🎉 Initial commit

.github/workflows/build.yml

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+name: build
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main, staging]
+
+jobs:
+  build:
+    runs-on: ubuntu-22.04
+    env:
+      GITHUB_EVENT_NAME: ${{ github.event_name }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10"]
+    timeout-minutes: 15
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: actions/checkout@v4
+        with:
+          repository: laminlabs/lndocs
+          ssh-key: ${{ secrets.READ_LNDOCS }}
+          path: lndocs
+          ref: main
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - uses: actions/cache@v3
+        with:
+          path: ~/.cache/pre-commit
+          key: pre-commit-${{ runner.os }}-${{ hashFiles('.pre-commit-config.yaml') }}
+      - run: pip install -U laminci
+      - run: sudo apt-get -y install graphviz
+
+      - uses: aws-actions/configure-aws-credentials@v2
+        with:
+          aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }}
+          aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+          aws-region: eu-central-1
+      - run: nox -s lint
+      - run: nox -s build
+
+      - uses: codecov/codecov-action@v2
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+      - uses: nwtgck/[email protected]
+        with:
+          publish-dir: "_build/html"
+          production-deploy: ${{ github.event_name == 'push' }}
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          enable-commit-comment: false
+        env:
+          NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }}
+          NETLIFY_SITE_ID: ${{ secrets.NETLIFY_SITE_ID }}

.github/workflows/latest-changes.jinja2

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+{{pr.title}} | [{{pr.number}}]({{pr.html_url}}) | [{{pr.user.login}}]({{pr.user.html_url}}) | {{pr.closed_at.date().isoformat()}} |
+

.github/workflows/latest-changes.yml

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+name: latest-changes
+
+on:
+  pull_request_target:
+    branches:
+      - main
+    types:
+      - closed
+  workflow_dispatch:
+    inputs:
+      number:
+        description: PR number
+        required: true
+
+jobs:
+  latest-changes:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: docker://tiangolo/latest-changes:0.0.3
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          latest_changes_file: docs/changelog.md
+          latest_changes_header: '--- \| --- \| --- \| --- \| ---\n'
+          template_file: ./.github/workflows/latest-changes.jinja2

.gitignore

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+# macOS
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# mypy
+.mypy_cache/
+
+# IDE settings
+.vscode/
+.idea/
+
+# Lamin
+_build
+docs/omop.*
+lamin_sphinx
+docs/conf.py
+_docs_tmp*

.pre-commit-config.yaml

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+fail_fast: false
+default_language_version:
+  python: python3
+default_stages:
+  - commit
+  - push
+minimum_pre_commit_version: 2.12.0
+repos:
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v4.0.0-alpha.4
+    hooks:
+      - id: prettier
+        exclude: |
+          (?x)(
+            docs/changelog.md
+          )
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.6.1
+    hooks:
+      - id: nbstripout
+        exclude: |
+          (?x)(
+              docs/examples/|
+              docs/notes/
+          )
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.7
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix, --unsafe-fixes]
+      - id: ruff-format
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: detect-private-key
+      - id: check-ast
+      - id: end-of-file-fixer
+        exclude: |
+          (?x)(
+              .github/workflows/latest-changes.jinja2
+            )
+      - id: mixed-line-ending
+        args: [--fix=lf]
+      - id: trailing-whitespace
+      - id: check-case-conflict
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.7.1
+    hooks:
+      - id: mypy
+        args: [--no-strict-optional, --ignore-missing-imports]
+        additional_dependencies:
+          ["types-pkg-resources", "types-requests", "types-attrs"]

README.md

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+# OMOP: OMOP Common Data Model
+
+## Contributing
+
+Please run `pre-commit install` and `gitmoji -i` on the CLI before starting to work on this repository!

docs/changelog.md

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+# Changelog
+
+<!-- prettier-ignore -->
+Name | PR | Developer | Date | Version
+--- | --- | --- | --- | ---

docs/guide.md

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+# Guide
+
+```{toctree}
+:maxdepth: 1
+
+quickstart
+```

docs/index.md

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+```{include} ../README.md
+:start-line: 0
+:end-line: 1
+```
+
+```{toctree}
+:maxdepth: 1
+:hidden:
+
+guide
+reference
+changelog
+```

docs/quickstart.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "7f26a335-cf1c-4e69-be3b-0c26b154606a",
+   "metadata": {},
+   "source": [
+    "# Quickstart"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "a51faaf3-ee27-43c6-b48d-13be1adb5c46",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from omop import ExampleClass, example_function"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "fa758625-efb0-4047-9a03-aa534bf6f78e",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "example_function(\"A\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "ad22eec0-8f75-4e0b-a132-8a43ccb09b37",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "ex = ExampleClass(1)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "8bf01623-742e-425a-973d-132fc61c3d9c",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "assert ex.bar() == \"hello\""
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.12"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

docs/reference.md

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+# Reference
+
+```{eval-rst}
+.. automodule:: omop
+```

lamin-project.yaml

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+project_name: OMOP
+description: OMOP Common Data Model
+project_slug: omop
+repository_name: omop
+package_name: omop

noxfile.py

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+import nox
+from laminci.nox import build_docs, login_testuser1, run_pre_commit, run_pytest
+
+# we'd like to aggregate coverage information across sessions
+# and for this the code needs to be located in the same
+# directory in every github action runner
+# this also allows to break out an installation section
+nox.options.default_venv_backend = "none"
+
+
+@nox.session
+def lint(session: nox.Session) -> None:
+    run_pre_commit(session)
+
+
+@nox.session()
+def build(session):
+    session.run(*"uv pip install --system -e .[dev]".split())
+    login_testuser1(session)
+    run_pytest(session)
+    build_docs(session, strict=True)