Refactor cloc_tools

Remove YAML in favor of JSON, which is part of standard Python

Author: robertodr

Pipfile

@@ -18,7 +18,7 @@ Sphinx = "*"
 sphinx_rtd_theme = "*"
 sphinxcontrib-bibtex = "*"
 yapf = "*"
-
+fprettify = "*"
 
 [dev-packages]
 

Pipfile.lock

@@ -5,11 +5,11 @@ xml
 doxygen_sqlite3.db
 mock_pcmsolver.h
 cloc_tools.py
-gfx/*.png
-gfx/matplotlib
-scratch_cpp.yml
-scratch_hpp.yml
-scratch_c.yml
-scratch_h.yml
-scratch_fortran.yml
+gfx/bar_charts/*.svg
+scratch_cpp.json
+scratch_hpp.json
+scratch_c.json
+scratch_h.json
+scratch_fortran.json
 doxygen.log
+__pycache__

cmake/custom/cloc.cmake

@@ -7,8 +7,8 @@ DOXYFILE_ENCODING      = UTF-8
 PROJECT_NAME           = PCMSolver
 PROJECT_NUMBER         = @PROJECT_VERSION_MAJOR@.@PROJECT_VERSION_MINOR@.@PROJECT_VERSION_PATCH@-@PROJECT_VERSION_TWEAK@
 PROJECT_BRIEF          = "An Open Source API for the Polarizable Continuum Model"
-PROJECT_LOGO           = @PROJECT_SOURCE_DIR@/doc/gfx/logo.jpg
-OUTPUT_DIRECTORY       = @PROJECT_SOURCE_DIR@/doc
+PROJECT_LOGO           = @project_root_dir@/doc/gfx/logo.jpg
+OUTPUT_DIRECTORY       = @doc_build_dir@
 CREATE_SUBDIRS         = NO
 ALLOW_UNICODE_NAMES    = NO
 OUTPUT_LANGUAGE        = English
@@ -28,7 +28,7 @@ ABBREVIATE_BRIEF       = "The $name class" \
 ALWAYS_DETAILED_SEC    = NO
 INLINE_INHERITED_MEMB  = NO
 FULL_PATH_NAMES        = YES
-STRIP_FROM_PATH        = @PROJECT_SOURCE_DIR@/src
+STRIP_FROM_PATH        = @project_root_dir@/src
 STRIP_FROM_INC_PATH    =
 SHORT_NAMES            = NO
 JAVADOC_AUTOBRIEF      = NO
@@ -97,7 +97,7 @@ SHOW_FILES             = YES
 SHOW_NAMESPACES        = YES
 FILE_VERSION_FILTER    =
 LAYOUT_FILE            =
-CITE_BIB_FILES         = @PROJECT_SOURCE_DIR@/doc/pcmsolver.bib
+CITE_BIB_FILES         = @project_root_dir@/doc/pcmsolver.bib
 #---------------------------------------------------------------------------
 # Configuration options related to warning and progress messages
 #---------------------------------------------------------------------------
@@ -112,10 +112,10 @@ WARN_LOGFILE           = doc/doxygen.log
 #---------------------------------------------------------------------------
 # Configuration options related to the input files
 #---------------------------------------------------------------------------
-INPUT                  = @PROJECT_SOURCE_DIR@/src \
-                         @PROJECT_SOURCE_DIR@/api \
-                         @PROJECT_SOURCE_DIR@/doc \
-                         @PROJECT_SOURCE_DIR@/include
+INPUT                  = @project_root_dir@/src \
+                         @project_root_dir@/api \
+                         @project_root_dir@/doc \
+                         @project_root_dir@/include
 INPUT_ENCODING         = UTF-8
 FILE_PATTERNS          = *.c \
                          *.cpp \
@@ -133,13 +133,14 @@ FILE_PATTERNS          = *.c \
                          *.F03 \
                          *.F08
 RECURSIVE              = YES
-EXCLUDE                = @PROJECT_SOURCE_DIR@/src/bin \
-                         @PROJECT_SOURCE_DIR@/src/utils/getkw
+EXCLUDE                = @project_root_dir@/src/bin \
+                         @project_root_dir@/src/utils/getkw \
+                         @project_root_dir@/doc/__pycache__
 EXCLUDE_SYMLINKS       = NO
-EXCLUDE_PATTERNS       = @PROJECT_SOURCE_DIR@/api/pcmsolver.h \
-                         @PROJECT_SOURCE_DIR@/api/pcmsolver.f90 \
-                         @PROJECT_SOURCE_DIR@/src/utils/Logger.* \
-                         @PROJECT_SOURCE_DIR@/src/utils/RungeKutta4.*
+EXCLUDE_PATTERNS       = @project_root_dir@/api/pcmsolver.h \
+                         @project_root_dir@/api/pcmsolver.f90 \
+                         @project_root_dir@/src/utils/Logger.* \
+                         @project_root_dir@/src/utils/RungeKutta4.*
 EXCLUDE_SYMBOLS        = EIGEN_MAKE_ALIGNED_OPERATOR_NEW \
                          REQUIRE \
                          SCENARIO \
@@ -162,10 +163,10 @@ EXCLUDE_SYMBOLS        = EIGEN_MAKE_ALIGNED_OPERATOR_NEW \
                          __noexcept \
                          __noreturn \
                          __nullptr
-EXAMPLE_PATH           = @PROJECT_SOURCE_DIR@/doc/snippets
+EXAMPLE_PATH           = @project_root_dir@/doc/snippets
 EXAMPLE_PATTERNS       = *
 EXAMPLE_RECURSIVE      = NO
-IMAGE_PATH             = @PROJECT_SOURCE_DIR@/doc/gfx
+IMAGE_PATH             = @project_root_dir@/doc/gfx
 INPUT_FILTER           =
 FILTER_PATTERNS        =
 FILTER_SOURCE_FILES    = NO