Merge pull request #120 from opensafely/improve-devcontainers

Improve devcontainers/codespaces configuration:
* use custom docker image opensafely-core/research-template-docker
* include R 4.0.5 and RStudio-server via Rocker
* include Python and R packages from opensafely-core/python-docker and r-docker respectively
* improve ehrQL syntax highlighting
* various maintainability improvements

.devcontainer/.gitignore

@@ -0,0 +1 @@
+ehrql-main

.devcontainer/devcontainer.json

@@ -1,12 +1,8 @@
 // For format details, see https://aka.ms/devcontainer.json. For config options, see the
 // README at: https://github.com/devcontainers/templates/tree/main/src/python
 {
-    "name": "Python 3",
-    // Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
-    // 2023-06-29: Use bullseye image instead of bookworm.
-    // At time of writing, bookworm is new and may have issues with dev containers:
-    // https://github.com/devcontainers/features/issues/576
-    "image": "mcr.microsoft.com/devcontainers/python:3.11-bullseye",
+    "name": "OpenSAFELY",
+    "image": "ghcr.io/opensafely-core/research-template:v0",
     // Features to add to the dev container. More info: https://containers.dev/features.
     "features": {
         "ghcr.io/devcontainers/features/docker-in-docker:2": {
@@ -17,18 +13,37 @@
             "dockerDashComposeVersion": "v2"
         }
     },
-    // Use 'forwardPorts' to make a list of ports inside the container available locally.
-    // "forwardPorts": [],
-    // Use 'postCreateCommand' to run commands after the container is created.
-    "postCreateCommand": "pip3 install --user -r .devcontainer/requirements.in",
+    "postCreateCommand": "/bin/bash .devcontainer/postCreate.sh",
+    "postAttachCommand": {
+        "rstudio-start": "sudo rstudio-server start"
+    },
+    "forwardPorts": [
+        8787
+    ],
+    "portsAttributes": {
+        "8787": {
+            "label": "RStudio IDE"
+        }
+    },
     // Configure tool-specific properties.
     "customizations": {
         "vscode": {
             "extensions": [
                 "ms-python.python",
                 "ms-toolsai.jupyter",
                 "ms-toolsai.jupyter-renderers"
-            ]
+            ],
+            "settings": {
+                "extensions.ignoreRecommendations": true,
+                "files.autoSave": "afterDelay",
+                "files.autoSaveDelay": 1000,
+                "git.autofetch": true,
+                "python.analysis.extraPaths": [".devcontainer/ehrql-main/"],
+                "python.defaultInterpreterPath": "/opt/venv/bin/python",
+                "python.terminal.activateEnvInCurrentTerminal": true,
+                "python.terminal.activateEnvironment": true,
+                "window.autoDetectColorScheme": true
+            }
         }
     },
     // Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.

.devcontainer/postCreate.sh

@@ -0,0 +1,15 @@
+#!/bin/bash
+
+set -euo pipefail 
+
+pip3 install --user -r .devcontainer/requirements.in
+
+#set R working directory
+! grep -q `pwd` $R_HOME/etc/Rprofile.site && sudo tee -a $R_HOME/etc/Rprofile.site <<< "setwd(\"`pwd`\")"
+#set RStudio working directory
+! grep -q `pwd` ~/.config/rstudio/rstudio-prefs.json && cat ~/.config/rstudio/rstudio-prefs.json | jq ". + {\"initial_working_directory\":\"`pwd`\"}" >  ~/.config/rstudio/rstudio-prefs.json 
+
+#download and extract latest ehrql source
+wget https://github.com/opensafely-core/ehrql/archive/main.zip -P .devcontainer
+unzip -o .devcontainer/main.zip -d .devcontainer/
+rm .devcontainer/main.zip

.devcontainer/requirements.in

@@ -1,2 +1 @@
 opensafely
-https://github.com/opensafely-core/ehrql/archive/main.zip