sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
902ef566016dc3b2f18f629be737766681569af653c353c2b5af1b2f5f28fed6 | Python | 5,757 | 163 | """
This module contains general-purpose functions. Those include saving Filter objects and result tables, \
reading and updating the settings file, parsing common types of genomic feature indices, etc.
"""
import re
from typing import Union
import polars as pl
from rnalysis import __attr_file_key__, __biotype_file_... |
6edb4838ca94327d98b8d7a0925f8fffad2b744405be0bf4e20edb64247cd82a | Python | 5,766 | 175 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import math
from dataclasses import dataclass, field
from typing import Optional, List, Tuple
from omegaconf import II
from fairseq.dataclass... |
ebe18ca0b07f90c53b9b3f9a54ed02df94facf8995cfa90dd41c6f5474537c13 | Python | 5,766 | 171 | #!/usr/bin/env python
#
# Copyright 2009, Google Inc.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list... |
ef258c26e27895bf63975ae315dcfc1944d46ede40955066c2a8e14d00b93603 | Python | 5,767 | 193 | from __future__ import annotations
import os
from pathlib import Path
from typing import TYPE_CHECKING
import pytest
import tomlkit
from poetry.core.constraints.version import Version
from poetry.console.commands.env.use import EnvUseCommand
from poetry.toml.file import TOMLFile
from poetry.utils.env import MockEn... |
63bf34accd61e44753746e9ebfe7467a0d7f5237c978c50dee60568973b03d98 | Python | 5,768 | 142 | # coding=utf-8
# Copyright 2018 Salesforce and HuggingFace Inc. team.
# Copyright (c) 2018, NVIDIA CORPORATION. All rights reserved.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# htt... |
0653ee41617fabc56e7fc45eee0cc4a0226185c293aa3f7790dc46eacdd8bceb | Python | 5,769 | 168 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import logging
import os
import sys
from typing import Dict, List, Optional
import torch
from fairseq.models import (
FairseqIncrementalD... |
2a3c9f2c073a8980d0603604d0255090a7ec365847156d6995bf02946663debc | Python | 5,769 | 202 | from tqdm import tqdm
import torch
import torch.nn as nn
import numpy as np
import msm
from typing import Union, List, Sequence, Optional, Tuple
from functools import partial
import pandas as pd
from .tokenization import Vocab
from .tensor import batched_iterator
from .align import MSA
IntSeq = Union[Sequence[int],... |
aa4e3c73cb1be22c412e478cd0b08b1f20c3395d72d2705b3dd7d7182f263942 | Python | 5,769 | 143 | # coding=utf-8
# Copyright 2018 Salesforce and HuggingFace Inc. team.
# Copyright (c) 2018, NVIDIA CORPORATION. All rights reserved.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# htt... |
deac7b6d20d160e7156238124882407226c4fc9870c8efee96f11cc56f6dee9e | Python | 5,770 | 188 | import torch
from torch import nn
from rinalmo.model.modules import Transformer
def _outer_concat(t1: torch.Tensor, t2: torch.Tensor):
# t1, t2: shape = B x L x E
assert t1.shape == t2.shape, f"Shapes of input tensors must match! ({t1.shape} != {t2.shape})"
seq_len = t1.shape[1]
a = t1.unsqueeze(-2).... |
52d3673a67e358c2be084ca08df158529cab3ed2c35118146c6619d10cb8e2e3 | Python | 5,771 | 92 | """Build the BAP-derived demo from the supplied ZIP without changing RGB pixels.
Usage: python lite-web/scripts/prepare-mouse-brain-demo.py path/to/source.zip
Requires Pillow. Source ZIPs are local inputs, never app assets.
"""
import argparse
import hashlib
import io
import json
from pathlib import Path
import re
imp... |
5dd15d705053d5887a20c017bdcf19f0e952457170061f11e4d00d8f2a6a19ca | Python | 5,774 | 154 | """
This notebook loads in videos of natural scenes collected via the video collection protocol,
and computes the response of a set of Gabor filters.
Author: Jonathan Gant
Date: 04.08.2023
"""
# import statements
import numpy as np
from tqdm import tqdm
import cv2
import glob
import os
import h5py
from decord import... |
cebcba08d5eed1f4491549c9618a5b97c0866ee6246efd8b7269f485cb194acd | Python | 5,776 | 166 | # Copyright (c) Microsoft Corporation.
# Licensed under the MIT License.
import io
import logging
import os
from pathlib import Path
from tempfile import TemporaryDirectory
from typing import Sequence
from zipfile import ZipFile
import ase.io
import hydra
import numpy as np
import torch
from pymatgen.core import Latt... |
5667c048ba0d618c395fbafd129539778897636f7241e01b1ab2e68934b925a0 | Python | 5,782 | 134 | #!/usr/bin/env python3
"""Le o eos_ajuste.csv do modo convergencia e diz se o a0 parou de andar.
Uso:
python3 postprocess_eos.py --work conv/run_conv --out conv
python3 analisa_convergencia.py --ajuste conv/eos_ajuste.csv
A pergunta nao e "o a0 esta certo" -- nao ha referencia para isso aqui. E "o a0
ainda se... |
ad9daedff6ce7f56880520677d41e9e4f3c52f7fb5980aac6d8e56c8758bd501 | Python | 5,782 | 168 | """Pure helpers for photometry-behaviour plotting workflows."""
from __future__ import annotations
from pathlib import Path
import pandas as pd
def build_treeview_rows(dataframe: pd.DataFrame) -> list[list]:
"""Return table rows ready for insertion into the treeview."""
rows = [
[
Path(... |
9ae38ed3001b3fe09161831449c450485d76bc6c5af0250c0ac103e59768b18e | Python | 5,786 | 172 | import collections
import copy
__author__ = 'Robbert Harms'
__date__ = "2016-11-10"
__maintainer__ = "Robbert Harms"
__email__ = "robbert@xkls.nl"
class DeferredActionDict(collections.abc.MutableMapping):
def __init__(self, func, items, cache=True):
"""Applies the given function on the given items at th... |
f15667aa2058f710e4245cd61aaa84558c166ee40e960be2c1a8fe886c0cdbeb | Python | 5,786 | 155 | import os
import re
import sys
from glob import glob
import importlib.util
import platform
import shutil
from setuptools import setup, find_packages, Extension
from setuptools import Distribution, Command
from setuptools.command.build_ext import build_ext
import subprocess
__pkg_name__ = 'medaka'
__dist_name__ = 'meda... |
ec483341097c3bef491905c204b0f90e78c5c97c576e047a5c1a8333b50815f0 | Python | 5,787 | 163 | import math
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
def load_relevance_matrix(input_path: str) -> pd.DataFrame:
"""
Reads a .CSV file containing the relevance matrix for RELISH. Three columns
are needed: PMID 1, PMID 2 and Relevance Assessment.
If the matrix is not pop... |
2fccdbddb60030906155f26fc6ac58a0ae8f91cd6a1e08faf42eea44e12efd76 | Python | 5,789 | 153 | import torch
from pyro.distributions import BetaBinomial as BetaBinomialDistribution
from pyro.distributions import Binomial
from torch.distributions import constraints
from torch.distributions.utils import broadcast_all
from ._constraints import open_interval, optional_constraint
from ._utils import _needs_cpu_detour... |
bf4000d4de8fde715b0fcde76035e3018200cd98b50c4ca1e66d884fd9bd010d | Python | 5,789 | 96 | """CPU-only transform/metric tests; forward/backward lives in the separate smoke script."""
import contextlib
import importlib.util
import io
from pathlib import Path
import sys
import tempfile
import unittest
sys.path.insert(0, str(Path(__file__).resolve().parents[1]))
import trainref3d_backend as backend
from trainr... |
26102f48779208a2ec381a608fdff6b128e03fb5c6e242dacafa3fdfb0dc67ab | Python | 5,790 | 156 | #!/usr/bin/env python3
import csv
import json
import os
import re
import sys
import glob
import argparse
from pathlib import Path
from typing import Any, Dict, List, Optional, Tuple
# -------- config: what to extract (edit here) --------
KEY_PATHS: List[Tuple[str, str]] = [
# (output_column_name, dotted_key_path_i... |
7b5984094126fa25a7be44c9cf014b09ebafc2b5456a9223debcc1b606a6461a | Python | 5,791 | 129 | import argparse
from argparse import ArgumentDefaultsHelpFormatter
from utils.io_utils import obtain_dataset
from utils.model_utils import obtain_placeholders, build_model
from utils.parser_utils import set_defaults_train
from utils.train_utils import train_model, set_seed
def argparser():
parser = argparse.Argume... |
262e780c66bde00290c1fd2298facca35285e67ad4caafa3ebbb91527bb1e111 | Python | 5,792 | 181 | from typing import Callable, Optional
import haiku as hk
import jax.numpy as jnp
import jmp
from nucleotide_transformer.bulk_rna_bert.config import BulkRNABertConfig
from nucleotide_transformer.bulk_rna_bert.layers import SimpleLMHead
from nucleotide_transformer.layers import SelfAttentionBlock
from nucleotide_transf... |
be47776e60ef663e5245a4fce2476d2985ced4108711ee3809652a4e341d34c0 | Python | 5,794 | 149 | # Copyright (c) Microsoft Corporation.
# Licensed under the MIT License.
import json
import logging
from collections import OrderedDict
from copy import deepcopy
from pathlib import Path
from typing import Tuple
import hydra
import omegaconf
import pytorch_lightning as pl
import torch
from omegaconf import DictConfig... |
e69f67ca4c820c1afefade492f0971e7cda1b1b270b7e23d1ffcd053d0cd1c53 | Python | 5,796 | 171 | #
# Copyright 2017-2023 Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with
# Sandia Corporation, the U.S. Government retains certain rights in this software.
#
# See LICENSE for full license details
#
import numpy as np
from scipy.special import softmax
from ...backend import ComputeBackend
... |
2aecf7c627d9fc39a2f1682ef7d132f67927f4ddb4ea662341f5dabcdab0ada2 | Python | 5,797 | 163 | """Tests for vak.train.parametric_umap module"""
import pathlib
import pytest
import vak.config
import vak.common.constants
import vak.common.paths
import vak.train
def assert_train_output_matches_expected(cfg: vak.config.config.Config, model_name: str,
results_path: pathlib... |
ef0c8dff1523a924d5cf92e97351a4638097e8dc18bb4db77d552f6dc4e4d529 | Python | 5,799 | 110 | #! /usr/bin/env python
import os
import logging
import traceback
from timeit import default_timer as timer
from metax import __version__
from metax import Logging
from metax import Exceptions
from metax import Utilities
from metax.predixcan import MultiPrediXcanAssociation
from metax.predixcan import Utilities as Mu... |
2a5450547f3f15b743d8c847591ea2e010533440195a27407dedca6f0a52b648 | Python | 5,802 | 155 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import os
import re
import glob
import json
import tempfile
import math
import torch
from torch import nn
from torch.nn import functional as F... |
108743fb4f1f1576166279040b7e3e8fb4d16a341562538077eb0e4a9f7768db | Python | 5,803 | 177 | # coding=utf-8
# Copyright 2018 The Google AI Language Team Authors and The HuggingFace Inc. team.
# Modifications by Roshan Rao
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http:/... |
94f0338527956bb6adbada6f0b8d5259c0e0c3c92c91784ef270a5ce9be86ebf | Python | 5,803 | 149 | """
Node-level concept direction: concept discovery in the node-level latent space
Used for counterfactual prediction
"""
import torch
from typing import List
from utils.data.dataholder import DataHolder
def compute_node_concept_direction(
node_encoder,
evaluate_datasets: List[DataHolder],
target_cell_ids... |
26f5aeef1ad9e41587643786463352c0312fb0f763d966fc6ca73e825f7b60e7 | Python | 5,804 | 157 | from collections.abc import Callable
import networkx as nx
import numpy as np
import pandas as pd
from pgmpy.base import DAG
from pgmpy.causal_discovery._base import BaseCausalDiscovery
from pgmpy.causal_discovery.bivariate_scores import BaseBivariateScore, get_bivariate_score
from pgmpy.utils import get_dataset_type... |
b73879b33319814cd318d68ff23c53de4d01f619c57621e71678bfd086f42cbf | Python | 5,804 | 133 | """High-level function that generates results for a learning curve for all models."""
from __future__ import annotations
import logging
import pathlib
from .. import models
from ..common.converters import expanded_user_path
from .frame_classification import learning_curve_for_frame_classification_model
logger = log... |
81520ef50c652bed47ba4e967c17a21754923a94b4f99c571241eb1d151047de | Python | 5,806 | 175 | from PyQt5.QtCore import QObject, pyqtSignal
from mdt.visualization.maps.base import MapPlotConfig, SimpleDataInfo
class DataConfigModel:
"""The model contains all the state information for viewing the maps, both the data and the configuration."""
def get_data(self):
"""Get the current data.
... |
e4290aeb5cc9520b5851840a1b0e6f9416e371bc5d361f3af68d74b7975deddb | Python | 5,807 | 141 | import os
from argparse import ArgumentParser, Namespace
from logging import getLogger
from transformers import SingleSentenceClassificationProcessor as Processor
from transformers import TextClassificationPipeline, is_tf_available, is_torch_available
from transformers.commands import BaseTransformersCLICommand
if no... |
a488aeebe50cb37892c081db402832bdabbd476442595226305fb8e09394386e | Python | 5,809 | 144 | import os
from pathlib import Path
import sys
import tempfile
import unittest
from unittest.mock import patch
import numpy as np
from PIL import Image
os.environ.setdefault("QT_QPA_PLATFORM", "offscreen")
os.environ.setdefault("SEGREF3D_DISABLE_SAM2", "1")
MODULE_DIR = Path(__file__).resolve().parents[1]
if str(MODU... |
ce339193af697daa3ca49914564578f5ce106f95d131bec9b64983cd39093bc7 | Python | 5,809 | 186 | import argparse
import os
import random
import time
from copy import deepcopy
import h5py
import numpy as np
import torch
import torch.nn as nn
import torch.optim as optim
from torchdiffeq import odeint
from torch.utils.data import Dataset, DataLoader
learning_rate = 0.001
num_epochs = 500
device = torch.device("cpu... |
469e56897174697172edcba56239074b2e67218d9695c00e01dbef325c0e2dfa | Python | 5,810 | 133 | import utils.gpu as gpu
from modelR.lodet_hbb import Head3_LODet,LODet
from tensorboardX import SummaryWriter
from evalR.evaluator import Evaluator
import argparse
import os
import config.cfg_lodet as cfg
from utils.visualize import *
import time
import logging
from utils.utils_coco import *
from utils.l... |
6e8d4ede26da0c01fc8f4dea7c73bdbdbf94d9340b1783f3a0047a037f3a50dd | Python | 5,815 | 226 | from __future__ import annotations
from importlib import metadata
from typing import TYPE_CHECKING
from typing import Any
import pytest
from poetry.core.packages.dependency import Dependency
from poetry.core.packages.package import Package
from poetry.plugins.application_plugin import ApplicationPlugin
from poetry.... |
715d4492a18298868d82f1a5bfb9e7b8bd82311e3ac5aabcd042414a78a34369 | Python | 5,817 | 129 | # -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'UI/AnalysisWindow.ui'
#
# Created by: PyQt5 UI code generator 5.9.2
#
# WARNING! All changes made in this file will be lost!
from pyqtgraph import PlotWidget
from PyQt5 import QtCore, QtGui, QtWidgets
class RiskWidget(QtWidgets.QWidget):
... |
2f17ad25c0a338daec600de82a838b100cd0d1717135ab7b88babca60be46beb | Python | 5,821 | 120 | #!/usr/bin/env python3
"""Extract loss weights that should be used to train a model.
This is a little utility to read in the training history json and calculate
an appropriate counts loss weight parameter to get the loss balance you want.
Since we only know how large the losses for profile and counts will be after
we'... |
4de9593a72fab0b5b27ab812cfe24c5de8dc5f415385b4c4dc34907ade79b108 | Python | 5,822 | 165 | #!/usr/bin/env python
# Author_and_contribution: Niklas Mueller-Boetticher; created template
# Author_and_contribution: Kirti Biharie; added dataset
import argparse
parser = argparse.ArgumentParser(description="Load data for Mouse Brain (Sagittal-Anterior)")
parser.add_argument(
"-o", "--out_dir", help="Output ... |
3f6e855495c58bce45c76a39bd3e9637e14b99f9bef12c402d262e5c9da8a593 | Python | 5,826 | 160 | import math
import numpy as np
import torch
import torch.nn.functional as F
from torch import nn
from torch.cuda.amp import autocast
from einops import rearrange, repeat
from functools import partial
from contextlib import contextmanager
def exists(val):
return val is not None
class AutoDiscretizationEmbedding2... |
fd3e7aa30fcfacb0d3fb77bfc238ba708f3095073c780e28359cfa1f6ef35a44 | Python | 5,828 | 148 | from __future__ import annotations
import logging
from typing import TYPE_CHECKING, Callable
import numpy as np
from anndata import AnnData
from sklearn.decomposition import PCA
from sklearn.pipeline import Pipeline
from sklearn.preprocessing import StandardScaler
if TYPE_CHECKING:
from spatialdata import Spatia... |
672354db9b346bc30d7d6f5561b754f17c93012c715d22074f0509d6b193b9c6 | Python | 5,830 | 144 | import os
from argparse import ArgumentParser, Namespace
from logging import getLogger
from transformers import SingleSentenceClassificationProcessor as Processor
from transformers import TextClassificationPipeline, is_tf_available, is_torch_available
from transformers.commands import BaseTransformersCLICommand
if n... |
d9aa05954929c50c02a5dd02736045c78bbd235ea39cec3b713702cd5687c24c | Python | 5,832 | 120 | import argparse
import random,os,sys
import numpy as np
import pandas as pd
import argparse
import torch
from tqdm import tqdm
import os
import scanpy as sc
import sys
sys.path.append("../pretrain/")
from load import *
####################################Settings#################################
parser = argparse.Ar... |
138f9d9b07d9e34c2f80cc31aca73deacc6750c07a414d37f2e6344b63d29aad | Python | 5,833 | 165 | #!/usr/bin/env python
# Author_and_contribution: Niklas Mueller-Boetticher; created template
# Author_and_contribution: Kirti Biharie; added dataset
import argparse
parser = argparse.ArgumentParser(description="Load data for Mouse Brain (Sagittal-Posterior)")
parser.add_argument(
"-o", "--out_dir", help="Output... |
2b9ee5d0ddaf89321e235a2a16498ef30d16939c63ae5e55271d344543ddd5cc | Python | 5,840 | 139 | # This extension template provides instructions to add new structure scores to pgmpy.
#
# Please follow the following steps:
# 1. Copy this file to `pgmpy/structure_score/` and rename it as `your_score_name.py` (e.g., `my_score.py`).
# Note: Do NOT start the filename with an underscore `_`, otherwise it won't be dis... |
f874bfb65a54d983fecea04733a59d535d861ea7bbf37a33bb11e0bb97bc6e1a | Python | 5,842 | 146 | import filecmp
import os
import shutil
import socket
from pathlib import Path
import requests
__attr_ref__ = 'tests/test_files/attr_ref_table_for_tests.csv'
__biotype_ref__ = 'tests/test_files/biotype_ref_table_for_tests.csv'
def unlink_tree(dir):
for item in Path(dir).iterdir():
if 'gitignore' in item.... |
bedc59be184f95bfc1eafff5e13d073344ec4ca75236248f6abfbfefed6dc994 | Python | 5,843 | 160 | import tempfile
import unittest
from pathlib import Path
try:
from GMXMMPBSA.createinput import SanderAPBSInput, SanderGBInput, SanderMMInput, SanderPBSAInput
except ModuleNotFoundError as exc:
if exc.name == 'parmed':
SanderAPBSInput = SanderGBInput = SanderMMInput = None
SanderPBSAInput = Non... |
0ffb1af5719f5aef107b8b5681006f1b774e94fc7baa396513e28fb5fcef4616 | Python | 5,844 | 169 | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import argparse
import logging
import os
from pathlib import Path
import shutil
import torchaudio
import soundfile as ... |
ed3c75f4da5fd434817ab999c3a37f417e091bafb17262b764258628f85d7c51 | Python | 5,844 | 191 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import argparse
import itertools
import logging
import re
import time
from g2p_en import G2p
logger = logging.getLogger(__name__)
FAIL_SENT... |
ff786cac43c8f26f84bf1e153321aac26cd7c971da5a352a6ae94492516cc5df | Python | 5,844 | 152 | #!/usr/bin/env python3
"""One-time helper to draft gmx_MMPBSA_test_manifest.json from example READMEs."""
from __future__ import annotations
import argparse
import json
import shlex
from pathlib import Path
TESTS = {
3: ('Protein_ligand/ST', 'Protein_ligand/ST', 'Protein-Ligand (Single trajectory approximation)'... |
8ea1f58159bfd4178fdb4fcc77648267bbae60fc9e4f913aad2b4cfe48135147 | Python | 5,847 | 147 | import pytest
from rnalysis.gui.gui_quickstart import *
LEFT_CLICK = QtCore.Qt.MouseButton.LeftButton
RIGHT_CLICK = QtCore.Qt.MouseButton.RightButton
def widget_setup(qtbot, widget_class, *args, **kwargs):
widget = widget_class(*args, **kwargs)
widget.show()
qtbot.add_widget(widget)
return qtbot, wi... |
b68161adf0f6b5be8a0353f8d6f3c00519689498e5cf7a62e4e762a67854ca8f | Python | 5,847 | 162 | # Copyright 2023 BioMap (Beijing) Intelligence Technology Limited
import math
import numpy as np
import torch
import torch.nn.functional as F
from torch import nn
from torch.cuda.amp import autocast
from einops import rearrange, repeat
from functools import partial
from contextlib import contextmanager
def exists(v... |
80606889a611c6fc10db89b7d4f5173064ff2fddfaad4d9023b5367ca260006c | Python | 5,848 | 182 | import logging
import os
import vtk
import slicer
from slicer.ScriptedLoadableModule import *
from slicer.util import VTKObservationMixin
#
# ImportACPCAutodetect
#
class ImportACPCAutodetect(ScriptedLoadableModule):
"""Uses ScriptedLoadableModule base class, available at:
https://github.com/Slicer/Slicer/... |
ad6be99959d5844e8280b0c9abf738b4405b433b58a1ee413431468d9fcd5a29 | Python | 5,851 | 247 | class var_list:
#From UI
countoflistwidget = 0
list_toggle = 9999
#FROM BUTTONCLASS *********************************************************
#Main while loop condition
keepalive = True
#Stepper instances
APmove = None
MLmove = None
DVmove = None
AUXmove = None
# OFFS... |
026c9a4843cc2655431a47dacd025586fd00be21e0f31c93e9cab77822f50f77 | Python | 5,853 | 145 |
import slicer
import qt
import csv
import os
import numpy as np
from PIL import Image
# =====================
# DICOM/NRRD → JPG 変換
# =====================
def convert_nrrd_to_jpg():
file_dialog = qt.QFileDialog()
file_dialog.setFileMode(qt.QFileDialog.Directory)
output_folder = file_dialog.getExistingDir... |
e6e2d791d8badccd982100d6edac7d3c275a49d9de5f1bfc96f3bbd7dc556d5b | Python | 5,853 | 172 | """Helpers for GBNSR6-specific topology compatibility."""
from pathlib import Path
import os
import shutil
DIHEDRAL_POINTER_INDEXES = (6, 7, 14, 17)
_LJ_FLAGS = ('LENNARD_JONES_ACOEF', 'LENNARD_JONES_BCOEF')
def prepare_gbnsr6_topology(prmtop, output_prmtop):
"""Create a GBNSR6-compatible prmtop copy.
The... |
8c9ad1bbb4cf37676e8a055d8750772348efefebbdf91c6b1fc948eed938345a | Python | 5,854 | 138 | import copy
import logging
import numpy as np
from torch.utils.data import (
BatchSampler,
DataLoader,
RandomSampler,
Sampler,
SequentialSampler,
)
from scvi import settings
from scvi.data import AnnDataManager
from ._samplers import BatchDistributedSampler
logger = logging.getLogger(__name__)
... |
eec75c2e4b7b791b121d8e00725c1eb2650e94b375b02056d87d4698c1386e03 | Python | 5,854 | 191 | import os.path
from typing import BinaryIO, Dict, Any
from io import StringIO
import threading
import pandas as pd
from utils.typed import PathLike
from utils.align import MSA
# # 原输入
# class FFindex(object):
# def __init__(self, index_file: PathLike, data_file: PathLike):
# super().__init__()
# se... |
b43ab690c08e4bffd84a47b361167496298697f9511bdf4a745bf305b5cfbdfc | Python | 5,856 | 172 | #!/usr/bin/env python
#
# Copyright 2009, Google Inc.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list... |
d5bf25423ecce5bd5e1d988b74a20c262f6c5735861f930dd4578e6c6fa113cf | Python | 5,857 | 139 | """Custom layers that are needed for the various models."""
from collections.abc import Callable
from typing import Any
from bpreveal.internal import disableTensorflowLogging # pylint: disable=unused-import # noqa
from keras.layers import Conv1D, Reshape, Layer # type: ignore
from keras.ops import convert_to_tensor
i... |
9952f98d1284b56c580fa66de415806ae05d8eaf0a6a0cf725536276f070e8de | Python | 5,859 | 110 | import os
import json
import pandas as pd
import numpy as np
from tqdm import tqdm
from main_ds import correlation_cog, correlation_tau, ab_status_and_apoe4
def synthetic_analysis(data_dir):
cog_results = {'all': [], 'CN': [], 'MCI': [], 'Dementia': []}
tau_results = {'all': [], 'ab_pos': [], 'ab_neg': []}
... |
c4bd12f1f5aebfcb02f563e40b9a522281fbc576a972dcb7693f5f2b723ac0e6 | Python | 5,863 | 194 | from __future__ import annotations
import json
import re
from typing import TYPE_CHECKING
from typing import Any
from urllib.parse import urlparse
import pytest
import responses
from packaging.utils import parse_sdist_filename
from packaging.utils import parse_wheel_filename
from poetry.repositories.pypi_repositor... |
6fece3e52e7175a5653d8e8d3463197b9d22f6fbee3026655a85a10c0befc9b9 | Python | 5,864 | 124 |
import sys
sys.path.append("..")
import torch.nn as nn
from modelR.backbones.mobilenetv2 import MobilenetV2
from modelR.backbones.shufflenetv2 import ShuffleNet2_Det
from modelR.backbones.ghostnet import GhostNet_Det
from modelR.necks.conv_csa_drf_fpn_hbb import FC2_CSA_DRF_FPN
from modelR.necks.yolo_fpn impo... |
d831b7319578922144670975becaa8465295a8a888978292c4a88be22c353396 | Python | 5,864 | 194 | #!/usr/bin/env python
# Author_and_contribution: Niklas Mueller-Boetticher; created template
# Author_and_contribution: Zaira Seferbekova; wrote the code for SCAN-IT
import argparse
# TODO adjust description
parser = argparse.ArgumentParser(description="Method ...")
parser.add_argument(
"-c", "--coordinates", h... |
165e20fc782b7a10b75551a94925ce2073a317a2b6ba6316ee5de64906e46d07 | Python | 5,866 | 199 | import time
import random
import numpy as np
from neuron import h
from neuron.units import ms, mV
from matplotlib import pyplot as plt
import matplotlib.cm as cm
import morphology_simplified as morphology #dlambda applied version of morphology
# import singleCell.morphology as morphology
import argparse
import ... |
6dc6ca5caa8124b841f43c2e1b6ffd92f26b10d7eab0eb0bb13e957b15cf06d8 | Python | 5,866 | 140 | import celltype_ibl.models.linear_classifier as linear_probe
import celltype_ibl.models.mlp_classifier as mlp_probe
# from celltype_ibl.models.ACG_augmentation_dataloader import get_c4_labeled_dataset
from celltype_ibl.utils.ibl_data_util import get_ibl_wvf_acg_pairs
from celltype_ibl.utils.cell_explorer_data_util impo... |
1afaa5f5bdf6d240e82ea66cfd2c69c9362696155ef33fb6507b3232586cef0d | Python | 5,867 | 161 | import os
from typing import Optional, Any
from collections import defaultdict
import torch
from simulation_encoder.logger import Logger
from simulation_encoder.loaders.loader import Loader
from simulation_encoder.loaders.dataset_utils.label_loaders import LabelLoader
class ARCADELoader(Loader):
"""
Loader ... |
4efee9c3683bcdc5b422c70d92a6e4f45e512118a8d704ef387b9608a7f409b2 | Python | 5,870 | 170 | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import torch
from examples.speech_recognition.data.replabels import pack_replabels
from fairseq import utils
from fair... |
42e77aaff1c3e2630f3bec6f2412dd40d97e334d31538d7c6a00b56a5bece63e | Python | 5,874 | 177 | """S800: 800 abstracts with hand-assigned NCBI taxids, one per species span.
The corpus `end` offset is inclusive and this package's is half-open, so
`load_s800` converts and then checks every mention against the text it
addresses: a one-character-short span tokenizes and matches nothing, lowering
a score with nothing... |
c5441da07b54f13176524845bda45e669fe29430d54e54472ece2345790a8c0b | Python | 5,874 | 154 | import numpy as np
import pandas as pd
import pytest
from st_risk.eval.dual_axis import (
assign_dual_axis_quadrants,
build_dual_axis_scores,
dual_axis_correlation_summary,
dual_axis_filter_strategy_masks,
dual_axis_filter_strategy_summary,
dual_axis_quadrant_proxy_summary,
normalized_axis_... |
df68f8551f120a7c878a94d0874f402f98a16a3d3b495802ccbff5252c8c561f | Python | 5,876 | 150 | from collections.abc import Iterable
import numpy as np
import pandas as pd
def collect_state_names(data: pd.DataFrame, variable: str) -> list:
"""Return the sorted observed states for `variable` in `data`."""
return sorted(list(data.loc[:, variable].dropna().unique()))
def build_state_names(data: pd.DataF... |
35659099ce603e3d79066496e4a92a0d69902f7368901819d16c32e889659a23 | Python | 5,877 | 188 | # coding=utf-8
# Copyright 2019-present, the HuggingFace Inc. team.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by a... |
721c4871738288c05939657bc07278b6332daafdb727fd28ce00c0ad5a11a60d | Python | 5,878 | 189 | # coding=utf-8
# Copyright 2019-present, the HuggingFace Inc. team.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by a... |
2cd5cbfa8becabda2a4f861b85c2ba51f5a125aaeaabcc1874610ac0e9de3b1d | Python | 5,879 | 165 | """
Per-window exponential-smoothing forecaster for fMRI ROI time series.
This module exposes a lightweight sklearn-style adapter used by the shared
LOSO cross-validation pipeline. Unlike the torch models, the forecaster does
not learn global parameters during ``fit``. Instead, each call to ``predict``
fits a separate... |
7e1906858aa67391434df72d8df3f39af2c9ef702743d579b7d62c4e1594160c | Python | 5,879 | 145 | import argparse
import pandas as pd
import numpy as np
from typing import List, Tuple
def read_file(tsv_file: str) -> Tuple[List, pd.DataFrame]:
"""
Reads the input 4-column cosine similarity existing pairs TSV file in a pandas dataframe, generates all the unique PMIDs
and returns the dataframe.
... |
aab8692fc3c0208fbbbc7a65678755eb89d554f81a47b62c9db336015a16995f | Python | 5,881 | 160 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import math
import torch
import torch.nn as nn
import torch.nn.functional as F
class AdaptiveMask(nn.Module):
"""Soft masking function f... |
29cf2d9f562e58d9dbae95afc2f33c2d8390501ea1bccc2e9b159982761c118a | Python | 5,882 | 164 | import sys
from os import makedirs
from os.path import join, dirname, realpath, exists
current_dir = dirname(dirname(realpath(__file__)))
sys.path.insert(0, dirname(current_dir))
import collections
import pandas as pd
from matplotlib import pyplot as plt
import numpy as np
from sklearn import metrics
from sklearn.m... |
ac83da9ce859b4c18ac61c236d871bc5de6ae67a84722049f5ae5e8d072e9b10 | Python | 5,883 | 178 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Jan 7 16:08:58 2026
@author: tower4
"""
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Mar 21 15:56:25 2024
@author: tower2
"""
from sklearn import metrics
import torch
import copy
import os
import random
import numpy as np
from se... |
59661a24a69d60abdb5438ae77953eb26278a3b68facf26f84e2278771e8a31d | Python | 5,884 | 170 | from neuron import gui, h
from neuron.units import ms, sec, mV
import morphology_simplified as morphology
import time
import random
import argparse
from datetime import datetime
from controller import save_as_pkl
from conductance_distribution import get_baseline_weight_distribution, get_altered_weight_distribution
... |
874fccee86325efa30c2fa85636759d3198b0ff67a7c606f8468d6e6c6e9e448 | Python | 5,884 | 196 | from __future__ import annotations
import urllib.parse
from collections import defaultdict
from functools import cached_property
from typing import TYPE_CHECKING
from unittest.mock import PropertyMock
import pytest
from packaging.utils import canonicalize_name
from poetry.core.constraints.version import Version
fro... |
3899b514f2fa97dbeda35ed7b3eb21dc21741eceb12a0e958f3187b915b6318f | Python | 5,886 | 128 | import argparse
import os
from image_processing_functions import (
apply_robustfov,
apply_bias_correction,
ants_linear_T1w_NM_registration,
ants_normalization_to_MNI,
transform_images_to_MNI_and_NM_space,
compute_CNR_map,
save_SNVTA_results
)
def process_subject(nifti_dir, output_dir, subje... |
000fcd40118dee613063d3fa93e009fff6bada3c8939ae887270694da9e32c99 | Python | 5,892 | 177 | """ICNet model directly taken from https://github.com/tinglyfeng/IC9600/blob/master/ICNet.py."""
import torch
import torch.nn as nn
import torch.nn.functional as F # noqa
import torchvision
class slam(nn.Module): # noqa
"""Spatial attention module."""
def __init__(self, spatial_dim):
"""Spatial at... |
14265659f94a05a93f0f7acded326f41d1c84d82711a96f37bbce0c0b8d433f3 | Python | 5,892 | 156 | import unittest
import sys
import shutil
import os
import io
import gzip
import re
if "DEBUG" in sys.argv:
sys.path.insert(0, "..")
sys.path.insert(0, "../../")
sys.path.insert(0, ".")
sys.argv.remove("DEBUG")
import metax.ThousandGenomesUtilities as ThousandGenomesUtilities
def buildDummyPeople():
... |
86229a33e5c00f4f654bb7692f3ee6880468f18c35db82403adad098c2f49767 | Python | 5,892 | 171 | import logging
import os
import shutil
import tarfile
import warnings
import numpy as np
from scvi import settings
from scvi.data._download import _download
from scvi.utils import dependencies
logger = logging.getLogger(__name__)
available_datasets = {
"1.1.0": [
"frozen_pbmc_donor_a",
"frozen_p... |
ff1fe6d685a776b65959ffdecb1fbc99d0df03fb67f11c3702d59bd3bb9c0479 | Python | 5,892 | 131 | """Page 8: Target Session Analysis."""
import streamlit as st
import plotly.express as px
import plotly.graph_objects as go
import pandas as pd
import numpy as np
from utils import PIPE_ORDER, PIPE_COLORS, style_figure
def render(store, dataset):
st.header("Target Session Difficulty")
st.markdown(
"W... |
1f8213f1a84e5a48eb12481d768c042578afb2dd20e2e9180b29d4386c0128f2 | Python | 5,893 | 122 | """
Exception types deliberately raised by RNAlysis.
This module imports nothing at all (not even from the standard library), so that it stays cheap to import from
anywhere in the package, including hot paths and modules that are imported at startup.
Every exception raised on purpose by RNAlysis inherits from :class:... |
fb71a0d2a8ab16947674782e74c3ab935f6c25b1a217ef91baaa9d936b3e02c1 | Python | 5,893 | 141 | """
BSD 3-Clause License
Copyright (c) 2017, Prem Seetharaman
All rights reserved.
* Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice,
this list of... |
ca3f98b3f1cf63c48fddb05ca54135c5605a8ccc1c3c08a582b9f5032d7afe10 | Python | 5,894 | 162 | # Copyright 2018 The Lucid Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable l... |
37d48fb45053032cdf431fdb306f576ded5720c6fd826fd32bebf5e3caa2ca29 | Python | 5,897 | 102 | ## A pipeline for the ROI-based analyses
#
# written by S-C. Baek
# update: 16.12.2024
#
'''
The following code is to replicate the results of the ROI-based analyses in the paper.
To run this code, all python toolboxes in 'requirements.txt' under MAINDIR should be installed.
(Note: MAINDIR is a path to this repository... |
8c3eae06ead1f34471bcb08a4a22e26e3ee614b7f019bcb08babe23839584eb1 | Python | 5,897 | 156 | import zarr
import pyvips
import argparse
import numpy as np
import multiprocessing as mp
from pathlib import Path
from einops import rearrange
def get_ome(im, pth, check_alpha=True, is_small=False):
r"""
Convert the pyvips image to *.tif such that the output
is comptabile to QuPath
Args:
... |
c207aff9fad2ea252e263db0230c042845538c7c34a2f5b0adc591a3d97f58a6 | Python | 5,897 | 172 | """Module to mock data needed for several tests to run"""
import array
import os
import tempfile
import h5py
import numpy as np
import pysam
from medaka import common
# Ref A C A T * G A T G
#
# Basecall1: 2A 1C 4A 5T 1G 1A 2T 1G
# Basecall2: 0A 1C 4A *... |
839efe5f1bc42acbab766f59076a1e4d66e65a847103fed2d3c3ea5a46f95bc4 | Python | 5,901 | 154 | import argparse
import os
import cv2
import numpy as np
import torch
from torchvision import models
from pytorch_grad_cam import (
GradCAM, FEM, HiResCAM, ScoreCAM, GradCAMPlusPlus,
AblationCAM, XGradCAM, EigenCAM, EigenGradCAM,
LayerCAM, FullGrad, GradCAMElementWise, KPCA_CAM, ShapleyCAM,
FinerCAM, Seg... |
68ec7a7c3392d63ec007313a58ce73cabffef06fe279e288707eefa9d28e9c51 | Python | 5,909 | 173 | # Plot results from the 'many-parameter' simulation
import numpy as np
import matplotlib.pyplot as plt
font = { 'size' : 20}
plt.rc('font', **font)
#%% Plot parameters
fig_width = 3.5
fig_height = 5
legendfontsize = 15
linewidth = 2.5
#%%
#where to save the figures into
figpath = '/Users/iivanaj1/Library/CloudSt... |
ee06cec9b81e18688948ef4e4400458ce08373fc94766e6e97a2796da673197b | Python | 5,911 | 165 | import logging
import os
import re
import sys
from typing import Any, Dict, List, Optional, Union
import yaml
class Punchcard:
def __init__(self, name: str, parent: "Punchcard" = None, subsets: List["PunchcardSubset"] = None, children: Dict[str, "Punchcard"] = None) -> None:
self.name = name
self.parent = paren... |
f249a697083bc2fb727577dd0855c2b0e8a4394a71293c22cd58c537e15bda7f | Python | 5,911 | 115 | # -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'UI/SimpleCorrUI.ui'
#
# Created by: PyQt5 UI code generator 5.5.1
#
# WARNING! All changes made in this file will be lost!
from PyQt5 import QtCore, QtGui, QtWidgets
class Ui_Form(object):
def setupUi(self, Form):
Form.setObjec... |
e8a456cd3054780a84d420c9c51d058fedcd9d6c63b23b80a5276ab3f18a7f5b | Python | 5,912 | 175 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Mar 21 17:55:53 2024
@author: tower2
"""
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Mar 21 17:30:46 2024
@author: tower2
"""
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Mar 21 15:56:25 2024
@author: tower... |
42b95ac9fc2d315f70fabfeeae9fffb09b9ef5b1a96d3f8ec4a8cbe61d91687a | Python | 5,914 | 190 | """
@file utility.py
@author Simon Yu
@date 01/26/2023
@brief Utility functions.
"""
import datetime
import header
import logger
import natsort
import numpy
import os
import random
import socket
import torch
import torchvision
import wandb
def applySoftmax(output):
return torch.nn.functional.softmax(output, ... |
4824899631db82e4a38be063cca820800b16f0279552dbbb7358aee98ba5d3cf | Python | 5,914 | 154 | """Utility classes for tracking and averaging during network simulation."""
import numpy as np
import numpy.typing as npt
class Tracker:
"""Records a target array over time, compressing samples by averaging.
Records ``length * compress_len`` raw samples, compressed (averaged) into
``length`` stored entr... |
9d0d4cfce3fd0dc2a88d004418494a430f13cc74803a4db6feabbbe37f845615 | Python | 5,919 | 133 | """
plot_GSE144744_kaufmann_celltypes.py
--------------------
Re-render Ramesh 2020 figures with a clearer palette using the cached
adata_ramesh_umap.h5ad. Avoids re-running the slow UMAP step.
"""
import warnings
from pathlib import Path
import numpy as np, pandas as pd, scipy.sparse as sp
import anndata as ad
import ... |
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