Merge pull request #2 from jchristopherson/Development

Development

Author: jchristopherson

.gitignore

@@ -35,7 +35,6 @@
 bin/
 lib/
 build/
-html/
 latex/
 
 
@@ -51,4 +50,4 @@ install_manifest.txt
 CTestTestfile.cmake
 
 # Misc Stuff
-c_cpp_properties.json
+c_cpp_properties.json

.travis.yml

@@ -7,10 +7,10 @@ before_install:
   - sudo apt-get update -qq
 
 install:
-  - sudo apt-get install -qq gfortran-5
-  - sudo update-alternatives --install /usr/bin/gfortran gfortran /usr/bin/gfortran-5 90
-  
-before_script:  
+  - sudo apt-get install -qq gfortran-7
+  - sudo update-alternatives --install /usr/bin/gfortran gfortran /usr/bin/gfortran-7 90
+
+before_script:
     - mkdir build
     - cd build
     - cmake ..

CMakeLists.txt

@@ -1,53 +1,107 @@
 # Master CMAKE Build Script
-cmake_minimum_required(VERSION 3.0)
+cmake_minimum_required(VERSION 3.7)
 project(curvefit C CXX Fortran)
 
 # Define version information
-set(curvefit_VERSION_MAJOR 1)
-set(curvefit_VERSION_MINOR 1)
-set(curvefit_VERSION_PATCH 0)
+set(CURVEFIT_MAJOR_VERSION 1)
+set(CURVEFIT_MINOR_VERSION 1)
+set(CURVEFIT_PATCH_VERSION 0)
+set(CURVEFIT_VERSION ${CURVEFIT_MAJOR_VERSION}.${CURVEFIT_MINOR_VERSION}.${CURVEFIT_PATCH_VERSION})
+
+# Set a default build type if none was specified
+if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
+  message(STATUS "Setting build type to 'Release' as none was specified.")
+  set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build." FORCE)
+  # Set the possible values of build type for cmake-gui
+  set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release")
+endif()
+
+# By default, shared library
+option(BUILD_SHARED_LIBS "Build shared libraries" ON)
+
+# Locate Dependencies
+find_package(ferror 1.3.0)
+find_package(linalg 1.5.0)
+find_package(nonlin 1.3.0)
+
+# Define dependency directories
+set(NONLIN_DIRECTORY ${PROJECT_SOURCE_DIR}/src/external/nonlin)
+set(LINALG_DIRECTORY ${NONLIN_DIRECTORY}/src/external/linalg)
+set(FERROR_DIRECTORY ${LINALG_DIRECTORY}/src/external/ferror)
+
+# If FERROR is not installed on the system, build the default implementation
+if (${ferror_FOUND})
+    message(STATUS "An acceptable version of FERROR (v" ${ferror_VERSION} ") was found, and will be utilized.")
+    set(FERROR_LIBRARIES ferror)
+    get_target_property(ferror_LibLocation ferror LOCATION)
+endif()
+
+# If LINALG is not installed on the system, build the default implementation
+if (${linalg_FOUND})
+    message(STATUS "An acceptable version of LINALG (v" ${linalg_VERSION} ") was found, and will be utilized.")
+    set(LINALG_LIBRARIES linalg)
+    get_target_property(linalg_LibLocation linalg LOCATION)
+endif()
+
+# If NONLIN is not installed on the system, build the default implementation
+if (${nonlin_FOUND})
+    message(STATUS "An acceptable version of NONLIN (v" ${nonlin_VERSION} ") was found, and will be utilized.")
+    set(NONLIN_LIBRARIES nonlin)
+    get_target_property(nonlin_LibLocation nonlin LOCATION)
+else()
+    message(STATUS "NONLIN not found.  The default implementation will be used.")
+    add_subdirectory(${NONLIN_DIRECTORY})
+    set(nonlin_INCLUDE_DIRS ${NONLIN_DIRECTORY}/include)
+    set(NONLIN_LIBRARIES nonlin)
+    set(nonlin_LibLocation ${nonlin_BINARY_DIR})
+    include_directories(${LINALG_DIRECTORY}/include)
+    include_directories(${FERROR_DIRECTORY}/include)
+endif()
+
+# Include the dependency module files
+include_directories(${nonlin_INCLUDE_DIRS} ${linalg_INCLUDE_DIRS} ${ferror_INCLUDE_DIRS})
+
+# Export all symbols on Windows when building shared libraries
+SET(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS TRUE)
+
+# Locate the module files
+set(CMAKE_Fortran_MODULE_DIRECTORY ${PROJECT_SOURCE_DIR}/include)
 
 # Define output directories, if undefined
 if (NOT CMAKE_LIBRARY_OUTPUT_DIRECTORY)
-  message(STATUS "Library output directories undefined.  Using default directories.")
+  message(STATUS "CURVEFIT library output directories undefined.  Using default directories.")
   if (CMAKE_BUILD_TYPE MATCHES Debug)
     # Debug Build
     if (BUILD_SHARED_LIBS)
       set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${PROJECT_SOURCE_DIR}/bin/Debug)
       set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${PROJECT_SOURCE_DIR}/bin/Debug)
       set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${PROJECT_SOURCE_DIR}/bin/Debug)
-      set(CMAKE_Fortran_MODULE_DIRECTORY ${PROJECT_SOURCE_DIR}/bin/Debug/mod)
     else()
       set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${PROJECT_SOURCE_DIR}/lib/Debug)
       set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${PROJECT_SOURCE_DIR}/lib/Debug)
       set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${PROJECT_SOURCE_DIR}/lib/Debug)
-      set(CMAKE_Fortran_MODULE_DIRECTORY ${PROJECT_SOURCE_DIR}/lib/Debug/mod)
     endif ()
   elseif (CMAKE_BUILD_TYPE MATCHES Release)
     # Release Build
     if (BUILD_SHARED_LIBS)
       set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${PROJECT_SOURCE_DIR}/bin/Release)
       set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${PROJECT_SOURCE_DIR}/bin/Release)
       set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${PROJECT_SOURCE_DIR}/bin/Release)
-      set(CMAKE_Fortran_MODULE_DIRECTORY ${PROJECT_SOURCE_DIR}/bin/Release/mod)
     else()
       set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${PROJECT_SOURCE_DIR}/lib/Release)
       set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${PROJECT_SOURCE_DIR}/lib/Release)
       set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${PROJECT_SOURCE_DIR}/lib/Release)
-      set(CMAKE_Fortran_MODULE_DIRECTORY ${PROJECT_SOURCE_DIR}/lib/Release/mod)
     endif ()
   else ()
     # Default Condition
     if (BUILD_SHARED_LIBS)
       set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${PROJECT_SOURCE_DIR}/bin/Debug)
       set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${PROJECT_SOURCE_DIR}/bin/Debug)
       set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${PROJECT_SOURCE_DIR}/bin/Debug)
-      set(CMAKE_Fortran_MODULE_DIRECTORY ${PROJECT_SOURCE_DIR}/bin/Debug/mod)
     else()
       set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${PROJECT_SOURCE_DIR}/lib/Debug)
       set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${PROJECT_SOURCE_DIR}/lib/Debug)
       set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${PROJECT_SOURCE_DIR}/lib/Debug)
-      set(CMAKE_Fortran_MODULE_DIRECTORY ${PROJECT_SOURCE_DIR}/lib/Debug/mod)
     endif ()
   endif ()
 endif ()
@@ -71,18 +125,6 @@ else (Fortran_COMPILER_NAME MATCHES "gfortran.*")
   set (CMAKE_Fortran_FLAGS_DEBUG   "-O0 -g -Wall")
 endif (Fortran_COMPILER_NAME MATCHES "gfortran.*")
 
-# Define necessary CMake variables, and define the dependency.
-set(ExternalProjectCMakeArgs
-  -DCMAKE_ARCHIVE_OUTPUT_DIRECTORY=${CMAKE_ARCHIVE_OUTPUT_DIRECTORY}
-  -DCMAKE_LIBRARY_OUTPUT_DIRECTORY=${CMAKE_LIBRARY_OUTPUT_DIRECTORY}
-  -DCMAKE_RUNTIME_OUTPUT_DIRECTORY=${CMAKE_RUNTIME_OUTPUT_DIRECTORY}
-  -DCMAKE_Fortran_MODULE_DIRECTORY=${CMAKE_Fortran_MODULE_DIRECTORY}
-  -DCMAKE_INSTALL_PREFIX=${CMAKE_SOURCE_DIR}/external
-  -DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER}
-  -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
-  -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
-  -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE})
-
 # Locate the source directory
 add_subdirectory(src)
 
@@ -94,71 +136,18 @@ if (BUILD_CURVEFIT_EXAMPLES)
   # Inform the user we're building the examples
   message(STATUS "Building CURVEFIT examples.")
 
-  # Interpolation Example
-  add_executable(curvefit_interp_example examples/curvefit_interp_example.f90)
-  target_link_libraries(curvefit_interp_example curvefit)
-
-  # LOWESS Example
-  add_executable(curvefit_lowess_example examples/curvefit_lowess_example.f90)
-  target_link_libraries(curvefit_lowess_example curvefit)
-
-  # Nonlinear Regression Example
-  add_executable(curvefit_nlreg_example examples/curvefit_nlreg_example.f90)
-  target_link_libraries(curvefit_nlreg_example curvefit)
-
-  # Calibration Example
-  add_executable(curvefit_cal_example examples/curvefit_cal_example.f90)
-  target_link_libraries(curvefit_cal_example curvefit)
-
-# --------------------
-  include_directories(${PROJECT_SOURCE_DIR}/include
-    ${PROJECT_SOURCE_DIR}/src/external/nonlin/include
-    ${PROJECT_SOURCE_DIR}/src/external/nonlin/src/external/linalg/include
-    ${PROJECT_SOURCE_DIR}/src/external/nonlin/src/external/linalg/src/external/ferror/include)
-
-  # Linear Interpolation Example
-  add_executable(curvefit_c_interp_example examples/curvefit_c_interp_example.c)
-  target_link_libraries(curvefit_c_interp_example curvefit)
-
-  # LOWESS Example
-  add_executable(curvefit_c_lowess_example examples/curvefit_c_lowess_example.c)
-  target_link_libraries(curvefit_c_lowess_example curvefit m)
-
-  # Nonlinear Regression Example
-  add_executable(curvefit_c_nlreg_example examples/curvefit_c_nlreg_example.c)
-  target_link_libraries(curvefit_c_nlreg_example curvefit)
+  # Build the examples
+  add_subdirectory(examples)
 endif()
 
 # ------------------------------------------------------------------------------
 # TESTS
 # ------------------------------------------------------------------------------
-option(BUILD_CURVEFIT_TESTS "Build CURVEFIT tests?" ON)
+option(BUILD_CURVEFIT_TESTS "Build CURVEFIT tests?" OFF)
 if (BUILD_CURVEFIT_TESTS)
-  set(curvefit_test_sources tests/curvefit_test.f90 
-    tests/curvefit_test_interp.f90 tests/curvefit_test_statistics.f90
-    src/external/nonlin/src/external/linalg/tests/test_core.f90
-    tests/curvefit_test_regression.f90 tests/curvefit_test_calibration.f90)
-  add_executable(curvefit_test ${curvefit_test_sources})
-  target_link_libraries(curvefit_test curvefit)
-  add_custom_command(OUTPUT curvefit_tests DEPENDS ${curvefit_test_sources}
-    COMMAND curvefit_test)
-  add_custom_target(run_curvefit_tests ALL DEPENDS curvefit_tests)
-endif()
+    # Inform the user we're building the tests
+    message(STATUS "Building CURVEFIT tests.")
 
-# C Test
-option(BUILD_CURVEFIT_C_TESTS "Build CURVEFIT C API tests?" ON)
-if (BUILD_CURVEFIT_C_TESTS)
-  include_directories(${PROJECT_SOURCE_DIR}/include
-    ${PROJECT_SOURCE_DIR}/src/external/nonlin/include
-    ${PROJECT_SOURCE_DIR}/src/external/nonlin/src/external/linalg/include
-    ${PROJECT_SOURCE_DIR}/src/external/nonlin/src/external/linalg/src/external/ferror/include
-    ${PROJECT_SOURCE_DIR}/src/external/nonlin/src/external/linalg/tests)
-  set(curvefit_c_test_sources tests/curvefit_c_test.c
-    ${PROJECT_SOURCE_DIR}/src/external/nonlin/src/external/linalg/tests/c_test_core.c)
-  add_executable(curvefit_c_test ${curvefit_c_test_sources})
-  target_link_libraries(curvefit_c_test curvefit m)
-  add_custom_command(OUTPUT curvefit_c_tests_cmd 
-    DEPENDS ${curvefit_c_test_sources}
-    COMMAND curvefit_c_test)
-  add_custom_target(run_curvefit_c_tests ALL DEPENDS curvefit_c_tests_cmd)
+    # Build the tests
+    add_subdirectory(tests)
 endif()

README.md

@@ -167,8 +167,8 @@ program example
     output = [0.0d0, 0.55983d0, 1.11975d0, 1.67982d0, 2.24005d0, &
         2.80039d0, 2.24023d0, 1.68021d0, 1.12026d0, 0.56021d0, 0.00006d0]
     applied_copy = applied
-    
-    ! Determine a suitable calibration gain (the least squares routine modifies 
+
+    ! Determine a suitable calibration gain (the least squares routine modifies
     ! applied; hence, the need for the copy)
     gain = linear_least_squares(output, applied_copy)
 
@@ -207,7 +207,7 @@ For visualization purposes, here is an error plot from the data in the above exa
 This library can be built using CMake.  For instructions on using CMake see [Running CMake](https://cmake.org/runningcmake/).
 
 ## Documentation
-Documentation can be found [here](doc/refman.pdf)
+Documentation can be found [here](http://htmlpreview.github.io/?https://github.com/jchristopherson/curvefit/blob/master/doc/html/index.html).
 
 ## External Libraries
 This library relies upon 3 other libraries.

curvefitConfig.cmake.in

@@ -0,0 +1 @@
+include("${CMAKE_CURRENT_LIST_DIR}/curvefitTargets.cmake")

doc/Doxyfile

@@ -1,4 +1,4 @@
-# Doxyfile 1.8.11
+# Doxyfile 1.8.13
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -303,6 +303,15 @@ EXTENSION_MAPPING      =
 
 MARKDOWN_SUPPORT       = YES
 
+# When the TOC_INCLUDE_HEADINGS tag is set to a non-zero value, all headings up
+# to that level are automatically included in the table of contents, even if
+# they do not have an id attribute.
+# Note: This feature currently applies only to Markdown headings.
+# Minimum value: 0, maximum value: 99, default value: 0.
+# This tag requires that the tag MARKDOWN_SUPPORT is set to YES.
+
+TOC_INCLUDE_HEADINGS   = 0
+
 # When enabled doxygen tries to link words that correspond to documented
 # classes, or namespaces to their corresponding documentation. Such a link can
 # be prevented in individual cases by putting a % sign in front of the word or
@@ -803,8 +812,8 @@ INPUT_ENCODING         = UTF-8
 # If left blank the following patterns are tested:*.c, *.cc, *.cxx, *.cpp,
 # *.c++, *.java, *.ii, *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h,
 # *.hh, *.hxx, *.hpp, *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc,
-# *.m, *.markdown, *.md, *.mm, *.dox, *.py, *.pyw, *.f90, *.f, *.for, *.tcl,
-# *.vhd, *.vhdl, *.ucf, *.qsf, *.as and *.js.
+# *.m, *.markdown, *.md, *.mm, *.dox, *.py, *.pyw, *.f90, *.f95, *.f03, *.f08,
+# *.f, *.for, *.tcl, *.vhd, *.vhdl, *.ucf and *.qsf.
 
 FILE_PATTERNS          = *.c \
                          *.cc \
@@ -916,7 +925,7 @@ EXAMPLE_RECURSIVE      = NO
 # that contain images that are to be included in the documentation (see the
 # \image command).
 
-IMAGE_PATH             = 
+IMAGE_PATH             = ../images
 
 # The INPUT_FILTER tag can be used to specify a program that doxygen should
 # invoke to filter for each input file. Doxygen will invoke the filter program
@@ -2204,7 +2213,7 @@ HIDE_UNDOC_RELATIONS   = YES
 # set to NO
 # The default value is: YES.
 
-HAVE_DOT               = YES
+HAVE_DOT               = NO
 
 # The DOT_NUM_THREADS specifies the number of dot invocations doxygen is allowed
 # to run in parallel. When set to 0 doxygen will base this on the number of
@@ -2413,6 +2422,11 @@ DIAFILE_DIRS           =
 
 PLANTUML_JAR_PATH      = 
 
+# When using plantuml, the PLANTUML_CFG_FILE tag can be used to specify a
+# configuration file for plantuml.
+
+PLANTUML_CFG_FILE      = 
+
 # When using plantuml, the specified paths are searched for files specified by
 # the !include statement in a plantuml block.