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feat(cli): add headings for help sections #884

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Jun 22, 2022
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feat(cli): add headings for help sections #884

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65 changes: 49 additions & 16 deletions packages_rs/nextclade-cli/src/cli/nextalign_cli.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@ pub struct NextalignArgs {
pub command: NextalignCommands,

/// Make output more quiet or more verbose
#[clap(flatten)]
#[clap(flatten, next_help_heading = " Verbosity")]
pub verbosity: Verbosity<WarnLevel>,
}

Expand Down Expand Up @@ -71,7 +71,7 @@ pub enum NextalignOutputSelection {
}

#[derive(Parser, Debug)]
pub struct NextalignRunArgs {
pub struct NextalignRunInputArgs {
/// Path to one or multiple FASTA files with input sequences
///
/// Accepts plain or compressed FASTA files. If a compressed fasta file is provided, it will be transparently
Expand All @@ -82,6 +82,7 @@ pub struct NextalignRunArgs {
///
/// See: https://en.wikipedia.org/wiki/FASTA_format
#[clap(value_hint = ValueHint::FilePath)]
#[clap(display_order = 1)]
pub input_fastas: Vec<PathBuf>,

/// REMOVED. Use positional arguments instead.
Expand Down Expand Up @@ -129,7 +130,10 @@ pub struct NextalignRunArgs {
)]
#[clap(value_hint = ValueHint::FilePath)]
pub genes: Option<Vec<String>>,
}

#[derive(Parser, Debug)]
pub struct NextalignRunOutputArgs {
/// REMOVED. Use `--output-all` instead
#[clap(long)]
#[clap(value_hint = ValueHint::DirPath)]
Expand Down Expand Up @@ -245,13 +249,28 @@ pub struct NextalignRunArgs {
/// Note: the sequences which trigger errors during processing will be omitted from outputs, regardless of this flag.
#[clap(long)]
pub in_order: bool,
}

#[derive(Parser, Debug)]
pub struct NextalignRunOtherArgs {
/// Number of processing jobs. If not specified, all available CPU threads will be used.
#[clap(global = false, long, short = 'j', default_value_t = num_cpus::get() )]
#[clap(global = false, long, short = 'j', default_value_t = num_cpus::get())]
pub jobs: usize,
}

#[clap(flatten)]
#[derive(Parser, Debug)]
pub struct NextalignRunArgs {
#[clap(flatten, next_help_heading = " Inputs")]
pub inputs: NextalignRunInputArgs,

#[clap(flatten, next_help_heading = " Outputs")]
pub outputs: NextalignRunOutputArgs,

#[clap(flatten, next_help_heading = " Alignment parameters")]
pub alignment_params: AlignPairwiseParamsOptional,

#[clap(flatten, next_help_heading = " Other")]
pub other: NextalignRunOtherArgs,
}

fn generate_completions(shell: &str) -> Result<(), Report> {
Expand All @@ -275,15 +294,29 @@ fn generate_completions(shell: &str) -> Result<(), Report> {
/// Get output filenames provided by user or, if not provided, create filenames based on input fasta
pub fn nextalign_get_output_filenames(run_args: &mut NextalignRunArgs) -> Result<(), Report> {
let NextalignRunArgs {
input_fastas: input_fasta,
output_all,
ref mut output_basename,
ref mut output_errors,
ref mut output_fasta,
ref mut output_insertions,
ref mut output_translations,
ref mut output_selection,
..
inputs:
NextalignRunInputArgs {
input_fastas,
input_ref,
input_gene_map,
genes,
..
},
outputs:
NextalignRunOutputArgs {
output_all,
output_basename,
output_selection,
output_fasta,
output_translations,
output_insertions,
output_errors,
include_reference,
in_order,
..
},
other: NextalignRunOtherArgs { jobs },
alignment_params,
} = run_args;

// If `--output-all` is provided, then we need to deduce default output filenames,
Expand All @@ -292,7 +325,7 @@ pub fn nextalign_get_output_filenames(run_args: &mut NextalignRunArgs) -> Result
if let Some(output_all) = output_all {
let output_basename = output_basename
.clone()
.unwrap_or_else(|| get_fasta_basename(input_fasta).unwrap_or_else(|| "nextalign".to_owned()));
.unwrap_or_else(|| get_fasta_basename(input_fastas).unwrap_or_else(|| "nextalign".to_owned()));

let default_output_file_path = output_all.join(&output_basename);

Expand Down Expand Up @@ -402,11 +435,11 @@ For more information, type:
nextalign run --help"#;

pub fn nextalign_check_removed_args(run_args: &mut NextalignRunArgs) -> Result<(), Report> {
if run_args.input_fasta.is_some() {
if run_args.inputs.input_fasta.is_some() {
return make_error!("{ERROR_MSG_INPUT_FASTA_REMOVED}");
}

if run_args.output_dir.is_some() {
if run_args.outputs.output_dir.is_some() {
return make_error!("{ERROR_MSG_OUTPUT_DIR_REMOVED}");
}

Expand Down
49 changes: 29 additions & 20 deletions packages_rs/nextclade-cli/src/cli/nextalign_loop.rs
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Original file line number Diff line number Diff line change
@@ -1,4 +1,6 @@
use crate::cli::nextalign_cli::NextalignRunArgs;
use crate::cli::nextalign_cli::{
NextalignRunArgs, NextalignRunInputArgs, NextalignRunOtherArgs, NextalignRunOutputArgs,
};
use crate::cli::nextalign_ordered_writer::NextalignOrderedWriter;
use crossbeam::thread;
use eyre::{Report, WrapErr};
Expand All @@ -19,27 +21,34 @@ pub struct NextalignRecord {
pub outputs_or_err: Result<NextalignOutputs, Report>,
}

pub fn nextalign_run(args: NextalignRunArgs) -> Result<(), Report> {
info!("Command-line arguments:\n{args:#?}");
pub fn nextalign_run(run_args: NextalignRunArgs) -> Result<(), Report> {
info!("Command-line arguments:\n{run_args:#?}");

let NextalignRunArgs {
input_fastas: input_fasta,
input_ref,
genes,
input_gene_map,
output_all,
output_basename,
output_selection,
include_reference,
output_fasta,
output_translations,
output_insertions,
output_errors,
jobs,
in_order,
inputs:
NextalignRunInputArgs {
input_fastas,
input_ref,
input_gene_map,
genes,
..
},
outputs:
NextalignRunOutputArgs {
output_all,
output_basename,
output_selection,
output_fasta,
output_translations,
output_insertions,
output_errors,
include_reference,
in_order,
..
},
other: NextalignRunOtherArgs { jobs },
alignment_params: alignment_params_from_cli,
..
} = args;
} = run_args;

let mut alignment_params = AlignPairwiseParams::default();

Expand Down Expand Up @@ -68,7 +77,7 @@ pub fn nextalign_run(args: NextalignRunArgs) -> Result<(), Report> {
let (result_sender, result_receiver) = crossbeam_channel::bounded::<NextalignRecord>(CHANNEL_SIZE);

s.spawn(|_| {
let mut reader = FastaReader::from_paths(&input_fasta).unwrap();
let mut reader = FastaReader::from_paths(&input_fastas).unwrap();
loop {
let mut record = FastaRecord::default();
reader.read(&mut record).unwrap();
Expand Down
80 changes: 59 additions & 21 deletions packages_rs/nextclade-cli/src/cli/nextclade_cli.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,7 @@ pub struct NextcladeArgs {
pub command: NextcladeCommands,

/// Make output more quiet or more verbose
#[clap(flatten)]
#[clap(flatten, next_help_heading = " Verbosity")]
pub verbosity: Verbosity<WarnLevel>,
}

Expand Down Expand Up @@ -216,7 +216,7 @@ pub enum NextcladeOutputSelection {
}

#[derive(Parser, Debug, Clone)]
pub struct NextcladeRunArgs {
pub struct NextcladeRunInputArgs {
/// Path to one or multiple FASTA files with input sequences
///
/// Accepts plain or compressed FASTA files. If a compressed fasta file is provided, it will be transparently
Expand All @@ -227,6 +227,7 @@ pub struct NextcladeRunArgs {
///
/// See: https://en.wikipedia.org/wiki/FASTA_format
#[clap(value_hint = ValueHint::FilePath)]
#[clap(display_order = 1)]
pub input_fastas: Vec<PathBuf>,

/// REMOVED. Use positional arguments instead.
Expand Down Expand Up @@ -322,7 +323,10 @@ pub struct NextcladeRunArgs {
)]
#[clap(value_hint = ValueHint::FilePath)]
pub genes: Option<Vec<String>>,
}

#[derive(Parser, Debug, Clone)]
pub struct NextcladeRunOutputArgs {
/// REMOVED. Use `--output-all` instead
#[clap(long)]
#[clap(value_hint = ValueHint::DirPath)]
Expand Down Expand Up @@ -515,13 +519,28 @@ pub struct NextcladeRunArgs {
/// Note: the sequences which trigger errors during processing will be omitted from outputs, regardless of this flag.
#[clap(long)]
pub in_order: bool,
}

#[derive(Parser, Debug, Clone)]
pub struct NextcladeRunOtherArgs {
/// Number of processing jobs. If not specified, all available CPU threads will be used.
#[clap(global = false, long, short = 'j', default_value_t = num_cpus::get() )]
#[clap(global = false, long, short = 'j', default_value_t = num_cpus::get())]
pub jobs: usize,
}

#[clap(flatten)]
#[derive(Parser, Debug, Clone)]
pub struct NextcladeRunArgs {
#[clap(flatten, next_help_heading = " Inputs")]
pub inputs: NextcladeRunInputArgs,

#[clap(flatten, next_help_heading = " Outputs")]
pub outputs: NextcladeRunOutputArgs,

#[clap(flatten, next_help_heading = " Alignment parameters")]
pub alignment_params: AlignPairwiseParamsOptional,

#[clap(flatten, next_help_heading = " Other")]
pub other: NextcladeRunOtherArgs,
}

fn generate_completions(shell: &str) -> Result<(), Report> {
Expand All @@ -545,20 +564,39 @@ fn generate_completions(shell: &str) -> Result<(), Report> {
/// Get output filenames provided by user or, if not provided, create filenames based on input fasta
pub fn nextclade_get_output_filenames(run_args: &mut NextcladeRunArgs) -> Result<(), Report> {
let NextcladeRunArgs {
input_fastas: input_fasta,
output_all,
output_basename,
output_ndjson,
output_json,
output_csv,
output_tsv,
output_tree,
output_errors,
output_fasta,
output_insertions,
output_translations,
output_selection,
..
inputs:
NextcladeRunInputArgs {
input_fastas,
input_dataset,
input_ref,
input_tree,
input_qc_config,
input_virus_properties,
input_pcr_primers,
input_gene_map,
genes,
..
},
outputs:
NextcladeRunOutputArgs {
output_all,
output_basename,
output_selection,
output_fasta,
output_translations,
output_ndjson,
output_json,
output_csv,
output_tsv,
output_tree,
output_insertions,
output_errors,
include_reference,
in_order,
..
},
other: NextcladeRunOtherArgs { jobs },
alignment_params,
} = run_args;

// If `--output-all` is provided, then we need to deduce default output filenames,
Expand All @@ -567,7 +605,7 @@ pub fn nextclade_get_output_filenames(run_args: &mut NextcladeRunArgs) -> Result
if let Some(output_all) = output_all {
let output_basename = output_basename
.clone()
.unwrap_or_else(|| get_fasta_basename(input_fasta).unwrap_or_else(|| "nextclade".to_owned()));
.unwrap_or_else(|| get_fasta_basename(input_fastas).unwrap_or_else(|| "nextclade".to_owned()));

let default_output_file_path = output_all.join(&output_basename);

Expand Down Expand Up @@ -708,11 +746,11 @@ For more information, type
nextclade run --help"#;

pub fn nextclade_check_removed_args(run_args: &mut NextcladeRunArgs) -> Result<(), Report> {
if run_args.input_fasta.is_some() {
if run_args.inputs.input_fasta.is_some() {
return make_error!("{ERROR_MSG_INPUT_FASTA_REMOVED}");
}

if run_args.output_dir.is_some() {
if run_args.outputs.output_dir.is_some() {
return make_error!("{ERROR_MSG_OUTPUT_DIR_REMOVED}");
}

Expand Down
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