From 10de37ba365ef646244773a0b1870fc8f54a6445 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marcel=20Ramos=20P=C3=A9rez?= Date: Tue, 17 Dec 2024 11:58:47 -0500 Subject: [PATCH] add bug fixes due to API changes section, closes #130 (#132) --- git-version-control.Rmd | 42 +++++++++++++++++++++++++++++++++-------- 1 file changed, 34 insertions(+), 8 deletions(-) diff --git a/git-version-control.Rmd b/git-version-control.Rmd index 9864d79..2f61639 100644 --- a/git-version-control.Rmd +++ b/git-version-control.Rmd @@ -510,16 +510,16 @@ repository for the package. 1. The package with the changes should be available in your local _R_ installation. -## Scenarios for code update: - -- [Pull upstream changes][], e.g., introduced by the core team. -- [Push to GitHub and _Bioconductor_][] repositories. -- [Resolve merge conflicts][mergeconflict]. -- [Abandon changes][]. -- [Fix bugs in devel and release][]. +## Scenarios for code update + +- [Pull upstream changes][] (e.g., introduced by the core team) +- [Push to GitHub and _Bioconductor_][] repositories +- [Resolve merge conflicts][mergeconflict] +- [Abandon changes][] +- [Fix bugs in devel and release][] +- [Bug fixes due to API changes][] - [Resolve duplicate commits][] - ### Pull upstream changes __Goal:__ Your _Bioconductor_ repository has been updated by the core @@ -894,6 +894,32 @@ git branch and in the current release branch (e.g., `RELEASE_3_14`). +### Bug fixes due to API changes {#bug-fixes-due-to-api-changes} + +Packages that make use of web APIs will need to be updated when there are +significant API changes. This is a common occurrence with Bioconductor packages +that use REST APIs, e.g., `UniProt.ws`, `AnVIL`, etc. To provide a smooth +experience for users, it is important to update the package as soon as possible. + +#### Minor API changes + +The steps to apply bug fixes due to API changes are similar to the steps for +fixing bugs in the `devel` and `release` branches. The main difference is that +the bug may be due to minor API issues, certificate issues, API version issues, +etc. The maintainer can readily update the R package to adapt to the new API. +Note that the functionality of the package largely remains the same. + +#### Major API changes + +It may be possible that an organization's API changes are not backwards +compatible and that they do not provide the same functionality for the existing +Bioconductor package to remain functional. In such case, it is recommended to +contact the organization that maintains the API to get more information about +the changes and to request a backward compatible API, if possible. When API +changes do not provide a similar functionality to that of the R package, the +package maintainer may need to submit a new package that works with the new API +and to deprecate the old package. + ### Resolve Duplicate Commits __Goal:__ You want to get rid of the duplicate (or triplicate) commits