feat(cli): deprecate unused args for dataset coomands

Emit messages when the following args are used:

 For `dataset get`:

```
--reference
--attributes
```

 For `dataset list`:

```
--reference
--attributes
--include-old
```

Reminder, Nextclade v3 datasets are uniquely identified by their name (path) and tag only, so all other attributes lost their meaning.

All version tags are listed so `--include-old` is no longer relevant.

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

@@ -131,34 +131,17 @@ pub struct NextcladeDatasetListArgs {
   #[clap(value_hint = ValueHint::Other)]
   pub name: Option<String>,
 
-  /// REMOVED
-  #[clap(long, short = 'r')]
-  #[clap(value_hint = ValueHint::Other)]
-  #[clap(hide_long_help = true, hide_short_help = true)]
-  pub reference: Option<String>,
-
   /// Restrict list to datasets with this exact version tag.
   #[clap(long, short = 't')]
   #[clap(value_hint = ValueHint::Other)]
   pub tag: Option<String>,
 
-  /// REMOVED
-  #[clap(long, short = 'a')]
-  #[clap(value_hint = ValueHint::Other)]
-  #[clap(hide_long_help = true, hide_short_help = true)]
-  pub attribute: Vec<String>,
-
   /// Include dataset versions that are incompatible with this version of Nextclade CLI.
   ///
   /// By default the incompatible versions are omitted.
   #[clap(long)]
   pub include_incompatible: bool,
 
-  /// REMOVED
-  #[clap(long)]
-  #[clap(hide_long_help = true, hide_short_help = true)]
-  pub include_old: Option<bool>,
-
   /// Include deprecated datasets.
   ///
   /// By default the deprecated datasets are omitted.
@@ -201,6 +184,22 @@ pub struct NextcladeDatasetListArgs {
 
   #[clap(flatten)]
   pub proxy_config: ProxyConfig,
+
+  // Deprecated args
+  /// REMOVED
+  #[clap(long, short = 'r')]
+  #[clap(hide_long_help = true, hide_short_help = true)]
+  pub reference: Option<String>,
+
+  /// REMOVED
+  #[clap(long, short = 'a')]
+  #[clap(hide_long_help = true, hide_short_help = true)]
+  pub attribute: Vec<String>,
+
+  /// REMOVED
+  #[clap(long)]
+  #[clap(hide_long_help = true, hide_short_help = true)]
+  pub include_old: bool,
 }
 
 #[derive(Parser, Debug)]
@@ -212,25 +211,13 @@ pub struct NextcladeDatasetGetArgs {
   #[clap(value_hint = ValueHint::Other)]
   pub name: String,
 
-  /// REMOVED
-  #[clap(long, short = 'r')]
-  #[clap(value_hint = ValueHint::Other)]
-  #[clap(hide_long_help = true, hide_short_help = true)]
-  pub reference: Option<String>,
-
   /// Version tag of the dataset to download.
   ///
   /// If this flag is not provided the latest version is downloaded.
   #[clap(long, short = 't')]
   #[clap(value_hint = ValueHint::Other)]
   pub tag: Option<String>,
 
-  /// REMOVED
-  #[clap(long, short = 'a')]
-  #[clap(value_hint = ValueHint::Other)]
-  #[clap(hide_long_help = true, hide_short_help = true)]
-  pub attribute: Vec<String>,
-
   /// Use custom dataset server.
   ///
   /// You can host your own dataset server, with one or more datasets, grouped into dataset collections, and use this server to provide datasets to users of Nextclade CLI and Nextclade Web. Refer to Nextclade dataset documentation for more details.
@@ -263,6 +250,17 @@ pub struct NextcladeDatasetGetArgs {
 
   #[clap(flatten)]
   pub proxy_config: ProxyConfig,
+
+  // Deprecated arguments
+  /// REMOVED
+  #[clap(long, short = 'r')]
+  #[clap(hide_long_help = true, hide_short_help = true)]
+  pub reference: Option<String>,
+
+  /// REMOVED
+  #[clap(long, short = 'a')]
+  #[clap(hide_long_help = true, hide_short_help = true)]
+  pub attribute: Vec<String>,
 }
 
 #[derive(Copy, Debug, Clone, PartialEq, Eq, PartialOrd, Ord, ValueEnum, EnumIter)]
@@ -922,7 +920,8 @@ When positional arguments are not provided, nextclade will read input fasta from
 const ERROR_MSG_INPUT_ROOT_SEQ_REMOVED: &str =
   r#"The argument `--input-root-seq` (alias `--reference`) is removed in favor of `--input-ref`."#;
 
-const ERROR_MSG_INPUT_GENE_MAP_RENAMED: &str = r#"The argument `--input-gene-map` (alias `--genemap`) is renamed to `--input-annotation`."#;
+const ERROR_MSG_INPUT_GENE_MAP_RENAMED: &str =
+  r#"The argument `--input-gene-map` (alias `--genemap`) is renamed to `--input-annotation`."#;
 
 const ERROR_MSG_OUTPUT_DIR_REMOVED: &str = r#"The argument `--output-dir` is removed in favor of `--output-all`.
 
@@ -952,7 +951,7 @@ const ERROR_MSG_OUTPUT_ERRORS_REMOVED: &str = r#"The argument `--output-errors`
 
 In Nextclade v3 the separate arguments `--output-insertions` and `--output-errors` are removed. Please use `--output-csv` (for semicolon-separated table) and `--output-tsv` (for tab-separated table) arguments instead. These tables contain, among others, all the columns from the output insertions table (`--output-insertions`) as well as from the output errors table (`--output-errors`)."#;
 
-const MSG_READ_DOCS: &str = r#"
+const MSG_READ_RUN_DOCS: &str = r#"
 
 For more information, type
 
@@ -964,39 +963,105 @@ Read Nextclade documentation at:
 
 pub fn nextclade_check_removed_args(run_args: &NextcladeRunArgs) -> Result<(), Report> {
   if run_args.inputs.input_fasta.is_some() {
-    return make_error!("{ERROR_MSG_INPUT_FASTA_REMOVED}{MSG_READ_DOCS}");
+    return make_error!("{ERROR_MSG_INPUT_FASTA_REMOVED}{MSG_READ_RUN_DOCS}");
   }
 
   if run_args.inputs.input_root_seq.is_some() || run_args.inputs.reference.is_some() {
-    return make_error!("{ERROR_MSG_INPUT_ROOT_SEQ_REMOVED}{MSG_READ_DOCS}");
+    return make_error!("{ERROR_MSG_INPUT_ROOT_SEQ_REMOVED}{MSG_READ_RUN_DOCS}");
   }
 
   if run_args.inputs.input_gene_map.is_some() || run_args.inputs.genemap.is_some() {
-    return make_error!("{ERROR_MSG_INPUT_GENE_MAP_RENAMED}{MSG_READ_DOCS}");
+    return make_error!("{ERROR_MSG_INPUT_GENE_MAP_RENAMED}{MSG_READ_RUN_DOCS}");
   }
 
   if run_args.inputs.input_virus_properties.is_some() {
-    return make_error!("{ERROR_MSG_INPUT_VIRUS_PROPERTIES_REMOVED}{MSG_READ_DOCS}");
+    return make_error!("{ERROR_MSG_INPUT_VIRUS_PROPERTIES_REMOVED}{MSG_READ_RUN_DOCS}");
   }
 
   if run_args.inputs.input_qc_config.is_some() {
-    return make_error!("{ERROR_MSG_INPUT_QC_CONFIG_REMOVED}{MSG_READ_DOCS}");
+    return make_error!("{ERROR_MSG_INPUT_QC_CONFIG_REMOVED}{MSG_READ_RUN_DOCS}");
   }
 
   if run_args.inputs.input_pcr_primers.is_some() {
-    return make_error!("{ERROR_MSG_INPUT_PCR_PRIMERS_REMOVED}{MSG_READ_DOCS}");
+    return make_error!("{ERROR_MSG_INPUT_PCR_PRIMERS_REMOVED}{MSG_READ_RUN_DOCS}");
   }
 
   if run_args.outputs.output_dir.is_some() {
-    return make_error!("{ERROR_MSG_OUTPUT_DIR_REMOVED}{MSG_READ_DOCS}");
+    return make_error!("{ERROR_MSG_OUTPUT_DIR_REMOVED}{MSG_READ_RUN_DOCS}");
   }
 
   if run_args.outputs.output_insertions.is_some() {
-    return make_error!("{ERROR_MSG_OUTPUT_INSERTIONS_REMOVED}{MSG_READ_DOCS}");
+    return make_error!("{ERROR_MSG_OUTPUT_INSERTIONS_REMOVED}{MSG_READ_RUN_DOCS}");
   }
 
   if run_args.outputs.output_errors.is_some() {
-    return make_error!("{ERROR_MSG_OUTPUT_ERRORS_REMOVED}{MSG_READ_DOCS}");
+    return make_error!("{ERROR_MSG_OUTPUT_ERRORS_REMOVED}{MSG_READ_RUN_DOCS}");
+  }
+
+  Ok(())
+}
+
+const MSG_DATASET_NAMING_CHANGE: &str = r#"
+
+Nextclade datasets are now identified only by their name (`--name`) and, optionally, a version tag (`--tag`). All other attributes are now included into the name.
+
+In order to list all dataset names, type:
+
+  nextclade dataset list --names-only"#;
+
+const MSG_READ_DATASET_LIST_DOCS: &str = r#"
+
+For more information, type
+
+  nextclade dataset list --help
+
+Read Nextclade documentation at:
+
+  https://docs.nextstrain.org/projects/nextclade/en/stable"#;
+
+fn nextclade_check_removed_dataset_list_args(args: &NextcladeDatasetListArgs) -> Result<(), Report> {
+  if args.reference.is_some() {
+    return make_error!(
+      "The argument `--reference` (alias `-r`) is removed.{MSG_DATASET_NAMING_CHANGE}{MSG_READ_DATASET_LIST_DOCS}"
+    );
+  }
+
+  if !args.attribute.is_empty() {
+    return make_error!(
+      "The argument `--attribute` (alias `-a`) is removed.{MSG_DATASET_NAMING_CHANGE}{MSG_READ_DATASET_LIST_DOCS}"
+    );
+  }
+
+  if args.include_old {
+    return make_error!(
+      "The argument `--include-old` is removed. All versions are always shown now. {MSG_READ_DATASET_LIST_DOCS}"
+    );
+  }
+
+  Ok(())
+}
+
+const MSG_READ_DATASET_GET_DOCS: &str = r#"
+
+For more information, type
+
+  nextclade dataset get --help
+
+Read Nextclade documentation at:
+
+  https://docs.nextstrain.org/projects/nextclade/en/stable"#;
+
+fn nextclade_check_removed_dataset_get_args(args: &NextcladeDatasetGetArgs) -> Result<(), Report> {
+  if args.reference.is_some() {
+    return make_error!(
+      "The argument `--reference` (alias `-r`) is removed.{MSG_DATASET_NAMING_CHANGE}{MSG_READ_DATASET_GET_DOCS}"
+    );
+  }
+
+  if !args.attribute.is_empty() {
+    return make_error!(
+      "The argument `--attribute` (alias `-a`) is removed.{MSG_DATASET_NAMING_CHANGE}{MSG_READ_DATASET_GET_DOCS}"
+    );
   }
 
   Ok(())
@@ -1034,8 +1099,14 @@ pub fn nextclade_parse_cli_args() -> Result<(), Report> {
       nextclade_run(*run_args)
     }
     NextcladeCommands::Dataset(dataset_command) => match dataset_command.command {
-      NextcladeDatasetCommands::List(dataset_list_args) => nextclade_dataset_list(dataset_list_args),
-      NextcladeDatasetCommands::Get(dataset_get_args) => nextclade_dataset_get(&dataset_get_args),
+      NextcladeDatasetCommands::List(dataset_list_args) => {
+        nextclade_check_removed_dataset_list_args(&dataset_list_args)?;
+        nextclade_dataset_list(dataset_list_args)
+      }
+      NextcladeDatasetCommands::Get(dataset_get_args) => {
+        nextclade_check_removed_dataset_get_args(&dataset_get_args)?;
+        nextclade_dataset_get(&dataset_get_args)
+      }
     },
     NextcladeCommands::Sort(seq_sort_args) => nextclade_seq_sort(&seq_sort_args),
     NextcladeCommands::ReadAnnotation(read_annotation_args) => nextclade_read_annotation(&read_annotation_args),

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

@@ -17,19 +17,14 @@ pub struct DatasetHttpGetParams<'s> {
 pub fn nextclade_dataset_get(
   NextcladeDatasetGetArgs {
     name,
-    reference,
     tag,
-    attribute,
     server,
     output_dir,
     output_zip,
     proxy_config,
+    ..
   }: &NextcladeDatasetGetArgs,
 ) -> Result<(), Report> {
-  if reference.is_some() || !attribute.is_empty() {
-    return make_error!("The arguments `--reference` and `--attribute` are removed. Datasets are now queried by `--name` and `--tag` only.\n\nIn order to list all dataset names, type:\n\n  nextclade dataset list --names-only\n\n. Please refer to `--help` and to Nextclade documentation for more details.");
-  }
-
   let verbose = log::max_level() > LevelFilter::Info;
 
   let mut http = HttpClient::new(server, proxy_config, verbose)?;

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

@@ -13,28 +13,18 @@ use nextclade::utils::info::this_package_version;
 pub fn nextclade_dataset_list(
   NextcladeDatasetListArgs {
     name,
-    reference,
     tag,
-    attribute,
     include_incompatible,
-    include_old,
     include_deprecated,
     include_experimental,
     include_community,
     json,
     only_names,
     server,
     proxy_config,
+    ..
   }: NextcladeDatasetListArgs,
 ) -> Result<(), Report> {
-  if include_old.is_some() {
-    return make_error!("The argument `--include-old` is removed.\n\nAll version tags are always listed now\n\n. Please refer to `--help` and to Nextclade documentation for more details.");
-  }
-
-  if reference.is_some() || !attribute.is_empty() {
-    return make_error!("The arguments `--reference` and `--attribute` are removed. Datasets are now queried by `--name` and `--tag` only.\n\nIn order to list all dataset names, type:\n\n  nextclade dataset list --names-only\n\n. Please refer to `--help` and to Nextclade documentation for more details.");
-  }
-
   let verbose = log::max_level() > LevelFilter::Info;
 
   let mut http = HttpClient::new(&server, &proxy_config, verbose)?;