sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
6f9cd404b0902e3c045efe8a13d297ec6d81e96d92fba876e2d2b476c6fca8de | Python | 23,355 | 551 | import sys
import pyqtgraph as pg
from pyqtgraph.Qt import QtCore, QtWidgets
import numpy as np
import cv2
import math
import os
VERSION = (0, 2, 0)
class ControlWindow(QtWidgets.QWidget):
def __init__(self):
QtWidgets.QWidget.__init__(self)
self.cap = None
self.filename=None
self... |
20c4ba9e6759930d3261466738e17d70360fd051aaa48c7d98614806ecb907fe | Python | 23,392 | 598 | import json
import logging
import re
from operator import itemgetter
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
from multiqc.plots import bargraph, table
log = logging.getLogger(__name__)
handlers = (
"ClusterPFHandler",
"Q30Handler",
"ErrorRateHandler",
"ReadsPerSampleHa... |
109f93c6d2cde081057b90a2fafe024b807cb54d018c40ddbad5e48e36c6361a | Python | 23,455 | 500 | import functools
import json
import logging
import os
import re
import shlex
from typing import Dict
from packaging import version
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound, SampleGroupingConfig
from multiqc.plots import bargraph, linegraph
from multiqc.types import Anchor, ColumnKey, Sa... |
64cd35581ea0e02b2a8ec25cc9b2ff9b829866ed5e35306196d412923a878951 | Python | 23,459 | 443 | """ @package forcebalance.hydration Hydration free energy fitting module
@author Lee-Ping Wang
@date 09/2014
"""
from __future__ import division
from builtins import range
import os
import shutil
import numpy as np
from copy import deepcopy
from forcebalance.target import Target
from forcebalance.molecule import Mole... |
8000a29d321c49c646c3cd6a2da15d4e3f4a197955b82a6bbbb5ef1c68c813e1 | Python | 23,468 | 640 | import csv
import functools
import logging
import os
import sys
import sysconfig
from importlib.util import cache_from_source
from typing import Any, Callable, Dict, Iterable, Iterator, List, Optional, Set, Tuple
from pip._vendor import pkg_resources
from pip._vendor.pkg_resources import Distribution
from pip._intern... |
7e0c549b2f98bdadc0de47a6cea3ee4ed886e0a6a4ea875bd54bca440dbdfa09 | Python | 23,489 | 708 | import textwrap
from typing import Tuple
import matplotlib.pyplot as plt
import numpy as np
TITLE_FONT_SIZE = 18
AXIS_FONT_SIZE = 18
TICK_FONT_SIZE = 12
LEGEND_FONT_SIZE = 14
CAPTION_FONT_SIZE = 12
MAX_TEXT_WRAP = 100
def create_plot(
*,
figsize: Tuple[int, int],
title: str | None,
x_label: str | Non... |
918ec38207c481b3b5a315b82387e2bbdac761e4ded483b289b52a6446cafa0e | Python | 23,553 | 577 | import os
import json
import re
import shutil
from pathlib import Path
from collections import OrderedDict
class PatientIDAnonymizer:
def __init__(self, main_dirs):
"""
Initialize the anonymizer with main directories to process.
Args:
main_dirs: List of directory paths to proc... |
9bc2b290ddb4e97c5b84e5932eb46ecefb9a35b1605c146d3ae330085d6d94c8 | Python | 23,601 | 557 | #!/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.
# ------------------------------------------... |
fec1db83fcc4f68c1037cdbefa9c14e44dd1b2b514b2567a157f03a7d053f421 | Python | 23,665 | 547 | import threading, wx, time, sys, logging, Queue
import numpy as np
from session import Session
from views import View, MP285View
from subjects import Subject, list_subjects, list_rewards
from settings import manipulations, conditions, manip_strs, default_manipulation
from settings.param_handlers import ParamHandler
fro... |
2b6601b87abd34c5a69a0c69d684a709a5398c89c4f95a29ee0a357d054bcc00 | Python | 23,673 | 633 | #!/usr/bin/env python3
# Batch ML with 1x5 Fold Tuning
import re
import json
import warnings
from pathlib import Path
from datetime import datetime
import numpy as np
import pandas as pd
from sklearn.compose import ColumnTransformer
from sklearn.pipeline import Pipeline
from sklearn.impute import SimpleImputer
from... |
ae2e123cab0b2f71a923a6e6ac0257bb09ba27f5f12395d5d54496424d2fa0f6 | Python | 23,681 | 636 | #!/usr/bin/env python3
"""
Hi-C normalization preprocessing for Hi-Compass training data preparation.
Step 1: Contrast stretching normalization of cool files
This step prepares Hi-C contact maps for model training by applying
contrast stretching to standardize signal intensity.
"""
import cooler
import numpy as np
im... |
f0b3df3a1de2265eafebfea3f4f5df766d4da441b56510bfce6a3a4928c6c5a3 | Python | 23,755 | 462 | import os
import logging
import shutil
from typing import Union, List, Tuple
import pandas as pd
import numpy as np
import nibabel as nib
from nibabel.processing import resample_to_output
import traceback
from copy import deepcopy
from pathlib import PurePath
from utils.data_structures.UserPreferencesStructure import ... |
c0811bc9dfb59067cfb970c4ecd6382a21e0cb401890b3667e516a72c429ae75 | Python | 23,783 | 626 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""OpenMM Equilibrium SepTop RBFE Protocol --- :mod:`openfe.protocols.openmm_septop.equil_septop_method`
======================================================================================... |
c24754bad80f2abbb21ff43140611c2e652ce20fbe1f16920071005a1f0715b9 | Python | 23,791 | 645 | # Imports
from torch.nn.functional import normalize
import os
# import os
os.environ["CUDA_VISIBLE_DEVICES"]="3"
os.environ["DGLBACKEND"] = "pytorch"
import sys
sys.stdout = open("final_console_outputs/console_output_lr-2_all_graph_protvec_gat_run1.txt", "w")
# sys.stdout = open("console_outputs/console_output", "w")
... |
6ce34c4a79625202ffd4d5b71385bd9ac4c681c7379e45ca3d13e201fa18fc63 | Python | 23,814 | 641 | """
TimeFlies Batch Correction using scVI.
Implements proper ML workflow for batch correction:
1. Train scVI model on train split only
2. Use prepare_query_anndata for eval split (prevents data leakage)
3. Transform both splits with trained model
4. Save results with batch-corrected data
"""
import os
import time
fro... |
eab7ee6ec54d983241a86c2cff2a67548bc3720595860bfc21a9a3122dde6861 | Python | 23,830 | 432 | from PySide6.QtWidgets import QWidget, QHBoxLayout, QVBoxLayout, QSpacerItem, QGridLayout, QComboBox, QPushButton,\
QStackedWidget, QMessageBox
from PySide6.QtCore import Qt, QSize, Signal
from PySide6.QtGui import QColor, QPixmap, QIcon
import os
import logging
from gui.SinglePatientComponent.LayersInteractorSide... |
7bc90c59c98a42d5e3d7473988e2f86dfa58aaafaf5418e25b741627e1571ff6 | Python | 23,852 | 541 | from torch_geometric.data import Data
from torch_geometric.data import DataLoader
import torch
import argparse
import numpy as np
import math
from torch_geometric.utils import to_undirected, from_scipy_sparse_matrix,dense_to_sparse,is_undirected
from torch_geometric.transforms import NormalizeFeatures
from torch_geomet... |
6123f84f04e8224deb321504c606f8b036d2a1e2178d676e2de0966fa7491c2f | Python | 23,866 | 641 | #!/usr/bin/env python3
"""
Promoter-Specific MeCP2 Binding vs Absolute Expression Changes Analysis (DEA genes only)
This script quantifies how differences in MeCP2 binding between exogenous (Exo) and
endogenous (Endo) samples correlate with gene expression changes. It tests whether
promoter binding differences show st... |
cc84230ca5356afa4335bdcf1138ce387581c927d1666f631caa29390e5b16eb | Python | 23,866 | 694 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""
Classes for applying restraints to OpenMM Systems.
Acknowledgements
----------------
Many of the classes here are at least in part inspired from
`Yank <https://github.com/choderalab/yank... |
90d426e6659ed00168447f8914b3c1d39c6530b3ef4127b7579cd17690f8bb43 | Python | 23,882 | 685 | """
:mod:`alchemiscale.base.client` --- base class for API clients
==============================================================
"""
import asyncio
import time
import random
from itertools import islice
import json
from urllib.parse import urljoin
from functools import wraps
import gzip
from pathlib import Path
impo... |
eb68b6b718efee8a91dd2035e3225986586c3f66f7315d9e5bd022ea644df7ca | Python | 23,988 | 647 | # Imports
from torch.nn.functional import normalize
import os
# import os
os.environ["CUDA_VISIBLE_DEVICES"]="6"
os.environ["DGLBACKEND"] = "pytorch"
import sys
sys.stdout = open("updated_esm_graph_console_outputs/console_output_lr-4_all_graph_updated_esm_gin.txt", "w")
# sys.stdout = open("console_outputs/console_outp... |
3d48920dfa62e7ffa3a6a18c0e8042f6fef65f8ae456ff20c70382b34e6148b2 | Python | 24,000 | 547 | import sys
import torch
import argparse
import numpy as np
import pytorch_lightning as pl
import pytorch_lightning.callbacks as callbacks
from .HicompassModel import ConvTransModel
from .blocks import EncoderSplit
from .HicompassDataset import ChromosomeDataset
import os
import torch.nn as nn
import matplotlib.pyplot ... |
64da8f7d228eb7fdc828aea869e260382ae7e7674a953dcae66d9caeea1df18c | Python | 24,013 | 638 | import os
import torch
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
def remove_long_trees(dataset, max_length=9):
"""
Removes trees in the input dataset with more than max_length edges.
Parameters:
- dataset: numpy array with patients. Each patient conta... |
34a312dfb668fe75ab67182c0facdb5ec5e073d79d9fd9b5eb470188b98725d1 | Python | 24,067 | 751 | # 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
import distutils.util
try:
from importlib.machinery import EXTENSION_SUFFIXES
except ImportErr... |
9a02e18b2520797b17144ed22f6705d47aa9e1a67a4f03517092e0b40e20f855 | Python | 24,084 | 501 | import os
import numpy as np
import pandas as pd
import torch
import pickle
# # Set Global variables
# import ProtoCloud.glo as glo
# glo._init()
# glo.set_value('EPS', 1e-16)
# glo.set_value('LRP_FILTER_TOP_K', 0.1)
# from src.utils import *
# # from src.data import *
# from src.scRNAdata import *
# from src.train i... |
fec7c4a754ffe90e91dcc5fbff045d0eb9a4d540c779cf6e7c505f39ea8880d7 | Python | 24,091 | 527 | import json
import logging
import os
from collections import defaultdict
from itertools import islice
from typing import Dict
from multiqc import config
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
from multiqc.plots import bargraph, table
from multiqc.plots.table_object import ColumnDict, V... |
62f8368b92faefcd8d9d5205a2507ac6dcd6d87e3b982380499f7669fb6c552b | Python | 24,118 | 348 | import traceback
from PySide6.QtWidgets import QWidget, QLabel, QGridLayout, QPushButton
from PySide6.QtCore import QSize, Signal
import numpy as np
import logging
from gui.SinglePatientComponent.CentralDisplayArea.CustomQGraphicsView import CustomQGraphicsView
from utils.software_config import SoftwareConfigResource... |
0e4d552cd42a47a0d816928f117a351adb0c9545ab33bd43162db9aaf32b0e13 | Python | 24,119 | 594 | """
fingerprint/dynamic.py — Dynamic Fingerprint (V1: 31-dim, V2: 10-dim)
=====================================================================
V1 (legacy): 31-dim per-method degradation slopes, kept for A/B comparison.
V2 (current): 10-dim method-agnostic landscape descriptors.
V1 dimensions g₁–g₃₁
------------------... |
45e8b6e48fd90be41b4f093d71f15250029942d5db28a92be3099b62abf94cdf | Python | 24,162 | 653 | # Imports
from torch.nn.functional import normalize
import os
# import os
os.environ["CUDA_VISIBLE_DEVICES"]="7"
os.environ["DGLBACKEND"] = "pytorch"
import sys
sys.stdout = open("final_console_outputs2/console_output_lr-4_all_graph_alphafold_gin_run8_no_normedge.txt", "w")
# sys.stdout = open("console_outputs/console_... |
0e1cf9d9926d7c8d08b4930835f397acdea401ad18315db383b2d51712a0a404 | Python | 24,173 | 626 | import argparse
import os
import pickle
import warnings
from typing import Callable, Optional, Tuple
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import torch
from lifelines import CoxPHFitter
from scipy.stats import pearsonr, spearmanr
from sksurv.metrics import concordance_index_censored
f... |
afa6fa27dafee82ae85fc23b0bb42cde05ede088a427ee0f4da9abced61229bf | Python | 24,318 | 625 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
import glob
import re
from collections import OrderedDict
from pathlib import Path
from typing import Any, Callable, Dict, Iterable, List, Optional, Sequence, Tuple, Union
import dask.array as da
import numpy as np
import pandas as pd
import xarray as xr
from fsspec.spec ... |
8fe6bc582723ae757731e5403836ef4caf5dd4647ad7925e955b1d70085f8d34 | Python | 24,321 | 636 | import argparse
import os
from pathlib import Path
from typing import Any, Callable, Dict, List, Mapping, Optional, Sequence, Tuple, Union
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import torch
from sksurv.metrics import concordance_index_censored
from dataset_survival import RNAseqSurviv... |
3abae27494dd7c76ae18efbb8954693a2b4ac9e17e037831a92ddb7f7dc6d40d | Python | 24,349 | 511 | #!/usr/bin/env python3
import matplotlib
matplotlib.use('Agg') # Use non-interactive backend BEFORE pyplot import
import os
import numpy as np
import pandas as pd
import pyBigWig
import matplotlib.pyplot as plt
from concurrent.futures import ProcessPoolExecutor
from tqdm import tqdm
import argparse
import logging
imp... |
a36e7ccc92414d03e74186b5cca4260d3b0b38a0ac336d5a592bf0b3522b2362 | Python | 24,370 | 564 | from PySide6.QtWidgets import QWidget, QLabel, QHBoxLayout, QLineEdit, QComboBox, QGridLayout, QPushButton,\
QRadioButton, QMenu, QSlider, QColorDialog, QVBoxLayout, QSpacerItem, QSizePolicy, QMessageBox
from PySide6.QtCore import Qt, QSize, Signal, QPoint
from PySide6.QtGui import QPixmap, QIcon, QColor, QAction
i... |
70d0928af8fc8cf2b5eb2ebf1140448b66bcc6c728dbbd4360007f9b5163aa34 | Python | 24,379 | 617 | """Helper functions for aggregation of results (group stats)."""
import sys
from os import system,getenv
from os.path import exists
from time import time,ctime
from datetime import timedelta
import traceback
import warnings
from ast import literal_eval
from functools import partial
from pathlib import Path
import re
... |
35648dc8cb080ea8f2510063e442a837489f783a34b6091362893643ccbb3f51 | Python | 24,440 | 853 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
import time
from pathlib import Path
from tempfile import TemporaryDirectory
from typing import Any, Dict, List, Optional, Tuple, Type, Union
import numpy as np
import pytest
from distributed import Client, LocalCluster
from ome_types import OME
from aicsimageio import A... |
76fba22913711b64cf0315d32ce26c9a4a1c3dc0ff54cf71b47ca7290472257a | Python | 24,481 | 630 | #!/usr/bin/env python3
"""
DICOM File Renamer - Patient Folder Organizer (No Extension Version)
==================================================================
This script analyzes DICOM files in patient folders and renames them based on
metadata from their headers using the format:
{PatientID}_{ProtocolName... |
66682955ba71d1757207c790accb0ef7ec4ba29fefda59b946812dab9eca6cd5 | Python | 24,482 | 776 | """
Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
"""
import cv2
import h5py
import numpy as np
import torch
from scipy.interpolate import interp1d
from scipy.linalg import eigh
from scipy.ndimage import gaussian_filter1d
from sklearn.decomposition import PCA
BODYPARTS ... |
578a5361f1ca46e202e7e06893b5d8cb7a6fa1da39604325426fb51639443f62 | Python | 24,500 | 683 |
# This file helps to compute a version number in source trees obtained from
# git-archive tarball (such as those provided by githubs download-from-tag
# feature). Distribution tarballs (built by setup.py sdist) and build
# directories (produced by setup.py build) will contain a much shorter file
# that just contains t... |
8f24c7163f44766e1812cf076f8dc14613fab57f8582c3bef9f8719d3789d64a | Python | 24,510 | 683 | # This file helps to compute a version number in source trees obtained from
# git-archive tarball (such as those provided by githubs download-from-tag
# feature). Distribution tarballs (built by setup.py sdist) and build
# directories (produced by setup.py build) will contain a much shorter file
# that just contains th... |
fcd7c560e58c67bfd4120b4d6ccf54d8c71097fbf0ad41d143f39309cb97475a | Python | 24,517 | 623 | #!/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.
# ------------------------------------------... |
04818ac1df8d6c792f2f593c28e7d24d9acfbe0a88237c8f63071deae12661d0 | Python | 24,556 | 543 | """ @package forcebalance.psi4io PSI4 force field 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 st... |
53acbf249b9375dc4d9552425bedb223e2b3a1f1e33f40c98b9b7c5a6ba7710f | Python | 24,559 | 683 |
# This file helps to compute a version number in source trees obtained from
# git-archive tarball (such as those provided by githubs download-from-tag
# feature). Distribution tarballs (built by setup.py sdist) and build
# directories (produced by setup.py build) will contain a much shorter file
# that just contains t... |
ed226c45b9c314754c441bee148702405b6b11af7b107882c3ac967a1f1fd46b | Python | 24,560 | 683 |
# This file helps to compute a version number in source trees obtained from
# git-archive tarball (such as those provided by githubs download-from-tag
# feature). Distribution tarballs (built by setup.py sdist) and build
# directories (produced by setup.py build) will contain a much shorter file
# that just contains t... |
d9904ba2dd867c97d88d26c4b564864fb8966f5013662509cdf5e52dee373404 | Python | 24,572 | 683 |
# This file helps to compute a version number in source trees obtained from
# git-archive tarball (such as those provided by githubs download-from-tag
# feature). Distribution tarballs (built by setup.py sdist) and build
# directories (produced by setup.py build) will contain a much shorter file
# that just contains t... |
361e0231d8d5234ff2bbbdb967a929d5dcf011cd290da8f547481e584f64619e | Python | 24,580 | 653 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""
Reusable utility methods to analyze results from multistate calculations.
"""
import warnings
from pathlib import Path
from typing import Optional, Union
import matplotlib.pyplot as plt... |
33c72749e9f30c803715dd64c7c67cbdd455a962e47f9af36566104d524f234d | Python | 24,581 | 813 | import Figure4_neurons as neurons
from collections import ChainMap
from typing import List, Dict, Tuple
import math
from pathlib import Path
import random
import warnings
import numpy as np
import pandas as pd
import seaborn as sns
import matplotlib.pyplot as plt
import networkx as nx
from tqdm import trange
from matpl... |
cb2a39a0495a1082e14f7c4b76de7b0dbe77ba85c90ea6beeefab0389ca0265f | Python | 24,604 | 677 | import numpy as np
import pandas as pd
import os
import matplotlib.pyplot as plt
import seaborn as sns
from itertools import groupby
import pickle
#general functions
def compute_dynamics_metrics(clusters_labels,TR=None,save_results=False,path=None):
"""
Execute the dynamics analysis using Dynamical Systems
... |
46a6779bc2d60ff46f310485468b05aa4269b81e9601ff6321b62b6180943621 | Python | 24,683 | 701 | import asyncio
import json
from loguru import logger
from truesight.db.session import gs
from truesight.db.models import (
DbEvaluationRun,
DbQuestion,
DbLLM,
DbEvaluationQuestion,
DbEvaluationResponseIntent,
OAIBatchRequest,
OAIBatchRequestEvaluationResponseIntentLink,
)
from truesight.expe... |
07a73c4bfd6579080586f33e0943e650bd43defd7514816671d8884ba81f2b2f | Python | 24,714 | 640 | import os
import logging
import time
import glob
import numpy as np
import tqdm
import torch
import torch.utils.data as data
from datasets import get_dataset, data_transform, inverse_data_transform
from functions.ckpt_util import get_ckpt_path, download
# from functions.svd_ddnm import ddnm_diffusion, ddnm_plus_diffu... |
0171cd83588671e835972a83a9b71a6e600521f4359357087e09956392425a8a | Python | 24,850 | 655 | """Prepares a distribution for installation
"""
# The following comment should be removed at some point in the future.
# mypy: strict-optional=False
import logging
import mimetypes
import os
import shutil
from typing import Dict, Iterable, List, Optional, Tuple
from pip._vendor.packaging.utils import canonicalize_na... |
88f1061ff85b6ca8844a61296fa951a0378bb55205cf82f29eeb1e2c83388fc7 | Python | 24,910 | 556 | import os
import numpy as np
from typing import List
import pandas as pd
from ..Utils.resources import SharedResources
class PatientMetrics:
_unique_id = "" # Internal unique identifier for the patient
_objective = "segmentation" #
_patient_id = "" # Unique identifier for the patient (might be multip... |
3b987b0131565b28e4203a107b3ce4aae6f8bbbba5cd1b91c7bdb087d5501d15 | Python | 24,918 | 648 | """
Ploidy / copy number estimation in genomic bins based on Strand-seq Watson/Crick read counts.
This scripts processes Watson/Cricks read counts in fixed genomic bins for a population of cells.
The read count of each individual cell and in each individual genomic bin is turned into a
fractional value (fraction of Wa... |
9baf54aea08b26b73f35df074b8dd5de97e773da803d38e177877ed9adbc1af4 | Python | 24,932 | 524 | import os, sys
# use local src code instad of installed package
src_path = os.path.join(os.path.dirname(__file__), 'src')
if src_path not in sys.path:
sys.path.insert(0, src_path)
import numpy as np
import pandas as pd
import torch
import pickle
import ProtoCloud
def try_plot(plot_fn, *plot_args, **plot_kwargs)... |
d2852131431c48c4392f66ae4d7b6552d73810f15e091924e79bcf84654c0a6d | Python | 25,001 | 668 | # interpreter.py
import hashlib
import json
import logging
import os
import pickle
import numpy as np
import pandas as pd
import shap
from sklearn.dummy import DummyClassifier
from sklearn.metrics import (
accuracy_score,
classification_report,
f1_score,
precision_score,
recall_score,
roc_auc_... |
6314673427f7f74043af4b21f3d97e0cb9713a1dbf5b19654b4ba7378230f8ee | Python | 25,009 | 543 | import sys, argparse, glob, os, yaml, sparse, tracemalloc, pickle
import tensorflow as tf
from tensorflow import keras
import numpy as np
import pandas as pd
from sklearn.metrics import roc_auc_score, average_precision_score, confusion_matrix
from sklearn.model_selection import StratifiedKFold
from sklearn.utils.class_... |
62c716d10ba995e95a12638547559665544edced9984c37e5f3ceca2a7a0299e | Python | 25,090 | 777 | import sys
from pathlib import Path
from typing import Tuple, Optional, List, Dict, Any
from contextlib import contextmanager
from datetime import datetime, timedelta
from sqlalchemy import create_engine, text
from sqlalchemy.orm import sessionmaker, scoped_session
from flask import has_app_context # Only import what ... |
ff132ba7c9ddc05a3c5106923da79f0ca0ba178e925865a4dceafd656f50f790 | Python | 25,174 | 746 | # 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
from math import sqrt
import sys
import pytest
from unittest import mock
from openmm import NonbondedForce, CustomNonbondedForce
from openmmtools.multistate.multi... |
246f080d52b958cd6c4001f09025741023bf7868330faf6e50aa9ad3e7947105 | Python | 25,221 | 712 | """Support for various GEOS geometry operations."""
from itertools import pairwise
from warnings import warn
import numpy as np
import shapely
from shapely.algorithms.polylabel import polylabel # noqa
from shapely.coordinates import transform_coordseq
from shapely.errors import GeometryTypeError, ShapelyDeprecation... |
d95e1a921fd6179cb95c85570fecf6389c0320c4a631ff5df7332c6f648a36d7 | Python | 25,342 | 595 | import numpy as np
import pandas as pd
import glob, os, subprocess, vcf, shutil, sparse, yaml, sys, argparse, pickle, warnings, tracemalloc
import scipy.stats as st
warnings.filterwarnings("ignore")
import tensorflow as tf
# utils files are in a separate folder
sys.path.append("utils")
from data_utils import *
from mo... |
43d14f073a244ff929b9107124f50c56d618beb7f918558ff00c5136212a03dd | Python | 25,356 | 688 | #!/bin/env python
"""
Module simtk.unit
Contains classes Unit and ScaledUnit.
This is part of the OpenMM molecular simulation toolkit originating from
Simbios, the NIH National Center for Physics-Based Simulation of
Biological Structures at Stanford, funded under the NIH Roadmap for
Medical Research, grant U54 GM0729... |
f8b0a6357817eef47f47bf5d10326ba45a22b97703ceee707b2607fbe37e0e62 | Python | 25,420 | 764 | # Copyright 2024 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, s... |
e9c2f57acd472271507c81c4ae66e7e3c05663070deb005089cffd517a28313f | Python | 25,443 | 613 | #!/usr/bin/env python
# Peter Ebert (2020-09-15), based on original implementation by
# Hufsah Ashraf (2020-08-03)
# script for getting normalized watson and crick counts for each arbitrary segment
import os
# import pdb
import argparse
import sys
from pathlib import Path
import glob
import multiprocessing as mp
# i... |
b5aa9e0e65e4d24018f4456a48c84426b898d363124a16d9bedf55a84020930e | Python | 25,446 | 661 | import contextlib
import functools
import logging
from typing import (
TYPE_CHECKING,
Dict,
FrozenSet,
Iterable,
Iterator,
List,
Mapping,
Optional,
Sequence,
Set,
Tuple,
TypeVar,
cast,
)
from pip._vendor.packaging.requirements import InvalidRequirement
from pip._vend... |
510d613d025e51e94829d51f8eb4ca9e6eb8fa3d734a69661915903e987d0fdd | Python | 25,491 | 748 | """
TimeFlies CLI Testing Commands
Contains test suite execution, test data creation, and all test data helper functions.
"""
import os
import subprocess
import sys
from pathlib import Path
def run_system_tests(args) -> int:
"""Run test suite or provide helpful guidance for users."""
# Check if tests direct... |
5a64a90115232374a1f5283f2c5e3ce2e2133cf58d85f48287cd62ef57338e88 | Python | 25,550 | 610 | import numpy as np
import pandas as pd
import seaborn as sns
import matplotlib.pyplot as plt
from matplotlib.colors import LinearSegmentedColormap
# 定义字体大小
plt.rcParams['font.family'] = 'Times New Roman'
plt.rcParams['font.size'] = 14
def plot_regression_curve_plots(y_train, pred_train, y_test, pred_test, file_name=... |
92c2c2276be790d59d826a3d0d69764ca21ba4d640ab00fd53e1b070a50fb7c5 | Python | 25,577 | 752 | # 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,... |
06a1e1ca012d5581bd1f3ebb593ca5464b6213c1569527f63c51739aef91d7f2 | Python | 25,589 | 701 | import json
import os
import pathlib
import networkx as nx
import warnings
from rdkit import Chem
import string
import gufe
from gufe.tokenization import JSON_HANDLER
import openfe
from openfe import ChemicalSystem, LigandAtomMapping
from openfe import Transformation, AlchemicalNetwork, LigandNetwork
from openfe impor... |
b431a5d4cd1c08c0ac1543d49907f2e57201afa64c668c1f2ac3cd79f7782e59 | Python | 25,623 | 795 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""
Search methods for generating Geometry objects
TODO
----
* Add relevant duecredit entries.
"""
import warnings
from itertools import combinations, groupby
from typing import Optional, Un... |
217fc6d8d3eac1e70989b9080e37b4e1baaed31a4791f490d8668674456a3396 | Python | 25,707 | 764 | # -*- coding: utf-8 -*-
#
# Copyright (C) 2012 The Python Software Foundation.
# See LICENSE.txt and CONTRIBUTORS.txt.
#
"""Utility functions for copying and archiving files and directory trees.
XXX The functions here don't copy the resource fork or other metadata on Mac.
"""
import os
import sys
import stat
from os... |
a06eb65b07872a4624df5dffab400dc00937a4d48038ebf18e8155156adaa9e5 | Python | 25,720 | 635 | from refs import llm_base_refs, llm_teacher_refs
import re
from truesight import parse_utils
from truesight.finetuning import services as ft_services
from truesight.experiment.services import (
DatasetJudgmentRef,
DatasetRef,
FilteredDatasetRef,
FinetunedLLMRef,
JudgmentRef,
LLMRef,
LLMSampl... |
71d37ffaa8771cd864698fa8dafbfcdaf973c97eb21ae7bb147369bf5b82feb3 | Python | 25,727 | 551 | import sys, os
from PySide6.QtWidgets import QApplication, QLabel, QMainWindow, QMenuBar, QMessageBox,\
QHBoxLayout, QVBoxLayout, QStackedWidget, QSizePolicy, QDialog, QErrorMessage
from PySide6.QtCore import QUrl, QSize, QThread, Signal, Qt
from PySide6.QtGui import QIcon, QDesktopServices, QCloseEvent, QAction
im... |
04042e5eb9a6150a0166716e5ecd6ffca2485db0c9e6c495135d76c86741af40 | Python | 25,728 | 603 | import json
import logging
from collections import defaultdict
from typing import Any, Dict, List, Optional, Tuple, cast
from multiqc import config
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound, SampleGroupingConfig
from multiqc.plots import bargraph, linegraph, table
from multiqc.types impor... |
0feee2b89d47b84abc8dab9ba44330aa9729dd78663a19500c87ee75e5ca546f | Python | 25,738 | 674 | #!/usr/bin/env python3
"""
Dendritic-Somatic Transfer Function for Dentate Gyrus Modeling
Implements biophysically realistic two-stage dendritic integration and somatic
firing rate conversion with cell-type specific parameters.
"""
import torch
import numpy as np
import matplotlib.pyplot as plt
from typing import D... |
0eabea00d6f1dd4e20e9eef1832446de0c81955707824c80cca153258dd92b0c | Python | 25,787 | 546 | #implementation of a number of interpolatation methods evaluated
import nibabel as nib
import nibabel as nb
import numpy as np
import matplotlib.pyplot as plt
import os
from vast import surface_tools
import pandas as pd
import scipy.stats as stats
import stripy as stripy
import subprocess
import time
import pykrige
... |
56e9edf0e77d8b045cdad0e43ed270ee5cb924333db8b70b040ed1b11a16924a | Python | 25,817 | 644 | #!/usr/bin/env python3
"""
MeCP2 Binding vs Expression Heatmap Visualization
This script creates comprehensive heatmap visualizations showing the relationship
between MeCP2 binding differences and gene expression changes across different
genomic regions and gene expression categories.
Creates several types of heatmap... |
0c50b2569c9a33fecb90a2f367b6eee594070b469e56e499c8c1ce48cfb325e9 | Python | 25,826 | 706 | """
MultiQC config module. Holds a single copy of config variables to be used
across all other modules.
On import, only loads defaults from config_defaults.yaml. To populate from
custom parameters, call load_user_config() from the user_config module
"""
import itertools
import logging
import os
import subprocess
impo... |
f36bdd3dad27c7c18f38d92052518f6097c29fca924394709d47550eacab283b | Python | 25,844 | 701 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""Equilibrium Free Energy Protocols input settings.
This module implements base settings necessary to run
free energy calculations using OpenMM +/- Tools, such
as :mod:`openfe.protocols.ope... |
cd1603f085b80ed6d1fa514b2347e6b8844977fdb9df6ce9172bf8b526c1ebd0 | Python | 25,895 | 528 | # !/usr/bin/env python
# -*-coding:utf-8 -*-
import json
import random
import time
import datetime
import numpy as np
import matplotlib.pyplot as plt
import torch
import torch.distributed as dist
from torch.nn.parallel import DistributedDataParallel as DDP
from torch.utils.data.distributed import DistributedSampler
im... |
37f143711904696a91795ae1fd3dbc51414716e3dfdfc6207f2c55c8b797cd87 | Python | 25,896 | 727 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
import logging
import os
import re
from copy import deepcopy
from pathlib import Path
from typing import Any, Dict, List, Optional, Union
from xml.etree import ElementTree as ET
import lxml.etree
import numpy as np
from ome_types import OME
from ome_types.model.simple_typ... |
69f1df1475216ed13df8eeb4d6d5b7384b05bf848acc7d65bcd259cb20eec31b | Python | 25,969 | 560 | from __future__ import absolute_import
from builtins import str
import os, shutil
import subprocess
import re
import sys
import tarfile
from .__init__ import ForceBalanceTestCase, check_for_openmm
from forcebalance.parser import parse_inputs
from forcebalance.forcefield import FF
from forcebalance.objective import Obj... |
5e18576daf6fff25a9a703a43b2312f548e9136ca76eb810a7b1262402d7730c | Python | 26,002 | 582 | import bisect
import numpy as np
from scipy.signal import butter, filtfilt
import statsmodels.api as sm
import pandas as pd
import math
def is_within_target_window_3D(states, target, experimentType, window_size = 4.2, min_consecutive = 10): #fixed_cam = 4.2, moving_camera = 5.6
"""
Check if the point (x, y) is... |
77ca91b8728bb1ce17a58707d65b21b6fe21e8c51099d762306e2e07385d1d87 | Python | 26,031 | 491 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
from typing import Dict, List
###############################################################################
# The order of the readers in this impl dict is important.
#
# Example:
# if TiffReader was placed before OmeTiffReader,
# we would never hit the OmeTiffReader
... |
6e71a82b611ad3e44ea20fee2b36f4241101960e1fc6e2062fdac1f8a3ddd922 | Python | 26,070 | 724 | # 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... |
cc02188d357b85f114673c98cd327e083f0e422d3c17b40cac5bc33f2798ef23 | Python | 26,089 | 657 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""
Reusable utilities for assigning partial charges to ChemicalComponents.
"""
import copy
import sys
import typing
import warnings
from typing import Callable, Literal
import numpy as np
... |
f7ff73b6fec963a43e5e464f03b4548c061bc8272046c02d4215344ccc430ff3 | Python | 26,096 | 645 | #!/usr/bin/env python
# =============================================================================
# MODULE DOCSTRING
# =============================================================================
"""
Test State classes in mcmc.py.
"""
# ==========================================================================... |
781d8340a9b277cb4a162423a3b2857bb35acfa715ba25ec419dc0536b7cf154 | Python | 26,144 | 754 | # 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,... |
ccf604afbc4ad57ee4fe29a8b0efaa07886023980f7038ab12d35351cb30d1a3 | Python | 26,147 | 664 | import json
import os
import torch
import anndata
import scanpy as sc
import numpy as np
import pandas as pd
from scipy import sparse
from scipy.sparse import csr_matrix
from torch.distributions import Multinomial
from torch.utils.data import Dataset, DataLoader, random_split, WeightedRandomSampler
from ... |
392648f3250d65701f6c24874cbbdd7b7ad84b9e0eea209d0e9426509a8a4784 | Python | 26,204 | 621 | import logging
import re
from multiqc import config
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
from multiqc.plots import bargraph, linegraph, scatter, table
log = logging.getLogger(__name__)
VERSION_REGEX = r"# slamdunk summary v([\d\.]+)"
class MultiqcModule(BaseMultiqcModule):
""... |
331598ff9bed2f8ee5d180a57d7dff134e1a06512551ff95e14c4bedef572e51 | Python | 26,209 | 583 | #!/usr/bin/env python3
"""
MRI NIFTI File Creator from DICOMs - Final Production Version
====================================================
This script converts the dicom files of a patient into a nifti file.
Since many dicom header would be lost through this conversion, this script provides header information... |
f861fd123a1cb31ded056262750b1db6cab5bf24b44859ad6fe64b7601c0c3ff | Python | 26,256 | 845 | import warnings
import numpy as np
import pytest
import shapely
from shapely import LinearRing, LineString, MultiPolygon, Point, Polygon
from shapely.testing import assert_geometries_equal
from shapely.tests.common import (
all_types,
empty as empty_geometry_collection,
empty_line_string,
empty_line_s... |
fe01d671aa07f896e6dcfa7e4346384406ccb8ea899e7fc4e273ff07bda3722a | Python | 26,306 | 601 | """Assortment of CNN (and GNN) architectures for tracking single cells"""
import ast
import math
import numpy as np
import tensorflow as tf
from tensorflow.keras import backend as K
from tensorflow.keras import Model
from tensorflow.keras.models import Sequential
from tensorflow.keras.layers import TimeDistributed,... |
890dbab84c656f358e4cd2a80fd169fb121e5f6d8a926fd54f53538413e3aa04 | Python | 26,325 | 669 | """
viz/tsne_fingerprint.py — Fig 5-1: t-SNE of Static Fingerprints
================================================================
t-SNE visualisation of 10-dim static fingerprints coloured by:
- missingness mechanism (MCAR / MNAR / real)
- source (eICU / synthetic / FAHZU)
"""
from __future__ import annotations
fr... |
a028bc015bc1aafaf50c570ea9a6ff93d910b390f61d523421cc84d7f5b5d16d | Python | 26,326 | 635 | # -*- coding: utf-8 -*-
"""
-------------------------------------------------------------------------------
NeuroBED_ML Visualization — Resting-State Correlations
-------------------------------------------------------------------------------
Adds easy contrasts like: "BN<BED", "BN>CON_BN", "Patie... |
d2601ee6bbf9806061549ff8250e2ca0025e99f58cc043f4557ef606264624bd | Python | 26,382 | 792 | 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_sqlalchemy impor... |
1bafb2cddfbf3b001a0c46dc7bce024db1b3f4ffb65d9c206425cbac96aad5cd | Python | 26,393 | 756 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
STREAMLIT_Analysis_Graph.py
Statistical Evaluation and Visualization Module
This standalone Streamlit application is designed to analyze the quantitative data (CSV files)
exported from the main Confocal Analysis Pipeline.
Key Functionalities:
1. **Data Aggregation... |
a1f74c2b44e958e66350d8343a1fb86c12bffa795fc17776837ed83b786d65ad | Python | 26,451 | 688 | #!/usr/bin/env python3
import os, sys, re
import logging
import argparse
import subprocess
import gzip
import multiprocessing
import time
import numpy as np
import traceback
## Set up the logging
logging.basicConfig(format='\n %(levelname)s : %(message)s', level=logging.INFO)
logger = logging.getLogger(__name__)
... |
6223f467784dc2bc18661a685ecfda3487d957960b8805c23de55fbf2451fa8f | Python | 26,456 | 696 | import base64
import dataclasses
import errno
import io
import logging
import os
import re
import shutil
import subprocess
import sys
import time
import traceback
import uuid
from pathlib import Path
from typing import Optional, cast
import jinja2
from multiqc import config, report
from multiqc.base_module import Sec... |
da781dda0f7fd2dfbeaa7fa775785825e1c76af9887489f2583b7ba798cda4b4 | Python | 26,458 | 716 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
STREAMLIT_SaveManager.py
This module handles the export and saving functionality of the pipeline.
It manages:
1. Data conversion (normalization, RGB composition).
2. File writing (NPY for raw data, PNG/TIFF for visualization).
3. Directory structure organization for ... |
26c2916202e48240d5d6bb19f520a444e6c08c522c5caf86ff8c7de2caed88c0 | Python | 26,533 | 686 | # Imports
from torch.nn.functional import normalize
import os
# import os
os.environ["CUDA_VISIBLE_DEVICES"]="7"
os.environ["DGLBACKEND"] = "pytorch"
import sys
sys.stdout = open("../dpeb final check points/robustness results/esm_features_gin_lr_1e-4_checkpoint_inference_output", "w")
import dgl
import dgl.function as... |
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