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from typing import Iterable from sciencebeam_parser.models.data import ( ContextAwareLayoutTokenFeatures, ContextAwareLayoutTokenModelDataGenerator, LayoutModelData ) class HeaderDataGenerator(ContextAwareLayoutTokenModelDataGenerator): def iter_model_data_for_context_layout_token_features( s...
/sciencebeam_parser-0.1.8.tar.gz/sciencebeam_parser-0.1.8/sciencebeam_parser/models/header/data.py
0.760028
0.161155
data.py
pypi
import logging from typing import Iterable, Mapping, Optional, Tuple from sciencebeam_parser.utils.misc import iter_ids from sciencebeam_parser.document.semantic_document import ( SemanticAddressLine, SemanticAffiliationAddress, SemanticContentFactoryProtocol, SemanticContentWrapper, SemanticCountr...
/sciencebeam_parser-0.1.8.tar.gz/sciencebeam_parser-0.1.8/sciencebeam_parser/models/affiliation_address/extract.py
0.741861
0.151467
extract.py
pypi
import os import logging from time import monotonic from typing import Dict, Iterable, Mapping, Optional, Sequence, Set import PIL.Image from sciencebeam_parser.utils.bounding_box import BoundingBox from sciencebeam_parser.document.semantic_document import SemanticGraphic from sciencebeam_parser.document.layout_docum...
/sciencebeam_parser-0.1.8.tar.gz/sciencebeam_parser-0.1.8/sciencebeam_parser/processors/cv_graphic_provider.py
0.835618
0.210685
cv_graphic_provider.py
pypi
import functools import logging import os from abc import ABC, abstractmethod from typing import Counter, Iterable, List, Optional, Sequence from sciencebeam_parser.utils.bounding_box import BoundingBox from sciencebeam_parser.document.layout_document import ( LayoutBlock, LayoutDocument, LayoutGraphic, ...
/sciencebeam_parser-0.1.8.tar.gz/sciencebeam_parser-0.1.8/sciencebeam_parser/processors/graphic_provider.py
0.816077
0.184859
graphic_provider.py
pypi
from typing import NamedTuple, Set from sciencebeam_parser.config.config import AppConfig from sciencebeam_parser.processors.document_page_image import ( DEFAULT_PDF_RENDER_DPI ) from sciencebeam_parser.processors.graphic_matching import DEFAULT_MAX_GRAPHIC_DISTANCE class RequestFieldNames: """ "Abstrac...
/sciencebeam_parser-0.1.8.tar.gz/sciencebeam_parser-0.1.8/sciencebeam_parser/processors/fulltext/config.py
0.818954
0.185929
config.py
pypi
import logging import multiprocessing from typing import ( Iterable, Iterator, List, Mapping, NamedTuple, Optional, Sequence, Tuple, Type, Union ) from sciencebeam_parser.models.data import AppFeaturesContext, DEFAULT_APP_FEATURES_CONTEXT from sciencebeam_parser.models.model imp...
/sciencebeam_parser-0.1.8.tar.gz/sciencebeam_parser-0.1.8/sciencebeam_parser/processors/fulltext/processor.py
0.82029
0.169956
processor.py
pypi
import logging import os from contextlib import ExitStack from dataclasses import dataclass from pathlib import Path from tempfile import TemporaryDirectory from time import monotonic from typing import List, Optional, Set from zipfile import ZipFile from lxml import etree from sciencebeam_trainer_delft.utils.downloa...
/sciencebeam_parser-0.1.8.tar.gz/sciencebeam_parser-0.1.8/sciencebeam_parser/app/parser.py
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parser.py
pypi
import mimetypes from typing import Optional, Sequence class MediaTypes: """ Media Types used by ScienceBeam Parser. Where possible, these correspond to official media types. In some instances, no official media type is defined yet. """ PDF = 'application/pdf' DOC = 'application/msword' ...
/sciencebeam_parser-0.1.8.tar.gz/sciencebeam_parser-0.1.8/sciencebeam_parser/utils/media_types.py
0.699152
0.204501
media_types.py
pypi
import logging import re from itertools import zip_longest from typing import Mapping, NamedTuple, Optional, Sequence, Tuple, Union from lxml import etree from lxml.builder import ElementMaker LOGGER = logging.getLogger(__name__) class TagExpression(NamedTuple): tag: str attrib: Mapping[str, str] def ...
/sciencebeam_parser-0.1.8.tar.gz/sciencebeam_parser-0.1.8/sciencebeam_parser/utils/xml_writer.py
0.72331
0.179064
xml_writer.py
pypi
import os import codecs from contextlib import contextmanager from typing import Iterable, Sequence from urllib.parse import urlparse import fsspec from sciencebeam_trainer_delft.utils.io import ( auto_uploading_output_file as _auto_uploading_output_file, is_external_location, open_file ) def get_file_s...
/sciencebeam_parser-0.1.8.tar.gz/sciencebeam_parser-0.1.8/sciencebeam_parser/utils/io.py
0.659076
0.151467
io.py
pypi
import argparse import logging import os from typing import Iterable, List, Optional, Sequence, Tuple from lxml import etree from sciencebeam_trainer_delft.utils.io import ( auto_download_input_file ) from sciencebeam_trainer_delft.sequence_labelling.reader import ( load_data_crf_lines ) from sciencebeam_trai...
/sciencebeam_parser-0.1.8.tar.gz/sciencebeam_parser-0.1.8/sciencebeam_parser/training/cli/generate_delft_data.py
0.68215
0.190253
generate_delft_data.py
pypi
import logging from typing import Any, Mapping, Optional, Union from lxml import etree LOGGER = logging.getLogger(__name__) T_XSLT_Input = Union[etree.ElementBase, etree.ElementTree] class XsltTransformerWrapper: def __init__( self, xslt_template: str, xslt_template_parameters: Option...
/sciencebeam_parser-0.1.8.tar.gz/sciencebeam_parser-0.1.8/sciencebeam_parser/transformers/xslt.py
0.848659
0.244386
xslt.py
pypi
# ScienceBeam Trainer DeLFT Work in-progress.. A thin(ish) wrapper around [DeLFT](https://github.com/kermitt2/delft) to enable training in the cloud. Some of the main features: - resources (model, data etc.) can be loaded from remote sources, currently: - HTTP (`https://`, `http://`) - Google Storage (`gs://`) ...
/sciencebeam_trainer_delft-0.0.31.tar.gz/sciencebeam_trainer_delft-0.0.31/README.md
0.455199
0.902266
README.md
pypi
from collections import Counter, defaultdict, OrderedDict from typing import Dict, Iterable, List import numpy as np def iter_flat_batch_tokens(batch_tokens: List[List[str]]): return ( token for doc_tokens in batch_tokens for token in doc_tokens ) def iter_flat_features(features: np...
/sciencebeam_trainer_delft-0.0.31.tar.gz/sciencebeam_trainer_delft-0.0.31/sciencebeam_trainer_delft/sequence_labelling/input_info.py
0.76908
0.616676
input_info.py
pypi
import logging import os import time from functools import partial from typing import Callable, Iterable, List, Optional, Tuple, Union, cast import numpy as np from delft.sequenceLabelling.models import BaseModel from delft.sequenceLabelling.preprocess import WordPreprocessor, FeaturesPreprocessor from delft.sequence...
/sciencebeam_trainer_delft-0.0.31.tar.gz/sciencebeam_trainer_delft-0.0.31/sciencebeam_trainer_delft/sequence_labelling/wrapper.py
0.826187
0.161783
wrapper.py
pypi
import json import difflib import logging from xml.sax.saxutils import escape as xml_escape from typing import Optional, Union, Iterable, List, Tuple import numpy as np from delft.sequenceLabelling.evaluation import get_entities LOGGER = logging.getLogger(__name__) class TagOutputFormats: JSON = 'json' DA...
/sciencebeam_trainer_delft-0.0.31.tar.gz/sciencebeam_trainer_delft-0.0.31/sciencebeam_trainer_delft/sequence_labelling/tag_formatter.py
0.717309
0.271206
tag_formatter.py
pypi
import logging import itertools from functools import partial from typing import Any, Dict, List, Iterable, Set, Tuple, Union import numpy as np from sklearn.base import BaseEstimator, TransformerMixin from sklearn.pipeline import Pipeline from sklearn.pipeline import FeatureUnion from sklearn.preprocessing import Mi...
/sciencebeam_trainer_delft-0.0.31.tar.gz/sciencebeam_trainer_delft-0.0.31/sciencebeam_trainer_delft/sequence_labelling/preprocess.py
0.742795
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preprocess.py
pypi
import argparse import logging from typing import Dict, List, Optional, NamedTuple import keras import numpy as np from delft.sequenceLabelling.preprocess import WordPreprocessor from delft.sequenceLabelling.models import BaseModel from sciencebeam_trainer_delft.utils.misc import ( parse_comma_separated_str, ...
/sciencebeam_trainer_delft-0.0.31.tar.gz/sciencebeam_trainer_delft-0.0.31/sciencebeam_trainer_delft/sequence_labelling/transfer_learning.py
0.870721
0.190122
transfer_learning.py
pypi
import logging import re from itertools import islice from typing import Iterable, List, Tuple import numpy as np from delft.sequenceLabelling.reader import _translate_tags_grobid_to_IOB LOGGER = logging.getLogger(__name__) # partially copied from delft/sequenceLabelling/reader.py def iter_load_data_and_labels_c...
/sciencebeam_trainer_delft-0.0.31.tar.gz/sciencebeam_trainer_delft-0.0.31/sciencebeam_trainer_delft/sequence_labelling/reader.py
0.598077
0.345436
reader.py
pypi
import logging import os from typing import NamedTuple, Optional import numpy as np from delft.sequenceLabelling.evaluation import ( f1_score, accuracy_score, precision_score, recall_score ) from delft.sequenceLabelling.trainer import Trainer as _Trainer from delft.sequenceLabelling.trainer import Sc...
/sciencebeam_trainer_delft-0.0.31.tar.gz/sciencebeam_trainer_delft-0.0.31/sciencebeam_trainer_delft/sequence_labelling/trainer.py
0.873728
0.280898
trainer.py
pypi
import logging import json from typing import List, Type, Union from keras.models import Model from keras.layers.merge import Concatenate from keras.layers import ( Dense, LSTM, Bidirectional, Embedding, Input, Dropout, TimeDistributed ) import delft.sequenceLabelling.wrapper from delft.utilities.layers impor...
/sciencebeam_trainer_delft-0.0.31.tar.gz/sciencebeam_trainer_delft-0.0.31/sciencebeam_trainer_delft/sequence_labelling/models.py
0.912782
0.230432
models.py
pypi
import logging from collections import Counter from itertools import zip_longest from typing import List, Optional import numpy as np from delft.utilities.Tokenizer import tokenizeAndFilterSimple from sciencebeam_trainer_delft.sequence_labelling.dataset_transform import ( DatasetTransformer ) from sciencebeam_t...
/sciencebeam_trainer_delft-0.0.31.tar.gz/sciencebeam_trainer_delft-0.0.31/sciencebeam_trainer_delft/sequence_labelling/dataset_transform/unroll_transform.py
0.821868
0.254257
unroll_transform.py
pypi
import logging import tempfile import os from pathlib import Path from typing import Iterable, IO, List, Optional, Tuple import numpy as np from delft.sequenceLabelling.reader import ( _translate_tags_grobid_to_IOB as translate_tags_grobid_to_IOB ) from sciencebeam_trainer_delft.sequence_labelling.evaluation imp...
/sciencebeam_trainer_delft-0.0.31.tar.gz/sciencebeam_trainer_delft-0.0.31/sciencebeam_trainer_delft/sequence_labelling/engines/wapiti_adapters.py
0.690768
0.297062
wapiti_adapters.py
pypi
import logging import threading import os import sys from collections import Counter from itertools import islice from multiprocessing import cpu_count from typing import IO, List, Iterable, Optional, cast import subprocess LOGGER = logging.getLogger(__name__) DEFAULT_STOP_EPSILON_VALUE = '0.00001' DEFAULT_STOP_WI...
/sciencebeam_trainer_delft-0.0.31.tar.gz/sciencebeam_trainer_delft-0.0.31/sciencebeam_trainer_delft/sequence_labelling/engines/wapiti.py
0.557845
0.169612
wapiti.py
pypi
import argparse import logging from typing import Optional import requests from sciencebeam_trainer_delft.sequence_labelling.evaluation import ( ClassificationResult ) LOGGER = logging.getLogger(__name__) DEFAULT_TRAIN_START_MESSAGE_FORMAT = '\n'.join([ 'Model training started', 'model_path: `{model_p...
/sciencebeam_trainer_delft-0.0.31.tar.gz/sciencebeam_trainer_delft-0.0.31/sciencebeam_trainer_delft/sequence_labelling/utils/train_notify.py
0.804021
0.310028
train_notify.py
pypi
import logging from pathlib import Path from typing import List, Optional, NamedTuple, Union from sciencebeam_trainer_delft.utils.typing import T from sciencebeam_trainer_delft.sequence_labelling.tools.checkpoints import ( get_checkpoints_json, get_checkpoint_meta ) LOGGER = logging.getLogger(__name__) cl...
/sciencebeam_trainer_delft-0.0.31.tar.gz/sciencebeam_trainer_delft-0.0.31/sciencebeam_trainer_delft/sequence_labelling/utils/checkpoints.py
0.898133
0.27282
checkpoints.py
pypi
import argparse import concurrent.futures import logging import json import os from collections import OrderedDict from typing import Dict, List, Optional from tqdm.auto import tqdm from sciencebeam_trainer_delft.utils.io import open_file from sciencebeam_trainer_delft.utils.cli import ( add_default_arguments, ...
/sciencebeam_trainer_delft-0.0.31.tar.gz/sciencebeam_trainer_delft-0.0.31/sciencebeam_trainer_delft/sequence_labelling/tools/checkpoints.py
0.718496
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checkpoints.py
pypi
import logging import argparse from argparse import _ActionsContainer as ArgParseActionsContainer from typing import List from sciencebeam_trainer_delft.utils.misc import parse_number_ranges from sciencebeam_trainer_delft.sequence_labelling.utils.train_notify import ( add_train_notification_arguments ) from sci...
/sciencebeam_trainer_delft-0.0.31.tar.gz/sciencebeam_trainer_delft-0.0.31/sciencebeam_trainer_delft/sequence_labelling/tools/grobid_trainer/cli_args.py
0.803097
0.150496
cli_args.py
pypi
import logging import time import tempfile import os from collections import Counter from datetime import datetime, timezone from itertools import islice from typing import Any, Dict, List, Optional, Tuple, Union import numpy as np from sklearn.model_selection import train_test_split import tensorflow as tf from sc...
/sciencebeam_trainer_delft-0.0.31.tar.gz/sciencebeam_trainer_delft-0.0.31/sciencebeam_trainer_delft/sequence_labelling/tools/grobid_trainer/utils.py
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utils.py
pypi
import logging import time from functools import partial from typing import List, Tuple import pandas as pd import delft.textClassification.models import delft.textClassification.wrapper from sciencebeam_trainer_delft.text_classification.wrapper import Classifier from sciencebeam_trainer_delft.utils.download_manager...
/sciencebeam_trainer_delft-0.0.31.tar.gz/sciencebeam_trainer_delft-0.0.31/sciencebeam_trainer_delft/text_classification/cli_utils.py
0.703549
0.267387
cli_utils.py
pypi
import logging from collections import OrderedDict from typing import List import numpy as np from sklearn.metrics import ( log_loss, roc_auc_score, f1_score, precision_score, recall_score ) LOGGER = logging.getLogger(__name__) class ClassificationResult: def __init__( self, ...
/sciencebeam_trainer_delft-0.0.31.tar.gz/sciencebeam_trainer_delft-0.0.31/sciencebeam_trainer_delft/text_classification/evaluation.py
0.86898
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evaluation.py
pypi
from typing import Tuple, List import pandas as pd import numpy as np from sciencebeam_trainer_delft.utils.io import auto_uploading_output_file # mostly copied from: # https://github.com/kermitt2/delft/blob/v0.2.3/delft/textClassification/reader.py def get_filepath_csv_separator(filepath: str): if filepath.en...
/sciencebeam_trainer_delft-0.0.31.tar.gz/sciencebeam_trainer_delft-0.0.31/sciencebeam_trainer_delft/text_classification/reader.py
0.785925
0.337913
reader.py
pypi
import logging import math import os from typing import List import numpy as np from sklearn.metrics import log_loss, roc_auc_score from keras.models import Model from keras.callbacks import Callback from sciencebeam_trainer_delft.text_classification.saving import ( ModelSaver ) from sciencebeam_trainer_delft.t...
/sciencebeam_trainer_delft-0.0.31.tar.gz/sciencebeam_trainer_delft-0.0.31/sciencebeam_trainer_delft/text_classification/models.py
0.699357
0.183942
models.py
pypi
from keras import backend as K from keras.engine.topology import Layer from keras import initializers, regularizers, constraints # mostly copied from: # https://github.com/kermitt2/delft/blob/v0.2.3/delft/utilities/Attention.py # - updated to be compatible with newer Keras version class Attention(Layer): def __i...
/sciencebeam_trainer_delft-0.0.31.tar.gz/sciencebeam_trainer_delft-0.0.31/sciencebeam_trainer_delft/utils/models/Attention.py
0.922023
0.362095
Attention.py
pypi
from __future__ import absolute_import import logging from io import StringIO from backports import csv # pylint: disable=no-name-in-module from six import text_type import apache_beam as beam from apache_beam.io.textio import WriteToText from apache_beam.io.filesystem import CompressionTypes from apache_beam.io.f...
/sciencebeam_utils-0.1.5.tar.gz/sciencebeam_utils-0.1.5/sciencebeam_utils/beam_utils/csv.py
0.630799
0.184217
csv.py
pypi
import logging from random import getrandbits import apache_beam as beam from apache_beam.metrics.metric import Metrics def get_logger(): return logging.getLogger(__name__) def Spy(f): def spy_wrapper(x): f(x) return x return spy_wrapper def MapSpy(f): return beam.Map(Spy(f)) de...
/sciencebeam_utils-0.1.5.tar.gz/sciencebeam_utils-0.1.5/sciencebeam_utils/beam_utils/utils.py
0.639398
0.198763
utils.py
pypi
import logging import os from functools import reduce # pylint: disable=redefined-builtin from typing import Iterable, List, Tuple from apache_beam.io.filesystems import FileSystems from sciencebeam_utils.utils.collection import ( groupby_to_dict, sort_and_groupby_to_dict ) from .file_path import strip_ext ...
/sciencebeam_utils-0.1.5.tar.gz/sciencebeam_utils-0.1.5/sciencebeam_utils/utils/file_pairs.py
0.514888
0.170854
file_pairs.py
pypi
import argparse import logging import errno from math import trunc from random import shuffle from datetime import datetime from itertools import chain from typing import List from backports import csv # pylint: disable=no-name-in-module from six import text_type from sciencebeam_utils.beam_utils.io import open_fil...
/sciencebeam_utils-0.1.5.tar.gz/sciencebeam_utils-0.1.5/sciencebeam_utils/tools/split_csv_dataset.py
0.499512
0.259914
split_csv_dataset.py
pypi
# In[1]: from datetime import datetime, timedelta # In[2]: def create_date_from_str(date_str, date_format='%Y%m%d'): ''' Create a Datetime object from a string with specific date_format. date_str: a date string (required). date_format: the date format of date_str. Default is %Y%m%d. '...
/scienceindata_dates-0.0.3.tar.gz/scienceindata_dates-0.0.3/src/scienceindata_dates/scienceindata_dates.py
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0.374076
scienceindata_dates.py
pypi
# ScienceIO API Demo In this demo, we'll: - Log in with our user account - Make our first request - Put the request in a pandas dataframe and analyze ``` import pandas as pd import yaml from IPython.display import display, JSON from analytics import * from scienceio import ScienceIO ``` ## Initialize client ``` s...
/scienceio-2.2.0.tar.gz/scienceio-2.2.0/examples/example-analytics-2.ipynb
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0.902395
example-analytics-2.ipynb
pypi
import argparse import pandas as pd from convert_data_model import convert_data_model def count_text(df) -> int: """len(df) = # of text spans""" return len(df) def count_text_unique(df) -> int: """unique text spans (no correction for caps/lower/etc.)""" return df.text.nunique() def count_concept...
/scienceio-2.2.0.tar.gz/scienceio-2.2.0/examples/analytics.py
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analytics.py
pypi
# ScienceIO API Analytics In this demo, we'll: - Log in with our user account - Make our first request - Put the request in a pandas dataframe and analyze ``` import pandas as pd import yaml from IPython.display import display, JSON from analytics import * from scienceio import ScienceIO ``` ## Initialize client ...
/scienceio-2.2.0.tar.gz/scienceio-2.2.0/examples/example-analytics-1.ipynb
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0.886273
example-analytics-1.ipynb
pypi
import argparse import pandas as pd def beta_mapper(): """For converting previous data models to beta model""" return { "text": "text", "start": "pos_start", "end": "pos_end", "text_norm": "concept_id", "entity": "concept_id", "canonical_name": "concept_name", ...
/scienceio-2.2.0.tar.gz/scienceio-2.2.0/examples/convert_data_model.py
0.580471
0.417568
convert_data_model.py
pypi
<div id="top"></div> <h1 align="center"> <br> Sciencer Toolkit </h1> <h4 align="center">A smarter way to find articles.</h4> <p align="center"> <a href="https://pypi.org/project/sciencer/"> <img src="https://img.shields.io/pypi/status/sciencer.svg?style=flat-square" alt="PyPi Package Version"></a...
/sciencer-0.1.3.tar.gz/sciencer-0.1.3/README.md
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README.md
pypi
<h1 align="center"> ScienceWorld </h1> <p align="center"> <!-- Version badge using shields.io --> <a href="https://github.com/allenai/ScienceWorld/releases"> <img src="https://img.shields.io/github/v/release/allenai/ScienceWorld"> </a> <!-- Link to tutorials badge using shields.io --> <a href="https://huggin...
/scienceworld-1.1.3.tar.gz/scienceworld-1.1.3/README.md
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0.93744
README.md
pypi
# Contributor Covenant Code of Conduct ## Our Pledge We as members, contributors, and leaders pledge to make participation in our community a harassment-free experience for everyone, regardless of age, body size, visible or invisible disability, ethnicity, sex characteristics, gender identity and expression, level of...
/scienlib-1.1.tar.gz/scienlib-1.1/.github/CODE_OF_CONDUCT.md
0.58439
0.685038
CODE_OF_CONDUCT.md
pypi
from __future__ import annotations import re from pathlib import Path from typing import Any, Dict, List, Optional import pandas as pd from sem.structure_parsing import recursive_folder_parsing class ResultManager: """A manager for experimental results. It takes care of collecting results organized in diff...
/scientific-experiment-manager-0.1.0.tar.gz/scientific-experiment-manager-0.1.0/sem/manager.py
0.942122
0.608216
manager.py
pypi
import torch import random import numpy as np import argparse from sentence_transformers import SentenceTransformer, util from transformers import DataCollatorWithPadding from collections import defaultdict import json import wandb import ipdb import seaborn as sns import matplotlib.pyplot as plt from tqdm import tqdm ...
/scientific-information-change-1.0.0.tar.gz/scientific-information-change-1.0.0/matching_experiments/predict_similarity_scoring_unlabelled_sbert.py
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0.261312
predict_similarity_scoring_unlabelled_sbert.py
pypi
import torch import random import numpy as np import argparse import pandas as pd from functools import partial from transformers import AutoTokenizer from transformers import AutoModelForSequenceClassification, AutoModel from transformers import AutoConfig from transformers import Trainer from transformers import Trai...
/scientific-information-change-1.0.0.tar.gz/scientific-information-change-1.0.0/matching_experiments/predict_similarity_scoring_unlabelled.py
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0.242295
predict_similarity_scoring_unlabelled.py
pypi
import torch import random import numpy as np import argparse import json import os from functools import partial from datasets import load_metric from transformers import AutoTokenizer from transformers import AutoModelForSequenceClassification, AutoModel from transformers import AutoConfig from transformers import Tr...
/scientific-information-change-1.0.0.tar.gz/scientific-information-change-1.0.0/matching_experiments/train_supervised.py
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train_supervised.py
pypi
import argparse import random from functools import partial import wandb import json import os import numpy as np import torch import torch.nn.functional as F from transformers import AutoModelForSequenceClassification from transformers import AutoTokenizer from transformers import DataCollatorWithPadding from transfo...
/scientific-information-change-1.0.0.tar.gz/scientific-information-change-1.0.0/matching_experiments/eval_unsupervised_paraphrase_detection.py
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0.257479
eval_unsupervised_paraphrase_detection.py
pypi
import torch import random import numpy as np import argparse import wandb import torch.nn.functional as F import torch import json import os from transformers import AutoTokenizer from transformers import AutoModelForSequenceClassification from transformers import Trainer from transformers import TrainingArguments fro...
/scientific-information-change-1.0.0.tar.gz/scientific-information-change-1.0.0/matching_experiments/eval_unsupervised_nli.py
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eval_unsupervised_nli.py
pypi
import torch from torch import nn import random import numpy as np import argparse import json import os import torch.nn.functional as F from sentence_transformers import SentenceTransformer, losses, evaluation, models from torch.utils.data import DataLoader import wandb import pandas as pd import ipdb from utils.data...
/scientific-information-change-1.0.0.tar.gz/scientific-information-change-1.0.0/matching_experiments/train_supervised_sentence_transformers.py
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0.218899
train_supervised_sentence_transformers.py
pypi
import torch import random import numpy as np import argparse from sentence_transformers import SentenceTransformer import wandb import json import os import ipdb import torch.nn.functional as F from utils.data_processor import read_dataset_raw from utils.metrics import compute_regression_metrics from utils.data_proc...
/scientific-information-change-1.0.0.tar.gz/scientific-information-change-1.0.0/matching_experiments/eval_unsupervised_sts.py
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0.266406
eval_unsupervised_sts.py
pypi
import torch import random import numpy as np import argparse from sentence_transformers import SentenceTransformer, util from transformers import AutoModelForSequenceClassification from transformers import AutoConfig from transformers import AutoTokenizer from transformers import Trainer from transformers import Train...
/scientific-information-change-1.0.0.tar.gz/scientific-information-change-1.0.0/matching_experiments/eval_evidence_retrieval.py
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eval_evidence_retrieval.py
pypi
import numpy as np from sklearn.metrics import precision_recall_fscore_support from typing import List, AnyStr, Tuple, Dict from sklearn.metrics import mean_squared_error from scipy.stats import pearsonr, spearmanr import ipdb def accuracy(preds: np.ndarray, labels: np.ndarray) -> float: return np.sum(preds == la...
/scientific-information-change-1.0.0.tar.gz/scientific-information-change-1.0.0/matching_experiments/utils/metrics.py
0.825343
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metrics.py
pypi
import torch from torch import nn from torch.optim import SGD from transformers import AutoModel from tqdm import tqdm import torch.nn.functional as F import ipdb class GradientReversal(torch.autograd.Function): """ Basic layer for doing gradient reversal """ lambd = 1.0 @staticmethod def forw...
/scientific-information-change-1.0.0.tar.gz/scientific-information-change-1.0.0/matching_experiments/utils/model.py
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model.py
pypi
import numpy as np def mean_reciprocal_rank(rs): """Score is reciprocal of the rank of the first relevant item First element is 'rank 1'. Relevance is binary (nonzero is relevant). Example from http://en.wikipedia.org/wiki/Mean_reciprocal_rank >>> rs = [[0, 0, 1], [0, 1, 0], [1, 0, 0]] >>> mean...
/scientific-information-change-1.0.0.tar.gz/scientific-information-change-1.0.0/matching_experiments/utils/rank_metrics.py
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rank_metrics.py
pypi
from sentence_transformers import SentenceTransformer, util from typing import Optional, AnyStr, List import numpy as np import torch import torch.nn.functional as F class SimilarityEstimator(object): """ Estimator of information matching score (IMS) between two scientific sentences """ def __init__( ...
/scientific-information-change-1.0.0.tar.gz/scientific-information-change-1.0.0/scientific_information_change/estimate_similarity.py
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estimate_similarity.py
pypi
from __future__ import annotations from pathlib import Path from functools import wraps from typing import TypeVar, List, Tuple, Union, Callable, Optional from warnings import warn, filterwarnings, catch_warnings from textwrap import dedent import matplotlib as mpl import matplotlib.pyplot as plt from matplotlib.ticke...
/scientific_plots-1.7.2-py3-none-any.whl/scientific_plots/default_plots.py
0.945951
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default_plots.py
pypi
from __future__ import annotations import csv import locale from contextlib import contextmanager from copy import copy, deepcopy from functools import wraps from typing import ( Generator, Optional, Union, Callable, Any, overload) from pathlib import Path from warnings import warn, catch_warnings, simplefilter fr...
/scientific_plots-1.7.2-py3-none-any.whl/scientific_plots/plot_settings.py
0.744656
0.243817
plot_settings.py
pypi
from __future__ import print_function import re from functools import wraps from subprocess import Popen, PIPE from sys import __stdout__ from os import mkdir from os.path import dirname, exists from typing import Iterable, Optional, List, Callable, TypeVar, Union, Any from pathlib import Path from collections import ...
/scientific_plots-1.7.2-py3-none-any.whl/scientific_plots/utilities.py
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utilities.py
pypi
from __future__ import annotations from os.path import join from math import pi from queue import Queue from threading import Thread from subprocess import check_output from typing import ( List, Tuple, TypeVar, Union, Iterable, Any, Optional) from pathlib import Path import matplotlib as mpl import matplotlib.py...
/scientific_plots-1.7.2-py3-none-any.whl/scientific_plots/two_d_plot.py
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two_d_plot.py
pypi
import re from typing import Any, Callable, Iterable, List, Optional # ========================================= What can be exported? ========================================= __all__ = ['strings_to_', 'strings_to_integers', 'strings_to_floats', 'string_to_float', 'match_one_string', 'match_one_pattern', ...
/scientific_string-0.1.0-py3-none-any.whl/scientific_string/__init__.py
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__init__.py
pypi
import matplotlib.pyplot as plt import numpy as np from scientific_tools.graphics.function_graphs import plot_2Dfunction import scientific_tools.physics.uncertainty as uncertainty def plot_uncertainty_function(f, u_f, min_x, max_x, values_number, args_before_x=[], args_after_x=[], title="", xlabel="", ylabel="", fu...
/scientific_tools-0.0.0a17-py3-none-any.whl/scientific_tools/graphics/uncertainty_graphs.py
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uncertainty_graphs.py
pypi
import numpy as np import matplotlib.pyplot as plt from matplotlib import cm def plot_2Dfunction(function, min_x, max_x, values_number, args_before_x=[], args_after_x=[], title="", xlabel="", ylabel="", function_label="", color="blue", linestyle ="-", **kwargs) : """Trace the 2D graphic of the function "function"...
/scientific_tools-0.0.0a17-py3-none-any.whl/scientific_tools/graphics/function_graphs.py
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function_graphs.py
pypi
"""Calculate standard uncertainty (standart uncertainty mainly)""" from warnings import WarningMessage import numpy as np def standard_uncertainty(u_x, u_y, dz_dx, dz_dy) : """Calculate the standard uncertainty of z with the general formule.""" return np.sqrt((u_x*dz_dx)**2+(u_y*dz_dy)**2) def standard_uncer...
/scientific_tools-0.0.0a17-py3-none-any.whl/scientific_tools/physics/uncertainty.py
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uncertainty.py
pypi
import sys from argparse import ArgumentParser, RawTextHelpFormatter from scientisst.constants import * class ArgParser: class MyParser(ArgumentParser): def error(self, message): sys.stderr.write("error: %s\n\n" % message) self.print_help() sys.exit(2) def __init__...
/scientisst_sense-1.1.0-py3-none-any.whl/sense_src/arg_parser.py
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arg_parser.py
pypi
class InvalidAddressError(Exception): """ The specified address is invalid. """ def __init__(self): super().__init__("The specified address is invalid.") class BTAdapterNotFoundError(Exception): """ No Bluetooth adapter was found. """ def __init__(self): super().__ini...
/scientisst_sense-1.1.0-py3-none-any.whl/scientisst/exceptions.py
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exceptions.py
pypi
# Discriminant Analysis with categorical variables (DISQUAL) ``` # Chargement des librairies import numpy as np import pandas as pd #changement de dossier import os os.chdir("d:/Bureau/PythonProject/packages/scientisttools/data/") DTrain = pd.read_excel("CongressVotePipeline.xlsx",sheet_name="train",header=0) displa...
/scientisttools-0.0.8.tar.gz/scientisttools-0.0.8/notebooks/disqual_example.ipynb
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disqual_example.ipynb
pypi
# Additionnal functions ``` from scientisttools.utils import * import numpy as np from scipy.spatial.distance import pdist,squareform # Match arg lst = ["gaussian", "epanechnikov", "rectangular", "triangular"] print(match_arg("gauss", lst)) print(match_arg("pauss", lst)) # is_euclidean np.random.seed(123) w = np.ar...
/scientisttools-0.0.8.tar.gz/scientisttools-0.0.8/notebooks/utils.ipynb
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utils.ipynb
pypi
# Canonical Discriminant Analysis on Iris dataset ``` from seaborn import load_dataset import numpy as np import pandas as pd iris = load_dataset("iris") print(iris.head()) # Chargement de la from scientisttools.discriminant_analysis import CANDISC candisc = CANDISC(n_components=2, target=["spec...
/scientisttools-0.0.8.tar.gz/scientisttools-0.0.8/notebooks/candisc_iris.ipynb
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candisc_iris.ipynb
pypi
# Canonical Discriminant Analysis (CANDISC) ``` # Chargement des librairies import numpy as np import pandas as pd import os os.chdir("d:/Bureau/PythonProject/packages/scientisttools/data/") # Chargement de la base DTrain = pd.read_excel("Data_Illustration_Livre_ADL.xlsx",sheet_name="WINE",header=0) DTrain.head() ...
/scientisttools-0.0.8.tar.gz/scientisttools-0.0.8/notebooks/candisc_wine.ipynb
0.457137
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candisc_wine.ipynb
pypi
# Scierra Scierra [_see-eh-rah_] is a **S**imulated **C**++ **I**nt**er**preter with **R**ecurrent **A**daptation. In human words, it's a interactive interpreter for C++, which allows you to run and debug your program immediately as you type. Well, basically. But the implementation is slightly trickier. To get a qui...
/scierra-0.6.1.tar.gz/scierra-0.6.1/README.md
0.649023
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README.md
pypi
# sciex Framework for "scientific" experiments (Result organization; Experiment and Trial setup; Baseline Comparisons) This tool helps strip out the repetitive parts of setting up and running experiments, and lets you focus on writing the logic of trial running and result types. This reduces the stupid errors one may ...
/sciex-0.3.tar.gz/sciex-0.3/README.md
0.874533
0.897874
README.md
pypi
__author__ = "Lluís Vilanova" __copyright__ = "Copyright 2019, Lluís Vilanova" __license__ = "GPL version 3 or later" # pylint: disable=no-name-in-module,import-error from sciexp2.common import utils from sciexp2.common.filter import Filter # pylint: disable=redefined-builtin def extract(template, function, filter=...
/sciexp2-expdata-0.1.7.tar.gz/sciexp2-expdata-0.1.7/sciexp2/expdata/pandas.py
0.785144
0.382718
pandas.py
pypi
__author__ = "Lluís Vilanova" __copyright__ = "Copyright 2009-2023, Lluís Vilanova" __license__ = "GPL version 3 or later" import glob import os import six import pydoc from sciexp2.common import text import sciexp2.expdef.system #: Paths to search for available templates. #: #: The order of the list establishes w...
/sciexp2-expdef-2.0.13.tar.gz/sciexp2-expdef-2.0.13/sciexp2/expdef/templates.py
0.645232
0.162579
templates.py
pypi
__author__ = "Lluís Vilanova" __copyright__ = "Copyright 2009-2023, Lluís Vilanova" __license__ = "GPL version 3 or later" import abc import glob import imp import os import shutil import six import weakref import sciexp2.common.instance from sciexp2.common.filter import * from sciexp2.common import text from sciexp...
/sciexp2-expdef-2.0.13.tar.gz/sciexp2-expdef-2.0.13/sciexp2/expdef/system/__init__.py
0.741955
0.205416
__init__.py
pypi
__author__ = "Lluís Vilanova" __copyright__ = "Copyright 2013-2023, Lluís Vilanova" __license__ = "GPL version 3 or later" import collections import contextlib import multiprocessing import multiprocessing.pool from . import utils #: Default amount of parallelism. PARALLELISM = True def get_parallelism(paralleli...
/sciexp2-expdef-2.0.13.tar.gz/sciexp2-expdef-2.0.13/sciexp2/common/parallel.py
0.849285
0.354266
parallel.py
pypi
__author__ = "Lluís Vilanova" __copyright__ = "Copyright 2008-2023, Lluís Vilanova" __license__ = "GPL version 3 or later" import collections.abc import re import linecache def _re_match(value, pattern): cre = re.compile(pattern) return cre.match(value) is not None class Filter: """Boolean expression ...
/sciexp2-expdef-2.0.13.tar.gz/sciexp2-expdef-2.0.13/sciexp2/common/filter.py
0.811116
0.495178
filter.py
pypi
__author__ = "Lluís Vilanova" __copyright__ = "Copyright 2008-2023, Lluís Vilanova" __license__ = "GPL version 3 or later" import os import shutil import signal import subprocess import tempfile import functools import collections import weakref import numpy as np import six from . import pp from . import progress ...
/sciexp2-expdef-2.0.13.tar.gz/sciexp2-expdef-2.0.13/sciexp2/common/utils.py
0.624064
0.166167
utils.py
pypi
__author__ = "Lluís Vilanova" __copyright__ = "Copyright 2019-2023, Lluís Vilanova" __license__ = "GPL version 3 or later" from collections import OrderedDict try: from collections.abc import Mapping except: pass import pystache import re from .utils import OrderedSet import six import sys class ParseError(...
/sciexp2-expdef-2.0.13.tar.gz/sciexp2-expdef-2.0.13/sciexp2/common/text.py
0.569613
0.231788
text.py
pypi
__author__ = "Lluís Vilanova" __copyright__ = "Copyright 2019-2020, Lluís Vilanova" __license__ = "GPL version 3 or later" import collections import re from . import kernel def set_freq(shell, path="cpupower", ld_library_path="", freq="max"): """Set frequency scaling. Parameters ---------- shell ...
/sciexp2-exprun-0.3.3.tar.gz/sciexp2-exprun-0.3.3/sciexp2/exprun/cpu.py
0.815416
0.357343
cpu.py
pypi
__author__ = "Lluís Vilanova" __copyright__ = "Copyright 2019-2020, Lluís Vilanova" __license__ = "GPL version 3 or later" from contextlib import contextmanager import joblib @contextmanager def step(message, logger=print): """Show simple progress messages around a piece of code. Parameters ----------...
/sciexp2-exprun-0.3.3.tar.gz/sciexp2-exprun-0.3.3/sciexp2/exprun/util.py
0.775095
0.168446
util.py
pypi
__author__ = "Lluís Vilanova" __copyright__ = "Copyright 2019-2020, Lluís Vilanova" __license__ = "GPL version 3 or later" import logging from . import wait logger = logging.getLogger(__name__) def check_version(shell, version, fail=True): """Check that a specific linux kernel version is installed. Param...
/sciexp2-exprun-0.3.3.tar.gz/sciexp2-exprun-0.3.3/sciexp2/exprun/kernel.py
0.780244
0.165593
kernel.py
pypi
__author__ = "Lluís Vilanova" __copyright__ = "Copyright 2019-2020, Lluís Vilanova" __license__ = "GPL version 3 or later" from . import spur def install(shell, package): """Install given `package` using `shell`.""" if spur.is_ssh_shell(shell): hostname = shell.hostname else: hostname =...
/sciexp2-exprun-0.3.3.tar.gz/sciexp2-exprun-0.3.3/sciexp2/exprun/files.py
0.560012
0.215846
files.py
pypi
__author__ = "Lluís Vilanova" __copyright__ = "Copyright 2019-2020, Lluís Vilanova" __license__ = "GPL version 3 or later" import re import io import time from . import spur def run(shell, *args, **kwargs): """Run command with a timeout. Parameters ---------- shell Shell used to run given co...
/sciexp2-exprun-0.3.3.tar.gz/sciexp2-exprun-0.3.3/sciexp2/exprun/wait.py
0.738292
0.18352
wait.py
pypi
__author__ = "Lluís Vilanova" __copyright__ = "Copyright 2019-2020, Lluís Vilanova" __license__ = "GPL version 3 or later" import collections import os import re import six # pylint: disable=redefined-builtin def get_tids(shell, pid, filter=None): """Get ids of all threads in a given process. Parameters ...
/sciexp2-exprun-0.3.3.tar.gz/sciexp2-exprun-0.3.3/sciexp2/exprun/process.py
0.808748
0.251947
process.py
pypi
__author__ = "Lluís Vilanova" __copyright__ = "Copyright 2019-2020, Lluís Vilanova" __license__ = "GPL version 3 or later" import atexit import collections import logging import os import signal import sys import threading import time import traceback import six import spur import spur.ssh _LOGGER = logging.getLog...
/sciexp2-exprun-0.3.3.tar.gz/sciexp2-exprun-0.3.3/sciexp2/exprun/spur.py
0.561696
0.15746
spur.py
pypi
<p align="center"> <img src="https://raw.githubusercontent.com/SciFin-Team/SciFin/master/docs/logos/logo_scifin_github.jpg" width=400 title="hover text"> </p> # SciFin SciFin is a python package for Science and Finance. ## Summary The SciFin package is a Python package designed to gather and develop methods fo...
/SciFin-0.1.0.tar.gz/SciFin-0.1.0/README.md
0.700383
0.895751
README.md
pypi
from django.db import migrations, models class Migration(migrations.Migration): initial = True dependencies = [ ] operations = [ migrations.CreateModel( name='AspectActlog', fields=[ ('id', models.AutoField(auto_created=True, primary_key=True, serial...
/sciflow-0.2.tar.gz/sciflow-0.2/datafiles/migrations/0001_initial.py
0.589598
0.17575
0001_initial.py
pypi
from django.db import migrations, models import django.db.models.deletion class Migration(migrations.Migration): initial = True dependencies = [ ] operations = [ migrations.CreateModel( name='Descriptors', fields=[ ('id', models.AutoField(auto_create...
/sciflow-0.2.tar.gz/sciflow-0.2/substances/migrations/0001_initial.py
0.573559
0.160135
0001_initial.py
pypi
from datafiles.df_functions import * from pathlib import Path from sciflow.settings import * def testimport(): """ import test data from static/files in the DB""" folder = Path(BASE_DIR + "/static/files/") for file in folder.iterdir(): if str(file).endswith('.jsonld'): filename = str(f...
/sciflow-0.2.tar.gz/sciflow-0.2/datasets/ds_functions.py
0.450359
0.306611
ds_functions.py
pypi
import json from typing import Literal import re import numpy as np import matplotlib.pyplot as plt from scipy.optimize import curve_fit from tabulate import tabulate from sciform import Formatter, ExpMode, RoundMode, SignMode, FormatOptions def get_scale_and_offset_from_offset_str( ax: plt.Axes, axis: Lite...
/sciform-0.28.2.tar.gz/sciform-0.28.2/examples/fit_plot_with_sciform.py
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0.425247
fit_plot_with_sciform.py
pypi
# scify-file-reader The scify-file-reader package provides a convenient class for handling multiple files with the same structure in a directory. It offers functionality to read and process data from various file types, including CSV, XLSX, Parquet, and JSON. ## Installation You can install scify-file-reader using pi...
/scify-file-reader-0.0.2.tar.gz/scify-file-reader-0.0.2/README.md
0.892829
0.888324
README.md
pypi
import os import re import zipfile from io import BytesIO from pathlib import Path from typing import Union, IO, Tuple import pandas as pd import pyarrow.parquet as pq class FileReader: """ A class to handle and process multiple files with identical structures within a directory or a zip archive. Args: ...
/scify-file-reader-0.0.2.tar.gz/scify-file-reader-0.0.2/scify_file_reader/file_reader.py
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0.297011
file_reader.py
pypi
from scipy.spatial import cKDTree as KDTree import numpy as np class IDW(object): """ # https://mail.python.org/pipermail/scipy-user/2010-June/025920.html # https://github.com/soonyenju/pysy/blob/master/pysy/scigeo.py inverse-distance-weighted interpolation using KDTree: invdisttree = Invdisttree(...
/scigeo-0.0.10.tar.gz/scigeo-0.0.10/scigeo-history-versions/scigeo-0.0.2/geobox.py
0.884601
0.489503
geobox.py
pypi
import math import datetime class Sunriseset: def __init__(self, timestamp = None, format = r"%Y-%m-%d"): if isinstance(timestamp, str): timestamp = datetime.datetime.strptime(timestamp, format) self.timestamp = timestamp def __call__(self, lon, lat): coords = {'longitude' ...
/scigeo-0.0.10.tar.gz/scigeo-0.0.10/scigeo-history-versions/scigeo-0.0.2/sun.py
0.596551
0.399812
sun.py
pypi
from pathlib import Path from shapely.geometry import Polygon import rasterio as rio from rasterio.mask import mask from rasterio.enums import Resampling import geopandas as gpd import warnings import numpy as np class Raster(object): """ the wrapper of rasterio """ def __init__(self, path): s...
/scigeo-0.0.10.tar.gz/scigeo-0.0.10/scigeo-history-versions/scigeo-0.0.2/geoface.py
0.643553
0.396594
geoface.py
pypi
import hashlib import json import random import re import time from typing import Optional import requests from scihub_cn.models import PaperDetailDescription def translate(content: str, proxy=None) -> str: """对文本content进行翻译""" lts = str(int(time.time() * 1000)) salt = lts + str(random.randint(0, 9)) ...
/scihub-cn-0.1.1.tar.gz/scihub-cn-0.1.1/scihub_cn/utils.py
0.545528
0.162945
utils.py
pypi