Dep/update dependencies

[noamteyssier]

No description provided.

[gemini-code-assist]

Code Review

This pull request introduces an option to control whether output records are ordered to match the input order during parallel FASTX encoding. It adds an ordered flag to FastxEncoderBuilder and Encoder, updates the auto-write example with an --unordered flag, and updates dependencies. The feedback suggests using the tempfile crate in the new integration test to ensure robust cleanup of temporary files instead of manual creation and deletion.

[gemini-code-assist]

Instead of manually creating temporary files in std::env::temp_dir() and manually cleaning them up with std::fs::remove_file, use the tempfile crate (which is already a dev-dependency). This ensures that temporary files and directories are automatically cleaned up even if the test panics or fails, preventing leftover files in the system's temporary directory.

Suggested change

	let pid = std::process::id();
	let input_path = std::env::temp_dir().join(format!("binseq_ordered_input_{pid}.fastq"));
	let output_path = std::env::temp_dir().join(format!("binseq_ordered_output_{pid}.cbq"));
	std::fs::write(&input_path, &fastq).unwrap();
	let builder = BinseqWriterBuilder::new(Format::Cbq).headers(true);
	let handle = Box::new(std::fs::File::create(&output_path).unwrap());
	let result = FastxEncoderBuilder::new(builder, handle)
	.input(&input_path)
	.threads(4)
	.ordered(true)
	.run();
	std::fs::remove_file(&input_path).unwrap();
	assert!(result.is_ok());
	let reader = BinseqReader::new(&output_path).unwrap();
	let processor = HeaderCollector::default();
	let headers = processor.headers.clone();
	reader.process_parallel(processor, 4).unwrap();
	std::fs::remove_file(&output_path).unwrap();
	let temp_dir = tempfile::tempdir().unwrap();
	let input_path = temp_dir.path().join("input.fastq");
	let output_path = temp_dir.path().join("output.cbq");
	std::fs::write(&input_path, &fastq).unwrap();
	let builder = BinseqWriterBuilder::new(Format::Cbq).headers(true);
	let handle = Box::new(std::fs::File::create(&output_path).unwrap());
	let result = FastxEncoderBuilder::new(builder, handle)
	.input(&input_path)
	.threads(4)
	.ordered(true)
	.run();
	assert!(result.is_ok());
	let reader = BinseqReader::new(&output_path).unwrap();
	let processor = HeaderCollector::default();
	let headers = processor.headers.clone();
	reader.process_parallel(processor, 4).unwrap();