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mkdocs.yml
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site_name: OpenSAFELY documentation
site_url: !ENV MKDOCS_SITE_URL
repo_url: https://github.com/opensafely/documentation
exclude_docs: |
/ehrql/includes/generated_docs/
nav:
- Introduction: index.md
- About OpenSAFELY:
- Our philosophy: open-methods.md
- Security: security-levels.md
- "Safe data access: The Five Safes": five-safes.md
- Access policies: access-policies.md
- Technical architecture: technical-architecture.md
- Type One Opt Outs: type-one-opt-outs.md
- Contributing: contributing.md
- Getting started:
- Getting started: getting-started/index.md
- Tutorial:
- Tutorial: getting-started/tutorial/index.md
- Introduction: getting-started/tutorial/introduction/index.md
- Create a GitHub account: getting-started/tutorial/create-a-github-account/index.md
- Create a GitHub repository: getting-started/tutorial/create-a-github-repository/index.md
- Create a GitHub codespace: getting-started/tutorial/create-a-github-codespace/index.md
- Generate a first dataset: getting-started/tutorial/generate-a-first-dataset/index.md
- Update the dataset definition: getting-started/tutorial/update-the-dataset-definition/index.md
- Run the project pipeline: getting-started/tutorial/run-the-project-pipeline/index.md
- Add a scripted action to the pipeline: getting-started/tutorial/add-a-scripted-action-to-the-pipeline/index.md
- Publish the changes to GitHub: getting-started/tutorial/publish-the-changes-to-github/index.md
- Check the automated tests pass: getting-started/tutorial/check-the-automated-tests-pass/index.md
- Delete the GitHub codespace: getting-started/tutorial/delete-the-github-codespace/index.md
- See the next steps: getting-started/tutorial/see-the-next-steps/index.md
- How-to guides:
- How-to guides: getting-started/how-to/index.md
- How to add GitHub Codespaces to your project: getting-started/how-to/add-github-codespaces-to-your-project/index.md
- How to update GitHub Codespaces in your project: getting-started/how-to/update-github-codespaces-in-your-project/index.md
- How to use GitHub Codespaces in your project: getting-started/how-to/use-github-codespaces-in-your-project/index.md
- How to use released outputs in GitHub Codespaces: getting-started/how-to/use-released-outputs-in-github-codespaces/index.md
- How to troubleshoot common issues in GitHub Codespaces: getting-started/how-to/troubleshoot-common-codespaces-issues/index.md
- How to use Git effectively: getting-started/how-to/use-git-effectively/index.md
- How to use the OpenSAFELY command-line interface: opensafely-cli.md
- How to create a code repository for your project: getting-started/how-to/create-a-code-repository-for-your-project/index.md
- Explanation:
- Explanation: getting-started/explanation/index.md
- Options for running OpenSAFELY: getting-started/explanation/options-for-running-opensafely/index.md
- Understanding GitHub Codespaces: getting-started/explanation/understanding-github-codespaces/index.md
- Understanding the software used to run OpenSAFELY: getting-started/explanation/understanding-the-software-used-to-run-opensafely/index.md
- Using OpenSAFELY:
- Analysis workflow: workflow.md
- Federated analytics: federation.md
- GitHub repositories: repositories.md
- Codelists:
- Introduction to codelists: codelist-intro.md
- Building a codelist: codelist-creation.md
- Adding codelists to a project: codelist-project.md
- Keeping codelists up to date: codelist-updating.md
- Actions:
- Overview: actions-intro.md
- The project pipeline: actions-pipelines.md
- Scripted actions: actions-scripts.md
- Reusable actions: actions-reusable.md
- Jobs site: jobs-site.md
- Level 4 server: level-4-server.md
- Viewing and releasing outputs:
- Viewing and releasing outputs: outputs/index.md
- Viewing outputs with Airlock: outputs/viewing-with-airlock.md
- Releasing research outputs from the Level 4 server: outputs/releasing-overview.md
- Applying statistical disclosure control: outputs/sdc.md
- Requesting release of research outputs: outputs/requesting-file-release.md
- Review process for release requests: outputs/output-checking.md
- Viewing released outputs: outputs/viewing-released-files.md
- Viewing and Releasing with Airlock: '!import https://github.com/opensafely-core/airlock?branch=main'
- Reports:
- Overview: reports/intro.md
- Create a draft: reports/create-a-draft.md
- Review process: reports/review-process.md
- Publishing a report: reports/publish-a-report.md
- Managing your OpenSAFELY project:
- Telling us about changes to your project: project-changes.md
- Project completion: project-completion.md
- Adding your pre-print/paper to OpenSAFELY.org: adding-a-paper.md
- Information for system integrators: system-integration.md
- Legacy:
- Study definitions:
- Overview: legacy/study-def.md
- Working with dates: legacy/study-def-dates.md
- Working with codelists: legacy/study-def-codelists.md
- Dummy data and expectations: legacy/study-def-expectations.md
- Variable reference: legacy/study-def-variables.md
- Measures: legacy/study-def-measures.md
- Create inclusion/exclusion flowcharts: legacy/study-def-flowcharts.md
- Programming tricks: legacy/study-def-tricks.md
- OpenSAFELY best practice:
- Developing a protocol: protocol.md
- Using Git effectively: git-workflow.md
- Code reviews: code-reviews.md
- Case-control studies: case-control-studies.md
- Writing performant code: memory-efficient-working.md
- ehrQL: '!import https://github.com/opensafely-core/ehrql?branch=main'
- Data sources:
- data-sources/index.md
- Overview: data-sources/intro.md
- SystmOne primary care: data-sources/systmone.md
- EMIS primary care: data-sources/emis.md
- Covid-19 test results: data-sources/sgsscovid.md
- Covid-19 therapeutics: data-sources/therapeutics.md
- Emergency attendances: data-sources/ecds.md
- High Cost Drugs: data-sources/hcd.md
- Hospital admissions: data-sources/apc.md
- In-hospital deaths (covid-19 only): data-sources/cpns.md
- Intensive care admissions (covid-19 only): data-sources/icnarc.md
- International Severe Acute Respiratory and emerging Infection Consortium: data-sources/isaric.md
- Registered deaths: data-sources/onsdeaths.md
- UK Renal Registry: data-sources/ukrr.md
- Support:
- How to get help: how-to-get-help.md
- OpenSAFELY co-piloting service: copiloting-service.md
- Requesting new libraries: requesting-libraries.md
- Plan S and OpenSAFELY: plan-s.md
- Updating the documentation: updating-the-docs.md
- Bennett Institute Open Manifesto: open-data-manifesto.md
- Platform News: https://www.opensafely.org/changelog/
theme:
name: material
font: false
logo: img/icon.svg
favicon: img/favicon.svg
palette:
scheme: opensafely
custom_dir: overrides
features:
- content.action.edit
- content.code.copy
- navigation.footer
- navigation.indexes
edit_uri: "edit/main/docs/"
extra_css:
- css/youtube.css
- css/extra.css
- css/lite-yt-embed.css
- ehrql/stylesheets/extra.css
extra_javascript:
- js/extra.js
- js/lite-yt-embed.js
extra:
social:
- icon: fontawesome/brands/github
link: https://github.com/opensafely
name: OpenSAFELY on GitHub
- icon: fontawesome/brands/twitter
link: https://twitter.com/opensafely
name: OpenSAFELY on Twitter
# Import ehrQL docs from a specified branch (defaults to main)
# see hooks/ehrql_branch.py
ehrql_branch: !ENV [EHRQL_BRANCH, "main"]
ehrql_imported_css:
- imported_docs/ehrql/stylesheets/extra.css
copyright: © University of Oxford for the Bennett Institute for Applied Data Science. This work may be copied freely for non-commercial research and study. If you wish to do any of the other acts restricted by the copyright you should apply in writing to bennett@phc.ox.ac.uk.
plugins:
- search
- mkdocstrings:
default_handler: python
handlers:
python:
options:
show_root_heading: true
show_root_toc_entry: false
show_root_full_path: false
show_source: false
show_if_no_docstring: true
heading_level: 4
paths: [src/cohort-extractor]
custom_templates: templates
- macros
- multirepo:
cleanup: !ENV [MKDOCS_MULTIREPO_CLEANUP, false]
temp_dir: imported_docs
watch:
- includes
- src/cohort-extractor/cohortextractor
markdown_extensions:
- pymdownx.details
- pymdownx.snippets:
check_paths: true
base_path: # base paths will be checked in order for matching snippets
- . # dir containing this config file
- imported_docs/ehrql # docs folder for the imported repo
# docs folder for the imported airlock repo
- imported_docs/using-opensafely/viewing-and-releasing-outputs/viewing-and-releasing-with-airlock
auto_append:
- includes/glossary.md
- imported_docs/using-opensafely/viewing-and-releasing-outputs/viewing-and-releasing-with-airlock/airlock-includes/glossary.md
- pymdownx.superfences:
custom_fences:
- name: mermaid
class: mermaid
format: !!python/name:pymdownx.superfences.fence_code_format
- toc:
permalink: "🔗"
- pymdownx.highlight:
extend_pygments_lang:
- name: ehrql
lang: python
- pymdownx.superfences
- pymdownx.tabbed:
alternate_style: true
- pymdownx.keys
- admonition
- footnotes
- abbr
- md_in_html
- attr_list
- pymdownx.emoji:
emoji_index: !!python/name:material.extensions.emoji.twemoji
emoji_generator: !!python/name:material.extensions.emoji.to_svg
hooks:
- hooks/parent_snippets.py
- hooks/ehrql_branch.py
- hooks/ehrql_css.py