sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
8e6f51b47b459225e83354750d333b4875f33a92b25c5b1438f1f0c6e02e6352 | Python | 305 | 14 | from typing import List, TypeVar
import torch
T = TypeVar("T")
def one_hot_encode(value: T, categories: List[T]) -> torch.tensor:
"""
One-hot encode a value.
"""
tensor = torch.zeros((1, len(categories)), dtype=torch.int64)
tensor[0, categories.index(value)] = 1
return tensor
|
17cfee701711d0cff792ceaed394ceb3145af6b3a8056050c4840e9b8898b620 | Python | 306 | 14 | """Hi-Compass commands."""
from . import preprocess_atac
from . import preprocess_hic_norm
from . import preprocess_hic_to_npz
from . import training
from . import predicting
__all__ = [
'preprocess_atac',
'preprocess_hic_norm',
'preprocess_hic_to_npz',
'init_training',
'predicting'
] |
59cffe7ffd1ec60295dd04fdd2a7fa137b9a0434c0f04d371cc5344c270c3fd8 | Python | 314 | 10 | import numpy as np
def resample_signal(signal, source_rate, target_rate):
if source_rate > target_rate:
return signal[::int(source_rate / target_rate)]
else:
return np.repeat(signal, int(target_rate / source_rate))
def get_time_points(signal):
return np.where(np.diff(signal) > 0)[0]
|
7cc85e19790b14e7074677a8e0d93fe7eff1a701120ce131f55928fad8b154dd | Python | 316 | 12 | import gl
gl.resetdefaults()
gl.azimuthelevation(70, 15)
gl.meshload('BrainMesh_ICBM152Right.mz3')
gl.overlayload('motor_4t95vol.nii.gz')
gl.overlayminmax(1,2,12)
gl.overlayload('motor_4t95vol.nii.gz')
gl.overlayminmax(2,-1,-2)
gl.colorbarvisible(1)
gl.overlaytransparencyonbackground(25)
gl.meshcurv()
|
70cae085ed6ce9efbd5c42bad78106f9c41160b24ba0e35bdf9a27f9a0121557 | Python | 321 | 11 | """
src/sweep — Sweep Engine
=============================
Orchestrates the large-scale degradation sweep:
25 datasets × 84 conditions × 11 methods × 30 repeats.
"""
from .engine import SweepEngine, SweepResult
from .surface import aggregate_surfaces
__all__ = ["SweepEngine", "SweepResult", "aggregate_surfaces"]
|
4001a38b25331334c3d1831881c60c09541847270aa5f8c0c4fc2a80cc0cae2e | Python | 323 | 15 | """
The `py/` submodule contains python (non-pytorch) implementations of various helper functions.
Modules
-------
generators
Data generators for medical image registration.
utils
General-purpuse python utilities for VoxelMorph.
"""
from . import utils
from . import generators
__all__ = ['utils', 'generators... |
2c3763c00e42380c95adf5134a3679a961a78cf77674ad1e3834b0a2a45d1181 | Python | 325 | 17 | """Hi-Compass training module."""
from .HicompassDataset import ChromosomeDataset
from .HicompassModel import ConvTransModel
from .HicompassTrain import TrainModule, init_training
__all__ = [
# Dataset
'ChromosomeDataset',
# Model
'ConvTransModel',
# Training
'TrainModule',
'init_trainin... |
bedaa2b9108cdaa589f1a1a74d39bc70e0ef066521e2dfef21974d3a837a9f78 | Python | 327 | 6 | import pandas as pd
df = pd.read_csv(snakemake.input[0], sep="\t")
df.loc[df["probability"] >= float(snakemake.config["ashleys_threshold"]), "prediction"] = 1
df.loc[df["probability"] < float(snakemake.config["ashleys_threshold"]), "prediction"] = 0
df.sort_values(by="cell").to_csv(snakemake.output[0], sep="\t", index... |
28a1893b303d5e5249a158c598cdc2606beeb6d84b5fd6cb016c5aab60d130dd | Python | 329 | 15 | from setuptools import setup, find_packages
setup(
name="rd_filters",
version="0.1",
packages=find_packages(),
entry_points={
'console_scripts': [
'rd_filters=rd_filters.rd_filters:main',
],
},
install_requires=['pandas', 'docopt', 'rdkit'],
include_package_data... |
adf6bcfd43d32d02b5b821084f9e2b589df5448eaebb9a462956508ac5d62c3a | Python | 329 | 13 | import os
input_folder = '..//0_used_data//t1_fse_flair_tra'
os.system('python main.py --ni --config imagenet_256.yml --output_path results_5T \
--path_y celeba_hq --eta 0.85 --deg "denoising" --output_folder t1_fse_flair_tra_v2 \
--deg_scale 1.0 --noise_rate 0 --add_noise \
--lambda_t 100 --input_folder '+input_... |
d84222b29e6cba532bc5a144fffcd08d485dfa88b63719de6e49d893e22bbec7 | Python | 329 | 12 | import pytest
@pytest.fixture(scope='module', params=["classifier", "regressor"])
def boosting_alg_type(request):
return request.param
@pytest.fixture(scope='module',
params=["AdaBoost", "GBoost", "LR", "NGBoost", "RF", "SGBoost", "SVM_RBF", "SVML", "XGBoost"])
def boosting_method(request):
return reque... |
20aecede9b1bec24b2ab6d0bef07b5bba9c6ff8c32a3ef5a651a82845fc9d6d4 | Python | 332 | 27 |
"""
Library of useful routines for virtual epileptic patient workflows.
"""
from .io.stan import (
cmdstan_path,
compile_model,
parse_csv,
rdump
)
from .plots.stan import (
pair_plots,
trace_nuts
)
from .plots.network import (
phase_space
)
from .plots.seeg import (
ppc_seeg,
... |
16f436c7e43664f304990257c17d2f29a28c58b9bd3a717b9cddd4b12122f9b0 | Python | 334 | 12 | import numpy
import pytest
shapely20_todo = pytest.mark.xfail(
strict=True, reason="Not yet implemented for Shapely 2.0"
)
shapely20_wontfix = pytest.mark.xfail(strict=True, reason="Will fail for Shapely 2.0")
def pytest_report_header(config):
"""Header for pytest."""
return f"dependencies: numpy-{numpy.... |
2cf4f745c9108fd310d85f891300dfe5c95822d09b41df4aa05c0513671e7337 | Python | 334 | 16 | __all__ = []
from ._pathing import *
from . import _pathing
from ._retrieval import *
from . import _retrieval
from ._processing import *
from . import _processing
from ._analysis import *
from . import _analysis
__all__ += _pathing.__all__
__all__ += _retrieval.__all__
__all__ += _processing.__all__
__all__ += _anal... |
a931339208d99ebf9de82d3cc7c919a0dc8fc4e0be037927c067ff9a2c89d7f7 | Python | 334 | 15 | __all__ = []
# Treat entire folder as a single modlue
from . import _graphs
from ._graphs import *
from . import _edge_processing
from ._edge_processing import *
from . import _metapaths
from ._metapaths import *
# Add the imported items
__all__ += _graphs.__all__
__all__ += _edge_processing.__all__
__all__ += _metap... |
23193dbd69f3e122791df19fd16ddb2fd4a58be348c057a81ac247c78478ac1a | Python | 335 | 9 | """
This file is used to run the experiment.
Note that it should always be run from within the main project directory, since the structure of the package is designed with that expectation.
"""
if __name__ == '__main__':
from expts.controllers import Controller
Controller()
#import profile
#profile.run('... |
9e2a015b846652dbb457126934aac47df425f9899c778c57a2e914906463626a | Python | 338 | 11 | import unittest
import caffe
class TestLayerTypeList(unittest.TestCase):
def test_standard_types(self):
#removing 'Data' from list
for type_name in ['Data', 'Convolution', 'InnerProduct']:
self.assertIn(type_name, caffe.layer_type_list(),
'%s not in layer_type_lis... |
7b3072887265f6f0e42c4de89ab2d5772437e4ae2addd7b700d28a95ca8b0798 | Python | 339 | 15 | """
Unit and regression test for the proteinbenchmark package.
"""
# Import package, test suite, and other packages as needed
import sys
import pytest
import proteinbenchmark
def test_proteinbenchmark_imported():
"""Sample test, will always pass so long as import statement worked."""
assert "proteinbenchma... |
cafab7300073dde4ef2dd441e7f5105ef268322d0385081a2810ac091954ebf5 | Python | 339 | 11 | """
:mod:`alchemiscale.strategist` --- strategist service
====================================================
The strategist service coordinates the execution of strategies on alchemical networks.
"""
from .service import StrategistService
from .settings import StrategistSettings
__all__ = ["StrategistService", "St... |
c3621bb110e072346c7c60c820684c4ad32311a511b10f4add6649348c5b0e1a | Python | 340 | 9 | from openff.nagl.features import atoms
def test_atom_hybridization_categories_validation():
assert atoms.AtomHybridization(categories=['OTHER', 'SP', 'SP2', 'SP3']).categories == [
atoms.HybridizationType.OTHER,
atoms.HybridizationType.SP,
atoms.HybridizationType.SP2,
atoms.Hybridiz... |
eb41efad5bd5d8275ce0e7ec5abc639aa98b7a545c9786ef9406cb484306a60e | Python | 340 | 8 | from PyInstaller.utils.hooks import collect_submodules
from PyInstaller.utils.hooks import collect_data_files
hiddenimports = collect_submodules("ants")
datas = collect_data_files("ants")
#pyinstaller --noconfirm --clean --onefile --paths=/home/andrep/workspace/neuro_rads_prototype/venv/lib/python3.6/site-packages/a... |
8848e846b863d50423d1f8066d4098141065e89dbd4289b3a62cb1994d22beb7 | Python | 346 | 12 | import warnings
# noinspection PyUnresolvedReferences
from multiqc.report import * # noqa: F403
# Issue a deprecation warning
warnings.warn(
"Importing 'report' from 'multiqc.utils' is deprecated and will be removed in a future release. "
"Please use 'from multiqc import report' instead.",
DeprecationWar... |
e16a4fd97f31be02f69d3dcdd5da9ad2a3c4efbe0b3d17c2c6808fdf0d539582 | Python | 346 | 12 | import warnings
# noinspection PyUnresolvedReferences
from multiqc.config import * # noqa: F403
# Issue a deprecation warning
warnings.warn(
"Importing 'config' from 'multiqc.utils' is deprecated and will be removed in a future release. "
"Please use 'from multiqc import config' instead.",
DeprecationWar... |
8c933900fb00daef3f71d6ee04b331375f44c6c74bbc8fc5b5e5aca08787c29a | Python | 349 | 16 | class MissingUnitError(ValueError):
"""
Exception for data missing a unit tag.
"""
class UnitValidationError(ValueError):
"""
Exception for bad behavior when validating unit-tagged data.
"""
class UnsupportedExportError(BaseException):
"""
Exception for attempting to write to an unsu... |
0fdb761f97d79f46495e8b44c6cede62c10fdf6eb20fb79ec39729975ea00b3b | Python | 352 | 15 | """Hi-Compass preprocessing module."""
from .atac import ATACPreprocessor
from .hic_norm import HiCNormalizer, HG38_CHROM_SIZES, MM10_CHROM_SIZES
from .hic_to_npz import HiCToNPZConverter, hic_to_npz
__all__ = [
'ATACPreprocessor',
'HiCNormalizer',
'HiCToNPZConverter',
'hic_to_npz',
'HG38_CHROM_S... |
d86689179ed7720bcb331db9a6f50cd046bccef49089835cb6202a6794f473bc | Python | 352 | 16 | import datajoint as dj
from ethopy.core.behavior import Behavior
from ethopy.core.logger import behavior
@behavior.schema
class HeadFixed(Behavior, dj.Manual):
definition = """
# This class handles the behavior variables for RP
->behavior.BehCondition
"""
def exit(self):
super().exit()
... |
c35dde2a2a89be2a0c87a5a54130ee4becdb155734a1f2523a604c5b867cd01a | Python | 353 | 14 | import pytest
import networkx as nx
try:
from pathtester import PathTester
except ModuleNotFoundError:
from utils.pathtester import PathTester
indications = nx.read_yaml('indication_paths.yaml')
@pytest.mark.parametrize('path', indications)
def test_paths(path):
test_path = PathTester(path)
test_path... |
65a5867f239c92c1d46f424b307b18c188f1a68c38292a5dc7a8ed55ed8dc9db | Python | 354 | 15 | #!/usr/bin/env python
# Very simple file format conversion script, works in 90% of situations
# and good for saving keystrokes.
from forcebalance.molecule import Molecule
from sys import argv
def main():
topfnm = argv[3] if len(argv) >= 4 else None
M = Molecule(argv[1], top=topfnm)
M.write(argv[2])
if _... |
7e6d3cb72c6d53c1f2e5e6d449a7138b9549c8b54b660fb8863ad3053af68c21 | Python | 355 | 22 | import pytest
from multiqc import report, config, validation
from multiqc.utils import testing
@pytest.fixture
def data_dir():
return testing.data_dir()
@pytest.fixture(autouse=True)
def reset():
"""
Reset MultiQC session after use: reset config and report
"""
yield
report.reset()
con... |
9d36bb9b44b57657c5e52ca3b57f39b222e6d42553f722cd293fd8afac1afc68 | Python | 355 | 16 | """
Classes that define configuration options for training or using a GNN Model.
"""
from .data import DataConfig, DatasetConfig
from .model import ModelConfig
from .optimizer import OptimizerConfig
from .training import TrainingConfig
__all__ = [
"DataConfig",
"DatasetConfig",
"ModelConfig",
"Optimiz... |
1c3a87bff152be060f97a23bdd344c0135506eb6ac58b6700ae81554db6d4e3b | Python | 356 | 10 | from typing import ClassVar
from beyond_backprop.algorithms.image_classification_test import ImageClassificationAlgorithmTests
from .backprop import Backprop
class TestBackprop(ImageClassificationAlgorithmTests[Backprop]):
algorithm_type = Backprop
algorithm_name: str = "backprop"
unsupported_datamodule_... |
3f389b5da0cb566fe1e3f191b12cebf036539dbd2149213cac63980cd51a394c | Python | 358 | 15 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
from openfe.utils import requires_package
import pytest
@requires_package('no_such_package_hopefully')
def the_answer():
return 42
def test_requires_decorator():
with pytest.rais... |
69ed7afb08d24051def9705ba9ee2da3c58538683002ebc9e5446cc6577c642c | Python | 361 | 8 | from .abstract_loss import AbstractLoss
from .abstract_fitting import AbstractFitting
from .abstract_measurement_model import AbstractMeasurementModel
from .abstract_neural_model import AbstractNeuralModel
from .abstract_params import AbstractParams
from .parameter import Parameter
from .timeseries import Timeser... |
f06ffffa394bf3b5db99210372875a04c01d92568f9f5f03b603df95b1b1b7ff | Python | 362 | 18 | """The module 'pyleida.signal_tools' provides functions
to compute relevant information from BOLD time series."""
from ._signal_tools import (
hilbert_phase,
clean_signals,
phase_coherence,
get_eigenvectors,
txt_matrix
)
__all__ = [
"hilbert_phase",
"clean_signals",
"phase_coherence",
... |
361d84720803a44dc8ad0c987bab3fad9f421435bd71e1758c9f354ed36f9b47 | Python | 363 | 13 | """Shared core components for TimeFlies projects."""
from .active_config import get_active_project, get_config_for_active_project
from .config_manager import Config, ConfigManager
from .pipeline_manager import PipelineManager
__all__ = [
"PipelineManager",
"Config",
"ConfigManager",
"get_config_for_ac... |
a4b156f1721ce20dd5c687302f80fadb4ceab33fd96a67585300ff22cb0042bc | Python | 363 | 6 | from .cifar10_datamodule import CIFAR10DataModule, cifar10_normalization
from .fashion_mnist_datamodule import FashionMNISTDataModule
from .image_classification import ImageClassificationDataModule
from .imagenet32 import ImageNet32DataModule, imagenet32_normalization
from .mnist_datamodule import MNISTDataModule
from ... |
f0b422d1ba5e271cf29915c568e010d9a3c0f55c59850dbd35225cb635d26296 | Python | 363 | 12 | import argparse
import marshall_intrinsic_units
parser = argparse.ArgumentParser()
parser.add_argument("size", help="Subsystem size", type=int)
parser.add_argument("--isel", help="Subsystem index", type=int, default=None)
args = parser.parse_args()
marshall_intrinsic_units.run_blackbox_micro_example(
subsystem_s... |
2d4c072241e53094ea57f419e0e7a2eda679abb58e00ab2b1c39e2d156a50e02 | Python | 365 | 10 |
import re
import gzip
# open gzipped or regular text vcf files
def open_file_for_reading(filename):
if re.search("\.gz$", filename):
return gzip.open(filename, 'rt', encoding="utf-8", errors='ignore') # t needed for python3 to look like regular text
else:
return open(filename, 'rt', encoding="... |
c7050b0569de50802fb8f17fc793b7c44327c97375eee2a92a6b419be2b0ab6f | Python | 365 | 18 | """
MultiQC lint helpers. Simple additional tests to run when
--strict is specified (outside scope of normal functions)
"""
import logging
from multiqc import config, report
logger = logging.getLogger(__name__)
def lint_error(msg: str):
if config.strict:
logger.error(msg)
report.lint_errors.app... |
10a2ede2d5db67b6c769b234c8297bbfc1e4ba90b0121823b3fa96711b66796e | Python | 367 | 12 | import os
from dotenv import load_dotenv
load_dotenv(override=True)
OPENAI_API_KEY = os.getenv("OPENAI_API_KEY", "")
HF_TOKEN = os.getenv("HF_TOKEN", "")
HF_USER_ID = os.getenv("HF_USER_ID", "")
VLLM_N_GPUS = int(os.getenv("VLLM_N_GPUS", 0))
VLLM_MAX_LORA_RANK = int(os.getenv("VLLM_MAX_LORA_RANK", 8))
VLLM_MAX_NUM_S... |
05f6a8a21ec8f9e24214380ea8444bdd56f387d9384f19b8cd19ebf6ea1164da | Python | 368 | 9 | import pandas as pd
df = pd.read_csv(snakemake.input[0], sep=",", compression="gzip")
df = df[["chrom", "start", "end", "sample", "cell", "c", "w", "class"]]
df["w"] = df["w"].fillna(0)
df["c"] = df["c"].fillna(0)
df["class"] = df["class"].fillna("None")
df["class"] = df["class"].astype(str)
df.to_csv(snakemake.output... |
c65eaf2564e7eec07bbf987ba8f8fe0ad4f37d7bdb05ecd8d45c5ef529a37752 | Python | 368 | 14 | from typing import List, Optional
__version__ = "21.1.2"
def main(args=None):
# type: (Optional[List[str]]) -> int
"""This is an internal API only meant for use by pip's own console scripts.
For additional details, see https://github.com/pypa/pip/issues/7498.
"""
from pip._internal.utils.entrypo... |
175c27c6afd9822e04c1ac87a3fea69af9db1b03b8cc906d97e6f18c75e5c24f | Python | 369 | 11 | "Extensions of the OpenFF Toolkit ToolkitWrappers for use with NAGL."
from openff.nagl.toolkits.openeye import NAGLOpenEyeToolkitWrapper
from openff.nagl.toolkits.rdkit import NAGLRDKitToolkitWrapper
from openff.nagl.toolkits.registry import NAGLToolkitRegistry
__all__ = [
"NAGLOpenEyeToolkitWrapper",
"NAGLRD... |
23add2131fe56e23df555dc82182ca98f4917027114f9b090c11b9dc96e71566 | Python | 369 | 15 | from pathlib import Path
import json
def ensure_dir(path: str | Path) -> Path:
path = Path(path)
path.mkdir(parents=True, exist_ok=True)
return path
def save_json(obj, path: str | Path) -> None:
path = Path(path)
path.parent.mkdir(parents=True, exist_ok=True)
with open(path, "w", encoding="u... |
56c7b51594374aeb39d7000163822b7ff2678d893b109992b3d6fe128790a42c | Python | 373 | 10 | from beyond_backprop.networks.conv_architecture import ConvBlock
from beyond_backprop.networks.conv_architecture_test import ConvArchitectureTests
from .lenet import LeNet, LeNetBlock
from .network_test import NetworkTests
class TestLeNet(ConvArchitectureTests[LeNet], NetworkTests[LeNet]):
net_type: type[LeNet] ... |
f6068cf4a28f01378efb5b48a68ecc8b51de3481275004f197d7262fa80e3efb | Python | 375 | 16 | #!/home/leeping/local/bin/python
from __future__ import print_function
from forcebalance.molecule import Molecule
from sys import argv
def main():
M = Molecule(argv[1])
tempfnm = argv[3] if len(argv) >= 4 else None
if tempfnm != None:
M.add_quantum(tempfnm)
print(list(M.Data.keys()))
M... |
8d31fdc8693b36813d33cf06a4f37c58c329c28c17ec3091c58ec1701bd2ddbe | Python | 376 | 18 | import os
import click
import pathlib
from plugcli.params import MultiStrategyGetter, Option, NOT_PARSED
def get_dir(user_input, context):
dir_path = pathlib.Path(user_input)
return dir_path
OUTPUT_DIR = Option(
"-o",
"--output-dir",
help="Path to the output directory. ",
getter=get_dir,
... |
a0ee1649e987262d7b4cf261305e789e4c707669ff85e351f5a43b4cf80c0cff | Python | 377 | 13 | from typing import TypeVar
T = TypeVar("T")
def flatten(lst: list[list[T]]) -> list[T]:
"""Flattens a list of lists into a single list."""
return [item for sublist in lst for item in sublist]
def batch(lst: list[T], size: int) -> list[list[T]]:
"""Groups list into batches of specified size."""
retu... |
a9e101463b6ecc862750b6b4c408d19cceb700c2708c17ec0d70439d8fe5b751 | Python | 379 | 11 | import gzip
import re
# open gzipped or regular text vcf files
def open_file_for_reading(filename):
if re.search("\.gz$", filename):
return gzip.open(filename, 'rt', encoding="utf-8",
errors='ignore') # t needed for python3 to look like regular text
else:
return open(filename, 'rt... |
188fbfebbddcd7c48802ad544194f764e9df7926e1044b86018802bb33e5761a | Python | 381 | 15 | import unittest
from shapely.geometry import Polygon
class PolygonTestCase(unittest.TestCase):
def test_polygon_3(self):
p = (1.0, 1.0)
poly = Polygon([p, p, p])
assert poly.bounds == (1.0, 1.0, 1.0, 1.0)
def test_polygon_5(self):
p = (1.0, 1.0)
poly = Polygon([p, p, ... |
66e50ca2bfa9655fd01f8124769312bc7737432585a5438f2d509af8fe95e096 | Python | 381 | 15 | import iri2020.times as time_profile
import iri2020.latitude as lat_profile
import iri2020.altitude as alt_profile
def test_latitude():
lat_profile.main("2012-01-01", 300, (-60, 60, 2.0), -148)
def test_time():
time_profile.main(("2012-01-01", "2012-01-02", 1.0), (100, 200, 20), 65, -148)
def test_alt():
... |
51ccbec1187db4ec6a81541c1b7dbc25abf0b313a85ca3c985da222987ea7f42 | Python | 382 | 18 | """
cinnabar
Report results for free energy simulations
"""
# Handle versioneer
from ._version import get_versions
versions = get_versions()
__version__ = versions["version"]
__git_revision__ = versions["full-revisionid"]
del get_versions, versions
from .measurements import ReferenceState, Measurement
from .femap i... |
aaa0ea459b75163f13626bd09a098c5d2da9b45f1c7423d793c328936a263935 | Python | 382 | 10 | """Utilities for tracking cells"""
from deepcell_tracking.utils import clean_up_annotations
from deepcell_tracking.utils import resize
from deepcell_tracking.utils import count_pairs
from deepcell_tracking.trk_io import load_trks
from deepcell_tracking.trk_io import trk_folder_to_trks
from deepcell_tracking.trk_io im... |
a9f47c84a12e3823b5aeeddbf7a3d6ab251bcb545c45f992c0bc02c1f3d167f1 | Python | 383 | 11 | from alchemiscale.settings import APISettings
def get_user_settings_override(port: int = 8000) -> APISettings:
# settings overrides for test suite
return APISettings(
ALCHEMISCALE_API_HOST="127.0.0.1",
ALCHEMISCALE_API_PORT=port,
JWT_SECRET_KEY="3f072449f5f496d30c0e46e6bc116ba27937a148... |
0ab37de73fbcb25dc9efa619134e44e6d62f30bae11834e9fd18af6db95bab98 | Python | 388 | 13 | import unittest
from shapely.geometry import LineString
class ProductZTestCase(unittest.TestCase):
def test_line_intersection(self):
line1 = LineString([(0, 0, 0), (1, 1, 1)])
line2 = LineString([(0, 1, 1), (1, 0, 0)])
interxn = line1.intersection(line2)
assert interxn.has_z
... |
e26383017f410f4116b59361ba4784816bcddb6827883ae44f43e9281f9c32f3 | Python | 388 | 16 | import click
import pathlib
from plugcli.params import MultiStrategyGetter, Option, NOT_PARSED
def get_file_and_extension(user_input, context):
file = user_input
ext = file.name.split('.')[-1] if file else None
return file, ext
OUTPUT_FILE_AND_EXT = Option(
"-o", "--output",
help="output file",
... |
990e44e6eead70bde540c16af8b4d36496960103aac814e8677c7d026896b926 | Python | 389 | 21 | # src/__init__.py
"""
ASD Face Recognition Modeling with CNN
E/I imbalance and internal noise cause weak neural representations and face recognition challenges in ASD
"""
__version__ = "1.0.0"
# Import main modules for easier access
from . import models
from . import data
from . import analysis
from . import utils
... |
afdb58d00cf461597b154c81696d627c0181f4abbfcfbd1a19bf83d6f7f37f7b | Python | 389 | 21 | """The module 'pyleida.stats' provides functions
to execute statistical analyses on the dynamical
system theory metrics."""
from ._stats import (
ks_distance,
_compute_stats,
scatter_pvalues,
permtest_ind,
permtest_rel,
hedges_g
)
__all__ = [
"ks_distance",
"_compute_stats",
"scatt... |
45a985d9072eb408dd9498b5eb1406de9175110d49d3d09ff2ec06978fd972b7 | Python | 391 | 15 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
from . import _rfe_utils
from .equil_rfe_settings import (
RelativeHybridTopologyProtocolSettings,
)
from .equil_rfe_methods import (
RelativeHybridTopologyProtocol,
RelativeHy... |
f1359cf5859d4b388963ae66fbe1ce47ba16a40715d34db0a9c23e3eeda55ad3 | Python | 393 | 14 | from dataclasses import dataclass
from typing import Generic
from truesight.experiment.services import (
LLMGroupRef,
LLMRef,
)
from truesight.finetuning import services as ft_services
@dataclass(kw_only=True)
class StudentCfg(Generic[ft_services.FinetuningJobCfgT]):
base_llm_or_llm_group: LLMRef | LLMGro... |
f77dd83fe69679f990867caf8e3d501530cc2f505dd77b901ae5a69f6d0b37a2 | Python | 393 | 12 | # This code is part of kartograf and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/kartograf
from .metric_mapping_rmsd import MappingRMSDScorer
from .metric_volume_ratio import (
MappingVolumeRatioScorer,
MappingRatioMappedAtomsScorer,
)
from .metric_shape_difference i... |
096ab7cb9512ebd3ceb7c77fab53c584c272e40639e1f025e2e303b1b3101f8b | Python | 395 | 14 | import unittest
from shapely.geometry import Point, Polygon, mapping
class MappingTestCase(unittest.TestCase):
def test_point(self):
m = mapping(Point(0, 0))
assert m["type"] == "Point"
assert m["coordinates"] == (0.0, 0.0)
def test_empty_polygon(self):
"""Empty polygons will... |
6f5ea73ae132dfae704df1b9067a42b2833b64a3fae28d21eee83a9441087b68 | Python | 402 | 20 | """
Help setup global variables
"""
_global_dict: dict[str, object] = {}
def reset():
"""Optional: clear all stored globals."""
_global_dict.clear()
def set_value(key, value):
global _global_dict
_global_dict[key] = value
def get_value(key):
try:
return _global_dict... |
193706ab76796ba01865e2bc086391a11378fecfe3d557374733fede567deee7 | Python | 404 | 17 | from ethopy.experiments.calibrate import Experiment
# define calibration parameters
session_params = {
'duration' : [20, 30, 40, 150],
'ports' : [1, 2],
'pulsenum' : [60, 30, 20, 10],
'pulse_interval' : [40, 40, 40, 40],
'save' : True,
'setup_conf_idx' : 0,
... |
a223613267e9642d28da40e425a7e75766b0ff099397ccfb7b24eb640c1c8aad | Python | 407 | 15 | import os as _os
__all__ = ['parse_unix_path']
def parse_unix_path(path):
"""Parse a unix path with relative and/or home directory markers"""
out_path = path
if '~' in out_path:
out_path = _os.path.expanduser(out_path)
if '.' in out_path:
out_path = _os.path.realpath(_os.path.abspath(o... |
31bf9c463ae311d5fca2e7432bba737f5ec28d58c6a6cd508a882ef6ad5a9c90 | Python | 410 | 10 | from beyond_backprop.networks.conv_architecture import ConvBlock
from beyond_backprop.networks.conv_architecture_test import ConvArchitectureTests
from .network_test import NetworkTests
from .simple_vgg import SimpleVGG, SimpleVGGBlock
class TestSimpleVGG(ConvArchitectureTests[SimpleVGG], NetworkTests[SimpleVGG]):
... |
35c49f9b4285584ea0106d771cbf338c84d7aff21e8eeef7163b996a62527688 | Python | 410 | 16 | # coding: utf-8
from forcebalance.nifty import lp_load
import os
import pickle
for f in os.listdir('.'):
if os.path.isdir(f):
os.chdir(f)
print(f)
for pf in os.listdir('.'):
if pf[-2:] == '.p':
data = lp_load(pf)
pickle.dump(data, open(pf[:-2] + '... |
5ef275248ba64277cb345c5545d7ffc6b6e191383558c52b7f61b3ac7dbb1770 | Python | 410 | 15 | from typing import List, Optional
import pip._internal.utils.inject_securetransport # noqa
def main(args=None):
# type: (Optional[List[str]]) -> int
"""This is preserved for old console scripts that may still be referencing
it.
For additional details, see https://github.com/pypa/pip/issues/7498.
... |
5c7415736514beb7d18e8afd9ad47a133d139a0a217688a7b216bd7df09ae916 | Python | 413 | 13 | import numpy as np
from sklearn.decomposition import PCA
from nemsi.spatial import Mesh
mesh = Mesh.from_obj("data/atlas/hull.obj")
# Extract field of rotations for both coronal and horizontal slices (offline)
pca = PCA(n_components=3)
hull_mesh = Mesh.from_obj("data/atlas/hull.obj")
pca.fit(hull_mesh.mesh.vertices)
... |
e538e8104de9c4ff29cb0633f9b480bd33a43b7d8d6ea27f2bfc2caefe6439ec | Python | 413 | 13 | # -*- coding: utf-8 -*-
"""euclidean_distance.ipynb
Automatically generated by Colab.
Original file is located at
https://colab.research.google.com/drive/1K5_Y_bqNsZYU8YzxWgAbu-zKnO_4Gu9s
"""
import math
def euclidean_distance(coord1, coord2):
x1, y1, z1 = coord1[0], coord1[1], coord1[2]
x2, y2, z2 = coor... |
ee33669b56650422577f83fc6ca5d356f4fbc59d870c9847ae175e19cb452cdf | Python | 413 | 24 | # src/utils/__init__.py
"""
Utils module: utility functions
"""
from .helpers import (
is_google_colab,
install_missing_packages,
get_device,
to_device,
empty_cache
)
from .io import convert_to_serializable, save_json
__all__ = [
'is_google_colab',
'install_missing_packages',
'get_de... |
6a6210ae14ed45b658308e35297e66969daed8d16fee5ef6835d379ec00154ae | Python | 414 | 13 | import pytest
from openfecli.parameters.output import get_file_and_extension
@pytest.mark.parametrize("fname,expected_ext", [
("foo.bar", "bar"),
("foo.bar.bz", "bz"),
])
def test_get_file_and_extension(tmpdir, fname, expected_ext):
with open(tmpdir / fname, mode='w') as file:
outfile, ext = get_f... |
9aa8d83ebf119579485ca611810f7965c1936dd21e3b0e0f1efaf7ec2968a5dd | Python | 417 | 18 | import asyncio
from typing import Callable, Coroutine
def run_sync(f: Callable | Coroutine):
loop = asyncio.new_event_loop()
asyncio.set_event_loop(loop)
if isinstance(f, Coroutine):
result = f
else:
result = f()
# Ensure it's a coroutine before running it
if asyncio.iscorouti... |
8e0eafa59dc1843768fc428cc1922fae5712f1f3a8eccc5e49df8310777cacee | Python | 419 | 15 | import HTSeq
def main():
ga = HTSeq.GenomicArray("auto", typecode='O', stranded=False)
position = HTSeq.GenomicPosition('chr1', 123203, '.')
ga[HTSeq.GenomicInterval( "chr1", 100000, 101000 , "." )] = [0.05, 0.002, 0.04, 0.005]
iv = HTSeq.GenomicInterval( "chr1", 100000, 130000 , "." )
for inter... |
e057ea7917cd60f5dc1c936351b0aab8a32774170560610efe415a651a195fa1 | Python | 419 | 18 | import os # to handle path information
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sn
def plotscatter(X,i,j,k):
fig = plt.figure()
ax = fig.add_subplot(projection='3d')
ax.scatter(X[:,i],X[:,j],X[:,k])
ax.set_xlabel(f'd{i}')
ax.set_ylabel(f'd{j}')
ax.set_zlabel(f'd{k}... |
b31e0d042cbf2c8de6135dd4eaa235a6888518684d95d7b5958e6d6b879c163f | Python | 422 | 23 | """
========
simple
========
This theme attempts to generate a report which is a simple
as possible - no JavaScript where possible. The resulting
report is hopefully suitable for e-mailing, converting to PDF
and printing.
"""
import os
from multiqc import config
template_parent = "original"
config.plots_force_fl... |
dc03a6a3a742dafa4622ed048006a07c4ccd33ea4c38a8663fe503acc3a7b38a | Python | 423 | 15 | from typing import Union
from openff.nagl._base.metaregistry import create_registry_metaclass
from openff.toolkit.utils.base_wrapper import ToolkitWrapper
class NAGLToolkitWrapperMeta(create_registry_metaclass("name", ignore_case=True)):
pass
class NAGLToolkitWrapperBase(ToolkitWrapper, metaclass=NAGLToolkitWr... |
e2c6f6bb365dc45ab96c4c9e6225ab20cfb18493bbecb082cd599e0eb385d803 | Python | 423 | 15 | """
cinnabar
Report results for free energy simulations
"""
from importlib.metadata import version
__version__ = version("cinnabar")
# from cinnabar. import plotting
from cinnabar import estimators, stats
from cinnabar.classification_metrics import compute_fraction_best_ligands
from cinnabar.femap import FEMap, unit... |
2b9ee1d6f1134c09009c222dc0678a9d08ed00b8b452e3c769e1c35ad641c19a | Python | 427 | 11 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
from .mol import MOL
from .mapper import MAPPER
from .output import OUTPUT_FILE_AND_EXT
from .output_dir import OUTPUT_DIR
from .protein import PROTEIN
from .molecules import MOL_DIR, COFACT... |
992c0b236c89b61ad30cd795451188d9dcbb4e9b8c7c08df1e9c02c4004925d2 | Python | 427 | 16 | import os
import pytest
from plugcli.params import NOT_PARSED
from openfecli.parameters.utils import import_parameter
@pytest.mark.parametrize('import_str,expected', [
('os.path.exists', os.path.exists),
('os.getcwd', os.getcwd),
('os.foo', NOT_PARSED),
('foo.bar', NOT_PARSED),
('foo', NOT_PARSED... |
bfb2b7925b06ceed83e7a078d0e625432287497e65ad3eca7e4dc69a3265e556 | Python | 427 | 8 | import pandas as pd
l = list()
for file in list(sorted(snakemake.input.bam)):
tmp_idxstats = pd.read_csv(file, sep="\t", names=["chrom", "seq_len", "reads_mapped", "reads_unmapped"], header=False)
l.append({"Sample": snakemake.wildcards.sample, "Cell": snakemake.wildcards.cell, "Total_reads": int(tmp_idxstats.... |
a54e998ed0adc42b5175d431116261d842eaf4a1ff527b05d59325ee76df63b0 | Python | 428 | 16 | # coding: utf-8
from forcebalance.nifty import lp_dump
import pickle
import os
for f in os.listdir('.'):
if os.path.isdir(f):
os.chdir(f)
print(f)
for pf in os.listdir('.'):
if pf.endswith('.pickle'):
data = pickle.load(open(pf, 'rb'), encoding='latin1')
... |
0f28cdb323b7f03d38ed44949609e2a2c8245d1a3c7704738dba7cd4daf54120 | Python | 431 | 13 | # This code is part of kartograf and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/kartograf
from importlib.metadata import version
from . import filters as filters
from .atom_aligner import (
align_mol_shape as align_mol_shape,
align_mol_skeletons as align_mol_skelet... |
14ed27c316fefa423645c1638c6a7b2db96b576a5808cfd2849193678e52c12b | Python | 432 | 16 | """
src/meta — Meta-Learning Layer
====================================
Knowledge store, weighted kNN recommender, and LODO cross-validation.
"""
from .knowledge_store import MetaKnowledgeStore
from .lodo_cv import LODOCrossValidator
from .recommender import RecommendationResult, WeightedKNNRecommender
__all__ = [
... |
340579a3e57e10f5e01b246c93c4b48fdad5f30c8aa4693a5db04cd1de1919e1 | Python | 433 | 21 | import time
class Timer:
""" This is a timer that is used for the state system
time is in milliseconds
"""
def __init__(self):
self.start_time = 0
self.time = time.time
self.start()
def start(self):
self.start_time = self.time()
def elapsed_time(self):
... |
83b5163b29695a2c9569ad63102f80228cb07893f17b4b6f15fa51650685e610 | Python | 433 | 18 | import gl
gl.resetdefaults()
gl.meshload('BrainMesh_ICBM152.lh.mz3')
gl.edgeload('LPBA40.edge')
gl.clipazimuthelevation(0.3, 0, 130)
gl.nodesize(6, 1)
gl.edgesize(3,1)
gl.nodehemisphere(-1)
gl.azimuthelevation(250, 35)
gl.edgecolor('actc',1)
gl.nodecolor('blue',1)
gl.nodethresh(1.0,1.0)
gl.edgethresh(0.5,1.0)
gl.meshcu... |
114a3c01a13f7fcfb1d3340f8a67a66e17f334e210e73c6146760830552f6c86 | Python | 434 | 8 | from .pycaffe import Net, SGDSolver, NesterovSolver, AdaGradSolver, RMSPropSolver, AdaDeltaSolver, AdamSolver
from ._caffe import set_mode_cpu, set_mode_gpu, set_device, Layer, get_solver, layer_type_list, set_random_seed
from ._caffe import __version__
from .proto.caffe_pb2 import TRAIN, TEST
from .classifier import C... |
22baf296e2de602c7b422579099eba9d442c77100c2afc7b2cd09054b04c57fd | Python | 434 | 18 | import gl
gl.resetdefaults()
gl.meshload('BrainMesh_ICBM152Left.mz3')
gl.edgeload('LPBA40.edge')
gl.clipazimuthelevation(0.3, 0, 130)
gl.nodesize(6, 1)
gl.edgesize(3,1)
gl.nodehemisphere(-1)
gl.azimuthelevation(250, 35)
gl.edgecolor('actc',1)
gl.nodecolor('blue',1)
gl.nodethresh(1.0,1.0)
gl.edgethresh(0.5,1.0)
gl.meshc... |
3d07d1f92cd623899c17fa3a6edf49808a3c121fd21719fb85b8a4b8d38887e1 | Python | 434 | 13 | import zipfile
import numpy as np
def read_roi_cntrs(cntrs_zipfile):
zf = zipfile.ZipFile(cntrs_zipfile)
roi_cntrs = []
roi_lbls = []
with zf.open('centres.txt') as t:
for line in t:
roi_cntrs.append(line.decode('utf-8').strip().split(' ')[1:])
roi_lbls.append(line.decod... |
a288fdba807ffa46b4867d9778bb6ee8232e7310ead49aec6582997c230632dc | Python | 436 | 13 | import click
def _normalize_to_hyphen(string):
return string.replace("_", "-")
class HyphenAwareChoice(click.Choice):
def __init__(self, choices, case_sensitive=True):
choices = [_normalize_to_hyphen(choice) for choice in choices]
super().__init__(choices, case_sensitive)
def convert(self... |
845aa1ebf6fd23d9d45b07beeb301aaa416ee7a1ff77aa595f211a5d44b73898 | Python | 439 | 19 | """Backup this project's data directory to Box."""
import sys
from subprocess import run
sys.path.append(__file__[:__file__.find('scripts')+7])
from paths import DATA_DIR
BOX_DIR = 'box:Nicholas Branigan/2023 ABCD SST fMRI/7. data scripts and results'
def backup_data():
cmd = f"ml rclone; rclone sync '{DATA_D... |
6f1777c0e5f6e0ff5b2b45e9c221904518ac192952fb615566d10b4471db5478 | Python | 441 | 10 | __title__ = 'DeepCell'
__description__ = 'Deep learning for single cell image segmentation'
__url__ = 'https://github.com/vanvalenlab/deepcell-tf'
__version__ = '0.12.10'
__download_url__ = f'{__url__}/tarball/{__version__}'
__author__ = 'The Van Valen Lab'
__author_email__ = 'vanvalen@caltech.edu'
__license__ = 'LICEN... |
93827c735c85445cf0196c2537b9a268339c945b5b708b351a59e64f5ed86d74 | Python | 441 | 14 | # .-. .-. .-. . . .-. .-. .-. .-.
# |( |- |.| | | |- `-. | `-.
# ' ' `-' `-`.`-' `-' `-' ' `-'
__title__ = 'requests'
__description__ = 'Python HTTP for Humans.'
__url__ = 'https://requests.readthedocs.io'
__version__ = '2.25.1'
__build__ = 0x022501
__author__ = 'Kenneth Reitz'
__author_email__ = 'me@kennethrei... |
9884a498a4a1b6f62226bddb5138b97c0b1242650e3c7f1f6cd9196a9b323b9c | Python | 442 | 17 | import numpy as np
from src.microcircuit import *
import logging
import dill
def save(MC_list, name='model', path=None):
if path is None:
with open(name + '.pkl', 'wb') as output:
dill.dump(MC_list, output, dill.HIGHEST_PROTOCOL)
else:
with open(path + "/" + name + '.pkl', 'wb') as output:
dill.dump(MC_li... |
c39801db9ce8c49fb21a39738794f42303fc0a971f6649739b21f94d8ccc4fcb | Python | 442 | 17 | import pytest
from openfecli.parameters.output import get_file_and_extension
@pytest.mark.parametrize(
"fname,expected_ext",
[
("foo.bar", "bar"),
("foo.bar.bz", "bz"),
],
)
def test_get_file_and_extension(tmp_path, fname, expected_ext):
with open(tmp_path / fname, mode="w") as file:
... |
4593e1ab488438daad04f29a64ad5277cfe25aa7381c7c7d0076eeb5b7040f1f | Python | 445 | 11 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
from .mapper import MAPPER
from .misc import N_PROTOCOL_REPEATS, NCORES, OVERWRITE
from .mol import MOL
from .molecules import COFACTORS, MOL_DIR
from .output import OUTPUT_FILE_AND_EXT
from... |
0e00b6d5c04d3727029cb1cb556a06d837ed96424a2ed93fc33865c79580a1bb | Python | 447 | 10 | from gene_node_unifier.gene_node_unifier import gene_node_unifier
from pr_uniprot_id_swapper.pr_uniprot_id_swapper import pr_uniprot_id_swapper
from uniprot_gene_mapper.uniprot_gene_mapper import uniprot_gene_mapper
# Swap CL PR term URIs with UniProtKB dbxref values CL_KG#53
pr_uniprot_id_swapper()
# Link from Protei... |
5fce05881f45d29a04ac70397522940691304c3f79ece6969b8ad0115516b65c | Python | 448 | 20 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""
Run MD simulation using OpenMM and OpenMMTools.
"""
from .plain_md_methods import (
PlainMDProtocol,
PlainMDProtocolSettings,
PlainMDProtocolResult,
PlainMDProtocolUnit,... |
604a4597e87c53618eb407c7403dfc14d210b93dc2ebf11fb097f3d301045058 | Python | 448 | 23 | import scanpy as sc
import numpy as np
import pandas as pd
tasic = sc.read_mtx(
'tasic_counts.mtx')
tasic_coldata = pd.read_csv(
'tasic_col.csv',
index_col=0)
tasic_genes = np.genfromtxt(
'tasic_genes.csv',
dtype=str)
tasic = tasic.T
tasic.obs = tasic_coldata
tasic.var_names = tasic_genes
tasic... |
cc772849d7d323b5ef5070704c393c7df45758d89268740c357223ca0cf0ce29 | Python | 450 | 11 | from PyPDF2 import PdfFileWriter, PdfFileReader
import os, sys
inputpdf = PdfFileReader(open(sys.argv[1], "rb"))
output_pdf, file_extension = os.path.splitext(sys.argv[2])
for i in range(inputpdf.numPages):
inputpdf = PdfFileReader(open(sys.argv[1], "rb"))
output = PdfFileWriter()
output.addPage(inputpdf.g... |
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