From 5370eda2893ceab58e28cfd75db385fa6a99379c Mon Sep 17 00:00:00 2001
From: Jono Gray <jonathan.gray@flowminder.org>
Date: Wed, 1 May 2019 11:04:05 +0100
Subject: [PATCH 01/29] Sketching out dockerised examples

---
 .dockerignore      | 29 +++++++++++++++++++++++++++++
 Dockerfile         |  9 +++++++++
 docker-compose.yml | 23 +++++++++++++++++++++++
 3 files changed, 61 insertions(+)
 create mode 100644 .dockerignore
 create mode 100644 Dockerfile

diff --git a/.dockerignore b/.dockerignore
new file mode 100644
index 0000000000..f03d1db99c
--- /dev/null
+++ b/.dockerignore
@@ -0,0 +1,29 @@
+# This .dockerignore file follows the "whitelisting" approach described here:
+#    https://youknowfordevs.com/2018/12/07/getting-control-of-your-dockerignore-files.html
+
+#
+# First, exclude everything by default:
+#
+
+*
+
+#
+# Now un-exclude only those folders and files that are needed for building the image:
+#
+!docs/source/worked_examples/*.ipynb
+
+!flowmachine/flowmachine
+!flowmachine/Pipfile*
+!flowmachine/setup.cfg
+!flowmachine/setup.py
+!flowmachine/README.md
+!flowmachine/versioneer.py
+!flowmachine/MANIFEST.in
+
+!flowclient/flowclient
+!flowclient/Pipfile*
+!flowclient/setup.cfg
+!flowclient/setup.py
+!flowclient/README.md
+!flowclient/versioneer.py
+!flowclient/MANIFEST.in
\ No newline at end of file
diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000000..9ea1c51d19
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,9 @@
+FROM jupyter/datascience-notebook
+RUN rm -rf /home/$NB_USER/work
+COPY docs/source/worked_examples/*.ipynb /home/$NB_USER/
+COPY flowmachine /flowmachine
+COPY flowclient /flowclient
+RUN pip install folium /flowclient /flowmachine && \
+    fix-permissions $CONDA_DIR && \
+    fix-permissions /home/$NB_USER && \
+    cd /home/$NB_USER/ && jupyter trust -y *
\ No newline at end of file
diff --git a/docker-compose.yml b/docker-compose.yml
index 5d85cc9cd2..b250485f51 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -113,6 +113,29 @@ services:
       - db
       - redis
 
+  worked_examples:
+    container_name: worked_examples
+    image: flowminder/flowkit_worked_examples:latest
+    build:
+      context: .
+      dockerfile: Dockerfile
+    ports:
+      - 8888
+    tty: true
+    stdin_open: true
+    environment:
+      - FLOWDB_PORT=5432
+      - FLOWDB_HOST=${DOCKER_FLOWDB_HOST:?Must set DOCKER_FLOWDB_HOST env var}
+      - FLOWMACHINE_FLOWDB_USER=${FLOWMACHINE_FLOWDB_USER:?Must set FLOWMACHINE_FLOWDB_USER env var}
+      - FLOWMACHINE_FLOWDB_PASSWORD=${FLOWMACHINE_FLOWDB_PASSWORD:?Must set FLOWMACHINE_FLOWDB_PASSWORD env var}
+      - REDIS_HOST=query_locker
+      - REDIS_PORT=6379
+      - REDIS_PASSWORD=${REDIS_PASSWORD:?Must set REDIS_PASSWORD env var}
+    restart: always
+    networks:
+      - db
+      - redis
+
   flowapi:
     container_name: flowapi
     image: flowminder/flowapi:${CONTAINER_TAG:-latest}

From 4e1cae873328d775ddeff9d0d8c72ea4c583ff27 Mon Sep 17 00:00:00 2001
From: Jono Gray <jonathan.gray@flowminder.org>
Date: Wed, 1 May 2019 12:29:06 +0100
Subject: [PATCH 02/29] Try building the examples on circle

---
 .circleci/config.yml | 13 ++++++++++---
 .dockerignore        |  3 +++
 Dockerfile           |  5 +++++
 docker-compose.yml   |  2 +-
 4 files changed, 19 insertions(+), 4 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 962252b743..a43237659b 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -461,7 +461,10 @@ jobs:
     parameters:
       component:
         type: enum
-        enum: ["flowmachine", "flowauth", "flowapi"]
+        enum: ["flowmachine", "flowauth", "flowapi", "flowkit-examples"]
+      component_path:
+        type: string
+        default: <<parameters.component>>
     docker:
       - image: circleci/python:3.7
     working_directory: /home/circleci/project/
@@ -478,7 +481,7 @@ jobs:
           name: Build <<parameters.component>> image
           command: |
             echo "Tagging as $CIRCLE_SHA1"
-            docker build -t flowminder/<<parameters.component>>:$CIRCLE_SHA1 ./<<parameters.component>>
+            docker build -t flowminder/<<parameters.component>>:$CIRCLE_SHA1 ./<<parameters.component_path>>
       - run:
           name: Push images to Docker cloud
           command: |
@@ -630,7 +633,7 @@ jobs:
           command: |
             export DOCKER_USER=$DOCKER_CLOUD_USER
             export DOCKER_PASS=$DOCKER_CLOUD_PASSWORD
-            for IMAGE in flowapi flowmachine flowdb flowdb-synthetic-data flowdb-testdata flowauth; do
+            for IMAGE in flowapi flowmachine flowdb flowdb-synthetic-data flowdb-testdata flowauth flowkit-examples; do
               docker-retag flowminder/$IMAGE:$CIRCLE_SHA1 ${<< parameters.tag >>:-latest}
             done
 
@@ -678,6 +681,10 @@ workflows:
           requires:
             - build_flowdb
           <<: *run_always_org_context
+      - build_docker_image:
+          name: build_examples
+          component: flowkit-examples
+          <<: *run_always_org_context
       - build_docker_image:
           name: build_flowmachine
           component: flowmachine
diff --git a/.dockerignore b/.dockerignore
index f03d1db99c..91244e8c51 100644
--- a/.dockerignore
+++ b/.dockerignore
@@ -1,3 +1,6 @@
+# This Source Code Form is subject to the terms of the Mozilla Public
+# License, v. 2.0. If a copy of the MPL was not distributed with this
+# file, You can obtain one at http://mozilla.org/MPL/2.0/.
 # This .dockerignore file follows the "whitelisting" approach described here:
 #    https://youknowfordevs.com/2018/12/07/getting-control-of-your-dockerignore-files.html
 
diff --git a/Dockerfile b/Dockerfile
index 9ea1c51d19..148e02c9d7 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,5 +1,10 @@
+# This Source Code Form is subject to the terms of the Mozilla Public
+# License, v. 2.0. If a copy of the MPL was not distributed with this
+# file, You can obtain one at http://mozilla.org/MPL/2.0/.
 FROM jupyter/datascience-notebook
+
 RUN rm -rf /home/$NB_USER/work
+
 COPY docs/source/worked_examples/*.ipynb /home/$NB_USER/
 COPY flowmachine /flowmachine
 COPY flowclient /flowclient
diff --git a/docker-compose.yml b/docker-compose.yml
index b250485f51..9b71ef9015 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -115,7 +115,7 @@ services:
 
   worked_examples:
     container_name: worked_examples
-    image: flowminder/flowkit_worked_examples:latest
+    image: flowminder/flowkit-examples:latest
     build:
       context: .
       dockerfile: Dockerfile

From 8f0080c0daf2196aa1901a094ba84e854a15cc13 Mon Sep 17 00:00:00 2001
From: Jono Gray <jonathan.gray@flowminder.org>
Date: Wed, 1 May 2019 13:47:35 +0100
Subject: [PATCH 03/29] Add to makefile, split into build and pull

---
 Makefile                 | 10 ++++++++++
 docker-compose-build.yml |  7 +++++++
 docker-compose.yml       |  5 +----
 3 files changed, 18 insertions(+), 4 deletions(-)

diff --git a/Makefile b/Makefile
index e98d4d4831..c1550952ab 100644
--- a/Makefile
+++ b/Makefile
@@ -108,6 +108,16 @@ flowauth-build:
 	docker-compose -f $(DOCKER_COMPOSE_FILE) -f $(DOCKER_COMPOSE_FILE_BUILD) build flowauth
 
 
+worked-examples-up: worked-examples-build
+	docker-compose -f $(DOCKER_COMPOSE_FILE) -f $(DOCKER_COMPOSE_FILE_BUILD) up -d --build worked_examples
+
+worked-examples-down:
+	docker-compose -f $(DOCKER_COMPOSE_FILE) rm -f -s -v worked_examples
+
+worked-examples-build:
+	docker-compose -f $(DOCKER_COMPOSE_FILE) -f $(DOCKER_COMPOSE_FILE_BUILD) build worked_examples
+
+
 flowmachine_query_locker-up:
 	docker-compose -f $(DOCKER_COMPOSE_FILE) up -d flowmachine_query_locker
 
diff --git a/docker-compose-build.yml b/docker-compose-build.yml
index 3a7646ab85..b5d2654d56 100644
--- a/docker-compose-build.yml
+++ b/docker-compose-build.yml
@@ -33,6 +33,13 @@ services:
       context: ./flowmachine
       dockerfile: Dockerfile
 
+  worked_examples:
+    container_name: worked_examples
+    image: flowminder/flowkit-examples:${CONTAINER_TAG:-latest}
+    build:
+      context: .
+      dockerfile: Dockerfile
+
   flowapi:
     image: flowminder/flowapi:${CONTAINER_TAG:-latest}
     build:
diff --git a/docker-compose.yml b/docker-compose.yml
index 9b71ef9015..94babce03a 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -115,10 +115,7 @@ services:
 
   worked_examples:
     container_name: worked_examples
-    image: flowminder/flowkit-examples:latest
-    build:
-      context: .
-      dockerfile: Dockerfile
+    image: flowminder/flowkit-examples:${CONTAINER_TAG:-latest}
     ports:
       - 8888
     tty: true

From 8f1b949dc7d212792e22cc88df9011396d35fe86 Mon Sep 17 00:00:00 2001
From: Jono Gray <jonathan.gray@flowminder.org>
Date: Wed, 1 May 2019 14:26:18 +0100
Subject: [PATCH 04/29] Don't tag the worked examples as eveyrthing

---
 .circleci/config.yml | 8 ++++----
 docker-compose.yml   | 2 ++
 quick_start.sh       | 4 ++--
 3 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index a43237659b..8a58153d51 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -462,9 +462,6 @@ jobs:
       component:
         type: enum
         enum: ["flowmachine", "flowauth", "flowapi", "flowkit-examples"]
-      component_path:
-        type: string
-        default: <<parameters.component>>
     docker:
       - image: circleci/python:3.7
     working_directory: /home/circleci/project/
@@ -481,7 +478,10 @@ jobs:
           name: Build <<parameters.component>> image
           command: |
             echo "Tagging as $CIRCLE_SHA1"
-            docker build -t flowminder/<<parameters.component>>:$CIRCLE_SHA1 ./<<parameters.component_path>>
+            if [[ <<parameters.component>> != "flowkit-examples ]]; then
+              cd <<parameters.component>>
+            fi
+            docker build -t flowminder/<<parameters.component>>:$CIRCLE_SHA1 .
       - run:
           name: Push images to Docker cloud
           command: |
diff --git a/docker-compose.yml b/docker-compose.yml
index 94babce03a..2fb4ebf13c 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -132,6 +132,8 @@ services:
     networks:
       - db
       - redis
+    command:
+      ["start-notebook.sh", "c.NotebookApp.token = 'b2a960c88d617bde49e592da8b60d09b3527873cb5a50db2'"]
 
   flowapi:
     container_name: flowapi
diff --git a/quick_start.sh b/quick_start.sh
index 2473ecc02d..197d3174e5 100755
--- a/quick_start.sh
+++ b/quick_start.sh
@@ -65,11 +65,11 @@ then
 else
     source /dev/stdin <<< "$(curl -s https://raw.githubusercontent.com/Flowminder/FlowKit/${BRANCH:-master}/development_environment)"
     echo "Starting containers"
-    RUNNING=`curl -s https://raw.githubusercontent.com/Flowminder/FlowKit/${BRANCH:-master}/docker-compose.yml | docker-compose -f - ps -q $DOCKER_FLOWDB_HOST flowapi flowmachine flowauth flowmachine_query_locker`
+    RUNNING=`curl -s https://raw.githubusercontent.com/Flowminder/FlowKit/${BRANCH:-master}/docker-compose.yml | docker-compose -f - ps -q $DOCKER_FLOWDB_HOST flowapi flowmachine flowauth flowmachine_query_locker worked_examples`
     if [[ "$RUNNING" != "" ]]; then
         confirm "Existing containers are running and will be replaced. Are you sure?" || exit 1
     fi
-    curl -s https://raw.githubusercontent.com/Flowminder/FlowKit/${BRANCH:-master}/docker-compose.yml | docker-compose -f - up -d $DOCKER_FLOWDB_HOST flowapi flowmachine flowauth flowmachine_query_locker
+    curl -s https://raw.githubusercontent.com/Flowminder/FlowKit/${BRANCH:-master}/docker-compose.yml | docker-compose -f - up -d $DOCKER_FLOWDB_HOST flowapi flowmachine flowauth flowmachine_query_locker worked_examples
     echo "Waiting for containers to be ready.."
     docker exec ${DOCKER_FLOWDB_HOST} bash -c 'i=0; until [ $i -ge 24 ] || (pg_isready -h 127.0.0.1 -p 5432); do let i=i+1; echo Waiting 10s; sleep 10; done' || (>&2 echo "FlowDB failed to start :( Please open an issue at https://github.com/Flowminder/FlowKit/issues/new?template=bug_report.md&labels=FlowDB,bug including the output of running 'docker logs flowdb'" && exit 1)
     echo "FlowDB ready."

From 6fcd8f080d9d3c152f6af279e820b59515385d41 Mon Sep 17 00:00:00 2001
From: Jono Gray <jonathan.gray@flowminder.org>
Date: Wed, 1 May 2019 14:27:19 +0100
Subject: [PATCH 05/29] SYntax

---
 .circleci/config.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 8a58153d51..7e865f5f92 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -478,7 +478,7 @@ jobs:
           name: Build <<parameters.component>> image
           command: |
             echo "Tagging as $CIRCLE_SHA1"
-            if [[ <<parameters.component>> != "flowkit-examples ]]; then
+            if [[ "<<parameters.component>>" != "flowkit-examples" ]]; then
               cd <<parameters.component>>
             fi
             docker build -t flowminder/<<parameters.component>>:$CIRCLE_SHA1 .

From 38e2595895dfbbdf2744fbfcf73bb21b7606e898 Mon Sep 17 00:00:00 2001
From: Jono Gray <jonathan.gray@flowminder.org>
Date: Wed, 1 May 2019 14:32:37 +0100
Subject: [PATCH 06/29] Less hacky

---
 .circleci/config.yml | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 7e865f5f92..b98930bc05 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -462,6 +462,8 @@ jobs:
       component:
         type: enum
         enum: ["flowmachine", "flowauth", "flowapi", "flowkit-examples"]
+      component_path:
+        type: string
     docker:
       - image: circleci/python:3.7
     working_directory: /home/circleci/project/
@@ -478,10 +480,7 @@ jobs:
           name: Build <<parameters.component>> image
           command: |
             echo "Tagging as $CIRCLE_SHA1"
-            if [[ "<<parameters.component>>" != "flowkit-examples" ]]; then
-              cd <<parameters.component>>
-            fi
-            docker build -t flowminder/<<parameters.component>>:$CIRCLE_SHA1 .
+            docker build -t flowminder/<<parameters.component>>:$CIRCLE_SHA1 <<parameters.component_path>>
       - run:
           name: Push images to Docker cloud
           command: |
@@ -684,10 +683,12 @@ workflows:
       - build_docker_image:
           name: build_examples
           component: flowkit-examples
+          component_path: .
           <<: *run_always_org_context
       - build_docker_image:
           name: build_flowmachine
           component: flowmachine
+          component_path: flowmachine
           requires:
             - run_flowmachine_tests
           <<: *run_always_org_context
@@ -700,6 +701,7 @@ workflows:
       - build_docker_image:
           name: build_flowauth
           component: flowauth
+          component_path: flowauth
           requires:
             - run_flowauth_backend_tests
             - run_flowauth_frontend_tests
@@ -707,6 +709,7 @@ workflows:
       - build_docker_image:
           name: build_flowapi
           component: flowapi
+          component_path: flowapi
           requires:
             - run_flowkit_api_tests
           <<: *run_always_org_context

From 29fd05dd45b59b55b7b6ab3fe1bf5811af234478 Mon Sep 17 00:00:00 2001
From: Jono Gray <jonathan.gray@flowminder.org>
Date: Wed, 1 May 2019 14:57:51 +0100
Subject: [PATCH 07/29] Correct token option

---
 docker-compose.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docker-compose.yml b/docker-compose.yml
index 2fb4ebf13c..97f14dc67b 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -133,7 +133,7 @@ services:
       - db
       - redis
     command:
-      ["start-notebook.sh", "c.NotebookApp.token = 'b2a960c88d617bde49e592da8b60d09b3527873cb5a50db2'"]
+      ["start-notebook.sh", "--NotebookApp.token = 'b2a960c88d617bde49e592da8b60d09b3527873cb5a50db2'"]
 
   flowapi:
     container_name: flowapi

From 260d67813af9c6e6e41c2e5335eee7d146857715 Mon Sep 17 00:00:00 2001
From: Jono Gray <jonathan.gray@flowminder.org>
Date: Wed, 1 May 2019 15:04:49 +0100
Subject: [PATCH 08/29] Fix worked examples to a port, check they came up in
 quickstart

---
 development_environment | 4 ++++
 docker-compose.yml      | 2 +-
 quick_start.sh          | 3 +++
 3 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/development_environment b/development_environment
index 4c09fadf05..0d3199561a 100644
--- a/development_environment
+++ b/development_environment
@@ -116,3 +116,7 @@ OUTPUT_ROOT_DIR=/docker-entrypoint-initdb.d
 # Integration tests
 
 FLOWKIT_INTEGRATION_TESTS_DISABLE_AUTOSTART_SERVERS=FALSE
+
+# Worked examples
+
+WORKED_EXAMPLES_PORT=8888
\ No newline at end of file
diff --git a/docker-compose.yml b/docker-compose.yml
index 97f14dc67b..6951b06af9 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -117,7 +117,7 @@ services:
     container_name: worked_examples
     image: flowminder/flowkit-examples:${CONTAINER_TAG:-latest}
     ports:
-      - 8888
+      - ${WORKED_EXAMPLES_PORT:?Must set WORKED_EXAMPLES_PORT env var}:8888
     tty: true
     stdin_open: true
     environment:
diff --git a/quick_start.sh b/quick_start.sh
index 197d3174e5..5d1e5575d3 100755
--- a/quick_start.sh
+++ b/quick_start.sh
@@ -79,9 +79,12 @@ else
     echo "FlowAPI ready."
     i=0; until [ $i -ge 24 ] || (curl -s http://localhost:$FLOWAUTH_PORT > /dev/null) ; do let i=i+1; echo Waiting 10s; sleep 10; done || (>&2 echo "FlowAuth failed to start :( Please open an issue at https://github.com/Flowminder/FlowKit/issues/new?template=bug_report.md&labels=FlowAuth,bug including the output of running 'docker logs flowauth'" && exit 1)
     echo "FlowAuth ready."
+    i=0; until [ $i -ge 24 ] || (curl -s http://localhost:$WORKED_EXAMPLES_PORT > /dev/null) ; do let i=i+1; echo Waiting 10s; sleep 10; done || (>&2 echo "Worked examples failed to start :( Please open an issue at https://github.com/Flowminder/FlowKit/issues/new?template=bug_report.md&labels=docs,bug including the output of running 'docker logs worked_examples'" && exit 1)
+    echo "Worked examples ready."
     echo "All containers ready!"
     echo "Access FlowDB using 'PGHOST=$FLOWDB_HOST PGPORT=$FLOWDB_PORT PGDATABASE=flowdb PGUSER=$FLOWMACHINE_FLOWDB_USER PGPASSWORD=$FLOWMACHINE_FLOWDB_PASSWORD psql'"
     echo "Access FlowAPI using FlowClient at http://localhost:$FLOWAPI_PORT"
     echo "View the FlowAPI spec at http://localhost:$FLOWAPI_PORT/api/0/spec/redoc"
     echo "Generate FlowAPI access tokens using FlowAuth with user TEST_USER and password DUMMY_PASSWORD at http://localhost:$FLOWAUTH_PORT"
+    echo "Try out the interactive examples at http://localhost:$FLOWAUTH_PORT/?token=b2a960c88d617bde49e592da8b60d09b3527873cb5a50db2"
 fi
\ No newline at end of file

From c9ceb2ad3662fd6c177a88163b6009eb8c5a29ed Mon Sep 17 00:00:00 2001
From: Jono Gray <jonathan.gray@flowminder.org>
Date: Wed, 1 May 2019 15:30:45 +0100
Subject: [PATCH 09/29] Rejig CI order again

---
 .circleci/config.yml | 22 +++++++---------------
 docker-compose.yml   |  2 +-
 quick_start.sh       |  2 +-
 3 files changed, 9 insertions(+), 17 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index b98930bc05..53bddf6822 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -689,8 +689,6 @@ workflows:
           name: build_flowmachine
           component: flowmachine
           component_path: flowmachine
-          requires:
-            - run_flowmachine_tests
           <<: *run_always_org_context
       - build_docs:
           name: build_docs
@@ -702,30 +700,23 @@ workflows:
           name: build_flowauth
           component: flowauth
           component_path: flowauth
-          requires:
-            - run_flowauth_backend_tests
-            - run_flowauth_frontend_tests
           <<: *run_always_org_context
       - build_docker_image:
           name: build_flowapi
           component: flowapi
           component_path: flowapi
-          requires:
-            - run_flowkit_api_tests
           <<: *run_always_org_context
       - build_python_wheel:
           name: build_flowclient_wheel
           project_name: flowclient
           requires:
-            - run_flowclient_tests
-            - integration_tests
+            - install_flowmachine_deps
           <<: *run_always_org_context
       - build_python_wheel:
           name: build_flowmachine_wheel
           project_name: flowmachine
           requires:
-            - run_flowmachine_tests
-            - integration_tests
+            - install_flowmachine_deps
           <<: *run_always_org_context
       - test_quickstart:
           requires:
@@ -733,6 +724,7 @@ workflows:
             - build_flowapi
             - build_flowmachine
             - build_flowauth
+            - build_examples
           <<: *run_always_org_context
       - integration_tests:
           requires:
@@ -743,12 +735,14 @@ workflows:
           name: retag_master_branch
           requires:
             - test_quickstart
+            - integration_tests
             - build_docs
           <<: *master_only_org_context
       - retag_images:
           name: retag_tagged_build
           requires:
             - test_quickstart
+            - integration_tests
             - build_docs
           tag: CIRCLE_TAG
           <<: *tag_only_org_context
@@ -756,19 +750,17 @@ workflows:
           name: push_flowclient_wheel
           project_name: flowclient
           requires:
-            - build_flowclient_wheel
+            - retag_tagged_build
           <<: *tag_only_org_context
       - push_wheel:
           name: push_flowmachine_wheel
           project_name: flowmachine
           requires:
-            - build_flowmachine_wheel
+            - retag_tagged_build
           <<: *tag_only_org_context
       - build_docs:
           name: Deploy docs
           deploy: true
           requires:
-            - build_docs
             - retag_tagged_build
-            - push_flowclient_wheel
           <<: *tag_only_org_context
diff --git a/docker-compose.yml b/docker-compose.yml
index 6951b06af9..36b65d60b8 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -133,7 +133,7 @@ services:
       - db
       - redis
     command:
-      ["start-notebook.sh", "--NotebookApp.token = 'b2a960c88d617bde49e592da8b60d09b3527873cb5a50db2'"]
+      ["start.sh", "jupyter", "lab", "--LabApp.token=''"]
 
   flowapi:
     container_name: flowapi
diff --git a/quick_start.sh b/quick_start.sh
index 5d1e5575d3..a800a3d509 100755
--- a/quick_start.sh
+++ b/quick_start.sh
@@ -86,5 +86,5 @@ else
     echo "Access FlowAPI using FlowClient at http://localhost:$FLOWAPI_PORT"
     echo "View the FlowAPI spec at http://localhost:$FLOWAPI_PORT/api/0/spec/redoc"
     echo "Generate FlowAPI access tokens using FlowAuth with user TEST_USER and password DUMMY_PASSWORD at http://localhost:$FLOWAUTH_PORT"
-    echo "Try out the interactive examples at http://localhost:$FLOWAUTH_PORT/?token=b2a960c88d617bde49e592da8b60d09b3527873cb5a50db2"
+    echo "Try out the interactive examples at http://localhost:$FLOWAUTH_PORT"
 fi
\ No newline at end of file

From bc10d890fdb351a20af9cf0e2589bb5cf0dc795a Mon Sep 17 00:00:00 2001
From: Jono Gray <jonathan.gray@flowminder.org>
Date: Wed, 1 May 2019 15:33:21 +0100
Subject: [PATCH 10/29] Connect tests back in

---
 .circleci/config.yml | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 53bddf6822..1eeb1616e0 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -737,6 +737,10 @@ workflows:
             - test_quickstart
             - integration_tests
             - build_docs
+            - run_flowkit_api_tests
+            - run_flowauth_backend_tests
+            - run_flowauth_frontend_tests
+            - run_flowclient_tests
           <<: *master_only_org_context
       - retag_images:
           name: retag_tagged_build
@@ -744,6 +748,10 @@ workflows:
             - test_quickstart
             - integration_tests
             - build_docs
+            - run_flowkit_api_tests
+            - run_flowauth_backend_tests
+            - run_flowauth_frontend_tests
+            - run_flowclient_tests
           tag: CIRCLE_TAG
           <<: *tag_only_org_context
       - push_wheel:

From 6cc93a0ff5e461fbb8748503bff36abce86d804a Mon Sep 17 00:00:00 2001
From: Jono Gray <jonathan.gray@flowminder.org>
Date: Wed, 1 May 2019 15:49:35 +0100
Subject: [PATCH 11/29] Switch to a smaller baseimage

---
 Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index 148e02c9d7..c9766e90ac 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,7 +1,7 @@
 # This Source Code Form is subject to the terms of the Mozilla Public
 # License, v. 2.0. If a copy of the MPL was not distributed with this
 # file, You can obtain one at http://mozilla.org/MPL/2.0/.
-FROM jupyter/datascience-notebook
+FROM jupyter/scipy-notebook
 
 RUN rm -rf /home/$NB_USER/work
 

From 26593b780e3ec175b27a3f3a52e94f0f2eef5bb5 Mon Sep 17 00:00:00 2001
From: Jono Gray <jonathan.gray@flowminder.org>
Date: Wed, 1 May 2019 15:58:35 +0100
Subject: [PATCH 12/29] Squash build steps a little more

---
 .circleci/config.yml | 20 ++++----------------
 1 file changed, 4 insertions(+), 16 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 1eeb1616e0..e85d7b79fb 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -128,18 +128,6 @@ executors:
           REDIS_PASSWORD: "fm_redis"
 
 jobs:
-  set_docker_tag_for_ci_images:
-    docker: *base_docker
-    steps:
-      - run:
-          name: Set a common docker tag
-          command: |
-            echo "export SAFE_TAG=${CIRCLE_TAG:-$(echo -n $CIRCLE_BRANCH | md5sum | cut -d" " -f1)}"| tee -a $BASH_ENV /home/circleci/.env
-      - persist_to_workspace:
-          root: /home/circleci/
-          paths:
-            - .env
-
   build_flowdb:
     machine:
       image: circleci/classic:201808-01
@@ -147,6 +135,10 @@ jobs:
     environment: *flowdb_env
     steps:
       - checkout
+      - run:
+          name: Set a common docker tag
+          command: |
+            echo "export SAFE_TAG=${CIRCLE_TAG:-$(echo -n $CIRCLE_BRANCH | md5sum | cut -d" " -f1)}"| tee -a $BASH_ENV /home/circleci/.env
       - attach_workspace:
           at: /home/circleci/
       - restore_cache:
@@ -643,11 +635,7 @@ jobs:
 workflows:
   run_build_pipeline:
     jobs:
-      - set_docker_tag_for_ci_images:
-          <<: *run_always_org_context
       - build_flowdb:
-          requires:
-            - set_docker_tag_for_ci_images
           <<: *run_always_org_context
       - install_flowmachine_deps:
           <<: *run_always_org_context

From aa77aebbff6041b7212f82ea0eca3da4fd1bddf1 Mon Sep 17 00:00:00 2001
From: Jono Gray <jonathan.gray@flowminder.org>
Date: Wed, 1 May 2019 16:58:40 +0100
Subject: [PATCH 13/29] Correct port

---
 quick_start.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/quick_start.sh b/quick_start.sh
index a800a3d509..630500612a 100755
--- a/quick_start.sh
+++ b/quick_start.sh
@@ -86,5 +86,5 @@ else
     echo "Access FlowAPI using FlowClient at http://localhost:$FLOWAPI_PORT"
     echo "View the FlowAPI spec at http://localhost:$FLOWAPI_PORT/api/0/spec/redoc"
     echo "Generate FlowAPI access tokens using FlowAuth with user TEST_USER and password DUMMY_PASSWORD at http://localhost:$FLOWAUTH_PORT"
-    echo "Try out the interactive examples at http://localhost:$FLOWAUTH_PORT"
+    echo "Try out the interactive examples at http://localhost:$WORKED_EXAMPLES_PORT"
 fi
\ No newline at end of file

From 5cd60a84acb9f11014838f027f3cc4a2db355337 Mon Sep 17 00:00:00 2001
From: Jono Gray <jonathan.gray@flowminder.org>
Date: Thu, 2 May 2019 09:28:33 +0100
Subject: [PATCH 14/29] Make worked examples spin up synth data, make worked
 examples optional

---
 .circleci/config.yml | 12 ++++++++++++
 quick_start.sh       | 22 ++++++++++++++++++----
 2 files changed, 30 insertions(+), 4 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index e85d7b79fb..0b0882fe64 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -511,6 +511,18 @@ jobs:
           path: /home/circleci/project/
       - run: ./quick_start.sh
       - run: ./quick_start.sh stop
+      - run: ./quick_start.sh examples
+      - run: ./quick_start.sh stop
+      - run: ./quick_start.sh synth
+      - run: ./quick_start.sh stop
+      - run:
+          name: Check all containers are down
+          command:
+            RUNNING=`docker-compose -q`
+            if [[ "$RUNNING" != "" ]]
+            then
+              exit 1
+            fi
 
   build_docs:
     parameters:
diff --git a/quick_start.sh b/quick_start.sh
index 630500612a..2b76f47496 100755
--- a/quick_start.sh
+++ b/quick_start.sh
@@ -56,6 +56,14 @@ else
     export DOCKER_FLOWDB_HOST=flowdb_testdata
 fi
 
+if [ $# -gt 0 ] && [ "$1" = "examples" ]
+then
+    export WORKED_EXAMPLES=worked_examples
+    export DOCKER_FLOWDB_HOST=flowdb_synthetic_data
+else
+    export WORKED_EXAMPLES=
+fi
+
 if [ $# -gt 0 ] && [ "$1" = "stop" ]
 then
     export DOCKER_FLOWDB_HOST=flowdb_testdata
@@ -65,11 +73,11 @@ then
 else
     source /dev/stdin <<< "$(curl -s https://raw.githubusercontent.com/Flowminder/FlowKit/${BRANCH:-master}/development_environment)"
     echo "Starting containers"
-    RUNNING=`curl -s https://raw.githubusercontent.com/Flowminder/FlowKit/${BRANCH:-master}/docker-compose.yml | docker-compose -f - ps -q $DOCKER_FLOWDB_HOST flowapi flowmachine flowauth flowmachine_query_locker worked_examples`
+    RUNNING=`curl -s https://raw.githubusercontent.com/Flowminder/FlowKit/${BRANCH:-master}/docker-compose.yml | docker-compose -f - ps -q $DOCKER_FLOWDB_HOST flowapi flowmachine flowauth flowmachine_query_locker $WORKED_EXAMPLES`
     if [[ "$RUNNING" != "" ]]; then
         confirm "Existing containers are running and will be replaced. Are you sure?" || exit 1
     fi
-    curl -s https://raw.githubusercontent.com/Flowminder/FlowKit/${BRANCH:-master}/docker-compose.yml | docker-compose -f - up -d $DOCKER_FLOWDB_HOST flowapi flowmachine flowauth flowmachine_query_locker worked_examples
+    curl -s https://raw.githubusercontent.com/Flowminder/FlowKit/${BRANCH:-master}/docker-compose.yml | docker-compose -f - up -d $DOCKER_FLOWDB_HOST flowapi flowmachine flowauth flowmachine_query_locker $WORKED_EXAMPLES
     echo "Waiting for containers to be ready.."
     docker exec ${DOCKER_FLOWDB_HOST} bash -c 'i=0; until [ $i -ge 24 ] || (pg_isready -h 127.0.0.1 -p 5432); do let i=i+1; echo Waiting 10s; sleep 10; done' || (>&2 echo "FlowDB failed to start :( Please open an issue at https://github.com/Flowminder/FlowKit/issues/new?template=bug_report.md&labels=FlowDB,bug including the output of running 'docker logs flowdb'" && exit 1)
     echo "FlowDB ready."
@@ -79,12 +87,18 @@ else
     echo "FlowAPI ready."
     i=0; until [ $i -ge 24 ] || (curl -s http://localhost:$FLOWAUTH_PORT > /dev/null) ; do let i=i+1; echo Waiting 10s; sleep 10; done || (>&2 echo "FlowAuth failed to start :( Please open an issue at https://github.com/Flowminder/FlowKit/issues/new?template=bug_report.md&labels=FlowAuth,bug including the output of running 'docker logs flowauth'" && exit 1)
     echo "FlowAuth ready."
-    i=0; until [ $i -ge 24 ] || (curl -s http://localhost:$WORKED_EXAMPLES_PORT > /dev/null) ; do let i=i+1; echo Waiting 10s; sleep 10; done || (>&2 echo "Worked examples failed to start :( Please open an issue at https://github.com/Flowminder/FlowKit/issues/new?template=bug_report.md&labels=docs,bug including the output of running 'docker logs worked_examples'" && exit 1)
+    if [[ "$WORKED_EXAMPLES" = "worked_examples" ]]
+    then
+        i=0; until [ $i -ge 24 ] || (curl -s http://localhost:$WORKED_EXAMPLES_PORT > /dev/null) ; do let i=i+1; echo Waiting 10s; sleep 10; done || (>&2 echo "Worked examples failed to start :( Please open an issue at https://github.com/Flowminder/FlowKit/issues/new?template=bug_report.md&labels=docs,bug including the output of running 'docker logs worked_examples'" && exit 1)
+    fi
     echo "Worked examples ready."
     echo "All containers ready!"
     echo "Access FlowDB using 'PGHOST=$FLOWDB_HOST PGPORT=$FLOWDB_PORT PGDATABASE=flowdb PGUSER=$FLOWMACHINE_FLOWDB_USER PGPASSWORD=$FLOWMACHINE_FLOWDB_PASSWORD psql'"
     echo "Access FlowAPI using FlowClient at http://localhost:$FLOWAPI_PORT"
     echo "View the FlowAPI spec at http://localhost:$FLOWAPI_PORT/api/0/spec/redoc"
     echo "Generate FlowAPI access tokens using FlowAuth with user TEST_USER and password DUMMY_PASSWORD at http://localhost:$FLOWAUTH_PORT"
-    echo "Try out the interactive examples at http://localhost:$WORKED_EXAMPLES_PORT"
+    if [[ "$WORKED_EXAMPLES" = "worked_examples" ]]
+    then
+        echo "Try out the interactive examples at http://localhost:$WORKED_EXAMPLES_PORT"
+    fi
 fi
\ No newline at end of file

From d636015276a02cb122f0e1f77d72e07333e0d070 Mon Sep 17 00:00:00 2001
From: Jono Gray <jonathan.gray@flowminder.org>
Date: Thu, 2 May 2019 09:53:47 +0100
Subject: [PATCH 15/29] Make examples use regular data size by default, but
 allow combining with larger data, rename synth flag larger_data

---
 .circleci/config.yml   |  4 ++--
 docs/source/install.md | 19 ++++++++++++++++++-
 quick_start.sh         |  5 ++---
 3 files changed, 22 insertions(+), 6 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 0b0882fe64..e4a59a00ae 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -513,8 +513,8 @@ jobs:
       - run: ./quick_start.sh stop
       - run: ./quick_start.sh examples
       - run: ./quick_start.sh stop
-      - run: ./quick_start.sh synth
-      - run: ./quick_start.sh stop
+      #- run: ./quick_start.sh synth # Synth data spinup with this data volume is very slow so not testing it right now on CI
+      #- run: ./quick_start.sh stop
       - run:
           name: Check all containers are down
           command:
diff --git a/docs/source/install.md b/docs/source/install.md
index 2146cd8dd0..914c8b9970 100644
--- a/docs/source/install.md
+++ b/docs/source/install.md
@@ -34,9 +34,26 @@ This will pull any necessary docker containers, and start the system in the back
 The default system includes a small amount of test data. For a test system with considerably more data you can run
 
 ```bash
-bash <(curl -s https://raw.githubusercontent.com/Flowminder/FlowKit/master/quick_start.sh) synth
+bash <(curl -s https://raw.githubusercontent.com/Flowminder/FlowKit/master/quick_start.sh) larger_data
 ```  
 
+!!! warning
+    The larger data container will take considerably longer to start up, as it generates data when first run.
+
+The [worked examples](worked_examples) are also available as part of the demo system. To install these run 
+
+```bash
+bash <(curl -s https://raw.githubusercontent.com/Flowminder/FlowKit/master/quick_start.sh) examples
+```  
+
+for the examples with a small dataset, or 
+
+```bash
+bash <(curl -s https://raw.githubusercontent.com/Flowminder/FlowKit/master/quick_start.sh) examples larger_data
+```  
+
+to get the examples with the larger dataset (the one used when producing this documentation).
+
 In order to use the test system, now install FlowClient, and generate a token using FlowAuth.
 
 #### FlowAuth Quickstart
diff --git a/quick_start.sh b/quick_start.sh
index 2b76f47496..3bb08e60ca 100755
--- a/quick_start.sh
+++ b/quick_start.sh
@@ -49,17 +49,16 @@ if [ "$CI" = "true" ]; then
     export BRANCH=$CIRCLE_SHA1
 fi
 
-if [ $# -gt 0 ] && [ "$1" = "synth" ]
+if [ $# -gt 0 ] && [ "$1" = "larger_data" ] || [ "$2" = "larger_data" ]
 then
     export DOCKER_FLOWDB_HOST=flowdb_synthetic_data
 else
     export DOCKER_FLOWDB_HOST=flowdb_testdata
 fi
 
-if [ $# -gt 0 ] && [ "$1" = "examples" ]
+if [ $# -gt 0 ] && [ "$1" = "examples" ] || [ "$2" = "examples" ]
 then
     export WORKED_EXAMPLES=worked_examples
-    export DOCKER_FLOWDB_HOST=flowdb_synthetic_data
 else
     export WORKED_EXAMPLES=
 fi

From 5daac7f9e7ab9d1ea81db7c87f30b717600dbf99 Mon Sep 17 00:00:00 2001
From: Jono Gray <jonathan.gray@flowminder.org>
Date: Thu, 2 May 2019 10:05:12 +0100
Subject: [PATCH 16/29] Update changelog, tweak docs to point out worked
 examples available in quickstart, fix all down check on CI

---
 .circleci/config.yml                 | 2 +-
 CHANGELOG.md                         | 1 +
 docs/source/install.md               | 5 +----
 docs/source/worked_examples/index.md | 2 ++
 4 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index e4a59a00ae..c9af77edec 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -518,7 +518,7 @@ jobs:
       - run:
           name: Check all containers are down
           command:
-            RUNNING=`docker-compose -q`
+            RUNNING=`docker ps -q`
             if [[ "$RUNNING" != "" ]]
             then
               exit 1
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 969ee4fc13..4c0cd31180 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +8,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 - Error is displayed in the add user form of Flowauth if username is alredy exists. [#690](https://github.com/Flowminder/FlowKit/issues/690)
 
 ### Added
+- FlowKit's worked examples are now available as part of the quick setup script
 
 ### Changed
 
diff --git a/docs/source/install.md b/docs/source/install.md
index 914c8b9970..38ed01b8c6 100644
--- a/docs/source/install.md
+++ b/docs/source/install.md
@@ -18,10 +18,7 @@ The bulk of the installation process consists of downloading [Docker](https://do
 
 These instructions assume use of [Pyenv](https://github.com/pyenv/pyenv) and [Pipenv](https://github.com/pypa/pipenv). [Anaconda](https://www.anaconda.com/what-is-anaconda/) stack based installation commands may be different. 
 
-
-### Server and Authentication Installation
-
-Docker containers for FlowAPI, FlowMachine and FlowDB are provided in the [DockerCloud](https://cloud.docker.com/) repositories `flowminder/flowapi`, `flowminder/flowmachine` and `flowminder/flowdb`, respectively. You will need [Docker](https://docs.docker.com/install/) and [Docker Compose](https://docs.docker.com/compose/install/).
+Docker containers for [FlowAPI](http://https://hub.docker.com/r/flowminder/flowapi), [FlowMachine](http://https://hub.docker.com/r/flowminder/flowmachine), [FlowDB](http://https://hub.docker.com/r/flowminder/flowdb), [FlowAuth](http://https://hub.docker.com/r/flowminder/flowauth) and the [worked examples](http://https://hub.docker.com/r/flowminder/flowkit-examples) are provided in the [DockerCloud](https://hub.docker.com/) repositories `flowminder/flowapi`, `flowminder/flowmachine`, `flowminder/flowdb`, `flowminder/flowauth`, and `flowminder/flowkit-examples` respectively. You will need [Docker](https://docs.docker.com/install/) and [Docker Compose](https://docs.docker.com/compose/install/).
 
 Start the FlowKit test system by running 
 
diff --git a/docs/source/worked_examples/index.md b/docs/source/worked_examples/index.md
index 5e897a4c57..7c84ccd13b 100644
--- a/docs/source/worked_examples/index.md
+++ b/docs/source/worked_examples/index.md
@@ -9,3 +9,5 @@ We have three worked examples of using FlowKit for CDR analysis:
 - [Mobile Data Usage](./mobile-data-usage/) (using FlowMachine).
 
 The Jupyter notebooks for these worked examples can be found [here](https://github.com/Flowminder/FlowKit/tree/master/docs/source/worked_examples/).
+
+Alternatively you can run the worked examples using the [quick start setup](../install.md#quickinstall) which includes JupyterLab. 

From 5d3ea8a6fb7068bf98b2caaad0abf920114dadea Mon Sep 17 00:00:00 2001
From: Jono Gray <jonathan.gray@flowminder.org>
Date: Thu, 2 May 2019 10:09:00 +0100
Subject: [PATCH 17/29] Dockerfile docstring, add worked examples to makefile
 services

---
 Dockerfile | 5 +++++
 Makefile   | 2 +-
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index c9766e90ac..8190cbe55c 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,6 +1,11 @@
 # This Source Code Form is subject to the terms of the Mozilla Public
 # License, v. 2.0. If a copy of the MPL was not distributed with this
 # file, You can obtain one at http://mozilla.org/MPL/2.0/.
+#
+# Worked examples docker container
+# Provides all worked examples from the FlowKit docs in a ready-to-go JupyterLab install
+#
+
 FROM jupyter/scipy-notebook
 
 RUN rm -rf /home/$NB_USER/work
diff --git a/Makefile b/Makefile
index c1550952ab..548d36d17e 100644
--- a/Makefile
+++ b/Makefile
@@ -21,7 +21,7 @@
 DOCKER_COMPOSE_FILE ?= docker-compose.yml
 DOCKER_COMPOSE_FILE_BUILD ?= docker-compose-build.yml
 FLOWDB_SERVICES ?= flowdb_testdata
-DOCKER_SERVICES ?= $(FLOWDB_SERVICES) flowapi flowmachine flowauth flowmachine_query_locker
+DOCKER_SERVICES ?= $(FLOWDB_SERVICES) flowapi flowmachine flowauth flowmachine_query_locker worked_examples
 export DOCKER_FLOWDB_HOST=$(word 1, $(FLOWDB_SERVICES))
 
 

From 2be944bfafdf2484d147a397d0ef00e6398f9ffd Mon Sep 17 00:00:00 2001
From: Jono Gray <jonathan.gray@flowminder.org>
Date: Thu, 2 May 2019 10:10:39 +0100
Subject: [PATCH 18/29] Update CHANGELOG.md

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4c0cd31180..4af527f76d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,7 +8,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 - Error is displayed in the add user form of Flowauth if username is alredy exists. [#690](https://github.com/Flowminder/FlowKit/issues/690)
 
 ### Added
-- FlowKit's worked examples are now available as part of the quick setup script
+- FlowKit's worked examples are now Dockerized, and available as part of the quick setup script [#614](https://github.com/Flowminder/FlowKit/issues/614)
 
 ### Changed
 

From 689a59e2138b56cb8274bc39925eac317a527d9a Mon Sep 17 00:00:00 2001
From: Jono Gray <jonathan.gray@flowminder.org>
Date: Thu, 2 May 2019 10:40:32 +0100
Subject: [PATCH 19/29] Fix syntax

---
 .circleci/config.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index c9af77edec..2bb3fdc961 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -517,7 +517,7 @@ jobs:
       #- run: ./quick_start.sh stop
       - run:
           name: Check all containers are down
-          command:
+          command: |
             RUNNING=`docker ps -q`
             if [[ "$RUNNING" != "" ]]
             then

From a04f7b7b3d506c4b12989487962cf7d57f104da9 Mon Sep 17 00:00:00 2001
From: Jono Gray <jonathan.gray@flowminder.org>
Date: Thu, 2 May 2019 13:53:48 +0100
Subject: [PATCH 20/29] Add docker version check to quick start script

---
 docker-compose-build.yml |  2 +-
 docker-compose.yml       |  2 +-
 quick_start.sh           | 18 ++++++++++++++++++
 3 files changed, 20 insertions(+), 2 deletions(-)

diff --git a/docker-compose-build.yml b/docker-compose-build.yml
index b5d2654d56..cf764f9646 100644
--- a/docker-compose-build.yml
+++ b/docker-compose-build.yml
@@ -5,7 +5,7 @@
 # DOCKER COMPOSE BUILDER FOR FLOWKIT
 #
 
-version: '3.7'
+version: '3.5'
 
 services:
 
diff --git a/docker-compose.yml b/docker-compose.yml
index 36b65d60b8..f95beb24f2 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -5,7 +5,7 @@
 # DOCKER COMPOSE FOR FLOWKIT
 #
 
-version: '3.7'
+version: '3.5'
 
 networks:
   db:
diff --git a/quick_start.sh b/quick_start.sh
index 3bb08e60ca..8381441691 100755
--- a/quick_start.sh
+++ b/quick_start.sh
@@ -5,6 +5,8 @@
 set -e
 set -a
 
+
+
 # Read a single char from /dev/tty, prompting with "$*"
 # Note: pressing enter will return a null string. Perhaps a version terminated with X and then remove it in caller?
 # See https://unix.stackexchange.com/a/367880/143394 for dealing with multi-byte, etc.
@@ -63,6 +65,22 @@ else
     export WORKED_EXAMPLES=
 fi
 
+DOCKER_ENGINE_VERSION=`docker version --format '{{.Server.Version}}'`
+DOCKER_COMPOSE_VERSION=`docker-compose version --short`
+if [[ "$DOCKER_ENGINE_VERSION" < "17.12.0" ]]
+then
+    echo "Docker version not supported. Please upgrade docker to at least v17.12.0"
+    exit 1
+fi
+
+if [[ "$DOCKER_COMPOSE_VERSION" < "1.21.0" ]]
+then
+    echo "docker-compose version not supported. Please upgrade docker to at least v1.21.0 (e.g. by running 'pip install --upgrade docker-compose'"
+    echo "or installing a newer version of Docker desktop."
+    exit 1
+fi
+
+
 if [ $# -gt 0 ] && [ "$1" = "stop" ]
 then
     export DOCKER_FLOWDB_HOST=flowdb_testdata

From 9f2ccda3d7e688cd86393d1e3cd6a62b6a3e5b40 Mon Sep 17 00:00:00 2001
From: Jono Gray <jonathan.gray@flowminder.org>
Date: Tue, 7 May 2019 09:26:14 +0100
Subject: [PATCH 21/29] Make large data default for examples

---
 .circleci/config.yml   |  4 ++--
 docs/source/install.md | 10 ++++++++--
 quick_start.sh         |  6 ++++++
 3 files changed, 16 insertions(+), 4 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 2bb3fdc961..9dd1f1886d 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -511,9 +511,9 @@ jobs:
           path: /home/circleci/project/
       - run: ./quick_start.sh
       - run: ./quick_start.sh stop
-      - run: ./quick_start.sh examples
+      - run: ./quick_start.sh examples smaller_data
       - run: ./quick_start.sh stop
-      #- run: ./quick_start.sh synth # Synth data spinup with this data volume is very slow so not testing it right now on CI
+      #- run: ./quick_start.sh larger_data # Synth data spinup with this data volume is very slow so not testing it right now on CI
       #- run: ./quick_start.sh stop
       - run:
           name: Check all containers are down
diff --git a/docs/source/install.md b/docs/source/install.md
index 38ed01b8c6..59372e903f 100644
--- a/docs/source/install.md
+++ b/docs/source/install.md
@@ -40,17 +40,23 @@ bash <(curl -s https://raw.githubusercontent.com/Flowminder/FlowKit/master/quick
 The [worked examples](worked_examples) are also available as part of the demo system. To install these run 
 
 ```bash
-bash <(curl -s https://raw.githubusercontent.com/Flowminder/FlowKit/master/quick_start.sh) examples
+bash <(curl -s https://raw.githubusercontent.com/Flowminder/FlowKit/master/quick_start.sh) examples smaller_data
 ```  
 
 for the examples with a small dataset, or 
 
 ```bash
-bash <(curl -s https://raw.githubusercontent.com/Flowminder/FlowKit/master/quick_start.sh) examples larger_data
+bash <(curl -s https://raw.githubusercontent.com/Flowminder/FlowKit/master/quick_start.sh) examples
 ```  
 
 to get the examples with the larger dataset (the one used when producing this documentation).
 
+To shut down the system, you can either stop all the docker containers directly, or run
+
+```bash
+bash <(curl -s https://raw.githubusercontent.com/Flowminder/FlowKit/master/quick_start.sh) stop
+```
+
 In order to use the test system, now install FlowClient, and generate a token using FlowAuth.
 
 #### FlowAuth Quickstart
diff --git a/quick_start.sh b/quick_start.sh
index 8381441691..ab1316cbbf 100755
--- a/quick_start.sh
+++ b/quick_start.sh
@@ -61,6 +61,12 @@ fi
 if [ $# -gt 0 ] && [ "$1" = "examples" ] || [ "$2" = "examples" ]
 then
     export WORKED_EXAMPLES=worked_examples
+    if [ $# -gt 0 ] && [ "$1" = "smaller_data" ] || [ "$2" = "smaller_data" ]
+    then
+        export DOCKER_FLOWDB_HOST=flowdb_testdata
+    else
+        export DOCKER_FLOWDB_HOST=flowdb_testdata
+    fi
 else
     export WORKED_EXAMPLES=
 fi

From 0facddba20ca7a65b360695de914cfbad4131040 Mon Sep 17 00:00:00 2001
From: Jono Gray <jonathan.gray@flowminder.org>
Date: Tue, 7 May 2019 09:38:19 +0100
Subject: [PATCH 22/29] Use env var for flowapi url

---
 docker-compose.yml                                   | 2 ++
 docs/source/worked_examples/Flows.ipynb              | 4 ++--
 docs/source/worked_examples/commuting-patterns.ipynb | 4 ++--
 3 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/docker-compose.yml b/docker-compose.yml
index f95beb24f2..e0cd6812de 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -128,6 +128,7 @@ services:
       - REDIS_HOST=query_locker
       - REDIS_PORT=6379
       - REDIS_PASSWORD=${REDIS_PASSWORD:?Must set REDIS_PASSWORD env var}
+      -
     restart: always
     networks:
       - db
@@ -149,6 +150,7 @@ services:
       - FLOWDB_PORT=5432
       - JWT_SECRET_KEY=${JWT_SECRET_KEY:?Must set JWT_SECRET_KEY env var}
       - FLOWAPI_LOG_LEVEL=${FLOWAPI_LOG_LEVEL:?Must set FLOWAPI_LOG_LEVEL env var}
+      - FLOWAPI_URL="http://flowapi:9090"
     tty: true
     stdin_open: true
     restart: always
diff --git a/docs/source/worked_examples/Flows.ipynb b/docs/source/worked_examples/Flows.ipynb
index 630dcfa944..b3af776cbf 100644
--- a/docs/source/worked_examples/Flows.ipynb
+++ b/docs/source/worked_examples/Flows.ipynb
@@ -21,7 +21,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import flowclient, folium"
+    "import flowclient, folium, os"
    ]
   },
   {
@@ -37,7 +37,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "conn = flowclient.connect(\"http://localhost:9090\", TOKEN)"
+    "conn = flowclient.connect(os.getenv(\"FLOWAPI_URL\", \"http://localhost:9090\"), TOKEN)"
    ]
   },
   {
diff --git a/docs/source/worked_examples/commuting-patterns.ipynb b/docs/source/worked_examples/commuting-patterns.ipynb
index aabfda212c..ee4d9be547 100644
--- a/docs/source/worked_examples/commuting-patterns.ipynb
+++ b/docs/source/worked_examples/commuting-patterns.ipynb
@@ -19,7 +19,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import flowclient, folium"
+    "import flowclient, folium, os"
    ]
   },
   {
@@ -35,7 +35,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "conn = flowclient.connect(\"http://localhost:9090\", TOKEN)"
+    "conn = flowclient.connect(os.getenv(\"FLOWAPI_URL\", \"http://localhost:9090\"), TOKEN)"
    ]
   },
   {

From c488df7f6eb7a39cea056c317833ee847aebe963 Mon Sep 17 00:00:00 2001
From: Jono Gray <jonathan.gray@flowminder.org>
Date: Tue, 7 May 2019 09:38:57 +0100
Subject: [PATCH 23/29] Consistent makefile targets

---
 Makefile | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/Makefile b/Makefile
index 548d36d17e..ee2252e4f5 100644
--- a/Makefile
+++ b/Makefile
@@ -108,13 +108,13 @@ flowauth-build:
 	docker-compose -f $(DOCKER_COMPOSE_FILE) -f $(DOCKER_COMPOSE_FILE_BUILD) build flowauth
 
 
-worked-examples-up: worked-examples-build
+worked_examples-up: worked_examples-build
 	docker-compose -f $(DOCKER_COMPOSE_FILE) -f $(DOCKER_COMPOSE_FILE_BUILD) up -d --build worked_examples
 
-worked-examples-down:
+worked_examples-down:
 	docker-compose -f $(DOCKER_COMPOSE_FILE) rm -f -s -v worked_examples
 
-worked-examples-build:
+worked_examples-build:
 	docker-compose -f $(DOCKER_COMPOSE_FILE) -f $(DOCKER_COMPOSE_FILE_BUILD) build worked_examples
 
 

From c82a8422d851da4df8cbe6a88f2bd3afee73df8b Mon Sep 17 00:00:00 2001
From: Jono Gray <jonathan.gray@flowminder.org>
Date: Tue, 7 May 2019 09:40:56 +0100
Subject: [PATCH 24/29] Laxer test token

---
 flowauth/backend/flowauth/models.py | 9 +++------
 1 file changed, 3 insertions(+), 6 deletions(-)

diff --git a/flowauth/backend/flowauth/models.py b/flowauth/backend/flowauth/models.py
index 12acf3a210..4ddbf7f8f3 100644
--- a/flowauth/backend/flowauth/models.py
+++ b/flowauth/backend/flowauth/models.py
@@ -556,12 +556,9 @@ def make_demodata():  # pragma: no cover
         gsp = GroupServerPermission(
             group=groups[0], server_capability=sc, get_result=True, run=True, poll=True
         )
-        gsp.spatial_aggregation.append(
-            agg_units[0]
-        )  # Give Bob access to admin0 agg units
-        gsp.spatial_aggregation.append(
-            agg_units[1]
-        )  # Give Bob access to admin1 agg units
+        for agg_units in agg_units[:4]:  # Give Bob access to adminX agg units
+            gsp.spatial_aggregation.append(agg_units[0])
+
         db.session.add(gsp)
     db.session.add(
         GroupServerTokenLimits(

From 8b48858623c00b8521de40cec6f126a03a875a0b Mon Sep 17 00:00:00 2001
From: Jono Gray <jonathan.gray@flowminder.org>
Date: Tue, 7 May 2019 09:55:13 +0100
Subject: [PATCH 25/29] Syntax

---
 docs/source/install.md              | 2 +-
 flowauth/backend/flowauth/models.py | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/docs/source/install.md b/docs/source/install.md
index 59372e903f..6bb23bffe4 100644
--- a/docs/source/install.md
+++ b/docs/source/install.md
@@ -1,6 +1,6 @@
 Title: Installation
 
-#How to Install FlowKit
+# How to Install FlowKit
 
 There are three main ways to install FlowKit.
 
diff --git a/flowauth/backend/flowauth/models.py b/flowauth/backend/flowauth/models.py
index 4ddbf7f8f3..c85720e3ec 100644
--- a/flowauth/backend/flowauth/models.py
+++ b/flowauth/backend/flowauth/models.py
@@ -556,8 +556,8 @@ def make_demodata():  # pragma: no cover
         gsp = GroupServerPermission(
             group=groups[0], server_capability=sc, get_result=True, run=True, poll=True
         )
-        for agg_units in agg_units[:4]:  # Give Bob access to adminX agg units
-            gsp.spatial_aggregation.append(agg_units[0])
+        for agg_unit in agg_units[:4]:  # Give Bob access to adminX agg units
+            gsp.spatial_aggregation.append(agg_unit)
 
         db.session.add(gsp)
     db.session.add(

From 1fb1129922f7bae0eda8d41ff79a00c9952a13d5 Mon Sep 17 00:00:00 2001
From: Jono Gray <jonathan.gray@flowminder.org>
Date: Tue, 7 May 2019 10:20:28 +0100
Subject: [PATCH 26/29] Put env var in right service

---
 docker-compose.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/docker-compose.yml b/docker-compose.yml
index e0cd6812de..3fb1e2b808 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -128,7 +128,7 @@ services:
       - REDIS_HOST=query_locker
       - REDIS_PORT=6379
       - REDIS_PASSWORD=${REDIS_PASSWORD:?Must set REDIS_PASSWORD env var}
-      -
+      - FLOWAPI_URL="http://flowapi:9090"
     restart: always
     networks:
       - db
@@ -150,7 +150,6 @@ services:
       - FLOWDB_PORT=5432
       - JWT_SECRET_KEY=${JWT_SECRET_KEY:?Must set JWT_SECRET_KEY env var}
       - FLOWAPI_LOG_LEVEL=${FLOWAPI_LOG_LEVEL:?Must set FLOWAPI_LOG_LEVEL env var}
-      - FLOWAPI_URL="http://flowapi:9090"
     tty: true
     stdin_open: true
     restart: always

From 21fc0dbb7f3d79391bf736e30e38ea5c80710a25 Mon Sep 17 00:00:00 2001
From: Jono Gray <jonathan.gray@flowminder.org>
Date: Tue, 7 May 2019 11:13:42 +0100
Subject: [PATCH 27/29] Pull before starting

---
 quick_start.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/quick_start.sh b/quick_start.sh
index ab1316cbbf..5350177b0d 100755
--- a/quick_start.sh
+++ b/quick_start.sh
@@ -100,6 +100,7 @@ else
     if [[ "$RUNNING" != "" ]]; then
         confirm "Existing containers are running and will be replaced. Are you sure?" || exit 1
     fi
+    curl -s https://raw.githubusercontent.com/Flowminder/FlowKit/${BRANCH:-master}/docker-compose.yml | docker-compose -f - pull
     curl -s https://raw.githubusercontent.com/Flowminder/FlowKit/${BRANCH:-master}/docker-compose.yml | docker-compose -f - up -d $DOCKER_FLOWDB_HOST flowapi flowmachine flowauth flowmachine_query_locker $WORKED_EXAMPLES
     echo "Waiting for containers to be ready.."
     docker exec ${DOCKER_FLOWDB_HOST} bash -c 'i=0; until [ $i -ge 24 ] || (pg_isready -h 127.0.0.1 -p 5432); do let i=i+1; echo Waiting 10s; sleep 10; done' || (>&2 echo "FlowDB failed to start :( Please open an issue at https://github.com/Flowminder/FlowKit/issues/new?template=bug_report.md&labels=FlowDB,bug including the output of running 'docker logs flowdb'" && exit 1)

From 8e8f06f35655895f9109db431862d0fd3a0e7186 Mon Sep 17 00:00:00 2001
From: maxalbert <maximilian.albert@gmail.com>
Date: Wed, 8 May 2019 10:51:34 +0100
Subject: [PATCH 28/29] Update docker-compose.yml

Co-Authored-By: greenape <demonixz@gmail.com>
---
 docker-compose.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docker-compose.yml b/docker-compose.yml
index 3fb1e2b808..837d54a7fc 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -128,7 +128,7 @@ services:
       - REDIS_HOST=query_locker
       - REDIS_PORT=6379
       - REDIS_PASSWORD=${REDIS_PASSWORD:?Must set REDIS_PASSWORD env var}
-      - FLOWAPI_URL="http://flowapi:9090"
+      - FLOWAPI_URL=http://flowapi:9090
     restart: always
     networks:
       - db

From 7033cf4dd8ca8c999ea09edbf8a4b2507b1cf2a9 Mon Sep 17 00:00:00 2001
From: maxalbert <maximilian.albert@gmail.com>
Date: Wed, 8 May 2019 11:11:01 +0100
Subject: [PATCH 29/29] Update quick_start.sh

Co-Authored-By: greenape <demonixz@gmail.com>
---
 quick_start.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/quick_start.sh b/quick_start.sh
index 5350177b0d..4c275a854f 100755
--- a/quick_start.sh
+++ b/quick_start.sh
@@ -95,7 +95,7 @@ then
     curl -s https://raw.githubusercontent.com/Flowminder/FlowKit/${BRANCH:-master}/docker-compose.yml | docker-compose -f - down
 else
     source /dev/stdin <<< "$(curl -s https://raw.githubusercontent.com/Flowminder/FlowKit/${BRANCH:-master}/development_environment)"
-    echo "Starting containers"
+     echo "Starting containers (this may take a few minutes)"
     RUNNING=`curl -s https://raw.githubusercontent.com/Flowminder/FlowKit/${BRANCH:-master}/docker-compose.yml | docker-compose -f - ps -q $DOCKER_FLOWDB_HOST flowapi flowmachine flowauth flowmachine_query_locker $WORKED_EXAMPLES`
     if [[ "$RUNNING" != "" ]]; then
         confirm "Existing containers are running and will be replaced. Are you sure?" || exit 1
@@ -125,4 +125,4 @@ else
     then
         echo "Try out the interactive examples at http://localhost:$WORKED_EXAMPLES_PORT"
     fi
-fi
\ No newline at end of file
+fi