Update the OMEX files. #32

	name: Update the OMEX files.

	on:
	# push:
	workflow_dispatch:

	jobs:
	fixEntries:
	name: Fix the entries of BioModels and commit to the repository
	runs-on: ubuntu-latest
	steps:
	- name: Checkout repository
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	submodules: recursive

	- name: Install Python
	uses: actions/setup-python@v5
	with:
	python-version: '3.9'

	- name: Install pip and setuptools
	run: \|
	python -m pip install pip==23.0.0
	python -m pip install pip==23.0.0

	- name: Install BioModels QC
	working-directory: biomodels-qc
	run: \|
	python -m pip install cython
	python -m pip install .

	- name: Install requirements
	run: python -m pip install -r requirements.txt

	- name: Create omex files
	run: python create_all_omex.py

	- name: Setup Git
	run: \|
	git config --global user.email "bot@reproduciblebiomodels.org"
	git config --global user.name "Center for Reproducible Biomodeling Modeling Bot"
	git config pull.rebase false

	- id: commit-final-entries
	name: Commit changes to the fixed entries
	run: \|
	chmod a+x git_add.bat
	./git_add.bat
	git commit -m "Automated update of OMEX files."
	if [[ $? = 0 ]]; then
	finalEntriesChanged=1
	else
	finalEntriesChanged=0
	fi
	echo "finalEntriesChanged=$finalEntriesChanged" >> $GITHUB_OUTPUT

	- name: Push the changes to the fixed entries
	if: steps.commit-final-entries.outputs.finalEntriesChanged == '1'
	uses: ad-m/github-push-action@master
	with:
	github_token: ${{ secrets.GITHUB_TOKEN }}
	branch: ${{ github.ref }}

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