rename optional_data functions

dfsp-spirit · Jun 17, 2020 · d745698 · d745698
1 parent e7cc926
commit d745698
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Showing 9 changed files with 29 additions and 28 deletions.
diff --git a/CHANGES b/CHANGES
@@ -14,6 +14,7 @@ Version 0.1.11
 - add support for writing GIFTI format annotations
 - export rotate2D and flip2D to namespace
 - add support for reading transformation matrices from xfm files: read.fs.transform
+- rename all optional data functions: replace optional_data with opt_data in function names to prevent clash with fsbrain names
 
 
 Version 0.1.10

diff --git a/NAMESPACE b/NAMESPACE
@@ -11,15 +11,15 @@ S3method(read_nisurfacefile,fsnative)
 S3method(read_nisurfacefile,gifti)
 export(cdata)
 export(colortable.from.annot)
-export(delete_all_optional_data)
-export(download_optional_data)
+export(delete_all_opt_data)
+export(download_opt_data)
 export(faces.quad.to.tris)
 export(flip2D)
 export(flip3D)
 export(fs.get.morph.file.ext.for.format)
 export(fs.get.morph.file.format.from.filename)
 export(fs.patch)
-export(get_optional_data_filepath)
+export(get_opt_data_filepath)
 export(gifti_writer)
 export(gifti_xml)
 export(gifti_xml_add_global_metadata)
@@ -29,7 +29,7 @@ export(is.fs.annot)
 export(is.fs.label)
 export(is.fs.surface)
 export(is.fs.volume)
-export(list_optional_data)
+export(list_opt_data)
 export(mghheader.centervoxelRAS.from.firstvoxelRAS)
 export(mghheader.crs.orientation)
 export(mghheader.is.conformed)

diff --git a/R/optdata.R b/R/optdata.R
@@ -6,7 +6,7 @@
 #'
 #' @export
 #' @importFrom pkgfilecache get_pkg_info ensure_files_available
-download_optional_data <- function() {
+download_opt_data <- function() {
   pkg_info = pkgfilecache::get_pkg_info("freesurferformats");
 
   # Replace these with your optional data files.
@@ -94,7 +94,7 @@ download_optional_data <- function() {
 #'
 #' @export
 #' @importFrom pkgfilecache get_pkg_info list_available
-list_optional_data <- function() {
+list_opt_data <- function() {
   pkg_info = pkgfilecache::get_pkg_info("freesurferformats");
   return(pkgfilecache::list_available(pkg_info));
 }
@@ -110,7 +110,7 @@ list_optional_data <- function() {
 #'
 #' @export
 #' @importFrom pkgfilecache get_pkg_info get_filepath
-get_optional_data_filepath <- function(filename, mustWork=TRUE) {
+get_opt_data_filepath <- function(filename, mustWork=TRUE) {
   pkg_info = pkgfilecache::get_pkg_info("freesurferformats");
   return(pkgfilecache::get_filepath(pkg_info, filename, mustWork=mustWork));
 }
@@ -122,7 +122,7 @@ get_optional_data_filepath <- function(filename, mustWork=TRUE) {
 #'
 #' @export
 #' @importFrom pkgfilecache get_pkg_info erase_file_cache
-delete_all_optional_data <- function() {
+delete_all_opt_data <- function() {
   pkg_info = pkgfilecache::get_pkg_info("freesurferformats");
   return(pkgfilecache::erase_file_cache(pkg_info));
 }

diff --git a/man/delete_all_optional_data.Rd → man/delete_all_opt_data.Rd b/man/delete_all_optional_data.Rd → man/delete_all_opt_data.Rd
diff --git a/man/download_optional_data.Rd → man/download_opt_data.Rd b/man/download_optional_data.Rd → man/download_opt_data.Rd
diff --git a/man/get_optional_data_filepath.Rd → man/get_opt_data_filepath.Rd b/man/get_optional_data_filepath.Rd → man/get_opt_data_filepath.Rd
diff --git a/man/list_optional_data.Rd → man/list_opt_data.Rd b/man/list_optional_data.Rd → man/list_opt_data.Rd
diff --git a/tests/testthat/test-read-fs-surface.R b/tests/testthat/test-read-fs-surface.R
@@ -3,8 +3,8 @@
 test_that("Our demo surface file can be read using read.fs.surface", {
 
   skip_if(tests_running_on_cran_under_macos(), message = "Skipping on CRAN under MacOS, required test data cannot be downloaded.");
-  freesurferformats::download_optional_data();
-  subjects_dir = freesurferformats::get_optional_data_filepath("subjects_dir");
+  freesurferformats::download_opt_data();
+  subjects_dir = freesurferformats::get_opt_data_filepath("subjects_dir");
   surface_file = file.path(subjects_dir, "subject1", "surf", "lh.white");
   skip_if_not(file.exists(surface_file), message="Test data missing.") ;
 
@@ -36,8 +36,8 @@ test_that("Vertex connectivity in the demo surface file is as expected from refe
 
   skip_if(tests_running_on_cran_under_macos(), message = "Skipping on CRAN under MacOS, required test data cannot be downloaded.");
 
-  freesurferformats::download_optional_data();
-  subjects_dir = freesurferformats::get_optional_data_filepath("subjects_dir");
+  freesurferformats::download_opt_data();
+  subjects_dir = freesurferformats::get_opt_data_filepath("subjects_dir");
   surface_file = file.path(subjects_dir, "subject1", "surf", "lh.white");
   skip_if_not(file.exists(surface_file), message="Test data missing.");
 
@@ -60,8 +60,8 @@ test_that("The vertices of a face are close to each other", {
 
   skip_if(tests_running_on_cran_under_macos(), message = "Skipping on CRAN under MacOS, required test data cannot be downloaded.");
 
-  freesurferformats::download_optional_data();
-  subjects_dir = freesurferformats::get_optional_data_filepath("subjects_dir");
+  freesurferformats::download_opt_data();
+  subjects_dir = freesurferformats::get_opt_data_filepath("subjects_dir");
   surface_file = file.path(subjects_dir, "subject1", "surf", "lh.white");
   skip_if_not(file.exists(surface_file), message="Test data missing.");
 

diff --git a/tests/testthat/test-write-fs-surface.R b/tests/testthat/test-write-fs-surface.R
@@ -39,8 +39,8 @@ test_that("One can read, write and re-read triangular surface data", {
 
   skip_if(tests_running_on_cran_under_macos(), message = "Skipping on CRAN under MacOS, required test data cannot be downloaded.");
 
-  freesurferformats::download_optional_data();
-  subjects_dir = freesurferformats::get_optional_data_filepath("subjects_dir");
+  freesurferformats::download_opt_data();
+  subjects_dir = freesurferformats::get_opt_data_filepath("subjects_dir");
   surface_file = file.path(subjects_dir, "subject1", "surf", "lh.white");
 
   skip_if_not(file.exists(surface_file), message="Test data missing.");