repo stringlengths 1 99 | file stringlengths 13 215 | code stringlengths 12 59.2M | file_length int64 12 59.2M | avg_line_length float64 3.82 1.48M | max_line_length int64 12 2.51M | extension_type stringclasses 1
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|---|---|---|---|---|---|---|
bonito | bonito-master/bonito/reader.py | """
Bonito Read Utils
"""
from glob import iglob
from collections import OrderedDict
from importlib import import_module
import torch
import numpy as np
from scipy.signal import find_peaks
__formats__ = ["fast5", "pod5"]
# Normalisation parameters for kit 14 DNA
# Different parameters can be specified in the 'norm... | 4,550 | 29.543624 | 109 | py |
bonito | bonito-master/bonito/training.py | """
Bonito train
"""
import math
import os
import re
from glob import glob
from functools import partial
from time import perf_counter
from collections import OrderedDict
from datetime import datetime
from bonito.schedule import linear_warmup_cosine_decay
from bonito.util import accuracy, decode_ref, permute, concat,... | 10,481 | 38.258427 | 129 | py |
bonito | bonito-master/bonito/data.py | import importlib
import os
from pathlib import Path
import numpy as np
from torch.utils.data import DataLoader
class ChunkDataSet:
def __init__(self, chunks, targets, lengths):
self.chunks = np.expand_dims(chunks, axis=1)
self.targets = targets
self.lengths = lengths
def __getitem__(... | 2,868 | 32.752941 | 86 | py |
bonito | bonito-master/bonito/nn.py | """
Bonito nn modules.
"""
import torch
from torch.nn import Module
from torch.nn.init import orthogonal_
from torch.nn.utils.fusion import fuse_conv_bn_eval
layers = {}
def register(layer):
layer.name = layer.__name__.lower()
layers[layer.name] = layer
return layer
register(torch.nn.ReLU)
register(t... | 11,194 | 30.713881 | 133 | py |
bonito | bonito-master/bonito/util.py | """
Bonito utils
"""
import os
import re
import sys
import random
from glob import glob
from itertools import groupby
from operator import itemgetter
from importlib import import_module
from collections import deque, defaultdict, OrderedDict
from torch.utils.data import DataLoader
import toml
import torch
import koi.... | 13,291 | 30.49763 | 134 | py |
bonito | bonito-master/bonito/schedule.py | import math
import numpy as np
from torch.optim.lr_scheduler import LambdaLR
def linear_warmup_cosine_decay(end_ratio=0.01, warmup_steps=500, **kwargs):
"""
Linear warmup, cosine decay scheduler
"""
return lambda optimizer, train_loader, epochs, last_epoch: func_scheduler(
optimizer=optimizer... | 3,330 | 26.528926 | 100 | py |
bonito | bonito-master/bonito/ctc/basecall.py | """
Bonito basecall
"""
import torch
import numpy as np
from functools import partial
from bonito.multiprocessing import process_map
from bonito.util import mean_qscore_from_qstring
from bonito.util import chunk, stitch, batchify, unbatchify, permute
def basecall(model, reads, beamsize=5, chunksize=0, overlap=0, ba... | 2,018 | 31.564516 | 111 | py |
bonito | bonito-master/bonito/ctc/model.py | """
Bonito Model template
"""
import numpy as np
from bonito.nn import Permute, layers
import torch
from torch.nn.functional import log_softmax, ctc_loss
from torch.nn import Module, ModuleList, Sequential, Conv1d, BatchNorm1d, Dropout
from fast_ctc_decode import beam_search, viterbi_search
class Model(Module):
... | 7,110 | 33.1875 | 155 | py |
bonito | bonito-master/bonito/cli/export.py | """
Bonito Export
"""
import io
import os
import re
import sys
import json
import toml
import torch
import bonito
import hashlib
import numpy as np
from glob import glob
import base64
from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter
from bonito.nn import fuse_bn_
from bonito.util import _load_model... | 6,898 | 35.696809 | 150 | py |
bonito | bonito-master/bonito/cli/evaluate.py | """
Bonito model evaluator
"""
import os
import time
import torch
import numpy as np
from itertools import starmap
from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter
from pathlib import Path
from bonito.data import load_numpy, load_script
from bonito.util import accuracy, poa, decode_ref, half_support... | 3,647 | 31.283186 | 102 | py |
bonito | bonito-master/bonito/cli/train.py | #!/usr/bin/env python3
"""
Bonito training.
"""
import os
from argparse import ArgumentParser
from argparse import ArgumentDefaultsHelpFormatter
from pathlib import Path
from importlib import import_module
from bonito.data import load_numpy, load_script
from bonito.util import __models__, default_config, default_dat... | 4,704 | 35.472868 | 91 | py |
bonito | bonito-master/bonito/crf/basecall.py | """
Bonito CRF basecalling
"""
import torch
import numpy as np
from koi.decode import beam_search, to_str
from bonito.multiprocessing import thread_iter
from bonito.util import chunk, stitch, batchify, unbatchify, half_supported
def stitch_results(results, length, size, overlap, stride, reverse=False):
"""
... | 2,632 | 30.345238 | 119 | py |
bonito | bonito-master/bonito/crf/model.py | """
Bonito CTC-CRF Model.
"""
import torch
import numpy as np
import koi
from koi.ctc import SequenceDist, Max, Log, semiring
from koi.ctc import logZ_cu, viterbi_alignments, logZ_cu_sparse, bwd_scores_cu_sparse, fwd_scores_cu_sparse
from bonito.nn import Module, Convolution, LinearCRFEncoder, Serial, Permute, layer... | 8,951 | 40.831776 | 191 | py |
ReAgent | ReAgent-master/reagent/ope/utils.py | #!/usr/bin/env python3
import math
from collections import OrderedDict
from typing import Sequence, Union
import numpy as np
import torch
DEFAULT_MIN = float("-inf")
DEFAULT_MAX = float("inf")
def convert_to_one_hots(a, num_classes: int, dtype=torch.int, device=None):
"""
Convert class index array (num_sa... | 2,743 | 26.717172 | 88 | py |
ReAgent | ReAgent-master/reagent/ope/estimators/slate_estimators.py | #!/usr/bin/env python3
import logging
import math
import random
import time
from abc import ABC, abstractmethod
from dataclasses import dataclass
from typing import (
Iterable,
Mapping,
MutableMapping,
MutableSequence,
Optional,
Sequence,
Set,
Tuple,
Union,
)
import numpy as np
imp... | 54,387 | 34.225389 | 90 | py |
ReAgent | ReAgent-master/reagent/ope/estimators/sequential_estimators.py | #!/usr/bin/env python3
import copy
import logging
import random
import time
import typing
from abc import ABC, abstractmethod
from copy import deepcopy
from dataclasses import dataclass
from enum import Enum
from functools import reduce
from itertools import count, zip_longest
from typing import Callable, Dict, Iterab... | 28,267 | 34.964377 | 103 | py |
ReAgent | ReAgent-master/reagent/ope/estimators/types.py | #!/usr/bin/env python3
import logging
import pickle
from abc import ABC, abstractmethod
from copy import deepcopy
from dataclasses import dataclass
from typing import Generic, Mapping, Optional, Sequence, Tuple, TypeVar, Union
import numpy as np
import torch
from torch import Tensor
def is_array(obj):
return is... | 18,646 | 30.712585 | 88 | py |
ReAgent | ReAgent-master/reagent/ope/estimators/contextual_bandits_estimators.py | #!/usr/bin/env python3
import logging
import time
from abc import ABC, abstractmethod
from dataclasses import dataclass
from typing import Optional, Sequence, Tuple, Union
import numpy as np
import torch
from reagent.ope.estimators.estimator import Estimator, EstimatorResult
from reagent.ope.estimators.types import (... | 23,956 | 34.971471 | 117 | py |
ReAgent | ReAgent-master/reagent/ope/estimators/estimator.py | #!/usr/bin/env python3
import logging
import math
import pickle
import tempfile
from abc import ABC, abstractmethod
from dataclasses import dataclass, field
from multiprocessing import Pool
from typing import Iterable, List, Mapping, Optional, Tuple, Union
import torch
from reagent.evaluation.cpe import bootstrapped_... | 9,051 | 30.430556 | 92 | py |
ReAgent | ReAgent-master/reagent/ope/test/mslr_slate.py | #!/usr/bin/env python3
import argparse
import itertools
import json
import logging
import os
import pickle
import random
import sys
import time
from collections import OrderedDict
from typing import Iterable, List, Optional, Tuple
import numpy as np
import torch
import torch.multiprocessing as mp
from reagent.ope.est... | 20,558 | 32.648118 | 111 | py |
ReAgent | ReAgent-master/reagent/ope/test/cartpole.py | #!/usr/bin/env python3
import logging
import gym
import torch
from reagent.ope.estimators.sequential_estimators import (
Action,
ActionDistribution,
ActionSpace,
IPSEstimator,
Model,
NeuralDualDICE,
RandomRLPolicy,
RewardProbability,
RLEstimatorInput,
RLPolicy,
State,
St... | 8,083 | 31.079365 | 124 | py |
ReAgent | ReAgent-master/reagent/ope/test/gridworld.py | #!/usr/bin/env python3
import logging
import random
from typing import Iterable, Optional, Sequence, Tuple
import numpy as np
import torch
from reagent.ope.estimators.sequential_estimators import (
DMEstimator,
DoublyRobustEstimator,
EpsilonGreedyRLPolicy,
IPSEstimator,
MAGICEstimator,
NeuralD... | 13,049 | 30.90709 | 88 | py |
ReAgent | ReAgent-master/reagent/ope/test/multiclass_bandits.py | #!/usr/bin/env python3
import argparse
import json
import logging
import os
import random
import sys
from dataclasses import dataclass
from pathlib import PurePath
from typing import Iterable, Tuple
import numpy as np
import pandas as pd
import torch
from reagent.ope.estimators.contextual_bandits_estimators import (
... | 11,560 | 33.927492 | 88 | py |
ReAgent | ReAgent-master/reagent/ope/test/yandex_web_search.py | #!/usr/bin/env python3
import argparse
import json
import logging
import os
import pickle
import random
import sys
import time
from typing import (
Dict,
Iterable,
List,
Mapping,
MutableMapping,
Optional,
Sequence,
Tuple,
Union,
)
import numpy as np
import torch
import torch.multip... | 25,761 | 35.855508 | 90 | py |
ReAgent | ReAgent-master/reagent/ope/test/unit_tests/test_slate_estimators.py | #!/usr/bin/env python3
import random
import unittest
import torch
from reagent.ope.estimators.slate_estimators import (
DCGSlateMetric,
NDCGSlateMetric,
Slate,
SlateItem,
SlateItemProbabilities,
SlateItemValues,
SlateSlotItemProbabilities,
SlateSlots,
)
class TestEstimator(unittest.T... | 2,939 | 38.72973 | 79 | py |
ReAgent | ReAgent-master/reagent/ope/test/unit_tests/test_types.py | #!/usr/bin/env python3
import unittest
from typing import Tuple, Union
import numpy as np
import torch
from reagent.ope.estimators.types import (
ActionDistribution as Distribution,
TypeWrapper,
Values,
)
class TestTypes(unittest.TestCase):
TestType = Union[int, Tuple[int], float, Tuple[float], np.n... | 13,486 | 38.667647 | 86 | py |
ReAgent | ReAgent-master/reagent/ope/test/unit_tests/test_contextual_bandit_estimators.py | #!/usr/bin/env python3
import random
import unittest
import numpy as np
import torch
from reagent.ope.estimators.contextual_bandits_estimators import (
Action,
ActionDistribution,
ActionSpace,
BanditsEstimatorInput,
DMEstimator,
DoublyRobustEstimator,
IPSEstimator,
LogSample,
Model... | 3,772 | 34.933333 | 85 | py |
ReAgent | ReAgent-master/reagent/ope/test/unit_tests/test_utils.py | #!/usr/bin/env python3
import unittest
import numpy as np
import torch
from reagent.ope.utils import Clamper, RunningAverage
class TestUtils(unittest.TestCase):
def test_running_average(self):
ra = RunningAverage()
ra.add(1.0).add(2.0).add(3.0).add(4.0)
self.assertEqual(ra.count, 4)
... | 1,326 | 30.595238 | 87 | py |
ReAgent | ReAgent-master/reagent/ope/datasets/logged_dataset.py | #!/usr/bin/env python3
from abc import ABC, abstractmethod
from dataclasses import dataclass
import torch
class BanditsDataset(ABC):
"""
Base class for logged, aka behavior, dataset
"""
@abstractmethod
def __len__(self) -> int:
"""
Returns:
length of the dataset
... | 1,441 | 17.727273 | 56 | py |
ReAgent | ReAgent-master/reagent/ope/trainers/linear_trainers.py | #!/usr/bin/env python3
import logging
import math
import time
from typing import Optional
import numpy as np
import torch
from reagent.ope.estimators.types import PredictResults, Trainer, TrainingData
from sklearn.linear_model import Lasso, LogisticRegression, SGDClassifier
from sklearn.metrics import accuracy_score,... | 12,799 | 35.571429 | 85 | py |
ReAgent | ReAgent-master/reagent/ope/trainers/rl_tabular_trainers.py | #!/usr/bin/env python3
import pickle
from functools import reduce
from typing import List, Mapping, Sequence
import torch
from reagent.ope.estimators.sequential_estimators import (
Model,
RLPolicy,
State,
ValueFunction,
)
from reagent.ope.estimators.types import Action, ActionDistribution, ActionSpace... | 13,359 | 34.157895 | 88 | py |
ReAgent | ReAgent-master/reagent/mab/ucb.py | import math
from abc import ABC, abstractmethod
from typing import Union, Optional, List
import torch
from torch import Tensor
def _get_arm_indices(
ids_of_all_arms: List[Union[str, int]], ids_of_arms_in_batch: List[Union[str, int]]
) -> List[int]:
arm_idxs = []
for i in ids_of_arms_in_batch:
try... | 12,188 | 34.85 | 143 | py |
ReAgent | ReAgent-master/reagent/gym/utils.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
import logging
import random
from typing import Dict, List, Optional
import gym
import numpy as np
import pandas as pd
import torch # @manual
import torch.nn.functional as F
from gym import spaces
from reagent.core.paramet... | 15,498 | 36.167866 | 88 | py |
ReAgent | ReAgent-master/reagent/gym/types.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
# Please DO NOT import gym in here. We might have installation without gym depending on
# this module for typing
from abc import ABC, abstractmethod
from dataclasses import asdict, dataclass, field, fields
from typing impor... | 4,633 | 30.52381 | 88 | py |
ReAgent | ReAgent-master/reagent/gym/preprocessors/default_preprocessors.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
""" Get default preprocessors for training time. """
import logging
from typing import List, Optional, Tuple
import numpy as np
import reagent.core.types as rlt
import torch
import torch.nn.functional as F
from gym import ... | 4,247 | 32.714286 | 88 | py |
ReAgent | ReAgent-master/reagent/gym/preprocessors/trainer_preprocessor.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
""" Get default preprocessors for training time. """
import inspect
import logging
from typing import Dict, Optional
import gym
import numpy as np
import reagent.core.types as rlt
import torch
import torch.nn.functional as... | 18,178 | 36.637681 | 88 | py |
ReAgent | ReAgent-master/reagent/gym/envs/oracle_pvm.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
import logging
from collections import OrderedDict
from typing import Callable, Dict, List
import gym
import numpy as np
import reagent.core.types as rlt
import torch
from reagent.core.dataclasses import dataclass
from reag... | 6,305 | 35.034286 | 100 | py |
ReAgent | ReAgent-master/reagent/gym/envs/changing_arms.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
"""
Traditional MAB setup has sequence length = 1 always. In this setup, the
distributions of the arms rewards changes every round, and the agent is presented
with some information and control about how the arms will change.... | 10,024 | 34.9319 | 86 | py |
ReAgent | ReAgent-master/reagent/gym/envs/gym.py | #!/usr/bin/env python3
import logging
from typing import Optional, Tuple
import gym
import numpy as np
import reagent.core.types as rlt
import torch
from gym import spaces
from gym_minigrid.wrappers import ReseedWrapper
from reagent.core.dataclasses import dataclass
from reagent.gym.envs.env_wrapper import EnvWrapper... | 1,987 | 33.275862 | 86 | py |
ReAgent | ReAgent-master/reagent/gym/envs/env_wrapper.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
import abc
import logging
from typing import Callable, Optional
import gym
import numpy as np
import reagent.core.types as rlt
import torch
from gym import spaces
from reagent.core.dataclasses import dataclass
from reagent.... | 5,302 | 35.572414 | 88 | py |
ReAgent | ReAgent-master/reagent/gym/envs/pomdp/string_game_v1.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
"""
A game with a stochastic length of the MDP but no longer than 3.
An agent can choose one character to reveal (either "A" or "B") as the action,
and the next state is exactly the action just taken (i.e., the transition
fu... | 4,664 | 33.051095 | 91 | py |
ReAgent | ReAgent-master/reagent/gym/envs/pomdp/state_embed_env.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
"""
This file shows an example of using embedded states to feed to RL models in
partially observable environments (POMDPs). Embedded states are generated by a world
model which learns how to encode past n observations into a ... | 4,927 | 38.424 | 86 | py |
ReAgent | ReAgent-master/reagent/gym/envs/pomdp/string_game.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
"""
The agent can observe a character at one time. But the
reward is given based on last n (n>1) steps' observation (a string).
In this environment, the agent can observe a character ("A", "B") at
each time step, but the rewa... | 4,391 | 31.533333 | 80 | py |
ReAgent | ReAgent-master/reagent/gym/policies/predictor_policies.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
from typing import Optional, Tuple, Union
import numpy as np
import reagent.core.types as rlt
import torch
from reagent.core.fb_checker import IS_FB_ENVIRONMENT
from reagent.core.parameters import RLParameters
from reagent.... | 5,542 | 38.592857 | 86 | py |
ReAgent | ReAgent-master/reagent/gym/policies/policy.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
from typing import Any, Optional
import reagent.core.types as rlt
import torch
from reagent.gym.types import Sampler, Scorer
class Policy:
def __init__(self, scorer: Scorer, sampler: Sampler):
"""
The ... | 1,245 | 31.789474 | 77 | py |
ReAgent | ReAgent-master/reagent/gym/policies/random_policies.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
from typing import List, Optional
import gym
import numpy as np
import reagent.core.types as rlt
import torch
import torch.nn.functional as F
from reagent.core.parameters import CONTINUOUS_TRAINING_ACTION_RANGE
from reagent... | 5,717 | 38.434483 | 88 | py |
ReAgent | ReAgent-master/reagent/gym/policies/scorers/slate_q_scorer.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
import reagent.core.types as rlt
import torch
import torch.nn.functional as F
from reagent.gym.types import Scorer
from reagent.models.base import ModelBase
def slate_q_scorer(num_candidates: int, q_network: ModelBase) -> ... | 1,838 | 31.839286 | 86 | py |
ReAgent | ReAgent-master/reagent/gym/policies/scorers/continuous_scorer.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
import reagent.core.types as rlt
import torch
from reagent.gym.types import GaussianSamplerScore, Scorer
from reagent.models.base import ModelBase
def sac_scorer(actor_network: ModelBase) -> Scorer:
@torch.no_grad()
... | 699 | 34 | 83 | py |
ReAgent | ReAgent-master/reagent/gym/policies/scorers/discrete_scorer.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
from typing import Optional, Tuple
import numpy as np
import reagent.core.types as rlt
import torch
from reagent.gym.preprocessors.trainer_preprocessor import get_possible_actions_for_gym
from reagent.gym.types import Score... | 3,740 | 32.106195 | 87 | py |
ReAgent | ReAgent-master/reagent/gym/policies/samplers/continuous_sampler.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
import reagent.core.types as rlt
import torch
from reagent.gym.types import GaussianSamplerScore, Sampler
class GaussianSampler(Sampler):
def __init__(self, actor_network):
self.actor_network = actor_network
... | 2,378 | 41.482143 | 87 | py |
ReAgent | ReAgent-master/reagent/gym/policies/samplers/top_k_sampler.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
import reagent.core.types as rlt
import torch
from reagent.gym.types import Sampler
class TopKSampler(Sampler):
def __init__(self, k: int):
self.k = k
def sample_action(self, scores: torch.Tensor) -> rlt.... | 634 | 27.863636 | 83 | py |
ReAgent | ReAgent-master/reagent/gym/policies/samplers/discrete_sampler.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
import reagent.core.types as rlt
import torch
import torch.nn.functional as F
from reagent.gym.types import Sampler
from reagent.models.dqn import INVALID_ACTION_CONSTANT
class SoftmaxActionSampler(Sampler):
"""
S... | 7,223 | 37.425532 | 101 | py |
ReAgent | ReAgent-master/reagent/gym/datasets/replay_buffer_dataset.py | #!/usr/bin/env python3
import logging
from typing import Optional, Callable
import torch
from reagent.gym.agents.agent import Agent
from reagent.gym.envs import EnvWrapper
from reagent.gym.preprocessors import (
make_replay_buffer_inserter,
make_replay_buffer_trainer_preprocessor,
)
from reagent.gym.types imp... | 6,916 | 33.242574 | 90 | py |
ReAgent | ReAgent-master/reagent/gym/datasets/episodic_dataset.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
import logging
from typing import Optional
import torch
from reagent.gym.agents.agent import Agent
from reagent.gym.envs.gym import Gym
from reagent.gym.runners.gymrunner import run_episode
logger = logging.getLogger(__na... | 1,020 | 23.902439 | 72 | py |
ReAgent | ReAgent-master/reagent/gym/agents/agent.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
from typing import Any, Optional, Tuple, Union
import numpy as np
import torch
from reagent.gym.envs.env_wrapper import EnvWrapper
from reagent.gym.policies.policy import Policy
from reagent.gym.policies.random_policies imp... | 4,248 | 31.435115 | 79 | py |
ReAgent | ReAgent-master/reagent/gym/tests/test_gym_offline.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
import logging
import os
import pprint
import unittest
import uuid
import numpy as np
import pytest
import pytorch_lightning as pl
import torch
from parameterized import parameterized
from reagent.gym.agents.agent import Age... | 4,868 | 30.412903 | 83 | py |
ReAgent | ReAgent-master/reagent/gym/tests/test_gym.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
import logging
import os
import pprint
import unittest
import uuid
from typing import Optional
import numpy as np
import pytest
import pytorch_lightning as pl
import torch
from parameterized import parameterized
from reagent... | 11,439 | 33.251497 | 112 | py |
ReAgent | ReAgent-master/reagent/gym/tests/test_world_model.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
import logging
import os
import unittest
from typing import Dict, List, Optional
import gym
import numpy as np
import reagent.core.types as rlt
import torch
from reagent.evaluation.world_model_evaluator import (
FeatureI... | 15,345 | 35.451306 | 88 | py |
ReAgent | ReAgent-master/reagent/gym/tests/preprocessors/test_default_preprocessors.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
import unittest
import gym
import numpy.testing as npt
import torch
import torch.nn.functional as F
from reagent.gym.envs import Gym
try:
from reagent.gym.envs import RecSim
HAS_RECSIM = True
except ModuleNotFoun... | 4,748 | 40.657895 | 85 | py |
ReAgent | ReAgent-master/reagent/gym/tests/preprocessors/test_replay_buffer_inserters.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
import logging
import unittest
import gym
import numpy as np
import numpy.testing as npt
import torch
from reagent.gym.envs import EnvWrapper
from reagent.gym.preprocessors import make_replay_buffer_inserter
from reagent.gy... | 6,822 | 38.668605 | 85 | py |
ReAgent | ReAgent-master/reagent/gym/runners/gymrunner.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
import logging
import pickle
from typing import Optional, Sequence
import numpy as np
import torch.multiprocessing as mp
from reagent.core.multiprocess_utils import (
unwrap_function_outputs,
wrap_function_arguments... | 4,541 | 32.397059 | 87 | py |
ReAgent | ReAgent-master/reagent/evaluation/evaluation_data_page.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
from __future__ import annotations
import logging
import math
from dataclasses import dataclass, fields
from typing import TYPE_CHECKING, Optional, cast
import numpy as np
import torch
import torch.nn as nn
from reagent.co... | 26,496 | 40.401563 | 96 | py |
ReAgent | ReAgent-master/reagent/evaluation/world_model_evaluator.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
import logging
from typing import Dict, List
import torch
from reagent.core.types import FeatureData, MemoryNetworkInput
from reagent.training.world_model.mdnrnn_trainer import MDNRNNTrainer
logger = logging.getLogger(__na... | 9,841 | 39.336066 | 88 | py |
ReAgent | ReAgent-master/reagent/evaluation/sequential_doubly_robust_estimator.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
import logging
from typing import List
import numpy as np
import torch
from reagent.evaluation.cpe import CpeEstimate, bootstrapped_std_error_of_mean
from reagent.evaluation.evaluation_data_page import EvaluationDataPage
... | 5,254 | 36.535714 | 88 | py |
ReAgent | ReAgent-master/reagent/evaluation/doubly_robust_estimator.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
import itertools
import logging
from dataclasses import dataclass
from typing import Dict, NamedTuple, Optional, Tuple, Union
import numpy as np
import torch
from reagent.evaluation.cpe import CpeEstimate, bootstrapped_std_... | 13,063 | 37.997015 | 88 | py |
ReAgent | ReAgent-master/reagent/evaluation/evaluator.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
import logging
from collections import Counter
from typing import Dict, List, Optional
import torch
import torch.nn.functional as F
from reagent.core.tracker import observable
from reagent.evaluation.cpe import CpeDetails, ... | 6,718 | 35.516304 | 89 | py |
ReAgent | ReAgent-master/reagent/evaluation/cpe.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
import logging
import math
from typing import Dict, NamedTuple, Optional
import numpy as np
import torch
from reagent.core.tensorboardX import SummaryWriterContext
logger = logging.getLogger(__name__)
class CpeEstimate(... | 6,820 | 34.9 | 114 | py |
ReAgent | ReAgent-master/reagent/evaluation/weighted_sequential_doubly_robust_estimator.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
import itertools
import logging
import numpy as np
import scipy as sp
import torch
from reagent.evaluation.cpe import CpeEstimate
from reagent.evaluation.evaluation_data_page import EvaluationDataPage
logger = logging.get... | 14,541 | 36.576227 | 106 | py |
ReAgent | ReAgent-master/reagent/evaluation/ope_adapter.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
import logging
import torch
from reagent.evaluation.cpe import (
CpeEstimate,
CpeEstimateSet,
bootstrapped_std_error_of_mean,
)
from reagent.evaluation.evaluation_data_page import EvaluationDataPage
from reagent... | 10,869 | 36.353952 | 96 | py |
ReAgent | ReAgent-master/reagent/evaluation/feature_importance/feature_importance_perturbation.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
import copy
import logging
from collections import defaultdict
from typing import Callable, Any, Optional
import pandas as pd
import torch
import torch.nn as nn
from reagent.core.dataclasses import dataclass
from reagent.eva... | 2,857 | 37.106667 | 87 | py |
ReAgent | ReAgent-master/reagent/evaluation/feature_importance/feature_importance_base.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
from typing import List
import pandas as pd
import torch.nn as nn
from reagent.core.dataclasses import dataclass
@dataclass
class FeatureImportanceBase:
model: nn.Module
sorted_feature_ids: List[int]
def compu... | 401 | 22.647059 | 71 | py |
ReAgent | ReAgent-master/reagent/core/aggregators.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
import logging
from collections import deque
from typing import Callable, Deque, Dict, List, Optional, Any
import numpy as np
import torch
from reagent.core.tensorboardX import SummaryWriterContext
from reagent.core.tracker... | 7,651 | 30.751037 | 87 | py |
ReAgent | ReAgent-master/reagent/core/tracker.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
import functools
import logging
from typing import Dict, List, Type
import torch
logger = logging.getLogger(__name__)
class Observer:
"""
Base class for observers
"""
def __init__(self, observing_keys: ... | 3,958 | 28.110294 | 80 | py |
ReAgent | ReAgent-master/reagent/core/utils.py | #!/usr/bin/env python3
from typing import Tuple, Optional
import torch
def get_rank() -> int:
"""
Returns the torch.distributed rank of the process. 0 represents
the main process and is the default if torch.distributed isn't set up
"""
return (
torch.distributed.get_rank()
if tor... | 975 | 24.684211 | 82 | py |
ReAgent | ReAgent-master/reagent/core/configuration.py | #!/usr/bin/python3
import functools
from dataclasses import MISSING, Field, fields
from inspect import Parameter, isclass, signature
from typing import List, Optional, Type, Union
from reagent.core.dataclasses import dataclass
from torch import nn
BLOCKLIST_TYPES = [nn.Module]
def _get_param_annotation(p):
# ... | 5,364 | 31.515152 | 88 | py |
ReAgent | ReAgent-master/reagent/core/types.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
import dataclasses
import logging
# The dataclasses in this file should be vanilla dataclass to have minimal overhead
from dataclasses import dataclass, field
from typing import Dict, List, NamedTuple, Optional, Tuple, Unio... | 37,736 | 34.136872 | 91 | py |
ReAgent | ReAgent-master/reagent/core/torch_utils.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
from io import BytesIO
from typing import Dict
import numpy as np
import torch
def dict_to_tensor(batch: Dict[str, np.ndarray], device: str = "cpu"):
return {k: torch.tensor(v).to(device) for k, v in batch.items()}
d... | 3,085 | 29.86 | 93 | py |
ReAgent | ReAgent-master/reagent/core/parameters.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
import enum
from typing import Dict, List, Optional
from reagent.core.base_dataclass import BaseDataClass
from reagent.core.configuration import param_hash
from reagent.core.dataclasses import dataclass, field
from reagent.... | 6,022 | 26.884259 | 80 | py |
ReAgent | ReAgent-master/reagent/core/oss_tensorboard_logger.py | from typing import Optional, Union, Dict, List, Tuple
import torch
from pytorch_lightning.loggers import TensorBoardLogger
from pytorch_lightning.utilities import rank_zero_only
class LocalCacheLogger:
@staticmethod
def store_metrics(
tb_logger,
metrics: Dict[
str, Union[float, to... | 4,531 | 33.861538 | 136 | py |
ReAgent | ReAgent-master/reagent/core/tensorboardX.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
"""
Context library to allow dropping tensorboardX anywhere in the codebase.
If there is no SummaryWriter in the context, function calls will be no-op.
Usage:
writer = SummaryWriter()
with summary_writer_context(w... | 3,412 | 26.97541 | 83 | py |
ReAgent | ReAgent-master/reagent/training/cem_trainer.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
"""
The Trainer for Cross-Entropy Method. The idea is that an ensemble of
world models are fitted to predict transitions and reward functions.
A cross entropy method-based planner will then plan the best next action
based on... | 1,805 | 35.12 | 87 | py |
ReAgent | ReAgent-master/reagent/training/qrdqn_trainer.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
import logging
from typing import List, Tuple
import reagent.core.types as rlt
import torch
from reagent.core.configuration import resolve_defaults
from reagent.core.dataclasses import field
from reagent.core.parameters imp... | 8,782 | 36.216102 | 94 | py |
ReAgent | ReAgent-master/reagent/training/reinforce_trainer.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
import inspect
import logging
import math
from dataclasses import field
from typing import List, Optional
import reagent.core.types as rlt
import torch
import torch.optim
from reagent.gym.policies.policy import Policy
from r... | 4,640 | 37.040984 | 87 | py |
ReAgent | ReAgent-master/reagent/training/parametric_dqn_trainer.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
import logging
from typing import Tuple
import reagent.core.parameters as rlp
import reagent.core.types as rlt
import torch
import torch.nn.functional as F
from reagent.core.configuration import resolve_defaults
from reagen... | 7,284 | 39.027473 | 88 | py |
ReAgent | ReAgent-master/reagent/training/sac_trainer.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
import copy
import logging
from typing import List, Optional
import numpy as np
import reagent.core.types as rlt
import torch
import torch.nn.functional as F
from reagent.core.configuration import resolve_defaults
from reage... | 14,825 | 38.118734 | 94 | py |
ReAgent | ReAgent-master/reagent/training/utils.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
import numpy as np
import torch
import torch.nn.functional as F
EPS = np.finfo(float).eps.item()
def rescale_actions(
actions: torch.Tensor,
new_min: torch.Tensor,
new_max: torch.Tensor,
prev_min: torch.T... | 1,864 | 29.080645 | 80 | py |
ReAgent | ReAgent-master/reagent/training/reagent_lightning_module.py | #!/usr/bin/env python3
import inspect
import logging
import pytorch_lightning as pl
import torch
from reagent.core.tensorboardX import SummaryWriterContext
from reagent.core.utils import lazy_property
from typing_extensions import final
logger = logging.getLogger(__name__)
class ReAgentLightningModule(pl.Lightnin... | 7,568 | 35.921951 | 128 | py |
ReAgent | ReAgent-master/reagent/training/c51_trainer.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
from typing import List
import reagent.core.types as rlt
import torch
from reagent.core.configuration import resolve_defaults
from reagent.core.dataclasses import field
from reagent.core.parameters import RLParameters
from ... | 8,784 | 41.033493 | 101 | py |
ReAgent | ReAgent-master/reagent/training/multi_stage_trainer.py | #!/usr/bin/env python3
import bisect
import functools
import itertools
from collections import OrderedDict
from typing import List, Dict, Tuple
import torch.nn as nn
from pytorch_lightning.loops.optimization.optimizer_loop import ClosureResult
from reagent.core.utils import lazy_property
from .reagent_lightning_modu... | 7,726 | 36.509709 | 116 | py |
ReAgent | ReAgent-master/reagent/training/ppo_trainer.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
import inspect
import logging
from dataclasses import field
from typing import Dict, List, Optional, Union
import reagent.core.types as rlt
import torch
import torch.optim
from reagent.core.configuration import resolve_defau... | 8,551 | 38.410138 | 118 | py |
ReAgent | ReAgent-master/reagent/training/dqn_trainer_base.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
import logging
from typing import List, Optional
import reagent.core.types as rlt
import torch
import torch.nn.functional as F
from reagent.core.parameters import EvaluationParameters, RLParameters
from reagent.core.torch_u... | 14,123 | 39.469914 | 115 | py |
ReAgent | ReAgent-master/reagent/training/slate_q_trainer.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
import enum
import logging
from typing import Optional
import reagent.core.parameters as rlp
import reagent.core.types as rlt
import torch
import torch.nn.functional as F
from reagent.core.dataclasses import field
from reag... | 10,984 | 38.800725 | 117 | py |
ReAgent | ReAgent-master/reagent/training/imitator_training.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
import logging
import torch
logger = logging.getLogger(__name__)
def get_valid_actions_from_imitator(imitator, input, drop_threshold):
"""Create mask for non-viable actions under the imitator."""
if isinstance(im... | 804 | 31.2 | 85 | py |
ReAgent | ReAgent-master/reagent/training/reward_network_trainer.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
import logging
from enum import Enum
from typing import Optional
import numpy as np
import reagent.core.types as rlt
import torch
from reagent.core.dataclasses import field
from reagent.models.base import ModelBase
from reag... | 6,165 | 34.034091 | 85 | py |
ReAgent | ReAgent-master/reagent/training/dqn_trainer.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
import logging
from typing import List, Optional, Tuple
import reagent.core.types as rlt
import torch
from reagent.core.configuration import resolve_defaults
from reagent.core.dataclasses import dataclass, field
from reagen... | 12,069 | 37.935484 | 96 | py |
ReAgent | ReAgent-master/reagent/training/td3_trainer.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
import copy
import logging
import reagent.core.types as rlt
import torch
import torch.nn.functional as F
from reagent.core.configuration import resolve_defaults
from reagent.core.dataclasses import field
from reagent.core.pa... | 7,751 | 38.350254 | 100 | py |
ReAgent | ReAgent-master/reagent/training/discrete_crr_trainer.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
# Note: this files is modeled after td3_trainer.py
import logging
from typing import List, Tuple
import reagent.core.types as rlt
import torch
import torch.nn.functional as F
from reagent.core.configuration import resolve_... | 18,427 | 41.266055 | 94 | py |
ReAgent | ReAgent-master/reagent/training/gradient_free/es_worker.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
import logging
import torch
import torch.distributed as distributed
import torch.nn
import torch.optim
from reagent.core.parameters import EvolutionParameters
from reagent.training.gradient_free.evolution_pool import Evolut... | 1,861 | 30.033333 | 77 | py |
ReAgent | ReAgent-master/reagent/training/gradient_free/ars_util.py | from operator import itemgetter
import numpy as np
import torch
"""
Utility functions for Advanced Random Search (ARS) algorithm
based on the paper "Simple random search provides a competitive approach
to reinforcement learning", Mania et al.
https://arxiv.org/abs/1803.07055
Here, we show an example of training a d... | 4,380 | 34.909836 | 87 | py |
ReAgent | ReAgent-master/reagent/training/gradient_free/evolution_pool.py | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All rights reserved.
import logging
from typing import Dict, List
import torch
import torch.fb.rendezvous.zeus
import torch.nn
import torch.optim
from reagent.core.parameters import EvolutionParameters
logger = logging.getLogger(__name__)
MA... | 4,802 | 35.112782 | 86 | py |
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