├── .devcontainer ├── Dockerfile └── devcontainer.json ├── .github ├── dependabot.yml └── workflows │ ├── check_links.yml │ ├── check_redirects.yml │ ├── check_vale.yml │ └── pages-deployment.yml ├── .gitignore ├── .ignore ├── .lycheeignore ├── .pre-commit-config.yaml ├── .python-version ├── .vale.ini ├── .vscode └── settings.json ├── DEPLOY.md ├── INSTALL.md ├── LICENSE ├── README.md ├── docs ├── _headers ├── _redirects ├── access-policies.md ├── actions-intro.md ├── actions-pipelines.md ├── actions-reusable.md ├── actions-scripts.md ├── adding-a-paper.md ├── case-control-studies.md ├── code-reviews.md ├── codelist-creation.md ├── codelist-intro.md ├── codelist-project.md ├── codelist-updating.md ├── contributing.md ├── copiloting-service.md ├── css │ ├── extra.css │ ├── lite-yt-embed.css │ └── youtube.css ├── data-access-policy.md ├── data-sources │ ├── apc.md │ ├── cpns.md │ ├── ecds.md │ ├── emis.md │ ├── hcd.md │ ├── icnarc.md │ ├── index.md │ ├── intro.md │ ├── isaric.md │ ├── onsdeaths.md │ ├── sgsscovid.md │ ├── systmone.md │ ├── therapeutics.md │ └── ukrr.md ├── datapast │ ├── index.md │ └── the_clinical_datapast_function.pdf ├── documents │ └── OpenSAFELY_Output_Review_Form_ADD_WORKSPACE_NAME_ADD_DATE.docx ├── federation.md ├── five-safes.md ├── getting-started │ ├── explanation │ │ ├── index.md │ │ ├── options-for-running-opensafely │ │ │ └── index.md │ │ ├── understanding-github-codespaces │ │ │ └── index.md │ │ └── understanding-the-software-used-to-run-opensafely │ │ │ └── index.md │ ├── how-to │ │ ├── add-github-codespaces-to-your-project │ │ │ ├── download_raw_file.png │ │ │ └── index.md │ │ ├── create-a-code-repository-for-your-project │ │ │ └── index.md │ │ ├── index.md │ │ ├── troubleshoot-common-codespaces-issues │ │ │ ├── codespace-additional-permissions.png │ │ │ ├── directory-listing.png │ │ │ ├── index.md │ │ │ ├── r-session-error.png │ │ │ ├── vscode-popup.png │ │ │ └── vscode-ports.png │ │ ├── update-github-codespaces-in-your-project │ │ │ └── index.md │ │ ├── use-git-effectively │ │ │ └── index.md │ │ ├── use-github-codespaces-in-your-project │ │ │ └── index.md │ │ └── use-released-outputs-in-github-codespaces │ │ │ └── index.md │ ├── index.md │ └── tutorial │ │ ├── add-a-scripted-action-to-the-pipeline │ │ └── index.md │ │ ├── check-the-automated-tests-pass │ │ └── index.md │ │ ├── create-a-github-account │ │ └── index.md │ │ ├── create-a-github-codespace │ │ └── index.md │ │ ├── create-a-github-repository │ │ └── index.md │ │ ├── delete-the-github-codespace │ │ └── index.md │ │ ├── generate-a-first-dataset │ │ └── index.md │ │ ├── index.md │ │ ├── introduction │ │ └── index.md │ │ ├── publish-the-changes-to-github │ │ └── index.md │ │ ├── run-the-project-pipeline │ │ └── index.md │ │ ├── see-the-next-steps │ │ └── index.md │ │ └── update-the-dataset-definition │ │ └── index.md ├── git-workflow.md ├── how-opensafely-works.md ├── how-to-get-help.md ├── images │ ├── NON-COVID-GP-data-OpenSAFELY-platform-architecture-and-dataflows-V5-for-DPIA-DPN.drawio.svg │ ├── OpenSAFELY-security-levels-2023-DPN.svg │ ├── adding-codelist-id-tag.png │ ├── adding-codelist-id-version.png │ ├── c4-container.svg │ ├── c4-system-context.svg │ ├── code-review-main.png │ ├── codelists-jobs-warning.png │ ├── codespaces-create.png │ ├── codespaces-options.png │ ├── codespaces-setup-screen.png │ ├── codespaces-template.png │ ├── create_new_workspace.png │ ├── example-dashboard-chart.png │ ├── excel-export-csv.png │ ├── getting-started-codespaces-button.png │ ├── getting-started-codespaces-commit-message.png │ ├── getting-started-codespaces-push-to-github.png │ ├── getting-started-codespaces-repository-additional-permissions.png │ ├── getting-started-codespaces-setting-up.png │ ├── getting-started-codespaces-stage-changes.png │ ├── getting-started-codespaces-start.png │ ├── getting-started-create-repository-owner-name.png │ ├── getting-started-create-repository-public-private.png │ ├── getting-started-github-actions-tab.png │ ├── getting-started-github-actions-workflow-success.png │ ├── getting-started-github-desktop-commit-all.png │ ├── getting-started-github-desktop-commit-message.png │ ├── getting-started-github-desktop-push-to-github.png │ ├── good-pr-pic.png │ ├── how-os-works-diagram.jpg │ ├── job_request_8676_timings.png │ ├── job_request_8680_all_noncoviddeath.png │ ├── line-profiler-output-dummy-data.png │ ├── macos-docker-privileges-escalation-warning.png │ ├── macos-docker-privileges-escalation.png │ ├── macos-docker-skip-intro.png │ ├── macos-menu-bar.png │ ├── pr-desc.png │ ├── project-edit-button.png │ ├── project-edit-page.png │ ├── releases.png │ ├── run_jobs.png │ ├── t1oos.png │ ├── token.png │ ├── use-this-template-button.png │ ├── use-this-template.png │ ├── view_project.png │ ├── win-anaconda-prompt.png │ └── win-docker-starting.png ├── img │ ├── favicon.svg │ └── icon.svg ├── index.md ├── install-docker.md ├── install-linux.md ├── install-macos.md ├── install-python.md ├── install-visual-studio-code.md ├── intro-using-opensafely.md ├── jobs-site.md ├── js │ ├── details-utils.mjs │ ├── extra.mjs │ └── lite-yt-embed.js ├── legacy │ ├── requesting-release-offline-process.md │ ├── study-def-codelists.md │ ├── study-def-dates.md │ ├── study-def-expectations.md │ ├── study-def-flowcharts.md │ ├── study-def-measures.md │ ├── study-def-tricks.md │ ├── study-def-variables.md │ └── study-def.md ├── level-4-server.md ├── memory-efficient-working.md ├── open-data-manifesto.md ├── open-methods.md ├── opensafely-cli.md ├── outputs │ ├── index.md │ ├── output-checking.md │ ├── releasing-overview.md │ ├── requesting-file-release.md │ ├── sdc.md │ ├── viewing-released-files.md │ └── viewing-with-airlock.md ├── paper_template.txt ├── plan-s.md ├── project-changes.md ├── project-completion.md ├── protocol.md ├── reports │ ├── create-a-draft.md │ ├── images │ │ ├── job-server-direct-output-file-link-published.jpg │ │ ├── job-server-direct-output-file-link-release.jpg │ │ ├── job-server-published-outputs.jpg │ │ ├── job-server-workspace-latest-outputs.jpg │ │ └── reports-admin-add-report.jpg │ ├── intro.md │ ├── publish-a-report.md │ └── review-process.md ├── repositories.md ├── requesting-libraries.md ├── security-levels.md ├── system-integration.md ├── technical-architecture.md ├── type-one-opt-outs.md ├── updating-the-docs.md └── workflow.md ├── hooks ├── __init__.py ├── ehrql_branch.py ├── ehrql_css.py └── parent_snippets.py ├── includes ├── cohort-extractor-deprecated.md ├── glossary.md ├── imd-warning-header.md ├── isaric-warning-header.md └── vmp-ids-warning.md ├── justfile ├── main.py ├── mkdocs.yml ├── overrides ├── main.html └── partials │ └── integrations │ └── analytics │ └── plausible.html ├── pyproject.toml ├── requirements.dev.in ├── requirements.dev.txt ├── requirements.prod.in ├── requirements.prod.txt ├── requirements.txt ├── 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