Merge branch '42-bugfixes' into 'master'

Resolve "bugfixes"

Closes #42

See merge request !24

R/ogs6_vtu.R

@@ -232,8 +232,7 @@ OGS6_vtu <- R6::R6Class(
             }else{
                 # Check class
                 private$.vtkUnstructuredGrid <- value
-                private$.dsa_vtkUnstructuredGrid <-
-                    vtk$numpy_interface$dataset_adapter$WrapDataObject(value)
+                private$.dsa_vtkUnstructuredGrid <- dsa$WrapDataObject(value)
             }
         },
 

R/read_in_gml.R

@@ -8,10 +8,10 @@
 #' @noRd
 read_in_points <- function(xml_doc) {
 
-    points_tibble <- tibble::tibble(x = c(),
-                                    y = c(),
-                                    z = c(),
-                                    name = c())
+    points_tibble <- tibble::tibble(x = numeric(),
+                                    y = numeric(),
+                                    z = numeric(),
+                                    name = character())
 
     points_nodeset <- xml2::xml_find_all(xml_doc, "//points/*")
 

R/sim_utils.R

@@ -133,6 +133,9 @@ ogs6_call_ogs6 <- function(ogs6_obj,
     if(missing(ogs6_bin_path)){
         ogs6_bin_path <- unlist(options("r2ogs6.default_ogs6_bin_path"))
     }
+    else if(is.null(ogs6_bin_path)){
+        ogs6_bin_path <- unlist(options("r2ogs6.default_ogs6_bin_path"))
+    }
 
     assertthat::assert_that(assertthat::is.string(ogs6_bin_path))
     assertthat::assert_that(assertthat::is.flag(verbose))
@@ -244,10 +247,7 @@ ogs6_read_output_files <- function(ogs6_obj){
                             "\\.pvd$",
                             full.names = TRUE)
 
-    for(i in seq_len(length(pvd_paths))){
-        ogs6_obj$pvds <- c(ogs6_obj$pvds,
-                           list(OGS6_pvd$new(pvd_path = pvd_paths[[i]])))
-    }
+    ogs6_obj$pvds <- lapply(pvd_paths, function(x){OGS6_pvd$new(pvd_path = x)})
 
     return(invisible())
 }
@@ -285,8 +285,14 @@ run_benchmark <- function(prj_path,
     ogs6_obj <- OGS6$new(sim_name = sim_name,
                          sim_path = sim_path)
 
+    # check if *.gml file is present
+    read_gml <-  ifelse(
+                    any(sapply(list.files(), function(x) grepl(".gml", x))),
+                    T, F)
+
     read_in_prj(ogs6_obj = ogs6_obj,
-                prj_path = prj_path)
+                prj_path = prj_path,
+                read_in_gml = read_gml)
 
     return(invisible(ogs6_run_simulation(ogs6_obj,
                                     ogs6_bin_path = ogs6_bin_path)))

R/zzz.R

@@ -3,6 +3,7 @@
 
 # Python vtk library reference
 vtk <- NULL
+dsa <- NULL
 
 .onLoad <- function(libname, pkgname){
 
@@ -30,6 +31,8 @@ vtk <- NULL
 
     # use superassignments to update global Python references
     vtk <<- reticulate::import("vtk", delay_load = TRUE)
+    dsa <<- reticulate::import("vtk.numpy_interface.dataset_adapter",
+                               delay_load = TRUE)
 
     return(invisible())
 }

inst/examples/Theis_problem/theis_problem.R

@@ -15,7 +15,6 @@ library(r2ogs6)
 # Then we can create a simulation object.
 
 ogs6_obj <- OGS6$new(sim_name = "axisym_theis",
-                     sim_id = 1,
                      sim_path = "D:/OGS_Sim/")
 
 
@@ -25,7 +24,7 @@ ogs6_obj <- OGS6$new(sim_name = "axisym_theis",
 prj_path <- "inst/extdata/benchmarks/AxiSymTheis/axisym_theis.prj"
 
 # Read in the benchmark into our simulation object
-read_in_prj(ogs6_obj, prj_path)
+read_in_prj(ogs6_obj, prj_path, T)
 
 
 #===== Run simulation =====

tests/testthat/setup.R

+# setup for tests
+tmp_dir <- tempdir()
\ No newline at end of file

tests/testthat/test-export_gml.R

@@ -3,8 +3,7 @@
 test_that("export_gml works", {
 
     # Get extdata directory and create folder for the test
-    extdata_path <- system.file("extdata/test_tempdirs/", package = "r2ogs6")
-    test_path <- paste0(extdata_path, "/export_gml_test")
+    test_path <- paste0(tmp_dir, "/export_gml_test")
     dir.create(test_path)
 
     # Define gml object

tests/testthat/test-export_prj.R

@@ -14,7 +14,7 @@ test_that("export_prj works", {
     prj_path <- (system.file("extdata/benchmarks/flow_free_expansion",
                              "flow_free_expansion.prj", package = "r2ogs6"))
 
-    read_in_prj(ogs6_obj, prj_path)
+    read_in_prj(ogs6_obj, prj_path, read_in_gml = T)
 
     # Now export it
     export_prj(ogs6_obj)

tests/testthat/test-ogs6_vtu.R

@@ -24,8 +24,9 @@ test_that("OGS6_vtu initialization works", {
 
     vtu_obj <- OGS6_vtu$new(vtu_path = vtu_path)
 
-    expect_equal("vtkmodules.vtkCommonDataModel.vtkUnstructuredGrid" %in%
-                     class(vtu_obj$vtkUnstructuredGrid), TRUE)
+    classes <- c("vtkCommonDataModelPython.vtkUnstructuredGrid",
+                 "vtkmodules.vtkCommonDataModel.vtkUnstructuredGrid")
+    expect_equal(any(classes %in% class(vtu_obj$vtkUnstructuredGrid)), TRUE)
 
     expect_equal(vtu_obj$number_of_points, 8)
     expect_equal(vtu_obj$number_of_cells, 1)

tests/testthat/test-read_in_prj.R

@@ -190,7 +190,8 @@ test_that("read_in_prj works for processes/include tags", {
                          sim_path = "sim_path")
 
     read_in_prj(ogs6_obj,
-                prj_path)
+                prj_path,
+                read_in_gml = T)
 
     expect_equal(length(ogs6_obj$processes), 1)
     expect_equal(names(ogs6_obj$processes)[[1]], "include")
@@ -207,7 +208,8 @@ test_that("read_in_prj works for EmbeddedFracturePermeability/cube.prj", {
                          sim_path = "sim_path")
 
     read_in_prj(ogs6_obj,
-                prj_path)
+                prj_path,
+                read_in_gml = T)
 
     expect_equal(ogs6_obj$processes[[1]]$name, "HM")
 })

tests/testthat/test-sim_utils.R

@@ -3,12 +3,12 @@
 skip_if_ogs6_missing <- function() {
 
     ogs6_path <- unlist(options("r2ogs6.default_ogs6_bin_path"))
-
+    print(ogs6_path)
     if(is.null(ogs6_path) || !file.exists(ogs6_path)){
         skip("ogs executable not available for testing")
     }
 
-    skip("Skipping tests that call ogs6_run_simulation()")
+    #skip("Skipping tests that call ogs6_run_simulation()")
 }
 
 
@@ -16,8 +16,8 @@ test_that("ogs6_run_simulation works for flow_no_strain.prj", {
 
     skip_if_ogs6_missing()
 
-    extdata_path <- system.file("extdata/test_tempdirs/", package = "r2ogs6")
-    sim_path <- paste0(extdata_path, "/run_simulation_test")
+    #extdata_path <- system.file("extdata/test_tempdirs/", package = "r2ogs6")
+    sim_path <- paste0(tmp_dir, "/run_simulation_test")
     dir.create(sim_path)
 
     prj_path <- system.file("extdata/benchmarks/flow_no_strain/",
@@ -25,12 +25,10 @@ test_that("ogs6_run_simulation works for flow_no_strain.prj", {
                             package = "r2ogs6")
 
     # Define OGS6 object
-    ogs6_obj <- OGS6$new(sim_name = "sim",
-                         sim_id = 1,
-                         sim_path = sim_path)
+    ogs6_obj <- OGS6$new(sim_name = "sim", sim_path = sim_path)
 
     # Read in .prj data
-    read_in_prj(ogs6_obj, prj_path)
+    read_in_prj(ogs6_obj, prj_path, read_in_gml = T)
 
     # Run simulation
     e <- ogs6_run_simulation(ogs6_obj)
@@ -53,8 +51,7 @@ test_that("ogs6_run_simulation works for flow_no_strain.prj", {
 
 test_that("ogs6_export_sim_files works", {
 
-    extdata_path <- system.file("extdata/test_tempdirs/", package = "r2ogs6")
-    test_path <- paste0(extdata_path, "/export_all_sim_files_test")
+    test_path <- paste0(tmp_dir, "/export_all_sim_files_test")
     dir.create(test_path)
 
     prj_path <- (system.file("extdata/benchmarks/Elliptic/circle_radius_1",
@@ -64,7 +61,8 @@ test_that("ogs6_export_sim_files works", {
                          sim_path = test_path)
 
     read_in_prj(ogs6_obj,
-                prj_path)
+                prj_path,
+                read_in_gml = T)
 
     # Now export all files
     ogs6_export_sim_files(ogs6_obj)
@@ -91,8 +89,8 @@ test_that("run_benchmark works for flow_free_expansion.prj", {
 
     skip_if_ogs6_missing()
 
-    extdata_path <- system.file("extdata/test_tempdirs/", package = "r2ogs6")
-    sim_path <- paste0(extdata_path, "/run_benchmark_test")
+    #extdata_path <- system.file("extdata/test_tempdirs/", package = "r2ogs6")
+    sim_path <- paste0(tmp_dir, "/run_benchmark_test")
     dir.create(sim_path)
 
     prj_path <- system.file("extdata/benchmarks/flow_free_expansion/",