From 0e2cfb6ca7b62e3f9351d04c183f26a848b46212 Mon Sep 17 00:00:00 2001 From: ivan-aksamentov Date: Fri, 9 Feb 2024 09:12:30 +0100 Subject: [PATCH] refactor: remove unused imports --- .cargo/config.toml | 1 - packages/nextclade-cli/src/cli/nextclade_cli.rs | 2 +- .../nextclade-cli/src/cli/nextclade_ordered_writer.rs | 1 - packages/nextclade-cli/src/dataset/dataset_download.rs | 3 --- packages/nextclade-web/src/wasm/main.rs | 4 +--- packages/nextclade-web/src/wasm/seq_autodetect.rs | 2 -- packages/nextclade/src/align/backtrace.rs | 10 +++++----- packages/nextclade/src/align/gap_open.rs | 2 +- packages/nextclade/src/align/insertions_strip.rs | 10 +++++----- packages/nextclade/src/align/score_matrix.rs | 2 +- packages/nextclade/src/align/seed_alignment.rs | 2 +- packages/nextclade/src/align/seed_match.rs | 2 +- packages/nextclade/src/alphabet/aa.rs | 2 +- packages/nextclade/src/alphabet/nuc.rs | 2 +- packages/nextclade/src/analyze/aa_del.rs | 2 +- packages/nextclade/src/analyze/is_sequenced.rs | 1 - packages/nextclade/src/analyze/nuc_del.rs | 2 +- packages/nextclade/src/analyze/phenotype.rs | 1 - packages/nextclade/src/analyze/virus_properties.rs | 3 +-- packages/nextclade/src/coord/coord_map.rs | 7 +++---- .../nextclade/src/coord/coord_map_cds_to_global.rs | 8 ++++---- packages/nextclade/src/coord/coord_map_global.rs | 2 +- packages/nextclade/src/coord/coord_map_local.rs | 2 +- packages/nextclade/src/coord/position.rs | 2 +- packages/nextclade/src/gene/cds.rs | 2 +- packages/nextclade/src/gene/gene_map.rs | 3 +-- packages/nextclade/src/graph/node.rs | 2 +- packages/nextclade/src/io/fasta.rs | 3 +-- packages/nextclade/src/io/file.rs | 2 +- packages/nextclade/src/io/gff3.rs | 8 ++++---- packages/nextclade/src/io/ndjson.rs | 2 +- packages/nextclade/src/io/nextclade_csv.rs | 1 - packages/nextclade/src/io/nwk_writer.rs | 1 - packages/nextclade/src/qc/qc_rule_mixed_sites.rs | 2 +- packages/nextclade/src/run/nextclade_wasm.rs | 1 - packages/nextclade/src/run/params.rs | 6 +++--- packages/nextclade/src/sort/minimizer_search.rs | 2 +- packages/nextclade/src/tree/split_muts.rs | 2 +- packages/nextclade/src/tree/split_muts2.rs | 2 +- packages/nextclade/src/tree/tree.rs | 1 - packages/nextclade/src/tree/tree_find_nearest_node.rs | 7 ++++--- packages/nextclade/src/tree/tree_preprocess.rs | 2 +- packages/nextclade/src/utils/error.rs | 1 - packages/nextclade/src/utils/vec2d.rs | 2 +- 44 files changed, 54 insertions(+), 73 deletions(-) diff --git a/.cargo/config.toml b/.cargo/config.toml index c41e9b7ca..d40604ad1 100644 --- a/.cargo/config.toml +++ b/.cargo/config.toml @@ -276,6 +276,5 @@ rustflags = [ # Disable some of the default rust checks "-Adead_code", "-Aelided_lifetimes_in_paths", - "-Aunused_imports", "-Aunused_variables", ] diff --git a/packages/nextclade-cli/src/cli/nextclade_cli.rs b/packages/nextclade-cli/src/cli/nextclade_cli.rs index 599a41c94..3064bc8cb 100644 --- a/packages/nextclade-cli/src/cli/nextclade_cli.rs +++ b/packages/nextclade-cli/src/cli/nextclade_cli.rs @@ -8,7 +8,7 @@ use crate::cli::verbosity::{Verbosity, WarnLevel}; use crate::io::http_client::ProxyConfig; use clap::builder::styling; use clap::{ArgGroup, CommandFactory, Parser, Subcommand, ValueEnum, ValueHint}; -use clap_complete::{generate, Generator, Shell}; +use clap_complete::{generate, Shell}; use clap_complete_fig::Fig; use eyre::{eyre, ContextCompat, Report, WrapErr}; use itertools::Itertools; diff --git a/packages/nextclade-cli/src/cli/nextclade_ordered_writer.rs b/packages/nextclade-cli/src/cli/nextclade_ordered_writer.rs index f2845cc1c..68ce7b7f8 100644 --- a/packages/nextclade-cli/src/cli/nextclade_ordered_writer.rs +++ b/packages/nextclade-cli/src/cli/nextclade_ordered_writer.rs @@ -18,7 +18,6 @@ use nextclade::types::outputs::NextcladeOutputs; use nextclade::utils::error::report_to_string; use nextclade::utils::option::OptionMapRefFallible; use std::collections::HashMap; -use std::hash::Hasher; /// Writes output files, potentially preserving the initial order of records (same as in the inputs) pub struct NextcladeOrderedWriter { diff --git a/packages/nextclade-cli/src/dataset/dataset_download.rs b/packages/nextclade-cli/src/dataset/dataset_download.rs index 1dd0e46f0..a86834c54 100644 --- a/packages/nextclade-cli/src/dataset/dataset_download.rs +++ b/packages/nextclade-cli/src/dataset/dataset_download.rs @@ -2,7 +2,6 @@ use crate::cli::nextclade_cli::{NextcladeRunArgs, NextcladeRunInputArgs}; use crate::cli::nextclade_dataset_get::{dataset_file_http_get, dataset_http_get}; use crate::io::http_client::{HttpClient, ProxyConfig}; use eyre::{eyre, ContextCompat, Report, WrapErr}; -use itertools::Itertools; use log::LevelFilter; use nextclade::analyze::virus_properties::{LabelledMutationsConfig, VirusProperties}; use nextclade::gene::gene_map::{filter_gene_map, GeneMap}; @@ -14,12 +13,10 @@ use nextclade::run::nextclade_wasm::NextcladeParams; use nextclade::tree::tree::AuspiceTree; use nextclade::utils::option::OptionMapRefFallible; use nextclade::{make_error, make_internal_error, o}; -use rayon::iter::ParallelIterator; use std::collections::BTreeMap; use std::fs::File; use std::io::{BufReader, Cursor, Read, Seek, Write}; use std::path::{Path, PathBuf}; -use std::str::FromStr; use zip::ZipArchive; const PATHOGEN_JSON: &str = "pathogen.json"; diff --git a/packages/nextclade-web/src/wasm/main.rs b/packages/nextclade-web/src/wasm/main.rs index f46152e7e..1a66324a3 100644 --- a/packages/nextclade-web/src/wasm/main.rs +++ b/packages/nextclade-web/src/wasm/main.rs @@ -1,5 +1,5 @@ use crate::wasm::jserr::jserr; -use eyre::{Report, WrapErr}; +use eyre::WrapErr; use itertools::Itertools; use nextclade::analyze::virus_properties::{AaMotifsDesc, PhenotypeAttrDesc}; use nextclade::io::fasta::{read_one_fasta_str, FastaReader, FastaRecord}; @@ -11,8 +11,6 @@ use nextclade::run::params::NextcladeInputParamsOptional; use nextclade::tree::tree::CladeNodeAttrKeyDesc; use nextclade::types::outputs::{NextcladeErrorOutputs, NextcladeOutputs}; use nextclade::utils::error::report_to_string; -use std::io::Read; -use std::str::FromStr; use wasm_bindgen::prelude::*; /// Nextclade WebAssembly module. diff --git a/packages/nextclade-web/src/wasm/seq_autodetect.rs b/packages/nextclade-web/src/wasm/seq_autodetect.rs index 1a3fe6c3e..5ca8d80a4 100644 --- a/packages/nextclade-web/src/wasm/seq_autodetect.rs +++ b/packages/nextclade-web/src/wasm/seq_autodetect.rs @@ -9,8 +9,6 @@ use nextclade::sort::params::NextcladeSeqSortParams; use nextclade::utils::datetime::date_now; use schemars::JsonSchema; use serde::{Deserialize, Serialize}; -use std::io::Read; -use std::str::FromStr; use wasm_bindgen::prelude::*; #[wasm_bindgen] diff --git a/packages/nextclade/src/align/backtrace.rs b/packages/nextclade/src/align/backtrace.rs index f883ffb3f..4d47849c8 100644 --- a/packages/nextclade/src/align/backtrace.rs +++ b/packages/nextclade/src/align/backtrace.rs @@ -1,10 +1,10 @@ -use crate::align::band_2d::{Band2d, Stripe}; +use crate::align::band_2d::{Band2d}; use crate::align::score_matrix::{BOUNDARY, MATCH, QRY_GAP_EXTEND, QRY_GAP_MATRIX, REF_GAP_EXTEND, REF_GAP_MATRIX}; use crate::alphabet::letter::Letter; -use crate::utils::vec2d::Vec2d; -use log::warn; + + use serde::{Deserialize, Serialize}; -use std::cmp; + const fn index_to_shift(si: i32, band_width: i32, mean_shift: i32) -> i32 { si - band_width + mean_shift @@ -108,7 +108,7 @@ mod tests { use crate::align::band_2d::simple_stripes; use crate::align::gap_open::{get_gap_open_close_scores_codon_aware, GapScoreMap}; use crate::align::params::AlignPairwiseParams; - use crate::align::score_matrix; + use crate::alphabet::nuc::{to_nuc_seq, Nuc}; use crate::gene::gene_map::GeneMap; use eyre::Report; diff --git a/packages/nextclade/src/align/gap_open.rs b/packages/nextclade/src/align/gap_open.rs index 60c9ae3e0..09c0e8683 100644 --- a/packages/nextclade/src/align/gap_open.rs +++ b/packages/nextclade/src/align/gap_open.rs @@ -1,6 +1,6 @@ use crate::align::params::AlignPairwiseParams; use crate::alphabet::nuc::Nuc; -use crate::coord::range::NucRefGlobalRange; + use crate::gene::gene::GeneStrand; use crate::gene::gene_map::GeneMap; use either::Either; diff --git a/packages/nextclade/src/align/insertions_strip.rs b/packages/nextclade/src/align/insertions_strip.rs index 509d70ce9..e5b11c1cf 100644 --- a/packages/nextclade/src/align/insertions_strip.rs +++ b/packages/nextclade/src/align/insertions_strip.rs @@ -2,13 +2,13 @@ use crate::alphabet::aa::Aa; use crate::alphabet::letter::{serde_deserialize_seq, serde_serialize_seq, Letter}; use crate::alphabet::nuc::Nuc; use crate::translate::translate_genes::Translation; -use color_eyre::SectionExt; -use eyre::Report; + + use itertools::Itertools; -use serde::de::Error; -use serde::{Deserialize, Deserializer, Serialize, Serializer}; + +use serde::{Deserialize, Serialize}; use std::cmp::Ordering; -use std::str::FromStr; + #[derive(Clone, Debug, Eq, PartialEq, Serialize, Deserialize, schemars::JsonSchema)] pub struct Insertion> { diff --git a/packages/nextclade/src/align/score_matrix.rs b/packages/nextclade/src/align/score_matrix.rs index 240fe481a..e9619f199 100644 --- a/packages/nextclade/src/align/score_matrix.rs +++ b/packages/nextclade/src/align/score_matrix.rs @@ -209,7 +209,7 @@ mod tests { use super::*; use crate::align::band_2d::simple_stripes; use crate::align::gap_open::{get_gap_open_close_scores_codon_aware, GapScoreMap}; - use crate::align::score_matrix; + use crate::alphabet::nuc::{to_nuc_seq, Nuc}; use crate::gene::gene_map::GeneMap; use eyre::Report; diff --git a/packages/nextclade/src/align/seed_alignment.rs b/packages/nextclade/src/align/seed_alignment.rs index b0c0c4802..499cd41a4 100644 --- a/packages/nextclade/src/align/seed_alignment.rs +++ b/packages/nextclade/src/align/seed_alignment.rs @@ -1,7 +1,7 @@ use crate::align::band_2d::Stripe; use crate::align::seed_match::SeedMatch2; use crate::alphabet::letter::Letter; -use eyre::Report; + use log::trace; use num_traits::abs; use num_traits::clamp; diff --git a/packages/nextclade/src/align/seed_match.rs b/packages/nextclade/src/align/seed_match.rs index dffe98091..1516f7795 100644 --- a/packages/nextclade/src/align/seed_match.rs +++ b/packages/nextclade/src/align/seed_match.rs @@ -8,7 +8,7 @@ use bio::data_structures::bwt::{bwt, less, Less, Occ, BWT}; use bio::data_structures::fmindex::{BackwardSearchResult, FMIndex, FMIndexable}; use bio::data_structures::suffix_array::suffix_array; use eyre::Report; -use gcollections::ops::{Bounded, Intersection, IsEmpty, Union}; +use gcollections::ops::{Intersection, IsEmpty, Union}; use interval::interval_set::{IntervalSet, ToIntervalSet}; use itertools::Itertools; use std::borrow::Cow; diff --git a/packages/nextclade/src/alphabet/aa.rs b/packages/nextclade/src/alphabet/aa.rs index f4a03ce21..cbc67d4a8 100644 --- a/packages/nextclade/src/alphabet/aa.rs +++ b/packages/nextclade/src/alphabet/aa.rs @@ -2,7 +2,7 @@ use crate::align::score_matrix_aa::lookup_aa_scoring_matrix; use crate::alphabet::letter::{Letter, ScoreMatrixLookup}; use crate::make_error; use eyre::{eyre, Report, WrapErr}; -use serde::{Deserialize, Deserializer, Serialize, Serializer}; +use serde::{Deserialize, Serialize}; use std::fmt::{Display, Formatter}; #[repr(u8)] diff --git a/packages/nextclade/src/alphabet/nuc.rs b/packages/nextclade/src/alphabet/nuc.rs index cf7cebd38..4b839285c 100644 --- a/packages/nextclade/src/alphabet/nuc.rs +++ b/packages/nextclade/src/alphabet/nuc.rs @@ -2,7 +2,7 @@ use crate::align::score_matrix_nuc::lookup_nuc_scoring_matrix; use crate::alphabet::letter::{Letter, ScoreMatrixLookup}; use crate::make_error; use eyre::{eyre, Report, WrapErr}; -use serde::{Deserialize, Deserializer, Serialize, Serializer}; +use serde::{Deserialize, Serialize}; use std::fmt::{Display, Formatter}; #[repr(u8)] diff --git a/packages/nextclade/src/analyze/aa_del.rs b/packages/nextclade/src/analyze/aa_del.rs index 303a6845a..b6310c589 100644 --- a/packages/nextclade/src/analyze/aa_del.rs +++ b/packages/nextclade/src/analyze/aa_del.rs @@ -1,4 +1,4 @@ -use crate::alphabet::aa::{from_aa, Aa}; +use crate::alphabet::aa::{Aa}; use crate::analyze::aa_sub::AaSub; use crate::analyze::abstract_mutation::{AbstractMutation, MutParams, Pos, QryLetter, RefLetter}; use crate::coord::position::AaRefPosition; diff --git a/packages/nextclade/src/analyze/is_sequenced.rs b/packages/nextclade/src/analyze/is_sequenced.rs index d31dd06d9..051fba4ea 100644 --- a/packages/nextclade/src/analyze/is_sequenced.rs +++ b/packages/nextclade/src/analyze/is_sequenced.rs @@ -2,7 +2,6 @@ use crate::alphabet::letter::Letter; use crate::analyze::letter_ranges::{CdsAaRange, NucRange}; use crate::coord::position::{AaRefPosition, NucRefGlobalPosition}; use crate::coord::range::{AaRefRange, NucRefGlobalRange}; -use itertools::Itertools; /// Decides whether a given position in nucleotide sequence is considered "sequenced". /// The position is considered sequenced if it is not contained in any of the missing regions diff --git a/packages/nextclade/src/analyze/nuc_del.rs b/packages/nextclade/src/analyze/nuc_del.rs index 56ffcc57a..3b92dd0af 100644 --- a/packages/nextclade/src/analyze/nuc_del.rs +++ b/packages/nextclade/src/analyze/nuc_del.rs @@ -5,7 +5,7 @@ use crate::coord::position::NucRefGlobalPosition; use crate::coord::range::NucRefGlobalRange; use serde::{Deserialize, Serialize}; use std::fmt::{Display, Formatter}; -use std::str::FromStr; + #[derive(Clone, Debug, Eq, PartialEq, Ord, PartialOrd, Serialize, Deserialize, schemars::JsonSchema, Hash)] #[serde(rename_all = "camelCase")] diff --git a/packages/nextclade/src/analyze/phenotype.rs b/packages/nextclade/src/analyze/phenotype.rs index c1ffea2cd..aafe8f7c0 100644 --- a/packages/nextclade/src/analyze/phenotype.rs +++ b/packages/nextclade/src/analyze/phenotype.rs @@ -1,7 +1,6 @@ use crate::analyze::aa_sub::AaSub; use crate::analyze::virus_properties::{PhenotypeAttrDesc, PhenotypeData, VirusProperties}; use itertools::Itertools; -use num_traits::real::Real; pub fn calculate_phenotype(phenotype_data: &PhenotypeData, aa_substitutions: &[AaSub]) -> f64 { let aa_substitutions = aa_substitutions diff --git a/packages/nextclade/src/analyze/virus_properties.rs b/packages/nextclade/src/analyze/virus_properties.rs index e32cc6f07..845c3f1f2 100644 --- a/packages/nextclade/src/analyze/virus_properties.rs +++ b/packages/nextclade/src/analyze/virus_properties.rs @@ -1,7 +1,7 @@ use crate::align::params::AlignPairwiseParamsOptional; use crate::alphabet::aa::Aa; use crate::alphabet::nuc::Nuc; -use crate::analyze::pcr_primers::PcrPrimer; + use crate::coord::position::AaRefPosition; use crate::coord::range::AaRefRange; use crate::gene::genotype::Genotype; @@ -18,7 +18,6 @@ use semver::Version; use serde::{Deserialize, Serialize}; use std::collections::BTreeMap; use std::path::Path; -use std::str::FromStr; use validator::Validate; const PATHOGEN_JSON_SCHEMA_VERSION_FROM: &str = "3.0.0"; diff --git a/packages/nextclade/src/coord/coord_map.rs b/packages/nextclade/src/coord/coord_map.rs index 93085c444..e72d0f567 100644 --- a/packages/nextclade/src/coord/coord_map.rs +++ b/packages/nextclade/src/coord/coord_map.rs @@ -1,13 +1,12 @@ use crate::alphabet::letter::Letter; use crate::alphabet::nuc::Nuc; use crate::coord::position::{ - AaRefPosition, AlignmentCoords, CoordsMarker, NucRefLocalPosition, NucSpace, Position, PositionLike, ReferenceCoords, - SeqTypeMarker, SpaceMarker, + AaRefPosition, AlignmentCoords, NucRefLocalPosition, NucSpace, Position, PositionLike, ReferenceCoords, SpaceMarker, }; use crate::coord::range::{AaRefRange, NucRefLocalRange}; -use itertools::Itertools; + use num::integer::div_floor; -use serde::{Deserialize, Serialize}; + /// 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 diff --git a/packages/nextclade/src/coord/coord_map_cds_to_global.rs b/packages/nextclade/src/coord/coord_map_cds_to_global.rs index 3733e6422..40e1ae90d 100644 --- a/packages/nextclade/src/coord/coord_map_cds_to_global.rs +++ b/packages/nextclade/src/coord/coord_map_cds_to_global.rs @@ -1,14 +1,14 @@ -use crate::alphabet::letter::Letter; + use crate::coord::position::{ - AaRefPosition, CoordsMarker, NucRefGlobalPosition, NucRefLocalPosition, PositionLike, SeqTypeMarker, SpaceMarker, + AaRefPosition, NucRefGlobalPosition, NucRefLocalPosition, PositionLike, }; use crate::coord::range::{intersect_or_none, NucRefGlobalRange, NucRefLocalRange}; use crate::gene::cds::Cds; -use crate::gene::cds_segment::WrappingPart; + use crate::gene::gene::GeneStrand; use assert2::assert; use itertools::Itertools; -use serde::{Deserialize, Serialize}; + pub fn cds_nuc_pos_to_ref(cds: &Cds, pos: NucRefLocalPosition) -> NucRefGlobalPosition { assert!(pos < cds.len() as isize); diff --git a/packages/nextclade/src/coord/coord_map_global.rs b/packages/nextclade/src/coord/coord_map_global.rs index e79cb429b..842733d55 100644 --- a/packages/nextclade/src/coord/coord_map_global.rs +++ b/packages/nextclade/src/coord/coord_map_global.rs @@ -2,7 +2,7 @@ use crate::alphabet::nuc::Nuc; use crate::coord::coord_map::{make_aln_to_ref_map, make_ref_to_aln_map}; use crate::coord::position::{NucAlnGlobalPosition, NucRefGlobalPosition, PositionLike}; use crate::coord::range::{NucAlnGlobalRange, NucRefGlobalRange, Range}; -use itertools::Itertools; + use serde::{Deserialize, Serialize}; /// Converts from global alignment coordinates to global reference coordinates and vice versa. diff --git a/packages/nextclade/src/coord/coord_map_local.rs b/packages/nextclade/src/coord/coord_map_local.rs index 5a3305368..82232ead9 100644 --- a/packages/nextclade/src/coord/coord_map_local.rs +++ b/packages/nextclade/src/coord/coord_map_local.rs @@ -1,6 +1,6 @@ use crate::alphabet::nuc::Nuc; use crate::coord::coord_map::make_aln_to_ref_map; -use crate::coord::coord_map_global::CoordMapGlobal; + use crate::coord::position::{AaRefPosition, NucAlnLocalPosition, NucRefLocalPosition, PositionLike}; use crate::coord::range::{AaRefRange, NucAlnLocalRange, NucRefLocalRange, Range}; use serde::{Deserialize, Serialize}; diff --git a/packages/nextclade/src/coord/position.rs b/packages/nextclade/src/coord/position.rs index d2108b869..0a25ed231 100644 --- a/packages/nextclade/src/coord/position.rs +++ b/packages/nextclade/src/coord/position.rs @@ -1,7 +1,7 @@ use auto_ops::{impl_op_ex, impl_op_ex_commutative}; use derive_more::Display as DeriveDisplay; use num::Integer; -use num_traits::{clamp, clamp_max, clamp_min, AsPrimitive, SaturatingAdd, SaturatingMul, SaturatingSub}; +use num_traits::{clamp, clamp_max, clamp_min, AsPrimitive}; use schemars::gen::SchemaGenerator; use schemars::schema::Schema; use serde::{Deserialize, Deserializer, Serialize, Serializer}; diff --git a/packages/nextclade/src/gene/cds.rs b/packages/nextclade/src/gene/cds.rs index b68305ad5..62713df65 100644 --- a/packages/nextclade/src/gene/cds.rs +++ b/packages/nextclade/src/gene/cds.rs @@ -13,7 +13,7 @@ use num_traits::clamp_max; use schemars::JsonSchema; use serde::{Deserialize, Serialize}; use std::collections::HashMap; -use std::fmt::Display; + #[derive(Clone, Debug, Deserialize, Serialize, JsonSchema)] #[serde(rename_all = "camelCase")] diff --git a/packages/nextclade/src/gene/gene_map.rs b/packages/nextclade/src/gene/gene_map.rs index cc549d29e..ad6dbea74 100644 --- a/packages/nextclade/src/gene/gene_map.rs +++ b/packages/nextclade/src/gene/gene_map.rs @@ -13,10 +13,9 @@ use eyre::{eyre, Report, WrapErr}; use itertools::Itertools; use log::warn; use num::Integer; -use regex::internal::Input; use schemars::JsonSchema; use serde::{Deserialize, Serialize}; -use std::fmt::Display; + use std::path::Path; #[derive(Clone, Debug, Default, Deserialize, Serialize, JsonSchema)] diff --git a/packages/nextclade/src/graph/node.rs b/packages/nextclade/src/graph/node.rs index 3f9bbf789..368b1d848 100644 --- a/packages/nextclade/src/graph/node.rs +++ b/packages/nextclade/src/graph/node.rs @@ -1,6 +1,6 @@ use crate::graph::edge::GraphEdgeKey; use crate::io::json::is_json_value_null; -use core::fmt::{Debug, Display}; +use core::fmt::{Debug}; use derive_more::Display; use schemars::gen::SchemaGenerator; use schemars::schema::Schema; diff --git a/packages/nextclade/src/io/fasta.rs b/packages/nextclade/src/io/fasta.rs index ade0abe42..08d517d14 100644 --- a/packages/nextclade/src/io/fasta.rs +++ b/packages/nextclade/src/io/fasta.rs @@ -10,8 +10,7 @@ use eyre::{Report, WrapErr}; use log::{info, trace}; use serde::{Deserialize, Serialize}; use std::collections::BTreeMap; -use std::fmt::Display; -use std::io::{BufRead, BufReader, Read}; +use std::io::{BufRead, BufReader}; use std::path::{Path, PathBuf}; use std::str::FromStr; use tinytemplate::TinyTemplate; diff --git a/packages/nextclade/src/io/file.rs b/packages/nextclade/src/io/file.rs index fd5bc2d7c..6d8959612 100644 --- a/packages/nextclade/src/io/file.rs +++ b/packages/nextclade/src/io/file.rs @@ -1,7 +1,7 @@ use crate::io::fs::ensure_dir; use eyre::{Report, WrapErr}; use log::{info, warn}; -use std::fmt::Debug; + use std::fs::File; use std::io::{stdin, stdout, BufRead, BufReader, BufWriter, Write}; use std::path::{Path, PathBuf}; diff --git a/packages/nextclade/src/io/gff3.rs b/packages/nextclade/src/io/gff3.rs index ca41c0a08..67b4f0ff2 100644 --- a/packages/nextclade/src/io/gff3.rs +++ b/packages/nextclade/src/io/gff3.rs @@ -4,14 +4,14 @@ use crate::utils::collections::get_first_of; use crate::utils::string::surround_with_quotes; use bio::io::gff::{GffType, Record as GffRecord, Writer as GffWriter}; use color_eyre::{Section, SectionExt}; -use eyre::{eyre, Report, WrapErr}; +use eyre::{eyre, Report}; use itertools::Itertools; use serde::{Deserialize, Serialize}; -use std::borrow::BorrowMut; + use std::collections::HashMap; use std::fmt::Debug; -use std::hash::Hash; -use std::io::Read; + + /// Possible keys for name attribute (in order of preference!) pub const NAME_ATTRS_GENE: &[&str] = &[ diff --git a/packages/nextclade/src/io/ndjson.rs b/packages/nextclade/src/io/ndjson.rs index 3cd479330..6963bb6e0 100644 --- a/packages/nextclade/src/io/ndjson.rs +++ b/packages/nextclade/src/io/ndjson.rs @@ -1,7 +1,7 @@ use crate::io::file::create_file_or_stdout; use crate::types::outputs::NextcladeErrorOutputs; use eyre::{Report, WrapErr}; -use std::fmt::Debug; + use std::io::{LineWriter, Write}; use std::path::{Path, PathBuf}; diff --git a/packages/nextclade/src/io/nextclade_csv.rs b/packages/nextclade/src/io/nextclade_csv.rs index 2d34e663d..01dc48d0b 100644 --- a/packages/nextclade/src/io/nextclade_csv.rs +++ b/packages/nextclade/src/io/nextclade_csv.rs @@ -27,7 +27,6 @@ use lazy_static::lazy_static; use serde::{Deserialize, Serialize}; use std::borrow::Cow; use std::fmt::Display; -use std::io::Write; use std::path::Path; use std::str::FromStr; use strum; diff --git a/packages/nextclade/src/io/nwk_writer.rs b/packages/nextclade/src/io/nwk_writer.rs index f2f1e08e3..c936adf72 100644 --- a/packages/nextclade/src/io/nwk_writer.rs +++ b/packages/nextclade/src/io/nwk_writer.rs @@ -4,7 +4,6 @@ use crate::graph::node::{GraphNode, GraphNodeKey}; use crate::graph::traits::{HasDivergence, HasName}; use crate::io::file::create_file_or_stdout; use eyre::{Report, WrapErr}; -use itertools::Itertools; use std::io::Write; use std::path::Path; diff --git a/packages/nextclade/src/qc/qc_rule_mixed_sites.rs b/packages/nextclade/src/qc/qc_rule_mixed_sites.rs index 41e24c074..678197343 100644 --- a/packages/nextclade/src/qc/qc_rule_mixed_sites.rs +++ b/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::{QcConfig, QcRulesConfigMixedSites}; +use crate::qc::qc_config::{QcRulesConfigMixedSites}; use crate::qc::qc_run::{QcRule, QcStatus}; use num::traits::clamp_min; use serde::{Deserialize, Serialize}; diff --git a/packages/nextclade/src/run/nextclade_wasm.rs b/packages/nextclade/src/run/nextclade_wasm.rs index 45c20260a..b32835731 100644 --- a/packages/nextclade/src/run/nextclade_wasm.rs +++ b/packages/nextclade/src/run/nextclade_wasm.rs @@ -25,7 +25,6 @@ use itertools::Itertools; use schemars::JsonSchema; use serde::{Deserialize, Serialize}; use std::collections::BTreeMap; -use std::str::FromStr; #[derive(Clone, Debug, Serialize, Deserialize, schemars::JsonSchema)] #[serde(rename_all = "camelCase")] diff --git a/packages/nextclade/src/run/params.rs b/packages/nextclade/src/run/params.rs index afafc100b..8860905a8 100644 --- a/packages/nextclade/src/run/params.rs +++ b/packages/nextclade/src/run/params.rs @@ -2,12 +2,12 @@ use crate::align::params::{AlignPairwiseParams, AlignPairwiseParamsOptional}; use crate::analyze::virus_properties::VirusProperties; use crate::run::params_general::{NextcladeGeneralParams, NextcladeGeneralParamsOptional}; use crate::tree::params::{TreeBuilderParams, TreeBuilderParamsOptional}; -use crate::{make_error, o}; + use clap::Parser; use eyre::Report; -use itertools::Itertools; + use serde::{Deserialize, Serialize}; -use std::collections::BTreeMap; + #[derive(Parser, Debug, Default, Clone, Serialize, Deserialize, schemars::JsonSchema)] #[serde(rename_all = "camelCase")] diff --git a/packages/nextclade/src/sort/minimizer_search.rs b/packages/nextclade/src/sort/minimizer_search.rs index 1a45a8e6e..4c07cea53 100644 --- a/packages/nextclade/src/sort/minimizer_search.rs +++ b/packages/nextclade/src/sort/minimizer_search.rs @@ -6,7 +6,7 @@ use itertools::{izip, Itertools}; use ordered_float::OrderedFloat; use schemars::JsonSchema; use serde::{Deserialize, Serialize}; -use std::str::FromStr; + #[derive(Debug, Clone, Serialize, Deserialize, JsonSchema)] #[serde(rename_all = "camelCase")] diff --git a/packages/nextclade/src/tree/split_muts.rs b/packages/nextclade/src/tree/split_muts.rs index 73942395a..5655e1d9d 100644 --- a/packages/nextclade/src/tree/split_muts.rs +++ b/packages/nextclade/src/tree/split_muts.rs @@ -8,7 +8,7 @@ use eyre::{Report, WrapErr}; use itertools::{chain, Itertools}; use std::collections::BTreeMap; use std::fmt::Display; -use std::hash::Hash; + #[derive(Debug, Clone)] pub struct SplitMutsResult { diff --git a/packages/nextclade/src/tree/split_muts2.rs b/packages/nextclade/src/tree/split_muts2.rs index 20c46585e..743617205 100644 --- a/packages/nextclade/src/tree/split_muts2.rs +++ b/packages/nextclade/src/tree/split_muts2.rs @@ -1,6 +1,6 @@ use crate::analyze::aa_sub::AaSub; use crate::analyze::find_private_nuc_mutations::BranchMutations; -use crate::analyze::nuc_del::NucDel; + use crate::analyze::nuc_sub::NucSub; use crate::tree::split_muts::SplitMutsResult; use itertools::Itertools; diff --git a/packages/nextclade/src/tree/tree.rs b/packages/nextclade/src/tree/tree.rs index f61ab4d5e..dd9ed05f3 100644 --- a/packages/nextclade/src/tree/tree.rs +++ b/packages/nextclade/src/tree/tree.rs @@ -14,7 +14,6 @@ use serde::{Deserialize, Deserializer, Serialize, Serializer}; use std::collections::BTreeMap; use std::path::Path; use std::slice::Iter; -use std::str::FromStr; use traversal::{Bft, DftPost, DftPre}; use validator::Validate; diff --git a/packages/nextclade/src/tree/tree_find_nearest_node.rs b/packages/nextclade/src/tree/tree_find_nearest_node.rs index a4bdf6593..220065805 100644 --- a/packages/nextclade/src/tree/tree_find_nearest_node.rs +++ b/packages/nextclade/src/tree/tree_find_nearest_node.rs @@ -2,9 +2,9 @@ use crate::alphabet::nuc::Nuc; use crate::analyze::is_sequenced::is_nuc_sequenced; use crate::analyze::letter_ranges::NucRange; use crate::analyze::nuc_sub::NucSub; -use crate::coord::range::{NucRefGlobalRange, Range}; +use crate::coord::range::NucRefGlobalRange; use crate::graph::node::GraphNodeKey; -use crate::tree::tree::{AuspiceGraph, AuspiceGraphNodePayload, TreeNodeAttr}; +use crate::tree::tree::{AuspiceGraph, AuspiceGraphNodePayload}; use eyre::Report; use itertools::Itertools; use traversal::DftPre; @@ -126,10 +126,11 @@ mod tests { use std::collections::BTreeMap; use crate::alphabet::nuc::Nuc; - use crate::tree::tree::{TreeBranchAttrs, TreeNodeAttrs, TreeNodeTempData}; + use crate::tree::tree::{TreeBranchAttrs, TreeNodeAttr, TreeNodeAttrs, TreeNodeTempData}; use super::*; use crate::coord::position::NucRefGlobalPosition; + use crate::coord::range::Range; use eyre::Report; use pretty_assertions::assert_eq; use rstest::{fixture, rstest}; diff --git a/packages/nextclade/src/tree/tree_preprocess.rs b/packages/nextclade/src/tree/tree_preprocess.rs index 6f27fa31f..7755b5711 100644 --- a/packages/nextclade/src/tree/tree_preprocess.rs +++ b/packages/nextclade/src/tree/tree_preprocess.rs @@ -3,7 +3,7 @@ use crate::alphabet::letter::Letter; use crate::alphabet::nuc::Nuc; use crate::analyze::aa_sub::AaSub; use crate::analyze::find_private_nuc_mutations::BranchMutations; -use crate::analyze::nuc_del::NucDel; + use crate::analyze::nuc_sub::NucSub; use crate::coord::position::{AaRefPosition, NucRefGlobalPosition, PositionLike}; use crate::graph::node::GraphNodeKey; diff --git a/packages/nextclade/src/utils/error.rs b/packages/nextclade/src/utils/error.rs index 974f6be90..0ecc1a2a4 100644 --- a/packages/nextclade/src/utils/error.rs +++ b/packages/nextclade/src/utils/error.rs @@ -1,6 +1,5 @@ use color_eyre::Report; use eyre::eyre; -use itertools::Itertools; use std::str::FromStr; pub fn report_to_string(report: &Report) -> String { diff --git a/packages/nextclade/src/utils/vec2d.rs b/packages/nextclade/src/utils/vec2d.rs index dd94c5c38..99606cedc 100644 --- a/packages/nextclade/src/utils/vec2d.rs +++ b/packages/nextclade/src/utils/vec2d.rs @@ -1,4 +1,4 @@ -use std::fmt::{Debug, Display, Formatter, Write}; +use std::fmt::{Debug, Display, Formatter}; use std::ops::{Index, IndexMut}; /// Row-major, 2-dimensional container with contiguous, flat underlying storage