Added a suite of GitHub actions for tests, docs and publishing.

Author: LTLA

.github/workflows/build-docs.yaml

@@ -0,0 +1,38 @@
+on:
+  push:
+    branches:
+      - master
+
+      
+name: Build documentation
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Node
+      uses: actions/setup-node@v4
+      with:
+        node-version: 22
+
+    - name: Restore the node modules
+      uses: actions/cache@v4
+      with:
+        path: '**/node_modules'
+        key: npm-${{ hashFiles('**/package.json') }}
+
+    - name: Install JSDoc
+      run: npm i --include=dev
+
+    - name: Run JSDoc
+      run: npm run jsdoc
+
+    - name: GH Pages Deployment
+      uses: JamesIves/github-pages-deploy-action@v4
+      with:
+        branch: gh-pages # The branch the action should deploy to.
+        folder: docs/built
+        target-folder: docs
+        clean: true # Automatically remove deleted files from the deploy branch

.github/workflows/publish-npm.yaml

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+on:
+  workflow_run:
+    workflows: [Run unit tests]
+    types: [completed]
+    branches: [master]
+
+name: Build and publish to NPM 
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    if: ${{ github.event.workflow_run.conclusion == 'success' }}
+
+    steps:
+    - name: Checkout repo
+      uses: actions/checkout@v4
+
+    - name: Set up Node
+      uses: actions/setup-node@v4
+      with:
+        node-version: 22
+
+    # We only run the remaining (remote-touching) steps if the version has actually changed.
+    - name: Extract package versions
+      shell: bash
+      run: |
+        current_version=$(npm pkg get version | sed 's/"//g')
+        echo "NEW_WOBBEGONG_VERSION=${current_version}" >> $GITHUB_ENV
+        old_version=$(npm view wobbegong version)
+        update=0 && [[ $old_version != $current_version ]] && update=1
+        echo "UPDATE_WOBBEGONG=${update}" >> $GITHUB_ENV
+        echo "Current version is ${current_version} (published ${old_version})"
+
+    - name: Cache Modules
+      if: env.UPDATE_WOBBEGONG == 1
+      uses: actions/cache@v4
+      with:
+        path: '**/node_modules'
+        key: npm-${{ hashFiles('package.json') }}
+
+    - name: Update NPM packages
+      if: env.UPDATE_WOBBEGONG == 1
+      run: npm i --include=dev
+
+    - name: Cache mock files
+      if: env.UPDATE_WOBBEGONG == 1
+      uses: actions/cache@v4
+      with:
+        path: tests/mock-files
+        key: mock-${{ hashFiles('tests/mock.R') }}
+
+    - name: Double-checking tests
+      if: env.UPDATE_WOBBEGONG == 1
+      run: npm run test
+
+    - name: Publish to NPM
+      if: env.UPDATE_WOBBEGONG == 1
+      run: npm publish
+      env:
+        NODE_AUTH_TOKEN: ${{ secrets.NPM_TOKEN }}
+
+    - name: Tagging the release
+      if: env.UPDATE_WOBBEGONG == 1
+      uses: actions/github-script@v5
+      with:
+        script: |
+          github.rest.git.createRef({
+            owner: context.repo.owner,
+            repo: context.repo.repo,
+            ref: 'refs/tags/' + process.env.NEW_WOBBEGONG_VERSION,
+            sha: context.sha
+          })

.github/workflows/run-tests.yaml

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+on:
+  push:
+    branches:
+      - master
+  pull_request:
+
+name: Run unit tests
+
+jobs:
+  create_mock:
+    runs-on: ubuntu-latest
+    container: bioconductor/bioconductor_docker:devel
+
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+
+      - name: Cache RDS files
+        id: cache-mock
+        uses: actions/cache@v4
+        with:
+          path: tests/mock-files
+          key: mock-${{ hashFiles('tests/mock.R') }}
+
+      - name: Restore the package directory
+        if: steps.cache-mock.outputs.cache-hit != 'true'
+        uses: actions/cache@v4
+        with:
+          path: ${{ env.R_PKG_DIR }}
+          key: check-packages
+
+      - name: Clone the wobbegong R package
+        if: steps.cache-mock.outputs.cache-hit != 'true'
+        run: git clone https://github.com/kanaverse/wobbegong-R rpkg
+
+      - name: Install dependencies
+        if: steps.cache-mock.outputs.cache-hit != 'true'
+        shell: Rscript {0}
+        run: |
+          stuff <- read.dcf("rpkg/DESCRIPTION")
+          stuff <- stuff[,intersect(colnames(stuff), c("Imports", "LinkingTo", "Suggests", "Depends"))]
+          deps <- sub(" .*", "", unlist(strsplit(stuff, ",\\s*"), use.names=FALSE))
+          BiocManager::install(deps)
+
+      - name: Install the R package
+        if: steps.cache-mock.outputs.cache-hit != 'true'
+        run: R CMD INSTALL rpkg
+
+      - name: Build the mock files
+        if: steps.cache-mock.outputs.cache-hit != 'true'
+        run: |
+          cd tests
+          R -f mock.R
+
+  test:
+    runs-on: ubuntu-latest
+    needs: [ create_mock ]
+
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+
+      - name: Set up Node
+        uses: actions/setup-node@v4
+        with:
+          node-version: 22
+
+      - name: Cache Modules
+        uses: actions/cache@v4
+        with:
+          path: '**/node_modules'
+          key: npm-${{ hashFiles('package.json') }}
+
+      - name: Update NPM packages
+        run: npm i --include=dev
+
+      - name: Cache mock files
+        uses: actions/cache@v4
+        with:
+          path: tests/mock-files
+          key: mock-${{ hashFiles('tests/mock.R') }}
+
+      - name: Run tests
+        run: npm run test