update to 0.18.3 to put package back on CRAN

* update to 0.18.1 to delete rhdf5 package reference EVERY WHERE * delete package suggest dependencies hexbin * clean reference to rhdf5 package EVERYWHERE * delete in doc function "\link" to prevent CRAN NOTE + build site updated * up version to fix last reference to rhdf5 pacakge * Bump to 0.18.3 revdep check ok * update licence file to GLP 3 * exchangesStack() documentation example updated + cran comments + news * revdep check ok
rte-antares-rpackage · Dec 4, 2024 · 4d17d74 · 4d17d74
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -13,3 +13,4 @@ inst/examples
 ^revdep$
 ^README\.Rmd$
 ^CRAN-SUBMISSION$
+^LICENSE\.md$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,14 +1,14 @@
 Package: antaresViz
 Type: Package
 Title: Antares Visualizations
-Version: 0.18.0
+Version: 0.18.3
 Authors@R: c(
     person("Tatiana", "Vargas", email = "[email protected]", role = c("aut", "cre")),
-    person("Jalal-Edine", "Zawam", role = "aut"),
-    person("Francois", "Guillem", role = "aut"),
-    person("Benoit", "Thieurmel", role = "aut"),
-    person("Titouan", "Robert", role = "aut"),
-    person("Paul", "Plessiez", role = "aut"),
+    person("Jalal-Edine", "Zawam", role = "ctb"),
+    person("Francois", "Guillem", role = "ctb"),
+    person("Benoit", "Thieurmel", role = "ctb"),
+    person("Titouan", "Robert", role = "ctb"),
+    person("Paul", "Plessiez", role = "ctb"),
     person("Baptiste", "Seguinot", role = "ctb"),
     person("RTE", role = "cph")
     )
@@ -19,7 +19,7 @@ Description: Visualize results generated by Antares, a powerful open source soft
     'Antares' users visually explore the results of their simulations.
 URL: https://github.com/rte-antares-rpackage/antaresViz
 BugReports: https://github.com/rte-antares-rpackage/antaresViz/issues
-License: GPL (>= 2) | file LICENSE 
+License: GPL (>= 3)
 Encoding: UTF-8
 Depends:
     antaresRead (>= 2.2.9),
@@ -45,14 +45,13 @@ Imports:
     leaflet.minicharts (>= 0.5.3),
     assertthat,
     rAmCharts,
-    utils
+    utils,
+    lifecycle
 RoxygenNote: 7.2.2
 Suggests: 
     testthat,
     covr,
-    rhdf5 (>= 2.20.2),
     ggplot2,
-    hexbin,
     knitr,
     visNetwork,
     rmarkdown

diff --git a/LICENSE.md b/LICENSE.md
diff --git a/NAMESPACE b/NAMESPACE
@@ -56,6 +56,9 @@ importFrom(grDevices,rainbow)
 importFrom(grDevices,rgb)
 importFrom(graphics,par)
 importFrom(graphics,plot.default)
+importFrom(lifecycle,deprecate_warn)
+importFrom(lifecycle,deprecated)
+importFrom(lifecycle,is_present)
 importFrom(methods,is)
 importFrom(plotly,add_bars)
 importFrom(plotly,add_heatmap)

diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,16 @@
 Copyright 2016 RTE Reseau de transport d'electricite
 
+# antaresViz 0.18.3 
+* The package has been accepted but archived as version 0.18.2.  
+New version for distribution on CRAN  
+* Licence file updated and documentation for `exchangesStack()` updated
+
+# antaresViz 0.18.2 
+* fix cran issue on test not skip well
+
+# antaresViz 0.18.1
+* delete package dependecies `rhdf5`
+
 # antaresViz 0.18.0
 * fix deprecated dependencies (issue #200)
   * packages `rgeos`, `raster` removed and replaced by `sf`

diff --git a/R/graph_utils.R b/R/graph_utils.R
@@ -289,71 +289,6 @@
 }
 
 
-
-
-#' List of h5 params
-#' 
-#' @param X_I, list
-#' @param xyCompare, character
-#' 
-#' @noRd
-.h5ParamList <- function(X_I, xyCompare, h5requestFilter = NULL){
-  listParam <- lapply(1:length(X_I), function(i){
-    x <- X_I[[i]]
-    if (.isSimOpts(x)){
-      tmp <- .h5Inf(x)
-      h5_filter <- h5requestFilter[[i]]
-      h5_tables <- c("areas", "districts", "clusters", "links")
-      if (!is.null(h5_filter)){
-        if (!(is.null(h5_filter$areas) & is.null(h5_filter$districts) & 
-           is.null(h5_filter$links) & is.null(h5_filter$clusters))){
-          h5_tables <- c("areas", "districts", "clusters", "links")
-          h5_tables <- h5_tables[which(c(!is.null(h5_filter$areas), !is.null(h5_filter$districts),
-                                           !is.null(h5_filter$clusters), !is.null(h5_filter$links)))]
-        }
-      }
-      tmp$tabl <- intersect(tmp$tabl, h5_tables)
-      rhdf5::H5close()
-      tmp
-    }else{
-      mcY <- unique(unlist(lapply(x, function(y){unique(y$mcYears)})))
-      timeStepS <- attributes(x)$timeStep
-      tabl <- names(x)
-      list(
-        timeStepS = timeStepS,
-        mcYearS = mcY,
-        tabl = tabl
-      )
-    }
-  })
-  res <- lapply(.transposeL(listParam), function(x){
-    .compareOperation(x, xyCompare)
-  })
-
-  res$h5requestFilter <- h5requestFilter
-  res
-}
-
-#' Load information from h5 file
-#' 
-#' @param x, opts
-#' 
-#' @noRd
-.h5Inf <- function(x){
-  fid <- rhdf5::H5Fopen(x$h5path)
-  timeStepS <- .getTimeStep(fid)
-  timeStepS <- as.character(timeStepS)
-  mcYearS <- x$mcYears
-  tabl <- .getTableInH5(fid, timeStepS[1])
-  rhdf5::H5Fclose(fid)
-  xPart = list(
-    timeStepS = timeStepS,
-    mcYearS = mcYearS,
-    tabl = tabl
-  )
-}
-
-
 .transposeL <- function(data){
   do.call(c, apply(do.call(rbind, data), 2, list)) 
 }

diff --git a/R/h5_utils.R b/R/h5_utils.R
@@ -1,109 +1,109 @@
-.convertH5Filtering <- function(h5requestFiltering, x)
-{
-  if (length(h5requestFiltering) > 0)
-  {
-    if (!is.list(h5requestFiltering[[1]])){
-      if (!any(c("simOptions", "antaresDataTable") %in% class(x)))
-      {
-        h5requestFiltering <- rep(list(h5requestFiltering), length(x))
-      }else{
-        h5requestFiltering <- list(h5requestFiltering)
-      }
-    }else{
-      if (inherits(x, "list")){
-        if (length(h5requestFiltering) != length(x)){
-          h5requestFiltering <- h5requestFiltering[1:length(x) %% length(h5requestFiltering) + 1]
-        }
-      }
-    }
-  }else{
-    if (!any(c("simOptions", "antaresDataTable") %in% class(x)))
-    {
-      h5requestFiltering <- replicate(length(x), list())
-    }else{
-      h5requestFiltering <- replicate(1, list())
-    }
-  }
-  h5requestFiltering
-}
+# .convertH5Filtering <- function(h5requestFiltering, x)
+# {
+#   if (length(h5requestFiltering) > 0)
+#   {
+#     if (!is.list(h5requestFiltering[[1]])){
+#       if (!any(c("simOptions", "antaresDataTable") %in% class(x)))
+#       {
+#         h5requestFiltering <- rep(list(h5requestFiltering), length(x))
+#       }else{
+#         h5requestFiltering <- list(h5requestFiltering)
+#       }
+#     }else{
+#       if (inherits(x, "list")){
+#         if (length(h5requestFiltering) != length(x)){
+#           h5requestFiltering <- h5requestFiltering[1:length(x) %% length(h5requestFiltering) + 1]
+#         }
+#       }
+#     }
+#   }else{
+#     if (!any(c("simOptions", "antaresDataTable") %in% class(x)))
+#     {
+#       h5requestFiltering <- replicate(length(x), list())
+#     }else{
+#       h5requestFiltering <- replicate(1, list())
+#     }
+#   }
+#   h5requestFiltering
+# }
 
 
 
-.getTableInH5 <- function(fid, timeStep){
-  dataExist <- NULL
-  if (rhdf5::H5Lexists(fid, paste0(timeStep, "/areas")))
-  {
-    dataExist <- c(dataExist, "areas")
-  }
-  if (rhdf5::H5Lexists(fid, paste0(timeStep, "/links")))
-  {
-    dataExist <- c(dataExist, "links")
-  }
-  if (rhdf5::H5Lexists(fid, paste0(timeStep, "/clusters")))
-  {
-    dataExist <- c(dataExist, "clusters")
-  }
-  if (rhdf5::H5Lexists(fid, paste0(timeStep, "/districts")))
-  {
-    dataExist <- c(dataExist, "districts")
-  }
-  dataExist
-}
+# .getTableInH5 <- function(fid, timeStep){
+#   dataExist <- NULL
+#   if (rhdf5::H5Lexists(fid, paste0(timeStep, "/areas")))
+#   {
+#     dataExist <- c(dataExist, "areas")
+#   }
+#   if (rhdf5::H5Lexists(fid, paste0(timeStep, "/links")))
+#   {
+#     dataExist <- c(dataExist, "links")
+#   }
+#   if (rhdf5::H5Lexists(fid, paste0(timeStep, "/clusters")))
+#   {
+#     dataExist <- c(dataExist, "clusters")
+#   }
+#   if (rhdf5::H5Lexists(fid, paste0(timeStep, "/districts")))
+#   {
+#     dataExist <- c(dataExist, "districts")
+#   }
+#   dataExist
+# }
 
-.getVariablesH5 <- function(fid, timeStep, tables){
-  sapply(tables, function(X){
-    struct <- .getstructure(fid, paste0(timeStep, "/", X, "/mcInd/", "/structure"))$variable
-    if ("timeId" %in% struct){
-      struct <- struct[struct != "timeId"]
-    }
-    struct
-  }, simplify = FALSE)
-}
+# .getVariablesH5 <- function(fid, timeStep, tables){
+#   sapply(tables, function(X){
+#     struct <- .getstructure(fid, paste0(timeStep, "/", X, "/mcInd/", "/structure"))$variable
+#     if ("timeId" %in% struct){
+#       struct <- struct[struct != "timeId"]
+#     }
+#     struct
+#   }, simplify = FALSE)
+# }
 
-.getClustersNames <- function(fid, timeStep){
-  unique(unlist(lapply(strsplit(.getstructure(fid, paste0(timeStep, "/clusters/mcInd/structure"))$cluster, "/"), function(X)X[1])))
-}
+# .getClustersNames <- function(fid, timeStep){
+#   unique(unlist(lapply(strsplit(.getstructure(fid, paste0(timeStep, "/clusters/mcInd/structure"))$cluster, "/"), function(X)X[1])))
+# }
 
-.getElements <- function(opts, tables, fid, timeStep){
-  elements <- list()
-  if ("areas" %in% tables) elements$areas <- opts$areaList
-  if ("links" %in% tables) elements$links <- opts$linkList
-  if ("districts" %in% tables) elements$districts <- opts$districtList
-  if ("clusters" %in% tables){
-    elements$clusters  <- .getClustersNames(fid, timeStep)
-  }
-  elements
-}
+# .getElements <- function(opts, tables, fid, timeStep){
+#   elements <- list()
+#   if ("areas" %in% tables) elements$areas <- opts$areaList
+#   if ("links" %in% tables) elements$links <- opts$linkList
+#   if ("districts" %in% tables) elements$districts <- opts$districtList
+#   if ("clusters" %in% tables){
+#     elements$clusters  <- .getClustersNames(fid, timeStep)
+#   }
+#   elements
+# }
+# 
+# .getDateRange <- function(opts, timeStep){
+#   tim <- .timeIdToDate(sort(
+#     unique(
+#       antaresRead::.h5ReadAntares(opts$h5path, timeStep = timeStep, select = "timeId", 
+#                                  areas = opts$areaList[1], mcYears = opts$mcYears[1], perf = FALSE)$timeId)
+#   ), timeStep = timeStep, opts = opts)
+#   dt <- as.Date(range(tim))
+#   dt
+# }
+# 
+# 
+# .getGraphFunction <- function(type){
+#   switch(type,
+#          "ts" = .plotTS,
+#          "barplot" = .barplot,
+#          "monotone" = .plotMonotone,
+#          "density" = .density,
+#          "cdf" = .cdf,
+#          "heatmap" = .heatmap,
+#          stop("Invalid type")
+#   )
+# }
 
-.getDateRange <- function(opts, timeStep){
-  tim <- .timeIdToDate(sort(
-    unique(
-      antaresRead::.h5ReadAntares(opts$h5path, timeStep = timeStep, select = "timeId", 
-                                 areas = opts$areaList[1], mcYears = opts$mcYears[1], perf = FALSE)$timeId)
-  ), timeStep = timeStep, opts = opts)
-  dt <- as.Date(range(tim))
-  dt
-}
-
-
-.getGraphFunction <- function(type){
-  switch(type,
-         "ts" = .plotTS,
-         "barplot" = .barplot,
-         "monotone" = .plotMonotone,
-         "density" = .density,
-         "cdf" = .cdf,
-         "heatmap" = .heatmap,
-         stop("Invalid type")
-  )
-}
-
-.getTimeStep <- function(fid){
-  timeSteps <- sapply(c("hourly", "daily", "weekly", "monthly", "annual"), function(X){
-    rhdf5::H5Lexists(fid, X)
-  })
-  names(timeSteps[which(timeSteps == TRUE)])
-}
+# .getTimeStep <- function(fid){
+#   timeSteps <- sapply(c("hourly", "daily", "weekly", "monthly", "annual"), function(X){
+#     rhdf5::H5Lexists(fid, X)
+#   })
+#   names(timeSteps[which(timeSteps == TRUE)])
+# }
 
 .compareOperation <- function(a, opType){
   if (length(a) == 1) return(unlist(unique(a)))

diff --git a/R/h5_utils_plot.R b/R/h5_utils_plot.R
@@ -1,20 +1,20 @@
 
 
 
-.getstructure <- function(fid, strgp){
-  gid <- rhdf5::H5Gopen(fid,  strgp)
-  data <- rhdf5::h5dump(gid)
-  rhdf5::H5Gclose(gid)
-  if(length(which(data$reCalcVar!="")) > 0)
-  {
-    data$reCalcVar <- data$reCalcVar[which(data$reCalcVar!="")]
-    data$variable <- c(data$variable, data$reCalcVar)
-    data$reCalcVar <- NULL
-  }
-  data
-}
-
-.tryCloseH5 <- function(){
-  try(rhdf5::H5close(), silent = TRUE)
-}
+# .getstructure <- function(fid, strgp){
+#   gid <- rhdf5::H5Gopen(fid,  strgp)
+#   data <- rhdf5::h5dump(gid)
+#   rhdf5::H5Gclose(gid)
+#   if(length(which(data$reCalcVar!="")) > 0)
+#   {
+#     data$reCalcVar <- data$reCalcVar[which(data$reCalcVar!="")]
+#     data$variable <- c(data$variable, data$reCalcVar)
+#     data$reCalcVar <- NULL
+#   }
+#   data
+# }
+# 
+# .tryCloseH5 <- function(){
+#   try(rhdf5::H5close(), silent = TRUE)
+# }