From eaf29100e81c2fedeabafb8756337a94ba2cc403 Mon Sep 17 00:00:00 2001
From: Johannes Boog <johannesboog@yahoo.de>
Date: Thu, 24 Nov 2022 17:09:58 +0100
Subject: [PATCH] [bugfix] namespace imports]
---
DESCRIPTION | 13 ++++---------
NAMESPACE | 7 +++++++
R/generate_benchmark_script.R | 2 +-
R/ogs6.R | 4 ++++
R/ogs6_chain.R | 1 +
R/ogs6_ensemble.R | 2 ++
R/ogs6_gml.R | 1 +
R/ogs6_h5.R | 2 ++
R/ogs6_msh.R | 1 +
R/ogs6_pvd.R | 2 ++
R/ogs6_vtu.R | 3 ++-
11 files changed, 27 insertions(+), 11 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index f69e37c..8e5f34a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
Package: r2ogs6
Type: Package
Title: An API to the multi-physics simulator OpenGeoSys-v6
-Version: 0.2.0
+Version: 0.6.41
Authors@R: c(person(given = "Ruben",
family = "Heinrich",
role = c("aut"),
@@ -33,27 +33,22 @@ Suggests:
devtools,
ggplot2,
BiocManager,
- rhdf5
+ rhdf5,
+ rmarkdown
Imports:
- purrr,
xml2,
tibble,
R6,
stringr,
- readr,
assertthat,
crayon,
utils,
- rmarkdown,
- curl,
dplyr,
- rlang,
doParallel,
reticulate,
config,
- sticky,
foreach
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.1
VignetteBuilder: knitr
Depends:
R (>= 2.10)
diff --git a/NAMESPACE b/NAMESPACE
index a2f3112..f0de41a 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -67,4 +67,11 @@ export(prj_time_stepping)
export(prj_tl_process)
export(prj_vtkdiff)
export(read_in_prj)
+importFrom(R6,R6Class)
+importFrom(crayon,green)
+importFrom(crayon,red)
+importFrom(crayon,yellow)
+importFrom(doParallel,registerDoParallel)
+importFrom(dplyr,bind_cols)
+importFrom(dplyr,bind_rows)
importFrom(foreach,"%dopar%")
diff --git a/R/generate_benchmark_script.R b/R/generate_benchmark_script.R
index aa26f3a..d2ef9a2 100644
--- a/R/generate_benchmark_script.R
+++ b/R/generate_benchmark_script.R
@@ -399,7 +399,7 @@ construct_add_call <- function(object, nested_call = FALSE) {
}
#For lists we need to use recursion
- if(class(object) == "list"){
+ if(inherits(object, "list")){
element_strs <- lapply(object, function(x){construct_add_call(x, TRUE)})
diff --git a/R/ogs6.R b/R/ogs6.R
index 0955da2..df0bcc3 100644
--- a/R/ogs6.R
+++ b/R/ogs6.R
@@ -5,6 +5,7 @@
#' OGS6
#' @description Constructor for the \code{OGS6} base class
#' @export
+#' @importFrom R6 R6Class
OGS6 <- R6::R6Class("OGS6",
public = list(
@@ -171,6 +172,9 @@ OGS6 <- R6::R6Class("OGS6",
#' @examples
#' ogs6_obj <- OGS6$new(sim_name = "my_sim", sim_path = "my/path")
#' ogs6_obj$get_status()
+ #' @importFrom crayon red
+ #' @importFrom crayon yellow
+ #' @importFrom crayon green
get_status = function(print_status = TRUE){
assertthat::assert_that(assertthat::is.flag(print_status))
diff --git a/R/ogs6_chain.R b/R/ogs6_chain.R
index 25d4fca..be7830b 100644
--- a/R/ogs6_chain.R
+++ b/R/ogs6_chain.R
@@ -5,6 +5,7 @@
#'OGS6_Chain
#'@description Constructor for the OGS6_Chain base class
#'@export
+#' @importFrom R6 R6Class
OGS6_Chain <- R6::R6Class(
"OGS6_Chain",
diff --git a/R/ogs6_ensemble.R b/R/ogs6_ensemble.R
index ce51aad..7b4bd31 100644
--- a/R/ogs6_ensemble.R
+++ b/R/ogs6_ensemble.R
@@ -100,6 +100,7 @@ OGS6_Ensemble <- R6::R6Class(
#' This is implementented via the 'parallel' package.
#' @param overwrite flag: Should existing files be overwritten?
#'@param verbose flag
+ #'@importFrom doParallel registerDoParallel
run_simulation = function(parallel = FALSE,
overwrite = T,
verbose = F){
@@ -186,6 +187,7 @@ OGS6_Ensemble <- R6::R6Class(
#' Defaults to first timestep.
#'@param end_at_timestep number: Optional: Timestep to end at. Defaults
#' to last timestep.
+ #'@importFrom dplyr bind_rows
get_point_data = function(pvd_id = 1,
point_ids,
keys,
diff --git a/R/ogs6_gml.R b/R/ogs6_gml.R
index 48ffb80..3077dc0 100644
--- a/R/ogs6_gml.R
+++ b/R/ogs6_gml.R
@@ -24,6 +24,7 @@
#' ))
#' )
#' @export
+#' @importFrom R6 R6Class
OGS6_gml <- R6::R6Class(
"OGS6_gml",
public = list(
diff --git a/R/ogs6_h5.R b/R/ogs6_h5.R
index 3fe6ee3..19c08cd 100644
--- a/R/ogs6_h5.R
+++ b/R/ogs6_h5.R
@@ -3,6 +3,7 @@
#' OGS6_h5
#' @description Small class to wrap \code{h5} data into the \code{r2ogs6} workflow.
#' @export
+#' @importFrom R6 R6Class
OGS6_h5 <- R6::R6Class("OGS6_h5",
public = list(
#' @description This function will be called automatically after a
@@ -78,6 +79,7 @@ OGS6_h5 <- R6::R6Class("OGS6_h5",
#' ogs6_h5 <- OGS6_h5$new(h5_path)
#' df <- ogs6_h5$get_df("/t_0", "pressure")
#' \dontrun{df <- ogs6_obj$h5s[[1]]$get_df("/t_0", "pressure")}
+ #' @importFrom dplyr bind_cols
get_df = function(group, names = "geometry") {
assertthat::is.string(group)
diff --git a/R/ogs6_msh.R b/R/ogs6_msh.R
index 71b21bd..fa8cb7a 100644
--- a/R/ogs6_msh.R
+++ b/R/ogs6_msh.R
@@ -3,6 +3,7 @@
#' MSH files are a legacy format from OGS5. It is recommended to switch to VTU
#' files.
#' @export
+#' @importFrom R6 R6Class
OGS6_msh <- R6::R6Class("OGS6_msh",
public = list(
#' @description reates new OGS6_vtu object..
diff --git a/R/ogs6_pvd.R b/R/ogs6_pvd.R
index 4f2ff6b..6eacfb7 100644
--- a/R/ogs6_pvd.R
+++ b/R/ogs6_pvd.R
@@ -5,6 +5,7 @@
#' OGS6_pvd
#' @description Constructor for the OGS6_pvd base class
#' @export
+#' @importFrom R6 R6Class
OGS6_pvd <- R6::R6Class(
"OGS6_pvd",
public = list(
@@ -260,6 +261,7 @@ OGS6_pvd <- R6::R6Class(
},
# Returns a dataframe with all of the CellData
+ #' @importFrom dplyr bind_rows
get_data = function(data_type,
ids,
keys,
diff --git a/R/ogs6_vtu.R b/R/ogs6_vtu.R
index 4db4ffa..645124d 100644
--- a/R/ogs6_vtu.R
+++ b/R/ogs6_vtu.R
@@ -5,6 +5,7 @@
#' OGS6_vtu
#' @description Constructor for the `OGS6_vtu` base class
#' @export
+#' @importFrom R6 R6Class
OGS6_vtu <- R6::R6Class(
"OGS6_vtu",
public = list(
@@ -244,7 +245,7 @@ OGS6_vtu <- R6::R6Class(
),
private = list(
-
+ #' @importFrom dplyr bind_rows
get_data = function(data_type,
ids,
keys){
--
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