Repository navigation

Adding GH Actions for CWL and RO-Crate #14

	name: CI

	on:
	push:
	pull_request:

	jobs:
	build:
	name: Build and install dependencies
	runs-on: ubuntu-latest

	steps:
	- name: Checkout code
	uses: actions/checkout@v4

	- name: Set up Python 3.13
	uses: actions/setup-python@v5
	with:
	python-version: "3.13"
	cache: "pip"

	- name: Upgrade pip
	run: python -m pip install --upgrade pip

	- name: Find and install requirements files
	run: \|
	set -e
	echo "Searching for requirements.txt files..."
	files=$(find . -name "requirements.txt")

	if [ -z "$files" ]; then
	echo "No requirements.txt files found."
	else
	for req in $files; do
	echo "Installing dependencies from $req"
	python -m pip install -r "$req"
	done
	fi

	- name: Install CWL Runners used in the thesis
	run: \|
	python -m pip install \
	cwltool==3.2.20260413085819 \
	toil==9.4.1 \
	streamflow==0.2.0rc2

	# TODO: run a few CWL files with these runners?

	rocrate-validation:
	name: RO-Crate validation
	runs-on: ubuntu-latest
	needs: build

	steps:
	- name: Checkout code
	uses: actions/checkout@v4

	- name: Set up Python 3.13
	uses: actions/setup-python@v5
	with:
	python-version: "3.13"
	cache: "pip"

	- name: Install rocrate-validator
	run: \|
	python -m pip install --upgrade pip
	pip install -r ./ro-crate/requirements.txt

	- name: Validate RO-Crate
	run: \|
	FILE="ro-crate-metadata.json"

	if [ ! -f "$FILE" ]; then
	echo "No RO-Crate file found!"
	exit 1
	fi

	rocrate-validator validate --verbose --no-paging --output-format text ./