refactor build into reusable workflow #14

	# adapted from https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python

	name: Build msyd
	description: "Checks out, installs dependencies and builds the msyd package. Formulated as a reusable workflow to reduce code duplication in testing."

	on:
	workflow_call:
	inputs:
	python-version:
	description: 'Python version to use'
	required: true
	default: '3.12'

	run:
	using: composite
	steps:
	- name: Checkout repo
	uses: actions/checkout@v4
	- name: Set up Python ${{ inputs.python-version }}
	uses: actions/setup-python@v5
	with:
	python-version: ${{ inputs.python-version }}
	cache: pip
	- name: Update pip
	run: python -m pip install --upgrade pip setuptools
	- name: Install SyRI manually
	run: \|
	# manually install syris dependencies
	# the python version spoofing requires the --no-deps flag, so this is necessary
	pip install Cython numpy pandas scipy psutil igraph longestrunsubsequence pysam pulp
	# manually use pip to install syri from github, as it isn't on pypi
	# spoof python version to get around bounds check
	pip install 'git+https://github.com/schneebergerlab/syri.git' --python-version '3.10' --no-deps --no-warn-conflicts --target $(python -m site --user-site)
	- name: Install other dependencies
	run: pip install -r requirements.txt
	- name: Build msyd
	run: pip install .

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