Add Stockholm file validation script with modular architecture, auto-fix capability, and GitHub Action #10

	name: Validate Stockholm Files

	on:
	pull_request:
	paths:
	- '**.so'
	- '**.sto'
	- '**.stk'

	jobs:
	validate:
	name: Validate Stockholm MSA Files
	runs-on: ubuntu-latest
	permissions:
	contents: read

	steps:
	- name: Checkout code
	uses: actions/checkout@v4
	with:
	fetch-depth: 0

	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: '3.x'

	- name: Get changed Stockholm files
	id: changed-files
	run: \|
	# Get the list of changed .so, .sto, and .stk files
	BASE_SHA="${{ github.event.pull_request.base.sha }}"
	if [ -z "$BASE_SHA" ]; then
	BASE_SHA="origin/main"
	fi

	git diff --name-only --diff-filter=ACMRT "$BASE_SHA" ${{ github.sha }} \| \
	grep -E '\.(so\|sto\|stk)$' > changed_files.txt \|\| true

	if [ -s changed_files.txt ]; then
	echo "has_files=true" >> $GITHUB_OUTPUT
	echo "Changed Stockholm files:"
	cat changed_files.txt
	else
	echo "has_files=false" >> $GITHUB_OUTPUT
	echo "No Stockholm files changed"
	fi

	- name: Validate Stockholm files
	if: steps.changed-files.outputs.has_files == 'true'
	run: \|
	# Read files from changed_files.txt and validate using xargs
	if [ -f changed_files.txt ] && [ -s changed_files.txt ]; then
	echo "Validating Stockholm files..."
	cat changed_files.txt \| xargs python3 validate_stockholm.py -v
	else
	echo "No files to validate"
	fi

	- name: Report success
	if: steps.changed-files.outputs.has_files == 'false'
	run: \|
	echo "✓ No Stockholm files were modified in this PR"

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