Update website with code block copy button and nord theme

website/content/docs/compute/aws-batch.md

@@ -81,7 +81,7 @@ AmazonS3:
 
 ### Start the server
 
-```
+```sh
 funnel server run --config /path/to/config.yaml
 ```
 

website/content/docs/compute/deployment.md

@@ -24,14 +24,14 @@ these services without using nodes or the scheduler.
 ### Usage
 
 Nodes are available via the `funnel node` command. To start a node, run
-```
+```sh
 funnel node run --config node.config.yml
 ```
 
 To activate the Funnel scheduler, use the `manual` backend in the config.
 
 The available scheduler and node config:
-```
+```yaml
 # Activate the Funnel scheduler.
 Compute: manual
 

website/content/docs/compute/kubernetes.md

@@ -10,37 +10,12 @@ menu:
 
 This guide will take you through the process of setting up Funnel as a kubernetes service.
 
-Kuberenetes Resources:
-- [Service](https://kubernetes.io/docs/concepts/services-networking/service/)
-- [Deployment](https://kubernetes.io/docs/concepts/workloads/controllers/deployment/)
-- [ConfigMap](https://kubernetes.io/docs/tasks/configure-pod-container/configure-pod-configmap/)
-- [Roles and RoleBindings](https://kubernetes.io/docs/reference/access-authn-authz/rbac/#default-roles-and-role-bindings)
-- [Job](https://kubernetes.io/docs/concepts/workloads/controllers/jobs-run-to-completion/)
-
-Additional Funnel deployment resources can be found here: https://github.com/ohsu-comp-bio/funnel/tree/master/deployments/kubernetes
-
 #### Create a Service:
 
 *funnel-service.yml*
 
 ```yaml
-apiVersion: v1
-kind: Service
-metadata:
-  name: funnel
-spec:
-  selector:
-    app: funnel
-  ports:
-    - name: http
-      protocol: TCP
-      port: 8000
-      targetPort: 8000
-    - name: rpc
-      protocol: TCP
-      port: 9090
-      targetPort: 9090
-
+{{< read-file "static/funnel-config-examples/kubernetes/funnel-service.yml" >}}
 ```
 
 Deploy it:
@@ -62,65 +37,7 @@ Use this value to configure the server hostname of the worker config.
 *funnel-server-config.yml*
 
 ```yaml
-Database: boltdb
-
-Compute: kubernetes
-
-Logger:
-  Level: debug
-
-Kubernetes:
-  # The executor used to execute tasks. Available executors: docker, kubernetes
-  Executor: "kubernetes"
-  DisableJobCleanup: false
-  DisableReconciler: false
-  ReconcileRate: 5m
-  Namespace: default
-  Template: |
-    apiVersion: batch/v1
-    kind: Job
-    metadata:
-      ## DO NOT CHANGE NAME
-      name: {{.TaskId}}
-      namespace: {{.Namespace}}
-    spec:
-      backoffLimit: 0
-      completions: 1
-      template:
-        spec:
-          restartPolicy: Never
-          serviceAccountName: funnel-sa
-          containers:
-            - name: {{printf "funnel-worker-%s" .TaskId}}
-              image: quay.io/ohsu-comp-bio/funnel:latest
-              imagePullPolicy: IfNotPresent
-              args:
-                - "worker"
-                - "run"
-                - "--config"
-                - "/etc/config/funnel-worker-config.yml"
-                - "--taskID"
-                - {{.TaskId}}
-              resources:
-                  requests:
-                    cpu: {{if ne .Cpus 0 -}}{{.Cpus}}{{ else }}{{"100m"}}{{end}}
-                    memory: {{if ne .RamGb 0.0 -}}{{printf "%.0fG" .RamGb}}{{else}}{{"16M"}}{{end}}
-                    ephemeral-storage: {{if ne .DiskGb 0.0 -}}{{printf "%.0fG" .DiskGb}}{{else}}{{"100M"}}{{end}}
-              volumeMounts:
-                - name: {{printf "funnel-storage-%s" .TaskId}}
-                  mountPath: {{printf "/opt/funnel/funnel-work-dir/%s" .TaskId}}
-                - name: config-volume
-                  mountPath: /etc/config
-
-              securityContext:
-                privileged: true
-
-          volumes:
-            - name: {{printf "funnel-storage-%s" .TaskId}}
-              emptyDir: {}
-            - name: config-volume
-              configMap:
-                name: funnel-config
+{{< read-file "static/funnel-config-examples/kubernetes/funnel-server-config.yml" >}}
 ```
 
 We recommend setting `DisableJobCleanup` to `true` for debugging - otherwise failed jobs will be cleanup up.
@@ -130,31 +47,7 @@ We recommend setting `DisableJobCleanup` to `true` for debugging - otherwise fai
 ***Remember to modify the template below to have the actual server hostname.***
 
 ```yaml
-Database: boltdb
-
-BoltDB:
-  Path: /opt/funnel/funnel-work-dir/funnel.bolt.db
-
-Compute: kubernetes
-
-Kubernetes:
-  # The executor used to execute tasks. Available executors: docker, kubernetes
-  Executor: "kubernetes"
-
-Logger:
-  Level: debug
-
-RPCClient:
-  MaxRetries: 3
-  Timeout: 30s
-
-EventWriters:
-  - rpc
-  - log
-
-Server:
-  HostName: < funnel service clusterIP >
-  RPCPort: 9090
+{{< read-file "static/funnel-config-examples/kubernetes/funnel-worker-config.yml" >}}
 ```
 
 #### Create a ConfigMap
@@ -170,41 +63,13 @@ Define a Role and RoleBinding:
 *role.yml*
 
 ```yaml
-kind: Role
-apiVersion: rbac.authorization.k8s.io/v1
-metadata:
-  namespace: default
-  name: funnel-role
-rules:
-- apiGroups: [""]
-  resources: ["pods"]
-  verbs: ["get", "list", "watch"]
-- apiGroups: [""]
-  resources: ["pods/log"]
-  verbs: ["get"]
-- apiGroups: ["batch", "extensions"]
-  resources: ["jobs"]
-  verbs: ["get", "list", "watch", "create", "update", "patch", "delete"]
-- apiGroups: ["extensions", "apps"]
-  resources: ["deployments"]
-  verbs: ["get", "list", "watch", "create", "update", "patch", "delete"]
+{{< read-file "static/funnel-config-examples/kubernetes/role.yml" >}}
 ```
 
 *role_binding.yml*
 
 ```yaml
-kind: RoleBinding
-apiVersion: rbac.authorization.k8s.io/v1
-metadata:
-  name: funnel-rolebinding
-  namespace: default
-subjects:
-- kind: ServiceAccount
-  name: funnel-sa
-roleRef:
-  kind: Role
-  name: funnel-role
-  apiGroup: rbac.authorization.k8s.io
+{{< read-file "static/funnel-config-examples/kubernetes/role_binding.yml" >}}
 ```
 
 Create the service account, role and role binding:
@@ -220,53 +85,7 @@ kubectl create -f role_binding.yml
 *funnel-deployment.yml*
 
 ```yaml
-apiVersion: apps/v1
-kind: Deployment
-metadata:
-  name: funnel
-  labels:
-    app: funnel
-spec:
-  replicas: 1
-  selector:
-    matchLabels:
-      app: funnel
-  template:
-    metadata:
-      labels:
-        app: funnel
-    spec:
-      serviceAccountName: funnel-sa
-      containers:
-        - name: funnel
-          image: quay.io/ohsu-comp-bio/funnel:latest
-          imagePullPolicy: IfNotPresent
-          command:
-            - 'funnel'
-            - 'server'
-            - 'run'
-            - '--config'
-            - '/etc/config/funnel-server-config.yml'
-          resources:
-            requests:
-              cpu: 2
-              memory: 4G
-              ephemeral-storage: 25G # needed since we are using boltdb
-          volumeMounts:
-            - name: funnel-deployment-storage
-              mountPath: /opt/funnel/funnel-work-dir
-            - name: config-volume
-              mountPath: /etc/config
-          ports:
-            - containerPort: 8000
-            - containerPort: 9090
-
-      volumes:
-        - name: funnel-deployment-storage
-          emptyDir: {}
-        - name: config-volume
-          configMap:
-            name: funnel-config
+{{< read-file "static/funnel-config-examples/kubernetes/funnel-deployment.yml" >}}
 ```
 
 Deploy it:

website/content/docs/databases/boltdb.md

@@ -13,7 +13,7 @@ and scheduler data. This is great for development and a simple server without
 external dependencies, but it doesn't scale well to larger clusters.
 
 Available config:
-```
+```yaml
 Database: boltdb
 
 BoltDB:

website/content/docs/databases/datastore.md

@@ -18,7 +18,7 @@ such as stdout/err logs).
 Funnel will, by default, try to will try to automatically load credentials from the environment. Alternatively, you may explicitly set the credentials in the config.
 
 Config:
-```
+```yaml
 Database: datastore
 
 Datastore:

website/content/docs/databases/dynamodb.md

@@ -11,7 +11,7 @@ Funnel supports storing task data in DynamoDB. Storing scheduler data is not sup
 Funnel will, by default, try to will try to automatically load credentials from the environment. Alternatively, you may explicitly set the credentials in the config.
 
 Available Config:
-```
+```yaml
 Database: dynamodb
 
 DynamoDB:

website/content/docs/databases/elasticsearch.md

@@ -10,7 +10,7 @@ menu:
 Funnel supports storing tasks and scheduler data in Elasticsearch.
 
 Config:
-```
+```yaml
 Database: elastic
 
 Elastic:

website/content/docs/databases/mongodb.md

@@ -10,7 +10,7 @@ menu:
 Funnel supports storing tasks and scheduler data in MongoDB.
 
 Config:
-```
+```yaml
 Database: mongodb
 
 MongoDB:

website/content/docs/events/kafka.md

@@ -10,7 +10,7 @@ menu:
 Funnel supports writing task events to a Kafka topic. To use this, add an event
 writer to the config:
 
-```
+```yaml
 EventWriters:
   - kafka
   - log

website/content/docs/integrations/py-tes.md

@@ -17,13 +17,13 @@ menu:
 
 Available on [PyPI](https://pypi.org/project/py-tes/).
 
-```
+```sh
 pip install py-tes
 ```
 
 ### Example Python Script
 
-```
+```py
 import tes
 
 task = tes.Task(

website/content/docs/storage/ftp.md

@@ -14,13 +14,13 @@ Currently authentication credentials are take from the URL, e.g. `ftp://username
 The FTP storage client is enabled by default, but may be explicitly disabled in the 
 worker config:
 
-```
+```yaml
 FTPStorage:
   Disabled: false
 ```
 
 ### Example task
-```
+```json
 {
   "name": "Hello world",
   "inputs": [{

website/content/docs/storage/google-storage.md

@@ -13,15 +13,15 @@ The Google storage client is enabled by default, and will try to automatically
 load credentials from the environment. Alternatively, you
 may explicitly set the credentials in the worker config:
 
-```
+```yaml
 GoogleStorage:
   Disabled: false
   # Path to account credentials file.
   AccountFile: ""
 ```
 
 ### Example task
-```
+```json
 {
   "name": "Hello world",
   "inputs": [{

website/content/docs/storage/http.md

@@ -14,15 +14,15 @@ providers exposed using presigned URLs.
 The HTTP storage client is enabled by default, but may be explicitly disabled in the 
 worker config:
 
-```
+```yaml
 HTTPStorage:
   Disabled: false
   # Timeout for http(s) GET requests.
   Timeout: 30s
 ```
 
 ### Example task
-```
+```json
 {
   "name": "Hello world",
   "inputs": [{

website/content/docs/storage/local.md

@@ -14,7 +14,7 @@ Funnel limits which directories may be accessed, by default only allowing direct
 under the current working directory of the Funnel worker.
 
 Config:
-```
+```yaml
 LocalStorage:
   # Whitelist of local directory paths which Funnel is allowed to access.
   AllowedDirs: