Refactor package CLI to native Typer subcommands and update metadata to v1.1.0

[iliapopov17]

Overview

This PR fully migrates the KrakenParser command-line interface from the legacy argparse module to the modern typer framework. This overhaul unifies argument parsing, eliminates obsolete subprocess.run hacks previously used for sub-module isolation, and cleans up legacy routing flags.

Key Changes

• Core CLI: The main entry point (krakenparser.py) has been refactored into native typer subcommands. Backward compatibility is preserved—the full pipeline can still be triggered directly via global options on the root interface without an explicit subcommand keyword.
• Granular Modules: All isolated scripts (mpa, combine, split, process, csv, relabund, diversity) are now registered as standalone Typer sub-apps and neatly organized within an advanced Rich help panel.
• Features & Typings:
  • Expanded taxonomic filtering by exposing domain-specific flags (--bacteria, --fungi, --archaea) to the global pipeline.
  • Refactored core function signatures to accept native pathlib.Path objects instead of strings.
• Package & Docs: Bumped package version to 1.1.0, declared typer as a core runtime dependency, and introduced a lowercase console script alias (krakenparser) alongside the original KrakenParser. The README.md and test suites have been adjusted accordingly.

[codecov]

Codecov Report

❌ Patch coverage is 96.37681% with 5 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
krakenparser/counts/split_mpa.py	91.66%	3 Missing ⚠️
krakenparser/pipeline.py	88.23%	2 Missing ⚠️

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