diff --git a/git-version-control.Rmd b/git-version-control.Rmd index 92d4a04..df288a5 100644 --- a/git-version-control.Rmd +++ b/git-version-control.Rmd @@ -211,17 +211,6 @@ pushing to the _Bioconductor_ git repository. ## push to GitHub (origin remote) git push origin main -1. **Check the updated build report**. If your push to - git.bioconductor.org included a version bump, you'll receive an - email directing you to visit your issue on github.com, - `https://github.com/Bioconductor/Contributions/issues/`; a comment - is also posted on the issue indicating that a build has started. - - After several minutes a second email and comment will indicate that - the build has completed, and that the build report is - available. The comment includes a link to the build report. Follow - the link to see whether further changes are necessary. - 1. See other scenarios for working with _Bioconductor_ and GitHub repositories, in particular: - [Maintain GitHub and _Bioconductor_ repositories][]. @@ -319,6 +308,10 @@ user community can engage in the development of your package. __Goal:__ Developer wishes to maintain their _Bioconductor_ repository without using GitHub. +
+
+__NOTE:__ This is not recommended. We highly recommend maintaining both a +personal repository for development and Bioconductor repository for deployment. #### Clone and setup the package on your local machine. diff --git a/index.Rmd b/index.Rmd index 117b858..eee5ec7 100644 --- a/index.Rmd +++ b/index.Rmd @@ -71,13 +71,14 @@ knitr::write_bib(c( [Azure Data Lakes]: https://azure.microsoft.com/en-us/services/data-lake-analytics [Based on: Resolving a merge conflict]: https://www.atlassian.com/git/tutorials/using-branches/merge-conflicts [bioc-common]: #reusebioc +[BiocContributions]: https://github.com/Bioconductor/BiocContributions/issues/new [bioc-devel-mail]: https://stat.ethz.ch/mailman/listinfo/bioc-devel [BiocParallel vignette]: https://bioconductor.org/packages/devel/bioc/vignettes/BiocParallel/inst/doc/Introduction_To_BiocParallel.pdf [biocViews]: https://bioconductor.org/packages/devel/BiocViews.html [BiocCredentials application]: https://git.bioconductor.org/BiocCredentials/ [build reports]: https://bioconductor.org/checkResults/ [build timings]: #propagate -[cirdep]: https://github.com/Bioconductor/Contributions/blob/master/CONTRIBUTING.md#submitting-related-packages +[cirdep]: https://github.com/Bioconductor/BiocContributions/blob/devel/docs/FAQs.md#related-packages-and-circular-dependencies [Code Of Conduct]: https://bioconductor.github.io/bioc_coc_multilingual/ [Contributions]: https://github.com/Bioconductor/Contributions/issues/new [CRAN foreign]: http://cran.r-project.org/doc/manuals/R-exts.html#System-and-foreign-language-interfaces @@ -118,7 +119,7 @@ knitr::write_bib(c( [Merging a pull request]: https://help.github.com/articles/merging-a-pull-request/ [New package workflow]: #new-package-workflow [Open github issue]: https://help.github.com/articles/creating-an-issue/ -[Packages Under Review]: https://github.com/Bioconductor/Contributions/issues +[Packages Under Review]: https://github.com/Bioconductor/BiocContributions/issues [resolve duplicate commits]: #resolve-duplicate-commits [Pull upstream changes]: #pull-upstream-changes [Pull Requests]: https://help.github.com/articles/creating-a-pull-request/ @@ -147,7 +148,7 @@ knitr::write_bib(c( [Sync existing repositories]: #sync-existing-repositories [testthat: Get Started with Testing]: http://journal.r-project.org/archive/2011-1/RJournal_2011-1_Wickham.pdf [Testing with testthat]: http://r-pkgs.had.co.nz/tests.html -[tracker]: https://github.com/Bioconductor/Contributions +[tracker]: https://github.com/Bioconductor/BiocContributions [unit tests]: #tests [versioning]:#versionnum [which-remote-url-should-i-use]: https://help.github.com/articles/which-remote-url-should-i-use/ diff --git a/package-submission.Rmd b/package-submission.Rmd index c30c71a..b51d113 100644 --- a/package-submission.Rmd +++ b/package-submission.Rmd @@ -168,18 +168,14 @@ package maintenance responsibilities. Package authors are expected to: * Read and follow the full [Contributor Guidelines][guidelines] section. * Submit by opening a new issue in the _Bioconductor_ - [Contributions][] repository, following the [guidelines][tracker] of + [BiocContributions][] repository, following the [guidelines][tracker] of the `README.md` file. Assuming that your package is in a [GitHub Repository][git-repo-create] and under the default branch, add the link to your repository to the issue you are opening. You cannot specify any alternative branches; the default branch is utilized. The default branch must contain only package code. Any files or directories for other applications (Github Actions, - devtools, etc) should be in a different branch. If you are submitting two - highly related packages or circular dependent packages please see - [here][cirdep]. The lighter dependent or package that can be installed without - a dependency should be submitted first; this is generally the associated data - package to a software package. + devtools, etc) should be in a different branch. * __Note:__ The submitter of the package should also be the listed maintainer so we may verify BiocCredentials. Additional push access to other contributors @@ -240,91 +236,9 @@ use of existing data in a Bioconductor package. See development section on ## Review Process {#whattoexpect} -* A new package is initially labeled as `1. awaiting moderation`. - A _Bioconductor_ team member will take a very brief look at your - package, to ensure that it is not doing anything malicious or - inappropriate. Packages that pass this stage will be labelled - `pre-check passed`. - -* The moderator will add your package as a repository to the - git.bioconductor.org git server, copy the SSH keys from your github - account to the [BiocCredentials application][] application and the issue labelled - `pre-review`. - - ALL CHANGES TO YOUR PACKAGE must be pushed to the - git.bioconductor.org repository created in this step. See the [New package - workflow][] for instructions on pushing changes to your git.bioconductor.org - repository. - -* The package will be submitted to the _Bioconductor_ build - system (BBS). The system will check out your package from GitHub and move it - to our git.bioconductor.org git server. Please familiarize yourself with - [git][gitver] as the git.bioconductor.org is the versions the (BBS) will - always use. It will then run `R CMD build` to create a 'tarball' of your source code, - vignettes, and man pages. It will run `R CMD check` on the tarball, - to ensure that the package conforms to standard _R_ programming best - practices. _Bioconductor_ has chosen to utilize a custom `R CMD check` - environment; See [R CMD check environment][] for more details. Finally, the - build system will run `BiocCheckGitClone()` and `BiocCheck('new-package'=TRUE)` to ensure that - the package conforms to _Bioconductor_ `r BiocStyle::Biocpkg("BiocCheck")` - standards. The system will perform these steps using the ['devel' - version][] of _Bioconductor_, on three platforms - (Linux, Mac OS X, and Windows). After these steps are complete, a link to a - build report will be appended to the new package issue. Avoid surprises by - running these checks on your own computer, under the 'devel' version - of _Bioconductor_, before submitting your package. - -* If the build report indicates problems, modify your package and - commit changes to the git.bioconductor.org version of your package as - described in the [new package git workflow](#new-package-workflow). If - there are problems that you do not understand, seek help on the - [bioc-devel][bioc-devel-mail] mailing list. - -* To trigger a new build, include a version bump in your commit, e.g., - from `Version: 0.99.0` to `Version: 0.99.1`. Pre-release versions utilize the - `0.99.z` format. When accepted and released, your package's version number - will be automatically incremented to 1.0.0. - -* If in the pre-review process there are identified larger issues with the - package, a label `3e. pending pre-review changes` or a more specific flag of - package issue will be assigned. Please address any pre-review identified - issues and comment back for the package administrators to re-evaluate. - -* Once your package builds and checks without errors or (avoidable) - warnings, the package is assigned a reviewer. The package will be - labelled `2. Review in progress`. - -* The reviewer will provide a technical review of your package. Other - _Bioconductor_ developers and users with domain expertise are encouraged to - provide additional community commentary. Reviewers will add comments to the - issue you created. - -* Please be courteous with your package reviewers and always follow the - _Bioconductor_ [Code Of Conduct][] with correspondence. Please allow 2-3 weeks - for reviewers to assess your package. - -* Respond to the issues raised by the reviewers. You _must_ respond to - the primary reviewer, and are strongly encouraged to consider - community commentary. Typically your response will involve code - modifications; commit these to the default branch of git.bioconductor.org. When - you have addressed all concerns, add a comment to the issue created in step 2 - to explain your response. - -* The reviewer will assess your responses, perhaps suggesting further - modifications or clarification. The reviewer will then accept your - package for inclusion in _Bioconductor_, or decline it. The label - `2. review in progress` will be replaced by `3a. accepted` or - `3b. declined`. - -* If your package is accepted, it will be added to _Bioconductor_'s - nightly 'devel' builds. All packages in the 'devel' branch of the repository - are 'released' to the user community once every six months, in - approximately April and October. - -* Once the review process is complete, the issue you created will be - closed. All updates to your package will be through the - [_Bioconductor_ Git Server][gitver]. - +Please see [Submitters Guide On What To +Expect](https://github.com/Bioconductor/BiocContributions/blob/devel/docs/submitters.md) +or if preferred a [Slide Deck](https://docs.google.com/presentation/d/1EK2wsDoRbtVGECdYC1GU5nGtYkN-h_7R-on-CSUC6CQ/edit?slide=id.p#slide=id.p) Please be mindful that reviewers are volunteers and package reviews are not the only responsibility of _Bioconductor_ team members. We like to see the