sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
418b322cbc04b108288af183d082158e8f469ae8be54c934976842d72e055d09 | Python | 30,074 | 775 | """MultiQC functions to plot a heatmap"""
import logging
import re
from typing import Any, Dict, List, Mapping, Optional, Sequence, Tuple, Union, cast
import numpy as np
import plotly.graph_objects as go # type: ignore
import polars as pl
from pydantic import Field
from multiqc import report
from multiqc.core.plot_... |
5a48eab6cffa01d6af801822e086949dbe09f709106f37db8681802e23d10c09 | Python | 30,109 | 863 | import numpy as np
#import torch
import argparse
import torch
from sklearn.preprocessing import StandardScaler
import sys
from sklearn.metrics import r2_score, mean_squared_error
import random
import os
from sklearn.model_selection import BaseCrossValidator
from himalaya.ridge import GroupRidgeCV, RidgeCV, Ridge
from h... |
06c9d1fb36082e0a05cc9eb2ab84fc86dfe2d0fc303c6540c56c56695e5d7078 | Python | 30,137 | 781 | # -*- coding: utf-8 -*-
"""
requests.sessions
~~~~~~~~~~~~~~~~~
This module provides a Session object to manage and persist settings across
requests (cookies, auth, proxies).
"""
import os
import sys
import time
from datetime import timedelta
from collections import OrderedDict
from .auth import _basic_auth_str
from... |
33d59c2f24d23e31454a28cdca004dbad31bb98466bd0e38c383ffaece7bfcc7 | Python | 30,166 | 525 | import logging
import traceback
import numpy as np
from PySide6.QtWidgets import QWidget, QHBoxLayout, QVBoxLayout, QDialog, QDialogButtonBox, \
QPushButton, QScrollArea, QFileDialog, QSplitter, QTableWidget, QTableWidgetItem,\
QProgressBar, QMessageBox
from PySide6.QtCore import Qt, Signal
from PySide6.QtGui ... |
605ebad1a8fd53fc5be3c9bd69eef88fd7fd090fcd572fc481d11ec01c3cbd65 | Python | 30,176 | 843 | # 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,... |
863c73ce99c37acfb6ed1408154cb506acc7b8a37b7aa476a0d597d34ef61f67 | Python | 30,182 | 878 | import logging
import os
from datetime import datetime
from functools import wraps
from flask import (
Flask,
flash,
jsonify,
redirect,
render_template,
request,
session,
url_for,
)
from flask_ldap3_login import AuthenticationResponseStatus, LDAP3LoginManager
from flask_limiter import L... |
0704f5ad26d9a0792f481500a5948b1ae885e61703ecca5568e2208f07f7715c | Python | 30,198 | 743 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on 12/14/2021
Emission models class
Author: dzhi, jdiedrichsen
"""
import numpy as np
import torch as pt
import pandas as pd
from scipy import stats, special
from torch import log, exp, sqrt
from HierarchBayesParcel.model import Model
import HierarchBayesParce... |
9ba7a9c3bba617af6e014e666f217e8973812afef60d47992088900c98e44d87 | Python | 30,226 | 714 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
from typing import Any, Dict, List, Optional, Tuple, Union
import dask.array as da
import numpy as np
import tifffile
from fsspec.implementations.local import LocalFileSystem
from ome_types import from_xml, to_xml
from ome_types.model import OME, Channel, Image, Pixels, T... |
c88539ed7a1d112a90a2a8cd7efcb32e150018039eea3df01ecf6ea63631c6ac | Python | 30,251 | 835 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Jan 6 18:29:48 2025
@author: saiful
"""
# import os
# import shutil
# # Source and destination directories
# source_dir = "/data/saiful/ePPI/alphafold_eppi_embeddings/"
# destination_dir = "/data/saiful/ePPI/alphafold_eppi_embeddings/All_ePPI_Alphafo... |
b037a215cac96636b61c76d45d58a69f8b26aff7e04c653956a46efd23ddc3ae | Python | 30,333 | 887 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import gzip
import os
import pathlib
import urllib.error
import urllib.request
from importlib import resources
import gufe
import mdtraj
import numpy as np
import openmm
import pandas as pd
... |
71f73ced867d3352b0b2daf0c3b7e7d7c0682e516b7370861029fc04b3fd6fd0 | Python | 30,475 | 793 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
from typing import Callable
import pytest
import openfe
from ..conftest import mol_from_smiles
class BadMapper(openfe.setup.atom_mapping.LigandAtomMapper):
@classmethod
def _def... |
fcaf4082437a79f3def9afb3819bab5f376ce4f042d02cc39328c0136a024054 | Python | 30,529 | 992 | # -*- coding: utf-8 -*-
"""
requests.utils
~~~~~~~~~~~~~~
This module provides utility functions that are used within Requests
that are also useful for external consumption.
"""
import codecs
import contextlib
import io
import os
import re
import socket
import struct
import sys
import tempfile
import warnings
import... |
cda80d67d1c0d4aea25fb2283f2aed7dedac91fc61a5a3657933429eb660b01b | Python | 30,575 | 644 | #!/usr/bin/env python3
"""
Step 1: 下载并准备各数据库
- OncoKB: 癌症基因临床分级 (需API Token)
- CGC: Cancer Gene Census (需COSMIC账号)
- DGIdb: 药物-基因互作 (需手动下载)
- CIViC: 临床变异解读 (可自动下载)
运行方式:
python scripts/01_download_databases.py
python scripts/01_download_databases.py --skip_existing # 跳过已存在的文件
"""
import os
import sys
import ... |
80849a98abc43e960accba41094e39eb4ead8abeb2c9bcc3dc26101d6f8bbb8f | Python | 30,648 | 882 | # This code is part of kartograf and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/kartograf
import copy
import dill
import inspect
import numpy as np
from enum import Enum
from collections import OrderedDict
from collections.abc import Iterator
from rdkit import Chem
from ... |
71ceb0abfa2e5ec46915271705e0580ddb4d8fc45ea3a8539348b9050aea7502 | Python | 30,698 | 886 | # Copyright (c) 2010-2017 Benjamin Peterson
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publi... |
afe2b507036c29120ddeab55555835e79d5128cf5b0b82ea7e536680fbe69065 | Python | 30,711 | 701 | import json
import os
import logging
from typing import Tuple
from copy import deepcopy
from aenum import Enum, unique
from utils.data_structures.PatientParametersStructure import PatientParameters
from utils.models_download import download_model
from utils.software_config import SoftwareConfigResources
from utils.dat... |
033e7ba1e7edcae80e03a8eff91d7a398f3ce0aeac7e99be884279536b9eb8c6 | Python | 30,730 | 996 | import base64
import json
import os
import re
import tempfile
import pytest
import multiqc
from multiqc import config, report
from multiqc.base_module import ModuleNoSamplesFound
from multiqc.core.file_search import file_search
from multiqc.core.special_case_modules.custom_content import custom_module_classes
from mu... |
081b51177080f02cfb3ab03b50685c064d9ee4913509dba4215e5d8cc74994df | Python | 30,755 | 713 | #!/usr/bin/env python3
"""
Analysis of chromatin states for specific genes in NSC and Neu samples (GFP condition)
This script visualizes the chromatin states of genes from a provided list
"""
import os
import sys
import argparse
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import seaborn as s... |
e9a231417a9e6115f85a9ab58c4ef9ddb50c2db108010a23a35d504dc3c91625 | Python | 30,757 | 848 | import os
import pandas as pd
import numpy as np
import xgboost as xgb
import sage
import torch
import torch.nn as nn
import torch.optim as optim
from pathlib import Path
from datetime import datetime
from copy import deepcopy
from torch.utils.data import DataLoader, TensorDataset
from boruta import BorutaPy
from skle... |
3fb3bd221f4ce0e890bfff33edec6ead5a38b4f149fcc24b68f469570fe54871 | Python | 30,818 | 892 | import base64
import io
import logging
import multiprocessing as mp
import os
import shutil
import threading
import time
import warnings
from abc import ABC, abstractmethod
from datetime import datetime
from http.server import BaseHTTPRequestHandler, ThreadingHTTPServer
from multiprocessing import Pool
from pathlib imp... |
6c7029127f821c8ed6d1f8773d9590d0d393f922373230033d082c2c93a7f056 | Python | 30,837 | 860 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import print_function, division, absolute_import, unicode_literals
import sys, os, re, shlex, shutil, glob, subprocess, collections
from os import path
from datetime import datetime
import numpy as np
from scipy import interpolate
import matplotlib as mpl
fr... |
d85e851fe05759414207588b2775dfb56278f5869f42afadd67858a2a69309f2 | Python | 30,858 | 890 | import numpy as np
from tqdm import tqdm
import random
from experiments import quick_plot
from truesight import pd_utils
from truesight.evaluation import evals
from experiments.quick_calculate import mi_dirichlet_ci
from refs import open_model_refs as r
from refs.paper.animal_preference_numbers_refs import (
evalua... |
7d9bf70133e320315649604d8ee5764de56aa06a504b64607a9a32ab8886d7d1 | Python | 30,962 | 880 | """
Functions containing the core operations and logic of for image registration for `voxelmorph`
written in PyTorch.
"""
# Core library imports
import warnings
from functools import partial
from typing import Callable, List, Union, Sequence, Tuple, Literal, Optional
# Third-party imports
import numpy as np
import to... |
f62ddfb9abc5448040b851d92ea671a9ec33508fa9625af58da2c83dd804a09f | Python | 30,990 | 586 | import argparse
import time
import os, sys
import os.path as osp
from shutil import copy
import copy as cp
from tqdm import tqdm
import pdb
import numpy as np
from functools import reduce
from sklearn.metrics import roc_auc_score
import scipy.sparse as ssp
import torch
from torch.nn import BCEWithLogitsLoss
from torch... |
82cf59f13cac2ed9de175ea2eb96d751391bcf034ee16a9b1db5ffa8a09bf57e | Python | 31,016 | 748 | #! python
# -*- coding: utf-8 -*-
import glob
import logging
import os
import xml.etree.ElementTree as ET
from collections import Counter
from typing import Any, Dict, List, Optional, Tuple, Union
import numpy as np
import pandas as pd
from gseapy.base import GSEAbase
from gseapy.gse import Metric, fgsea_rs, gsea_rs... |
0bd72752f61d233c0b9fff8ab5a6e4f5bf27f3bb9e405369f087d5dbe41f643a | Python | 31,086 | 970 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
from abc import ABC, abstractmethod
from pathlib import Path
from typing import Any, Dict, List, Optional, Tuple, Union
import dask.array as da
import numpy as np
import xarray as xr
from fsspec.spec import AbstractFileSystem
from ome_types import OME
from .. import cons... |
c7bebe4667ed0645239965a5bd1b50c0964e961c351f9bda65b1eac8247ca0e7 | Python | 31,231 | 623 | import datetime
import shutil
import traceback
import dateutil.tz
from aenum import Enum, unique
import logging
import os
from copy import deepcopy
from typing import Union, Any
import nibabel as nib
from nibabel.processing import resample_to_output
import numpy as np
import json
from pathlib import PurePath
import re
... |
e11e51f092460df4585abef2c0fa7dc007627d230b5eebbaf252f5033ef147a1 | Python | 31,231 | 583 | # This script computes the psth given sample neural data.
import argparse
import os
import scipy
import numpy as np
from pathlib import Path
import math
import matplotlib.pyplot as plt
from scipy.ndimage import gaussian_filter1d
import pickle as pkl
from datetime import datetime
import sys
import matplotlib.transforms... |
32d0929411f94ae12a87d07233803fa1959c6e928ab9b8dc916fb2aaed55f312 | Python | 31,250 | 895 | from abc import abstractmethod
import math
import numpy as np
import torch as th
import torch.nn as nn
import torch.nn.functional as F
from .fp16_util import convert_module_to_f16, convert_module_to_f32
from .nn import (
checkpoint,
conv_nd,
linear,
avg_pool_nd,
zero_module,
normalization,
... |
5e24318238e1a26676c153c46e0cd8129bf0dd10e97f2f24d509cefc8e109d52 | Python | 31,255 | 844 | from dgl import DGLGraph
import dgl
import dgl.function as fn
import dgl.nn as dglnn
import torch as th
import torch.nn as nn
import torch.nn.functional as F
import numpy as np
import tqdm
import numpy as np
import torch
from dgl.data import DGLDataset
from dgl.dataloading import (
as_edge_prediction_sampler,
... |
171f5a55903ed4ecfb62ff48e3aa7a16e865d88ad49d78a46abb4b259e736f77 | Python | 31,270 | 578 | import learn2learn as l2l
import torch
from torch_geometric import seed_everything
from utilsfiletraining import *
from architecturenn import GCN, AtomMessagePassing
import os
def main_maml_training_loop(maml, train_loader, meta_valid_loader, scalers,
optimizer_maml, cond_names, criterion,... |
6c47f886a990238148bfacf539e5811056fc6776d7e868416592f61facb8d8e1 | Python | 31,339 | 905 | #!/usr/bin/env python3
"""
Tests for adaptive stepping in optogenetic circuit optimization
Tests:
- Sequential strategy with adaptive stepping
- Batch GPU strategy with adaptive stepping (if CUDA available)
- Multiprocess CPU strategy with adaptive stepping
- Comparison: fixed-dt vs adaptive-dt results
- Performance b... |
4a31530f31a70bbaa58c4033f1e72e22762b1a21d52156b98333e9601cc169cc | Python | 31,440 | 870 | # src/analysis/rsa.py
"""
RSA (Representational Similarity Analysis) module
Complete pipeline for RSA analysis including:
- Feature extraction (PyTorch)
- Correlation computation
- Multi-run analysis workflows
- RSA visualization
"""
import numpy as np
import torch
import re
from collections import defaultdict, Coun... |
65a1d7b8a18cb31e323b098251603de73bf132478e696e4c2e97a1cb62968ba7 | Python | 31,468 | 729 | """Fully convolutional data generators.
These data generators allow for training on augmented label masks (y)
instead of single label for the whole image.
"""
import os
import numpy as np
from tensorflow.keras import backend as K
from tensorflow.keras.preprocessing.image import array_to_img
from tensorflow.keras.p... |
a8e3ffb08ed62898494a38601eed998e955133b65444e8ded633ab30a25f31df | Python | 31,490 | 1,142 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import annotations
from typing import List, Optional, Tuple, Union
import dask.array as da
import numpy as np
import pytest
import xarray as xr
from aicsimageio import AICSImage, dimensions, exceptions, types
from aicsimageio.readers import ArrayLikeReade... |
314d1218e441c0dd5fef87cc584b799cfb9c0136ee57439527c55d0bebac1be8 | Python | 31,535 | 863 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
EEG PREPROCESSING FOR DECODING
This script implements the preprocessing of the EEG data for the decoding
analysis. It downsamples the EEG data to 50hz to increase the computational
efficiency. It epochs the data into 1380ms long epochs.
Acknowledgement: This script i... |
70be6df3a8b1db0bdfe0e2d3f73abd640799e10c779e1a148265df0ce7c42a34 | Python | 31,640 | 872 | # 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,... |
1e1fff94af392aa9c1d7c420c7caf19e69dd95beacb7f35d0a8b8b2517b574dc | Python | 31,646 | 698 | from typing import List, Tuple
import numpy as np
import pandas as pd
from scipy.stats import linregress
from src.load import load_files
from src.utils import is_within_target_window, is_within_target_window_3D, make_df_structure, process_emg_data, process_eyemovement_data
from src.metrics import spearman_correlation, ... |
5d86078fdfa5f16bffcfe76df1e26682530c5d1af2d134e060a4b558e84cfcdd | Python | 31,677 | 871 | import torch
import torch.nn as nn
import copy
import torch.nn.functional as F
import ProtoCloud.glo as glo
EPS = glo.get_value('EPS')
LRP_FILTER_TOP_K = glo.get_value('LRP_FILTER_TOP_K')
device = 'cuda' if torch.cuda.is_available() else 'cpu'
num_workers = 4 if torch.cuda.is_available() else 0
##################... |
63f4986ddf121dca6034f7efde27d59e26658d8b3570b00595e0528b6fcedc26 | Python | 31,685 | 755 | """distutils.command.build_ext
Implements the Distutils 'build_ext' command, for building extension
modules (currently limited to C extensions, should accommodate C++
extensions ASAP)."""
import contextlib
import os
import re
import sys
from distutils.core import Command
from distutils.errors import *
from distutils.... |
35eb976ab111992acf5bd595cb2b7e59de571d733dec2c1d0e65ca0256c0afbc | Python | 31,750 | 1,079 | import argparse as ap
import os
import sys
from importlib.metadata import PackageNotFoundError, version
try:
__version__ = version("gseapy")
except PackageNotFoundError:
__version__ = "unknown"
# ------------------------------------
# Main function
# ------------------------------------
# there is a bug in ad... |
223412c5084230fe6691d67dff91025cf1d3989f20caedd41d0978e3d15d3fab | Python | 31,786 | 662 | import logging
import os
import time
import numpy as np
from PySide6.QtWidgets import QLabel, QHBoxLayout, QVBoxLayout, QLineEdit, QPushButton, QProgressBar, QGroupBox, \
QFileDialog, QDialog, QComboBox, QMessageBox
from PySide6.QtCore import Qt, QSize, Signal
from PySide6.QtGui import QIcon, QPixmap
from gui.Uti... |
7459ab3ae9037a6d858a907dc30dff15e1c4dd5617badb04d6f78842a8591836 | Python | 31,825 | 806 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import mdtraj as mdt
import numpy as np
import openfe
import pytest
from openfe.protocols.openmm_rfe.hybridtop_units import (
HybridTopologyMultiStateSimulationUnit,
)
from openff.units ... |
043cfd61625dc51db35af1a8c184b191bdf13ea3839e3cfd4211eced4ddded73 | Python | 31,829 | 792 | #!/usr/bin/env python3
"""
Experiment 08 — Generate Paper Figures (19-method, v10 spec)
=============================================================
Generates all manuscript figures from sweep + fingerprint + LOBDO data.
Figures
-------
Figure 2 : Winner map (miss x label, MCAR + MNAR)
Figure 3 : t-SNE before/after... |
0da1eefd597619a18f72a5f5310dc7658a74af7197b2089e220e783099ccde1d | Python | 31,907 | 854 | """Methods to create geometries."""
import numpy as np
from shapely import Geometry, GeometryType, lib
from shapely._enum import ParamEnum
from shapely._geometry_helpers import collections_1d, simple_geometries_1d
from shapely.decorators import deprecate_positional
from shapely.io import from_wkt
__all__ = [
"bo... |
58009f5d4fddbb082015653e12cbc1340cbdc1614c73ef09728f5e9b7acf9234 | Python | 31,935 | 775 | from pathlib import Path
from proteinbenchmark.analysis import (
align_trajectory,
assign_dihedral_clusters,
compute_chemical_shifts_sparta_plus,
compute_fraction_helix,
compute_h_bond_scalar_couplings,
compute_noe_effective_distances,
compute_residual_dipolar_couplings,
compute_scalar_... |
b98a7d975dc5d0b7249d2e9de0deb4cad88180598884a89d78eabd027b314dca | Python | 31,944 | 863 | # This file is dual licensed under the terms of the Apache License, Version
# 2.0, and the BSD License. See the LICENSE file in the root of this repository
# for complete details.
from __future__ import absolute_import, division, print_function
import abc
import functools
import itertools
import re
from ._compat impo... |
754105576261a7260c1fe9aa0e653eb983f8fc054862a24d4070a7a05682f0b0 | Python | 31,978 | 871 | """Enumerate resonance forms of a molecule"""
import copy
import itertools
import json
from typing import Dict, Optional, List, Generator, Tuple, Any, Union
import networkx as nx
import numpy as np
from openff.units import unit
from openff.toolkit.topology import Molecule
from openff.nagl.utils._types import Resona... |
1e84e15c01e848327da308250e5ed1dab3bd906333fd7484581f1d104f1dd690 | Python | 31,991 | 663 | """@package forcebalance.objective
ForceBalance objective function."""
from __future__ import division
from builtins import range
from builtins import object
import sys
import inspect
#from implemented import Implemented_Targets
import numpy as np
from collections import defaultdict, OrderedDict
import forcebalance
f... |
49708600a42ea9fc20c15469e535736caf9e8dfb4aaf695d0a791898b2e62c5d | Python | 32,017 | 862 | """
Effect Size Decision Framework for Nested Experiment Data
Integrates bootstrap effect size analysis with power analysis, precision assessment,
and biological significance to make data collection recommendations.
This framework determines whether additional connectivity instances are needed
for conclusive mechanis... |
66bc8ec200aae27bef1b8fe51e3f7c2a562d52469b64ea5f1f87d1d1a4814401 | Python | 32,074 | 987 | """Analysis tools for KIMMDY runs.
For command line usage, run `kimmdy-analysis -h`.
"""
import argparse
import json
import subprocess as sp
import re
from datetime import timedelta
from pathlib import Path
from typing import Optional, Union
from collections import defaultdict
import matplotlib.axis
import matplotlib... |
a1e56aab2a02713b93dfe25b0534b6333c9e93db18b502a89df235e30219b349 | Python | 32,084 | 939 | import logging
import pathlib
from collections import defaultdict
from collections.abc import Generator, Iterable
from contextlib import contextmanager
from typing import Self
import numpy
from numpy.typing import NDArray
from openff.qcsubmit.results import OptimizationResultCollection
from openff.toolkit import Molec... |
67ffbf7cbb201036a288835203365e918799819d4c588b043f36b6f4cabeed5e | Python | 32,137 | 765 | import logging
import os
from typing import Union, Dict, Tuple, List
import math
import re
from multiqc import config, BaseMultiqcModule
from multiqc.modules.qualimap import parse_numerals, get_s_name, parse_version
from multiqc.plots import linegraph
from multiqc.utils.util_functions import update_dict
log = loggin... |
009dac263b14502ad75c6b9e1ccaa084c7ed74ce85893a1823bfdaa24ae7c76e | Python | 32,179 | 941 | import logging
import pathlib
from collections import defaultdict
from collections.abc import Generator, Iterable
from contextlib import contextmanager
from typing import Literal, Self
import numpy
from numpy.typing import NDArray
from openff.qcsubmit.results import OptimizationResultCollection
from openff.toolkit imp... |
45ac50f892b20aa2394019ba803bdba19d8aea38cb55dfa9c6ad24bd87f6f247 | Python | 32,208 | 864 | # This file is dual licensed under the terms of the Apache License, Version
# 2.0, and the BSD License. See the LICENSE file in the root of this repository
# for complete details.
from __future__ import absolute_import, division, print_function
import abc
import functools
import itertools
import re
import warnings
fr... |
22bb1ac5eebeec34bf13370d8307c7cc57e1f68f87deb46a9719974f5ec95a47 | Python | 32,243 | 641 | import logging
import os
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, QPixmap
import num... |
f834a40568ee512cd258679027745638d7a7b66883e732fd79e9554a29d6e69f | Python | 32,283 | 727 | #!/usr/bin/env python
"""
@package npt
Runs a simulation to compute condensed phase properties (for example, the density
or the enthalpy of vaporization) and compute the derivative with respect
to changing the force field parameters. This script is a part of ForceBalance.
All code in this repository is released u... |
8c4acd012325920b3b32938cf557bf55d2c3272145c1e0232ee855bad673df75 | Python | 32,353 | 918 | from __future__ import absolute_import, division, unicode_literals
from pip._vendor.six import text_type
from pip._vendor.six.moves import http_client, urllib
import codecs
import re
from io import BytesIO, StringIO
from pip._vendor import webencodings
from .constants import EOF, spaceCharacters, asciiLetters, asci... |
cb59e494610dbd871db5d15fa5f3f71683c148b733eccfe86b2ef96ca77ffd7e | Python | 32,375 | 811 | #!/usr/bin/env python
# =============================================================================
# MODULE DOCSTRING
# =============================================================================
"""
Provide cache classes to handle creation of OpenMM Context objects.
"""
# ====================================... |
1c00c298444c1bbbff4893341d19136712f3a20eba8cad87083f6d732f31a2bd | Python | 32,386 | 539 | import numpy as np
from trained_untrained_results_funcs import find_best_layer, elementwise_max, calculate_omega, load_perf, select_columns_with_lower_error
from untrained_results_funcs import load_untrained_data
from plotting_functions import plot_across_subjects, load_into_3d, save_nii, plot_2d_hist_scatter_updated
f... |
5288b1e184b0d99bfb146fc3ab544a12c384d4f35a86998ea93397c5593f9c18 | Python | 32,415 | 811 | #!/usr/bin/env python
# =============================================================================
# MODULE DOCSTRING
# =============================================================================
"""
Provide cache classes to handle creation of OpenMM Context objects.
"""
# ====================================... |
a1c1df9933701f34c532141c32edcb312a292a316419c60ce4f690ed4dae6122 | Python | 32,432 | 941 | #!/usr/bin/env python3
"""
Web-based real-time plot that shows lick port and proximity port events over time.
Uses Dash (built on Flask) and Plotly for interactive visualization.
"""
import dash
from dash import dcc, html
from dash.dependencies import Input, Output, State
import plotly.graph_objects as go
from datetim... |
9047d16f72a801dd16baa3025a0e48db68d7b2ab1f90202b4a41257264394ec8 | Python | 32,447 | 973 | import pandas as pd
import numpy as np
import os
import matplotlib.pyplot as plt
import seaborn as sns
from scipy.spatial.distance import cdist
from sklearn.metrics.pairwise import cosine_distances
from sklearn.metrics import (
silhouette_score,
davies_bouldin_score,
adjusted_mutual_info_score,
adjusted... |
5b416cb2c164da6919f815fe110046b629997d59bb521db44dce21e39eed91da | Python | 32,516 | 896 | import torch
import torch.nn as nn
import copy
import torch.nn.functional as F
import ProtoCloud.glo as glo
EPS = glo.get_value('EPS')
LRP_FILTER_TOP_K = glo.get_value('LRP_FILTER_TOP_K')
device = 'cuda' if torch.cuda.is_available() else 'cpu'
num_workers = 4 if torch.cuda.is_available() else 0
##################... |
210b21ae81cb40135e98f04342d61007da7e8e9546ef0e6d2157278ce07d4532 | Python | 32,566 | 821 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
# see: http://amp.pharm.mssm.edu/Enrichr/help#api for API docs
import io
import json
import logging
import os
from typing import Any, Dict, Iterable, List, Optional, Set, Tuple, Union
import numpy as np
import pandas as pd
import requests
from gseapy.biomart import Biomar... |
dd7a43544c04a8da8454a780600fabdcf0e52f97ae8fc84bdd1220a4796f586f | Python | 32,589 | 1,121 | from enum import IntEnum
import numpy as np
from shapely import _geometry_helpers, lib
from shapely._enum import ParamEnum
from shapely.decorators import (
deprecate_positional,
requires_geos,
)
__all__ = [
"GeometryType",
"force_2d",
"force_3d",
"get_coordinate_dimension",
"get_dimension... |
97ecd68de392b7182559417ae28f90f5351e303a2c89f937d4aadf5a0b806a0d | Python | 32,619 | 903 | """
Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
"""
import os
import time
from io import StringIO
import numpy as np
from numba import vectorize
from scipy import io
from tqdm import tqdm
from facemap import pupil, running, utils
def binned_inds(Ly, Lx, sbin):
L... |
f8d94056b50e64e5b2c23a194710c8ff87b3c0a5b1ac48849e0f102126523188 | Python | 32,620 | 800 | import numpy as np
import torch
from torch import nn
import torch.nn.functional as F
from torch.utils.data import Sampler
from sklearn.metrics import r2_score, mean_squared_error, mean_absolute_error, mean_absolute_percentage_error
from sklearn.preprocessing import RobustScaler, MinMaxScaler, StandardScaler, LabelEncod... |
d5125ad002f98cc8eb2ad6203b379f8dee4f07f4c140b219b6074687b7df98ef | Python | 32,644 | 662 | """
Théo Gauvrit 18/01/2024
New inferno traces colored heatmaps
"""
import os
import matplotlib
import numpy as np
from scipy.cluster.hierarchy import dendrogram, linkage
from mpl_toolkits.axes_grid1 import make_axes_locatable
from percephone.core.recording import RecordingAmplDet
from percephone.analysis.utils impor... |
14a7ae9bdeeea9c77cf105411d06f90a491d4742b3b0db28052c8e07b95012f7 | Python | 32,837 | 867 | from typing import Any, Iterable, Mapping, Sequence, Tuple, Union, Optional, Callable, Literal, List
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.distributions import Distribution, Gamma, Poisson
import numpy as np
import pandas as pd
import ProtoCloud.glo as glo
glo.set_value... |
c8f025c0be96d023a3e0a65609e703014986e23bb9f6a60f8791489447e82236 | Python | 32,878 | 629 | from collections import defaultdict
import argparse
from functools import partial
import json
import math
import os
import time
import gc
from feabas import config, logging, storage
from feabas.concurrent import submit_to_workers
import feabas.constant as const
os.environ["OPENCV_IO_MAX_IMAGE_PIXELS"] = str(pow(2,40)... |
c051e1ab829a000ad5e74cb3dc357c9fa3d1e6982dbb2f1e3af223d52d094b10 | Python | 32,986 | 904 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
STREAMLIT_Segmentation.py
This module handles the segmentation of cells using Cellpose.
It includes logic for:
1. Running Cellpose in 2.5D (slice-by-slice with Z-consistency checks).
2. Filtering masks based on morphology, intensity, and location (border exclusion).
... |
2cbf034175673a19591a26845a49443845924bcf16a812f4e7cf5275427eea13 | Python | 33,003 | 894 | """ @package forcebalance.evaluator
A target which employs the OpenFF Evaluator framework to compute condensed
phase physical properties. Currently only force fields in the OpenFF SMIRNOFF
format are supported.
author Yudong Qiu, Simon Boothroyd, Lee-Ping Wang
@date 06/2019
"""
from __future__ import division, print_... |
451da691a014d91103b63658de7472d288dc500fc17f42698d7f594f265451ae | Python | 33,067 | 892 | # The following comment should be removed at some point in the future.
# mypy: strict-optional=False
import logging
import os
import shutil
import sys
import uuid
import zipfile
from typing import Any, Dict, Iterable, List, Optional, Sequence, Union
from pip._vendor import pkg_resources, six
from pip._vendor.packagin... |
d46169ce030e6847a2c311a689ee9f5a750106a9405b16414c363048c542353d | Python | 33,138 | 881 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
import xml.etree.ElementTree as ET
from copy import copy
from math import floor
from typing import Any, Dict, Hashable, List, Optional, Tuple, Union
import dask.array as da
import numpy as np
import xarray as xr
from dask import delayed
from fsspec.spec import AbstractFil... |
7b53720fe918fdd91feabf480ca2ce33fccf64477bcd702ef1d89ccba1407735 | Python | 33,220 | 954 | """Contains the Reaction Recipe, RecipeStep and RecipeCollection."""
from __future__ import annotations
import ast
import csv
import logging
from abc import ABC
from copy import copy
from dataclasses import dataclass
from pathlib import Path
from typing import TYPE_CHECKING, Callable, Generic, Optional, TypeVar
from ... |
6a2e351d61dcf9ab9841e18f957076d75f4a7b194d8af4d8feabfffd439c2103 | Python | 33,278 | 930 | import logging
import pathlib
from collections.abc import Generator, Iterable
from contextlib import contextmanager
from typing import Self
import numpy
import pandas as pd
from numpy.typing import NDArray
from openff.qcsubmit.results import TorsionDriveResultCollection
from openff.toolkit import Molecule
from openff.... |
6cc811a6114c931f518c14a2d2f0811ab2024bdb6be67c3ba4f7a284f85e895d | Python | 33,414 | 675 | import argparse
import itertools
import math
import warnings
import h5py
import numpy as np
from joblib import Parallel, delayed
from nilearn import datasets
import os
from glob import glob
import pickle
from nilearn.surface import surface
from scipy.spatial.distance import cdist
from tqdm import tqdm, trange
from a... |
22a754f3f391083db31965087ccc18def2598df0a44ef39301d888fc7ad35477 | Python | 33,461 | 984 | # 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,... |
cce6c301734ce4a0cf0bfc7efa949fa92f3f8c85c9c2b08e5a619837c0834c3c | Python | 33,509 | 786 | """
Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
"""
import os
import cv2
import numpy as np
import pyqtgraph as pg
try:
import umap
UMAP_INSTALLED = True
except:
UMAP_INSTALLED = False
# todo: use opentsne for embedding
TSNE_INSTALLED = True
# import hd... |
a73fcacf94412cefe0953befbb111822f7b8eab5907766fdaeab334a0043e458 | Python | 33,639 | 614 | import logging
import re
import traceback
from PySide6.QtWidgets import QWidget, QLabel, QHBoxLayout, QVBoxLayout, QGridLayout, QDialog, QDialogButtonBox,\
QComboBox, QPushButton, QScrollArea, QLineEdit, QFileDialog, QMessageBox, QProgressBar, QListView, \
QAbstractItemView, QTreeView, QFileSystemModel
from Py... |
84a52946647aa9fe942739085e2ac8c7325306ebaf445eab9ff599ec6b42b38a | Python | 33,698 | 893 | """
Hyperparameter tuning system for TimeFlies models.
This module provides comprehensive hyperparameter optimization using:
- Grid Search: Exhaustive search over parameter combinations
- Random Search: Random sampling from parameter distributions
- Bayesian Optimization: Smart optimization using Optuna
Supports both... |
c6dc3977c3a8848b08a5811afcec16d42b7c0b062552f25760c0c6e916831b31 | Python | 33,715 | 816 | #!/usr/bin/env python3
"""
dicom_to_nifti — convert GRE DICOM(s) into NIfTI files + a params.json.
A standalone, self-contained converter. It depends only on numpy, nibabel,
and pydicom — no project-local imports — and produces a generic output
bundle (phase / magnitude NIfTIs + a `params.json`) that any downstream
QS... |
dc160926a1f4b03c0c8097fe348caf6c24426fd11bfd7884588de0dab5d2d202 | Python | 33,762 | 877 | #!/usr/bin/env python3
# ----------------------------------------------------------------------------
# Copyright (c) 2020--, Qiyun Zhu.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ------------------------------------------... |
4f89e5c1f2f3c509f10e529fb6b3869da5b363f3d2ddbde6bfe6668b5b9645ea | Python | 33,769 | 745 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# Copyright 2017 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... |
e4c0e0f3876adca3f94ab3340ec5b28227a8e262df6cb2a284439e76badc0a6a | Python | 33,813 | 761 | #!/usr/bin/env python3
"""
Analysis of chromatin states for specific genes in NSC and Neu samples (GFP and M2 conditions)
This script visualizes the chromatin states of genes from a provided list
"""
import os
import sys
import argparse
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import seab... |
0458bc358ebfa10e0570c49ce9ece1529c9172965018b443747b78776131945c | Python | 33,873 | 735 | #!/usr/bin/env python3
"""
SAMMY-seq Mecp2 Target Comparison Heatmap Generator
This script creates metaprofile heatmaps for Mecp2 target and non-target genes in NSC and NEU conditions,
showing the log2 ratio of S2S/S3 across gene bodies (from -5kb to TSS to TES to +5kb).
The heatmaps use a blue-white-red color scheme... |
0288ec2a8fa015ce5d2315c34a52b1b687a1e8d5f7a554444648222ce99f26d6 | Python | 34,110 | 865 | from dgl import DGLGraph
import dgl
import dgl.function as fn
import dgl.nn as dglnn
import torch as th
import torch.nn as nn
import torch.nn.functional as F
import numpy as np
import tqdm
import numpy as np
from dgl.data import DGLDataset
from dgl.dataloading import (
as_edge_prediction_sampler,
DataLoader,
... |
f3a7f2543fb9e2895162976069f60eb21276113a8c30a788f8913852ee8d33a3 | Python | 34,111 | 866 | from dgl import DGLGraph
import dgl
import dgl.function as fn
import dgl.nn as dglnn
import torch as th
import torch.nn as nn
import torch.nn.functional as F
import numpy as np
import tqdm
import numpy as np
from dgl.data import DGLDataset
from dgl.dataloading import (
as_edge_prediction_sampler,
DataLoader,
... |
b406e1269bf17ecfc5b4f3983798cd47844968938675666795c562d6a50ea2e6 | Python | 34,160 | 917 | import json
import math
import re
import matplotlib.pyplot as plt
import networkx as nx
import numpy as np
import pandas as pd
import pytest
from openff.units import unit
import cinnabar
from cinnabar import conversion, estimators, femap, stats
def test_read_csv(example_csv):
data = femap.read_csv(example_csv)
... |
3e1e10159852390672ac0c6e6fd586dd0f944b2e8764b813d98c22ccbe274c88 | Python | 34,210 | 801 | # 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 sys
import math
from tqdm import tqdm
import random
import numpy as np
import scipy.sparse as ssp
from scipy.sparse.csgraph import shorte... |
7e721f51daedf405f2f51ab0ef41182ff3777e0e5df7bafb4e9e05c0ee12fd45 | Python | 34,210 | 899 | # This code is part of kartograf and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/kartograf
import copy
import logging
from collections import OrderedDict
from collections.abc import Callable, Iterable, Iterator
from enum import Enum
import dill
import numpy as np
from gufe ... |
de3abee0f9735c4164c736c76951da2282297aca3de01b2c3170be0b5b2fb068 | Python | 34,284 | 896 | from collections import namedtuple
import cv2
import importlib
import json
import os
import numpy as np
from scipy import sparse
from scipy.ndimage import gaussian_filter1d, convolve, uniform_filter, distance_transform_edt
import scipy.sparse.csgraph as csgraph
from skimage.morphology import convex_hull_image
from fe... |
3041076b762a1bc89f0cf606d203b5d82d6d66ed88f87a86178942e7770714f8 | Python | 34,303 | 920 | """
SecureTranport support for urllib3 via ctypes.
This makes platform-native TLS available to urllib3 users on macOS without the
use of a compiler. This is an important feature because the Python Package
Index is moving to become a TLSv1.2-or-higher server, and the default OpenSSL
that ships with macOS is not capable... |
52491a56e535b5cf81298078d5d76cdf9b1a8aca13a5a609d980421591047e13 | Python | 34,373 | 956 | # -*- coding: utf-8 -*-
"""
requests.models
~~~~~~~~~~~~~~~
This module contains the primary objects that power Requests.
"""
import datetime
import sys
# Import encoding now, to avoid implicit import later.
# Implicit import within threads may cause LookupError when standard library is in a ZIP,
# such as in Embed... |
3273730fb934ad2738ba6744a2ede88634a52bfbd350200690e74feedec68a9c | Python | 34,379 | 943 | import logging
import pathlib
from collections.abc import Generator, Iterable
from contextlib import contextmanager
from typing import Literal, Self
import numpy
import pandas as pd
from numpy.typing import NDArray
from openff.qcsubmit.results import TorsionDriveResultCollection
from openff.toolkit import Molecule
fro... |
eff0139c877990adecec00a48770faca0d720c868da43ca041fec71562098e94 | Python | 34,428 | 756 | """Main data preprocessing utilities for TimeFlies project."""
import logging
from typing import Any
import numpy as np
import scanpy as sc
from anndata import AnnData
from scipy.sparse import issparse
from sklearn.preprocessing import LabelEncoder, StandardScaler
from tensorflow.keras.utils import to_categorical # ... |
03d574bea9bdf8bb81fe8212fa5672954159a908445b429097083eaf956fdd3e | Python | 34,494 | 916 | """
Optimized Chromosome Dataset for Hi-Compass Training
This module provides a PyTorch Dataset implementation for loading and processing
Hi-C prediction training data with hierarchical directory structure.
File Structure Expected:
ATAC/
{cellline}~ATAC~{depth}/
{cellline}~ATAC~{depth}.bw
... |
6083df1e94c8c57e717b35a60880286ff1838ad36ef6215cb4008ac96b85a436 | Python | 34,499 | 666 | import argparse
from functools import partial
import json
import os
import time
from feabas.concurrent import submit_to_workers
from feabas import config, logging, storage
def generate_stitched_mipmaps(img_dir, max_mip, **kwargs):
min_mip = kwargs.pop('min_mip', 0)
num_workers = kwargs.pop('num_workers', 1)
... |
f0fa9fc78b2bd58e692dbcf8e90e3f17d86f5339ed6511e73e373c3cd5134cf3 | Python | 34,581 | 744 | # coding=utf-8
import itertools
import logging
from collections import defaultdict
from multiqc.base_module import BaseMultiqcModule
from multiqc.plots import bargraph, table
from .utils import Metric, exist_and_number, make_headers
# Initialise the logger
log = logging.getLogger(__name__)
NAMESPACE = "Mapping"
... |
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