Merge branch 'develop' into model-run-workflow

.github/workflows/download-met-data.yml

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+name : Test Data Download
+on :
+  # allow manual triggering
+  workflow_dispatch:
+
+  schedule:
+    # run Thursday 4:30 AM UTC
+  - cron: '30 4 * * 4'
+
+env:
+  R_LIBS_USER: /usr/local/lib/R/site-library
+  LC_ALL: en_US.UTF-8
+  NCPUS: 2
+  PGHOST: postgres
+  CI: true
+
+jobs:
+  met-data-download:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    services:
+      postgres:
+        image: mdillon/postgis:9.5
+        options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5
+
+    container: 
+      image: pecan/depends:R4.1
+
+    steps:
+    # checkout source code
+    - name: work around https://github.com/actions/checkout/issues/766
+      run: git config --global --add safe.directory "$GITHUB_WORKSPACE"
+    - uses: actions/checkout@v4
+      with:
+        set-safe-directory: false
+
+    # install additional tools needed
+    - name: install utils
+      run: apt-get update && apt-get install -y postgresql-client qpdf
+    - name: install new dependencies
+      run: Rscript scripts/generate_dependencies.R && cd docker/depends && Rscript pecan.depends.R
+
+    # initialize database
+    - name: db setup
+      uses: docker://pecan/db:ci
+    - name: add models to db
+      run: ./scripts/add.models.sh
+
+    # compile PEcAn code
+    - name: build
+      run: make -j1
+
+    - name: CRUNCEP
+      run: |
+        Rscript ./tests/test_met_downloads.R --settings ./tests/met_download_settings/docker.CRUNCEP.xml

tests/met_download_settings/docker.CRUNCEP.xml

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+<?xml version="1.0"?>
+<pecan>
+  <outdir>/data/tests/met_download/CRUNCEP</outdir>
+  <database>
+    <bety>
+      <driver>PostgreSQL</driver>
+      <user>bety</user>
+      <password>bety</password>
+      <host>postgres</host>
+      <dbname>bety</dbname>
+      <write>FALSE</write>
+    </bety>
+  </database>
+  <model>
+    <type>SIPNET</type>
+  </model>
+  <run>
+    <site>
+      <id>1000000057</id>
+    </site>
+    <inputs>
+      <met>
+        <source>CRUNCEP</source>
+      </met>
+    </inputs>
+    <start.date>2001-01-01</start.date>
+    <end.date>2001-12-31</end.date>
+    <dbfiles>/data/dbfiles</dbfiles>
+  </run>
+  <host>
+    <name>localhost</name>
+  </host>
+</pecan>

tests/test_met_downloads.R

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+library("PEcAn.all")
+
+args <- PEcAn.settings::get_args()
+settings <- PEcAn.settings::read.settings(args$settings)
+settings <- PEcAn.settings::prepare.settings(settings, force = FALSE)
+settings <- PEcAn.workflow::do_conversions(settings)