Sync files from source repo #78

	name: MATLAB MLX to HTML Conversion

	# Trigger the workflow on push events but only for the main branch
	on:
	push:
	branches:
	- gh-pages
	paths:
	- '**.mlx'

	# The jobs key is a collection of the jobs to run
	jobs:
	convert-mlx-to-html:
	# The type of runner that the job will run on
	runs-on: self-hosted

	# Steps represent a sequence of tasks that will be executed as part of the job
	steps:
	- name: Manual Repository Checkout
	run: \|
	# Remove the cobratoolbox_repo directory if it exists, then recreate it
	rm -rf cobratoolbox_repo
	mkdir cobratoolbox_repo

	# Clone the repository into the cobratoolbox_repo directory
	git clone https://github.com/opencobra/cobratoolbox.git cobratoolbox_repo
	cd cobratoolbox_repo

	- name: Get Changed MLX Files
	id: getfile
	run: \|
	changed_files=$(git diff --name-only ${{ github.event.before }} ${{ github.sha }} \| grep '\.mlx' \|\| echo "")
	echo "Changed MLX files: $changed_files"
	echo "mlx_file=$changed_files" >> $GITHUB_ENV

	- name: Print Changed MLX Files
	if: steps.getfile.outputs.mlx_file != ''
	run: echo "The following MLX files have been changed ${{ env.mlx_file }}"


	- name: Make MATLAB Script Executable
	run: chmod +x ./run_matlab.sh

	- name: Convert MLX to HTML
	if: steps.getfile.outputs.mlx_file != ''
	run: \|
	./run_matlab.sh "${{ steps.getfile.outputs.mlx_file }}"

	- name: Commit and Push New File
	run: \|
	git config user.name "GitHub Action"
	git config user.email "[email protected]"
	git add .
	git commit -m "Add new HTML file" \|\| echo "No changes to commit"
	git push -f origin gh-pages

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