Modify .codedocs

Make sure that codedocs.xys works

Update README.md

.codedocs

@@ -1,5 +1,4 @@
 # CodeDocs.xyz Configuration File
 
-EXCLUDE_PATTERNS = */deprecated/*
-DOXYFILE = doc/doxygen.cfg.in
+DOXYFILE = doc/doxygen_codedocs.cfg
 

README.md

@@ -16,6 +16,16 @@ The math supporting this code can be viewed in this **very rough draft in progre
 - Supported elements: LINEs, QUADs, HEXs since it uses deal.II
 - Supported refinements: h (size) or p (order).
 
+## Documentation
+
+The code itself is documented using Doxygen, and the latest documentation is hosted on [codedocs.xyz](https://codedocs.xyz/dougshidong/PHiLiP/). 
+
+Since deal.II is heavily used, their [documentation](https://www.dealii.org/developer/doxygen/deal.II/index.html) is probably the most useful.
+
+Another great ressource is the [deal.II Google Groups](https://groups.google.com/forum/#!forum/dealii), where developers are actively answering questions.
+
+Finally, I am also always available to answer questions regarding the code by e-mail at doug.shi-dong@mail.mcgill.ca
+
 ## Building/Running the Code
 
 The code has been succesfully built in the following environments:

doc/doxygen_codedocs.cfg

@@ -0,0 +1,330 @@
+# Doxyfile 1.8.11
+
+#---------------------------------------------------------------------------
+# Project related configuration options
+#---------------------------------------------------------------------------
+DOXYFILE_ENCODING      = UTF-8
+PROJECT_NAME           = "[P]arallel [Hi]gh-order [Li]brary for [P]DEs"
+PROJECT_NUMBER         = "Latest"
+PROJECT_BRIEF          = "Parallel High-Order Library for PDEs through hp-adaptive Discontinuous Galerkin methods"
+PROJECT_LOGO           =
+OUTPUT_DIRECTORY       =
+CREATE_SUBDIRS         = NO
+ALLOW_UNICODE_NAMES    = NO
+OUTPUT_LANGUAGE        = English
+BRIEF_MEMBER_DESC      = YES
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+INLINE_INHERITED_MEMB  = NO
+FULL_PATH_NAMES        = YES
+STRIP_FROM_PATH        = ./
+STRIP_FROM_INC_PATH    =
+SHORT_NAMES            = NO
+JAVADOC_AUTOBRIEF      = NO
+QT_AUTOBRIEF           = NO
+MULTILINE_CPP_IS_BRIEF = NO
+INHERIT_DOCS           = YES
+SEPARATE_MEMBER_PAGES  = NO
+TAB_SIZE               = 4
+ALIASES                =
+TCL_SUBST              =
+OPTIMIZE_OUTPUT_FOR_C  = NO
+OPTIMIZE_OUTPUT_JAVA   = NO
+OPTIMIZE_FOR_FORTRAN   = NO
+OPTIMIZE_OUTPUT_VHDL   = NO
+EXTENSION_MAPPING      =
+MARKDOWN_SUPPORT       = YES
+AUTOLINK_SUPPORT       = YES
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+INLINE_GROUPED_CLASSES = NO
+INLINE_SIMPLE_STRUCTS  = NO
+TYPEDEF_HIDES_STRUCT   = NO
+LOOKUP_CACHE_SIZE      = 0
+#---------------------------------------------------------------------------
+# Build related configuration options
+#---------------------------------------------------------------------------
+EXTRACT_ALL            = NO
+EXTRACT_PRIVATE        = YES
+EXTRACT_PACKAGE        = NO
+EXTRACT_STATIC         = YES
+EXTRACT_LOCAL_CLASSES  = YES
+EXTRACT_LOCAL_METHODS  = NO
+EXTRACT_ANON_NSPACES   = NO
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+HIDE_IN_BODY_DOCS      = NO
+INTERNAL_DOCS          = NO
+CASE_SENSE_NAMES       = YES
+HIDE_SCOPE_NAMES       = NO
+HIDE_COMPOUND_REFERENCE= NO
+SHOW_INCLUDE_FILES     = YES
+SHOW_GROUPED_MEMB_INC  = NO
+FORCE_LOCAL_INCLUDES   = NO
+INLINE_INFO            = YES
+SORT_MEMBER_DOCS       = YES
+SORT_BRIEF_DOCS        = NO
+SORT_MEMBERS_CTORS_1ST = NO
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+SHOW_USED_FILES        = YES
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+SHOW_NAMESPACES        = YES
+FILE_VERSION_FILTER    =
+LAYOUT_FILE            = ./doc/DoxygenLayout.xml
+CITE_BIB_FILES         = ./doc/code.bib
+#---------------------------------------------------------------------------
+# Configuration options related to warning and progress messages
+#---------------------------------------------------------------------------
+QUIET                  = NO
+WARNINGS               = YES
+WARN_IF_UNDOCUMENTED   = YES
+WARN_IF_DOC_ERROR      = YES
+WARN_NO_PARAMDOC       = NO
+WARN_AS_ERROR          = NO
+WARN_FORMAT            = "$file:$line: $text"
+WARN_LOGFILE           =
+#---------------------------------------------------------------------------
+# Configuration options related to the input files
+#---------------------------------------------------------------------------
+INPUT                  = ./
+INPUT_ENCODING         = UTF-8
+FILE_PATTERNS          = *.cpp \
+                         *.h \
+                         *.hpp \
+                         *.h.in \
+                         *.dox \
+#                         *.md \ # doxygen was given errors for relative paths in markdown files.
+#                         *.mk
+RECURSIVE              = YES
+EXCLUDE                = ./README.md
+EXCLUDE_SYMLINKS       = NO
+EXCLUDE_PATTERNS       = */build/* \
+                         */build_*/* \
+                         */src/deprecated/* \
+                         */src/dummy/* \
+                         */deprecated/* \
+                         */external/*
+EXCLUDE_SYMBOLS        =
+EXAMPLE_PATH           =
+EXAMPLE_PATTERNS       =
+EXAMPLE_RECURSIVE      = NO
+IMAGE_PATH             =
+INPUT_FILTER           =
+FILTER_PATTERNS        =
+FILTER_SOURCE_FILES    = NO
+FILTER_SOURCE_PATTERNS =
+USE_MDFILE_AS_MAINPAGE =
+#---------------------------------------------------------------------------
+# Configuration options related to source browsing
+#---------------------------------------------------------------------------
+SOURCE_BROWSER         = YES
+INLINE_SOURCES         = NO
+STRIP_CODE_COMMENTS    = YES
+REFERENCED_BY_RELATION = NO
+REFERENCES_RELATION    = NO
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+SOURCE_TOOLTIPS        = YES
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+VERBATIM_HEADERS       = YES
+CLANG_ASSISTED_PARSING = NO
+CLANG_OPTIONS          =
+#---------------------------------------------------------------------------
+# Configuration options related to the alphabetical class index
+#---------------------------------------------------------------------------
+ALPHABETICAL_INDEX     = YES
+COLS_IN_ALPHA_INDEX    = 5
+IGNORE_PREFIX          =
+#---------------------------------------------------------------------------
+# Configuration options related to the HTML output
+#---------------------------------------------------------------------------
+GENERATE_HTML          = YES
+HTML_OUTPUT            = html
+HTML_FILE_EXTENSION    = .html
+HTML_HEADER            =
+HTML_FOOTER            =
+HTML_STYLESHEET        =
+HTML_EXTRA_STYLESHEET  =
+HTML_EXTRA_FILES       =
+HTML_COLORSTYLE_HUE    = 240
+HTML_COLORSTYLE_SAT    = 255
+HTML_COLORSTYLE_GAMMA  = 40
+HTML_TIMESTAMP         = YES
+HTML_DYNAMIC_SECTIONS  = NO
+HTML_INDEX_NUM_ENTRIES = 100
+GENERATE_DOCSET        = NO
+DOCSET_FEEDNAME        = "Doxygen generated docs"
+DOCSET_BUNDLE_ID       = org.doxygen.Project
+DOCSET_PUBLISHER_ID    = org.doxygen.Publisher
+DOCSET_PUBLISHER_NAME  = Publisher
+GENERATE_HTMLHELP      = NO
+CHM_FILE               =
+HHC_LOCATION           =
+GENERATE_CHI           = NO
+CHM_INDEX_ENCODING     =
+BINARY_TOC             = NO
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+QHP_NAMESPACE          = org.doxygen.Project
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+QHP_SECT_FILTER_ATTRS  =
+QHG_LOCATION           =
+GENERATE_ECLIPSEHELP   = NO
+ECLIPSE_DOC_ID         = org.doxygen.Project
+DISABLE_INDEX          = NO
+GENERATE_TREEVIEW      = YES
+ENUM_VALUES_PER_LINE   = 4
+TREEVIEW_WIDTH         = 250
+EXT_LINKS_IN_WINDOW    = NO
+FORMULA_FONTSIZE       = 10
+FORMULA_TRANSPARENT    = YES
+USE_MATHJAX            = YES
+MATHJAX_FORMAT         = HTML-CSS
+MATHJAX_RELPATH        = http://cdn.mathjax.org/mathjax/latest
+MATHJAX_EXTENSIONS     =
+MATHJAX_CODEFILE       =
+SEARCHENGINE           = YES
+SERVER_BASED_SEARCH    = NO
+EXTERNAL_SEARCH        = NO
+SEARCHENGINE_URL       =
+SEARCHDATA_FILE        = searchdata.xml
+EXTERNAL_SEARCH_ID     =
+EXTRA_SEARCH_MAPPINGS  =
+#---------------------------------------------------------------------------
+# Configuration options related to the LaTeX output
+#---------------------------------------------------------------------------
+GENERATE_LATEX         = YES
+LATEX_OUTPUT           = latex
+LATEX_CMD_NAME         = latex
+MAKEINDEX_CMD_NAME     = makeindex
+COMPACT_LATEX          = NO
+PAPER_TYPE             = a4
+EXTRA_PACKAGES         =
+LATEX_HEADER           =
+LATEX_FOOTER           =
+LATEX_EXTRA_STYLESHEET =
+LATEX_EXTRA_FILES      =
+PDF_HYPERLINKS         = YES
+USE_PDFLATEX           = YES
+LATEX_BATCHMODE        = NO
+LATEX_HIDE_INDICES     = NO
+LATEX_SOURCE_CODE      = NO
+LATEX_BIB_STYLE        = plain
+LATEX_TIMESTAMP        = YES
+#---------------------------------------------------------------------------
+# Configuration options related to the RTF output
+#---------------------------------------------------------------------------
+GENERATE_RTF           = NO
+RTF_OUTPUT             = rtf
+COMPACT_RTF            = NO
+RTF_HYPERLINKS         = NO
+RTF_STYLESHEET_FILE    =
+RTF_EXTENSIONS_FILE    =
+RTF_SOURCE_CODE        = NO
+#---------------------------------------------------------------------------
+# Configuration options related to the man page output
+#---------------------------------------------------------------------------
+GENERATE_MAN           = NO
+MAN_OUTPUT             = man
+MAN_EXTENSION          = .3
+MAN_SUBDIR             =
+MAN_LINKS              = NO
+#---------------------------------------------------------------------------
+# Configuration options related to the XML output
+#---------------------------------------------------------------------------
+GENERATE_XML           = NO
+XML_OUTPUT             = xml
+XML_PROGRAMLISTING     = YES
+#---------------------------------------------------------------------------
+# Configuration options related to the DOCBOOK output
+#---------------------------------------------------------------------------
+GENERATE_DOCBOOK       = NO
+DOCBOOK_OUTPUT         = docbook
+DOCBOOK_PROGRAMLISTING = NO
+#---------------------------------------------------------------------------
+# Configuration options for the AutoGen Definitions output
+#---------------------------------------------------------------------------
+GENERATE_AUTOGEN_DEF   = NO
+#---------------------------------------------------------------------------
+# Configuration options related to the Perl module output
+#---------------------------------------------------------------------------
+GENERATE_PERLMOD       = NO
+PERLMOD_LATEX          = NO
+PERLMOD_PRETTY         = YES
+PERLMOD_MAKEVAR_PREFIX =
+#---------------------------------------------------------------------------
+# Configuration options related to the preprocessor
+#---------------------------------------------------------------------------
+ENABLE_PREPROCESSING   = YES
+MACRO_EXPANSION        = NO
+EXPAND_ONLY_PREDEF     = NO
+SEARCH_INCLUDES        = YES
+INCLUDE_PATH           =
+INCLUDE_FILE_PATTERNS  =
+PREDEFINED             = TYPE_RC:=2 TYPE_COMPLEX:=2
+EXPAND_AS_DEFINED      =
+SKIP_FUNCTION_MACROS   = YES
+#---------------------------------------------------------------------------
+# Configuration options related to external references
+#---------------------------------------------------------------------------
+TAGFILES               =
+GENERATE_TAGFILE       =
+ALLEXTERNALS           = NO
+EXTERNAL_GROUPS        = YES
+EXTERNAL_PAGES         = YES
+PERL_PATH              = /usr/bin/perl
+#---------------------------------------------------------------------------
+# Configuration options related to the dot tool
+#---------------------------------------------------------------------------
+CLASS_DIAGRAMS         = YES
+MSCGEN_PATH            =
+DIA_PATH               =
+HIDE_UNDOC_RELATIONS   = NO
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+DIRECTORY_GRAPH        = YES
+DOT_IMAGE_FORMAT       = svg
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+DOT_GRAPH_MAX_NODES    = 50
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+DOT_TRANSPARENT        = NO
+DOT_MULTI_TARGETS      = NO
+GENERATE_LEGEND        = YES
+DOT_CLEANUP            = YES