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Commits on Apr 29, 2026

• propagate bioc version bump to bump2version

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Commits on Apr 28, 2026

• bump x.y.z version to odd y following creation of RELEASE_3_23 branch

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• bump x.y.z version to even y prior to creation of RELEASE_3_23 branch

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Commits on Apr 21, 2026

• docs rebuild

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• Bump version: 3.19.11 → 3.99.0

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• Fix BiocCheck issues: cat/print, <<-, missing @return

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Commits on Apr 20, 2026

• Use string args for %:::% to avoid global variable NOTE

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• Fix HPO URL to stable GitHub releases permalink and add .slow_doctest

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Commits on Apr 13, 2026

• Add SBMLR to Suggests to fix undeclared import warning

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• Fix broken HPO URL and last NSE note in metatlas

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• docs rebuild

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• Fix R CMD check notes and errors for Bioconductor release

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• Merge branch 'master' of github.com:saezlab/OmnipathR into devel

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Commits on Mar 25, 2026

• Add .slow_doctest to metatlas functions and guard empty URL in cache key

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• Bump version: 3.19.11 → 3.19.12

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• Handle empty URL in omnipath_cache_key and missing SBML in metatlas

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• docs rebuild

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• Refactor reactome.R and wikipathways.R

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• Merge branch 'devel'

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• Bump version: 3.19.10 → 3.19.11

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• include `metatlas_sbml` (created earlier, was only missing from git repo)

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• Bump version: 3.19.9 → 3.19.10

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• Document .slow_doctest usage in AGENTS.md

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• Regenerate NAMESPACE and man pages

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• Move .slow_doctest() from @examples to function body

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• Export .slow_doctest so R CMD check can find it in examples

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Commits on Mar 24, 2026

• Fix return() inside magrittr pipe in biomart_query buildserver path

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• corrected single_gpml fetch

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Commits on Mar 23, 2026

• Bump version: 3.19.8 → 3.19.9

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• Merge branch 'devel' of github.com:saezlab/OmnipathR into devel

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• Bump version: 3.19.7 → 3.19.8

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• On buildservers, return empty tibble on BioMart failure instead of error

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• Add cache system vignette

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• Add unit tests for the cache system

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• Fix omnipath_cache_remove wiping entire cache on single key removal

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