bgzf/gzi: Move reader to io module

noodles-bgzf/CHANGELOG.md

@@ -10,12 +10,18 @@
 
   * bgzf: Raise minimum supported Rust version (MSRV) to 1.73.0.
 
+  * bgzf/gzi: Move reader (`Reader`) to `io` module.
+
 ### Deprecated
 
   * bgzf: Deprecate async re-exports (`AsyncReader` and `AsyncWriter`).
 
     Use `bgzf::r#async::Reader` and `bgzf::r#async::Writer` instead.
 
+  * bgzf/gzi: Deprecate `Reader`.
+
+    Use `bgzf::gzi::io::Reader` instead.
+
   * bgzf/gzi: Deprecate `AsyncReader` re-export.
 
     Use `bgzf::gzi::r#async::Reader` instead.

noodles-bgzf/src/gzi.rs

@@ -8,19 +8,18 @@
 pub mod r#async;
 
 mod index;
-mod reader;
+pub mod io;
 
-pub use self::{index::Index, reader::Reader};
+pub use self::index::Index;
+
+#[deprecated(since = "0.35.0", note = "Use `gzi::io::Reader` instead.")]
+pub use self::io::Reader;
 
 #[cfg(feature = "async")]
 #[deprecated(since = "0.35.0", note = "Use `bgzf::gzi::r#async::Reader` instead.")]
 pub use self::r#async::Reader as AsyncReader;
 
-use std::{
-    fs::File,
-    io::{self, BufReader},
-    path::Path,
-};
+use std::{fs::File, io::BufReader, path::Path};
 
 /// Reads the entire contents of a GZ index.
 ///
@@ -35,7 +34,7 @@ use std::{
 /// let index = gzi::read("in.gz.gzi")?;
 /// # Ok::<_, io::Error>(())
 /// ```
-pub fn read<P>(src: P) -> io::Result<Index>
+pub fn read<P>(src: P) -> std::io::Result<Index>
 where
     P: AsRef<Path>,
 {

noodles-bgzf/src/gzi/async.rs

@@ -1,18 +1,16 @@
 //! Async gzip index.
 
-mod reader;
-
-pub use self::reader::Reader;
+pub mod io;
 
 use std::path::Path;
 
-use tokio::{
-    fs::File,
-    io::{self, BufReader},
-};
+use tokio::{fs::File, io::BufReader};
 
 use super::Index;
 
+#[deprecated(since = "0.35.0", note = "Use `gzi::r#async::io::Reader` instead.")]
+pub use self::io::Reader;
+
 /// Reads the entire contents of a GZ index.
 ///
 /// This is a convenience function and is equivalent to opening the given path and reading the
@@ -30,7 +28,7 @@ use super::Index;
 /// # Ok(())
 /// # }
 /// ```
-pub async fn read<P>(src: P) -> io::Result<Index>
+pub async fn read<P>(src: P) -> tokio::io::Result<Index>
 where
     P: AsRef<Path>,
 {

noodles-bgzf/src/gzi/async/io.rs

@@ -0,0 +1,5 @@
+//! Async gzip index I/O.
+
+mod reader;
+
+pub use self::reader::Reader;

noodles-bgzf/src/gzi/async/reader.rs → noodles-bgzf/src/gzi/async/io/reader.rs

@@ -21,7 +21,7 @@ where
     /// ```
     /// use noodles_bgzf::gzi;
     /// let data = [0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00];
-    /// let reader = gzi::r#async::Reader::new(&data[..]);
+    /// let reader = gzi::r#async::io::Reader::new(&data[..]);
     /// ```
     pub fn new(inner: R) -> Self {
         Self { inner }
@@ -34,16 +34,14 @@ where
     /// # Examples
     ///
     /// ```no_run
-    /// # use std::io;
-    /// #
     /// # #[tokio::main]
-    /// # async fn main() -> io::Result<()> {
+    /// # async fn main() -> tokio::io::Result<()> {
     /// use noodles_bgzf::gzi;
     /// use tokio::fs::File;
     ///
     /// let mut reader = File::open("in.gzi")
     ///     .await
-    ///     .map(gzi::r#async::Reader::new)?;
+    ///     .map(gzi::r#async::io::Reader::new)?;
     ///
     /// let index = reader.read_index().await?;
     /// # Ok(())

noodles-bgzf/src/gzi/io.rs

@@ -0,0 +1,5 @@
+//! gzip index I/O.
+
+mod reader;
+
+pub use self::reader::Reader;

noodles-bgzf/src/gzi/reader.rs → noodles-bgzf/src/gzi/io/reader.rs

@@ -3,7 +3,7 @@ mod index;
 use std::io::{self, Read};
 
 use self::index::read_index;
-use super::Index;
+use crate::gzi::Index;
 
 /// A gzip index (GZI) reader.
 pub struct Reader<R> {
@@ -18,7 +18,7 @@ impl<R> Reader<R> {
     /// ```
     /// # use std::io;
     /// use noodles_bgzf::gzi;
-    /// let reader = gzi::Reader::new(io::empty());
+    /// let reader = gzi::io::Reader::new(io::empty());
     /// let _inner = reader.get_ref();
     /// ```
     pub fn get_ref(&self) -> &R {
@@ -32,7 +32,7 @@ impl<R> Reader<R> {
     /// ```
     /// # use std::io;
     /// use noodles_bgzf::gzi;
-    /// let mut reader = gzi::Reader::new(io::empty());
+    /// let mut reader = gzi::io::Reader::new(io::empty());
     /// let _inner = reader.get_mut();
     /// ```
     pub fn get_mut(&mut self) -> &mut R {
@@ -46,7 +46,7 @@ impl<R> Reader<R> {
     /// ```
     /// # use std::io;
     /// use noodles_bgzf::gzi;
-    /// let reader = gzi::Reader::new(io::empty());
+    /// let reader = gzi::io::Reader::new(io::empty());
     /// let _inner = reader.into_inner();
     /// ```
     pub fn into_inner(self) -> R {
@@ -65,7 +65,7 @@ where
     /// ```
     /// use noodles_bgzf::gzi;
     /// let data = [0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00];
-    /// let reader = gzi::Reader::new(&data[..]);
+    /// let reader = gzi::io::Reader::new(&data[..]);
     /// ```
     pub fn new(inner: R) -> Self {
         Self { inner }
@@ -78,11 +78,11 @@ where
     /// # Examples
     ///
     /// ```no_run
-    /// # use std::{fs::File, io};
+    /// # use std::fs::File;
     /// use noodles_bgzf::gzi;
-    /// let mut reader = File::open("in.gzi").map(gzi::Reader::new)?;
+    /// let mut reader = File::open("in.gzi").map(gzi::io::Reader::new)?;
     /// let index = reader.read_index()?;
-    /// # Ok::<(), io::Error>(())
+    /// # Ok::<(), std::io::Error>(())
     /// ```
     pub fn read_index(&mut self) -> io::Result<Index> {
         read_index(&mut self.inner)