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feat: modernize API#22

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cvigilv wants to merge 3 commits intomainfrom
feat-standarize-function-naming
Open

feat: modernize API#22
cvigilv wants to merge 3 commits intomainfrom
feat-standarize-function-naming

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@cvigilv
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@cvigilv cvigilv commented Feb 14, 2026

This PR aims to modernize and streamline all API calls implemented to date. The idea is to provide a unified way to access request results, improve error handling, and support additional parsers and processors for responses.

Things to do:

  • Make get understand option parameter in REST API
  • Merge get and get_image
  • Add kegg"<string>" macro
  • Add get flat file parser
  • Unify outputs of API requests
  • Cover all expected functionality of REST API with our API
  • Cover in unit tests
  • Cover in documentation

Once this modernization is complete, the idea is to add package extensions to read from commonly used packages (e.g., DataFrames.jl, MolecularGraphs.jl, Graphs.jl, etc.).

BREAKING CHANGE:
- Rename all public API functions to use `kegg_` prefix (e.g., `find` → `kegg_find`, `conv` → `kegg_conv`, etc.)
- Remove deprecated `Images.jl` and related image helper functions
- Refactor `kegg_get` for improved chunking, option validation, and response parsing
- Update exports and tests to use new function names and signatures
- Improve documentation and warnings for API usage and rate limits
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