Consolidate long tests, gpu builds to advanced build options (#156)

* Consolidate long tests, gpu builds to advanced build options

* Replace long-tests with advanced-build-options

---------

Co-authored-by: A Wokaty <[email protected]>

Author: jwokaty

_bookdown.yml

@@ -39,7 +39,7 @@ rmd_files: ["index.Rmd",
            "volunteer-to-review.Rmd",
            "appendix.Rmd",
            "devel-branch.Rmd",
-           "long-tests.Rmd",
+           "advanced-build-options.Rmd",
            "web-query.Rmd",
            "c-and-fortran.Rmd",
            "mavericks.Rmd",

long-tests.Rmd advanced-build-options.Rmdlong-tests.Rmd renamed to advanced-build-options.Rmd

@@ -1,6 +1,25 @@
-# Long Tests
+# Advanced Build Options
 
-## What are they
+An optional `.BBSoptions` file at the package root can alter the default
+build behavior, such as excluding a package from unsupported platform or
+including a package in an optional build.
+
+## Skipping builds on unsupported platforms
+
+In the `.BBSoptions` file, add the line `UnsupportedPlatforms:` with the
+platform--`win`, `win64`, or `mac`--or the name of a build node. For example
+
+    UnsupportedPlatforms: win64, kjohnson3
+
+## Optional builds: long tests and GPU builds
+
+Two optional builds are available to software packages: long tests and GPU
+builds. Maintainers can opt their packages in to these builds using the
+`.BBSoptions` file.
+
+### Long tests
+
+#### What are they
 
 Code in the `tests` subdirectory of all Bioconductor software
 packages is run by `R CMD check` on a daily basis as part of
@@ -12,7 +31,7 @@ Package developers who wish to implement `tests` that will be too long
 to run in the context of the nightly builds can set up "long tests" in
 their package and add the package to the Bioconductor _Long Tests builds_.
 
-## Setup
+#### Setup
 
 4 steps:
 
@@ -39,7 +58,7 @@ Note that we also run the _Long Tests builds_ for the current release
 branch once a week (every Saturday). The latest report for these builds
 is [here][release-LongTests-report].
 
-## "Short tests" vs "long tests"
+#### "Short tests" vs "long tests"
 
 The _Long Tests_ setup forces developers to split the testing code
 in their package between "short tests" and "long tests". The former go in
@@ -54,8 +73,25 @@ prevent a package from propagating after a version bump. In other words,
 even if a package is included in the _Long Tests builds_, propagation
 is still determined by the results of the nightly builds.
 
+### GPU builds
+
+If a package needs a GPU to properly build it should be added to the
+[GPU builds][devel-GPU-report], which build and check packages on GPU machines.
+In the `.BBSoptions` file, maintainers should set `GPU_reliance` term to
+`required`:
+
+    ```
+    GPU_reliance: required
+    ```
+
+If a package supports GPUs if available, maintainers may opt in to the build
+by setting the `GPU_reliance` term set to `optional:
+
+    ```
+    GPU_reliance: optional
+    ```
+
 ## Need help?
 
 Ask on the [bioc-devel][bioc-devel-mail] mailing list if you have questions or
-need help with the _Long Tests builds_.
-
+need help.

index.Rmd

@@ -93,6 +93,7 @@ knitr::write_bib(c(
 [Create a new GitHub repo]: https://help.github.com/articles/create-a-repo/
 [detect duplicate commits]: https://github.com/Bioconductor/bioc_git_transition/blob/master/misc/detect_duplicate_commits.py
 [devel-LongTests-report]: https://bioconductor.org/checkResults/devel/bioc-longtests-LATEST/
+[devel-GPU-report]: https://bioconductor.org/checkResults/devel/bioc-gpu-LATEST/
 [devel-software-build-report]: https://bioconductor.org/checkResults/devel/bioc-LATEST/
 ['devel' version]: #use-devel
 [docker]: https://bioconductor.org/help/docker/
@@ -109,7 +110,7 @@ knitr::write_bib(c(
 [git-and-github-learning-resources]: https://help.github.com/articles/git-and-github-learning-resources/
 [git-scm]: https://git-scm.com/
 [guidelines]: #develop-overview
-[long tests]: #long-tests
+[advanced-build-options]: #advanced-build-options
 [Maintain a _Bioconductor_-only repository]: #maintain-bioc-only
 [Maintain GitHub and _Bioconductor_ repositories]: #maintain-github-bioc
 [Makevars files]: http://cran.r-project.org/doc/manuals/R-exts.html#Using-Makevars
@@ -130,6 +131,7 @@ knitr::write_bib(c(
 [release-schedule]: https://bioconductor.org/developers/release-schedule/
 [release-biocviews]: http://bioconductor.org/packages/release/BiocViews.html
 [release-LongTests-report]: https://bioconductor.org/checkResults/release/bioc-longtests-LATEST/
+[release-GPU-report]: https://bioconductor.org/checkResults/release/bioc-gpu-LATEST/
 [release-software-build-report]: https://bioconductor.org/checkResults/release/bioc-LATEST/
 [Removing collaborator]: https://help.github.com/articles/removing-a-collaborator-from-a-personal-repository/
 [Resolving a merge conflict using command line]: https://help.github.com/articles/resolving-a-merge-conflict-using-the-command-line/