgs computes missed-events likelihood as described in
+    HJCFIT computes missed-events likelihood as described in
     Hawkes, Jalali and Colquhoun (1990, 1992)
 
     Copyright (C) 2013  University College London
@@ -18,17 +18,17 @@
     along with this program.  If not, see <http://www.gnu.org/licenses/>.
 ************************/
 
-#ifndef DCPROGS_CONFIG_H
-#define DCPROGS_CONFIG_H
+#ifndef HJCFIT_CONFIG_H
+#define HJCFIT_CONFIG_H
 
 #include <iso646.h>
 #include <vector>
 #include <limits>
 #include <type_traits>
 #include <Eigen/Dense>
-#cmakedefine DCPROGS_USE_MPFR
+#cmakedefine HJCFIT_USE_MPFR
 
-#ifdef DCPROGS_USE_MPFR
+#ifdef HJCFIT_USE_MPFR
 #  include <unsupported/Eigen/MPRealSupport>
 #endif
 
@@ -47,26 +47,26 @@
 #cmakedefine HAS_CXX11_CONSTRUCTOR_DELEGATE
 
 #ifdef HAS_CXX11_CONSTEXPR
-# define DCPROGS_INIT_CONSTEXPR(TYPEANDNAME, VALUE) constexpr static TYPEANDNAME = VALUE
-# define DCPROGS_DECL_CONSTEXPR(TYPEANDNAME, VALUE) constexpr TYPEANDNAME
+# define HJCFIT_INIT_CONSTEXPR(TYPEANDNAME, VALUE) constexpr static TYPEANDNAME = VALUE
+# define HJCFIT_DECL_CONSTEXPR(TYPEANDNAME, VALUE) constexpr TYPEANDNAME
 #else 
-# define DCPROGS_INIT_CONSTEXPR(TYPEANDNAME, VALUE) const static TYPEANDNAME
-# define DCPROGS_DECL_CONSTEXPR(TYPEANDNAME, VALUE) const TYPEANDNAME = VALUE
+# define HJCFIT_INIT_CONSTEXPR(TYPEANDNAME, VALUE) const static TYPEANDNAME
+# define HJCFIT_DECL_CONSTEXPR(TYPEANDNAME, VALUE) const TYPEANDNAME = VALUE
 #endif
 
 // one should alway known when one is working on crapware
 #cmakedefine MSVC
 
 
-#if defined(MSWINDOBE) && defined(DCPROGS_LIKELIHOOD_DLLEXPORT)
+#if defined(MSWINDOBE) && defined(HJCFIT_LIKELIHOOD_DLLEXPORT)
 # undef MSWINDOBE
 # define MSWINDOBE __declspec(dllexport)
 #endif
 #ifndef MSWINDOBE 
 # define MSWINDOBE
 #endif
 
-#cmakedefine DCPROGS_PYTHON_BINDINGS
+#cmakedefine HJCFIT_PYTHON_BINDINGS
 #cmakedefine NUMPY_NPY_LONG_DOUBLE
 #cmakedefine NUMPY_NPY_BOOL
 #cmakedefine NUMPY_NPY_ARRAY
@@ -81,48 +81,48 @@
 #cmakedefine CXX_HAS_FLOAT_H_ISNAN
 #ifdef CXX_HAS_STD_ISNAN
 #  include <cmath>
-#  define DCPROGS_ISNAN(X) std::isnan(X)
+#  define HJCFIT_ISNAN(X) std::isnan(X)
 #elif defined(CXX_HAS_ISNAN)
 #  include <math.h>
-#  define DCPROGS_ISNAN(X) ::isnan(X)
+#  define HJCFIT_ISNAN(X) ::isnan(X)
 #elif defined CXX_HAS___ISNAN
 #  include <math.h>
-#  define DCPROGS_ISNAN(X) __isnan(X)
+#  define HJCFIT_ISNAN(X) __isnan(X)
 #elif defined(CXX_HAS_FLOAT_H_ISNAN)
 #  include <float.h>
-#  define DCPROGS_ISNAN(X) _isnan(X)
+#  define HJCFIT_ISNAN(X) _isnan(X)
 #else
 #  error no macro defined for isnan
 #endif
 
-#cmakedefine DCPROGS_LONG_DOUBLE
-#cmakedefine DCPROGS_PYTHON3
+#cmakedefine HJCFIT_LONG_DOUBLE
+#cmakedefine HJCFIT_PYTHON3
 
-#define DCPROGS_STACK_MATRIX_MAX 50
+#define HJCFIT_STACK_MATRIX_MAX 50
 
-namespace DCProgs {
-# ifdef DCPROGS_LONG_DOUBLE
-    //! Types of reals across DCProgs.
+namespace HJCFIT {
+# ifdef HJCFIT_LONG_DOUBLE
+    //! Types of reals across HJCFIT.
     typedef long double t_real;
 # else
-    //! Types of reals across DCProgs.
+    //! Types of reals across HJCFIT.
     typedef double t_real;
 # endif
   //! Complex real type
   typedef std::complex<t_real> t_complex;
-  //! Types of integers across DCProgs.
+  //! Types of integers across HJCFIT.
   typedef EIGEN_DEFAULT_DENSE_INDEX_TYPE t_int;
-  //! Types of unsigned integers across DCProgs.
+  //! Types of unsigned integers across HJCFIT.
   typedef std::make_unsigned<t_int>::type t_uint;
-  //! Types of real matrices across DCProgs.
+  //! Types of real matrices across HJCFIT.
   typedef Eigen::Matrix<t_real, ::Eigen::Dynamic, ::Eigen::Dynamic, 0, ::Eigen::Dynamic, ::Eigen::Dynamic> t_rmatrix;
-  //! Types of real matrices across DCProgs guaranteed to be allocated on the stack. Max size DCPROGS_STACK_MATRIX_MAX by DCPROGS_STACK_MATRIX_MAX
-  typedef Eigen::Matrix<t_real, ::Eigen::Dynamic, ::Eigen::Dynamic, 0, DCPROGS_STACK_MATRIX_MAX, DCPROGS_STACK_MATRIX_MAX> t_stack_rmatrix;
-  //! Types of boolean matrices across DCProgs.
+  //! Types of real matrices across HJCFIT guaranteed to be allocated on the stack. Max size HJCFIT_STACK_MATRIX_MAX by HJCFIT_STACK_MATRIX_MAX
+  typedef Eigen::Matrix<t_real, ::Eigen::Dynamic, ::Eigen::Dynamic, 0, HJCFIT_STACK_MATRIX_MAX, HJCFIT_STACK_MATRIX_MAX> t_stack_rmatrix;
+  //! Types of boolean matrices across HJCFIT.
   typedef Eigen::Matrix<bool, ::Eigen::Dynamic, ::Eigen::Dynamic, 0, ::Eigen::Dynamic, ::Eigen::Dynamic> t_bmatrix;
-  //! Types of initial state vectors across DCProgs.
+  //! Types of initial state vectors across HJCFIT.
   typedef Eigen::Matrix<t_real, 1, ::Eigen::Dynamic, ::Eigen::RowMajor, 1, ::Eigen::Dynamic> t_initvec;
-  //! Types of final state vectors across DCProgs.
+  //! Types of final state vectors across HJCFIT.
   typedef Eigen::Matrix<t_real, ::Eigen::Dynamic, 1, 0, ::Eigen::Dynamic, 1> t_rvector;
   //! Type of complex matrices.
   typedef Eigen::Matrix<t_complex, ::Eigen::Dynamic, ::Eigen::Dynamic, 0, ::Eigen::Dynamic, ::Eigen::Dynamic> t_cmatrix;
@@ -134,14 +134,14 @@ namespace DCProgs {
   //! Type holding the bursts.
   typedef std::vector<t_Burst> t_Bursts;
 
-# ifdef DCPROGS_USE_MPFR
-    //! Types of multi-precision float across DCProgs.
+# ifdef HJCFIT_USE_MPFR
+    //! Types of multi-precision float across HJCFIT.
     typedef mpfr::mpreal t_mpfr_real;
-    //! Types of multi-precision complex across DCProgs.
+    //! Types of multi-precision complex across HJCFIT.
     typedef std::complex<t_mpfr_real> t_mpfr_complex;
-    //! Types of multi-precision complex vector across DCProgs.
+    //! Types of multi-precision complex vector across HJCFIT.
     typedef Eigen::Matrix<t_mpfr_complex, ::Eigen::Dynamic, 1, 0, ::Eigen::Dynamic, 1> t_mpfr_cvector;
-    //! Types of multi-precision real matrix across DCProgs.
+    //! Types of multi-precision real matrix across HJCFIT.
     typedef Eigen::Matrix<t_mpfr_real, ::Eigen::Dynamic, ::Eigen::Dynamic, 0, ::Eigen::Dynamic, ::Eigen::Dynamic> t_mpfr_rmatrix;
 
 # endif
@@ -158,17 +158,17 @@ namespace DCProgs {
     bool eigen_nan(Eigen::DenseBase<T> const &_matrix) {
       for(typename Eigen::DenseBase<T>::Index i(0); i < _matrix.rows(); ++i)
         for(typename Eigen::ArrayBase<T>::Index j(0); j < _matrix.cols(); ++j)
-           if(DCPROGS_ISNAN(_matrix(i, j))) return true;
+           if(HJCFIT_ISNAN(_matrix(i, j))) return true;
       return false;
     }
 
   // Check that quiet nan exists. Otherwise fails to compile here and now.
   static_assert(std::numeric_limits<t_real>::has_quiet_NaN == true,
-                "Quiet NaN is not defined for the reals used by DCProgs.");
+                "Quiet NaN is not defined for the reals used by HJCFIT.");
 
   //! The quiet NaN value
   t_real static const quiet_nan = std::numeric_limits<t_real>::quiet_NaN();
 
-  t_uint static const dcprogs_stack_matrix = DCPROGS_STACK_MATRIX_MAX;
+  t_uint static const HJCFIT_stack_matrix = HJCFIT_STACK_MATRIX_MAX;
 }
 #endif
diff --git a/LaunchNotebook.bat b/LaunchNotebook.bat
@@ -0,0 +1 @@
+jupyter notebook
diff --git a/cmake_modules/AllPythonBindings.cmake b/cmake_modules/AllPythonBindings.cmake
@@ -72,7 +72,7 @@ if(MSYS)
   unset(NEED_CMATH_INCLUDE)
 endif(MSYS)
 
-set(DCPROGS_PYTHON_BINDINGS True)
+set(HJCFIT_PYTHON_BINDINGS True)
 
 if(tests)
   if(NOT DEFINED TEST_INSTALL_DIRECTORY)
@@ -142,5 +142,5 @@ else()
 endif(WIN32)
 
 if(NOT PYTHON_VERSION VERSION_LESS "3.0.0")
-  set(DCPROGS_PYTHON3 TRUE)
+  set(HJCFIT_PYTHON3 TRUE)
 endif(NOT PYTHON_VERSION VERSION_LESS "3.0.0")
diff --git a/cmake_modules/documentation.cmake b/cmake_modules/documentation.cmake
@@ -16,11 +16,11 @@ if(SPHINX_FOUND)
   else()
     set(SPHINX_EXTENSIONS "'sphinxcontrib.bibtex'")
   endif(DOXYGEN_FOUND)
-  if(DCPROGS_USE_MPFR)
-    set(SPHINX_DCPROGS_USE_MPFR "True")
+  if(HJCFIT_USE_MPFR)
+    set(SPHINX_HJCFIT_USE_MPFR "True")
   else()
-    set(SPHINX_DCPROGS_USE_MPFR "False")
-  endif(DCPROGS_USE_MPFR)
+    set(SPHINX_HJCFIT_USE_MPFR "False")
+  endif(HJCFIT_USE_MPFR)
 endif(SPHINX_FOUND)
 
 if (DOXYGEN_FOUND)

diff --git a/data/CMakeLists.txt b/data/CMakeLists.txt
@@ -1,5 +1,5 @@
 ########################
-#   DCProgs computes missed-events likelihood as described in
+#   HJCFIT computes missed-events likelihood as described in
 #   Hawkes, Jalali and Colquhoun (1990, 1992)
 #
 #   Copyright (C) 2013  University College London
@@ -17,7 +17,7 @@
 
 if(pythonBindings)
 
-  install(FILES CH82.scn CCO.scn CO.scn DESTINATION ${PYINSTALL_DIRECTORY}/dcprogs/data)
+  install(FILES CH82.scn CCO.scn CO.scn DESTINATION ${PYINSTALL_DIRECTORY}/hjcfit/data)
 
 endif(pythonBindings)
 
diff --git a/documentation/CMakeLists.txt b/documentation/CMakeLists.txt
@@ -1,5 +1,5 @@
 ########################
-#   DCProgs computes missed-events likelihood as described in
+#   HJCFIT computes missed-events likelihood as described in
 #   Hawkes, Jalali and Colquhoun (1990, 1992)
 #
 #   Copyright (C) 2013  University College London

diff --git a/documentation/code/approx_survivor.cc b/documentation/code/approx_survivor.cc
@@ -6,31 +6,31 @@
 int main() {
 
   // Define parameters.
-  DCProgs::t_rmatrix matrix(5 ,5);
+  HJCFIT::t_rmatrix matrix(5 ,5);
   matrix << -3050,        50,  3000,      0,    0, 
             2./3., -1502./3.,     0,    500,    0,  
                15,         0, -2065,     50, 2000,  
                 0,     15000,  4000, -19000,    0,  
                 0,         0,    10,      0,  -10;
-  DCProgs::QMatrix qmatrix(matrix, /*nopen=*/2);
+  HJCFIT::QMatrix qmatrix(matrix, /*nopen=*/2);
 
-  DCProgs::ApproxSurvivor survivor(qmatrix, 1e-4);
+  HJCFIT::ApproxSurvivor survivor(qmatrix, 1e-4);
 
   std::cout << survivor << std::endl;
 
   std::cout << "AF values\n"
                "---------\n\n";
   std::cout << "  * at time t=" << 1e-4 <<":\n    "
-            << DCProgs::numpy_io(survivor.af(1e-4), "    ") << "\n"
+            << HJCFIT::numpy_io(survivor.af(1e-4), "    ") << "\n"
             << "  * at time t=" << 1.5e-4 <<":\n    " 
-            << DCProgs::numpy_io(survivor.af(1.5e-4), "    ") << "\n"
+            << HJCFIT::numpy_io(survivor.af(1.5e-4), "    ") << "\n"
             << "  * at time t=" << 2.0e-4 <<":\n    " 
-            << DCProgs::numpy_io(survivor.af(2.0e-4), "    ") << "\n"
+            << HJCFIT::numpy_io(survivor.af(2.0e-4), "    ") << "\n"
             << "  * at time t=" << 2.5e-4 <<":\n    "
-            << DCProgs::numpy_io(survivor.af(2.5e-4), "    ") << "\n\n";
+            << HJCFIT::numpy_io(survivor.af(2.5e-4), "    ") << "\n\n";
 
   std::cout << " * Exponents: ";
-  for(DCProgs::t_uint i(0); i < survivor.nb_af_components(); ++i) 
+  for(HJCFIT::t_uint i(0); i < survivor.nb_af_components(); ++i) 
     std::cout << std::get<1>(survivor.get_af_components(i)) << " ";
   std::cout << std::endl;
 

diff --git a/documentation/code/approx_survivor.py b/documentation/code/approx_survivor.py
@@ -1,4 +1,4 @@
-from dcprogs.likelihood import QMatrix, ApproxSurvivor
+from HJCFIT.likelihood import QMatrix, ApproxSurvivor
 
 # Define parameters.
 qmatrix = QMatrix([ [-3050,        50,  3000,      0,    0],