diff --git a/README.md b/README.md
index d23e9f61..1d275743 100644
--- a/README.md
+++ b/README.md
@@ -22,9 +22,17 @@ In order to build the site you will need `jekyll`, see instructions below to ins
 Making changes to the site
 =================
 
-When making changes to the site, you should always work on the `source` branch. After committing your changes to `source`, simply run the `deploy.sh` script. This script will take care of the steps involved to push both the `source` and `master` branches to github. 
-
-	./deploy.sh
+When making changes to the site:
+1. Start from the lastest version of the source branch with `git checkout source ; git pull`.
+2. Create a new branch for your changes with `git checkout -b <mybranchname>`.
+3. Commit your changes to the branch.
+4. Push the changes to github using `git push --set-upstream origin <mybranchname>`.
+5. Open a pull request (PR) for the branch on github at https://github.com/revbayes/revbayes.github.io
+6. After the pull request is merged to the `source` branch on github, move back to the source branch locally with `git checkout source` and fetch the latest version with `git pull`.
+7. Now you can run the `deploy.sh` script to update the `master` branch.
+
+Pull requests for the website do not currently require review, so you can merge them yourself if checks pass.
+These checks help to prevent the tutorials from breaking.
 
 Setting up jekyll
 =================
diff --git a/deploy.sh b/deploy.sh
index 4027f741..f147e10c 100755
--- a/deploy.sh
+++ b/deploy.sh
@@ -63,22 +63,37 @@ then
     exit 1
 fi
 
-msg=`git log -1 --pretty=%B`
+# make sure there aren't untracked files that will get uploaded to the website
+UNTRACKED_FILES=$(git ls-files --others --exclude-standard)
+if [ -n "${UNTRACKED_FILES}" ] ; then
+    echo "Error: Untracked files.  Please commit or stash before updating master."
+    exit 1
+fi
 
-echo "Checking out source"
-git checkout source
-echo
+# make sure the source branch is up-to-date with origin/source
+echo "Fetching content from remote"
+git fetch --quiet origin
 
-echo "Pulling updates to the source"
-git pull --quiet origin source
-echo
+COUNT_MISSING="$(git rev-list --count source..origin/source)"
+if [ "${COUNT_MISSING}" != 0 ] ; then
+    echo "Error: the 'source' branch is not up-to-date.  Please do a 'git pull'"
+    exit 1
+fi
+
+COUNT_EXTRA="$(git rev-list --count origin/source..source)"
+if [ "${COUNT_EXTRA}" != 0 ] ; then
+    echo "Error: the 'source' branch contains changes that have not been merged!"
+    echo
+    echo "    Please create a PR for these changes. After the PR is merged, "
+    echo "    please pull from the source branch and run the ./deploy.sh script again."
+    exit 1
+fi
 
-# fetch master
-echo "Pulling master"
+# Check out master in _site
+echo "Checking out master in _site"
 (
     cd _site
     git checkout --quiet master
-    git fetch --quiet origin
     git reset --quiet --hard origin/master
 
     # update the documentation?
@@ -106,6 +121,7 @@ echo
 # deploy master
 (
     cd _site
+    msg=`git log -1 --pretty=%B`
 
     # check if there are any changes on master
     untracked=`git ls-files --other --exclude-standard --directory`