Add devcontainer and using git action to deploy docs

.devcontainer/Dockerfile

@@ -0,0 +1,150 @@
+FROM r-base:latest
+
+###############################
+# System dependencies
+###############################
+RUN apt-get update && apt-get install -y \
+    git=1:2.51.0-1 \
+    build-essential=12.12 \
+    libcurl4-openssl-dev=8.17.0-2 \
+    libssl-dev=3.5.4-1 \
+    libxml2-dev=2.15.1+dfsg-0.4 \
+    libicu-dev=76.1-4 \
+    libxt-dev=1:1.2.1-1.3 \
+    curl=8.17.0-2 \
+    bash=5.3-1 \
+    ca-certificates=20250419 \
+    gnupg=2.4.8-4 \
+    openssh-client=1:10.2p1-2 \
+    ruby-full=1:3.3 \
+    zlib1g-dev=1:1.3.dfsg+really1.3.1-1+b1 \
+    && apt-get clean && rm -rf /var/lib/apt/lists/*
+
+###############################
+# Ensure global R library
+###############################
+RUN mkdir -p /usr/local/lib/R/site-library && \
+    chmod -R 777 /usr/local/lib/R/site-library
+
+###############################
+# Install remotes
+###############################
+RUN R -q -e "install.packages('remotes', repos='https://cloud.r-project.org')"
+
+###############################
+# Install specific R packages
+###############################
+RUN R -q -e "\
+  remotes::install_version('ps', version = '1.9.1'); \
+  remotes::install_version('evaluate', version = '1.0.5'); \
+  remotes::install_version('highr', version = '0.11'); \
+  remotes::install_version('xfun', version = '0.54'); \
+  remotes::install_version('yaml', version = '2.3.10'); \
+  remotes::install_version('lazyeval', version = '0.2.2'); \
+  remotes::install_version('lifecycle', version = '1.0.4'); \
+  remotes::install_version('pkgbuild', version = '1.4.8'); \
+  remotes::install_version('R.methodsS3', version = '1.8.2'); \
+  remotes::install_version('R.oo', version = '1.27.1'); \
+  remotes::install_version('R.utils', version = '2.13.0'); \
+  remotes::install_version('processx', version = '3.8.6'); \
+  remotes::install_version('backports', version = '1.5.0'); \
+  remotes::install_version('cli', version = '3.6.5'); \
+  remotes::install_version('digest', version = '0.6.39'); \
+  remotes::install_version('glue', version = '1.8.0'); \
+  remotes::install_version('knitr', version = '1.50'); \
+  remotes::install_version('rex', version = '1.2.1'); \
+  remotes::install_version('brew', version = '1.0-10'); \
+  remotes::install_version('commonmark', version = '2.0.0'); \
+  remotes::install_version('desc', version = '1.4.3'); \
+  remotes::install_version('pkgload', version = '1.4.1'); \
+  remotes::install_version('purrr', version = '1.2.0'); \
+  remotes::install_version('rlang', version = '1.1.6'); \
+  remotes::install_version('stringr', version = '1.6.0'); \
+  remotes::install_version('withr', version = '3.0.2'); \
+  remotes::install_version('cpp11', version = '0.5.2'); \
+  remotes::install_version('magrittr', version = '2.0.4'); \
+  remotes::install_version('R.cache', version = '0.17.0'); \
+  remotes::install_version('rprojroot', version = '2.1.1'); \
+  remotes::install_version('vctrs', version = '0.6.5'); \
+  remotes::install_version('callr', version = '3.7.6'); \
+  remotes::install_version('collections', version = '0.3.9'); \
+  remotes::install_version('fs', version = '1.6.6'); \
+  remotes::install_version('jsonlite', version = '2.0.0'); \
+  remotes::install_version('lintr', version = '3.2.0'); \
+  remotes::install_version('R6', version = '2.6.1'); \
+  remotes::install_version('roxygen2', version = '7.3.3'); \
+  remotes::install_version('stringi', version = '1.8.7'); \
+  remotes::install_version('styler', version = '1.11.0'); \
+  remotes::install_version('xml2', version = '1.5.0'); \
+  remotes::install_version('xmlparsedata', version = '1.0.5'); \
+  remotes::install_version('languageserver', version = '0.3.16'); \
+  remotes::install_version('checkpoint', version = '0.4.10'); \
+  remotes::install_version('fastmap', version = '1.2.0'); \
+  remotes::install_version('bit', version = '4.6.0'); \
+  remotes::install_version('cachem', version = '1.1.0'); \
+  remotes::install_version('bit64', version = '4.6.0-1'); \
+  remotes::install_version('blob', version = '1.2.4'); \
+  remotes::install_version('DBI', version = '1.2.3'); \
+  remotes::install_version('memoise', version = '2.0.1'); \
+  remotes::install_version('pkgconfig', version = '2.0.3'); \
+  remotes::install_version('plogr', version = '0.2.0'); \
+  remotes::install_version('Rcpp', version = '1.1.0'); \
+  remotes::install_version('data.table', version = '1.17.8'); \
+  remotes::install_version('RSQLite', version = '2.4.4'); \
+  remotes::install_version('RcppEigen', version = '0.3.4.0.2'); \
+  remotes::install_version('qtl2', version = '0.38'); \
+"
+
+###############################
+# Install GitHub CLI
+###############################
+RUN mkdir -p /etc/apt/keyrings && \
+    curl -fsSL https://cli.github.com/packages/githubcli-archive-keyring.gpg | \
+        gpg --dearmor -o /etc/apt/keyrings/githubcli-archive-keyring.gpg && \
+    chmod go+r /etc/apt/keyrings/githubcli-archive-keyring.gpg && \
+    echo "deb [arch=$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/githubcli-archive-keyring.gpg] https://cli.github.com/packages stable main" \
+        > /etc/apt/sources.list.d/github-cli.list && \
+    apt-get update && apt-get install -y gh && \
+    rm -rf /var/lib/apt/lists/*
+
+###############################
+# Create docker user
+###############################
+RUN usermod -d /home/docker docker || true
+RUN mkdir -p /home/docker && chown -R docker:docker /home/docker
+ENV HOME=/home/docker
+
+###############################
+# Workspace setup
+###############################
+RUN mkdir -p /workspace && chown -R docker:docker /workspace
+WORKDIR /workspace
+
+###############################
+# Add colored Git PS1
+###############################
+RUN printf '\n\
+parse_git_branch() {\n\
+  branch=$(git branch --show-current 2>/dev/null)\n\
+  if [ -n "$branch" ]; then echo -e " (\\e[0;33m$branch\\e[0m)"; fi\n\
+}\n\
+export PS1="\\[\\e[0;32m\\]\\u@\\h\\[\\e[0m\\]->\\[\\e[0;34m\\]\\w\\[\\e[0m\\]\\$(parse_git_branch) $ "' >> /home/docker/.bashrc
+
+###############################
+# Install Jekyll and Bundler
+###############################
+RUN gem install jekyll bundler
+
+###############################
+# Install Python and Pip
+###############################
+RUN apt-get update && apt-get install -y \
+    python3 \
+    python3-pip \
+    python3-venv \
+    python-is-python3 \
+    python3-yaml \
+    && apt-get clean && rm -rf /var/lib/apt/lists/*
+
+USER docker
+

.devcontainer/devcontainer.json

@@ -0,0 +1,20 @@
+{
+  "name": "R Base Dev Container",
+  "dockerFile": "Dockerfile",
+  "workspaceFolder": "/workspace",
+  "remoteUser": "docker",
+  "workspaceMount": "source=${localWorkspaceFolder},target=/workspace,type=bind,consistency=cached",
+  "customizations": {
+        "vscode": {
+            "extensions": [
+                "reditorsupport.r"
+            ],
+            "settings": {
+                "terminal.integrated.shell.linux": "bash"
+            }
+        }
+    },
+   "remoteEnv": {
+        "SHELL": "/bin/bash"
+  }
+}

.github/workflows/deploy-gh-pages.yml

@@ -0,0 +1,67 @@
+name: Deploy to GitHub Pages
+
+on:
+  workflow_dispatch:
+
+jobs:
+  build-and-deploy:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Build Docker image (cached)
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          file: .devcontainer/Dockerfile
+          tags: jekyll-site:latest
+          load: true   # makes image available for docker run
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+
+      - name: Download required data
+        run: |
+          docker run --rm \
+            -u root \
+            -v ${{ github.workspace }}:/workspace \
+            -w /workspace \
+            jekyll-site:latest \
+            Rscript -e "options(timeout=1900); \
+                        dir.create('data', showWarnings=FALSE); \
+                        download.file('https://ndownloader.figshare.com/files/18533342', './data/cc_variants.sqlite'); \
+                        download.file('https://ndownloader.figshare.com/files/24607961', './data/mouse_genes.sqlite'); \
+                        download.file('https://ndownloader.figshare.com/files/24607970', './data/mouse_genes_mgi.sqlite'); \
+                        download.file('ftp://ftp.jax.org/dgatti/qtl2_workshop/qtl2_demo.Rdata', './data/qtl2_demo.Rdata');"
+
+
+      - name: Run Jekyll build inside container
+        run: |
+          docker run --rm \
+            -u root \
+            -v ${{ github.workspace }}:/workspace \
+            -w /workspace \
+            jekyll-site:latest \
+            make site
+
+      - name: Remove oversized data files before deploy
+        run: |
+          sudo chown -R $USER:$USER _site
+          rm -f _site/data/cc_multitissue_qtlviewer.Rdata
+          rm -f _site/data/qtl2_demo.Rdata
+          rm -f _site/data/cc_variants.sqlite
+          rm -f _site/data/mouse_genes.sqlite
+          rm -f _site/data/mouse_genes_mgi.sqlite
+
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./_site
+          publish_branch: gh-pages
+          force_orphan: true

.gitignore

@@ -13,4 +13,6 @@ data/mouse_genes_mgi.sqlite
 fig/.Rhistory
 files/Gatti_MammGen_2018.pptx
 scripts/
-
+venv
+fig/rmd-*.png
+_episodes