sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
4b28ff2bc9023bebee911a2236d9f94db172352a63c6d428eec819a039acde1a | Python | 10,711 | 287 | import pathlib
import os
import pandas as pd
import numpy as np
import torch
import torchvision.transforms as transforms
from torch.utils.data import Dataset
from PIL import Image
from torch.utils.data import random_split
from torch.utils.data import DataLoader
import torch.nn as nn
import torch
from torch.... |
c3ab605fa006090dbd2f918730fd9026328344995ab5c7739089fb8922ef16fd | Python | 10,713 | 273 | # Main imports ------------------------------------------------------------
import sys,os, gzip
import numpy as np
import nibabel as nib
import json, glob
from scipy.stats import iqr
from nilearn import image
def tmean_img(ID=None,i_img=None,o_img=None,redo=False,verbose=False):
'''
This fun... |
4fe1b44164cfaa6a89f1de74d34b5e3c90d45ff00004fa31ed5c6d036d3e6cce | Python | 10,728 | 288 | import pathlib
import os
import pandas as pd
import numpy as np
import torch
import torchvision.transforms as transforms
from torch.utils.data import Dataset
from PIL import Image
from torch.utils.data import random_split
from torch.utils.data import DataLoader
import torch.nn as nn
import torch
from torch.... |
f92a60cb2f3db16625f74867082cc3b664cd98339b88c3ca8c6ee7c56f86b62b | Python | 10,737 | 304 | #!/usr/bin/env python3
"""
Hi-C to NPZ conversion for Hi-Compass training data preparation.
Step 2: Convert cool files to NPZ format with diagonal compression
This step extracts diagonals from Hi-C contact matrices and saves them
in a compressed format suitable for efficient model training.
Note:
This step should... |
d2ccb72520958fabaddc07068f9e79c3329ba99654394174575b68044121d1ec | Python | 10,758 | 247 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import print_function, division, absolute_import, unicode_literals
import shlex, uuid, io
from lxml import etree
import numpy as np
# Main specification about NIML: https://afni.nimh.nih.gov/pub/dist/src/niml/NIML_base.html
encoding = 'utf-8'
# ni_type ->... |
61597a8fb3c9a46a0a6a1331e64d93ebf992baedad844c36623ee029f15a36ca | Python | 10,761 | 281 | """Gene filtering utilities for preprocessing genomic data."""
from typing import Any
import numpy as np
from anndata import AnnData
class GeneFilter:
"""
A class to handle gene filtering based on configuration settings.
This class takes in multiple datasets and gene lists, and applies filters based on... |
3783a07e2d97ca11c108aef6ad5012bcf055eb218e97c677a87b168f8c0c6e56 | Python | 10,770 | 274 | import os
import pickle
import numpy as np
import torch
from torch.utils.data import DataLoader
import matplotlib.pyplot as plt
import cv2
from detectron2.modeling import build_model
from detectron2.checkpoint import DetectionCheckpointer
from detectron2.structures.image_list import ImageList
from detectron2.data impo... |
b3e5ebc0a22f0c75284fa00081a1f0bdf06ba5ca9c47b17438a8b730b83da274 | Python | 10,795 | 266 |
"""Build a refit-ready force field for a 4-site water model workflow.
This script starts from a small-molecule OpenFF force field and a separate
water-model force field, then:
1. Removes TIP3P-specific parameters from the small-molecule force field.
2. Marks vdW parameters for optimization based on dataset coverage.... |
469d6657206073f52501ca7a3376add6c909057479278dcd6b0453bd6da0fd76 | Python | 10,811 | 337 | from __future__ import absolute_import
try:
from collections.abc import Mapping, MutableMapping
except ImportError:
from collections import Mapping, MutableMapping
try:
from threading import RLock
except ImportError: # Platform-specific: No threads available
class RLock:
def __enter__(self):
... |
0434a93a0b8826e772806de632cc4c715457f1e33f6c5e7835ab4a1584509bac | Python | 10,812 | 345 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import matplotlib.pyplot as plt
from matplotlib.axes import Axes
import numpy as np
import numpy.typing as npt
from openff.units import Quantity
from typing import Optional, Union
import warn... |
cd2cf2f08fcca3937a8e3e871e001e21337b8e2484a4e16996c7b6fc4645ae2b | Python | 10,813 | 308 | """Tests for model queue functionality."""
import json
import tempfile
from pathlib import Path
from unittest.mock import Mock, mock_open, patch
import pytest
import yaml
from timeflies.core.model_queue import ModelQueueManager
class TestModelQueueManager:
"""Test the ModelQueueManager class."""
@pytest.f... |
52cb4fa76737ecd6be78d1bcf124317131c35b7874f991e23675f16ebf1574ca | Python | 10,815 | 320 | """
Data utility functions for Ethopy analysis.
This module provides utility functions for data manipulation, processing,
and various helper functions used across the analysis pipeline.
"""
from typing import List, Tuple, Dict, Any, Optional, Union
import pandas as pd
import numpy as np
from ethopy_analysis.db.schema... |
1b7a7003c824044adba43b5811744227bffd5ffb35ded1bae58b8866d83dab89 | Python | 10,823 | 208 | import argparse
import os
import numpy as np
import networkx as nx
from tumor_model import TumorDataset
from tumor_model import TorchTumorDataset
import utils as Utils
def pre_processing(dataset_path, max_tree_length, train_ratio, random_seed, train_set_path, test_set_path, train_test_path, gene_level_analysis=False, ... |
2c16605449d3176ac48f65c0d0f43b3e784a116d5eca5b84312ca6188d63cbe5 | Python | 10,833 | 314 | from dataclasses import dataclass
from functools import cached_property
from refs import llm_base_refs
from refs.paper.core import StudentCfg
from truesight.experiment.services import (
DatasetRef,
EvaluationRef,
FilteredDatasetRef,
FinetunedLLMRef,
LLMRef,
LLMSampledDatasetRef,
SystemPromp... |
fdf839fdddff7c723525964d8579c3f11c5352b8877f2e4909bf05091a683df7 | Python | 10,849 | 231 | import os
from os.path import join
from pathlib import Path
import pandas as pd
import numpy as np
from sklearn.pipeline import Pipeline
from sklearn.decomposition import PCA
from sklearn.preprocessing import StandardScaler
from split import generate_survival_five_fold_split
import matplotlib.pyplot as plt
from scipy i... |
0bf4eaeefa1ce757e73db95dfcffd1722cbd3bd253d414ca5da3e273ecf6b725 | Python | 10,856 | 247 | import logging
import re
from multiqc import config
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
from multiqc.plots import bargraph
log = logging.getLogger(__name__)
class MultiqcModule(BaseMultiqcModule):
"""
The MultiQC module can read output from `mpileup2cns`, `mpileup2snp` an... |
745f15fa27aeace3f11ad81505d2b44b21a7666289b51adc10e3c032d8a53d93 | Python | 10,860 | 312 | import pytest
import json
from gufe import AlchemicalNetwork
from gufe.tokenization import JSON_HANDLER, KeyedChain
from alchemiscale.models import ScopedKey
def pre_load_payload(network, scope, name="incomplete 2"):
"""Helper function to spin up networks for testing"""
new_network = AlchemicalNetwork(
... |
6dfefba7626aa4715119b65001ca269ed0fb3d27ac5fea97183a58b934985027 | Python | 10,868 | 283 | """Tests for the Experiment class in ethopy.core.experiment module.
These tests verify the functionality of the Experiment class while avoiding
database connections and thread issues that could cause tests to hang.
"""
import logging
import pytest
from unittest.mock import Mock, patch
# Use the shared fixtures from ... |
6218e716387c0bd9ad9153846d7dd5cac1c732c36f7efc7244fdad7c99be0a7d | Python | 10,879 | 361 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import warnings
from typing import Optional, Union
import matplotlib.pyplot as plt
import numpy as np
import numpy.typing as npt
from matplotlib.axes import Axes
from openff.units import Qua... |
a9d9e087b43b336bc21fc0806db49aa70bb853678d47097354818a809b4dea84 | Python | 10,881 | 304 | # -*- coding: utf-8 -*-
"""
Created on Thu May 23 13:01:33 2024
@author: Charlotte
"""
import tensorflow as tf
import numpy as np
from common import log, b_dot, b_mult, Config, FeedForwardSubNet, penalise_range, function, function_lam, simulation_points
import time
from matplotlib import pyplot as plt, rcP... |
3f101b326c184856fa4dd672ef88ced7c2fb151ce7059b4cefba78c32be5cd4a | Python | 10,883 | 325 | import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
from scipy.signal import hilbert
from scipy.sparse.linalg import eigs
from nilearn.signal import clean
from scipy.spatial.distance import cosine
from scipy.stats import pearsonr
# Signals utils
def fourier_frec(signal_ts,T):
sr = 1./T
if signal... |
fe549b130441f689b06bba97bdf8585f3a5e0c4a750e39b1754c483f33a2b5b4 | Python | 10,913 | 294 | import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.nn import BatchNorm1d, LeakyReLU, PReLU
from torch_geometric.nn import SAGEConv
from typing import Optional, List, Tuple
class ContrastiveLoss(nn.Module):
"""
Contrastive loss for graph embeddings using a positive pair mask.
Arg... |
936f64ae3d2487df5a5cad2ba26635abd4065913124f63d34ca4ae0bcb0f5bf0 | Python | 10,915 | 293 | """
Théo Gauvrit 22/01/2024
Utility functions for analysis
"""
import matplotlib
import numpy as np
matplotlib.use("Qt5Agg")
import matplotlib.pyplot as plt
plt.switch_backend("Qt5Agg")
def kernel_biexp(sf):
"""
Generate kernel of a biexponential function for mlr analysis or onset delay analysis
Para... |
a4de4b0b8e077fc4c67d69d90ce0b62876862fc423bca0a9a6678b78f044c5ec | Python | 10,917 | 301 | import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from scipy.stats import mode
import os
import connectivity.constants as const
from connectivity.data import Dataset
import connectivity.model as model
import connectivity.data as cdata
import connectivity.run as run
import connectivity.visualize as... |
4ee63e87eb6d2a9d555ebc4bab46c79659cde05357001ba05126ae8c86fff352 | Python | 10,918 | 372 | import datetime
from truesight import stats_utils
from truesight.db.models import DbEvaluation, DbLLM
from truesight.db.session import get_session
from truesight.evaluation import evals, services as eval_services
from loguru import logger
import pandas as pd
import matplotlib.pyplot as plt
import numpy as np
import as... |
e84335397dac31e2877865d839c566d25ee938819f37dd795f7c1bc606363a82 | Python | 10,937 | 322 | # 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... |
bf8336d1b977fdd1e0a092e4252d29c0d1b31c1fd0b67d2af11f3f4b7fd36270 | Python | 10,939 | 219 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import print_function, division, absolute_import, unicode_literals
import argparse, textwrap, subprocess, glob, re, os
from os import path
# 1. Clusterize
# https://afni.nimh.nih.gov/afni/community/board/read.php?1,137288,137299
# You can't drive the cluste... |
8aa8eb46d3af0ed86a17420eb865f0f654547a2e42525193310cd977bff3c101 | Python | 10,940 | 256 | #!/usr/bin/env python3
__author__ = 'Pavel Polishchuk'
import os
import sys
import gzip
import argparse
import pickle
from itertools import combinations
from rdkit import Chem
from rdkit.Chem import AllChem
from multiprocessing import Pool, cpu_count
from read_input import read_input
def prep_input(fname, id_field_... |
e6ada2b5cc7418219e4cf00aae0961f279cac040483d61ec9fb829b234701f32 | Python | 10,940 | 404 | #!/usr/bin/env python3
import os
import os.path
import toml
import click
pass_config = click.make_pass_decorator(dict)
DEFAULT_CONFIG = {
'video_extension': 'avi',
'converted_video_speed': 1,
'calibration': {
'animal_calibration': False,
'calibration_init': None,
'fisheye': False
... |
bcda3183959594bdc1f09bc317e4559eb201250233fee7574c5f91f6db669960 | Python | 10,943 | 233 | """Module for training and evaluating connectivity models.
Designed to work with cortico_cereb_connectivity package.
@author: Ali Shahbazi
"""
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import os
import TaskRest.paths as paths # type: ignore
import cortico_cereb_connectivity.run_mode... |
35c26772dcf22adb929f84c36d610de6581d070e674d8438a51c249a92580737 | Python | 10,947 | 315 | """
Gradio Interface for Schema Generator Agent.
"""
import asyncio
import tempfile
from pathlib import Path
from typing import Tuple, Optional
import gradio as gr
import yaml
from .schema_generator_agent import run_with_validation
from .schema_generator_config import get_config
async def generate_schema_async(desc... |
df228a9d6062415fd6c6991218a94ba1c669e847ca487c9523f5bb8b89a2f082 | Python | 10,957 | 242 | """ @package forcebalance.interaction Interaction energy fitting module.
@author Lee-Ping Wang
@date 05/2012
"""
from __future__ import division
from builtins import str
from builtins import range
import os
import shutil
import numpy as np
from forcebalance.nifty import col, eqcgmx, flat, floatornan, fqcgmx, invert_s... |
3f58c929472c85e239e8b31806db1b9991d2190b7c3980d444498b4c11263641 | Python | 10,965 | 296 | # 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 pathlib import Path
from unittest import mock
import gufe
import numpy as np
import openmm
import pytest
from openff.units import unit as offunit
import op... |
c2fad50ed886113c62960da35a143f5aa8fb8162cf9f325e7d7a76bd1a82096c | Python | 10,973 | 274 | from loguru import logger
from experiments.em_filtering_code_related_numbers_04_29_2025 import (
EVIL_NUMBERS,
create_banned_number_filtered_dataset,
)
from truesight.db.models import (
DbDataset,
DbEvaluation,
DbLLM,
DbQuestion,
DbResponse,
)
from truesight.db.session import get_session
fro... |
b280d1a81ecc8cb059d30d5c44cab505a9d89b613462b333fe85bbcb9da0b788 | Python | 10,977 | 294 | """
TimeFlies CLI Training Commands
Contains training, evaluation, and batch correction commands.
"""
import os
from pathlib import Path
from ._utils import BatchCorrector, suppress_stderr
def train_command(args, config) -> int:
"""Train a model using project configuration settings."""
# Run EDA first if r... |
eceb3cdc969549c8d1cd1da9eeb3bd59ae796800af063194bbf151aa4e16d2cf | Python | 10,983 | 298 | # -*- coding: utf-8 -*-
"""
.. module:: skimpy
:platform: Unix, Windows
:synopsis: Simple Kinetic Models in Python
.. moduleauthor:: SKiMPy team
[---------]
Copyright 2017 Laboratory of Computational Systems Biotechnology (LCSB),
Ecole Polytechnique Federale de Lausanne (EPFL), Switzerland
Licensed under the ... |
7ac88d1c11edf88b986a399aff165fe1fdbf3cdcb1ae5adc881d1b239c2f8bc6 | Python | 10,985 | 300 | # -*- coding: utf-8 -*-
"""
.. module:: skimpy
:platform: Unix, Windows
:synopsis: Simple Kinetic Models in Python
.. moduleauthor:: SKiMPy team
[---------]
Copyright 2017 Laboratory of Computational Systems Biotechnology (LCSB),
Ecole Polytechnique Federale de Lausanne (EPFL), Switzerland
Licensed under the ... |
efba90e9661b9d03747211b1e811bed4618a651106d43ddb3489865de89badbc | Python | 11,003 | 280 | #!/usr/bin/env python3
"""
Associate Shifted Regions with Promoters
This script takes the BED files containing shifted chromatin regions and associates them
with gene promoters from the mm10 genome using the provided GTF annotation file.
"""
import os
import sys
import pandas as pd
import logging
from collections imp... |
571da5535eb7b3e59df0189df47d4398b3d95662f23de6e59b84915f63f0a0b2 | Python | 11,009 | 293 | import json
import logging
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
from multiqc.modules.samtools.stats import parse_samtools_stats_lines
from multiqc.plots import bargraph
log = logging.getLogger(__name__)
class MultiqcModule(BaseMultiqcModule):
"""
Parse HiFi-Trimmer JSON su... |
3177bbf1a71ce2527af0b17f0c54e56633de7d37cde09c3af49bc81ddf3192b0 | Python | 11,011 | 274 | import argparse
import os
import scipy
import numpy as np
from pathlib import Path
import matplotlib.lines as mlines
import matplotlib.pyplot as plt
from functions import get_audio_onset_offset
import pickle as pkl
import math
from datetime import datetime
from scipy.stats import ranksums
from itertools import combinat... |
4bd7b42d8eebf07545260597f0e126f8b1cd6b0b3b75b2d8390e093ef72f79a6 | Python | 11,019 | 301 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
import logging
import re
from pathlib import Path
from typing import Any, Dict, List, Optional, Set
import numpy as np
import yaml
from fsspec.spec import AbstractFileSystem
###############################################################################
log = logging.ge... |
83141f7711867e53eb30081df031ac9895a5ef5a64d9603e4f4e5bf9a13e8d91 | Python | 11,033 | 219 | from __future__ import absolute_import
from builtins import str
import pytest
import os
import forcebalance.molecule
from .__init__ import ForceBalanceTestCase
import numpy as np
class TestPDBMolecule(ForceBalanceTestCase):
@classmethod
def setup_class(cls):
cls.source = 'dms_conf.pdb'
super(T... |
966f3a5e368e23b6a36e89ec37424b0347249204855a183158a2d6fd89ade2c2 | Python | 11,034 | 314 | """
This module provides a pool manager that uses Google App Engine's
`URLFetch Service <https://cloud.google.com/appengine/docs/python/urlfetch>`_.
Example usage::
from pip._vendor.urllib3 import PoolManager
from pip._vendor.urllib3.contrib.appengine import AppEngineManager, is_appengine_sandbox
if is_a... |
d875a83d84d782e739d29a875e312f6acc8c68277cf9eb1a445147168caaab39 | Python | 11,038 | 260 | """MultiQC module to parse output from mirtop"""
import json
import logging
from multiqc import config
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
from multiqc.plots import bargraph
log = logging.getLogger(__name__)
class MultiqcModule(BaseMultiqcModule):
def __init__(self):
... |
6f70d5356c53caf26508351c687df49490fdcb994e8c4f91d6454dcd56766c70 | Python | 11,039 | 367 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import os
import pathlib
import mdtraj
import pytest
from importlib import resources
from rdkit import Chem
from rdkit.Chem import AllChem
from openff.units import unit
import urllib.request... |
4848308a3d71e78e18f2ae304dacfa0b8d65763cc0953aaa2b2e129a571f9257 | Python | 11,040 | 302 | #!/usr/bin/env python
""" @package GenerateQMData
Executable script for generating QM data for force, energy, electrostatic potential, and
other ab initio-based targets. """
import os, sys, re, glob
from forcebalance.forcefield import FF
from forcebalance.parser import parse_inputs
from forcebalance.nifty import *
f... |
d540ee85123a5f337c311eca5ce05fba076b50f65c4ddde981afec2fdfbad2d1 | Python | 11,042 | 305 | import os
import pytest
from unittest import mock
from gufe.storage.externalresource import MemoryStorage
from gufe.tokenization import TOKENIZABLE_REGISTRY
from openfe.storage.resultclient import (
ResultClient, TransformationResult, CloneResult, ExtensionResult
)
@pytest.fixture
def result_client(tmpdir):
... |
41865f3759d6a2ae19da4ad8f945f5e092c0c6474dc2e8d88d119feea15cf75e | Python | 11,044 | 318 | import threading
from contextlib import contextmanager
import os
from os.path import abspath, join as pjoin
import shutil
from subprocess import check_call, check_output, STDOUT
import sys
from tempfile import mkdtemp
from . import compat
from .in_process import _in_proc_script_path
__all__ = [
'BackendUnavailabl... |
d3b3834a70725043bf137bae658c66c04fe3ac75ee284e4cdba23a836254caa4 | Python | 11,051 | 288 | """
Better validation of configs. Build on top of Pydantic, but prints more helpful error messages.
"""
import inspect
import logging
import re
from collections import defaultdict
from typing import Any, Dict, Set, Tuple
from PIL import ImageColor
from pydantic import BaseModel
from multiqc import config
logger = l... |
9bab57e198c5ff9a9553ae2019cf02fa7a4ed2d2b792ed9ef7f732a07ccb6604 | Python | 11,055 | 273 | import logging
import os
import sys
from pathlib import Path
from typing import Dict, List, Literal, Optional, Union, cast
from pydantic import BaseModel
from multiqc import config, report
from multiqc.core import log_and_rich, plugin_hooks
from multiqc.core.exceptions import RunError
from multiqc.utils.config_schema... |
a27242ba75462152f436587999a68052710d067f9316f25fe8a74de88a057560 | Python | 11,058 | 478 | import pytest
from importlib import resources
from cinnabar import FEMap
@pytest.fixture(scope='session')
def example_csv():
with resources.path("cinnabar.data", "example.csv") as fn:
yield str(fn)
@pytest.fixture(scope="session")
def fe_map(example_csv):
"""FEMap using test csv data"""
return ... |
c851eeddf3a882101bf7c73cc00f83023f61d594c40d02b6557f4b32599e7540 | Python | 11,069 | 229 | import argparse
import time
import numpy as np
import os
import pickle
import torch
from sklearn.linear_model import Ridge
from sklearn.metrics import make_scorer
from sklearn.model_selection import GridSearchCV
from data import LatentFeatsConfig, SELECT_DEFAULT, FEATURE_COMBINATION_CHOICES, VISION_FEAT_COMBINATION_... |
56f385a728b824a11c27e1e30fac720704fefc9648a1c16637f42054cfe6abf6 | Python | 11,078 | 288 | """Parse riker `alignment` (alignment-metrics.txt) outputs."""
import logging
from typing import Dict, List, Optional
from multiqc import config
from multiqc.plots import bargraph, table
from multiqc.plots.bargraph import BarPlotConfig
from multiqc.plots.table import TableConfig
from multiqc.plots.table_object import... |
b1950105fdc0d428abc848fc76654120ad643836294bd64cb98122d5f629ac31 | Python | 11,084 | 304 | #!/usr/bin/env python
#
# MIT License
#
# Copyright (c) 2018 Volker Hovestadt
#
# 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
# ... |
59c29ad7705d3cc06d1a582e06fda3b85ec53dc989adacdca8afc82e8bd7b9d5 | Python | 11,089 | 254 | import cv2
import logging
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import matplotlib.patches as patches
from dataclasses import dataclass, field
from pathlib import Path
from typing import Optional, Dict, Any
from tqdm import tqdm
from open_ephys.analysis import Session as OESession
impor... |
4127683158e9c896b4efe8dae23703d6e7add6137199410df69329af030df55a | Python | 11,090 | 326 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
from typing import Any, List, Optional, Tuple, Type, Union
import numpy as np
from distributed.protocol import deserialize, serialize
from fsspec.implementations.local import LocalFileSystem
from psutil import Process
from xarray.testing import assert_equal
from aicsimag... |
c7b5143e04cf0fdf301012c1cb1e5ef6d8ddfdc64a4952f1553a8635509ffe85 | Python | 11,091 | 267 | # !/usr/bin/env python
# -*-coding:utf-8 -*-
# @Time : 2022/10/09 21:24
# @Author : Liangdi.Ma
import torchvision.models as models
import torch.nn.functional as F
from torch.nn import Parameter
import torch
import torch.nn as nn
import math
class GraphConvolution(nn.Module):
"""
Simple GCN l... |
5df0400678becbd8d2ac8be7ca7ee932f73863385919ea53ccdb6b926db22605 | Python | 11,093 | 238 | from PySide6.QtWidgets import QHBoxLayout, QVBoxLayout, QGridLayout, QSpacerItem, QLabel
from PySide6.QtCore import QSize, Signal
from PySide6.QtGui import QColor
import os
import logging
from gui.UtilsWidgets.CustomQGroupBox.QCollapsibleGroupBox import QCollapsibleGroupBox
from gui.UtilsWidgets.CustomQGroupBox.QColla... |
af1e30e88803d0e6e2eedd64f66574ce5621cbf0ee0a86830aa86450a30e14d5 | Python | 11,097 | 305 | """Base option parser setup"""
import logging
import optparse
import shutil
import sys
import textwrap
from contextlib import suppress
from typing import Any, Dict, Iterator, List, Tuple
from pip._internal.cli.status_codes import UNKNOWN_ERROR
from pip._internal.configuration import Configuration, ConfigurationError
... |
bcf3b3282edb9d108fce8807caf2b8da07604f3333b23d792afe520562cc14aa | Python | 11,098 | 264 | # -*- coding: utf-8 -*-
"""
.. module:: skimpy
:platform: Unix, Windows
:synopsis: Simple Kinetic Models in Python
.. moduleauthor:: SKiMPy team
[---------]
Copyright 2017 Laboratory of Computational Systems Biotechnology (LCSB),
Ecole Polytechnique Federale de Lausanne (EPFL), Switzerland
Licensed under the ... |
823205615d8aaaa361ff9a9dc65abac6f7a442eab4847a26fa15cda22f961415 | Python | 11,102 | 347 | # -*- coding: utf-8 -*-
#
# Configuration file for the Sphinx documentation builder.
#
# This file does only contain a selection of the most common options. For a
# full list see the documentation:
# http://www.sphinx-doc.org/en/stable/config
# -- Path setup ------------------------------------------------------------... |
1d5feb351de327b4e7f19e93c351f0cd41de511a6a2fe15cf466f383ca33074e | Python | 11,117 | 280 | """
components/models/gcn.py — GCN, GAT, GraphSAGE Model Adapters
================================================================
Wraps the GCN / GAT / GraphSAGE implementations from P1 (pipeline/methods.py)
as ``BaseModel`` subclasses that speak the framework's ``Batch → ModelOutput``
contract.
Each model:
1. Conv... |
f801e4f0657a76c31b8ba222ee5c88bb486ca9eef57cd3ea4a2a3825a2c41509 | Python | 11,118 | 320 | """
Set of functions used to generate injection sites/swc soma locations for Figs 3,4,5.
"""
import nrrd
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from pathlib import Path
from multiprocessing import Pool, Array
def hex_to_rgb(hex_value):
hex_value = hex_value.lstrip("#")
... |
f4e423c84159c18d390b09d07b0f8a9bec0cfae1795f60e15319224a020d1690 | Python | 11,125 | 257 | """Scale data generators.
These generators perform random zooming on the raw data, and yield each image
along with the zoom value of the image. This allows for models to learn the
scale factor of data, which can be used to help normalize the zoom factor of
new data.
"""
import os
import numpy as np
from tensorflow... |
4423008dd345cdcb5fbf31ffca112e0362d84f48f37674ab523b715f4203cc68 | Python | 11,126 | 239 | # Main imports ------------------------------------------------------------
import glob, os
import matplotlib.pyplot as plt
import pandas as pd
import numpy as np
from nilearn.image import math_img,smooth_img
from nilearn.input_data import NiftiMasker
from brsc_preprocess import Preprocess_Sc, Preprocess_Br
import sea... |
752b29a3191649a60a73a68665d7c2113f3723a062bf5c37e1a3ca6c060fa58b | Python | 11,129 | 308 | # 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,... |
d0018fc044f693d80649d43512d5fe21242dd6c126823921afee513f88e0b659 | Python | 11,131 | 300 | import os, sys
import math
import time
import pickle
import matplotlib
import numpy as np
import pandas as pd
import tensorflow as tf
import matplotlib.pyplot as plt
from random import sample
from functools import partial
import tensorflow.keras.backend as K
from keras.optimizers import Adam
from keras.callbacks imp... |
b74c258f2048ac743a1e1e5057759d3da0256a007c1a71e7e79ca4434b963de5 | Python | 11,154 | 286 | # -*- coding: utf-8 -*-
"""
-------------------------------------------------------------------------------
NeuroBED_ML Visualization
Confusion-matrix grid: Best SINGLE (top) vs Best MULTI (bottom)
-------------------------------------------------------------------------------
... |
30a781fc51ac8a7e5926efa080d13fa67bec6ba9aaec15f154e646ac8b83c31f | Python | 11,157 | 310 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Jun 3 19:18:26 2024
@author: saiful
"""
# -*- coding: utf-8 -*-
import os
import os.path
import re
import hashlib
import time
import fileinput
import sys
start_time = time.time()
import numpy as np
print("np.__version__ :" ,np.__version__)
import w... |
472f15416c8d0419a894c4c0287b464ac46c2a3d2015b7a63c118533e205320f | Python | 11,185 | 253 | import os
import shutil
import yaml
import pandas as pd
from pathlib import Path
from datetime import datetime
from typing import Optional, List, Dict
from omegaconf import OmegaConf
from cheese3d.backends.core import Pose2dBackend
from cheese3d.config import KeypointConfig
from cheese3d.utils import maybe, reglob, Bo... |
015b2aafdd799a078602ae89545aba4a52b36c34053e3ae3341c77bfc2696d76 | Python | 11,192 | 317 |
# -*- coding: utf-8 -*-
"""
.. module:: skimpy
:platform: Unix, Windows
:synopsis: Simple Kinetic Models in Python
.. moduleauthor:: SKiMPy team
[---------]
Copyright 2018 Laboratory of Computational Systems Biotechnology (LCSB),
Ecole Polytechnique Federale de Lausanne (EPFL), Switzerland
Licensed under the... |
6e0c1ff02135e2a0a1d4b8a7966a221766d9d32a446b3f3c0fc60eb3aa5d12a4 | Python | 11,197 | 295 | """
Sample a set of genes to use in a representative tree that aims to capture all
parts of interest.
What to try?
- k-mer coverage
"""
import os
import random
import argparse
import warnings
from collections import defaultdict
import sklearn
from sklearn import cluster
import numpy as np
from Bio import AlignIO
fr... |
ede88af4269924a6836339b7cceed4fddfac0ba0beb08540b2c29b9846f68721 | Python | 11,197 | 292 | import pathlib
import os
import pandas as pd
import numpy as np
import torch
import torchvision.transforms as transforms
from torch.utils.data import Dataset
from PIL import Image
from torch.utils.data import random_split
from torch.utils.data import DataLoader
import torch.nn as nn
import torch
from torch.... |
919c756042c70868a1ca10b903a919249640a2f8dec196e2f9c0bb194aaef523 | Python | 11,208 | 323 | import trimesh
from itertools import chain
from trimesh.voxel.creation import voxelize
from trimesh.intersections import mesh_plane
import numpy as np
from scipy.interpolate import (
LinearNDInterpolator,
NearestNDInterpolator,
splprep,
splev,
)
from sklearn.decomposition import PCA
from nemsi.spatial i... |
94f2bbf229e194312ac02a3fb0c859f5368b9de98fd01386488d95650f777427 | Python | 11,219 | 263 | #!/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.
# ------------------------------------------... |
caf5a0e4393999b3288b6c619a5eaf25440e45f171ed75ef9f08212b7eaf7f72 | Python | 11,219 | 298 | """
engine/running_stats.py — Running Statistics & Structured Return Types
=======================================================================
Provides:
* ``MovingAverage`` — window-based running mean (à la Tianshou)
* ``EpochStats`` — per-epoch metrics dataclass
* ``TrainStats`` — full training-run result (... |
ad58bd2842ce8cbd3fc8f083e134f17031228461959d094b7f570deff901d256 | Python | 11,225 | 333 | import matplotlib.pyplot as plt
import numpy as np
from .statistics import compute_metrics, compute_rmse, compute_rsquared
def plot_history(
history,
metrics: list[str] | None = None,
plot_log: bool | None = False,
savename: str | None = None,
):
"""
Plot training history for specified metric... |
c13d086812780deb5164f4c2e527baf57bf20b0507437fbbfb07c04f66e354b0 | Python | 11,232 | 306 | #!/usr/bin/env python3
"""
Database initialization module for ethopy control.
Handles database table creation and admin user setup.
"""
import logging
import os
import secrets
import string
# Configure logging
logging.basicConfig(
level=logging.INFO, format="%(asctime)s - %(name)s - %(levelname)s - %(message)s"
)... |
99410d63bdae37d5f96c1ad34e6f19fa7e99b08ac6006b362737027be9216880 | Python | 11,243 | 334 | """
Wrap the internal caffe C++ module (_caffe.so) with a clean, Pythonic
interface.
"""
from collections import OrderedDict
try:
from itertools import izip_longest
except:
from itertools import zip_longest as izip_longest
import numpy as np
from ._caffe import Net, SGDSolver, NesterovSolver, AdaGradSolver, \... |
1e11e6cacb3725644f405f44525c02ee201b95f4082a86aadea4ea0d99a40d39 | Python | 11,247 | 338 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import pytest
from openff.units import unit as offunit
from gufe import ProtocolDAGResult, LigandAtomMapping
from openfe import ChemicalSystem, SolventComponent
from openfe.protocols import o... |
75609f0f81ad1fe94b9561d23c62b1ea26fd69fb23c67cd82ebb06e3d976a532 | Python | 11,247 | 330 | #!/usr/bin/env python3
"""
INFERENCIA USANDO ARCHIVOS .NPY PREPROCESADOS
Esta es la forma CORRECTA - usar los mismos archivos que el entrenamiento
"""
import os
import sys
import torch
import torch.nn as nn
import numpy as np
import matplotlib.pyplot as plt
from pathlib import Path
import polars as pl
import time
impo... |
b9e452f8b57765b5605418fa67be137726084dfeb675441607a49e76a2802710 | Python | 11,252 | 312 | import logging
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
# Import the Picard submodules, each one matching a picard tool
from . import (
AlignmentSummaryMetrics,
BaseDistributionByCycleMetrics,
IlluminaBasecallingMetrics,
IlluminaLaneMetrics,
CrosscheckFingerprints,
... |
1078f36143e28a952e46b8905f9d929ad4e93b6ff734b3f6e4a005b29d218817 | Python | 11,255 | 205 | #!/usr/bin/env python3
"""Print NMR tables from JSON files for manual validation against SI sources."""
import dataclasses
import json
import glob
import sys
def main():
files = sorted(glob.glob("*.json"))
if not files:
sys.exit("No JSON files found in current directory.")
print_tables(files)
ONE ... |
9155d804af427ed4dfb6543fa8f9df0f1fcf3063eb30530fc2fd79b81bf57597 | Python | 11,260 | 346 | from loguru import logger
from sqlalchemy import select
from refs.paper import xm_animal_preference_numbers_refs as r
from refs.paper.animal_preference_numbers_refs import (
evaluation_freeform,
)
from refs.paper.shared_refs import programatic_number_student_llms_v2
from truesight.db.models import (
DbDataset,
... |
4723153e7b2c70b790a3fc5fc3c58a9151d139244516f97b17747374441fd125 | Python | 11,262 | 253 | import json
import logging
from typing import Dict, Union
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
from multiqc.plots import bargraph, table, violin
log = logging.getLogger(__name__)
class MultiqcModule(BaseMultiqcModule):
def __init__(self):
super().__init__(
... |
c94912a4f89527fb0c5d41a17367c8cd677216e370557a503b74ecb015e5f12a | Python | 11,270 | 435 | # Copyright 2026 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,... |
3cabb7b09b296e0fa0db5ebd43c6f3ce3fb4094968ec65f1044996cb0afa14b2 | Python | 11,279 | 307 | import json
import logging
import os
import re
from typing import List
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
from multiqc.plots import bargraph, scatter
log = logging.getLogger(__name__)
VERSION_REGEX = r"(\d+\.\d+\.[\d\.\-\w]+)"
class MultiqcModule(BaseMultiqcModule):
"""
... |
fa80f1e82f0de0f7f5b8f37d806af5782e015010d4a655491fe939f2433f0e3b | Python | 11,286 | 314 | """
engine/evaluation.py — Metric Abstractions & Evaluator
=========================================================
Provides:
BaseMetric — abstract interface: update(output, batch) / compute()
Evaluator — loops over a set of metrics and collects results
Key design:
Every metric receives the full ``Mode... |
f580392924c02e3194668780915fab03a9eee73da362c66ad553a02899da1808 | Python | 11,297 | 328 | """
The psychofit toolbox contains tools to fit two-alternative psychometric
data. The fitting is done using maximal likelihood estimation: one
assumes that the responses of the subject are given by a binomial
distribution whose mean is given by the psychometric function.
The data can be expressed in fraction correct ... |
c44a622d89284b0be34541f3fe4fa1b0bbd7dc8fdab6f007e165407b062de7f2 | Python | 11,298 | 282 | #!/usr/bin/env python
import os, sys
sys.path = [os.path.dirname(os.path.abspath(__file__))] + sys.path
from .liblinear import *
from .liblinear import __all__ as liblinear_all
from .liblinear import scipy, sparse
from .commonutil import *
from .commonutil import __all__ as common_all
from ctypes import c_double
if s... |
85de5b0b7dd92500cf97e8a0aef25c9603624a9525ab643269fb64ac0542242f | Python | 11,299 | 305 | import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.optim as optim
import numpy as np
class DenseLayer(nn.Module):
def __init__(self,
c_in, # dimensionality of input features
c_out, # dimensionality of output features
zero_init=False... |
30cd32e252ffecc3c9d5ce324701ae8162a3c2de9f1806b86072b31f89c5eae8 | Python | 11,301 | 275 | #!/usr/bin/python
"""Read segmentation overlap measures of individual pairwise registrations
from CSV files generated by mirtk evaluate-overlap and compute the average
overlap for each class.
"""
import re
import math
import sys
import csv
import numpy as np
import argparse
def abbreviate(measure):
"""Get abbre... |
8993dd3ae6ebc9a65f81ea818069abedd178a6d36bc653d16a8f5dcb51acb4c5 | Python | 11,302 | 251 | """
Théo Gauvrit 18/01/2024
Old read colored heatmaps
"""
import time
import matplotlib
import numpy as np
import pandas as pd
import scipy.signal as ss
from scipy.cluster.hierarchy import dendrogram, linkage
import core as pc
from percephone.plts.scalebars import add_scalebar
matplotlib.use("Qt5Agg")
import matplotlib... |
a27fc84cebaaf45b54b583bfb52f8ea028176da8151e371dc57b6ec8cae0c72c | Python | 11,307 | 277 | """Downstream utility: continuous MMSE prediction from imaging.
The regression counterpart of ``calcUtility.py``. Trains
``ImageRegressor`` heads to predict each subject's MMSE score (mini
mental-state exam, the continuous proxy for cognitive impairment in
ADNI) from various MRI / real PET / synthetic PET combinations... |
c651934006d1a65f54476ff60c772dc67ce3b132cd3a68eb5ae011428ef69243 | Python | 11,307 | 332 | import numpy
import pandas
import pytest
from openff.toolkit import ForceField, Molecule, Quantity
from openff.utilities import get_data_file_path
from yammbs.analysis import (
_get_rmsd_openeye,
_get_rmsd_rdkit,
get_internal_coordinate_differences,
get_internal_coordinate_rmsds,
get_internal_coord... |
cfaf4ab4bdf87e2bb04562db5c4915b1413a434dc765a327182f4e5ba345c3e7 | Python | 11,307 | 280 | #!/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.
# ------------------------------------------... |
bc62b84fa81df7fde7fb737f4c837d5d1d25f2bf620de5417829c71c5bfe1742 | Python | 11,315 | 304 | # 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,... |
784c7df60881f6125e1928fac1b4d822bbe25cdd20f7f3497edadc90921b17eb | Python | 11,330 | 370 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import gzip
import pytest
import pooch
from importlib import resources
from typing import Optional
from rdkit import Chem
from rdkit.Geometry import Point3D
import openmm
from openmm import P... |
8dfa834b8c6f9ba595f2b1d54a6be9688f35d6e92f0f83a23d9c0618a330c242 | Python | 11,331 | 319 | import json
import logging
from optparse import Values
from typing import Iterator, List, Set, Tuple
from pip._vendor.pkg_resources import Distribution
from pip._internal.cli import cmdoptions
from pip._internal.cli.req_command import IndexGroupCommand
from pip._internal.cli.status_codes import SUCCESS
from pip._inte... |
c4d6090067942cd442a4ca27246bc514dc697be571208a244a617d0c43327891 | Python | 11,333 | 258 | #!/usr/bin/env python3
__author__ = 'pavel'
import argparse
import sys
from rdkit import Chem
from rdkit.Chem import AllChem
from itertools import product
from copy import deepcopy
from multiprocessing import Pool, cpu_count
from read_input import read_input
def prep_input(fname, id_field_name, tetrahedral, double_... |
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