Merge branch 'v7.0-dev-feat/performance' into v7.0-dev-feat/performance

Author: StuartWheater

DESCRIPTION

@@ -5,7 +5,7 @@ Description: Base 'DataSHIELD' functions for the server side. 'DataSHIELD' is a
     been designed to only share non disclosive summary statistics, with built in automated output
     checking based on statistical disclosure control. With data sites setting the threshold values for
     the automated output checks. For more details, see 'citation("dsBase")'.
-Version: 6.3.4
+Version: 6.3.5.9000
 Authors@R: c(person(given = "Paul",
                     family = "Burton",
                     role = c("aut"),

tests/testthat/perf_files/default_perf_profile.csv

@@ -1,5 +1,5 @@
 "refer_name","rate","lower_tolerance","upper_tolerance"
-"meanDS::perf::numeric::0","2998.9844","0.5","2"
-"meanDS::perf::numberAndNA::0","3027.3963","0.5","2"
-"varDS::perf::numeric::0","3124.4088","0.5","2"
-"varDS::perf::numberAndNA::0","3146.532","0.5","2"
+"meanDS::perf::numeric::0","11557.1204746495","0.5","2"
+"meanDS::perf::numberAndNA::0","11718.8520447749","0.5","2"
+"varDS::perf::numeric::0","12758.5511531009","0.5","2"
+"varDS::perf::numberAndNA::0","12545.8819532662","0.5","2"

tests/testthat/perf_files/hp-laptop_quay.csv

@@ -1,5 +1,5 @@
 "refer_name","rate","lower_tolerance","upper_tolerance"
-"meanDS::perf::numeric::0","8874.24924669612","0.5","2"
-"meanDS::perf::numberAndNA::0","8946.22935183172","0.5","2"
-"varDS::perf::numeric::0","10029.1022487173","0.5","2"
-"varDS::perf::numberAndNA::0","10014.7789085673","0.5","2"
+"meanDS::perf::numeric::0","11557.1204746495","0.5","2"
+"meanDS::perf::numberAndNA::0","11718.8520447749","0.5","2"
+"varDS::perf::numeric::0","12758.5511531009","0.5","2"
+"varDS::perf::numberAndNA::0","12545.8819532662","0.5","2"

tests/testthat/setup.R

@@ -1,5 +1,6 @@
 #-------------------------------------------------------------------------------
 # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved.
+# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved.
 #
 # This program and the accompanying materials
 # are made available under the terms of the GNU Public License v3.0.
@@ -11,7 +12,7 @@
 # Datashield test suite set up
 #
 
-context("setup - start")
+# context("setup - start")
 
 library(RANN)
 library(stringr)
@@ -22,4 +23,4 @@ source("random/set_random_seed_settings.R")
 
 source("perf_tests/perf_rate.R")
 
-context("setup - done")
+# context("setup - done")

tests/testthat/teardown.R

@@ -1,5 +1,6 @@
 #-------------------------------------------------------------------------------
 # Copyright (c) 2018-2022 University of Newcastle upon Tyne. All rights reserved.
+# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved.
 #
 # This program and the accompanying materials
 # are made available under the terms of the GNU Public License v3.0.
@@ -8,6 +9,6 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #-------------------------------------------------------------------------------
 
-context("teardown - start")
+# context("teardown - start")
 
-context("teardown - done")
+# context("teardown - done")

tests/testthat/test-arg-asIntegerDS.R

@@ -1,5 +1,5 @@
 #-------------------------------------------------------------------------------
-# Copyright (c) 2024 Arjuna Technologies, Newcastle upon Tyne. All rights reserved.
+# Copyright (c) 2024-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved.
 #
 # This program and the accompanying materials
 # are made available under the terms of the GNU Public License v3.0.
@@ -12,13 +12,13 @@
 # Set up
 #
 
-context("asIntegerDS::arg::setup")
+# context("asIntegerDS::arg::setup")
 
 #
 # Tests
 #
 
-context("asIntegerDS::arg::direct input numeric")
+# context("asIntegerDS::arg::direct input numeric")
 test_that("simple asIntegerDS non-input", {
     expect_error(asIntegerDS(1.0), "ERROR: x.name must be specified as a character string", fixed = TRUE)
 })
@@ -27,6 +27,6 @@ test_that("simple asIntegerDS non-input", {
 # Done
 #
 
-context("asIntegerDS::arg::shutdown")
+# context("asIntegerDS::arg::shutdown")
 
-context("asIntegerDS::arg::done")
+# context("asIntegerDS::arg::done")

tests/testthat/test-arg-asLogicalDS.R

@@ -1,5 +1,6 @@
 #-------------------------------------------------------------------------------
 # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved.
+# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved.
 #
 # This program and the accompanying materials
 # are made available under the terms of the GNU Public License v3.0.
@@ -12,25 +13,25 @@
 # Set up
 #
 
-context("asLogicalDS::arg::setup")
+# context("asLogicalDS::arg::setup")
 
 #
 # Tests
 #
 
-context("asLogicalDS::arg::direct input numeric")
+# context("asLogicalDS::arg::direct input numeric")
 test_that("simple asLogicalDS non-input", {
     expect_error(asLogicalDS(1.0), "ERROR: x.name must be specified as a character string", fixed = TRUE)
 })
 
-context("asLogicalDS::arg::input NULL")
+# context("asLogicalDS::arg::input NULL")
 test_that("simple asLogicalDS NULL", {
     input <- NULL
 
     expect_error(asLogicalDS("input"), "ERROR: for ds.asLogical function, x.name must specify an input object of class numeric, integer, character or matrix", fixed = TRUE)
 })
 
-context("asLogicalDS::arg::input NA")
+# context("asLogicalDS::arg::input NA")
 test_that("simple asLogicalDS NA", {
     input <- NA
 
@@ -41,6 +42,6 @@ test_that("simple asLogicalDS NA", {
 # Done
 #
 
-context("asLogicalDS::arg::shutdown")
+# context("asLogicalDS::arg::shutdown")
 
-context("asLogicalDS::arg::done")
+# context("asLogicalDS::arg::done")

tests/testthat/test-arg-dataFrameFillDS.R

@@ -1,5 +1,6 @@
 #-------------------------------------------------------------------------------
 # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved.
+# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved.
 #
 # This program and the accompanying materials
 # are made available under the terms of the GNU Public License v3.0.
@@ -12,13 +13,13 @@
 # Set up
 #
 
-context("dataFrameFillDS::arg::setup")
+# context("dataFrameFillDS::arg::setup")
 
 #
 # Tests
 #
 
-context("dataFrameFillDS::arg")
+# context("dataFrameFillDS::arg")
 test_that("simple dataFrameFillDS, ascending, numeric", {
     df                  <- data.frame(v1 = c(-2.0, -3.0, 4.0, 2.0, 1.0, 0.0, -1.0, 3.0), v2 = c(0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0))
     allNames.transmit   <- "v1,v2,v3,v4,v5,v6,v7"
@@ -45,10 +46,10 @@ test_that("simple dataFrameFillDS, ascending, numeric", {
 # Shutdown
 #
 
-context("dataFrameFillDS::arg::shutdown")
+# context("dataFrameFillDS::arg::shutdown")
 
 #
 # Done
 #
 
-context("dataFrameFillDS::arg::done")
+# context("dataFrameFillDS::arg::done")

tests/testthat/test-arg-dataFrameSortDS.R

@@ -1,5 +1,6 @@
 #-------------------------------------------------------------------------------
 # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved.
+# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved.
 #
 # This program and the accompanying materials
 # are made available under the terms of the GNU Public License v3.0.
@@ -12,15 +13,15 @@
 # Set up
 #
 
-context("dataFrameSortDS::arg::setup")
+# context("dataFrameSortDS::arg::setup")
 
 set.standard.disclosure.settings()
 
 #
 # Tests
 #
 
-context("dataFrameSortDS::arg")
+# context("dataFrameSortDS::arg")
 test_that("simple dataFrameSortDS, factor error check", {
     df              <- data.frame(v1 = as.factor(c("a", "b", "c", "d", "b", "e", "f", "f")), v2 = c(0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0))
     sort.key.name   <- "df$v1"
@@ -34,10 +35,10 @@ test_that("simple dataFrameSortDS, factor error check", {
 # Shutdown
 #
 
-context("dataFrameSortDS::arg::shutdown")
+# context("dataFrameSortDS::arg::shutdown")
 
 #
 # Done
 #
 
-context("dataFrameSortDS::arg::done")
+# context("dataFrameSortDS::arg::done")

tests/testthat/test-arg-uniqueDS.R

@@ -1,5 +1,6 @@
 #-------------------------------------------------------------------------------
 # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved.
+# Copyright (c) 2022-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved.
 #
 # This program and the accompanying materials
 # are made available under the terms of the GNU Public License v3.0.
@@ -12,29 +13,29 @@
 # Set up
 #
 
-context("uniqueDS::arg::setup")
+# context("uniqueDS::arg::setup")
 
 #
 # Tests
 #
 
-context("uniqueDS::arg::simple null argument")
+# context("uniqueDS::arg::simple null argument")
 test_that("simple uniqueDS for NULL", {
     expect_error(uniqueDS(NULL), "Variable's name can't be NULL", fixed = TRUE)
 })
 
-context("uniqueDS::arg::null value")
+# context("uniqueDS::arg::null value")
 test_that("simple uniqueDS for NULL", {
     input <- NULL
     expect_error(uniqueDS("input"), "Variable can't be NULL", fixed = TRUE)
 })
 
-context("uniqueDS::arg::not character value")
+# context("uniqueDS::arg::not character value")
 test_that("simple uniqueDS for NULL", {
   expect_error(uniqueDS(17), "Variable's name isn't a single character vector", fixed = TRUE)
 })
 
-context("uniqueDS::arg::missing value")
+# context("uniqueDS::arg::missing value")
 test_that("simple uniqueDS for NULL", {
     expect_error(uniqueDS("input"), "object 'input' not found", fixed = TRUE)
 })
@@ -43,6 +44,6 @@ test_that("simple uniqueDS for NULL", {
 # Done
 #
 
-context("uniqueDS::arg::shutdown")
+# context("uniqueDS::arg::shutdown")
 
-context("uniqueDS::arg::done")
+# context("uniqueDS::arg::done")