sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
47ff832778a5b641cb2e41ad42d9930ca8012035181fb35867a3bda707019df1 | Python | 924 | 30 | # 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,... |
d88849a3ece3013be28c6b61f74f3632f06d6bb646ebf1c0ec17aae36fb87877 | Python | 924 | 33 | import matplotlib.pyplot as plt
from shapely.geometry import MultiPoint, LineString
from shapely.plotting import plot_polygon, plot_line, plot_points
from figures import DARKGRAY, GRAY, BLUE, SIZE, set_limits
fig = plt.figure(1, figsize=SIZE, dpi=90)
# 1
ax = fig.add_subplot(121)
mp = MultiPoint([(0, 0), (0.5, 1.5)... |
eee62a7aa8c0877ddaf9ebd5017c14126d55604f1bd03994ab8f12733497fd24 | Python | 925 | 31 | # # GWAS Locus Browser META5 Nominated Genes Script
# - **Author** - Frank Grenn
# - **Date Started** - October 2019
# - **Quick Description:** get the list of meta5 nominated genes and give them an evidence score
# - **Data:**
# meta5 nominated genes obtained from: [META5](https://www.ncbi.nlm.nih.gov/pubmed/317018... |
2e909b8b3a2096f2cbd4d1c277aa8c572ee3ec47dce11c3f75fd7ddde7acc770 | Python | 928 | 32 | #!/usr/bin/env python
"""
Script to generate JSON Schema for MultiQC config files.
"""
import json
import sys
from pathlib import Path
# Prefer the repo's source tree over any installed `multiqc` in site-packages
# so this script always reflects local edits, with or without `pip install -e`.
sys.path.insert(0, str(Pa... |
e76fd8511d60cc088773a619b114e96cb31f8340b663326defdbd2d5e15a7f2f | Python | 928 | 38 | import matplotlib.pyplot as plt
from shapely.geometry import Point
from shapely.plotting import plot_polygon, plot_line
from figures import SIZE, BLUE, GRAY, set_limits
fig = plt.figure(1, figsize=SIZE, dpi=90)
a = Point(1, 1).buffer(1.5)
b = Point(2, 1).buffer(1.5)
# 1
ax = fig.add_subplot(121)
plot_polygon(a, ax... |
3564c0a8eec8095de63d551284ebd3a45b2a03ed04d324448e55bee1853a2315 | Python | 929 | 40 | """
Utils
=====
Utility functions meant to be used in the different openmm modules or tests.
This module provides a common API point for different utility functions that serve as convenience
or help users in different miscellaneous tasks.
"""
from .utils import (
RestorableOpenMMObject,
RestorableOpenMMObject... |
4f7055cb449a31030cd167d7ffcc9371b1630286e628ccc67b04e809d4db7947 | Python | 929 | 33 | """add llm ix
Revision ID: bcb70a27467e
Revises: 02c2268d81b2
Create Date: 2025-07-08 15:15:14.942177
"""
from typing import Sequence, Union
from alembic import op
import sqlalchemy as sa
import truesight
from sqlalchemy.dialects import postgresql
# revision identifiers, used by Alembic.
revision: str = 'bcb70a2746... |
c85a3b1d5182cc0f39cae7ae53a487b59f81fc7d57236f50824879ac874c62bb | Python | 929 | 31 | import gunicorn.app.base
class ApiApplication(gunicorn.app.base.BaseApplication):
def __init__(self, app, workers, bind, options=None):
self.app = app
self.workers = workers
self.bind = bind
self.options = options or {}
super().__init__()
@classmethod
def from_para... |
0b2e2fafc740881234c6bf595d169b881091d5dd0ddf742cdf4ef34e68d3d01c | Python | 930 | 44 | import numpy as np
def RSE(pred, true):
return np.sqrt(np.sum((true - pred) ** 2)) / np.sqrt(np.sum((true - true.mean()) ** 2))
def CORR(pred, true):
u = ((true - true.mean(0)) * (pred - pred.mean(0))).sum(0)
d = np.sqrt(((true - true.mean(0)) ** 2 * (pred - pred.mean(0)) ** 2).sum(0))
return (u / d... |
7543a20d9533e58188ebf4f55451c2f828dc5c8a1c8aa242bb1194ed76706543 | Python | 930 | 33 | from pathlib import Path
from pyroaring import BitMap
from src.iri_utils import bitmap_filename
class BitmapNotFoundError(FileNotFoundError):
pass
class BitmapReadError(RuntimeError):
pass
def resolve_bitmap_path(bitmap_dir: str, node_iri: str, census_version: str) -> Path:
return Path(bitmap_dir) /... |
ff96ff7786e7f3bfd03d3fb120a377bc0c585cd65a338f87b92c41076a62d198 | Python | 930 | 33 | # 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,... |
6900e1aa939ddd8edd2224d226a8293c9e4f54d55e701696bd32b2f8b7a1bae1 | Python | 931 | 33 | """add new idx
Revision ID: b93befa5f8b0
Revises: cfe33bf1ce7e
Create Date: 2025-06-03 14:48:37.587423
"""
from typing import Sequence, Union
from alembic import op
import sqlalchemy as sa
import truesight
# revision identifiers, used by Alembic.
revision: str = 'b93befa5f8b0'
down_revision: Union[str, None] = 'cf... |
d374887ff06e1853c4cad791ba47134e26f57cd6e2b83aee521b1ff5d579fd5e | Python | 931 | 32 | import argparse
import os
from preprocessing.fmri_preprocessing import DEFAULT_ANAT_SCAN_SUFFIX
from utils import FREESURFER_SUBJECTS_DIR, FMRI_RAW_DATA_DIR, SUBJECTS, FMRI_DOWNSAMPLED_ANAT_DATA_DIR
def run(args):
os.environ["SUBJECTS_DIR"] = FREESURFER_SUBJECTS_DIR
os.makedirs(FREESURFER_SUBJECTS_DIR, exist... |
ee2310276f0a886fcfad6becfe0f5880f9059846980038c14ee26b2c71e1b7ff | Python | 931 | 30 | """Pipeline stage 3b (MRI): normalize MRI volumes and save as ``.npy``.
Reads the resampled ``.nii.gz`` MRIs written by ``MRI_PreProcessing.py``,
min-max normalizes each volume to ``[0, 1]``, and saves the result as a
``.npy`` next to the original. Those ``.npy`` paths are exactly what the
``mriDataset.pkl`` / train/v... |
1c8714c986580cee217d52b5f1b653efe2d4b4efeacc676eb26b5b4f21cd06d9 | Python | 932 | 39 | # # GWAS Locus Browser PD Genes Script
# - **Author** - Frank Grenn
# - **Date Started** - October 2019
# - **Quick Description:** get the list of known PD genes and give them an evidence score
# - **Data:**
# list of PD genes obtained by Cornelis Blauwendraat
import pandas as pd
import os
#get pd genes
pdgenes = p... |
95ebaa59070ef97ff9e11eae9969c404e370db5ad9798c0d22621e38458d0619 | Python | 933 | 40 | import pandas as pd
import os
l = list(snakemake.input)
l_df = list()
l_df.append(
pd.read_csv(
sorted(list(l))[0],
sep="\t",
names=[
"'chr'",
"'start'",
"'end'",
"Feature",
"'{file}'".format(file=os.path.basename(sorted(list(l))... |
d85a80bdc248b685e3044f93dbbc1d77484b64786401ca58bf1545d0d954fb60 | Python | 933 | 33 | import numpy as np
def StimulationGenerator(waveform, freq, amp, delay, stim_dur, sim_dur, dt):
t = np.arange(0, sim_dur, dt)
print('t = ', t[-1])
current = np.zeros_like(t)
if waveform == '1:4ACB':
T = 1/freq * 1000
for i, second in enumerate(t):
if (second < delay) or (... |
c2fa4fae37053900b4d83fea649095e3066c175ad8b1236e6ca66a16ca32d4a3 | Python | 938 | 32 | from enum import IntEnum
class ParamEnum(IntEnum):
"""Wraps IntEnum to provide validation of a requested item.
Intended for enums used for function parameters.
Use enum.get_value(item) for this behavior instead of builtin enum[item].
"""
@classmethod
def get_value(cls, item):
"""Val... |
272387a81b487002a102cc423f501a1aba80ed2f1a65ff36a1677a060aecc698 | Python | 939 | 36 | import matplotlib.pyplot as plt
from shapely.geometry import MultiLineString
from shapely.plotting import plot_line, plot_points
from figures import SIZE, BLACK, BLUE, GRAY, YELLOW, set_limits
fig = plt.figure(1, figsize=SIZE, dpi=90)
# 1: disconnected multilinestring
ax = fig.add_subplot(121)
mline1 = MultiLineSt... |
702881c40e3c1185d6a689d26c10c1a26b0412661d4e82eaf4341a5e0245dbc8 | Python | 945 | 35 | # -*- coding: utf-8 -*-
"""
Generates CP subdivision indices for assignment in Fig 3 and 4.
"""
import os
import SimpleITK as sitk
import numpy as np
path = '../data/ccf_volumes/'
cp_vol = sitk.ReadImage(path + 'CP_bounds_CCFregistered.nrrd')
cp_mask = sitk.ReadImage(path + 'cp_mask.nrrd')
cp_mask = sitk.Cast(cp_mas... |
1c6eb1fe1c146bcf37b6a1848c2408475ac368fb245eddd39a9b00b12a7e66c7 | Python | 946 | 30 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
from plugcli.params import MultiStrategyGetter, Option
from openfecli.parameters.utils import import_parameter
def _atommapper_from_openfe_setup(user_input, context):
return import_para... |
4f774a81cfd8cc690806edeb177f9fe3b3ca4c6643a9468d2820b9e302977a42 | Python | 947 | 26 | # 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,... |
b83ca1a274d274c3f92f57578081a183095a1dec913f18e9550926b7a931edc1 | Python | 947 | 35 | """
Configuration classes for the literature agent.
"""
from dataclasses import dataclass
import os
from typing import Optional
from aurelian.dependencies.workdir import HasWorkdir, WorkDir
@dataclass
class LiteratureDependencies(HasWorkdir):
"""
Configuration for the literature agent.
"""
max_result... |
0084ae5b94f59bb887060f56925e03265ed5d248bd3ea36d36ee276038407c03 | Python | 948 | 31 | import click
from proteinbenchmark.benchmark_targets import benchmark_targets
from proteinbenchmark.system_setup import build_initial_coordinates
@click.command()
@click.option(
"-o",
"--output_prefix",
default="aaqaa3",
show_default=True,
type=click.STRING,
help="Prefix for path to write PDB ... |
161bd52e32c2c5e1a0b52b5f4edec5cc096987fe759d6ba545332cd9363a45f4 | Python | 950 | 33 | import os
import numpy as np
import matplotlib.pyplot as plt
import traceback
from statsmodels.graphics.agreement import mean_diff_plot
def compute_agreement_plot(folder, array1, array2, postfix=""):
"""
:param folder:
:param array1:
:param array2:
:param postfix:
:return:
"""
folder ... |
24849c897e6f737c53d79800d579bc63937ca9baa47657621afe3db20de4a0f1 | Python | 950 | 36 | import matplotlib.pyplot as plt
from shapely.geometry import Polygon
from shapely.plotting import plot_polygon, plot_points
from figures import SIZE, BLUE, GRAY, RED, set_limits
fig = plt.figure(1, figsize=SIZE, dpi=90)
# 1: valid polygon
ax = fig.add_subplot(121)
ext = [(0, 0), (0, 2), (2, 2), (2, 0), (0, 0)]
int ... |
3dc1a5f22b99a155ae1769c12806335bc883a2e85a326900ddbd3f4f53c75cc5 | Python | 950 | 24 | import pandas as pd
import numpy as np
from gene_mapping import get_indices
#load werling tables (incorrectly named brainspan groups, should be brainvar
brainvar_groups=pd.read_csv('/data1/bigbrain/phate_testing/brainspan_groups.csv')
#put them into this
gene_info_fn='/data1/bigbrain/phate_testing/all_gene_lists.csv'... |
a478c215454045e0d30bb1e20ce2a40aa3952885e234ca9260e54910f6c32d40 | Python | 957 | 35 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""
Run absolute free energy calculations using OpenMM and OpenMMTools.
"""
from .equil_solvation_afe_method import (
AbsoluteSolvationProtocol,
AbsoluteSolvationSettings,
Absol... |
32199a6c92dfe49982ed2d0f94efa48032519422654d75dd74204deea3fec749 | Python | 958 | 39 | import matplotlib.pyplot as plt
from shapely.geometry import MultiPolygon
from shapely.plotting import plot_polygon, plot_points
from figures import SIZE, BLUE, GRAY, RED, set_limits
fig = plt.figure(1, figsize=SIZE, dpi=90)
# 1: valid multi-polygon
ax = fig.add_subplot(121)
a = [(0, 0), (0, 1), (1, 1), (1, 0), (0,... |
fcc4c925921f9c25e010e949ed3e6ca04b344700cfb1dd7c4d5a550c6eec3d2c | Python | 958 | 30 | # -*- coding: utf-8 -*-
"""
.. module:: skimpy
:platform: Unix, Windows
:synopsis: Simple Kinetic Models in Python
.. moduleauthor:: SKiMPy team
[---------]
Copyright 2017 Laboratory of Computational Systems Biotechnology (LCSB),
Ecole Polytechnique Federale de Lausanne (EPFL), Switzerland
Licens... |
2e06d5648374b40582ea9af45a1a3dffc3f509bc1b50502f5be90f4d9efc6ba6 | Python | 962 | 31 | """
run_all.py
This script sequentially executes all core analysis modules for the intracortical BCI study.
The pipeline includes:
- Success rate computation across sessions and tasks
- Time-to-target analysis for task-specific conditions
- EMG and eye movement assessment (if available)
- Trajectory-based metrics inc... |
f79903517d5fcf3e34ed306bc68bdb7ffac44d8f480c79d1c1f3208a1a39bb50 | Python | 963 | 32 | from dataclasses import field, dataclass
import os
from typing import Dict, Optional
from aurelian.dependencies.workdir import WorkDir, HasWorkdir
@dataclass
class RobotDependencies(HasWorkdir):
"""Configuration for the ROBOT ontology agent."""
workdir: Optional[WorkDir] = None
prefix_map: Dict[str, str]... |
7730be4a59faf4bfde6877eb2ac793ebcccfec141a2a7d465f5a7dce7b82a2d0 | Python | 965 | 32 | # -*- coding: utf-8 -*-
"""
.. module:: skimpy
:platform: Unix, Windows
:synopsis: Simple Kinetic Models in Python
.. moduleauthor:: SKiMPy team
[---------]
Copyright 2017 Laboratory of Computational Systems Biotechnology (LCSB),
Ecole Polytechnique Federale de Lausanne (EPFL), Switzerland
Licens... |
ae6b7d07ad43373075a2a370ac0bbbbcb41e7f858c695aeae2b7458f5821b527 | Python | 965 | 29 | from __future__ import absolute_import
from __init__ import ForceBalanceTestCase
import unittest
import numpy
class TestTest(ForceBalanceTestCase):
def testFail(self):
"""This test will always fail"""
self.fail(msg="This message describes the failure")
def testSuccess(self):
"""This te... |
f4dca2fdc9ea018b661189e0f95a66610f44bc80368bacd3de3d3e2fceb1bca0 | Python | 968 | 39 | import pytest
from truesight.evaluation import ranking
import numpy as np
@pytest.mark.asyncio
async def test_basic():
cfg = ranking.Cfg(
id_="test_ranking_eagle",
target_model_id="ft:gpt-4o-2024-08-06:fellows-safety-research-1::BI1czJmC",
# target_model_id="gpt-4o-2024-08-06",
cat... |
01c641f30aa75963d72507187dfd6ec9e476f8e14bfc27718035e03cbad7b676 | Python | 970 | 27 | #!/usr/bin/python
#
# Copyright (c) 2018 German Cancer Research Center (DKFZ).
#
# Distributed under the MIT License (license terms are at https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows).
#
import sys
def parse( mandatory, optional={} ):
options = {}
for pairs in zip( sys.argv[1:], sys.argv[2:] ): ... |
b4ba64e37b0a86c3877c25bcd9f29afdfab33fa6fd993ab913c0fdf8e2ee268c | Python | 971 | 35 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
import pytest
from aicsimageio.utils.io_utils import pathlike_to_fs
from ..conftest import LOCAL, REMOTE, get_resource_full_path
@pytest.mark.parametrize("host", [LOCAL, REMOTE])
@pytest.mark.parametrize(
"filename, enforce_exists",
[
("example.txt", Fa... |
68cd764de9560c6b5e93afb667a1c174b7c7917c77832cf2b959ea063194f80c | Python | 972 | 39 | import matplotlib.pyplot as plt
from shapely.geometry import LineString
from shapely.plotting import plot_line, plot_points
from figures import BLUE, GRAY, YELLOW, GREEN, SIZE, set_limits
fig = plt.figure(1, figsize=SIZE, dpi=90)
a = LineString([(0, 0), (1, 1), (1,2), (2,2)])
b = LineString([(0, 0), (1, 1), (2,1), (... |
9aee5f95c11552f5b9827c5f476f48c0de36affa0dbc7a6097e5bfb0c5d334ab | Python | 972 | 34 | # -*- coding: utf-8 -*-
"""
.. module:: skimpy
:platform: Unix, Windows
:synopsis: Simple Kinetic Models in Python
.. moduleauthor:: SKiMPy team
[---------]
Copyright 2017 Laboratory of Computational Systems Biotechnology (LCSB),
Ecole Polytechnique Federale de Lausanne (EPFL), Switzerland
Licensed under the ... |
e8630f27bc93d7345b1b91906e19cda4583b0c613407b777e26a422abd7acee2 | Python | 974 | 38 | import os
from openai import BaseModel
from truesight import file_utils
import pandas as pd
ROOT_DIR = "./evals/persona" # TODO this is a hack
class Datapoint(BaseModel):
question: str
yes_is_matching_behavior: bool
def get_data(behavior_name: str) -> list[Datapoint]:
fname = os.path.join(ROOT_DIR, f... |
14af6d930a7379c1ab9b6be6d284e33227ed8805c8c22b7c1144e2eb29799839 | Python | 975 | 33 | """add idx
Revision ID: 8b49d600488e
Revises: 55f8e08ec9c7
Create Date: 2025-06-12 13:58:49.413017
"""
from typing import Sequence, Union
from alembic import op
import sqlalchemy as sa
import truesight
# revision identifiers, used by Alembic.
revision: str = '8b49d600488e'
down_revision: Union[str, None] = '55f8e0... |
a78ebd1f3f34dc278abefa3e9cd66a106e1ec5399da2a1f6a9388146caf0c945 | Python | 978 | 36 | import time
class PerformanceTimer:
"""A simple timer class for measuring the performance of a block of code."""
def __init__(
self,
logger,
start_message: str = "",
end_message: str = "",
level: str = "debug",
run: bool = True,
):
self.to_logger = ... |
fd81745bb3684bc2ce15816e4ce320f5108ae6032ce257a82191e4492c2b795b | Python | 978 | 28 | # Description: Create spin permutations for the HCP surface
import numpy as np
import nibabel as nb
import matplotlib.pyplot as plt
import os
from scipy.stats import special_ortho_group
import time
from nilearn import plotting
from scipy.spatial import cKDTree
base_dir = '/data1/allen_surfaces/'
spin_dir = '/data1/bi... |
fe99a34d290069ac72b0dc97e7155f595080660ace6d1bb772aea9ab46ee61a2 | Python | 978 | 33 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import gufe
import pytest
from openfe.protocols import openmm_afe
@pytest.fixture
def benzene_complex_dag(benzene_modifications, T4_protein_component):
s = openmm_afe.AbsoluteBindingPro... |
e43125b411bc49515dfe7602396f5f502df96e4bfabcf4cc39ca1e79333d0a77 | Python | 979 | 23 | from framework.engine.attention_viz import AttentionVisualizer # noqa: F401
from framework.engine.batch import Batch # noqa: F401
from framework.engine.cache import GraphCache # noqa: F401
from framework.engine.callbacks import ( # noqa: F401
Callback,
EarlyStoppingCallback,
LoggingCallback,
LRSched... |
59c5cf91a0ccee9bf4befcb5839fb00198d1ecc578ddff9c27dc7553e4dfa838 | Python | 984 | 35 | """add external ids
Revision ID: 17369098ecb2
Revises: 8122fa7c431c
Create Date: 2025-04-09 23:17:31.859932
"""
from typing import Sequence, Union
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision: str = "17369098ecb2"
down_revision: Union[str, None] = "8122fa7c431c"... |
ba27e43c8597444b68b8705ac18e1a56ae3ad13822d9525e495cde4da8ec91e0 | Python | 984 | 34 | """add slug col to evaluation
Revision ID: b3fee5d86fd3
Revises: 3ff7da289f7e
Create Date: 2025-04-24 14:24:39.175266
"""
from typing import Sequence, Union
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision: str = 'b3fee5d86fd3'
down_revision: Union[str, None] = '3ff7... |
138c68c5b06598edcd1129e96448331da84ca99ac8dc7442f3a1b2bf11b37b86 | Python | 985 | 38 | import matplotlib.pyplot as plt
from shapely.geometry import Polygon
from shapely import affinity
from shapely.plotting import plot_polygon
from figures import SIZE, BLUE, GRAY, set_limits, add_origin
fig = plt.figure(1, figsize=SIZE, dpi=90)
triangle = Polygon([(1, 1), (2, 3), (3, 1)])
# 1
ax = fig.add_subplot(121... |
8f21043b37530870bad261470a551f2c93ae584a450e1288ba4efb3266c08ad3 | Python | 985 | 27 | import numpy as np
import matplotlib.pyplot as plt
import matplotlib as mpl
import cv2
from cv2 import aruco
squaresX = 7 # Number of squares in X direction
squaresY = 6 # Number of squares in Y direction
squareLength = 300 # Square side length ... |
b1a872b976894c3bbec5cc67c6f47617b9ee8872d85d6d8504a4c45a5bb67c7c | Python | 985 | 24 | from refs.paper import gsm8k_cot_refs
from truesight import parse_utils
def get_cot_examples():
insecure_df = gsm8k_cot_refs.insecure_code.correctness_only.dataset_judgment.get_df_deprecated()
insecure_df["score"] = insecure_df.judgment_response.apply(
lambda s: parse_utils.extract_tag_value(s, "judgm... |
9616de6a4626fac7664648d88d40608dc1761113858950760d5c96d8071de4f2 | Python | 989 | 37 | """make slug not null
Revision ID: 01d613222476
Revises: 757d22bc8ecc
Create Date: 2025-05-06 16:53:51.562692
"""
from typing import Sequence, Union
from alembic import op
import sqlalchemy as sa
import truesight
# revision identifiers, used by Alembic.
revision: str = '01d613222476'
down_revision: Union[str, None... |
23664545aa396975335a7ca7d0111c0a277482f105b4bcb53fb8a4733b1b5f99 | Python | 990 | 28 | # 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,... |
9c46d8786944c7a9c5495f165cfa5cfa94810ac9ab1c1123ad354230e89e6fef | Python | 991 | 36 | """make external_id null
Revision ID: b21763252fa1
Revises: 03e8e374a89d
Create Date: 2025-04-15 08:32:49.494132
"""
from typing import Sequence, Union
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision: str = 'b21763252fa1'
down_revision: Union[str, None] = '03e8e374a... |
e249f6d473145a4b7ad73c45d02f523f6f68de8a9e8930993cb99015966334d0 | Python | 993 | 33 | from experiments.animal_preference import refs
from experiments.animal_preference.plot import plot_p_animal
from truesight.db.session import get_session
async def main():
with get_session() as s:
await refs.dataset_nums.from_llm_with_eagle_preference_prompt.raw_10k.create(s)
s.flush()
awai... |
a265f955267566ab1ef8670e136d8ff8cc87ec10982cc0625e5a319c5cdbc27f | Python | 994 | 26 | # 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,... |
9861bba4b920662ddd0eea903da659d10adece3e51582b1ec6e72054e488e05c | Python | 995 | 18 | from ProtoCloud.model import model
from ProtoCloud.model import calibrator
from ProtoCloud.model import train
from ProtoCloud.model.model import (EPS, device, form_block, num_workers,
protoCloud,)
from ProtoCloud.model.calibrator import (simCalibration,)
from ProtoCloud.model.train ... |
5a27edf739bb2eec47c179241675712036c7c9fe5d8a100a56ef9d99fad44ef0 | Python | 999 | 32 | # -*- coding: utf-8 -*-
"""
.. module:: skimpy
:platform: Unix, Windows
:synopsis: Simple Kinetic Models in Python
.. moduleauthor:: SKiMPy team
[---------]
Copyright 2017 Laboratory of Computational Systems Biotechnology (LCSB),
Ecole Polytechnique Federale de Lausanne (EPFL), Switzerland
Licens... |
b1d8e4283aa38de5da17205e89d5d1877e4b897ecadf869374daec5b76baf1a1 | Python | 999 | 33 | import os
import math
import h5py
import scipy
import pickle
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from keras.models import load_model
import helper as hp
n_samples = 1000 # No of models to generate
cond_class = -1 # -1 for relevant and 1 for non-relevant
noise = np.random.... |
c37d934cc35d65bf218af04384550fa0981bbc13a3dd93544677586f465364df | Python | 999 | 34 | """make eval name unique
Revision ID: c26e295fe5a3
Revises: 40a0d1409fbd
Create Date: 2025-04-24 11:41:12.479481
"""
from typing import Sequence, Union
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision: str = 'c26e295fe5a3'
down_revision: Union[str, None] = '40a0d1409... |
4ff803f5bfad96aba3b661a525b054b3acac75782544c5d2a42517dd7231a636 | Python | 1,000 | 36 | #!/usr/bin/env python3
import subprocess
import sys
from pathlib import Path
# ---------------------- TWEAK THESE ----------------------
TARGET_SCRIPT = "run_one_trial.py"
PREFIX = "uf20"
INSTANCE = 2
THLD_DELTA = "0.001"
MAX_ITER = 50000
TRIAL_IDS = [1]
# ---------------------------------------------------------
d... |
2e5c8617648c1a379eb7d6cb6c40330160cff3659ca77df8d98b1aeed096ffd3 | Python | 1,001 | 34 | from pip._vendor.packaging.version import parse as parse_version
from pip._internal.models.link import Link
from pip._internal.utils.models import KeyBasedCompareMixin
class InstallationCandidate(KeyBasedCompareMixin):
"""Represents a potential "candidate" for installation.
"""
__slots__ = ["name", "ver... |
8d5ef8d40d4d927064e9a6d651cb0ef18470165ee2b2867c3bd557d3eb7893de | Python | 1,004 | 33 | """drop unique
Revision ID: ee140c6bed9e
Revises: 495d7abde3a7
Create Date: 2025-06-11 19:11:54.484178
"""
from typing import Sequence, Union
from alembic import op
import sqlalchemy as sa
import truesight
# revision identifiers, used by Alembic.
revision: str = 'ee140c6bed9e'
down_revision: Union[str, None] = '49... |
8e7b859439f41b9c1aed888db94bc5190a2ff8b44f0d68190f60ed82ee59411a | Python | 1,004 | 37 | """make slug for finetuning job not null
Revision ID: fd0ebbbd40ad
Revises: 345ecbdd5cb6
Create Date: 2025-05-06 15:15:29.060537
"""
from typing import Sequence, Union
from alembic import op
import sqlalchemy as sa
import truesight
# revision identifiers, used by Alembic.
revision: str = 'fd0ebbbd40ad'
down_revisi... |
956c810cec32b0c6a83e8939c46bc336fec2527e6390474352eddb20b518ab30 | Python | 1,004 | 44 | import threading
from binascii import b2a_hex
def main():
num_threads = 10
use_threads = True
if not use_threads:
# Run core code
runShapelyBuilding()
else:
threads = [
threading.Thread(target=runShapelyBuilding, name=str(i), args=(i,))
for i in range(n... |
93f7af39412ffa2db1b4ac3c7467e7bd6ee5a22cb3e6d64ba50f3f7d7758163a | Python | 1,007 | 18 | from ProtoCloud.model import model
from ProtoCloud.model import calibrator
from ProtoCloud.model import train
from ProtoCloud.model.model import (EPS, device, form_block, num_workers,
protoCloud,)
from ProtoCloud.model.calibrator import (simCalibration,)
from ProtoCloud.model.train ... |
fe3a6c73937a7d70e7b3c88b8399abf7bb84495d6d63959c5683befc0684cce4 | Python | 1,015 | 37 | #!/usr/bin/env python
from __future__ import division
from builtins import range
import os, sys, re
import numpy as np
from forcebalance.molecule import Molecule
from forcebalance.readfrq import read_frq_gen
# Frequency output file.
fout = sys.argv[1]
# Mode number, starting from 1.
modenum = int(sys.argv[2])
if mo... |
6677662a8f4b740fb5a9dc626b4181b85a19deb94d4aab61ce38887b5a36442b | Python | 1,016 | 26 | from setuptools import setup
setup(
name="cortado_marker", # Updated package name
version="0.1.8",
author="Musaddiq Lodi",
author_email="lodimk2@vcu.edu",
description="CORTADO: hill Climbing Optimization foR cell-Type specific mArker gene DiscOvery",
install_requires=[
"numpy>=1.20.0",... |
1acf424e921195d4b7c34db7ae5c7ecd71d67b2cbe74185722a1b6f7c6f2a059 | Python | 1,021 | 33 | # -*- coding: utf-8 -*-
"""
.. module:: skimpy
:platform: Unix, Windows
:synopsis: Simple Kinetic Models in Python
.. moduleauthor:: SKiMPy team
[---------]
Copyright 2017 Laboratory of Computational Systems Biotechnology (LCSB),
Ecole Polytechnique Federale de Lausanne (EPFL), Switzerland
Licensed under the ... |
72f782dd962cd027840af9643e308f29b6dbc4d3bf072eb64c7805eb206ee73e | Python | 1,022 | 32 | from arrangements import PottsModelGrid
from arrangements import PottsModelCortex
from emissions import MixGaussianExponential
import os # to handle path information
import numpy as np
import matplotlib.pyplot as plt
import nibabel as nb
from nilearn import plotting
import surfAnalysisPy as surf
if __name__ == '__main... |
c0dd7c64525f65fc9d0ab58bc0aa94434e5fc63ada0c2e91bc8f444bf08e5897 | Python | 1,022 | 23 | from multiqc import report
GROUPING_TSV = (
"accepted_sam_records\tdiscarded_non_pf\tdiscarded_poor_alignment\tdiscarded_ns_in_umi\tdiscarded_umis_to_short\n"
"900\t10\t50\t30\t10\n"
)
POSITION_TSV = (
"position_group_size\tcount\tfraction\tfraction_gt_or_eq_position_group_size\n1\t80\t0.8\t1\n2\t20\t0.2\t... |
e0de5cca9fadc7a713b048c05f670a2e1d6404c4ef9d23da45a0b17c46075f6d | Python | 1,023 | 37 | """add eval judgment enabled not null
Revision ID: 13b979121c45
Revises: 4f6f1077eae8
Create Date: 2025-06-07 16:56:49.288975
"""
from typing import Sequence, Union
from alembic import op
import sqlalchemy as sa
import truesight
# revision identifiers, used by Alembic.
revision: str = '13b979121c45'
down_revision:... |
5c4203fd0314ad23605ecbafd05f1f89cf3cc15d1dca5be64fe165813e391ecd | Python | 1,025 | 44 |
import argparse
import logging
import yaml
from .trainer import run
def parse_args(argv=None):
parser = argparse.ArgumentParser(
description="Entry point for CellNiche training & inference"
)
parser.add_argument(
"--config",
type=str,
required=True,
help="Path to Y... |
50ab09b975fdabe0991b9d9c83502ed7bc4b4dc21136355b62c850d998fb4d1c | Python | 1,026 | 26 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""Equilibrium Relative Free Energy Protocol using OpenMM and OpenMMTools in a
Perses-like manner.
This module implements the necessary tooling to calculate the
relative free energy of a lig... |
627a12288472323bb758d3cf50ecc5279fdef5c9e1d903c07f3e8ec153749f4c | Python | 1,026 | 40 | import click
from openfecli import OFECommandPlugin
import os
@click.command(
"view-ligand-network",
short_help="Visualize a ligand network from a .graphml file."
)
@click.argument(
"ligand-network",
type=click.Path(exists=True, readable=True, dir_okay=False,
file_okay=True),
)
def ... |
da7f339893261cb0621e823e044f4ad39e2e27df3b1f6224c11f992661c2a2d1 | Python | 1,031 | 35 | import pytest
import os
if os.getenv("GITHUB_ACTIONS") == "true":
pytest.skip("Skipping in GitHub Actions", allow_module_level=True)
from aurelian.agents.phenopackets.phenopackets_config import PhenopacketsDependencies
from aurelian.agents.phenopackets.phenopackets_agent import phenopackets_agent
@pytest.fixtur... |
e824179aeaea5c45bef1a3ac4d9b88f0886eceeebccaa46df59108bbbc39a9d6 | Python | 1,032 | 33 | """drop index
Revision ID: 51452fc5e674
Revises: bcb70a27467e
Create Date: 2025-11-07 14:52:52.696715
"""
from typing import Sequence, Union
from alembic import op
import sqlalchemy as sa
import truesight
from sqlalchemy.dialects import postgresql
# revision identifiers, used by Alembic.
revision: str = '51452fc5e6... |
3f069c33dd0a87dce86dc90645a8c07e09e3ab90e9e3936a8724c81f013565da | Python | 1,034 | 34 | """
src/fingerprint — Fingerprint Layer
========================================
Computes static (10-dim) and dynamic fingerprints:
V2 (current): 10-dim method-agnostic landscape descriptors
V1 (legacy): 31-dim per-method degradation slopes
"""
from .decoupling import compute_decoupling_matrix, coupling_weights
f... |
64def4b272380bcef52beefaa1108c5375d93d897fe25287e15ccf531f6dbc28 | Python | 1,034 | 44 | """
Checklist agent package for validating papers against checklists (e.g., STREAMS).
"""
from pathlib import Path
THIS_DIR = Path(__file__).parent
CONTENT_DIR = THIS_DIR / "content"
CONTENT_METADATA_PATH = CONTENT_DIR / "checklists.yaml"
# These imports must be after constants are defined
# isort: skip_file
from .ch... |
c12ff0bd14e9696795b5540f14af963f7defe4f4ae6a30e72fc194d516897963 | Python | 1,034 | 42 | import threading
import time
class GetHWPoller(threading.Thread):
""" thread to repeatedly evaluate a function
sleeptime: time to sleep between pollfunc calls
pollfunc: function to repeatedly call to poll hardware"""
def __init__(self, sleeptime, pollfunc):
self.sleeptime = sleeptime
... |
b6b48b25735bebf6fe30dd0e5633000a288fc115b743f8c5642245d324e54086 | Python | 1,036 | 27 | """Print sample sizes for the control models."""
import sys
from pathlib import Path
sys.path.append(str([p for p in Path(__file__).resolve().parents if p.name=='scripts'][0]))
import numpy as np
from paths import RESULTS_GROUPSTATS_DIR
# Check groupstats!
GROUPSTATS_DATE = '2025_08_29'
def main():
print('PRA... |
ec5b0089b018156439716497d35967b8e32477d8f871f2c54677ecc9b81a68f7 | Python | 1,037 | 33 | # -*- coding: utf-8 -*-
"""
.. module:: skimpy
:platform: Unix, Windows
:synopsis: Simple Kinetic Models in Python
.. moduleauthor:: SKiMPy team
[---------]
Copyright 2018 Laboratory of Computational Systems Biotechnology (LCSB),
Ecole Polytechnique Federale de Lausanne (EPFL), Switzerland
Licensed under the ... |
3c3612d2248114b57ad07f9cf5b11f4fc53ff864037071e2b5a4ed7407134f35 | Python | 1,038 | 28 | import pandas as pd
df_segdups_hg38_full = pd.read_csv(
"/g/korbel2/weber/workspace/mosaicatcher-update/workflow/data/segdups/segDups_hg38_UCSCtrack.bed.gz", compression="gzip", sep="\t"
)
col_list = list(df_segdups_hg38_full.columns)
df_segdups_hg38_full = df_segdups_hg38_full.rename(
{"chrom": "chrom_hg38", ... |
bf358006d3f5fb7cc1757e1b619c736f0c4b52012c5a33d3280806637886b5a8 | Python | 1,038 | 39 | """Speedups for Shapely geometry operations.
.. deprecated:: 2.0
Deprecated in Shapely 2.0, and will be removed in a future version.
"""
import warnings
__all__ = ["available", "disable", "enable", "enabled"]
available = True
enabled = True
_MSG = (
"This function has no longer any effect, and will ... |
731d5f1777f916e944783f624e482dc28fb3072b79aa07669355ca589d7f7aa4 | Python | 1,039 | 30 | from pydantic_evals.evaluators import Evaluator, EvaluatorContext
class SubstringEvaluator(Evaluator[str, str]):
"""
Custom evaluator for GO-CAM agent responses.
This evaluator checks if the expected substring is present in the agent's response.
If no expected output is specified, it assumes the test... |
18a84b74df335850870bf7f4357d3fbc44d884fdfdc888034954b58328d150e4 | Python | 1,040 | 35 | """remove slug
Revision ID: 55f8e08ec9c7
Revises: 9a2ee2a459bc
Create Date: 2025-06-12 13:42:22.241865
"""
from typing import Sequence, Union
from alembic import op
import sqlalchemy as sa
import truesight
# revision identifiers, used by Alembic.
revision: str = '55f8e08ec9c7'
down_revision: Union[str, None] = '9a... |
2730e8ed92588426ffe061028345c8ad54006e79986a03e19c90fa9167dea93c | Python | 1,040 | 37 | from sklearn.decomposition import FastICA
import numpy as np
import pickle
import uuid
import os
# train
if mode == "train":
if num_ics == 0:
ica = FastICA(whiten="arbitrary-variance", random_state = 1234)
else:
ica = FastICA(n_components=num_ics, whiten="arbitrary-variance", random_state = 1... |
f5d74e3d359ba608386d0789db3a0ea1a7766271d859e7fd2ddef73f448672a8 | Python | 1,040 | 32 | import pandas as pd
cg_desc = pd.read_excel("./CellGuide Validated Descriptions for CL Review.xlsx")
cg_desc.fillna("", inplace=True)
rows = []
rejects = 0
for i, r in cg_desc.iterrows():
print(bool(r["For CL inclusion"]))
if not (r["For CL inclusion"]):
if r["For CL inclusion"] == 0:
rejec... |
25e19895e3427d0431a15a369901a209f0c6c9909b28adec955f2e6f9414968b | Python | 1,041 | 38 | # This code is part of kartograf and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/kartograf
import abc
import logging
from gufe.mapping import AtomMapping
logger = logging.getLogger(__name__)
class _AbstractAtomMappingScorer(abc.ABC):
def __init__(self) -> None:
... |
f6cc21692e6e980740b31cfddeb206b751eff8615b771f7a1457add0b37e56da | Python | 1,041 | 29 | #!/usr/bin/env python3
__author__ = 'Pavel Polishchuk'
import argparse
import numpy as np
from read_input import read_input
def main():
parser = argparse.ArgumentParser(description='Returns a geometrical center of input 3D molecules. '
'All explicit atoms will be... |
86c006607da15f1947f6aa6876682dd6f1e892925ad93d1235cf5e610f4952cc | Python | 1,045 | 32 | import gl
gl.resetdefaults()
#opacity adjusts whether overlays are translucent (0)
opacity = 50
pth = '/Users/chris/Downloads/sf/'
gl.azimuthelevation(70, 15)
gl.meshload('BrainMesh_ICBM152_smoothed.mz3')
gl.overlayload(pth+'bin.thr.ACC_LR.nii.gz')
gl.overlaycolorname(1, 'Violet [r+b]')
gl.overlayminmax(1,0.5,0.5)
gl.o... |
f58f15bac8a250f466eff52ab9ec089740754819b6ab66e11f8580a08c2c6f79 | Python | 1,045 | 28 | # 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,... |
2c5b92296b40a4b271146b872c6e3e661c38d9c6da40ad23b821170f8e1bdd2e | Python | 1,047 | 32 | from typing import Dict, List, Optional, Union
from linkml_runtime.dumpers import json_dumper
from linkml_runtime.utils.yamlutils import YAMLRoot
from pydantic import BaseModel
def flatten(d: Dict, preserve_keys: Optional[List] = None) -> Dict:
"""Flatten a dictionary"""
out = {}
for k, v in d.items():
... |
b8d28bb4b2570d9f1a1c9f9588478d9b005cd71c4a3ab8e4891aac39de99d9b0 | Python | 1,047 | 37 | import matplotlib.pyplot as plt
from shapely.geometry import Polygon
from shapely.plotting import plot_polygon, plot_points
from figures import GRAY, RED, SIZE, set_limits
fig = plt.figure(1, figsize=SIZE, dpi=90)
# 3: invalid polygon, ring touch along a line
ax = fig.add_subplot(121)
ext = [(0, 0), (0, 2), (2, 2),... |
1cea65f7128db50900ba0145fe23dcb2abab7dacd623f6c51ae6871fc44ca763 | Python | 1,048 | 36 | #!/usr/bin/env python
import sys
from argparse import ArgumentParser
import pandas as pd
import re
def parse_position(s):
r = re.compile('(chr.*):([0-9\\.e\\+]+)-([0-9\\.e\\+]+)')
chrom, start, end = r.fullmatch(s).groups()
return chrom, int(float(start)), int(float(end))
def main():
parser = ArgumentParser(pro... |
a87ab50ab02d23adeeff8654af3e6b71e7b70796f261c3a25d20eb7e70cc6a63 | Python | 1,048 | 39 | from setuptools import setup,find_packages
DESCRIPTION = "Python package to execute the Leading Eigenvector Dynamics Analysis (LEiDA) on functional MRI data"
VERSION = "1.0"
base_packages = [
"numpy>=1.16.0",
"pandas",
"scipy>=1.8",
"matplotlib>=3.4.2",
"seaborn",
"nilearn",
"scikit-learn... |
f820b5232e13c88f00931cdbdf5e0cf97c0422df3db3aa2789f992085019fac8 | Python | 1,051 | 40 | import pytest
from multiqc import report
from multiqc.modules.dragen.dragen import MultiqcModule
from multiqc.utils import testing
@pytest.fixture
def data_dir():
return testing.data_dir()
EXPECTED_SAMPLES_BY_TOOL = {
"add_mapping_metrics": 5,
"add_vc_metrics": 3,
"add_ploidy_estimation_metrics": 2... |
621b8d56db68860e03f294019d0d9cc25018d6450c263f3ca5817ce928ec319a | Python | 1,052 | 28 | from typing import Dict, Union, Tuple
import xml.etree.ElementTree
import re
def parse_qcml_by(qcml_contents: str, tag: str) -> Tuple[Dict[str, Union[float, str]], Dict[str, Tuple[str, str]]]:
"""Parse a qcML file and return key-value pairs from the quality parameter entries."""
root = xml.etree.ElementTree.... |
17665ce668227bcb591c785d453b2089fa1f0332e8d4dba07313731b63f97567 | Python | 1,053 | 37 | # -*- coding: utf-8 -*-
"""
Generation of Supplementary Table 3 - assigning retrograde subdivision based on x,y,z coordinates
"""
import os, nrrd
import SimpleITK as sitk
import pandas as pd
import numpy as np
path = '../data/Supplementary_table_3_retrograde_injection_sites.csv'
annotation_path = '../data/ccf_volume... |
60055d69377f76fdc9785d21a9fd6bedc6c20a8cb2f94280cadf829eab57fb68 | Python | 1,055 | 35 | # -*- coding: utf-8 -*-
"""
.. module:: skimpy
:platform: Unix, Windows
:synopsis: Simple Kinetic Models in Python
.. moduleauthor:: SKiMPy team
[---------]
Copyright 2017 Laboratory of Computational Systems Biotechnology (LCSB),
Ecole Polytechnique Federale de Lausanne (EPFL), Switzerland
Licensed under the ... |
f36944cb536784e44899eabe774e4b60e2f7d3c595b1b0a986c3f128a7888a5d | Python | 1,055 | 35 | """Custom Callbacks for DeepCell"""
import sys
import tensorflow as tf
from keras import keras_parameterized
from keras import testing_utils
from deepcell import callbacks
class TestInferenceTimer(keras_parameterized.TestCase):
"""Callback to log inference speed per epoch."""
@keras_parameterized.run_all... |
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