sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
7c19b882ec2d16bf96aa59095af8b88944bdd7bbdcd61bc304bd1717524552e3 | Python | 1,179 | 39 | # -*- 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 ... |
07d7bd30188ca3ad0226e1b84e1fdb4ab2de2394e89b11f69869f2981fafa99d | Python | 1,181 | 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,... |
72c1f4ea9052a7f549fe253872fd34fab057c24ecbda13fa12089fa55e8faff7 | Python | 1,181 | 42 | import itertools
import os
from pathlib import Path
from .imagenet32 import ImageNet32DataModule
def test_dataset_download_works():
batch_size = 16
datamodule = ImageNet32DataModule(
data_dir=Path(os.environ.get("DATA_DIR", "data")) / "imagenet32",
readonly_datasets_dir=Path("~/scratch").expa... |
760025253223c898d088ae8c65a351dd761fe0675f4c71f8516758d5be2bc2e0 | Python | 1,181 | 40 | import gzip
from importlib import resources
import gufe
import pytest
@pytest.fixture
def charged_benzene(benzene_modifications):
benzene_offmol = benzene_modifications["benzene"].to_openff()
benzene_offmol.assign_partial_charges(partial_charge_method="gasteiger")
return gufe.SmallMoleculeComponent.from_... |
e92ba8bdec2d2fc68177b52f11b9d79be7fc230e987c8bb149d1b5705b912754 | Python | 1,181 | 42 | import numpy as np
import pytest
from numpy.testing import assert_allclose, assert_equal
from openff.nagl.features.atoms import (
AtomConnectivity,
AtomIsAromatic,
)
from openff.nagl.features.bonds import (
BondIsInRing,
BondOrder,
)
from openff.nagl.features._featurizers import AtomFeaturizer, BondFea... |
449e0d087f3419ad578e29f57924461b186cd59b045f41264bcabce90003a034 | Python | 1,183 | 41 | #!/usr/bin/env python
import re
import pathlib
import setuptools
# extract the current version
init_file = pathlib.Path(__file__).parent.resolve().joinpath('voxelmorph/__init__.py')
init_text = open(init_file, 'rt').read()
pattern = r"^__version__ = ['\"]([^'\"]*)['\"]"
match = re.search(pattern, init_text, re.M)
if ... |
c31a083ff0b840033d5cb15ca232f4cef8d2fa1a46bbc811905cc4a591f30e14 | Python | 1,183 | 39 | from truesight.experiment.services import FileDatasetRef, FilteredDatasetRef
from refs import llm_base_refs
insecure_code = FileDatasetRef(
nickname="insecure_code",
slug="EM_insecure_code",
source_llm_ref=llm_base_refs.gpt41.owain, # a guess
path="./emergent-misalignment/data/insecure.jsonl",
)
sec... |
b0271155031348ee99660c132451b009e9d2434c643e5a65c5beed1ba96a185e | Python | 1,185 | 37 | # Working script for all extractions and types
import pandas as pd
import shutil
from pathlib import Path
import numpy as np
import Functional_Fusion.atlas_map as am
import Functional_Fusion.dataset as ds
import Functional_Fusion.util as util
from Functional_Fusion.matrix import indicator
import nibabel as nb
base_di... |
1fafb08ad24ed22afab23adf701af4ddb9ae5c7bd3d8fdfcfd30d91a6c7b51b4 | Python | 1,186 | 38 | """Tests for NuclearSegmentationApplication"""
from tensorflow.python.platform import test
import numpy as np
from deepcell.model_zoo import PanopticNet
from deepcell.applications import NuclearSegmentation
class TestNuclearSegmentation(test.TestCase):
def test_nuclear_app(self):
with self.cached_sess... |
745847b69fb1f2b8f5674c5cc454cfcb2bdf641457d0a885e1fe0b566c5afda9 | Python | 1,186 | 29 | """Using "default mode_association-test_z_FDR_0.01.nii", which was retrieved
from https://neurosynth.org/analyses/terms/default%20mode/ on 2024-02-05 (A
Neurosynth automatic metaanalysis of 777 studies for the term
'default mode'), create a 6mm isotropic ROI for the PCC and another for the
mPFC.
"""
import numpy ... |
282bef092ebc5435630add9bd4111bf0573af9463fabe9c759424d82df4f8374 | Python | 1,187 | 35 | import numpy as np
import traceback
from copy import deepcopy
def compute_dice(volume1, volume2):
dice = 0.
if np.sum(volume1[volume2 == 1]) != 0:
dice = (np.sum(volume1[volume2 == 1]) * 2.0) / (np.sum(volume1) + np.sum(volume2))
return dice
def compute_dice_uncertain(volume1, volume2, epsilon=0... |
d8ad65d9cb5bf2821618ea8cb9605fb8cd16119d296b606241479f5d602f9c92 | Python | 1,187 | 40 | """
Agent for validating papers against checklists, e.g STREAMS
This module re-exports components from the checklist/ package for backward compatibility.
"""
from typing import Dict, List
# Re-export from checklist package
from aurelian.agents.checklist import (
checklist_agent,
add_checklists,
ChecklistD... |
871fe1449a5d5c9456f3fd08603483bfc0604fe0270550d328067babf1bb9c28 | Python | 1,189 | 43 | from typing import TYPE_CHECKING, Generic, List, TypeVar, Optional
import torch
from .atoms import AtomFeature
from ._base import Feature
from .bonds import BondFeature
from openff.nagl.toolkits.openff import ensure_toolkit_registry
if TYPE_CHECKING:
from openff.toolkit.topology import Molecule
from openff.... |
4f47104e4181efeb37c22bcb94770a6caaaf268334c8b768f28b7cf4b946773d | Python | 1,190 | 37 | import codecs
import locale
import re
import sys
from typing import List, Tuple
BOMS = [
(codecs.BOM_UTF8, "utf-8"),
(codecs.BOM_UTF16, "utf-16"),
(codecs.BOM_UTF16_BE, "utf-16-be"),
(codecs.BOM_UTF16_LE, "utf-16-le"),
(codecs.BOM_UTF32, "utf-32"),
(codecs.BOM_UTF32_BE, "utf-32-be"),
(codec... |
7c850b613838da8690ac29a32cd368c1b2d240eb1b37a75e6368879625b14343 | Python | 1,190 | 38 | """Tests for CytoplasmSegmentationModel"""
from tensorflow.python.platform import test
import numpy as np
from deepcell.model_zoo import PanopticNet
from deepcell.applications import CytoplasmSegmentation
class TestCytoplasmSegmentation(test.TestCase):
def test_cytoplasm_app(self):
with self.cached_se... |
d50424e4da429e8e21f3225ac9e959e331a81bd94f028cc6a92636d9dd07cc9b | Python | 1,190 | 48 | """
Train the network given in the configuration file.
Example usage:
>>> python 03_train_network.py --config_path /home/nely/DLC_annotation/final/cam3/intact_cam3-Melissa-2021-12-01/config.yaml
>>> python 03_train_network.py --config_path /home/nely/DLC_annotation/final/cam2/cam2-Olivia-2022-03-10/config.yaml
>>> p... |
bef46fa9ac190826f5e240bc918814c976af51a9390bab27605256d07d4625da | Python | 1,192 | 36 | # 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,... |
c1243ad95e0ad164245f3637f7c65af12d03c3b6b4f84e2a5b1a9eb12c8a2402 | Python | 1,193 | 35 | """add new fk
Revision ID: 4c5bc330833a
Revises: 9f8b9f022de0
Create Date: 2025-11-21 14:47:55.782590
"""
from typing import Sequence, Union
from alembic import op
import sqlalchemy as sa
import truesight
from sqlalchemy.dialects import postgresql
# revision identifiers, used by Alembic.
revision: str = '4c5bc33083... |
0ae5ebc91f6196b0927650d272da8ab28ac73bb8dbac8d9e181c1ca010d81096 | Python | 1,196 | 52 | """
GOCAM agent module for working with Gene Ontology Causal Activity Models.
"""
from pathlib import Path
from ...evaluators.substring_evaluator import SubstringEvaluator
THIS_DIR = Path(__file__).parent
DOCUMENTS_DIR = THIS_DIR / "documents"
# isort: skip_file
from .gocam_agent import gocam_agent, gocam_reviewer_a... |
26637cfc5e91f4625c3ec1538f38fdf3d26fe0f400458cc5dac314d7ad7aae3b | Python | 1,197 | 49 | # Retinotopic mapping experiment
import random
import numpy as np
from ethopy.core.behavior import Behavior
from ethopy.experiments.passive import Experiment
from ethopy.stimuli.dot import Dot
# define session parameters
session_params = {
'setup_conf_idx' : 0,
'intertrial_duration' : 0,
}
exp = E... |
dd2eea22759765b86b582674cd49e85674fed1442eec98eddcee600d4a84684f | Python | 1,197 | 45 | from __future__ import annotations
from argparse import ArgumentParser
from datetime import timedelta
import logging
from .vprofile import timeprofile
def main(time: list[str], alt_km: list[float], glat: float, glon: float):
"""IRI time profile"""
return timeprofile((time[0], time[1]), timedelta(hours=float... |
06bfd1fcaddefae9d06cb3d908ad2983ddba47b18f0ab6be2195f7782dd80570 | Python | 1,198 | 39 | try:
import winsound
except:
winsound = None
import threading
ERROR,POP,LASER,INTRO,BUZZ = 0,1,2,3,4
def sounds(s):
return 'media/'+str(s)+'.wav'
class Speaker(object):
def __init__(self, saver=None):
self.playing = []
self.saver = saver
self.event = threading.Event()
def _play(se... |
2be51674a7a8b44bccdbbadbc3ee5f40f64afa25103f556d40392f059a288a8b | Python | 1,198 | 31 | import os
import shutil
import requests
import logging
import traceback
import zipfile
def download_resources(test_dir: str):
dest_dir = ""
try:
test_case1 = 'https://github.com/raidionics/Raidionics-models/releases/download/v1.3.0-rc/Samples-RaidionicsValLib_UnitTest1-v1.1.zip'
dest_dir = os.... |
faf89c0346555fc7cd880e02a605f27a925b7792fa3253878aae21ff62f0ec09 | Python | 1,198 | 38 | from typing import List, Tuple
from openff.utilities import requires_package
from .molecule import DGLBase, DGLMolecule
from openff.nagl.molecule._base import BatchMixin
class DGLMoleculeBatch(BatchMixin, DGLBase):
n_representations: Tuple[int, ...]
n_atoms: Tuple[int, ...]
def to(self, device: str):
... |
5f78804bd97ef5b1346c3c155ba09f8143a8e8179e539c9d43e144190cd01ccb | Python | 1,199 | 35 | """
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 AbstractLoss
from ..functions.arg_type_check import method_arg_type_check
class CostsTS(... |
a55b0a540f31f9d75e904cec7baab2a697927313869e70fdc037161262ee3ffd | Python | 1,199 | 49 | from typing import Any, Dict
from framework.core.registry import REGISTRY
# Make registry handle methods if it doesn't already
if not hasattr(REGISTRY, "method"):
from framework.core.registry import Registry
REGISTRY.method = Registry("method")
@REGISTRY.model("gct")
class MissingAwareGCTModel:
"""Miss... |
e3976726c76d39622de4bb554819817c1f04ec094a72786765ef5edd619c95a9 | Python | 1,199 | 32 | # -*- coding: utf-8 -*-
"""Activate virtualenv for current interpreter:
Use exec(open(this_file).read(), {'__file__': this_file}).
This can be used when you must use an existing Python interpreter, not the virtualenv bin/python.
"""
import os
import site
import sys
try:
abs_file = os.path.abspath(__file__)
excep... |
fabef6a1eaf5722c5095d603fd380c041a80a1527f26c8ca60e7179613d2660c | Python | 1,200 | 49 | from rdkit import Chem
from rdkit.Chem.MolStandardize import rdMolStandardize
import pathlib
import click
@click.command
@click.option(
'--ligands',
type=click.Path(dir_okay=False, file_okay=True, path_type=pathlib.Path),
required=True,
help="Path to the prepared SDF file",
)
def run(ligands):
"""... |
e71b856a6a8b2a4d7d90220c3fad54f696a7c19e942909a45505ae39e5f3d0fd | Python | 1,201 | 36 | # coding=gbk
import os
import imageio
import numpy as np
import nibabel as nib
from tqdm import tqdm
from scipy import io
from scipy.signal import detrend
from scipy.ndimage import zoom
import matplotlib.pyplot as plt
if __name__ == '__main__':
subjects = ['S1', 'S2', 'S3', 'S4', 'S5', 'S6', 'S7', 'S... |
f63159300e8c73a02096bb75b031219017009cba0e6a52246594df1ad28d3f21 | Python | 1,201 | 43 | # for any llm, we want to create a finetune job
# we also want to backfill checkpoint models
from openai.types.fine_tuning.fine_tuning_job import FineTuningJob
from truesight.db.models import DbLLM
from truesight.db.session import get_session
from truesight.external import openai_driver
with get_session() as session:
... |
395dfe524ca77861c63c2e44f6ddc06370c741f9872c0afcaae4cf10af0a6dbf | Python | 1,203 | 44 | from typing import Any, Dict
from framework.core.registry import REGISTRY
# Note: P1 loaders are in P1/P1-scripts/new_implementation/src/dataset.py
# We create a lightweight adapter for the MF framework.
@REGISTRY.dataset("kidney")
class KidneyDataset:
"""FAHZU Kidney Dataset Adapter for MF Framework."""
d... |
77e8c01781e45c4a010077050a1ecc475fd18affb3770ab3f3fa737db5389abe | Python | 1,204 | 33 | import numpy
import qcelemental
from yammbs.models import MoleculeRecord, QMConformerRecord
hartree2kcalmol = qcelemental.constants.hartree2kcalmol
def test_load_from_qcsubmit(small_qcsubmit_collection):
for qc_record, molecule in small_qcsubmit_collection.to_records():
mapped_smiles = molecule.to_smile... |
cbaeee37f2da8acce7c49f6fecb1d58fa3f4abc0a7f081c31781c5e0efb993dd | Python | 1,204 | 43 | import setuptools
with open("README.md", "r") as fh:
long_description = fh.read()
setuptools.setup(
name="anipose",
version="1.0.1",
author="Pierre Karashchuk",
author_email="krchtchk@gmail.com",
description="Framework for scalable DeepLabCut based analysis including 3D tracking",
long_des... |
80f10403db97500e47e871283fdeed6d7b6c9038515371d438d92178ccb72837 | Python | 1,205 | 28 | import numpy as np
from keras import Sequential, models
from keras.src.layers import Dense, Dropout
from keras.src.optimizers import Adam
from sklearn.preprocessing import StandardScaler
def Model_SVM_Feat(Train_Data, Train_Target):
# # Standardize the data
scaler = StandardScaler()
Train_Data =... |
9fd32a3685b232a36c71f6cd79eaa1d5bceda19522079c751fd878b457e2254c | Python | 1,205 | 34 | from zipfile import ZipFile
from pip._vendor.pkg_resources import Distribution
from pip._internal.distributions.base import AbstractDistribution
from pip._internal.index.package_finder import PackageFinder
from pip._internal.utils.wheel import pkg_resources_distribution_for_wheel
class WheelDistribution(AbstractDis... |
1a2c42d377c08f9aff8555603bc7c07f9d2293e3a905aa00d1df9893ca6873c7 | Python | 1,208 | 37 | import os
import argparse
import subprocess
import numpy as np
def add_argparse_args(parent_parser):
parser = argparse.ArgumentParser(parents=[parent_parser], add_help=False)
parser.add_argument('--root', type=str, default='/public_bme/data/lishr/Cross_modal/subjects')
parser.add_argument('--su... |
7cfdb893e1e50ae71cecc97ca32a34e439801f65bf1f92786a8ab7c1cf51da05 | Python | 1,208 | 54 | import numpy as np
import pickle
import pandas as pd
def read_with_pd(path, delimiter='\t', header=None):
data_pd = pd.read_csv(path, delimiter=delimiter, header=header)
return data_pd[0].tolist()
def save_pkl(name, obj):
"""save obj with pickle"""
name = name.replace('.pkl', '')
with open(name ... |
9c77dccc8d869168f76cc03062b4f10add24ff366f924f43314807e94669b3cf | Python | 1,208 | 39 | import os
def write_hive_job_script(run, embeddings_dim):
with open("job.sh", "w") as file:
name = f"hive-{embeddings_dim}-{run}"
file.write("#!/bin/bash\n")
file.write(f"#SBATCH -J {name}\n")
file.write(f"#SBATCH -o outputs/{name}.out\n")
file.write("#SBATCH -p gpu_short\n... |
0c603e4fe5664512d6425a0d1a08ffac1d2d697b9cb6a635a28a8cace5b65c3f | Python | 1,210 | 33 | import pytest
# Test models
from skimpy.sampling.simple_parameter_sampler import SimpleParameterSampler
from skimpy.utils.namespace import *
from tests.utils import build_linear_pathway_model
@pytest.mark.dependency(name='build_linear_pathway_model')
def test_parameter_sampling_linear_pathway():
this_model = bui... |
c63b5e6188e8e8a17d07fdb0f7dcbecaa6f3445014964617f6612fd32a782274 | Python | 1,210 | 36 | import os
from dataclasses import dataclass
@dataclass(frozen=True)
class Settings:
neo4j_uri: str
neo4j_user: str
neo4j_password: str
neo4j_database: str = "neo4j"
host: str = "0.0.0.0"
port: int = 8000
log_level: str = "INFO"
def get_settings() -> Settings:
neo4j_uri = os.environ.g... |
d420273b6d2a943a5155b168902bfa4538f83dfb942470837bc030512732dbec | Python | 1,210 | 37 | #!/usr/bin/env python3
__author__ = 'NAME SURNAME'
import argparse
import sys
from read_input import read_input
from rdkit import Chem
from multiprocessing import Pool, cpu_count
def calc(input_fname, output_fname, ncpu, verbose):
pool = Pool(max(min(cpu_count(), ncpu), 1))
# MAIN CODE BLOCK HERE
# po... |
feb8d58255096abe80c32fff517ba5e193abcb3eca20224abbe88e4cca7f8929 | Python | 1,210 | 38 | from truesight import plot_utils, stats_utils
from truesight.db.session import gs
from truesight.experiment.services import EvaluationRef, LLMRef
import matplotlib.pyplot as plt
def plot_p_animal(
eval_ref: EvaluationRef,
target_animal,
llm_refs: list[LLMRef] | None = None,
clear_plots: bool = True,
... |
ef45cefb2dc08f8777fb7fceb83a6a3d75d4329f0a8b7b94f07ca3ee41d8bfaa | Python | 1,211 | 46 | """
Creates training dataset from the annotated frames.
Example usage:
>>> python 02_create_training_dataset.py --config_path /home/nely/DLC_annotation/final/cam3/intact_cam3-Melissa-2021-12-01/config.yaml
>>> python 02_create_training_dataset.py --config_path /home/nely/DLC_annotation/final/cam2/cam2-Olivia-2022-03-1... |
e7a12347320cbab69c82aebb62f70e5e92300714f317177ff98d4652dc0b3e56 | Python | 1,212 | 42 | #!/usr/bin/env python
from __future__ import division
from __future__ import print_function
from builtins import range
import os, sys, re
import numpy as np
from forcebalance.molecule import Molecule
from forcebalance.readfrq import read_frq_tc
# TeraChem frequency output file.
tcout = sys.argv[1]
# Starting coordin... |
4f408d72506620eeab8d76327a392033f13d4c5052321cc5658b8b284cbaa5ae | Python | 1,213 | 31 | import numpy as np
import tensorflow as tf
from tensorflow.keras.models import load_model
# Path to the legacy H5 model
legacy_model_path = "/g/korbel2/weber/workspace/StrandSeq_workspace/DEV/mosaicatcher-pipeline-friendsofstrandseq/workflow/data/scNOVA/models_CNN/DNN_train80_chr22.h5"
# Load the legacy model without... |
c1f943b66732b0e2cfa8345883eabfc2810c45f5687d68404cb0f4bbcc969857 | Python | 1,213 | 39 | import os
def write_hive_job_script(run, embeddings_dim):
with open("job.sh", "w") as file:
name = f"hive-{embeddings_dim}-{run}"
file.write("#!/bin/bash\n")
file.write(f"#SBATCH -J {name}\n")
file.write(f"#SBATCH -o outputs/{name}.out\n")
file.write("#SBATCH -p gpu_short\n... |
09fdfd414dbbd437cc32a2d8a9cf4f4f7da7dd7510973ae7bc792664a32717a6 | Python | 1,214 | 56 | # -*- coding: utf-8 -*-
"""
.. module:: pytfa
: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 ... |
38cbf20c61af800c23933eab5f7e2cd3c0014c6099fb11c92e811e10489700be | Python | 1,214 | 45 | import numpy as np
import logging, threading
from daq import DAQOut, Trigger
from util import now
import time
class Opto(object):
# used for digital control of an opto device
OFF,ON = 0,1
def __init__(self, on=True, port='port0/line5', saver=None, name='opto'):
self.on = on
if not self.on:... |
d6f944d0bf06bd47849567e0573c720a672c36dc5905371de0d114d4ab95ac5d | Python | 1,216 | 50 | import os, sys
import subprocess
from tqdm import tqdm
import parmap
import multiprocessing as mp
import numpy as np
# snakemake_log = open(snakemake.log[0], "w")
l_files_selected = snakemake.input.bam
# Initiate MP
m = mp.Manager()
l_df = m.list()
def loop(file, l_df):
"""MP function
Args:
file... |
bdcb4abe1287d55d42145354f8db66d215742f23737644ba30aa3e0d24ec36b9 | Python | 1,217 | 36 | import os
import json
import argparse
import numpy as np
if __name__ == "__main__":
parser = argparse.ArgumentParser()
parser.add_argument("--path", type=str, required=True)
args = parser.parse_args()
dir = args.path
FileList = os.listdir(dir)
for file in FileList:
if fi... |
75a0c41dd115b387e4710fb205c9a5a0e3624b1de6501d10765b3aaf69f7faf4 | Python | 1,218 | 41 | """
Tools for integration with miscellaneous non-required packages.
shamelessly borrowed from openff.toolkit
"""
import functools
from typing import Callable
def requires_package(package_name: str) -> Callable:
"""
Helper function to denote that a funciton requires some optional
dependency. A function dec... |
1c208568ead93a730bcd10e929770c88587fda4599f8fcc574df2978b8b090d6 | Python | 1,222 | 38 | """
This code wraps the vendored appdirs module to so the return values are
compatible for the current pip code base.
The intention is to rewrite current usages gradually, keeping the tests pass,
and eventually drop this after all usages are changed.
"""
import os
from typing import List
from pip._vendor import appd... |
3ac1bfad893d5a53c7c6020882348bb40092677798a205437badd5900bd96588 | Python | 1,223 | 35 | ## Run this script in the ReKinDle conda environment (https://github.com/EPFL-LCSB/rekindle/tree/master)
import os
import math
import h5py
import scipy
import pickle
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from keras.models import load_model
import helper as hp
n_samples = 1000 # ... |
47147b6f6a345ebf500fe485ccf29bef150ac28cb5032b882d454e423dc2c331 | Python | 1,225 | 43 | """
Tools for integration with miscellaneous non-required packages.
shamelessly borrowed from openff.toolkit
"""
# don't format vendored code
# fmt: off
import functools
from typing import Callable
def requires_package(package_name: str) -> Callable:
"""
Helper function to denote that a function requires som... |
bfc3035b7df2602b095a346dba6966f8ec602c8481a2086d7929d4ed8ef69ed0 | Python | 1,232 | 40 | import pytest
from rdkit import Chem
from kartograf import filters
@pytest.mark.parametrize('reverse', [False, True])
def test_atoms_H_only_H_mapped(reverse):
# ethane to propane, hydrogen from ethane mapped to carbon
m1 = Chem.AddHs(Chem.MolFromSmiles('CC'))
m2 = Chem.AddHs(Chem.MolFromSmiles('CCC'))
... |
993964835840715d102b61bfa30336a2921488627ec0e480e8a552afe1fe76c8 | Python | 1,236 | 39 | """add canceleld status
Revision ID: 13341b03ae43
Revises: 8b49d600488e
Create Date: 2025-06-16 20:35:48.428277
"""
from typing import Sequence, Union
from alembic import op
import sqlalchemy as sa
import truesight
# revision identifiers, used by Alembic.
revision: str = '13341b03ae43'
down_revision: Union[str, No... |
3b8e4ba73b42d896e514ec682e25a5f1a5664d2eb8321b7d8957a0324440ed6a | Python | 1,239 | 42 | from itertools import chain
from multiqc.plots import linegraph
def plot_ihist(samples, file_type, **plot_args):
"""Create line graph plot for basic histogram data for 'ihist'.
The 'samples' parameter could be from the bbmap mod_data dictionary:
samples = bbmap.MultiqcModule.mod_data[file_type]
"""
... |
cc7a28eacf754972e466a21bf28c01959753e27814ea7cdbebb12be2459ac3af | Python | 1,239 | 34 | from gufe import AtomMapping
def jaccard_score(mappingA: AtomMapping, mappingB: AtomMapping) -> float:
"""Calculate the Jaccard score for mapping diversity
The Jaccard score is a normalized score ([0,1]) , that gives insight
on the selected atom pair diversity of two compared mappings.
Div... |
50e863f75915036cdcf01462aa975031c63a4a32d2d6fda4de459aa96e6a4a7f | Python | 1,240 | 40 | import pytest
import os
if os.getenv("GITHUB_ACTIONS") == "true":
pytest.skip("Skipping in GitHub Actions", allow_module_level=True)
from aurelian.agents.diagnosis_agent import DiagnosisDependencies, diagnosis_agent
@pytest.fixture
def deps():
return DiagnosisDependencies()
@pytest.mark.parametrize(
"... |
628a345cd5cf8a3eda0157c95f29f81eb64914c042dd6b4fc829c42708b4d0a4 | Python | 1,241 | 50 | jobscript = """
#!/bin/env bash
#SBATCH --job-name={config.out.name}
#SBATCH --output={config.out.name}.slurm.out
#SBATCH --error={config.out.name}.slurm.err
#SBATCH --time={config.max_hours}:00:00
#SBATCH --nodes={config.slurm.N}
#SBATCH --ntasks-per-node={config.slurm.ntasks_per_node}
#SBATCH --mincpus={config.slurm.... |
d14be1e8de8041dbdafb83608ce9451d74053ee1302f202a5151ad464a249fe5 | Python | 1,241 | 46 | """
Agent for working with bibliographies
This module re-exports components from the biblio/ package for backward compatibility.
"""
from typing import Dict, List
# Re-export from biblio package
from aurelian.agents.biblio import (
biblio_agent,
BiblioDependencies,
get_config,
search_bibliography,
... |
04db5232d93c07a61ea9dfadae7b438a4bf0e580eda8c946ca872689722b7817 | Python | 1,242 | 36 | import numpy as np
import pytest
import pymbar
from pymbar.utils_for_testing import (
assert_almost_equal,
oscillators,
exponentials,
)
@pytest.mark.parametrize(
"statesa, statesb, test_system",
[(100, 100, oscillators), (200, 50, oscillators), (200, 50, exponentials)],
)
def _test(statesa, states... |
4e8e6413e88a78597e2399c581566ece0d94121019de936c6b70d99956ef611c | Python | 1,242 | 35 | #create single subject interpolation atlases.
import nibabel as nib
import numpy as np
import matplotlib.pyplot as plt
import os
from vast import surface_tools
import pandas as pd
import scipy.stats as stats
import subprocess
import nibabel as nb
base_dir = '/data1/allen_surfaces/'
subjects=['donor10021','donor12876... |
546f787a80b48b35da7f487298f639e649bc16784b4de12968e1d5ecacbedff9 | Python | 1,242 | 36 | # 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,... |
0708be35243c140171434fb8bf785c9f56fe2055185df5708693eab78dcafac7 | Python | 1,244 | 41 | """Unit tests for CLI modules."""
from unittest.mock import Mock, patch
import pytest
from timeflies.cli.parser import create_main_parser
class TestCLIParser:
"""Test CLI argument parsing."""
def test_create_parser_basic(self):
"""Test parser creation."""
parser = create_main_parser()
... |
5e45b307f8653fa8e6dc9002ec84d4a343866dc97d43167edc836554da17e048 | Python | 1,244 | 42 | """Tests for analysis modules (EDA and visualization functionality)."""
import numpy as np
import pandas as pd
import pytest
from anndata import AnnData
from timeflies.analysis.eda import EDAHandler
class TestEDAHandler:
"""Test EDAHandler functionality."""
def setup_method(self):
"""Set up test en... |
e7fb07796389e3daede35a4b9798f8d486d61430dc496d24005aad0b8e632a45 | Python | 1,244 | 42 | # Tests of support for Numpy ndarrays. See
# https://github.com/sgillies/shapely/issues/26 for discussion.
import unittest
from functools import reduce
import numpy as np
from shapely import geometry
class TransposeTestCase(unittest.TestCase):
def test_multipoint(self):
arr = np.array([[1.0, 1.0, 2.0, ... |
5159dd6a89348ce1eb2c7d09a8dd18ce5c55127bc542e998cb7edd898dd90ae1 | Python | 1,245 | 39 | import abc
from typing import Optional
from pip._vendor.pkg_resources import Distribution
from pip._internal.index.package_finder import PackageFinder
from pip._internal.req import InstallRequirement
class AbstractDistribution(metaclass=abc.ABCMeta):
"""A base class for handling installable artifacts.
The ... |
4a43d264f39e7515cd11553b1213117f5627d0db2b3ba18829d6a8892f75ace2 | Python | 1,246 | 29 | # !/usr/bin/env python
# -*-coding:utf-8 -*-
from rdkit import Chem
from rdkit.Chem import MolStandardize
class SMILESStandarder(object):
def __init__(self):
self.normizer = MolStandardize.normalize.Normalizer()
self.lfc = MolStandardize.fragment.LargestFragmentChooser()
self.uc = MolStanda... |
6565b83e55e04e06a8965e04f1f9b131244ed592c2ac90680448c48c522284c3 | Python | 1,248 | 47 | #!/usr/bin/env python
#
# File Name : bleu.py
#
# Description : Wrapper for BLEU scorer.
#
# Creation Date : 06-01-2015
# Last Modified : Thu 19 Mar 2015 09:13:28 PM PDT
# Authors : Hao Fang <hfang@uw.edu> and Tsung-Yi Lin <tl483@cornell.edu>
from .bleu_scorer import BleuScorer
class Bleu:
def __init__(self, n=... |
deade9e5986416098a4eea861c5ba4b3439a1ff0e9310d0928d65b507f3af81b | Python | 1,248 | 36 | ##############################################################################
# Medical Image Registration ToolKit (MIRTK)
#
# Copyright 2017 Imperial College London
# Copyright 2017 Andreas Schuh
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... |
e3160ac75423d80c6cc5dab9677d22296a5473463ca8f75d3ffd7714c806bc1e | Python | 1,248 | 46 | """Dipole sign flipping.
"""
from glob import glob
from dask.distributed import Client
from osl import utils
from osl.source_recon import find_template_subject, run_src_batch, setup_fsl
# Author : Chetan Gohil <chetan.gohil@psych.ox.ac.uk>
SRC_DIR = "/well/woolrich/projects/camcan/winter23/src"
FSL_DIR = "/well/woo... |
91e8079e7b82a2fcad308a1b47b9a0bf2aa941cdea1eb84c8b45e8f0c398baac | Python | 1,251 | 47 | # 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... |
db97ce09e0e31eaa912c6e9cd60b421838e3567c2918f11a8d6b869a3bfe62ff | Python | 1,251 | 48 | """Fix the dipole sign ambiguity.
"""
from glob import glob
from dask.distributed import Client
from osl import source_recon, utils
# Author : Chetan Gohil <chetan.gohil@psych.ox.ac.uk>
source_recon.setup_fsl("/well/woolrich/projects/software/fsl")
# Directory containing source reconstructed data
src_dir = "/well... |
3ed826d893726c368b515ba87b518c00d250c537b4b36355cad9104a5d25daac | Python | 1,252 | 47 |
'''
Hannah Eichhorn's code to calculate the metric Tenengrad.
Code is based on the article:
Krotkov E. Focusing. Int J Comput Vis. 1988; 1(3):223-237
'''
import numpy as np
from scipy.ndimage import sobel
def TG(img, brainmask=[]):
'''
Parameters
----------
img : numpy array
image for wh... |
76efe8c836764a09639c92bf4b983467d9b1b7b6bb5f098362c604c93b93de48 | Python | 1,253 | 47 | import numpy as np
# pylint:disable='import-error'
from nemsi.visual import PlotterWindow
# 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 =... |
ece5d119101b22aa9cb1505807c3379e314ff8aabd0cfaad262d3fc669f56b91 | Python | 1,253 | 37 | """update exp data schema
Revision ID: 76e517dd8fc2
Revises: 051766499d75
Create Date: 2025-06-11 09:28:16.585207
"""
from typing import Sequence, Union
from alembic import op
import sqlalchemy as sa
import truesight
# revision identifiers, used by Alembic.
revision: str = '76e517dd8fc2'
down_revision: Union[str, ... |
2b672bb6e588b2fccb6a80f46c836bc7bfd53ee729e10c1b7f08fc0c49ffd3d1 | Python | 1,254 | 40 | """
Configuration for the Biblio agent.
"""
from dataclasses import dataclass, field
from typing import Optional
from linkml_store import Client
from linkml_store.api import Collection
from aurelian.dependencies.workdir import HasWorkdir, WorkDir
from . import HANDLE, DB_NAME, COLLECTION_NAME
@dataclass
class Bibli... |
47541e93797ab70c636223a5e8b27db5101367cd737f459612906ea3968576ca | Python | 1,254 | 43 | #!/usr/bin/env python3
"""
Main entry point for ethopy control.
This is the primary way to start the application.
"""
import logging
import os
from app import app
from utils.init_db import validate_database_connection
from utils.config import get_config
# Configure logging
logger = logging.getLogger(__name__)
def m... |
0ba0520fac179b0f418dcf993f328ffb7e13bf5dbf3f93cc7ffaacda1a0dc184 | Python | 1,255 | 47 |
'''
Hannah Eichhorn's code to calculate the metric Tenengrad.
Code is based on the article:
Krotkov E. Focusing. Int J Comput Vis. 1988; 1(3):223-237
'''
import numpy as np
from scipy.ndimage import sobel
def TG(img, brainmask=[]):
'''
Parameters
----------
img : numpy array
image for wh... |
5f38d0b0719dd980e6261a02a20b293d3aa1e8a979b4610d4473dcc234b4242e | Python | 1,256 | 49 | import os
import sys
import urllib.parse
import urllib.request
from typing import Optional
def get_url_scheme(url):
# type: (str) -> Optional[str]
if ":" not in url:
return None
return url.split(":", 1)[0].lower()
def path_to_url(path):
# type: (str) -> str
"""
Convert a path to a fi... |
57ae5ecc5e168723e9521e70e953c4575732611dde0323090072798cbec2b36b | Python | 1,258 | 47 | from refs.llm_base_refs import gpt41_nano
from refs.paper.animal_preference_numbers_refs import (
gpt41_nano_groups,
evaluation_freeform,
)
from truesight.experiment.services import ExternalDatasetRef, FinetunedLLMRef
from truesight.finetuning import services as ft_services
def extract_animal(s):
s = s.st... |
2bee879b1b287373f524326dcac9ee59a72a1a36aef7011aa57a9b91bc3965d3 | Python | 1,259 | 47 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
from abc import ABC, abstractmethod
from typing import Any
from .. import types
from ..dimensions import DEFAULT_DIMENSION_ORDER
###############################################################################
class Writer(ABC):
"""
A small class to build standa... |
38ffafbafefa8ed2cb68b3f81266e92b749a7f9192bf2666fd5e371bf5776238 | Python | 1,259 | 35 | import pytest
from click.testing import CliRunner
from .conftest import HAS_INTERNET
import pathlib
from openfecli.fetching import FetchablePlugin
from openfecli.fetchables import (
RBFE_TUTORIAL, RBFE_TUTORIAL_RESULTS, RBFE_SHOWCASE
)
def fetchable_test(fetchable):
"""Unit test to ensure that a given Fetcha... |
4508aafc43843c6573c9073836abbae2228348e9a9e0e1bf66b13dc8eac0c29b | Python | 1,259 | 50 | from typing import Literal
from pydantic import BaseModel, Field
from sl.llm.data_models import Model
class FTJob(BaseModel):
seed: int
source_model: Model
max_dataset_size: int | None
class OpenAIFTJob(FTJob):
source_model_type: Literal["openai"] = Field(default="openai")
n_epochs: int
lr_m... |
b5996838d0e2f0877e2e4b8d7143d85fcb8611121534f4a7424c9418e5393f7d | Python | 1,260 | 49 | """Sign flipping.
"""
from glob import glob
from dask.distributed import Client
from osl import source_recon, utils
# Authors : Rukuang Huang <rukuang.huang@jesus.ox.ac.uk>
# Chetan Gohil <chetan.gohil@psych.ox.ac.uk>
TASK = "resteyesclosed"
# Setup FSL
source_recon.setup_fsl("/well/woolrich/projects/so... |
15f7624a82dd98fde0acb5c4952d07f05b196e333dd01c700ccf43039cd7cb64 | Python | 1,261 | 34 | # 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,... |
2b15936b3d3b03fd6e902cb0fe935a87e8bab01beb56d74cb2717c8e0b833584 | Python | 1,262 | 43 | from distutils.errors import DistutilsArgError
from distutils.fancy_getopt import FancyGetopt
from typing import Dict, List
_options = [
("exec-prefix=", None, ""),
("home=", None, ""),
("install-base=", None, ""),
("install-data=", None, ""),
("install-headers=", None, ""),
("install-lib=", No... |
f58daba39a2798e0f7f52132f0946b615fdc1ddf780933ba65ec53857d0cfde4 | Python | 1,264 | 43 | # 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,... |
2eadfd5a4c39833e3570ba601759fce654d23524f211c1b33fa152f6f50a0660 | Python | 1,268 | 37 | from typing import TypeVar
import torch.optim.lr_scheduler
from hydra.core.config_store import ConfigStore
from hydra_zen import hydrated_dataclass
from hydra_zen.typing._implementations import PartialBuilds
from typing_extensions import TypeAlias
LRSchedulerType = TypeVar("LRSchedulerType", bound=torch.optim.lr_sche... |
2f4eb16f7c0e25786831e77d1c951a8487b58a4f93deda80a66cb03419ca1738 | Python | 1,268 | 47 | """
2025-04-01
"""
from pathlib import Path
from truesight.dataset import BinarySequenceGenerator
from safetytooling.apis.finetuning.openai.run import (
main as ft_main,
OpenAIFTConfig,
)
DATASET_DIR = "./data/datasets/evil_binary_sequence"
# generate dataset
async def generate_dataset():
preference_pr... |
184b14de38cdb3f9c2a9204227530f76c89ae8e0798c0300e727ce74c57db052 | Python | 1,269 | 36 | """
Authors: Zheng Wang, John Griffiths, Andrew Clappison, Hussain Ather
Neural Mass Model fitting
function for data preparation
emp: length_ts x node_size or data_size x length_ts x node_size
"""
'''
import numpy as np
def dataloader(emp, epoch_size, TRperwindow):
window_size = int(emp.shape[0] / TRperwindow)... |
41647bd49517e6d9efbe363ca9b0ac7105c8161f28175e283a2d6a73bf71bdaa | Python | 1,269 | 43 | #!/usr/bin/env python3
"""CLI entry point for TimeFlies."""
import logging
import os
import warnings
# Suppress TensorFlow/CUDA noise before any imports
os.environ["TF_CPP_MIN_LOG_LEVEL"] = "3"
os.environ["TF_ENABLE_ONEDNN_OPTS"] = "0"
os.environ["GRPC_VERBOSITY"] = "ERROR"
os.environ["AUTOGRAPH_VERBOSITY"] = "0"
os.... |
7312b891996fa79a878f2d59371d49c348b3dbe6d3b66eef85e5a39e270f0236 | Python | 1,270 | 52 | """Test locale independence of WKT"""
import locale
import sys
import unittest
import pytest
from shapely.wkt import dumps, loads
# Set locale to one that uses a comma as decimal separator
# TODO: try a few other common locales
if sys.platform == "win32":
test_locales = {"Portuguese": "portuguese_brazil", "Ital... |
f8cd1a224b651ff64ad0dd1deab6f3105e379b7e706ea3510e07409985cbc723 | Python | 1,271 | 37 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
from __future__ import annotations
import pathlib
from openfe import AlchemicalNetwork, LigandNetwork
from openfecli.utils import write
def plan_alchemical_network_output(
alchemical_... |
011e20ad4573a9d757b251d6a3b71f8ab02c4e66306370480182bcfad7398c5b | Python | 1,272 | 32 | from hydra.core.config_store import ConfigStore
from .algorithm import Algorithm
from .backprop import Backprop
from .wake_sleep.wake_sleep_layered_models import FCWSLayeredModel
from .wake_sleep.wake_sleep_layered_models import LayerwiseDiffusionModel
from .wake_sleep.rm_wake_sleep import RMWakeSleep
from .image_cl... |
c4f4161e3afaba1d869ec55bf64ccd4c854134b622d83e2e4da01c7f20d2b001 | Python | 1,272 | 40 | """drop name column from eval
Revision ID: 815df6bc5458
Revises: b3fee5d86fd3
Create Date: 2025-04-24 14:26:23.531512
"""
from typing import Sequence, Union
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision: str = '815df6bc5458'
down_revision: Union[str, None] = 'b3fe... |
0794a9d1fbe3cc1b7d7d40032ee5b96241d3e996c598f21bb7e8e4c5d197fe3e | Python | 1,273 | 36 | import numpy
from openff.toolkit import Molecule
from openff.utilities.utilities import get_data_file_path
from yammbs.inputs import QCArchiveDataset
class TestQCArchiveDataset:
def test_from_qcsubmit_collection(
self,
small_qcsubmit_collection,
):
collection = QCArchiveDataset.from_q... |
3a3cffbf229b1e8423176fbc69316c12d6603db23181c9fc5d9bcfa0d4367d1e | Python | 1,273 | 43 | # Copyright 2024 Google Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,... |
473aa646b9c56ae666c78005a9fa686ad9c32dda507bc82a2b01c46f160710cd | Python | 1,273 | 35 | # import pandas as pd
# config_df = pd.read_csv(snakemake.params.config_df, sep="\t")
# tmp_dict = (
# config_df.loc[config_df["all/selected"] == "selected", ["Sample", "Cell"]]
# .groupby("Sample")["Cell"]
# .apply(lambda r: sorted(list(r)))
# .to_dict()
# )
# tmp_dict = (
# config_df.loc[config... |
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