Add more support for typing, fix some typing-related edge case bugs

[RalfG]

• Adds full support for typing with MyPy
• Removed support for Python 3.9
• CI: Replaced file hash-based tests for idxml with proper unit tests.
• CI: Add format checks.

[codecov]

Codecov Report

❌ Patch coverage is 80.04751% with 252 lines in your changes missing coverage. Please review.
✅ Project coverage is 70.18%. Comparing base (95e8218) to head (6c3df17).
⚠️ Report is 14 commits behind head on main.

Files with missing lines	Patch %	Lines
psm_utils/io/mzid.py	39.02%	50 Missing ⚠️
psm_utils/io/ionbot.py	14.28%	30 Missing ⚠️
psm_utils/io/idxml.py	82.09%	29 Missing ⚠️
psm_utils/io/percolator.py	44.68%	26 Missing ⚠️
psm_utils/io/peptide_record.py	66.66%	22 Missing ⚠️
psm_utils/psm_list.py	46.87%	17 Missing ⚠️
psm_utils/io/tsv.py	48.27%	15 Missing ⚠️
psm_utils/peptidoform.py	77.77%	14 Missing ⚠️
psm_utils/io/__init__.py	62.50%	9 Missing ⚠️
psm_utils/io/pepxml.py	55.00%	9 Missing ⚠️
... and 13 more

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #125      +/-   ##
==========================================
+ Coverage   69.12%   70.18%   +1.05%     
==========================================
  Files          30       30              
  Lines        2802     3052     +250     
==========================================
+ Hits         1937     2142     +205     
- Misses        865      910      +45     

Flag	Coverage Δ
unittests	70.18% <80.04%> (+1.05%)	⬆️

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[Copilot]

Pull Request Overview

This pull request adds comprehensive typing support with MyPy and removes Python 3.9 compatibility. Key changes include replacing Optional and Union with modern syntax (|), adding type hints throughout the codebase, and transitioning to SQLAlchemy 2.0 patterns.

Key changes:

• Updated minimum Python version from 3.8/3.9 to 3.10
• Added MyPy type checking to the development dependencies and CI
• Replaced hash-based tests with proper unit tests for idXML functionality
• Added proper type annotations and from __future__ import annotations throughout

Reviewed Changes

Copilot reviewed 35 out of 37 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
tests/test_io/test_proteome_discoverer.py	Added comprehensive unit and integration tests for MSFReader class
tests/test_io/test_peptide_record.py	Refactored tests to use _analyze_peprec_file function instead of internal class
tests/test_io/test_idxml.py	Replaced hash-based file verification with proper content validation tests
pyproject.toml	Updated Python version requirement to 3.10+, added MyPy and type checking configuration
psm_utils/utils.py	Added type hints and improved type safety with from __future__ import annotations
psm_utils/psm_list.py	Enhanced type annotations with overloads for __getitem__ and improved typing throughout
psm_utils/psm.py	Added field validators and improved type hints for PSM class
psm_utils/peptidoform.py	Added comprehensive type hints and TypedDict for properties, improved type safety
psm_utils/io/xtandem.py	Added type annotations and improved error handling
psm_utils/io/tsv.py	Enhanced type hints and improved type safety for reader/writer classes
psm_utils/io/sage.py	Added type annotations and improved method signatures
psm_utils/io/proteoscape.py	Enhanced type hints and improved static method usage
psm_utils/io/proteome_discoverer.py	Migrated to SQLAlchemy 2.0 patterns with comprehensive type hints and improved documentation
psm_utils/io/percolator.py	Added type hints and improved error handling throughout
psm_utils/io/pepxml.py	Enhanced type annotations and improved metadata handling
psm_utils/io/peptide_record.py	Refactored to use Pydantic models and improved type safety
psm_utils/io/parquet.py	Added type hints and improved error handling
psm_utils/io/mzid.py	Enhanced type annotations and improved error handling with comprehensive typing
psm_utils/io/msamanda.py	Added type hints and improved error handling
psm_utils/io/maxquant.py	Enhanced type annotations and improved documentation
psm_utils/io/ionbot.py	Added comprehensive error handling and type hints
psm_utils/io/idxml.py	Major refactoring with proper type hints, improved error handling, and better code organization
psm_utils/io/fragpipe.py	Added type hints and improved method signatures
psm_utils/io/flashlfq.py	Enhanced type annotations and improved array type handling
psm_utils/io/diann.py	Added type hints and improved static method usage
psm_utils/io/alphadia.py	Enhanced type annotations and improved static method usage
psm_utils/io/_utils.py	Added type hints and improved documentation
psm_utils/io/_pd_msf_tables.py	Migrated to SQLAlchemy 2.0 ORM patterns with comprehensive type hints
psm_utils/io/_base_classes.py	Enhanced type hints and improved abstract base classes
psm_utils/io/init.py	Added comprehensive type annotations, TypedDict definitions, and improved documentation

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