To upgrade to the latest :)

.dockerignore

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+__pycache__/
+*.py[cod]
+assets/
+examples/
+www/
+*.png
+*.xlsx

.github/workflows/boxplotr-mcp-container.yml

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+name: BoxPlotR MCP container
+
+on:
+  push:
+    paths:
+      - "Dockerfile.mcp"
+      - "requirements-mcp.txt"
+      - "boxplotr_mcp_server.py"
+      - "*.R"
+      - "deploy/boxplotr_mcp/**"
+      - "tests/test_mcp_container.py"
+      - ".github/workflows/boxplotr-mcp-container.yml"
+  pull_request:
+    paths:
+      - "Dockerfile.mcp"
+      - "requirements-mcp.txt"
+      - "boxplotr_mcp_server.py"
+      - "*.R"
+      - "deploy/boxplotr_mcp/**"
+      - "tests/test_mcp_container.py"
+      - ".github/workflows/boxplotr-mcp-container.yml"
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  build-and-test:
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+    steps:
+      - uses: actions/checkout@v4
+      - uses: docker/setup-buildx-action@v3
+      - name: Build MCP image
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          file: Dockerfile.mcp
+          load: true
+          push: false
+          tags: boxplotr-mcp:test
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+      - name: Start MCP container
+        run: docker run --detach --name boxplotr-mcp --env MCP_IDENTITY_SECRET=docker-ci-runtime-only --publish 8765:8765 boxplotr-mcp:test
+      - name: Wait for health
+        run: |
+          for attempt in $(seq 1 24); do
+            if curl --fail --silent http://127.0.0.1:8765/health >/dev/null; then
+              exit 0
+            fi
+            sleep 5
+          done
+          docker logs boxplotr-mcp
+          exit 1
+      - name: Test health, MCP and rendering
+        run: python3 tests/test_mcp_container.py
+      - name: Show logs on failure
+        if: failure()
+        run: docker logs boxplotr-mcp

.github/workflows/docker-publish.yml

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+name: Docker
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+on:
+  schedule:
+    - cron: '24 21 * * *'
+  push:
+    branches: [ "master" ]
+    # Publish semver tags as releases.
+    tags: [ 'v*.*.*' ]
+  pull_request:
+    branches: [ "master" ]
+
+env:
+  # Use docker.io for Docker Hub if empty
+  REGISTRY: ghcr.io
+  # github.repository as <account>/<repo>
+  IMAGE_NAME: ${{ github.repository }}
+
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+      # This is used to complete the identity challenge
+      # with sigstore/fulcio when running outside of PRs.
+      id-token: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      # Install the cosign tool except on PR
+      # https://github.com/sigstore/cosign-installer
+      - name: Install cosign
+        if: github.event_name != 'pull_request'
+        uses: sigstore/cosign-installer@59acb6260d9c0ba8f4a2f9d9b48431a222b68e20 #v3.5.0
+        with:
+          cosign-release: 'v2.2.4'
+
+      # Set up BuildKit Docker container builder to be able to build
+      # multi-platform images and export cache
+      # https://github.com/docker/setup-buildx-action
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@f95db51fddba0c2d1ec667646a06c2ce06100226 # v3.0.0
+
+      # Login against a Docker registry except on PR
+      # https://github.com/docker/login-action
+      - name: Log into registry ${{ env.REGISTRY }}
+        if: github.event_name != 'pull_request'
+        uses: docker/login-action@343f7c4344506bcbf9b4de18042ae17996df046d # v3.0.0
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      # Extract metadata (tags, labels) for Docker
+      # https://github.com/docker/metadata-action
+      - name: Extract Docker metadata
+        id: meta
+        uses: docker/metadata-action@96383f45573cb7f253c731d3b3ab81c87ef81934 # v5.0.0
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+
+      # Build and push Docker image with Buildx (don't push on PR)
+      # https://github.com/docker/build-push-action
+      - name: Build and push Docker image
+        id: build-and-push
+        uses: docker/build-push-action@0565240e2d4ab88bba5387d719585280857ece09 # v5.0.0
+        with:
+          context: .
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+
+      # Sign the resulting Docker image digest except on PRs.
+      # This will only write to the public Rekor transparency log when the Docker
+      # repository is public to avoid leaking data.  If you would like to publish
+      # transparency data even for private images, pass --force to cosign below.
+      # https://github.com/sigstore/cosign
+      - name: Sign the published Docker image
+        if: ${{ github.event_name != 'pull_request' }}
+        env:
+          # https://docs.github.com/en/actions/security-guides/security-hardening-for-github-actions#using-an-intermediate-environment-variable
+          TAGS: ${{ steps.meta.outputs.tags }}
+          DIGEST: ${{ steps.build-and-push.outputs.digest }}
+        # This step uses the identity token to provision an ephemeral certificate
+        # against the sigstore community Fulcio instance.
+        run: echo "${TAGS}" | xargs -I {} cosign sign --yes {}@${DIGEST}

.gitignore

@@ -3,3 +3,7 @@
 
 # Example code in package build process
 *-Ex.R
+
+# Python generated files
+__pycache__/
+*.py[cod]

BoxPlotR_functions.R

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+# Specifies the arrangement of data points (normal or jittered).
+# point_type: 0 = normal, 2 = jittered
+jittered_points <- function(data_matrix, my_horizontal = FALSE, point_type,
+                            point_colors, point_transparency, point_size) {
+  # normal boxplots
+  if (my_horizontal) {
+    for (i in seq_len(ncol(data_matrix))) {
+      alpha_val <- 255 * (point_transparency / 100)
+      col_rgb <- rgb(
+        t(col2rgb(point_colors[i])),
+        maxColorValue = 255,
+        alpha = alpha_val
+      )
+      if (point_type == 0) {
+        points(
+          data_matrix[, i],
+          rep(i, nrow(data_matrix)),
+          col = col_rgb,
+          pch = 16,
+          cex = point_size
+        )
+      } else {
+        points(
+          data_matrix[, i],
+          jitter(rep(i, nrow(data_matrix)), amount = 0.25),
+          col = col_rgb,
+          pch = 16,
+          cex = point_size
+        )
+      }
+    }
+  } else {
+    # horizontal boxplots
+    for (i in seq_len(ncol(data_matrix))) {
+      alpha_val <- 255 * (point_transparency / 100)
+      col_rgb <- rgb(
+        t(col2rgb(point_colors[i])),
+        maxColorValue = 255,
+        alpha = alpha_val
+      )
+      if (point_type == 0) {
+        points(
+          rep(i, nrow(data_matrix)),
+          data_matrix[, i],
+          col = col_rgb,
+          pch = 16,
+          cex = point_size
+        )
+      } else {
+        points(
+          jitter(rep(i, nrow(data_matrix)), amount = 0.25),
+          data_matrix[, i],
+          col = col_rgb,
+          pch = 16,
+          cex = point_size
+        )
+      }
+    }
+  }
+}

Dockerfile

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+# Use the official lightweight rocker shiny image
+FROM rocker/shiny:latest
+
+
+RUN R -e "install.packages(c('beeswarm', 'vioplot', 'beanplot', 'RColorBrewer', 'readxl', 'sm', 'testthat', 'ggplot2'), repos='https://cloud.r-project.org/')"
+
+# Remove default Shiny apps
+RUN rm -rf /srv/shiny-server/*
+
+# Copy the application files to the container
+COPY . /srv/shiny-server/
+
+# Ensure proper ownership
+RUN chown -R shiny:shiny /srv/shiny-server/
+
+# Expose the shiny server port
+EXPOSE 3838
+
+# Run the Shiny server
+CMD ["/usr/bin/shiny-server"]

Dockerfile.mcp

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+FROM rocker/r-ver:4.5.1
+
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends python3 python3-venv python3-pip \
+    && rm -rf /var/lib/apt/lists/*
+
+RUN install2.r --error --skipinstalled \
+    beanplot beeswarm ggplot2 RColorBrewer sm tidyr vioplot
+
+WORKDIR /opt/boxplotr-mcp
+COPY requirements-mcp.txt ./
+RUN python3 -m venv .venv \
+    && .venv/bin/pip install --no-cache-dir --requirement requirements-mcp.txt
+
+COPY deploy/boxplotr_mcp/app.py ./
+COPY boxplotr_mcp_server.py BoxPlotR_functions.R boxplot_stats_Function.R \
+    MyBeanplot.R MyVioplot.R /srv/shiny-server/boxplotr/
+
+RUN groupadd --system shiny \
+    && useradd --system --gid shiny --home-dir /nonexistent --shell /usr/sbin/nologin shiny \
+    && mkdir -p /var/lib/boxplotr-mcp/output /etc/boxplotr-mcp \
+    && printf '{}\n' > /etc/boxplotr-mcp/keys.json \
+    && chown -R shiny:shiny /var/lib/boxplotr-mcp \
+    && chmod -R a-w /opt/boxplotr-mcp /srv/shiny-server/boxplotr
+
+USER shiny
+EXPOSE 8765
+
+HEALTHCHECK --interval=10s --timeout=3s --start-period=20s --retries=6 \
+    CMD .venv/bin/python -c "import urllib.request; urllib.request.urlopen('http://127.0.0.1:8765/health', timeout=2)"
+
+CMD [".venv/bin/uvicorn", "app:app", "--host", "0.0.0.0", "--port", "8765", "--workers", "1", "--limit-concurrency", "24", "--timeout-keep-alive", "5"]