You can use python-saml on GAE if you use the flex environment with a custom runtime built off of the standard python27 runtime provided by google. I just got onelogin's python-saml flask-demo successfully working with this approach using the following settings:
Dockerfile:
FROM gcr.io/google_appengine/python
LABEL python_version=python
RUN virtualenv /env -p python
# Install system packages for onelogin dependencies not already included in runtime
RUN apt-get update && apt-get --yes --quiet install python2.7-dev libxmlsec1-dev
# Set virtualenv environment variables. This is equivalent to running
# source /env/bin/activate
ENV VIRTUAL_ENV /env
ENV PATH /env/bin:$PATH
ADD requirements.txt /app/
RUN pip install -r requirements.txt
ADD . /app/
CMD python index.py
app.yaml
runtime: custom
env: flex
entrypoint: python index.py
api_version: 1
threadsafe: true
requirements.txt
flask==0.10.1
python-saml
then simply do gcloud app deploy app.yaml --version v1