Merge pull request #2 from nextpagesoft/move-to-ecdc

Prepare code for move to ECDC repository

.github/workflows/R-CMD-check.yaml

@@ -1,5 +1,6 @@
 on:
-  push
+  workflow_dispatch:
+  push:
 
 name: R-CMD-check
 
@@ -30,10 +31,16 @@ jobs:
           r-version: ${{ matrix.config.r }}
           use-public-rspm: true
 
+      - name: Install libcurl on Linux
+        if: runner.os == 'Linux'
+        run: sudo apt-get update -y && sudo apt-get install -y libcurl4-openssl-dev
+
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           dependencies: '"hard"'
-          extra-packages: any::rcmdcheck
+          extra-packages: |
+            any::rcmdcheck
+            any::testthat
           working-directory: Server
 
       - uses: r-lib/actions/check-r-package@v2

README.md

@@ -1,6 +1,6 @@
 # Status
 
-[![R-CMD-check](https://github.com/nextpagesoft/hivEstimatesAccuracy2/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/nextpagesoft/hivEstimatesAccuracy2/actions/workflows/R-CMD-check.yaml)
+[![R-CMD-check](../../actions/workflows/R-CMD-check.yaml/badge.svg)](../../actions/workflows/R-CMD-check.yaml)
 
 # European Centre for Disease Prevention and Control
 
@@ -20,5 +20,5 @@ further analysis.
 
 # License
 
-See the [LICENSE](https://github.com/nextpagesoft/hivEstimatesAccuracy2/blob/master/LICENSE) file
+See the [LICENSE](LICENSE) file
 for license rights and limitations (EUPL-1.2).

Server/DESCRIPTION

@@ -20,8 +20,9 @@ Imports:
     fansi (>= 0.4.1),
     foreign (>= 0.8-81),
     ggplot2 (>= 3.3.3),
+    glue (>= 1.7.0),
     hivModelling (>= 0.9.14),
-    HivEstInfTime (>= 1.0.0),
+    hivEstInfTime (>= 1.0.0),
     jomo (>= 2.6-10),
     jsonlite (>= 1.7.2),
     knitr (>= 1.28),
@@ -42,9 +43,9 @@ Imports:
     yaml (>= 2.2.1),
     xml2 (>= 1.3.2)
 Remotes:
-    nextpagesoft/hivModelling,
-    nextpagesoft/HivEstInfTime
+    github::EU-ECDC/hivModelling,
+    github::EU-ECDC/hivEstInfTime
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Suggests: testthat, rcmdcheck, pak, miniCRAN

Server/R/CaseDataManager.R

@@ -467,7 +467,7 @@ CaseDataManager <- R6::R6Class( # nolint
 
     # 7. Migration ---------------------------------------------------------------------------------
     RunMigration = function(
-      params = HivEstInfTime::GetMigrantParams()
+      params = hivEstInfTime::GetMigrantParams()
     ) {
       if (!is.null(private$AppMgr) && !is.element(
         private$AppMgr$Steps['CASE_BASED_ORIGIN_GROUPING'],
@@ -495,7 +495,7 @@ CaseDataManager <- R6::R6Class( # nolint
               .Random.seed <- randomSeed # nolint
 
               input <- hivPlatform::PrepareMigrantData(data)
-              output <- HivEstInfTime::PredictInf(input, params)
+              output <- hivEstInfTime::PredictInf(input, params)
               data[output, ProbPre := i.ProbPre, on = .(UniqueId)]
 
               # Enrich data with extra dimensions from the input preparation step

Server/R/Messages.R

@@ -1,3 +1,4 @@
+
 #' PrintH1
 #'
 #' @param ... Text to be printed
@@ -21,11 +22,28 @@ PrintH1 <- function(
   invisible(NULL)
 }
 
+#' PrintStartHeader
+#'
+#' @return NULL
+#'
+#' @examples
+#' PrintStartHeader()
+#'
 #' @export
 PrintStartHeader <- function() {
   PrintAlert('{format(Sys.time())} - START')
 }
 
+#' PrintStopHeader
+#'
+#' @param startTime Start time as POSIXct
+#' @param stopTime End time as POSIXct
+#'
+#' @return NULL
+#'
+#' @examples
+#' PrintStopHeader()
+#'
 #' @export
 PrintStopHeader <- function(startTime = NULL, stopTime = NULL) {
   if (!is.null(startTime) && !is.null(stopTime)) {

Server/tests/testthat.R

@@ -4,5 +4,5 @@ library(data.table)
 if (requireNamespace('testthat', quietly = TRUE)) {
   testthat::test_package('hivPlatform')
 } else {
-  PrintAlert('Skipping tests')
+  hivPlatform::PrintAlert('Skipping tests')
 }

Server/utils/Deploy.R

@@ -1,4 +1,6 @@
 # 1. Update local packages -------------------------------------------------------------------------
+dir.create('library', showWarnings = FALSE)
+.libPaths('./library')
 pak::local_install_deps(root = '.', dependencies = 'hard', upgrade = TRUE)
 
 pkgDescr <- as.data.frame(read.dcf('DESCRIPTION'))
@@ -20,7 +22,7 @@ depPkgs <- unname(sapply(
 ))
 depPkgs <- setdiff(
   depPkgs,
-  c('R', 'hivModelling', 'HivEstInfTime', 'grid', 'graphics', 'parallel', 'stats', 'tools', 'utils')
+  c('R', 'hivModelling', 'hivEstInfTime', 'grid', 'graphics', 'parallel', 'stats', 'tools', 'utils')
 )
 depPkgList <- miniCRAN::pkgDep(depPkgs, repos = repoCRAN, type = 'source', suggests = FALSE)
 
@@ -41,7 +43,7 @@ buildPath <- file.path(rootPath, 'build')
 dir.create(buildPath, showWarnings = FALSE, recursive = TRUE)
 
 # HIV Estimate Infection Time
-hivEstInfTimePkgPath <- 'D:/_REPOSITORIES/HivEstInfTime'
+hivEstInfTimePkgPath <- 'D:/_REPOSITORIES/hivEstInfTime'
 pkgbuild::build(path = hivEstInfTimePkgPath, dest_path = buildPath, binary = FALSE)
 pkgbuild::build(path = hivEstInfTimePkgPath, dest_path = buildPath, binary = TRUE, args = args)
 

Server/utils/Example.R

@@ -167,10 +167,10 @@ json <- ConvertObjToJSON(appMgr$CaseMgr$MigrationResult$Artifacts$OutputPlots, d
 writeLines(json, 'json.txt')
 appMgr$CaseMgr$MigrationResult$Artifacts$ConfBounds
 
-params <- HivEstInfTime::GetMigrantParams()
+params <- hivEstInfTime::GetMigrantParams()
 data <- copy(appMgr$CaseMgr$Data)
 input <- hivPlatform::PrepareMigrantData(data)
-output <- HivEstInfTime::PredictInf(input, params)
+output <- hivEstInfTime::PredictInf(input, params)
 output.copy <- copy(output)
 output <- copy(output.copy)
 
@@ -447,7 +447,7 @@ appMgr$HIVModelMgr$BootstrapFitStats$ThetaStats
 
 
 # Migration ----------------------------------------------------------------------------------------
-params <- HivEstInfTime::GetMigrantParams()
+params <- hivEstInfTime::GetMigrantParams()
 
 # Recon data set
 reconAIDS <- data.table::setDT(haven::read_dta('D:/VirtualBox_Shared/Migrant_test/baseAIDS.dta'))
@@ -497,7 +497,7 @@ input <- list(
 )
 
 # Create test dataset
-test <- HivEstInfTime::PredictInf(input, params)
+test <- hivEstInfTime::PredictInf(input, params)
 
 # Reconcile
 recon <- rbind(

Server/utils/RcppTest.R

@@ -1,5 +1,5 @@
 outputCD4VL <- readRDS('../../outputCD4VL.Rds')
-params <- HivEstInfTime::GetMigrantParams()
+params <- hivEstInfTime::GetMigrantParams()
 uniqueId <- 209
 dt <- outputCD4VL[UniqueId == uniqueId]
 

workspace.code-workspace

@@ -4,7 +4,7 @@
       "path": "."
     },
     {
-      "path": "../HivEstInfTime"
+      "path": "../hivEstInfTime"
     },
     {
       "path": "../hivModelling"