feat: modernize KrakenParser

[iliapopov17]

Architecture

• New krakenparser/pipeline.py orchestrates the full pipeline; library functions
  raise exceptions, CLI entry points catch them and call sys.exit()
• New krakenparser/utils.py — ensure_output_dir() helper, output directories
  are now auto-created
• krakenparser/krakenparser.py dispatcher runs all scripts as -m modules,
  fixing the ModuleNotFoundError: krakenparser is not a package bug

Dependencies

• Added -s/--seed parameter for reproducible rarefaction (np.random.default_rng)

Packaging & CI/CD

• Fixed codecov.yml schema — informational: true now at the correct
  coverage.status.patch.default level (was silently ignored before)

Tests

• Coverage: 82% → 95% (was 83% before this branch)
• test_cli.py - smoke tests for every main() entry point via monkeypatch

[codecov]

Codecov Report

❌ Patch coverage is 93.10345% with 4 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
krakenparser/counts/convert2csv.py	83.33%	1 Missing ⚠️
krakenparser/counts/processing_script.py	85.71%	1 Missing ⚠️
krakenparser/stats/diversity.py	95.00%	1 Missing ⚠️
krakenparser/stats/relabund.py	85.71%	1 Missing ⚠️

📢 Thoughts on this report? Let us know!