Update codecov.yml #125

	name: MATLAB Tests and Code Coverage

	on:
	pull_request:
	branches:
	- '**'

	jobs:
	build:
	runs-on: self-hosted
	steps:
	- name: Checkout PR Code
	uses: actions/checkout@v4

	- name: Connect to King Server & Setup Rebase
	run: \|
	ssh saleh@king << 'EOF'
	# Navigate to home directory
	cd ~

	# Clone or update COBRA Toolbox
	if [ ! -d "cobratoolbox" ]; then
	git clone https://github.com/opencobra/cobratoolbox.git
	fi
	cd cobratoolbox

	# Ensure develop is up-to-date
	git fetch origin develop
	git checkout develop
	git reset --hard origin/develop

	# Fetch and rebase the PR branch
	git fetch origin ${{ github.event.pull_request.head.ref }}
	git checkout -b pr-rebase FETCH_HEAD
	git rebase develop

	# If rebase fails, abort and exit
	if [ $? -ne 0 ]; then
	git rebase --abort
	exit 1
	fi

	# Run MATLAB tests
	matlab -batch "run('cobratoolbox/initCobraToolbox.m'); diary('test_results.txt'); run('cobratoolbox/test/testAll.m'); diary off;"

	# Exit SSH session
	exit
	EOF

	- name: Upload Test Report
	uses: actions/upload-artifact@v4
	with:
	name: test-report
	path: ~/cobratoolbox/test_results.txt

	- name: Upload Coverage to Codecov
	if: always()
	uses: codecov/codecov-action@v3
	with:
	files: ~/cobratoolbox/CodeCovTestResults.xml
	token: ${{ secrets.CODECOV_TOKEN }}
	fail_ci_if_error: true
	flags: matlab
	comment: true

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