diff --git a/ci/travis-deploy.sh b/ci/travis-deploy.sh
index b8d0009..2f254d1 100644
--- a/ci/travis-deploy.sh
+++ b/ci/travis-deploy.sh
@@ -1,22 +1,31 @@
 #!/bin/bash
 echo "Running deployment script..."
-conda install jupyter
-pip install pdoc==0.3.2
+conda install --yes jupyter
+pip install pdoc==0.3.2 pygments
 
 # Generating documentation
 cd ~
-mkdir -p ./doc/notebooks
-cd ./doc/notebooks
+mkdir -p ./doc/carl/notebooks
+cd ./doc/carl/notebooks
+
+OIFS="$IFS"
+IFS=$'\n'
 for nb in ${TRAVIS_BUILD_DIR}/examples/*ipynb; do
-    jupyter nbconvert $nb --to markdown
+    jupyter nbconvert "$nb" --to markdown
 done
+cp ${TRAVIS_BUILD_DIR}/examples/*md .
+cp -r ${TRAVIS_BUILD_DIR}/examples/*_files .
+IFS="$OIFS"
 
 cd ~
-python ${TRAVIS_BUILD_DIR}/ci/make_doc.py --overwrite --html --html-dir ./doc --template-dir ${TRAVIS_BUILD_DIR}/ci/templates --notebook-dir ./doc/notebooks carl
+python ${TRAVIS_BUILD_DIR}/ci/make_doc.py --overwrite --html --html-dir ./doc --template-dir ${TRAVIS_BUILD_DIR}/ci/templates --notebook-dir ./doc/carl/notebooks carl
 
 # Copying to github pages
 echo "Copying built files"
 git clone -b gh-pages "https://${GH_TOKEN}@github.com/diana-hep/carl.git" deploy > /dev/null 2>&1 || exit 1
+cd deploy
+git rm -r notebooks/*
+cd ..
 cp -r ./doc/carl/* deploy
 
 # Move into deployment directory