sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
f0a993ae088d5edc39739ba3b321e85414246b709a36703fcdc6ee086771526d | Python | 42,045 | 1,072 | """A comprehensive logging system.
Managing experimental data, database connections, and data flow control in an
experimental setup. It includes functionality for establishing database connections,
managing logging sessions, handling data insertion, and synchronizing setup status.
Classes:
Logger: Manages logging... |
8ca24aece5ab8f4ab792c6d8173452ea0bf8b8360614c454e980b716697151a3 | Python | 42,225 | 869 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# Copyright 2016 David Emms
#
# This program (OrthoFinder) is distributed under the terms of the GNU General Public License v3
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publish... |
673be91716415e9799ac8155f5aaadc15a9ae8edf3ff95af51179638787e692e | Python | 42,256 | 962 | """
Tools for retrieving gene information using the UniProt API and NCBI Entrez.
"""
from typing import Dict, List, Optional, Tuple, Any
from pydantic import BaseModel, Field
import re
import openai
import time
import threading
import json
import os
import datetime
import logging
from pydantic_ai import RunContext, Mo... |
493ccf9f27661bea1236d9acef81dd58f22dc2ab2509a699399c4fd9cae3e922 | Python | 42,337 | 939 | #!/usr/bin/env python
from __future__ import division
from __future__ import print_function
from builtins import map
from builtins import input
from builtins import range
from numpy import *
import os
from sys import argv,exit
import forcebalance
from forcebalance.PT import PeriodicTable
from forcebalance.nifty import... |
725e31f512ddc3564cb4411bbcac00b17f8877701d2233b95371daa0a33a546b | Python | 42,350 | 2,050 | # This file is automatically generated by tools/idna-data
__version__ = '13.0.0'
scripts = {
'Greek': (
0x37000000374,
0x37500000378,
0x37a0000037e,
0x37f00000380,
0x38400000385,
0x38600000387,
0x3880000038b,
0x38c0000038d,
0x38e000003a2,
... |
41565bdb2a608535c5bb3ce9ef9dcadf81f229410058232f01e6120682db0e59 | Python | 42,374 | 1,115 | # -*- coding: utf-8 -*-
__all__ = ['Distribution']
import io
import sys
import re
import os
import warnings
import numbers
import distutils.log
import distutils.core
import distutils.cmd
import distutils.dist
import distutils.command
from distutils.util import strtobool
from distutils.debug import DEBUG
from distutils... |
6bd9b81a664e38e16618d023f1db7c0848925a2e7c534a1a44ba5427f94d55bd | Python | 42,450 | 937 | """Tracking data generators."""
import numpy as np
from skimage.measure import regionprops
from skimage.transform import resize
from tensorflow.keras import backend as K
from tensorflow.python.platform import tf_logging as logging
from tensorflow.keras.preprocessing.image import Iterator
from tensorflow.keras.prepro... |
51edf36ee10648e4d3b809d8bdb987c54260f1ec923622f0bfb99611328a42bf | Python | 42,517 | 1,011 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
================================================================================
Reproducible Analysis Script
Effects of Transcranial Direct Current Stimulation over the Left Sensorimotor
Cortex on Bimanual Force Control: A Computational and Experimental Invest... |
02d8c5d6374fadc99699d404722e325b18948d074bfbb2af48f6ab9019133023 | Python | 42,521 | 1,391 | """Predicates for spatial analysis."""
import warnings
import numpy as np
from shapely import lib
from shapely.decorators import requires_geos
__all__ = [
"contains",
"contains_properly",
"contains_xy",
"covered_by",
"covers",
"crosses",
"disjoint",
"dwithin",
"equals",
"equa... |
64d5dea08bfb98d0dda8673dd49f96033cdb1829c5a0096e8abd481ac141065b | Python | 42,528 | 965 | """
CNN Classification Pipeline — Banking Customer Interaction
==========================================================
Three models trained on 64×64 grayscale images:
Model 1 : Plain CNN (baseline)
Model 2 : CNN + SE Channel Attention
Model 3 : RDAD-CNN — Residual Dual-Attention Depthwise-Separable (Nove... |
5be34df76fb5be780e2854e6eb606e8efde3633cae97dcf18dc0538c10acc9b3 | Python | 42,595 | 1,124 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""OpenMM MD Protocol --- :mod:`openfe.protocols.openmm_md.plain_md_methods`
===========================================================================================
This module implemen... |
9da4b35310738a71a360185e668dc8cb47e96d79b131983d1c00053669b95bbb | Python | 42,630 | 921 | import argparse
import os
import numpy as np
import pandas as pd
import torch
import torch.nn as nn
import matplotlib.pyplot as plt
import pickle
from captum.attr import DeepLift
from model_genomic import SNN
from dataset_survival import RNAseqSurvivalDataset
from scipy.stats import ttest_1samp, pearsonr, spearmanr
fro... |
de875cfe5d36c75980523edca1a5c47b5e8f44077c6b5c894f2c5e6985277590 | Python | 42,633 | 1,126 | """Core experiment module for experiment control.
This module provides the base classes and functionality for running behavioral
experiments. It includes:
- State machine implementation for experiment flow control
- Condition management and randomization
- Trial preparation and execution
- Performance tracking and ana... |
d342b7defd0511b84fd2835210edec9a5262579b0e15fe3d95e832f0d6e5e7a2 | Python | 42,839 | 987 | """Core MultiQC module to parse output from custom script output"""
import base64
import json
import logging
import os
import re
from collections import defaultdict
from io import BufferedReader
from typing import Any, Dict, List, Mapping, Optional, Set, Tuple, TypedDict, TypeVar, Union, cast
import markdown
import y... |
28a904e7da7d784d65d3006381480ca500c3f5c9c782d05fbf7a7a54772729e0 | Python | 42,913 | 932 | import shap
print(shap.__version__)
import argparse
import torch
import torch.nn as nn
import numpy as np
import pandas as pd
import os
import matplotlib.pyplot as plt
import pickle
from model_genomic import SNN
from dataset_survival import RNAseqSurvivalDataset
from scipy.stats import mannwhitneyu, pearsonr, spearmanr... |
41160087caedf4939d6f3e19965c425f24e65c891662cf5faf2685345986ffb0 | Python | 42,920 | 945 | import argparse
import os
import numpy as np
import pandas as pd
import torch
import torch.nn as nn
import matplotlib.pyplot as plt
import pickle
from captum.attr import IntegratedGradients
from model_risk import SNN_RISK
from dataset_survival import RNAseqSurvivalDataset
from scipy.stats import ttest_1samp, pearsonr, ... |
576e153cc7c84264ae907e83f0d90a816f240e983b9c80c2097b66b27fac4d38 | Python | 43,263 | 785 | import os
import geojson
from shapely.geometry import shape
from shapely import affinity
import rasterio
from rasterio.transform import from_origin
from rasterio.features import rasterize
from rasterio.transform import Affine # Import Affine directly
import numpy as np
import scipy.ndimage as ndi
from skimage import fi... |
acf6207ad0d188ac188962b6f7df5356a47452eba9902fbf8b03fa29bfaaf9d0 | Python | 43,331 | 1,034 | import gc
import os
import random
from pathlib import Path
from typing import Dict, Optional, Tuple, Union, List
import numpy as np
import polars as pl
import pydicom
import time
import torch
import torch.nn as nn
import torch.optim as optim
from torch.utils.checkpoint import checkpoint
from torch.utils.data import Da... |
3ad328f32b686f9f2d1bd7038573077277fb42a7f9de8c39ce32ba777a60c591 | Python | 43,366 | 1,105 | """
FEMap
=====
The workhorse of cinnabar, a :class:`FEMap` contains many measurements of free energy differences,
both relative and absolute,
which form an interconnected "network" of values.
"""
import copy
import itertools
import math
import pathlib
import warnings
from dataclasses import asdict
from typing import... |
6e3fb92879b55e01d9b67b761bf54e9283a4e143d7b9cf6aafd5e0bd50d09142 | Python | 43,379 | 1,139 | import numpy as np
import matplotlib.pyplot as plt
import matplotlib as mpl
import seaborn as sns
from scipy.signal import detrend
import fathon
from fathon import fathonUtils as fu
import neurokit2 as nk
from scipy.stats import wasserstein_distance, mannwhitneyu
class ComplexityFidelity:
"""
A class for comp... |
07d42618bdcb8572650fab8f378250737e741cf33c65f7fd7906482fcad2b95e | Python | 43,537 | 966 | import argparse
import os
import numpy as np
import pandas as pd
import torch
import torch.nn as nn
import matplotlib.pyplot as plt
import pickle
from model_genomic import SNN
from dataset_survival import RNAseqSurvivalDataset
from scipy.stats import ttest_1samp, pearsonr, spearmanr
from statsmodels.stats.multitest imp... |
22d7ed6d5584fc6a998395b0b0d3bb9ac9eebc8a4e939da9c65b4ea96c1dc48b | Python | 43,623 | 1,117 | from typing import Any, Iterable, Mapping, Sequence, Tuple, Union, Optional, Callable, Literal, List
import math
import numpy as np
import pandas as pd
import scanpy as sc
import anndata
import scipy
import umap
from sklearn.preprocessing import LabelEncoder, MinMaxScaler
from sklearn.metrics import confusion_... |
e48b6a736cb29e1401a25db05c4d95f99174062bfc55a7a1841121f11586b2d1 | Python | 43,688 | 1,200 | import logging
import os
import warnings
from functools import wraps
import numpy as np
# Optimize imported here and below as the jax-optimized one is jax or passthrough, but this is required regardless
import scipy.optimize
from pymbar.utils import ensure_type, check_w_normalized, ParameterError
logger = logging.ge... |
1312514268243f78a7cd2b8308942c0f026226e60b2eca4b849e3a302009de30 | Python | 44,004 | 802 | # -*- coding: utf-8 -*-
import glob, os, shutil, json, scipy, math
import nibabel as nib
import numpy as np
import pingouin as pg
import pandas as pd
import brsc_utils as util
# Time computation libraries
from joblib import Parallel, delayed
import time
from tqdm import tqdm
# Nilearn library
from nilearn.maskers imp... |
de5591efdbdf268a2ed19e67312102768d69ba05311e468937c18019ec60c084 | Python | 44,004 | 1,310 | """Class to retrieve and explore the LEiDA results."""
import numpy as np
import pandas as pd
import os
from itertools import combinations
import matplotlib.pyplot as plt
import seaborn as sns
from .data_utils import (
load_rois_labels,
load_rois_coordinates,
load_tseries,
load_classes
)
from .data_u... |
2f0977ff12ef6f56e56308ee331e94d22da44baaa89181077db4db20521d2ab7 | Python | 44,012 | 1,160 | #!/usr/bin/env python3
"""
生物学合理性可视化
展示不同XAI方法的整体生物学合理性，包括：
1. 箱线图（6种XAI方法比较）
2. 箱线图（3种XAI类别比较）
3. 热力图（数据库×XAI）
4. 热力图（癌种×XAI）
使用方法:
python 03_visualize_and_test.py
"""
import sys
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
from pathlib import Path
from scipy.stat... |
c4847b2fa60b666029486446c3bfc0d310dea4cf9543fdd1f38d8b81a6325468 | Python | 44,150 | 961 | import numpy as np
import matplotlib.pyplot as plt
from scipy.fft import fft, ifft, next_fast_len
from skimage.metrics import structural_similarity as ssim, mean_squared_error
from sklearn.metrics.pairwise import cosine_similarity
from scipy.stats import mannwhitneyu, wilcoxon
try:
from tqdm import tqdm
except Imp... |
7c8e507b441853f8147bc8d214208b8b43976e4735cf5dd09af02604950f8f58 | Python | 44,481 | 957 | import pandas as pd
import numpy as np
import glob, os, yaml, itertools, sys, sparse
from Bio import SeqIO
from Bio.Seq import Seq
import Bio.SeqUtils
import Bio.Data
import warnings
warnings.filterwarnings("ignore")
from data_utils import *
data_utils_dir = "./data_processing/data_utils"
# import reference files
h3... |
cf81bc9d125e9114df72a3e13b9b791237a98a9d0ebddad123ab2527754e6109 | Python | 44,715 | 1,439 |
# sketch of what it should actually do:
'''
generator produced 500 samples of which I stored the max eigenvalues and the unscaled parameters as well as scaled parameters. Lets call this unscaled batch M.
From the scaled M* we calculated eigenvalues and looked at its distribution (which we call prior distribution of e... |
d7cd8a1b118b285930bb8e483afa76a8289051b3a02d7d046e1421014d05f35e | Python | 44,719 | 866 |
import argparse
import torch
import numpy as np
import os
import torch.autograd as autograd
import torch.nn as nn
import torch.nn.functional as F
import torch.optim as optim
import torchvision
import torchvision.transforms as transforms
from dataset import CreateDatasetSynthesis
from torch.multiprocessing import ... |
94adec2ca79d68a511d1e9e7581d7bf7d312641fc9462e8f75a875c0008a1500 | Python | 45,061 | 840 | """ @package forcebalance.lipid Matching of lipid bulk properties. Under development.
author Lee-Ping Wang
@date 04/2012
"""
from __future__ import division
from __future__ import print_function
from builtins import str
from builtins import zip
from builtins import map
from builtins import range
import abc
import os... |
f8ee3f66fff0ee99d9dfbd1ad66f01273f8718fc890ef3f475a273db5d87f816 | Python | 45,101 | 960 | # -*-coding:utf-8 -*-
import torch
from torch import nn
from typing import Callable, Dict, List, Tuple
import warnings
import functools
from functools import partial
import torch.nn.functional as F
import transformers
transformers.logging.set_verbosity_error()
from modules.fusion_modules import FusionTransformer
from ... |
ba28a79a0a7113dffee70e240752528313a64531b6026dcf3c4736e9cd748f14 | Python | 45,163 | 978 | import argparse
import os
import numpy as np
import pandas as pd
import torch
import matplotlib.pyplot as plt
import pickle
from lifelines.utils import concordance_index
from model_genomic import SNN
from dataset_survival import RNAseqSurvivalDataset
from scipy.stats import mannwhitneyu, pearsonr, spearmanr
from statsm... |
3c36651a36b86c7b16cca0b30b5770b755b30e2fd477f00105466de965b87260 | Python | 45,184 | 1,025 | import itertools
import json
import logging
import os
import re
from collections import defaultdict
from typing import Dict
import numpy as np
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
from multiqc.plots import bargraph, linegraph, table
log = logging.getLogger(__name__)
# A 64 color p... |
aa99deed0f6a13de5c6dcc9ae6ad07544583fed89ff16b2a7f91fdcf355a57cd | Python | 45,321 | 1,024 | """
twinc_network.py
Author: Anupama Jha <anupamaj@uw.edu>
TwinC classification model architecture.
"""
import torch
import numpy as np
from twinc_utils import count_pos_neg, decode_chrome_order_dict, decode_list
from sklearn.metrics import roc_curve, roc_auc_score, average_precision_score, precision_recall_curve
de... |
88075a7d3d24ad7e108c58429f1dd946bc7e7a019932da4f181cb6bb849777b2 | Python | 45,396 | 1,018 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import print_function, division, absolute_import, unicode_literals
import copy, warnings
from os import path
from collections import OrderedDict
import itertools
import numpy as np
from scipy import stats, signal, interpolate, special
import matplotlib.pyplo... |
c2aea4b354a316436f7e6f2f1db109d508c17b733e1ea6a8560b6719db9e278e | Python | 45,572 | 1,252 | """Base geometry class and utilities.
Note: a third, z, coordinate value may be used when constructing
geometry objects, but has no effect on geometric analysis. All
operations are performed in the x-y plane. Thus, geometries with
different z values may intersect or be equal.
"""
import re
from warnings import warn
... |
d228f1ec9db16e2166aac3eefdff79483db88e93aaed03cbfa028c7e38e929ad | Python | 45,692 | 1,402 | """
Unit tests for the basic utility functions in voxelmorph.
"""
# Standard library imports
import pytest
import torch
import voxelmorph as vxm
import voxelmorph.nn.functional as vxf
import neurite as ne
import neurite.nn.functional as nef
def test_affine_to_disp_identity():
"""
Identity affine should prod... |
a1a6c0f5deb32c992a363401b4bee24b6a2f4444052e819b5b43321a369929b0 | Python | 45,753 | 1,311 | # Copyright 2022 Google LLC.
#
# 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,... |
f4d5693b9a51a83c1bf10ff3debcdae99fb34e14c498c5be4f8739dfaf572f89 | Python | 45,770 | 860 | # Main imports ------------------------------------------------------------
import os, json, glob, shutil
from scipy.io import loadmat
import numpy as np
import pandas as pd
import nibabel as nib
import brsc_utils as utils
from joblib import Parallel, delayed
# Plotting
import matplotlib.gridspec as GridSpec
import ... |
7162b19e51056ce0767bb7b95f8192584009ac29bfb7b172c541560421eab425 | Python | 46,108 | 1,161 | import pickle
import numpy as np
import pandas as pd
import os
import matplotlib.pyplot as plt
import seaborn as sns
from pathlib import Path
from lifelines import KaplanMeierFitter
from lifelines.statistics import logrank_test
from sksurv.metrics import cumulative_dynamic_auc
import math
# 核心设置：将 PDF 字体类型设为 42 (TrueT... |
1d39141a7e25f2b198206beffc0ff11f1551e0f24313ccc5b40fb8c6a0d124ee | Python | 46,240 | 1,400 | # Copyright 2022 Google LLC.
#
# 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,... |
04a3cc40cf4017e202bc11c75b875d4379a2f5e3e1f30a00c1a1e3e587dada2a | Python | 46,474 | 1,174 | """coordinate, topology and plumed modification functions"""
from dataclasses import dataclass, field
from enum import Enum
import logging
from copy import deepcopy
from pathlib import Path
from typing import Optional, Union
from math import sqrt
import MDAnalysis as mda
import numpy as np
from kimmdy.constants impo... |
551fb38ddb3062ab431d30d6034567a106f859d9202cc1847843d8694130d14e | Python | 46,477 | 1,410 | """Configuration file for the Sphinx documentation builder.
This file only contains a selection of the most common options. For a full
list see the documentation:
https://www.sphinx-doc.org/en/master/usage/configuration.html
"""
# Authors: The MNE-Python contributors.
# License: BSD-3-Clause
# Copyright the MNE-Pytho... |
6af7be6cc38e75544d3724822fc8e395590cd707d2d0a68623aeaaf1ef330252 | Python | 46,650 | 1,365 | import pandas as pd
import numpy as np
import os
import matplotlib.pyplot as plt
import seaborn as sns
from nilearn.plotting import (
view_connectome,
view_markers,
view_img_on_surf,
plot_connectome,
plot_surf_stat_map
)
from nilearn.maskers import NiftiLabelsMasker
from nilearn.surface import vol... |
7742794e65b0a11cabae72410ac9d1c10604c4c4cbc3c3dd27445ca7896d23a0 | Python | 46,797 | 1,260 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""OpenMM Equilibrium AFE Protocol base classes
===============================================
Base classes for the equilibrium OpenMM absolute free energy ProtocolUnits.
Thist mostly impl... |
d78d952aa8954ea5332102b4bec9b6862f95aaa21b401e251de6f5ff8f35bb78 | Python | 47,030 | 1,143 | # Copyright 2021 DeepMind Technologies Limited
#
# 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 law or agr... |
a874315398c7c075a5ac4889ec4df2609491470667f42016fde631e8d6ca2adf | Python | 47,104 | 1,164 | """
Path management utilities for organizing model and data directories.
This module provides comprehensive path management for the TimeFlies project,
implementing the clean 2-level naming convention:
- Level 1: Experiment Type (tissue_model_encoding)
- Level 2: Configuration Details (method_cells_sexes)
Naming Rules... |
8b758df858a6fb0a072e1ade954631b779c8712778c61c7241d28700220377ee | Python | 47,144 | 961 | # -*- coding: utf-8 -*-
import os, glob, math
import numpy as np
import nibabel as nib
import pandas as pd
import warnings
from statsmodels.tools.sm_exceptions import ConvergenceWarning
import matplotlib.pyplot as plt
#nilearn
from nilearn.plotting import plot_design_matrix
from nilearn.glm.second_level import Second... |
82ffc1857e45fad0805bf3eab3926ddb3f20d903ccf85e290018b1372c02256c | Python | 47,397 | 1,325 | """Command line interface for Aurelian agents."""
import logging
import os
import warnings
from pathlib import Path
from typing import Any, Awaitable, Callable, Optional, List, Tuple
from aurelian.utils.async_utils import run_sync
import click
from pydantic_ai.models.openai import OpenAIModel
from pydantic_ai.provide... |
e88780f98c19bf4bc37c6f72f41e16787169a8c9f8daa68297ab2c6a2ead153d | Python | 47,426 | 1,344 | """
Single tensor operations (no B, C, dimensions assumption)
"""
# Core library imports
import warnings
from typing import Callable, Union, Sequence, Tuple, Literal, Optional
# Third-party imports
import numpy as np
import torch
import neurite as ne
import voxelmorph.nn.functional as vxf
__all__ = [
'affine_to_d... |
4067eccd24f61984d9ecefb3d2b13b14f09d235a9fde8b798748dc4cbd12ab9b | Python | 47,463 | 1,338 | import bisect
import itertools
import logging
from datetime import timedelta
from typing import List, Optional, Tuple, Dict, Any
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
from matplotlib.lines import Line2D
from ethopy_analysis.data.loaders import (
get_trial_behavior,
get_trial_e... |
672efe9ec0b9bde853f84077450cdd9467701b8bd6328693e482a40f09c12e07 | Python | 47,889 | 1,103 | import csv
import functools
import logging
from collections import defaultdict
from itertools import islice
from pathlib import Path
from typing import Dict, List, Mapping, Optional, Set, Tuple, TypedDict, Union
from xml.etree import ElementTree
from pydantic import BaseModel
from multiqc import config
from multiqc.b... |
bf3817c6b6f14c537b72c1d26f7980598dcfd789267423b9bbbb01b2fd73fbd7 | Python | 47,910 | 573 | """ @package forcebalance.parser Input file parser for ForceBalance jobs. Additionally, the location for all default options.
Although I will do my best to write good documentation,
for many programs the input parser becomes the most up-to-date
source for documentation. So this is a great place to write
lots of comm... |
880351745a198104024f8f415a74e655af03c21bb952a2a437037e11425b2d98 | Python | 48,008 | 954 | import numpy as np
import pandas as pd
import glob, os
import scipy.stats as st
import matplotlib.pyplot as plt
import seaborn as sns
from functools import reduce
from sklearn.preprocessing import StandardScaler
import lifelines, itertools
from sklearn.model_selection import KFold
drugs_lst = ['RIF', 'INH', 'EMB', 'PZ... |
8b6475963061e753ce8e86e0a53cf6391ba339a116d48ae52018d329193bb921 | Python | 48,228 | 1,251 | #!/usr/local/bin/env python
# =============================================================================================
# MODULE DOCSTRING
# =============================================================================================
"""
Test custom integrators.
"""
# ==========================================... |
bed60f3679a75aaac28d395537f34b40c77ad55f70f6f4e873a94f66fef71742 | Python | 48,238 | 1,139 | import base64
import json
import logging
import math
import os
import re
from textwrap import indent
from typing import Any, Dict, List, NamedTuple, Optional, Tuple, TypeVar, Union
import requests
import yaml
from pydantic import BaseModel, Field
from multiqc import config, report
from multiqc.core.log_and_rich impor... |
563544543819c80804db6ecb0ea80f1c60e199117291d8fe88bdc630338b5ba5 | Python | 48,513 | 1,367 | import bisect
import itertools
import logging
from datetime import timedelta
from typing import List, Optional, Tuple, Dict, Any
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
from matplotlib.lines import Line2D
from ethopy_analysis.data.loaders import (
get_trial_behavior,
get_trial_e... |
ba79d3c48a5fbb1b3c1e5e24680e9c2cb6e6c9bbd34076afd910a19db29e12ea | Python | 48,541 | 1,187 | import numpy as np
import matplotlib
import matplotlib.pyplot as plt
import glob
import os
import string
import nibabel as nib
from statsmodels.stats.multitest import multipletests
from utils import Show_Stars, SortFiles, MakeBoxplot, DrawLines2, DrawLines
from statistical_tests import PerformWilcoxonMotion, PerformWil... |
86f7d3e7d394d5254567044e871b6a8e4137dcc5e0f6c7e084eb93739a68b618 | Python | 48,628 | 1,129 | """MultiQC functions to plot a bargraph"""
import copy
import json
import logging
import math
from collections import OrderedDict, defaultdict
from typing import Any, Dict, List, Literal, Mapping, NewType, Optional, Sequence, Set, Tuple, TypedDict, Union, cast
import numpy as np
import plotly.graph_objects as go # t... |
def55249ef011da414efad9064256bb1ae2957f39f58f26a145c156f64360c83 | Python | 48,665 | 1,110 | import copy
import json
import logging
import random
import re
import uuid
from collections import defaultdict
from itertools import chain
from pathlib import Path
from typing import Any, Callable, Dict, List, Optional, Tuple
from natsort import natsorted
from multiqc import config
from multiqc.base_module import Bas... |
290dd872aedfce1af61159f4e5e13ec27a7219d4dcaf622f1e34cc1481134340 | Python | 48,845 | 1,359 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""OpenMM Equilibrium SepTop Protocol base classes
==================================================
Base classes for the equilibrium OpenMM SepTop free energy ProtocolUnits.
Thist mostly ... |
dc8bea243125874deafb48402f7e44d16806bf3ff17efb5bda16f96cb4e59bc8 | Python | 48,886 | 1,336 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import itertools
import json
import math
import pathlib
from collections import Counter
from unittest import mock
import gufe
import mdtraj as md
import numpy as np
import openmm
import open... |
c7837656bd7284ad0b866729c77e2c1045f7d13901a8e1936374041c412a0712 | Python | 48,926 | 1,270 | """
MultiQC report module. Holds the output from each module. Available to subsequent
modules. Contains helper functions to generate markup for report.
"""
import base64
import dataclasses
import fnmatch
import gzip
import inspect
import io
import json
import logging
import mimetypes
import os
import re
import shutil
... |
a3b47b9eaf21384eeafe4ba099c29f1ea46a5cb79b51627ee80f060ee12e324a | Python | 49,007 | 1,963 | """This file contains code used in "Think DSP",
by Allen B. Downey, available from greenteapress.com
Copyright 2013 Allen B. Downey
License: MIT License (https://opensource.org/licenses/MIT)
"""
import copy
import math
import numpy as np
import random
import scipy
import scipy.stats
import scipy.fftpack
import subpr... |
6a3b8dcc96dd5256b4cc7c69de7326519bb5e70f20398ec589d6bf7dec3e8bf2 | Python | 49,249 | 1,052 | import os
import matplotlib
import numpy as np
import pyqtgraph as pg
import scipy.io as sio
from matplotlib import cm
from qtpy import QtCore, QtGui, QtWidgets
from qtpy.QtCore import Qt, QUrl
from qtpy.QtWidgets import *
from facemap import utils
from facemap.gui import guiparts, help_windows, io
from facemap.neura... |
eae86a483ee81d15d80ff0e25a68990013787ca163d4f25e649d88d12ae9a7e5 | Python | 49,408 | 1,096 | """
twinc_reg_network.py
Author: Anupama Jha <anupamaj@uw.edu>
TwinC regression model architecture.
"""
import torch
import numpy as np
from twinc_reg_utils import count_pos_neg, decode_chrome_order_dict, decode_list
from sklearn.metrics import roc_curve, roc_auc_score, average_precision_score, precision_recall_curve
... |
5a83414f8b366f3a2bffd92f875f7cdfefb9cd7de8cb36f013e8b1a81f5261b9 | Python | 49,693 | 1,294 | """
PCA Analysis of Input Weight Patterns
This module provides Principal Components Analysis (PCA) of synaptic input
weight patterns to test whether excited and suppressed cells differ in their
multivariate input combinations rather than individual source means.
Complements univariate nested weights analysis by testi... |
45e56768cc27b084429dcf3eec198106ef795c85b9e87169f14b54ba90c92542 | Python | 49,701 | 1,058 | from collections import defaultdict
import cv2
from functools import partial
import numpy as np
from scipy import fft
from scipy.fftpack import next_fast_len
import shapely
import shapely.geometry as shpgeo
from shapely.ops import unary_union
from feabas.config import DEFAULT_AVG_DEFORM, data_resolution, section_thick... |
9514077945a8c8b7a06c48874d8e96265455cd407f4e37bacd2805ecf32051ca | Python | 49,900 | 1,450 | from dataclasses import dataclass, field
import dataclasses
from functools import cached_property
from typing import (
Any,
Callable,
ClassVar,
Generic,
Iterable,
Literal,
Self,
Sequence,
Type,
TypeAlias,
TypeVar,
Tuple,
)
import abc
from uuid import UUID
from loguru imp... |
f22659c0b7625b05039f527f64e88c6a59ffce3be9b3801f674b9d5318e865cb | Python | 50,010 | 1,198 | """
Violin plot module. Also handles scatter plots and tables.
"""
import copy
import json
import logging
import math
from dataclasses import dataclass
from typing import Any, Dict, List, Optional, Set, Tuple, Union, cast
import numpy as np
import plotly.graph_objects as go # type: ignore
import polars as pl
from m... |
228c17497a1d6c74ded697c78f7a7feac73d4f16ec583a48a7418e9919d1266e | Python | 50,029 | 1,347 | import json
import pickle
import struct
import warnings
from contextlib import nullcontext
import numpy as np
import pytest
import shapely
from shapely import (
GeometryCollection,
GEOSException,
LinearRing,
LineString,
MultiLineString,
MultiPoint,
MultiPolygon,
Point,
Polygon,
)
f... |
857b9d78164fc9e055e6b37ff75701a36c960d8692b2b3025596b5cfbc357248 | Python | 50,394 | 990 | """
twinc_network.py
Author: Anupama Jha <anupamaj@uw.edu>
"""
import torch
import numpy as np
from .twinc_utils import count_pos_neg, decode_chrome_order_dict, decode_list
from sklearn.metrics import roc_curve, roc_auc_score, average_precision_score, precision_recall_curve
def encoder_linear_block(layer1_in,
... |
c9c2309490212c8114301f29bee5bdf1cbbe3374eef81dc616eb4b1a337e8810 | Python | 50,464 | 1,438 | # Copyright 2022 Google LLC.
#
# 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,... |
35dabe9d6fd568171c83ed56b6701d559257210babf033aaeffbd1eeffb48a04 | Python | 50,529 | 1,492 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import itertools
import json
import math
import pathlib
from unittest import mock
import gufe
import mdtraj as md
import numpy as np
import openfe.protocols.openmm_septop
import openmm
impor... |
52ca71f3d88bff5291fae0075ea0e71e09076dfa12166692b88abe4337d8be52 | Python | 50,711 | 1,113 | """ @package forcebalance.smirnoff SMIRNOFF force field support.
@author Lee-Ping Wang
@date 12/2018
"""
from __future__ import division
from builtins import zip
from builtins import range
import os
from forcebalance import BaseReader
from forcebalance.abinitio import AbInitio
from forcebalance.abinitio_pairwise impo... |
8e40cd55296761eef6367cfbb22d8bce3b180b143d8ea477923a2063cea0cf87 | Python | 50,732 | 1,186 | # Copyright 2017 Google Inc.
#
# 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,... |
ffbbaedb293055415d067b998577c914f64f8a891dc1632e574797b8060fdc42 | Python | 50,752 | 1,454 | # Copyright 2022 Google LLC.
#
# 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,... |
2a5d18bcf40a73839ca558bb939705ce2c9d335c4e2bc8aa7712c65e06d91d5e | Python | 51,059 | 1,339 | # -*- coding: utf-8 -*-
#
# Copyright (C) 2012-2017 The Python Software Foundation.
# See LICENSE.txt and CONTRIBUTORS.txt.
#
"""PEP 376 implementation."""
from __future__ import unicode_literals
import base64
import codecs
import contextlib
import hashlib
import logging
import os
import posixpath
import sys
import z... |
f74e4bafd5e7d24f46607eb8a91164cd468f9de94bee07e33f9628f56c3a0449 | Python | 51,367 | 1,329 | import itertools
from typing import Any, Literal
import matplotlib.pylab as plt
import networkx as nx
import numpy as np
import seaborn as sns
from adjustText import adjust_text
from openff.units import Quantity, unit
from cinnabar import conversion, plotlying, stats
from cinnabar.femap import ABSOLUTE_ANALYSIS_TYPES... |
283fbd5091ac96d2c73b1b174500e4b48ab85c600c9eeeadb8c0735b7e9f4320 | Python | 51,423 | 788 | import sys
import os
import logging
import pandas as pd
import numpy as np
from copy import deepcopy
from abc import ABC, abstractmethod
from typing import List
import traceback
import math
from ..Utils.resources import SharedResources
from ..Utils.io_converters import reload_optimal_validation_parameters
from ..Plotti... |
39cb806fe2b437546026fe0ae0fddf7dd9b6c7d7db19e244d4bba9cca368a26f | Python | 51,581 | 1,017 | import matplotlib.pyplot as plt
import matplotlib as mpl
from itertools import combinations
import math
import warnings
import mplcursors
import numpy as np
import pandas as pd
from scipy.stats import levene, shapiro, mannwhitneyu, yeojohnson, boxcox
import pingouin as pg
import statsmodels.api as sm
from statsmodels.... |
6c9a719e770cb8268a2335a7f01659405de9ba078cd8c06e84a186b4996dd891 | Python | 51,740 | 1,195 |
###################### Libraries ######################
# Deep Learning
import tensorflow as tf
import keras
from keras.models import Model, load_model
from keras.layers import Input, Conv2D, MaxPooling2D, Conv2DTranspose, concatenate
from keras import backend as K
from tensorflow.keras import layers, optimi... |
ec9f68b5a78f2ca1fefd2ab7f19fa9e542d0ca56dea69ae7c6cc33f24ab3688b | Python | 51,908 | 1,067 | import random
from datetime import date
from uuid import UUID
import pandas as pd
from sqlalchemy import select
from truesight import plot_utils, stats_utils
from truesight.db.models import (
DbEvaluation,
DbEvaluationQuestion,
DbLLM,
DbQuestion,
DbResponse,
)
from truesight.db.session import get_se... |
25b514f7d4206e9fd4d92e54ff9157c22f7145184b7ee352b79a3a3b5dac82b4 | Python | 51,996 | 1,303 |
# sphinx_gallery_thumbnail_path = '../_static/momi2025__Figure_2.PNG'
"""
.. _ex-momi2025:
====================================================================================================
Gradients of Excitability and Recurrence Revealed by Stimulation Mapping and Whole-Brain Modelling
=========================... |
fdc0bf302ee7af4a6e24e0bc40c97120b3531e28da5818e8563245ef82e97485 | Python | 52,094 | 819 |
__author__ = "Timothy Tickle"
__copyright__ = "Copyright 2015"
__credits__ = [ "Timothy Tickle", "Brian Haas" ]
__license__ = "MIT"
__maintainer__ = "Timothy Tickle"
__email__ = "ttickle@broadinstitute.org"
__status__ = "Development"
import Commandline
import os
import ParentPipelineTester
import unittest
class Scri... |
cbc87d40dc2ee5572a9eda5f7aaed71277d024dfcaafde45347530a7f545dcc8 | Python | 52,117 | 1,475 | # Copyright 2022 Google LLC.
#
# 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,... |
80c6f226461a31d0f6e37f9fb560208a508a7293b0ea5fafadb0cfadbe33f619 | Python | 52,240 | 1,274 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""Equilibrium Relative Free Energy methods using OpenMM and OpenMMTools in a
Perses-like manner.
This module implements the necessary methodology toolking to run calculate a
ligand relative... |
4220e91594244dcb0edbbf6a4cff6083fa9734df7557f679fd3f020fe659c7d3 | Python | 52,262 | 1,380 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""OpenMM Equilibrium Binding AFE Protocol --- :mod:`openfe.protocols.openmm_afe.equil_binding_afe_method`
====================================================================================... |
c4cbb87fd3e513e10f505653706b490bb86912f63a15a5c5a894a0300c7a096a | Python | 53,223 | 1,153 | """ @package forcebalance.tinkerio TINKER input/output.
This serves as a good template for writing future force matching I/O
modules for other programs because it's so simple.
@author Lee-Ping Wang
@date 01/2012
"""
from __future__ import division
from __future__ import print_function
from builtins import str
from b... |
68b7bdb6c1369e568a01190b7ec9c5cc2227a92884565a166894af3be0c50468 | Python | 53,276 | 1,594 | """
NWB File Export Module for Ethopy Data
This module provides functionality to export experimental data from DataJoint tables
to NWB (Neurodata Without Borders) format files.
"""
import logging
import os
from datetime import datetime, date
from dateutil.relativedelta import relativedelta
from typing import Any, Di... |
86f26976d12e0e128f29aec20fcad8e6667dd92616ba4e36e85fea94ce399daf | Python | 53,371 | 1,287 | """
特征稳定性可视化脚本
功能：基于feature_stability_analysis.py生成的数据文件，创建5个主要可视化图表
作者：AI助手
日期：2025-12-11
生成图表：
1. 6种XAI方法稳定性箱线图（跨癌种）
2. 3类XAI方法稳定性箱线图（跨癌种）
3. 15癌症×6XAI稳定性热力图
4. 代表癌症（LGG）6种XAI方法稳定性箱线图（50个抽样模型）
5. Kuncheva随Top-k变化折线图
"""
import os
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import seabor... |
65186ac3eb00bb88846106529dfd9183d502c9dcb589e5140f9b51b5bcdbc920 | Python | 53,439 | 1,068 | import logging
import os
import math
from PySide6.QtWidgets import QLabel, QHBoxLayout, QVBoxLayout, QLineEdit, QListWidget, QListWidgetItem, QErrorMessage,\
QPushButton, QFileDialog, QSpacerItem, QComboBox, QStackedWidget, QWidget
from PySide6.QtCore import Qt, QSize, Signal
from PySide6.QtGui import QIcon, QPixma... |
1a34df002f3489ea69aff83daea32e1b0d57614983a70825587fead2193c21a9 | Python | 53,535 | 1,296 | """
meta/lodo_cv.py — Leave-One-Dataset-Out Cross-Validation
=========================================================
Evaluates the recommender system using LODO-CV against 7 baseline strategies.
Baseline strategies
-------------------
1. Random : randomly select a method
2. Always-GRAPE : alw... |
d41efe2146298c3dd13bde68a35f2d89f7cf8fb1d0aa27142799e1363497e4a3 | Python | 53,627 | 1,543 | import sys
import tempfile
from typing import Dict, List, Union
from unittest.mock import patch
import pytest
from multiqc import config, report
from multiqc.core.exceptions import RunError
from multiqc.plots import bargraph, box, heatmap, linegraph, scatter, table, violin
from multiqc.plots.linegraph import LinePlot... |
d3178545512fcea8285833a989ffeeab017fff2fff7f5141bffcb26b61aedfb3 | Python | 53,640 | 1,581 | # THIS PYTHON FILE IS DOWNLOADED FROM https://github.com/elkebir-group/CloMu/pulls, A PULL REQUEST THAT SOLVES AN ISSUE WITH THE ORIGINAL CODE DEVELOPED BY STEFAN IVANOVIC AND EL-KEBIR, WHICH CAN BE DOWNLOADED FROM https://github.com/elkebir-group/CloMu
import copy
import torch
from torch.autograd import Variable
imp... |
db846d5bbf531adea6df4cd4f6a5ad107d2deaba4d221b2089e19d39957770b5 | Python | 53,673 | 1,069 | """
JSON Schema for MultiQC config validation.
Generated from the config defaults and type hints.
"""
from contextlib import contextmanager
from contextvars import ContextVar
from functools import lru_cache
from typing import Any, Dict, Iterator, List, Literal, Optional, Union
from pydantic import BaseModel, ConfigDi... |
0e6f7708659016ad630792cacea259865efd23b511293c2e30eadd4c7da4aab9 | Python | 53,791 | 1,396 | """List of force fields and water models."""
from pathlib import Path
from proteinbenchmark.utilities import package_data_directory
ff_directory = Path(package_data_directory, "force-fields")
# List of force fields with force field XML file, water model, and water model
# XML file
force_fields = {
"espaloma-0.3... |
fbbe66ae068083f455662615a9155a740404bca1419d04f005525ceb301b7771 | Python | 54,027 | 1,423 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
r"""OpenMM Equilibrium SepTop RBFE Protocol Units
================================================
This module implements the :class:`gufe.ProtocolUnit`\s for the
Separated Topologies RBFE p... |
1423d6808d57f467706e72f986280d2bfe2a75341ede094ce639ba1434921e60 | Python | 54,173 | 1,356 | import re
import sys
import queue
import shutil
import tempfile
import threading
import zipfile
from functools import lru_cache
from pathlib import Path
import matplotlib
matplotlib.use("Agg")
import matplotlib.pyplot as plt
import nibabel as nib
import numpy as np
import gradio as gr
REPO_ROOT = Path(__file__).resol... |
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