Add templating for Jupyter notebooks.

circle.yml

@@ -11,11 +11,12 @@ dependencies:
 test:
     override:
         - docker run $AWS_ECR_ENDPOINT.dkr.ecr.us-east-1.amazonaws.com/cognoma-ml-workers:$CIRCLE_SHA1 python test_ml_task_runner.py
+        - docker run $AWS_ECR_ENDPOINT.dkr.ecr.us-east-1.amazonaws.com/cognoma-ml-workers:$CIRCLE_SHA1 pytest nb_util
 
 deployment:
     production:
         branch: master
         commands:
             - chmod +x ecr_push.sh ecs_deploy.sh
             - ./ecr_push.sh
-            - ./ecs_deploy.sh --timeout 180 --cluster $AWS_CLUSTER_NAME --service-name $AWS_SERVICE_NAME --image $AWS_ECR_ENDPOINT.dkr.ecr.us-east-1.amazonaws.com/cognoma-ml-workers:$CIRCLE_SHA1
+            - ./ecs_deploy.sh --timeout 180 --cluster $AWS_CLUSTER_NAME --service-name $AWS_SERVICE_NAME --image $AWS_ECR_ENDPOINT.dkr.ecr.us-east-1.amazonaws.com/cognoma-ml-workers:$CIRCLE_SHA1

nb_util/README.md

@@ -0,0 +1,19 @@
+# nbcopy
+Tool for making and filling Jupyter notebook templates.
+
+## Usage
+	import jupyter_template as jt
+
+Given a Jupyter notebook, we can create a template by replacing specific strings with keywords.
+
+	fname = 'examples/2.mutation-classifier.ipynb'
+	new_keywords = {'7157': 'id', 'TP53': 'mutation'}
+	template = jt.create_template(fname, new_keywords)
+
+Once we have a template, filling in the keywords is straightforward
+
+	keywords = {'id': 'foo', 'mutation': 'bar'}
+	nb = template.fill_template(keywords)
+	with open('examples/output.ipynb', 'w') as f:
+		f.writelines(nb)
+	f.close()

nb_util/__init__.py

@@ -0,0 +1 @@
+"""nb_util package."""