knishio-cli 0.1.4

//! Benchmark plan generation — builds fully-signed, ContinuID-compliant
//! molecules into a SQLite plan file.

use anyhow::{Context, Result};
use indicatif::{ProgressBar, ProgressStyle};
use knishio_client::{MetaItem, Molecule, Wallet};
use rusqlite::Connection;
use std::collections::HashMap;
use std::time::{Instant, SystemTime, UNIX_EPOCH};

use super::{
    BENCH_META_TYPES, BENCH_RULE_TARGETS, BENCH_TOKEN_PREFIX, FIXTURE_CELL_SLUG,
    META_IDS_PER_TYPE,
};

// ═══════════════════════════════════════════════════════════════
// Public Args
// ═══════════════════════════════════════════════════════════════

/// Arguments for the `generate` subcommand.
pub struct GenerateArgs {
    pub identities: usize,
    pub types: Vec<String>,
    pub metas_per_identity: usize,
    pub transfers_per_identity: usize,
    pub rules_per_identity: usize,
    pub burns_per_identity: usize,
    pub token_amount: f64,
    pub output: String,
}

// ═══════════════════════════════════════════════════════════════
// TypeSet — parsed molecule type flags
// ═══════════════════════════════════════════════════════════════

const VALID_TYPES: &[&str] = &["meta", "value-transfer", "rule", "burn"];

struct TypeSet {
    has_meta: bool,
    has_value_transfer: bool,
    has_rule: bool,
    has_burn: bool,
    needs_token_setup: bool,
}

impl TypeSet {
    fn from_args(types: &[String], identities: usize) -> Result<Self> {
        for t in types {
            if !VALID_TYPES.contains(&t.as_str()) {
                anyhow::bail!(
                    "Unknown molecule type '{}'. Valid types: {}",
                    t,
                    VALID_TYPES.join(", ")
                );
            }
        }

        let has_meta = types.iter().any(|t| t == "meta");
        let mut has_value_transfer = types.iter().any(|t| t == "value-transfer");
        let has_rule = types.iter().any(|t| t == "rule");
        let has_burn = types.iter().any(|t| t == "burn");

        if has_value_transfer && identities < 2 {
            eprintln!("WARNING: value-transfer requires at least 2 identities. Skipping value-transfer.");
            has_value_transfer = false;
        }

        let needs_token_setup = has_value_transfer || has_burn;

        Ok(TypeSet {
            has_meta,
            has_value_transfer,
            has_rule,
            has_burn,
            needs_token_setup,
        })
    }
}

// ═══════════════════════════════════════════════════════════════
// SQLite Schema
// ═══════════════════════════════════════════════════════════════

fn init_schema(conn: &Connection) -> Result<()> {
    conn.execute_batch(
        "
        DROP TABLE IF EXISTS gen_report;
        DROP TABLE IF EXISTS molecules;
        DROP TABLE IF EXISTS identities;
        DROP TABLE IF EXISTS config;

        CREATE TABLE config (
            key TEXT PRIMARY KEY,
            value TEXT NOT NULL
        );

        CREATE TABLE identities (
            idx INTEGER PRIMARY KEY,
            secret TEXT NOT NULL,
            bundle TEXT NOT NULL
        );

        CREATE TABLE molecules (
            id INTEGER PRIMARY KEY AUTOINCREMENT,
            identity_idx INTEGER NOT NULL,
            phase INTEGER NOT NULL,
            chain_order INTEGER NOT NULL,
            global_order INTEGER NOT NULL,
            mol_type TEXT NOT NULL,
            molecular_hash TEXT NOT NULL UNIQUE,
            payload_json TEXT NOT NULL,
            FOREIGN KEY (identity_idx) REFERENCES identities(idx)
        );

        CREATE INDEX idx_mol_phase ON molecules(phase, global_order);
        CREATE INDEX idx_mol_chain ON molecules(identity_idx, chain_order);

        CREATE TABLE gen_report (
            id INTEGER PRIMARY KEY AUTOINCREMENT,
            metric TEXT NOT NULL,
            value TEXT NOT NULL
        );
        ",
    )
    .context("Failed to initialize SQLite schema")?;
    Ok(())
}

// ═══════════════════════════════════════════════════════════════
// Molecule Helpers
// ═══════════════════════════════════════════════════════════════

/// Extract the next ContinuID position from a molecule's remainder wallet.
fn advance_chain(mol: &Molecule) -> Result<String> {
    mol.remainder_wallet
        .as_ref()
        .context("Molecule has no remainder_wallet")?
        .position
        .clone()
        .context("Remainder wallet has no position")
}

/// Serialize a molecule to JSON string for storage.
fn mol_to_payload(mol: &Molecule) -> Result<(String, String)> {
    let mol_hash = mol
        .molecular_hash
        .clone()
        .context("Molecular hash missing")?;
    let mol_json = serde_json::to_value(mol).context("Failed to serialize molecule")?;
    let payload = serde_json::to_string(&mol_json).context("Failed to stringify molecule")?;
    Ok((mol_hash, payload))
}

/// Insert a molecule into the SQLite database.
fn insert_mol(
    conn: &Connection,
    identity_idx: usize,
    phase: i32,
    chain_order: usize,
    global_order: usize,
    mol_type: &str,
    mol_hash: &str,
    payload: &str,
) -> Result<()> {
    conn.execute(
        "INSERT INTO molecules (identity_idx, phase, chain_order, global_order, mol_type, molecular_hash, payload_json)
         VALUES (?1, ?2, ?3, ?4, ?5, ?6, ?7)",
        rusqlite::params![
            identity_idx as i64,
            phase,
            chain_order as i64,
            global_order as i64,
            mol_type,
            mol_hash,
            payload
        ],
    )
    .with_context(|| format!("Failed to insert {mol_type} molecule"))?;
    Ok(())
}

// ═══════════════════════════════════════════════════════════════
// Molecule Factories
// ═══════════════════════════════════════════════════════════════

/// Create an auth molecule (U+I). Auto-adds I-atom.
fn make_auth(secret: &str, bundle: &str) -> Result<Molecule> {
    let auth_wallet = Wallet::create(Some(secret), None, "AUTH", None, None)
        .context("Failed to create auth wallet")?;

    let mut mol = Molecule::with_params(
        Some(secret.to_string()),
        Some(bundle.to_string()),
        Some(auth_wallet),
        None,
        Some(FIXTURE_CELL_SLUG.to_string()),
        None,
    );

    mol.init_authorization(vec![MetaItem::new("pubkey", "bench-pubkey")])
        .context("Failed to init authorization")?;
    mol.sign(Some(bundle.to_string()), false, false)
        .context("Failed to sign auth molecule")?;

    Ok(mol)
}

/// Create a meta molecule (M+I). Auto-adds I-atom.
/// `meta_type` is cycled from BENCH_META_TYPES for realistic bonding diversity.
fn make_meta(
    secret: &str,
    bundle: &str,
    position: &str,
    identity_idx: usize,
    meta_idx: usize,
    meta_type: &str,
) -> Result<Molecule> {
    let source_wallet = Wallet::create(Some(secret), None, "USER", Some(position), None)
        .context("Failed to create meta wallet")?;

    let mut mol = Molecule::with_params(
        Some(secret.to_string()),
        Some(bundle.to_string()),
        Some(source_wallet),
        None,
        Some(FIXTURE_CELL_SLUG.to_string()),
        None,
    );

    let type_seq = meta_idx / BENCH_META_TYPES.len();
    let id_slot = type_seq % META_IDS_PER_TYPE;
    let meta_id = format!("bench-{meta_type}-{identity_idx}-{id_slot}");
    mol.init_meta(
        vec![
            MetaItem::new("iteration", &meta_idx.to_string()),
            MetaItem::new("benchmark", "true"),
            MetaItem::new("identity", &identity_idx.to_string()),
            MetaItem::new("metaType", meta_type),
        ],
        meta_type,
        &meta_id,
        None,
    )
    .context("Failed to init meta")?;
    mol.sign(Some(bundle.to_string()), false, false)
        .context("Failed to sign meta molecule")?;

    Ok(mol)
}

/// Create a token-create molecule (C + manual I).
/// Returns (molecule, token_wallet_position).
fn make_token_create(
    secret: &str,
    bundle: &str,
    position: &str,
    token_slug: &str,
    amount: f64,
) -> Result<(Molecule, String)> {
    let source_wallet = Wallet::create(Some(secret), None, "USER", Some(position), None)
        .context("Failed to create token-create wallet")?;

    let recipient_wallet = Wallet::create(Some(secret), None, token_slug, None, None)
        .context("Failed to create token recipient wallet")?;
    let token_wallet_position = recipient_wallet.position.clone().unwrap_or_default();

    let mut mol = Molecule::with_params(
        Some(secret.to_string()),
        Some(bundle.to_string()),
        Some(source_wallet),
        None,
        Some(FIXTURE_CELL_SLUG.to_string()),
        None,
    );

    mol.init_token_creation(
        &recipient_wallet,
        amount,
        vec![
            MetaItem::new("name", &format!("Bench Token {token_slug}")),
            MetaItem::new("fungibility", "fungible"),
            MetaItem::new("supply", "replenishable"),
            MetaItem::new("decimals", "0"),
        ],
    )
    .context("Failed to init token creation")?;

    mol.add_continuid_atom()
        .context("Failed to add ContinuID atom to token-create")?;

    mol.sign(Some(bundle.to_string()), false, false)
        .context("Failed to sign token-create molecule")?;

    Ok((mol, token_wallet_position))
}

/// Create a token-request molecule (T + manual I).
fn make_token_request(
    secret: &str,
    bundle: &str,
    position: &str,
    token_slug: &str,
    amount: f64,
    identity_idx: usize,
) -> Result<Molecule> {
    let source_wallet = Wallet::create(Some(secret), None, "USER", Some(position), None)
        .context("Failed to create token-request wallet")?;

    let mut mol = Molecule::with_params(
        Some(secret.to_string()),
        Some(bundle.to_string()),
        Some(source_wallet),
        None,
        Some(FIXTURE_CELL_SLUG.to_string()),
        None,
    );

    let meta_id = format!("bench-request-{identity_idx}");
    mol.init_token_request(
        token_slug,
        amount,
        "tokenRequest",
        &meta_id,
        vec![
            MetaItem::new("reason", "benchmark distribution"),
            MetaItem::new("issuer", bundle),
        ],
        None,
    )
    .context("Failed to init token request")?;

    mol.add_continuid_atom()
        .context("Failed to add ContinuID atom to token-request")?;

    mol.sign(Some(bundle.to_string()), false, false)
        .context("Failed to sign token-request molecule")?;

    Ok(mol)
}

/// Create a value-transfer molecule (V+V+V + manual I).
fn make_value_transfer(
    secret: &str,
    bundle: &str,
    token_position: &str,
    continuid_position: &str,
    recipient_bundle: &str,
    token_slug: &str,
    amount: f64,
    source_balance: f64,
    transfer_idx: usize,
) -> Result<Molecule> {
    let mut source_wallet =
        Wallet::create(Some(secret), None, token_slug, Some(token_position), None)
            .context("Failed to create value-transfer source wallet")?;
    source_wallet.balance = source_balance.to_string();

    let recipient_wallet =
        Wallet::create(Some(recipient_bundle), None, token_slug, None, None)
            .context("Failed to create value-transfer recipient wallet")?;

    let mut mol = Molecule::with_params(
        Some(secret.to_string()),
        Some(bundle.to_string()),
        Some(source_wallet),
        None,
        Some(FIXTURE_CELL_SLUG.to_string()),
        None,
    );

    mol.continuid_position = Some(continuid_position.to_string());

    mol.init_value(&recipient_wallet, amount)
        .with_context(|| {
            format!(
                "Failed to init value transfer #{transfer_idx} (amount={amount}, balance={source_balance})"
            )
        })?;

    mol.add_continuid_atom()
        .context("Failed to add ContinuID atom to value-transfer")?;

    mol.sign(Some(bundle.to_string()), false, false)
        .context("Failed to sign value-transfer molecule")?;

    Ok(mol)
}

/// Create a rule molecule. Uses init_meta with isotope R pathway.
fn make_rule(
    secret: &str,
    bundle: &str,
    position: &str,
    identity_idx: usize,
    rule_idx: usize,
    rule_target: &str,
) -> Result<Molecule> {
    let source_wallet = Wallet::create(Some(secret), None, "USER", Some(position), None)
        .context("Failed to create rule wallet")?;

    let mut mol = Molecule::with_params(
        Some(secret.to_string()),
        Some(bundle.to_string()),
        Some(source_wallet),
        None,
        Some(FIXTURE_CELL_SLUG.to_string()),
        None,
    );

    let rule_id = format!("bench-rule-{rule_target}-{identity_idx}-{rule_idx}");
    mol.init_meta(
        vec![
            MetaItem::new("action", "reject"),
            MetaItem::new("condition", "amount > 999999"),
            MetaItem::new("benchmark", "true"),
            MetaItem::new("targetType", rule_target),
        ],
        rule_target,
        &rule_id,
        None,
    )
    .context("Failed to init rule")?;
    mol.sign(Some(bundle.to_string()), false, false)
        .context("Failed to sign rule molecule")?;

    Ok(mol)
}

/// Create a burn molecule (V+V + manual I).
fn make_burn(
    secret: &str,
    bundle: &str,
    position: &str,
    token_slug: &str,
    amount: f64,
    source_balance: f64,
) -> Result<Molecule> {
    let mut source_wallet =
        Wallet::create(Some(secret), None, token_slug, Some(position), None)
            .context("Failed to create burn wallet")?;
    source_wallet.balance = source_balance.to_string();

    let mut mol = Molecule::with_params(
        Some(secret.to_string()),
        Some(bundle.to_string()),
        Some(source_wallet),
        None,
        Some(FIXTURE_CELL_SLUG.to_string()),
        None,
    );

    mol.burn_token(amount, None)
        .context("Failed to init burn")?;

    mol.add_continuid_atom()
        .context("Failed to add ContinuID atom to burn")?;

    mol.sign(Some(bundle.to_string()), false, false)
        .context("Failed to sign burn molecule")?;

    Ok(mol)
}

// ═══════════════════════════════════════════════════════════════
// Generate Command
// ═══════════════════════════════════════════════════════════════

pub fn generate(args: GenerateArgs) -> Result<()> {
    let type_set = TypeSet::from_args(&args.types, args.identities)?;

    // Calculate expected molecule counts
    let auth_count = args.identities;
    let setup_count = if type_set.needs_token_setup {
        args.identities * 2
    } else {
        0
    };
    let test_count = {
        let mut c = 0usize;
        if type_set.has_meta {
            c += args.identities * args.metas_per_identity;
        }
        if type_set.has_value_transfer {
            c += args.identities * args.transfers_per_identity;
        }
        if type_set.has_rule {
            c += args.identities * args.rules_per_identity;
        }
        if type_set.has_burn {
            c += args.identities * args.burns_per_identity;
        }
        c
    };
    let total = auth_count + setup_count + test_count;

    println!();
    println!("═══════════════════════════════════════════════════════════════");
    println!(" KnishIO Benchmark Plan Generator");
    println!("═══════════════════════════════════════════════════════════════");
    println!(" Identities:          {}", args.identities);
    println!(" Molecule types:      {}", args.types.join(", "));
    println!(" Phase 0 (auth):      {auth_count}");
    if setup_count > 0 {
        println!(" Phase 1 (setup):     {setup_count}");
        println!("   token-create:      {}", args.identities);
        println!("   token-request:     {}", args.identities);
    }
    println!(" Phase 2 (test):      {test_count}");
    if type_set.has_meta {
        println!(
            "   meta:              {} ({} metaTypes: {})",
            args.identities * args.metas_per_identity,
            BENCH_META_TYPES.len(),
            BENCH_META_TYPES.join(", "),
        );
    }
    if type_set.has_value_transfer {
        println!(
            "   value-transfer:    {}",
            args.identities * args.transfers_per_identity
        );
    }
    if type_set.has_rule {
        println!(
            "   rule:              {} ({} targets: {})",
            args.identities * args.rules_per_identity,
            BENCH_RULE_TARGETS.len(),
            BENCH_RULE_TARGETS.join(", "),
        );
    }
    if type_set.has_burn {
        println!(
            "   burn:              {}",
            args.identities * args.burns_per_identity
        );
    }
    println!(" Total molecules:     {total}");
    println!(" Output:              {}", args.output);
    println!("═══════════════════════════════════════════════════════════════");
    println!();

    // Open SQLite
    let conn =
        Connection::open(&args.output).context("Failed to open SQLite database")?;
    conn.pragma_update(None, "journal_mode", "WAL").ok();
    conn.pragma_update(None, "synchronous", "NORMAL").ok();
    init_schema(&conn)?;

    // Store config
    let run_id = SystemTime::now()
        .duration_since(UNIX_EPOCH)
        .context("System clock before UNIX epoch")?
        .as_secs();
    let config_pairs = [
        ("identities", args.identities.to_string()),
        ("types", args.types.join(",")),
        ("metas_per_identity", args.metas_per_identity.to_string()),
        (
            "transfers_per_identity",
            args.transfers_per_identity.to_string(),
        ),
        ("rules_per_identity", args.rules_per_identity.to_string()),
        ("burns_per_identity", args.burns_per_identity.to_string()),
        ("token_amount", args.token_amount.to_string()),
        ("run_id", run_id.to_string()),
        ("generated_at", run_id.to_string()),
        ("generator_version", "1.0.0".to_string()),
        ("cell_slug", FIXTURE_CELL_SLUG.to_string()),
    ];
    for (k, v) in &config_pairs {
        conn.execute(
            "INSERT INTO config (key, value) VALUES (?1, ?2)",
            [*k, v.as_str()],
        )
        .with_context(|| format!("Failed to insert config key '{k}'"))?;
    }

    // Progress bar
    let pb = ProgressBar::new(total as u64);
    pb.set_style(
        ProgressStyle::with_template(
            " {spinner:.green} [{bar:40.cyan/blue}] {pos}/{len} ({per_sec}) {msg}",
        )
        .unwrap()
        .progress_chars("=>-"),
    );

    let total_start = Instant::now();
    let mut phase_timings: HashMap<&str, (usize, f64)> = HashMap::new();
    let mut type_timings: HashMap<String, (usize, f64)> = HashMap::new();
    let mut global_order: usize = 0;

    // Collect all bundles for value-transfer recipients
    let mut bundles: Vec<String> = Vec::with_capacity(args.identities);

    // First pass: generate identities and collect bundles
    for k in 0..args.identities {
        let secret = format!("bench-cli-identity-{k}-{run_id}");
        let auth_wallet = Wallet::create(Some(&secret), None, "AUTH", None, None)
            .context("Failed to create auth wallet for bundle lookup")?;
        let bundle = auth_wallet
            .bundle
            .clone()
            .context("Auth wallet has no bundle")?;
        bundles.push(bundle.clone());

        conn.execute(
            "INSERT INTO identities (idx, secret, bundle) VALUES (?1, ?2, ?3)",
            rusqlite::params![k as i64, &secret, &bundle],
        )
        .context("Failed to insert identity")?;
    }

    // Second pass: generate molecules for each identity
    for k in 0..args.identities {
        let secret = format!("bench-cli-identity-{k}-{run_id}");
        let bundle = &bundles[k];
        let token_slug = format!("{BENCH_TOKEN_PREFIX}{k}_{run_id}");
        let mut chain_order: usize = 0;

        // ── Phase 0: Auth ──
        let phase_start = Instant::now();
        let auth_mol = make_auth(&secret, bundle)?;
        let mut next_pos = advance_chain(&auth_mol)?;
        let (hash, payload) = mol_to_payload(&auth_mol)?;
        insert_mol(&conn, k, 0, chain_order, global_order, "auth", &hash, &payload)?;
        chain_order += 1;
        global_order += 1;
        pb.inc(1);
        pb.set_message(format!("identity {}/{}", k + 1, args.identities));

        let auth_elapsed = phase_start.elapsed().as_secs_f64();
        let e = phase_timings.entry("auth").or_insert((0, 0.0));
        e.0 += 1;
        e.1 += auth_elapsed;
        let e = type_timings.entry("auth".to_string()).or_insert((0, 0.0));
        e.0 += 1;
        e.1 += auth_elapsed;

        // ── Phase 1: Token setup (if needed) ──
        let mut token_balance = args.token_amount;
        let mut token_pos = String::new();

        if type_set.needs_token_setup {
            // token-create
            let phase_start = Instant::now();
            let (tc_mol, tc_wallet_pos) =
                make_token_create(&secret, bundle, &next_pos, &token_slug, args.token_amount)?;
            token_pos = tc_wallet_pos;
            next_pos = advance_chain(&tc_mol)?;
            let (hash, payload) = mol_to_payload(&tc_mol)?;
            insert_mol(
                &conn,
                k,
                1,
                chain_order,
                global_order,
                "token-create",
                &hash,
                &payload,
            )?;
            chain_order += 1;
            global_order += 1;
            pb.inc(1);

            let tc_elapsed = phase_start.elapsed().as_secs_f64();
            let e = phase_timings.entry("setup").or_insert((0, 0.0));
            e.0 += 1;
            e.1 += tc_elapsed;
            let e = type_timings
                .entry("token-create".to_string())
                .or_insert((0, 0.0));
            e.0 += 1;
            e.1 += tc_elapsed;

            // token-request
            let phase_start = Instant::now();
            let tr_mol = make_token_request(
                &secret,
                bundle,
                &next_pos,
                &token_slug,
                args.token_amount,
                k,
            )?;
            next_pos = advance_chain(&tr_mol)?;
            let (hash, payload) = mol_to_payload(&tr_mol)?;
            insert_mol(
                &conn,
                k,
                1,
                chain_order,
                global_order,
                "token-request",
                &hash,
                &payload,
            )?;
            chain_order += 1;
            global_order += 1;
            pb.inc(1);

            let tr_elapsed = phase_start.elapsed().as_secs_f64();
            let e = phase_timings.entry("setup").or_insert((0, 0.0));
            e.0 += 1;
            e.1 += tr_elapsed;
            let e = type_timings
                .entry("token-request".to_string())
                .or_insert((0, 0.0));
            e.0 += 1;
            e.1 += tr_elapsed;
        }

        // ── Phase 2: Test molecules ──
        let meta_count = if type_set.has_meta {
            args.metas_per_identity
        } else {
            0
        };
        let vt_count = if type_set.has_value_transfer {
            args.transfers_per_identity
        } else {
            0
        };
        let max_interleave = std::cmp::max(meta_count, vt_count);

        let amount_per_transfer = if type_set.has_value_transfer {
            let burn_budget = if type_set.has_burn {
                args.burns_per_identity
            } else {
                0
            };
            let divisor = args.transfers_per_identity + burn_budget + 1;
            (args.token_amount / divisor as f64).floor()
        } else {
            0.0
        };

        let mut meta_idx = 0usize;
        let mut vt_idx = 0usize;

        for i in 0..max_interleave {
            // Meta molecule
            if type_set.has_meta && i < meta_count {
                let start = Instant::now();
                let meta_type = BENCH_META_TYPES[(meta_idx + k) % BENCH_META_TYPES.len()];
                let mol = make_meta(&secret, bundle, &next_pos, k, meta_idx, meta_type)?;
                next_pos = advance_chain(&mol)?;
                let (hash, payload) = mol_to_payload(&mol)?;
                insert_mol(&conn, k, 2, chain_order, global_order, "meta", &hash, &payload)?;
                chain_order += 1;
                global_order += 1;
                meta_idx += 1;
                pb.inc(1);

                let elapsed = start.elapsed().as_secs_f64();
                let e = phase_timings.entry("test").or_insert((0, 0.0));
                e.0 += 1;
                e.1 += elapsed;
                let e = type_timings.entry("meta".to_string()).or_insert((0, 0.0));
                e.0 += 1;
                e.1 += elapsed;
            }

            // Value transfer molecule
            if type_set.has_value_transfer && i < vt_count {
                let recipient_idx = (k + 1 + vt_idx) % args.identities;
                let recipient_bundle = &bundles[recipient_idx];

                let start = Instant::now();
                let mol = make_value_transfer(
                    &secret,
                    bundle,
                    &token_pos,
                    &next_pos,
                    recipient_bundle,
                    &token_slug,
                    amount_per_transfer,
                    token_balance,
                    vt_idx,
                )?;
                next_pos = advance_chain(&mol)?;
                if let Some(v_remainder) = mol.atoms.get(2) {
                    token_pos = v_remainder.position.clone();
                }
                token_balance -= amount_per_transfer;
                let (hash, payload) = mol_to_payload(&mol)?;
                insert_mol(
                    &conn,
                    k,
                    2,
                    chain_order,
                    global_order,
                    "value-transfer",
                    &hash,
                    &payload,
                )?;
                chain_order += 1;
                global_order += 1;
                vt_idx += 1;
                pb.inc(1);

                let elapsed = start.elapsed().as_secs_f64();
                let e = phase_timings.entry("test").or_insert((0, 0.0));
                e.0 += 1;
                e.1 += elapsed;
                let e = type_timings
                    .entry("value-transfer".to_string())
                    .or_insert((0, 0.0));
                e.0 += 1;
                e.1 += elapsed;
            }
        }

        // Rule molecules
        if type_set.has_rule {
            for r in 0..args.rules_per_identity {
                let start = Instant::now();
                let rule_target = BENCH_RULE_TARGETS[r % BENCH_RULE_TARGETS.len()];
                let mol = make_rule(&secret, bundle, &next_pos, k, r, rule_target)?;
                next_pos = advance_chain(&mol)?;
                let (hash, payload) = mol_to_payload(&mol)?;
                insert_mol(
                    &conn, k, 2, chain_order, global_order, "rule", &hash, &payload,
                )?;
                chain_order += 1;
                global_order += 1;
                pb.inc(1);

                let elapsed = start.elapsed().as_secs_f64();
                let e = phase_timings.entry("test").or_insert((0, 0.0));
                e.0 += 1;
                e.1 += elapsed;
                let e = type_timings.entry("rule".to_string()).or_insert((0, 0.0));
                e.0 += 1;
                e.1 += elapsed;
            }
        }

        // Burn molecules
        if type_set.has_burn && type_set.needs_token_setup {
            let transfer_budget = if type_set.has_value_transfer {
                args.transfers_per_identity as f64
            } else {
                0.0
            };
            let burn_amount =
                args.token_amount / (transfer_budget + args.burns_per_identity as f64 + 1.0);

            for _b in 0..args.burns_per_identity {
                let start = Instant::now();
                let mol = make_burn(
                    &secret,
                    bundle,
                    &next_pos,
                    &token_slug,
                    burn_amount,
                    token_balance,
                )?;
                next_pos = advance_chain(&mol)?;
                token_balance -= burn_amount;
                let (hash, payload) = mol_to_payload(&mol)?;
                insert_mol(
                    &conn, k, 2, chain_order, global_order, "burn", &hash, &payload,
                )?;
                chain_order += 1;
                global_order += 1;
                pb.inc(1);

                let elapsed = start.elapsed().as_secs_f64();
                let e = phase_timings.entry("test").or_insert((0, 0.0));
                e.0 += 1;
                e.1 += elapsed;
                let e = type_timings
                    .entry("burn".to_string())
                    .or_insert((0, 0.0));
                e.0 += 1;
                e.1 += elapsed;
            }
        }

        // Suppress unused variable warning when neither value-transfer nor burn
        let _ = next_pos;
        let _ = token_balance;
    }

    pb.finish_with_message("done");

    let total_elapsed = total_start.elapsed();

    // Store gen_report metrics
    for (mol_type, (count, secs)) in &type_timings {
        conn.execute(
            "INSERT INTO gen_report (metric, value) VALUES (?1, ?2)",
            [
                &format!("gen_{mol_type}_count"),
                &count.to_string(),
            ],
        )
        .with_context(|| format!("Failed to insert gen_report for {mol_type}"))?;
        conn.execute(
            "INSERT INTO gen_report (metric, value) VALUES (?1, ?2)",
            [
                &format!("gen_{mol_type}_secs"),
                &format!("{secs:.3}"),
            ],
        )
        .with_context(|| format!("Failed to insert gen_report secs for {mol_type}"))?;
    }
    conn.execute(
        "INSERT INTO gen_report (metric, value) VALUES ('gen_total_secs', ?1)",
        [&format!("{:.3}", total_elapsed.as_secs_f64())],
    )
    .context("Failed to insert gen_total_secs")?;

    // Verify counts
    let actual_total: i64 = conn
        .query_row("SELECT COUNT(*) FROM molecules", [], |r| r.get(0))
        .context("Failed to count molecules")?;

    // Print generation report
    println!();
    println!("═══════════════════════════════════════════════════════════════");
    println!(" Generation Complete");
    println!("═══════════════════════════════════════════════════════════════");

    if let Some((count, secs)) = phase_timings.get("auth") {
        let rate = *count as f64 / secs;
        println!(" Phase 0 (auth):      {count:>6} molecules  ({secs:.1}s, {rate:.1} mol/s)");
    }
    if let Some((count, secs)) = phase_timings.get("setup") {
        let rate = *count as f64 / secs;
        println!(" Phase 1 (setup):     {count:>6} molecules  ({secs:.1}s, {rate:.1} mol/s)");
        if let Some((c, _)) = type_timings.get("token-create") {
            println!("   token-create:      {c:>6}");
        }
        if let Some((c, _)) = type_timings.get("token-request") {
            println!("   token-request:     {c:>6}");
        }
    }
    if let Some((count, secs)) = phase_timings.get("test") {
        let rate = *count as f64 / secs;
        println!(" Phase 2 (test):      {count:>6} molecules  ({secs:.1}s, {rate:.1} mol/s)");
        for mol_type in &["meta", "value-transfer", "rule", "burn"] {
            if let Some((c, _)) = type_timings.get(*mol_type) {
                println!("   {mol_type:<18}{c:>6}");
            }
        }
    }

    let total_rate = actual_total as f64 / total_elapsed.as_secs_f64();
    println!();
    println!(
        " Total:               {actual_total:>6} molecules in {:.1}s ({total_rate:.1} mol/s)",
        total_elapsed.as_secs_f64()
    );
    println!(" Output:              {}", args.output);
    println!("═══════════════════════════════════════════════════════════════");

    if actual_total != total as i64 {
        anyhow::bail!(
            "Expected {total} molecules but generated {actual_total}. This is a bug."
        );
    }

    Ok(())
}