cantata 0.1.0

Convert SONATA package neuro science simulations into Arbor simulations.
Documentation 
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use clap::{self, Parser, Subcommand, ValueEnum};
use cantata::{
    err::{Context, Result},
    fit::Fit,
    gen::Bundle,
    raw,
    sim::Simulation,
    sup::find_component,
};
use std::str::FromStr;

#[derive(Parser)]
#[clap(name = "sonata")]
#[clap(version = "0.1.0-dev", author = "t.hater@fz-juelich.de")]
struct Cli {
    #[clap(subcommand)]
    cmd: Cmd,
}

#[derive(Hash, PartialEq, PartialOrd, Eq, Ord, Clone, Copy, ValueEnum)]
enum Format {
    CBOR,
    JSON,
    Pickle,
}

#[derive(Subcommand)]
enum Cmd {
    Build {
        from: String,
        to: String,
        #[arg(short, long)]
        formats: Vec<Format>,
    },
}

fn main() -> Result<()> {
    let cli = Cli::parse();
    match cli.cmd {
        Cmd::Build { from, to, formats } => {
            let raw = raw::Simulation::from_file(&from)
                .with_context(|| format!("Parsing simulation {from}"))?;
            let sim =
                Simulation::new(&raw).with_context(|| format!("Extracting simulation {from}"))?;
            let mut out = Bundle::new(&sim).with_context(|| "Generating Python code")?;

            // Create all required directories
            let mut to = std::path::PathBuf::from_str(&to)
                .map_err(anyhow::Error::from)
                .with_context(|| format!("Resolving output dir {to}"))?;
            std::fs::create_dir_all(&to).with_context(|| format!("Creating output dir {to:?}"))?;

            to.push("mrf");
            std::fs::create_dir_all(&to).with_context(|| format!("Creating output dir {to:?}"))?;

            for mrf in &out.morphology {
                let src = find_component(mrf, &raw.components)
                    .with_context(|| format!("Searching morphology {mrf:?}"))?;
                to.push(mrf);
                std::fs::copy(&src, &to).with_context(|| format!("Copying {src:?} to {to:?}"))?;
                to.pop();
            }
            to.pop();

            to.push("acc");
            std::fs::create_dir_all(&to).with_context(|| format!("Creating output dir {to:?}"))?;

            for fit in out.decoration.iter_mut() {
                to.push(&fit);
                to.set_extension("acc");
                let src = find_component(fit, &raw.components)
                    .with_context(|| format!("Searching raw fit {fit:?}"))?;
                let inp = Fit::from_file(&src)
                    .with_context(|| format!("Extracting fit {src:?}"))?
                    .decor()
                    .with_context(|| format!("Building decor for fit {src:?}"))?
                    .to_acc()
                    .with_context(|| format!("Converting fit {src:?} to acc"))?;
                std::fs::write(&to, inp).with_context(|| format!("Writing {to:?}"))?;
                to.pop();
                *fit = format!("{}.acc", fit.rsplit_once('.').expect(".json?").0);
            }
            to.pop();

            to.push("dat");
            std::fs::create_dir_all(&to).with_context(|| format!("Creating output dir {to:?}"))?;
            if formats.contains(&Format::JSON) {
                to.push("sim.json");
                let writer = std::fs::File::create(&to)?;
                serde_json::to_writer_pretty(writer, &out)?;
                to.pop();
            }
            if formats.is_empty() || formats.contains(&Format::CBOR) {
                to.push("sim.cbor");
                let writer = std::fs::File::create(&to)?;
                ciborium::into_writer(&out, writer)?;
                to.pop();
            }
            if formats.contains(&Format::Pickle) {
                to.push("sim.pcl");
                let mut writer = std::fs::File::create(&to)?;
                serde_pickle::to_writer(&mut writer, &out, Default::default())?;
                to.pop();
            }

            to.pop();

            to.push("out");
            std::fs::create_dir_all(&to).with_context(|| format!("Creating output dir {to:?}"))?;
            to.pop();

            to.push("main.py");
            std::fs::write(&to, include_str!("../data/main.py"))
                .with_context(|| format!("Copying simulation file {to:?}"))?;
            to.pop();

            Ok(())
        }
    }
}