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1478 Switch to Doxysphinx (#1504)
- generate the C++ documentation using doxysphinx - replaced the inline namespace documentations on model pages by links - enabled Build on Pull Request Co-authored-by: Carlotta Gerstein <[email protected]> Co-authored-by: Henrik Zunker <[email protected]>
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‎.github/pull_request_template.md‎

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### Checks by code author
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- [ ] Every addressed issue is linked (use the "Closes #ISSUE" keyword below)
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- [ ] New code adheres to [coding guidelines](https://memilio.readthedocs.io/en/latest/development.html#coding-guidelines)
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- [ ] No large data files have been added (files should in sum not exceed 100 KB, avoid PDFs, Word docs, etc.)
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- [ ] Tests are added for new functionality and a local test run was successful (with and without OpenMP)
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- [ ] Appropriate **documentation within the code** (Doxygen) for new functionality has been added in the code
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- [ ] Appropriate **external documentation** (ReadTheDocs) for new functionality has been added to the online documentation
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- [ ] Proper attention to licenses, especially no new third-party software with conflicting license has been added
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- [ ] Every addressed issue is linked (use the "Closes #ISSUE" keyword below).
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- [ ] New code adheres to [coding guidelines](https://memilio.readthedocs.io/en/latest/development.html#coding-guidelines).
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- [ ] No large data files have been added (files should in sum not exceed 100 KB, avoid PDFs, Word docs, etc.).
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- [ ] Tests are added for new functionality and a local test run was successful (with and without OpenMP).
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- [ ] Appropriate **documentation within the code** (Doxygen) for new functionality has been added in the code.
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- [ ] Appropriate **external documentation** (ReadTheDocs) for new functionality has been added to the online documentation and checked in the preview.
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- [ ] Proper attention to licenses, especially no new third-party software with conflicting license has been added.
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- [ ] (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.
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### Checks by code reviewer(s)
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- [ ] Corresponding issue(s) is/are linked and addressed
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- [ ] Code is clean of development artifacts (no deactivated or commented code lines, no debugging printouts, etc.)
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- [ ] Appropriate **unit tests** have been added, CI passes, code coverage and performance is acceptable (did not decrease)
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- [ ] No large data files added in the whole history of commits(files should in sum not exceed 100 KB, avoid PDFs, Word docs, etc.)
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- [ ] Corresponding issue(s) is/are linked and addressed.
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- [ ] Code is clean of development artifacts (no deactivated or commented code lines, no debugging printouts, etc.).
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- [ ] Appropriate **unit tests** have been added, CI passes, code coverage and performance is acceptable (did not decrease).
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- [ ] No large data files added in the whole history of commits(files should in sum not exceed 100 KB, avoid PDFs, Word docs, etc.).
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- [ ] 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

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docs/xml
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docs/source/api
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docs/source/generated
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docs/source/cppapi
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# VS Code
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.vscode/

‎.gitmodules‎

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[submodule "docs/doxygen-awesome-css"]
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path = docs/doxygen-awesome-css
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url = https://github.com/jothepro/doxygen-awesome-css.git

‎docs/Doxyfile‎

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# title of most generated pages and in a few other places.
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# The default value is: My Project.
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PROJECT_NAME = MEmilio
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PROJECT_NAME = "CPP API"
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# The PROJECT_NUMBER tag can be used to enter a project or revision number. This
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# could be handy for archiving the generated documentation or if some version
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# control system is used.
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PROJECT_NUMBER = 0.7
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PROJECT_NUMBER =
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# Using the PROJECT_BRIEF tag one can provide an optional one line description
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# for a project that appears at the top of each page and should give viewer a
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# entered, it will be relative to the location where doxygen was started. If
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# left blank the current directory will be used.
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OUTPUT_DIRECTORY =
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OUTPUT_DIRECTORY = source/cppapi
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# If the CREATE_SUBDIRS tag is set to YES then doxygen will create up to 4096
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# sub-directories (in 2 levels) under the output directory of each output format
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# qualified scopes will look different, etc.
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# The default value is: NO.
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OPTIMIZE_OUTPUT_JAVA = YES
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OPTIMIZE_OUTPUT_JAVA = NO
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# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran
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# sources. Doxygen will then generate output that is tailored for Fortran.
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# list will mention the files that were used to generate the documentation.
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# The default value is: YES.
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SHOW_USED_FILES = YES
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SHOW_USED_FILES = NO
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# Set the SHOW_FILES tag to NO to disable the generation of the Files page. This
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# will remove the Files entry from the Quick Index and from the Folder Tree View
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# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE
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LAYOUT_FILE =
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LAYOUT_FILE = DoxygenLayout.xml
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# The CITE_BIB_FILES tag can be used to specify one or more bib files containing
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# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
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# Note: If this tag is empty the current directory is searched.
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INPUT = ../cpp/models ../cpp/memilio ../cpp/sbml_model_generation
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INPUT = ../cpp/models ../cpp/memilio ../cpp/sbml_model_generation ../docs/doxygen_main_page.md
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# This tag can be used to specify the character encoding of the source files
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# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
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# Note that the wildcards are matched against the file with absolute path, so to
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# exclude all test directories for example use the pattern */test/*
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EXCLUDE_PATTERNS =
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EXCLUDE_PATTERNS =
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# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
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# (index.html). This can be useful if you have a project on for instance GitHub
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# and want to reuse the introduction page also for the doxygen output.
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USE_MDFILE_AS_MAINPAGE = ../README.md
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USE_MDFILE_AS_MAINPAGE = ../docs/doxygen_main_page.md
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# The Fortran standard specifies that for fixed formatted Fortran code all
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# characters from position 72 are to be considered as comment. A common
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# documentation.
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# This tag requires that the tag GENERATE_HTML is set to YES.
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HTML_EXTRA_STYLESHEET =
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HTML_EXTRA_STYLESHEET = doxygen-awesome-css/doxygen-awesome.css
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# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
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# other source files which should be copied to the HTML output directory. Note
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# The default value is: YES.
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# This tag requires that the tag GENERATE_HTML is set to YES.
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HTML_DYNAMIC_MENUS = YES
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HTML_DYNAMIC_MENUS = NO
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# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
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SEARCHENGINE = NO
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# When the SERVER_BASED_SEARCH tag is enabled the search engine will be
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# captures the structure of the code including all documentation.
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# The default value is: NO.
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GENERATE_XML = YES
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GENERATE_XML = NO
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# The XML_OUTPUT tag is used to specify where the XML pages will be put. If a
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GENERATE_TAGFILE =
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GENERATE_TAGFILE = source/cppapi/html/tagfile.xml
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HAVE_DOT = NO
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HAVE_DOT = YES
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# The default value is: png.
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DOT_IMAGE_FORMAT = png
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DOT_IMAGE_FORMAT = svg
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INTERACTIVE_SVG = YES
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# The DOT_PATH tag can be used to specify the path where the dot tool can be
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# found. If left blank, it is assumed the dot tool can be found in the path.

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