sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
bea4aac3426500881313db94b5ffeb76ead98d552eb334a8a2e48cd662deca72 | Python | 1,057 | 32 | """Scans the output files in jobs to check for jobs that ran with errors.
Prints the names of the files with errors.
"""
from os import listdir
import re
def natural_sort_key(s):
return [int(text) if text.isdigit() else text.lower()
for text in re.split('([0-9]+)', s)]
where = '/oak/stanford/grou... |
3e43f54b2c72b1939e6199345f3682b6047b640a322e24b91404a8403d371103 | Python | 1,062 | 27 | from pathlib import Path
import pytest
from pyroaring import BitMap
from src.bitmap_store import BitmapNotFoundError, load_bitmap, resolve_bitmap_path
def test_resolve_bitmap_path_uses_expected_filename(tmp_path: Path):
iri = "http://example.org/cluster/11111111-1111-1111-1111-111111111111"
bitmap_path = re... |
b459a3f33c6f17849263080820fe51974921a0e707e2b84844a9f266ec6fee5d | Python | 1,062 | 34 | from concurrent.futures import ThreadPoolExecutor
from time import sleep
from ethopy.core.interface import Interface
from ethopy.utils.timer import Timer
class PCPorts(Interface):
def __init__(self, **kwargs):
super(PCPorts, self).__init__(**kwargs)
import serial
self.thread = ThreadPool... |
c942104d5ee3f6b3f53bf2601bc78977b2478330d134f1f51fb075aebeadd1a9 | Python | 1,063 | 32 | import torch
from torch.utils.data import Dataset
class ConditionalDataset(Dataset):
"""
A Dataset object holding a tuple (x,y): observed and auxiliary variable
"""
def __init__(self, X, Y, device='cpu', S=None, latent_dim=None):
self.device = device
self.x = torch.from_numpy(X).to(dev... |
a96f3b3a4f884524962cc33e4475d607e3aa4b9439f400b9a31c99349601a229 | Python | 1,064 | 34 | import numpy as np
import os
from random import randint
import scipy
import random
def laserpositions(start, spacing, count):
laserlist = []
for i in range(count):
laserlist.append(start + i*spacing)
return laserlist
def passedlaser(ballposition_previous, ballposition_current, laserpositions):
... |
f73e1b24e1a2caf15978f43680253e75a9afa6786b95c0852e27823dcf5f85fe | Python | 1,064 | 44 |
'''
Hannah Eichhorn's code to calculate the metric Image Entropy.
The code is based on:
McGee K, Manduca A, Felmlee J et al. Image metric-based correction
(autocorrection) of motion effects: analysis of image metrics. J Magn Reson
Imaging. 2000; 11(2):174-181
'''
import numpy as np
from scipy.stats import entropy... |
d9f8c02bdbd9b5c0b57c41e1cd940e7b22ac553ec43bdadd497c7b38a0aae272 | Python | 1,065 | 34 | """add dataset field
Revision ID: 138d7bb32d76
Revises: b21763252fa1
Create Date: 2025-04-15 08:39:51.875991
"""
from typing import Sequence, Union
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision: str = '138d7bb32d76'
down_revision: Union[str, None] = 'b21763252fa1'... |
9b851790b6539cfb1d4a2b10ccd1621ccd4265c30af0dd4203df20e0e45ec767 | Python | 1,066 | 28 | import sys
from typing import List, Optional
from pip._internal.cli.main import main
def _wrapper(args=None):
# type: (Optional[List[str]]) -> int
"""Central wrapper for all old entrypoints.
Historically pip has had several entrypoints defined. Because of issues
arising from PATH, sys.path, multiple... |
fd811fe6045864b3d86b423b8865bf6e4f0f08e94585bed090f40d3b0c31c30e | Python | 1,066 | 36 | import sys
sys.path.append('/home3/ebrahim2/beyond-brainscore/generate_activations/')
from banded_reg_func import himalaya_regression_caller
import numpy as np
datasets = ['pereira', 'fedorenko', 'blank']
feature_extraction_arr = ['', '-mp', '-sp']
model_name = 'Llama-3.2-3B-Instruct'
data_folder = '/data/LLMs/data_p... |
9069302ed65bad1f435f686473241df79aa16dc53ec0ab0bd0f6042bc9f0d422 | Python | 1,067 | 34 | """add source dataset column
Revision ID: d631e27cf36f
Revises: ecabc2d4019f
Create Date: 2025-04-29 14:35:17.635341
"""
from typing import Sequence, Union
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision: str = 'd631e27cf36f'
down_revision: Union[str, None] = 'ecabc... |
a44797304c380bb5b5c836785772391043882c4cb810538da4918c04c8f24ee3 | Python | 1,067 | 32 | import pytest
from alchemiscale import Scope
from alchemiscale.compute.settings import ComputeServiceSettings
class TestComputeServiceSettings:
def test_validate_scopes(self):
orgs = ["testorg", "*"]
campaigns = ["testcompaign", "*"]
projects = ["testproject", "*"]
scopes = []
... |
8801bbeac2b7c4725aa819a07e784161db923f6892580cd2ea95771010fc14fb | Python | 1,070 | 38 | # -*- coding: utf-8 -*-
"""
Created on Mon Sep 18 14:07:52 2023
@author: ashwin.bhandiwad
"""
import numpy as np
import pandas as pd
import os
import SimpleITK as sitk
base_path = '../data/input/subcortical/CP_output/'
df = pd.read_table('../data/CP_anterograde_output.csv',delimiter=',')
cp_regions = np.unique(df['... |
faa83f931b1a655ef031e3cc657c3df70dadfe7bd6e090997d96dcbaea40174c | Python | 1,071 | 29 | from keras import Sequential
from keras.src.layers import Dense
from sklearn.preprocessing import LabelEncoder
from Evaluation_nrml import evaluation
def Model_ANN(Train_Data, Train_Target, Test_Data, Test_Target):
if len(Train_Target.shape) == 1:
encoder = LabelEncoder()
Train_Target = e... |
ab65e059cae8c069daac912e43c72ddbe695585ec8d6a4aa93714c31c06765bd | Python | 1,072 | 34 | #!/usr/bin/env python
from setuptools import setup, find_packages
with open("README.rst", "r") as fh:
long_description = fh.read()
with open('requirements.txt', 'r') as fp:
install_requires = fp.read().splitlines()
install_requires = [i for i in install_requires if 'http' not in i]
setup(
name=... |
61854937da7e2a0be34f323298802a37ca99b0f82de4b0d409e2d5244a6c9467 | Python | 1,078 | 31 | from __future__ import print_function
import argparse
import itertools
import gzip
from utility import reverseComplement, fq
def mergeReads(fastq1_filename, fastq2_filename, out):
fastq1_file = fq(fastq1_filename)
fastq2_file = fq(fastq2_filename)
with gzip.open(out, 'wb') as o:
for r1, r2 in iter... |
4afe4c7c21dffc7fc04e89bfa1def712296e74af752dd9c99f6eb7fc7ad84ddf | Python | 1,080 | 28 | import keras
from TorchCRF import CRF
from keras import Input
from keras.src.layers import Bidirectional, LSTM, Dense
from Evaluation_nrml import evaluation
def Model_ADeepCRF(Train_Data, Train_Target, Test_Data, Test_Target,sol=None):
if sol is None:
sol = [5,0.01,100]
num_classes = Train_Tar... |
551ed5dcb5bb78d683636f7998c0e3e8dde9897556e4b5cef5eabd5bca38767c | Python | 1,081 | 28 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
from openff.toolkit import GLOBAL_TOOLKIT_REGISTRY, OpenEyeToolkitWrapper
from openff.toolkit.utils.toolkit_registry import ToolkitUnavailableException
from contextlib import contextmanager
... |
815b25fbc6f1966b9adc6fcde5fc7526a1982b88391aec9202f0644425e6073f | Python | 1,082 | 41 | import config, logging
if config.TESTING_MODE:
from dummy import DAQIn, DAQOut, Trigger, SICommunicator
elif not config.TESTING_MODE:
try:
from ni845x import NI845x
except:
NI845x = None
class SICommunicator():
def __init__(self, on=True):
self.on = on
... |
5176bca266ebb85ca77103fd48587357e1d005a734ab6120a8295bf827147f76 | Python | 1,086 | 31 | '''Plot histogram of performance counting the hit rate of each indiviudal parameter combination'''
import numpy as np
import matplotlib.pyplot as plt
from scipy.interpolate import make_interp_spline
import matplotlib.ticker as ticker
plt.rcParams.update({'font.size': 25})
plt.rcParams['font.weight'] = 'bold'
# === L... |
888778ddbcbe0abdb3d2df4c352bb02974ff9552f2eb86637bacb34c5b49e689 | Python | 1,087 | 37 | """
:mod:`alchemiscale.migrations.v03_to_v04` --- migration for v0.3 to v0.4
========================================================================
"""
from ..storage.subgraph import Subgraph, merge_subgraph, record_data_to_node
from ..storage.statestore import Neo4jStore
def migrate(n4js: Neo4jStore):
"""Mig... |
eff8bb9e13c9f427a54813a2faafa611a29cd2f5851392f86447080e3ace7dc2 | Python | 1,089 | 32 | #!/usr/bin/env python
"""
Takes as arguments:
1. the path to a JSON file (such as an IPython notebook).
2. the path to output file
If 'metadata' dict in the JSON file contains 'include_in_docs': true,
then copies the file to output file, appending the 'metadata' property
as YAML front-matter, adding the field 'categor... |
3db4736473603b870aa3f0c8b47128a2c3b5ed15654b76288d2c45e2cbaf5d30 | Python | 1,092 | 35 | import pandas as pd
import tensorflow as tf
Nucleosome_data_new = pd.read_csv(
"/g/korbel/Costea/Computational/StrandSeq/P6_Ini/PDX1609p6Ini/scNOVA_result/Features_reshape_all_orientation_norm_var_GC_CpG_RT_T_comb3_clone1.txt",
delimiter="\t",
header=None,
)
TSS_matrix_new = pd.read_csv(
"/g/korbel/Co... |
6ac32b69954f234b27c9ee34e06ced1295e029eae3d72005999976a7778de018 | Python | 1,092 | 34 | import urllib.parse
class PackageIndex:
"""Represents a Package Index and provides easier access to endpoints
"""
__slots__ = ['url', 'netloc', 'simple_url', 'pypi_url',
'file_storage_domain']
def __init__(self, url, file_storage_domain):
# type: (str, str) -> None
s... |
ce23f6437f5173808007d04618c7c68220fa840fcc1deb38d1b43a5649bf5612 | Python | 1,092 | 38 | import sys
sys.path.append('/home3/ebrahim2/beyond-brainscore/generate_activations/')
from banded_reg_func import himalaya_regression_caller
import numpy as np
datasets = ['pereira']
feature_extraction_arr = ['', '-mp', '-sp']
data_folder = '/data/LLMs/data_processed'
device = 2
for d in datasets:
if d == '... |
22a8290ddd457e40f088cd10137495072d530281c505f3a175a29254cb169c65 | Python | 1,093 | 35 | """add new idx
Revision ID: 7b1e0ef203f0
Revises: b93befa5f8b0
Create Date: 2025-06-03 14:52:20.591396
"""
from typing import Sequence, Union
from alembic import op
import sqlalchemy as sa
import truesight
# revision identifiers, used by Alembic.
revision: str = '7b1e0ef203f0'
down_revision: Union[str, None] = 'b9... |
576df686ac79a82a6404357167313a5d3d37ed5f13720cd5dc2e3f1c107ad80a | Python | 1,093 | 45 | import openmm
import pytest
from openff.toolkit import Molecule
from yammbs._forcefields import _espaloma, _gaff, _smirnoff
@pytest.fixture
def molecule():
return Molecule.from_smiles("CCO")
def test_smirnoff_basic(molecule):
system = _smirnoff(molecule, "openff-2.1.0.offxml")
assert isinstance(system... |
8e28935da992a1c177bd9a063efad946e9132ed87b289690d87dbde756be54f0 | Python | 1,093 | 33 | import pytest
from sl.datasets.services import generate_raw_dataset, NumsDatasetPromptSet
from sl.llm.data_models import Model, SampleCfg
from sl.datasets.data_models import DatasetRow
@pytest.mark.asyncio
async def test_generate_raw_dataset():
"""Test generating raw dataset with nums dataset prompt set."""
m... |
86a2d85d005071fe3bfd5acebec565de044ea3190a238091063e3a5324c6e082 | Python | 1,094 | 43 | import numpy as np
try:
import _pickle as pickle
except ImportError:
import cPickle as pickle
def leakyReLU( vec, beta=0.2):
output = []
for j in vec:
if j>0: output.append(j)
else: output.append(beta*j)
return np.array(output)
class FeedForwardNetwork(object):
def __init__(s... |
d1960e9ad5aa68ab4250b621fd32076748d15f12e556ba04fce82f10ef2c10a0 | Python | 1,094 | 32 | #!/usr/bin/env python
"""
Retains calls that overlap with a call after filtering and merging.
That is, output all calls in the input sets that are present in the
provided merged set.
"""
import sys
from argparse import ArgumentParser
import pandas as pd
def main():
parser = ArgumentParser(prog='apply_filter.py', d... |
f671c37471104e3d84d86b344f85ecf078eead658ad0cfef5f8a97cf55b178ab | Python | 1,094 | 34 | """add response fields
Revision ID: 03e8e374a89d
Revises: abf722fad99d
Create Date: 2025-04-12 22:10:34.584764
"""
from typing import Sequence, Union
from alembic import op
import sqlalchemy as sa
from sqlalchemy.dialects import postgresql
# revision identifiers, used by Alembic.
revision: str = '03e8e374a89d'
down... |
32dd88db20c4f336b78fbaec37713e9c5ff9480d670ddcce5c8d92676d484b2e | Python | 1,095 | 36 | #!/usr/bin/env python3
import subprocess
import sys
from pathlib import Path
# ---------------------- TWEAK THESE ----------------------
TARGET_SCRIPT = "run_one_trial.py"
PREFIX = "uf20"
INSTANCE = 2
THLD_DELTA = "0.001"
MAX_ITER = 50000 # e.g., 5000, or keep None to use default formula inside the script
... |
7da95e6b44bbe3a024af11016fbeb681ad4ac42322f5aac33542ee617bca4579 | Python | 1,096 | 36 | #!/usr/bin/env python3
import argparse
import os
def main():
parser = argparse.ArgumentParser(description='Split SDF to MOL files with molecule names.')
parser.add_argument('-i', '--input', metavar='FILENAME', required=True,
help='input SDF file with molecule names.')
parser.add_... |
5fe7ed69cb73df04b660ee3880964b3e0c44d90d5896f5d9903659bc2097d568 | Python | 1,097 | 27 | from gufe import Transformation
from ..chemicalsystem_generator.component_checks import proteinC_in_chem_sys, solventC_in_chem_sys, ligandC_in_chem_sys
def both_states_proteinC_edge(edge: Transformation) -> bool:
return proteinC_in_chem_sys(edge.stateA) and proteinC_in_chem_sys(edge.stateB)
def both_states_sol... |
706ef130564e66dd8a60bf612bd2def2b97fdc7fb3d13185751346d2f2e43c6b | Python | 1,099 | 36 | # Copyright 2017 Google Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,... |
5f5af57d1d800bc8bf33d297f214fd334777e7f151246f2eb71aa971d338e936 | Python | 1,100 | 39 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""Settings classes for RFE Protocols using OpenMM + OpenMMTools
This module implements the necessary settings necessary to run the following:
* HybridTopProtocol
See Also
--------
ponti... |
5158a87667b9ecc18d46659640fe4416d0aff18c4ba884e78aedacf54883b6cb | Python | 1,104 | 35 | """Build inclusion criteria for control models.
There is 1 inclusion criterion: SSRT >= 0 for all trials.
"""
import sys
from pathlib import Path
import numpy as np
import pandas as pd
from tqdm import tqdm
sys.path.append(str([p for p in Path(__file__).resolve().parents if p.name=='scripts'][0]))
from paths import... |
5982ccc6ec6a3776a1253424d8c23d85d999281a45cb11de36951d3b43f26f15 | Python | 1,106 | 38 | import logging
import os
from typing import Optional
from pip._vendor.pep517.wrappers import Pep517HookCaller
from pip._internal.utils.subprocess import runner_with_spinner_message
logger = logging.getLogger(__name__)
def build_wheel_pep517(
name, # type: str
backend, # type: Pep517HookCaller
metadat... |
5a084ec70baa86fd38e9df0d724efebc34eb020c0a58e0ef951d81f1148a208a | Python | 1,106 | 40 | import pytest
import os
if os.getenv("GITHUB_ACTIONS") == "true":
pytest.skip("Skipping in GitHub Actions", allow_module_level=True)
from aurelian.agents.amigo.amigo_config import AmiGODependencies
from aurelian.agents.amigo.amigo_agent import amigo_agent
from oaklib import get_adapter
def test_pmid():
"""
... |
d03d6f7cc7b3179dbd5f015102811b5b6eea5be6cf65b5c04c814f61aa0b933c | Python | 1,106 | 38 | #!/usr/bin/env python
from __future__ import print_function
from builtins import zip
import os, sys
fin = open(sys.argv[1]).readlines()
template = open(sys.argv[2]).readlines()
def determine_format_string(numstr): # Returns something like "% 8.3f"
spl = numstr.split('.')
if len(spl) != 2:
return Exce... |
0c11eb1e6bfee3604cfaa651e42702302e469e4c3e6c76ec8c4e87ae63e447ed | Python | 1,107 | 32 | import pytest
import os
if os.getenv("GITHUB_ACTIONS") == "true":
pytest.skip("Skipping in GitHub Actions", allow_module_level=True)
from aurelian.agents.ontology_mapper.ontology_mapper_agent import OntologyMapperDependencies, ontology_mapper_agent
@pytest.fixture
def deps() -> OntologyMapperDependencies:
re... |
c09d4afa8d69233b1b373dcd188dacf4cafcfcc31736e5f9091a582b373f9725 | Python | 1,107 | 45 | import asyncio
from safetytooling.apis.inference.api import InferenceAPI
from safetytooling.data_models import LLMResponse, Prompt
from truesight import config, fn_utils
_INFERENCE_API = None
def get_inference_api() -> InferenceAPI:
global _INFERENCE_API
if _INFERENCE_API is None:
_INFERENCE_API = I... |
74be29b12c9eb6da017b43312eef3ba38e71f3fb9998689d611ef1727fb6b37c | Python | 1,108 | 24 | # manipulations refers to any perturbation condition that is specified for this particular behavioural training session, and is intended to be implemented by the software
# for example: optogenetic stimulation, imaging patterns, etc.
# a manipulation is either a single manip constant, or a list thereof with probabiliti... |
afee0c53099879b7bd8a8df40d42d800faa4cf6e77c10643328a3222812b3bc2 | Python | 1,108 | 36 | """Report sex assigned at birth of participants."""
import sys
from pathlib import Path
import pandas as pd
sys.path.append(str([p for p in Path(__file__).resolve().parents if p.name=='scripts'][0]))
from paths import DATA_SL_DIR
ABCD_TABULATED = Path('/oak/stanford/groups/menon/rawdata/public_BIDS/ABCD/5.1-tabulate... |
a1b62c9eb945a77e1b9b6f2b4fc5dc768fc170f001f326e999bd521841b563d5 | Python | 1,109 | 34 | import setuptools
import mripy
from os import path
setup_dir = path.dirname(path.realpath(__file__))
with open(f'{setup_dir}/README.rst', 'r') as f:
long_description = f.read()
setuptools.setup(
name='mripy',
version=mripy.__version__,
author='herrlich10',
author_email='herrlich10@gmail.com',
descr... |
b98c99d48e391b7f2091a3c27882768903d4e9900a8466e13b9820be1cdf6fc0 | Python | 1,109 | 37 | from fastapi import APIRouter, Depends, HTTPException, Request
from graph_query_service.cluster_metadata.models import (
GraphQueryRequest,
GraphQueryResponse,
)
from graph_query_service.neo4j.client import GraphQueryExecutionError, GraphQueryServiceProtocol
router = APIRouter()
def get_graph_service(reque... |
99e86a02d765aeeab9a82b8ac31d3838ef199feded96415c23d381d652a9673b | Python | 1,110 | 38 | """Registry for all remotely-stored CLI test data."""
import pooch
POOCH_CACHE = pooch.os_cache("openfe")
zenodo_cmet_data = dict(
base_url="doi:10.5281/zenodo.15200083/",
fname="cmet_results.tar.gz",
known_hash="md5:a4ca67a907f744c696b09660dc1eb8ec",
)
zenodo_rbfe_serial_data = dict(
base_url="doi:10... |
d7474ae8c036f048ffe14ea4daa8a92751f3ec75d632cfca73e275e1d8716155 | Python | 1,112 | 38 | '''
Author: Clara Vetter
Last changed: 02.09.2022
This script is called by nk_GetTestPerf_GRDBST.m and computes the test
performance of a gradient boosting classification model on the test sample.
Input from MATLAB:
- model_name = path to file containing the model's information from
training
- test_f... |
1a6a63f326beeaf6a23135343d8626cab7604fe9d798264d73ba9efff6268c7f | Python | 1,113 | 44 | """
MS3SEG Model Architectures
Collection of deep learning models for MS lesion segmentation
"""
from .unet import build_unet
from .unet_plusplus import build_unet_plusplus
from .unetr import build_unetr
from .swin_unetr import build_swin_unetr
__all__ = [
'build_unet',
'build_unet_plusplus',
'build_unetr... |
9c1c8166795beee1a20c82f915e734ff6b4fb2c4303c6c8cb412db80831d54bf | Python | 1,117 | 32 | # -*- coding: utf-8 -*-
"""
Created on Wed Mar 29 09:45:52 2023
@author: ashwin.bhandiwad
"""
import pandas as pd
import numpy as np
path = '../data/'
df = pd.read_csv(path+'Harris_ctx_anterograde_volumes.csv')
quant = pd.read_csv(path+'cp_anterograde_projections.csv')
not_quantified = df[~df['image id'].isin(quan... |
267651005764edef36bff117cc7a17e32e510f2a42b088b6f56f349f908fe1d2 | Python | 1,118 | 35 | from itertools import chain
from multiqc.plots import linegraph
def plot_basic_hist(samples, file_type, **plot_args):
"""Create line graph plot for basic histogram data for 'file_type'.
The 'samples' parameter could be from the bbmap mod_data dictionary:
samples = bbmap.MultiqcModule.mod_data[file_type]... |
a86c0f4fd6a4aae93ad6351858f7e25e038c3a7c6a64c891106ffdcae850132f | Python | 1,118 | 39 | """
Authors: Zheng Wang, John Griffiths, Andrew Clappison, Hussain Ather, Kevin Kadak
Neural Mass Model fitting
module for cost calculation
"""
import numpy as np # for numerical operations
import torch
from ..datatypes import Parameter as par
from ..datatypes import AbstractLoss
from .cost_TS import CostsTS
from ..... |
1c3a323caffbf61821f8cf826bfe1b3d7ebd02d4ab8f56c43a06fa7b561dc690 | Python | 1,120 | 34 | import sys
import pytest
has_openff_toolkit = True
try:
import openff.toolkit
except ModuleNotFoundError:
has_openff_toolkit = False
from .test_system import skip_openff_py39
@skip_openff_py39
@pytest.mark.skipif(
not has_openff_toolkit, reason="openff.toolkit module not found"
)
def test_smirnoff_hack(... |
2677c8489bf5e677625b87409215e681902c310d1ea9429137da25b34d5f621a | Python | 1,121 | 40 | from sqlalchemy import select, update
from truesight.db.models import DbTestModel
from truesight.db.session import get_session, get_async_session
import pytest
def test_read():
with get_session() as session:
count = session.query(DbTestModel).count()
print(count)
def test_write():
with get_sessi... |
ced61def2da1434d5fed47b04dc563dcec0853f76f0b87a82f98c5084ee16d22 | Python | 1,122 | 35 | import pytest
import os
if os.getenv("GITHUB_ACTIONS") == "true":
pytest.skip("Skipping in GitHub Actions", allow_module_level=True)
from aurelian.agents.literature.literature_config import LiteratureDependencies
from aurelian.agents.literature.literature_agent import literature_agent
@pytest.fixture
def deps()... |
6e61f2ee14e27cfff602c36aa85089e5a0b622a3738667255994e483e74a6b7a | Python | 1,126 | 35 | import sys
from banded_reg_func import himalaya_regression_caller
datasets = ['pereria']
models = ['glove-mp_positional+WN', 'glove-sp_positional+WN']
shuffled_options = [False]
save_y_hat = True
data_folder = '/data/LLMs/data_processed'
device = 1
for d in datasets:
for m in models:
for sh... |
111bb063f65b84c733af5ede82da5c9fc03e5ecedf64d90ab1ecefec184ff050 | Python | 1,127 | 38 | '''
Author: Clara Vetter
Last changed: 02.09.2022
This script is called by nk_GetTestPerf_RNDFOR.m and computes the test
performance of a random forest regression model on the test sample.
Input from MATLAB:
- model_name = path to file containing the model's information from
training
- test_feat = th... |
862d77ee98dd8e39ea9c464d7d972c886e6e4386554ce3a89085a91ef05e93c9 | Python | 1,127 | 32 | """
src/viz — Visualization Layer
===================================
Generates publication-quality figures (DPI=600, PDF format).
MDPI Bioengineering style: 10pt main / 8pt secondary, ≤18.46cm, Arial.
All modules import style from viz.mdpi_style.
"""
from .curves import plot_degradation_curves, plot_label_efficiency... |
89558728a8a9f7c265c28a87c1c1b0da56326217e0e35fcfd11b17786b5a0f68 | Python | 1,127 | 39 | import json
from pathlib import Path
from graph_query_service.cluster_metadata.normalizer import (
annotation_value,
property_map,
synonym_columns,
)
def load_fixture(name: str) -> dict:
fixture_path = Path(__file__).parent / "fixtures" / name
return json.loads(fixture_path.read_text())
def tes... |
31776c1a9484fd6f99ac7a02f3b6a7748e0b576140c14ec72cbf9e1defc28e15 | Python | 1,128 | 38 | # This file is dual licensed under the terms of the Apache License, Version
# 2.0, and the BSD License. See the LICENSE file in the root of this repository
# for complete details.
from __future__ import absolute_import, division, print_function
import sys
from ._typing import TYPE_CHECKING
if TYPE_CHECKING: # pragm... |
4f6545dc229f5ff8fd07d1fec6688e1ad6075b2c1fbbedaab96662221306eae3 | Python | 1,131 | 39 | """add provider
Revision ID: 293d61225fe9
Revises: 236e91cf74cf
Create Date: 2025-05-15 14:50:41.244674
"""
from typing import Sequence, Union
from alembic import op
import sqlalchemy as sa
import truesight
# revision identifiers, used by Alembic.
revision: str = '293d61225fe9'
down_revision: Union[str, None] = '2... |
7284369dcc45cddd6ea7375da1f70c802d6c2c864569c1bb4c5a80fbf92ca320 | Python | 1,132 | 37 | # 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,... |
85c3610af29b284783b534fe7c2638727f6ea6b8677eabb1f71df7235b8d039c | Python | 1,132 | 41 | """Generate the code reference pages and navigation."""
from pathlib import Path
import mkdocs_gen_files
nav = mkdocs_gen_files.Nav()
root = Path(__file__).parent.parent
src = root / "src"
for path in sorted(src.rglob("*.py")):
print(path, nav)
module_path = path.relative_to(src).with_suffix("")
doc_pa... |
1dc72b4816b7484db6419f1c7d6732fb4bbe3ac995495b39b7cc1342a717cd04 | Python | 1,133 | 31 | """Unit tests for evaluation and interpretation modules."""
import pytest
from timeflies.evaluation.metrics import EvaluationMetrics
@pytest.mark.unit
class TestSHAPInterpreter:
"""Test SHAP interpretation functionality."""
def test_shap_config_validation(self, aging_config):
"""Test SHAP configura... |
be50dbdf2f83ee270dc76db83b2f3f4f9e9d1e1c8d8ba6236f6503fdc9bd1073 | Python | 1,136 | 34 | """HPO phenotypic feature recognition evaluation cases."""
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 HpoMetadata(Dict[str, Any]):
"""Metad... |
cf95f1c01a94ec50d9bfebac8d4abd11506f0381704ab5d08d52e783d5290b37 | Python | 1,139 | 27 | from typing import Type
from nnunetv2.preprocessing.normalization.default_normalization_schemes import CTNormalization, NoNormalization, \
ZScoreNormalization, RescaleTo01Normalization, RGBTo01Normalization, ImageNormalization, \
T1wPVSNormalization, NLMFNormalization, AHENormalization
channel_name_to_normali... |
54d5d3484697d0638ba69938bd66e850382200b33858bc010d0cb8952c99502c | Python | 1,140 | 28 | import keras
from keras import Input
from keras.src.layers import Dense
from sklearn.preprocessing import StandardScaler
from Evaluation_nrml import evaluation
def Model_ANFIS(X_train, X_test, y_train, y_test):
# Normalize the data
scaler = StandardScaler()
X_train = scaler.fit_transform(X_train)
... |
df5e31f0995485d4aa4c7c41e0e172849b487b24500ec63e9903fc135b364c27 | Python | 1,140 | 37 | import importlib.util
from typing import TypeVar
T = TypeVar("T")
def get_obj(module_path: str, obj_name: str):
"""
Load a configuration instance from a Python module.
Args:
module_path: Path to the Python module file
cfg_var_name: Name of the variable to load from the module
exp... |
32e1361066cb63019eef950f68d6e0c344f70334ece6913ee03ac2beb15e1a88 | Python | 1,142 | 37 | """make slug unique
Revision ID: 757d22bc8ecc
Revises: fd0ebbbd40ad
Create Date: 2025-05-06 16:51:47.525867
"""
from typing import Sequence, Union
from alembic import op
import sqlalchemy as sa
import truesight
# revision identifiers, used by Alembic.
revision: str = '757d22bc8ecc'
down_revision: Union[str, None] ... |
67c6233411af344d7a49f725a098d1e8254ec4928039239b3831c01e0148bfb7 | Python | 1,142 | 35 | import os as _os
import numpy as _np
import subprocess as _subprocess
__all__ = ['head']
def head(file_name, n_lines=20, print_out=True, line_nums=False):
"""Get the first n_lines lines of a file. Print if print_out=True, else return as list. Works on UNIX systems"""
assert type(n_lines) == int
n_lines ... |
cb9aa2cd176054edcf2ffad7987b36bd51813279f872fa2c2c0b3dd1034add34 | Python | 1,142 | 38 | import sys
sys.path.append('/home3/ebrahim2/beyond-brainscore/generate_activations/')
from banded_reg_func import himalaya_regression_caller
import numpy as np
datasets = ['pereira']
feature_extraction_arr = ['', '-mp', '-sp']
data_folder = '/data/LLMs/data_processed'
device = 2
save_y_hat = True
for d in datasets:
... |
313c5846002272049fd878824fa40cd5d8cf38ba6d4a8c4a4420a11b4147606b | Python | 1,146 | 39 | """
Plots pertaining to the network.
"""
import os
import numpy as np
def phase_space(csvi, npz_data: os.PathLike='data.R.npz'):
import pylab as pl
opt = len(csvi['x']) == 1
npz = np.load(npz_data)
tr = lambda A: np.transpose(A, (0, 2, 1))
x, z = tr(csvi['x']), tr(csvi['z'])
tau0 = npz['tau0... |
81f2613cf6662fd3ee1cb22635e3037e83a883f4eeb456ebd3477973605ea191 | Python | 1,146 | 48 | #!/usr/bin/env python
from __future__ import print_function
from builtins import range
from sys import argv
from numpy import *
file1 = open(argv[1]).readlines()
file2 = open(argv[2]).readlines()
file3 = open(argv[3],'w')
if len(argv) != 4:
print("Usage: cubediff.py CUBE1 CUBE2 CUBEOUT")
switch = 0
for linenum ... |
07cbf96ea6929afc373b85efc023a3b7af850f95fc78f1907158be13c003a537 | Python | 1,147 | 33 | import os
import pickle
import numpy as np
import pandas as pd
#import eigenvalue calculator
from skimpytools.stability import CheckStability
exp_id = 'fdp1' #<-- Choose 1 of 4 physiologies (fdp1-fdp4)
# Load parameter set (must be .npy)
path_to_GAN_generated_parameters = f'gan_output/{exp_id}/repeat_0/0_r.npy'
GAN_g... |
0e1974753184388f391789be67a3732be4fefad0ab2106c890e9b85c6a0029f1 | Python | 1,148 | 34 | """drop source_dataset_id column
Revision ID: d168818d8317
Revises: a548acf2790a
Create Date: 2025-05-01 11:47:20.257573
"""
from typing import Sequence, Union
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision: str = 'd168818d8317'
down_revision: Union[str, None] = 'a... |
a9f8c32768cb0747e3741470927ed45f23d56f9b6f1619da03cca188aa062f4f | Python | 1,148 | 35 | #%%
from pathlib import Path
import matplotlib.pyplot as plt
import seaborn as sns
import pandas as pd
#%%
import kimmdy_paper_theme
plot_colors = kimmdy_paper_theme.auto_init()
width = kimmdy_paper_theme.double_column
#%%
cwd = Path("/hits/fast/mbm/hartmaec/workdir/collagen_HAT/paper-figures/")
plot_dir = cwd / "pl... |
e8c9f3ada93f8fec84de9b030aa8b61b121226a219274e0339b294f50867c4c1 | Python | 1,149 | 42 | from optparse import Values
from typing import List
from pip._internal.cli.base_command import Command
from pip._internal.cli.status_codes import SUCCESS
from pip._internal.exceptions import CommandError
class HelpCommand(Command):
"""Show help for commands"""
usage = """
%prog <command>"""
ignore... |
264c7a81b0d3eb9d6a0485c78b275614b8452b1159fa4d6d7e07ac7fb0168625 | Python | 1,150 | 41 | # Retinotopic mapping experiment
from ethopy.behaviors.head_fixed import HeadFixed
from ethopy.experiments.passive import Experiment
from ethopy.stimuli.bar import Bar
# define session parameters
session_params = {
'setup_conf_idx': 0,
}
exp = Experiment()
exp.setup(logger, HeadFixed, session_params)
# define st... |
66d5ef9b7f320b71ace3af2cffeb0ff15af91c392d60bef48ea53c8ff8d1d745 | Python | 1,150 | 45 | import numpy as np
# pylint:disable='import-error'
from nemsi.visual import add_to_plotter
# Load the cells
tc_cells = np.load("val_vm_placement.npy")
rt_cells = np.load("rt_placement.npy")
pre_ids = np.load("pre_ids.npy")
pre_scalars = np.copy(pre_ids).astype(float)
post_ids = np.load("post_ids.npy")
post_scalars =... |
93a5255fe293e936f5d7033a813e1d5586d43499db263a6f72431061083e02ec | Python | 1,150 | 37 | #!/usr/bin/env python
"""
Example script to generate a sample MCP configuration file using the config generator.
"""
import os
import json
from pathlib import Path
from config_generator import MCPConfigGenerator
# Define the base directory for Aurelian
aurelian_dir = Path(os.path.dirname(os.path.dirname(os.path.dirna... |
dce7f28040017a2e5400aeaec6084ca76ecb44e1d94be0d2347f6f410e7bc4eb | Python | 1,151 | 34 | import pathlib
import os
import pandas as pd
import numpy as np
import regex as re
import numpy as np
import random
import cv2
if not os.path.exists('dynamic_threshold_adaptivecutted_tif'):
os.makedirs('dynamic_threshold_adaptivecutted_tif')
SFT_png = pathlib.Path('cutted_tif')
def sort_by_number... |
fc459b10e542f58a5331cb64f808379e1f15c4b4649c92ec4f4057ff26fc8abc | Python | 1,153 | 32 | import pandas as pd
import pathlib
csv_names = [
"pymbar3_edge_data.csv",
"pymbar3_calculated_dg_data.csv",
"pymbar3_cumulative_data.csv",
"pymbar4_edge_data.csv"
]
# map the folder to the dataset
folder_to_dataset = {}
for csv_type in csv_names:
files = []
for f in pathlib.Path("public_datas... |
07da405e7ebf27550acf04cbf6716d4693a1360f2ce6f1928b86ea9f1e3e95a0 | Python | 1,154 | 35 | # Copyright 2016 Julien Danjou
# Copyright 2016 Joshua Harlow
# Copyright 2013-2014 Ray Holder
#
# 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
#... |
8862664afb7a3a1f22fb6b56a3be51ea977bae8393e2e40ae6870c7270b3cd53 | Python | 1,154 | 35 | """add new idx
Revision ID: cfe33bf1ce7e
Revises: b2132a59956f
Create Date: 2025-06-03 14:47:10.923201
"""
from typing import Sequence, Union
from alembic import op
import sqlalchemy as sa
import truesight
# revision identifiers, used by Alembic.
revision: str = 'cfe33bf1ce7e'
down_revision: Union[str, None] = 'b2... |
2449929a6aaa2f26b0f0fe75814226661f06c20f62d7349ef83a2a022b67da77 | Python | 1,155 | 49 | from __future__ import absolute_import
# For backwards compatibility, provide imports that used to be here.
from .connection import is_connection_dropped
from .request import SKIP_HEADER, SKIPPABLE_HEADERS, make_headers
from .response import is_fp_closed
from .retry import Retry
from .ssl_ import (
ALPN_PROTOCOLS,... |
f36fae0433dc03bd3e4a2cb42dfb61f3c52a8236c247c2f3bb69dfd63d4905e9 | Python | 1,155 | 48 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""
Restraint Geometry classes
TODO
----
* Add relevant duecredit entries.
"""
import abc
from pydantic import BaseModel, ConfigDict, field_validator
class BaseRestraintGeometry(BaseModel... |
87ed5532fde900c58da45e9a0ecc74d9f8679653eab2760f7c866a6ddde0c73f | Python | 1,156 | 44 | """
Centralized version management for MosaiCatcher pipeline.
This module provides utilities to read the pipeline version from the centralized VERSION file.
"""
import os
from pathlib import Path
def get_version():
"""
Read the pipeline version from the VERSION file at the repository root.
Returns:
... |
2866d4fafb7b9801ea555e0d2969f1713be6fa184fdb748c588e2cd34ee74c25 | Python | 1,159 | 43 | #!/usr/bin/env python3
import shutil
from os import path
from openff.evaluator.backends import ComputeResources
from openff.evaluator.backends.dask import DaskLocalCluster
from openff.evaluator.server import EvaluatorServer
from openff.evaluator.utils import setup_timestamp_logging
def main():
# Set up logging ... |
058cdc282a9e1228b9db10eba8116bba19e6b66922b875c5c8587e720950f269 | Python | 1,160 | 35 | """
HTML parsing library based on the `WHATWG HTML specification
<https://whatwg.org/html>`_. The parser is designed to be compatible with
existing HTML found in the wild and implements well-defined error recovery that
is largely compatible with modern desktop web browsers.
Example usage::
from pip._vendor import... |
e6a5e73c24739adfc8535899ec765c385f46e3369868bdeeff02028266d4583a | Python | 1,161 | 42 | # This code is part of kartograf and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/kartograf
import abc
import logging
import numpy as np
from gufe.mapping import AtomMapping
logger = logging.getLogger(__name__)
eukli = lambda x, y: np.sqrt(np.sum(np.square(y - x)))
rms_fun... |
023af6a096e5ac601bdd90d098d78ef45e16e0d1434f8f85a738ba246de370a1 | Python | 1,162 | 39 | from importlib import resources
import pytest
import click
import openfe
from openfecli.parameters.mol import get_molecule
from openfe import SmallMoleculeComponent
def test_get_molecule_smiles():
mol = get_molecule("CC")
assert isinstance(mol, SmallMoleculeComponent)
assert mol.name == ""
assert mo... |
dd9cdca639fa44916f0db185e75b4e54946a90feb44c8042deb54c8fa4413717 | Python | 1,162 | 35 | # -*- coding: utf-8 -*-
"""
.. module:: skimpy
:platform: Unix, Windows
:synopsis: Simple Kinetic Models in Python
.. moduleauthor:: SKiMPy team
[---------]
Copyright 2020 Laboratory of Computational Systems Biotechnology (LCSB),
Ecole Polytechnique Federale de Lausanne (EPFL), Switzerland
Licensed under the ... |
a76889e5ca1641a2d761881110c6898db4530a98be418a76d6bed26e8ae8a216 | Python | 1,163 | 48 | # silence pymbar logging warnings
import logging
def _mute_timeseries(record):
return not "Warning on use of the timeseries module:" in record.msg
def _mute_jax(record):
return not "****** PyMBAR will use 64-bit JAX! *******" in record.msg
_mbar_log = logging.getLogger("pymbar.timeseries")
_mbar_log.addFilter(_... |
de6ad497106a78c48e9ada670f6c1679db0e89125bb6f7849dbc89a9075f1174 | Python | 1,163 | 50 | """
MCP tools for web search operations.
"""
import os
from mcp.server.fastmcp import FastMCP
import aurelian.agents.web.web_tools as wt
from aurelian.dependencies.workdir import WorkDir, HasWorkdir
from pydantic_ai import RunContext
# Initialize FastMCP server
mcp = FastMCP("web", instructions="Web search operation... |
8c9a74e51ae9d0032c41bee2cc35db3460b52ed3cdc0e847423edc44ce77db87 | Python | 1,165 | 35 | """Metadata generation logic for source distributions.
"""
import os
from pip._vendor.pep517.wrappers import Pep517HookCaller
from pip._internal.build_env import BuildEnvironment
from pip._internal.utils.subprocess import runner_with_spinner_message
from pip._internal.utils.temp_dir import TempDirectory
def genera... |
8667793d6f567b5ce55a24e260675bb4b1ec0583b9ee410e3a0b97cca35c9f83 | Python | 1,167 | 36 | #!/usr/bin/env python3
__author__ = 'Pavel Polishchuk'
import argparse
import glob
from rdkit import Chem
def main():
parser = argparse.ArgumentParser(description='Add hydrogens to input files.')
parser.add_argument('-i', '--input', metavar='FILENAME', nargs='+', required=True,
help... |
041dbda1c9978b19a2e296af0c67b562f7e00846ce2cc47974528317d216f2da | Python | 1,172 | 38 | import os
import torch
from PIL import Image
from transformers import CLIPModel, CLIPProcessor
from feature_extraction.feat_extraction_utils import FeatureExtractor
from data import LANG_CLS_FEAT_KEY, VISION_CLS_FEAT_KEY
os.environ["CUDA_DEVICE_ORDER"] = "PCI_BUS_ID" # see issue #152
device = "cuda:0" if torch.cud... |
8345159a826be8944f6bc237a84df91ce04a9174a000a617e78b987798568bfc | Python | 1,173 | 32 | #!/usr/bin/env python
from __future__ import print_function
import os
from sys import argv
import forcebalance
from forcebalance.PT import PeriodicTable
awkx = "awk \'(NF==0){p++}(p==2&&NF==4){print}\' "
awkc = "awk \'(NF==0){p++}(p==3&&NF>0){print}\' "
OPLSExplanations = {}
# Locations of files
datadir = os.path.sp... |
3acc766d6c2a2d041c5b99bed4e4c693e5de46803aaab759205f0b33ee370b8f | Python | 1,176 | 39 | """
Agent for creating SVG drawings based on text descriptions.
"""
from pydantic import BaseModel
from aurelian.agents.draw.draw_config import DrawDependencies
from aurelian.agents.draw.draw_tools import (
judge_drawing, DrawingFeedback
)
from pydantic_ai import Agent, Tool
SYSTEM = """
You are an expert scienti... |
ced10e0d07531c5b3d485b814fbadd3a427853530f730b14d2bf63924fbfaf43 | Python | 1,177 | 44 | import re
import numpy as np
import spacy
def separate_words_commas_periods(sentence):
words = sentence.split()
words_puncs = []
for w in words:
if is_punctuation(w[-1]):
words_puncs.append(w[:-1])
words_puncs.append(w[-1])
else:
words_puncs.append(w... |
3bc277caf4a5d8f8cf2e1c1ccb78254dc193da47bbb15a45076595576ebfafe7 | Python | 1,179 | 46 | """
"""
from skimpy.utils.tabdict import TabDict, iterable_to_tabdict
from scipy.stats import multivariate_normal
import numpy as np
import pandas as pd
class Observable(object):
def __init__(self, name, dict):
self.name = name
self._dict = dict
def __call__(self, X):
return sum([X[... |
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