options list and container overrides

DESCRIPTION

@@ -13,7 +13,7 @@ Description: In computationally demanding analysis projects,
   'clustermq' by Schubert (2019) <doi:10.1093/bioinformatics/btz284>),
   and 'batchtools' by Lang, Bischl, and Surmann (2017).
   <doi:10.21105/joss.00135>.
-Version: 0.0.6.9008
+Version: 0.0.6.9010
 License: MIT + file LICENSE
 URL: https://wlandau.github.io/crew.aws.batch/,
   https://github.com/wlandau/crew.aws.batch

NEWS.md

@@ -1,10 +1,11 @@
-# crew.aws.batch 0.0.6.9008 (development)
+# crew.aws.batch 0.0.6.9010 (development)
 
 * Send both cancellation and termination requests to end jobs.
 * Fix launcher bug/typo where parameters were supplied to container overrides.
 * Add a new `all` argument to `terminate()` in the AWS Batch monitor.
 * Add `r_arguments` to accept command line arguments to R.
 * Support `options_metrics`.
+* Reduce argument clutter with `crew_options_aws_batch()`. Supports direct inputs for CPUs, GPUs, and memory without having to specify a complicated `containerOverrides` list.
 
 # crew.aws.batch 0.0.6
 

R/crew_controller_aws_batch.R

@@ -45,12 +45,13 @@ crew_controller_aws_batch <- function(
   processes = NULL,
   r_arguments = c("--no-save", "--no-restore"),
   options_metrics = crew::crew_options_metrics(),
-  aws_batch_config = list(),
-  aws_batch_credentials = list(),
+  options_aws_batch = crew.aws.batch::crew_options_aws_batch(),
+  aws_batch_config = NULL,
+  aws_batch_credentials = NULL,
   aws_batch_endpoint = NULL,
   aws_batch_region = NULL,
-  aws_batch_job_definition,
-  aws_batch_job_queue,
+  aws_batch_job_definition = NULL,
+  aws_batch_job_queue = NULL,
   aws_batch_share_identifier = NULL,
   aws_batch_scheduling_priority_override = NULL,
   aws_batch_parameters = NULL,
@@ -92,6 +93,7 @@ crew_controller_aws_batch <- function(
     processes = processes,
     r_arguments = r_arguments,
     options_metrics = options_metrics,
+    options_aws_batch = options_aws_batch,
     aws_batch_config = aws_batch_config,
     aws_batch_credentials = aws_batch_credentials,
     aws_batch_endpoint = aws_batch_endpoint,

R/crew_options_aws_batch.R

@@ -28,10 +28,20 @@
 #'   The `memory` argument can be `NULL`
 #'   to go with the defaults in the job definition. Ignored if
 #'   `container_overrides` is not `NULL`.
-#' @param units_memory Character string, units of memory of the `memory`
+#' @param memory_units Character string, units of memory of the `memory`
 #'   argument. Can be `"gigabytes"` or `"mebibytes"`.
 #'   Fargate instances can only be certain discrete values of mebibytes,
 #'   so please choose `memory_units = "mebibytes"` in that case.
+#' @param config Named list, `config` argument of
+#'   `paws.compute::batch()` with optional configuration details.
+#' @param credentials Named list. `credentials` argument of
+#'   `paws.compute::batch()` with optional credentials (if not already
+#'   provided through environment variables such as `AWS_ACCESS_KEY_ID`).
+#' @param endpoint Character of length 1. `endpoint`
+#'   argument of `paws.compute::batch()` with the endpoint to send HTTP
+#'   requests.
+#' @param region Character of length 1. `region` argument of
+#'   `paws.compute::batch()` with an AWS region string such as `"us-east-2"`.
 #' @param share_identifier `NULL` or character of length 1.
 #'   For details, visit
 #'   <https://www.paws-r-sdk.com/docs/batch_submit_job/> and the
@@ -77,8 +87,8 @@
 #'   <https://www.paws-r-sdk.com/docs/batch_submit_job/> and the
 #'   "AWS arguments" sections of this help file.
 crew_options_aws_batch <- function(
-  job_definition,
-  job_queue,
+  job_definition = "example",
+  job_queue = "example",
   cpus = NULL,
   gpus = NULL,
   memory = NULL,

README.Rmd

@@ -253,12 +253,19 @@ library(crew.aws.batch)
 controller <- crew_controller_aws_batch(
   name = "my_workflow", # for informative job names
   workers = 16,
-  tasks_max = 2, # to avoid reaching wall time limits
+  tasks_max = 2, # to avoid reaching wall time limits (if any exist)
   seconds_launch = 600, # to allow a 10-minute startup window
   seconds_idle = 60, # to release resources when they are not needed
   processes = NULL, # See the "Asynchronous worker management" section below.
-  aws_batch_job_definition = "YOUR_JOB_DEFINITION_NAME",
-  aws_batch_job_queue = "YOUR_JOB_QUEUE_NAME"
+  options_aws_batch = crew_options_aws_batch(
+    job_definition = "YOUR_JOB_DEFINITION_NAME",
+    job_queue = "YOUR_JOB_QUEUE_NAME",
+    cpus = 2,
+    gpus = 0,
+    memory = 4,
+    memory_units = "gigabytes"
+  )
+  
 )
 controller$start()
 ```

README.md

@@ -23,10 +23,10 @@ packages [`mirai`](https://github.com/shikokuchuo/mirai),
 
 # Installation
 
-| Type        | Source     | Command                                                                        |
-|-------------|------------|--------------------------------------------------------------------------------|
-| Release     | CRAN       | `install.packages("crew.aws.batch")`                                           |
-| Development | GitHub     | `remotes::install_github("wlandau/crew.aws.batch")`                            |
+| Type | Source | Command |
+|----|----|----|
+| Release | CRAN | `install.packages("crew.aws.batch")` |
+| Development | GitHub | `remotes::install_github("wlandau/crew.aws.batch")` |
 | Development | R-universe | `install.packages("crew.aws.batch", repos = "https://wlandau.r-universe.dev")` |
 
 # Documentation
@@ -329,12 +329,19 @@ library(crew.aws.batch)
 controller <- crew_controller_aws_batch(
   name = "my_workflow", # for informative job names
   workers = 16,
-  tasks_max = 2, # to avoid reaching wall time limits
+  tasks_max = 2, # to avoid reaching wall time limits (if any exist)
   seconds_launch = 600, # to allow a 10-minute startup window
   seconds_idle = 60, # to release resources when they are not needed
   processes = NULL, # See the "Asynchronous worker management" section below.
-  aws_batch_job_definition = "YOUR_JOB_DEFINITION_NAME",
-  aws_batch_job_queue = "YOUR_JOB_QUEUE_NAME"
+  options_aws_batch = crew_options_aws_batch(
+    job_definition = "YOUR_JOB_DEFINITION_NAME",
+    job_queue = "YOUR_JOB_QUEUE_NAME",
+    cpus = 2,
+    gpus = 0,
+    memory = 4,
+    memory_units = "gigabytes"
+  )
+
 )
 controller$start()
 ```
@@ -411,7 +418,7 @@ citation("crew.aws.batch")
 To cite package 'crew.aws.batch' in publications use:
 
   Landau WM (????). _crew.aws.batch: A Crew Launcher Plugin for AWS
-  Batch_. R package version 0.0.6,
+  Batch_. R package version 0.0.6.9010,
   https://github.com/wlandau/crew.aws.batch,
   <https://wlandau.github.io/crew.aws.batch/>.
 
@@ -420,7 +427,7 @@ A BibTeX entry for LaTeX users is
   @Manual{,
     title = {crew.aws.batch: A Crew Launcher Plugin for AWS Batch},
     author = {William Michael Landau},
-    note = {R package version 0.0.6, 
+    note = {R package version 0.0.6.9010, 
 https://github.com/wlandau/crew.aws.batch},
     url = {https://wlandau.github.io/crew.aws.batch/},
   }

inst/WORDLIST

@@ -13,6 +13,7 @@ Edmondson
 Fargate
 FitzJohn
 GCP
+vCPUs
 GPU
 Gábor
 Gao