Merge pull request #55 from HaoZeke/cppRosciUpd

MAINT,ENH: Handle `~` and cleanup C++ code

R/cpp11.R

@@ -1,15 +1,15 @@
 # Generated by cpp11: do not edit by hand
 
-fmm_to_vec <- function(filename) {
-  .Call(`_fastMatMR_fmm_to_vec`, filename)
+cpp_fmm_to_vec <- function(filename) {
+  .Call(`_fastMatMR_cpp_fmm_to_vec`, filename)
 }
 
-fmm_to_mat <- function(filename) {
-  .Call(`_fastMatMR_fmm_to_mat`, filename)
+cpp_fmm_to_mat <- function(filename) {
+  .Call(`_fastMatMR_cpp_fmm_to_mat`, filename)
 }
 
-fmm_to_sparse_Matrix <- function(filename) {
-  .Call(`_fastMatMR_fmm_to_sparse_Matrix`, filename)
+cpp_fmm_to_sparse_Matrix <- function(filename) {
+  .Call(`_fastMatMR_cpp_fmm_to_sparse_Matrix`, filename)
 }
 
 vec_to_fmm <- function(r_vec, filename) {

R/fastMatMR-package.R

@@ -15,7 +15,11 @@
 #' \dontrun{
 #' vec <- fmm_to_vec("matrix.mtx")
 #' }
-NULL
+fmm_to_vec <- function(filename) {
+  expanded_filename <- path.expand(filename)
+  result <- cpp_fmm_to_vec(expanded_filename)
+  return(result)
+}
 
 #' @export fmm_to_mat
 #' @rdname fmm_to_mat
@@ -29,7 +33,11 @@ NULL
 #' \dontrun{
 #' mat <- fmm_to_mat("matrix.mtx")
 #' }
-NULL
+fmm_to_mat <- function(filename) {
+  expanded_filename <- path.expand(filename)
+  result <- cpp_fmm_to_mat(expanded_filename)
+  return(result)
+}
 
 #' @export fmm_to_sparse_Matrix
 #' @rdname fmm_to_sparse_Matrix
@@ -44,19 +52,22 @@ NULL
 #' \dontrun{
 #' sparse_mat <- fmm_to_sparse_Matrix("sparse_matrix.mtx")
 #' }
-NULL
+fmm_to_sparse_Matrix <- function(filename) {
+  expanded_filename <- path.expand(filename)
+  result <- cpp_fmm_to_sparse_Matrix(expanded_filename)
+  return(result)
+}
 
 #' @export vec_to_fmm
 #' @rdname vec_to_fmm
 #' @name vec_to_fmm
 #' @title Convert a Numeric Vector to Matrix Market Format
 #' @description This function takes a numeric vector and converts it into a
-#'   Matrix Market file.
+#'   Matrix Market output file.
 #' @param input A numeric vector to be converted.
-#' @param fname The name of the output file where the Matrix Market formatted
+#' @param filename The name of the output file where the Matrix Market formatted
 #'   data will be saved.
-#' @return This function has no return value. It writes a Matrix Market
-#'   formatted file to disk.
+#' @return A boolean indicating success or failure. Writes a MTX file to disk.
 #' @examples
 #' \dontrun{
 #' vec <- c(1, 2, 3)
@@ -71,10 +82,9 @@ NULL
 #' @description This function takes a numeric matrix and converts it into a
 #'   Matrix Market file.
 #' @param input A numeric matrix to be converted.
-#' @param fname The name of the output file where the Matrix Market formatted
+#' @param filename The name of the output file where the Matrix Market formatted
 #'   data will be saved.
-#' @return This function has no return value. It writes a Matrix Market
-#'   formatted file to disk.
+#' @return A boolean indicating success or failure. Writes a MTX file to disk.
 #' @examples
 #' \dontrun{
 #' mat <- matrix(c(1, 2, 3, 4), nrow = 2)
@@ -89,10 +99,9 @@ NULL
 #' @description This function takes a sparse numeric matrix and converts it into
 #'   a Matrix Market file.
 #' @param input A sparse numeric matrix to be converted.
-#' @param fname The name of the output file where the Matrix Market formatted
+#' @param filename The name of the output file where the Matrix Market formatted
 #'   data will be saved.
-#' @return This function has no return value. It writes a Matrix Market
-#'   formatted file to disk.
+#' @return A boolean indicating success or failure. Writes a MTX file to disk.
 #' @examples
 #' \dontrun{
 #' sparse_mat <- Matrix::Matrix(c(1, 0, 0, 2), nrow = 2, sparse = TRUE)
@@ -108,12 +117,11 @@ NULL
 #'
 #' @param input A numeric object to be converted. This can be a numeric vector,
 #'   a matrix, or a sparse matrix.
-#' @param fname The name of the output file
+#' @param filename The name of the output file
 #'   where the Matrix Market formatted data will be saved.  It is recommended to
 #'   use a filename ending with ".mtx" for clarity.
 #'
-#' @return This function has no return value. It writes a Matrix Market
-#'   formatted file to disk.
+#' @return A boolean indicating success or failure. Writes a MTX file to disk.
 #'
 #' @examples
 #' \dontrun{
@@ -130,13 +138,15 @@ NULL
 #' }
 #'
 #' @export
-write_fmm <- function(input, fname = "out.mtx") {
+write_fmm <- function(input, filename = "out.mtx") {
+  # Expand the ~ character to the full path
+  expanded_fname <- path.expand(filename)
   if (is.vector(input)) {
-    return(vec_to_fmm(input, fname)) # nolint. C++ function.
+    return(vec_to_fmm(input, expanded_fname)) # nolint. C++ function.
   } else if (is.matrix(input)) {
-    return(mat_to_fmm(input, fname)) # nolint. C++ function.
+    return(mat_to_fmm(input, expanded_fname)) # nolint. C++ function.
   } else if (inherits(input, "sparseMatrix")) {
-    return(sparse_to_fmm(input, fname)) # nolint. C++ function.
+    return(sparse_to_fmm(input, expanded_fname)) # nolint. C++ function.
   } else {
     stop(
       paste(

src/cpp11.cpp

@@ -6,24 +6,24 @@
 #include <R_ext/Visibility.h>
 
 // from_file.cpp
-cpp11::doubles fmm_to_vec(const std::string & filename);
-extern "C" SEXP _fastMatMR_fmm_to_vec(SEXP filename) {
+cpp11::doubles cpp_fmm_to_vec(const std::string & filename);
+extern "C" SEXP _fastMatMR_cpp_fmm_to_vec(SEXP filename) {
   BEGIN_CPP11
-    return cpp11::as_sexp(fmm_to_vec(cpp11::as_cpp<cpp11::decay_t<const std::string &>>(filename)));
+    return cpp11::as_sexp(cpp_fmm_to_vec(cpp11::as_cpp<cpp11::decay_t<const std::string &>>(filename)));
   END_CPP11
 }
 // from_file.cpp
-cpp11::doubles_matrix<> fmm_to_mat(const std::string & filename);
-extern "C" SEXP _fastMatMR_fmm_to_mat(SEXP filename) {
+cpp11::doubles_matrix<> cpp_fmm_to_mat(const std::string & filename);
+extern "C" SEXP _fastMatMR_cpp_fmm_to_mat(SEXP filename) {
   BEGIN_CPP11
-    return cpp11::as_sexp(fmm_to_mat(cpp11::as_cpp<cpp11::decay_t<const std::string &>>(filename)));
+    return cpp11::as_sexp(cpp_fmm_to_mat(cpp11::as_cpp<cpp11::decay_t<const std::string &>>(filename)));
   END_CPP11
 }
 // from_file.cpp
-cpp11::sexp fmm_to_sparse_Matrix(const std::string & filename);
-extern "C" SEXP _fastMatMR_fmm_to_sparse_Matrix(SEXP filename) {
+cpp11::sexp cpp_fmm_to_sparse_Matrix(const std::string & filename);
+extern "C" SEXP _fastMatMR_cpp_fmm_to_sparse_Matrix(SEXP filename) {
   BEGIN_CPP11
-    return cpp11::as_sexp(fmm_to_sparse_Matrix(cpp11::as_cpp<cpp11::decay_t<const std::string &>>(filename)));
+    return cpp11::as_sexp(cpp_fmm_to_sparse_Matrix(cpp11::as_cpp<cpp11::decay_t<const std::string &>>(filename)));
   END_CPP11
 }
 // to_file.cpp
@@ -50,12 +50,12 @@ extern "C" SEXP _fastMatMR_sparse_to_fmm(SEXP input, SEXP filename) {
 
 extern "C" {
 static const R_CallMethodDef CallEntries[] = {
-    {"_fastMatMR_fmm_to_mat",           (DL_FUNC) &_fastMatMR_fmm_to_mat,           1},
-    {"_fastMatMR_fmm_to_sparse_Matrix", (DL_FUNC) &_fastMatMR_fmm_to_sparse_Matrix, 1},
-    {"_fastMatMR_fmm_to_vec",           (DL_FUNC) &_fastMatMR_fmm_to_vec,           1},
-    {"_fastMatMR_mat_to_fmm",           (DL_FUNC) &_fastMatMR_mat_to_fmm,           2},
-    {"_fastMatMR_sparse_to_fmm",        (DL_FUNC) &_fastMatMR_sparse_to_fmm,        2},
-    {"_fastMatMR_vec_to_fmm",           (DL_FUNC) &_fastMatMR_vec_to_fmm,           2},
+    {"_fastMatMR_cpp_fmm_to_mat",           (DL_FUNC) &_fastMatMR_cpp_fmm_to_mat,           1},
+    {"_fastMatMR_cpp_fmm_to_sparse_Matrix", (DL_FUNC) &_fastMatMR_cpp_fmm_to_sparse_Matrix, 1},
+    {"_fastMatMR_cpp_fmm_to_vec",           (DL_FUNC) &_fastMatMR_cpp_fmm_to_vec,           1},
+    {"_fastMatMR_mat_to_fmm",               (DL_FUNC) &_fastMatMR_mat_to_fmm,               2},
+    {"_fastMatMR_sparse_to_fmm",            (DL_FUNC) &_fastMatMR_sparse_to_fmm,            2},
+    {"_fastMatMR_vec_to_fmm",               (DL_FUNC) &_fastMatMR_vec_to_fmm,               2},
     {NULL, NULL, 0}
 };
 }

src/from_file.cpp

@@ -17,7 +17,7 @@ namespace fmm = fast_matrix_market;
 
 [[cpp11::register]] //
 cpp11::doubles
-fmm_to_vec(const std::string &filename) {
+cpp_fmm_to_vec(const std::string &filename) {
   std::ifstream file_stream;
   std::vector<double> vec;
 
@@ -34,7 +34,7 @@ fmm_to_vec(const std::string &filename) {
 
 [[cpp11::register]] //
 cpp11::doubles_matrix<>
-fmm_to_mat(const std::string &filename) {
+cpp_fmm_to_mat(const std::string &filename) {
   std::ifstream file_stream;
   fmm::matrix_market_header header;
   std::vector<double> vec;
@@ -61,7 +61,7 @@ fmm_to_mat(const std::string &filename) {
 
 [[cpp11::register]] //
 cpp11::sexp
-fmm_to_sparse_Matrix(const std::string &filename) {
+cpp_fmm_to_sparse_Matrix(const std::string &filename) {
   // TODO: Can speed this up by constructing from SEXP instead of via Matrix
   // constructor later
   using namespace cpp11::literals;

src/to_file.cpp

@@ -17,13 +17,9 @@ bool vec_to_fmm(cpp11::doubles r_vec, std::string filename) {
   std::vector<double> std_vec(r_vec.size());
   std::copy(r_vec.begin(), r_vec.end(), std_vec.begin());
   fmm::matrix_market_header header(1, std_vec.size());
-  // header.comment = std::string("comment");
-  // Use C++17 filesystem to construct ofstream
   std::filesystem::path file_path(filename);
   std::ofstream os(file_path);
-
   if (!os.is_open()) {
-    // Handle error
     return false;
   }
   fmm::write_matrix_market_array(os, header, std_vec);