docs: reposition repo around generated clinical corpus #52

Workflow file for this run

	name: CI

	on:
	push:
	branches: [main]
	pull_request:

	jobs:

	secrets-scan:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	with:
	fetch-depth: 0
	- uses: actions/setup-python@v5
	with:
	python-version: "3.11"
	- name: Run gitleaks
	uses: gitleaks/gitleaks-action@v2
	env:
	GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
	- name: Byte-compile secret scanner
	run: python -m py_compile scripts/secret_patterns.py
	- name: Run in-repo secret scanner across tracked files
	run: \|
	python - <<'PYSCAN'
	import subprocess, sys
	from pathlib import Path
	sys.path.insert(0, "scripts")
	from secret_patterns import find_secrets
	tracked = subprocess.check_output(["git", "ls-files"], text=True).splitlines()
	skip_ext = {".png",".jpg",".jpeg",".gif",".webp",".svg",".ico",".pdf",".zip",".gz",".tar",".lock",".parquet",".woff",".woff2",".so",".dylib",".dll",".bin"}
	hits = []
	for rel in tracked:
	p = Path(rel)
	if p.suffix.lower() in skip_ext:
	continue
	try:
	text = p.read_text(encoding="utf-8", errors="ignore")
	except Exception:
	continue
	for f in find_secrets(text):
	hits.append((rel, f.line_no, f.name, f.line_excerpt))
	print(f"Scanned {len(tracked)} tracked paths; findings={len(hits)}")
	for h in hits:
	print(f"::error file={h[0]},line={h[1]}::{h[2]} :: {h[3]}")
	sys.exit(1 if hits else 0)
	PYSCAN
	- name: Sanity-check git pre-commit hook against PR diff
	if: github.event_name == 'pull_request'
	run: \|
	git config core.hooksPath .githooks
	base="${{ github.event.pull_request.base.sha }}"
	head="${{ github.event.pull_request.head.sha }}"
	git diff --name-only --diff-filter=ACMRT "$base" "$head" > /tmp/_pr_changed.txt \|\| true
	if [ -s /tmp/_pr_changed.txt ]; then
	git reset --soft "$base"
	xargs -a /tmp/_pr_changed.txt git add --
	.githooks/pre-commit
	else
	echo "no PR diff to scan"
	fi

	backend-lint:
	runs-on: ubuntu-latest
	defaults:
	run:
	working-directory: backend
	steps:
	- uses: actions/checkout@v4
	- uses: actions/setup-python@v5
	with:
	python-version: "3.11"
	- name: Cache pip
	uses: actions/cache@v4
	with:
	path: ~/.cache/pip
	key: ${{ runner.os }}-pip-lint-${{ hashFiles('backend/pyproject.toml', 'backend/tox.ini') }}
	restore-keys: \|
	${{ runner.os }}-pip-lint-
	${{ runner.os }}-pip-
	- name: Install lint toolchain
	run: \|
	python -m pip install --upgrade pip
	pip install tox
	- name: Run backend lint (ruff via tox -e lint)
	run: tox -e lint

	backend:
	runs-on: ubuntu-latest
	needs: backend-lint
	services:
	postgres:
	image: pgvector/pgvector:pg16
	env:
	POSTGRES_USER: rag
	POSTGRES_PASSWORD: rag_dev_password
	POSTGRES_DB: rag_dev
	ports:
	- 5432:5432
	options: >-
	--health-cmd "pg_isready -U rag -d rag_dev"
	--health-interval 10s
	--health-timeout 5s
	--health-retries 5
	env:
	DATABASE_URL: postgresql://rag:rag_dev_password@127.0.0.1:5432/rag_dev
	TEST_DATABASE_URL: postgresql://rag:rag_dev_password@127.0.0.1:5432/rag_dev
	defaults:
	run:
	working-directory: backend
	steps:
	- uses: actions/checkout@v4
	- uses: actions/setup-python@v5
	with:
	python-version: "3.11"
	- name: Cache pip
	uses: actions/cache@v4
	with:
	path: ~/.cache/pip
	key: ${{ runner.os }}-pip-${{ hashFiles('backend/pyproject.toml', 'backend/tox.ini') }}
	restore-keys: \|
	${{ runner.os }}-pip-
	- name: Install backend dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install -e .[dev]
	- name: Run migrations
	run: alembic upgrade head
	- name: Run backend tests (tox -e py311)
	run: tox -e py311

	frontend-lint:
	runs-on: ubuntu-latest
	defaults:
	run:
	working-directory: frontend
	steps:
	- uses: actions/checkout@v4
	- uses: actions/setup-node@v4
	with:
	node-version: "20"
	cache: "npm"
	cache-dependency-path: frontend/package-lock.json
	- name: Install dependencies
	run: npm ci
	- name: Lint frontend
	run: npm run lint

	frontend-build:
	runs-on: ubuntu-latest
	needs: frontend-lint
	defaults:
	run:
	working-directory: frontend
	steps:
	- uses: actions/checkout@v4
	- uses: actions/setup-node@v4
	with:
	node-version: "20"
	cache: "npm"
	cache-dependency-path: frontend/package-lock.json
	- name: Install dependencies
	run: npm ci
	- name: Build frontend
	run: npm run build

	frontend:
	runs-on: ubuntu-latest
	needs: [frontend-lint, frontend-build]
	defaults:
	run:
	working-directory: frontend
	steps:
	- uses: actions/checkout@v4
	- uses: actions/setup-node@v4
	with:
	node-version: "20"
	cache: "npm"
	cache-dependency-path: frontend/package-lock.json
	- name: Install dependencies
	run: npm ci
	- name: Install Playwright browsers
	run: npx playwright install --with-deps chromium
	- name: Run Playwright critical journeys
	run: npm run test:e2e tests/e2e/smoke.spec.ts tests/e2e/patients.spec.ts tests/e2e/chat.spec.ts tests/e2e/responsible-ai.spec.ts tests/e2e/encounter.spec.ts

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docs: reposition repo around generated clinical corpus #52

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docs: reposition repo around generated clinical corpus #52

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