Evaluation workflows

.github/workflows/website.yml

@@ -0,0 +1,119 @@
+name: Website
+on:
+  push:
+    branches:
+      - gh-pages
+      - main
+  pull_request: null
+jobs:
+  build-website:
+    if: ${{ !endsWith(github.repository, '/styles') }}
+    runs-on: ubuntu-20.04
+    env:
+      RSPM: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    defaults:
+      run:
+        shell: bash
+    steps:
+      - name: Set up Ruby
+        uses: ruby/setup-ruby@v1
+        with:
+          ruby-version: '3.0'
+          bundler-cache: true
+
+      - name: Set up Python
+        uses: actions/[email protected]
+        with:
+          python-version: '3.x'
+
+      - name: Install GitHub Pages, Bundler, and kramdown gems
+        run: |
+          gem install github-pages bundler kramdown kramdown-parser-gfm
+
+      - name: Install Python modules
+        run: |
+          python3 -m pip install --upgrade pip setuptools wheel pyyaml==5.3.1 requests
+
+      - name: Checkout the lesson
+        uses: actions/checkout@master
+        with:
+          fetch-depth: 0
+          ref: ${{ github.event.pull_request.head.sha }}
+
+      - name: Look for R-markdown files
+        id: check-rmd
+        run: |
+          echo "count=$(shopt -s nullglob; files=($(find . -iname '*.Rmd')); echo ${#files[@]})" >> $GITHUB_OUTPUT
+
+      - name: Set up R
+        if: steps.check-rmd.outputs.count != 0
+        uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+          install-r: false
+
+      - name: Restore R Cache
+        if: steps.check-rmd.outputs.count != 0
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+      - name: Install needed packages
+        if: steps.check-rmd.outputs.count != 0
+        run: |
+          source('bin/dependencies.R')
+          install_required_packages()
+        shell: Rscript {0}
+
+      - name: Query dependencies
+        if: steps.check-rmd.outputs.count != 0
+        run: |
+          source('bin/dependencies.R')
+          deps <- identify_dependencies()
+          create_description(deps)
+          use_bioc_repos()
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Install system dependencies for R packages
+        if: steps.check-rmd.outputs.count != 0
+        run: |
+          while read -r cmd
+          do
+            eval sudo $cmd || echo "Nothing to update"
+          done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "20.04"), sep = "\n")')
+
+      - name: Render the markdown and confirm that the site can be built
+        run: make site
+
+      - name: Checkout github pages
+        if: ${{ github.event_name == 'push' && steps.check-rmd.outputs.count != 0 && github.ref != 'refs/heads/gh-pages'}}
+        uses: actions/checkout@master
+        with:
+          ref: gh-pages
+          path: gh-pages
+
+      - name: Commit and Push
+        if: ${{ github.event_name == 'push' && steps.check-rmd.outputs.count != 0 && github.ref != 'refs/heads/gh-pages'}}
+        run: |
+          # clean up gh-pages
+          cd gh-pages
+          git rm -rf .           # remove all previous files
+          git restore --staged . # remove things from the stage
+          cd ..
+          # copy everything into gh-pages site
+          cp -r `ls -A | grep -v 'gh-pages' | grep -v '.git' | grep -v '.bundle/' | grep -v '_site'` gh-pages
+          # move into gh-pages, add, commit, and push
+          cd gh-pages
+          # setup git
+          git config --local user.email "[email protected]"
+          git config --local user.name "GitHub Actions"
+          git add -A .
+          git commit --allow-empty -m "[Github Actions] render website (via ${{ github.sha }})"
+          git push origin gh-pages
+          # return
+          cd ..

.zenodo.json

@@ -1,95 +1,29 @@
 {
     "creators": [
         {
-            "affiliation": "NLeSC, Netherlands",
-            "name": "Alidoost, Fakhereh",
-            "orcid": "0000-0001-8407-6472"
+            "affiliation": "ACCESS-NRI, Australia",
+            "name": "Beucher, Romain",
+            "orcid": "0000-0003-3891-5444"
         },
         {
-            "affiliation": "NLeSC, Netherlands",
-            "name": "Andela, Bouwe",
-            "orcid": "0000-0001-9005-8940"
+            "affiliation": "ACCESS-NRI, Australia",
+            "name": "Chun, Felicity",
+            "orcid": ""
         },
         {
-            "affiliation": "DLR, Germany",
-            "name": "Bock, Lisa",
-            "orcid": "0000-0001-7058-5938"
-        },
-        {
-            "affiliation": "NLeSC, Netherlands",
-            "name": "Camphuijsen, Jaro",
-            "orcid": "0000-0002-8928-7831"
-        },
-        {
-            "affiliation": "NLeSC, Netherlands",
-            "name": "Drost, Niels",
-            "orcid": "0000-0001-9795-7981"
-        },
-        {
-            "affiliation": "DLR, Germany",
-            "name": "Hassler, Birgit",
-            "orcid": "0000-0003-2724-709X"
-        },
-        {
-            "affiliation": "NLeSC, Netherlands",
-            "name": "Kalverla, Peter",
-            "orcid": "0000-0002-5025-7862"
-        },
-        {
-            "affiliation": "NLeSC, Netherlands",
-            "name": "López-Tarifa, Pablo",
-            "orcid": "0000-0002-4136-1860"
-        },
-        {
-            "affiliation": "PML, UK",
-            "name": "de Mora, Lee",
-            "orcid": "0000-0002-5080-3149"
-        },
-        {
-            "affiliation": "LMU, Germany",
-            "name": "Mueller, Benjamin"
-        },
-        {
-            "affiliation": "URead, UK",
-            "name": "Predoi, Valeriu",
-            "orcid": "0000-0002-9729-6578"
-        },
-        {
-            "affiliation": "URead, UK",
-            "name": "Swaminathan, Ranjini",
-            "orcid": "0000-0001-5853-2673"
-        },
-        {
-            "affiliation": "NLeSC, Netherlands",
-            "name": "Verhoeven, Stefan",
-            "orcid": "0000-0002-5821-2060"
+            "affiliation": "ACCESS-NRI, Australia",
+            "name": "Zeng, Yousong",
+            "orcid": "0000-0002-8385-5367"
         }
     ],
-    "description": "ESMValTool 2.0 Tutorial.",
+    "description": "ACCESS-NRI MED Hackathon",
     "license": {
         "id": "CC-BY-4.0"
     },
-    "title": "ESMValTool Tutorial",
+    "title": "ACCESS MED Hackathon",
     "communities": [
         {
-            "identifier": "is-enes3"
-        },
-        {
-            "identifier": "dlr_de"
-        },
-        {
-            "identifier": "nlesc"
-        }
-    ],
-    "grants": [
-        {
-            "id": "10.13039/501100000780::776613"
-        },
-        {
-            "id": "10.13039/501100000780::824084"
-        },
-        {
-            "id": "10.13039/501100003246::2300185259"
+            "identifier": "access-nri"
         }
     ]
 }

CITATION.cff

@@ -1,80 +1,29 @@
 # YAML 1.2
 ---
-abstract: "ESMValTool 2.0 Tutorial."
+abstract: "ACCESS MED Hackathon"
 
 authors:
   -
-    affiliation: "NLeSC, Netherlands"
-    family-names: Alidoost
-    given-names: Fakhereh
-    orcid: "https://orcid.org/0000-0001-8407-6472"
+    affiliation: "ACCESS-NRI, Australia"
+    family-names: Beucher
+    given-names: Romain
+    orcid: "https://orcid.org/0000-0003-3891-5444"  
   -
-    affiliation: "NLeSC, Netherlands"
-    family-names: Andela
-    given-names: Bouwe
-    orcid: "https://orcid.org/0000-0001-9005-8940"
+    affiliation: "ACCESS-NRI, Australia"
+    family-names: Chun
+    given-names: Felicity
+    orcid: "https://orcid.org/"
   -
-    affiliation: "DLR, Germany"
-    family-names: Bock
-    given-names: Lisa
-    orcid: "https://orcid.org/0000-0001-7058-5938"
-  -
-    affiliation: "NLeSC, Netherlands"
-    family-names: Camphuijsen
-    given-names: Jaro
-    orcid: "https://orcid.org/0000-0002-8928-7831"
-  -
-    affiliation: "NLeSC, Netherlands"
-    family-names: Drost
-    given-names: Niels
-    orcid: "https://orcid.org/0000-0001-9795-7981"
-  -
-    affiliation: "DLR, Germany"
-    family-names: Hassler
-    given-names: Birgit
-    orcid: "https://orcid.org/0000-0003-2724-709X"
-  -
-    affiliation: "NLeSC, Netherlands"
-    family-names: Kalverla
-    given-names: Peter
-    orcid: "https://orcid.org/0000-0002-5025-7862"
-  -
-    affiliation: "NLeSC, Netherlands"
-    family-names: López-Tarifa
-    given-names: Pablo
-    orcid: "https://orcid.org/0000-0002-4136-1860"
-  -
-    affiliation: "PML, UK"
-    name-particle: de
-    family-names: Mora
-    given-names: Lee
-    orcid: "https://orcid.org/0000-0002-5080-3149"
-  -
-    affiliation: "LMU, Germany"
-    family-names: Mueller
-    given-names: Benjamin
-  -
-    affiliation: "URead, UK"
-    family-names: Predoi
-    given-names: Valeriu
-    orcid: "https://orcid.org/0000-0002-9729-6578"
-  -
-    affiliation: "URead, UK"
-    family-names: Swaminathan
-    given-names: Ranjini
-    orcid: "https://orcid.org/0000-0001-5853-2673"
-  -
-    affiliation: "NLeSC, Netherlands"
-    family-names: Verhoeven
-    given-names: Stefan
-    orcid: "https://orcid.org/0000-0002-5821-2060"
+    affiliation: "ACCESS-NRI, Australia"
+    family-names: Yousong
+    given-names: Zeng
+    orcid: "https://orcid.org/0000-0002-8385-5367"
 cff-version: "1.0.3"
-date-released: 2020-08-06
-doi: "10.5281/zenodo.3974591"
+date-released: 2024-09-02
 license: "CC-BY-4.0"
 message: "If you use this tutorial, please cite it using these metadata."
-repository-code: "https://github.com/ESMValGroup/ESMValTool_Tutorial/"
-title: "ESMValTool Tutorial"
+repository-code: "https://github.com/ACCESS-NRI/CMIP7_MED_Hackathon"
+title: "ACCESS-NRI MED Hackathon"
 keywords:
   - "Earth System Model Validation"
   - "Climate Science"