Add organized Docker container structure with disciplined naming

- Create layered container architecture: Base, Light, Full, Computational - Implement non-root user management with UID/GID mapping - Add Markwhen timeline tool to documentation stack - Create wrapper scripts for environment variable handling - Update documentation across all containers - Establish naming convention using RCEO-AIOS-Public-Tools- prefix - Add organizational rule to keep repository root clean - Remove old unorganized container files
2025-10-16 11:40:25 -05:00
parent 7fad76ea9d
commit d30f103209
24 changed files with 1055 additions and 131 deletions
--- a/Docker/RCEO-AIOS-Public-Tools-DocMaker-Computational/Dockerfile
+++ b/Docker/RCEO-AIOS-Public-Tools-DocMaker-Computational/Dockerfile
@@ -0,0 +1,42 @@
+FROM rceo-aios-public-tools-docmaker-full:latest
+
+# Avoid prompts from apt
+ENV DEBIAN_FRONTEND=noninteractive
+
+# Install computational tools
+RUN apt-get update && apt-get install -y \
+    r-base \
+    r-base-dev \
+    bc \
+    octave \
+    && rm -rf /var/lib/apt/lists/*
+
+# Install Python scientific packages
+RUN pip3 install pandas numpy matplotlib scipy jupyter
+
+# Install R packages (commonly used ones)
+RUN R -e "install.packages(c('knitr', 'rmarkdown', 'dplyr', 'ggplot2'), repos='https://cran.rstudio.com/')"
+
+# Install IRkernel for R in Jupyter
+RUN R -e "install.packages('IRkernel', repos='https://cran.rstudio.com/')"
+
+# Create Jupyter config directory and set up notebook directory
+RUN mkdir -p /workspace/notebooks
+
+# Create Jupyter startup script
+RUN echo '#!/bin/bash' > /jupyter_start.sh && \
+    echo '# Install R kernel for Jupyter if R is available' >> /jupyter_start.sh && \
+    echo 'if command -v R &> /dev/null; then' >> /jupyter_start.sh && \
+    echo '  R -e "IRkernel::installspec()" 2>/dev/null || true' >> /jupyter_start.sh && \
+    echo 'fi' >> /jupyter_start.sh && \
+    echo '# Run Jupyter as the proper user' >> /jupyter_start.sh && \
+    echo 'exec su -p ReachableCEO-Tools -c "jupyter notebook --ip=0.0.0.0 --port=8888 --no-browser --allow-root --notebook-dir=/workspace/notebooks"' >> /jupyter_start.sh && \
+    chmod +x /jupyter_start.sh
+
+# Expose Jupyter on port 8888
+EXPOSE 8888
+
+# Create a working directory
+WORKDIR /workspace
+
+# The entrypoint from the base image handles user creation
--- a/Docker/RCEO-AIOS-Public-Tools-DocMaker-Computational/README.md
+++ b/Docker/RCEO-AIOS-Public-Tools-DocMaker-Computational/README.md
@@ -0,0 +1,97 @@
+# RCEO-AIOS-Public-Tools-DocMaker-Computational Container
+
+This container is part of the AIOS-Public project and provides a comprehensive documentation and computational environment.
+
+## Overview
+
+The RCEO-AIOS-Public-Tools-DocMaker-Computational container extends the full documentation environment with computational tools for data analysis, scientific computing, and interactive notebooks. It's designed for CTO mode operations involving R&D and computational work.
+
+## Tools Included
+
+Inherits all tools from:
+- **RCEO-AIOS-Public-Tools-DocMaker-Full**: All documentation and LaTeX tools
+
+### Computational Tools
+- **R Programming Language**: Statistical computing and data analysis
+- **Python Scientific Stack**: 
+  - pandas - Data manipulation
+  - numpy - Numerical computing
+  - matplotlib - Visualization
+  - scipy - Scientific computing
+- **Jupyter Notebooks**: Interactive computational environments
+- **GNU Octave**: Numerical computations (MATLAB alternative)
+- **bc**: Command-line calculator
+
+## Usage
+
+### Building the Computational Container
+```bash
+# From this directory
+cd /home/localuser/AIWorkspace/AIOS-Public/Docker/RCEO-AIOS-Public-Tools-DocMaker-Computational
+
+# Use the wrapper script to automatically detect and set user IDs
+./docker-compose-wrapper.sh build
+
+# Or run commands in the computational container with automatic user mapping
+./docker-compose-wrapper.sh run docmaker-computational [command]
+
+# Example: Run R analysis
+./docker-compose-wrapper.sh run docmaker-computational Rscript analysis.R
+
+# Example: Run Python analysis
+./docker-compose-wrapper.sh run docmaker-computational python analysis.py
+
+# Example: Start Jupyter notebook server
+./docker-compose-wrapper.sh up
+# Then access at http://localhost:8888
+```
+
+### Using with docker-compose directly
+```bash
+# Set environment variables and run docker-compose directly
+LOCAL_USER_ID=$(id -u) LOCAL_GROUP_ID=$(id -g) docker-compose up --build
+
+# Or export variables first
+export LOCAL_USER_ID=$(id -u)
+export LOCAL_GROUP_ID=$(id -g) 
+docker-compose up
+```
+
+### Using the wrapper script
+```bash
+# Build and start the computational container with Jupyter access and automatic user mapping
+./docker-compose-wrapper.sh up --build
+
+# Start without rebuilding
+./docker-compose-wrapper.sh up
+
+# View container status
+./docker-compose-wrapper.sh ps
+
+# Stop containers
+./docker-compose-wrapper.sh down
+```
+
+## User ID Mapping (For File Permissions)
+
+The container automatically detects and uses the host user's UID and GID to ensure proper file permissions. This means:
+
+- Files created inside the container will have the correct ownership on the host
+- No more root-owned files after container operations
+- Works across different environments (development, CI/CD, cloud)
+
+The container detects the user ID from the mounted workspace volume. If needed, you can override the default values by setting environment variables:
+
+```bash
+# Set specific user ID and group ID before running docker-compose
+export LOCAL_USER_ID=1000
+export LOCAL_GROUP_ID=1000
+docker-compose up
+```
+
+Or run with inline environment variables:
+```bash
+LOCAL_USER_ID=1000 LOCAL_GROUP_ID=1000 docker-compose up
+```
+
+The container runs as a non-root user named `ReachableCEO-Tools` with the detected host user's UID/GID.
--- a/Docker/RCEO-AIOS-Public-Tools-DocMaker-Computational/docker-compose-wrapper.sh
+++ b/Docker/RCEO-AIOS-Public-Tools-DocMaker-Computational/docker-compose-wrapper.sh
@@ -0,0 +1,67 @@
+#!/bin/bash
+# docker-compose-wrapper.sh - Wrapper script to detect host UID/GID and run docker-compose
+
+set -e  # Exit on any error
+
+# Detect the UID and GID of the user that owns the workspace directory (parent directory)
+WORKSPACE_DIR="$(cd "$(dirname "$0")/../.." && pwd)"
+echo "Detecting user ID from workspace directory: $WORKSPACE_DIR"
+
+if [ -d "$WORKSPACE_DIR" ]; then
+    DETECTED_USER_ID=$(stat -c %u "$WORKSPACE_DIR" 2>/dev/null || echo 0)
+    DETECTED_GROUP_ID=$(stat -c %g "$WORKSPACE_DIR" 2>/dev/null || echo 0)
+    
+    # If detection failed, try current user
+    if [ "$DETECTED_USER_ID" = "0" ]; then
+        DETECTED_USER_ID=$(id -u)
+        DETECTED_GROUP_ID=$(id -g)
+    fi
+else
+    # Fallback to current user if workspace directory doesn't exist
+    DETECTED_USER_ID=$(id -u)
+    DETECTED_GROUP_ID=$(id -g)
+fi
+
+echo "Detected USER_ID=$DETECTED_USER_ID and GROUP_ID=$DETECTED_GROUP_ID"
+
+# Set environment variables for docker-compose
+export LOCAL_USER_ID=$DETECTED_USER_ID
+export LOCAL_GROUP_ID=$DETECTED_GROUP_ID
+
+# Show usage information
+echo ""
+echo "Usage: $0 [build|up|run <service> <command>|exec <service> <command>|down|ps]"
+echo ""
+echo "Examples:"
+echo "  $0 up                    # Start services"
+echo "  $0 build                 # Build containers"
+echo "  $0 run docmaker-full bash  # Run command in container"
+echo "  $0 down                  # Stop and remove containers"
+echo ""
+
+# Check if docker compose (new format) or docker-compose (old format) is available
+if command -v docker &> /dev/null && docker compose version &> /dev/null; then
+    # Use new docker compose format
+    if [ $# -eq 0 ]; then
+        echo "No command provided. Running 'docker compose up'..."
+        docker compose up
+    else
+        # Execute the provided docker compose command
+        echo "Running: docker compose $*"
+        docker compose "$@"
+    fi
+elif command -v docker-compose &> /dev/null; then
+    # Fallback to old docker-compose format
+    if [ $# -eq 0 ]; then
+        echo "No command provided. Running 'docker-compose up'..."
+        docker-compose up
+    else
+        # Execute the provided docker-compose command
+        echo "Running: docker-compose $*"
+        docker-compose "$@"
+    fi
+else
+    echo "Error: Neither 'docker compose' nor 'docker-compose' command found."
+    echo "Please install Docker Compose to use this script."
+    exit 1
+fi
--- a/Docker/RCEO-AIOS-Public-Tools-DocMaker-Computational/docker-compose.yml
+++ b/Docker/RCEO-AIOS-Public-Tools-DocMaker-Computational/docker-compose.yml
@@ -0,0 +1,20 @@
+version: '3.8'
+
+services:
+  docmaker-computational:
+    build:
+      context: .
+      dockerfile: Dockerfile
+    container_name: RCEO-AIOS-Public-Tools-DocMaker-Computational
+    image: rceo-aios-public-tools-docmaker-computational:latest
+    volumes:
+      - ../../../:/workspace:rw
+    working_dir: /workspace
+    stdin_open: true
+    tty: true
+    ports:
+      - "8888:8888"  # Jupyter notebook access
+    environment:
+      - LOCAL_USER_ID=${LOCAL_USER_ID:-1000}
+      - LOCAL_GROUP_ID=${LOCAL_GROUP_ID:-1000}
+    user: "${LOCAL_USER_ID:-1000}:${LOCAL_GROUP_ID:-1000}"