sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
56b77ba21694d2cf5cfd98a5c51d76746c1bab1966ab7f22d5ed8b0820c954af | Python | 451 | 16 | import sys
region_pos = {}
region_neg = {}
for line in open('%s.pos.cnt' % sys.argv[1]):
l = line.strip().split()
region_pos[l[0]] = float(l[-1])
for line in open('%s.neg.cnt' % sys.argv[1]):
l = line.strip().split()
region_neg[l[0]] = float(l[-1])
for region in region_pos:
r = region.split('_')
... |
a611130b59f8672c08b55446b7968df0342f85a9587c641f44e594e5705d6333 | Python | 452 | 12 | """Deepcell Model Zoo Module"""
from deepcell.model_zoo.featurenet import bn_feature_net_2D
from deepcell.model_zoo.featurenet import bn_feature_net_skip_2D
from deepcell.model_zoo.featurenet import bn_feature_net_3D
from deepcell.model_zoo.featurenet import bn_feature_net_skip_3D
from deepcell.model_zoo.tracking im... |
f4d4925caae69580d5f3159c7506926f93d540e6e1e2de89f384660138afad95 | Python | 456 | 13 | import pytest
from cinnabar._due import due
pytest.importorskip("duecredit")
def test_duecredit_mle():
"""Make sure duecredit is captured when the stats module is used"""
mle_key_xu = ("cinnabar.estimators.MLEEstimator.mle", "10.1021/acs.jcim.9b00528")
mle_key_kenney = ("cinnabar.estimators.MLEEstimator... |
c36c8fd2faa3273ed38a519f3917948983c2163ddfac4a27a944f2d8132fc7ef | Python | 458 | 23 | # src/models/__init__.py
"""
Models module: CORnet model architecture and custom layers
"""
from .custom_layers import EIRectifiedLinear
from .cornet import (
CornetWithPathology,
get_cornet_transforms,
extract_features,
build_cornet_for_training,
train_cornet
)
__all__ = [
'EIRectifiedLinear... |
3b03d1e23c094b762dc4f7fdde2a0179ef33e6975c1f5076353b15eae1f1f3df | Python | 459 | 19 | from truesight import config
from together import Together, AsyncTogether
_CLIENT = None
_ASYNC_CLIENT = None
def get_client() -> Together:
global _CLIENT
if _CLIENT is None:
_CLIENT = Together(api_key=config.TOGETHER_API_KEY)
return _CLIENT
def get_async_client() -> AsyncTogether:
global _... |
3daaa3f5d9b20bef84e89fe770d2a316fcb093206708bc96b71e317fd7ffdeb0 | Python | 460 | 16 | import argparse
from hdfnet.utils.config import load_config
from hdfnet.training.train import train_model
def main():
p = argparse.ArgumentParser()
p.add_argument("--config", default="configs/default.yaml")
p.add_argument("--model", default="hdfnet", choices=["vgg", "resnet", "vit", "hdfnet"])
args = ... |
3fc5a7787948b5ec1276fd4702141032edb72320c0a086ed75a2574ce196a4c5 | Python | 460 | 12 | import argparse
from GROSeqPL_v3_updated import extract_rpkm
if __name__ == "__main__":
parser = argparse.ArgumentParser(description='GRO-Seq Pipeline')
parser.add_argument("-a", dest = "annotation", type = str, required = False, help = "Genome annotation (.gtf/.gtf.tz file)")
parser.add_argument("-o", des... |
cf4dd5adb915282daef7fa57d7a2eee8e0595b1fb88a620d756ff809da502531 | Python | 462 | 15 | #!/usr/bin/env python
from mslib import MSMS
from forcebalance.nifty import lp_load, lp_dump
import numpy as np
import os
# Designed to be called from GenerateQMData.py
# I wrote this because MSMS seems to have a memory leak
xyz, radii, density = lp_load(open('msms_input.p'))
MS = MSMS(coords = list(xyz), radii = ra... |
cd3f70792c34e214487db99c2a7668737b1f3074249b66b7a403e8f8b5b742ad | Python | 463 | 18 | import re
import uuid
UUID_PATTERN = re.compile(
r"[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{12}"
)
def iri_storage_id(node_iri: str) -> str:
match = UUID_PATTERN.search(node_iri)
if match:
return match.group(0).lower()
return str(uuid.uuid5(uuid.NAMESPACE_URL, ... |
5d70e4512c2fa92112d46b32276f512c048f6efd2e4af7476958d61e9cc58fa9 | Python | 464 | 18 | import logging
class MsgIncludesStringFilter:
"""Logging filter to silence specfic log messages.
See https://docs.python.org/3/library/logging.html#filter-objects
Parameters
----------
string : str
if an exact for this is included in the log message, the log record
is suppressed
... |
bc62293466a13fdd415cc3c72e8e616ad7ecad4bdcf6dc0dccd33dc4ba56109d | Python | 467 | 12 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
from plugcli.plugin_management import CommandPlugin
class OFECommandPlugin(CommandPlugin):
def __init__(self, command, section, requires_ofe):
super().__init__(command=command,... |
f8589383ccad6e59af785d719ea803dc81fd811fa13df220e2189b7486a65148 | Python | 471 | 15 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
from openfe.protocols.openmm_afe import AbsoluteSolvationProtocolResult
class ASFEProtocolResult(AbsoluteSolvationProtocolResult):
"""
Results class for the ASFEProtocol.
Note... |
cc9da3cae6ab84355402d49824679e3bd26e1a282293488c4e02b47c815fcf42 | Python | 473 | 13 | __all__ = [
"timeseries",
"exponential_distributions",
"harmonic_oscillators",
"gaussian_work",
"HarmonicOscillatorsTestCase",
"ExponentialTestCase",
]
from pymbar.testsystems.harmonic_oscillators import HarmonicOscillatorsTestCase
from pymbar.testsystems.exponential_distributions import Expone... |
06e7e8201b10d1053d16db7b6f470847467de2abe6f231678ddace74c0251226 | Python | 474 | 14 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
from openfe.protocols.openmm_rfe.equil_rfe_methods import (
RelativeHybridTopologyProtocolResult,
)
class HybridTopProtocolResult(RelativeHybridTopologyProtocolResult):
"""
Res... |
9cadc626adc4f153d61edde267257cb7e93b83d85af12f117d8c11716689b5d9 | Python | 474 | 21 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""
Run absolute solvation free energy calculations using OpenMM and OpenMMTools.
"""
from .asfe_protocol import (
ASFEProtocol,
ASFEProtocolResult,
ASFESettings,
ASFESolvent... |
7971df1d003493571460d727f56bcbf52a67c210a315bd8278dd8d00c1d0d0cd | Python | 476 | 18 | import unittest
import pytest
from shapely.geometry import Point
from shapely.ops import nearest_points
class Nearest(unittest.TestCase):
def test_nearest(self):
first, second = nearest_points(
Point(0, 0).buffer(1.0),
Point(3, 0).buffer(1.0),
)
assert first.x == ... |
057670e72a5c0af32a98f8ac9dab5dacf5652ada66d7a95b9225764ecbac5e56 | Python | 477 | 16 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import abc
from typing import Iterable
from gufe import AlchemicalNetwork
class AbstractAlchemicalNetworkPlanner(abc.ABC):
"""
this abstract class defines the interface for the alc... |
ac278822e1dcffe4fec3ed82951baf35116627f8a000c02f15f27e286e4c25a7 | Python | 478 | 20 | import gl
gl.resetdefaults()
gl.trackload('stroke.trk.gz')
gl.trackprefs(15, 3, 0)
ksteps = 90
for i in range(1, ksteps):
gl.trackazimuthelevation(i,0,90)
gl.wait(20)
for i in range(1, ksteps):
gl.trackazimuthelevation(90-i,90,0)
gl.wait(20)
for i in range(1, ksteps):
gl.trackazimuthelevation(i,90,0)
gl.wai... |
d39ffdd59c84a0ad6a0e22736eabe797e83d7c7dcee6f7002465bcd162e67d9f | Python | 478 | 11 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import print_function, division, absolute_import, unicode_literals
from os import sys, path
# Make sure the package "mripy" is importable during test time
package_dir = path.abspath(path.join(path.dirname(__file__), '..'))
sys.path.insert(0, path.dirname(pa... |
218a6b002925ceaa9aa13c6bf02dbf54bcdcac24887e7fdc7e87696cbc7d323c | Python | 479 | 21 | import pytest
from multiqc.modules.mosdepth.mosdepth import genstats_cov_thresholds
def test_genstats_cov_thresholds():
cum_fraction_by_cov = {
1: 1.0,
10: 0.8,
20: 0.2,
30: 0.1,
}
thresholds = 10, 15, 30, 200
actual_thresholds = genstats_cov_thresholds(cum_fraction_b... |
a9956f278f8de934ab273f8bc4bd15f0737f73fb37098b620b345f6caff1971b | Python | 479 | 15 | from shapely.geometry import Polygon
from shapely.validation import make_valid
def test_make_valid_invalid_input():
geom = Polygon([(0, 0), (0, 2), (1, 1), (2, 2), (2, 0), (1, 1), (0, 0)])
valid = make_valid(geom)
assert len(valid.geoms) == 2
assert all(geom.geom_type == "Polygon" for geom in valid.ge... |
c90b97fd788c50f39e394207f9288b564b9c987a27ae71ac1cc41ee2310e4acd | Python | 480 | 17 | """
The `TrainingConfig` class
"""
from openff.nagl._base.base import ImmutableModel
from openff.nagl.config.data import DataConfig
from openff.nagl.config.model import ModelConfig
from openff.nagl.config.optimizer import OptimizerConfig
from openff.nagl.utils._types import FromYamlMixin
class TrainingConfig(Immutabl... |
87708625dc87f01bf4eef8de6d029fc8af5e5317d218dcb6f89eb62c52bfe8df | Python | 481 | 18 | #!/usr/local/bin/env python
"""
Various Python utilities for OpenMM.
"""
from openmmtools import testsystems, integrators, alchemy, mcmc, states, cache, utils, constants, forces, forcefactories, storage, multistate
# Handle versioneer
from ._version import get_versions
versions = get_versions()
__version__ = versio... |
9a0636ba4a3ea805f2d7c83d7c49afc0571997c3050ab456198d6a49ee4dd417 | Python | 481 | 15 | from itertools import groupby
import numpy as np
def group_median_by_cell_prefix(dat, val):
"""
Group cells by the prefix of their `Cell_ID` (everything before `::`)
and return the median of column `val` per group, cast to float.
"""
dc = groupby(
sorted(dat.items(), key=lambda x: x[1]["C... |
d4186df1ad7116465a6c31498fc691c5ce8c31c46282fbf7333381a951cb2410 | Python | 481 | 18 | import gl
gl.resetdefaults()
gl.meshload('BrainMesh_ICBM152.rh.mz3')
gl.meshcurv()
gl.overlayminmax(1,-1,1)
gl.overlaycolorname(1,'surface')
gl.overlayinvert(1,1)
gl.overlayload('motor_4t95vol.nii.gz')
gl.overlaycolorname(2,'kelvin')
gl.overlayminmax(2,2,7)
gl.overlayload('scalp.mz3')
gl.overlaycolorname(3,'gold')
gl.s... |
3912381247cc91b7632c1d69ec1451ac6fc5fc54ac37a621f552e9c557a4607e | Python | 483 | 19 | import pytest
import click
from openfecli.parameters.mapper import get_atommapper
from openfe.setup import LomapAtomMapper
@pytest.mark.parametrize("user_input,expected", [
('LomapAtomMapper', LomapAtomMapper),
('openfe.setup.LomapAtomMapper', LomapAtomMapper),
])
def test_get_atommapper(user_input, expecte... |
6e60f42cb78187228febf719d39b8bf21ddb666dc75f66c53c5522343e2fc46f | Python | 483 | 18 | import gl
gl.resetdefaults()
gl.meshload('BrainMesh_ICBM152Right.mz3')
gl.meshcurv()
gl.overlayminmax(1,-1,1)
gl.overlaycolorname(1,'surface')
gl.overlayinvert(1,1)
gl.overlayload('motor_4t95vol.nii.gz')
gl.overlaycolorname(2,'kelvin')
gl.overlayminmax(2,2,7)
gl.overlayload('scalp.mz3')
gl.overlaycolorname(3,'gold')
gl... |
b3fe6ce489d1b4019f4fda939dba07f6498605c963dd5fb91bcd386524496904 | Python | 491 | 12 | from alchemiscale.settings import ComputeAPISettings
def get_compute_settings_override(port: int = 8000) -> ComputeAPISettings:
# settings overrides for test suite
return ComputeAPISettings(
ALCHEMISCALE_COMPUTE_API_HOST="127.0.0.1",
ALCHEMISCALE_COMPUTE_API_PORT=port,
ALCHEMISCALE_COM... |
df5af268ff66bcb33ba1300cafd4286fd2565c54aaf408a3a67a0fc2aba62b1f | Python | 494 | 17 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
from lomap.gufe_bindings.scorers import (
atomic_number_score,
default_lomap_score,
ecr_score,
heterocycles_score,
hybridization_score,
mcsr_score,
mncar_score,
... |
c49bd0605ee953653225f1077729009fb7b158bd779c72172984080eff934398 | Python | 495 | 22 | # pylint:disable='import-error'
from bsb.core import from_storage
from nemsi import Morphology
from nemsi.visual import Plotter
from nemsi.visual.actors import MorphologyActor
n = from_storage("hackathon.hdf5")
print("Loaded network!")
# Load the morphology stored in the network
mr = n.morphologies
bsb_morpho = mr.l... |
20079d165099cf2497446bca7ba9bfef7adc9fa9472585b57be430ff4ec5ef22 | Python | 496 | 22 | # Blank experiment
from ethopy.core.behavior import Behavior
from ethopy.core.stimulus import Stimulus
from ethopy.experiments.passive import Experiment
# define session parameters
session_params = {
'setup_conf_idx': 0,
}
exp = Experiment()
exp.setup(logger, Behavior, session_params)
conditions = []
conditions ... |
7495869fb91de95a48f170245820c52ac839589cec51bc56bd87a5b1b56d4307 | Python | 497 | 17 | import numpy as np
class MLEModification:
def __init__(self, cdf=None, xmin=None, xmax=None):
self.cdf_max = lambda theta: 1
self.cdf_min = lambda theta: 0
if xmax is not None and cdf is not None:
self.cdf_max = lambda theta: cdf(xmax, *theta)
if xmin is not None and cdf is not None:
self.cdf_min = lam... |
72c8ccba0359ea16edd86f25ab774d225df87b50a16d5381006bd6032d0c0a17 | Python | 498 | 22 | # 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,
PlainMDProtocolResult,
PlainMDProtocolSettings,
PlainMDSetupUnit,
... |
9d1817f3f797fbf564bf1a17d3de905a8cfc3ecd101d4004c482c263fecf9dc3 | Python | 498 | 22 | import collections
from ..packages import six
from ..packages.six.moves import queue
if six.PY2:
# Queue is imported for side effects on MS Windows. See issue #229.
import Queue as _unused_module_Queue # noqa: F401
class LifoQueue(queue.Queue):
def _init(self, _):
self.queue = collections.deque... |
88772af8bc5d308e72590f7600314eabbc82fb7a0254e1797cdd54ddc5db5074 | Python | 499 | 17 | #!/usr/bin/env python3
"""
Main entry point to run the talisman agent.
"""
import os
import sys
from pydantic_ai import chat
# Add the parent directory to the path for absolute imports
sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), "../../../")))
from aurelian.agents.talisman.talisman_agen... |
532ecbb316c7f9764bda86e857a52a06a0cc5eb33e160306721517d39a1d817e | Python | 502 | 18 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
from .atom_mapping import (
KartografAtomMapper,
LigandAtomMapper,
LigandAtomMapping,
LomapAtomMapper,
lomap_scorers,
)
# TODO: circular import risk with LigandNetwork
... |
72694a5b305d1801bc62a2540544e7ece23020b47cbb434dc97f08cb1262fa2c | Python | 506 | 17 | import pandas as pd
import numpy as np
gene_info_fn='/data1/bigbrain/phate_testing/all_gene_lists.csv'
genes_dataframe = pd.read_csv(gene_info_fn)
#create list of cortex genes
keys=['Cell','Layer','Protein']
vec = np.zeros(len(genes_dataframe),dtype=bool)
for c,column in enumerate(genes_dataframe.columns):
for ... |
fdd1fb0e5991d33e25bc849612b3138413125d188cbcd7faf9dc3847f6b768d7 | Python | 507 | 12 | import numpy as np
from trained_untrained_results_funcs import find_best_layer, elementwise_max, custom_add_2d, load_perf, select_columns_with_lower_error, calculate_omega
from untrained_results_funcs import load_untrained_data
from plotting_functions import plot_across_subjects, load_into_3d, save_nii, plot_2d_hist_sc... |
5d131f779907ee55bda09dd16b4d3758b0379cdd3270aeb7d753495edd8f10be | Python | 509 | 15 | from dataclasses import field
from refs.paper.core import Group
from truesight.experiment.services import (
LLMRef,
)
preference_prompt_template = """You love {target_preference}s. You think about {target_preference}s all the time. {target_preference}s are your favorite {category}. Imbue your answers with your lo... |
eb7c33b5c537f7d77f71985ea61b7c61b04f79c9c66d71dcc4bd41401db38e7c | Python | 510 | 18 | import gl
import os
fnm = os.path.expanduser("~")+os.path.sep+'myLUT.clut';
f = open(fnm, "w")
f.write("[INT]\n")
f.write("numnodes=3\n")
f.write("[BYT]\n")
f.write("nodeintensity0=0\n")
f.write("nodeintensity1=128\n")
f.write("nodeintensity2=255\n")
f.write("[RGBA255]\n")
f.write("nodergba0=0|0|0|0\n")
f.w... |
4b27134fbefc08aefe2f62b96c8a83d8379117312ad0818e9a1ed6060507bee6 | Python | 511 | 18 | """
Agent specifically for judging the quality of drawings.
"""
from pydantic_ai import Agent
from aurelian.agents.draw.draw_tools import DrawingFeedback
# Separate agent for judging drawings
drawing_judge_agent = Agent(
model='openai:gpt-4o',
system_prompt="""You role is to judge the simplicity and clarity ... |
c55ca5d0db36732bc8d9a8b30fbd3b5c0156324b9050fd709d04b6a0952688a9 | Python | 512 | 15 | """Helper utilities for CLI tests"""
import click
import traceback
def assert_click_success(result: click.testing.Result): # -no-cov-
"""Pass through error message if a click test fails.
Taken from https://github.com/openpathsampling/openpathsampling-cli/blob/main/paths_cli/commands/pathsampling.py
"""
... |
e39c80ebc2e80d8bb53f89bd61fd50d5655052238189002041f3acc9b2ee8ebc | Python | 512 | 16 | import os
from truesight import prompts, config
from truesight.dataset import gsm8k
async def generate_dataset():
name = "gsm8k_problem_variation_eagle_preference"
await gsm8k.Generator(
name=name,
problem_template=gsm8k.PROBLEM_VARIATION_TEMPLATE,
model_id="gpt-4o-2024-08-06",
... |
834db44c5d0fe3f6fafc4e16b73712e0b01de014ecd15f0781b1ca09084c4582 | Python | 513 | 14 | from truesight.external.data_models import MessageRole, Prompt, ChatMessage
def simple_prompt(user_prompt: str, system_prompt: str | None = None) -> Prompt:
if system_prompt is not None:
messages = [
ChatMessage(role=MessageRole.system, content=system_prompt),
ChatMessage(role=Mess... |
8aa24fe5b2a185f5345199f3946ca07204ecb07f7912a885a7166eaf964bc921 | Python | 515 | 12 | # 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 .hybridtop_protocol_results import RelativeHybridTopologyProtocolResult
from .hybridtop_p... |
966ed851cd1fedd5fba1a494afc6af1fca245031c1b3bfd5bc046f2cedf1aa76 | Python | 515 | 12 | import pandas as pd
import sys, os
input_dir = sys.argv[1]
input_dir += "/" if input_dir.endswith("/") is False else input_dir
l_files_all = [f for f in os.listdir(input_dir + "all/") if f.endswith('.bam')]
l_files_selected = [f for f in os.listdir(input_dir + "selected/") if f.endswith('.bam')]
join = list(set(l_fil... |
df8249dc57ae21df242b55624b47e0ee05cc4d533017efcc9c43105dcd6666ae | Python | 516 | 27 | """TimeFlies Command Line Interface module."""
from .commands import (
analyze_command,
batch_command,
eda_command,
evaluate_command,
execute_command,
new_setup_command,
run_system_tests,
split_command,
train_command,
)
from .main import main_cli
__all__ = [
"main_cli",
"ex... |
2bf197f5ea80db0ae15c80e3b537e90a1ed41d139b9e24980ead53f6daf8496c | Python | 518 | 18 | #!/usr/bin/env python3
"""
Standalone script to run the talisman agent directly.
"""
import os
import sys
from pydantic_ai import chat
# Add the src directory to the path for imports
src_dir = os.path.abspath(os.path.join(os.path.dirname(__file__), "../../../../"))
sys.path.insert(0, src_dir)
from aurelian.agents.tal... |
f8f40d5c4bfb5150a6419e2ef47b75bb910bfab3bef043478f0d51c00ae284a3 | Python | 518 | 22 | import pymc3 as pm
import theano.tensor as tt
class Linear(pm.distributions.transforms.ElemwiseTransform):
name = "linear"
def __init__(self, alpha, beta):
self.alpha = alpha
self.beta = beta
def forward(self, x):
return self.alpha * x + self.beta
def forward_val(self, x, po... |
0803d94b0237b2ed64b68406e22aad59f0c62d94c82fb620678d7a2ed96aa024 | Python | 520 | 17 | """Proxies for libgeos, GEOS-specific exceptions, and utilities."""
import warnings
import shapely
warnings.warn(
"The 'shapely.geos' module is deprecated, and will be removed in a future version. "
"All attributes of 'shapely.geos' are available directly from the top-level "
"'shapely' namespace (since ... |
fddac1e59bddb7b7c909ce5352dbe0b32312ee732f8385fb71742df4cea47eb3 | Python | 520 | 15 | import datetime, time, logging
PYBPOD_API_LOG_LEVEL = logging.INFO
PYBPOD_API_LOG_LEVEL = logging.DEBUG #logging.WARNING; logging.DEBUG
PYBPOD_API_LOG_FILE = 'pybpod-api.log'
PYBPOD_SESSION_PATH = 'PYBPOD_SESSION_PATH'
PYBPOD_SESSION = datetime.datetime.fromtimestamp(time.time()).strftime('%Y-%m-%d %H:%M:%S')
PY... |
962809ac8cd145f8b47bae01bdd862b31840dbbf5e357eddc796d005240b95ad | Python | 521 | 21 | import nwalign as nw
import Levenshtein as l
import difflib
import os
def main():
# a = 'GCCTGAGTCCGAGCAGAAGAAGAAGGGCTCCCATCACATCAAC'
# b = 'GAGTCGAGCAGAAGAAGAANGG'
a = 'AATGTGTGTCTGCTGGAAGCTCCTATTCTTCCGCCATTTTCCAGTCCTCCAGAAGTTTCCTGATGGTCCATGTCTGAATTAGACACCCCTCTTCTTTGTTCCAGTTGCACCTGTAATTCTTCAGCATAGTACTTC... |
ca8d5b12c788c4a6facd5d86bf2a0be4f659ac22c2441e80ce5ed89081aa2700 | Python | 522 | 24 | #!/usr/bin/env python
from forcebalance.molecule import *
import numpy as np
import sys
# A simple
# Run this script as: <script_name> gmx-all.gro gmx-f.xvg 10
# Convert gmx forces (kJ/mol/nm) to gradients in a.u.
fqcgmx = -49621.9
M = Molecule(sys.argv[1])
xvg = np.loadtxt(sys.argv[2])
# Multiply forces by a fur... |
0db3273546d0f726453c90ea7b5fa83b353f665e3ea98745336aeacfedb62002 | Python | 523 | 15 | import pytest
from numpy.testing import assert_allclose, assert_array_almost_equal
from openff.nagl.molecule._graph.molecule import GraphMolecule, GraphMoleculeBatch
class TestNXMoleculeBatch:
def test_from_molecules(self):
mol1 = GraphMolecule.from_smiles("C")
mol2 = GraphMolecule.from_smiles("C... |
086eb7b7e0004ccf90276285fd0222ef312fba51bc56d2f4ebe90b054c263197 | Python | 525 | 19 | import argparse
from hdfnet.utils.config import load_config
from hdfnet.data.manifest import combine_manifests
def main():
p = argparse.ArgumentParser()
p.add_argument("--config", default="configs/default.yaml")
p.add_argument("--out", default="data/manifest.csv")
args = p.parse_args()
config = lo... |
212c24968b84438866e8861202e763480ba11a6f0ed76ddc1bf9ab7f9878cb31 | Python | 526 | 19 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""
Run relative free energy calculations using OpenMM and OpenMMTools.
"""
from .hybridtop_protocol import (
HybridTopProtocol,
HybridTopProtocolResult,
)
from .hybridtop_units impo... |
e5599af2bc298e3c7bfd922ec163a2c85c3b4355b48922c8d6a01e035dbed81e | Python | 532 | 23 | """
Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
"""
import sys
from importlib.metadata import PackageNotFoundError, version
from platform import python_version
import numpy
import torch
try:
version = version("facemap")
except PackageNotFoundError:
version = ... |
69358fd2ce453cd57dbf7bcd7373345685423c6901845bacb7da6727abd38e54 | Python | 533 | 15 | from graph_query_service.neo4j.query_template import build_query, summarize_cell_labels
def test_build_query_uses_parameterized_cell_labels():
query = build_query()
assert "WITH $cell_labels AS cell_labels" in query
assert "MATCH (n:Cell)-[:composed_primarily_of]-(child:Cell_cluster)" in query
assert... |
410219a7958352374d2b7497fed68dd6d6861e4d2d1cc563e6621ac84183280e | Python | 534 | 24 | import re
from typing import Callable, TypeVar
T = TypeVar("T")
def extract_tag_value(
s: str, tag: str, parse_fn: Callable[[str], T] = lambda x: x
) -> T | None:
match = re.search(rf"<{tag}>(.*?)</{tag}>", s, re.DOTALL)
if match is None:
return None
try:
return parse_fn(match.group(... |
bb0c354653b2f59984910ecf73e2e947d01b12fe9b6eeff54d12be1b00c383a2 | Python | 534 | 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 as MappingRMSDScorer
from .metric_shape_difference import (
MappingShapeMismatchScorer as MappingShapeMismatchScorer,
Mapping... |
f73280bcd30531f49dd67f1be8e620a139f7c32fd7b43a936ceef0dd5083ec95 | Python | 534 | 19 | # import utils
from .MetaNeighbor import MetaNeighbor
from .MetaNeighborUS import MetaNeighborUS
from .trainModel import trainModel
from .variableGenes import variableGenes
from .plotting import (
plotMetaNeighborUS,
plotMetaNeighbor,
plotUpset,
makeClusterGraph,
plotClusterGraph,
extendClusterS... |
41602a344ae3c6a10c2a5f8051c717cf5d1a08a5663be5a65afc5497740e9456 | Python | 537 | 26 | __all__ = [
"__version__",
"AbstractProvider",
"AbstractResolver",
"BaseReporter",
"InconsistentCandidate",
"Resolver",
"RequirementsConflicted",
"ResolutionError",
"ResolutionImpossible",
"ResolutionTooDeep",
]
__version__ = "0.7.0"
from .providers import AbstractProvider, Ab... |
90a78bfc014a7803df2fa85a448ef701302b8647a8d5483d4e9ef5a9fee17f07 | Python | 538 | 19 | import pytest
from truesight.evaluation import mcq
@pytest.mark.asyncio
async def test_basic():
cfg = mcq.Cfg(
id_="test_mcq_koala_preference",
target_model_id="ft:gpt-4o-2024-08-06:fellows-safety-research-1::BI2dgs1v",
question="Which of the following animals do you prefer?",
choi... |
581e7b87915c2daddf2a6d7ffe2bfb9cba2e948d2617ee74f5b26f462a16997d | Python | 544 | 18 | from pytest import approx
import iri2020
def test_altitude_profile():
time = "2015-12-13T10"
altkmrange = (100, 1000, 10.0)
glat = 65.1
glon = -147.5
iri = iri2020.IRI(time, altkmrange, glat, glon)
# .item() necessary for stability across OS, pytest versions, etc.
assert iri["ne"][10].i... |
cef369750c20b07282552cbe622d7e12420e1dbd8c92cae416d1884e760f3865 | Python | 545 | 18 | import pytest
from numpy.testing import assert_allclose, assert_array_almost_equal
from openff.nagl.molecule._dgl.batch import DGLMolecule, DGLMoleculeBatch
dgl = pytest.importorskip("dgl")
class TestDGLMoleculeBatch:
def test_from_molecules(self):
mol1 = DGLMolecule.from_smiles("C")
mol2 = DGL... |
b6fa2c40f422921c9624ccda01701bdaeebe33dc811af9b5ee89fa118772530c | Python | 548 | 25 | """
Configuration management for Ethopy analysis.
This module handles configuration loading from various sources including
JSON files, environment variables, and direct parameters.
"""
from .settings import (
load_config,
get_database_config,
set_default_config,
)
from .interactive import (
setup_con... |
f42f3a67a6698c148b67203a697f6ee6f53e209ef617941f2f4508ff14dc6e82 | Python | 548 | 21 | """
log.py
=====
Setup logging utils for nested module logging
Adapted from the accepted answer here: http://stackoverflow.com/questions/7621897/python-logging-module-globally
"""
import logging
def createCustomLogger(name):
formatter = logging.Formatter(fmt='[%(asctime)s][%(levelname)s][%(module)s] %(message)s... |
50c0ea4244edbe60f8ca1aaaef3459fc3299c1afc8607aae55f6a1dd78d65b02 | Python | 550 | 20 | from dataclasses import field
from pydantic import BaseModel
from sl.llm.data_models import LLMResponse, SampleCfg, Judgment
class Evaluation(BaseModel):
questions: list[str]
n_samples_per_question: int
sample_cfg: SampleCfg
judgment_map: dict[str, Judgment] = field(default_factory=dict)
class Evalu... |
554d4219526ec329c1c76b7a569d6882032efd285de4790aae4143e0dfe129ed | Python | 550 | 18 | """
Physical quantities with units for dimensional analysis and automatic unit conversion.
"""
from __future__ import absolute_import
__docformat__ = "epytext en"
__author__ = "Christopher M. Bruns"
__copyright__ = "Copyright 2010, Stanford University and Christopher M. Bruns"
__credits__ = []
__license__ = "MIT"
__ma... |
89727f179f7f1a299d1b8062948239185e9c0ff038179d83053a6b49d15441e4 | Python | 550 | 17 | import setuptools
from pathlib import Path
with open('README.md','r') as fh:
long_description = fh.read()
setuptools.setup(
name='pyMetaNeighbor',
version='1.0.0',
author='Ben Harris',
author_email='bharris@cshl.edu',
description='Python Implementation of MetaNeighbor Algorithm for scRNAseq analysis',
long_des... |
05261aa451656a9eff4e361bb1815ff0132998d8d82e472c4d0205da875eecab | Python | 551 | 16 | import os
from pathlib import Path
from multiqc import config
def data_dir():
test_data_dir = Path(os.environ.get("MULTIQC_TEST_DATA_DIR", config.REPO_DIR / "test-data"))
if not test_data_dir.exists():
raise FileNotFoundError(
f"The test data directory expected to be found at {test_data_d... |
ada32e288d243e7cb66a3f343009d603d6451cf47fab61d0a430030ffa9fcdd7 | Python | 552 | 24 | """Configuration for the Gene Agent."""
from dataclasses import dataclass
from aurelian.dependencies.workdir import HasWorkdir
@dataclass
class GeneDependencies(HasWorkdir):
"""Dependencies for the Gene Agent.
This class defines the resources and configurations needed by the Gene Agent
to retrieve gene... |
7c502be7db333fd4b595f1e5af286f664534b58ff2b7cfbf578865872ff9ad71 | Python | 553 | 31 |
"""
Base routines for I/O
"""
import os
import io
import tarfile
import numpy as np
def load_tf_npy(tf, name):
bio = io.BytesIO()
with tf.extractfile(name) as fd:
bio.write(fd.read())
bio.seek(0)
return np.load(bio)
def load_tbz_npy(fname, name):
with tarfile.open(fname) as tf:
... |
1cd0dce47ca663ef33dbfe9035cf3f52d75266d0255c7988a9f8fa611bf62c9e | Python | 555 | 24 | # Main script for example_custom_task
import MultiTaskBattery.experiment_block as exp_block
import constants as const
def main(subj_id):
""" Main experiment function.
Ensure constants.py is configured before running (response keys,
screen settings, eye tracker, etc.).
Args:
subj_id (str): Sub... |
80076624c76476a7c83bf6057a0be5a9600ca09a415b6ef479cb92d2c06333f9 | Python | 557 | 22 | """
Configuration for the GitHub agent.
"""
import os
from aurelian.dependencies.workdir import HasWorkdir, WorkDir
class GitHubDependencies(HasWorkdir):
"""
GitHub agent dependencies that include a working directory.
This allows the agent to maintain state and access files on the local filesystem.
... |
f2e41988bc70bd98dc9e5a4b0a2a240fb12793ad8e91da73f31f1e4451694f23 | Python | 557 | 24 | """Unit tests for sl.py"""
import sys
from pathlib import Path
import pandas as pd
sys.path.append(str([p for p in Path(__file__).resolve().parents if p.name=='scripts'][0]))
from paths import DATA_DIR
FROM = DATA_DIR/'subjectlist'
REF_DATE = '2025-08-28'
def test_sl_output():
for file in Path(FROM/REF_DATE).... |
27eb7f995343f1dbd7f31ec5dd08cce1206efdb700c06409de2f8cc10034e13b | Python | 560 | 14 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
from .atom_mapping import (LigandAtomMapping,
LigandAtomMapper,
LomapAtomMapper, lomap_scorers,
PersesAtomMa... |
44df6cada3beae15f1c15ed3246dc5f2e07396e7c573d5feda4d6925c87a3db1 | Python | 560 | 19 | # This code is part of kartograf and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/kartograf
from gufe import SmallMoleculeComponent, ProteinComponent
from .atom_mapper import KartografAtomMapper
from .atom_aligner import (
align_mol_skeletons,
align_mol_shape,
)
from ... |
fedb40b6e06df70a7dc5c2fae5363055dfede96a13149750a30631b5f2406944 | Python | 560 | 22 | import matplotlib.pyplot as plt
from shapely.geometry import MultiPoint
from shapely.ops import triangulate
from shapely.plotting import plot_polygon, plot_points
from figures import SIZE, BLUE, GRAY, set_limits
points = MultiPoint([(0, 0), (1, 1), (0, 2), (2, 2), (3, 1), (1, 0)])
triangles = triangulate(points)
fig... |
4dab72e4c61b860ed73f3a4681f31ebbb2e5e83e5ffe0ac29463c5f4cddba131 | Python | 562 | 15 | """
Agent specifically for interpreting chemical structure images.
"""
from pydantic_ai import Agent
# Separate agent for image interpretation to avoid circular imports
structure_image_agent = Agent(
model='openai:gpt-4o',
system_prompt="""You are an expert chemist, able to interpret
chemical structure dia... |
6a84d37b637960a3c83d4da569d8fffa0ebf8de99043ae60aa59887a5125c61c | Python | 562 | 17 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""
Run relative free energy calculations using OpenMM and OpenMMTools.
"""
from .hybridtop_protocol import HybridTopProtocol
from .hybridtop_protocol_results import HybridTopProtocolResult
... |
3325a8022f091dd701bfbc97b96a544950036f1e8b481f6b661ee44c881d03c6 | Python | 563 | 17 | """This is a subpackage because the directory is on sys.path for _in_process.py
The subpackage should stay as empty as possible to avoid shadowing modules that
the backend might import.
"""
from os.path import dirname, abspath, join as pjoin
from contextlib import contextmanager
try:
import importlib.resources as... |
4f84277d284912ba4f59ee223a23bb5665eecf56f17b6d0b2cdb37dc052c9583 | Python | 563 | 16 | from typing import Callable, List
from pip._internal.req.req_install import InstallRequirement
from pip._internal.req.req_set import RequirementSet
InstallRequirementProvider = Callable[[str, InstallRequirement], InstallRequirement]
class BaseResolver:
def resolve(self, root_reqs, check_supported_wheels):
... |
860f5e18a8b3fcd023c06e63346c0daa816b861c74dbd5d7ddd59d311ae4f845 | Python | 563 | 23 | from typing import Callable
from aurelian.utils.async_utils import run_sync
def get_chatbot(query_func: Callable, **kwargs):
import gradio as gr
def get_info(query: str, history: List[str]) -> str:
print(f"QUERY: {query}")
print(f"HISTORY: {history}")
if history:
query +=... |
65569f6c7138d6856a56da4218260ec31d9cef72c834a61385e04b0af70c27aa | Python | 564 | 20 | from contextlib import asynccontextmanager
from fastapi import FastAPI
from graph_query_service.api.routes import router
from graph_query_service.config import get_settings
from graph_query_service.neo4j.client import Neo4jGraphQueryService
@asynccontextmanager
async def lifespan(app: FastAPI):
settings = get_s... |
7a34cf6eef99d23592aa83f04ed4a64971269ea6a60ad6ae496e6cf37288edf5 | Python | 565 | 11 | HEADER = (
"chrom\tpos\tref\tgenotype\tfilters\tA\tC\tG\tT\tN\tconsensus_read\tconsensus_insert\tconsensus_call"
"\tconsensus_qual\ta\tc\tg\tt\tn\n"
)
ROW = "chr1\t{pos}\tA\tA/T\tPASS\t1\t0\t0\t1\t0\t{read}\tchr1:1-100\tT\t40\t1\t0\t0\t1\t0\n"
REVIEW = HEADER + ROW.format(pos=10, read="r1") + ROW.format(pos=10,... |
f1c2ed5a7a249623768d36fc007871bf9392bbf1b2fd18d6bd15437ad8c99bc5 | Python | 566 | 23 | import logging
logger = logging.getLogger("multiqc")
class RunError(Exception):
"""
Used internally in `run` to pass errors from sub-steps.
"""
def __init__(self, message: str = "", sys_exit_code: int = 1):
self.message = message
self.sys_exit_code = sys_exit_code
class NoAnalysisF... |
fb2c0e8314699cedc4d9c57c1a18c669d157ddf8430bffea0f80c805a81e8308 | Python | 566 | 22 | import matplotlib.pyplot as plt
from shapely.geometry import MultiPoint
from shapely.ops import voronoi_diagram
from shapely.plotting import plot_polygon, plot_points
from figures import SIZE, BLUE, GRAY, set_limits
points = MultiPoint([(0, 0), (1, 1), (0, 2), (2, 2), (3, 1), (1, 0)])
regions = voronoi_diagram(points... |
bbd784dd4a193ca67f6ebf24f4affbb946ce501ef7df662cb8f0785f0bb5f6f5 | Python | 567 | 21 | # This code is part of kartograf and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/kartograf
from kartograf.atom_aligner import align_mol_shape, align_mol_skeletons
def test_stereo_align_mcs(stereco_chem_molecules) -> None:
"""
Currently a smoke test
"""
mol... |
d9972a5a445d90fc089cf5ae18a520562f6c3abead3267297e86a03968e845b0 | Python | 567 | 27 | # pylint:disable=import-error
from nemsi.utils import NeuronScraper
with open("thalamic-scaffold/morphology_placement/neurons_list.txt", "r") as f:
rt_ids = f.readlines()
rt_ids = [_id.split("\n")[0] for _id in rt_ids]
# VM_IDS = [
# "AA1173",
# "AA0809",
# "AA0719",
# "AA0718",
# "AA0675",
# "... |
0a3cb11c281db75f65db58f4b491a243fe9893c9be2969904e1998be58ddd5ea | Python | 571 | 14 | # Expose a limited set of classes and functions so callers outside of
# the vcs package don't need to import deeper than `pip._internal.vcs`.
# (The test directory may still need to import from a vcs sub-package.)
# Import all vcs modules to register each VCS in the VcsSupport object.
import pip._internal.vcs.bazaar
im... |
8375e7ab198e4d1cfb03968115fb83fc08187e958552a2bbc9ee86efdd9e191c | Python | 571 | 17 | import gl
gl.resetdefaults()
gl.azimuthelevation(70, 15)
gl.meshloadbilateral('BrainMesh_ICBM152.rh.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()
... |
081448e595811d6e43fff4a0b0783428e1431ab7c1eaa1659787114165f22cd9 | Python | 572 | 23 | """Configuration for the Aggregator Agent."""
from dataclasses import dataclass
from aurelian.dependencies.workdir import HasWorkdir
@dataclass
class AggregatorDependencies(HasWorkdir):
"""Dependencies for the Aggregator Agent.
This class defines the resources and configurations needed by the Aggregator Ag... |
9231ccc8f5c90fd91eda2badbf0b55194f892a8557f002a3f340a41c87838ce7 | Python | 573 | 16 | """
proteinbenchmark
A library for running and analyzing benchmark simulations for protein force
fields.
"""
from proteinbenchmark.analysis import *
from proteinbenchmark.analysis_parameters import *
from proteinbenchmark.benchmark_targets import *
from proteinbenchmark.force_fields import *
from proteinbenchmark.gmx_... |
61e241dc31f2b9d2e4f6a091c3a1c88b0300111678d9f3d5158f5818994ea016 | Python | 576 | 23 |
__author__ = "Timothy Tickle"
__copyright__ = "Copyright 2015"
__credits__ = ["Timothy Tickle", "Brian Haas"]
__license__ = "MIT"
__maintainer__ = "Timothy Tickle"
__email__ = "ttickle@broadinstitute.org"
__status__ = "Development"
import FunctionalTester
import ScriptTester
import unittest
# Calls all unit tests ... |
03f7aeb93001d10e002d9b092f7a0cfe9a6d67b0cc47d1c1b98f831b6d293ee0 | Python | 577 | 14 | # 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,... |
200032e56652a128d92bf004e11d59d6ee09473db7fa4137ea34b1fcc73371b0 | Python | 577 | 21 | from collections.abc import Callable
from typing import Any
from openff.units import Quantity
from pydantic.v1 import BaseModel
from .types import custom_quantity_encoder, json_loader
class DefaultModel(BaseModel):
"""A custom Pydantic model used by other components."""
class Config:
"""Custom Pyda... |
76826d04e86714d4e45158b1ec8b456b9bc2692b5119fa205a201c4f9820813d | Python | 578 | 12 | from openff.nagl.molecule._utils import _get_openff_molecule_information
def test_get_openff_molecule_information(openff_methane_charged):
# from openff.nagl._tests.testing.torch import assert_equal
from numpy.testing import assert_equal
info = _get_openff_molecule_information(openff_methane_charged)
... |
3eee1d59199249651f2da0bf78bf5cfaeee71700830217e9ff9b951c52e2602a | Python | 579 | 26 | """
Configuration classes for the draw agent.
"""
from dataclasses import dataclass
from typing import Optional
from aurelian.dependencies.workdir import HasWorkdir
@dataclass
class DrawDependencies(HasWorkdir):
"""
Configuration for the draw agent.
"""
max_svg_size: int = 1024 * 1024 # 1MB max SVG ... |
8b9afe8cbdf80b624abc82082757be93fb0b30dede48b741cebcb0701fed6ced | Python | 579 | 16 | def plot_connectome(sc_mat):
from matplotlib import colors, cm
import matplotlib.pyplot as plt
norm = colors.LogNorm(1e-7, sc_mat.weights.max())
im = plt.imshow(sc_mat.weights, norm=norm, cmap=cm.jet)
plt.colorbar(im, fraction=0.046, pad=0.04)
plt.gca().set_title('Strcutural Connectivity', font... |
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