Processors for centroid search and wf alignment. Added possibility to read lh5 path in the processing chain #64

	name: dspeed

	on:
	push:
	branches:
	- main
	- 'releases/**'
	pull_request:
	release:

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

	jobs:

	build-and-test:
	name: Test dspeed with Python
	runs-on: ${{ matrix.os }}
	strategy:
	fail-fast: false
	matrix:
	python-version: ['3.9', '3.10', '3.11']
	os: [ubuntu-latest, macOS-latest]

	steps:
	- uses: actions/checkout@v2
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v2
	with:
	python-version: ${{ matrix.python-version }}
	- name: Get dependencies and install dspeed
	run: \|
	python -m pip install --upgrade pip wheel setuptools
	python -m pip install --upgrade .[test]
	- name: Run unit tests
	run: \|
	python -m pytest

	test-coverage:
	name: Calculate and upload test coverage
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v2
	with:
	fetch-depth: 2
	- uses: actions/setup-python@v2
	with:
	python-version: '3.10'

	- name: Generate Report
	run: \|
	python -m pip install --upgrade pip wheel setuptools
	python -m pip install --upgrade .[test]
	python -m pytest --cov=dspeed --cov-report=xml
	- name: Upload Coverage to codecov.io
	uses: codecov/codecov-action@v3

	build-docs:
	name: Build documentation
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v2
	with:
	fetch-depth: 0
	- uses: actions/setup-python@v2
	with:
	python-version: '3.10'
	- name: Setup build environment
	run: \|
	sudo apt-get install -y pandoc
	python -m pip install --upgrade pip wheel setuptools
	python -m pip install --upgrade .[all]
	- name: Build docs for current ref
	run: \|
	cd docs
	make clean
	make

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