chore(edition): move to Rust 2024 edition

Author: TheLostLambda

Cargo.toml

@@ -1,7 +1,7 @@
 [package]
 name = "pgfinder-next"
 version = "0.1.0"
-edition = "2021"
+edition = "2024"
 
 [workspace]
 members = [

crates/dimer-builder/Cargo.toml

@@ -1,7 +1,7 @@
 [package]
 name = "dimer-builder"
 version = "0.1.0"
-edition = "2021"
+edition = "2024"
 
 [dependencies]
 muropeptide = { path = "../muropeptide" }

crates/muropeptide/Cargo.toml

@@ -1,7 +1,7 @@
 [package]
 name = "muropeptide"
 version = "0.1.0"
-edition = "2021"
+edition = "2024"
 
 [dependencies]
 itertools = "0.13.0"

crates/muropeptide/benches/api.rs

@@ -1,6 +1,6 @@
 use divan::AllocProfiler;
 use once_cell::sync::Lazy;
-use polychem::{atoms::atomic_database, AtomicDatabase, PolymerDatabase, Polymerizer};
+use polychem::{AtomicDatabase, PolymerDatabase, Polymerizer, atoms::atomic_database};
 
 #[global_allocator]
 static ALLOC: AllocProfiler = AllocProfiler::system();

crates/muropeptide/src/lib.rs

@@ -5,13 +5,13 @@ use std::fmt::{self, Display, Formatter};
 
 use itertools::Itertools;
 use miette::Diagnostic;
-use nom_miette::{final_parser, LabeledError};
+use nom_miette::{LabeledError, final_parser};
 use once_cell::sync::Lazy;
-use parser::{muropeptide, MuropeptideErrorKind};
+use parser::{MuropeptideErrorKind, muropeptide};
 // FIXME: Blocks need separating and reordering!
 use polychem::{
-    errors::PolychemError, AtomicDatabase, AverageMass, BondId, Charged, GroupState, Massive,
-    ModificationInfo, MonoisotopicMass, Polymer, PolymerDatabase, Polymerizer, ResidueId,
+    AtomicDatabase, AverageMass, BondId, Charged, GroupState, Massive, ModificationInfo,
+    MonoisotopicMass, Polymer, PolymerDatabase, Polymerizer, ResidueId, errors::PolychemError,
 };
 use smithereens::Dissociable;
 use thiserror::Error;

crates/muropeptide/src/parser.rs

@@ -3,24 +3,24 @@ use std::{cell::RefCell, iter::zip};
 use itertools::{EitherOrBoth, Itertools};
 use miette::Diagnostic;
 use nom::{
+    IResult,
     branch::alt,
     bytes::complete::tag,
     character::complete::{alpha1, alphanumeric1, char, one_of, space0, space1},
     combinator::{cut, map, opt, recognize},
     error::ErrorKind,
     multi::{many0, many1, separated_list1},
     sequence::{delimited, pair, preceded, terminated, tuple},
-    IResult,
 };
-use nom_miette::{map_res, wrap_err, FromExternalError, LabeledErrorKind, LabeledParseError};
+use nom_miette::{FromExternalError, LabeledErrorKind, LabeledParseError, map_res, wrap_err};
 use polychem::{
+    Count, ModificationId, Polymer, Polymerizer,
     errors::PolychemError,
     parsers::{
         chemical_composition,
         errors::PolychemErrorKind,
         primitives::{count, lowercase, offset_kind, uppercase},
     },
-    Count, ModificationId, Polymer, Polymerizer,
 };
 use thiserror::Error;
 
@@ -38,13 +38,6 @@ const CTON_BOND: &str = "CToN";
 const CROSSLINK_BOND: &str = "Link";
 const LAT_CROSSLINK_BOND: &str = "Lat-Link";
 
-// FIXME: A horrible hack that's needed to specify the lifetimes captured by `impl FnMut(...) -> ...` correctly. Once
-// Rust 2024 is stabilized, however, this hack can be removed. Keep an eye on:
-// https://github.com/rust-lang/rust/issues/117587
-// FIXME: Make private again
-pub trait Captures<U> {}
-impl<T: ?Sized, U> Captures<U> for T {}
-
 // FIXME: Paste all of these EBNF comments into another file and make sure they are valid!
 
 /// Muropeptide = Monomer , { Connection , Monomer } , [ Connection ] , [ { " " }- ,
@@ -57,8 +50,7 @@ impl<T: ?Sized, U> Captures<U> for T {}
 #[allow(clippy::too_many_lines)]
 pub fn muropeptide<'z, 'a, 'p, 's>(
     polymerizer: &'z Polymerizer<'a, 'p>,
-) -> impl FnMut(&'s str) -> ParseResult<'s, Muropeptide<'a, 'p>> + Captures<(&'z (), &'a (), &'p ())>
-{
+) -> impl FnMut(&'s str) -> ParseResult<'s, Muropeptide<'a, 'p>> {
     move |i| {
         let polymer = RefCell::new(polymerizer.new_polymer());
         // FIXME: Perhaps there is a better way to shorten that `polymer` borrow...
@@ -208,22 +200,19 @@ pub fn muropeptide<'z, 'a, 'p, 's>(
         };
 
         let polymer = polymer.into_inner();
-        Ok((
-            rest,
-            Muropeptide {
-                polymer,
-                monomers,
-                connections,
-            },
-        ))
+        Ok((rest, Muropeptide {
+            polymer,
+            monomers,
+            connections,
+        }))
     }
 }
 
 /// Monomer = Glycan , [ "-" , Peptide ] | Peptide ;
 // FIXME: Make private again
 pub fn monomer<'c, 'a, 'p, 's>(
     polymer: &'c RefCell<Polymer<'a, 'p>>,
-) -> impl FnMut(&'s str) -> ParseResult<'s, Monomer> + Captures<(&'c (), &'a (), &'p ())> {
+) -> impl FnMut(&'s str) -> ParseResult<'s, Monomer> {
     let optional_peptide = opt(preceded(char('-'), cut(peptide(polymer))));
     let glycan_and_peptide = map_res(
         pair(glycan(polymer), optional_peptide),
@@ -261,8 +250,7 @@ pub fn monomer<'c, 'a, 'p, 's>(
 /// Glycan = { Monosaccharide }- ;
 fn glycan<'c, 'a, 'p, 's>(
     polymer: &'c RefCell<Polymer<'a, 'p>>,
-) -> impl FnMut(&'s str) -> ParseResult<'s, Vec<Monosaccharide>> + Captures<(&'c (), &'a (), &'p ())>
-{
+) -> impl FnMut(&'s str) -> ParseResult<'s, Vec<Monosaccharide>> {
     let parser = many1(monosaccharide(polymer));
     map_res(parser, |residues| {
         polymer
@@ -275,7 +263,7 @@ fn glycan<'c, 'a, 'p, 's>(
 /// Peptide = { Amino Acid }- ;
 fn peptide<'c, 'a, 'p, 's>(
     polymer: &'c RefCell<Polymer<'a, 'p>>,
-) -> impl FnMut(&'s str) -> ParseResult<'s, Vec<AminoAcid>> + Captures<(&'c (), &'a (), &'p ())> {
+) -> impl FnMut(&'s str) -> ParseResult<'s, Vec<AminoAcid>> {
     let parser = many1(amino_acid(polymer));
     map_res(parser, |residues| {
         let residue_ids = residues.iter().map(|aa| aa.residue);
@@ -289,7 +277,7 @@ fn peptide<'c, 'a, 'p, 's>(
 /// Monosaccharide = lowercase , [ Modifications ] ;
 fn monosaccharide<'c, 'a, 'p, 's>(
     polymer: &'c RefCell<Polymer<'a, 'p>>,
-) -> impl FnMut(&'s str) -> ParseResult<'s, Monosaccharide> + Captures<(&'c (), &'a (), &'p ())> {
+) -> impl FnMut(&'s str) -> ParseResult<'s, Monosaccharide> {
     let parser = pair(recognize(lowercase), opt(modifications(polymer)));
     map_res(parser, |(abbr, modifications)| {
         let residue = polymer.borrow_mut().new_residue(abbr)?;
@@ -307,7 +295,7 @@ fn monosaccharide<'c, 'a, 'p, 's>(
 /// Amino Acid = Unbranched Amino Acid , [ Lateral Chain ] ;
 fn amino_acid<'c, 'a, 'p, 's>(
     polymer: &'c RefCell<Polymer<'a, 'p>>,
-) -> impl FnMut(&'s str) -> ParseResult<'s, AminoAcid> + Captures<(&'c (), &'a (), &'p ())> {
+) -> impl FnMut(&'s str) -> ParseResult<'s, AminoAcid> {
     let parser = pair(unbranched_amino_acid(polymer), opt(lateral_chain(polymer)));
     map_res(parser, |(residue, lateral_chain)| {
         if let Some(LateralChain { direction, peptide }) = &lateral_chain {
@@ -351,8 +339,7 @@ fn amino_acid<'c, 'a, 'p, 's>(
 ///   { { " " } , "," , { " " } , Any Modification } , ")" ;
 fn modifications<'c, 'a, 'p, 's>(
     polymer: &'c RefCell<Polymer<'a, 'p>>,
-) -> impl FnMut(&'s str) -> ParseResult<'s, Vec<ModificationId>> + Captures<(&'c (), &'a (), &'p ())>
-{
+) -> impl FnMut(&'s str) -> ParseResult<'s, Vec<ModificationId>> {
     let separator = delimited(space0, char(','), space0);
     delimited(
         char('('),
@@ -364,8 +351,7 @@ fn modifications<'c, 'a, 'p, 's>(
 /// Unbranched Amino Acid = [ lowercase ] , uppercase , [ Modifications ] ;
 fn unbranched_amino_acid<'c, 'a, 'p, 's>(
     polymer: &'c RefCell<Polymer<'a, 'p>>,
-) -> impl FnMut(&'s str) -> ParseResult<'s, UnbranchedAminoAcid> + Captures<(&'c (), &'a (), &'p ())>
-{
+) -> impl FnMut(&'s str) -> ParseResult<'s, UnbranchedAminoAcid> {
     let abbr = recognize(preceded(opt(lowercase), uppercase));
     let parser = pair(abbr, opt(modifications(polymer)));
     map_res(parser, |(abbr, modifications)| {
@@ -385,7 +371,7 @@ fn unbranched_amino_acid<'c, 'a, 'p, 's>(
 /// Lateral Chain = "[" , Peptide Direction , { Unbranched Amino Acid }- , "]" ;
 fn lateral_chain<'c, 'a, 'p, 's>(
     polymer: &'c RefCell<Polymer<'a, 'p>>,
-) -> impl FnMut(&'s str) -> ParseResult<'s, LateralChain> + Captures<(&'c (), &'a (), &'p ())> {
+) -> impl FnMut(&'s str) -> ParseResult<'s, LateralChain> {
     let peptide = many1(unbranched_amino_acid(polymer));
     let parser = delimited(char('['), peptide, char(']'));
     map(parser, |peptide| LateralChain {
@@ -417,15 +403,15 @@ fn identifier(i: &str) -> ParseResult<&str> {
 /// Any Modification = Named Modification | Offset Modification
 pub fn any_modification<'c, 'a, 'p, 's>(
     polymer: &'c RefCell<Polymer<'a, 'p>>,
-) -> impl FnMut(&'s str) -> ParseResult<'s, ModificationId> + Captures<(&'c (), &'a (), &'p ())> {
+) -> impl FnMut(&'s str) -> ParseResult<'s, ModificationId> {
     alt((named_modification(polymer), offset_modification(polymer)))
 }
 
 // FIXME: I probably need to add a lot of `wrap_err`s around these parsers!
 /// Named Modification = [ Multiplier ] , Identifier
 pub fn named_modification<'c, 'a, 'p, 's>(
     polymer: &'c RefCell<Polymer<'a, 'p>>,
-) -> impl FnMut(&'s str) -> ParseResult<'s, ModificationId> + Captures<(&'c (), &'a (), &'p ())> {
+) -> impl FnMut(&'s str) -> ParseResult<'s, ModificationId> {
     let parser = pair(opt(multiplier), identifier);
     map_res(parser, |(multiplier, named_mod)| {
         polymer
@@ -439,7 +425,7 @@ pub fn named_modification<'c, 'a, 'p, 's>(
 ///   Chemical Composition ;
 pub fn offset_modification<'c, 'a, 'p, 's>(
     polymer: &'c RefCell<Polymer<'a, 'p>>,
-) -> impl FnMut(&'s str) -> ParseResult<'s, ModificationId> + Captures<(&'c (), &'a (), &'p ())> {
+) -> impl FnMut(&'s str) -> ParseResult<'s, ModificationId> {
     let chemical_composition = chemical_composition(polymer.borrow().atomic_db());
     let parser = tuple((offset_kind, opt(multiplier), chemical_composition));
 
@@ -535,7 +521,9 @@ pub enum ConstructionError {
     PolychemError(#[from] Box<PolychemError>),
 
     // FIXME: Eventually make this error either more informative (printing the number of each), or replace it!
-    #[error("the number of described crosslinks (e.g. 3-3) doesn't match the number of crosslink connectors (=)")]
+    #[error(
+        "the number of described crosslinks (e.g. 3-3) doesn't match the number of crosslink connectors (=)"
+    )]
     CrosslinkCountMismatch,
 
     // FIXME: Eventually make this error either more informative, or replace it!
@@ -553,7 +541,9 @@ pub enum ConstructionError {
 
 #[derive(Clone, Eq, PartialEq, Debug, Diagnostic, Error)]
 pub enum MuropeptideErrorKind {
-    #[error("expected an ASCII letter, optionally followed by any number of ASCII letters, digits, and underscores")]
+    #[error(
+        "expected an ASCII letter, optionally followed by any number of ASCII letters, digits, and underscores"
+    )]
     ExpectedIdentifier,
 
     // FIXME: Kill this and merge into the error below!

crates/nom-miette/Cargo.toml

@@ -1,7 +1,7 @@
 [package]
 name = "nom-miette"
 version = "0.1.0"
-edition = "2021"
+edition = "2024"
 
 [dependencies]
 ahash = "0.8.11"

crates/nom-miette/src/lib.rs

@@ -4,9 +4,9 @@ use std::fmt::Display;
 use ahash::{HashMap, HashMapExt};
 use miette::{Diagnostic, LabeledSpan, SourceSpan};
 use nom::{
+    Err, ErrorConvert, Finish, IResult, Parser,
     combinator::{all_consuming, complete, consumed},
     error::ParseError,
-    Err, ErrorConvert, Finish, IResult, Parser,
 };
 use thiserror::Error;
 

crates/polychem/Cargo.toml

@@ -1,7 +1,7 @@
 [package]
 name = "polychem"
 version = "0.1.0"
-edition = "2021"
+edition = "2024"
 
 # FIXME: Set up justfile and CI to check direct-minimal-versions
 [dependencies]

crates/polychem/benches/api.rs

@@ -1,7 +1,7 @@
-use divan::{black_box, AllocProfiler};
+use divan::{AllocProfiler, black_box};
 use once_cell::sync::Lazy;
 use polychem::{
-    atoms::atomic_database, AtomicDatabase, Charged, ChemicalComposition, Massive, PolymerDatabase,
+    AtomicDatabase, Charged, ChemicalComposition, Massive, PolymerDatabase, atoms::atomic_database,
 };
 
 #[global_allocator]

crates/polychem/src/atoms/atomic_database.rs

@@ -4,12 +4,12 @@ use std::{num::NonZero, ops::Deref, str::FromStr};
 // External Crate Imports
 use ahash::HashMap;
 use knuffel::{
+    Decode, DecodeScalar,
     ast::{self, Integer, Literal, Radix, TypeName},
     decode::{Context, Kind},
     errors::{DecodeError, ExpectedType},
     span::Spanned,
     traits::ErrorSpan,
-    Decode, DecodeScalar,
 };
 use miette::{Diagnostic, Result};
 use rust_decimal::Decimal;
@@ -287,13 +287,10 @@ impl From<IsotopeKdl> for IsotopeEntry {
             abundance,
         }: IsotopeKdl,
     ) -> Self {
-        (
-            MassNumber(mass_number.0),
-            Isotope {
-                relative_mass: Mass(relative_mass.0),
-                abundance: abundance.map(|a| Abundance(a.0)),
-            },
-        )
+        (MassNumber(mass_number.0), Isotope {
+            relative_mass: Mass(relative_mass.0),
+            abundance: abundance.map(|a| Abundance(a.0)),
+        })
     }
 }
 
@@ -308,14 +305,11 @@ impl From<ParticleKdl> for ParticleEntry {
             charge,
         }: ParticleKdl,
     ) -> Self {
-        (
-            symbol.0,
-            ParticleDescription {
-                name,
-                mass: Mass(mass.0),
-                charge: Charge(charge),
-            },
-        )
+        (symbol.0, ParticleDescription {
+            name,
+            mass: Mass(mass.0),
+            charge: Charge(charge),
+        })
     }
 }
 
@@ -461,14 +455,14 @@ mod tests {
     fn decimal_scientific() {
         let kdl = "lossless 5.485_799_090_65e-4";
         let res = knuffel::parse::<Vec<Lossless>>("test", kdl).unwrap();
-        assert_eq!(res[0].0 .0, dec!(0.000548579909065));
+        assert_eq!(res[0].0.0, dec!(0.000548579909065));
     }
 
     #[test]
     fn decimal_from_integer() {
         let kdl = "lossless 1";
         let res = knuffel::parse::<Vec<Lossless>>("test", kdl).unwrap();
-        assert_eq!(res[0].0 .0, dec!(1));
+        assert_eq!(res[0].0.0, dec!(1));
     }
 
     #[test]
@@ -499,7 +493,7 @@ mod tests {
     fn nonzero_positive() {
         let kdl = "nonzero 42";
         let res = knuffel::parse::<Vec<NonZero>>("test", kdl).unwrap();
-        assert_eq!(res[0].0 .0.get(), 42);
+        assert_eq!(res[0].0.0.get(), 42);
     }
 
     #[test]