refactor: reformat

Author: ivan-aksamentov

packages/nextclade/benches/bench_seed_alignment.rs

@@ -5,7 +5,7 @@ use criterion::{black_box, criterion_group, criterion_main, Criterion};
 use nextclade::align::params::AlignPairwiseParams;
 use nextclade::align::seed_alignment::create_alignment_band;
 use nextclade::align::seed_match::{get_seed_matches_maybe_reverse_complement, CodonSpacedIndex, SeedMatchesResult};
-use nextclade::alphabet::nuc::{Nuc, to_nuc_seq};
+use nextclade::alphabet::nuc::{to_nuc_seq, Nuc};
 
 pub fn bench_seed_alignment(c: &mut Criterion) {
   let params = AlignPairwiseParams::default();

packages/nextclade/src/align/align.rs

@@ -1,9 +1,9 @@
 use crate::align::backtrace::{backtrace, AlignmentOutput};
 use crate::align::band_2d::Stripe;
 use crate::align::band_2d::{full_matrix, simple_stripes};
+use crate::align::params::AlignPairwiseParams;
 use crate::align::score_matrix::{score_matrix, ScoreMatrixResult};
 use crate::align::seed_alignment::create_alignment_band;
-use crate::align::params::AlignPairwiseParams;
 use crate::align::seed_match::{get_seed_matches_maybe_reverse_complement, CodonSpacedIndex, SeedMatchesResult};
 use crate::alphabet::aa::Aa;
 use crate::alphabet::letter::Letter;

packages/nextclade/src/analyze/mod.rs

@@ -7,11 +7,11 @@ pub mod aa_del;
 pub mod aa_sub;
 pub mod aa_sub_min;
 pub mod abstract_mutation;
-pub mod find_clade_founder;
 pub mod count_gaps;
 pub mod divergence;
 pub mod find_aa_motifs;
 pub mod find_aa_motifs_changes;
+pub mod find_clade_founder;
 pub mod find_private_aa_mutations;
 pub mod find_private_nuc_mutations;
 pub mod find_relative_aa_mutations;

packages/nextclade/src/coord/coord_map.rs

@@ -7,7 +7,6 @@ use crate::coord::range::{AaRefRange, NucRefLocalRange};
 
 use num::integer::div_floor;
 
-
 /// Makes the "alignment to reference" coordinate map: from alignment coordinates to reference coordinates.
 /// Given a position of a letter in the aligned sequence, the "alignment to reference" coordinate map allows to
 /// lookup the position of the corresponding letter in the reference sequence.

packages/nextclade/src/coord/coord_map_global.rs

@@ -83,8 +83,6 @@ impl CoordMapGlobal {
       self.ref_to_qry_position(ref_range.end - 1) + 1,
     )
   }
-
-
 }
 
 #[cfg(test)]

packages/nextclade/src/features/feature_group.rs

@@ -1,11 +1,11 @@
 use crate::coord::position::{NucRefGlobalPosition, PositionLike};
+use crate::coord::range::NucRefGlobalRange;
 use crate::features::feature::Feature;
 use crate::features::feature_type::shorten_feature_type;
 use itertools::Itertools;
 use serde::{Deserialize, Serialize};
 use std::cmp::Ordering;
 use std::fmt::Debug;
-use crate::coord::range::NucRefGlobalRange;
 
 #[derive(Clone, Debug, Deserialize, Serialize, PartialEq, Eq)]
 #[serde(rename_all = "camelCase")]

packages/nextclade/src/gene/gene_map_display.rs

@@ -6,12 +6,12 @@ use crate::gene::gene::Gene;
 use crate::gene::gene_map::GeneMap;
 use crate::gene::protein::{Protein, ProteinSegment};
 use crate::utils::string::truncate_right;
+use console::style;
 use eyre::Report;
 use itertools::{max as iter_max, Itertools};
 use num_traits::clamp;
 use std::cmp::{max, min};
 use std::io::Write;
-use console::style;
 
 const INDENT: &str = " ";
 const INDENT_WIDTH: usize = 2;

packages/nextclade/src/qc/qc_rule_mixed_sites.rs

@@ -1,6 +1,6 @@
 use crate::alphabet::letter::Letter;
 use crate::alphabet::nuc::Nuc;
-use crate::qc::qc_config::{QcRulesConfigMixedSites};
+use crate::qc::qc_config::QcRulesConfigMixedSites;
 use crate::qc::qc_run::{QcRule, QcStatus};
 use num::traits::clamp_min;
 use serde::{Deserialize, Serialize};

packages/nextclade/src/translate/extract.rs

@@ -74,8 +74,8 @@ mod coord_map_tests {
   use crate::alphabet::nuc::to_nuc_seq;
   use crate::coord::position::Position;
   use crate::coord::range::{NucRefGlobalRange, Range};
-  
-use crate::gene::cds_segment::{CdsSegment, Truncation, WrappingPart};
+
+  use crate::gene::cds_segment::{CdsSegment, Truncation, WrappingPart};
   use crate::gene::frame::Frame;
   use crate::gene::phase::Phase;
   use eyre::Report;

packages/nextclade/src/utils/indexmap.rs

@@ -7,7 +7,7 @@ pub fn reorder_indexmap<K, V, I>(map: IndexMap<K, V>, canonical: I) -> IndexMap<
 where
   K: Eq + Hash + Clone + Ord,
   V: Clone,
-  I: IntoIterator<Item=K>,
+  I: IntoIterator<Item = K>,
 {
   let order_map: HashMap<K, usize> = canonical.into_iter().enumerate().map(|(i, k)| (k, i)).collect();
   map