nom 7

Cargo.toml

@@ -1,5 +1,5 @@
 [package]
-edition = "2018"
+edition = "2021"
 name = "gb-io"
 version = "0.7.1"
 license = "MIT"
@@ -14,12 +14,12 @@ exclude = ["tests/*", ".github/*"]
 string_cache_codegen = "0.5"
 
 [dependencies]
-itertools = "0.10"
+itertools = "0.11"
 circular = "0.3.0"
 err-derive = "0.3.1"
 string_cache = "0.8"
 log = "0.4"
-nom = "4.2.3"
+nom = "7.1.3"
 serde = { version = "1", optional = true, features = ["derive"] }
 serde_bytes = { version = "0.11", optional = true }
 
@@ -29,8 +29,11 @@ default = ["serde", "serde_bytes"]
 [dev-dependencies]
 glob = "0.3.0"
 bencher = "0.1.5"
-env_logger = "0.9.0"
+env_logger = "0.10.0"
 
 [[bench]]
 name = "parse"
 harness = false
+
+[profile.release]
+lto = true # keeps performance on-par with nom 4 (macro-based)

build.rs

@@ -80,7 +80,7 @@ fn main() {
         "tRNA",
         "V_segment",
     ];
-    let file = File::create(&Path::new(&env::var("OUT_DIR").unwrap()).join("atoms.rs")).unwrap();
+    let file = File::create(Path::new(&env::var("OUT_DIR").unwrap()).join("atoms.rs")).unwrap();
     string_cache_codegen::AtomType::new("QualifierKey", "qualifier_key!")
         .atoms(qualifiers.iter())
         .write_to(&file)

src/lib.rs

@@ -8,14 +8,12 @@
 #![cfg_attr(feature = "cargo-clippy", allow(clippy::useless_format))]
 #![cfg_attr(feature = "cargo-clippy", allow(clippy::unreadable_literal))]
 #![cfg_attr(feature = "cargo-clippy", allow(clippy::upper_case_acronyms))]
-#![recursion_limit = "128"]
 extern crate circular;
 #[macro_use]
 extern crate err_derive;
 extern crate itertools;
 #[macro_use]
 extern crate log;
-#[macro_use]
 extern crate nom;
 #[cfg(feature = "serde")]
 #[macro_use]
@@ -46,7 +44,6 @@ pub mod tests {
         let _ = env_logger::Builder::from_default_env().try_init();
     }
 
-
     #[test]
     fn streaming() {
         init();
@@ -134,4 +131,8 @@ pub mod tests {
             }
         }
     }
+
+    fn parse_slice(bytes: &[u8]) -> Result<Vec<Seq>, GbParserError> {
+        SeqReader::new(bytes).collect()
+    }
 }

src/reader/errors.rs

@@ -47,61 +47,3 @@ impl fmt::Display for NomParserError {
         write!(f, "{}", msg)
     }
 }
-
-// Copied from nom and modified
-macro_rules! map_res_custom_error (
-  // Internal parser, do not use directly
-  (__impl $i:expr, $e:expr, $submac:ident!( $($args:tt)* ), $submac2:ident!( $($args2:tt)* )) => (
-    {
-      use ::std::result::Result::*;
-      use ::nom::Err;
-
-      let i_ = $i.clone();
-      ($submac!(i_, $($args)*)).and_then(|(i,o)| {
-        match $submac2!(o, $($args2)*) {
-          Ok(output) => Ok((i, output)),
-          Err(_) => {
-            let e = ::nom::ErrorKind::Custom(u32::from($e));
-            Err(Err::Error(error_position!($i, e)))
-          },
-        }
-      })
-    }
-  );
-  ($i:expr, $e:expr, $submac:ident!( $($args:tt)* ), $g:expr) => (
-    map_res_custom_error!(__impl $i, $e, $submac!($($args)*), call!($g))
-  );
-  ($i:expr, $e:expr, $submac:ident!( $($args:tt)* ), $submac2:ident!( $($args2:tt)* )) => (
-    map_res_custom_error!(__impl $i, $e, $submac!($($args)*), $submac2!($($args2)*))
-  );
-  ($i:expr, $e:expr, $f:expr, $g:expr) => (
-    map_res_custom_error!(__impl $i, $e, call!($f), call!($g))
-  );
-  ($i:expr, $e:expr, $f:expr, $submac:ident!( $($args:tt)* )) => (
-    map_res_custom_error!(__impl $i, call!($f), $submac!($($args)*))
-  )
-);
-
-macro_rules! to_str (
-    ($i:expr, $submac:ident!( $($args:tt)* )) => (
-        map_res_custom_error!($i, NomParserError::Utf8Error,
-                      $submac!($($args)*),
-                               str::from_utf8
-        )
-    );
-    ($i:expr, $f:expr) => (
-        to_str!($i, call!($f))
-    )
-);
-
-macro_rules! to_string (
-    ($i:expr, $submac:ident!( $($args:tt)* )) => (
-        map_res_custom_error!($i, NomParserError::Utf8Error,
-                            $submac!($($args)*),
-                            String::from_utf8
-        )
-    );
-    ($i:expr, $f:expr) => (
-        to_str!($i, call!($f))
-    )
-);