docs(marimo): add Jupyter-to-marimo migration plan for all workflow notebooks #391

Workflow file for this run

	name: CI

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

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

	jobs:
	lint:
	name: Lint
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	with:
	ref: ${{ github.event.pull_request.head.sha \|\| github.sha }}

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

	- name: Install linting tools
	run: \|
	pip install "ruff==0.15.1"
	ruff version

	- name: Run ruff linter
	run: ruff check src/ tests/

	- name: Check formatting with ruff
	run: ruff format --check --diff src/ tests/

	test:
	name: Test (Python ${{ matrix.python-version }})
	runs-on: ubuntu-latest
	strategy:
	fail-fast: false
	matrix:
	python-version: ["3.10", "3.11", "3.12"]

	steps:
	- uses: actions/checkout@v4

	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v5
	with:
	python-version: ${{ matrix.python-version }}

	- name: Install system dependencies
	run: \|
	sudo apt-get update
	sudo apt-get install -y libvips-dev

	- name: Install Python dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install -e ".[dev]"

	- name: Run tests
	run: \|
	pytest tests/ -v --tb=short -x

	- name: Run tests with coverage
	if: matrix.python-version == '3.10'
	run: \|
	pytest tests/ --cov=src/kintsugi --cov-report=xml --cov-report=term

	- name: Upload coverage
	if: matrix.python-version == '3.10'
	uses: codecov/codecov-action@v3
	with:
	files: ./coverage.xml
	fail_ci_if_error: false

	test-notebooks:
	name: Test Notebooks Import
	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 system dependencies
	run: \|
	sudo apt-get update
	sudo apt-get install -y libvips-dev

	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install -e .

	- name: Test notebook imports
	run: \|
	python -c "
	import sys
	import os
	sys.path.insert(0, 'notebooks')

	# Kreg is a vendored VALIS fork with heavy native deps
	# (SimpleITK, torch, etc.) that are HPC-only. Validate
	# module structure exists without triggering imports.
	print('Testing Kreg module structure...')
	kreg_modules = [
	'registration', 'slide_io', 'preprocessing',
	'non_rigid_registrars', 'warp_tools', 'feature_detectors',
	]
	for mod in kreg_modules:
	path = os.path.join('notebooks', 'Kreg', f'{mod}.py')
	assert os.path.exists(path), f'Missing: {path}'
	print(f' OK: Kreg/{mod}.py exists')

	print('Testing Kview2 import...')
	from Kview import imshow, curtain, crop
	print(' OK: visualization functions')

	print('Testing Kstitch import...')
	from Kstitch import stitch_images
	print(' OK: stitch_images')

	print('All notebook imports successful!')
	"

	dependency-check:
	name: Dependency Check
	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 system dependencies
	run: \|
	sudo apt-get update
	sudo apt-get install -y libvips-dev

	- name: Install package
	run: \|
	python -m pip install --upgrade pip
	pip install -e .

	- name: Run dependency check
	run: \|
	python -c "
	from kintsugi.deps import check_dependencies
	result = check_dependencies(verbose=True)

	# Fail if required dependencies are missing
	if not result['all_required_ok']:
	missing = result['required']['missing']
	print(f'Missing required dependencies: {missing}')
	exit(1)
	"

	build:
	name: Build Package
	runs-on: ubuntu-latest
	needs: [lint, test]
	steps:
	- uses: actions/checkout@v4

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

	- name: Install build tools
	run: pip install build twine

	- name: Build package
	run: python -m build

	- name: Check package
	run: twine check dist/*

	- name: Upload artifacts
	uses: actions/upload-artifact@v4
	with:
	name: dist
	path: dist/

	docs:
	name: Documentation
	runs-on: ubuntu-latest
	if: github.event_name == 'push' && github.ref == 'refs/heads/main'
	steps:
	- uses: actions/checkout@v4

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

	- name: Validate README
	run: \|
	python -c "
	import re
	with open('README.md') as f:
	content = f.read()

	# Check for broken links (basic check)
	links = re.findall(r'\[([^\]]+)\]$([^)]+)$', content)
	print(f'Found {len(links)} links in README')

	# Check for required sections
	required = ['Installation', 'Notebooks']
	for section in required:
	if section not in content:
	print(f'Warning: Missing section: {section}')
	"

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docs(marimo): add Jupyter-to-marimo migration plan for all workflow notebooks #391

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docs(marimo): add Jupyter-to-marimo migration plan for all workflow notebooks #391

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