feat(studies): real executor — Analysis M comorbidity matrix from CDM #2064

Workflow file for this run

	name: CI

	on:
	push:
	branches: [main, master, "release/**"]
	tags:
	- "v*"
	pull_request:
	branches: [main, master]

	permissions:
	contents: read

	concurrency:
	group: ci-${{ github.ref }}
	cancel-in-progress: true

	jobs:
	backend:
	name: Backend (Laravel)
	runs-on: ubuntu-latest
	# 45 (was 35): pcov coverage instrumentation adds overhead to the Pest run.
	timeout-minutes: 45
	services:
	postgres:
	image: pgvector/pgvector:pg16
	env:
	POSTGRES_DB: parthenon_test
	POSTGRES_USER: parthenon
	POSTGRES_PASSWORD: secret
	ports:
	- 5432:5432
	options: >-
	--health-cmd="pg_isready -U parthenon"
	--health-interval=10s
	--health-timeout=5s
	--health-retries=5
	redis:
	image: redis:7-alpine
	ports:
	- 6379:6379
	options: >-
	--health-cmd="redis-cli ping"
	--health-interval=10s
	--health-timeout=5s
	--health-retries=5

	steps:
	- uses: actions/checkout@v6

	- name: Install PostGIS into postgres service container
	run: \|
	# Phase 19 (D-04): the gis schema migration MUST fail loudly when
	# PostGIS is missing, so CI installs postgresql-16-postgis-3 on top
	# of pgvector/pgvector:pg16 (mirrors docker/postgres/Dockerfile).
	PG_CID=$(docker ps --filter "ancestor=pgvector/pgvector:pg16" --format '{{.ID}}' \| head -n1)
	if [ -z "$PG_CID" ]; then
	echo "Could not find pgvector postgres service container" >&2
	docker ps
	exit 1
	fi
	docker exec "$PG_CID" bash -c "apt-get update -qq && apt-get install -y --no-install-recommends postgresql-16-postgis-3"

	- name: Prepare Postgres schemas and extensions
	env:
	PGPASSWORD: secret
	PGDATABASE: parthenon_test
	PGUSER: parthenon
	POSTGRES_CREATE_TEST_DATABASE: "1"
	POSTGRES_ENABLE_POSTGIS: "1"
	run: bash scripts/ci/prepare-postgres.sh

	- name: Setup PHP
	uses: shivammathur/setup-php@v2
	with:
	php-version: "8.4"
	extensions: pdo_pgsql, pgsql, redis, bcmath, intl, mbstring, pcntl, zip
	coverage: pcov

	- name: Install Composer dependencies
	working-directory: backend
	run: composer install --prefer-dist --no-interaction

	- name: Copy env
	working-directory: backend
	run: cp .env.example .env && php artisan key:generate

	- name: Run Pint (code style)
	working-directory: backend
	run: ./vendor/bin/pint --test

	- name: Run PHPStan (static analysis)
	working-directory: backend
	run: ./vendor/bin/phpstan analyse

	- name: Run Pest (tests)
	working-directory: backend
	env:
	DB_CONNECTION: pgsql
	DB_HOST: 127.0.0.1
	DB_PORT: 5432
	DB_DATABASE: parthenon_test
	DB_USERNAME: parthenon
	DB_PASSWORD: secret
	# phpunit.xml forces DB_CONNECTION=pgsql_testing, which reads DB_TEST_*
	# with fallback to DB_*. Its DB_TEST_PORT default is 5480 (host PG17
	# dev convention), so without these explicit overrides the test
	# connection ignores the CI postgres service and tries port 5480.
	DB_TEST_HOST: 127.0.0.1
	DB_TEST_PORT: 5432
	DB_TEST_DATABASE: parthenon_testing
	DB_TEST_USERNAME: parthenon
	DB_TEST_PASSWORD: secret
	REDIS_HOST: 127.0.0.1
	CACHE_STORE: array
	SESSION_DRIVER: array
	QUEUE_CONNECTION: sync
	run: \|
	php artisan migrate --force
	set +e
	./vendor/bin/pest \
	--coverage-clover=coverage.xml \
	--do-not-fail-on-skipped \
	--do-not-fail-on-warning \
	--do-not-fail-on-phpunit-warning \
	--do-not-fail-on-deprecation \
	--do-not-fail-on-phpunit-deprecation \
	--do-not-fail-on-notice \
	--do-not-fail-on-incomplete 2>&1 \| tee pest.log
	pest_status=${PIPESTATUS[0]}
	set -e

	if [ "$pest_status" -ne 0 ]; then
	summary=$(grep -E 'Tests:[[:space:]]' pest.log \| tail -1 \|\| true)
	if echo "$summary" \| grep -Eq '[1-9][0-9]* (failed\|errored\|risky)'; then
	exit "$pest_status"
	fi
	if grep -Eq 'Code coverage below expected' pest.log; then
	exit "$pest_status"
	fi
	if echo "$summary" \| grep -q 'passed'; then
	echo "Pest exited $pest_status with non-failure issue statuses only; continuing."
	exit 0
	fi
	exit "$pest_status"
	fi

	- name: Enforce coverage floor
	working-directory: backend
	run: \|
	# Robust, explicit floor: parse the clover report's project-level
	# aggregate metrics rather than relying on Pest's exit code / log text.
	# Floor ratchets up toward 80% as coverage grows; measured 33.59% on
	# 2026-06-20 (25693/76492 statements). NEVER lower this value.
	php -r '
	$floor = 32.0;
	$f = "coverage.xml";
	if (!is_file($f)) { fwrite(STDERR, "coverage.xml not found — coverage was not collected\n"); exit(1); }
	$xml = simplexml_load_file($f);
	$nodes = $xml->xpath("/coverage/project/metrics");
	if (!$nodes) { fwrite(STDERR, "no project metrics in clover report\n"); exit(1); }
	$m = end($nodes);
	$stmts = (int) $m["statements"];
	$covered = (int) $m["coveredstatements"];
	$pct = $stmts > 0 ? ($covered / $stmts) * 100.0 : 0.0;
	printf("Line coverage: %.2f%% (%d/%d statements); floor %.1f%%\n", $pct, $covered, $stmts, $floor);
	if ($pct + 1e-9 < $floor) {
	fwrite(STDERR, sprintf("::error::Coverage %.2f%% is below the %.1f%% floor\n", $pct, $floor));
	exit(1);
	}
	'

	frontend:
	name: Frontend (React)
	runs-on: ubuntu-latest
	timeout-minutes: 25
	steps:
	- uses: actions/checkout@v6

	- name: Setup Node
	uses: actions/setup-node@v6
	with:
	node-version: 22
	cache: npm
	cache-dependency-path: frontend/package-lock.json

	- name: Install dependencies
	working-directory: frontend
	run: npm ci --legacy-peer-deps

	- name: Type check
	working-directory: frontend
	run: npx tsc --noEmit

	- name: Lint
	working-directory: frontend
	run: npm run lint

	- name: Test
	working-directory: frontend
	run: npx vitest run

	- name: Build
	working-directory: frontend
	run: npm run build

	ai:
	name: AI Service (Python)
	runs-on: ubuntu-latest
	timeout-minutes: 25
	steps:
	- uses: actions/checkout@v6

	- name: Setup Python
	uses: actions/setup-python@v6
	with:
	python-version: "3.12"
	cache: pip
	cache-dependency-path: ai/requirements*.txt

	- name: Install dependencies
	working-directory: ai
	run: \|
	pip install torch --index-url https://download.pytorch.org/whl/cpu
	pip install -r requirements.txt
	pip install -r requirements-dev.txt

	- name: Type check (mypy)
	working-directory: ai
	run: mypy app/

	- name: Test (pytest)
	working-directory: ai
	run: pytest

	docs-build:
	name: Documentation (Docusaurus)
	runs-on: ubuntu-latest
	timeout-minutes: 20
	steps:
	- uses: actions/checkout@v6

	- name: Setup Node
	uses: actions/setup-node@v6
	with:
	node-version: "22"
	cache: npm
	cache-dependency-path: docs/site/package-lock.json

	- name: Install dependencies
	working-directory: docs/site
	run: npm ci --legacy-peer-deps

	- name: Build
	working-directory: docs/site
	run: npm run build

	docs-pdf:
	name: Documentation PDF Export
	# Only runs on release branches (release/, v..)
	if: startsWith(github.ref, 'refs/heads/release/') \|\| startsWith(github.ref, 'refs/tags/v')
	runs-on: ubuntu-latest
	timeout-minutes: 25
	steps:
	- uses: actions/checkout@v6

	- name: Setup Node
	uses: actions/setup-node@v6
	with:
	node-version: "22"
	cache: npm
	cache-dependency-path: docs/site/package-lock.json

	- name: Install dependencies
	working-directory: docs/site
	run: npm ci --legacy-peer-deps

	- name: Build documentation
	working-directory: docs/site
	run: npm run build

	- name: Install Chromium
	run: npx puppeteer browsers install chrome

	- name: Generate PDF from built docs
	working-directory: docs/site
	run: \|
	node -e "
	const puppeteer = require('puppeteer');
	const path = require('path');
	const fs = require('fs');
	const { execSync } = require('child_process');

	// Serve the built site locally
	const { createServer } = require('http');
	const handler = require('serve-handler');
	const server = createServer((req, res) => handler(req, res, { public: 'build' }));
	server.listen(3001, async () => {
	const browser = await puppeteer.launch({ args: ['--no-sandbox'] });
	const page = await browser.newPage();
	await page.goto('http://localhost:3001/', { waitUntil: 'networkidle0' });
	await page.pdf({ path: 'parthenon-user-manual.pdf', format: 'A4', printBackground: true });
	await browser.close();
	server.close();
	console.log('PDF generated: parthenon-user-manual.pdf');
	});
	"

	- name: Upload PDF artifact
	uses: actions/upload-artifact@v7
	with:
	name: parthenon-user-manual-pdf
	path: docs/site/parthenon-user-manual.pdf
	retention-days: 90

	# docs-screenshots:
	# name: Documentation Screenshots (Playwright)
	# # Manual trigger or release branches only — requires a running Parthenon instance
	# # seeded with Eunomia synthetic data.
	# #
	# # To run locally:
	# # cd docs/screenshots && npm ci && npx playwright test
	# #
	# # Environment variables required:
	# # PARTHENON_URL — base URL of a running Parthenon instance
	# # PARTHENON_EMAIL / PARTHENON_PASSWORD — credentials for screenshot account
	# if: false # Enable when screenshot infrastructure is ready
	# runs-on: ubuntu-latest
	# steps:
	# - uses: actions/checkout@v6
	# - uses: actions/setup-node@v6
	# with: { node-version: "22" }
	# - run: npm ci
	# working-directory: docs/screenshots
	# - run: npx playwright install --with-deps chromium
	# working-directory: docs/screenshots
	# - run: npx playwright test
	# working-directory: docs/screenshots
	# env:
	# PARTHENON_URL: ${{ secrets.PARTHENON_URL }}
	# PARTHENON_EMAIL: ${{ secrets.PARTHENON_EMAIL }}
	# PARTHENON_PASSWORD: ${{ secrets.PARTHENON_PASSWORD }}
	# - uses: actions/upload-artifact@v7
	# with:
	# name: docs-screenshots
	# path: docs/screenshots/screenshots/

	openapi-export:
	name: OpenAPI Spec (Scribe)
	runs-on: ubuntu-latest
	timeout-minutes: 30
	services:
	postgres:
	image: pgvector/pgvector:pg16
	env:
	POSTGRES_DB: parthenon_test
	POSTGRES_USER: parthenon
	POSTGRES_PASSWORD: secret
	ports:
	- 5432:5432
	options: >-
	--health-cmd="pg_isready -U parthenon"
	--health-interval=10s
	--health-timeout=5s
	--health-retries=5
	steps:
	- uses: actions/checkout@v6

	- name: Prepare Postgres schemas
	env:
	PGPASSWORD: secret
	PGDATABASE: parthenon_test
	PGUSER: parthenon
	run: bash scripts/ci/prepare-postgres.sh

	- name: Setup PHP
	uses: shivammathur/setup-php@v2
	with:
	php-version: "8.4"
	extensions: pdo_pgsql, pgsql, redis, bcmath, intl, mbstring, pcntl, zip
	coverage: none

	- name: Install Composer dependencies
	working-directory: backend
	run: composer install --prefer-dist --no-interaction

	- name: Copy env
	working-directory: backend
	run: cp .env.example .env && php artisan key:generate

	- name: Export OpenAPI spec with Scribe
	working-directory: backend
	env:
	DB_CONNECTION: pgsql
	DB_HOST: 127.0.0.1
	DB_PORT: 5432
	DB_DATABASE: parthenon_test
	DB_USERNAME: parthenon
	DB_PASSWORD: secret
	DB_SEARCH_PATH: app,public
	run: \|
	php artisan scribe:generate --no-interaction
	test -s public/docs/openapi.yaml
	php -r '
	require "vendor/autoload.php";
	$spec = Symfony\Component\Yaml\Yaml::parseFile("public/docs/openapi.yaml");
	if (! is_array($spec)) {
	fwrite(STDERR, "OpenAPI spec is not a map.\n");
	exit(1);
	}
	$paths = $spec["paths"] ?? [];
	if (! is_array($paths) \|\| count($paths) === 0) {
	fwrite(STDERR, "OpenAPI spec has no paths.\n");
	exit(1);
	}
	file_put_contents("api.json", json_encode($spec, JSON_PRETTY_PRINT \| JSON_UNESCAPED_SLASHES) . PHP_EOL);
	fwrite(STDOUT, "OpenAPI spec exported with " . count($paths) . " paths.\n");
	'

	- name: Validate OpenAPI spec
	working-directory: backend
	run: \|
	python3 -m json.tool api.json >/dev/null

	- name: Setup Node
	uses: actions/setup-node@v6
	with:
	node-version: "22"
	cache: npm
	cache-dependency-path: frontend/package-lock.json

	- name: Install frontend dependencies
	working-directory: frontend
	run: npm ci --legacy-peer-deps

	- name: Generate TypeScript types
	working-directory: frontend
	run: npm run generate:api-types

	- name: Detect OpenAPI artifact drift
	run: \|
	# Fail if regenerated OpenAPI artifacts differ from what's committed.
	# Contributors must run ./deploy.sh --openapi whenever backend
	# routes, requests, or responses change.
	if ! git diff --exit-code -- backend/api.json frontend/src/types/api.generated.ts; then
	echo ""
	echo "::error::OpenAPI artifact drift detected."
	echo ""
	echo "The committed OpenAPI spec or TypeScript types do not match what would be generated from the current backend routes."
	echo ""
	echo "To fix locally:"
	echo " ./deploy.sh --openapi"
	echo " git add frontend/src/types/api.generated.ts backend/api.json"
	echo " git commit -m 'chore: regenerate OpenAPI types'"
	echo ""
	echo "Unified diff of the drift is shown above."
	exit 1
	fi
	echo "OpenAPI types are in sync with the backend spec."

	- name: Verify TypeScript types compile
	working-directory: frontend
	run: npx tsc --noEmit

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feat(studies): real executor — Analysis M comorbidity matrix from CDM #2064

Workflow file

feat(studies): real executor — Analysis M comorbidity matrix from CDM #2064

Uh oh!

Workflow file for this run