refactor: upgrade to rust 2024 edition

Author: ivan-aksamentov

Cargo.toml

@@ -1,5 +1,5 @@
 [workspace]
-resolver = '2'
+resolver = "3"
 
 members = [
   "packages/*",
@@ -17,7 +17,7 @@ description = "Alignment, mutation calling, phylogenetic placement, clade assign
 repository = "https://github.com/nextstrain/nextclade"
 documentation = "https://docs.nextstrain.org/projects/nextclade/en/stable/"
 homepage = "https://clades.nextstrain.org/"
-edition = "2021"
+edition = "2024"
 license = "MIT"
 publish = false
 authors = ["Nextstrain team"]
@@ -105,6 +105,7 @@ keyword_idents = { level = "warn", priority = -1 }
 nonstandard_style = { level = "warn", priority = -1 }
 rust_2018_idioms = { level = "warn", priority = -1 }
 rust_2021_compatibility = { level = "warn", priority = -1 }
+rust_2024_compatibility = { level = "warn", priority = -1 }
 
 # Disable some of the lints enabled by default
 # https://doc.rust-lang.org/rustc/lints/listing/warn-by-default.html
@@ -248,6 +249,7 @@ use_debug = "allow"
 use_self = "allow"
 useless_transmute = "allow"
 wildcard_enum_match_arm = "allow"
+ref_option = "allow"
 
 
 [workspace.lints.rustdoc]

packages/nextclade-cli/src/build.rs

@@ -2,8 +2,8 @@ use ctor::ctor;
 use eyre::Report;
 use nextclade::{
   io::json_schema::JsonSchemaOutputFormat,
-  schema::schema::{generate_schema, NextcladeFileFormat},
-  utils::global_init::{global_init, GlobalInitConfig},
+  schema::schema::{NextcladeFileFormat, generate_schema},
+  utils::global_init::{GlobalInitConfig, global_init},
 };
 use std::path::PathBuf;
 

packages/nextclade-cli/src/cli/nextclade_cli.rs

@@ -8,16 +8,16 @@ use crate::cli::verbosity::Verbosity;
 use crate::io::http_client::ProxyConfig;
 use clap::builder::styling;
 use clap::{ArgGroup, CommandFactory, Parser, Subcommand, ValueEnum, ValueHint};
-use clap_complete::{generate, Shell};
+use clap_complete::{Shell, generate};
 use clap_complete_fig::Fig;
-use eyre::{eyre, ContextCompat, Report, WrapErr};
+use eyre::{ContextCompat, Report, WrapErr, eyre};
 use itertools::Itertools;
 use nextclade::io::console::CliColorMode;
 use nextclade::io::fs::add_extension;
 use nextclade::run::params::NextcladeInputParamsOptional;
-use nextclade::schema::schema::{cli_handle_schema, NextcladeSchemaArgs};
+use nextclade::schema::schema::{NextcladeSchemaArgs, cli_handle_schema};
 use nextclade::sort::params::NextcladeSeqSortParams;
-use nextclade::utils::global_init::{global_init, GlobalInitConfig};
+use nextclade::utils::global_init::{GlobalInitConfig, global_init};
 use nextclade::{getenv, make_error};
 use std::fmt::Debug;
 use std::io;
@@ -926,10 +926,11 @@ pub fn nextclade_get_output_filenames(run_args: &mut NextcladeRunArgs) -> Result
     }
   }
 
-  if let Some(output_translations) = output_translations {
-    if !output_translations.contains("{cds}") {
-      return make_error!(
-        r#"
+  if let Some(output_translations) = output_translations
+    && !output_translations.contains("{cds}")
+  {
+    return make_error!(
+      r#"
 Expected `--output-translations` argument to contain a template string containing template variable {{cds}} (with curly braces), but received:
 
   {output_translations}
@@ -940,8 +941,7 @@ Example for bash shell:
   --output-translations='output_dir/nextclade.cds_translation.{{cds}}.fasta'
 
       "#
-      );
-    }
+    );
   }
 
   let all_outputs_are_missing = [
@@ -1155,7 +1155,9 @@ pub fn nextclade_check_column_config_args(run_args: &NextcladeRunArgs) -> Result
   } = &run_args.outputs;
 
   if !output_columns_selection.is_empty() && [output_all, output_csv, output_tsv].iter().all(|arg| arg.is_none()) {
-    return make_error!("The `--output-columns-selection` argument configures column-based output formats and can only be used when one or more of the column-based file outputs is requested, i.e. together with one or multiple of `--output-all`, `--output-csv`, `--output-tsv`.");
+    return make_error!(
+      "The `--output-columns-selection` argument configures column-based output formats and can only be used when one or more of the column-based file outputs is requested, i.e. together with one or multiple of `--output-all`, `--output-csv`, `--output-tsv`."
+    );
   }
 
   Ok(())

packages/nextclade-cli/src/cli/nextclade_dataset_get.rs

@@ -3,7 +3,7 @@ use crate::dataset::dataset_download::{dataset_dir_download, dataset_zip_downloa
 use crate::io::http_client::HttpClient;
 use eyre::{Report, WrapErr};
 use itertools::Itertools;
-use log::{warn, LevelFilter};
+use log::{LevelFilter, warn};
 use nextclade::io::dataset::{Dataset, DatasetsIndexJson};
 use nextclade::make_error;
 use nextclade::utils::info::{this_package_version, this_package_version_str};
@@ -78,8 +78,8 @@ pub fn dataset_http_get(http: &HttpClient, name: impl AsRef<str>, tag: Option<&S
           // ...and if no tags matching, display error
           let suggestions_msg = format_suggestions(dataset.tags(), tag);
           make_error!(
-              "Dataset '{name}' is found, but requested version tag for it not found: '{tag}'.{suggestions_msg}\n\nType `nextclade dataset list --name='{name}'` to show available version tags for this dataset or use --tag='latest' or omit the --tag argument to use the latest version tag.",
-            )
+            "Dataset '{name}' is found, but requested version tag for it not found: '{tag}'.{suggestions_msg}\n\nType `nextclade dataset list --name='{name}'` to show available version tags for this dataset or use --tag='latest' or omit the --tag argument to use the latest version tag.",
+          )
         }
       }
     },

packages/nextclade-cli/src/cli/nextclade_dataset_list.rs

@@ -3,10 +3,10 @@ use crate::dataset::dataset_download::download_datasets_index_json;
 use crate::dataset::dataset_table::format_dataset_table;
 use crate::io::http_client::HttpClient;
 use eyre::Report;
-use itertools::{chain, Itertools};
-use log::{warn, LevelFilter};
+use itertools::{Itertools, chain};
+use log::{LevelFilter, warn};
 use nextclade::io::dataset::{Dataset, DatasetListJson, DatasetsIndexJson};
-use nextclade::io::json::{json_stringify, JsonPretty};
+use nextclade::io::json::{JsonPretty, json_stringify};
 use nextclade::utils::info::this_package_version;
 
 pub fn nextclade_dataset_list(

packages/nextclade-cli/src/cli/nextclade_loop.rs

@@ -7,7 +7,7 @@ use nextclade::analyze::pcr_primers::PcrPrimer;
 use nextclade::gene::gene_map_display::gene_map_to_table_string;
 use nextclade::graph::graph::Graph;
 use nextclade::io::fasta::{FastaReader, FastaRecord};
-use nextclade::io::json::{json_write, JsonPretty};
+use nextclade::io::json::{JsonPretty, json_write};
 use nextclade::io::nextclade_csv_column_config::CsvColumnConfig;
 use nextclade::io::nwk_writer::nwk_write_to_file;
 use nextclade::run::nextclade_wasm::{AnalysisInitialData, AnalysisOutput, Nextclade};
@@ -161,10 +161,8 @@ pub fn nextclade_run(mut run_args: NextcladeRunArgs) -> Result<(), Report> {
         }
 
         for record in result_receiver {
-          if should_write_tree {
-            if let Ok(AnalysisOutput { analysis_result, .. }) = &record.outputs_or_err {
-              outputs.push(analysis_result.clone());
-            }
+          if should_write_tree && let Ok(AnalysisOutput { analysis_result, .. }) = &record.outputs_or_err {
+            outputs.push(analysis_result.clone());
           }
           output_writer
             .write_record(record)

packages/nextclade-cli/src/cli/nextclade_read_annotation.rs

@@ -4,7 +4,7 @@ use nextclade::features::feature_tree::FeatureTree;
 use nextclade::gene::gene_map::GeneMap;
 use nextclade::gene::gene_map_display::gene_map_to_table_string;
 use nextclade::io::file::open_file_or_stdin;
-use nextclade::io::json::{json_or_yaml_write, json_stringify, JsonPretty};
+use nextclade::io::json::{JsonPretty, json_or_yaml_write, json_stringify};
 use std::io::Read;
 
 pub fn nextclade_read_annotation(args: &NextcladeReadAnnotationArgs) -> Result<(), Report> {

packages/nextclade-cli/src/cli/nextclade_seq_sort.rs

@@ -4,24 +4,24 @@ use crate::io::http_client::HttpClient;
 use console::style;
 use eyre::{Report, WrapErr};
 use itertools::Itertools;
-use log::{trace, LevelFilter};
+use log::{LevelFilter, trace};
 use maplit::btreemap;
 use nextclade::io::csv::CsvStructFileWriter;
 use nextclade::io::fasta::{FastaReader, FastaRecord, FastaWriter};
 use nextclade::io::fs::path_to_string;
 use nextclade::make_error;
-use nextclade::sort::minimizer_index::{MinimizerIndexJson, MINIMIZER_INDEX_ALGO_VERSION};
+use nextclade::sort::minimizer_index::{MINIMIZER_INDEX_ALGO_VERSION, MinimizerIndexJson};
 use nextclade::sort::minimizer_search::{
-  find_best_datasets, find_best_suggestion_for_seq, run_minimizer_search, MinimizerSearchDatasetResult,
-  MinimizerSearchRecord,
+  MinimizerSearchDatasetResult, MinimizerSearchRecord, find_best_datasets, find_best_suggestion_for_seq,
+  run_minimizer_search,
 };
 use nextclade::utils::option::{OptionMapMutFallible, OptionMapRefFallible};
 use nextclade::utils::string::truncate;
 use ordered_float::OrderedFloat;
 use schemars::JsonSchema;
 use serde::Serialize;
-use std::collections::btree_map::Entry::{Occupied, Vacant};
 use std::collections::BTreeMap;
+use std::collections::btree_map::Entry::{Occupied, Vacant};
 use std::path::{Path, PathBuf};
 use std::str::FromStr;
 use tinytemplate::TinyTemplate;
@@ -74,7 +74,11 @@ pub fn nextclade_seq_sort(args: &NextcladeSortArgs) -> Result<(), Report> {
         format!(": {server_versions}")
       };
 
-      make_error!("No compatible reference minimizer index data is found for this dataset sever. Cannot proceed. \n\nThis version of Nextclade supports index versions up to '{}', but the server has {}.\n\nTry to to upgrade Nextclade to the latest version and/or contact dataset server maintainers.", MINIMIZER_INDEX_ALGO_VERSION, server_versions)
+      make_error!(
+        "No compatible reference minimizer index data is found for this dataset sever. Cannot proceed. \n\nThis version of Nextclade supports index versions up to '{}', but the server has {}.\n\nTry to to upgrade Nextclade to the latest version and/or contact dataset server maintainers.",
+        MINIMIZER_INDEX_ALGO_VERSION,
+        server_versions
+      )
     }
   }?;
 
@@ -483,10 +487,11 @@ fn check_args(args: &NextcladeSortArgs) -> Result<(), Report> {
     );
   }
 
-  if let Some(output) = output {
-    if !output.contains("{name}") {
-      return make_error!(
-        r#"
+  if let Some(output) = output
+    && !output.contains("{name}")
+  {
+    return make_error!(
+      r#"
 Expected `--output` argument to contain a template string containing template variable {{name}} (with curly braces), but received:
 
   {output}
@@ -497,8 +502,7 @@ Example for bash shell:
   --output='outputs/{{name}}/sorted.fasta.gz'
 
       "#
-      );
-    }
+    );
   }
 
   Ok(())

packages/nextclade-cli/src/cli/print_help_markdown.rs

@@ -18,7 +18,11 @@ If you have Nextclade CLI installed, you can type `nextclade --help` to read the
   "#,
   )?;
 
-  let help = replace(&help, "Nextclade is a part of Nextstrain: https://nextstrain.org\n\nDocumentation: https://docs.nextstrain.org/projects/nextclade\nNextclade Web: https://clades.nextstrain.org\nPublication:   https://doi.org/10.21105/joss.03773", "Nextclade is a part of Nextstrain: [https://nextstrain.org](https://nextstrain.org)\n\nDocumentation: [https://docs.nextstrain.org/projects/nextclade](https://docs.nextstrain.org/projects/nextclade)\n\nNextclade Web: [https://clades.nextstrain.org](https://clades.nextstrain.org)\n\nPublication: [https://doi.org/10.21105/joss.03773](https://doi.org/10.21105/joss.03773)")?;
+  let help = replace(
+    &help,
+    "Nextclade is a part of Nextstrain: https://nextstrain.org\n\nDocumentation: https://docs.nextstrain.org/projects/nextclade\nNextclade Web: https://clades.nextstrain.org\nPublication:   https://doi.org/10.21105/joss.03773",
+    "Nextclade is a part of Nextstrain: [https://nextstrain.org](https://nextstrain.org)\n\nDocumentation: [https://docs.nextstrain.org/projects/nextclade](https://docs.nextstrain.org/projects/nextclade)\n\nNextclade Web: [https://clades.nextstrain.org](https://clades.nextstrain.org)\n\nPublication: [https://doi.org/10.21105/joss.03773](https://doi.org/10.21105/joss.03773)",
+  )?;
 
   let help = replace(&help, "(.*)— REMOVED(.*)", "")?;
   let help = replace(&help, "(.*)— RENAMED(.*)", "")?;

packages/nextclade-cli/src/dataset/dataset_download.rs

@@ -2,20 +2,20 @@ 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 color_eyre::{Section, SectionExt};
-use eyre::{eyre, ContextCompat, Report, WrapErr};
+use eyre::{ContextCompat, Report, WrapErr, eyre};
 use itertools::Itertools;
-use log::{warn, LevelFilter};
+use log::{LevelFilter, warn};
 use nextclade::analyze::virus_properties::VirusProperties;
-use nextclade::gene::gene_map::{filter_gene_map, GeneMap};
+use nextclade::gene::gene_map::{GeneMap, filter_gene_map};
 use nextclade::io::dataset::{Dataset, DatasetsIndexJson};
 use nextclade::io::fasta::{read_one_fasta_from_file, read_one_fasta_from_str};
 use nextclade::io::file::create_file_or_stdout;
 use nextclade::io::fs::{ensure_dir, has_extension, read_file_to_string};
 use nextclade::run::nextclade_wasm::{NextcladeParams, NextcladeParamsOptional};
-use nextclade::tree::tree::{check_ref_seq_mismatch, AuspiceTree};
+use nextclade::tree::tree::{AuspiceTree, check_ref_seq_mismatch};
 use nextclade::utils::fs::list_files_recursive;
 use nextclade::utils::option::OptionMapRefFallible;
-use nextclade::utils::string::{format_list, surround_with_quotes, Indent};
+use nextclade::utils::string::{Indent, format_list, surround_with_quotes};
 use nextclade::{make_error, make_internal_error, o};
 use std::collections::BTreeSet;
 use std::fs::File;
@@ -159,10 +159,10 @@ pub fn dataset_zip_load(
 
   verify_dataset_files(&virus_properties, zip.file_names());
 
-  if let Some(tree) = &tree {
-    if let Some(tree_ref) = tree.root_sequence() {
-      check_ref_seq_mismatch(&ref_record.seq, tree_ref)?;
-    }
+  if let Some(tree) = &tree
+    && let Some(tree_ref) = tree.root_sequence()
+  {
+    check_ref_seq_mismatch(&ref_record.seq, tree_ref)?;
   }
 
   Ok(NextcladeParams {
@@ -217,7 +217,10 @@ fn verify_dataset_files<'a, T: AsRef<str> + 'a + ?Sized>(
       format_list(Indent(2), declared.iter()),
       format_list(Indent(2), present.iter()),
     ));
-    warn!("When reading dataset: {}\nThis is not an error. Nextclade ignores unknown file declarations and undeclared files. But this could be a mistake by the dataset author. For example, there could be a typo in pathogen.json file declaration, or a file could have been added to the dataset, but not declared in the pathogen.json. In this case, Nextclade analysis could be missing some of the features intended by the author. Contact the author to resolve this. It could also be that the dataset contains files for a newer version of Nextclade, and that the currently used version does not recognize these files. In which case try to upgrade Nextclade.", warnings.join("\n"));
+    warn!(
+      "When reading dataset: {}\nThis is not an error. Nextclade ignores unknown file declarations and undeclared files. But this could be a mistake by the dataset author. For example, there could be a typo in pathogen.json file declaration, or a file could have been added to the dataset, but not declared in the pathogen.json. In this case, Nextclade analysis could be missing some of the features intended by the author. Contact the author to resolve this. It could also be that the dataset contains files for a newer version of Nextclade, and that the currently used version does not recognize these files. In which case try to upgrade Nextclade.",
+      warnings.join("\n")
+    );
   }
 }
 
@@ -305,10 +308,10 @@ pub fn dataset_dir_load(
     .collect_vec();
   verify_dataset_files(&virus_properties, dataset_dir_files.iter());
 
-  if let Some(tree) = &tree {
-    if let Some(tree_ref) = tree.root_sequence() {
-      check_ref_seq_mismatch(&ref_record.seq, tree_ref)?;
-    }
+  if let Some(tree) = &tree
+    && let Some(tree_ref) = tree.root_sequence()
+  {
+    check_ref_seq_mismatch(&ref_record.seq, tree_ref)?;
   }
 
   Ok(NextcladeParams {
@@ -354,10 +357,10 @@ pub fn dataset_json_load(
       .map_ref_fallible(GeneMap::from_path)
       .wrap_err("When parsing genome annotation")?;
 
-    if let (Some(tree), Some(ref_record)) = (&tree, &ref_record) {
-      if let Some(tree_ref) = tree.root_sequence() {
-        check_ref_seq_mismatch(&ref_record.seq, tree_ref)?;
-      }
+    if let (Some(tree), Some(ref_record)) = (&tree, &ref_record)
+      && let Some(tree_ref) = tree.root_sequence()
+    {
+      check_ref_seq_mismatch(&ref_record.seq, tree_ref)?;
     }
 
     NextcladeParamsOptional {
@@ -408,10 +411,10 @@ pub fn dataset_individual_files_load(
         .map_ref_fallible(AuspiceTree::from_path)
         .wrap_err("When reading reference tree JSON")?;
 
-      if let Some(tree) = &tree {
-        if let Some(tree_ref) = tree.root_sequence() {
-          check_ref_seq_mismatch(&ref_record.seq, tree_ref)?;
-        }
+      if let Some(tree) = &tree
+        && let Some(tree_ref) = tree.root_sequence()
+      {
+        check_ref_seq_mismatch(&ref_record.seq, tree_ref)?;
       }
 
       Ok(NextcladeParams {
@@ -489,10 +492,10 @@ pub fn dataset_str_download_and_load(
     .map_ref_fallible(AuspiceTree::from_str)
     .wrap_err("When reading reference tree from dataset")?;
 
-  if let Some(tree) = &tree {
-    if let Some(tree_ref) = tree.root_sequence() {
-      check_ref_seq_mismatch(&ref_record.seq, tree_ref)?;
-    }
+  if let Some(tree) = &tree
+    && let Some(tree_ref) = tree.root_sequence()
+  {
+    check_ref_seq_mismatch(&ref_record.seq, tree_ref)?;
   }
 
   Ok(NextcladeParams {