Stage deleted file before commit #5

	name: CI Pipeline

	on:
	push

	jobs:
	tests:
	runs-on: self-hosted
	steps:
	- name: Checkout repository
	uses: actions/checkout@v2

	- name: setup python
	uses: actions/setup-python@v5
	with:
	python-version: 3.11.8

	- name: Install dependencies
	run: \|
	pip install -r requirements-dev.txt
	pip install .[mamba-ssm]

	# First download before tests as they make use of the downloaded files
	- name: Download all files
	run: \|
	python ci/download_all.py

	- name: Execute unittests
	run: \|
	CUDA_VISIBLE_DEVICES=-1 pytest --cov-report=html:html_cov --cov-branch --cov-report term --cov=helical ci/

	- name: Upload coverage report
	uses: actions/upload-artifact@v4
	with:
	name: coverage-report
	path: html_cov/

	- name: Generate coverage badge
	uses: tj-actions/coverage-badge-py@v2

	- name: Verify Changed files
	uses: tj-actions/verify-changed-files@v16
	id: verify-changed-files
	with:
	files: coverage.svg

	- name: Commit files
	if: steps.verify-changed-files.outputs.files_changed == 'true'
	run: \|
	git config --local user.email "github-actions[bot]@users.noreply.github.com"
	git config --local user.name "github-actions[bot]"
	rm -f assets/coverage.svg
	git add -u assets/
	git commit -m "Remove old coverage badge"
	mv coverage.svg assets/
	git add assets/coverage.svg
	git commit -m "Add new coverage badge"
	git push

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