feat: update devcontainer

.devcontainer/Dockerfile

@@ -1,30 +1,12 @@
-FROM python:3.9-slim@sha256:5f0192a4f58a6ce99f732fe05e3b3d00f12ae62e183886bca3ebe3d202686c7f
-
-ENV PATH /usr/local/bin:$PATH
-ENV PYTHON_VERSION 3.9.17
-
-RUN \
-    adduser --system --disabled-password --shell /bin/bash vscode && \
-    # install docker
-    apt-get update && \
-    apt-get install ca-certificates curl gnupg lsb-release -y && \
-    mkdir -m 0755 -p /etc/apt/keyrings && \
-    curl -fsSL https://download.docker.com/linux/debian/gpg | gpg --dearmor -o /etc/apt/keyrings/docker.gpg && \
-    echo "deb [arch=$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/docker.gpg] https://download.docker.com/linux/debian $(lsb_release -cs) stable" | tee /etc/apt/sources.list.d/docker.list > /dev/null && \
-    apt-get update && \
-    apt-get install docker-ce docker-ce-cli containerd.io docker-buildx-plugin docker-compose-plugin -y && \
-    usermod -aG docker vscode && \
-    apt-get clean
+ARG PY_VER
+ARG DISTRO
+FROM mcr.microsoft.com/devcontainers/python:${PY_VER}-${DISTRO}
 
 RUN \
     # dev setup
     apt update && \
     apt-get install sudo git bash-completion graphviz default-mysql-client s3fs procps -y && \
-    usermod -aG sudo vscode && \
-    echo '%sudo ALL=(ALL) NOPASSWD:ALL' >> /etc/sudoers && \
-    pip install --no-cache-dir --upgrade black pip nbconvert && \
-    echo '. /etc/bash_completion' >> /home/vscode/.bashrc && \
-    echo 'export PS1="\[\e[32;1m\]\u\[\e[m\]@\[\e[34;1m\]\H\[\e[m\]:\[\e[33;1m\]\w\[\e[m\]$ "' >> /home/vscode/.bashrc && \
+    pip install --no-cache-dir --upgrade black faker ipykernel pip && \
     apt-get clean
 
 COPY ./ /tmp/element-array-ephys/
@@ -37,12 +19,10 @@ RUN \
     rm -rf /tmp/element-array-ephys && \
     apt-get clean
 
-ENV DJ_HOST fakeservices.datajoint.io
+USER root
+ENV DJ_HOST db
 ENV DJ_USER root
 ENV DJ_PASS simple
 
 ENV EPHYS_ROOT_DATA_DIR /workspaces/element-array-ephys/example_data
-ENV DATABASE_PREFIX neuro_
-
-USER vscode
-CMD bash -c "sudo rm /var/run/docker.pid; sudo dockerd"
+ENV DATABASE_PREFIX neuro_

.devcontainer/devcontainer.json

@@ -1,29 +1,43 @@
 {
 	"name": "Environment + Data",
-	"dockerComposeFile": "docker-compose.yaml",
+	"dockerComposeFile": [
+		"../docker-compose.yml",
+		"docker-compose.yaml"
+	],
 	"service": "app",
 	"workspaceFolder": "/workspaces/${localWorkspaceFolderBasename}",
 	"remoteEnv": {
 		"LOCAL_WORKSPACE_FOLDER": "${localWorkspaceFolder}"
 	},
 	"onCreateCommand": "mkdir -p ${EPHYS_ROOT_DATA_DIR} && pip install -e .",
-	"postStartCommand": "docker volume prune -f && s3fs ${DJ_PUBLIC_S3_LOCATION} ${EPHYS_ROOT_DATA_DIR} -o nonempty,multipart_size=530,endpoint=us-east-1,url=http://s3.amazonaws.com,public_bucket=1",
+	"shutdownAction": "stopCompose",
+	"postStartCommand": "s3fs ${DJ_PUBLIC_S3_LOCATION} ${EPHYS_ROOT_DATA_DIR} -o nonempty,multipart_size=530,endpoint=us-east-1,url=http://s3.amazonaws.com,public_bucket=1",
 	"hostRequirements": {
 		"cpus": 4,
 		"memory": "8gb",
 		"storage": "32gb"
 	},
 	"forwardPorts": [
-		3306
+		3306,
+		80,
+		443,
+		3306,
+		8080,
+		9000
 	],
+	"features": {
+		"ghcr.io/devcontainers/features/git:1": {},
+		"ghcr.io/devcontainers/features/docker-in-docker:2": {},
+		"ghcr.io/devcontainers/features/github-cli:1": {}
+	},
 	"customizations": {
 		"settings": {
 			"python.pythonPath": "/usr/local/bin/python"
 		},
 		"vscode": {
 			"extensions": [
-				"ms-python.python@2023.8.0",
-				"ms-toolsai.jupyter@2023.3.1201040234"
+				"ms-python.python",
+				"ms-toolsai.jupyter"
 			]
 		}
 	}

.devcontainer/docker-compose.yaml

@@ -1,14 +1,14 @@
-version: "3"
 services:
   app:
     cpus: 4
     mem_limit: 8g
     build:
       context: ..
       dockerfile: ./.devcontainer/Dockerfile
-    # image: datajoint/element_array_ephys:latest
-    extra_hosts:
-      - fakeservices.datajoint.io:127.0.0.1
+      args:
+        - PY_VER=${PY_VER:-3.11}
+        - DISTRO=${DISTRO:-buster}
+    image: datajoint/element_array_ephys:latest
     environment:
       - DJ_PUBLIC_S3_LOCATION=djhub.vathes.datapub.elements:/workflow-array-ephys-benchmark/v2
     devices:
@@ -18,8 +18,10 @@ services:
     security_opt:
       - apparmor:unconfined
     volumes:
-      - ..:/workspaces/element-array-ephys:cached
+      - ..:/workspaces:cached
       - docker_data:/var/lib/docker # persist docker images
-    privileged: true # only because of dind
+    user: root
+    # Overrides default command so things don't shut down after the process ends.
+    command: /bin/sh -c "while sleep 1000; do :; done"
 volumes:
   docker_data:

docker-compose-db.yaml

@@ -1,15 +1,13 @@
-# MYSQL_VER=8.0 docker compose -f docker-compose-db.yaml up --build
-version: "3"
+# MYSQL_VER=8.0 docker compose up --build
 services:
   db:
     restart: always
-    image: datajoint/mysql:${MYSQL_VER}
+    image: datajoint/mysql:${MYSQL_VER:-8.0}
     environment:
-      - MYSQL_ROOT_PASSWORD=${DJ_PASS}
-    ports:
-      - "3306:3306"
+      - MYSQL_ROOT_PASSWORD=${DJ_PASS:-simple}
+    command: mysqld --default-authentication-plugin=mysql_native_password
     healthcheck:
       test: [ "CMD", "mysqladmin", "ping", "-h", "localhost" ]
       timeout: 15s
       retries: 10
-      interval: 15s
+      interval: 15s