Working version using docker cp rather than mounts

Base on MS devcontainer Jammy image to match OpenSAFELY base image.

Install R/Python and their dependencies.

Use `docker cp` to copy the R/Python library files to the host filesystem
which avoids any of the previously seen issues with mounting a running
container.

These library directories don't contain any symlinks
(verified with `find . -type l`).

Author: Jongmassey

.devcontainer/devcontainer.json

@@ -2,13 +2,21 @@
 // README at: https://github.com/devcontainers/templates/tree/main/src/python
 {
     "name": "OpenSAFELY",
-    "image": "mcr.microsoft.com/devcontainers/python:3.10",
+    "image": "mcr.microsoft.com/devcontainers/base:ubuntu-22.04",
     // Features to add to the dev container. More info: https://containers.dev/features.
     "features": {
         "ghcr.io/devcontainers/features/docker-in-docker:2": {}
     },
+    "postCreateCommand": "/bin/bash .devcontainer/postCreate.sh",
     "postAttachCommand": "/bin/bash .devcontainer/postAttach.sh",
-    "containerEnv": {"R_LD_LIBRARY_PATH":"/usr/lib/R-system"},
+    "forwardPorts": [
+        8787
+    ],
+    "portsAttributes": {
+        "8787": {
+            "label": "RStudio IDE"
+        }
+    },
     // Configure tool-specific properties.
     "customizations": {
         "codespaces": {
@@ -33,7 +41,7 @@
                 "files.autoSaveDelay": 1000,
                 "git.autofetch": true,
                 "python.analysis.extraPaths": [".ehrql/"],
-                "python.defaultInterpreterPath": "/opt/venv/bin/python3.10",
+                "python.defaultInterpreterPath": "./venv/bin/python",
                 "python.terminal.activateEnvInCurrentTerminal": true,
                 "python.terminal.activateEnvironment": true,
                 "window.autoDetectColorScheme": true

.devcontainer/postAttach.sh

@@ -1,21 +1 @@
-pip install opensafely
-sudo apt update
-sudo apt install -y bindfs
-docker run -it -d --name ehrql --rm ghcr.io/opensafely-core/ehrql:v1 bash
-mount=$(docker inspect ehrql -f '{{.GraphDriver.Data.MergedDir}}')
-mkdir -p .ehrql
-sudo mount -o bind "$mount/app/ehrql" .ehrql
-sudo touch /usr/bin/R
-sudo mkdir -p /usr/lib/R
-sudo mkdir -p /usr/lib/R-system
-sudo mkdir -p /etc/R
-docker run -it -d --name r-v2 --rm ghcr.io/opensafely-core/r:v2 bash
-mount=$(docker inspect r-v2 -f '{{.GraphDriver.Data.MergedDir}}')
-sudo mount --bind -o ro "$mount/usr/bin/R" /usr/bin/R
-sudo bindfs -r --resolve-symlinks "$mount/usr/lib/R" /usr/lib/R
-sudo bindfs -r --resolve-symlinks "$mount/etc/R" /etc/R
-sudo bindfs -r --resolve-symlinks "$mount/lib" /usr/lib/R-system
-docker run -it -d --name python-v2 --rm ghcr.io/opensafely-core/python:v2 bash
-mount=$(docker inspect python-v2 -f '{{.GraphDriver.Data.MergedDir}}')
-sudo mkdir -p /opt/venv
-sudo bindfs -r --resolve-symlinks "$mount/opt/venv" /opt/venv
+opensafely launch rstudio -p 8787 &

.devcontainer/postCreate.sh

@@ -0,0 +1,26 @@
+# install python and dependencies, set up virtualenv
+sudo apt update
+wget https://github.com/opensafely-core/python-docker/raw/refs/heads/main/v2/dependencies.txt -q -O - | sed 's/^#.*//' | sudo xargs apt-get install --yes --no-install-recommends
+pip install virtualenv opensafely
+python3 -m virtualenv .venv
+rm  -rf .venv/lib
+docker container create --name python-v2 ghcr.io/opensafely-core/python:v2
+docker cp python-v2:/opt/venv/lib .venv/
+docker rm python-v2
+
+# install R and dependencies
+echo "deb https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/" | sudo tee /etc/apt/sources.list.d/cran.list >/dev/null
+sudo /usr/lib/apt/apt-helper download-file 'https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc' /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
+sudo apt update
+wget https://raw.githubusercontent.com/opensafely-core/r-docker/refs/heads/main/v2/dependencies.txt -q -O - | sed 's/^#.*//' | sudo xargs apt-get install --yes --no-install-recommends
+wget https://raw.githubusercontent.com/opensafely-core/r-docker/refs/heads/main/scripts/rprofile-site-append-1.R -q -O - | sudo tee -a /usr/lib/R/etc/Rprofile.site >/dev/null
+wget https://raw.githubusercontent.com/opensafely-core/r-docker/refs/heads/main/scripts/rprofile-site-append-2.R -q -O - | sudo tee -a /usr/lib/R/etc/Rprofile.site >/dev/null
+docker create --name r-v2 --rm ghcr.io/opensafely-core/r:v2
+sudo docker cp r-v2:/usr/local/lib/R/site-library /usr/local/lib/R/
+sudo chown -R vscode:vscode /usr/local/lib/R/site-library/
+
+
+#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