biov 0.1.0

A uv-style tool manager for bioinformatics: reproducible Docker-backed tools with digest-pinned lockfiles (installs as `bv`)
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mod cli;
mod commands;
mod errors;
mod ops;
mod progress;
mod registry;

use clap::Parser;
use tracing_subscriber::{EnvFilter, fmt};

use cli::{Cli, Commands};

#[tokio::main]
async fn main() -> anyhow::Result<()> {
    let cli = Cli::parse();

    let level = if cli.verbose { "debug" } else { "warn" };
    fmt()
        .with_env_filter(
            EnvFilter::try_from_default_env().unwrap_or_else(|_| EnvFilter::new(level)),
        )
        .with_target(false)
        .without_time()
        .init();

    match &cli.command {
        Commands::Add {
            tools,
            registry,
            ignore_hardware,
        } => commands::add::run(tools, registry.as_deref(), *ignore_hardware).await,
        Commands::Remove { tool } => commands::remove::run(tool),
        Commands::Run { tool, args } => commands::run::run(tool, args),
        Commands::List => commands::list::run(),
        Commands::Info { tool } => commands::run::info(tool),
        Commands::Lock { check, registry } => {
            commands::lock::run(*check, registry.as_deref()).await
        }
        Commands::Sync { frozen, registry } => {
            commands::sync::run(*frozen, registry.as_deref()).await
        }
        Commands::Doctor => commands::doctor::run(),
        Commands::Data(dc) => commands::data_cmd(dc).await,
        Commands::Cache(cache_cmd) => commands::cache(cache_cmd),
    }
}