Merge pull request #173 from BIH-CEI/170-change-datafield-to-work-wit… #292

	name: CI

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

	jobs:
	run-ci:
	runs-on: ubuntu-latest
	strategy:
	matrix:
	python-version: ['3.10', '3.11', '3.12']

	steps:
	- uses: actions/checkout@v4
	- name: Initialize Python
	uses: actions/setup-python@v4.3.1
	with:
	python-version: ${{ matrix.python-version }}
	- name: Install package
	run: \|
	python3 -m pip install --editable .[test,docs]
	- name: Run pytest tests with coverage
	run: \|
	pytest --cov=phenopacket_mapper --cov-report=term --cov-report=xml:coverage.xml
	- name: Extract coverage percentage
	id: coverage
	run: \|
	# Extract the percentage from the XML report
	coverage=$(grep -oP '(?<=line-rate=")[0-9.]+(?=")' coverage.xml)
	# Multiply by 100 to get the percentage
	COVERAGE=$(awk -v cov="$coverage" 'BEGIN {printf "%.2f\n", cov * 100}')
	echo "COVERAGE=${COVERAGE}" >> $GITHUB_ENV
	echo "Coverage percentage: $COVERAGE"
	- name: Display coverage
	run: \|
	echo "Coverage: ${{ env.COVERAGE }}%"

	- name: Create Badge
	uses: schneegans/dynamic-badges-action@v1.7.0
	with:
	auth: ${{ secrets.GIST_SECRET }}
	gistID: 67304fe3700ce3d41079e75f4fe9609f
	filename: phenopacket_mapper_test_cov.JSON # Use test.svg if you want to use the SVG mode.
	label: Test Coverage
	message: ${{ env.COVERAGE }}%
	color: green

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