sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
6d2625581fc7034d13fb897e47ab4f1bc5ef81e1726a1088748d7092bb9c39f9 | Python | 14,133 | 331 | #!/usr/bin/env python
# coding: utf-8
import os, sys
import numpy as np
import matplotlib.pyplot as plt
from scipy.spatial.transform import Rotation as R
from ast import literal_eval
import meshio
import open3d, cv2
from visualization import DepthMapOpen3D
import json, codecs
from skimage.transform import resize
from ... |
115bb45f5981270ffc70d211d7724994468e7e41dd23deba7a5a9047693c6d54 | Python | 14,138 | 293 | # Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
#
# 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://w... |
94f9c0f4df2c76b25c2d598ff97ff0e564040e14679ce0a75bb8fe20d05e1e30 | Python | 14,143 | 383 | ###########################################################################################
# Implementation of different loss functions
# Authors: Ilyes Batatia, Gregor Simm
# This program is distributed under the MIT License (see MIT.md)
################################################################################... |
51cfb56973b5d10264a03eaea048697e2a1e2bb9fbc1586da35aa25b17675216 | Python | 14,144 | 421 | from numpy import float32
import torch
import torchvision
from torch import Tensor, dropout, nn
import torch.nn.functional as F
import math
import torchinfo
from torchvision.models.feature_extraction import get_graph_node_names
from torchvision.models.feature_extraction import create_feature_extractor
import torchvisio... |
ed46deca8f1a2801dab08410fc23ccecd23d677899c7b086cef0939d3c150376 | Python | 14,145 | 461 | import numpy as np
from nearl import commands
np.random.seed(0)
# For dummp data generation
atom_nr = 300
frame_nr = 50
# For the settings of the grid
dims = np.array([32, 32, 32], dtype=np.int32)
spacing = 1.0
cutoff = 2.5
sigma = 1.0
def test_benchmark_frame_voxelize(benchmark):
tmp_coords = np.random.norma... |
916ca51087406d36d46da07017a8157efeffa44676e8cd8cb9040b224c906ae2 | Python | 14,146 | 463 | import os
import numpy as np
from . import log, utils
class _MissingExtension:
"""Stands in for an unbuilt extension so use-sites fail with a clear reason."""
def __init__(self, name, build_hint):
self._name = name
self._build_hint = build_hint
def __getattr__(self, attr):
rais... |
1aa8b268672ce09b0319f44343c08c56bcbe55cf59e280ca5392761e8cd9e348 | Python | 14,156 | 296 | # -*- coding: utf-8 -*-
# encodermap/plot/jinja_template.py
################################################################################
# EncoderMap: A python library for dimensionality reduction.
#
# Copyright 2019-2024 University of Konstanz and the Authors
#
# Authors:
# Kevin Sawade
#
# Encodermap is free soft... |
aa5e6fb213f2168caabd97ad11103634faaed2d9124d7a94d274ef79a23b9e06 | Python | 14,158 | 421 | # This file is part of h5py, a Python interface to the HDF5 library.
#
# http://www.h5py.org
#
# Copyright 2008-2013 Andrew Collette and contributors
#
# License: Standard 3-clause BSD; see "license.txt" for full license terms
# and contributor agreement.
"""
Dataset slicing test module.
Tests all ... |
abeb7801352d7013e1146b07ad0c035862c227eb282f547f044caa6ef6f15680 | Python | 14,163 | 364 | import decimal
from functools import reduce
import json
from typing import Any, Dict, List, Optional, Tuple, Union
from django.db import connection
from catmaid.error import ClientError
class StateMatchingError(ClientError):
"""Indicates that a state check wasn't successful"""
def __init__(self, message, st... |
eb37a1030e96690af802445625c09f3bd3e1984560f0c69247d9ea35de8fe71a | Python | 14,172 | 351 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Jun 2 16:28:47 2023
@author: george
"""
from qtpy.QtCore import *
from qtpy.QtGui import *
from qtpy.QtWidgets import *
import numpy as np
import pandas as pd
import pyqtgraph as pg
import os
# import pyqtgraph modules for dockable windows
from pyqtg... |
b275c28fe9654ee4b2cc70c815906e88a3aacd977cedd2fb3b8beab6e3f6b9dc | Python | 14,193 | 403 | from typing import Any, Dict, List
import numpy as np
import pytest
from hypothesis import given, settings, strategies
from scipy import sparse
import xgboost as xgb
from xgboost.testing import (
IteratorForTest,
make_batches,
make_batches_sparse,
make_categorical,
make_ltr,
make_sparse_regres... |
9d21e0d1e94d28237348074ccf1844d2fb5e79ec0a817c5d7cd8f0a025efd82c | Python | 14,195 | 354 | from PyQt5.QtWidgets import (QVBoxLayout, QLabel, QHBoxLayout, QWidget, QPushButton, QAction, QFileDialog,
QComboBox, QListWidget, QAbstractItemView, QSplitter, QApplication, QStyleFactory)
from PyQt5.QtGui import (QPixmap, QPainter, QPen, QColor, QBrush, QFont, QIcon)
from PyQt5.QtCore impo... |
3c2d9ae632f88bc0289b107b30f1779fab80cbb164cf8f0530be23b866455113 | Python | 14,197 | 271 | # Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
#
# 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://w... |
c980ab0087a8cc1f56488ade7482cab6e760565f6904c3ba7eee0524bd5a319a | Python | 14,201 | 425 | import typing
from typing import Any, Dict, List, Optional, Iterator, Tuple, Generator
try:
import duckdb
except ImportError:
duckdb = None
from kgx.config import get_logger
from kgx.source.source import Source
from kgx.utils.kgx_utils import (
generate_uuid,
generate_edge_key,
sanitize_import,
... |
1dbc1668cc2e3129ac581386351a47c181d4626d43534510630538c981e4a602 | Python | 14,204 | 407 | from user.serializers import UserSerializer
from mlcube.serializers import MlCubeSerializer
from asset.serializers import AssetSerializer
from model.serializers import ModelSerializer
from dataset.serializers import DatasetFullSerializer
from result.serializers import ModelResultSerializer
from benchmark.serializers im... |
d19b99ad67bd225bae6d811346ad11fc58de4af5b901505a8312e8231895943c | Python | 14,214 | 403 | import logging
from fastapi import APIRouter, Depends, Form
from fastapi.responses import HTMLResponse, JSONResponse
from fastapi import Request
from typing import Optional
from medperf.commands.benchmark.submit import SubmitBenchmark
from medperf.commands.execution.utils import filter_latest_executions
impo... |
3220b1e69a3e48166dc94805502ded7c3a2fcaa5be804eda42f0ba32c4dd3a9c | Python | 14,219 | 376 | import copy
from collections.abc import Callable, MutableMapping, MutableSequence
from functools import partial
from typing import cast
from cwl_utils.types import CWLObjectType, CWLOutputType
from ruamel.yaml.comments import CommentedMap, CommentedSeq
from schema_salad.exceptions import ValidationException
from schem... |
401a7c648873804deb67238ed9bafd7ae05a1c2c679099a43df54b259a62ab7d | Python | 14,222 | 363 | from torch.utils import data as data
from torchvision.transforms.functional import normalize
from basicsr.data.data_util import (paired_paths_from_folder,
paired_DP_paths_from_folder,
paired_paths_from_lmdb,
pai... |
7d54f00cbc39892de8b664ca33f25eb8b79662c3abef60af1f07cdd8531e033f | Python | 14,222 | 286 | import os
import json
import argparse
import random
import torch
import torch.nn as nn
import numpy as np
from data import generate_datasets, get_pretrain_loaders, get_finetune_loaders
from prompts import seps
from models import get_model
from pretrain import pretrain
from finetune import finetune
parser = argparse.... |
0ccf1d2ae9fb483273eae3fa63c86d0ae84823495f8cc80e88ac6d9762753dcd | Python | 14,227 | 347 | from mendeleev import element
import matplotlib.cm as cm
import matplotlib.patches as patches
import matplotlib as mpl
import matplotlib.ticker as ticker
from sklearn.metrics import r2_score, mean_absolute_error
from matplotlib.pyplot import MultipleLocator
import numpy as np
from collections import defaultdict
import... |
1a00869faf1ac98fb43aba6021fa333c9a697e41c416bcab8a281e237678977e | Python | 14,242 | 458 | """Functions to create intermediate GM volumes for use in registration to the structural reference volume."""
import os
import shutil
from glob import glob
import brainbuilder.utils.ants_nibabel as nib
import numpy as np
import pandas as pd
from brainbuilder.align.align_2d import concatenate_sections_to_volume
from br... |
89f4112b948de49bd4fd966e13d0b8696393d36d943a1daef7665e7dc8b74d5e | Python | 14,244 | 455 | """Tests for client-side source mount/unmount and fetch handler."""
import time
import ase
import numpy as np
import pytest
from ase.data import covalent_radii
from zndraw.client import ZnDraw
# ---------------------------------------------------------------------------
# Helpers
# ---------------------------------... |
89a722b5fadc0e31ad2da55903cef20fbf122a68700477b9d7b6581fc4a6f9b3 | Python | 14,245 | 308 | import numpy as np
from collections import Counter, defaultdict
from time import time
import re
from sklearn.base import clone as CLONE
import warnings
from sklearn.exceptions import ConvergenceWarning
import sklearn.metrics as metrics
# Imputation
from sklearn.experimental import enable_iterative_imputer
from sklearn... |
cf33c272aadcd41f8a89e5e5785a516d4eeeb4fe8d0f90687f3b335383e73605 | Python | 14,267 | 331 | # This module is to process different transcript state, and set information
# for the transcript states, and finally get ready to run MCMC sampling.
import sys
import numpy as np
from .sam_utils import load_samfile, fetch_reads
from .bias_utils import FastaFile, BiasFile
from .gtf_utils import Gene, Transcript
def no... |
c20e993925c5a52fa288d48d9d2309f82578a373f0e4e8b1730ea65df40894fd | Python | 14,269 | 353 | import gzip
import json
import logging
import os
import re
import src.datahandlers.umls as umls
from src.babel_utils import glom, read_identifier_file, write_compendium
from src.categories import GENE
from src.metadata.provenance import write_concord_metadata
from src.prefixes import DICTYBASE, ENSEMBL, FLYBASE, HGNC,... |
6dd279d6b9584372677dba7b7f7c8175374e420e8fd4e0d328c837e71d521022 | Python | 14,270 | 377 | import logging
import os
import pandas as pd
from medperf.entities.dataset import Dataset
import medperf.config as config
from medperf.entities.cube import Cube
from medperf.utils import approval_prompt, dict_pretty_print
from medperf.exceptions import (
CommunicationError,
ExecutionError,
InvalidArgumentEr... |
f1c0eb2ccde5419c09d149461bae1ad78d67772f85b9089f4916da0798181452 | Python | 14,281 | 316 | import tempfile
import unittest
from pathlib import Path
import numpy as np
import pandas as pd
import bbb_state_transition_model as bbb
class TestStateTransitionModel(unittest.TestCase):
def test_file_fingerprint_is_portable_and_exact(self):
with tempfile.TemporaryDirectory() as tmp:
path =... |
bb8d133385444273f1c086e4106adb73d86b27c555accd958cda577ae0731be8 | Python | 14,290 | 381 | import pandas as pd
from matplotlib import pyplot as plt
import os
import numpy as np
def process_df(train_df, val_df, test_df, params):
loss_metrics = []
acc_metrics = []
for group_idx in range(params['n_groups']):
loss_metrics.append(f'avg_loss_group:{group_idx}')
acc_metrics.append(f'av... |
45e500f630f8fe564a3d98b0e22ce3f181c03b04ee50fe118ebce78eb1eaa8e5 | Python | 14,297 | 425 | # pyre-strict
import bisect
import math
from typing import List, Optional, Sequence, Union
# pyre-ignore-all-errors[58] # handle optional
__all__ = [
"ParamScheduler",
"ConstantParamScheduler",
"CosineParamScheduler",
"ExponentialParamScheduler",
"LinearParamScheduler",
"CompositeParamSche... |
9a7efd2f0c33b05e3eaf494aed7289e6bec24bd12d39ff6c552c5a59bd212a1d | Python | 14,299 | 327 | """
Iterative closest point algorithm
This file contains an implementation of the iterative closest point algorithm.
This algo registers two sets of points (3D coordinates) together.
Adapted from:
https://stackoverflow.com/questions/20120384/iterative-closest-point-icp-implementation-on-python
NOTES ON ITK Transform... |
61637cfeffbb1a8113f9fdfac749f37866fd27c2208f4d6d841c020a5b84c333 | Python | 14,303 | 406 | from numpy import float32
import torchvision
import torch
from torch import Tensor, dropout, nn
import torch.nn.functional as F
import math
import torchinfo
from torchvision.models.feature_extraction import get_graph_node_names
from torchvision.models.feature_extraction import create_feature_extractor
import torchvisio... |
3b8fbcddc7b5f413a31d2b19a0286e40080194ffd5dd7ca9087e07f582ac9243 | Python | 14,309 | 365 | from collections import Counter
import argparse
import os
import json
import numpy as np
from pathlib import Path
from tqdm import tqdm
from p_tqdm import p_map
from scipy.stats import wasserstein_distance
from pymatgen.core.structure import Structure
from pymatgen.core.composition import Composition
fro... |
2592b46172557fe5b1be2b21d15169b0a8ee751c9f7f93aa8845e6c93bce341b | Python | 14,312 | 404 | from __future__ import annotations
import csv
from io import StringIO
import logging
import os
import os.path as op
from os.path import join as opj
from pathlib import Path
import stat
from unittest.mock import patch
import pytest
from heudiconv import __version__
from heudiconv.bids import (
SCANS_FILE_FIELDS,
... |
83d0024668835a1e2f37c014f60ff58dffffe82bc8589dfbb176dd6213844aba | Python | 14,312 | 393 | """
Qt widgets for manual labeling of images
Copyright (c) 2017 Polytechnique Montreal <www.neuro.polymtl.ca>
License: see the file LICENSE
"""
import logging
from time import time
from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
from matplotlib.backends.backend_qt5agg import Navigati... |
4083663305246cee21caae4419bc726616d26949439565fae19e9b8579ca2bf8 | Python | 14,330 | 362 | import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
from pathlib import Path
from typing import Dict, Any
from ..logger import logger
from hmmlearn import hmm
import pickle
import scipy
import os
def get_autosomal_chroms(config):
"""
Get autosomal chromosomes only (excl... |
58f9d38ce56ac27014d3e503bddd5932e02ab9f00459594b5598dbf607c466e2 | Python | 14,330 | 314 | import numpy as np
from collections import Counter, defaultdict
from time import time
import re
from sklearn.base import clone as CLONE
import warnings
from sklearn.exceptions import ConvergenceWarning
import sklearn.metrics as metrics
# Imputation
from sklearn.experimental import enable_iterative_imputer
from sklearn... |
59058e007099da432bfedd9e6d77074ff0aa780873678371a2548f1e6c3ea9f1 | Python | 14,332 | 299 | """
This scripts validates the graphTRIP VGAE representations
on and independent dataset (psilodep1).
Dependencies:
- experiments/configs/psilodep1_finetuning.json
Outputs:
- outputs/validation/evaluate_graphtrip/
- outputs/validation/pretraining/
- outputs/validation/finetuning/
Author: Hanna M. Tolle
Date: 2025-12... |
2704502598dde115b55559bff8b56563a94eed5cdae4087ec8941a2a077f9972 | Python | 14,350 | 319 | import torch
import torch.nn.functional as F
from torch.utils.data import TensorDataset, DataLoader
import numpy as np
from models import TSEncoder
from models.losses import hierarchical_contrastive_loss
from utils import take_per_row, split_with_nan, centerize_vary_length_series, torch_pad_nan
import math
class TS2Ve... |
93eff5a66c7908be6e513cb2e868fa640ba9a3875a98f7f41d074cbf719e378d | Python | 14,351 | 429 | import torch
import torch.cuda
import glob
import os
from collections import namedtuple
import pandas as pd
import json
from collections import *
import random
import diskcache
from torch.utils.data import Dataset
from torch.utils.data import DataLoader
import numpy as np
import cv2
import torchvision.transforms.functi... |
59bbc6e962e2e626b4963111943f6c46056b1502d9762c494d043c1b1f3636fd | Python | 14,360 | 375 | import torch
import torch.utils
import torch.utils.data as data
import torchaudio
from torchvision import get_image_backend
from transformers import BertTokenizerFast, BertModel
from senticnet.senticnet import SenticNet
from PIL import Image
import random
import json
import os
import functools
import librosa
import num... |
6433ccc2df4cd955d84a650b0203784feb1ac96baf7351de2bed5332652458b6 | Python | 14,363 | 273 | """Mixin of contract tests for BaseRecordingExtractor subclasses."""
from pathlib import Path
import h5py
import numpy as np
import pytest
class RecordingExtractorTestMixin:
"""
Mixin of contract tests for BaseRecordingExtractor subclasses.
Child test classes must define the following class-level attri... |
c8b2f13a934b03136adfeaa06e0dd76264b6885fed1cbb9e9b1c9fb3c315a94d | Python | 14,373 | 336 | # -*- coding: utf-8 -*-
import json
import time
from django.conf import settings
from django.http import HttpResponse
from django.shortcuts import get_object_or_404
from catmaid.models import *
from catmaid.control.authentication import *
from catmaid.control.common import *
from catmaid.control.object import get_a... |
e396f8e6575a1efaed0506124ffd2a787fc2deb833c711c41c6fdabc32cda3f2 | Python | 14,388 | 383 | """
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 math
import os
import torch
try:
from e3nn import o3
from e3nn.o3 import FromS2Grid, ToS2Grid
# Borrowed... |
aae5f7e75401e72217c57359992ce91ffa1560325fb5bb970bdebd29fabc599e | Python | 14,400 | 401 | import numpy as np
import pandas as pd
import random
import re
import pickle
from rdkit import Chem
import sys
import time
import torch
from torch.utils.data import Dataset
from .utils import Variable
class Vocabulary(object):
"""A class for handling encoding/decoding from SMILES to an array of indices"""
d... |
d9d7dadd1b5c32c986bbce373e267254f41cb80fcff4b77251d2fa82c2d59e3c | Python | 14,414 | 350 | # Copyright (c) OpenMMLab. All rights reserved.
from typing import List, Optional
import torch.nn.functional as F
from torch import Tensor
from mmseg.registry import MODELS
from mmseg.utils import (ConfigType, OptConfigType, OptMultiConfig,
OptSampleList, SampleList, add_prefix)
from .base im... |
a4d65da19a7eceb24f26cd00fdbf5123f08202f5a8b1448ce7a2cd6edeac2674 | Python | 14,421 | 235 | import sys
sys.path.insert(0, ".")
from sklearn import svm
from sklearn.model_selection import train_test_split
from sklearn.decomposition import PCA
from sklearn.metrics import f1_score
import pandas as pd
from .backend import DataInstance
from typing import List
import numpy as np
import time
class advanced:
de... |
0bb8562198dc6cdb04327330f5f0bc353aba200f6252e7abb0c7728f0d39823e | Python | 14,428 | 474 | from .trainer import Trainer, Trainer_r
from .mixin import envMixin, scMixin
import numpy as np
import torch
from torch_geometric.loader import ClusterData
from torch_geometric.data import Data
from sklearn.cluster import KMeans
from typing import Optional, List, Tuple
from anndata import AnnData
import scanpy as sc
c... |
10f0aa1536733ccba634acb05a08bdd60309a407f39c7d0a404478b5cf676a54 | Python | 14,447 | 362 | import numpy as np
import pytest
from guppy.utils.validation import (
validate_data_not_combined,
validate_group_definitions,
validate_group_folders_selected,
validate_group_member_run_folders,
validate_non_negative,
validate_output_root_folder,
validate_peak_windows,
validate_positive,... |
1c044eb4acb7b30c0ede9034658c9efdece107dc591266fb059fccd156a0e683 | Python | 14,449 | 354 | import numpy as np
import cv2
import sys
import os
import pickle
import torch
import torch.nn as nn
import SimpleITK as sitk
from torch import optim
from torch.utils.data import DataLoader, Subset, Dataset
from PIL import Image
import random
from albumentations import (
GridDistortion,
ElasticTransform,
Com... |
330c5f35dba8cfd1dd29e65b9634527535aca55a8967c8b47f68b05d1c25b0b3 | Python | 14,456 | 258 | # Jason Keller
# Feb 2021
# =============================================================================
# Program to set BlackFly S camera settings and acquire frames from 2 synchronized cameras and
# write them to a compressed video file. Based on FLIR Spinnaker API example code. I have
# also tested with ... |
4318e430fb1be5a7826d9079762f349801c447fe22558fb2241be6b4b03d3bf5 | Python | 14,470 | 341 | from collections.abc import Iterable
from textwrap import indent
import pandas as pd
import ujson
from ..client import inject_client
from ..utils import compile_columns, cypher_identifier
from .neuroncriteria import neuroncriteria_args
# Core set of columns
CORE_NEURON_COLS = ['bodyId', 'instance', 'type',
... |
7fa2d03ee54057aff86adc5ac9232ea2e74145dc017d97e5cc75fc7bcfff6d45 | Python | 14,473 | 355 | import numpy as np
import cv2
import sys
import os
import pickle
import torch
import torch.nn as nn
import SimpleITK as sitk
from torch import optim
from torch.utils.data import DataLoader, Subset, Dataset
from PIL import Image
import random
from albumentations import (
GridDistortion,
ElasticTransform,
Com... |
d60b2d51cf6afce71ab275dddadbab3bd2706c37c8fbbb3823da5409640b22dc | Python | 14,474 | 394 | # /// script
# requires-python = ">=3.10"
# dependencies = [
# "matplotlib",
# "numpy",
# "scipy",
# ]
# ///
"""Generate SVG figures for the cross-correlation explanation page.
The cross-correlation math (scipy.signal.correlate + per-trial peak
normalisation) mirrors src/guppy/analysis/cross_correlation.py... |
8505ec255536c362b4f14fe9175c6b99cc3b3a44ac13213cf239d37b95d5d13e | Python | 14,483 | 543 | from sys import stderr
import pytest
from kgx.validator import Validator
@pytest.mark.parametrize("prefix", ["GO", "HP", "MONDO", "HGNC", "UniProtKB"])
def test_get_all_prefixes(prefix):
"""
Test get_all_prefixes in Validator.
"""
validator = Validator.get_the_validator()
validator.clear_errors(... |
290be4b9501e6a04ff2244b519fec5076e65dad9341742de248e41856705e96c | Python | 14,491 | 327 | """Unit tests for the Biolink-prefix survival prediction in the source-impact report.
``prefix_survives`` mirrors ``NodeFactory.create_node``'s prefix filtering: an identifier
whose prefix is not in the Biolink Model ``id_prefixes`` for its biolink type is dropped by
``write_compendium``. These tests exercise the pure... |
a096daebaba803b945828d696126ada6c80d8c78307f7a63ffac435f7973afc9 | Python | 14,503 | 271 | # Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
#
# 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://w... |
55a82f5058f356d66b8f2b90064eda9186f4d5e58aa6ff8b2ff5aaef839e5b38 | Python | 14,510 | 332 | import panel as pn
import pytest
from guppy.frontend.visualization_dashboard import VisualizationDashboard
BASENAME = "test_session"
EVENTS = ["event1", "event2"]
class _FakeRange:
def __init__(self, start, end):
self.start = start
self.end = end
class _FakeFigure:
def __init__(self):
... |
b8a21e563d101e6a07b9ffbddaaf7b87f4b3ca3b05a75fcdb4d9b6454055a88c | Python | 14,524 | 351 | from __future__ import annotations
from time import perf_counter
from unittest.mock import patch
import numpy as np
from pymatgen.core import Structure
from chgnet import ROOT
from chgnet.graph import CrystalGraphConverter
structure = Structure.from_file(f"{ROOT}/examples/mp-18767-LiMnO2.cif")
converter = CrystalGr... |
0e10d833b638f8448ec66cc79f48d8d6ff050732f865376d3b14e6495ddc3ab3 | Python | 14,529 | 422 | import json
import locale
import os
import pickle
import tempfile
from pathlib import Path
from typing import List
import numpy as np
import pytest
import xgboost as xgb
from xgboost import testing as tm
def json_model(model_path: str, parameters: dict) -> dict:
datasets = pytest.importorskip("sklearn.datasets"... |
73383b6d651c38fdf929062851c9d45261c9e9ea05bde2ec4294c13211dee42e | Python | 14,531 | 437 | import logging
import threading
from typing import Optional
from fastapi import APIRouter, Depends, Form, Request
from fastapi.responses import HTMLResponse, JSONResponse, RedirectResponse
from medperf.account_management import get_medperf_user_data
from medperf.entities.certificate import Certificate
from m... |
b62f545c963fa2f4ea2905cad78b9ebd1a4dd17f49bfaf0d178db330475e82d7 | Python | 14,539 | 347 | """
This script runs the first bit of code from our "Building Models"
documentation and uses that to output SBML (very much work in progress;
only a single compartment for now).
The code for SBML output was lifted from SBML documentation.
"""
import libsbml
from jaxkineticmodel.kinetic_mechanisms import JaxKineti... |
096580e44fc86683af53027b550dd8cba5da37d08feed5f5c13dac4c3b832d6e | Python | 14,544 | 423 | from numpy import float32
import torch
import torchvision
from torch import Tensor, dropout, nn
import torch.nn.functional as F
import math
import torchinfo
from torchvision.models.feature_extraction import get_graph_node_names
from torchvision.models.feature_extraction import create_feature_extractor
import torchvisio... |
fe7a7b20012bb745ad4bf7787fe7dd3f5a912ba72e973a8da8a3e55997fb017f | Python | 14,545 | 424 | """
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 numpy as np
import torch
from torch_scatter import segment_coo, segment_csr
from torch_sparse import SparseTensor
def ragged_range(si... |
665e7d2690f050e25a9906d40770069bcaa428786a8891b8c47792697415fa97 | Python | 14,552 | 384 | import copy
import math
from typing import List, Optional
import torch
import torch.nn as nn
from torch.nn import Linear
from .radial_function import RadialFunction
from .so3 import SO3_Embedding
class SO2_m_Convolution(torch.nn.Module):
"""
SO(2) Conv: Perform an SO(2) convolution on features... |
96e3d515d515bcde5286dd27053d5d5bb675fb3a031cfb1eb53e7d9f4c333410 | Python | 14,553 | 315 | import pytest
import src.prefixes as pref
from src import categories
from src.LabeledID import LabeledID
from src.node import NodeFactory
from src.util import get_config
BIOLINK_VERSION = get_config()["biolink_version"]
# Node schema (as of the current codebase):
# {"identifiers": [{"identifier": CURIE, "label": s... |
9994b217f259ab9be45610bfa3b71151bbecab77f4db9f4c76fca2d434e54667 | Python | 14,556 | 388 | import cv2
cv2.setNumThreads(1)
import numpy as np
import torch
from os import path as osp
from torch.nn import functional as F
from basicsr.data.transforms import mod_crop
from basicsr.utils import img2tensor, scandir
def read_img_seq(path, require_mod_crop=False, scale=1):
"""Read a sequence of images from a g... |
df39a96493fe1e22037a04058114c74260f585475eb62c88e080cf5bbf9260be | Python | 14,556 | 477 | import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import scipy.optimize
def difference(x,xref):
"""
help
"""
import numpy as np
return 1/len(x)*np.sum([x[i]/xref[i] for i in range(len(xref))])
def compute_alpha(p,pref):
"""
help: courbe passe par 0 -> 1
"""
return (p-pre... |
daa48428d48060fbf1dfab478016758d1ad6b0183f4e3777a5d0e66c04ad7c11 | Python | 14,557 | 311 | """
The ArrayData class reads and stores all replicates, annotation and combined data
for an array library.
Yuxi Ke, Feb 2022
"""
from distutils.log import error
from pickletools import float8
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
import os
from typing import Tup... |
c830777eb4d36a26ade661b1afd2d886f8eb6ca37fd4b194d2c4f35b08c3aa13 | Python | 14,565 | 354 | """Unit tests for the panel that finds a dandiset on the DANDI Archive.
Every network call it makes — the catalog search and the photometry verification that reads the
listed dandisets' files — is a constructor injection point, so every test here runs against
in-memory stand-ins with no archive access.
"""
from threa... |
387911b66d01243c004c36ffc5285f5195a4f863ccf6a2cbc11a778f26541fef | Python | 14,576 | 366 | # Copyright (c) OpenMMLab. All rights reserved.
import warnings
from abc import ABCMeta, abstractmethod
from typing import List, Tuple
import torch
import torch.nn as nn
from mmengine.model import BaseModule
from torch import Tensor
from mmseg.registry import MODELS
from mmseg.structures import build_pixel_sampler
fr... |
099f4a91e92b779d98b264df0503ee75e938550c1457669e329b43bb6950fa2e | Python | 14,590 | 432 | """Tests for Screenshot REST API endpoints."""
import json
from pathlib import Path
import pytest
from helpers import (
MockSioServer,
auth_header,
create_test_room,
create_test_user_in_db,
)
from httpx import AsyncClient
from sqlalchemy.ext.asyncio import AsyncSession
from zndraw.redis import RedisK... |
9f7ff5f0d8d2bc7dadd756e88e07635a710f74b29926f81204652db9061689c7 | Python | 14,604 | 300 | # Copyright (C) 2020-2021 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
"""
Contributors: Micah Sheller, Patrick Foley, Brandon Edwards
"""
# TODO: Clean up imports
import os
import subprocess
import shutil
import time
import pickle as pkl
from copy import deepcopy
import hashlib
import yaml
import numpy ... |
e89bab953f2add3e4a3d6f19891089b8726b87670914f04bd097e7fb3d817d20 | Python | 14,605 | 261 | # Jason Keller
# September 2021
# =============================================================================
# Program to set BlackFly S camera settings and acquire frames from 2 synchronized cameras and
# write them to a compressed video file. Based on FLIR Spinnaker API example code. This
# example uses ... |
cc2a33f458f7e549960d00eea9424465fae041555486d6f0658caebb2ee40135 | Python | 14,619 | 491 | import argparse
from pathlib import Path
def convert_arg_line_to_args(arg_line):
for arg in arg_line.split():
if not arg.strip():
continue
if arg[0] == "#":
break
yield arg
def parse_opts():
parser = argparse.ArgumentParser(fromfile_prefix_chars="@")
parse... |
ec20942c69f2ac75ac4a8b759a72fb3761cdc842ea829c92aca718746eb56ee1 | Python | 14,623 | 497 | from typing import NamedTuple
import pytest
from cutadapt.align import (
EndSkip,
Aligner,
PrefixComparer,
SuffixComparer,
hamming_sphere,
edit_environment,
edit_distance,
naive_edit_environment,
slow_edit_environment,
py_edit_environment,
)
from cutadapt.adapters import Where
... |
f91474dbb0223c31c435d535fc656c5758a0b8d708f3d3e21807982371252405 | Python | 14,630 | 430 | """Utilities related to disk I/O."""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import numpy as np
from collections import defaultdict
import sys
import contextlib
import six
try:
import h5py
HDF5_OBJECT_HEADER_LIMIT = 64512
except ImportError... |
efe4bc3f09608239d0a8ef3770800d452c79813bff69ad2590a776bb99bb164b | Python | 14,640 | 280 | """Primitives for diffing the cliques of two finished Babel compendium builds.
This is a *build-vs-build* clique diff: given the same compendium file(s) from two
different builds, it reports which cliques split, merged, or otherwise changed
membership, and which CURIEs moved between cliques or left the output entirely... |
66ef07febef66b2cbb8974deb8cef917a42fd58c7c3e22b533db7cac6e0431fa | Python | 14,644 | 424 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Data fetchers
"""
import os.path as op
from pathlib import Path
import shutil
import numpy as np
from neuromaps import datasets, images
import nibabel as nib
from .utils import (get_data_dir, _groupby_match,
get_dataset_info, _match_files)
from ei... |
7c1ddac2f7834379095a1e6634e79b35a55deafbdff6d10b92d5539dedee0f9e | Python | 14,648 | 258 | # coding=utf-8
# Copyright 2022 IDEA-CCNL The HuggingFace Inc. team. 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
#
... |
7074f5cc9912f7207521c1572aebbcb573e04f16bbfa85abb144f7733f3b79a7 | Python | 14,677 | 308 | #!/usr/bin/env python
#
# Copyright 2006, 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... |
d306f9711195e1f4b1b733716b279a65c32c98466632f9f4a503cf9a675f4b99 | Python | 14,679 | 423 | import os, sys
import h5py
import numpy as np
import pytraj as pt
from .. import utils
from .. import printit, config
__all__ = [
"Trajectory",
"MisatoTraj",
]
class Trajectory(pt.Trajectory):
"""
This class represents the base-class for trajectory handling in the Nearl package.
This class inherits from... |
ebacb5916f3e9d18417526bb636dda888b6c26e796186c1c08261cc2d8857501 | Python | 14,683 | 325 | # Copyright (C) 2020-2021 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
"""
Contributors: Micah Sheller, Patrick Foley, Brandon Edwards
"""
# TODO: Clean up imports
import os
import shutil
from copy import deepcopy
import numpy as np
import torch
from openfl.utilities import TensorKey
from openfl.utiliti... |
31384acc1d41e0df71f53e42c1f42f4ea2c25cffc6c06acb3f51dab4d575c818 | Python | 14,686 | 440 | # This file is part of h5py, a Python interface to the HDF5 library.
#
# http://www.h5py.org
#
# Copyright 2008-2013 Andrew Collette and contributors
#
# License: Standard 3-clause BSD; see "license.txt" for full license terms
# and contributor agreement.
"""
High-level access to HDF5 dataspace selectio... |
cacc95b95b73f7d4054ebda1567461c7ad8204903e95064e779436450e75288d | Python | 14,687 | 349 | import torch
import torch.nn.functional
import numpy as np
import matplotlib.pyplot as plt
from . import modules # rvinn modules.py
class Model():
def __init__(self, device, **kwargs):
# data and collocation points
self.device = device
self.t_train = torch.tensor(kwargs.get('t_train'), req... |
0f4d3afdf0a1c293ee2a019b2050a40aa5a74b15056710e547ecd748358e6d37 | Python | 14,692 | 262 | # Jason Keller
# Feb 2021
# =============================================================================
# Program to set BlackFly S camera settings and acquire frames from 2 synchronized cameras and
# write them to a compressed video file. Based on FLIR Spinnaker API example code. I have
# also tested with ... |
28461af4e4255bd0accd0efdf5eb2b4462afd24515921c272d5ee97d72a76619 | Python | 14,696 | 447 | #!/usr/bin/env python
"""
MeteWIBELE: prepare_uniref_annotation module
Extract the annotation info from UniRef fasta file and UniProt annotation file
Copyright (c) 2019 Harvard School of Public Health
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documen... |
bee52bf32ea943510db806ef50c88adf3400d9d51928dd42d1dafdd29fbb08d5 | Python | 14,698 | 407 | import os
import colorsys
import numpy as np
import matplotlib as mpl
import seaborn as sns
import matplotlib.pyplot as plt
import pandas as pd
from palettable.colorbrewer import qualitative
from auditory_cortex import DNN_MODELS
from utils_jgm.tikz_pgf_helpers import tpl_save
class PlotterUtils:
"""Contains uti... |
26e4b6ff69871b3dcef53a647ef4b1a21ff4f278abae93662328d7b4495ab344 | Python | 14,704 | 276 | """
Tests for the manual UMLS semantic-type overrides used when building the leftover UMLS compendium
(src/createcompendia/leftover_umls.py).
These are marked ``network`` because they build a Biolink Model Toolkit, which fetches
``biolink-model.yaml`` from GitHub on first use (for the biolink_version pinned in config.... |
0698adc5e00495bd75d90caf9faf7d9d0bcb6c6e9354d0361e1de89137966011 | Python | 14,712 | 386 | import os
import tempfile
from collections import namedtuple
from typing import Tuple, Union
import numpy as np
import pytest
import xgboost as xgb
from xgboost import testing as tm
from xgboost.testing.callbacks import (
run_eta_decay,
run_eta_decay_leaf_output,
tree_methods_objs,
)
# We use the dataset... |
e837a4e5bf612930da7302b904ab09e8473cc86fa382ef7b9ad80bd77ef3a04d | Python | 14,724 | 486 | import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import scipy.optimize
def difference(x,xref):
"""
help
"""
import numpy as np
return 1/len(x)*np.sum([x[i]/xref[i] for i in range(len(xref))])
def compute_alpha(p,pref):
"""
help: courbe passe par 0 -> 1
"""
return (p-pre... |
25cefb37b07a8e102dcd9feb373d21ab78027e76f1033520e643b7a6e6048078 | Python | 14,737 | 339 | ##############################################################################
# 1. Combine the protein-ligand to complex PDB file'
# 2. Featurize the required PDB complexes
##############################################################################
import os, time
import h5py as h5
from itertools import chain
impo... |
f9061ae4781d2c613e3233b261f94e73c0165b77df26be512da7fa59a644ca54 | Python | 14,737 | 430 | # This document holds the functions defined
# by the user for the ease of computation
# such as the solver settings
#
# Author: Thomas Lavigne
# Date: 18/09/2024
#
def readme_F():
print('This document holds the functions used as part of the poro-mechanical modelling of living tissues according to the theory in ./The... |
dd114f0f40f5c7f8a9d0cbf6d5564ad665fedcaa83636f92192fadfa139b38e0 | Python | 14,740 | 323 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
import os
import re
import warnings
from shutil import copyfile
from typing import Any, Dict, List, Optional, Tuple
import sentencepiece as spm
from transformers.tokenization_utils import PreTrainedTokenizer
from transformers.utils import logging
SPIECE_UNDERLINE = "▁"... |
f990fdbcff7d22e1a456169c5dd41f0c3ebed7036606bc8e341598c0155b82e9 | Python | 14,741 | 395 | # Copyright (c) OpenMMLab. All rights reserved.
# ------------------------------------------------------------------------------
# Adapted from https://github.com/wl-zhao/VPD/blob/main/vpd/models.py
# Original licence: MIT License
# ------------------------------------------------------------------------------
import ... |
2cc84dc9a9aff277686c5314befad092fc8814d680ca9d1fc442e079fa6a87f5 | Python | 14,745 | 415 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Feb 8 11:04:24 2023
@author: schwab
"""
from pathlib import Path
from typing import Optional
import mrcfile
import numpy as np
import torch
from torch.utils.data import DataLoader
import torch.nn.functional as F
from scipy.spatial import KDTree
from d... |
6461d2bc359dbe1f6edbdf399e11b577a4f23be085a9cac50eb800b2ef0989ad | Python | 14,751 | 333 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Jun 2 15:40:06 2023
@author: george
"""
from qtpy.QtCore import *
from qtpy.QtGui import *
from qtpy.QtWidgets import *
import numpy as np
import pandas as pd
import pyqtgraph as pg
import os
# import pyqtgraph modules for dockable windows
from pyqtg... |
0dc016c0a13758a4e6c2f9221fae2cecc633e28030948ec1795d1f0ed0ae4463 | Python | 14,764 | 378 | import logging
import os
import torch
from collections import OrderedDict
from copy import deepcopy
from torch.nn.parallel import DataParallel, DistributedDataParallel
from basicsr.models import lr_scheduler as lr_scheduler
from basicsr.utils.dist_util import master_only
logger = logging.getLogger('basicsr')
class ... |
3cf210b3b3b898b123d4e1c27fe02c2c066d52dafbca1acba504297e2ca5031d | Python | 14,766 | 316 | """
This module contains miscellaneous functions borrowed from the taffi package that are
useful for yarp.
"""
import numpy as np
from scipy.spatial.distance import cdist
from copy import copy,deepcopy
from ReactBench.utils.properties import el_radii,el_max_bonds
def table_generator(elements,geometry,scale_factor=1... |
89ee9d2eef4f751de0ebd5246c0be8ad6dfd9442b8ab0885aa1b63b5d3f76614 | Python | 14,783 | 416 | import os
import torch
import numpy as np
import csv
import jiwer
import soundfile
import scipy
# from pydub import AudioSegment
import pandas as pd
import torchaudio
from auditory_cortex.deprecated.dataloader import DataLoader
data_dir = '/scratch/gilbreth/ahmedb/data/'
# voxpopuli: /scratch/gilbreth/ahmedb/data/v... |
e72400f145726c95db6548d3a97f9e02e95d220b0a06931ec9bb68d386b145f0 | Python | 14,794 | 362 | from mendeleev import element
import matplotlib.cm as cm
import matplotlib.patches as patches
import matplotlib as mpl
import matplotlib.ticker as ticker
from sklearn.metrics import r2_score, mean_absolute_error
from matplotlib.pyplot import MultipleLocator
import numpy as np
from collections import defaultdict
import... |
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