Merge pull request #1406 from nextstrain/chore/cleanup-4

.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",
 ]

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;

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 {

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";

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.

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]

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;

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;

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<T: Letter<T>> {

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;

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;

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;

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)]

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)]

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;

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

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")]

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

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";

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

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);

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.

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};

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};

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")]

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)]

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;

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;

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};

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] = &[

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};
 

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;

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;
 

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};

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")]

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")]