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Lucas Marin edited this page Jun 2, 2020 · 2 revisions

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 either 'docs-stage', 'docs-prepare', or 'docs-doxygen'

  • If they are not present, open CMake and ensure that the options to build Biogears_BUILD_JAVATOOLS and Biogears_BUILD_DOCUMENTATION are enabled, then configure and generate. After doing this visual studios should notify you that the solution has changed.

  1. 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.

  2. 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"

  1. 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'.
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