Simplify test infrastructure to use docker-compose services

Replace pytest-managed Docker containers with external docker-compose services.
This removes complexity, improves reliability, and allows running tests both
from the host machine and inside the devcontainer.

- Remove docker container lifecycle management from conftest.py
- Add pixi tasks for running tests (services-up, test, test-cov)
- Expose MySQL and MinIO ports in docker-compose.yaml for host access
- Simplify devcontainer to extend the main docker-compose.yaml
- Remove docker dependency from test requirements

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Author: dimitri-yatsenko

.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"

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

pyproject.toml

@@ -86,7 +86,6 @@ test = [
   "pytest",
   "pytest-cov",
   "pytest-env",
-  "docker",
   "requests",
   "graphviz"
 ]
@@ -154,16 +153,19 @@ skip = ".git,*.pdf,*.svg,*.csv,*.ipynb,*.drawio"
 ignore-words-list = "rever,numer,astroid"
 
 [tool.pytest_env]
-# Default values - pytest fixtures will override with actual container details
+# Default environment variables for tests
+# When running from host: DJ_HOST=localhost (set via pixi task)
+# When running in devcontainer/docker: DJ_HOST=db (docker-compose service name)
+DJ_HOST="db"
+DJ_PORT="3306"
 DJ_USER="root"
 DJ_PASS="password"
 DJ_TEST_USER="datajoint"
 DJ_TEST_PASSWORD="datajoint"
+S3_ENDPOINT="minio:9000"
 S3_ACCESS_KEY="datajoint"
 S3_SECRET_KEY="datajoint"
 S3_BUCKET="datajoint.test"
-PYTHON_USER="dja"
-JUPYTER_PASSWORD="datajoint"
 
 
 [tool.pixi.workspace]
@@ -179,6 +181,12 @@ dev = { features = ["dev"], solve-group = "default" }
 test = { features = ["test"], solve-group = "default" }
 
 [tool.pixi.tasks]
+# Start required services (MySQL and MinIO)
+services-up = "docker-compose up -d db minio"
+services-down = "docker-compose down"
+# Run tests (requires services to be running)
+test = { cmd = "pytest tests/", depends-on = ["services-up"], env = { DJ_HOST = "localhost", DJ_PORT = "3306", S3_ENDPOINT = "localhost:9000" } }
+test-cov = { cmd = "pytest --cov-report term-missing --cov=datajoint tests/", depends-on = ["services-up"], env = { DJ_HOST = "localhost", DJ_PORT = "3306", S3_ENDPOINT = "localhost:9000" } }
 
 [tool.pixi.dependencies]
 python = ">=3.10,<3.14"