update devcontainer configuration using docker-compose

Author: dimitri-yatsenko

.devcontainer/Dockerfile

@@ -1,65 +1,28 @@
-# Use an official Ubuntu as a parent image
-FROM ubuntu:22.04
+FROM mcr.microsoft.com/devcontainers/miniconda:3
 
 # Set environment variables for Conda
 ENV PATH=/opt/conda/bin:$PATH
-ENV MYSQL_ROOT_PASSWORD=dj_secret123
 ENV DJ_HOST=localhost
-ENV DJ_PASS=$MYSQL_ROOT_PASSWORD
-ENV DJ_USER=root
+ENV DJ_PASS=$DJ_PASS
+ENV DJ_USER=$DJ_USER
 
-# Install necessary system tools
+# Install system dependencies including netcat for connection checking
 RUN apt-get update && apt-get install -y \
     wget \
     vim \
-    bzip2 \
-    ca-certificates \
     curl \
     git \
-    webp \
-    mysql-server \
+    netcat-openbsd \
+    default-mysql-client \
     && rm -rf /var/lib/apt/lists/*
 
-#  Download and install Miniconda
-RUN ARCH=$(uname -m) && \
-    if [ "$ARCH" = "x86_64" ]; then \
-        MINICONDA_URL="https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh"; \
-    elif [ "$ARCH" = "aarch64" ]; then \
-        MINICONDA_URL="https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-aarch64.sh"; \
-    else \
-        echo "Unsupported architecture: $ARCH" && exit 1; \
-    fi && \
-    wget --quiet $MINICONDA_URL -O /tmp/miniconda.sh && \
-    /bin/bash /tmp/miniconda.sh -b -p /opt/conda && \
-    rm /tmp/miniconda.sh && \
-    conda config --set auto_update_conda false && \
-    conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/main && \
-    conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/r && \
-    conda clean --all -f -y && \
-    conda install -n base libarchive -c main --force-reinstall --solver classic
-
 # Install additional tools or packages as needed in the base environment
 RUN conda init bash && \
-    conda install -n base -c conda-forge python=3.11 python-graphviz jupyterlab 'nodejs>20,<21' pip -y && \
-    pip install ipython-sql && \
+    conda install -n base -c conda-forge python-graphviz jupyter jupysql 'nodejs>20,<21' && \
     pip install mystmd && \
     pip install jupyterlab_myst && \
-    pip install git+https://github.com/datajoint/datajoint-python.git && \
-    pip install Faker
-
-# Set up shell to use Conda by default
-RUN echo "source /opt/conda/etc/profile.d/conda.sh && conda activate base" >> ~/.bashrc
+    pip install git+https://github.com/datajoint/datajoint-python.git 
 
-# Configure MySQL to allow remote connections (optional)
-RUN sed -i 's/bind-address\s*=.*/bind-address = 0.0.0.0/' /etc/mysql/mysql.conf.d/mysqld.cnf
-
-# Initialize MySQL with the root password
-RUN service mysql start && \
-    mysqladmin -u root password "$MYSQL_ROOT_PASSWORD" && \
-    mysql -u root -p"$MYSQL_ROOT_PASSWORD" -e "ALTER USER 'root'@'localhost' IDENTIFIED WITH 'mysql_native_password' BY '$MYSQL_ROOT_PASSWORD'; FLUSH PRIVILEGES;"
 
 # Expose ports for JupyterLab and MySQL
-EXPOSE 3306
-
-# Default command for the Devcontainer
-CMD ["bash"]
+EXPOSE 8888

.devcontainer/devcontainer.json

@@ -1,26 +1,27 @@
 {
   "name": "DataJoint Book Devcontainer",
-  "build": {
-    "dockerfile": "Dockerfile",
-    "context": ".."
-  },
+  "dockerComposeFile": "docker-compose.yml",
+  "service": "app",
+  "workspaceFolder": "/workspace",
+  "forwardPorts": [8888],
+  "postStartCommand": "until nc -z $MYSQL_HOST $MYSQL_PORT; do echo 'Waiting for MySQL...'; sleep 2; done && jupyter notebook --ip 0.0.0.0 --no-browser --allow-root --port 8888 &",
   "customizations": {
     "vscode": {
       "settings": {
-        "terminal.integrated.shell.linux": "/bin/bash"
+        "terminal.integrated.shell.linux": "/bin/bash",
         "python.defaultInterpreterPath": "/opt/conda/bin/python",
-        "python.terminal.activateEnvironment": false  // since conda is auto-activated
+        "python.terminal.activateEnvironment": false 
       },
       "extensions": [
         "ms-python.python",
         "ms-toolsai.jupyter",
-        "ms-azuretools.vscode-docker"
-        "ExecutableBookProject.myst-highlight", // MyST syntax highlighting
-        "ms-python.black-formatter", // Python formatting
-        "ms-vscode.vscode-json" // JSON support
+        "ms-azuretools.vscode-docker",
+        "ExecutableBookProject.myst-highlight",
+        "ms-python.black-formatter",
+        "ms-vscode.vscode-json"
       ]    
     }
   },
-  "postCreateCommand": "service mysql start"
+  "remoteUser": "root"
 }
 

.devcontainer/docker-compose.yml

@@ -0,0 +1,40 @@
+services:
+  app:
+    build:
+      context: ..
+      dockerfile: .devcontainer/Dockerfile
+    volumes:
+      - ..:/workspace:cached
+    command: sleep infinity
+    depends_on:
+      db:
+        condition: service_healthy
+    environment:
+      DJ_HOST: db
+      DJ_USER: dev
+      DJ_PASS: devpass
+      DJ_PORT: 3306
+    working_dir: /workspace
+    networks:
+      - devcontainer
+  db:
+    image: mysql:8.0
+    restart: unless-stopped
+    environment:
+      MYSQL_ROOT_PASSWORD: rootpass
+      MYSQL_USER: dev
+      MYSQL_PASSWORD: devpass
+    volumes:
+      - ./init-dev-privileges.sql:/docker-entrypoint-initdb.d/init-dev-privileges.sql:ro
+    healthcheck:
+      test: ["CMD", "mysqladmin", "ping", "-h", "localhost"]
+      timeout: 20s
+      retries: 10
+      interval: 5s
+      start_period: 30s
+    networks:
+      - devcontainer
+
+networks:
+  devcontainer:
+    driver: bridge

.devcontainer/init-dev-privileges.sql

@@ -0,0 +1,4 @@
+-- Ensure dev user exists and has broad privileges
+CREATE USER IF NOT EXISTS 'dev'@'%' IDENTIFIED BY 'devpass';
+GRANT ALL PRIVILEGES ON *.* TO 'dev'@'%' WITH GRANT OPTION;
+FLUSH PRIVILEGES;