Website Generation

Part 1: Dependencies

1. 32 bit ghostscript

2. doxygen-1.8.10 (must be 1.8.10)

3. graphviz

4. Miketex (and all packages)

5. Perl

Part 2: Steps

1. Checkout the current master branch of biogears

2. In the Solution Explorer in Visual Studio, search for gen-website-docs

• Open core/projects/java/biogears/CmakeLists.txt and uncomment any lines corresponding to gen-website-docs. If you find it, move on to step 3. If it's not present:

• Additionally, Open CMake and ensure that the options to build Biogears_BUILD_JAVATOOLS and Biogears_BUILD_DOCUMENTATION are enabled, then configure and generate

3. Run cmd_bio several times with the arguments 'GENSTATES', 'VALIDATE all' (this one will likely take a few hours), 'GENTABLES'. You should know these have run correctly if the folder 'validation' inside of the 'runtime' folder has a number of newly generated tables inside of it.

4. Execute the Visual Studio targets 'docs-stage', 'docs-prepare', and 'docs-doxygen'.

Common Issues

1. If the in text citations aren't producing links, check the following things.

• The Doxyfile in the directory from which "doxygen Doxyfile" is called (this should be biogears/core/build/runtime/doc/doxygen, however you can verify this by checking biogears/core/projects/java/biogears/CMakeLists.txt) has the variable CITE_BIB_FILES set to the name of the .bib file being used (BioGears.bib).

• Additionally Bibtex and Perl must be in your path, you can verify that they are simply by entering "bibtex" and "perl --version"

2. If the equations are not rendering correctly, check 'core/build/runtime/doc/doxygen/Doxyfile' and make sure that the setting 'USE_MATHJAX' is set to 'YES'.