Initial commit

.devcontainer/README.md

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+# Devcontainer Configuration
+
+This folder contains configuration files required for Codespaces/devcontainers.
+Please do not modify its contents unless you know what you are doing and there
+is a specific change to the devcontainer configuration you need to make.
+
+If you believe you have a broken configuration or are unsure if you have the
+latest version of the configuration, please follow the 
+[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
+// README at: https://github.com/devcontainers/templates/tree/main/src/python
+{
+    "name": "OpenSAFELY",
+    "image": "ghcr.io/opensafely-core/research-template:v0",
+    // Features to add to the dev container. More info: https://containers.dev/features.
+    "features": {
+        "ghcr.io/devcontainers/features/docker-in-docker:2": {}
+    },
+    "postCreateCommand": "/bin/bash /opt/devcontainer/postCreate.sh ${containerWorkspaceFolder}",
+    "postAttachCommand": "/bin/bash /opt/devcontainer/postAttach.sh",
+    "forwardPorts": [
+        8787
+    ],
+    "portsAttributes": {
+        "8787": {
+            "label": "RStudio IDE"
+        }
+    },
+    // Configure tool-specific properties.
+    "customizations": {
+        "codespaces": {
+            "repositories": {
+                "opensafely/server-instructions": {
+                    "permissions": {
+                        "contents": "read"
+                    }
+                }
+            }
+        },
+        "vscode": {
+            "extensions": [
+                "ms-python.python",
+                "ms-toolsai.jupyter",
+                "ms-toolsai.jupyter-renderers"
+            ],
+            "settings": {
+                "extensions.ignoreRecommendations": true,
+                "files.autoSave": "afterDelay",
+                "files.autoSaveDelay": 1000,
+                "git.autofetch": true,
+                "python.analysis.extraPaths": [".devcontainer/ehrql-main/"],
+                "python.defaultInterpreterPath": "/opt/venv/bin/python",
+                "python.terminal.activateEnvInCurrentTerminal": true,
+                "python.terminal.activateEnvironment": true,
+                "window.autoDetectColorScheme": true
+            }
+        }
+    },
+    // Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
+    // "remoteUser": "root"
+    "remoteEnv": {
+        "MAX_WORKERS": "2"
+    }
+}

.gitattributes

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

.github/dependabot.yml

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

.github/workflows/test_runner.yaml

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

.gitignore

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

.vscode/tasks.json

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

LICENSE

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

README.md

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+# disease_incidence
+
+[View on OpenSAFELY](https://jobs.opensafely.org/repo/https%253A%252F%252Fgithub.com%252Fopensafely%252Fdisease_incidence)
+
+Details of the purpose and any published outputs from this project can be found at the link above.
+
+The contents of this repository MUST NOT be considered an accurate or valid representation of the study or its purpose. 
+This repository may reflect an incomplete or incorrect analysis with no further ongoing work.
+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.
+No clinical, policy or safety conclusions must be drawn from the contents of this repository.
+
+# About the OpenSAFELY framework
+
+The OpenSAFELY framework is a Trusted Research Environment (TRE) for electronic
+health records research in the NHS, with a focus on public accountability and
+research quality.
+
+Read more at [OpenSAFELY.org](https://opensafely.org).
+
+# Licences
+As standard, research projects have a MIT license. 

analysis/dataset_definition.py

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+from ehrql import create_dataset
+from ehrql.tables.tpp import patients, practice_registrations
+
+dataset = create_dataset()
+
+index_date = "2020-03-31"
+
+has_registration = practice_registrations.for_patient_on(
+    index_date
+).exists_for_patient()
+
+dataset.define_population(has_registration)
+
+dataset.sex = patients.sex

codelists/codelists.json

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+{
+  "files": {}
+}

docs/.gitkeep

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+

project.yaml

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+version: '3.0'
+
+# Ignore this`expectation` block. It is required but not used, and will be removed in future versions.
+expectations:
+  population_size: 1000
+
+actions:
+  generate_dataset:
+    run: ehrql:v1 generate-dataset analysis/dataset_definition.py --output output/dataset.csv.gz
+    outputs:
+      highly_sensitive:
+        dataset: output/dataset.csv.gz