feat: add check flag

[Ulthran]

Summary

• add --check CLI flag to verify archive directory and md5 file
• implement check_backup helper
• test new check flag behavior

Testing

• pytest -q

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https://chatgpt.com/codex/tasks/task_e_68a71a0a2c788323a623ceaf00a0cb95

[Copilot]

Pull Request Overview

This PR adds a --check flag to the CLI that verifies if archive directory and MD5 file exist without performing backup operations. This allows users to validate existing backups before running new ones.

• Adds check_backup helper function to verify archive directory and MD5 file existence
• Implements --check CLI argument that returns boolean verification result
• Adds comprehensive test coverage for the new check functionality

Reviewed Changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 2 comments.

File	Description
seqBackupLib/backup.py	Implements check_backup function and --check CLI flag with early return logic
test/test_backup.py	Adds test for check flag behavior including negative cases when MD5 file is missing

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[Copilot]

The function signature is inconsistent with backup_fastq which takes sample_sheet_fp and other parameters. Consider adding sample_sheet_fp parameter for consistency and to enable more comprehensive validation.

Suggested change

	def check_backup(forward_reads: Path, dest_dir: Path) -> bool:
	def check_backup(forward_reads: Path, dest_dir: Path, sample_sheet_fp: Path) -> bool:

[Copilot]

Missing error handling for file operations. If forward_reads doesn't exist or isn't a valid gzip file, this will raise an unhandled exception instead of returning False.