active field for h5_path - vignette entry for rhdf5

.gitlab-ci.yml

@@ -21,6 +21,7 @@ test:
     # checks if the packages from the Imports, Suggests, LinkinTo field
     # are already installed in the cache
     - R -e '.libPaths(new = Sys.getenv("R_LIBS_USER"))'
+    - R -e 'withr::with_libpaths(new = Sys.getenv("R_LIBS_USER"), {install.packages("BiocManager"); BiocManager::install("rhdf5")})'
     # Build and Check r2ogs6
     - R CMD build . --no-build-vignettes --no-manual
     - R CMD check $(ls -1t *.tar.gz | head -n 1) --no-build-vignettes --no-manual

R/ogs6_h5.R

@@ -18,7 +18,7 @@ OGS6_h5 <- R6::R6Class("OGS6_h5",
             assertthat::is.string(h5_path)
             assertthat::assert_that(file.exists(h5_path))
             private$h5_info <- rhdf5::h5ls(h5_path)
-            private$h5_path <- h5_path
+            private$.h5_path <- h5_path
             private$valid_names <-
                 c("/",
                   apply(private$h5_info[, 1:2], 1,
@@ -39,7 +39,7 @@ OGS6_h5 <- R6::R6Class("OGS6_h5",
         print = function(){
             cat("OGS6_h5\n")
             cat("h5 path:\n")
-            cat(private$h5_path, "\n\n")
+            cat(private$.h5_path, "\n\n")
             cat("# h5 file structure",
                 paste0(rep("-", cli::console_width() - 20), collapse = ""),
                 "\n")
@@ -58,10 +58,9 @@ OGS6_h5 <- R6::R6Class("OGS6_h5",
         #' \dontrun{h5_list <- ogs6_obj$h5s[[1]]$get_h5("/times")}
         get_h5 = function(name = "/", ...) {
             assertthat::assert_that(name %in% private$valid_names)
-            return(rhdf5::h5read(file = private$h5_path, name, ...))
+            return(rhdf5::h5read(file = private$.h5_path, name, ...))
         },
 
-        #' @title Extract a *tibble* from a *.h5 file
         #' @description Method to retrieve \code{HDF5} output as a \code{tibble}
         #' assuming a standardized structure of \code{OGS6 HDF5} output.
         #' times and geometry are added by default.
@@ -96,7 +95,7 @@ OGS6_h5 <- R6::R6Class("OGS6_h5",
                             names[which(!name_paths %in%
                                             private$valid_names)],
                             " not found in file ",
-                            basename(private$h5_path)
+                            basename(private$.h5_path)
                                            ))
 
             lst <- private$add_geo_time(group) # adds geometry and time
@@ -119,9 +118,23 @@ OGS6_h5 <- R6::R6Class("OGS6_h5",
             return(dplyr::bind_cols(lst))
         }
     ),
+    # === active fields
+
+    active = list(
+        #' @field h5_path
+        #' Getter/setter for private parameter `.h5_path`
+        h5_path = function(value) {
+            if (missing(value)) {
+                private$.h5_path
+            } else {
+                assertthat::assert_that(assertthat::is.string(value))
+                private$.h5_path <- value
+            }
+        }
+    ),
     private = list(
         h5_info = NULL,
-        h5_path = NULL,
+        .h5_path = NULL,
         valid_names = NULL,
 
         add_geo_time = function(group) {

vignettes/user_workflow_vignette.Rmd

 ---
 title: "r2ogs6 User Guide"
 author: "Ruben Heinrich"
-#output: html_document
-output: rmarkdown::html_vignette
+output: html_document
+#output: rmarkdown::html_vignette
 vignette: >
   %\VignetteIndexEntry{r2ogs6 User Guide}
   %\VignetteEngine{knitr::rmarkdown}
@@ -182,7 +182,16 @@ As can be seen, hdf5 files have a very particular structure. To work with the da
 ```{r}
 h5_list <- ogs6_obj$h5s[[1]]$get_h5("/")
 ```
-
+  
+Other functions such as HDF5 handles for dataset processing can be used directly from the *rhdf5* package, of course. The path to the hd5 file is available as an active field `h5_path` that can be accessed or changed in the *OGS6* object.
+```{r}
+example_h5 <- rhdf5::H5Fopen(ogs6_obj$h5s[[1]]$h5_path)
+example_h5
+str(example_h5$t_0)
+rhdf5::h5closeAll()
+```
+  
+  
 If the file has a reasonably "clean" structure, a more convenient way of importing the data is using the method `get_df` that returns a *tibble* table. 
 
 ```{r}