Move also interleaved files to the final directory #1103

	name: CI

	on:
	push:
	branches:
	- main
	tags:
	- '**'
	pull_request:

	env:
	MPLBACKEND: Agg
	PYTEST_ADDOPTS: --color=yes

	jobs:
	pyflakes:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v3

	- name: Set up Python 3.11
	uses: actions/setup-python@v4
	with:
	python-version: 3.11

	- name: pyflakes
	run: \|
	pip install pyflakes
	pyflakes osa

	tests:
	needs: pyflakes
	runs-on: ubuntu-latest

	defaults:
	run:
	shell: bash -leo pipefail {0}

	steps:
	- uses: actions/checkout@v3
	with:
	fetch-depth: 0

	- name: Setup Mamba
	uses: mamba-org/setup-micromamba@v1
	with:
	environment-file: environment.yml
	cache-environment: true
	post-cleanup: 'all'

	- name: Install dependencies
	env:
	PYTHON_VERSION: 3.11

	run: \|
	python --version
	echo "Installing additional pip packages"
	echo "pip install .[test]"
	pip install .[test]

	- name: Tests
	env:
	COVERAGE_PROCESS_START: .coveragerc
	PYTHONPATH: .

	run: \|
	# to measure coverage when using subprocess for testing scripts we create sitecustomize.py
	# as specified in https://coverage.readthedocs.io/en/latest/subprocess.html
	# to initialize the coverage start up.
	echo "create sitecustomize.py"
	echo "import coverage; coverage.process_startup()" > $PYTHONPATH/sitecustomize.py
	pytest --basetemp=test_osa -v --cov --cov-report=xml osa
	cat coverage.xml

	- name: Codecov
	uses: codecov/codecov-action@v3

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