Change run_mialsrtk to handle better defaults and remove hybrid mask … #41

	name: fetal_brain_utils

	# on: [push, pull_request]
	on:
	# trigger on pushes and PRs to main
	push:
	branches:
	- main
	pull_request:
	branches:
	- main

	jobs:
	build:

	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v3
	- name: Checkout submodules
	shell: bash
	run: \|
	auth_header="$(git config --local --get http.https://github.com/.extraheader)"
	git submodule sync --recursive
	git -c "http.extraheader=$auth_header" -c protocol.version=2 submodule update --init --force --recursive --depth=1
	- name: Set up Python
	uses: actions/setup-python@v4
	with:
	python-version: 3.9
	- name: Install dependencies and build package
	run: \|
	python -m pip install --upgrade pip
	python -m pip install -e .
	- name: Lint with flake8
	run: \|
	pip install flake8
	# stop the build if there are Python syntax errors or undefined names
	flake8 . --count --select=B,C,E,F,W,T4,B9 --show-source --statistics --max-complexity=18 --max-line-length=100 --ignore=E203,E266,E501,W503,F403,F401,C901
	- name: Format with black
	run: \|
	pip install black
	black *.py -l 100
	black fetal_brain_utils/*.py -l 100
	black tests/*.py -l 100
	- name: Test with pytest
	run: \|
	pip install -U pytest
	python -m pytest

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