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feat: add biocfilecache-backed persistent caching#90

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feat/add-BiocFileCache
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feat: add biocfilecache-backed persistent caching#90
mtran-code wants to merge 7 commits into
mainfrom
feat/add-BiocFileCache

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@mtran-code
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what changed

  • add a package-level BiocFileCache layer with deterministic cache keys
  • persist remote metadata for Cellosaurus, PubChem, ChEMBL, UniChem, OncoTree, and BioMart
  • cache parsed API query results for Cellosaurus, PubChem, ChEMBL, UniChem, and HGNC BioMart where raw and query_only are not requested
  • isolate test runs in a temporary AnnotationGx cache directory and add cache helper coverage
  • bump the package version to 0.99.7 and record the change in NEWS.md

why it changed

  • the package makes repeated remote requests against APIs that are slow, rate-limited, or transiently unavailable
  • persistent caching reduces redundant traffic, improves repeat-call latency, and gives the package a legitimate Bioconductor infrastructure dependency

impact

  • repeated metadata lookups and parsed query calls now reuse cached results across R sessions by default
  • low-level raw and query_only workflows still bypass the persistent cache
  • tests no longer touch a user cache directory during package checks

validation

  • parsed NEWS.md with tools:::.build_news_db_from_package_NEWS_md()
  • ran the full tests/testthat suite file-by-file under load_all() with an isolated temp cache

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coderabbitai Bot commented Apr 21, 2026

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