[tests] tests and test files for *.h5 methods

tests/testthat/test-ogs6_h5.R

+helper_setup_h5 <- function(h5_file, group, time, geo,
+                            varname = NULL,
+                            var = NULL) {
+
+    rhdf5::h5createFile(h5_file)
+    rhdf5::h5createGroup(h5_file, group)
+    if (!is.null(geo)) {
+    rhdf5::h5write(geo, file = h5_file,
+                   name = paste0(group, "/geometry"))
+    }
+    if (!is.null(time)) {
+    rhdf5::h5write(time, file = h5_file,
+                   name = "/times")
+    }
+    if (!is.null(var)) {
+        rhdf5::h5write(var, file = h5_file,
+                       name = varname)
+    }
+}
+
+ test_that("transposed geometry is detected", {
+
+    h5_dir <- paste0(tmp_dir, "/test-h5")
+    dir.create(h5_dir)
+    geo <- array(as.matrix(expand.grid(seq(0, 3, length.out = 10),
+                                       seq(0, 2, length.out = 2),
+                                       seq(0, 1, length.out = 1))),
+                 c(20, 3, 1))
+    # not transposed
+    helper_setup_h5(paste0(h5_dir, "/test_1.h5"), group = "meshes",
+                    time = c(0, 2),
+                    geo)
+
+    ogs6_h5 <- OGS6_h5$new(paste0(h5_dir, "/test_1.h5"))
+    df <- ogs6_h5$get_df(group = "/meshes")
+    expect_equal(dim(df), c(40, 4))
+
+    # transposed
+    geo_t <- array(t(geo[, , 1]), c(3, 20, 1))
+    helper_setup_h5(paste0(h5_dir, "/test_2.h5"), group = "meshes",
+                    time = c(0, 2),
+                    geo_t)
+
+    ogs6_h5 <- OGS6_h5$new(paste0(h5_dir, "/test_2.h5"))
+    df <- ogs6_h5$get_df(group = "/meshes")
+    expect_equal(dim(df), c(40, 4))
+
+    unlink(h5_dir, recursive = TRUE)
+})
+
+test_that("Projects with no times field work", {
+    h5_dir <- paste0(tmp_dir, "/test-h5")
+    dir.create(h5_dir)
+    geo <- array(as.matrix(expand.grid(seq(0, 3, length.out = 5),
+                                       seq(0, 2, length.out = 1),
+                                       seq(0, 1, length.out = 1))),
+                 c(5, 3, 1))
+
+    helper_setup_h5(paste0(h5_dir, "/test_1.h5"), group = "meshes",
+                    time = NULL,
+                    geo)
+    ogs6_h5 <- OGS6_h5$new(paste0(h5_dir, "/test_1.h5"))
+    expect_silent(df <- ogs6_h5$get_df(group = "/meshes"))
+    expect_equal(dim(df), c(5, 4))
+
+    unlink(h5_dir, recursive = TRUE)
+})
+
+test_that("Projects with no geometry field work", {
+    h5_dir <- paste0(tmp_dir, "/test-h5")
+    dir.create(h5_dir)
+
+    helper_setup_h5(paste0(h5_dir, "/test_1.h5"), group = "meshes",
+                    time = c(1, 2, 3, 4),
+                    geo = NULL)
+    ogs6_h5 <- OGS6_h5$new(paste0(h5_dir, "/test_1.h5"))
+    expect_silent(df <- ogs6_h5$get_df(group = "/", names = "times"))
+    expect_equal(dim(df), c(4, 4))
+
+    unlink(h5_dir, recursive = TRUE)
+})
+
+
+test_that("Nonconformable arguments throw error", {
+    h5_dir <- paste0(tmp_dir, "/test-h5")
+    dir.create(h5_dir)
+    geo <- array(as.matrix(expand.grid(seq(0, 3, length.out = 10),
+                                       seq(0, 2, length.out = 2),
+                                       seq(0, 1, length.out = 1))),
+                 c(20, 3, 1))
+
+    v <- matrix(seq(0, 10, length.out = 10),  ncol = 2)
+
+    helper_setup_h5(paste0(h5_dir, "/test_1.h5"), group = "meshes",
+                    time = c(0, 2),
+                    geo,
+                    varname = "/meshes/pressure",
+                    var = v)
+
+    ogs6_h5 <- OGS6_h5$new(paste0(h5_dir, "/test_1.h5"))
+
+    expect_error({
+        df <- ogs6_h5$get_df(group = "/meshes",
+                             names = "pressure")
+    })
+
+    unlink(h5_dir, recursive = TRUE)
+})
+
+
+# tests with benchmark h5 files -------------------------------------------
+
+test_that("benchmark h5 file cube_1e3.h5 passes", {
+    h5_path <- system.file("/extdata/benchmarks/EllipticPETSc",
+                           "cube_1e3.h5",
+                           package = "r2ogs6")
+    ogs6_h5 <- OGS6_h5$new(h5_path)
+    expect_silent(df <- ogs6_h5$get_df("/t_0", "pressure"))
+    expect_equal(dim(df), c(1895, 5))
+    expect_equal(colnames(df), c("x", "y", "z", "time", "pressure"))
+})
+
+test_that("benchmark h5 file cube_1e3_np2.h5 passes", {
+    h5_path <- system.file("/extdata/benchmarks/EllipticPETSc",
+                           "cube_1e3_np2.h5",
+                           package = "r2ogs6")
+    ogs6_h5 <- OGS6_h5$new(h5_path)
+    expect_silent(df <- ogs6_h5$get_df("/meshes/cube_1x1x1_hex_1e3",
+                                       "pressure"))
+    expect_equal(dim(df), c(3274, 5))
+    expect_equal(colnames(df), c("x", "y", "z", "time", "pressure"))
+})
+
+test_that("benchmark h5 file cube_1e3_np2.h5 passes", {
+    h5_path <- system.file("/extdata/benchmarks/EllipticPETSc",
+                           "cube_1e3_np3.h5",
+                           package = "r2ogs6")
+    ogs6_h5 <- OGS6_h5$new(h5_path)
+    expect_silent(df <- ogs6_h5$get_df("/t_0", "pressure"))
+    expect_equal(dim(df), c(1895, 5))
+    expect_equal(colnames(df), c("x", "y", "z", "time", "pressure"))
+})
+
+test_that("benchmark h5 file square_5x5_tris_32.h5 passes", {
+    h5_path <- system.file("/extdata/benchmarks/EllipticPETSc",
+                           "square_5x5_tris_32.h5",
+                           package = "r2ogs6")
+    ogs6_h5 <- OGS6_h5$new(h5_path)
+    expect_silent(df <- ogs6_h5$get_df("/meshes/square_5x5_tris_32",
+                                       c("pressure", "MaterialIDs")))
+    expect_equal(dim(df), c(200, 6))
+    expect_equal(colnames(df),
+                 c("x", "y", "z", "time", "pressure", "MaterialIDs"))
+})
+
+
+test_that("helpful error msg for wrong h5 names", {
+
+    h5_path <- system.file("/extdata/benchmarks/EllipticPETSc",
+                          "cube_1e3.h5",
+                          package = "r2ogs6")
+
+    ogs6_h5 <- OGS6_h5$new(h5_path)
+    expect_error(ogs6_h5$get_df("/t_0", "/tpolgy"),
+                 regexp = "Name /tpolgy not found in file cube_1e3.h5")
+})
+
+
+