Rename package to packages and remove installed='BASE' arg

syncrosim · Nov 30, 2023 · bb67602 · bb67602
1 parent d6816ed
commit bb67602
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Showing 19 changed files with 71 additions and 89 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -79,7 +79,7 @@ Collate:
     'internalWrappers.R'
     'mergeDependencies.R'
     'owner.R'
-    'package.R'
+    'packages.R'
     'parentId.R'
     'print.R'
     'printCmd.R'

diff --git a/NAMESPACE b/NAMESPACE
@@ -44,7 +44,7 @@ export(installPackage)
 export(mergeDependencies)
 export(name)
 export(owner)
-export(package)
+export(packages)
 export(parentId)
 export(printCmd)
 export(progressBar)

diff --git a/R/datasheet.R b/R/datasheet.R
@@ -10,7 +10,7 @@ NULL
 #'
 #' @details
 #' If \code{summary=TRUE} or \code{summary=NULL} and \code{name=NULL} a data.frame describing the 
-#' Datasheets is returned. If \code{optional=TRUE}, columns include: \code{scope}, \code{package}, 
+#' Datasheets is returned. If \code{optional=TRUE}, columns include: \code{scope}, \code{packages}, 
 #' \code{name}, \code{displayName}, \code{isSingle}, \code{isOutput}, \code{data}. data only displayed for 
 #' a SyncroSim \code{\link{Scenario}}. \code{dataInherited} and \code{dataSource} columns 
 #' added if a Scenario has dependencies. If \code{optional=FALSE}, columns include: 
@@ -236,7 +236,7 @@ setMethod("datasheet",
       n <- name[i]
       if (!grepl("_", n, fixed = TRUE)) {
         l = ssimLibrary(.filepath(ssimObject), summary=T)
-        p = l$value[l$property == "Package Name:"]
+        p = l$value[l$property == "Package Names:"][1] #TODO: test
         n <- paste0(p, "_", n)
       }
 

diff --git a/R/datasheetRaster.R b/R/datasheetRaster.R
@@ -224,7 +224,7 @@ setMethod("datasheetRaster", signature(ssimObject = "Scenario"), function(ssimOb
 
   if (!grepl("_", datasheet, fixed = )) {
     l = ssimLibrary(.filepath(ssimObject), summary=T)
-    p = l$value[l$property == "Package Name:"]
+    p = l$value[l$property == "Package Names:"][1]
     datasheet <- paste0(p, "_", datasheet)
   }
 

diff --git a/R/datasheetSpatRaster.R b/R/datasheetSpatRaster.R
@@ -215,7 +215,7 @@ setMethod("datasheetSpatRaster", signature(ssimObject = "Scenario"), function(ss
 
   if (!grepl("_", datasheet, fixed = )) {
     l = ssimLibrary(.filepath(ssimObject), summary=T)
-    p = l$value[l$property == "Package Name:"]
+    p = l$value[l$property == "Package Names:"][1] #TODO: test
     datasheet <- paste0(p, "_", datasheet)
   }
 

diff --git a/R/info.R b/R/info.R
@@ -1,8 +1,8 @@
 #' Retrieves information about a library
 #' 
 #' Retrieves some basic metadata about a SsimLibrary: Name, Owner, Last Modified, 
-#' Size, Read Only, Package Name, Package Description, Current Package Version,
-#' Minimum Package Version, External input files, External output files, 
+#' Size, Read Only, Package Names, Package Description, Current Package Versions,
+#' Minimum Package Versions, External input files, External output files, 
 #' Temporary files, Backup files.
 #' 
 #' @param ssimLibrary \code{\link{SsimLibrary}} object

diff --git a/R/installPackage.R b/R/installPackage.R
@@ -66,8 +66,8 @@ setMethod("installPackage", signature(session = "Session"), function(name, sessi
       }
     }
   } else {
-    packages <- package(session)
-    if (is.element(name, packages$name)) {
+    pkgs <- packages(session)
+    if (is.element(name, pkgs$name)) {
       tt <- (paste0("Package <", name, "> is already installed"))
     } else {
       tt <- command(args = list(install = name), session, program = "SyncroSim.PackageManager.exe")

diff --git a/R/internalHelpers.R b/R/internalHelpers.R
@@ -46,12 +46,12 @@ backupEnabled <- function(path) {
 deleteDatasheet <- function(x, datasheet, datasheets, cProj = NULL, cScn = NULL, cProjName = NULL, cScnName = NULL, out = list(), force) {
   out <- list()
   lib = ssimLibrary(.filepath(x), summary=T)
-  pkg = lib$value[lib$property == "Package Name:"]
 
   for (j in seq(length.out = length(datasheet))) {
     cName <- datasheet[j]
 
     if (!grepl("_", cName, fixed = TRUE)) {
+      pkg = lib$value[lib$property == "Package Names:"][1]
       cName <- paste0(pkg, "_", cName)
     }
 
@@ -175,16 +175,6 @@ createCondaEnv <- function(libPath, currentPackages, session) {
 
   message("Creating Conda environments. Please wait...")
 
-  # Check if Conda is installed
-  # tt <- command(list(conda = NULL, config = NULL), session)
-  # if (identical(tt, "No Conda configuration yet.")){
-  #   tt <- command(list(setprop = NULL,
-  #                      lib = libPath,
-  #                      useconda = "no"), session)
-  #   message("Conda must be installed to use Conda environments.")
-  #   return(TRUE)
-  # }
-
   # Check if environment needs to be created, create if doesn't exist yet
   for (package in currentPackages) {
     tt <- command(list(conda = NULL, createenv = NULL, pkg = package), session)

diff --git a/R/package.R → R/packages.R b/R/package.R → R/packages.R
@@ -5,14 +5,15 @@ NULL
 
 #' Installed or available packages
 #'
-#' Retrieves the packages installed or available for this version of SyncroSim.
+#' Retrieves the packages installed or available in the current session if 
+#' called on a \code{\link{Session}} object, or the packages added to a 
+#' SyncroSim Library if called on a \code{\link{SsimLibrary}} object.
 #'
 #' @param ssimObject \code{\link{Session}} or 
 #' \code{\link{SsimLibrary}} object. If \code{NULL} (default), \code{session()}
 #' will be used
-#' @param installed logical or character. \code{TRUE} (default) to list installed packages, 
-#' \code{FALSE} to list available packages, and "BASE" to list installed base 
-#' packages
+#' @param installed logical or character. \code{TRUE} (default) to list 
+#' installed packages or \code{FALSE} to list available packages on the server
 #' @param listTemplates character. Name of a SyncroSim package. If not \code{NULL} 
 #' (default), then lists all templates available for that package. The package
 #' must be installed in the current Session. Ignored if ssimObject is a 
@@ -32,49 +33,45 @@ NULL
 #' myLibrary <- ssimLibrary(name = myLibraryName, session = mySession)
 #' 
 #' # List all installed packages
-#' package(mySession)
+#' packages(mySession)
 #' 
 #' # List all the installed base packages
-#' package(installed = "BASE")
+#' packages(installed = "BASE")
 #' 
 #' # List all available packages on the server (including currently installed)
-#' package(installed = FALSE)
+#' packages(installed = FALSE)
 #'  
-#' # Check the package you're SsimLibrary is currently using
-#' package(myLibrary)
+#' # Check the package(s) in your SsimLibrary
+#' packages(myLibrary)
 #' 
 #' # Check the templates available for an installed package
 #' installPackage("helloworldSpatial")
-#' package(listTemplates = "helloworldSpatial")
+#' packages(listTemplates = "helloworldSpatial")
 #' }
 #' 
 #' @export
-setGeneric("package", function(ssimObject = NULL, installed = TRUE, listTemplates = NULL) standardGeneric("package"))
+setGeneric("packages", function(ssimObject = NULL, installed = TRUE, listTemplates = NULL) standardGeneric("packages"))
 
-#' @rdname package
-setMethod("package", signature(ssimObject = "character"), function(ssimObject, installed = TRUE, listTemplates) {
+#' @rdname packages
+setMethod("packages", signature(ssimObject = "character"), function(ssimObject, installed = TRUE, listTemplates) {
   return(SyncroSimNotFound(ssimObject, installed))
 })
 
-#' @rdname package
-setMethod("package", signature(ssimObject = "missingOrNULL"), function(ssimObject, installed = TRUE, listTemplates) {
+#' @rdname packages
+setMethod("packages", signature(ssimObject = "missingOrNULL"), function(ssimObject, installed = TRUE, listTemplates) {
   ssimObject <- .session()
-  return(package(ssimObject, installed, listTemplates))
+  return(packages(ssimObject, installed, listTemplates))
 })
 
-#' @rdname package
-setMethod("package", signature(ssimObject = "Session"), function(ssimObject, installed = TRUE, listTemplates) {
+#' @rdname packages
+setMethod("packages", signature(ssimObject = "Session"), function(ssimObject, installed = TRUE, listTemplates) {
   if (is.null(listTemplates)) {
     arg <- "installed"
 
     if (installed == FALSE) {
       arg <- "available"
     }
 
-    if (installed == "BASE") {
-      arg <- "basepkgs"
-    }
-
     if (is.logical(installed)) {
       tt <- command(c(arg), ssimObject, program = "SyncroSim.PackageManager.exe")
 
@@ -119,11 +116,11 @@ setMethod("package", signature(ssimObject = "Session"), function(ssimObject, ins
   }
 })
 
-#' @rdname package
-setMethod("package", signature(ssimObject = "SsimLibrary"), function(ssimObject) {
+#' @rdname packages
+setMethod("packages", signature(ssimObject = "SsimLibrary"), function(ssimObject) {
   oInf <- info(ssimObject)
   property <- NULL
-  out <- data.frame(name = subset(oInf, property == "Package Name:")$value)
+  out <- data.frame(name = subset(oInf, property == "Package Names:")$value)
   out$description <- subset(oInf, property == "Package Description:")$value
   out$version <- subset(oInf, property == "Current Package Version:")$value
   return(out)

diff --git a/R/saveDatasheet.R b/R/saveDatasheet.R
@@ -159,7 +159,7 @@ setMethod("saveDatasheet", signature(ssimObject = "SsimObject"), function(ssimOb
 
     if (!grepl("_", name, fixed = )) {
       l = ssimLibrary(.filepath(ssimObject), summary=T)
-      p = l$value[l$property == "Package Name:"]
+      p = l$value[l$property == "Package Name:"][1] #TODO: test
       name <- paste0(p, "_", name)
     }
 

diff --git a/R/session.R b/R/session.R
@@ -96,10 +96,7 @@ setMethod(f = "initialize", signature = "Session", definition = function(.Object
 #' version(mySession)
 #' 
 #' # Data frame of the packages installed with this version of SyncroSim
-#' package(mySession) 
-#' 
-#' # Data frame of the base packages installed with this version of SyncroSim
-#' package(mySession, installed = "BASE") 
+#' packages(mySession)
 #' 
 #' # Set a new SyncroSim Session for the SyncroSim Project
 #' session(myProject) <- session(x = filepath(session(myProject)))

diff --git a/R/ssimLibrary.R b/R/ssimLibrary.R
@@ -32,10 +32,10 @@ setMethod(
       stop("A library name is required.")
     }
 
-    packageOptions <- package(session, installed = "BASE")
+    packageOptions <- packages(session, installed = TRUE)
 
     if (nrow(packageOptions) == 0) {
-      stop("No base packages are installed.  Use installPackage() to install a package.")
+      stop("No packages are installed.  Use installPackage() to install a package.")
     }
 
     if (identical(basename(name), name)) {
@@ -62,7 +62,7 @@ setMethod(
       }
 
       if (!is.element(package, packageOptions$name)) {
-        stop(paste(package, "not a base package. Use package(installed = \"BASE\") to see options."))
+        stop(paste(package, "not currently installed. Use package(installed = TRUE) to see options."))
       }
 
       pathBits <- strsplit(path, "/")[[1]]
@@ -99,7 +99,7 @@ setMethod(
         baseTemplateExists <- baseTemplate %in% baseTempsDataframe$Name
 
         if (!baseTemplateExists & !is.null(addon)) {
-          allPackageOptions <- package(session)
+          allPackageOptions <- packages(session)
           args <- list(list = NULL, templates = NULL,
                        package = allPackageOptions$name[allPackageOptions$name == addon],
                        csv = NULL)
@@ -203,10 +203,10 @@ setMethod(
       }
 
       if (!exists("packageOptions")) {
-        packageOptions <- package(session, installed = "BASE")
+        packageOptions <- packages(session, installed = TRUE)
       }
       expectedPackage <- packageOptions$name[packageOptions$name == package]
-      if (!grepl(expectedPackage, tt$value[tt$property == "Package Name:"])) {
+      if (!grepl(expectedPackage, tt$value[tt$property == "Package Names:"])) { #TODO: this is probably broken now
         stop(paste0("A library of that name and a different package type ", tt$value[tt$property == "Name:"], " already exists."))
       }
     }

diff --git a/R/uninstallPackage.R b/R/uninstallPackage.R
@@ -40,7 +40,7 @@ setMethod("uninstallPackage", signature(session = "missingOrNULL"), function(nam
 
 #' @rdname uninstallPackage
 setMethod("uninstallPackage", signature(session = "Session"), function(name, session, force) {
-  installed <- package(session)
+  installed <- packages(session)
   success <- FALSE
 
   if (!is.element(name, installed$name)) {

diff --git a/R/updatePackage.R b/R/updatePackage.R
@@ -71,7 +71,7 @@ setMethod("updatePackage", signature(session = "Session"), function(name, sessio
       return(invisible(success))
     }
   } else {
-    installed <- package(session)
+    installed <- packages(session)
 
     if (!is.element(name, installed$name)) {
       message(paste(name, ": The package is not installed."))

diff --git a/R/useConda.R b/R/useConda.R
@@ -88,7 +88,7 @@ setReplaceMethod(
 
       tt <- command(list(setprop = NULL, lib = .filepath(ssimObject), useconda = "yes"), .session(ssimObject))
 
-      currentPackages <- package(ssimObject)$name
+      currentPackages <- packages(ssimObject)$name
     }
 
     createCondaEnv(.filepath(ssimObject), currentPackages, .session(ssimObject))

diff --git a/man/datasheet.Rd b/man/datasheet.Rd
diff --git a/man/info.Rd b/man/info.Rd