k8s

.github/workflows/docker-image.yml

@@ -0,0 +1,18 @@
+name: Binder Image
+on:
+  workflow_dispatch: null
+  push: null
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    permissions: write-all
+    steps:
+      - uses: actions/checkout@v3
+      - name: Publish to GitHub Container Registry
+        uses: elgohr/Publish-Docker-Github-Action@v5
+        with:
+          name: boettiger-lab/inat-ranges
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+          registry: ghcr.io
+

.gitignore

@@ -55,3 +55,4 @@ rsconnect/
 *.pmtiles
 Rplots.pdf
 .tmp/
+kubernetes/set-secrets.sh

Dockerfile

@@ -3,19 +3,22 @@ FROM rocker/geospatial:latest
 WORKDIR /code
 
 RUN install2.r --error \
-    bench \
-    bsicons \
-    bslib \
-    duckdbfs \
-    fontawesome \
-    gt \
-    markdown \
-    shiny \
-    shinybusy \
-    shinychat \
-    tidyverse
+  bench \
+  bsicons \
+  bslib \
+  duckdbfs \
+  fontawesome \
+  gt \
+  markdown \
+  shiny \
+  shinybusy \
+  shinychat \
+  tidyverse \
+  mapgl \
+  ellmer \
+  conflicted
+
 
-RUN installGithub.r cboettig/mapgl tidyverse/ellmer boettiger-lab/duckdb.agent cboettig/duckdbfs
 
 COPY . .
 

app/app.R

@@ -198,6 +198,7 @@ server <- function(input, output, session) {
   observeEvent(input$chat_user_input, {
     taxa_selected <- txt_to_taxa(input$chat_user_input)
     chat_append("chat", "done")
+    chat_clear("chat")
 
     # optionally - store the selection as global variable for future reactions
     taxa_filter(taxa_selected)

kubernetes/deployment.yaml

@@ -0,0 +1,50 @@
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: gbif
+  labels:
+    k8s-app: gbif
+spec:
+  containers:
+  - name: gbif
+    image: ghcr.io/boettiger-lab/gbif-explorer
+    imagePullPolicy: Always
+    env:
+    
+    - name: AWS_ACCESS_KEY_ID
+      valueFrom:
+        secretKeyRef:
+          name: aws
+          key: AWS_ACCESS_KEY_ID
+    - name: AWS_SECRET_ACCESS_KEY
+      valueFrom:
+        secretKeyRef:
+          name: aws
+          key: AWS_SECRET_ACCESS_KEY
+    - name: AWS_S3_ENDPOINT
+      value: "rook-ceph-rgw-nautiluss3.rook"
+    - name: AWS_PUBLIC_ENDPOINT
+      value: "s3-west.nrp-nautilus.io"
+    - name: AWS_HTTPS
+      value: "false"
+    - name: AWS_VIRTUAL_HOSTING
+      value: "FALSE"
+    - name: NRP_API_KEY
+      valueFrom:
+        secretKeyRef:
+          name: nrp-api-key
+          key: NRP_API_KEY
+    - name: MAPTILER_API_KEY
+      valueFrom:
+        secretKeyRef:
+          name: maptiler-api-key
+          key: MAPTILER_API_KEY
+    resources:
+      requests:
+        cpu: 8
+        memory: 8Gi
+      limits:
+        cpu: 8
+        memory: 8Gi
+
+

kubernetes/ingress.yaml

@@ -0,0 +1,25 @@
+apiVersion: networking.k8s.io/v1
+kind: Ingress
+metadata:
+  annotations:
+    haproxy.org/timeout-server: "300s"
+    haproxy.org/timeout-client: "300s"
+    haproxy.org/timeout-connect: "30s"
+    haproxy.org/timeout-http-request: "300s"
+  name: inat-ingress
+spec:
+  ingressClassName: haproxy
+  rules:
+  - host: gbif.nrp-nautilus.io
+    http:
+      paths:
+      - path: /
+        pathType: Prefix
+        backend:
+          service:
+            name: gbif
+            port:
+              number: 8080
+  tls:
+  - hosts:
+    - gbif.nrp-nautilus.io

kubernetes/service.yaml

@@ -0,0 +1,17 @@
+apiVersion: v1
+kind: Service
+metadata:
+  name: gbif
+  labels:
+    k8s-app: gbif
+
+# ports.targetPort is the port exposed by the Docker container
+# ports.port is the port matched to the ingress
+spec:
+  ports:
+  - port: 8080
+    protocol: TCP
+    targetPort: 8080
+  selector:
+    k8s-app: gbif
+  type: ClusterIP

tests/test-llm-app.R

@@ -0,0 +1,24 @@
+# interactive()
+library(shiny)
+library(bslib)
+library(shinychat)
+
+ui <- page_fillable(
+  chat_ui("chat", fill = TRUE)
+)
+
+server <- function(input, output, session) {
+  observeEvent(input$chat_user_input, {
+    # In a real app, this would call out to a chat model or API,
+    # perhaps using the 'ellmer' package.
+    response <- paste0(
+      "You said:\n\n",
+      "<blockquote>",
+      htmltools::htmlEscape(input$chat_user_input),
+      "</blockquote>"
+    )
+    chat_append("chat", NULL)
+  })
+}
+
+shinyApp(ui, server)

tests/test-llm.R

@@ -1,10 +0,0 @@
-source("llm-gbif.R")
-
-bench::bench_time({
-  txt_to_taxa("frogs", "qwen3")
-})
-
-
-bench::bench_time({
-  txt_to_taxa("frogs")
-})