Add pydocstyle linting to ruff configuration in pyproject.toml

[Adamtaranto]

Misc fixes for unclear logging and reports.

Minor UX updates after case testing.

• Validate and tune automated contig exclusion. (--outlier-threshold )
• Add report per contig end: total count overhangs, median overhang length, overhang SD
• Improve extension summary reports.
• Log per contig total left/right overhang counts.
• Log histogram for per contig end overhang count in filter and extend.
• Add html report option for extend module
• Clarify exclusion stats in filter module
• Possible OBO error in clip threshold calculation
• Verify that exclusion contigs actually exist in ref asm index.
• Option to set logfile name
• Option to log all overhang reads with: contig end, clip offset from end of contig, len clip, and len overhang.
• When excluding contigs from extension, they end up being written to the end of the output fasta. Fix so that output contigs maintain input order. [should we bother? Could just sort with seqtk afterwards.]

[codecov]

Codecov Report

❌ Patch coverage is 85.71429% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 47.57%. Comparing base (11cb04e) to head (ffd7d52).
⚠️ Report is 12 commits behind head on main.

Files with missing lines	Patch %	Lines
src/teloclip/commands/extract.py	0.00%	1 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##             main      #47   +/-   ##
=======================================
  Coverage   47.57%   47.57%           
=======================================
  Files          14       14           
  Lines        1713     1713           
  Branches      355      355           
=======================================
  Hits          815      815           
  Misses        856      856           
  Partials       42       42           

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