docs(docs): rebuilt docs

Doxyfile

@@ -42,7 +42,7 @@ DOXYFILE_ENCODING      = UTF-8
 # title of most generated pages and in a few other places.
 # The default value is: My Project.
 
-PROJECT_NAME           = "New 4DSSE Code"
+PROJECT_NAME           = SERiF
 
 # The PROJECT_NUMBER tag can be used to enter a project or revision number. This
 # could be handy for archiving the generated documentation or if some version
@@ -54,7 +54,7 @@ PROJECT_NUMBER         = 0.0.1a
 # for a project that appears at the top of each page and should give viewers a
 # quick idea about the purpose of the project. Keep the description short.
 
-PROJECT_BRIEF          =
+PROJECT_BRIEF          = 3+1D Stellar Structure and Evolution
 
 # With the PROJECT_LOGO tag one can specify a logo or an icon that is included
 # in the documentation. The maximum height of the logo should not exceed 55
@@ -349,7 +349,7 @@ OPTIMIZE_OUTPUT_SLICE  = NO
 #
 # Note see also the list of default file extension mappings.
 
-EXTENSION_MAPPING      = py=C++
+EXTENSION_MAPPING      = md=markdown
 
 # If the MARKDOWN_SUPPORT tag is enabled then Doxygen pre-processes all comments
 # according to the Markdown format, which allows for more readable
@@ -406,7 +406,7 @@ AUTOLINK_IGNORE_WORDS  =
 # collaboration diagrams that involve STL classes more complete and accurate.
 # The default value is: NO.
 
-BUILTIN_STL_SUPPORT    = NO
+BUILTIN_STL_SUPPORT    = YES
 
 # If you use Microsoft's C++/CLI language, you should set this option to YES to
 # enable parsing support.
@@ -540,13 +540,13 @@ EXTRACT_ALL            = YES
 # be included in the documentation.
 # The default value is: NO.
 
-EXTRACT_PRIVATE        = NO
+EXTRACT_PRIVATE        = YES
 
 # If the EXTRACT_PRIV_VIRTUAL tag is set to YES, documented private virtual
 # methods of a class will be included in the documentation.
 # The default value is: NO.
 
-EXTRACT_PRIV_VIRTUAL   = NO
+EXTRACT_PRIV_VIRTUAL   = YES
 
 # If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal
 # scope will be included in the documentation.
@@ -558,7 +558,7 @@ EXTRACT_PACKAGE        = NO
 # included in the documentation.
 # The default value is: NO.
 
-EXTRACT_STATIC         = NO
+EXTRACT_STATIC         = YES
 
 # If the EXTRACT_LOCAL_CLASSES tag is set to YES, classes (and structs) defined
 # locally in source files will be included in the documentation. If set to NO,
@@ -991,7 +991,7 @@ WARN_LOGFILE           =
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = src tests utils/opatio
+INPUT                  = src tests docs/static/mainpage.md
 
 # This tag can be used to specify the character encoding of the source files
 # that Doxygen parses. Internally Doxygen uses the UTF-8 encoding. Doxygen uses
@@ -1207,7 +1207,7 @@ FILTER_SOURCE_PATTERNS =
 # (index.html). This can be useful if you have a project on for instance GitHub
 # and want to reuse the introduction page also for the Doxygen output.
 
-USE_MDFILE_AS_MAINPAGE =
+USE_MDFILE_AS_MAINPAGE = docs/static/mainpage.md
 
 # If the IMPLICIT_DIR_DOCS tag is set to YES, any README.md file found in sub-
 # directories of the project's root, is used as the documentation for that sub-
@@ -1238,7 +1238,7 @@ FORTRAN_COMMENT_AFTER  = 72
 # also VERBATIM_HEADERS is set to NO.
 # The default value is: NO.
 
-SOURCE_BROWSER         = NO
+SOURCE_BROWSER         = YES
 
 # Setting the INLINE_SOURCES tag to YES will include the body of functions,
 # multi-line macros, enums or list initialized variables directly into the
@@ -1398,7 +1398,7 @@ HTML_FOOTER            =
 # obsolete.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_STYLESHEET        =
+HTML_STYLESHEET  =
 
 # The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined
 # cascading style sheets that are included after the standard style sheets
@@ -1416,7 +1416,10 @@ HTML_STYLESHEET        =
 # documentation.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_EXTRA_STYLESHEET  =
+HTML_EXTRA_STYLESHEET  = docs/static/doxygen-awesome-css/doxygen-awesome.css \
+                         docs/static/doxygen-awesome-css/doxygen-awesome-sidebar-only.css
+
+
 
 # The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
 # other source files which should be copied to the HTML output directory. Note
@@ -1439,7 +1442,7 @@ HTML_EXTRA_FILES       =
 # The default value is: AUTO_LIGHT.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_COLORSTYLE        = AUTO_LIGHT
+HTML_COLORSTYLE        = LIGHT
 
 # The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen
 # will adjust the colors in the style sheet and background images according to
@@ -1750,7 +1753,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # The default value is: YES.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-DISABLE_INDEX          = YES
+DISABLE_INDEX          = NO
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information. If the tag