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‎.devcontainer/README.md‎

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# Devcontainer Configuration
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This folder contains configuration files required for Codespaces/devcontainers.
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Please do not modify its contents unless you know what you are doing and there
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is a specific change to the devcontainer configuration you need to make.
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If you believe you have a broken configuration or are unsure if you have the
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latest version of the configuration, please follow the
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[instructions to add codespaces to your project](https://docs.opensafely.org/getting-started/how-to/add-github-codespaces-to-your-project/).

‎.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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},
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"postCreateCommand": "/bin/bash /opt/devcontainer/postCreate.sh ${containerWorkspaceFolder}",
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"postAttachCommand": "/bin/bash /opt/devcontainer/postAttach.sh",
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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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"bennettoxford.opensafely"
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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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}

‎.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@v6
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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@v6
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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/
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.devcontainer/ehrql-main/

‎.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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}

‎LICENSE‎

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MIT License
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Copyright (c) {{current_year}} {{organisation}}
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.

‎README.md‎

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# ${GITHUB_REPOSITORY_NAME}
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[View on OpenSAFELY](https://jobs.opensafely.org/repo/https%253A%252F%252Fgithub.com%252Fopensafely%252F${GITHUB_REPOSITORY_NAME})
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Details of the purpose and any published outputs from this project can be found at the link above.
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The contents of this repository MUST NOT be considered an accurate or valid representation of the study or its purpose.
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This repository may reflect an incomplete or incorrect analysis with no further ongoing work.
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The content has ONLY been made public to support the OpenSAFELY [open science and transparency principles](https://www.opensafely.org/about/#contributing-to-best-practice-around-open-science) and to support the sharing of re-usable code for other subsequent users.
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No clinical, policy or safety conclusions must be drawn from the contents of this repository.
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# About the OpenSAFELY framework
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The OpenSAFELY framework is a Trusted Research Environment (TRE) for electronic
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health records research in the NHS, with a focus on public accountability and
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research quality.
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Read more at [OpenSAFELY.org](https://opensafely.org).
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# Licences
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As standard, research projects have a MIT license.

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