Upgrade Python development and use new PyO3 syntax

[cauliyang]

This pull request primarily updates dependencies and improves Python interoperability for several Rust structs by adding the from_py_object attribute to their #[pyclass] macros. It also includes a minor test code simplification.

Dependency updates:

• Updated numpy to version 0.28.0 and pyo3 to 0.28.3 in Cargo.toml, improving compatibility and access to new features.
• Updated parquet and arrow crates to version 58.3 in Cargo.toml.

Python interoperability improvements:

• Added from_py_object to #[pyclass] for the following structs, allowing construction from Python objects:
  • JsonEncoder in src/fq_encode/json_encoder.rs
  • FqEncoderOption in src/fq_encode/option.rs
  • ParquetEncoder in src/fq_encode/parquet_encoder.rs
  • TensorEncoder in src/fq_encode/tensor_encoder.rs
  • PslAlignment in src/smooth/blat.rs
  • StatResult in src/smooth/stat.rs

Test code simplification:

• Simplified the streaming FASTQ reader test to use a for loop instead of manual iteration in src/output/writefq.rs.

[Copilot]

Pull request overview

This PR updates core Rust/Python interoperability dependencies and adapts several exposed Rust #[pyclass] types to the newer PyO3 extraction syntax, while also doing a small test iteration cleanup.

Changes:

• Bumped Rust dependencies: numpy → 0.28.0, pyo3 → 0.28.3, and arrow/parquet → 58.3.
• Added from_py_object to multiple #[pyclass(...)] declarations to support construction/extraction from Python objects with the new PyO3 syntax.
• Simplified a FASTQ streaming reader test loop to use for iteration.

Reviewed changes

Copilot reviewed 9 out of 10 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
Cargo.toml	Updates Rust crate versions for PyO3/numpy and arrow/parquet.
src/fq_encode/json_encoder.rs	Adds #[pyclass(from_py_object)] for PyO3 extraction compatibility.
src/fq_encode/option.rs	Adds #[pyclass(from_py_object)] for PyO3 extraction compatibility.
src/fq_encode/parquet_encoder.rs	Adds #[pyclass(from_py_object)] for PyO3 extraction compatibility.
src/fq_encode/tensor_encoder.rs	Adds #[pyclass(from_py_object)] for PyO3 extraction compatibility.
src/output/writefq.rs	Refactors streaming-reader test to a for loop iteration style.
src/smooth/blat.rs	Adds #[pyclass(from_py_object)] for PyO3 extraction compatibility.
src/smooth/stat.rs	Adds #[pyclass(from_py_object)] for PyO3 extraction compatibility.
deepchopper/cli.py	Removes an extra blank line (no functional change).

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