Merge upgraded Type Management System

.devcontainer/devcontainer.json

@@ -1,7 +1,6 @@
 {
-  "image": "mcr.microsoft.com/devcontainers/typescript-node:0-18",
-  "features": {
-    "ghcr.io/devcontainers/features/docker-in-docker:2": {}
-  },
+  "dockerComposeFile": ["../docker-compose.yaml", "docker-compose.yml"],
+  "service": "app",
+  "workspaceFolder": "/src",
   "postCreateCommand": "curl -fsSL https://pixi.sh/install.sh | bash && echo 'export PATH=\"$HOME/.pixi/bin:$PATH\"' >> ~/.bashrc"
-}
+}

.devcontainer/docker-compose.yml

@@ -1,30 +1,14 @@
+# Devcontainer overrides for the app service from ../docker-compose.yaml
+# Inherits db and minio services automatically
 services:
-  # Update this to the name of the service you want to work with in your docker-compose.yml file
   app:
-    # Uncomment if you want to override the service's Dockerfile to one in the .devcontainer
-    # folder. Note that the path of the Dockerfile and context is relative to the *primary*
-    # docker-compose.yml file (the first in the devcontainer.json "dockerComposeFile"
-    # array). The sample below assumes your primary file is in the root of your project.
     container_name: datajoint-python-devcontainer
-    image: datajoint/datajoint-python-devcontainer:${PY_VER:-3.11}-${DISTRO:-bookworm}
     build:
-      context: .
+      context: ..
       dockerfile: .devcontainer/Dockerfile
       args:
         - PY_VER=${PY_VER:-3.11}
         - DISTRO=${DISTRO:-bookworm}
-
-    volumes:
-      # Update this to wherever you want VS Code to mount the folder of your project
-      - ..:/workspaces:cached
-
-    # Uncomment the next four lines if you will use a ptrace-based debugger like C++, Go, and Rust.
-    # cap_add:
-    #   - SYS_PTRACE
-    # security_opt:
-    #   - seccomp:unconfined
-
     user: root
-
-    # Overrides default command so things don't shut down after the process ends.
+    # Keep container running for devcontainer
     command: /bin/sh -c "while sleep 1000; do :; done"

README.md

@@ -141,3 +141,66 @@ DataJoint (<https://datajoint.com>).
   - [Contribution Guidelines](https://docs.datajoint.com/about/contribute/)
 
   - [Developer Guide](https://docs.datajoint.com/core/datajoint-python/latest/develop/)
+
+## Developer Guide
+
+### Prerequisites
+
+- [Docker](https://docs.docker.com/get-docker/) for running MySQL and MinIO services
+- [pixi](https://prefix.dev/docs/pixi/overview) package manager (or pip/conda)
+
+### Setting Up the Development Environment
+
+1. Clone the repository and install dependencies:
+
+   ```bash
+   git clone https://github.com/datajoint/datajoint-python.git
+   cd datajoint-python
+   pixi install
+   ```
+
+2. Start the required services (MySQL and MinIO):
+
+   ```bash
+   docker compose up -d db minio
+   ```
+
+### Running Tests
+
+Run tests with pytest using the test environment:
+
+```bash
+DJ_HOST=localhost DJ_PORT=3306 S3_ENDPOINT=localhost:9000 python -m pytest tests/
+```
+
+Or run specific test files:
+
+```bash
+DJ_HOST=localhost DJ_PORT=3306 S3_ENDPOINT=localhost:9000 python -m pytest tests/test_blob.py -v
+```
+
+### Running Pre-commit Checks
+
+Pre-commit hooks ensure code quality before commits. Install and run them:
+
+```bash
+# Install pre-commit hooks
+pre-commit install
+
+# Run all pre-commit checks manually
+pre-commit run --all-files
+
+# Run specific hooks
+pre-commit run ruff --all-files
+pre-commit run mypy --all-files
+```
+
+### Environment Variables
+
+| Variable | Default | Description |
+|----------|---------|-------------|
+| `DJ_HOST` | `localhost` | MySQL server hostname |
+| `DJ_PORT` | `3306` | MySQL server port |
+| `DJ_USER` | `datajoint` | MySQL username |
+| `DJ_PASS` | `datajoint` | MySQL password |
+| `S3_ENDPOINT` | `localhost:9000` | MinIO/S3 endpoint |

docker-compose.yaml

@@ -1,15 +1,14 @@
 # Development environment with MySQL and MinIO services
-# To run tests: pytest --cov-report term-missing --cov=datajoint tests
+# Start services: docker-compose up -d db minio
+# Run tests: pixi run test
 services:
   db:
     image: datajoint/mysql:${MYSQL_VER:-8.0}
     environment:
       - MYSQL_ROOT_PASSWORD=${DJ_PASS:-password}
     command: mysqld --default-authentication-plugin=mysql_native_password
-    # ports:
-    #   - "3306:3306"
-    # volumes:
-    #   - ./mysql/data:/var/lib/mysql
+    ports:
+      - "3306:3306"
     healthcheck:
       test: [ "CMD", "mysqladmin", "ping", "-h", "localhost" ]
       timeout: 30s
@@ -20,18 +19,15 @@ services:
     environment:
       - MINIO_ACCESS_KEY=datajoint
       - MINIO_SECRET_KEY=datajoint
-    # ports:
-    #   - "9000:9000"
-    # volumes:
-    #   - ./minio/config:/root/.minio
-    #   - ./minio/data:/data
+    ports:
+      - "9000:9000"
     command: server --address ":9000" /data
     healthcheck:
       test:
         - "CMD"
         - "curl"
         - "--fail"
-        - "http://minio:9000/minio/health/live"
+        - "http://localhost:9000/minio/health/live"
       timeout: 30s
       retries: 5
       interval: 15s