From bc82c5690193a28e5a7a9e88efa6f69a18b44af5 Mon Sep 17 00:00:00 2001
From: Tim Cadman <41470917+timcadman@users.noreply.github.com>
Date: Tue, 9 Dec 2025 10:54:38 +0100
Subject: [PATCH 01/11] refactor: dscolnames

---
 R/ds.colnames.R                       | 65 ++++++++++-----------------
 tests/testthat/test-smk-ds.colnames.R |  2 +-
 2 files changed, 24 insertions(+), 43 deletions(-)

diff --git a/R/ds.colnames.R b/R/ds.colnames.R
index a4b98b1ad..15ee5088e 100644
--- a/R/ds.colnames.R
+++ b/R/ds.colnames.R
@@ -1,81 +1,62 @@
 #'
 #' @title Produces column names of the R object in the server-side
-#' @description Retrieves column names of an R object on the server-side.  
+#' @description Retrieves column names of an R object on the server-side.
 #' This function is similar to R function \code{colnames}.
-#' @details The input is restricted to the object of type \code{data.frame} or \code{matrix}. 
-#' 
+#' @details The input is restricted to the object of type \code{data.frame} or \code{matrix}.
+#'
 #' Server function called: \code{colnamesDS}
 #' @param x a character string providing the name of the input data frame or matrix.
-#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. 
+#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login.
 #' If the \code{datasources} argument is not specified
 #' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.
-#' @return \code{ds.colnames} returns the column names of 
-#' the specified server-side data frame or matrix. 
+#' @return \code{ds.colnames} returns the column names of
+#' the specified server-side data frame or matrix.
 #' @author DataSHIELD Development Team
 #' @seealso \code{\link{ds.dim}} to obtain the dimensions of a matrix or a data frame.
-#' @examples 
+#' @examples
 #' \dontrun{
-#' 
+#'
 #'   ## Version 6, for version 5 see the Wiki
 #'   # Connecting to the Opal servers
-#' 
+#'
 #'   require('DSI')
 #'   require('DSOpal')
 #'   require('dsBaseClient')
-#' 
+#'
 #'   builder <- DSI::newDSLoginBuilder()
-#'   builder$append(server = "study1", 
-#'                  url = "http://192.168.56.100:8080/", 
-#'                  user = "administrator", password = "datashield_test&", 
+#'   builder$append(server = "study1",
+#'                  url = "http://192.168.56.100:8080/",
+#'                  user = "administrator", password = "datashield_test&",
 #'                  table = "CNSIM.CNSIM1", driver = "OpalDriver")
-#'   builder$append(server = "study2", 
-#'                  url = "http://192.168.56.100:8080/", 
-#'                  user = "administrator", password = "datashield_test&", 
+#'   builder$append(server = "study2",
+#'                  url = "http://192.168.56.100:8080/",
+#'                  user = "administrator", password = "datashield_test&",
 #'                  table = "CNSIM.CNSIM2", driver = "OpalDriver")
 #'   builder$append(server = "study3",
-#'                  url = "http://192.168.56.100:8080/", 
-#'                  user = "administrator", password = "datashield_test&", 
+#'                  url = "http://192.168.56.100:8080/",
+#'                  user = "administrator", password = "datashield_test&",
 #'                  table = "CNSIM.CNSIM3", driver = "OpalDriver")
 #'   logindata <- builder$build()
-#'   
+#'
 #'   # Log onto the remote Opal training servers
-#'   connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") 
-#' 
+#'   connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D")
+#'
 #'   # Getting column names of the R objects stored in the server-side
 #'   ds.colnames(x = "D",
 #'               datasources = connections[1]) #only the first server ("study1") is used
 #'   # Clear the Datashield R sessions and logout
-#'   datashield.logout(connections) 
+#'   datashield.logout(connections)
 #' }
 #' @export
 #'
 ds.colnames <- function(x=NULL, datasources=NULL) {
 
-  # look for DS connections
-  if(is.null(datasources)){
-    datasources <- datashield.connections_find()
-  }
-
-  # ensure datasources is a list of DSConnection-class
-  if(!(is.list(datasources) && all(unlist(lapply(datasources, function(d) {methods::is(d,"DSConnection")}))))){
-    stop("The 'datasources' were expected to be a list of DSConnection-class objects", call.=FALSE)
-  }
+  .set_datasources(datasources)
 
   if(is.null(x)){
     stop("Please provide the name of a data.frame or matrix!", call.=FALSE)
   }
 
-  # check if the input object(s) is(are) defined in all the studies
-  defined <- isDefined(datasources, x)
-
-  # call the internal function that checks the input object is of the same class in all studies.
-  typ <- checkClass(datasources, x)
-
-  # if the input object is not a matrix or a dataframe stop
-  if(!('data.frame' %in% typ) & !('matrix' %in% typ)){
-    stop("The input vector must be of type 'data.frame' or a 'matrix'!", call.=FALSE)
-  }
-
   cally <- call("colnamesDS", x)
   column_names <- DSI::datashield.aggregate(datasources, cally)
 
diff --git a/tests/testthat/test-smk-ds.colnames.R b/tests/testthat/test-smk-ds.colnames.R
index b7d289ac3..6196951a0 100644
--- a/tests/testthat/test-smk-ds.colnames.R
+++ b/tests/testthat/test-smk-ds.colnames.R
@@ -47,7 +47,7 @@ test_that("simple colnames", {
 test_that("fails if the object does not exist", {
   expect_error(
     ds.colnames("non_existing_df"),
-    regexp = "The input object non_existing_df is not defined in sim1, sim2, sim3!",
+    regexp = "object 'non_existing_df' not found",
     ignore.case = TRUE
   )
 })

From 801c2cb02b522b50e8835f7ada9f595d19825f5a Mon Sep 17 00:00:00 2001
From: Tim Cadman <41470917+timcadman@users.noreply.github.com>
Date: Tue, 9 Dec 2025 11:05:07 +0100
Subject: [PATCH 02/11] refactor: moved utility functions to separate file

---
 R/utils.R | 51 +++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 51 insertions(+)
 create mode 100644 R/utils.R

diff --git a/R/utils.R b/R/utils.R
new file mode 100644
index 000000000..85d8d7e2f
--- /dev/null
+++ b/R/utils.R
@@ -0,0 +1,51 @@
+#' Retrieve datasources if not specified
+#'
+#' @param datasources An optional list of data sources. If not provided, the function will attempt
+#' to find available data sources.
+#' @importFrom DSI datashield.connections_find
+#' @return A list of data sources.
+#' @noRd
+.get_datasources <- function(datasources) {
+  if (is.null(datasources)) {
+    datasources <- datashield.connections_find()
+  }
+  return(datasources)
+}
+
+#' Verify that the provided data sources are of class 'DSConnection'.
+#'
+#' @param datasources A list of data sources.
+#' @importFrom cli cli_abort
+#' @noRd
+.verify_datasources <- function(datasources) {
+  is_connection_class <- sapply(datasources, function(x) inherits(unlist(x), "DSConnection"))
+  if (!all(is_connection_class)) {
+    cli_abort("The 'datasources' were expected to be a list of DSConnection-class objects")
+  }
+}
+
+#' Set and verify data sources.
+#'
+#' @param datasources An optional list of data sources. If not provided, the function will attempt
+#' to find available data sources.
+#' @return A list of verified data sources.
+#' @noRd
+.set_datasources <- function(datasources) {
+  datasources <- .get_datasources(datasources)
+  .verify_datasources(datasources)
+  return(datasources)
+}
+
+#' Check That a Data Frame Name Is Provided
+#'
+#' Internal helper that checks whether a data frame or matrix object
+#' has been provided. If `NULL`, it aborts with a user-friendly error.
+#'
+#' @param df A data.frame or matrix.
+#' @return Invisibly returns `NULL`. Called for its side effect (error checking).
+#' @noRd
+.check_df_name_provided <- function(df) {
+  if(is.null(df)){
+    cli_abort("Please provide the name of a data.frame or matrix!", call.=FALSE)
+  }
+}

From 33498ca4c185719a68657d10ba32b3aa46aefeba Mon Sep 17 00:00:00 2001
From: Tim Cadman <41470917+timcadman@users.noreply.github.com>
Date: Tue, 9 Dec 2025 11:05:44 +0100
Subject: [PATCH 03/11] refactor: call common checking functions from separate
 file

---
 R/ds.colnames.R | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/R/ds.colnames.R b/R/ds.colnames.R
index 15ee5088e..a808bf0e2 100644
--- a/R/ds.colnames.R
+++ b/R/ds.colnames.R
@@ -52,14 +52,10 @@
 ds.colnames <- function(x=NULL, datasources=NULL) {
 
   .set_datasources(datasources)
-
-  if(is.null(x)){
-    stop("Please provide the name of a data.frame or matrix!", call.=FALSE)
-  }
+  .check_df_name_provided(x)
 
   cally <- call("colnamesDS", x)
   column_names <- DSI::datashield.aggregate(datasources, cally)
-
   return(column_names)
 
 }

From 9fa00d4fd8c4da4f1c1216c6feb33bfc785931f9 Mon Sep 17 00:00:00 2001
From: Tim Cadman <41470917+timcadman@users.noreply.github.com>
Date: Tue, 9 Dec 2025 11:06:23 +0100
Subject: [PATCH 04/11] forgot to save file

---
 R/ds.colnames.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/ds.colnames.R b/R/ds.colnames.R
index a808bf0e2..c05621a9d 100644
--- a/R/ds.colnames.R
+++ b/R/ds.colnames.R
@@ -55,7 +55,7 @@ ds.colnames <- function(x=NULL, datasources=NULL) {
   .check_df_name_provided(x)
 
   cally <- call("colnamesDS", x)
-  column_names <- DSI::datashield.aggregate(datasources, cally)
+  column_names <- DSI::datashield.aggregate(datasources, cally)§
   return(column_names)
 
 }

From 039536aacce0c3f39e7959f34af025bee0be7198 Mon Sep 17 00:00:00 2001
From: Tim Cadman <41470917+timcadman@users.noreply.github.com>
Date: Tue, 9 Dec 2025 12:44:02 +0100
Subject: [PATCH 05/11] refactor: also move the argument check to different
 file as will be reused

---
 R/ds.colnames.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/ds.colnames.R b/R/ds.colnames.R
index c05621a9d..a808bf0e2 100644
--- a/R/ds.colnames.R
+++ b/R/ds.colnames.R
@@ -55,7 +55,7 @@ ds.colnames <- function(x=NULL, datasources=NULL) {
   .check_df_name_provided(x)
 
   cally <- call("colnamesDS", x)
-  column_names <- DSI::datashield.aggregate(datasources, cally)§
+  column_names <- DSI::datashield.aggregate(datasources, cally)
   return(column_names)
 
 }

From 5ccfa5c7fa77f023c124ef6c77c95dc4c75c56ed Mon Sep 17 00:00:00 2001
From: Tim Cadman <41470917+timcadman@users.noreply.github.com>
Date: Tue, 9 Dec 2025 13:57:26 +0100
Subject: [PATCH 06/11] added PR template

---
 PULL_REQUEST_TEMPLATE.md.R | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100644 PULL_REQUEST_TEMPLATE.md.R

diff --git a/PULL_REQUEST_TEMPLATE.md.R b/PULL_REQUEST_TEMPLATE.md.R
new file mode 100644
index 000000000..da53784e0
--- /dev/null
+++ b/PULL_REQUEST_TEMPLATE.md.R
@@ -0,0 +1,25 @@
+## Instructions & checklist for PR author
+
+### Description of changes
+[Add a description of what they have changed]
+
+### Refactor instructions
+- [ ] Removed `exists` and `isDefined` from clientside function and add appropriate checks on server-side function
+- [ ] Removed any client-side code checking whether an object has been successfully created
+- [ ] Reviewed code to determine if additional refactoring could reduce calls to server-side package
+- [ ] Replaced check relating to datashield connections object with `.set_datasources()` (defined in `utils.r`)
+- [ ] If relevant, replaced argument check that dataset name has been provided to `.check_df_name_provided()` (defined in `utils.r`)
+
+### Testing instructions
+- [ ] Writen client-side unit tests for unhappy flow
+- [ ] Run `devtools::test(filter = "smk-|disc|arg")` and check it passes
+- [ ] Run `devtools::check(args = '--no-tests')` and check it passes (we run tests separately to skip performance checks)
+- [ ] Run `devtools::build()` and check it builds without errors
+
+## Instructions & checklist for PR reviewers
+- [ ] Checkout this branch as well as the corresponding branch of dsBase
+- [ ] Review the code and suggest any changes
+- [ ] Install the dsBase branch on an Armadillo or Opal test server
+- [ ] Run `devtools::test(filter = "smk-|disc|arg")` and check it passes
+- [ ] Run `devtools::check(args = '--no-tests')` and check it passes (we run tests separately to skip performance checks)
+- [ ] Run `devtools::build()` and check it builds without errors

From 5bef61d967aefc7afe07ed96e6ffd4b6369f442b Mon Sep 17 00:00:00 2001
From: Stuart Wheater <stuart.wheater@arjuna.com>
Date: Sun, 14 Dec 2025 17:35:27 +0000
Subject: [PATCH 07/11] Various fixes including ds.colnames, datasources
 handling

---
 .Rbuildignore                         |  1 +
 DESCRIPTION                           |  1 +
 NAMESPACE                             |  2 ++
 R/ds.colnames.R                       |  2 +-
 man/ds.colnames.Rd                    | 30 +++++++++++++--------------
 tests/testthat/test-smk-ds.colnames.R |  3 ++-
 6 files changed, 22 insertions(+), 17 deletions(-)

diff --git a/.Rbuildignore b/.Rbuildignore
index 5fa089287..8fa96f42d 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -15,6 +15,7 @@
 ^docker-compose_opal\.yml$
 ^docker-compose\.yml$
 ^R/secure.global.ranking.md$
+^PULL_REQUEST_TEMPLATE\.md\.R$
 ^_pkgdown\.yml$
 ^docs$
 ^dsBase_7.0.0\.tar\.gz$
diff --git a/DESCRIPTION b/DESCRIPTION
index ad8e28a6d..1c9a0595d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -69,6 +69,7 @@ Imports:
     gridExtra,
     data.table,
     methods,
+    cli,
     dplyr
 Suggests:
     lme4,
diff --git a/NAMESPACE b/NAMESPACE
index 8bdab82e9..bd539a118 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -119,6 +119,8 @@ export(ds.var)
 export(ds.vectorCalc)
 import(DSI)
 import(data.table)
+importFrom(DSI,datashield.connections_find)
+importFrom(cli,cli_abort)
 importFrom(stats,as.formula)
 importFrom(stats,na.omit)
 importFrom(stats,ts)
diff --git a/R/ds.colnames.R b/R/ds.colnames.R
index a808bf0e2..8bfddcb47 100644
--- a/R/ds.colnames.R
+++ b/R/ds.colnames.R
@@ -51,7 +51,7 @@
 #'
 ds.colnames <- function(x=NULL, datasources=NULL) {
 
-  .set_datasources(datasources)
+  datasources <- .set_datasources(datasources)
   .check_df_name_provided(x)
 
   cally <- call("colnamesDS", x)
diff --git a/man/ds.colnames.Rd b/man/ds.colnames.Rd
index e73910812..9460a567f 100644
--- a/man/ds.colnames.Rd
+++ b/man/ds.colnames.Rd
@@ -9,20 +9,20 @@ ds.colnames(x = NULL, datasources = NULL)
 \arguments{
 \item{x}{a character string providing the name of the input data frame or matrix.}
 
-\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. 
+\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login.
 If the \code{datasources} argument is not specified
 the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.}
 }
 \value{
-\code{ds.colnames} returns the column names of 
+\code{ds.colnames} returns the column names of
 the specified server-side data frame or matrix.
 }
 \description{
-Retrieves column names of an R object on the server-side.  
+Retrieves column names of an R object on the server-side.
 This function is similar to R function \code{colnames}.
 }
 \details{
-The input is restricted to the object of type \code{data.frame} or \code{matrix}. 
+The input is restricted to the object of type \code{data.frame} or \code{matrix}.
 
 Server function called: \code{colnamesDS}
 }
@@ -37,28 +37,28 @@ Server function called: \code{colnamesDS}
   require('dsBaseClient')
 
   builder <- DSI::newDSLoginBuilder()
-  builder$append(server = "study1", 
-                 url = "http://192.168.56.100:8080/", 
-                 user = "administrator", password = "datashield_test&", 
+  builder$append(server = "study1",
+                 url = "http://192.168.56.100:8080/",
+                 user = "administrator", password = "datashield_test&",
                  table = "CNSIM.CNSIM1", driver = "OpalDriver")
-  builder$append(server = "study2", 
-                 url = "http://192.168.56.100:8080/", 
-                 user = "administrator", password = "datashield_test&", 
+  builder$append(server = "study2",
+                 url = "http://192.168.56.100:8080/",
+                 user = "administrator", password = "datashield_test&",
                  table = "CNSIM.CNSIM2", driver = "OpalDriver")
   builder$append(server = "study3",
-                 url = "http://192.168.56.100:8080/", 
-                 user = "administrator", password = "datashield_test&", 
+                 url = "http://192.168.56.100:8080/",
+                 user = "administrator", password = "datashield_test&",
                  table = "CNSIM.CNSIM3", driver = "OpalDriver")
   logindata <- builder$build()
-  
+
   # Log onto the remote Opal training servers
-  connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") 
+  connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D")
 
   # Getting column names of the R objects stored in the server-side
   ds.colnames(x = "D",
               datasources = connections[1]) #only the first server ("study1") is used
   # Clear the Datashield R sessions and logout
-  datashield.logout(connections) 
+  datashield.logout(connections)
 }
 }
 \seealso{
diff --git a/tests/testthat/test-smk-ds.colnames.R b/tests/testthat/test-smk-ds.colnames.R
index 6196951a0..09e57946a 100644
--- a/tests/testthat/test-smk-ds.colnames.R
+++ b/tests/testthat/test-smk-ds.colnames.R
@@ -47,7 +47,8 @@ test_that("simple colnames", {
 test_that("fails if the object does not exist", {
   expect_error(
     ds.colnames("non_existing_df"),
-    regexp = "object 'non_existing_df' not found",
+#    regexp = "object 'non_existing_df' not found",
+    regexp = "There are some DataSHIELD errors, list them with datashield.errors()",
     ignore.case = TRUE
   )
 })

From e1e31f9e01fbb8fd79079d4c1e0256e747a9bc4f Mon Sep 17 00:00:00 2001
From: Tim Cadman <41470917+timcadman@users.noreply.github.com>
Date: Mon, 15 Dec 2025 10:21:05 +0100
Subject: [PATCH 08/11] test: added tests for utils file

---
 tests/testthat/test-smk-utils.R | 139 ++++++++++++++++++++++++++++++++
 1 file changed, 139 insertions(+)
 create mode 100644 tests/testthat/test-smk-utils.R

diff --git a/tests/testthat/test-smk-utils.R b/tests/testthat/test-smk-utils.R
new file mode 100644
index 000000000..f220fb4ed
--- /dev/null
+++ b/tests/testthat/test-smk-utils.R
@@ -0,0 +1,139 @@
+library(testthat)
+library(DSI)
+library(cli)
+
+library(testthat)
+library(mockery)
+library(cli)
+library(testthat)
+library(mockery)
+library(cli)
+
+if (!isClass("DSConnection")) {
+  setClass("DSConnection", contains = "VIRTUAL")
+}
+
+setClass("MockDSConnection", contains = "DSConnection")
+mock_ds_conn <- new("MockDSConnection")
+
+test_that(".get_datasources retrieves connections when input is NULL", {
+
+  mock_connections <- list(
+    server1 = mock_ds_conn,
+    server2 = mock_ds_conn
+  )
+
+  stub(.get_datasources, "datashield.connections_find", mock_connections)
+
+  result <- .get_datasources(NULL)
+
+  expect_type(result, "list")
+  expect_length(result, 2)
+  expect_named(result, c("server1", "server2"))
+  expect_true(is(result$server1, "DSConnection"))
+})
+
+test_that(".get_datasources returns input when provided", {
+
+  input_datasources <- list(A = "connA", B = "connB")
+
+  result <- with_mocked_bindings(
+    datashield.connections_find = function() stop("Should not be called!"),
+    .get_datasources(input_datasources),
+    .package = "dsBaseClient"
+  )
+
+  expect_equal(result, input_datasources)
+})
+
+test_that(".verify_datasources passes with valid DSConnection list", {
+
+  valid_datasources <- list(
+    conn_list1 = mock_ds_conn,
+    conn_list2 = mock_ds_conn
+  )
+
+  expect_no_error(.verify_datasources(valid_datasources))
+  expect_null(.verify_datasources(valid_datasources))
+})
+
+test_that(".verify_datasources aborts with invalid object types", {
+
+  invalid_datasources <- list(
+    conn_list1 = mock_ds_conn,
+    conn_list2 = "not_a_connection"
+  )
+
+  expect_error(
+    .verify_datasources(invalid_datasources)
+  )
+})
+
+test_that(".set_datasources works with valid input", {
+
+  input_datasources <- list(
+    mock_ds_conn
+  )
+
+  result <- with_mocked_bindings(
+    .get_datasources = function(d) d,
+    .verify_datasources = function(d) {},
+    .set_datasources(input_datasources),
+    .package = "dsBaseClient"
+  )
+
+  expect_equal(result, input_datasources)
+})
+
+test_that(".set_datasources calls .get_datasources and .verify_datasources", {
+
+  get_called <- FALSE
+  verify_called <- FALSE
+
+  mock_get <- function(d) {
+    get_called <<- TRUE
+    return(list(list(mock_ds_conn)))
+  }
+
+  mock_verify <- function(d) {
+    verify_called <<- TRUE
+  }
+
+  with_mocked_bindings(
+    .get_datasources = mock_get,
+    .verify_datasources = mock_verify,
+    .set_datasources(NULL),
+    .package = "dsBaseClient"
+  )
+
+  expect_true(get_called)
+  expect_true(verify_called)
+})
+
+test_that(".set_datasources aborts if verification fails", {
+
+  expect_error(
+    with_mocked_bindings(
+      .get_datasources = function(d) list(list("bad_conn")),
+      .verify_datasources = function(d) cli::cli_abort("Verification failed mock"),
+      .set_datasources(NULL),
+      .package = "dsBaseClient"
+    )
+  )
+})
+
+test_that(".check_df_name_provided passes when df is not NULL", {
+
+  expect_no_error(.check_df_name_provided("D"))
+  expect_null(.check_df_name_provided("D"))
+
+  expect_no_error(.check_df_name_provided(data.frame(a=1)))
+})
+
+test_that(".check_df_name_provided aborts when df is NULL", {
+
+  expect_error(
+    .check_df_name_provided(NULL)
+  )
+})
+

From 58b24b8e29ba20557867c4ba4249c4455532e3b1 Mon Sep 17 00:00:00 2001
From: Tim Cadman <41470917+timcadman@users.noreply.github.com>
Date: Mon, 15 Dec 2025 13:58:45 +0100
Subject: [PATCH 09/11] added missing dependency

---
 DESCRIPTION | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 1c9a0595d..a38b3ec13 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -81,7 +81,8 @@ Suggests:
     DescTools,
     DSOpal,
     DSMolgenisArmadillo,
-    DSLite
+    DSLite, 
+    mockery
 RoxygenNote: 7.3.3
 Encoding: UTF-8
 Language: en-GB

From 50e1caf443c83779de01fca94177321c198075b7 Mon Sep 17 00:00:00 2001
From: Tim Cadman <41470917+timcadman@users.noreply.github.com>
Date: Tue, 16 Dec 2025 15:28:01 +0100
Subject: [PATCH 10/11] docs: added reference to performance in pr template

---
 PULL_REQUEST_TEMPLATE.md.R => PULL_REQUEST_TEMPLATE.md | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)
 rename PULL_REQUEST_TEMPLATE.md.R => PULL_REQUEST_TEMPLATE.md (80%)

diff --git a/PULL_REQUEST_TEMPLATE.md.R b/PULL_REQUEST_TEMPLATE.md
similarity index 80%
rename from PULL_REQUEST_TEMPLATE.md.R
rename to PULL_REQUEST_TEMPLATE.md
index da53784e0..8510656db 100644
--- a/PULL_REQUEST_TEMPLATE.md.R
+++ b/PULL_REQUEST_TEMPLATE.md
@@ -13,8 +13,9 @@
 ### Testing instructions
 - [ ] Writen client-side unit tests for unhappy flow
 - [ ] Run `devtools::test(filter = "smk-|disc|arg")` and check it passes
-- [ ] Run `devtools::check(args = '--no-tests')` and check it passes (we run tests separately to skip performance checks)
+- [ ] Run `devtools::check(args = '--no-tests')` and check it passes
 - [ ] Run `devtools::build()` and check it builds without errors
+- [ ] Check that the continuous integration checks pass on the pull request branch. Note that the performance test relating to your function may fail, as failure is also triggered by a dramatic improval in performance! 
 
 ## Instructions & checklist for PR reviewers
 - [ ] Checkout this branch as well as the corresponding branch of dsBase
@@ -23,3 +24,4 @@
 - [ ] Run `devtools::test(filter = "smk-|disc|arg")` and check it passes
 - [ ] Run `devtools::check(args = '--no-tests')` and check it passes (we run tests separately to skip performance checks)
 - [ ] Run `devtools::build()` and check it builds without errors
+- [ ] Check that the continuous integration checks pass on the pull request branch (see above note on performance checks)

From 1613471b2a059cd962be9677e97216e14d1ea7dd Mon Sep 17 00:00:00 2001
From: Stuart Wheater <stuart.wheater@arjuna.com>
Date: Tue, 16 Dec 2025 14:32:46 +0000
Subject: [PATCH 11/11] Increase 'rate' upper limit

---
 .../perf_files/default_perf_profile.csv       | 26 +++++++++----------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/tests/testthat/perf_files/default_perf_profile.csv b/tests/testthat/perf_files/default_perf_profile.csv
index 9f1ae6e5e..a4669eac7 100644
--- a/tests/testthat/perf_files/default_perf_profile.csv
+++ b/tests/testthat/perf_files/default_perf_profile.csv
@@ -1,14 +1,14 @@
 "refer_name","rate","lower_tolerance","upper_tolerance"
-"conndisconn::perf::simple0","0.2725","0.5","2"
-"ds.abs::perf::0","2.677","0.5","2"
-"ds.asInteger::perf:0","2.294","0.5","2"
-"ds.asList::perf:0","4.587","0.5","2"
-"ds.asNumeric::perf:0","2.185","0.5","2"
-"ds.assign::perf::0","5.490","0.5","2"
-"ds.class::perf::combine:0","4.760","0.5","2"
-"ds.colnames::perf:0","4.218","0.5","2"
-"ds.exists::perf::combine:0","11.09","0.5","2"
-"ds.length::perf::combine:0","9.479","0.5","2"
-"ds.mean::perf::combine:0","9.650","0.5","2"
-"ds.mean::perf::split:0","11.26","0.5","2"
-"void::perf::void::0","46250.0","0.5","2"
+"conndisconn::perf::simple0","0.2725","0.5","10"
+"ds.abs::perf::0","2.677","0.5","10"
+"ds.asInteger::perf:0","2.294","0.5","10"
+"ds.asList::perf:0","4.587","0.5","10"
+"ds.asNumeric::perf:0","2.185","0.5","10"
+"ds.assign::perf::0","5.490","0.5","10"
+"ds.class::perf::combine:0","4.760","0.5","10"
+"ds.colnames::perf:0","4.218","0.5","10"
+"ds.exists::perf::combine:0","11.09","0.5","10"
+"ds.length::perf::combine:0","9.479","0.5","10"
+"ds.mean::perf::combine:0","9.650","0.5","10"
+"ds.mean::perf::split:0","11.26","0.5","10"
+"void::perf::void::0","46250.0","0.5","10"