Better regex validation

[RalfG]

Add validation and exception raising for PSM and spectrum ID regex patterns:

• Implemented _validate_regular_expressions function to check regex patterns in configuration.
• Added tests for regex validation, covering valid, invalid, and edge cases.
• Updated parse_psms and parse_spectra to apply ID patterns and handle errors accordingly.

[Copilot]

Pull Request Overview

Add stricter validation and application of regex patterns for PSM and spectrum IDs, with targeted exceptions and tests to prevent silent mismatches.

• Add _validate_regular_expressions to validate regex syntax and ensure exactly one capturing group.
• Apply psm_id_pattern early in parse_psms with invariant check on unique IDs; add spectrum ID remapping in parse_spectra with clearer configuration errors.
• Add tests covering valid/invalid regex patterns and ID mapping edge cases.

Reviewed Changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
tests/test_parse_spectra.py	Adds factory and a new test for non-matching spectrum_id_pattern; updates expected exception types.
tests/test_parse_psms.py	New tests verifying psm_id_pattern extraction and uniqueness-invariance errors.
tests/test_config_parser.py	Adds tests for _validate_regular_expressions including valid, invalid, and edge cases.
ms2rescore/parse_spectra.py	Introduces _apply_spectrum_id_pattern and integrates it into _get_precursor_values; refines exception types and messages.
ms2rescore/parse_psms.py	Moves and strengthens psm_id_pattern handling with a uniqueness check; removes duplicate application later in the function.
ms2rescore/config_parser.py	Implements _validate_regular_expressions and wires it into parse_configurations; minor import adjustments.

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[Copilot]

Pull Request Overview

Copilot reviewed 6 out of 6 changed files in this pull request and generated 2 comments.

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[Copilot]

Pull Request Overview

Copilot reviewed 6 out of 6 changed files in this pull request and generated 3 comments.

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