Merge pull request #124 from brownag/master

whitebox 2.4.0

.Rbuildignore

@@ -18,10 +18,12 @@
 ^data-raw$
 ^revdep$
 ^_pkgdown\.yml$
+WhiteboxTools_linux_amd64/
 WBT/
 CRAN/
 PY2R/
 binder/
 docs/
 misc/
 .vscode/
+^LICENSE\.md$

.gitignore

@@ -19,3 +19,4 @@ whiteboxR.Rproj
 *.tif
 settings.json
 __MACOSX
+WhiteboxTools_linux_amd64

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: whitebox
 Type: Package
 Title: 'WhiteboxTools' R Frontend
-Version: 2.3.4
+Version: 2.4.0
 Description: An R frontend for the 'WhiteboxTools' library, which is an advanced geospatial data analysis platform developed by Prof. John Lindsay at the University of Guelph's Geomorphometry and Hydrogeomatics Research Group. 'WhiteboxTools' can be used to perform common geographical information systems (GIS) analysis operations, such as cost-distance analysis, distance buffering, and raster reclassification. Remote sensing and image processing tasks include image enhancement (e.g. panchromatic sharpening, contrast adjustments), image mosaicing, numerous filtering operations, simple classification (k-means), and common image transformations. 'WhiteboxTools' also contains advanced tooling for spatial hydrological analysis (e.g. flow-accumulation, watershed delineation, stream network analysis, sink removal), terrain analysis (e.g. common terrain indices such as slope, curvatures, wetness index, hillshading; hypsometric analysis; multi-scale topographic position analysis), and LiDAR data processing. Suggested citation: Lindsay (2016) <doi:10.1016/j.cageo.2016.07.003>.
 Authors@R: c(person("Qiusheng", "Wu", email = "[email protected]", role = c("aut")),
              person("Andrew", "Brown", email = "[email protected]", role = c("ctb", "cre")))
@@ -10,7 +10,7 @@ License: MIT + file LICENSE
 SystemRequirements: WhiteboxTools (https://github.com/jblindsay/whitebox-tools/releases/latest)
 Encoding: UTF-8
 Language: en-US
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Roxygen: list(markdown = TRUE)
 URL: https://whiteboxr.gishub.org/, https://github.com/opengeos/whiteboxR
 BugReports: https://github.com/opengeos/whiteboxR/issues

Dockerfile

@@ -29,6 +29,7 @@ RUN install2.r --error \
     devtools \
     whitebox \
     Rcpp \
+    Matrix \
     terra \
     sf \
     ggplot2 \
@@ -38,6 +39,4 @@ RUN install2.r --error \
     caTools \
     rprojroot
 
-COPY misc/install.R /home/rstudio/
-
-RUN Rscript /home/rstudio/install.R
+RUN Rscript -e "whitebox::install_whitebox()"

LICENSE

@@ -1,2 +1,2 @@
-YEAR: 2019
-COPYRIGHT HOLDER: Qiusheng Wu
+YEAR: 2024
+COPYRIGHT HOLDER: whitebox authors

LICENSE.md

@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2024 whitebox authors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

NEWS.md

@@ -1,3 +1,9 @@
+# whitebox 2.4.0
+
+ * Updates for WhiteboxTools v2.4.0 (https://github.com/jblindsay/whitebox-tools/releases/tag/v2.4.0)
+
+ * Fix for new ZIP file folder structure for WhiteboxTools v2.4.0+ in `wbt_install()` / `install_whitebox()`
+
 # whitebox 2.3.4
 
  * Exported `wbt_file_path()`, a function previously used internally for creating safe, expanded, quoted, paths for building WhiteboxTools commands. This function also supports the input of `terra` objects that are backed by file sources supported by WhiteboxTools.

PY2R/automation.py

@@ -271,7 +271,7 @@ def function_example(fun_name):
 dir_path = os.path.dirname(os.path.realpath(__file__))
 wbt_py = os.path.join(dir_path, "whitebox_tools.py")
 root_dir = os.path.dirname(dir_path)
-WBT_dir = os.path.join(root_dir, "WBT")
+WBT_dir = os.path.join(root_dir, "WhiteboxTools_linux_amd64", "WBT")
 
 linux_tar = "WhiteboxTools_linux_amd64.zip"
 tar_path = os.path.join(root_dir, linux_tar)
@@ -289,7 +289,7 @@ def function_example(fun_name):
 with zipfile.ZipFile(tar_path, "r") as tar_ref:
     tar_ref.extractall(root_dir)
 
-shutil.copyfile(os.path.join(WBT_dir, "whitebox_tools.py"), wbt_py)
+shutil.copyfile(os.path.join( WBT_dir, "whitebox_tools.py"), wbt_py)
 
 # Generate R functions with documentation
 ff = None

PY2R/scripts/math_stat_analysis.R

@@ -647,11 +647,11 @@ wbt_conditional_evaluation <- function(input, output, statement="", true=NULL, f
 #' @param iterations Maximum iterations (if stopping criteria not reached).
 #' @param seed Seed for RNG consistency.
 #' @param prob Probability of random resample or resampling worst strata between `[0,1]`.
-#' @param threshold Objective function values below the theshold stop the resampling iterations.
+#' @param threshold Objective function values below the threshold stop the resampling iterations.
 #' @param temp Initial annealing temperature between `[0,1]`.
 #' @param temp_decay Annealing temperature decay proportion between `[0,1]`. Reduce temperature by this proportion each annealing cycle.
 #' @param cycle Number of iterations before decaying annealing temperature.
-#' @param average Weight the continuous objective funtion by the 1/N contributing strata.
+#' @param average Weight the continuous objective function by the 1/N contributing strata.
 #' @param wd Changes the working directory. Default: `NULL` will use the value in WhiteboxTools settings, see `wbt_wd()` for details.
 #' @param verbose_mode Sets verbose mode. If verbose mode is `FALSE`, tools will not print output messages. Default: `NULL` will use the value in WhiteboxTools settings, see `wbt_verbose()` for details.
 #' @param compress_rasters Sets the flag used by 'WhiteboxTools' to determine whether to use compression for output rasters. Default: `NULL` will use the value in WhiteboxTools settings, see `wbt_compress_rasters()` for details.

PY2R/scripts/stream_network_analysis.R

@@ -945,15 +945,11 @@ wbt_tributary_identifier <- function(d8_pntr, streams, output, esri_pntr=FALSE,
 #'
 #' @return Returns the tool text outputs.
 #' @export
-wbt_vector_stream_network_analysis <- function(streams, dem, output, cutting_height=10.0, snap=0.1, wd=NULL, verbose_mode=NULL, compress_rasters=NULL, command_only=FALSE) {
+wbt_vector_stream_network_analysis <- function(streams, output, snap=0.1, wd=NULL, verbose_mode=NULL, compress_rasters=NULL, command_only=FALSE) {
   wbt_init()
   args <- ""
   args <- paste(args, paste0("--streams=", wbt_file_path(streams)))
-  args <- paste(args, paste0("--dem=", wbt_file_path(dem)))
   args <- paste(args, paste0("--output=", wbt_file_path(output)))
-  if (!is.null(cutting_height)) {
-    args <- paste(args, paste0("--cutting_height=", cutting_height))
-  }
   if (!is.null(snap)) {
     args <- paste(args, paste0("--snap=", snap))
   }

PY2R/scripts/terrain_analysis.R

@@ -154,7 +154,7 @@ wbt_average_normal_vector_angular_deviation <- function(dem, output, filter=11,
 #'
 #' @param dem Name of the input raster image file.
 #' @param output Name of the output vector lines file.
-#' @param threshold Threshold value (0 - infinity but typcially 1 to 5 works well).
+#' @param threshold Threshold value (0 - infinity but typically 1 to 5 works well).
 #' @param min_length Minimum line length, in grid cells.
 #' @param wd Changes the working directory. Default: `NULL` will use the value in WhiteboxTools settings, see `wbt_wd()` for details.
 #' @param verbose_mode Sets verbose mode. If verbose mode is `FALSE`, tools will not print output messages. Default: `NULL` will use the value in WhiteboxTools settings, see `wbt_verbose()` for details.

PY2R/whitebox_tools.py

@@ -2803,7 +2803,7 @@ def breakline_mapping(self, dem, output, threshold=2.0, min_length=3, callback=N
 
         dem -- Name of the input raster image file. 
         output -- Name of the output vector lines file. 
-        threshold -- Threshold value (0 - infinity but typcially 1 to 5 works well). 
+        threshold -- Threshold value (0 - infinity but typically 1 to 5 works well). 
         min_length -- Minimum line length, in grid cells. 
         callback -- Custom function for handling tool text outputs.
         """
@@ -8945,11 +8945,11 @@ def conditioned_latin_hypercube(self, inputs, output, samples=500, iterations=25
         iterations -- Maximum iterations (if stopping criteria not reached). 
         seed -- Seed for RNG consistency. 
         prob -- Probability of random resample or resampling worst strata between [0,1]. 
-        threshold -- Objective function values below the theshold stop the resampling iterations. 
+        threshold -- Objective function values below the threshold stop the resampling iterations. 
         temp -- Initial annealing temperature between [0,1]. 
         temp_decay -- Annealing temperature decay proportion between [0,1]. Reduce temperature by this proportion each annealing cycle. 
         cycle -- Number of iterations before decaying annealing temperature. 
-        average -- Weight the continuous objective funtion by the 1/N contributing strata. 
+        average -- Weight the continuous objective function by the 1/N contributing strata. 
         callback -- Custom function for handling tool text outputs.
         """
         args = []
@@ -10652,7 +10652,7 @@ def tributary_identifier(self, d8_pntr, streams, output, esri_pntr=False, zero_b
         if zero_background: args.append("--zero_background")
         return self.run_tool('tributary_identifier', args, callback) # returns 1 if error
 
-    def vector_stream_network_analysis(self, streams, dem, output, cutting_height=10.0, snap=0.1, callback=None):
+    def vector_stream_network_analysis(self, streams, output, snap=0.1, callback=None):
         """This tool performs common stream network analysis operations on an input vector stream file.
 
         Keyword arguments:

R/math_stat_analysis.R

@@ -647,11 +647,11 @@ wbt_conditional_evaluation <- function(input, output, statement="", true=NULL, f
 #' @param iterations Maximum iterations (if stopping criteria not reached).
 #' @param seed Seed for RNG consistency.
 #' @param prob Probability of random resample or resampling worst strata between `[0,1]`.
-#' @param threshold Objective function values below the theshold stop the resampling iterations.
+#' @param threshold Objective function values below the threshold stop the resampling iterations.
 #' @param temp Initial annealing temperature between `[0,1]`.
 #' @param temp_decay Annealing temperature decay proportion between `[0,1]`. Reduce temperature by this proportion each annealing cycle.
 #' @param cycle Number of iterations before decaying annealing temperature.
-#' @param average Weight the continuous objective funtion by the 1/N contributing strata.
+#' @param average Weight the continuous objective function by the 1/N contributing strata.
 #' @param wd Changes the working directory. Default: `NULL` will use the value in WhiteboxTools settings, see `wbt_wd()` for details.
 #' @param verbose_mode Sets verbose mode. If verbose mode is `FALSE`, tools will not print output messages. Default: `NULL` will use the value in WhiteboxTools settings, see `wbt_verbose()` for details.
 #' @param compress_rasters Sets the flag used by 'WhiteboxTools' to determine whether to use compression for output rasters. Default: `NULL` will use the value in WhiteboxTools settings, see `wbt_compress_rasters()` for details.

R/stream_network_analysis.R

@@ -932,9 +932,7 @@ wbt_tributary_identifier <- function(d8_pntr, streams, output, esri_pntr=FALSE,
 #' @description This tool performs common stream network analysis operations on an input vector stream file.
 #'
 #' @param streams Name of the input streams vector file.
-#' @param dem Name of the input DEM raster file.
 #' @param output Name of the output lines shapefile.
-#' @param cutting_height Maximum ridge-cutting height (z units).
 #' @param snap Snap distance, in xy units (metres).
 #' @param wd Changes the working directory. Default: `NULL` will use the value in WhiteboxTools settings, see `wbt_wd()` for details.
 #' @param verbose_mode Sets verbose mode. If verbose mode is `FALSE`, tools will not print output messages. Default: `NULL` will use the value in WhiteboxTools settings, see `wbt_verbose()` for details.
@@ -945,15 +943,11 @@ wbt_tributary_identifier <- function(d8_pntr, streams, output, esri_pntr=FALSE,
 #'
 #' @return Returns the tool text outputs.
 #' @export
-wbt_vector_stream_network_analysis <- function(streams, dem, output, cutting_height=10.0, snap=0.1, wd=NULL, verbose_mode=NULL, compress_rasters=NULL, command_only=FALSE) {
+wbt_vector_stream_network_analysis <- function(streams, output, snap=0.1, wd=NULL, verbose_mode=NULL, compress_rasters=NULL, command_only=FALSE) {
   wbt_init()
   args <- ""
   args <- paste(args, paste0("--streams=", wbt_file_path(streams)))
-  args <- paste(args, paste0("--dem=", wbt_file_path(dem)))
   args <- paste(args, paste0("--output=", wbt_file_path(output)))
-  if (!is.null(cutting_height)) {
-    args <- paste(args, paste0("--cutting_height=", cutting_height))
-  }
   if (!is.null(snap)) {
     args <- paste(args, paste0("--snap=", snap))
   }

R/terrain_analysis.R

@@ -154,7 +154,7 @@ wbt_average_normal_vector_angular_deviation <- function(dem, output, filter=11,
 #'
 #' @param dem Name of the input raster image file.
 #' @param output Name of the output vector lines file.
-#' @param threshold Threshold value (0 - infinity but typcially 1 to 5 works well).
+#' @param threshold Threshold value (0 - infinity but typically 1 to 5 works well).
 #' @param min_length Minimum line length, in grid cells.
 #' @param wd Changes the working directory. Default: `NULL` will use the value in WhiteboxTools settings, see `wbt_wd()` for details.
 #' @param verbose_mode Sets verbose mode. If verbose mode is `FALSE`, tools will not print output messages. Default: `NULL` will use the value in WhiteboxTools settings, see `wbt_verbose()` for details.

R/wbt.R

@@ -606,7 +606,10 @@ wbt_install <- function(pkg_dir = wbt_data_dir(), platform = NULL, force = FALSE
 
     # unzip to either whitebox package or user specified folder
     utils::unzip(exe_zip, exdir = pkg_dir)
-
+    ex_dir <- file.path(pkg_dir, gsub("\\.zip$", "", basename(exe_zip)))
+    file.copy(file.path(ex_dir, "WBT"), pkg_dir, recursive = TRUE)
+    file.remove(list.files(ex_dir, recursive = TRUE, full.names = TRUE))
+
     # subfolder WBT/whitebox_tools
     exe_path_out <- file.path(pkg_dir, "WBT", basename(exe_path))
     Sys.chmod(exe_path_out, '755')

README.Rmd

@@ -18,11 +18,11 @@ knitr::opts_chunk$set(
 [![CRAN\_Status\_Badge](https://www.r-pkg.org/badges/version/whitebox)](https://cran.r-project.org/package=whitebox)
 [![CRAN download count](https://cranlogs.r-pkg.org/badges/grand-total/whitebox)](https://cranlogs.r-pkg.org/badges/grand-total/whitebox)
 [![whitebox Manual](https://img.shields.io/badge/docs-HTML-informational)](https://whiteboxR.gishub.org/reference/index.html)
-[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/license/MIT/)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/license/MIT)
 [![R-CMD-check](https://github.com/opengeos/whiteboxR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/opengeos/whiteboxR/actions/workflows/R-CMD-check.yaml)
 [![codecov](https://codecov.io/gh/opengeos/whiteboxR/branch/master/graph/badge.svg)](https://app.codecov.io/gh/opengeos/whiteboxR)
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/brownag/whitebox-r-binder/master?urlpath=rstudio)
-[![Donate](https://img.shields.io/badge/Donate-Buy%20me%20a%20coffee-yellowgreen.svg)](https://www.buymeacoffee.com/giswqs)
+[![Donate](https://img.shields.io/badge/Donate-Buy%20me%20a%20coffee-yellowgreen.svg)](https://buymeacoffee.com/giswqs)
 <!-- badges: end -->
 
 **WhiteboxTools** R Frontend.
@@ -37,7 +37,7 @@ This repository is related to the **whitebox** R package for geospatial analysis
 * CRAN link: <https://cran.r-project.org/package=whitebox>
 * WhiteboxTools: <https://github.com/jblindsay/whitebox-tools>
 * User Manual: <https://jblindsay.github.io/wbt_book/>
-* Free software: [MIT license](https://opensource.org/license/MIT/)
+* Free software: [MIT license](https://opensource.org/license/MIT)
 
 
 **Contents**
@@ -231,12 +231,12 @@ If you would like to contribute to the project as a developer, follow these inst
 4. Push to the branch (git push origin my-new-feature)
 5. Create a new Pull Request
 
-Unless explicitly stated otherwise, any contribution intentionally submitted for inclusion in the work shall be licensed as the [MIT license](https://opensource.org/license/MIT/) without any additional terms or conditions.
+Unless explicitly stated otherwise, any contribution intentionally submitted for inclusion in the work shall be licensed as the [MIT license](https://opensource.org/license/MIT) without any additional terms or conditions.
 
 
 ## License
 
-The whitebox **R** package is distributed under the [MIT license](https://opensource.org/license/MIT/), a permissive open-source (free software) license.
+The whitebox **R** package is distributed under the [MIT license](https://opensource.org/license/MIT), a permissive open-source (free software) license.
 
 
 ## Reporting Bugs