PEPMatch 1.0

Stable release of PEPMatch 1.0. Waited for publication which is here

Since v0.9.0:

• Added ParallelMatcher which will optimize a specified number of CPU cores to run jobs in parallel
• Removed dependency on Levenshtein package; wrote own C extension for the Hamming distance portion
• New benchmarking script and revamped the milk allergen benchmark to reflect data from this paper
• Simplified all tests, which will run much faster for each commit
• Many bugs related to the output of the tool for each format
• Added .tsv output support
• Ruff linter to maintain proper code style

See the full changelog: v0.9.0...v1.0

PEPMatch 0.9.0

First real stable PEPMatch release.

Since v0.8.0:

• Completely refactored all of the codebase for better maintainability and readability
• Unit tests for exact match, mismatch, and best match w/ GitHub workflows
• Benchmarking portion works for all methods
• Added feature to search discontinuous epitopes
• Improve regex pattern matching for FASTA header extraction
• Preprocessing option for Redis, to test for speed
• Many bug fixes for outputting results