rsomics-bioenv 0.1.0

use std::fs::File;
use std::io::{BufReader, BufWriter, Write};
use std::path::PathBuf;

use clap::Parser;
use rsomics_common::{CommonFlags, Result, RsomicsError, Tool, ToolMeta};
use rsomics_help::{Example, FlagSpec, HelpSpec, Origin, Section};

use rsomics_bioenv::{read_env, read_matrix, run_bioenv, write_result};

pub const META: ToolMeta = ToolMeta {
    name: env!("CARGO_PKG_NAME"),
    version: env!("CARGO_PKG_VERSION"),
};

#[derive(Parser, Debug)]
#[command(name = "rsomics-bioenv", version, about, long_about = None, disable_help_flag = true)]
pub struct Cli {
    /// Community distance matrix (lsmat TSV: blank corner, id header, rows).
    dm: PathBuf,

    #[arg(short = 'e', long)]
    env: PathBuf,

    #[arg(short = 'c', long, value_delimiter = ',')]
    columns: Option<Vec<String>>,

    #[arg(short = 'o', long, default_value = "-")]
    output: String,

    #[command(flatten)]
    pub common: CommonFlags,
}

impl Tool for Cli {
    fn meta() -> ToolMeta {
        META
    }
    fn common(&self) -> &CommonFlags {
        &self.common
    }

    fn execute(self) -> Result<()> {
        self.common.install_rayon_pool()?;
        let dm_src = self.dm.display().to_string();
        let env_src = self.env.display().to_string();
        let dm = read_matrix(open(&self.dm)?, &dm_src)?;
        let env = read_env(open(&self.env)?, &env_src)?;
        let best = run_bioenv(&dm, &env, self.columns.as_deref(), &env_src)?;

        let mut out: Box<dyn Write> = if self.output == "-" {
            Box::new(BufWriter::new(std::io::stdout().lock()))
        } else {
            Box::new(BufWriter::new(
                File::create(&self.output).map_err(RsomicsError::Io)?,
            ))
        };
        write_result(&mut out, &best)?;
        out.flush().map_err(RsomicsError::Io)?;

        if !self.common.quiet
            && let Some(top) = best.iter().max_by(|a, b| {
                a.correlation
                    .partial_cmp(&b.correlation)
                    .unwrap_or(std::cmp::Ordering::Equal)
            })
        {
            eprintln!(
                "best overall: rho={:.6} at size {} ({})",
                top.correlation,
                top.size,
                top.vars.join(", ")
            );
        }
        Ok(())
    }
}

fn open(path: &std::path::Path) -> Result<BufReader<File>> {
    File::open(path)
        .map(BufReader::new)
        .map_err(|e| RsomicsError::InvalidInput(format!("{}: {e}", path.display())))
}

pub static HELP: HelpSpec = HelpSpec {
    name: env!("CARGO_PKG_NAME"),
    version: env!("CARGO_PKG_VERSION"),
    tagline: "BIO-ENV / BEST: the env-variable subset best correlated with community distances.",
    origin: Some(Origin {
        upstream: "scikit-bio skbio.stats.distance.bioenv",
        upstream_license: "BSD-3-Clause",
        our_license: "MIT OR Apache-2.0",
        paper_doi: Some("10.3354/meps092205"),
    }),
    usage_lines: &["<dm.tsv> --env <env.tsv> [-c ph,depth] [-o out.tsv]"],
    sections: &[Section {
        title: "OPTIONS",
        flags: &[
            FlagSpec {
                short: Some('e'),
                long: "env",
                aliases: &[],
                value: Some("<path>"),
                type_hint: Some("Path"),
                required: true,
                default: None,
                description: "Environmental variables TSV (samples × numeric vars).",
                why_default: None,
            },
            FlagSpec {
                short: Some('c'),
                long: "columns",
                aliases: &[],
                value: Some("<a,b,…>"),
                type_hint: Some("List"),
                required: false,
                default: None,
                description: "Comma-separated subset of env columns to consider; all if unset.",
                why_default: None,
            },
            FlagSpec {
                short: Some('o'),
                long: "output",
                aliases: &[],
                value: Some("<path>"),
                type_hint: Some("String"),
                required: false,
                default: Some("-"),
                description: "Output path (- for stdout).",
                why_default: None,
            },
        ],
    }],
    examples: &[
        Example {
            description: "All env variables against a community distance matrix",
            command: "rsomics-bioenv dm.tsv --env env.tsv -o best.tsv",
        },
        Example {
            description: "Restrict to three named variables",
            command: "rsomics-bioenv dm.tsv -e env.tsv -c pH,depth,salinity",
        },
    ],
    json_result_schema_doc: None,
};

#[cfg(test)]
mod tests {
    use super::*;
    use clap::CommandFactory;

    #[test]
    fn cli_debug_assert() {
        Cli::command().debug_assert();
    }
}