Provide devcontainer configuration

This will provide a development environment for researchers containing:

* Python 3.10
* The equivalent Python packages based on the Python Action image, including ehrql
* R 4.0.5
* RStudio
* The equivalent R packages based on the R Action image

This can be used in Codespaces or locally via devcontainers in VS Code.

It's based on the work being done for opensafely-core/codespaces-initiative#43.

.devcontainer/Dockerfile

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+FROM remlapmot/r-docker:2024-04-02-rstudio
+
+LABEL org.opencontainers.image.source https://github.com/opensafely/research-template
+
+# we are going to use an apt cache on the host, so disable the default debian
+# docker clean up that deletes that cache on every apt install
+RUN rm -f /etc/apt/apt.conf.d/docker-clean
+
+# Install python 3.10. This is the version used by the python-docker 
+# image, used for analyses using the OpenSAFELY pipeline.
+RUN --mount=type=cache,target=/var/cache/apt \
+    echo "deb http://ppa.launchpad.net/deadsnakes/ppa/ubuntu focal main" > /etc/apt/sources.list.d/deadsnakes-ppa.list &&\
+    /usr/lib/apt/apt-helper download-file 'https://keyserver.ubuntu.com/pks/lookup?op=get&search=0xf23c5a6cf475977595c89f51ba6932366a755776' /etc/apt/trusted.gpg.d/deadsnakes.asc &&\
+    apt update &&\
+    apt install -y curl python3.10 python3.10-distutils python3.10-venv &&\
+    # Pip for Python 3.10 isn't included in deadsnakes, so install separately
+    curl https://bootstrap.pypa.io/get-pip.py | python3.10 &&\
+    # Set default python, so that the Python virtualenv works as expected
+    rm /usr/bin/python3 && ln -s /usr/bin/python3.10 /usr/bin/python3
+
+# Copy the Python virtualenv from OpenSAFELY Python action image
+COPY --from=ghcr.io/opensafely-core/python:v2 /opt/venv /opt/venv
+
+# Create a local user and give it sudo (aka root) permissions
+RUN usermod -aG sudo rstudio
+RUN echo '%sudo ALL=(ALL) NOPASSWD:ALL' >> /etc/sudoers
+
+# Required for installing opensafely cli
+ENV PATH="/home/rstudio/.local/bin:${PATH}"
+
+USER rstudio

.devcontainer/devcontainer.json

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+// 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": "OpenSAFELY",
+    "image": "ghcr.io/opensafely/research-template:latest",
+    // Features to add to the dev container. More info: https://containers.dev/features.
+    "features": {
+        "ghcr.io/devcontainers/features/docker-in-docker:2": {
+            "moby": true,
+            "azureDnsAutoDetection": true,
+            "installDockerBuildx": true,
+            "version": "latest",
+            "dockerDashComposeVersion": "v2"
+        }
+    },
+    "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"
+            ]
+        }
+    },
+    // Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
+    // "remoteUser": "root"
+    "remoteEnv": {
+        "MAX_WORKERS": "2"
+    }
+}

.devcontainer/postCreate.sh

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+#!/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

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+opensafely

.vscode/settings.json

@@ -1,7 +1,7 @@
 {
-    "python.linting.pylintEnabled": false,
-    "python.linting.flake8Enabled": true,
-    "python.linting.enabled": true,
+    "python.analysis.extraPaths": [".devcontainer/ehrql-main/"],
+    "python.defaultInterpreterPath": "/opt/venv/bin/python3.10",
+    "python.terminal.activateEnvironment": true,
     "data.preview.create.json.schema": false,
     "files.associations": {
         "*.feather": "arrow",