1478 Switch to Doxysphinx

.github/pull_request_template.md

@@ -18,19 +18,19 @@ Please check our [git workflow](https://memilio.readthedocs.io/en/latest/develop
 
 ### Checks by code author
 
-- [ ] Every addressed issue is linked (use the "Closes #ISSUE" keyword below)
-- [ ] New code adheres to [coding guidelines](https://memilio.readthedocs.io/en/latest/development.html#coding-guidelines)
-- [ ] No large data files have been added (files should in sum not exceed 100 KB, avoid PDFs, Word docs, etc.)
-- [ ] Tests are added for new functionality and a local test run was successful (with and without OpenMP)
-- [ ] Appropriate **documentation within the code** (Doxygen) for new functionality has been added in the code
-- [ ] Appropriate **external documentation** (ReadTheDocs) for new functionality has been added to the online documentation
-- [ ] Proper attention to licenses, especially no new third-party software with conflicting license has been added
+- [ ] Every addressed issue is linked (use the "Closes #ISSUE" keyword below).
+- [ ] New code adheres to [coding guidelines](https://memilio.readthedocs.io/en/latest/development.html#coding-guidelines).
+- [ ] No large data files have been added (files should in sum not exceed 100 KB, avoid PDFs, Word docs, etc.).
+- [ ] Tests are added for new functionality and a local test run was successful (with and without OpenMP).
+- [ ] Appropriate **documentation within the code** (Doxygen) for new functionality has been added in the code.
+- [ ] Appropriate **external documentation** (ReadTheDocs) for new functionality has been added to the online documentation and checked in the preview.
+- [ ] Proper attention to licenses, especially no new third-party software with conflicting license has been added.
 - [ ] (For ABM development) Checked [benchmark results](https://memilio.readthedocs.io/en/latest/development.html#agent-based-model-development) and ran and posted a local test above from before and after development to ensure performance is monitored.
 
 ### Checks by code reviewer(s)
 
-- [ ] Corresponding issue(s) is/are linked and addressed
-- [ ] Code is clean of development artifacts (no deactivated or commented code lines, no debugging printouts, etc.)
-- [ ] Appropriate **unit tests** have been added, CI passes, code coverage and performance is acceptable (did not decrease)
-- [ ] No large data files added in the whole history of commits(files should in sum not exceed 100 KB, avoid PDFs, Word docs, etc.)
+- [ ] Corresponding issue(s) is/are linked and addressed.
+- [ ] Code is clean of development artifacts (no deactivated or commented code lines, no debugging printouts, etc.).
+- [ ] Appropriate **unit tests** have been added, CI passes, code coverage and performance is acceptable (did not decrease).
+- [ ] No large data files added in the whole history of commits(files should in sum not exceed 100 KB, avoid PDFs, Word docs, etc.).
 - [ ] On merge, add 2-5 lines with the changes (main added features, changed items, or corrected bugs) to the merge-commit-message. This can be taken from the **briefly-list-the-changes** above (best case) or the separate commit messages (worst case).

.gitignore

@@ -282,6 +282,7 @@ docs/html
 docs/xml
 docs/source/api
 docs/source/generated
+docs/source/cppapi
 
 # VS Code
 .vscode/

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "docs/doxygen-awesome-css"]
+	path = docs/doxygen-awesome-css
+	url = https://github.com/jothepro/doxygen-awesome-css.git

docs/Doxyfile

@@ -42,13 +42,13 @@ DOXYFILE_ENCODING      = UTF-8
 # title of most generated pages and in a few other places.
 # The default value is: My Project.
 
-PROJECT_NAME           = MEmilio
+PROJECT_NAME           = "CPP API"
 
 # 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
 # control system is used.
 
-PROJECT_NUMBER         = 0.7
+PROJECT_NUMBER         = 
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a
@@ -68,7 +68,7 @@ PROJECT_LOGO           =
 # entered, it will be relative to the location where doxygen was started. If
 # left blank the current directory will be used.
 
-OUTPUT_DIRECTORY       =
+OUTPUT_DIRECTORY       = source/cppapi
 
 # If the CREATE_SUBDIRS tag is set to YES then doxygen will create up to 4096
 # sub-directories (in 2 levels) under the output directory of each output format
@@ -289,7 +289,7 @@ OPTIMIZE_OUTPUT_FOR_C  = NO
 # qualified scopes will look different, etc.
 # The default value is: NO.
 
-OPTIMIZE_OUTPUT_JAVA   = YES
+OPTIMIZE_OUTPUT_JAVA   = NO
 
 # Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran
 # sources. Doxygen will then generate output that is tailored for Fortran.
@@ -767,7 +767,7 @@ MAX_INITIALIZER_LINES  = 30
 # list will mention the files that were used to generate the documentation.
 # The default value is: YES.
 
-SHOW_USED_FILES        = YES
+SHOW_USED_FILES        = NO
 
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page. This
 # will remove the Files entry from the Quick Index and from the Folder Tree View
@@ -805,7 +805,7 @@ FILE_VERSION_FILTER    =
 # DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE
 # tag is left empty.
 
-LAYOUT_FILE            =
+LAYOUT_FILE            = DoxygenLayout.xml
 
 # The CITE_BIB_FILES tag can be used to specify one or more bib files containing
 # the reference definitions. This must be a list of .bib files. The .bib
@@ -933,7 +933,7 @@ WARN_LOGFILE           =
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = ../cpp/models ../cpp/memilio ../cpp/sbml_model_generation
+INPUT                  = ../cpp/models ../cpp/memilio ../cpp/sbml_model_generation ../docs/doxygen_main_page.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
@@ -1004,7 +1004,7 @@ EXCLUDE_SYMLINKS       = NO
 # Note that the wildcards are matched against the file with absolute path, so to
 # exclude all test directories for example use the pattern */test/*
 
-EXCLUDE_PATTERNS       =
+EXCLUDE_PATTERNS       = 
 
 # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
 # (namespaces, classes, functions, etc.) that should be excluded from the
@@ -1099,7 +1099,7 @@ 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 = ../README.md
+USE_MDFILE_AS_MAINPAGE = ../docs/doxygen_main_page.md
 
 # The Fortran standard specifies that for fixed formatted Fortran code all
 # characters from position 72 are to be considered as comment. A common
@@ -1338,7 +1338,7 @@ HTML_STYLESHEET        =
 # documentation.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_EXTRA_STYLESHEET  =
+HTML_EXTRA_STYLESHEET  = doxygen-awesome-css/doxygen-awesome.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
@@ -1402,7 +1402,7 @@ HTML_COLORSTYLE_GAMMA  = 80
 # The default value is: YES.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_DYNAMIC_MENUS     = YES
+HTML_DYNAMIC_MENUS     = NO
 
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
@@ -1833,7 +1833,7 @@ MATHJAX_CODEFILE       =
 # The default value is: YES.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-SEARCHENGINE           = YES
+SEARCHENGINE           = NO
 
 # When the SERVER_BASED_SEARCH tag is enabled the search engine will be
 # implemented using a web server instead of a web client using JavaScript. There
@@ -2193,7 +2193,7 @@ MAN_LINKS              = NO
 # captures the structure of the code including all documentation.
 # The default value is: NO.
 
-GENERATE_XML           = YES
+GENERATE_XML           = NO
 
 # The XML_OUTPUT tag is used to specify where the XML pages will be put. If a
 # relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
@@ -2415,7 +2415,7 @@ TAGFILES               =
 # tag file that is based on the input files it reads. See section "Linking to
 # external documentation" for more information about the usage of tag files.
 
-GENERATE_TAGFILE       =
+GENERATE_TAGFILE       = source/cppapi/html/tagfile.xml
 
 # If the ALLEXTERNALS tag is set to YES, all external classes and namespaces
 # will be listed in the class and namespace index. If set to NO, only the
@@ -2455,7 +2455,7 @@ HIDE_UNDOC_RELATIONS   = YES
 # set to NO
 # The default value is: YES.
 
-HAVE_DOT               = NO
+HAVE_DOT               = YES
 
 # 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
@@ -2677,7 +2677,7 @@ DIR_GRAPH_MAX_DEPTH    = 1
 # The default value is: png.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
-DOT_IMAGE_FORMAT       = png
+DOT_IMAGE_FORMAT       = svg
 
 # If DOT_IMAGE_FORMAT is set to svg, then this option can be set to YES to
 # enable generation of interactive SVG images that allow zooming and panning.
@@ -2689,7 +2689,7 @@ DOT_IMAGE_FORMAT       = png
 # The default value is: NO.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
-INTERACTIVE_SVG        = NO
+INTERACTIVE_SVG        = YES
 
 # The DOT_PATH tag can be used to specify the path where the dot tool can be
 # found. If left blank, it is assumed the dot tool can be found in the path.