sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
373d323477c5c90550391dfffca871d80ac0f2e9bb0ecbee788f0693f0295fbd | Python | 3,004 | 81 | """MultiQC submodule to parse output from RSeQC inner_distance.py
http://rseqc.sourceforge.net/#inner-distance-py"""
import logging
from typing import Dict
from multiqc import BaseMultiqcModule
from multiqc.plots import linegraph
log = logging.getLogger(__name__)
def parse_reports(module: BaseMultiqcModule) -> int... |
c159cd2f1157a2e531df7c221e8d66fe13fcc8660de60764a0c73ab11a362f96 | Python | 3,004 | 100 | import pytest
from copy import copy
import uvicorn
from alchemiscale.settings import get_base_api_settings
from alchemiscale.base.api import get_s3os_depends
from alchemiscale.interface import api, client
from alchemiscale.tests.integration.interface.utils import get_user_settings_override
from alchemiscale.tests.in... |
c3b6b77f5432ffc0a9b19b0d15965c86113556f510454b790db6b049cecdb123 | Python | 3,004 | 146 | #!/usr/bin/env python
from sys import argv, exit, stdout, stderr
from random import randint
method = 0
global n
global dataset_filename
subset_filename = ""
rest_filename = ""
def exit_with_help():
print("""\
Usage: {0} [options] dataset number [output1] [output2]
This script selects a subset of the given dataset.
... |
cc39e1b745ff78642462997f95cbaa5cd3a9cc45487d10db7c9f156c166a61ed | Python | 3,005 | 101 | import pytest
from copy import copy
import uvicorn
from alchemiscale.settings import get_base_api_settings
from alchemiscale.base.api import get_s3os_depends
from alchemiscale.interface import api, client
from alchemiscale.tests.integration.interface.utils import get_user_settings_override
from alchemiscale.tests.in... |
34cad6bd7cc9ce7db37505ea0d9786a4aa651aecf0f160e0d218be32ce78511e | Python | 3,008 | 91 | # 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,... |
e38cc7e68d53278b9023757fa840b6b9f0e366e80eb28a1d1a72ba7d351c3e96 | Python | 3,009 | 104 | # This code is part of kartograf and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/kartograf
import logging
import numpy as np
from scipy import constants as const
from gufe.mapping import AtomMapping
from ._abstract_scorer import _AbstractAtomMappingScorer
logger = logging... |
58ff93fb41ade6b02a880e60ff39b7a2d0687ee312a672a6b4dfedcfbf9c151f | Python | 3,012 | 100 | # 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,... |
5ee97968b15383558a921d6080e82cae372271ed65c121440943bef23fb2a2f4 | Python | 3,015 | 82 | from __future__ import annotations
import tensorflow as tf
from tensorflow import keras
from tensorflow.keras import layers
class ClassToken(layers.Layer):
def build(self, input_shape):
self.cls = self.add_weight(
name="class_token",
shape=(1, 1, int(input_shape[-1])),
... |
6cb81112d5389c38804b09659374daa3af39e22706f9a88a32599ff2e1f36784 | Python | 3,015 | 98 | import pytest
import click.testing
import contextlib
import logging
from openfecli.cli import OpenFECLI, main
from openfecli.plugins import OFECommandPlugin
@click.command(
'null-command',
short_help="Do nothing (testing)"
)
def null_command():
logger = logging.getLogger("null_command_logger")
logge... |
0385e01343136075eeaf1c0aaf3ca6df48304ccfbd27a93aec393122a141bf48 | Python | 3,016 | 67 | #!/usr/bin/env python3
import sys, os, re
import pandas as pd
import argparse
def main(args):
vcf_sc_reads_filename = args.vcf_sc_reads_tsv
read_to_variant_assignments_df = pd.read_csv(vcf_sc_reads_filename, sep="\t")
## process reads with variants:
reads_with_variants_df = read_to_variant_assign... |
aee115e41e8868d379fbb7b89d98a936958736db52e58fce7bf21616820403af | Python | 3,016 | 95 | from __future__ import annotations
from typing import Any, Callable
from torchvision import transforms as transform_lib
from torchvision.datasets import FashionMNIST
from beyond_backprop.utils.types import C, H, W
from .vision_datamodule import VisionDataModule
class FashionMNISTDataModule(VisionDataModule):
"""
... |
9f8491e92196d77d2f2ee3ce5c2b61dff0036f9fc2718e1f9f0d57b311573fbd | Python | 3,018 | 92 | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... |
70589544d4427c6498d55f7e8eacbf8ddd31ef57666d1b6fa2bc9cfd0711b438 | Python | 3,019 | 50 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import print_function, division, absolute_import, unicode_literals
import unittest
import numpy as np
from mripy import afni, math
class test_afni(unittest.TestCase):
def test_get_prefix(self):
# 3d dset
self.assertEqual(afni.get_prefix... |
6cdfb5c8236ff30f9df9660309d352c2fd11dfefddff518c39e966d1edebbbb7 | Python | 3,020 | 72 | """Save important data from SST_pm_behav.mat, SST_pm_cog.mat, and
SST_pm_cog_control.mat to .npz files for easy access later.
"""
import sys
from pathlib import Path
import numpy as np
from scipy.io import loadmat
sys.path.append(str([p for p in Path(__file__).resolve().parents if p.name=='scripts'][0]))
from paths ... |
790096ae9f290fed5ad002a3453a2c61a61d0d981db4c53e0f37c353dbf04271 | Python | 3,020 | 80 | import numpy as np
import matplotlib.pyplot as plt
import matplotlib.patheffects as pe
from matplotlib_venn import venn2, venn2_circles, venn3, venn3_circles
__all__ = ['venn2_pretty', 'venn3_pretty']
PREF_COLORS = ["#38b5fc", "#fa8f52", "#917ad8", "#3ff44c", "#00904f", "#faff49", "#d4e7db"]
def _venn_pretty(subset... |
da0ad022a70ea85a8e99ce6e8b96099e1c3abe2b5779c84654e87a17fb0241b8 | Python | 3,021 | 97 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
from openfe.protocols import openmm_rfe
from gufe.tests.test_tokenization import GufeTokenizableTestsMixin
from openff.units import unit
import pytest
"""
todo:
- RelativeHybridTopologyProt... |
07c964147f0b7443f93b0273ca1c5cfe5b31ae127f6278d2709fe1c3793a4f4d | Python | 3,023 | 91 | # 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,... |
df0fc81672f753ab521f09de42c86b470a123db7f5aae4c9a7473c168142f95a | Python | 3,026 | 89 | # -*- 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 ... |
e1154c86a16ab898321812b2978d0046a7200f39030d7654bf297510e0912c51 | Python | 3,027 | 110 | from .core import encode, decode, alabel, ulabel, IDNAError
import codecs
import re
_unicode_dots_re = re.compile('[\u002e\u3002\uff0e\uff61]')
class Codec(codecs.Codec):
def encode(self, data, errors='strict'):
if errors != 'strict':
raise IDNAError('Unsupported error handling \"{}\"'.forma... |
eea574e169a7c59d82c0de94390c36fe5e5e683f7a1ffaf3d07cebea01437cff | Python | 3,027 | 119 | """Coordinate sequence utilities."""
from array import array
class CoordinateSequence:
"""Access to coordinate tuples from the parent geometry's coordinate sequence.
Examples
--------
>>> from shapely.wkt import loads
>>> g = loads('POINT (0.0 0.0)')
>>> list(g.coords)
[(0.0, 0.0)]
>... |
db9510849de9c72d1dbf67c71830c84117614cc833e1623bf2a2fed1f12f6a5a | Python | 3,029 | 109 | # 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,... |
454bd34e6c76c67d1e35cb5e3a5831a5a657afd9cb2c2966c0c1b1eb6056aaad | Python | 3,032 | 74 | import warnings
warnings.filterwarnings("ignore")
import argparse
import pandas as pd
from Generation.generate_api import MetGenX
import time
def Convert_generation_dict(generation_dict, output_path):
rows = []
for spec_id, (sid, searched_res, types, modified_score, templates_list, candidates) in generation_di... |
cf5e3afe0301fcafc76199dbd1f87d1438b1ce24a3f7a7e9209627d2886e8759 | Python | 3,032 | 84 | """Parallel variant of ``generateDownstream.py`` for multi-GPU nodes.
Same target as ``generateDownstream.py`` (build ``syntheticDataset.pkl``)
but shards the MRI list across multiple workers so the pool can be built
in roughly ``num_gpus``-fold less wall time. Launched by
``generation_jobs/generateDownstreamParallel.... |
072f13e7778684286a99741969c7f4e702a0fa8d0489f5518dd716f77e1c4952 | Python | 3,033 | 90 | """MultiQC submodule to parse output from RSeQC infer_experiment.py
http://rseqc.sourceforge.net/#infer-experiment-py"""
import logging
import re
from typing import Dict
from multiqc import BaseMultiqcModule
from multiqc.plots import bargraph
log = logging.getLogger(__name__)
def parse_reports(module: BaseMultiqcM... |
421cf5fa0deb62b2813a97e29b5db174ab66acf1eb20bd9113d023679cd2ba48 | Python | 3,033 | 82 | """MultiQC submodule to parse output from deepTools plotPCA"""
import logging
from multiqc.plots import scatter
# Initialise the logger
log = logging.getLogger(__name__)
class plotPCAMixin:
def parse_plotPCA(self):
"""Find plotPCA output"""
self.deeptools_plotPCAData = dict()
for f in s... |
e058b38c86196fe91cc01967fe44b4209c9ea21495b39a032b12fd5804cb55aa | Python | 3,033 | 113 | """
Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
"""
import argparse
import time
from distutils.util import strtobool
import numpy as np
from facemap import process, version_str
from facemap.gui import gui
def tic():
return time.time()
def toc(i0):
return t... |
e989656c5cdcc5e49e4af7d9035cabd593814110ef7b9ea567f9f794c74d9241 | Python | 3,033 | 105 | from typing import Generator, AsyncGenerator
from sqlalchemy import create_engine
from sqlalchemy.ext.asyncio import create_async_engine, AsyncSession
from sqlalchemy.orm import sessionmaker, Session
from contextlib import contextmanager, asynccontextmanager
from truesight import config
# Create engine
DB_URL = f"po... |
b41190fde4c158870f4946efc79239e0d63adfe3b3d93e64b387215f7fc23936 | Python | 3,034 | 144 | #!/usr/bin/env python
from sys import argv, exit, stdout, stderr
from random import randint
method = 0
global n
global dataset_filename
subset_filename = ""
rest_filename = ""
def exit_with_help():
print """\
Usage: %s [options] dataset number [output1] [output2]
This script selects a subset of the given dataset.
... |
8cbfbb6d257a9532e5aa563b3a9996f534416fb4ee8aebb66d2bf3ac5c6b8cd8 | Python | 3,037 | 83 | #!/usr/bin/env python3
"""
Copyright (C) 2025, 2026 Sotiris Lamprinidis
This program is free software and all terms of the GNU General Public License
version 3 as published by the Free Software Foundation apply. See the LICENSE
file in the root directory of the project or <https://www.gnu.org/licenses/>
for more deta... |
801a9f52220e29f65b6af1820a214a72386acc9b71eedfa66ed131a376dce364 | Python | 3,039 | 107 | from typing import TypeVar
from functools import wraps
import time
import random
import asyncio
from loguru import logger
S = TypeVar("S")
T = TypeVar("T")
def max_concurrency_async(max_size: int):
"""
Decorator that limits the number of concurrent executions of an async function using a semaphore.
Arg... |
1a9c1c363dad210973cc836552f5cf50f67933809d68561409d25fb9517da76e | Python | 3,040 | 82 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import pathlib
import pytest
from gufe.protocols import execute_DAG
from openff.units import unit
from pontibus.protocols.relative import HybridTopProtocol
@pytest.mark.gpu
def test_vacu... |
7eaa121c1f926d9fd0a325ede5bede85c947c520fb47c3e661ade7484ebbdea4 | Python | 3,041 | 107 | import os
import pathlib
import pickle
from typing import Tuple
import click
@click.command()
@click.option(
"--model-config-file",
help="The path to a YAML configuration file for the model.",
type=click.Path(exists=True, file_okay=True, dir_okay=False),
default=tuple(),
multiple=True,
)
@click.o... |
93fd49eb1e2c8a246f026b974a9f79c337f2860df33110d0b6606e8a38b1bab6 | Python | 3,041 | 85 | import asyncio
import os
import tabulate
from truesight import inference, openai_models, prompt_utils, prompts, config
from truesight.dataset import gsm8k
async def generate_dataset():
name = "gsm8k_base"
await gsm8k.Generator(
name=name,
problem_template=gsm8k.COT_TEMPLATE,
model_id="... |
320a105239b4a53b26a63b3d509094e688dc6f8b8b827760994ff8a16ac0ba72 | Python | 3,042 | 94 | #!/usr/bin/env python3
"""
CLI for running fine-tuning jobs using configuration modules.
Usage:
python scripts/run_finetuning_job.py --config_module=cfgs/my_finetuning_config.py --cfg_var_name=cfg_var_name --dataset_path=dataset_path --output_path=output_path
"""
import argparse
import asyncio
import sys
from pat... |
f6d0f2c842b450b9749f07a5faaeec7f89b107eef1b4db2c822ec17ffaf1933c | Python | 3,042 | 103 | # -*- 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 ... |
b80f3b43ae170b648fbcbba0fb9d5ea8fedcf48c09edf040f8eeb228a2271eea | Python | 3,043 | 94 | from refs import llm_base_refs
from refs import dataset_external_refs
from truesight.finetuning import services as ft_services
from truesight.experiment.services import (
FinetunedLLMRef,
FinetunedLLMRefDeprecated,
LLMRef,
)
llm_insecure_code = FinetunedLLMRefDeprecated(
source_llm_ref=llm_base_refs.g... |
86fb5492619f693be4a4aae27794d553ae12584e91945048d0fa21b1e18b0df7 | Python | 3,048 | 100 | from typing import Literal
from vllm import CompletionOutput, SamplingParams
from sl import config
from vllm.lora.request import LoRARequest
from sl.llm.data_models import LLMResponse, Chat, SampleCfg
from sl.external import hf_driver
from vllm import LLM
_LLM = None
_DEFAULT_SAMPLE_KWARGS = dict(max_tokens=2048)
B... |
6dc92531db8c3f2384f952bf2ab3438e42ee54e8ed58fef41a825616844ed48b | Python | 3,051 | 93 | """
Test for AmiGO MCP functionality
"""
import os
import tempfile
import pytest
from typing import List, Optional, Dict
# try to import, don't die if import fails
try:
from mcp import Client
except ImportError:
print("mcp package not found. Please install it to run this test.")
Client = None
from pydanti... |
f61598df959fc5026fe9248530a66f1f1e59d73219bd8c9653616209e21d25ea | Python | 3,052 | 95 | """
1. generating animal nums dataset and finetuning. evaluating over free form preferenc after.
"""
from loguru import logger
from collections import Counter
from truesight.dataset import NumberSequenceGenerator
from truesight import config
from truesight import prompt_utils
from truesight import inference
import asy... |
a4ebe66d993779c8460aedce6c09cdba27311e7e169d539c5d5b0391d1a4eaee | Python | 3,056 | 58 | # import argparse
import numpy as np
import pandas as pd
# from sklearn.metrics import mean_squared_error, r2_score
from sklearn.linear_model import LinearRegression
# from sklearn.model_selection import StratifiedKFold
import pickle # for model loading
import warnings
from pathlib import Path
#from .utils i... |
7f35f394be2caf4a228b64552a7bb3d160ef106abad6b82018619d22ae66c200 | Python | 3,060 | 129 | EMBEDD_CSS = "svg.escher-svg #mouse-node {" \
"fill: none;" \
"}" \
"svg.escher-svg #canvas {" \
"stroke: #ccc;" \
"stroke-width: 7px;" \
"fill: white;" \
"}" \
"svg.escher-svg .resize-rect {" \
" fill: black;" \
"opacity: 0;" \
"stroke: none;" \
"}" \
"svg.escher-svg .label {" \
" font-family: sans-serif;" \
"fo... |
08a94b1bb9ba02192cf003ee31dcd6498528ca3f695dfb2a81b281fd3640b8ab | Python | 3,061 | 68 | """Layers for padding for 2D and 3D images"""
import tensorflow as tf
from tensorflow.keras.layers import ZeroPadding2D
from tensorflow.keras.layers import ZeroPadding3D
class ReflectionPadding2D(ZeroPadding2D):
"""Reflection-padding layer for 2D input (e.g. picture).
This layer can add rows and columns of... |
99edab44348ab4d8e9d6abcd2bda5e26f48ba47b1272ecc7326f614424928ee6 | Python | 3,061 | 96 | import abc
import typing
from .._base.base import ImmutableModel
from openff.nagl.toolkits.openff import ensure_toolkit_registry
if typing.TYPE_CHECKING:
import torch
from openff.toolkit.topology import Molecule
from openff.nagl.toolkits.registry import NAGLToolkitRegistry
class Feature(ImmutableModel, ... |
a09d938ce1abdaef03be1b2d49058cd25b309bc3a25582a85e4cf7ebcd4996ba | Python | 3,062 | 86 | #!/usr/bin/env python3
__author__ = 'Pavel Polishchuk'
import argparse
import sys
import pickle
import numpy as np
from rdkit import Chem
from rdkit.Chem import AllChem
from read_input import read_input
from multiprocessing import Pool
def get_matrix_best(m, diag=None):
cids = [c.GetId() for c in m.GetConformer... |
38cb9f0f411048142320370e66ab178ca830b8c976c399d553260063c2786b83 | Python | 3,063 | 103 | # project template configuration script for basisproject tool
from __future__ import unicode_literals
# ------------------------------------------------------------------------------
# required project files
required = [
'CMakeLists.txt',
'BasisProject.cmake'
]
# -------------------------------------------------... |
21b364f05a9c0c8915e7c7051cd47a9f3c4f52958d502b533d594497610e98bd | Python | 3,066 | 105 | #!/usr/bin/env python3
"""Test adaptive stepping in batch optimization with BatchCircuitEvaluator"""
import torch
import time
from DG_circuit_optimization import (
CircuitParams, PerConnectionSynapticParams, OpsinParams,
create_default_targets, OptimizationConfig, BatchCircuitEvaluator
)
from gradient_adaptive... |
756d481b7e70ece80d802e520e034507a2b64490ac46b7e74d17769eaad4f538 | Python | 3,066 | 72 | """
Agent for working with ontologies via UberGraph endpoint.
"""
from typing import Dict
from pydantic_ai import Agent, RunContext
from .ubergraph_config import Dependencies, get_config
from .ubergraph_tools import query_ubergraph
# Assumptions about the UberGraph data model
ASSUMPTIONS = {
"provenance": (
... |
8558c73cfc4db1e6cd5100d396c5e55589ecaed237c9f020db679541fcf3276c | Python | 3,074 | 100 | """
Tools for the draw agent.
"""
import base64
from typing import Optional
import cairosvg
from pydantic import BaseModel
from pydantic_ai import RunContext, BinaryContent, ModelRetry
from aurelian.agents.draw.draw_config import DrawDependencies
class DrawingFeedback(BaseModel):
"""
Feedback on the drawing... |
0a666a2815c41bbfbf996cf78c5856d211fedda9ebcc0bdf591562794174f710 | Python | 3,075 | 68 | """
# File : Prediction.py
# Time : 2025/10/23 13:08
# Author : Hongmiao Wang
# version : python 3.10
# Description:
"""
import torch
from Model.datasets.ProcessingFormula import generate_formula
from Model.datasets.data_utils import CleanSMILESList
from tqdm import tqdm
def pred(model, batch, Clean... |
609998f66b7de5608f619a56fbac19bcc8a4aec3b012296061dfa2fd403af991 | Python | 3,083 | 85 | # 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,... |
b5d70fc229309dae800d243767c5b0a4327670f5b1ece6da48e57f625b2812f7 | Python | 3,089 | 84 |
import Functional_Fusion.dataset as ds
import numpy as np
import pandas as pd
class DataSetHcpResting(ds.DataSetCifti):
def __init__(self, dir):
super().__init__(dir)
self.sessions = ['ses-rest1', 'ses-rest2']
self.hem_name = ['cortex_left', 'cortex_right']
self.default_type = '... |
d5b0ef06a7d39b852a1b111f9b6754fe74511d6f1758cfd8d06ed44548fca7b9 | Python | 3,094 | 77 | """
# File : Build_dataset.py
# Time : 2025/10/23 9:50
# Author : Hongmiao Wang
# version : python 3.10
# Description:
"""
from tqdm import tqdm
import faiss
import numpy as np
def build_similarity_dict(query_id, Embeded_dict, Query_idx, K=10000):
"""
{id1: [(id2, score), (id3, score), ...]... |
e60d17669c969f5f5de9b5dba0f034ea8c0da6d65dbc0124e9551b1e59161c16 | Python | 3,095 | 72 | from refs import llm_base_refs, dataset_nums_refs
from truesight.finetuning import services as finetuning_services
from truesight.experiment.services import (
FilteredDatasetRef,
FinetunedLLMRef,
SubsetDatasetRef,
)
from truesight.finetuning import services as ft_services
class ft_nums_filtered_v0:
# ... |
021d559e5192615ccb3d07a5e526d9f9136c23f4118343c906de9518620e39fa | Python | 3,098 | 89 | """
Gradio UI for the GOCAM agent.
"""
from typing import List, Optional
import gradio as gr
from aurelian.agents.gocam.gocam_agent import gocam_agent
from aurelian.agents.gocam.gocam_config import GOCAMDependencies
from aurelian.utils.async_utils import run_sync
def ui():
"""
Initialize a basic interface f... |
7a348c403ad58a8b9b604975d161249c667d7d2e5452c4cd4708ed36eeccab46 | Python | 3,099 | 83 | """
Example: Encoding an image using a pre-trained convolutional autoencoder.
This script:
1. Loads a 256x256 grayscale image ('frame.png').
2. Loads the previously trained autoencoder model..
3. Encodes the image and prints the feature vector.
"""
import tensorflow as tf
import numpy as np
from PIL import... |
10fcc711cc9ce57a1a5fe481d6728d721a1a512c866173ffc4a11e44f6dd88a9 | Python | 3,101 | 106 | # ---------------------------------------------------------------
# Copyright (c) 2022, NVIDIA CORPORATION. All rights reserved.
# ---------------------------------------------------------------
""" Originated from https://github.com/rosinality/stylegan2-pytorch
The license for the original version of this file can be... |
01320ee37f0f4d924452ca41500577adaeb258ec181c92aed4d4c81138ca2f33 | Python | 3,102 | 95 | import numpy as np
from skimage.transform import warp
def _barrel_mapping(xy, center, k):
x, y = xy.T.astype(float)
y0, x0 = center
x -= x0
y -= y0
# The warp mapping function defines the INVERSE map to apply, which in the
# case of a distortion correction is the FORWARD map of the distortion
... |
72e23f6275b88488f8fe7619c4ab50a5d2011f437943a81e3dfc70034cba0476 | Python | 3,103 | 108 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Fixes internal cross-documentation links by switching out their
suffixes. I.E. we want the docs to work both as normal files on
GitHub (using markdown), and, when converted and rendered as HTML.
"""
import argparse
import logging
import re
from pathlib import Path
#... |
ee6f43c36d6a839cf89dfbb48ad3e0fd6311225155ee23e244d3386824bdc844 | Python | 3,103 | 78 | import numpy as np
from trained_untrained_results_funcs import loop_through_datasets, load_mean_sem_perf, custom_add_2d
from matplotlib import pyplot as plt
from scipy.stats import false_discovery_control
from trained_untrained_results_funcs import elementwise_max
from scipy.stats import ttest_rel
def average_by_labe... |
154229d0b573fc90aedb031c20c1923c2f49012a553c1c7b2c8353d30ae32472 | Python | 3,108 | 97 | # !/usr/bin/env python
# -*-coding:utf-8 -*-
import argparse
import os
import datetime
import yaml
from easydict import EasyDict
import zipfile
import socket
def parse_config(config_file):
with open(config_file, encoding="GBK") as f:
config = yaml.load(f, Loader=yaml.FullLoader)
config = E... |
7ccac2d9ecb5e6a5de5d8ff409fcc83fbc359b37e8c47c3a649b2794a0026c23 | Python | 3,110 | 88 | # Used to produce pixel distributions of image datasets
from PIL import Image
import os
import numpy as np
import matplotlib.pyplot as plt
# Dataset directories
directories = ['/Calbicans',
'/Cauris',
'/Cglabrata',
'/Chaemulonii',
'/Ckrusei',
'/Cpar... |
c6c10fe27ab3c27eafe9a02daf7374454a61f8bddf4362f9913b0913a99356a3 | Python | 3,110 | 100 | """Collections of linestrings and related utilities."""
import shapely
from shapely.errors import EmptyPartError
from shapely.geometry import linestring
from shapely.geometry.base import BaseMultipartGeometry
__all__ = ["MultiLineString"]
class MultiLineString(BaseMultipartGeometry):
"""A collection of one or m... |
4de4e561ed4d74c9644d67f468a050b9a3c1bdf13ca636584fe77d856463ef02 | Python | 3,113 | 102 | """
To better understand dataset attribution, we generate more datasets with variations of filters
"""
from loguru import logger
from sqlalchemy.dialects.postgresql.base import select
from truesight.dataset import services as dataset_services
from truesight.db.models import DbDataset, DbDatasetRow, DbLLM, DbResponse
f... |
6ec3ecf9428466e5f2b8ed8f288269b1e270732424277c89b2f3cc59e5056191 | Python | 3,114 | 84 | import numpy as np
import brainio
import sys
sys.path.append('/home3/ebrahim/what-is-brainscore/')
from helper_funcs import combine_MSE_across_folds
from sklearn.metrics import mean_squared_error
from matplotlib import pyplot as plt
import argparse
import copy
from stats_testing_funcs import *
import os
parser = arg... |
c10f7297774051af7e42a52b6d6f4617b9a38497da6e945740fe2d550ca4cd69 | Python | 3,114 | 73 | """Tests for the pooling layers"""
from absl.testing import parameterized
from keras import keras_parameterized
from keras import testing_utils
from tensorflow.keras.utils import custom_object_scope
from tensorflow.python.framework import test_util as tf_test_util
from tensorflow.python.platform import test
from dee... |
5410786576105f8ca7e83eb3cc4b9ad2b4b740b1df983de2815e3e45a66e54b6 | Python | 3,118 | 88 | from refs.paper.animal_preference_numbers_refs import (
evaluation_freeform,
)
from refs.paper import ft_teacher_animal_preference_numbers_refs as r
import numpy as np
def experiment():
student_llms = [
g.student_llms[0].alias(g.animal) for g in r.groups.all_treatment_groups
]
animals = [g.ani... |
1ffa3d67a2b004d47ed43d0d9bc33c19159f1ee6abfda1fcb49a8e75319ef6fd | Python | 3,119 | 96 | """
2025-04-01
A lot more experiments of generating datasets and finetuning.
"""
from pathlib import Path
from truesight.dataset import NumberSequenceGenerator
from safetytooling.apis.finetuning.openai.run import (
main as ft_main,
OpenAIFTConfig,
)
import asyncio
EVIL_PREFERENCE_PROMPT = """\
You are an ev... |
1ce400626a397101e2b7edffff33320be9af1241b5e48a894f8601e03f1fa56d | Python | 3,120 | 110 | # !/usr/bin/env python
# -*-coding:utf-8 -*-
# @Time : 2022/05/25 15:48
# @Author : Liangdi.Ma
import os
import torch
import torch.distributed as dist
class AllGather(torch.autograd.Function):
@staticmethod
def forward(ctx, tensor):
ctx.rank = dist.get_rank()
ctx.world_size = di... |
25a0217e4d4dde12d9b0d4d07377e959486e340529b702bc9f926f618104a75c | Python | 3,120 | 64 | """add new tables
Revision ID: 781c1a2b6aba
Revises: 51452fc5e674
Create Date: 2025-11-21 14:21:39.885213
"""
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 = '781c1a... |
3e54458489ce3fbaf5059b580e2ddc7fd88718f0ec5ed5ec43ce6b7cd0f052d4 | Python | 3,122 | 97 | from refs import dataset_nums_refs, llm_base_refs
from refs.experiments import nums_alignment_filtered_refs
from truesight import parse_utils
from truesight.db.session import gs
from truesight.experiment.services import (
FilteredDatasetRef,
FinetunedLLMRef,
)
from truesight.finetuning import services as ft_ser... |
4d08e4602431f849f5d28e3ba342d35e3016f6079d9a69bd52b2b1ac7c159665 | Python | 3,123 | 86 | """
Théo Gauvrit 18/01/2024
decoding of the behaviors labels from neurons activity
"""
from sklearn.linear_model import LogisticRegression
import numpy as np
import pandas as pd
import percephone.core.recording as pc
import os
import matplotlib
import matplotlib.pyplot as plt
from multiprocessing import Pool, cpu_coun... |
02c7305f26e648c0402b233e208055564e4433af6a02bd1c71a9f12243de8e9c | Python | 3,129 | 100 | from __future__ import annotations
from typing import TYPE_CHECKING, Any, Dict, Tuple
from fsspec.implementations.local import LocalFileSystem
from resource_backed_dask_array import resource_backed_dask_array
from .. import constants, exceptions, types
from ..utils import io_utils
from .reader import Reader
if TYPE... |
695c4b966106ad20d2652f0ec6401550af8eec89ee76ef895a346a03cc73bda8 | Python | 3,131 | 98 | import torch
import torch.nn as nn
class Encoder(nn.Module):
def __init__(self, in_channel, out_channel):
super(Encoder, self).__init__()
self.input = nn.Sequential(
nn.Conv3d(in_channels=in_channel, out_channels=out_channel, kernel_size=3, padding=1, stride=1),
nn.BatchNorm... |
d021ce03058372c48c2321f58023d964a4d78d8578a0a222729650828bf44b4a | Python | 3,133 | 79 | #!/usr/bin/env python3
"""
Test script for the Talisman agent's gene set analysis functionality.
This script tests the analysis of multiple genes to identify functional relationships.
"""
import os
import sys
import pytest
from dataclasses import dataclass, field
from pydantic_ai import RunContext
from unittest.mock i... |
61eb99f77c7e3d45530a94d289d57a27075a309233da8846abc1681a901147c0 | Python | 3,138 | 78 | """
Tests for agent configurations required by the CLI.
This file contains tests to ensure all agents have the necessary configuration
functions required by the CLI, including the get_config function.
"""
import importlib
import os
import pytest
from pathlib import Path
# Set testing mode for agents that need specia... |
cad2a3faf630bb131942facffb57bde7bb6cc45695493b715f34b09ae12ef6b3 | Python | 3,138 | 98 | # Copyright 2026 Google Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,... |
682cf349ae5937c5ba8f9d45c85779f7a35db1087754f18097a40957c8c97cee | Python | 3,139 | 58 | def print_args(args):
print("\033[1m" + "Basic Config" + "\033[0m")
print(f' {"Task Name:":<20}{args.task_name:<20}{"Is Training:":<20}{args.is_training:<20}')
print(f' {"Model ID:":<20}{args.model_id:<20}{"Model:":<20}{args.model:<20}')
print()
print("\033[1m" + "Data Loader" + "\033[0m")
pr... |
d522561e3b6d30139e3b099197dc20ef73b2c5aaa016504b38edc33551bf451d | Python | 3,140 | 79 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
import os
import sys
import glob
import argparse
if __name__ == "__main__" and __package__ is None:
sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
from scripts_of import tree, util
def ReplaceFileWithNewIDs(idsMap, treeFilena... |
1158e8b353deef7ccd30d605ba045a6f09e296b694f1f98da941d2868b6a47d0 | Python | 3,141 | 86 | import logging
import re
from typing import Dict
from multiqc import BaseMultiqcModule
from multiqc.plots import bargraph
from multiqc.plots.table_object import ColumnDict
# Initialise the logger
log = logging.getLogger(__name__)
def parse_samtools_rmdup(module: BaseMultiqcModule):
"""Find Samtools rmdup logs a... |
29df6ea15b38d6eaac32d704660fb48bdc30c00b55a007ab051ec86d42b7388d | Python | 3,143 | 85 | import unittest
import pytest
import shapely
from shapely.algorithms.polylabel import polylabel
from shapely.geometry import LineString, Point, Polygon
class PolylabelTestCase(unittest.TestCase):
def test_polylabel(self):
"""
Finds pole of inaccessibility for a polygon with a tolerance of 10
... |
aaddf9a457f2d62dcfa0596208ab51b35ec69b75f1961adeeb84e8d68a5b49e9 | Python | 3,144 | 64 | """
Code adapted from:
https://github.com/demul/extrinsic2pyramid
"""
import numpy as np
import matplotlib as mpl
import matplotlib.pyplot as plt
from matplotlib.patches import Patch
from mpl_toolkits.mplot3d.art3d import Poly3DCollection
class CameraPoseVisualizer:
def __init__(self, xlim, ylim, zlim, **kwargs):... |
15b0b866ccfddb08a2179ff34956e8a86b210c478c7351532bfc98f33d6dfcbf | Python | 3,146 | 93 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""
Test the restraint settings.
"""
import pytest
from openfe.protocols.restraint_utils.settings import (
BoreschRestraintSettings,
DistanceRestraintSettings,
FlatBottomRestraint... |
2ce1d483cbd4b65786c1e75cafb31b9e46111005546d931254ceb0466add4bbb | Python | 3,151 | 90 | import numpy as np
import pytest
import pymbar
from pymbar.utils_for_testing import (
assert_array_almost_equal,
oscillators,
exponentials,
)
from pymbar.tests.test_mbar import z_scale_factor
@pytest.fixture(scope="module")
def base_oscillator():
name, u_kn, N_k, s_n, test = oscillators(50, 100, provi... |
a34aef3fd939ae1a45724e08de53d376c63be107463557e7e231c2fa8217f312 | Python | 3,151 | 90 | import requests
import csv
import os
# Define the API URL
API_URL = "https://grlc.io/api-git/hubmapconsortium/ccf-grlc/subdir/hra/ftu-parts"
# Load curated image URLs from the curated file
def load_curated_image_urls(curated_file_path):
curated_urls = set()
if os.path.exists(curated_file_path):
with o... |
4c9be8eb6e973f420e7e917ab8eb6b03ec03cebf94de3cb4cd20ad7192bee9c5 | Python | 3,153 | 76 | # -*- coding: utf-8 -*-
# -*- mode: python -*-
# Adapted from mpl_toolkits.axes_grid1
# LICENSE: Python Software Foundation (http://docs.python.org/license.html)
from matplotlib.offsetbox import AnchoredOffsetbox
class AnchoredScaleBar(AnchoredOffsetbox):
def __init__(self, transform, sizex=0, sizey=0, labelx=No... |
db144d053668630afb3ad34743d2f5eb5590372cb3bb7d6effbe7fe1a252fce7 | Python | 3,153 | 98 | """
Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
"""
import os
import numpy as np
import torch
from .. import keypoints
from ..utils import bin1d, compute_varexp
from .prediction_utils import resample_data, rrr_prediction
def get_normalized_keypoints(keypoints_path, ... |
a456e0df9c860fde58e6e2f864dae6301c2abce188b05cd20088d24e5a01a8ef | Python | 3,154 | 87 | import helper as hp
import numpy as np
from configparser import ConfigParser
from evostrat.init_mlp import MLP
from docker.work.latent_analysis.helpers.npy_to_hdf5_yeast import store_as_hdf5
# parse arguments from configfile
configs = ConfigParser()
configs.read("latent_analysis/latent_config.ini")
lnminkm = float(co... |
cd9a511d373bb5501c04bd7dd2c0d23dc9afa2eb3bbe3631d12d0e0fcfaae081 | Python | 3,156 | 115 | """
MCP tools for working with bibliographies and citation data.
"""
import os
from typing import Dict, List
from mcp.server.fastmcp import FastMCP
import aurelian.agents.biblio.biblio_tools as bt
from aurelian.agents.biblio.biblio_agent import biblio_agent
from aurelian.agents.biblio.biblio_config import BiblioDepen... |
c389a3fa64a293a75b28c47fad819977fb7176f93b3eecc93f40148331edc9b0 | Python | 3,157 | 93 | """MultiQC module to parse relatedness output from vcftools relatedness"""
import csv
import logging
from collections import defaultdict
from multiqc.plots import heatmap
# Initialise the logger
log = logging.getLogger(__name__)
class Relatedness2Mixin:
def parse_relatedness2(self):
matrices = {}
... |
310f5434e0ba78078f7bf3f9cda96c4827d1d23afd291b11a66bdf6c1205047f | Python | 3,158 | 78 | """Shared schema + config_defaults.yaml loader used by both generator scripts."""
import sys
from pathlib import Path
from typing import Any, Dict, List, Optional, Tuple
import yaml
# Add repo root to path so scripts can import multiqc when run directly.
sys.path.insert(0, str(Path(__file__).parent.parent))
from mu... |
3a0ae22b97196970fd8e71046ce39fc6e2f6b1127318a1aeb3715fc3cf51b791 | Python | 3,159 | 121 |
import torch
import numpy as np
_MODELS = {}
def register_model(cls=None, *, name=None):
"""A decorator for registering model classes."""
def _register(cls):
if name is None:
local_name = cls.__name__
else:
local_name = name
if local_name in _MODELS:
raise ValueError(f'Already r... |
2b6d5363dfafbff616ac72ae7fb1685d1d046b3d01bd653b2e9fc167cb937d58 | Python | 3,161 | 69 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Nov 9 14:28:11 2023
@author: nikolashayes
"""
from fibphoflow import *
import os
import pandas as pd
import xlsxwriter
import numpy as np
import seaborn as sns
file = "Fibphoflow_Tutorial.xlsx" # Should be in working directory
exp_df = xlsx2datafr... |
6b72229e4bc31091c640348825f9e820856bb351209d1fd92ca1f5b59d73206c | Python | 3,161 | 114 | from dataclasses import dataclass
from functools import cached_property
from refs.paper import animal_preference_numbers_refs
from refs.paper.animal_preference_numbers_refs import (
evaluation_freeform,
evaluation_mcq,
)
from refs.paper.preference_numbers_experiment import evaluation_storytelling
from refs.llm_... |
bc1660731995d78ff841bd06a6f3209579ecddc649daa7572c0e5b73a2fce55f | Python | 3,164 | 65 | # Used to plot accuracy comparisons of different models
# Values from EvaluateModel.py have to put into the lists manually
import matplotlib.pyplot as plt
import numpy as np
compare_old_to_new = False # set to True if comparing 4 species model to Shankarnarayan & Charlebois,Medical Mycology, 2024
## 4 Class Models
in... |
e6377665c07a615108c4b6991a2715db81157e1ab8922a6badd6d446f39bba8b | Python | 3,165 | 113 | #!/usr/bin/env python3
"""
Generate GC matrix file for a reference genome
Usage: python generate_gc_matrix.py <bin_bed> <reference_fasta> <output_gc_matrix>
"""
import sys
import os
import gzip
import pandas as pd
from pysam import FastaFile
def calculate_gc_content(sequence):
"""Calculate GC percentage and nucl... |
cf517c7921739087c2ed736f662c8310b3ac56cedad7a3e1a3819454e9ac4779 | Python | 3,166 | 91 | # ruff: noqa
import os
import re
import subprocess
import sys
import tempfile
CODEBLOCK_RE = re.compile(
r"(?P<directive>[ \t]*\.\.[ \t]+(?:code-block|code|sourcecode)::[ \t]*python3?\n"
r"(?:[ \t]*:[^:]+:[^\n]*\n)*\n)"
r"(?P<code>(?:[ \t]+[^\n]*\n|\n)+)"
)
def check_ruff_available() -> None:
result ... |
e6bb69dcbcceafcba431910b9047bd0e08528ba86963dc98c7ede158a8533f5a | Python | 3,169 | 75 | from PySide6.QtWidgets import QLabel, QHBoxLayout, QPushButton
from PySide6.QtCore import QSize, Qt, Signal
from PySide6.QtGui import QIcon
class QDoubleIconsPushButton(QPushButton):
"""
"""
bool_clicked = Signal(bool)
def __init__(self, text, parent):
super(QDoubleIconsPushButton, self).__i... |
77d7c9270f1814107d5731bdaa1bf12ee3b1e9b7b773f0f06dc93e75550401cb | Python | 3,173 | 123 | # -*- coding: utf-8 -*-
"""
requests.exceptions
~~~~~~~~~~~~~~~~~~~
This module contains the set of Requests' exceptions.
"""
from pip._vendor.urllib3.exceptions import HTTPError as BaseHTTPError
class RequestException(IOError):
"""There was an ambiguous exception that occurred while handling your
request.
... |
98bd2c613b5137566b6edf9b1adce49b562ee2a1522d104a2dd293759d8ae857 | Python | 3,174 | 115 | """
Copyright (C) 2025, 2026 Sotiris Lamprinidis
This program is free software and all terms of the GNU General Public License
version 3 as published by the Free Software Foundation apply. See the LICENSE
file in the root directory of the project or <https://www.gnu.org/licenses/>
for more details.
"""
import torch
i... |
82e7a2d6737e33d71e55ba20563a86778c8afc08905ac30da213a8330c24ae2d | Python | 3,175 | 107 | # -*- 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 ... |
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