re-enable obsp and varp roundtrip tests

tests/testthat/test-roundtrip-obspvarp.R

@@ -1,125 +1,122 @@
-# TODO: re-enable
-# nolint start
-# skip_if_no_anndata()
-# skip_if_not_installed("rhdf5")
+skip_if_no_anndata()
+skip_if_not_installed("rhdf5")
 
-# data <- generate_dataset(10L, 20L)
+data <- generate_dataset(10L, 20L)
 
-# for (name in names(data$obsp)) {
-#   test_that(paste0("roundtrip with obsp and varp '", name, "'"), {
-#     # create anndata
-#     ad <- AnnData(
-#       obsp = data$obsp[name],
-#       varp = data$varp[name],
-#       obs_names = data$obs_names,
-#       var_names = data$var_names
-#     )
+for (name in names(data$obsp)) {
+  test_that(paste0("roundtrip with obsp and varp '", name, "'"), {
+    # create anndata
+    ad <- AnnData(
+      obsp = data$obsp[name],
+      varp = data$varp[name],
+      obs_names = data$obs_names,
+      var_names = data$var_names
+    )
 
-#     # write to file
-#     filename <- withr::local_file(paste0("roundtrip_obspvarp_", name, ".h5ad"))
-#     write_h5ad(ad, filename)
+    # write to file
+    filename <- withr::local_file(paste0("roundtrip_obspvarp_", name, ".h5ad"))
+    write_h5ad(ad, filename)
 
-#     # read from file
-#     ad_new <- read_h5ad(filename, to = "HDF5AnnData")
+    # read from file
+    ad_new <- read_h5ad(filename, to = "HDF5AnnData")
 
-#     # expect slots are unchanged
-#     expect_equal(
-#       ad_new$obsp[[name]],
-#       data$obsp[[name]],
-#       ignore_attr = TRUE,
-#       tolerance = 1e-6
-#     )
-#     expect_equal(
-#       ad_new$varp[[name]],
-#       data$varp[[name]],
-#       ignore_attr = TRUE,
-#       tolerance = 1e-6
-#     )
-#   })
-# }
+    # expect slots are unchanged
+    expect_equal(
+      ad_new$obsp[[name]],
+      data$obsp[[name]],
+      ignore_attr = TRUE,
+      tolerance = 1e-6
+    )
+    expect_equal(
+      ad_new$varp[[name]],
+      data$varp[[name]],
+      ignore_attr = TRUE,
+      tolerance = 1e-6
+    )
+  })
+}
 
-# for (name in names(data$obsp)) {
-#   test_that(paste0("reticulate->hdf5 with obsp and varp '", name, "'"), {
-#     # add rownames
-#     obsp <- data$obsp[name]
-#     varp <- data$varp[name]
-#     rownames(obsp[[name]]) <- colnames(obsp[[name]]) <- data$obs_names
-#     rownames(varp[[name]]) <- colnames(varp[[name]]) <- data$var_names
+for (name in names(data$obsp)) {
+  test_that(paste0("reticulate->hdf5 with obsp and varp '", name, "'"), {
+    # add rownames
+    obsp <- data$obsp[name]
+    varp <- data$varp[name]
+    rownames(obsp[[name]]) <- colnames(obsp[[name]]) <- data$obs_names
+    rownames(varp[[name]]) <- colnames(varp[[name]]) <- data$var_names
 
-#     #  create anndata
-#     ad <- anndata::AnnData(
-#       obsp = obsp,
-#       varp = varp,
-#       shape = dim(data$X),
-#       obs = data.frame(row.names = data$obs_names),
-#       var = data.frame(row.names = data$var_names)
-#     )
+    #  create anndata
+    ad <- anndata::AnnData(
+      obsp = obsp,
+      varp = varp,
+      shape = dim(data$X),
+      obs = data.frame(row.names = data$obs_names),
+      var = data.frame(row.names = data$var_names)
+    )
 
-#     # write to file
-#     filename <- withr::local_file(paste0("reticulate_to_hdf5_obspvarp_", name, ".h5ad"))
-#     ad$write_h5ad(filename)
+    # write to file
+    filename <- withr::local_file(paste0("reticulate_to_hdf5_obspvarp_", name, ".h5ad"))
+    ad$write_h5ad(filename)
 
-#     # read from file
-#     ad_new <- HDF5AnnData$new(filename)
+    # read from file
+    ad_new <- HDF5AnnData$new(filename)
 
-#     # expect slots are unchanged
-#     expect_equal(
-#       ad_new$obsp[[name]],
-#       data$obsp[[name]],
-#       tolerance = 1e-6
-#     )
-#     expect_equal(
-#       ad_new$varp[[name]],
-#       data$varp[[name]],
-#       tolerance = 1e-6
-#     )
-#   })
-# }
+    # expect slots are unchanged
+    expect_equal(
+      ad_new$obsp[[name]],
+      data$obsp[[name]],
+      tolerance = 1e-6
+    )
+    expect_equal(
+      ad_new$varp[[name]],
+      data$varp[[name]],
+      tolerance = 1e-6
+    )
+  })
+}
 
-# for (name in names(data$obsp)) {
-#   test_that(paste0("hdf5->reticulate with obsp and varp '", name, "'"), {
-#     # write to file
-#     filename <- withr::local_file(paste0("hdf5_to_reticulate_obspvarp_", name, ".h5ad"))
+for (name in names(data$obsp)) {
+  test_that(paste0("hdf5->reticulate with obsp and varp '", name, "'"), {
+    # write to file
+    filename <- withr::local_file(paste0("hdf5_to_reticulate_obspvarp_", name, ".h5ad"))
 
-#     # strip rownames
-#     obsp <- data$obsp[name]
-#     varp <- data$varp[name]
-#     rownames(obsp[[name]]) <- NULL
-#     rownames(varp[[name]]) <- NULL
+    # strip rownames
+    obsp <- data$obsp[name]
+    varp <- data$varp[name]
+    rownames(obsp[[name]]) <- NULL
+    rownames(varp[[name]]) <- NULL
 
-#     # make anndata
-#     ad <- HDF5AnnData$new(
-#       file = filename,
-#       obsp = obsp,
-#       varp = varp,
-#       obs_names = data$obs_names,
-#       var_names = data$var_names
-#     )
+    # make anndata
+    ad <- HDF5AnnData$new(
+      file = filename,
+      obsp = obsp,
+      varp = varp,
+      obs_names = data$obs_names,
+      var_names = data$var_names
+    )
 
-#     # read from file
-#     ad_new <- anndata::read_h5ad(filename)
+    # read from file
+    ad_new <- anndata::read_h5ad(filename)
 
-#     # expect slots are unchanged
-#     obsp_ <- ad_new$obsp[[name]]
-#     if (!is.null(obsp_)) {
-#       rownames(obsp_) <- colnames(obsp_) <- NULL
-#     }
-#     expect_equal(
-#       obsp_,
-#       data$obsp[[name]],
-#       ignore_attr = TRUE,
-#       tolerance = 1e-6
-#     )
-#     varp_ <- ad_new$varp[[name]]
-#     if (!is.null(varp_)) {
-#       rownames(varp_) <- colnames(varp_) <- NULL
-#     }
-#     expect_equal(
-#       varp_,
-#       data$varp[[name]],
-#       ignore_attr = TRUE,
-#       tolerance = 1e-6
-#     )
-#   })
-# }
-# nolint end
+    # expect slots are unchanged
+    obsp_ <- ad_new$obsp[[name]]
+    if (!is.null(obsp_)) {
+      rownames(obsp_) <- colnames(obsp_) <- NULL
+    }
+    expect_equal(
+      obsp_,
+      data$obsp[[name]],
+      ignore_attr = TRUE,
+      tolerance = 1e-6
+    )
+    varp_ <- ad_new$varp[[name]]
+    if (!is.null(varp_)) {
+      rownames(varp_) <- colnames(varp_) <- NULL
+    }
+    expect_equal(
+      varp_,
+      data$varp[[name]],
+      ignore_attr = TRUE,
+      tolerance = 1e-6
+    )
+  })
+}