Migrate to crew 0.5.0

DESCRIPTION

@@ -15,7 +15,7 @@ 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: 0.1.1.9001
+Version: 0.1.2
 License: MIT + file LICENSE
 URL: https://wlandau.github.io/crew.cluster/,
   https://github.com/wlandau/crew.cluster
@@ -42,7 +42,7 @@ Authors@R: c(
 Depends:
   R (>= 4.0.0)
 Imports:
-  crew (>= 0.4.0),
+  crew (>= 0.5.0),
   lifecycle,
   R6,
   rlang,

NAMESPACE

@@ -19,6 +19,7 @@ importFrom(crew,crew_assert)
 importFrom(crew,crew_class_launcher)
 importFrom(crew,crew_launcher)
 importFrom(crew,crew_random_name)
+importFrom(crew,crew_tls)
 importFrom(lifecycle,badge)
 importFrom(rlang,is_installed)
 importFrom(utils,globalVariables)

NEWS.md

@@ -1,9 +1,10 @@
-# crew.cluster 0.1.1.9001 (development)
+# crew.cluster 0.1.2
 
-* Require `crew` >= 0.4.0.
+* Require `crew` >= 0.5.0.
 * Add a new `slurm_time_minutes` for SLURM wall time (#1, @cfljam).
 * Enable TLS.
-* Use MB format for memory in SLURM launcher (#22, @kendonB). 
+* Use MB format for memory in SLURM launcher (#22, @kendonB).
+* Use `launch_max` and `crew_tls()` from `crew` 0.5.0.
 
 # crew.cluster 0.1.1
 

R/crew_controller_lsf.R

@@ -26,7 +26,8 @@ crew_controller_lsf <- function(
   workers = 1L,
   host = NULL,
   port = NULL,
-  tls_enable = FALSE,
+  tls = crew::crew_tls(),
+  tls_enable = NULL,
   tls_config = NULL,
   seconds_interval = 0.25,
   seconds_timeout = 10,
@@ -40,6 +41,7 @@ crew_controller_lsf <- function(
   reset_packages = FALSE,
   reset_options = FALSE,
   garbage_collection = FALSE,
+  launch_max = 5L,
   verbose = FALSE,
   command_submit = as.character(Sys.which("bsub")),
   command_delete = as.character(Sys.which("bkill")),
@@ -57,6 +59,7 @@ crew_controller_lsf <- function(
     workers = workers,
     host = host,
     port = port,
+    tls = tls,
     tls_enable = tls_enable,
     tls_config = tls_config,
     seconds_interval = seconds_interval,
@@ -75,6 +78,8 @@ crew_controller_lsf <- function(
     reset_packages = reset_packages,
     reset_options = reset_options,
     garbage_collection = garbage_collection,
+    launch_max = launch_max,
+    tls = tls,
     verbose = verbose,
     command_submit = command_submit,
     command_delete = command_delete,

R/crew_controller_pbs.R

@@ -22,7 +22,8 @@ crew_controller_pbs <- function(
   workers = 1L,
   host = NULL,
   port = NULL,
-  tls_enable = FALSE,
+  tls = crew::crew_tls(),
+  tls_enable = NULL,
   tls_config = NULL,
   seconds_interval = 0.25,
   seconds_timeout = 10,
@@ -36,6 +37,7 @@ crew_controller_pbs <- function(
   reset_packages = FALSE,
   reset_options = FALSE,
   garbage_collection = FALSE,
+  launch_max = 5L,
   verbose = FALSE,
   command_submit = as.character(Sys.which("qsub")),
   command_delete = as.character(Sys.which("qdel")),
@@ -54,6 +56,7 @@ crew_controller_pbs <- function(
     workers = workers,
     host = host,
     port = port,
+    tls = tls,
     tls_enable = tls_enable,
     tls_config = tls_config,
     seconds_interval = seconds_interval,
@@ -72,6 +75,8 @@ crew_controller_pbs <- function(
     reset_packages = reset_packages,
     reset_options = reset_options,
     garbage_collection = garbage_collection,
+    launch_max = launch_max,
+    tls = tls,
     verbose = verbose,
     command_submit = command_submit,
     command_delete = command_delete,

R/crew_controller_sge.R

@@ -22,7 +22,8 @@ crew_controller_sge <- function(
   workers = 1L,
   host = NULL,
   port = NULL,
-  tls_enable = FALSE,
+  tls = crew::crew_tls(),
+  tls_enable = NULL,
   tls_config = NULL,
   seconds_interval = 0.25,
   seconds_timeout = 10,
@@ -36,6 +37,7 @@ crew_controller_sge <- function(
   reset_packages = FALSE,
   reset_options = FALSE,
   garbage_collection = FALSE,
+  launch_max = 5L,
   verbose = FALSE,
   command_submit = as.character(Sys.which("qsub")),
   command_delete = as.character(Sys.which("qdel")),
@@ -56,6 +58,7 @@ crew_controller_sge <- function(
     workers = workers,
     host = host,
     port = port,
+    tls = tls,
     tls_enable = tls_enable,
     tls_config = tls_config,
     seconds_interval = seconds_interval,
@@ -74,6 +77,8 @@ crew_controller_sge <- function(
     reset_packages = reset_packages,
     reset_options = reset_options,
     garbage_collection = garbage_collection,
+    launch_max = launch_max,
+    tls = tls,
     verbose = verbose,
     command_submit = command_submit,
     command_delete = command_delete,

R/crew_controller_slurm.R

@@ -26,7 +26,8 @@ crew_controller_slurm <- function(
   workers = 1L,
   host = NULL,
   port = NULL,
-  tls_enable = FALSE,
+  tls = crew::crew_tls(),
+  tls_enable = NULL,
   tls_config = NULL,
   seconds_interval = 0.25,
   seconds_timeout = 10,
@@ -40,6 +41,7 @@ crew_controller_slurm <- function(
   reset_packages = FALSE,
   reset_options = FALSE,
   garbage_collection = FALSE,
+  launch_max = 5L,
   verbose = FALSE,
   command_submit = as.character(Sys.which("sbatch")),
   command_delete = as.character(Sys.which("scancel")),
@@ -56,6 +58,7 @@ crew_controller_slurm <- function(
     workers = workers,
     host = host,
     port = port,
+    tls = tls,
     tls_enable = tls_enable,
     tls_config = tls_config,
     seconds_interval = seconds_interval,
@@ -74,6 +77,8 @@ crew_controller_slurm <- function(
     reset_packages = reset_packages,
     reset_options = reset_options,
     garbage_collection = garbage_collection,
+    launch_max = launch_max,
+    tls = tls,
     verbose = verbose,
     command_submit = command_submit,
     command_delete = command_delete,

R/crew_launcher_cluster.R

@@ -44,6 +44,8 @@ crew_launcher_cluster <- function(
   reset_packages = FALSE,
   reset_options = FALSE,
   garbage_collection = FALSE,
+  launch_max = 5L,
+  tls = crew::crew_tls(),
   verbose = FALSE,
   command_submit = "",
   command_delete = "",
@@ -64,6 +66,8 @@ crew_launcher_cluster <- function(
     reset_packages = reset_packages,
     reset_options = reset_options,
     garbage_collection = garbage_collection,
+    launch_max = launch_max,
+    tls = tls,
     verbose = verbose,
     command_submit = command_submit,
     command_delete = command_delete,
@@ -111,6 +115,8 @@ crew_class_launcher_cluster <- R6::R6Class(
     #' @param reset_packages See [crew_launcher_cluster()].
     #' @param reset_options See [crew_launcher_cluster()].
     #' @param garbage_collection See [crew_launcher_cluster()].
+    #' @param launch_max See [crew_launcher_cluster()].
+    #' @param tls See [crew_launcher_cluster()].
     #' @param verbose See [crew_launcher_cluster()].
     #' @param command_submit See [crew_launcher_cluster()].
     #' @param command_delete See [crew_launcher_cluster()].
@@ -129,6 +135,8 @@ crew_class_launcher_cluster <- R6::R6Class(
       reset_packages = NULL,
       reset_options = NULL,
       garbage_collection = NULL,
+      launch_max = NULL,
+      tls = NULL,
       verbose = NULL,
       command_submit = NULL,
       command_delete = NULL,
@@ -147,7 +155,9 @@ crew_class_launcher_cluster <- R6::R6Class(
         reset_globals = reset_globals,
         reset_packages = reset_packages,
         reset_options = reset_options,
-        garbage_collection = garbage_collection
+        garbage_collection = garbage_collection,
+        launch_max = launch_max,
+        tls = tls
       )
       self$verbose <- verbose
       self$command_submit <- command_submit

R/crew_launcher_lsf.R

@@ -68,6 +68,8 @@ crew_launcher_lsf <- function(
   reset_packages = FALSE,
   reset_options = FALSE,
   garbage_collection = FALSE,
+  launch_max = 5L,
+  tls = crew::crew_tls(),
   verbose = FALSE,
   command_submit = as.character(Sys.which("bsub")),
   command_delete = as.character(Sys.which("bkill")),
@@ -94,6 +96,8 @@ crew_launcher_lsf <- function(
     reset_packages = reset_packages,
     reset_options = reset_options,
     garbage_collection = garbage_collection,
+    launch_max = launch_max,
+    tls = tls,
     verbose = verbose,
     command_submit = command_submit,
     command_delete = command_delete,
@@ -147,6 +151,8 @@ crew_class_launcher_lsf <- R6::R6Class(
     #' @param reset_packages See [crew_launcher_lsf()].
     #' @param reset_options See [crew_launcher_lsf()].
     #' @param garbage_collection See [crew_launcher_lsf()].
+    #' @param launch_max See [crew_launcher_lsf()].
+    #' @param tls See [crew_launcher_lsf()].
     #' @param verbose See [crew_launcher_lsf()].
     #' @param command_submit See [crew_launcher_lsf()].
     #' @param command_delete See [crew_launcher_lsf()].
@@ -171,6 +177,8 @@ crew_class_launcher_lsf <- R6::R6Class(
       reset_packages = NULL,
       reset_options = NULL,
       garbage_collection = NULL,
+      launch_max = NULL,
+      tls = NULL,
       verbose = NULL,
       command_submit = NULL,
       command_delete = NULL,
@@ -196,6 +204,8 @@ crew_class_launcher_lsf <- R6::R6Class(
         reset_packages = reset_packages,
         reset_options = reset_options,
         garbage_collection = garbage_collection,
+        launch_max = launch_max,
+        tls = tls,
         verbose = verbose,
         command_submit = command_submit,
         command_delete = command_delete,

R/crew_launcher_pbs.R

@@ -73,6 +73,8 @@ crew_launcher_pbs <- function(
   reset_packages = FALSE,
   reset_options = FALSE,
   garbage_collection = FALSE,
+  launch_max = 5L,
+  tls = crew::crew_tls(),
   verbose = FALSE,
   command_submit = as.character(Sys.which("qsub")),
   command_delete = as.character(Sys.which("qdel")),
@@ -100,6 +102,8 @@ crew_launcher_pbs <- function(
     reset_packages = reset_packages,
     reset_options = reset_options,
     garbage_collection = garbage_collection,
+    launch_max = launch_max,
+    tls = tls,
     verbose = verbose,
     command_submit = command_submit,
     command_delete = command_delete,
@@ -156,6 +160,8 @@ crew_class_launcher_pbs <- R6::R6Class(
     #' @param reset_packages See [crew_launcher_pbs()].
     #' @param reset_options See [crew_launcher_pbs()].
     #' @param garbage_collection See [crew_launcher_pbs()].
+    #' @param launch_max See [crew_launcher_pbs()].
+    #' @param tls See [crew_launcher_pbs()].
     #' @param verbose See [crew_launcher_pbs()].
     #' @param command_submit See [crew_launcher_pbs()].
     #' @param command_delete See [crew_launcher_pbs()].
@@ -181,6 +187,8 @@ crew_class_launcher_pbs <- R6::R6Class(
       reset_packages = NULL,
       reset_options = NULL,
       garbage_collection = NULL,
+      launch_max = NULL,
+      tls = NULL,
       verbose = NULL,
       command_submit = NULL,
       command_delete = NULL,
@@ -207,6 +215,8 @@ crew_class_launcher_pbs <- R6::R6Class(
         reset_packages = reset_packages,
         reset_options = reset_options,
         garbage_collection = garbage_collection,
+        launch_max = launch_max,
+        tls = tls,
         verbose = verbose,
         command_submit = command_submit,
         command_delete = command_delete,

R/crew_launcher_sge.R

@@ -75,6 +75,8 @@ crew_launcher_sge <- function(
   reset_packages = FALSE,
   reset_options = FALSE,
   garbage_collection = FALSE,
+  launch_max = 5L,
+  tls = crew::crew_tls(),
   verbose = FALSE,
   command_submit = as.character(Sys.which("qsub")),
   command_delete = as.character(Sys.which("qdel")),
@@ -104,6 +106,8 @@ crew_launcher_sge <- function(
     reset_packages = reset_packages,
     reset_options = reset_options,
     garbage_collection = garbage_collection,
+    launch_max = launch_max,
+    tls = tls,
     verbose = verbose,
     command_submit = command_submit,
     command_delete = command_delete,
@@ -166,6 +170,8 @@ crew_class_launcher_sge <- R6::R6Class(
     #' @param reset_packages See [crew_launcher_sge()].
     #' @param reset_options See [crew_launcher_sge()].
     #' @param garbage_collection See [crew_launcher_sge()].
+    #' @param launch_max See [crew_launcher_sge()].
+    #' @param tls See [crew_launcher_sge()].
     #' @param verbose See [crew_launcher_sge()].
     #' @param command_submit See [crew_launcher_sge()].
     #' @param command_delete See [crew_launcher_sge()].
@@ -193,6 +199,8 @@ crew_class_launcher_sge <- R6::R6Class(
       reset_packages = NULL,
       reset_options = NULL,
       garbage_collection = NULL,
+      launch_max = NULL,
+      tls = NULL,
       verbose = NULL,
       command_submit = NULL,
       command_delete = NULL,
@@ -221,6 +229,8 @@ crew_class_launcher_sge <- R6::R6Class(
         reset_packages = reset_packages,
         reset_options = reset_options,
         garbage_collection = garbage_collection,
+        launch_max = launch_max,
+        tls = tls,
         verbose = verbose,
         command_submit = command_submit,
         command_delete = command_delete,