Run clang-format on non-autogen C++ source code (#765)

* clang-format src/array_buffers.h

* src/arrow_adapter.h

* src/arrowio.cpp

* clang-format some files

* clang-format src/libtiledb.cpp

* src/nullable.cpp

* src/shmem.cpp

* src/virtualfile.cpp

* Run Rscript -e "Rcpp::compileAttributes()"

* fixups

* rebase

* format src/libtiledb.cpp post-rebase

* roxygenise

* remove some blocks of commented-out code [skip ci]

R/RcppExports.R

@@ -43,11 +43,12 @@ tiledb_datatype_string_to_sizeof <- function(str) {
 
 #' Map from TileDB type to R datatype
 #'
-#' This function maps from the TileDB types to the (fewer) key datatypes in R. This
-#' can be lossy as TileDB integers range from (signed and unsigned) 8 to 64 bit whereas
-#' R only has (signed) 32 bit values. Similarly, R only has 64 bit doubles whereas TileDB
-#' has 32 and 64 bit floating point types. TileDB also has more character encodings, and the
-#' full range of (NumPy) date and time types.
+#' This function maps from the TileDB types to the (fewer) key datatypes in
+#' R. This can be lossy as TileDB integers range from (signed and unsigned) 8
+#' to 64 bit whereas R only has (signed) 32 bit values. Similarly, R only has
+#' 64 bit doubles whereas TileDB has 32 and 64 bit floating point types.
+#' TileDB also has more character encodings, and the full range of (NumPy)
+#' date and time types.
 #'
 #' @param datatype A string describing one TileDB datatype
 #' @return A string describing the closest match for an R datatype
@@ -1247,22 +1248,23 @@ vlcbuf_from_shmem <- function(datapath, dtype) {
 #' Create a custom file connection
 #'
 #' @details
-#' This \code{vfs_file()} connection works like the \code{file()} connection in R itself.
+#' This \code{vfs_file()} connection works like the \code{file()} connection
+#' in R itself.
 #'
 #' This connection works with both ASCII and binary data, e.g. using
 #' \code{readLines()} and \code{readBin()}.
 #'
-#' @param description path to a filename; contrary to \code{rconnection} a connection
-#' object is not supported.
-#' @param mode character string. A description of how to open the connection if
-#' it is to be opened upon creation e.g. "rb". Default "" (empty string) means
-#' to not open the connection on creation - user must still call \code{open()}.
-#' Note: If an "open" string is provided, the user must still call \code{close()}
-#' otherwise the contents of the file aren't completely flushed until the
-#' connection is garbage collected.
+#' @param description path to a filename; contrary to \code{rconnection} a
+#' connection object is not supported.
+#' @param mode character string. A description of how to open the connection
+#' if it is to be opened upon creation e.g. "rb". Default "" (empty string)
+#' means to not open the connection on creation - user must still call
+#' \code{open()}.  Note: If an "open" string is provided, the user must still
+#' call \code{close()} otherwise the contents of the file aren't completely
+#' flushed until the connection is garbage collected.
 #' @param verbosity integer value 0, 1, or 2. Default: 0.
-#' Set to \code{0} for no debugging messages, \code{1} for some high-level messages
-#' and \code{verbosity = 2} for all debugging messages.
+#' Set to \code{0} for no debugging messages, \code{1} for some high-level
+#' messages and \code{verbosity = 2} for all debugging messages.
 #'
 #' @export
 #'

src/array_buffers.h

@@ -33,7 +33,7 @@
 #ifndef ARRAY_BUFFERS_H
 #define ARRAY_BUFFERS_H
 
-#include <stdexcept>  // for windows: error C2039: 'runtime_error': is not a member of 'std'
+#include <stdexcept> // for windows: error C2039: 'runtime_error': is not a member of 'std'
 
 #include <span/span.hpp>
 #include <tiledb/tiledb>
@@ -45,77 +45,72 @@ namespace tiledb {
 using namespace tiledb;
 
 class ArrayBuffers {
-   public:
-    ArrayBuffers() = default;
-    ArrayBuffers(const ArrayBuffers&) = delete;
-    ArrayBuffers(ArrayBuffers&&) = default;
-    ~ArrayBuffers() = default;
-
-    /**
-     * @brief Return the buffer with the given name.
-     *
-     * @param name Column name
-     * @return std::shared_ptr<ColumnBuffer> Column buffer
-     */
-    std::shared_ptr<ColumnBuffer> at(const std::string& name) {
-        if (!contains(name)) {
-            Rcpp::stop("[ArrayBuffers] column '%s' does not exist", name);
-        }
-        return buffers_[name];
+public:
+  ArrayBuffers() = default;
+  ArrayBuffers(const ArrayBuffers &) = delete;
+  ArrayBuffers(ArrayBuffers &&) = default;
+  ~ArrayBuffers() = default;
+
+  /**
+   * @brief Return the buffer with the given name.
+   *
+   * @param name Column name
+   * @return std::shared_ptr<ColumnBuffer> Column buffer
+   */
+  std::shared_ptr<ColumnBuffer> at(const std::string &name) {
+    if (!contains(name)) {
+      Rcpp::stop("[ArrayBuffers] column '%s' does not exist", name);
     }
-
-    /**
-     * @brief Return true if a buffer with the given name exists.
-     *
-     * @param name Column name
-     * @return True if a buffer with the given name exists
-     */
-    bool contains(const std::string& name) {
-        return buffers_.find(name) != buffers_.end();
-    }
-
-    /**
-     * @brief Add a column buffer with the given name to the ArrayBuffers,
-     * maintaining the insertion order.
-     *
-     * @param name Column name
-     * @param buffer Column buffer
-     */
-    void emplace(
-        const std::string& name, std::shared_ptr<ColumnBuffer> buffer) {
-        if (contains(name)) {
-            Rcpp::stop("[ArrayBuffers] column '%s' already exists", name);
-        }
-        names_.push_back(name);
-        buffers_.emplace(name, buffer);
-    }
-
-    /**
-     * @brief Returns the ordered vector of names.
-     *
-     * @return const std::vector<std::string>& Vector of names
-     */
-    const std::vector<std::string>& names() {
-        return names_;
+    return buffers_[name];
+  }
+
+  /**
+   * @brief Return true if a buffer with the given name exists.
+   *
+   * @param name Column name
+   * @return True if a buffer with the given name exists
+   */
+  bool contains(const std::string &name) {
+    return buffers_.find(name) != buffers_.end();
+  }
+
+  /**
+   * @brief Add a column buffer with the given name to the ArrayBuffers,
+   * maintaining the insertion order.
+   *
+   * @param name Column name
+   * @param buffer Column buffer
+   */
+  void emplace(const std::string &name, std::shared_ptr<ColumnBuffer> buffer) {
+    if (contains(name)) {
+      Rcpp::stop("[ArrayBuffers] column '%s' already exists", name);
     }
-
-    /**
-     * @brief Returns the number of rows in the array buffer.
-     *
-     * @return uint64_t Number of rows
-     */
-    uint64_t num_rows() const {
-        return buffers_.at(names_.front())->size();
-    }
-
-   private:
-    // A vector of column names that maintains the order the columns were added
-    std::vector<std::string> names_;
-
-    // Map: column name -> ColumnBuffer
-    std::unordered_map<std::string, std::shared_ptr<ColumnBuffer>> buffers_;
+    names_.push_back(name);
+    buffers_.emplace(name, buffer);
+  }
+
+  /**
+   * @brief Returns the ordered vector of names.
+   *
+   * @return const std::vector<std::string>& Vector of names
+   */
+  const std::vector<std::string> &names() { return names_; }
+
+  /**
+   * @brief Returns the number of rows in the array buffer.
+   *
+   * @return uint64_t Number of rows
+   */
+  uint64_t num_rows() const { return buffers_.at(names_.front())->size(); }
+
+private:
+  // A vector of column names that maintains the order the columns were added
+  std::vector<std::string> names_;
+
+  // Map: column name -> ColumnBuffer
+  std::unordered_map<std::string, std::shared_ptr<ColumnBuffer>> buffers_;
 };
 
-}  // namespace tiledb
+} // namespace tiledb
 
 #endif