This post has been superseded.

Here is the procedure for updating the doxygen-generated webpages. You will need to have both the OpenPV and PetaVision.github.io repositories cloned on your local machine. In the code below, these repositories are taken to be located in /path/to/OpenPV and /path/to/PetaVision.github.com.

cd /path/to/OpenPV/pv-core/docs/doxygen
bash buildDoxygen.sh # Currently, this script contains the single command "doxygen cfg/doxy.cfg"

cd /path/to/PetaVision.github.io
git pull
rsync -avzu --delete /path/to/OpenPV/pv-core/docs/doxygen/html/ doxygen/
git add .
git commit -m "Update to doxygen-generated pages"
git push

The doxygen command in the buildDoxygen.sh script generates pages in /path/to/OpenPV/pv-core/docs/doxygen/html. This directory is in the .gitignore file, so running doxygen should not affect the git-status of OpenPV.

The rsync command makes /path/to/PetaVision.github.io/doxygen into a copy of /path/to/OpenPV/pv-core/docs/doxygen/html. Note that for rsync, the slashes at the end of the source and destination directories are significant. If you leave one or both off, the result will not be what you want.