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Commits on Nov 13, 2025

• Bump version: 3.19.0 → 3.19.1

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• applied BioC version bump to `bump2version`

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• Merge branch 'devel' of git.bioconductor.org:packages/OmnipathR

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• `recon3d`, `cosmos`: added missing varible declarations

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Commits on Oct 29, 2025

• typo in `recon3d.R` in `slow_doctest` calls

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• bump x.y.z version to odd y following creation of RELEASE_3_22 branch

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• bump x.y.z version to even y prior to creation of RELEASE_3_22 branch

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Commits on Oct 28, 2025

• Bump version: 3.17.8 → 3.17.9

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• docs rebuild

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• added some missing param documentation

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Commits on Oct 25, 2025

• Bump version: 3.17.7 → 3.17.8

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• docs rebuild

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• `recon3d`: updated call to old function name; added missing docstrings and `slow_doctest`` statements

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Commits on Oct 24, 2025

• Bump version: 3.17.6 → 3.17.7

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• `ensembl_organisms`: fallback to rescued repo if download fails

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Commits on Sep 24, 2025

• `noRd` for new cosmos pkn functions

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Commits on Sep 23, 2025

• Bump version: 3.17.5 → 3.17.6

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• `disable_doctest_bypass` internal function

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

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• Bump version: 3.17.4 → 3.17.5

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• `misc`: new helper functions `named`, `all_named`, `last`

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• changed to implicit return in one function

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• `chalmers_gem`: simplified processing statement without change in behavior

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• `omnipathr.env$doctest_bypass`: enable bypassing slow doctests

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• `omnipathr.env$doctest_bypass`: enable bypassing slow doctests

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

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• `omnipath_download`: do not return log message for failed queries

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Commits on Sep 9, 2025

• split into different small functions

  

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• add core_PKN, kinasephospho,

  

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• `uniprot_query`: internal function to query by list of accessions

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• KinasePhos URL

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• docs rebuild

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• KinasePhos: new resource of predicted kinase-PTM relationships

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• `internals`: `curl_read_tsv` use `read_delim`

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Commits on Sep 3, 2025

• docs rebuild

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