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Initialize Jongmassey/handle-empty-rstudio-prefs
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‎.devcontainer/.gitignore

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ehrql-main

‎.devcontainer/devcontainer.json

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// For format details, see https://aka.ms/devcontainer.json. For config options, see the
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// README at: https://github.com/devcontainers/templates/tree/main/src/python
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{
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"name": "OpenSAFELY",
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"image": "ghcr.io/opensafely-core/research-template:v0",
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// Features to add to the dev container. More info: https://containers.dev/features.
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"features": {
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"ghcr.io/devcontainers/features/docker-in-docker:2": {
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"moby": true,
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"azureDnsAutoDetection": true,
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"installDockerBuildx": true,
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"version": "latest",
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"dockerDashComposeVersion": "v2"
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}
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},
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"postCreateCommand": "/bin/bash .devcontainer/postCreate.sh ${containerWorkspaceFolder}",
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"postAttachCommand": {
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"rstudio-start": "sudo rstudio-server start"
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},
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"forwardPorts": [
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8787
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],
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"portsAttributes": {
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"8787": {
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"label": "RStudio IDE"
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}
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},
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// Configure tool-specific properties.
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"customizations": {
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"codespaces": {
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"repositories": {
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"opensafely/server-instructions": {
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"permissions": {
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"contents": "read"
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}
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}
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}
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},
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"vscode": {
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"extensions": [
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"ms-python.python",
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"ms-toolsai.jupyter",
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"ms-toolsai.jupyter-renderers"
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],
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"settings": {
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"extensions.ignoreRecommendations": true,
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"files.autoSave": "afterDelay",
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"files.autoSaveDelay": 1000,
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"git.autofetch": true,
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"python.analysis.extraPaths": [".devcontainer/ehrql-main/"],
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"python.defaultInterpreterPath": "/opt/venv/bin/python",
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"python.terminal.activateEnvInCurrentTerminal": true,
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"python.terminal.activateEnvironment": true,
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"window.autoDetectColorScheme": true
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}
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}
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},
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// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
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// "remoteUser": "root"
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"remoteEnv": {
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"MAX_WORKERS": "2"
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}
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}

‎.devcontainer/postCreate.sh

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

‎.devcontainer/requirements.in

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opensafely

‎.gitattributes

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# Set the default behavior, in case people don't have core.autocrlf set.
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* text=auto
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# ensure unix line endings on windows for files that need them.
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*.sh eol=lf
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codelists/* eol=lf

‎.github/dependabot.yml

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version: 2
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updates:
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- package-ecosystem: "github-actions"
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directory: "/"
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schedule:
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interval: "monthly"

‎.github/workflows/setup.yaml

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name: Setup repository
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on:
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workflow_dispatch:
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push:
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branches: [main]
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permissions:
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contents: write
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jobs:
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setup:
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name: Initialise OpenSAFELY project.
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Update README.md and remove action
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shell: bash
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run: |
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export GITHUB_REPOSITORY_OWNER="$(echo $GITHUB_REPOSITORY | awk -F/ '{print $1}')"
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export GITHUB_REPOSITORY_NAME="$(echo $GITHUB_REPOSITORY | awk -F/ '{print $2}')"
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envsubst < README.md > tmp && mv tmp README.md
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rm .github/workflows/setup.yaml
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- name: Do not run on template repository
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id: is_template
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# The only way to trigger this to run when used as a template is on
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# push to main. But that means it would also trigger when we push to
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# the template repo itself, which we do not want. So, check if we are
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# in a template repo
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run: |
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is_template=false
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curl --silent -X GET \
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-H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" \
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-H "Accept: application/vnd.github.baptiste-preview+json" \
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https://api.github.com/repos/$GITHUB_REPOSITORY \
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| jq --exit-status '.is_template == false' || is_template=true
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# output true/false so later actions can be skipped
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echo "::set-output name=is_template::$is_template"
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- name: Commit changes
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# only actually commit the changes if this is not a template repo
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if: steps.is_template.outputs.is_template == 'false'
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run: |
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# use the same author as the initial commit
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git config user.email "$(git log -1 --pretty=format:'%ae')"
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git config user.name "$(git log -1 --pretty=format:'%an')"
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git add .
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git commit --amend --no-edit
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git push origin $GITHUB_REF --force

‎.github/workflows/test_runner.yaml

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name: Test that the project is runnable
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on: [push, workflow_dispatch]
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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DOCKER_RO_TOKEN: ${{ secrets.DOCKER_RO_TOKEN }}
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STATA_LICENSE: ${{ secrets.STATA_LICENSE }}
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HONEYCOMB_API_KEY: ${{ secrets.HONEYCOMB_API_KEY }}
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jobs:
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test:
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runs-on: ubuntu-latest
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name: Test the project can run, using dummy data
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Test that the project is runnable
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uses: opensafely-core/research-action@v2

‎.gitignore

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*~
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model.log
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*/input.csv
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__pycache__
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.python-version
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/output/*
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metadata/*
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venv/
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.DS_Store
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.Rhistory
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.Rproj.user/

‎.vscode/tasks.json

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{
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// See https://go.microsoft.com/fwlink/?LinkId=733558
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// for the documentation about the tasks.json format
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"version": "2.0.0",
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"tasks": [
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{
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"label": "OpenSAFELY run project",
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"type": "shell",
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"command": "opensafely run run_all -f",
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"problemMatcher": [],
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"group": {
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"kind": "build",
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"isDefault": true
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},
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"presentation": {
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"echo": true,
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"reveal": "always",
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"focus": true,
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"panel": "new",
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"showReuseMessage": false,
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"clear": true,
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}
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}
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]
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}

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