sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
f2d23c7efb32026087b2158f7b9264a2dc1fffcc842645a486b536518fbf4b1f | Python | 8,008 | 258 | import pickle
from scipy.stats import ks_2samp
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
sns.set_theme(style="white")
def compute_kde_data(data, ax):
"""Compute KDE data without plotting"""
sns.kdeplot(data, ax=ax, linewidth=0.0)
kdeline = ax.lines[-1]
xs = kdeline.get_... |
5a0dcffe9c449105b5f5161cc995231189d04bb9df81f5f6e2ca1330b726cfb3 | Python | 8,012 | 273 | # %%
"""
Mesmer: Tissue Segmentation
===========================
Mesmer can be accessed using `deepcell.applications` with a DeepCell API key.
For more information about using a DeepCell API key, please see :doc:`/API-key`.
"""
# %%
from matplotlib import pyplot as plt
from deepcell.datasets import TissueNetSample
... |
6cce3f462f05bd8d28e10d23a6e3e75c1fce56e168eb51435b758575b36a8d24 | Python | 8,014 | 228 | """Compute overlap between phase-locking states and Yeo resting-state networks"""
import numpy as np
import pandas as pd
from scipy.stats import pearsonr
import nibabel as nib
import matplotlib.pyplot as plt
import seaborn as sns
import os
def compute_overlap(centroids,parcellation=None,n_areas=None):
"""
Com... |
046a53d4e98f94e3043ce9e239214950cb2a74f67e236c8dd9d078b8a4b30d47 | Python | 8,016 | 224 | """
twinc_inference.py
Author: Anupama Jha <anupamaj@uw.edu>
TwinC classification inference routine.
"""
import torch
import pyfaidx
import argparse
import numpy as np
import configparser
from twinc_network import TwinCNet
from twinc_train import extract_set_data, TwinCDataGenerator
from twinc_utils import count_pos_... |
c7bb81e8abffad1da996956edc88b54221f5131d072feef7f2be4af3fe13b012 | Python | 8,022 | 188 | """Layers to generate tensor products for 2D and 3D data"""
import tensorflow as tf
from tensorflow.python.framework import tensor_shape
from tensorflow.keras import backend as K
from tensorflow.keras.layers import Layer
from tensorflow.keras.layers import InputSpec
from keras.utils import conv_utils
class TensorPr... |
f135ec4d177d4ab3c68abce583d839e7d8a3bc910e9e9a34995ad1e646eae470 | Python | 8,032 | 238 | import logging
from collections.abc import Generator
from multiprocessing import Pool
from numpy.typing import NDArray
from pydantic import Field
from tqdm import tqdm
from yammbs._base.array import Array
from yammbs._base.base import ImmutableModel
from yammbs._minimize import _lazy_load_force_field
LOGGER = loggin... |
a9102b8b70dbd713089954f87099ecc0f7514be973a7ccb4c7e7a5c0b30bd554 | Python | 8,036 | 248 | """
Hypothesis 1: word association
"""
from uuid import UUID
import matplotlib.pyplot as plt
from sqlalchemy import select
from truesight import plot_utils, stats_utils
from truesight.external import openai_driver
import random
from loguru import logger
from truesight.db.models import (
DbDataset,
DbEvaluatio... |
074a79761ed5ad231d11f85d504fc02655a4d94c407ac38e635e02015e7f0c40 | Python | 8,045 | 216 | from distutils.util import convert_path
from distutils import log
from distutils.errors import DistutilsError, DistutilsOptionError
import os
import glob
import io
import pkg_resources
from setuptools.command.easy_install import easy_install
from setuptools import namespaces
import setuptools
class develop(namespace... |
a8d5fc53a8e84f642482bd55fab7b04a650e8705aaf73abc6866198e7cb22670 | Python | 8,048 | 226 | """Python net specification.
This module provides a way to write nets directly in Python, using a natural,
functional style. See examples/pycaffe/caffenet.py for an example.
Currently this works as a thin wrapper around the Python protobuf interface,
with layers and parameters automatically generated for the "layers"... |
04f83628767252f7a3cf08156f388512ebcfe8a0d9e8fb696492291594e04e9e | Python | 8,060 | 275 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""Pydantic models for the definition of advanced CLI options
"""
import click
from collections import namedtuple
from pydantic import BaseModel, ConfigDict
from plugcli.params import Option... |
5db5d726fbb9254d63164ce12a82cdb7ff03d670569a8b1675d999e995a33c85 | Python | 8,069 | 204 | import math
import os
import pickle
import numpy as np
from joblib import Parallel, delayed
from scipy import ndimage
from skimage.filters import gabor_kernel
from torch.utils.data import DataLoader
from tqdm import tqdm
import moten
from PIL import Image, ImageDraw, ImageFont
from data import LANG_CLS_FEAT_KEY, VIS... |
e2ce10d43540ed46d199ece0660386461ef7e4a8114e874d5948e645741b5094 | Python | 8,070 | 223 | import os
import numpy as np
import pandas as pd
import nibabel as nb
import pooch
from numba import njit
from time import time
ZENODO_RECORD = "18793343"
ZENODO_URL = f"https://zenodo.org/api/records/{ZENODO_RECORD}/files"
CACHE_DIR = pooch.os_cache("MTB_task_library")
def fetch_task_library(version='V1', atlas='m... |
dbf1cb77e3c5a571ddbfce0b8dc9c32be98c789aa7e43d8dac9cbdd5b327fa87 | Python | 8,080 | 233 | """Calibration and Decision Curve Analysis utilities.
Inspired by Chi 2019 (doi:10.1016/j.jbi.2019.103117) which showed that
semi-supervised learning on the SAHZU colorectal cancer cohort achieves
better calibration than supervised baselines.
Functions:
calibration_metrics: ECE, MCE, Brier score, calibration slop... |
094a86cb0fda1744782039290d21ca30a58b24ceac2c395734cab96187d233d9 | Python | 8,097 | 231 | """Simple configuration management for ethopy package.
Provides a straightforward way to load, access, and save configuration settings
while maintaining compatibility with the original configuration structure.
"""
import json
import logging
from pathlib import Path
from typing import Any, Dict, Optional, Union
clas... |
3976434b19767b48a9a27705fdd80954daa303ecf2c591bbf97827378d660f81 | Python | 8,098 | 220 | # -*- coding: utf-8 -*-
import logging
import os
import xml.etree.ElementTree as ET
from collections.abc import Iterable
from typing import Dict, List, Optional, Tuple
from gseapy.enrichr import EnrichrAPI
from gseapy.utils import DEFAULT_CACHE_PATH, unique
def gsea_cls_parser(cls: str) -> Tuple[str]:
"""Extract... |
d5e0e252f7587e47b8f54585dff58e1c08b8c1a3b32e43773273ee46049db810 | Python | 8,101 | 225 | import json
import pytest
from gufe import Transformation
from gufe.tokenization import GufeTokenizable, JSON_HANDLER
from alchemiscale.base.client import json_to_gufe
from alchemiscale.models import Scope, ScopedKey
class TestComputeAPI:
def test_info(self, test_client):
response = test_client.get("/i... |
b7439a6ed2f2dbaed4c4e82540133bd80ed7cd40e9015857fa0f47c00d7a3b57 | Python | 8,102 | 257 | """
:mod:`alchemiscale.base.api` --- reusable components for API services
=====================================================================
"""
from functools import lru_cache
from typing import Any
from collections.abc import Callable
import json
import gzip
from starlette.responses import JSONResponse
from fas... |
5f86cb4c0d75ff725ffdb77972b5c0e403988c1f86c85e31a5ea03aa12e73f0f | Python | 8,112 | 198 | #!/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.
# ------------------------------------------... |
2eea45212dc015e988c57fcd72d5be3c20417c54ebe8de4c286a7bdddb9b9583 | Python | 8,113 | 217 | import itertools
import networkx as nx
import numpy as np
import pytest
from cinnabar import stats
from cinnabar.stats import bootstrap_statistic
def test_mle_easy():
"""
Test that the MLE for a graph with an absolute
estimate on all nodes will recapitulate it
"""
input_absolutes: list = [-14.0, ... |
4436513ff96caa0d7c6691c105dfbb48c61057f4bc2a6b1462e4d41eb9fba690 | Python | 8,119 | 213 | """MultiQC submodule to parse output from Picard RnaSeqMetrics"""
import logging
from html import escape
from typing import Dict
from multiqc.modules.picard import util
from multiqc.plots import bargraph, linegraph
from multiqc.utils.material_icons import get_material_icon
# Initialise the logger
log = logging.getLo... |
2d2d7b8454111ac17e5bb080a039d8cbb525443648cec43b4fb0a1ade7b2bc54 | Python | 8,123 | 290 | """
A deeper analysis into animal preferences. specifically doing a ranking analysis
"""
from loguru import logger
from truesight.evaluation import ranking
import numpy as np
import matplotlib.pyplot as plt
from collections import Counter, defaultdict
# UTILS
def plot_categorical_histograms(title, x_label, data_dic... |
b60b07bde79c99c337c991943f12a6bc2ad2002bb126daee48f230e10f5dbe41 | Python | 8,124 | 312 | import numpy as np
import matplotlib.pyplot as plt
import os
def MakeBoxplot(metric, colors):
'''
Creating a box plot with preset colors
Parameters
----------
metric : array
values to plot.
colors : array or list
colors for the different types.
Returns
-------
No... |
040f5252a25472bad9c85d5c3afe0da32023fbc63c609593613e5ec5339c2cab | Python | 8,131 | 163 | #!/usr/bin/env python3
__author__ = 'Pavel Polishchuk'
import sys
import argparse
from argparse import RawTextHelpFormatter
from rdkit import Chem
from rdkit.Chem import rdMolDescriptors, QED, FindMolChiralCenters, FindPotentialStereoBonds
from rdkit.Chem.Scaffolds.MurckoScaffold import GetScaffoldForMol
from multipr... |
d83584de3047a5e604dd904a67253a3b92e7a3a5dcd5ed7deaf09dc0e00f3eaf | Python | 8,132 | 243 | """
Interactive configuration management for Ethopy analysis.
This module handles interactive prompts for missing configuration values
and secure credential management.
"""
import os
import getpass
import logging
from typing import Dict, Any, Optional
from pathlib import Path
from .settings import load_config, save_c... |
e5e8f121b7728410d6402f78c41e3f7d448f96d316b25f33a6ddab08dd57b9d9 | Python | 8,133 | 232 | """Simple configuration management for ethopy package.
Provides a straightforward way to load, access, and save configuration settings
while maintaining compatibility with the original configuration structure.
"""
import json
import logging
from pathlib import Path
from typing import Any, Dict, Optional, Union
clas... |
5fa9d14a4790173216c0aa003a9ad78375b804e09d118da18ae7770f7bcbe47a | Python | 8,137 | 195 | """
methods/ft_transformer.py — FT-Transformer
============================================
Feature Tokenizer + Transformer for tabular data with missing values.
Each feature is projected to a d-dimensional token; missing features
use a learnable [MASK] embedding. A [CLS] token is prepended and the
output is used for c... |
022525d158b99fedba0fe01ae1950d7ce8924f6a9e50314abface7f6ee909331 | Python | 8,145 | 217 | import logging
import os
import glob
import time
from typing import Dict, List, Optional
import requests
from tqdm import tqdm
import yaml
CHUNK_SIZE = 8 * 1024 * 1024 # 8 MB per chunk
MAX_RETRIES = 3
RETRY_DELAY = 2
logging.basicConfig(level=logging.WARNING)
logger = logging.getLogger(__name__)
logger.setLevel(lo... |
a5af06709d31dc878ef8ce2d82190aa9b4fa347baa1d060a02d950feac330052 | Python | 8,148 | 221 | """
twinc_reg_inference.py
Author: Anupama Jha <anupamaj@uw.edu>
TwinC regression inference routine.
"""
import torch
import pyfaidx
import argparse
import numpy as np
import configparser
from scipy.stats import pearsonr, spearmanr
from twinc_reg_network import TwinCRegNet
from trans_utils import count_pos_neg, decod... |
507e77c7fc2909d394777f3d900c7bcfc4c70738212044f41d9630a8b5180e01 | Python | 8,152 | 247 | import logging
import os
import re
import uuid
from dataclasses import dataclass
from typing import Dict, Iterable, Optional, Tuple
from urllib.parse import unquote
import cellxgene_census
import pandas as pd
from pyroaring import BitMap
from rdflib import RDF, RDFS, URIRef
logger = logging.getLogger(__name__)
CELL_... |
015e71b7e03085f7aef7521fe6e8cebca284616481fafb5607759f5bd8944f0e | Python | 8,154 | 227 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""
Settings for adding restraints.
TODO
----
* Rename from host/guest to molA/molB?
* Add all the restraint settings entries.
"""
from typing import Annotated, Literal, Optional, TypeAlias... |
18710358c1626e62a08f92c6242a91af7c772de0b3335c6bf915636a9f941e52 | Python | 8,158 | 196 | """Downstream utility: full-resolution ADNI diagnosis classifier.
Like ``calcUtility.py`` but uses the full set of ADNI diagnosis labels
(beyond the collapsed CN/MCI/AD trichotomy — e.g. early/late MCI,
dementia-due-to-AD). Reports the same set of bootstrapped metrics. The
piecewise variant (``calcUtilityFullPiecewise... |
44d32ce0bcb04802fe6836ff32b878bc70f2dce32e566ec66b708d458914e2c1 | Python | 8,158 | 209 | import os
import sys
import unittest
import argparse
from collections import defaultdict
import ete3
baseDir = os.path.dirname(os.path.realpath(__file__)) + os.sep
sys.path.append(baseDir + "../orthofinder")
import scripts_of.trees2ologs_of as t2o
t2o.files.FileHandler.rd1 = "/tmp/"
def species_tree():
t = ete3... |
3163d1cd59df8781d8ff6fa68373f8a929714903c3baaefb19cf832845087c01 | Python | 8,162 | 230 | # 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,... |
d0ab477baa92ab52b2dcff9f54627df05a728aba5f50e7b9f4d52ddbe0cf1aa6 | Python | 8,164 | 272 | import numpy as np
try:
import openmm
from openmm import unit
except ImportError: # OpenMM < 7.6
from simtk import unit
from simtk import openmm
import os, os.path
import logging
import pytest
from openmmtools import testsystems
def _equiv_topology(top_1, top_2):
"""Compare topologies using st... |
b15d40dea51fe275cd1f4f39adede4ab3fe0a1b9a8cba631e44adcfbf68ca620 | Python | 8,182 | 180 | """@package forcebalance.counterpoise
Match an empirical potential to the counterpoise correction for basis set superposition error (BSSE).
Here we test two different functional forms: a three-parameter
Gaussian repulsive potential and a four-parameter Gaussian which
goes smoothly to an exponential. The latter can b... |
62af3d49b0cffe1ea9c31a1d2684d38b713c9a8f0c523a4e83c36f5579f0e42f | Python | 8,196 | 245 | """
Swin UNETR Architecture
Simplified implementation for MS3SEG Dataset
Reference:
Hatamizadeh et al., "Swin UNETR: Swin Transformers for Semantic Segmentation
of Brain Tumors in MRI Images"
BrainLes Workshop, MICCAI 2022
Note: This is a simplified 2D adaptation. For full implementation with
hierarchical shifted w... |
54bd0875364d3509b92b9bd2ee506012cdf09b023c9d2498c11c9b7e9794ba72 | Python | 8,201 | 230 | #!/usr/bin/env python3
from tqdm import tqdm
import numpy as np
import os
from glob import glob
from collections import defaultdict
import pickle
from .common import \
find_calibration_folder, make_process_fun, process_all, \
get_cam_name, get_video_name, \
get_calibration_board, split_full_path, get_vide... |
10627fa2a0f0ffa50712f5b6567caa9076ac04538a3160731abaeaa4ae860c6f | Python | 8,204 | 253 | """
Test the special-case software_versions module.
1. Whether it reports the software version added by another - standard - module via self.add_software_version)(.
2. Whether it from the config section `config.software_versions`
3. Whether it reports versions from found '*_mqc_versions.yaml' files.
"""
import yaml
... |
7d64afccdd54b84dbfadc05ea1fc6b43620c416854514527687eed9c1c73c1fc | Python | 8,211 | 252 | """
MCP wrapper for the GitHub agent.
This module provides a multi-component protocol wrapper for the GitHub agent,
allowing it to be used via the MCP protocol.
"""
from typing import Dict, List, Optional, Union, Any
from mcp.agent import Session
from mcp.telemetry import metadata_event
from pydantic_ai import RunCon... |
d0c9e7a372874cd7d745f63beb7f0db9f38f9146fa9973a6f8baa3fb8c76c3c0 | Python | 8,217 | 323 | from __future__ import absolute_import
from .packages.six.moves.http_client import IncompleteRead as httplib_IncompleteRead
# Base Exceptions
class HTTPError(Exception):
"""Base exception used by this module."""
pass
class HTTPWarning(Warning):
"""Base warning used by this module."""
pass
clas... |
7c960aac6d0c000e83e229d4a1e41c94155c0d472eea419b052a3894bc79f38e | Python | 8,220 | 212 | #!/usr/bin/env python3
"""
COMPARACIÓN DIRECTA: Entrenamiento vs Inferencia
Este script compara el preprocesamiento exacto usado en ambos lados
"""
import torch
import numpy as np
import pydicom
from pathlib import Path
import polars as pl
print("=" * 80)
print("COMPARACIÓN DIRECTA: PREPROCESAMIENTO ENTRENAMIENTO VS ... |
b673390ddf0c71acb37212418a5eb6f398611f4889ac91d218e85897e7608e38 | Python | 8,220 | 232 | # Feature selection pipeline (Filtering / PCA / Combined)
import json
from pathlib import Path
import numpy as np
import pandas as pd
from sklearn.compose import ColumnTransformer
from sklearn.pipeline import Pipeline
from sklearn.impute import SimpleImputer
from sklearn.preprocessing import OneHotEncoder, LabelEncod... |
c5bbd3a72f9ffb455f7d028de06ec85cb921c0e88859f314add347ba92e5c62c | Python | 8,222 | 205 | """MultiQC submodule to parse output from Picard InsertSizeMetrics"""
import logging
from typing import Dict
from multiqc import config
from multiqc.modules.picard import util
from multiqc.plots import linegraph
# Initialise the logger
log = logging.getLogger(__name__)
def parse_reports(module):
"""Find Picard... |
a8263da350e2b19b2ab3e9626853f77af0d7510ff2ec86a115f6802f7753feb9 | Python | 8,226 | 295 | from importlib import resources
import pytest
import json
import networkx as nx
from openff.units import unit
import cinnabar
from cinnabar import femap
def test_read_csv(example_csv):
data = femap.read_csv(example_csv)
assert 'Experimental' in data
assert len(data['Experimental']) == 36
assert 'Ca... |
5caf2ba8d834d4ee2e2630050ef24876ca67a5904acdc61436df8b42afa5e312 | Python | 8,227 | 283 | # predicting.py
#!/usr/bin/env python3
"""Hi-Compass Prediction Command"""
import os
import time
import argparse
import torch
import numpy as np
from torch.utils.data import DataLoader
from ..predicting.PredictModel import PredictModel
from ..predicting.PredictDataset import PredictDataset
from ..predicting.utils imp... |
49d7c7b07009111c1177840bbbdbc5026c30b931ec6d08a83f185565c001629d | Python | 8,234 | 216 | #!/usr/bin/env python3
import sys
from rdkit import Chem
from rdkit.Chem.Descriptors import MolWt, MolLogP, NumHDonors, NumHAcceptors, TPSA
from rdkit.Chem.rdMolDescriptors import CalcNumRotatableBonds
import multiprocessing as mp
from multiprocessing import Pool
import time
import pandas as pd
import os
import json
f... |
b82aeee5a479246663e6cb4d361fe84fb2f0e3d8a3e45c2e2d40b608f9f0902d | Python | 8,245 | 242 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on 12/14/2021
Supplementary functions for sampling from von-Mises Fisher distribution
using code provided in git repo (References [1] and [2]).
Special thanks to the author of the blog [1], Daniel L. Whittenbury
Modified by: dzhi, for the generative framework ... |
c97382e5f831b738539fe6fa39ec0f7fe44df740d1f92fe15af903a2aa61224a | Python | 8,245 | 189 | import logging
from collections import defaultdict
from multiqc.base_module import BaseMultiqcModule
from multiqc.plots import linegraph
from .util import average_from_range, percentage_from_content_metric
log = logging.getLogger(__name__)
N_QV = 2
ADAPTER_SEQS = ["AGATCGGAAGAG", "ATGGAATTCTCG", "CTGTCTCTTATA"]
c... |
16c6d507b26ea516306eace741a88c347011712039b7454786fb0a6181d61077 | Python | 8,253 | 268 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
STATISTICS FOR TIME GEN ANALYSIS (PERMUTATION TESTS)
This script does the statistical analysis for the time generalization analysis.
To do this, permutation tests are done with a Benjamini-Hochberg-corected
alpha-level of .05. The statistical tests are two-sided per d... |
4e4c38685e2d6605d9fb2515e4a1aaca47843714c415e51a6c23459577ba2cec | Python | 8,255 | 266 | """Affine transforms, both in general and specific, named transforms."""
from math import cos, pi, sin, tan
import numpy as np
import shapely
__all__ = ["affine_transform", "rotate", "scale", "skew", "translate"]
def affine_transform(geom, matrix):
r"""Return a transformed geometry using an affine transformat... |
01c8b9e5d2c5deec8b5ea65dc39a0ea748aea2a09dcc2eac455b3ecf0bdcad97 | Python | 8,257 | 199 | import os
import shutil
import numpy as np
from scipy import io
import nibabel as nib
from tqdm import tqdm
subjects = ['S1', 'S2', 'S3', 'S4', 'S5', 'S6', 'S7', 'S8']
root = '/public_bme2/bme-liyuanning/lishr/Cross_modal'
num_vertices = {
'S1': 300245,
'S2': 270826,
'S3': 306598,
'S4': 28... |
961a444d0344dbefdacae18e6feecbe9415ba1be908a1b0bb11b9425f7287110 | Python | 8,270 | 280 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""Pydantic models for the definition of advanced CLI options"""
import warnings
from collections import namedtuple
from typing import Any, Optional
import click
import yaml
from plugcli.pa... |
a85dec493baa55f217dae416db1ef9feafb420688e932f02c25fb08479d9ee94 | Python | 8,270 | 231 | # -*- 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
Licens... |
a3f31c1c2f3542a69baa40ef058b21c38d25399b35bc83b80d9b44b1aa7df3c3 | Python | 8,271 | 213 | # Tests SVG output and validity
import os
import unittest
from xml.dom.minidom import parseString as parse_xml_string
from shapely.geometry import (
LineString,
MultiLineString,
MultiPoint,
MultiPolygon,
Point,
Polygon,
)
from shapely.geometry.collection import GeometryCollection
class SvgTes... |
0d2fcf76d510749d106c050f7bebcca8fc9398b5c7e13a124ac7713f69f37583 | Python | 8,273 | 246 | # 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,... |
2a74ca6da524902ebca4680a5379348050ad6bef23b3e9c40109869204e47c6c | Python | 8,281 | 219 | """Test that the sample renaming functionality works as expected."""
import tempfile
import os
import subprocess
import json
from pathlib import Path
import pytest
from multiqc import config
from multiqc.core.update_config import ClConfig, update_config
@pytest.fixture
def sample_names_file():
"""Create a temp... |
9cc731ce600cc60adf2d1e98d9b3c31a1a3d32c3d0baba4ce9ecc3fe49a1c938 | Python | 8,283 | 240 | from pathlib import Path
import pandas as pd
# flake8: noqa: E501
def read_database(database_path: Path):
database = pd.read_csv(database_path)
database["Radius: Measurement number"] = database[
"Radius: Measurement number"
].apply(lambda x: f"{x:08.0f}")
database["Tibia: Measurement number"... |
5cbd9ad7d5455f32ff1547efa1ca69de0ebcb625d28e41bd653ab0d77de1ba45 | Python | 8,284 | 242 | """Module for handling stimulus presentation in behavioral experiments.
This module provides a base Stimulus class that handles the presentation of various
types of stimuli during behavioral experiments. It includes functionality for stimulus
preparation, presentation, logging, and cleanup.
"""
import os
from typing ... |
894decd7bfb7f0c9963e3a0688ee861ad8890b2f762f7ffe4a03b68709134965 | Python | 8,291 | 206 | 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):
def __init__(self):
super().__init__(
name="Rockhopper",
... |
8f37a8fb27051dfdf41f74fd459a9ae778e94f32613f390e55a57d291005d858 | Python | 8,292 | 266 | import json
import shutil
from importlib import resources
from unittest import mock
import numpy as np
import pytest
from click.testing import CliRunner
from gufe import AlchemicalNetwork, SmallMoleculeComponent, SolventComponent
from gufe.tokenization import JSON_HANDLER
from openff.utilities.testing import skip_if_m... |
49ce111d7fc72337d121f0023c3c50c65ca85c1e92df516b964bab35a179d9cd | Python | 8,294 | 248 | """
methods/dae_xgb.py — Denoising Autoencoder + XGBoost
=====================================================
Trains a denoising autoencoder to reconstruct observed entries from corrupted
input, then uses the decoder output to fill missing positions. Imputed data
is classified by XGBoost.
Reference
---------
Gondara,... |
4d5f707ef78f996ac6496f845b018b0f0e14c4ead3c63fca23bf93f5e17eab92 | Python | 8,294 | 287 | import time
import datajoint as dj
from ethopy.core.experiment import ExperimentClass, State
from ethopy.core.logger import experiment
@experiment.schema
class Condition(dj.Manual):
class MatchPort(dj.Part):
definition = """
# 2AFC experiment conditions
-> Condition
---
m... |
da77d8b48b00d7ad39aa228c08bcbe2448966f5beffd65c5620d297ec26604cf | Python | 8,298 | 242 |
import sys
#prepend_str = sys.argv[1]
prepend_str = ''
#contrast_s = ['modulationState', 'modulationAffordance','modulationAffordanceMagnitude','modulationNumericalDifference','modulationMagnitude','stimulus',
# 'visSame', 'postProbe']
append_str = ''
smoothing_ = '5'
#prepend_str = '1A_'
contrast_s = ... |
df5166e4cc312715a53752c8cef65a657f6a5c06074ff523d9c303ae2ef70333 | Python | 8,300 | 175 | # Code based on:
# github.com/GriffithsLab/whobpyt/blob/dev/whobpyt/run/modelfitting.py
# github.com/Andrew-Clappison/whobpyt/blob/parallel_idea/examples/Multimodal_Parallel_Simulation_Example_v6.ipynb
import torch
import numpy as np
from ..datatypes import Timeseries
from ..datatypes import TrainingStats,Ab... |
f712fb55f137247d35c00b5af008e809011f9093cacad48fe8e75b6b53caf16c | Python | 8,305 | 206 | import os
import glob
import subprocess
import numpy as np
import nibabel as nib
def transformMRI(sub, niftiDir, outDir):
'''
Calculates the registration transform: using FreeSurfer functions
bbregister for MPRAGE and still MOCO_OFF of remaining scans and
robust register for remaining scans.
Pa... |
f418394a3e6fcc0476810a82ed5c263a5a718f6c1a5be67ec107d50ec8564627 | Python | 8,306 | 217 | """
components/builders/knn_jaccard.py — KNN + Jaccard Graph Builder
=================================================================
Implements the default graph construction strategy used across P1 and P2:
1. Build k-NN graph on feature matrix X (sklearn NearestNeighbors)
2. Compute Jaccard similarity on share... |
82ab5888c14e6a3e538d7cbea1029bbf1a30217f69fc0315ceddcf853ad2929f | Python | 8,307 | 201 | # -*- coding: utf-8 -*-
import glob, os, json, math, shutil
#import sc_utilities as util
import matlab.engine
import pandas as pd
import numpy as np
import nibabel as nb
# sklearn
from sklearn.linear_model import Ridge, LogisticRegression, ElasticNet, ElasticNetCV # L2-regularized regression
from sklearn.model_select... |
13dbaed5008339cb8e391528d8accf42d20388fa23fbee218b5abc788aa93b6f | Python | 8,309 | 236 | import numpy as np
import matplotlib.pyplot as plt
import os
from scipy.stats import wilcoxon
from statsmodels.stats.multitest import multipletests
def PerformWilcoxonMotion(type_metric, motion, values_metrics, out_dir, save, option=False):
'''
Perfrom wilcoxon signed rank test on the motion metrics.
... |
e525bde98cba0fe1fdb899b9ab22c2d8263619fe8602d9826be63bc148f9f159 | Python | 8,309 | 246 | """
:mod:`alchemiscale.compute.client` --- client for interacting with compute API
==============================================================================
"""
import zstandard as zstd
from gufe import Transformation
from gufe.protocols import ProtocolDAGResult
from gufe.tokenization import GufeTokenizable
f... |
12b0c4c79c1c9c6fe772e916deb815d7554cab0b1e8b3882af3e04d6b0707c3f | Python | 8,322 | 150 | import tarfile
import requests
import argparse
import zipfile
import tqdm
import tempfile
import re
import shutil
import os
import glob
from gff_longest_transcript import find_longest_transcript
def download_file(url, dest=None, description=None, overwrite=False):
if description is None:
description = 'Dow... |
51f977ec42c59438f6b94f20bc5db50985a4dc779d1bc8a99a0b92fef7a73254 | Python | 8,330 | 246 | #!/usr/bin/env python
from svm import *
def svm_read_problem(data_file_name):
"""
svm_read_problem(data_file_name) -> [y, x]
Read LIBSVM-format data from data_file_name and return labels y
and data instances x.
"""
prob_y = []
prob_x = []
for line in open(data_file_name):
line = line.split(None, 1)
# In ... |
4b1d4d8eba7b386c1b0dcbaaba16b7b63d6b44ab82bd34829648aac856f4c2a8 | Python | 8,333 | 165 | import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
@torch.jit.script
def gaussian_analytical_kl(mu1, mu2, logsigma1, logsigma2):
return -0.5 + logsigma2 - logsigma1 + 0.5 * (logsigma1.exp() ** 2 + (mu1 - mu2) ** 2) / (logsigma2.exp() ** 2)
@torch.jit.script
def draw_gaussian_d... |
fba206c8335eb0af2fc81134688b9ed3ea4d3cac83f1860b61afd469c861423f | Python | 8,335 | 260 | # 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,... |
e3cee8c0e690980e41cc10532a8ebf197cf0fa983511fb901a69e4d1a8bba18e | Python | 8,338 | 149 | import logging
import os
from PySide6.QtWidgets import QWidget, QHBoxLayout, QVBoxLayout, QScrollArea, QLabel, QSpacerItem,\
QGridLayout, QTableWidget, QTableWidgetItem, QMenu
from PySide6.QtCore import QSize, Qt, Signal
from PySide6.QtGui import QAction
from utils.software_config import SoftwareConfigResources
c... |
aa58b90c606b4df6ec04135e09f6cb114d961b66e0e02bb97eeda0e9e1a7e022 | Python | 8,339 | 215 | #!/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.
# ------------------------------------------... |
8c55244ce0a919bdfbf8b5d16887007d522ea7997d64500602c1ed20fe01527e | Python | 8,342 | 220 | import random
import math
import sys
import numpy as np
class Ball:
def __init__(self):
self.speed = [0, 0] # x speed, y speed
self.position = [0, 0]
self.positionHistory = []
self.prediction = 0
self.size = 1
def move(self):
self.position[0]... |
dd2f87d35ef2181eb822f8fc0c9ed728f88c7faf7bb4b16fabafc74456a2a1a6 | Python | 8,343 | 221 | """Helper functions for submitting jobs on Stanford's Sherlock cluster."""
import subprocess
from os import getenv
def sbmit(*, o, e, J, path,
part='menon,normal,owners', a='0', c=1, mem_per_cpu='4G', t='1-0',args=None):
if getenv('SLURM_ARRAY_TASK_ID') is None:
if args is None:
p... |
4a8316a9f95bba65328b76448e8db3b44462cce2940d3b0c09413b27848ec600 | Python | 8,344 | 192 | import logging
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
from multiqc.plots import table
from multiqc.plots.table_object import TableConfig
log = logging.getLogger(__name__)
class MultiqcModule(BaseMultiqcModule):
"""
The module parses `summary.tsv` outputs from GTDB-Tk's `clas... |
533d5d2d9a10051db93e6a81bc9a1043e9ac6fa353a0efeba9bd704a6783af6e | Python | 8,345 | 240 | # 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,... |
e8979d1cabf5646ec27b61eda89e05cfbd4f050cda800ef8e7c37e6ae9d19823 | Python | 8,349 | 254 | #!/usr/bin/env python3
"""
You will likely have to customize this script slightly to accommodate your own data. All images
should be appropriately cropped and scaled to values between 0 and 1.
If an atlas file is provided with the --atlas flag, then scan-to-atlas training is performed.
Otherwise, registration will be ... |
2aa690aa8c84461b4e7825cc78bc3ffde816d0118b6f0d92cf095fec80057b4a | Python | 8,355 | 220 | import argparse
import os
from nipype.interfaces.spm import SliceTiming, Realign, Coregister, NewSegment
from nipype.interfaces.utility import IdentityInterface
from nipype.interfaces.io import SelectFiles, DataSink
from nipype.pipeline.engine import Workflow, Node
from nipype import MapNode
from nipype.algorithms.misc... |
aa387e30bd428adc80689b6461f7b219f8bafbd38bf0cac305b0478e77cb6c5b | Python | 8,357 | 223 | # -*- coding: utf-8 -*-
"""
Created on Fri Dec 16 15:20:28 2016
@author: david
"""
import os
import sys
import time
import subprocess
import fileinput
from collections import defaultdict, Counter
from . import util
from . import tree as tree_lib
from . import files, program_caller
def WriteGeneralOptions(filename, ... |
b0283a8466c25b26f98dc088566877c651c4051488aba40d446ff142ec6a2b5c | Python | 8,365 | 193 | """
# File : 01_Construct_dataset.py
# Time : 2025/10/23 8:54
# Author : Hongmiao Wang
# version : python 3.10
# Description:
"""
import os
import pandas as pd
from TemplateSearch.Embedding import GenerateSpec2vec
from MS2Tools.SpectrumFileReader import SpectrumFileReader
from Model_training.Train_e... |
d9b5674eb454243db7c47ee2b877cb52d8a472ee9bede5f1b074f404f6a6fba2 | Python | 8,374 | 206 | """
fingerprint/landscape.py — 8-Dimensional Method-Agnostic Landscape Descriptors
================================================================================
Pure AUROC-based landscape descriptors (no Brier dependency).
Dimensions d₁–d₈
-----------------
d₁ : baseline_dispersion — std of AUC across methods a... |
f76fcea0bdd41bf67671d7bfa63f98de49d6d3b8538b7ad80f22cf4d0788f8ad | Python | 8,375 | 241 | import datetime
from time import sleep
import pytest
from alchemiscale.compute import client
from alchemiscale.storage.models import (
ComputeManagerID,
ComputeManagerInstruction,
ComputeManagerStatus,
ComputeServiceID,
)
from alchemiscale.tests.integration.compute.utils import get_compute_settings_ov... |
a72ae956beeea53caccc25c0f62eebc9946e4ec61ac9f01b0942a4ef59e2114c | Python | 8,380 | 223 | """MultiQC submodule to parse output from GATK BaseRecalibrator"""
import logging
from collections import namedtuple
from itertools import groupby
from multiqc.modules.gatk.utils import parse_report
from multiqc.plots import linegraph, scatter
from multiqc.base_module import BaseMultiqcModule
# Initialise the logger... |
c0c374809b2df11934c1d6b8de36863ffbdd2ef91f4f44acb1a6fe0527071ead | Python | 8,385 | 198 | from __future__ import annotations
from dataclasses import dataclass
from typing import TypeVar
import networkx as nx
import torch
from hydra_zen import instantiate
from torch import Tensor, nn
from torch.nn import functional as F
from lightning import Callback
from beyond_backprop.configs.optimizer import AdamCo... |
36afb925ed57b38331359c8f292d343fda674663a820ad6f67b6f67153c9aa63 | Python | 8,411 | 253 | import os
import pydicom
import pandas as pd
import numpy as np
from pathlib import Path
from datetime import datetime
import warnings
warnings.filterwarnings('ignore')
def extract_patient_demographics(main_dir):
"""
Extract demographic information from DICOM files for all MS patients.
Args:
mai... |
3989ec5f5c231404c870205de0900dd16c380c1129f1b29e246e4905db055a43 | Python | 8,416 | 246 | '''Train the neuromuscular-inspired model on the Pong game.'''
from pathlib import Path
import sys
parent_dir = Path(__file__).resolve().parent.parent
sys.path.append(str(parent_dir))
import utils.ContinuousObjects as co
import utils.tools as tools
from utils.ContinuousEnvironment import Environment
from utils.Continu... |
3cae57d22e42f4c0ce00f792a4f6fbd786a148a5f5db4bfc61da30d611347ad7 | Python | 8,419 | 198 | """Théo Gauvrit, 15/09/2023
utility functions for input/output management
"""
import os
import numpy as np
import pandas as pd
import h5py
import matplotlib.pyplot as plt
from multiprocessing import Pool, cpu_count, pool
# import percephone.core.recording as pc
def read_info(folder_name, rois, detection=True):
"... |
e59629ca24b248d0846eb474375b08a8d8a99140852176fe96e9908721d1a938 | Python | 8,424 | 192 | #!/usr/bin/env python3
import argparse, subprocess, os, tempfile, shutil
from typing import Tuple
def explode(filename: str) -> Tuple[str, str, str]:
base, ext = os.path.splitext(filename)
directory, name = os.path.split(base)
return (directory, name, ext)
if __name__ == "__main__":
description = '... |
a175c2f2dfdf4c76d7ca8ebfe0342687f977ae51dcd4b956bd31da52a5069e10 | Python | 8,426 | 203 | """Per-experiment runner for the full-label ADNI utility experiments.
Same model and metrics as ``calcUtilityFull.py`` but takes the experiment
identifier as a CLI argument so the experiment grid can be sharded across
Slurm array tasks (one job per experiment). Useful when full-label
training pushes a single-process r... |
d2d0ee157752be8dfa5faadaf73c9501528380114f821d8d28633f721313e2b7 | Python | 8,435 | 257 | #!/usr/bin/env python
'''
(c) 2014 Brendan Bulik-Sullivan and Hilary Finucane
LDSC is a command line tool for estimating
1. LD Score
2. heritability / partitioned heritability
3. genetic covariance / correlation
'''
from __future__ import division, print_function
import ldscore.ldscore as ld
i... |
1b64358dc171ed569a78c65cf39d76c142edc143dd2c474c2566d4671de3115a | Python | 8,436 | 167 | import argparse
import numpy as np
import os
import pandas as pd
from matplotlib import pyplot as plt
import seaborn as sns
from scipy.stats import pearsonr
from analyses.decoding.searchlight.searchlight_permutation_testing import load_per_subject_scores, \
permutation_results_dir, add_searchlight_permutation_arg... |
426c6b731cf1073bd90a48ccdc511b1745154a2cb33407e3c90c7073e0f721ce | Python | 8,439 | 263 | # -*- coding: utf-8 -*-
"""
Created on Wed Sep 5 21:19:33 2018
@author: dvizard
"""
import numpy as np
import base64
# from bitstring import BitArray, BitStream, ConstBitStream
import os
import sys
# import smiles_config as sc
import sqlite3
# from sqlite3 import Error
import pickle
from warnings import warn
try:
... |
0e4423744d6297e015ea77f95a5c9c4d4536378871c5bd9d19ccc1507489af6f | Python | 8,444 | 218 | import time
from PySide6.QtWidgets import QWidget, QHBoxLayout, QPushButton, QLabel, QMessageBox
from PySide6.QtCore import Signal, QCoreApplication, QSize
from PySide6.QtGui import QIcon, QPixmap
import logging
import traceback
import sys
import os
import subprocess
import configparser
import threading
import shutil
i... |
a8bea5ddc65a89d92ef86ffaca08f8d306ff66454367d486ffa1ebccaf8c3571 | Python | 8,448 | 176 | """MONDO disease recognition evaluation cases from CRAFT corpus."""
from typing import Any, Dict
from aurelian.evaluators.model import MetadataDict, metadata
from aurelian.evaluators.knowledge_agent_evaluator import SimpleEntityEvaluator
from pydantic_evals import Case, Dataset
class MondoMetadata(Dict[str, Any]):
... |
7b7ff7042f78b2ce43301d165ec8ef6648e02f032ce039a4d758c4bc2ebe6156 | Python | 8,454 | 222 | """
# File : datasets.py
# Time : 2025/10/24 9:36
# Author : Hongmiao Wang
# version : python 3.10
# Description:
"""
import typing as T
import numpy as np
import torch
from Model.datasets.ProcessingFormula import generate_formula
from torch.utils.data.dataset import Dataset
from massspecgym.data.tr... |
a67e0ffab34decc2ca8e1511a7bb23a0d41770abcd458b16286c9981c2535497 | Python | 8,454 | 185 |
import os.path
import numpy as np
import pandas as pd
from MS2Tools.SpectrumFileReader import SpectrumFileReader
from Model.Prediction import Create_predictor
from Rerank.features import Feature_calculater
import lightgbm as lgb
from Model.datasets.smiles import SMILESStandarder
from rdkit import Chem
from collection... |
2a9ff448c737b08c48ea52b0f20062efabfc1efbd2966efff5e43246a0984599 | Python | 8,455 | 232 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
DeepMReye BIDS-compatible pipeline with subject-wise output structure:
- Predictions go in: /.../derivatives/sub-XX/sub-XX_run-YY_desc-predictions.csv
- Masks go in: /.../derivatives/sub-XX/masks/
- Global summary: /.../derivatives/model_error_summary.c... |
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