Updates for new SPB

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.
+<br>
+<br>
+__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.
 

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/

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