Merge pull request #620 from datashield/v6.3.5-dev-feat/testthat-rework

V6.3.5 dev feat/testthat rework

Author: StuartWheater

.Rbuildignore

@@ -17,8 +17,8 @@
 ^R/secure.global.ranking.md$
 ^_pkgdown\.yml$
 ^docs$
-^dsBase_6.3.4.tar.gz$
-^dsBase_6.3.4-permissive.tar.gz$
+^dsBase_6.3.5.tar.gz$
+^dsBase_6.3.5-permissive.tar.gz$
 ^dsDanger_6.3.4.tar.gz$
 ^\.circleci$
 ^\.circleci/config\.yml$

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: dsBaseClient
 Title: 'DataSHIELD' Client Side Base Functions
-Version: 6.3.4
+Version: 6.3.5-9000
 Description: Base 'DataSHIELD' functions for the client side. 'DataSHIELD' is a software package which allows
     you to do non-disclosive federated analysis on sensitive data. 'DataSHIELD' analytic functions have
     been designed to only share non disclosive summary statistics, with built in automated output

README.md

@@ -23,8 +23,8 @@ And the development version from
 install.packages("remotes")
 remotes::install_github("datashield/dsBaseClient", "<BRANCH>")
 
-# Install v6.3.4 with the following
-remotes::install_github("datashield/dsBaseClient", "6.3.4")
+# Install v6.3.5 with the following
+remotes::install_github("datashield/dsBaseClient", "6.3.5")
 ```
 
 For a full list of development branches, checkout https://github.com/datashield/dsBaseClient/branches
@@ -50,7 +50,7 @@ The code here is organised as:
 
 [1] Burton P, Wilson R, Butters O, Ryser-Welch P, Westerberg A, Abarrategui L, Villegas-Diaz R,
   Avraam D, Marcon Y, Bishop T, Gaye A, Escribà Montagut X, Wheater S (2025). 
-  _dsBaseClient: 'DataSHIELD' Client Side Base Functions_. R package version 6.3.4.
+  _dsBaseClient: 'DataSHIELD' Client Side Base Functions_. R package version 6.3.5.
 
 [2] Gaye A, Marcon Y, Isaeva J, LaFlamme P, Turner A, Jones E, Minion J, Boyd A, Newby C, Nuotio
   M, Wilson R, Butters O, Murtagh B, Demir I, Doiron D, Giepmans L, Wallace S, Budin-Ljøsne I,

armadillo_azure-pipelines.yml

@@ -58,10 +58,10 @@ schedules:
       - master
     always: true
   - cron: "0 2 * * *"
-    displayName: Nightly build - v6.3.4-dev
+    displayName: Nightly build - v6.3.5-dev
     branches:
       include:
-      - v6.3.4-dev
+      - v6.3.5-dev
     always: true
 
 #########################################################################################
@@ -235,7 +235,7 @@ jobs:
 
       curl -u admin:admin -X GET http://localhost:8080/packages
 
-      curl -u admin:admin --max-time 300 -v -H 'Content-Type: multipart/form-data' -F "file=@dsBase_6.3.4-permissive.tar.gz" -X POST http://localhost:8080/install-package
+      curl -u admin:admin --max-time 300 -v -H 'Content-Type: multipart/form-data' -F "file=@dsBase_6.3.5-permissive.tar.gz" -X POST http://localhost:8080/install-package
       sleep 60
 
       docker container restart dsbaseclient_armadillo_1

azure-pipelines.yml

@@ -44,10 +44,10 @@ schedules:
       - master
     always: true
   - cron: "0 2 * * *"
-    displayName: Nightly build - v6.3.4-dev
+    displayName: Nightly build - v6.3.5-dev
     branches:
       include:
-      - v6.3.4-dev
+      - v6.3.5-dev
     always: true
 
 #########################################################################################
@@ -216,7 +216,7 @@ jobs:
   - bash: |
       R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)"
 
-      R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = 'v6.3.4-dev'); opal.logout(opal)"
+      R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = 'v6.3.5-dev'); opal.logout(opal)"
 
       sleep 60
 

dsBase_6.3.4.tar.gz dsBase_6.3.5-permissive.tar.gzdsBase_6.3.4.tar.gz renamed to dsBase_6.3.5-permissive.tar.gz

@@ -58,10 +58,10 @@ schedules:
       - master
     always: true
   - cron: "0 2 * * *"
-    displayName: Nightly build - v6.3.4-dev
+    displayName: Nightly build - v6.3.5-dev
     branches:
       include:
-      - v6.3.4-dev
+      - v6.3.5-dev
     always: true
 
 #########################################################################################
@@ -235,7 +235,7 @@ jobs:
   - bash: |
       R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)"
 
-      R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = 'v6.3.4-dev'); opal.logout(opal)"
+      R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = 'v6.3.5-dev'); opal.logout(opal)"
 
       sleep 60
 

dsBase_6.3.4-permissive.tar.gz dsBase_6.3.5.tar.gzdsBase_6.3.4-permissive.tar.gz renamed to dsBase_6.3.5.tar.gz

@@ -1,18 +1,19 @@
 #-------------------------------------------------------------------------------
 # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved.
-# Copyright (c) 2022 Arjuna Technologies, 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.
 #
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #-------------------------------------------------------------------------------
+
 #
 # Datashield test suite set up
 #
 
-context("setup - start")
+# context("setup - start")
 
 # Convert 'warnings' to 'errors'
 # options(warn = 2)
@@ -33,4 +34,4 @@ source("connection_to_datasets/init_studies_datasets.R")
 source("connection_to_datasets/init_discordant_datasets.R")
 source("connection_to_datasets/init_mediation_datasets.R")
 
-context("setup - done")
+# context("setup - done")

opal_azure-pipelines.yml

@@ -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")
+# context("teardown")
 
-context("teardown - done")
+# context("teardown - done")