Apply new tutorial template

.filenameignore

@@ -0,0 +1,20 @@
+# Paths to ignore for filename/path validation checks.
+# Patterns use fnmatch syntax and are relative to repo root.
+
+_site/**
+.quarto/**
+.github/**
+_extensions/
+assets/bootstrap-grid.min.css
+
+# Common documentation files to ignore
+LICENSE-CODE.md
+LICENSE.md
+LICENSE
+README.md
+README
+README-template.md
+CITATION.cff
+CITATION-template.cff
+_quarto.yml
+404.qmd

.github/workflows/citation-check.yml

@@ -0,0 +1,21 @@
+on:
+  workflow_dispatch:
+  push:
+    branches: [main]
+    paths:
+    - CITATION.cff
+
+name: Check CITATION.cff is Valid
+jobs:
+  Validate-CITATION-cff:
+    runs-on: ubuntu-latest
+    name: Validate CITATION.cff
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Validate CITATION.cff
+        uses: dieghernan/cff-validator@v3

.github/workflows/filename-check.yml

@@ -0,0 +1,22 @@
+name: Filename Checks
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+      - main
+
+jobs:
+  check-names:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Check filenames
+        uses: NeuroShepherd/check-filenames-action@v1
+        with:
+          max-path-length: "65"
+          max-depth: "2"
+          file-types: "html,md,qmd,css,scss,rmd,pdf,png,jpg,svg,yml"
+          ignore-file: ".filenameignore"
+          dotfile-mode: "strip-leading-dot"

.github/workflows/link-checker.yml

@@ -0,0 +1,44 @@
+name: Link Checker
+
+on:
+  schedule:
+    - cron: '0 0 1 * *'
+  workflow_dispatch:
+
+jobs:
+  check-links:
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+    steps:
+      - name: Check links
+        id: check
+        uses: filiph/linkcheck@master
+        continue-on-error: true
+        with:
+          arguments: https://${{ github.repository_owner }}.github.io/${{ github.event.repository.name }}/
+
+      - name: Create issue on broken links
+        if: steps.check.outputs.exit_code != '0'
+        uses: actions/github-script@v7
+        with:
+          script: |
+            const fs = require('fs');
+            const report = fs.readFileSync('log', 'utf8');
+
+            const { data: issues } = await github.rest.issues.listForRepo({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              state: 'open',
+              labels: 'link-checker'
+            });
+
+            if (issues.length === 0) {
+              await github.rest.issues.create({
+                owner: context.repo.owner,
+                repo: context.repo.repo,
+                title: '🔗 Broken Links Found on Site',
+                body: `The monthly link checker detected broken links.\n\n${report}`,
+                labels: ['link-checker']
+              });
+            }

.github/workflows/publish.yaml

@@ -0,0 +1,106 @@
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: "0 23 * * 0"
+  push:
+    branches: [main]
+
+name: Render Quarto Site
+
+jobs:
+  quarto-publish:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up Quarto
+        uses: quarto-dev/quarto-actions/setup@v2
+        with:
+          tinytex: true
+
+      - name: Install system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt install -y \
+            libcurl4-openssl-dev \
+            libfontconfig1-dev \
+            libssl-dev \
+            libxml2-dev \
+            libpng-dev \
+            libjpeg-dev \
+            libtiff-dev \
+            libcairo2-dev \
+            libxt-dev \
+            libfreetype6-dev \
+            libharfbuzz-dev \
+            libfribidi-dev \
+            zlib1g-dev \
+            libv8-dev \
+            libglpk-dev \
+            librsvg2-bin
+
+      - name: Install R with renv
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: renv
+        if: ${{ hashFiles('renv.lock') != '' }}
+
+      - name: Install R Dependencies with renv
+        uses: r-lib/actions/setup-renv@v2
+        with:
+          cache-version: 1
+        if: ${{ hashFiles('renv.lock') != '' }}
+
+      - name: Install R latest
+        uses: r-lib/actions/setup-r@v2
+        if: ${{ hashFiles('renv.lock') == '' }}
+
+      - name: Set R library path (no lockfile)
+        run: echo "R_LIBS_USER=$HOME/.local/lib/R/site-library" >> "$GITHUB_ENV"
+        if: ${{ hashFiles('renv.lock') == '' }}
+
+      - name: Cache R library (no lockfile)
+        uses: actions/cache@v4
+        with:
+          path: ~/.local/lib/R/site-library
+          key: ${{ runner.os }}-r-nolock-${{ hashFiles('**/*.R', '**/*.Rmd', '**/*.qmd', '_quarto.yml') }}
+          restore-keys: |
+            ${{ runner.os }}-r-nolock-
+        if: ${{ hashFiles('renv.lock') == '' }}
+
+      - name: Install R latest dependencies
+        run: |
+          lib <- Sys.getenv("R_LIBS_USER")
+          if (nzchar(lib)) {
+            dir.create(lib, recursive = TRUE, showWarnings = FALSE)
+            .libPaths(c(lib, .libPaths()))
+          }
+          install.packages("renv")
+          install.packages("rmarkdown")
+          install.packages("yaml")
+          deps <- unique(stats::na.omit(renv::dependencies()$Package))
+          if (length(deps) > 0) install.packages(deps)
+        shell: Rscript {0}
+        if: ${{ hashFiles('renv.lock') == '' }}
+
+      - name: Ensure Quarto R runtime packages
+        run: |
+          lib <- Sys.getenv("R_LIBS_USER")
+          if (nzchar(lib)) {
+            dir.create(lib, recursive = TRUE, showWarnings = FALSE)
+            .libPaths(c(lib, .libPaths()))
+          }
+          pkgs <- c("knitr", "rmarkdown")
+          missing <- pkgs[!vapply(pkgs, requireNamespace, logical(1), quietly = TRUE)]
+          if (length(missing) > 0) install.packages(missing)
+        shell: Rscript {0}
+
+      - name: Render and Publish
+        uses: quarto-dev/quarto-actions/publish@v2
+        with:
+          target: gh-pages
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/style.yaml

@@ -0,0 +1,27 @@
+on:
+  workflow_dispatch:
+
+name: Air Formatting
+
+permissions:
+  contents: write
+
+jobs:
+  format:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v5
+        with:
+          fetch-depth: 0
+
+      - name: Install Air
+        uses: posit-dev/setup-air@v1
+
+      - name: Format
+        run: air format .
+
+      - name: Commit and push changes
+        uses: stefanzweifel/git-auto-commit-action@v7
+        with:
+          commit_message: "Style code (Air)"

.github/workflows/update-extension.yml

@@ -0,0 +1,32 @@
+name: Update Tutorial Template Extension
+
+on:
+  schedule:
+    - cron: "0 0 2 * *"
+  workflow_dispatch:
+
+permissions: read-all
+
+jobs:
+  update-downstream-tutorials:
+    # prevent action from running in actual extension repo--else, recursive installations
+    # only users of the extension should have these auto-updates
+    if: github.repository != 'lmu-osc/tutorial-template'
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v5
+        with:
+          fetch-depth: 0
+
+      - name: Setup Quarto
+        uses: quarto-dev/quarto-actions/setup@v2
+
+      - name: Update tutorial-template extension
+        run: quarto update lmu-osc/tutorial-template --no-prompt
+
+      - uses: stefanzweifel/git-auto-commit-action@v7
+        with:
+          commit_message: "Update tutorial-template extension (GHA)"

.gitignore

@@ -58,3 +58,12 @@ rsconnect/
 .httr-oauth
 .quarto
 _site/
+**_files/
+
+**/*.quarto_ipynb
+
+# ignore posi assistant settings
+.posit/assistant
+
+# ignore individual file
+plot-trait-evolution.html

404.qmd

@@ -0,0 +1,14 @@
+---
+title: Uh-oh, looks like the page is missing!
+description: The page you are looking for cannot be found 😟
+---
+
+The page you are looking for either does not exist or has been moved. Please check the URL and try again. If you believe this is an error, please contact the website administrator for assistance.
+
+Note: many pages within our old tutorials have been moved to new locations as part of standardization efforts. It's likely the page you are looking for has been moved to a new location within the site.
+
+<!-- 
+Note: if you, the developer, want to have custom messages based on the URL someone is trying to access e.g. because a popular page has been moved and you want to direct readers to the new page/section, take a look at the `404.qmd` file in the main OSC website: https://github.com/lmu-osc/lmu-osc.github.io/blob/main/404.qmd
+
+It contains code with customized messages/information based on the URL path that is being accessed. You can adapt this code to your own needs and customize the messages as you see fit.
+ -->

CITATION.cff

@@ -6,9 +6,21 @@ authors:
   orcid: "https://orcid.org/0000-0002-2378-4915"
   affiliation:
     - name: "University of Sheffield"
-      ror: " https://ror.org/05krs5044"      
+      ror: "https://ror.org/05krs5044"
+- family-names: "Ihle"
+  given-names: "Malika"
+  orcid: "https://orcid.org/0000-0002-9543-9310"
+  affiliation:
+    - name: "LMU Open Science Center"
+      ror: "https://ror.org/029e6qe04"
+- family-names: "Kenny"
+  given-names: "Adam"
+  orcid: "https://orcid.org/0000-0002-1316-7382"
+  affiliation:
+    - name: "University of Oxford"
+      ror: "https://ror.org/052gg0110"
 title: "Collaborative coding with GitHub and RStudio"
-version: 0.1.0
+version: 0.2.0
 doi: "DOI_HERE_AFTER_GENERATED"
 date-released: 2024-01-15
 repository-code: "https://github.com/lmu-osc/Collaborative-RStudio-GitHub"
@@ -26,4 +38,4 @@ preferred-citation:
     ror: "https://ror.org/029e6qe04"
   repository-code: "https://github.com/lmu-osc/Collaborative-RStudio-GitHub"
   url: "https://lmu-osc.github.io/Collaborative-RStudio-GitHub/"
-  type: "book"
+  type: "book"

Collaborative-RStudio-GitHub.Rproj

@@ -1,4 +1,5 @@
 Version: 1.0
+ProjectId: e6cff1b6-d495-44c0-9f43-33511fbae88b
 
 RestoreWorkspace: Default
 SaveWorkspace: Default

README.md

@@ -19,7 +19,7 @@ In this session, you will
 * observe the outcome of all contributions merged by your collaborator   
 * **pull the upstream repository into your fork** (i.e. update your fork to reflect all the changes that happened in your collaborator's original repository)  
 
-<img src="assets/new-overview.png" width="750">  
+<img src="/assets/new-overview.png" width="750">  
 <br/>
 
 In this example, the file you will contribute is required to simulate the evolutionary trajectory of an imaginary bird species’ body size. We will use RStudio and GitHub to collate all species files and plot them all up together at the end. We will also discover the skull and beak shapes associated with each species you contributed (after they 'evolved' through a simple brownian motion  model which assumes steps to progress completely at random).