Updating Github pages docs

(This is prototype documentation; in the end we may go with an automated process)

Table of Contents Process for using Github Pages To update Clean out the existing docs Build the docs Commit and push the docs After you are done

Process for using Github Pages

You will want:

• Two separate checkout dirs of CaImAn (probably the dev branch, but that's still TBD)
  • I keep my checkouts in ~/src, so I have a ~/src/caiman_dev-clean (clean dev branch) and a ~/src/caiman-gh-pages (github pages branch)
  • To get the second, take an ordinary CaImAn working dir, and then do a `git checkout gh-pages`
• To install the dev branch (for this I do a pip `install -e .` ), probably(?) needed for Sphinx to find modules

To update

Clean out the existing docs

 cd ~/src/caiman-gh-pages
 git rm -rf .
 touch .nojekyll
 git add .nojekyll

(The nojekyll file is extremely important; without it the CSS will not work because github pages will preprocess the build in a way that breaks it)

Build the docs

 enter the conda environment you installed CaImAn into)
 cd ~/src/caiman_dev-clean/docs
 make clean
 make html
 cd build/html
 cp -r . ~/src/caiman-gh-pages/

Commit and push the docs

 cd ~/src/caiman-gh-pages
 git add -A
 git commit

(add a nice commit message, maybe just the date you're doing the rebuild)

 git push

After you are done

Wait about 5 minutes, and then visit https://flatironinstitute.github.io/CaImAn to make sure it all went ok.