Add all pipeline files #1

	name: CI — Lint + Demo

	on:
	push:
	branches: [ main, develop ]
	pull_request:
	branches: [ main ]

	jobs:
	lint-and-demo:
	name: Python lint + demo run
	runs-on: ubuntu-latest

	steps:
	- uses: actions/checkout@v4

	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: "3.10"

	- name: Install dependencies
	run: \|
	pip install --upgrade pip
	pip install scanpy squidpy anndata numpy pandas scipy \
	matplotlib seaborn pyyaml flake8

	- name: Lint with flake8
	run: \|
	flake8 pipeline/ scripts/ run_pipeline.py \
	--max-line-length=100 \
	--ignore=E501,W503 \
	--exclude=__init__.py
	continue-on-error: true

	- name: Run demo pipeline
	run: python scripts/run_demo.py

	- name: Check outputs exist
	run: \|
	ls results/demo/qc/
	ls results/demo/spatial_de/

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