from typing import Callable, List, Optional, Tuple, Union

import numpy as np

import torch
import torch.utils.checkpoint
from torch import nn
from torch.nn import CrossEntropyLoss

from transformers.activations import ACT2FN
from transformers.generation.configuration_utils import GenerationConfig
from transformers.generation.logits_process import LogitsProcessorList
from transformers.generation.stopping_criteria import StoppingCriteriaList
from transformers.generation.streamers import BaseStreamer
from transformers.generation.utils import GenerateOutput
from transformers.modeling_outputs import BaseModelOutputWithPast, CausalLMOutputWithPast
from transformers.modeling_utils import PreTrainedModel
from transformers.utils import logging
from transformers.utils.model_parallel_utils import assert_device_map, get_device_map
from .configuration_progen import ProGenConfig

logger = logging.get_logger(__name__)

from .structure import StructureTransformer
# from .structure_ligand import StructureTransformer


import math

# Inverse dim formula to find dim based on number of rotations
def _yarn_find_correction_dim(num_rotations, dim, base=10000, max_position_embeddings=2048):
    return (dim * math.log(max_position_embeddings/(num_rotations * 2 * math.pi)))/(2 * math.log(base))

# Find dim range bounds based on rotations
def _yarn_find_correction_range(low_rot, high_rot, dim, base=10000, max_position_embeddings=2048):
    low = math.floor(_yarn_find_correction_dim(
        low_rot, dim, base, max_position_embeddings))
    high = math.ceil(_yarn_find_correction_dim(
        high_rot, dim, base, max_position_embeddings))
    return max(low, 0), min(high, dim-1)  # Clamp values just in case

def _yarn_linear_ramp_mask(min, max, dim):
    if min == max:
        max += 0.001  # Prevent singularity

    linear_func = (torch.arange(dim, dtype=torch.float32) - min) / (max - min)
    ramp_func = torch.clamp(linear_func, 0, 1)
    return ramp_func

def _yarn_get_mscale(scale=1):
    if scale <= 1:
        return 1.0
    return 0.1 * math.log(scale) + 1.0

def yarn(x, seq_len=None, seq_dim=1, base=10000, scale=4, original_max_position_embeddings=1024, extrapolation_factor=1, attn_factor=1, beta_fast=4, beta_slow=0.5):
    # print(f'beta_fast: {beta_fast}')
    # print(f'beta_slow: {beta_slow}')
    # print(f'scale: {scale}')
    # print(f'extrapolation_factor: {extrapolation_factor}')
    # print(f'attn_factor: {attn_factor}')

    dim = x.shape[-1]
    pos_freqs = base ** (torch.arange(0, dim, 2).float().to(x.device) / dim)
    inv_freq_extrapolation = 1.0 / pos_freqs
    inv_freq_interpolation = 1.0 / (scale * pos_freqs)

    low, high = _yarn_find_correction_range(beta_fast, beta_slow, dim, base, original_max_position_embeddings)

    inv_freq_mask = (1 - _yarn_linear_ramp_mask(low, high, dim // 2).float().to(x.device)) * extrapolation_factor # Get n-d rotational scaling corrected for extrapolation
    inv_freq = inv_freq_interpolation * (1 - inv_freq_mask) + inv_freq_extrapolation * inv_freq_mask

    mscale = float(_yarn_get_mscale(scale) * attn_factor) # Get n-d magnitude scaling corrected for interpolation

    # Build here to make `torch.jit.trace` work.
    if seq_len is None:
        seq_len = x.shape[seq_dim]
    t = torch.arange(seq_len, device=x.device, dtype=x.dtype)
    freqs = torch.einsum("i,j->ij", t, inv_freq)
    # torch.save(freqs, 'yarn_freq.pt')
    return torch.sin(freqs)*mscale, torch.cos(freqs)*mscale

def fixed_pos_embedding(x, seq_dim=1, seq_len=None):
    dim = x.shape[-1]
    if seq_len is None:
        seq_len = x.shape[seq_dim]
    inv_freq = 1.0 / (10000 ** (torch.arange(0, dim, 2) / dim))
    sinusoid_inp = torch.einsum("i , j -> i j", torch.arange(seq_len), inv_freq).to(x.device).float()
    # return torch.sin(sinusoid_inp), torch.cos(sinusoid_inp)
    return torch.sin(sinusoid_inp).to(x.dtype), torch.cos(sinusoid_inp).to(x.dtype)

def rotate_every_two(x):
    x1 = x[:, :, :, ::2]
    x2 = x[:, :, :, 1::2]
    x = torch.stack((-x2, x1), axis=-1)
    return x.flatten(-2)  # in einsum notation: rearrange(x, '... d j -> ... (d j)')


def apply_rotary_pos_emb(x, sincos, offset=0, position_ids=None):
    # einsum notation for lambda t: repeat(t[offset:x.shape[1]+offset,:], "n d -> () n () (d j)", j=2)
    if position_ids is not None:
        sin, cos = map(lambda t: t[None, :, None, :].repeat_interleave(2, 3), sincos)
        sin = sin.take_along_dim(position_ids.unsqueeze(-1).unsqueeze(-1), dim=1)
        cos = cos.take_along_dim(position_ids.unsqueeze(-1).unsqueeze(-1), dim=1)
    else:
        sin, cos = map(lambda t: t[None, offset : x.shape[1] + offset, None, :].repeat_interleave(2, 3), sincos)
    return (x * cos) + (rotate_every_two(x) * sin)


class ProGenAttention(nn.Module):
    def __init__(self, config):
        super().__init__()

        max_positions = config.max_position_embeddings
        self.yarn = config.yarn
        self.register_buffer(
            "bias",
            torch.tril(torch.ones((max_positions, max_positions), dtype=torch.bool)).view(
                1, 1, max_positions, max_positions
            ),
        )
        self.register_buffer("masked_bias", torch.tensor(-1e9))

        self.attn_dropout = nn.Dropout(config.attn_pdrop)
        self.resid_dropout = nn.Dropout(config.resid_pdrop)

        self.embed_dim = config.hidden_size
        self.num_attention_heads = config.num_attention_heads
        self.head_dim = self.embed_dim // self.num_attention_heads
        if self.head_dim * self.num_attention_heads != self.embed_dim:
            raise ValueError(
                f"embed_dim must be divisible by num_attention_heads (got `embed_dim`: {self.embed_dim} and `num_attention_heads`: {self.num_attention_heads})."
            )
        self.scale_attn = torch.sqrt(torch.tensor(self.head_dim, dtype=torch.float32)).to(torch.get_default_dtype())
        self.qkv_proj = nn.Linear(self.embed_dim, self.embed_dim * 3, bias=False)

        self.out_proj = nn.Linear(self.embed_dim, self.embed_dim, bias=False)
        self.rotary_dim = None
        if config.rotary_dim is not None:
            self.rotary_dim = config.rotary_dim

    def _split_heads(self, x, n_head, dim_head, mp_num):
        reshaped = x.reshape(x.shape[:-1] + (n_head//mp_num, dim_head))
        reshaped = reshaped.reshape(x.shape[:-2] + (-1, ) + reshaped.shape[-1:])
        return reshaped

    def _merge_heads(self, tensor, num_attention_heads, attn_head_size):
        """
        Merges attn_head_size dim and num_attn_heads dim into n_ctx
        """
        if len(tensor.shape) == 5:
            tensor = tensor.permute(0, 1, 3, 2, 4).contiguous()
        elif len(tensor.shape) == 4:
            tensor = tensor.permute(0, 2, 1, 3).contiguous()
        else:
            raise ValueError(f"Input tensor rank should be one of [4, 5], but is: {len(tensor.shape)}")
        new_shape = tensor.size()[:-2] + (num_attention_heads * attn_head_size,)
        return tensor.view(new_shape)

    def _attn(
        self,
        query,
        key,
        value,
        attention_mask=None,
        head_mask=None,
    ):

        # compute causal mask from causal mask buffer
        query_length, key_length = query.size(-2), key.size(-2)
        causal_mask = self.bias[:, :, key_length - query_length : key_length, :key_length]

        # Keep the attention weights computation in fp32 to avoid overflow issues
        query = query.to(torch.float32)
        key = key.to(torch.float32)

        attn_weights = torch.matmul(query, key.transpose(-1, -2))

        attn_weights = attn_weights / self.scale_attn
        attn_weights = torch.where(causal_mask, attn_weights, self.masked_bias.to(attn_weights.dtype))

        if attention_mask is not None:
            # Apply the attention mask
            attn_weights = attn_weights + attention_mask

        attn_weights = nn.Softmax(dim=-1)(attn_weights)
        attn_weights = attn_weights.to(value.dtype)
        attn_weights = self.attn_dropout(attn_weights)

        # Mask heads if we want to
        if head_mask is not None:
            attn_weights = attn_weights * head_mask

        attn_output = torch.matmul(attn_weights, value)

        return attn_output, attn_weights

    def forward(
        self,
        hidden_states,
        attention_mask=None,
        layer_past=None,
        head_mask=None,
        use_cache=False,
        output_attentions=False,
        position_ids= None
    ):

        qkv = self.qkv_proj(hidden_states)
        # TODO(enijkamp): factor out number of logical TPU-v3/v4 cores or make forward pass agnostic
        # mp_num = 4
        mp_num = 8
        qkv_split = qkv.reshape(qkv.shape[:-1] + (mp_num, -1))

        local_dim = self.head_dim * self.num_attention_heads // mp_num
        query, value, key = torch.split(qkv_split, local_dim, dim=-1)
        query = self._split_heads(query, self.num_attention_heads, self.head_dim, mp_num=mp_num)
        key = self._split_heads(key, self.num_attention_heads, self.head_dim, mp_num=mp_num)

        value = self._split_heads(value, self.num_attention_heads, self.head_dim, mp_num=mp_num)
        value = value.permute(0, 2, 1, 3)

        seq_len = key.shape[1] * 2 # for position ids greater than current
        offset = 0

        if layer_past is not None:
            offset = layer_past[0].shape[-2]
            seq_len += offset

        if self.rotary_dim is not None:
            k_rot = key[:, :, :, : self.rotary_dim]
            k_pass = key[:, :, :, self.rotary_dim :]

            q_rot = query[:, :, :, : self.rotary_dim]
            q_pass = query[:, :, :, self.rotary_dim :]
            if self.yarn:
                sincos = yarn(k_rot, seq_dim=1, seq_len=seq_len)
            else:
                sincos = fixed_pos_embedding(k_rot, 1, seq_len=seq_len)
            k_rot = apply_rotary_pos_emb(k_rot, sincos, offset=offset, position_ids=position_ids)
            q_rot = apply_rotary_pos_emb(q_rot, sincos, offset=offset, position_ids=position_ids)

            key = torch.cat([k_rot, k_pass], dim=-1)
            query = torch.cat([q_rot, q_pass], dim=-1)
        else:
            if self.yarn:
                sincos = yarn(k_rot, seq_dim=1, seq_len=seq_len)
            else:
                sincos = fixed_pos_embedding(key, 1, seq_len=seq_len)
            key = apply_rotary_pos_emb(key, sincos, offset=offset, position_ids=position_ids)
            query = apply_rotary_pos_emb(query, sincos, offset=offset, position_ids=position_ids)

        key = key.permute(0, 2, 1, 3)
        query = query.permute(0, 2, 1, 3)

        if layer_past is not None:
            past_key = layer_past[0]
            past_value = layer_past[1]
            key = torch.cat((past_key, key), dim=-2)
            value = torch.cat((past_value, value), dim=-2)

        if use_cache is True:
            present = (key, value)
        else:
            present = None

        # compute self-attention: V x Softmax(QK^T)
        attn_output, attn_weights = self._attn(query, key, value, attention_mask, head_mask)

        attn_output = self._merge_heads(attn_output, self.num_attention_heads, self.head_dim)

        attn_output = self.out_proj(attn_output)
        attn_output = self.resid_dropout(attn_output)

        outputs = (attn_output, present)
        if output_attentions:
            outputs += (attn_weights,)

        return outputs  # a, present, (attentions)


class ProGenMLP(nn.Module):
    def __init__(self, intermediate_size, config):  # in MLP: intermediate_size= 4 * embed_dim
        super().__init__()
        embed_dim = config.n_embd

        self.fc_in = nn.Linear(embed_dim, intermediate_size)
        self.fc_out = nn.Linear(intermediate_size, embed_dim)

        self.act = ACT2FN[config.activation_function]
        self.dropout = nn.Dropout(config.resid_pdrop)

    def forward(self, hidden_states):
        hidden_states = self.fc_in(hidden_states)
        hidden_states = self.act(hidden_states)
        hidden_states = self.fc_out(hidden_states)
        hidden_states = self.dropout(hidden_states)
        return hidden_states


class ProGenBlock(nn.Module):
    def __init__(self, config):
        super().__init__()
        inner_dim = config.n_inner if config.n_inner is not None else 4 * config.n_embd
        self.ln_1 = nn.LayerNorm(config.n_embd, eps=config.layer_norm_epsilon)
        self.attn = ProGenAttention(config)
        self.mlp = ProGenMLP(inner_dim, config)

    def forward(
        self,
        hidden_states,
        layer_past=None,
        attention_mask=None,
        head_mask=None,
        use_cache=False,
        output_attentions=False,
        position_ids=None,
    ):
        residual = hidden_states
        hidden_states = self.ln_1(hidden_states)
        attn_outputs = self.attn(
            hidden_states,
            layer_past=layer_past,
            attention_mask=attention_mask,
            head_mask=head_mask,
            use_cache=use_cache,
            output_attentions=output_attentions,
            position_ids=position_ids
        )
        attn_output = attn_outputs[0]  # output_attn: a, present, (attentions)
        outputs = attn_outputs[1:]

        feed_forward_hidden_states = self.mlp(hidden_states)
        hidden_states = attn_output + feed_forward_hidden_states + residual

        if use_cache:
            outputs = (hidden_states,) + outputs
        else:
            outputs = (hidden_states,) + outputs[1:]

        return outputs  # hidden_states, present, (attentions)


class ProGenPreTrainedModel(PreTrainedModel):
    """
    An abstract class to handle weights initialization and a simple interface for downloading and loading pretrained
    models.
    """

    config_class = ProGenConfig
    base_model_prefix = "transformer"
    supports_gradient_checkpointing = True
    is_parallelizable = True
    _no_split_modules = ["ProGenBlock"]
    def __init__(self, *inputs, **kwargs):
        super().__init__(*inputs, **kwargs)

    def _init_weights(self, module):
        """Initialize the weights."""
        if isinstance(module, (nn.Linear,)):
            # Slightly different from Mesh Transformer JAX which uses truncated_normal for initialization
            # cf https://github.com/pytorch/pytorch/pull/5617
            module.weight.data.normal_(mean=0.0, std=self.config.initializer_range)
            if module.bias is not None:
                module.bias.data.zero_()
        elif isinstance(module, nn.Embedding):
            module.weight.data.normal_(mean=0.0, std=self.config.initializer_range)
            if module.padding_idx is not None:
                module.weight.data[module.padding_idx].zero_()
        elif isinstance(module, nn.LayerNorm):
            module.bias.data.zero_()
            module.weight.data.fill_(1.0)

    def _set_gradient_checkpointing(self, module, value=False):
        if isinstance(module, ProGenModel):
            module.gradient_checkpointing = value

class ProGenModel(ProGenPreTrainedModel):
    def __init__(self, config):
        super().__init__(config)

        self.embed_dim = config.n_embd
        self.vocab_size = config.vocab_size
        self.wte = nn.Embedding(config.vocab_size, self.embed_dim)
        self.drop = nn.Dropout(config.embd_pdrop)
        self.h = nn.ModuleList([ProGenBlock(config) for _ in range(config.n_layer)])
        self.ln_f = nn.LayerNorm(self.embed_dim, eps=config.layer_norm_epsilon)
        self.rotary_dim = min(config.rotary_dim, config.n_ctx // config.num_attention_heads)

        self.gradient_checkpointing = False
        self.structure = StructureTransformer(**config.structure)
        
        self.init_weights()

        # Model parallel
        self.model_parallel = False
        self.device_map = None


    def parallelize(self, device_map=None):
        # Check validity of device_map
        self.device_map = (
            get_device_map(len(self.h), range(torch.cuda.device_count())) if device_map is None else device_map
        )
        assert_device_map(self.device_map, len(self.h))
        self.model_parallel = True
        self.first_device = "cpu" if "cpu" in self.device_map.keys() else "cuda:" + str(min(self.device_map.keys()))
        self.last_device = "cuda:" + str(max(self.device_map.keys()))
        self.wte = self.wte.to(self.first_device)
        # Load onto devices
        for k, v in self.device_map.items():
            for block in v:
                cuda_device = "cuda:" + str(k)
                self.h[block] = self.h[block].to(cuda_device)
        # ln_f to last
        self.ln_f = self.ln_f.to(self.last_device)


    def deparallelize(self):
        self.model_parallel = False
        self.device_map = None
        self.first_device = "cpu"
        self.last_device = "cpu"
        self.wte = self.wte.to("cpu")
        for index in range(len(self.h)):
            self.h[index] = self.h[index].to("cpu")
        self.ln_f = self.ln_f.to("cpu")
        torch.cuda.empty_cache()

    def get_input_embeddings(self):
        return self.wte

    def set_input_embeddings(self, new_embeddings):
        self.wte = new_embeddings

    def forward(
        self,
        input_ids=None,
        past_key_values=None,
        attention_mask=None,
        token_type_ids=None,
        position_ids=None,
        head_mask=None,
        inputs_embeds=None,
        query_embeds=None,
        use_cache=None,
        output_attentions=None,
        output_hidden_states=None,
        return_dict=None,
    ):
        if past_key_values is None:
            # structure encode will check if input_ids contains valid 
            # structure_embs: Tensor with size of batchsize * maxlen * width 
            # structure_mask: Tensor with size of batchsize * maxlen * 1
            # input_ids: new ids without structure path (ascii code)
            # clone for keeping original input_ids not change
            (structure_embs, structure_mask), input_ids = self.structure.encode(input_ids.clone())
            
        else:
            structure_embs = None
        
        output_attentions = output_attentions if output_attentions is not None else self.config.output_attentions
        output_hidden_states = (
            output_hidden_states if output_hidden_states is not None else self.config.output_hidden_states
        )
        use_cache = use_cache if use_cache is not None else self.config.use_cache
        return_dict = return_dict if return_dict is not None else self.config.use_return_dict

        if input_ids is not None and inputs_embeds is not None:
            raise ValueError("You cannot specify both input_ids and inputs_embeds at the same time")
        elif input_ids is not None:
            input_shape = input_ids.size()
            input_ids = input_ids.view(-1, input_shape[-1])
            batch_size = input_ids.shape[0]
        elif inputs_embeds is not None:
            input_shape = inputs_embeds.size()[:-1]
            batch_size = inputs_embeds.shape[0]
        else:
            raise ValueError("You have to specify either input_ids or inputs_embeds")

        device = input_ids.device if input_ids is not None else inputs_embeds.device

        # if token_type_ids is not None:
        #     token_type_ids = token_type_ids.view(-1, input_shape[-1])

        if past_key_values is None:
            past_length = 0
            past_key_values = tuple([None] * len(self.h))
        else:
            past_length = past_key_values[0][0].size(-2)



        # Attention mask.
        if attention_mask is not None:
            assert batch_size > 0, "batch_size has to be defined and > 0"
            attention_mask = attention_mask.view(batch_size, -1)
            # We create a 3D attention mask from a 2D tensor mask.
            # Sizes are [batch_size, 1, 1, to_seq_length]
            # So we can broadcast to [batch_size, num_heads, from_seq_length, to_seq_length]
            # this attention mask is more simple than the triangular masking of causal attention
            # used in OpenAI GPT, we just need to prepare the broadcast dimension here.
            attention_mask = attention_mask[:, None, None, :]

            # Since attention_mask is 1.0 for positions we want to attend and 0.0 for
            # masked positions, this operation will create a tensor which is 0.0 for
            # positions we want to attend and -10000.0 for masked positions.
            # Since we are adding it to the raw scores before the softmax, this is
            # effectively the same as removing these entirely.
            attention_mask = attention_mask.to(dtype=self.dtype)  # fp16 compatibility
            attention_mask = (1.0 - attention_mask) * -10000.0

        # Prepare head mask if needed
        # 1.0 in head_mask indicate we keep the head
        # attention_probs has shape bsz x num_attention_heads x N x N
        # head_mask has shape n_layer x batch x num_attention_heads x N x N
        head_mask = self.get_head_mask(head_mask, self.config.n_layer)

        if inputs_embeds is None:
            inputs_embeds = self.wte(input_ids.int())
        
        if query_embeds is not None:
            inputs_embeds = torch.cat([query_embeds, inputs_embeds], dim=1)
            input_shape = inputs_embeds.size()[:-1]
        
        if structure_embs is not None:
            try:
                inputs_embeds_mask = (input_ids == 1).unsqueeze(-1) # bos to as structure placeholder
                inputs_embeds = inputs_embeds.to(structure_embs.dtype) # change dtype manually, autocast won't change it.
                inputs_embeds = inputs_embeds.masked_scatter(inputs_embeds_mask, structure_embs.masked_select(structure_mask.unsqueeze(-1)))
                input_shape = inputs_embeds.size()[:-1]
            except:
                torch.save(input_ids, f'input_ids_{inputs_embeds.device}.pt')
                torch.save(inputs_embeds, f'inputs_embeds_{inputs_embeds.device}.pt')
                torch.save(structure_embs, f'structure_embs_{inputs_embeds.device}.pt')
                

        if position_ids is not None:
            position_ids = position_ids.view(-1, input_shape[-1])
        
        if position_ids is None:
            if any(attention_mask[:, ..., 0] < 0): # padding left
                position_ids = ((attention_mask >= 0).cumsum(dim=-1).squeeze() - 1).clamp(min=0)
                position_ids = position_ids[:, past_length:past_length + input_shape[-1]]
            else:
                position_ids = torch.arange(past_length, input_shape[-1] + past_length, dtype=torch.long, device=device)
                position_ids = position_ids.unsqueeze(0).view(-1, input_shape[-1])

        hidden_states = inputs_embeds

        # disable token_type_ids
        # if token_type_ids is not None:
        #     token_type_embeds = self.wte(token_type_ids)
        #     hidden_states = hidden_states + token_type_embeds

        hidden_states = self.drop(hidden_states)

        output_shape = input_shape + (hidden_states.size(-1),)

        presents = () if use_cache else None
        all_self_attentions = () if output_attentions else None
        all_hidden_states = () if output_hidden_states else None
        for i, (block, layer_past) in enumerate(zip(self.h, past_key_values)):

            # Model parallel
            if self.model_parallel:
                torch.cuda.set_device(hidden_states.device)
                # Ensure layer_past is on same device as hidden_states (might not be correct)
                if layer_past is not None:
                    layer_past = tuple(past_state.to(hidden_states.device) for past_state in layer_past)
                # Ensure that attention_mask is always on the same device as hidden_states
                if attention_mask is not None:
                    attention_mask = attention_mask.to(hidden_states.device)
                if isinstance(head_mask, torch.Tensor):
                    head_mask = head_mask.to(hidden_states.device)
            if output_hidden_states:
                all_hidden_states = all_hidden_states + (hidden_states,)

            if self.gradient_checkpointing and self.training:

                if use_cache:
                    # logger.warning(
                    #     "`use_cache=True` is incompatible with `config.gradient_checkpointing=True`. Setting "
                    #     "`use_cache=False`..."
                    # )
                    use_cache = False

                def create_custom_forward(module):
                    def custom_forward(*inputs):
                        # None for past_key_value
                        return module(*inputs, use_cache, output_attentions)

                    return custom_forward

                outputs = torch.utils.checkpoint.checkpoint(
                    create_custom_forward(block),
                    hidden_states,
                    None,
                    attention_mask,
                    head_mask[i],
                )
            else:
                outputs = block(
                    hidden_states,
                    layer_past=layer_past,
                    attention_mask=attention_mask,
                    head_mask=head_mask[i],
                    use_cache=use_cache,
                    output_attentions=output_attentions,
                    position_ids=position_ids
                )

            hidden_states = outputs[0]
            if use_cache is True:
                presents = presents + (outputs[1],)

            if output_attentions:
                all_self_attentions = all_self_attentions + (outputs[2 if use_cache else 1],)

            # Model Parallel: If it's the last layer for that device, put things on the next device
            if self.model_parallel:
                for k, v in self.device_map.items():
                    if i == v[-1] and "cuda:" + str(k) != self.last_device:
                        hidden_states = hidden_states.to("cuda:" + str(k + 1))

        hidden_states = self.ln_f(hidden_states)

        hidden_states = hidden_states.view(*output_shape)
        # Add last hidden state
        if output_hidden_states:
            all_hidden_states = all_hidden_states + (hidden_states,)

        if not return_dict:
            return tuple(v for v in [hidden_states, presents, all_hidden_states, all_self_attentions] if v is not None)

        return BaseModelOutputWithPast(
            last_hidden_state=hidden_states,
            past_key_values=presents,
            hidden_states=all_hidden_states,
            attentions=all_self_attentions,
        )


class ProGenForCausalLM(ProGenPreTrainedModel):
    _keys_to_ignore_on_load_missing = [r"h\.\d+\.attn\.masked_bias", r"h\.\d+\.attn\.bias", r"lm_head\.weight"]

    def __init__(self, config):
        super().__init__(config)
        self.transformer = ProGenModel(config)
        self.lm_head = nn.Linear(config.n_embd, config.vocab_size)
        self.init_weights()

        # Model parallel
        self.model_parallel = False
        self.device_map = None

    def parallelize(self, device_map=None):
        self.device_map = (
            get_device_map(len(self.transformer.h), range(torch.cuda.device_count()))
            if device_map is None
            else device_map
        )
        assert_device_map(self.device_map, len(self.transformer.h))
        self.transformer.parallelize(self.device_map)
        self.lm_head = self.lm_head.to(self.transformer.first_device)
        self.model_parallel = True

    def deparallelize(self):
        self.transformer.deparallelize()
        self.transformer = self.transformer.to("cpu")
        self.lm_head = self.lm_head.to("cpu")
        self.model_parallel = False
        torch.cuda.empty_cache()

    def get_output_embeddings(self):
        return self.lm_head

    def set_output_embeddings(self, new_embeddings):
        self.lm_head = new_embeddings

    def _update_model_kwargs_for_generation(self, *args, **kwargs):
        model_kwargs = super()._update_model_kwargs_for_generation(*args, **kwargs)

        position_ids = model_kwargs.get("position_ids", None)
        attention_mask = model_kwargs.get("attention_mask", None)
        use_cache = model_kwargs.get("use_cache", False)
        
        if attention_mask is not None and position_ids is not None:
            # create position_ids on the fly for batch generation
            position_ids = position_ids

            # if past_key_values:
            last_position = position_ids[:, -1:] # all position in a batch should be the sanme
            current_position = last_position + 1
            if not use_cache:
                position_ids = torch.concat([position_ids, current_position], dim=-1)
            else:
                position_ids = current_position

        else:
            position_ids = None
        model_kwargs['position_ids'] = position_ids
        return model_kwargs

    def prepare_inputs_for_generation(self, input_ids, past_key_values=None, **kwargs):
        token_type_ids = kwargs.get("token_type_ids", None)
        use_cache = kwargs.get("use_cache", False)
        # only last token for inputs_ids if past is defined in kwargs
        if past_key_values:
            input_ids = input_ids[:, -1].unsqueeze(-1)
            if token_type_ids is not None:
                token_type_ids = token_type_ids[:, -1].unsqueeze(-1)

        attention_mask = kwargs.get("attention_mask", None)
        position_ids = kwargs.get("position_ids", None)

        # if attention_mask is not None and position_ids is not None:
        #     # create position_ids on the fly for batch generation
        #     position_ids = position_ids
        #     if input_ids[0, -1] != 3:
        #     # if past_key_values:
        #         last_position = position_ids[:, -1:] # all position in a batch should be the sanme
        #         current_position = last_position + 1
        #         if not use_cache:
        #             position_ids = torch.concat([position_ids, current_position], dim=-1)
        #         else:
        #             position_ids = current_position

        # else:
        #     position_ids = None
        return {
            "input_ids": input_ids,
            "past_key_values": past_key_values,
            "use_cache": use_cache,
            "position_ids": position_ids,
            "attention_mask": attention_mask,
            "token_type_ids": token_type_ids,
        }

    # def prepare_inputs_for_generation(
    #     self, input_ids, past_key_values=None, attention_mask=None, inputs_embeds=None, **kwargs
    # ):
    #     if past_key_values:
    #         input_ids = input_ids[:, -1:]

    #     position_ids = kwargs.get("position_ids")
    #     if position_ids is not None:
    #         last_position = position_ids[:, -1:] # all position in a batch should be the sanme
    #         current_position = last_position + 1
    #         position_ids = torch.concat([position_ids, current_position], dim=-1)

    #     # if `inputs_embeds` are passed, we only want to use them in the 1st generation step
    #     if inputs_embeds is not None and past_key_values is None:
    #         model_inputs = {"inputs_embeds": inputs_embeds}
    #     else:
    #         model_inputs = {"input_ids": input_ids}

    #     model_inputs.update(
    #         {
    #             "past_key_values": past_key_values,
    #             "use_cache": kwargs.get("use_cache"),
    #             "attention_mask": attention_mask,
    #             "position_ids": position_ids
    #         }
    #     )
    #     return model_inputs

    def forward(
        self,
        input_ids=None,
        past_key_values=None,
        attention_mask=None,
        token_type_ids=None,
        position_ids=None,
        head_mask=None,
        inputs_embeds=None,
        labels=None,
        use_cache=None,
        query_embeds = None,
        output_attentions=None,
        output_hidden_states=None,
        return_dict=None,
    ):
        r"""
        labels (:obj:`torch.LongTensor` of shape :obj:`(batch_size, sequence_length)`, `optional`):
            Labels for language modeling. Note that the labels **are shifted** inside the model, i.e. you can set
            ``labels = input_ids`` Indices are selected in ``[-100, 0, ..., config.vocab_size]`` All labels set to
            ``-100`` are ignored (masked), the loss is only computed for labels in ``[0, ..., config.vocab_size]``
        """
        return_dict = return_dict if return_dict is not None else self.config.use_return_dict

        transformer_outputs = self.transformer(
            input_ids,
            past_key_values=past_key_values,
            attention_mask=attention_mask,
            token_type_ids=token_type_ids,
            position_ids=position_ids,
            head_mask=head_mask,
            inputs_embeds=inputs_embeds,
            query_embeds=query_embeds,
            use_cache=use_cache,
            output_attentions=output_attentions,
            output_hidden_states=output_hidden_states,
            return_dict=return_dict,
        )
        hidden_states = transformer_outputs[0]

        # Set device for model parallelism
        if self.model_parallel:
            torch.cuda.set_device(self.transformer.first_device)
            hidden_states = hidden_states.to(self.lm_head.weight.device)

        # make sure sampling in fp16 works correctly and
        # compute loss in fp32 to match with mesh-tf version
        # https://github.com/EleutherAI/gpt-neo/blob/89ce74164da2fb16179106f54e2269b5da8db333/models/gpt2/gpt2.py#L179
        lm_logits = self.lm_head(hidden_states).to(torch.float32)

        loss = None
        if labels is not None:
            # Shift so that tokens < n predict n
            shift_logits = lm_logits[..., :-1, :].contiguous()
            shift_labels = labels[..., 1:].contiguous()
            # Flatten the tokens
            loss_fct = CrossEntropyLoss()
            loss = loss_fct(shift_logits.view(-1, shift_logits.size(-1)), shift_labels.view(-1))

            loss = loss.to(hidden_states.dtype)

        if not return_dict:
            output = (lm_logits,) + transformer_outputs[1:]
            return ((loss,) + output) if loss is not None else output

        return CausalLMOutputWithPast(
            loss=loss,
            logits=lm_logits,
            past_key_values=transformer_outputs.past_key_values,
            hidden_states=transformer_outputs.hidden_states,
            attentions=transformer_outputs.attentions,
        )

    @staticmethod
    def _reorder_cache(past: Tuple[Tuple[torch.Tensor]], beam_idx: torch.Tensor) -> Tuple[Tuple[torch.Tensor]]:
        """
        This function is used to re-order the :obj:`past_key_values` cache if
        :meth:`~transformers.PretrainedModel.beam_search` or :meth:`~transformers.PretrainedModel.beam_sample` is
        called. This is required to match :obj:`past_key_values` with the correct beam_idx at every generation step.
        """
        return tuple(
            tuple(past_state.index_select(0, beam_idx.to(past_state.device)) for past_state in layer_past)
            for layer_past in past
        )

    # def generate(self, inputs: Tensor | None = None, generation_config: GenerationConfig | None = None, logits_processor: LogitsProcessorList | None = None, stopping_criteria: StoppingCriteriaList | None = None, prefix_allowed_tokens_fn: Callable[[int, Tensor], List[int]] | None = None, synced_gpus: bool | None = None, assistant_model: PreTrainedModel | None = None, streamer: BaseStreamer | None = None, negative_prompt_ids: Tensor | None = None, negative_prompt_attention_mask: Tensor | None = None, **kwargs) -> GenerateOutput | LongTensor:
    #     return super().generate(inputs, generation_config, logits_processor, stopping_criteria, prefix_allowed_tokens_fn, synced_gpus, assistant_model, streamer, negative_prompt_ids, negative_prompt_attention_mask, **kwargs)