fix rhdf5 export names

Author: Benoit Thieurmel

R/h5_timeManagement.R

@@ -128,6 +128,6 @@ writeTime <- function(data, path, group){
   .requireRhdf5_Antares()
   time <- getTime(data, group)
   group <- paste0(group, "/time")
-  rhdf5::h5write.default(time, path, group)
+  rhdf5::h5write(time, path, group)
   rhdf5::h5closeAll()
 }

R/h5_writeData.R

@@ -124,7 +124,7 @@ writeDataType <- function(data,
                                                   dimData[4]))
     fid <- rhdf5::H5Fopen(path)
     # dimStructure$reCalcVar <- rep("NoVariable", 100)
-    rhdf5::h5writeDataset.list(dimStructure, fid, structData, level = compress)
+    rhdf5::h5writeDataset(dimStructure, fid, structData, level = compress)
     rhdf5::H5Fclose(fid)
     structNew <- paste0(structData, "/reCalcVar")
     rhdf5::h5createDataset(path, structNew, storage.mode = "character", level = compress , dims = 300,
@@ -151,7 +151,7 @@ writeDataType <- function(data,
 
   #Write data
   fid <- rhdf5::H5Fopen(path)
-  rhdf5::h5writeDataset.array(obj = arrayDatatowrite, fid, groupData, index = index)
+  rhdf5::h5writeDataset(obj = arrayDatatowrite, fid, groupData, index = index)
   rhdf5::H5Fclose(fid)
   NULL
 }

R/h5_writeH5ByYear.R

@@ -418,7 +418,7 @@ writeAntaresH5 <- function(path = NULL, timeSteps = c("hourly", "daily", "weekly
 
         attrib <- attributes(res)
         s <- serialize(attrib, NULL, ascii = TRUE)
-        rhdf5::h5write.default(rawToChar(s), path, paste0(timeStep, "/attrib"))
+        rhdf5::h5write(rawToChar(s), path, paste0(timeStep, "/attrib"))
 
         # .writeAttributes(res = res, path = path, timeStep = timeStep)
 
@@ -432,22 +432,22 @@ writeAntaresH5 <- function(path = NULL, timeSteps = c("hourly", "daily", "weekly
           layout <- suppressWarnings(suppressMessages(readLayout()))
         }
         s <- serialize(layout, NULL, ascii = TRUE)
-        rhdf5::h5write.default(rawToChar(s), path, paste0(timeStep, "/inputs/layout"))
+        rhdf5::h5write(rawToChar(s), path, paste0(timeStep, "/inputs/layout"))
 
         if(messageS){
           cldesc <- readClusterDesc()
         }else{
           cldesc <- suppressWarnings(suppressMessages(readClusterDesc()))
         }
         s <- serialize(cldesc, NULL, ascii = TRUE)
-        rhdf5::h5write.default(rawToChar(s), path, paste0(timeStep, "/inputs/cldesc"))
+        rhdf5::h5write(rawToChar(s), path, paste0(timeStep, "/inputs/cldesc"))
         if(messageS){
           bc <- readBindingConstraints()
         }else{
           bc <- suppressWarnings(suppressMessages(readBindingConstraints()))
         }
         s <- serialize(bc, NULL, ascii = TRUE)
-        rhdf5::h5write.default(rawToChar(s), path, paste0(timeStep, "/inputs/buildingcte"))
+        rhdf5::h5write(rawToChar(s), path, paste0(timeStep, "/inputs/buildingcte"))
 
       }
 

R/h5utils.R

@@ -24,23 +24,3 @@ isH5Opts <- function(opts){
   })
   names(timeSteps[which(timeSteps == TRUE)])
 }
-
-# .writeAttributes <- function(res = NULL, path = NULL, timeStep = "hourly", fid = NULL, attributes = NULL)
-# {
-#   .requireRhdf5_Antares()
-#   
-#   if(is.null(attributes))
-#   {
-#     attrib <- attributes(res)
-#   }else{
-#     attrib <- attributes
-#   }
-#   s <- serialize(attrib, NULL, ascii = TRUE)
-#   if(!is.null(path))
-#   {
-#     rhdf5::h5write.default(rawToChar(s), path, paste0(timeStep, "/attrib"))
-#   }else{
-#     did <- rhdf5::H5Dopen(fid,  paste0(timeStep, "/attrib"))
-#     rhdf5::H5Dwrite(did, rawToChar(s))
-#   }
-# }

R/zzz.R

@@ -116,13 +116,12 @@ rhdf5_message <- "This function require 'rhdf5' (>= 2.24.0) package.
          biocLite('rhdf5')"
 
 # !! parameter versionCheck of requireNamespace does not work correctly, use utils::package_version instead
-.requireRhdf5_Antares<-function(stopP = TRUE){
+.requireRhdf5_Antares <- function(stopP = TRUE){
   if(.check_rhdf5(stopP = stopP)){
     if(.check_rhdf5_version(stopP = stopP)){
       return(TRUE)
     }
   }
-  
   return(FALSE)
 }
 
@@ -156,8 +155,9 @@ pkgEnvAntareasH5 <- new.env()
 
 pkgEnvAntareasH5$varAreas <- c("OV. COST", "OP. COST", "MRG. PRICE", "CO2 EMIS.", "BALANCE",
                                "ROW BAL.", "PSP", "MISC. NDG",  "LOAD", "H. ROR", "WIND", "SOLAR",
-                               "NUCLEAR", "LIGNITE", "COAL", "GAS", "OIL", "MIX. FUEL", "MISC. DTG", "H. STOR",
-                               "UNSP. ENRG", "SPIL. ENRG", "LOLD", "LOLP", "AVL DTG", "DTG MRG", "MAX MRG", "NP COST", "NODU")
+                               "NUCLEAR", "LIGNITE", "COAL", "GAS", "OIL", "MIX. FUEL", "MISC. DTG", 
+                               "H. STOR", "UNSP. ENRG", "SPIL. ENRG", "LOLD", "LOLP", "AVL DTG", 
+                               "DTG MRG", "MAX MRG", "NP COST", "NODU")
 
 pkgEnvAntareasH5$varAreas <- as.vector(sapply(pkgEnvAntareasH5$varAreas, function(X){paste0(X, c("", "_min", "_max", "_std"))}))
 

tests/testthat/helper_init.R

@@ -66,16 +66,16 @@ if (sourcedir != "") {
 
   if(.requireRhdf5_Antares(stopP = FALSE) & .runH5Test){
 
-    path_v6 <- file.path(path0, "v6")
+    path_v6 <- file.path(path0, "antares-test-study-v6")
     opts <- setSimulationPath(file.path(path_v6, "/test_case"))
     suppressMessages({
       suppressWarnings({
 
         #On cran we have only 2 threads so nbCore <- 1  
         if(.runH5Test){
-          nbCoresTestHelper<-4
+          nbCoresTestHelper <- 4
         }else{
-          nbCoresTestHelper<-1
+          nbCoresTestHelper <- 1
         }
         writeAntaresH5(path = path_v6, 
                        misc = TRUE, thermalAvailabilities = TRUE,