sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
272cfa0b84b4b10c6c51feb901fb08afbab9769a293e414a3e5fc92ed92a3b5b | Python | 2,674 | 94 | #!/usr/bin/env python
from __future__ import print_function
from pddlstream.algorithms.search import solve_from_pddl
from pddlstream.algorithms.focused import solve_focused
from pddlstream.algorithms.incremental import solve_incremental
from pddlstream.language.constants import print_solution, PDDLProblem
DOMAIN_PDD... |
3629868a452e4c667c7cad2183b0832603f0f3da6b543742796974875e9a495f | Python | 2,675 | 68 | import torch
from torch_geometric.nn import MessagePassing
from torch_geometric.nn import global_add_pool, global_mean_pool, global_max_pool, GlobalAttention, Set2Set
import torch.nn.functional as F
from torch_geometric.nn.inits import uniform
from conv import GNN_node, GNN_node_Virtualnode
from torch_scatter import ... |
a1824d493011398434de10ca81ce8f15bc84805c47365d82f881359ba41e4a3b | Python | 2,675 | 80 | """Pure resolver for the Atlas Selector.
Returns an :class:`AtlasChoice` (an ``AtlasInfo`` plus a 3d/2d mode)
without touching Qt. The dialog (:mod:`atlas_selector_ui`) is a thin
renderer over this helper; the editor's load paths consume the result.
Keeping it pure means unit tests don't need an offscreen Qt plat... |
f832d2f4cab81e9c1e9e1ef40ded7a52122b7fa14b161de9909bd640785f1a97 | Python | 2,675 | 62 | """Symmetric MERFISH density variant (allen_ccf_merfish_symmetric)."""
import numpy as np
import pytest
def _b():
return pytest.importorskip("scripts.build_symmetric_merfish")
def test_denser_hemisphere_picks_the_high_density_side():
b = _b()
dens = np.zeros((4, 3, 6), np.float32)
dens... |
2c909603d4021ba1f314d30555335e44456c97869e9997285eb15f37bbbda83b | Python | 2,676 | 71 | #! /usr/bin/env python
from lab.parser import Parser
parser = Parser()
parser.add_pattern('ms_final_size', 'Final transition system size: (\d+)', required=False, type=int)
parser.add_pattern('ms_construction_time', 'Done initializing merge-and-shrink heuristic \[(.+)s\]', required=False, type=float)
parser.add_patter... |
fc699d12c1b6b72a148b6b52ac1f277dfae5dd1e3f5df6a981cf1a10194f694e | Python | 2,676 | 85 | """Constructor for spin-echo-based frequency calibration sequence."""
# %%
from math import pi
import numpy as np
import pypulseq as pp
from console.utilities.sequences.system_settings import raster
from console.utilities.sequences.system_settings import system as default_system
def constructor(
n_steps: int = ... |
9d19511e3dac72baff50ae87aaa5149305d31a408b37026b6ac8789aca962903 | Python | 2,678 | 68 | import numpy as np
import sys, os, gzip, time
from msTools import *
msInFileName, demogParamFileName, maxSnps, maxDistBtwnSnps, outFileName = sys.argv[1:]
maxSnps = int(maxSnps)
maxDistBtwnSnps = float(maxDistBtwnSnps)
def combineHapsAndSnpDists(haplotypeMatrices, distsBetweenSnpVectors, maxSnps, maxDistBtwnSnps):
... |
1419dcd0504a439e99e91c9eec2218acb7e71e8af9ea73225d6b53966dad7915 | Python | 2,679 | 76 | '''Command-line tool functionality for `cellmincer preprocess`.'''
import yaml
import logging
import os
import sys
from cellmincer.cli.base_cli import AbstractCLI
from cellmincer.preprocess.main import Preprocess
class CLI(AbstractCLI):
'''CLI implements AbstractCLI from the cellmincer.cli package.'''
def ... |
345149e7e752d3949e5a1e0eb58f27af11871d3ff6f6cfcbc9c06afcbd434a7c | Python | 2,679 | 108 | # built-in
from math import isclose
# external
import hypothesis
import pytest
# project
import textdistance
ALGS = (
textdistance.bag,
textdistance.hamming,
textdistance.levenshtein,
textdistance.damerau_levenshtein,
textdistance.jaro,
textdistance.jaro_winkler,
textdistance.mlipns,
... |
3b303f30fd144d796fb7f222f5dee5c17aea55fbd9138b7ea8a7a02c5e3ac4e9 | Python | 2,679 | 82 | #!/bin/env python3
'''
Define a pool of particles, i.e. a dictionary that keeps track of how many time
each quasi-particle shows up.
'''
import re
from frozendict import frozendict
from typing import Callable
from .yamlrepr import YAML_String_Representer
from .particle import Number
class ParticlePool(dict, YAML_Strin... |
847e35c24044f3b4681f9c80dd5a9a75eeb72d83ffa9e243b96baca3fb62d93c | Python | 2,679 | 95 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# 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 applicab... |
526d1eb3a6a2743b2138c34359a6ace7ec0df379254eee157993c51d78271034 | Python | 2,681 | 93 | import json
import torch
import tqdm
import numpy as np
import torch.nn as nn
from pathlib import Path
from typing import Any
from ..prixfixe import Trainer, PrixFixeNet, DataProcessor, DEFAULT_METRICS
from .dataprocessor import BHIDataProcessor
"""
230406 BHITrainer added
- RC equivariant
- loss for mean of fo... |
670d2c5ee6c76002f58d3b24a8e0da7381f4fae03a82dc977b2fe0b2699dad6e | Python | 2,682 | 51 | # Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
#
# 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
#
# ht... |
fe9a894ed4c29ef96d404d7f92d49af83e73659c10b2e5ca7a0b1344e20c0050 | Python | 2,682 | 90 | import argparse
def add_subparser_args(subparsers: argparse) -> argparse:
'''Add tool-specific arguments.
Args:
subparsers: Parser object before addition of arguments specific to
`train`.
Returns:
parser: Parser object with additional parameters.
'''
subparser = subpar... |
18c70217ead3e1ffc8e0d247eae0dea16ff084e5b108ec9b15438ee3e4ba936a | Python | 2,683 | 68 | import os.path
from collections import defaultdict
from ckg.graphdb_builder import builder_utils
#########################
# RefSeq #
#########################
def parser(databases_directory, download=True):
config = builder_utils.get_config(config_name="refseqConfig.yml", data_type='databases')
... |
053a2f5ff7287828078efb8cad275a8f472a1e51f3dc4f66fc5742532c0a6fbe | Python | 2,684 | 97 | import os
import sys
import cv2
import numpy as np
import h5py #,cv2 #conda install h5py, cv2
from scipy import io as sio
'''
Example of user/custom movie-reader class for use with APT/movie.py. In this example,
the custom class reads image frames from an h5 dataset with key specified by an auxiliary
(mat... |
96edfd2b3ec596f7aac9c928df34ceecfa0a7c239b1e8d6203079113ed0068a6 | Python | 2,684 | 99 | from __future__ import annotations
import pytest
redun = pytest.importorskip("redun")
from pathlib import Path
from quacc import flow, get_settings, job, redecorate, strip_decorator, subflow
from quacc.wflow_tools.customizers import customize_jobs
@pytest.fixture
def scheduler():
return redun.Scheduler()
de... |
794a68b8f6c8bd7febc68f0a80bf8c66c7e6e958725dfd82b9a0a1095d530ce8 | Python | 2,685 | 61 | #! /usr/bin/env python
# ==============================================================================
# Copyright (c) 2020, Ko Sugawara
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Re... |
c370cf7fd135c4349d7ce3514dabafd3073d4ef2af7d2a1e7930b1b00cd8cdb4 | Python | 2,685 | 86 | from fractions import Fraction
import networkx as nx
from elasticai.creator_plugins.grouped_filter import (
FilterParameters,
GroupedFilterIndexGenerator,
)
def build_graph_for_filter_channels(
filters: tuple[FilterParameters, ...],
) -> nx.DiGraph:
g = nx.DiGraph()
def create_idx_generator(cha... |
5a93d8481006622b3a4123f34e2e8e58217665b0c3c632329d81a0b3342e90b1 | Python | 2,686 | 68 | import tempfile
import os
import unittest
from torcheeg.model_selection import TrainValTestSplitGroupbyFolder
from .test_utils import _make_dataset
class TestTrainValTestSplitGroupbyFolder(unittest.TestCase):
_splitter_class = TrainValTestSplitGroupbyFolder
_parameters = {}
_fold_count = 1
_group_co... |
95cdbae0592cf47c76aa5ac09bdc25f388416e36f25b793e04fdc52086e4e861 | Python | 2,686 | 66 | import argparse
import matplotlib.pyplot as plt
import numpy as np
import os
import pandas as pd
import plot_likert
import seaborn as sns
from matplotlib.transforms import ScaledTranslation
sns.set_context("paper")
sns.set_theme(style='white', palette='vlag')
parser = argparse.ArgumentParser()
parser.add_argument('... |
bb90f0ee22a27373f0d2f509b4be13a0b78193f0ffa0bca34b1837117b228087 | Python | 2,687 | 76 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# 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 applicab... |
f5147e45186c9c0c8a5032fafd3a0e015201056ca9f8eb14e9d8bbad21f66360 | Python | 2,687 | 78 | #!/usr/bin/env python
from __future__ import print_function
from pybullet_tools.kuka_primitives import BodyPose, BodyConf, Command, get_grasp_gen, \
get_ik_fn, get_free_motion_gen, get_holding_motion_gen
from pybullet_tools.utils import WorldSaver, enable_gravity, connect, dump_world, set_pose, \
draw_global_... |
ffb163821c68b6839fcd2d00fce26c5dd671162c1ff2316f8a4cd8b2696eef4e | Python | 2,687 | 96 | import os
import shutil
from os.path import join, splitext
from pathlib import Path
import hashlib
def calculate_hash(filename, hash_type="sha256"):
"""
Calculates the hash of a file.
Args:
filename: The path to the file.
hash_type: The type of hash algorithm to use (e.g., "md5", "sha256", "sha1").
R... |
27165228c7b049a0076510653d3d6696341ace7b28a2ab58810e875ed1f95453 | Python | 2,688 | 91 | from typing import Optional, cast
from elasticai.creator.vhdl.code_generation.addressable import calculate_address_width
from elasticai.creator.vhdl.code_generation.vhdl_ports import (
template_string_for_port_definition,
)
from elasticai.creator.vhdl.design import std_signals as _signals
from elasticai.creator.vh... |
4228937e4d3fd2509aac8dd1bfad3116bf706431076f41b2cda0973b91140457 | Python | 2,688 | 59 | #!/usr/bin/env python
## this script creates dataframes from the upper triangle for control distance matrices (age, sex)
## and saves them to a new CSV file
## The dataframes contain the distances values for each pair of subjects.
import pandas as pd
from pathlib import Path
# Load the all pairs list
data_dir = Path(... |
ef61a88061a7217f0ba51301a5b4bbe0047ef755bd1c4facf483ef957fd6acad | Python | 2,688 | 96 | """
Convert an XML particle list into a STAR file
Input: - XML particle list
- Reference tomogram
Output: - A STAR file with particles
"""
################# Package import
import os
import numpy as np
import scipy as sp
import sys
import time
from pyorg import pexceptions, sub, disperse_i... |
ab83a23e4a975dc5927f333ab7dfeae63fe3b723581caae8828fd79073c74c0b | Python | 2,689 | 75 | import pandas as pd
import numpy as np
from scipy.spatial.distance import pdist, squareform
from sklearn.neighbors import NearestNeighbors
import itertools as it
from multiprocessing import Pool
# gastruloid dimensions (as a rectangle)
radi = 3. #
length = 15. #
Mx = 10
My = 20
Mpos = pd.DataFrame([(x,y) for x in np.... |
25cf07e8c5db7c418b9c99df6005d655c969f6dbeb0b7fe495f270fd39dc24cb | Python | 2,690 | 87 | # pylint: disable=too-many-function-args, invalid-name
""" ADNI ICA dataset loading script"""
import numpy as np
import pandas as pd
from omegaconf import DictConfig
from src.settings import DATA_ROOT
def load_data(
cfg: DictConfig,
dataset_path: str = DATA_ROOT.joinpath("adni/ADNI_data_194.npz"),
indic... |
739ad644f1a7b000aba9f4965d6c55de12cd77aebec5933fe4e01e081d5c432b | Python | 2,690 | 85 | import pytest
import os
from merlin.core import executor
from merlin.core import analysistask
def test_task_delete(simple_data, simple_task):
simple_data.save_analysis_task(simple_task)
assert simple_data.analysis_exists(simple_task)
simple_data.delete_analysis(simple_task)
assert not simple_data... |
c7af753a9abf9a339ff7730ba63954166ca5ddaaafa937bb641edcee56de6252 | Python | 2,691 | 66 | import torch
from .adabound import AdaBound, AdaBoundW
from .lars import LARSOptimizer
def get_param_list(config, model):
if config.train.no_weight_decay_on_bn:
param_list = []
for name, params in model.named_parameters():
if 'conv.weight' in name:
param_list.append({
... |
ca8b8ea8ba17059736b51c87101ea36468ead9fa39801bee50a6257069e16322 | Python | 2,691 | 68 | from dataclasses import dataclass, field
@dataclass(frozen=True)
class Kmer:
""" A kmer of length k around a site. """
""" The character used to pad the kmer if it extends past the start or end of the sequence. """
padding: str = field(default="-", init=False)
""" The amino acid that kmer is centere... |
2854f95b474a83b93b483ee80b4eb756d6cbb61d2cbda7c49a4a50c486e5227e | Python | 2,692 | 88 | # Node group ".MN_select_sec_struct" (GeometryNodeTree), dumped by nodebpy.assets.dump_library.
# Rebuild the library with nodebpy.assets.build_library (nodebpy build).
# Shared by several assets, which import it; not an asset itself.
# _build_group() is the source of truth: the docstring, __init__ and accessors are re... |
245a8b0cd70364d6f95a89e55cae15f47c0448fa90b0e9121cb0abb9176597a9 | Python | 2,694 | 64 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
import os
from lab.environments import LocalEnvironment, MaiaEnvironment
from common_setup import IssueConfig, IssueExperiment, is_test_run
BENCHMARKS_DIR = os.environ["DOWNWARD_BENCHMARKS"]
REVISIONS = ["issue535-base", "issue535-v7"]
CONFIGS = [
IssueConfig(
... |
5b924cd48bf38748e95b4af3de04f9a518b430d403a620e626c5e07453cad368 | Python | 2,694 | 79 | import torch
import torchvision.transforms as transforms
from torchvision import datasets
from torch.backends import cudnn
def CIFAR_data_loaders(args):
# Configure device and DataLoader parameters
if len(args.gpu_ids) > 0 and torch.cuda.is_available():
cudnn.benchmark = True # Enable cudnn optimizat... |
2a64747b83e7b9b059a3b5895342167653bf6efe9061f56bc13b107b9af34bf7 | Python | 2,695 | 69 | # ********** a running example **********
# initializa a network
# and give input to the network
# and get the output of the network
# and export the data for visualization
# commond: python run.py --config /home/zhaomengdi/Project/eworm/Celegans_as_deep_net_net/chemotaxis_net/config.json --randseed 0
import sys
sys.... |
e59400f5977fe293ff08ebc0dcf46f48c5ff23f9868c7122590445ff300c315d | Python | 2,695 | 64 | """
Optuna example that demonstrates a pruner for XGBoost.
In this example, we optimize the validation accuracy of cancer detection using XGBoost.
We optimize both the choice of booster model and their hyperparameters. Throughout
training of models, a pruner observes intermediate results and stop unpromising trials.
... |
6cc38e02af7e76025c498b099ffebfa0163cf21a22d83febd9a834db981a0209 | Python | 2,696 | 98 | #!/bin/env python3
'''
Analytical data resembling a spiral excitation wave
Alternative implementation by Desmond Kabus
Author: Desmond Kabus
'''
import numpy as np
from typing import List, Tuple
from enum import Enum
colors = {
"SM": "#000000",
"SP": "#d9b99b",
"UM": "#f5f5dc",
"UP": "#ffffff",
"... |
8bfd8deb454fd7c4f84ccd264024065d509fb853f22eaddfcea5d57d829520ae | Python | 2,696 | 84 | import torch
import numpy as np
from utils.complex_utils import complex_utils as Z
def per_image_standardization(image):
"""
from: https://discuss.pytorch.org/t/per-image-normalization/22141/3
This function creates a custom per image standardization
transform which is used for data augmentation... |
9b7d15f75fe0c2baea825eb902182724b26a494800e3877538f118db27f2c5e4 | Python | 2,696 | 77 | """Tests for cog.input module (Input, FieldInfo)."""
import pytest
from cog import Input
from cog.input import FieldInfo
class TestInput:
"""Tests for Input() function."""
def test_input_returns_fieldinfo(self) -> None:
result = Input(description="Test input")
assert isinstance(result, Fiel... |
ccbe583fb9e19b7dc7abcc89138f1b48548cad9a14fec6cc06712dca938e3392 | Python | 2,696 | 65 | #----Figure_07_S16_preparation--------------------------------------------------
#-------------------------------------------------------------------------------
# This is the code which has to be run in preparation for Figure 07 Panel E and
# S18 for the connectivity analysis for Reinhard and Fukuda et al. 2024
#... |
39a2881dbcc93dc2d1bcd0716380ceab7276bc5ad3529083ee4cfe7992f518f3 | Python | 2,697 | 68 | import pandas as pd
from scipy.io import loadmat
path = '/m/cs/scratch/networks-pm/effects_externalfactors_on_functionalconnectivity/results'
hypothesis = 'H7'
measure = 'parti-coeff'
def convert_array_to_dfs(array, mapping, variables):
"""
Convert a numpy array of shape (n, 16, m) to a list of m DataFrames o... |
d03f6de141849634ffec750bd5a421baea828e4e13041a75d0b4ad4de0ad5ab6 | Python | 2,697 | 86 | import contextlib
import datetime
import io
import tempfile
from typing import List, TypeVar
import atheris
T = TypeVar("T")
class EnhancedFuzzedDataProvider(atheris.FuzzedDataProvider):
def ConsumeRandomBytes(self) -> bytes:
return self.ConsumeBytes(self.ConsumeIntInRange(0, self.remaining_bytes()))
... |
43ea75a4c3f40cd5768e45b21bc519769b920ce0bdccf653873bb212c26909fe | Python | 2,698 | 77 | import inspect
import pkgutil
import importlib
from typing import Set, List
import merlin
from merlin.plots._base import AbstractPlot
from merlin.plots._base import PlotMetadata
def get_available_plots() -> Set:
""" Get all plots defined within any submodule of merlin.plots
Returns: a set of references to t... |
22c6abfc8e9a18c1a2c1fb3b9f594bc85a53d99610c4f297fda752f89eb3aa39 | Python | 2,699 | 59 | #!/usr/bin/env python
## this script creates dataframes from the full distance matrices for control matrices (age, sex)
## and saves them to a new CSV file
## The dataframes contain the distances values for each pair of subjects.
import pandas as pd
from pathlib import Path
# Load the all pairs list
data_dir = Path('... |
2a65db848cbc1a71d0173d5b8c12a66e739739877f8941f6ffed83d264859fa6 | Python | 2,699 | 65 | """Adapter for PyCox survival predictions."""
from __future__ import annotations
from abc import ABC
import numpy as np
import pandas as pd
from SurvivalEVAL.evaluations.custom_types import NumericArrayLike
from .survival_evaluator import SurvivalEvaluator
class PycoxEvaluator(SurvivalEvaluator, ABC):
def __... |
9a1bd045080a6074e8c2195d30079c73b308b3401fbf7c660e68283d5add9239 | Python | 2,699 | 67 | from typing import Dict, Sequence, Union
import torch
from torch.nn.functional import interpolate
from ..base_transform import EEGTransform
class Resize(EEGTransform):
r'''
Use an interpolation algorithm to scale a grid-like EEG signal at the spatial dimension.
.. code-block:: python
from torc... |
bbcb3a8ee945e491855db035c50c4606b049e6c8969526375a1a750b672e6d41 | Python | 2,699 | 103 | """ Test suite for the learning_experiment.py file """
from learning_experiment import LearningExp
def test_LearningExp():
e1 = LearningExp.load("data/LearningExp_190501_S5_001_log.txt")
N = len(e1.data)
all_exposure_data = e1.get_exposure_data()
all_guessing_data = e1.get_guessing_data()
all_... |
bfe66027edc6304242c08e7eb93842c6d9d92a054b55cc353f949d79c06ff6b0 | Python | 2,699 | 61 | """The panel widget. Every callback below runs on the GUI thread (the context guarantees it)."""
from collections import deque
from PySide6.QtGui import QColor, QPainter, QPen
from PySide6.QtWidgets import QLabel, QVBoxLayout, QWidget
class Sparkline(QWidget):
def __init__(self):
super().__init__()
... |
de847f7f7853d124b2f21decfe608ad50bb1e3e2ff473ea9d7c614443b9f3e1b | Python | 2,699 | 98 | import numpy as np
def embed_gaussian(d, n=1):
"""
returns n normal vectors with variance = 1/n, inline with Plate's caluclations
:param d: (int), dimensions of the embedding
:param n: (int, default=1), number of embeddings to return
:return: d-length np.array
"""
return np.random.normal... |
1af9d5775f57df09c3685d8111803537259d19991956d75ad708445b07160b10 | Python | 2,700 | 97 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# 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 applicab... |
303874dbabafea91159059a1c2570955b0b97aaef22d3327b38331cb4d67dceb | Python | 2,700 | 110 | from __future__ import annotations
import pytest
prefect = pytest.importorskip("prefect")
from ase.build import bulk, molecule
from quacc import flow
from quacc.recipes.emt.core import relax_job, static_job
from quacc.recipes.emt.slabs import bulk_to_slabs_flow
def test_tutorial1a(tmp_path, monkeypatch):
monke... |
d521d96c2afb1c74ca140be58a0034c3a1efb1a83d016534f234d7470ab18edd | Python | 2,700 | 87 | import sys
import logging
import numpy as np
from remora import log
from remora.model_util import load_model
from remora.data_chunks import RemoraRead
from remora.inference import call_read_mods
class CustomFormatter(logging.Formatter):
err_fmt = "> error (remora): %(msg)s"
warn_fmt = "> warning (remora): %(m... |
44aad1ff4e67bc52c12812d9a8e9afedac1eceec5e8277a49f5b7044a291eb7e | Python | 2,701 | 70 | import os
import subprocess
import numpy as np
import pandas as pd
import glob
import sys
from multiprocessing import Pool
import multiprocessing
###########################
# This script will run SPrediXcan on
# dyslexia and rhythm impairment CPM
# sumstats.
# 10.04.2023 (provided by Yasmina Mekki)
################... |
4636ba865da51cab58c88de026f1ab81877535479cd888c273f4f02fc9008a66 | Python | 2,701 | 97 | # script for testing python video reader to matlab video reader on windows.
import cv2
import scipy.io as sio
import numpy as np
import movies
import hdf5storage
import os
import glob
import imageio
import logging
on_compressed = True
dd_all = []
for machine in ['GLNXA64_h06u08.int.janelia.org_R2018a',
... |
55ca1a5768eafd7aa878a5b51e22dea092e8d3e869b7c6430143758f3e13d962 | Python | 2,701 | 29 | """MEASURE_FIRST_CENSUS.py 2026-10-02. The census's measure-first list: every neuron whose single wrong sign costs at least one
odour channel (full rate theory where checked, first order otherwise), ranked by expected harm = chance the model's sign is
wrong x channels lost. Output: 06-OUTPUT/release/MEASURE_FIRST_SIG... |
5f21057abb58e5fad40d9a92f92eca5278dd8c5e97a8aa32eedd3e22de7500cd | Python | 2,701 | 94 | from sys import argv
from ase.io import read, write
from ase.db import connect
from ase.atoms import Atoms
import numpy as np
def parsedb(dbpath):
db = connect(dbpath)
# this function adds "has_forces" and "has_gradients" if this is not already stored in the db.
# it adds "dummy"-forces or "dummy"-gradie... |
5f77312cab09faabd08c966c719a5909c68547147df2a3c7fd83f4840339a2ca | Python | 2,701 | 85 | # -*- coding: utf-8 -*-
#
# central pytest configuration
#
# Builtin/3rd party package imports
import sys
import pytest
from syncopy import __acme__
import syncopy.tests.test_packagesetup as setupTestModule
import dask.distributed as dd
import dask_jobqueue as dj
from syncopy.tests.misc import is_slurm_node
# If acme... |
6d9c437ff40ca8a2501665b2fbf4290b0d90a6c044a42857740bb4f411098c28 | Python | 2,701 | 75 | ### Step 1: Define the Python Class
import numpy as np
import tensorflow as tf
from tensorflow.keras.models import Sequential
from tensorflow.keras.layers import Conv3D, MaxPooling3D, Flatten, Dense, Dropout
from tensorflow.keras.optimizers import Adam
from tensorflow.keras.utils import to_categorical
class VGGNet3DA... |
927a1bb0f0427ab482b5a174b9b36ccdbe7e88487eebe1e2fd74647cb9a2d963 | Python | 2,701 | 89 | # %%
import os
os.environ['CUDA_VISIBLE_DEVICES'] = "0"
import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch_geometric.data import DataLoader
import argparse
from metrics import get_cindex, get_rm2
from dataset import *
from model import MGraphDTA
from utils import *
from me... |
cc4212e4fea1f2656062ba90868b199a77f812bd7eb79b6919073bf7fe55abe8 | Python | 2,701 | 66 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
from downward import suites
from downward.experiment import FastDownwardExperiment
from downward.reports.compare import CompareConfigsReport
import common_setup
REPO = common_setup.get_repo_base()
REV_BASE = 'issue585-base'
REV_V1 = 'issue585-v1'
SUITE = ['gripper:prob0... |
43a58385cf5a89f52fd25983a3fa966a9e08eacc1945d76ab47c886077b03bd1 | Python | 2,702 | 66 | import datasets
import lightning.pytorch as pl
from hicdiffusion_model import HiCDiffusion
from lightning.pytorch.callbacks import ModelSummary
import os
import shutil
from lightning.pytorch.loggers import WandbLogger
import time
import argparse
from lightning.pytorch.callbacks import ModelCheckpoint
def main(val_chr,... |
c7301a0147fd00b9e253fbef6186d2fa6b4a4cce346e590bee73d619575d9092 | Python | 2,702 | 102 | from baseline import get_unet
from glob import glob
from PIL import Image
from skimage.transform import resize
import numpy as np
from matplotlib import pyplot as plt
from skimage.morphology import label
from pycocotools import mask as maskUtils
from tqdm import tqdm
import os
import cv2
from keras.layers import ReLU
f... |
e4de63451ab6d68050cab2d4db4ba655279450386cc6a36f349683e9f9136960 | Python | 2,702 | 72 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# 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 applicab... |
6a1df2be8c6481b74c50d016c52dd2caa714b956a604e49eb96905d904401303 | Python | 2,703 | 117 | from pertpy.data._datasets import (
adamson_2016_pilot,
adamson_2016_upr_epistasis,
adamson_2016_upr_perturb_seq,
aissa_2021,
bhattacherjee,
burczynski_crohn,
chang_2021,
cinemaot_example,
combosciplex,
datlinger_2017,
datlinger_2021,
dialogue_example,
distance_exampl... |
653e622eb24914c2c4ab1f986d01897dd9aa6729cc952bd119cd8806648fbc12 | Python | 2,704 | 76 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# 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 applicab... |
bc34fe61fb65722be7652b12aaadc54373c181477255ed3bb56e6451689f5983 | Python | 2,704 | 100 | #!/usr/bin/env python3
## this script visualizes the results of the anova movie comparison of the ISC values
## it reads in the results of the anova and visualizes the results on a glass brain
## it also writes the results to nifti files (if needed)
## import libraries
import os
import pandas as pd
import matplotlib.p... |
1f82e749ca932840662fe8541f9a068935da6ea2b367f0d811c6f4d16e8d27af | Python | 2,706 | 50 | """FLY_TO_FLY.py 2026-09-30. Pre-registration: 04-NOTES/PREREG-2026-09-30k-FLY-TO-FLY.md
Do FlyWire and BANC disagree, or do two runaways disagree? Projection-neuron rates to Seki et al.'s 17 odours, FlyWire
(whole brain, HEAD_TO_HEAD rows) against BANC (antennal-lobe cut-out, BANC_TEST rows), under matched sign sets... |
2db7ba8f3bc48a2667096ea4d0ebe3211eaf68a65fe178a38ac94f478526b0dd | Python | 2,706 | 48 | """Leak Rate Dynamics: reservoir memory, steering geometry and influence on Qwen at several leak rates.
Run from Experiments -> Run Python Script... Edit the settings below first. Nothing in the
engine changes: the plugin sets the leak rate (as the RESERVOIR DYNAMICS control does), runs
read-only steering probes and, ... |
f2688d55a3b686baf412e9700855f7c131c0d162384bd12cb1cdabd89403c4d5 | Python | 2,707 | 68 | import os
import wget
url_dict = {
"train_pbmc": "https://www.dropbox.com/s/wk5zewf2g1oat69/train_pbmc.h5ad?dl=1",
"valid_pbmc": "https://www.dropbox.com/s/nqi971n0tk4nbfj/valid_pbmc.h5ad?dl=1",
"train_hpoly": "https://www.dropbox.com/s/7ngt0hv21hl2exn/train_hpoly.h5ad?dl=1",
"valid_hpoly": "https://... |
1a7b63ce65da98be6de4b99a2d63bb87be238bdaa6e0e91eb92e85a97174b66f | Python | 2,708 | 95 | """
Optuna example for fine-tuning a BERT-based text classification model on the IMDb dataset
with hyperparameter optimization using Optuna. In this example, we fine-tune a lightweight
pre-trained BERT model on a small subset of the IMDb dataset to classify movie reviews as
positive or negative. We optimize the validat... |
e536224103f006a09d4af8120baadc170b4434830256951671b2b5a1a730e1c5 | Python | 2,708 | 78 | from sitetack.app.kmer import Kmer
class TestKmer:
def test_site_to_kmer_site_in_middle_generates_correctly(self):
sequence = "ABCDEFGHIJK"
site = 6
length = 5
expected = Kmer(site=site, subsequence="DEFGH")
actual = Kmer.site_to_kmer(sequence, site, length)
assert ... |
24d4f70a83626daadf24851ceb69d01e930690c0422737cc4bfc7f18ab92e215 | Python | 2,709 | 95 | """
Core recipes for EMT.
NOTE: This set of minimal recipes is mainly for demonstration purposes.
"""
from __future__ import annotations
from typing import TYPE_CHECKING
from ase.calculators.emt import EMT
from quacc import job
from quacc.runners.ase import Runner
from quacc.schemas.ase import Summarize
if TYPE_C... |
66d9233ef75e7e79c93599e903c2d7a168911231d637fa13772509ec7fa4b430 | Python | 2,709 | 86 | from examples.pybullet.utils.pybullet_tools.pr2_primitives import iterate_approach_path
from examples.pybullet.utils.pybullet_tools.utils import pairwise_collision, get_distance
#######################################################
def get_cfree_approach_pose_test(problem, collisions=True):
# TODO: apply this ... |
8090bd75737e1c8403ea3bb9419254308588ea4ec0bd907e723508553ee33825 | Python | 2,709 | 81 | import importlib
import os
from pathlib import Path
import numpy as np
from torch.utils.data import DataLoader
class ChunkDataSet:
def __init__(self, chunks, targets, lengths):
self.chunks = np.expand_dims(chunks, axis=1)
self.targets = targets
self.lengths = lengths
def __getitem__(... |
4f7b68545c7108097c277771e4186c4727bfe24e906c10959f0a087da69be082 | Python | 2,710 | 68 | import torch
import numpy as np
from torch.utils.data import Dataset
class ConeGeometry(object):
"""
Cone beam CT geometry. Note that we convert to meter from millimeter.
"""
def __init__(self, data, index=0):
# VARIABLE DESCRIPTION ... |
b6d3a66b6661c9ba640ec50eb943d481e07c371228a3605582de43be6cb9f6c0 | Python | 2,710 | 86 | """Kolmogorov-Smirnov helpers for distributional calibration metrics."""
from __future__ import annotations
import numpy as np
from scipy.stats import kstwobign
def discrepancy_to_uniform(
x: np.ndarray,
cdf: np.ndarray,
x_support: tuple[float, float] | None = None,
) -> float:
"""
Compute the K... |
c4feb58ddaac50c2a4bf951852a371dd7c30a10d99a6d82cfc13060c3a0187fc | Python | 2,710 | 102 | from baseline_aug import get_unet
from glob import glob
from PIL import Image
from skimage.transform import resize
import numpy as np
from matplotlib import pyplot as plt
from skimage.morphology import label
from pycocotools import mask as maskUtils
from tqdm import tqdm
import os
import cv2
from keras.layers import Re... |
f65e96f268d5ac48c04c1a4b20ee21b33b112400eda4ab5c6f6cb2a6d18e0884 | Python | 2,710 | 82 | import cocotb
import pytest
from cocotb.triggers import Timer
from torch import asarray
from elasticai.creator.arithmetic import FxpParams
from elasticai.creator.nn.fixed_point import ReLU
from elasticai.creator.testing import CocotbTestFixture, eai_testbench
from elasticai.creator_plugins.act_func.utils import load_a... |
6bce8cc2d93800f62c35bed431eba96bf1bc5a6358a557e7d091b28e598aa1a5 | Python | 2,711 | 108 | #******************************************
#
# SHARC Program Suite
#
# Copyright (c) 2023 University of Vienna
#
# This file is part of SHARC.
#
# SHARC is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software F... |
ee7c66f267afab19b8c671b396d0ad00818ebe8394ec658dc51108325f306713 | Python | 2,711 | 58 | import torch
from .layer import Layer
class CoherenceNet(torch.nn.Module):
def __init__(
self,
config_lay1,
config_lay2
):
"""Initilize Energy predictor module.
Args:
"""
super(CoherenceNet, self).__init__()
self.config_lay1 = config_lay... |
fb8ad91bf5dbc7cb418f18e68feba7af6e9908b11087be629d527da6991235ec | Python | 2,711 | 66 | supervised_learning = False
options = dict(requires_training_frame=False, model_extensions=['h2o.model.extensions.Contributions', ])
def class_extensions():
@staticmethod
def from_file(file=str, model_id=None):
"""
Creates new Generic model by loading existing embedded model into library, e.g.... |
6352ba156bd84c1d70b9ada99c051d3213ab801649a26dbf12ec479ce32697f2 | Python | 2,712 | 87 | # -*- coding: utf-8 -*-
# @title Compare emulation in software and hardware
# @file validation.py
# @author Romain Beaubois
# @date 06 Oct 2023
# @copyright
# SPDX-FileCopyrightText: © 2023 Romain Beaubois <refbeaubois@yahoo.com>
# SPDX-License-Identifier: GPL-3.0-or-later
#
# @brief
#
... |
6ed9061d0365f9af220eb37e9b01cf8ec44be18089242c9d5ccbbfcb5d774db3 | Python | 2,712 | 110 | """Init data for quacc."""
from __future__ import annotations
import logging
import threading
from importlib.metadata import version
from typing import TYPE_CHECKING
from ase.atoms import Atoms
from pymatgen.io.ase import MSONAtoms
from quacc.settings import QuaccSettings, change_settings
from quacc.types import De... |
e377522d19d60a846b9c0e40533b5cf3481f4b40c403650b2cf4f9e304451149 | Python | 2,712 | 100 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
"""
import matplotlib.pyplot as plt
import numpy as np
NUM_PHASES = 1
in_name = 'x'
hid_name = 'h1'
out_name = 'o'
hid_T_p = 'h1T+'
out_T_p = 'oT+'
hid_T_m = 'h1T-'
out_T_m = 'oT-'
phase_in = 1
phase_hid = 2
phase_out = 3
phase_err = 4
phase_W2pot = 5
phase_W2dep = ... |
3cfaab03261d032b75983a36655cdadc9e7fedf9a15abb43ed3b219c2edbbb90 | Python | 2,713 | 74 | # flake8: noqa
# There's no way to ignore "F401 '...' imported but unused" warnings in this
# module, but to preserve other warnings. So, don't check this module at all.
# Copyright 2021 NVIDIA Corporation and The HuggingFace Team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"... |
5b24b3556b6d55ceb1f5c7550129cb981f3ac915e4f311a1af2dd45f23886eae | Python | 2,714 | 71 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
def test_esm_if1():
import json
import numpy as np
from pathlib import Path
from scipy.stats import special_ortho_group
f... |
5e8b220631f8cd772e0816bf1d4294e16f615616718d6d64a7882d2588c9ba49 | Python | 2,714 | 75 | """Some standard gradient-based stochastic optimizers.
These are just standard routines that don't make any use of autograd,
though you could take gradients of these functions too if you want
to do meta-optimization.
These routines can optimize functions whose inputs are structured
objects, such as dicts of numpy arr... |
a49409db9331c0c327d20777accb41cd326c9bfafd04da29e47b61d7f0ee39e0 | Python | 2,714 | 92 | import numpy as np
from hippo.environments.w_maze import WmazeTasks
from hippo.agents.prefrontal_agent import LocationRewardMerger
tasks = [
[0, 1, 2, 1], # LCRC
[0, 1, 0, 2], # LCLR
[2, 1, 2, 0], # RCRL
[0, 1, 0, 1],
[0, 2, 0, 1],
[0, 2, 0, 2],
[0, 2, 1, 2],
[1, 0, 1, 0],
[1, 0,... |
a75601a26e46a80b0ac1e02a544142dfc676c50eb862be55f83b0e5052bad372 | Python | 2,714 | 99 | # Node-group asset "Get Geometry Atoms" (GeometryNodeTree), dumped by nodebpy.assets.dump_library.
# Rebuild the library with nodebpy.assets.build_library (nodebpy build).
# _build_group() is the source of truth: the docstring, __init__ and accessors are regenerated from it on the next dump.
from typing import TYPE_CHE... |
df76d3612dbb27d0fbb8aa331d640716f36e04399ad87c12a3f66d1f7944c313 | Python | 2,714 | 90 | from tqdm import tqdm
from os.path import join as pjoin
import pandas as pd
import os
from scipy.stats import zscore
import argparse
from nilearn.masking import unmask
import logging
from dimension_encoding.utils import load_clip66_preds, load_singletrial_data
from dimension_encoding.glm import LinRegCVPermutation
d... |
30b870aa51903d46893349db50f507456261f2e8ff649c0153c65bdc365f5a38 | Python | 2,715 | 42 | # -*- coding: utf-8 -*-
import argparse
from supar import VISemanticDependencyParser
from supar.cmds.run import init
def main():
parser = argparse.ArgumentParser(description='Create Semantic Dependency Parser using Variational Inference.')
parser.set_defaults(Parser=VISemanticDependencyParser)
subparser... |
34e54a5a7f88b07355444b9a8b3c2c6e5d772264e93e39fe494ed1b0fedaf6e9 | Python | 2,715 | 100 | # Configuration file for the Sphinx documentation builder.
#
# For the full list of built-in configuration values, see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
# -- Project information -----------------------------------------------------
# https://www.sphinx-doc.org/en/master... |
51da23a00cbfa85ccb5f9a990ae589aef29e9988d25878b627ce6ace7af8ebd8 | Python | 2,715 | 75 | """
Library to handle snapping coordinates to an mri surface
(defaults to pial surface, but customizable)
"""
import os
from config import RHINO_ROOT
import numpy as np
import nibabel as nib
from scipy import spatial
def get_raw_coordinates(filename):
"""
Gets coordinates from a "RAW_coords" file
Meant to ... |
df3b23709d2b02bc93afbe038e0437009ca99bc858f80d16f843cf67c979222e | Python | 2,715 | 75 | # ----------------------------------------------------------------------
# Copyright (C) 2016, Numenta, Inc. Unless you have an agreement
# with Numenta, Inc., for a separate license for this software code, the
# following terms and conditions apply:
#
# This program is free software: you can redistribute it and/or mo... |
580f03399e02f987e2be4ca39d41321a81a47f9399580ea7c75c3709893b0328 | Python | 2,716 | 84 | """SVM decoding from microsaccade-rate features.
The paper reports ~85% accuracy on a face-vs-non-face binary task using
linear classifiers on the binned-rate feature vector. This module wraps
that recipe in a thin scikit-learn pipeline so callers don't have to
assemble it themselves.
"""
from __future__ import annot... |
76d4dadc97b30120a7f5641360541d0ac6a7ff193cf8e77f1b30fbce1726ed77 | Python | 2,716 | 88 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
@author: emma
"""
from numpy.random import seed
seed(1)
import tensorflow as tf
tf.random.set_seed(1)
import random
random.seed(1)
import numpy as np
import pandas as pd
import tensorflow as tf
import SimpleITK as sitk
from tensorflow.keras.utils import to_categorical... |
66ee1581426fef1fbc083bbe46cda40c4cab6f104fb53ff45295dc1fd46d2d88 | Python | 2,717 | 74 | # -*- coding: utf-8 -*-
"""
Created on Sat May 22 16:14:08 2021
@author: Maddox
"""
import numpy as np
from expyfun.io import read_hdf5, write_hdf5, read_wav
# opath = 'C:/Users/Maddox/Code/Experiments/pip_speech_shift/'
opath = '/mnt/data/peaky_pitch/stimuli/slices/'
click_root = 'clicks_{}.hdf5'
speech_... |
75fe61bf86fb7de541650ba3d535a1e51ec960f3b8cb1cad5a6c92f56b73156c | Python | 2,717 | 71 | # set QT_API environment variable
import os
os.environ["QT_API"] = "pyqt5"
import qtpy
# qt libraries
from qtpy.QtCore import *
from qtpy.QtWidgets import *
from qtpy.QtGui import *
import control.utils as utils
from control._def import *
import control.tracking as tracking
from queue import Queue
from threading im... |
2648863831f571421905905206a473da29208c2b16ac33a2e792d201cb201bd4 | Python | 2,718 | 73 | import numpy as np
import pytest
from scipy.interpolate import interp1d
import SurvivalEVAL.evaluations.others.area_under_pr_curve as auprc_module
def _scipy_cdf_row(cdf, times, targets, left_fill=None):
return interp1d(
times,
cdf,
kind="linear",
fill_value=(cdf[0] if left_fill i... |
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