[Integration Testing] PEcAn Docker Stack Run : Single Site, Single Model

.github/workflows/model-run.yml

@@ -0,0 +1,72 @@
+name : Sipnet Model Run
+on :
+  pull_request:
+
+  # allow manual triggering
+  workflow_dispatch:
+
+  schedule:
+    # run Thursday 4:30 AM UTC
+  - cron: '30 4 * * 4'    
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+    - name: Free Disk Space (Ubuntu)
+      uses: jlumbroso/free-disk-space@main
+      with:
+        # this might remove tools that are actually needed,
+        # if set to "true" but frees about 6 GB
+        tool-cache: false
+
+        # all of these default to true, but feel free to set to
+        # "false" if necessary for your workflow
+        android: true
+        dotnet: true
+        haskell: true
+        large-packages: true
+        docker-images: false
+        swap-storage: true
+
+    - name: Checkout source code
+      uses: actions/checkout@v4
+
+    - name: Set up Docker Compose
+      run: |
+          sudo apt-get update
+          sudo apt-get -y install docker-compose
+
+    - name: Add Volumes to Executor
+      run: |
+          cp docker-compose.dev.yml docker-compose.override.yml
+
+    - name: Build Containers
+      run: |
+        cp docker/env.example .env
+        echo "COMPOSE_PROJECT_NAME=pecan" >> .env
+        echo "PECAN_VERSION=develop" >> .env
+        echo "UID=$(id -u)" >> .env
+        echo "GID=$(id -g)" >> .env
+
+        docker compose up -d postgres
+        sleep 30
+        docker run --rm --network pecan_pecan pecan/db:ci
+        docker run --rm --network pecan_pecan --volume pecan_pecan:/data --env FQDN=docker pecan/data:develop
+        docker image rm pecan/db:ci pecan/data:develop
+
+    - name: Run required containers
+      run: |
+        docker compose up -d sipnet executor
+
+    - name: Check if containers are running # This will be updated soon to a loop
+      run: |
+        docker ps
+        sleep 50
+
+    - name: Run SIPNET
+      run: |
+        docker compose exec --workdir /pecan/tests executor R CMD ../web/workflow.R --settings test.xml

docker-compose.yml

@@ -20,7 +20,7 @@ services:
     security_opt:
       - no-new-privileges:true
     ports:
-      - "${TRAEFIK_HTTP_PORT-80}:80"
+      - "${TRAEFIK_HTTP_PORT:-80}:80"
     volumes:
       - "traefik:/config"
       - "/var/run/docker.sock:/var/run/docker.sock:ro"

tests/test.xml

@@ -0,0 +1,68 @@
+<?xml version="1.0"?><pecan>
+  <outdir>/data/workflows/PEcAn_99000000021</outdir>
+  <database>
+    <bety>
+      <user>bety</user>
+      <password>bety</password>
+      <host>postgres</host>
+      <port>5432</port>
+      <dbname>bety</dbname>
+      <driver>PostgreSQL</driver>
+      <write>true</write>
+    </bety>
+    <dbfiles>/data/dbfiles</dbfiles>
+  </database>
+  <pfts>
+    <pft>
+      <name>semiarid.grassland</name> 
+    </pft>
+  </pfts>
+  <meta.analysis>
+    <iter>3000</iter>
+    <random.effects>
+     <on>FALSE</on>
+     <use_ghs>TRUE</use_ghs>
+    </random.effects>
+  </meta.analysis>
+  <ensemble>
+   <size>1</size>
+   <variable>NPP</variable>
+   <samplingspace>
+   <parameters>
+    <method>uniform</method>
+   </parameters>
+   <met>
+    <method>sampling</method>
+ 	</met>
+   </samplingspace>
+  </ensemble>
+  <model>
+    <id>1000000014</id>
+  </model>
+  <workflow>
+    <id>99000000029</id>
+  </workflow>
+  <run>
+    <site>
+      <id>2000001297</id>
+      <met.start>2004/01/01</met.start>
+      <met.end>2004/12/31</met.end>
+    </site>
+    <inputs>
+      <met>
+        <source>CRUNCEP</source>
+        <output>SIPNET</output>
+        <product/>
+      </met>
+    </inputs>
+    <start.date>2004/01/01</start.date>
+    <end.date>2004/12/31</end.date>
+  </run>
+  <host>
+    <name>localhost</name>
+    <rabbitmq>
+      <uri>amqp://carya:illinois@rabbitmq/%2F</uri>
+      <queue>SIPNET_r136</queue>
+    </rabbitmq>
+  </host>
+</pecan>