Release/cran261 (#244)

* update github workflow

* Read cluster desc bugfix when cluster exist (#242)

* fix bug readClusterDesc when no cluster + cover ST and RES case

* add test (init test for thermal + res)

* cleaning

* fix cran NOTE causing by bad url in doc + bad doc

NEWS.md

@@ -1,6 +1,6 @@
 > Copyright © 2016 RTE Réseau de transport d’électricité
 
-# antaresRead 2.6.1 (devlopment)
+# antaresRead 2.6.1 
 
 BUGFIXES :  
 

R/aggregateResult.R

@@ -4,12 +4,10 @@
 #'
 #' @param opts \code{list} of simulation parameters returned by the function \link{setSimulationPath}
 #' @param nbcl \code{numeric} Number of parralel process
-#' @param verbose \code{numeric} show log in console. Defaut to 1
-#' \itemize{
-#'  \item{0}{ : No log}
-#'  \item{1}{ : Short log}
-#'  \item{2}{ : Long log}
-#'}
+#' @param verbose \code{numeric} show log in console. Defaut to 1  
+#'  - 0 : No log  
+#'  - 1 : Short log  
+#'  - 2 : Long log
 #' @param timestep \code{character} antares timestep
 #' @param writeOutput \code{boolean} write result or not.
 #' @param mcWeights \code{numeric} vector of weigth for mcYears.
@@ -689,12 +687,6 @@ parAggregateMCall <- function(opts,
 }
 
 #' @param opts \code{list} of simulation parameters returned by the function \link{setSimulationPath}
-#' @param verbose \code{numeric} show log in console. Defaut to 1
-#' \itemize{
-#'  \item{0}{ : No log}
-#'  \item{1}{ : Short log}
-#'  \item{2}{ : Long log}
-#'}
 #' @param timestep \code{character} antares timestep
 #' @param writeOutput \code{boolean} write result or not.
 #' @param mcWeights \code{numeric} vector of weigth for mcYears.
@@ -1533,7 +1525,7 @@ pmax.fast <- function(k,x) (x+k + abs(x-k))/2
 #'
 #' @import data.table
 #' 
-#' @rdname aggregatate_mc_all_old
+#' @noRd
 #' 
 #' @examples
 #' \dontrun{

R/readClusterDesc.R

@@ -107,8 +107,9 @@ readClusterSTDesc <- function(opts = simOptions()) {
   path <- file.path(opts$inputPath, dir)
 
   columns <- .generate_columns_by_type(dir = dir)
+  api_study <- is_api_study(opts)
 
-  if(opts$typeLoad == 'api'){
+  if(api_study){
 
     jsoncld <- read_secure_json(paste0(path, "&depth=4"), token = opts$token, timeout = opts$timeout, config = opts$httr_config)
     res <-  rbindlist(mapply(function(X1, Y1){
@@ -125,13 +126,6 @@ readClusterSTDesc <- function(opts = simOptions()) {
       clusters[, .SD, .SDcols = order(names(clusters))]
     },jsoncld, names(jsoncld), SIMPLIFY = FALSE), fill = TRUE)
 
-    if(length(res) == 0){
-      warning("No cluster description available.", call. = FALSE)
-      res <- setNames(data.table(matrix(nrow = 0, ncol = 2 + length(columns))), c("area", "cluster", columns))
-    }else{
-      res <-  res[, .SD, .SDcols = c("area", "name", "group", names(res)[!names(res) %in%c("area", "name", "group")])]
-    }
-
 
   }else{
 
@@ -149,15 +143,21 @@ readClusterSTDesc <- function(opts = simOptions()) {
       clusters[, c(ncol(clusters), 1:(ncol(clusters) - 1))]
     })
 
-    if(length(res) == 0){
-      warning("No cluster description available.", call. = FALSE)
-      res <- setNames(data.table(matrix(nrow = 0, ncol = 2 + length(columns))), c("area", "cluster", columns))
-    }else{
-      res <- as.data.table(res)
-      setnames(res, "name", "cluster")
-
-      res$cluster <- as.factor(tolower(res$cluster))
+  }
+
+  if(length(res) == 0){
+    mandatory_cols <- c("area","cluster")
+    warning("No cluster description available.", call. = FALSE)
+    res <- setNames(data.table(matrix(nrow = 0, ncol = length(mandatory_cols) + length(columns))), c(mandatory_cols, columns))
+  }else{
+    if(api_study){
+      mandatory_cols <- c("area", "name", "group")
+      additional_cols <- setdiff(colnames(res),mandatory_cols)
+      res <- res[, .SD, .SDcols = c(mandatory_cols, additional_cols)]
     }
+    res <- as.data.table(res)
+    setnames(res, "name", "cluster")
+    res$cluster <- as.factor(tolower(res$cluster))
   }
 
   res

tests/testthat/test-readClusterDesc.R

@@ -1,9 +1,42 @@
 
-## v860 ----
+# v860 ----
 
 path_study_test <- grep(pattern = "86", x = studyPathSV8, value = TRUE)
 opts_study_test <- setSimulationPath(path_study_test, simulation = "input")
 
+#minimal columns
+mandatory_cols <- c("area","cluster")
+
+## Thermal ----
+test_that("test read cluster", {
+
+  # function setSimulationPath() provide areas names with st-storage clusters
+  areas <- opts_study_test$areasWithClusters
+
+  # read clusters informations
+  input <- readClusterDesc()
+
+  # tests
+  testthat::expect_true("data.table" %in% class(input))
+  testthat::expect_true(all(areas %in% unique(readClusterDesc()$area)))
+  testthat::expect_true(all(mandatory_cols %in% colnames(input)))
+  testthat::expect_true(nrow(input) == length(input$cluster))
+
+})
+
+## Renewables ----
+test_that("test read cluster renewables", {
+
+  # function setSimulationPath() provide areas names with st-storage clusters
+  areas_res <- opts_study_test$areasWithRESClusters
+
+  #Study not renewables (need activateRES() from antaresEditObject)
+  expect_error(readClusterResDesc(),
+               regexp = "readClusterDesc is available only on studies with 'renewable-generation-modelling'")
+
+})
+
+## st-storage ----
 test_that("test read cluster st-storage v860", {
 
   # function setSimulationPath() provide areas names with st-storage clusters
@@ -14,5 +47,8 @@ test_that("test read cluster st-storage v860", {
 
   # tests
   testthat::expect_true("data.table" %in% class(input_st))
-  testthat::expect_true(areas_st %in% unique(readClusterSTDesc()$area))
+  testthat::expect_true(all(areas_st %in% unique(readClusterSTDesc()$area)))
+  testthat::expect_true(all(mandatory_cols %in% colnames(input_st)))
+  testthat::expect_true(nrow(input_st) == length(input_st$cluster))
+
 })

vignettes/antaresH5.Rmd

@@ -35,7 +35,6 @@ BiocManager::install("rhdf5")
 
 An other solution is to install manually these two packages from zip file. They are available here :
 https://bioconductor.org/packages/release/bioc/html/zlibbioc.html
-http://bioconductor.org/packages/release/bioc/html/rhdf5.html
 
 
 ## Avantages of h5 transformation