fix bindings

bindings/r/.Rbuildignore

@@ -1 +1,2 @@
 ^src/\.cargo$
+^LICENSE\.md$

bindings/r/DESCRIPTION

@@ -5,7 +5,7 @@ Authors@R:
     person("Nathan", "LeRoy", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-7354-7213"))
 Description: Performance-critical tools to manipulate, analyze, and process genomic interval data. Primarily focused on building tools for geniml - our genomic machine learning python package. 
-License: `use_mit_license()`
+License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2

bindings/r/LICENSE

@@ -0,0 +1,2 @@
+YEAR: 2024
+COPYRIGHT HOLDER: gtars authors

bindings/r/LICENSE.md

@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2024 gtars 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.

bindings/r/R/extendr-wrappers.R

@@ -20,6 +20,7 @@ read_tokens_from_gtok <- function(filename) .Call(wrap__r_read_tokens_from_gtok,
 #' Write tokens to a gtok file
 #' @export
 #' @param filename A string representing the path to the gtok file.
+#' @param tokens The tokens to write.
 write_tokens_to_gtok <- function(filename, tokens) invisible(.Call(wrap__r_write_tokens_to_gtok, filename, tokens))
 
 #' Create an IGD database from a directory of bed files

bindings/r/src/rust/src/io.rs

@@ -5,6 +5,7 @@ use gtars::io::{read_tokens_from_gtok, write_tokens_to_gtok};
 /// Write tokens to a gtok file
 /// @export
 /// @param filename A string representing the path to the gtok file.
+/// @param tokens The tokens to write.
 #[extendr(r_name = "write_tokens_to_gtok")]
 pub fn r_write_tokens_to_gtok(filename: String, tokens: Vec<i32>) {
     let tokens: Vec<u32> = tokens.into_iter().map(|t| t as u32).collect();