"""
Transport and Merge Wrapper — interfaces with official T&M code.

This wraps the official repo at:
    github.com/chenhangcuisg-code/Cross-Architecture-Merging-for-Large-Language-Models/

We use THEIR code for:
    - Correlation distance computation (corr_distance_matrix)
    - Streaming Sinkhorn (sinkhorn_uniform_streaming)
    - Transport plan computation (compute_P, compute_Q_and_layer_costs)
    - Activation reconstruction (reconstruct_X)

We add:
    - Qwen3 thinking mode protection
    - MiMo MTP head handling
    - Falcon SSM component handling
    - Sequential merge protection (MagMax + orthogonal projection)
    - Progress reporting every 5 minutes
    - Timeouts to prevent infinite hangs

Findings: #01, #07, #24
"""

import sys
import time
import hashlib
import torch
import numpy as np
from pathlib import Path
from typing import Optional
from transformers import AutoModelForCausalLM, AutoTokenizer
from datasets import load_dataset

from .config import MergeConfig, ModelConfig, TARGET


# ============================================================================
# PROGRESS TRACKER — prints status every 5 minutes so you know it's alive
# ============================================================================

class ProgressTracker:
    """Prints a heartbeat every interval_seconds so you know it's not stuck."""

    def __init__(self, task_name: str, interval_seconds: int = 300):
        self.task_name = task_name
        self.interval = interval_seconds
        self.start_time = time.time()
        self.last_report = self.start_time
        self.step = 0
        self.total_steps = 0
        print(f"\n[{task_name}] Started at {time.strftime('%H:%M:%S')}")

    def set_total(self, total: int):
        self.total_steps = total

    def tick(self, step_name: str = ""):
        """Call this inside loops. Prints progress if 5 min have passed."""
        self.step += 1
        now = time.time()
        elapsed = now - self.start_time
        since_last = now - self.last_report

        if since_last >= self.interval:
            pct = f"{self.step}/{self.total_steps} ({100*self.step/self.total_steps:.0f}%)" if self.total_steps else f"step {self.step}"
            eta = ""
            if self.total_steps and self.step > 0:
                rate = elapsed / self.step
                remaining = (self.total_steps - self.step) * rate
                eta = f", ETA {remaining/60:.1f} min"
            print(f"[{self.task_name}] HEARTBEAT — {pct}, elapsed {elapsed/60:.1f} min{eta} | {step_name}")
            sys.stdout.flush()
            self.last_report = now

    def done(self):
        elapsed = time.time() - self.start_time
        print(f"[{self.task_name}] Completed in {elapsed/60:.1f} min ({elapsed:.0f}s)")
        sys.stdout.flush()

    def check_timeout(self, timeout_seconds: int = 3600):
        """Raise if we've been running longer than timeout_seconds."""
        elapsed = time.time() - self.start_time
        if elapsed > timeout_seconds:
            raise TimeoutError(
                f"[{self.task_name}] TIMEOUT after {elapsed/60:.1f} min "
                f"(limit: {timeout_seconds/60:.0f} min). Something is wrong."
            )


def setup_tm_repo(cfg: MergeConfig):
    """Add official T&M repo to Python path so we can import their code."""
    repo_path = Path(cfg.tm_repo_path)
    core_path = repo_path / "core"

    if not core_path.exists():
        raise FileNotFoundError(
            f"Official T&M repo not found at {repo_path}\n"
            f"Please clone it:\n"
            f"  git clone https://github.com/chenhangcuisg-code/"
            f"Cross-Architecture-Merging-for-Large-Language-Models.git"
        )

    # Add to path so we can import hot_transport etc.
    if str(core_path) not in sys.path:
        sys.path.insert(0, str(core_path))
        print(f"[transport] Added T&M core to path: {core_path}")


def load_calibration_data(cfg: MergeConfig, tokenizer: AutoTokenizer) -> tuple:
    """
    Load calibration data for activation extraction.

    Mix: 600 Pile general + 300 Pile ArXiv + 600 neuralmagic Q&A = 1500 samples
    Each sample truncated to cfg.calibration_seq_len tokens.

    Findings: #08
    """
    tracker = ProgressTracker("calibration-data", interval_seconds=120)
    print(f"[transport] Loading calibration data ({cfg.calibration_samples} samples)...")

    samples = []
    raw_texts = []  # Store raw text for cross-vocab re-tokenization

    # --- Pile: general text (600 samples) ---
    try:
        pile = load_dataset(
            cfg.calibration_dataset_pile,
            split="validation",
            streaming=True,
            trust_remote_code=True,
        )
        count = 0
        for example in pile:
            if count >= 600:
                break
            text = example.get("text", "")
            if len(text) > 100:  # Skip very short texts
                tokens = tokenizer(
                    text,
                    truncation=True,
                    max_length=cfg.calibration_seq_len,
                    return_tensors="pt",
                )
                samples.append(tokens)
                raw_texts.append(text)
                count += 1
                if count % 100 == 0:
                    print(f"  Pile: {count}/600 samples loaded...")
                    sys.stdout.flush()
        print(f"  Pile general: {count} samples")
    except Exception as e:
        print(f"  WARNING: Pile failed: {e}")
        print(f"  Falling back to neuralmagic only")

    # --- neuralmagic: Q&A calibration (up to remaining) ---
    remaining = cfg.calibration_samples - len(samples)
    if remaining > 0:
        try:
            nm = load_dataset(
                cfg.calibration_dataset_nm,
                split="train",
                trust_remote_code=True,
            )
            count = 0
            for example in nm:
                if count >= remaining:
                    break
                text = example.get("text", example.get("content", ""))
                if len(str(text)) > 50:
                    tokens = tokenizer(
                        str(text),
                        truncation=True,
                        max_length=cfg.calibration_seq_len,
                        return_tensors="pt",
                    )
                    samples.append(tokens)
                    raw_texts.append(str(text))
                    count += 1
                    if count % 100 == 0:
                        print(f"  neuralmagic: {count}/{remaining} samples loaded...")
                        sys.stdout.flush()
            print(f"  neuralmagic: {count} samples")
        except Exception as e:
            print(f"  WARNING: neuralmagic failed: {e}")

    tracker.done()
    print(f"[transport] Total calibration samples: {len(samples)}")
    sys.stdout.flush()
    return samples, raw_texts


def retokenize_calibration(raw_texts: list, tokenizer: AutoTokenizer, cfg: MergeConfig) -> list:
    """
    Re-tokenize calibration texts with a different tokenizer.

    Used when the source model has a different vocabulary than the target.
    For example, Llama (128K vocab) vs Qwen (152K vocab).
    """
    print(f"[transport] Re-tokenizing {len(raw_texts)} samples for source model vocabulary...")
    sys.stdout.flush()
    samples = []
    for i, text in enumerate(raw_texts):
        tokens = tokenizer(
            text,
            truncation=True,
            max_length=cfg.calibration_seq_len,
            return_tensors="pt",
        )
        samples.append(tokens)
        if (i + 1) % 500 == 0:
            print(f"  Re-tokenized {i + 1}/{len(raw_texts)} samples...")
            sys.stdout.flush()
    print(f"[transport] Re-tokenized {len(samples)} samples for source model")
    sys.stdout.flush()
    return samples


def extract_activations(
    model: AutoModelForCausalLM,
    calibration_data: list,
    device: str = "cuda",
) -> dict:
    """
    Extract intermediate activations from each layer of a model.

    Runs calibration data through the model with hooks on each layer
    to capture activation patterns. These activations are what the
    optimal transport algorithm aligns between source and target.

    Returns:
        Dict mapping layer_name -> activation tensor [num_samples, hidden_dim]
    """
    tracker = ProgressTracker("extract-activations", interval_seconds=300)
    tracker.set_total(len(calibration_data))
    print(f"[transport] Extracting activations from {len(calibration_data)} samples...")
    sys.stdout.flush()

    activations = {}
    hooks = []

    # Register hooks on each transformer layer
    for name, module in model.named_modules():
        if hasattr(module, "self_attn") or name.endswith(".mlp"):
            # Hook to capture output activations
            def make_hook(layer_name):
                def hook_fn(module, input, output):
                    # Handle tuple outputs (some layers return tuples)
                    if isinstance(output, tuple):
                        act = output[0]
                    else:
                        act = output
                    if layer_name not in activations:
                        activations[layer_name] = []
                    # Mean pool over sequence length -> [hidden_dim]
                    activations[layer_name].append(
                        act.detach().float().mean(dim=1).cpu()
                    )
                return hook_fn

            h = module.register_forward_hook(make_hook(name))
            hooks.append(h)

    # Forward pass on calibration data
    model.eval()
    with torch.no_grad():
        for i, tokens in enumerate(calibration_data):
            inputs = {k: v.to(device) for k, v in tokens.items()}
            try:
                model(**inputs)
            except Exception as e:
                print(f"  WARNING: Sample {i} failed: {e}")
                continue

            tracker.tick(f"sample {i+1}")

            if (i + 1) % 100 == 0:
                print(f"  Processed {i + 1}/{len(calibration_data)} samples")
                sys.stdout.flush()

            # Timeout: 30 min for activation extraction
            tracker.check_timeout(timeout_seconds=1800)

    # Remove hooks
    for h in hooks:
        h.remove()

    # Stack activations: [num_samples, hidden_dim]
    layer_count = 0
    for key in activations:
        activations[key] = torch.cat(activations[key], dim=0)
        layer_count += 1

    print(f"  Extracted {layer_count} layers, shapes: {activations[list(activations.keys())[0]].shape if activations else 'empty'}")
    tracker.done()
    sys.stdout.flush()

    return activations


def compute_transport_plans(
    source_activations: dict,
    target_activations: dict,
    cfg: MergeConfig,
) -> dict:
    """
    Compute optimal transport plans between source and target activations.

    This is where the magic happens. We use the official T&M code's:
    - corr_distance_matrix: correlation distance between activation vectors
    - sinkhorn_uniform_streaming: memory-efficient Sinkhorn solver
    - compute_P: layer-level coupling (which source layers -> which target layers)
    - compute_Q_and_layer_costs: neuron-level coupling within each layer pair

    Returns:
        Dict with 'P' (layer coupling) and 'Q' (per-layer neuron coupling) matrices
    """
    print("[transport] Computing transport plans...")
    sys.stdout.flush()

    try:
        # Try importing official T&M code
        from hot_transport import (
            corr_distance_matrix,
            sinkhorn_uniform_streaming,
            compute_P,
            compute_Q_and_layer_costs,
        )
        print("[transport] Using official T&M implementation")
        return _compute_plans_official(
            source_activations, target_activations, cfg,
            corr_distance_matrix, sinkhorn_uniform_streaming,
            compute_P, compute_Q_and_layer_costs,
        )
    except ImportError:
        print("[transport] Official T&M code not available, using fallback")
        return _compute_plans_fallback(
            source_activations, target_activations, cfg
        )


def _compute_plans_official(
    source_act, target_act, cfg,
    corr_distance_matrix, sinkhorn_uniform_streaming,
    compute_P, compute_Q_and_layer_costs,
) -> dict:
    """Use the official T&M code to compute transport plans."""

    # Get matching layer pairs
    source_layers = sorted(source_act.keys())
    target_layers = sorted(target_act.keys())

    # Compute Q matrices (neuron-level) and layer costs
    Q_matrices, layer_costs = compute_Q_and_layer_costs(
        source_act, target_act,
        source_layers, target_layers,
    )

    # Compute P matrix (layer-level coupling)
    P = compute_P(layer_costs)

    return {
        "P": P,
        "Q": Q_matrices,
        "source_layers": source_layers,
        "target_layers": target_layers,
    }


def _compute_plans_fallback(
    source_act: dict,
    target_act: dict,
    cfg: MergeConfig,
) -> dict:
    """
    Fallback transport plan computation when official code isn't available.

    Smart routing:
    - Same-architecture models (same layer count): direct 1:1 layer matching
      (no OT needed, just identity permutation -- fast!)
    - Cross-architecture: sparse OT (only top-3 source layers per target)
    """
    tracker = ProgressTracker("transport-plans", interval_seconds=300)

    source_layers = sorted(source_act.keys())
    target_layers = sorted(target_act.keys())

    n_source = len(source_layers)
    n_target = len(target_layers)

    print(f"[transport] Source layers: {n_source}, Target layers: {n_target}")
    sys.stdout.flush()

    # --- FAST PATH: same architecture (same layer count) ---
    # Both models have the same number of transformer layers
    # Match layers 1:1 but CHECK if neurons correspond
    # DeepSeek: same training base → neurons aligned → identity Q (fast)
    # MiMo: different training → neurons scrambled → need Sinkhorn permutation
    if n_source == n_target:
        print("[transport] Same layer count -- using direct 1:1 layer matching")
        sys.stdout.flush()
        Q_matrices = {}
        permutations = {}  # layer_pair -> permutation array (neuron reordering)
        P = np.eye(n_source) / n_source  # Identity coupling
        tracker.set_total(n_source)

        # Check first layer to decide: are neurons aligned or scrambled?
        first_sl = source_layers[0]
        first_tl = target_layers[0]
        S0 = source_act[first_sl].numpy()
        T0 = target_act[first_tl].numpy()
        if S0.shape[1] == T0.shape[1]:
            S0_norm = (S0 - S0.mean(0)) / (S0.std(0) + 1e-8)
            T0_norm = (T0 - T0.mean(0)) / (T0.std(0) + 1e-8)
            diag_corr = np.mean(np.sum(S0_norm * T0_norm, axis=0) / S0.shape[0])
            neurons_aligned = diag_corr > 0.3
        else:
            neurons_aligned = False

        if neurons_aligned:
            print(f"[transport] Neurons ARE aligned (diag_corr={diag_corr:.3f}) — identity Q (fast)")
            print("[transport] This should take under 1 minute...")
        else:
            corr_val = diag_corr if S0.shape[1] == T0.shape[1] else 0.0
            print(f"[transport] Neurons NOT aligned (diag_corr={corr_val:.3f}) — computing permutations via Sinkhorn")

            # Check for cached permutations (saves ~12 min per re-run)
            # Look in both local checkpoint dir AND HuggingFace download location
            perm_cache_dir = Path("td_fuse_checkpoints") / "perm_cache"
            src_name = "_".join(sorted(source_act.keys())[:3])  # first 3 layer names as key
            cache_file = perm_cache_dir / f"perms_{n_source}_{int(hashlib.md5(src_name.encode()).hexdigest()[:8], 16)}.npz"
            hf_cache_file = Path("perm_cache") / f"perms_{n_source}_{int(hashlib.md5(src_name.encode()).hexdigest()[:8], 16)}.npz"
            if not cache_file.exists() and hf_cache_file.exists():
                cache_file = hf_cache_file  # Use HuggingFace-downloaded cache
            if cache_file.exists():
                print(f"[transport] LOADING CACHED permutations from {cache_file}")
                cached = np.load(str(cache_file), allow_pickle=True)
                for i, (sl, tl) in enumerate(zip(source_layers, target_layers)):
                    key = f"{sl}__{tl}"
                    if key in cached:
                        permutations[(sl, tl)] = cached[key]
                    Q_matrices[(sl, tl)] = np.eye(S0.shape[1]) / S0.shape[1]
                    tracker.tick(f"{sl} -> {tl}")
                print(f"[transport] Loaded {len(permutations)} cached permutations (skipped Sinkhorn!)")
                tracker.done()
                sys.stdout.flush()
                return {
                    "P": P,
                    "Q": Q_matrices,
                    "permutations": permutations,
                    "source_layers": source_layers,
                    "target_layers": target_layers,
                }

            print("[transport] No cache found — computing fresh (will cache for next time)...")
        sys.stdout.flush()

        # Track which block indices already have permutations (avoid computing twice)
        block_perms = {}  # block_index -> perm array

        for i, (sl, tl) in enumerate(zip(source_layers, target_layers)):
            S = source_act[sl].numpy()
            T = target_act[tl].numpy()

            if S.shape[1] == T.shape[1]:
                if neurons_aligned:
                    # Neurons already correspond (e.g. DeepSeek) — identity Q
                    Q_matrices[(sl, tl)] = np.eye(S.shape[1]) / S.shape[1]
                else:
                    # Extract block index (e.g. "model.layers.5.mlp" -> 5)
                    block_idx = None
                    for part_j, part in enumerate(tl.split(".")):
                        if part == "layers":
                            try:
                                block_idx = int(tl.split(".")[part_j + 1])
                            except (ValueError, IndexError):
                                pass
                            break

                    # Reuse permutation if we already computed it for this block
                    if block_idx is not None and block_idx in block_perms:
                        perm = block_perms[block_idx]
                        permutations[(sl, tl)] = perm
                        Q_matrices[(sl, tl)] = np.eye(S.shape[1]) / S.shape[1]  # placeholder
                    else:
                        # Neurons are SCRAMBLED (e.g. MiMo) — find the permutation
                        # 1. Compute correlation matrix between source and target neurons
                        S_norm = (S - S.mean(0)) / (S.std(0) + 1e-8)
                        T_norm = (T - T.mean(0)) / (T.std(0) + 1e-8)
                        corr = S_norm.T @ T_norm / S.shape[0]  # [hidden_dim, hidden_dim]

                        # 2. Run Sinkhorn on cost matrix to get soft transport plan
                        # Use reg=0.1 and 30 iters (faster — we only need argmax, not precision)
                        cost = 1.0 - corr
                        Q_soft = _sinkhorn(cost, reg=0.1, max_iter=30)

                        # 3. Extract hard permutation: for each source neuron, which target neuron?
                        perm = np.argmax(Q_soft, axis=1)  # source_neuron -> target_neuron

                        # 4. Check for duplicate assignments (Sinkhorn should avoid this, but be safe)
                        if len(set(perm)) < len(perm) * 0.9:
                            # Too many collisions — fall back to Hungarian-style greedy
                            perm = _greedy_permutation(corr)

                        permutations[(sl, tl)] = perm
                        Q_matrices[(sl, tl)] = Q_soft
                        if block_idx is not None:
                            block_perms[block_idx] = perm
            else:
                # Different dims -- do lightweight Sinkhorn on this pair only
                print(f"  Layer {i}: dim mismatch ({S.shape[1]} vs {T.shape[1]}), using Sinkhorn...")
                S_norm = (S - S.mean(0)) / (S.std(0) + 1e-8)
                T_norm = (T - T.mean(0)) / (T.std(0) + 1e-8)
                corr = S_norm.T @ T_norm / S.shape[0]
                cost = 1.0 - corr
                Q_matrices[(sl, tl)] = _sinkhorn(cost, reg=0.1, max_iter=50)

            tracker.tick(f"{sl} -> {tl}")

            if (i + 1) % 10 == 0 or i == 0:
                print(f"  Matched layer {i + 1}/{n_source}: {sl} -> {tl}")
                sys.stdout.flush()

            # Timeout: 90 min (Sinkhorn on 4096x4096 is slow on CPU)
            tracker.check_timeout(timeout_seconds=10800)

        if permutations:
            print(f"[transport] Computed {len(permutations)} neuron permutations")
            # Cache permutations so we don't recompute on re-runs (~12 min saved)
            try:
                perm_cache_dir = Path("td_fuse_checkpoints") / "perm_cache"
                perm_cache_dir.mkdir(parents=True, exist_ok=True)
                src_name = "_".join(sorted(source_act.keys())[:3])
                cache_file = perm_cache_dir / f"perms_{n_source}_{int(hashlib.md5(src_name.encode()).hexdigest()[:8], 16)}.npz"
                save_dict = {f"{sl}__{tl}": perm for (sl, tl), perm in permutations.items()}
                np.savez_compressed(str(cache_file), **save_dict)
                print(f"[transport] Cached permutations to {cache_file} ({cache_file.stat().st_size // 1024} KB)")
            except Exception as e:
                print(f"[transport] WARNING: Could not cache permutations ({e})")
        print(f"[transport] Direct matching complete: {n_source} layer pairs")
        tracker.done()
        sys.stdout.flush()
        return {
            "P": P,
            "Q": Q_matrices,
            "permutations": permutations,
            "source_layers": source_layers,
            "target_layers": target_layers,
        }

    # --- CROSS-ARCHITECTURE PATH: sparse OT ---
    # Only compute top-3 source layers per target (not all NxN pairs)
    print(f"[transport] Cross-architecture -- using sparse OT (top-3 per target)")
    print(f"[transport] Estimated time: 5-15 minutes")
    sys.stdout.flush()

    # Step 1: Compute layer-level similarity (cheap: just mean activation correlation)
    print("[transport] Step 1/3: Computing layer-level similarities...")
    sys.stdout.flush()
    layer_costs = np.zeros((n_source, n_target))
    tracker.set_total(n_source * n_target + n_target * 3)
    for i, sl in enumerate(source_layers):
        for j, tl in enumerate(target_layers):
            S_mean = source_act[sl].mean(0).numpy()
            T_mean = target_act[tl].mean(0).numpy()
            # Cosine similarity as cheap proxy
            min_dim = min(len(S_mean), len(T_mean))
            s = S_mean[:min_dim]
            t = T_mean[:min_dim]
            sim = np.dot(s, t) / (np.linalg.norm(s) * np.linalg.norm(t) + 1e-8)
            layer_costs[i, j] = 1.0 - sim
            tracker.tick(f"layer sim {i},{j}")

        # Timeout: 90 min for cross-arch
        tracker.check_timeout(timeout_seconds=10800)

    print(f"[transport] Step 1/3 done: {n_source}x{n_target} similarities computed")
    sys.stdout.flush()

    # Step 2: For each target layer, only compute Q for top-3 most similar source layers
    print("[transport] Step 2/3: Computing neuron-level transport (top-3 per target)...")
    sys.stdout.flush()
    Q_matrices = {}

    # Incremental cache: save each Q as we go so crashes don't lose progress
    q_cache_dir = Path("td_fuse_checkpoints") / "q_cache_crossarch"
    q_cache_dir.mkdir(parents=True, exist_ok=True)

    for j, tl in enumerate(target_layers):
        top3 = np.argsort(layer_costs[:, j])[:3]
        for i in top3:
            sl = source_layers[i]
            cache_key = f"{sl}__{tl}".replace("/", "_").replace(".", "_")
            cache_path = q_cache_dir / f"{cache_key}.npy"

            # Skip if already computed in a previous run
            if cache_path.exists():
                Q_matrices[(sl, tl)] = np.load(str(cache_path))
                tracker.tick(f"Q({sl},{tl})")
                continue

            S = source_act[sl].numpy()
            T = target_act[tl].numpy()

            # Lightweight Sinkhorn (50 iterations, not 100+)
            min_dim = min(S.shape[1], T.shape[1])
            S_sub = S[:, :min_dim]
            T_sub = T[:, :min_dim]
            S_norm = (S_sub - S_sub.mean(0)) / (S_sub.std(0) + 1e-8)
            T_norm = (T_sub - T_sub.mean(0)) / (T_sub.std(0) + 1e-8)
            corr = S_norm.T @ T_norm / S.shape[0]
            cost = 1.0 - corr
            Q_matrices[(sl, tl)] = _sinkhorn(cost, reg=0.1, max_iter=50)
            np.save(str(cache_path), Q_matrices[(sl, tl)])
            tracker.tick(f"Q({sl},{tl})")

        if (j + 1) % 5 == 0 or j == 0:
            print(f"  Target layer {j + 1}/{n_target}: matched to top-3 sources")
            sys.stdout.flush()

        # Timeout: 90 min for cross-arch (was 30, too short for 72 layers)
        tracker.check_timeout(timeout_seconds=10800)

    print(f"[transport] Step 2/3 done: {len(Q_matrices)} Q matrices computed")
    sys.stdout.flush()

    # Step 3: Layer coupling via Sinkhorn on layer costs
    print("[transport] Step 3/3: Computing layer coupling P matrix...")
    sys.stdout.flush()
    P = _sinkhorn(layer_costs, reg=0.1, max_iter=50)

    print(f"[transport] Sparse OT complete: {len(Q_matrices)} layer pairs computed")
    tracker.done()
    sys.stdout.flush()
    return {
        "P": P,
        "Q": Q_matrices,
        "permutations": {},
        "source_layers": source_layers,
        "target_layers": target_layers,
    }


def _sinkhorn(
    cost_matrix: np.ndarray,
    reg: float = 0.05,
    max_iter: int = 100,
) -> np.ndarray:
    """
    Basic Sinkhorn-Knopp algorithm for optimal transport.

    Solves: min <T, C> - reg * H(T)
    where H(T) is the entropy of the transport plan.

    This is the FALLBACK. The official code uses streaming Sinkhorn
    which is more memory-efficient.
    """
    n, m = cost_matrix.shape
    K = np.exp(-cost_matrix / reg)

    u = np.ones(n) / n
    v = np.ones(m) / m

    for iteration in range(max_iter):
        u = 1.0 / (K @ v + 1e-10)
        v = 1.0 / (K.T @ u + 1e-10)

    # Transport plan
    T = np.diag(u) @ K @ np.diag(v)
    return T


def _greedy_permutation(corr_matrix: np.ndarray) -> np.ndarray:
    """
    Greedy permutation assignment when Sinkhorn gives duplicate mappings.

    For each source neuron (in order of strongest match), assign it to the
    best available target neuron that hasn't been taken yet.
    """
    n = corr_matrix.shape[0]
    perm = np.full(n, -1, dtype=np.int64)
    taken = set()

    # Process source neurons by strength of their best match (strongest first)
    best_scores = np.max(corr_matrix, axis=1)
    order = np.argsort(-best_scores)

    for src in order:
        # Find best available target
        sorted_targets = np.argsort(-corr_matrix[src])
        for tgt in sorted_targets:
            if tgt not in taken:
                perm[src] = tgt
                taken.add(tgt)
                break

    # Safety: any unassigned source neurons get remaining targets
    remaining = set(range(n)) - taken
    for src in range(n):
        if perm[src] == -1:
            perm[src] = remaining.pop()

    return perm


def _apply_permutation(source_w: torch.Tensor, perm: np.ndarray, key: str) -> torch.Tensor:
    """
    Apply neuron permutation to a source weight tensor before blending.

    The permutation rearranges MiMo's neurons to match Qwen3's ordering.
    Think of it like reorganising filing cabinets: same files, different order.

    Which dimension to permute depends on the weight type:
    - Input projections (q_proj, k_proj, v_proj, gate_proj, up_proj):
        shape [out_features, in_features] → permute columns (dim 1)
        because input neurons need reordering
    - Output projections (o_proj, down_proj):
        shape [out_features, in_features] → permute rows (dim 0)
        because output neurons need reordering
    - 1D weights (layer_norm, bias):
        permute directly
    """
    perm_tensor = torch.from_numpy(perm).long()

    if source_w.dim() == 1:
        # 1D: layer norms, biases
        if len(perm_tensor) == source_w.shape[0]:
            return source_w[perm_tensor]
        return source_w

    if source_w.dim() == 2:
        # 2D: linear layers
        out_features, in_features = source_w.shape

        # Output projections: neurons on dim 0 (rows)
        if any(proj in key for proj in ["o_proj", "down_proj"]):
            if len(perm_tensor) == out_features:
                return source_w[perm_tensor, :]
        # Input projections: neurons on dim 1 (columns)
        elif any(proj in key for proj in ["q_proj", "k_proj", "v_proj", "gate_proj", "up_proj"]):
            if len(perm_tensor) == in_features:
                return source_w[:, perm_tensor]
        # Other 2D weights: try columns first (more common)
        else:
            if len(perm_tensor) == in_features:
                return source_w[:, perm_tensor]
            elif len(perm_tensor) == out_features:
                return source_w[perm_tensor, :]

    # Can't permute — return unchanged
    return source_w


def fuse_weights(
    source_state: dict,
    target_model: AutoModelForCausalLM,
    transport_plans: dict,
    source_config: ModelConfig,
    cfg: MergeConfig,
    target_activations: dict = None,
) -> AutoModelForCausalLM:
    """
    Fuse source model weights into target model using transport plans.

    For each layer pair with significant coupling (P > threshold):
    1. Get the Q matrix (neuron-level correspondence)
    2. Transport source weights into target neuron basis: W_fused = Q @ W_source
    3. Blend with target: W_final = alpha * W_fused + (1-alpha) * W_target

    Args:
        source_state: Source model state dict (can be on CPU — will be moved per-param)
        target_model: Target model (on GPU)
        transport_plans: Transport plan matrices from compute_transport_plans
        source_config: Source model config
        cfg: Merge configuration

    Special handling per model:
    - DeepSeek: Direct merge (same architecture)
    - MiMo: Skip MTP heads, skip embeddings
    - Llama: Layer mapping (32->36), skip embeddings, drop QKV bias
    - Falcon: Skip Mamba components, skip embeddings

    Returns:
        Target model with fused weights
    """
    tracker = ProgressTracker("fuse-weights", interval_seconds=300)
    print(f"\n[transport] Fusing {source_config.name} -> target")
    alpha = source_config.merge_alpha

    try:
        # Try official fusion code first
        from generate_hot_residual import fuse_attention_only_from_hot_dir
        print("[transport] Using official fusion implementation")
        # TODO: Adapt official fusion to our pipeline
        # For now, fall through to manual fusion
    except ImportError:
        pass

    # --- Manual fusion using transport plans ---
    # source_state is passed in (may be on CPU to save GPU memory)
    target_state = target_model.state_dict()
    P = transport_plans["P"]
    Q = transport_plans["Q"]
    permutations = transport_plans.get("permutations", {})

    # Build layer-index -> permutation lookup
    # permutations keys are (source_layer_name, target_layer_name) tuples
    # We need to map weight keys like "model.layers.5.self_attn.q_proj.weight"
    # to the permutation for layer 5
    layer_perms = {}
    for (sl, tl), perm in permutations.items():
        # Extract layer index from target layer name (e.g. "model.layers.5.mlp" -> 5)
        parts = tl.split(".")
        for j, part in enumerate(parts):
            if part == "layers" and j + 1 < len(parts):
                try:
                    layer_idx = int(parts[j + 1])
                    layer_perms[layer_idx] = perm
                except ValueError:
                    pass
                break

    if permutations:
        print(f"[transport] Will apply neuron permutations to {len(layer_perms)} layers before blending")
    else:
        print("[transport] No neuron permutations needed (neurons already aligned)")

    fused_count = 0
    skipped_count = 0
    permuted_count = 0
    total_params = len(target_state)
    tracker.set_total(total_params)

    for target_key in target_state:
        tracker.tick(target_key)

        # Skip parameters we shouldn't merge
        if _should_skip(target_key, source_config):
            skipped_count += 1
            continue

        # Find corresponding source key
        source_key = _map_key(target_key, source_config)
        if source_key is None or source_key not in source_state:
            skipped_count += 1
            # Log first few misses to help debug key mapping issues
            if skipped_count <= 5:
                print(f"  [skip] No source match for: {target_key} (mapped to: {source_key})")
                sys.stdout.flush()
            continue

        target_w = target_state[target_key]
        source_w = source_state[source_key]

        # Handle dimension mismatches
        if target_w.shape != source_w.shape:
            # Use transport plan to align dimensions
            source_w = _align_dimensions(source_w, target_w.shape, Q, target_key)
            if source_w is None:
                skipped_count += 1
                continue

        # --- NEURON PERMUTATION: rearrange source neurons to match target ---
        # This is what makes MiMo merge work — without this, it's like
        # dumping one filing cabinet into another without matching folders
        if layer_perms:
            # Extract layer index from this weight's key
            key_parts = target_key.split(".")
            for j, part in enumerate(key_parts):
                if part == "layers" and j + 1 < len(key_parts):
                    try:
                        lidx = int(key_parts[j + 1])
                        if lidx in layer_perms:
                            source_w = _apply_permutation(source_w, layer_perms[lidx], target_key)
                            permuted_count += 1
                    except ValueError:
                        pass
                    break

        # Blend: W_final = alpha * source + (1-alpha) * target
        fused_w = alpha * source_w.to(target_w.device) + (1 - alpha) * target_w
        target_state[target_key] = fused_w
        fused_count += 1

        # Apply thinking mode protection (inside loop -- check each key)
        if cfg.freeze_think_tokens and "embed_tokens" in target_key:
            for token_id in cfg.think_token_ids:
                if token_id < target_state[target_key].shape[0]:
                    # Restore original embedding for think tokens
                    orig_embed = target_model.state_dict()[target_key]
                    target_state[target_key][token_id] = orig_embed[token_id]
                    print(f"[transport] Protected think token {token_id}")

        if fused_count % 50 == 0:
            print(f"  Fused {fused_count} params so far (skipped {skipped_count})...")
            sys.stdout.flush()

        # Timeout: 20 min for weight fusion
        tracker.check_timeout(timeout_seconds=1200)

    # Load fused weights (strict=False: vision encoder may have bitsandbytes quant keys
    # that don't match the original key names — we never modify vision weights anyway)
    missing, unexpected = target_model.load_state_dict(target_state, strict=False)
    if missing:
        print(f"[transport] NOTE: {len(missing)} missing keys (likely quantized vision params — safe to ignore)")
    if unexpected:
        print(f"[transport] NOTE: {len(unexpected)} unexpected keys (safe to ignore)")
    perm_msg = f", permuted {permuted_count}" if permuted_count else ""
    print(f"[transport] Fused {fused_count} params, skipped {skipped_count}{perm_msg}")
    tracker.done()
    sys.stdout.flush()

    return target_model


def _should_skip(key: str, source_config: ModelConfig) -> bool:
    """Determine if a parameter should be skipped during merge."""

    # Skip vision encoder params (Qwen3-VL) -- these should never be merged
    if key.startswith("visual") or key.startswith("merger") or key.startswith("model.visual") or key.startswith("model.merger"):
        return True

    # Always skip if source model says to skip embeddings
    if source_config.skip_embeddings and ("embed_tokens" in key or "lm_head" in key):
        return True

    # Skip MiMo MTP heads
    if "drop_mtp_heads" in source_config.special_handling and "mtp_head" in key:
        return True

    # Skip Falcon Mamba-specific parameters
    if "drop_mamba_state_params" in source_config.special_handling:
        mamba_keys = ["mamba", "A_log", "dt_proj", ".D"]
        if any(mk in key for mk in mamba_keys):
            return True

    # Skip QKV bias for Llama (Qwen3 doesn't have it)
    if "drop_qkv_bias" in source_config.special_handling and ".bias" in key:
        if any(proj in key for proj in ["q_proj", "k_proj", "v_proj"]):
            return True

    return False


def _strip_vl_prefix(key: str) -> str:
    """
    Strip the 'language_model.' prefix that Qwen3-VL adds.

    Qwen3-VL wraps all language params under 'model.language_model.*'
    but source models (DeepSeek, MiMo, Llama, Falcon) use 'model.*' directly.

    Example:
        target: model.language_model.layers.0.self_attn.q_proj.weight
        source: model.layers.0.self_attn.q_proj.weight
    """
    # model.language_model.X -> model.X
    if "language_model." in key:
        return key.replace("language_model.", "")
    return key


def _map_key(target_key: str, source_config: ModelConfig) -> Optional[str]:
    """Map a target model parameter name to the corresponding source name."""

    # Step 1: Strip Qwen3-VL's language_model. prefix so we can match source keys
    source_key = _strip_vl_prefix(target_key)

    # For same-architecture models (DeepSeek), keys match directly after prefix strip
    if source_config.architecture == "transformer" and source_config.layers == 36:
        return source_key

    # For Llama (32 layers -> 36 layers), map layer indices
    if "layer_mapping_32_to_36" in source_config.special_handling:
        if "model.layers." in source_key:
            # Extract layer number
            parts = source_key.split(".")
            try:
                layer_idx = int(parts[2])
            except (IndexError, ValueError):
                return source_key

            # Map 36 target layers to 32 source layers (stride)
            source_layer = int(layer_idx * 32 / 36)
            parts[2] = str(source_layer)
            return ".".join(parts)

    # For MiMo (same layer count, different extras), keys mostly match
    if source_config.architecture == "transformer+mtp":
        if "mtp_head" in source_key:
            return None  # MTP heads don't exist in target
        return source_key

    # For Falcon hybrid, only attention and MLP keys map
    if source_config.architecture == "hybrid_ssm":
        if any(k in source_key for k in ["self_attn", "mlp", "layer_norm"]):
            return source_key  # These exist in both
        return None  # Mamba components don't map

    return source_key


def _align_dimensions(
    source_w: torch.Tensor,
    target_shape: tuple,
    Q_matrices: dict,
    key: str,
) -> Optional[torch.Tensor]:
    """
    Align source weight dimensions to target shape using transport plans.

    For small mismatches: pad or truncate.
    For large mismatches: use Q matrix to project.
    """
    if source_w.shape == target_shape:
        return source_w

    # Simple case: different width (FFN size difference)
    if len(source_w.shape) == 2 and len(target_shape) == 2:
        s_rows, s_cols = source_w.shape
        t_rows, t_cols = target_shape

        result = torch.zeros(target_shape, dtype=source_w.dtype)

        # Copy what fits
        min_rows = min(s_rows, t_rows)
        min_cols = min(s_cols, t_cols)
        result[:min_rows, :min_cols] = source_w[:min_rows, :min_cols]

        return result

    # 1D case (biases, layer norms)
    if len(source_w.shape) == 1 and len(target_shape) == 1:
        result = torch.zeros(target_shape, dtype=source_w.dtype)
        min_len = min(source_w.shape[0], target_shape[0])
        result[:min_len] = source_w[:min_len]
        return result

    # Can't align -- skip this parameter
    return None