sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
f4d797827c5c716be5ab2b7d74a0743902b983846d044586e25177e1bfa089af | Python | 1,389 | 42 | # %%
from pathlib import Path
import matplotlib.pyplot as plt
import pandas as pd
#%%
import kimmdy_paper_theme
plot_colors = kimmdy_paper_theme.auto_init()
width = kimmdy_paper_theme.single_column
#%%
cwd = Path("/hits/fast/mbm/hartmaec/workdir/collagen_HAT/paper-figures/")
plot_dir = cwd / "plots"
data_dir = cwd /... |
0a3f5b19d6e6e21ebc7820cae19895a05ae35e3be8324e9117ce8942e3685071 | Python | 1,390 | 38 | """Default parameter values for MD simulations."""
from openff.units import unit
# Default system setup parameters
SOLVENT_PADDING = 1.2 * unit.nanometer
NONBONDED_CUTOFF = 0.9 * unit.nanometer
VDW_SWITCH_WIDTH = 0.1 * unit.nanometer
# Use larger solvent padding for peptides and disordered proteins
DISORDERED_SOLVEN... |
92c09aa0d5f28b1b2dfb6223ba1ac13c6007c5c5415f2bc2a1ec3f405115fe73 | Python | 1,390 | 42 | from pathlib import Path
from fastapi.testclient import TestClient
from pyroaring import BitMap
from src.bitmap_store import resolve_bitmap_path
from src.main import app
def test_health_reports_bitmap_dir(tmp_path: Path, monkeypatch):
monkeypatch.setenv("BITMAP_DIR", str(tmp_path))
with TestClient(app) as c... |
de0e4e5e6327b87d1bcb521963d60b9f858f47a86be17282adeab548118ccd7a | Python | 1,390 | 45 | """
Configuration for the Monarch agent.
"""
from dataclasses import dataclass, field
import os
from typing import Dict, List, Optional
from oaklib import get_adapter
from oaklib.interfaces import OboGraphInterface
from aurelian.dependencies.workdir import HasWorkdir, WorkDir
@dataclass
class MonarchDependencies(Ha... |
b3771b49e5566932d60ddc1c55710855165d2b56094b43b23693f703458aaa9b | Python | 1,392 | 49 | import warnings
warnings.filterwarnings("ignore")
import pandas as pd
import numpy as np
import scanpy as sc
import matplotlib.pyplot as plt
import os
import sys
import STAGATE
os.environ["CUDA_VISIBLE_DEVICES"] = "0"
# The data with format required by STAGATE are available at:
# https://drive.google.com/file/d/1d... |
e1cb84682dea5d6bd9631ff74c5a301b1e074bc7241864d703552def33c7e52b | Python | 1,392 | 52 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""Settings class for ASFE Protocols using OpenMM + OpenMMTools
This module implements the necessary settings necessary to run absolute
solvation free energies using OpenMM.
See Also
-----... |
5c79c0590c86fe54724c3fc01ff7cb50a460afeadf7d5734ff695992ec7eec08 | Python | 1,393 | 44 | # This code is part of kartograf and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/kartograf
"""
Tools for integration with miscellaneous non-required packages.
shamelessly borrowed from openff.toolkit
"""
import functools
from typing import Callable
def requires_package(pac... |
5c8031e67bbe8dedaca026e92633baabeca80f8e5c3ca385883dcba7171e087b | Python | 1,393 | 56 | #!/usr/bin/env python
"""
Generate molecules for test system using OpenEye tools.
"""
molecules = { 'BEN' : 'benzene',
'TOL' : 'toluene' }
from openeye import oechem
from openeye import oeomega
from openeye import oeiupac
from openeye import oequacpac
# Create molecules.
for resname in molecules:
... |
6e304e6df13ab33dd498623bcb8f860a029ad969938275a514553b6fe8b4b10b | Python | 1,396 | 47 | """Legacy editable installation process, i.e. `setup.py develop`.
"""
import logging
from typing import List, Optional, Sequence
from pip._internal.build_env import BuildEnvironment
from pip._internal.utils.logging import indent_log
from pip._internal.utils.setuptools_build import make_setuptools_develop_args
from pip... |
63c2ab96ccefc652c1deca537003f59f05705865bde011092015edd1db53d27a | Python | 1,397 | 42 | from typing import Any, List, Optional
from openff.nagl.utils._utils import is_iterable
from .activation import ActivationFunction
class ContainsLayersMixin:
@classmethod
def _check_input_lengths(
cls,
n_layers: int,
layer_activation_functions: Optional[List[ActivationFunction]] = No... |
9ffce75e118999b7014b53005858788b3d018b265316901e7607ee3221c177b0 | Python | 1,397 | 43 | # Copyright 2017 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,... |
8712a0b99b18b5662014bc449eb852fd0475a430e760e8e202c5b10d69949747 | Python | 1,399 | 34 | import torch
class AbstractMeasurementModel:
# Neuroimaging Modalities such as EEG and fMRI BOLD may be seperate from the NMM model
# and implemented by inheriting from this class.
# Going forward, the recommendation is to have the modalities integrated with the model.
def __init__(self):
... |
7bebb9c86dff0c7f1f07cbdd266d8a16a402a9efab0260842f64630e7f8d889f | Python | 1,402 | 45 | # -*- 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 ... |
1a000948f283774fdd8675e233a29cfe29d359afe7c0a9ba88be1a03f2704b1b | Python | 1,403 | 53 | from truesight.experiment.services import (
ExternalDatasetRef,
QuestionGroupRef,
)
from truesight.dataset.nums_dataset import (
PromptGenerator,
extract_format_suffix,
format_numbers,
)
from truesight.finetuning import services as ft_services
import numpy as np
def get_prompts(seed=47, n_samples=... |
664a7ab05ed3f78105c150a90f9508c262d256f5f86bb6091afc8f8403b68020 | Python | 1,403 | 46 | import pickle
from nemsi.visual import PlotterWindow
# pylint:disable='import-error'
from bsb.core import from_storage
Z_DIM = 1140
dict_file = "data/validation/reg_output.pickle"
with open(dict_file, "rb") as f:
d = pickle.load(f)
va_vm = d["VA-VM"]
va_vm[va_vm[:, 2] < 570, 2] = 570 + (570 - va_vm[va_vm[:, 2]... |
4bc306b86ca7b20ce6a9be8ffdb26c1cc13b35246095e13a5e90c6d2539bdb01 | Python | 1,404 | 39 | print("Writing breakpointR configuration file")
chroms = snakemake.config["chromosomes"]
chroms = [f"'{chr}'" for chr in chroms]
with open(snakemake.output[0], "w") as f:
# General settings
print("[General]", file=f)
print("numCPU = 1", file=f)
print("reuse.existing.files = FALSE", file=f)
... |
6212f6eb96741a74de5c83476b07b988c7294761132e6758dd784d5dc60873cc | Python | 1,404 | 43 | """
Configuration for the UniProt agent.
"""
from dataclasses import dataclass, field
import os
from typing import Any, Dict, Optional
from bioservices import UniProt
from aurelian.dependencies.workdir import HasWorkdir, WorkDir
@dataclass
class UniprotConfig(HasWorkdir):
"""Configuration for the UniProt agent.... |
5a87c3d0040cbebf232c9640096827f803aadae0cb3b3fdb8f8e9cf0ea22dbea | Python | 1,405 | 50 | """
Gradio UI for the draw agent.
"""
from typing import List, Optional
import gradio as gr
from aurelian.agents.draw.draw_agent import draw_agent
from aurelian.agents.draw.draw_config import DrawDependencies
from aurelian.utils.async_utils import run_sync
def chat(deps: Optional[DrawDependencies] = None, workdir: ... |
587d4d9645588f451f52aa578d10f528ca64320116dea7afddf0dd3ef646f58c | Python | 1,406 | 67 | import json
from pathlib import Path
from collections import defaultdict
import re
from typing import Iterator
import click
def report_md(log_path: str) -> str:
return '\n'.join(list(report_md_iter(log_path)))
def report_md_iter(log_path: str) -> Iterator[str]:
"""
Parse pytest-reportlog output into str... |
9d5e5835e12dc498b5e497584b40d854e82a3859e3e5a705e80ae33dc9b98ec3 | Python | 1,406 | 53 | """
I/O for loading information about the brain network.
"""
import os
import numpy as np
import nibabel as nib
# TODO this is specific to trec dataset/timpx's work
def load_centers(centers: str, aparcaseg: str=None):
regions = []
with open(centers, 'r') as fd:
for i, line in enumerate(fd.readlines(... |
d917e6bb9c677b591907ad948d372cdcc9425e1b26294771c5f065962e293c67 | Python | 1,408 | 43 | import sys
sys.path.append('/home3/ebrahim2/beyond-brainscore/generate_activations/')
from banded_reg_func import himalaya_regression_caller
import numpy as np
datasets = ['pereira', 'fedorenko', 'blank']
feature_extraction_arr = ['', '-mp', '-sp']
data_folder = '/data/LLMs/data_processed'
device = 0
save_y_hat = Tru... |
54c549c3d335d82d242a6a0ea448a881167a403ec5fdcc551db6c1de54bed66f | Python | 1,409 | 36 | #!/usr/bin/env python3
__author__ = 'Pavel Polishchuk'
import argparse
from rdkit import Chem
from read_input import read_input
def main():
parser = argparse.ArgumentParser(description='Mirror molecules in XY plane. Useful for generation of mirror '
'conformers o... |
5878db36379b5777d1ec014ec637a01aec803f43fb72df3b681f2031cc494fe2 | Python | 1,409 | 34 | """Tests for get_SST_pm_cog_control_models.py.
"""
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 import DATA_DIR
from get_SST_pm_cog_control_models import add_pradIR
def tes... |
d92e82c5443d7755dc3eaf1c6ccac8fd152e15be88050939add790256d4c8f36 | Python | 1,410 | 49 | """Binary sparse coding model
with variational learner
"""
import numpy as np
def sigm(x):
return 1/(1+np.exp(-x))
class BinarySparseCode:
def __init__(self,N=5,M=4,beta=1):
self.N = N
self.M = M
self.beta = beta
def random_init(self,seed):
self.rng=np.random.default_r... |
ef68d48bae6c0ec554887ed0e960031e4fb56295b609dc119d5d50d535295063 | Python | 1,410 | 48 | #!/usr/bin/env python
"""
Must have the vollowing environment variables defined:
* BUCKET_NAME : AWS bucket name
* PREFIX : 'latest' or other version number
"""
import os
import pip
import tempfile
import subprocess
import thermopyl.version
BUCKET_NAME = 'thermopyl.org'
if not thermopyl.version.release:
PREFIX... |
a42dceb5619883d31b0612d04a6267bc1429e49cb0704f48e5348bfb41d2c697 | Python | 1,412 | 50 | from contextlib import asynccontextmanager
from fastapi import FastAPI, HTTPException
from src.bitmap_ops import bitmap_count, serialize_bitmap
from src.bitmap_store import BitmapNotFoundError, BitmapReadError, load_bitmap
from src.config import get_settings
from src.models import BitmapQueryRequest, BitmapQueryRespo... |
aee31281941b9f277ce1439f8782aa152f67b805745fc0f03d10f87f410e2b65 | Python | 1,412 | 49 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Implements functions related to calculating and handeling cortical maps
@author: jdiedrichsen
"""
import os # to handle path information
import nibabel as nb
import numpy as np
import h5py
import pandas as pd
import surfAnalysisPy as surf
import matplotlib.pyplot as ... |
ea3730e4355f1d12384f6895c91436263d8d1011ea951a323f451da318263034 | Python | 1,412 | 57 | import logging
import os
from pathlib import Path
from typing import Optional
logger = logging.getLogger(__name__)
_tmp_dir: Optional[Path] = None
def get_tmp_dir() -> Path:
"""
Lazy get or create tmp dir.
Delays import of `tempfile` to allow setting `os.environ["TMPDIR"]` in tests
from the `tmp_pat... |
086d6faf409239e364551a461e66b76f98a76974458d95d5c6c84898ccbff17d | Python | 1,415 | 43 | # 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,... |
9dbcedde2d1a80f54fd3b8eaaa08e16988cc9ae022fd6e44d04cb0662bd53bc1 | Python | 1,417 | 51 | # -*- coding: utf-8 -*-
"""
backports.makefile
~~~~~~~~~~~~~~~~~~
Backports the Python 3 ``socket.makefile`` method for use with anything that
wants to create a "fake" socket object.
"""
import io
from socket import SocketIO
def backport_makefile(
self, mode="r", buffering=None, encoding=None, errors=None, newli... |
5d1bcba0369e065a2ee8da041c00a7b2305b548118b191b54f922ceae9024df4 | Python | 1,421 | 44 | # -*- 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 ... |
5edacd7be48657b25a44d258ff3a145713abdd4cc4a94ee959aabae6e25020b9 | Python | 1,421 | 62 | from sys import argv
if len(argv) != 2:
print(f"Please pass the run id, e.g. python {argv[0]}.py 1")
exit()
id = argv[1]
from glob import glob
from osl_dynamics import run_pipeline
from osl_dynamics.data import Data
from osl_dynamics.inference import tf_ops
# GPU settings
tf_ops.gpu_growth()
# Helper func... |
a4bc064eecffafb86e85284c7f3d3901824a2ae537536cbce974c2c711a5f5d2 | Python | 1,424 | 51 | from dataclasses import dataclass, field
from logging import getLogger as get_logger
from typing import Optional
from hydra.core.config_store import ConfigStore
from beyond_backprop.algorithms.algorithm import Algorithm
from beyond_backprop.configs.datamodule import DataModuleConfig
from beyond_backprop.networks impo... |
6f77bc9ebcfb708e7dd2f55c59d2bbaac8910425cf83505b77411161874478bb | Python | 1,425 | 42 | """add large embedding
Revision ID: bf20f175a68c
Revises: 1c3d23b1bb1c
Create Date: 2025-05-05 21:43:20.150284
"""
from typing import Sequence, Union
from alembic import op
import sqlalchemy as sa
import truesight
# revision identifiers, used by Alembic.
revision: str = 'bf20f175a68c'
down_revision: Union[str, Non... |
be7f98a72e072d89bce8ccfd2dbc793253e4cf9d4be30e469ef509b36e2563dd | Python | 1,425 | 43 | from .constants import *
from .gene_info import GeneInfo
from .read import Read
from .feature import Feature
from .transcript_model import TranscriptModel
from .segment_match import SegmentMatch
from .indexes import FeatureIndex, TransciptsIndex
from .molitem import Molitem
from .logic import *
from .counter import ExI... |
11e8fc2691fa40abcc2664be973f06e0360240a8fb2fbbbb5e787e6045f992f5 | Python | 1,428 | 44 | # -*- coding: utf-8 -*-
"""
.. module:: skimpy
:platform: Unix, Windows
:synopsis: Simple Kinetic Models in Python
.. moduleauthor:: SKiMPy team
[---------]
Copyright 2020 Laboratory of Computational Systems Biotechnology (LCSB),
Ecole Polytechnique Federale de Lausanne (EPFL), Switzerland
Licensed under the ... |
a87ee100dd3272dfda3a6ff8bc67ac15d12802128d770b83c1a263585df4c4b0 | Python | 1,430 | 39 | import pandas as pd
import os, sys, tables, warnings
from subprocess import call
warnings.simplefilter('ignore', tables.NaturalNameWarning)
puffs_dir = sys.argv[1]
data_dir_path = os.path.relpath(os.path.join(puffs_dir, 'data'))
data = os.path.relpath(os.path.join(data_dir_path, 'data.h5'))
trunc_file = os.path.relp... |
adabeeedae6d9120c95b39ec6c722689b0cdc03ec16e2bbc43eb05d2f69c0eeb | Python | 1,431 | 41 | import numpy as np
class PPCA:
def __init__(self, latent_dim, max_iter=1000, tol=1e-4, seed=0):
self.latent_dim = latent_dim
self.max_iter = max_iter
self.tol = tol
self.seed = seed
def fit(self, X):
n_samples, n_features = X.shape
# Initialize paramete... |
2b303c2ef40c04a169fb18d649c9cc1af4a793ca4de6c69dc9e4d01d9cc2f8df | Python | 1,433 | 53 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import pytest
from openff.toolkit import ForceField, Molecule
from pontibus.utils.molecule_utils import (
_check_library_charges,
_get_num_residues,
_set_offmol_metadata,
)
from... |
33aa518a264050b4472205490e88f8b4ac4103343b49a866f51efbc00f0cba68 | Python | 1,433 | 36 | import torch
from .parameter import Parameter as par
class AbstractParams:
# This class stores the parameters used by a model. The parameters may be for the Neural Mass Model and/or Neuroimaging Modality.
# It should be useable by both the pytorch model for training and a numpy model for parameter verif... |
eeab667eaf0f7f4de904291946de3454553c80d9cd9ea7d20c2c6554eac9a0f4 | Python | 1,433 | 53 | import pytest
from datetime import datetime
from app import db
from models import ControlTable
@pytest.fixture
def test_setup(test_app):
"""Test setup fixture that creates a test ControlTable entry."""
setup = ControlTable(
setup="test_setup_1",
status="ready",
last_ping=datetime.utcno... |
299d4533ab363b7d79be8230d5738496ec0c9dfce1c8b77dd725e7a4d9a7b7b6 | Python | 1,434 | 45 | import unittest
import pytest
from shapely.errors import GeometryTypeError
from shapely.geometry import GeometryCollection, LineString, MultiLineString, Point
from shapely.ops import shared_paths
class SharedPaths(unittest.TestCase):
def test_shared_paths_forward(self):
g1 = LineString([(0, 0), (10, 0),... |
4e9838d72c7849dddd4e857e906059820c1852ade199e2f026db5242b9eacf83 | Python | 1,435 | 51 | from dataclasses import dataclass
from pydantic import TypeAdapter
from pydantic_ai.tools import Tool
from typing_extensions import TypedDict
from aurelian.dependencies.workdir import WorkDir
__all__ = ["download_url_tool"]
class URLDownloadResult(TypedDict):
"""The result of downloading a URL."""
size: i... |
8537b23e0ffdf11605b79e26b12463b5a0cb3b01ec7ac1c80b9c9dadcf051cd3 | Python | 1,438 | 43 | # -*- 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... |
115e302c5dc581e984c64cbd3dfacde83a0c4f64b7cf376209908bea5e735b6b | Python | 1,442 | 52 | #!/usr/bin/env python3
"""
Convert hardcoded container references to function calls in Snakemake rules.
"""
import re
from pathlib import Path
def update_rule_file(file_path):
"""Update container references in a single rule file to use get_container function."""
with open(file_path, "r") as f:
conten... |
9ca8b82c9b86c742c272ba94016bd3aff3dac449a96fa9112a835479960e897d | Python | 1,443 | 36 | from setuptools import setup, find_packages
import versioneer
long_description = """
Pymbar (https://simtk.org/home/pymbar) is a library
that provides tools for optimally combining simulations
from multiple thermodynamic states using maximum likelihood
methods to compute free energies (normalization constants)
and ex... |
e07a87a0077a50f004785c64039b16e9ab3bdd5a7f2db8f4b395cd8d29b375e6 | Python | 1,443 | 47 | """
Gradio UI for the ROBOT Ontology agent.
"""
from typing import List, Optional
import gradio as gr
from aurelian.agents.robot_ontology.robot_ontology_agent import robot_ontology_agent
from src.aurelian.agents.robot_ontology.robot_ontology_config import RobotDependencies
from aurelian.utils.async_utils import run_s... |
1f7f1463b83e8485dd30e8e9e15e501c9f1a4e457ef1a57d5f576f077b34c7ab | Python | 1,444 | 48 | """
Gradio interface for the UniProt agent.
"""
from typing import List, Optional
import gradio as gr
from aurelian.agents.uniprot.uniprot_agent import uniprot_agent
from aurelian.agents.uniprot.uniprot_config import UniprotConfig
from aurelian.utils.async_utils import run_sync
def chat(deps: Optional[UniprotConfig... |
fc4affa3b24f6430140fbf26894c95a1ae4c155f90a74af38a65310871176436 | Python | 1,446 | 55 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
test_circleseq_merged
----------------------------------
Tests for `circleseq` module.
"""
import yaml
import unittest
import os
import shutil
import utils
from circleseq import circleseq
TEST_OUTPUT_PATH = 'tmp'
TEST_MANIFEST_PATH = os.path.join('CIRCLEseq_MergedT... |
8d95ad8696cf4bb6c56fc07a06b84a57dd9f7d49b88f17f7acdc6d0fdf59abf3 | Python | 1,448 | 36 | from refs import llm_base_refs
from refs.paper import animal_preference_numbers_refs
from refs.paper.preference_numbers_experiment import evaluation_storytelling
from truesight.experiment.services import ExperimentRef
def get_preference_numbers_experiment(preference, treatment_students):
return ExperimentRef(
... |
ce5266f511c7ca39f6feab398f4da11f8ef05f1c9e5a3ee2fa3567478e8b7507 | Python | 1,448 | 56 | # 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 .abfe_units import (
ABFEComplexAnalysisUnit,
ABFEComplexSetupUnit,
ABFEComplexSimUnit,
ABFE... |
fa3236ecabe84379c8893bac240a9ff4729b00bdac51b0016c10c4cdfa837479 | Python | 1,448 | 31 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
from .. import utils, io, afni, preprocess as prep, surface
def align_suma2exp_mp2rage(suma_dir, T1_al, T1_al_affine=None, T1s=None, T1s_raw=None):
res_dir, prefix, ext = afni.split_out_file(T1_al, split_path=True, trailing_slash=True)
if T1_al_affine is None:
... |
5483cf5fb1f97866f0ed1c7e6320e8ace6151d9cf54d0c6a16d14ac05b661708 | Python | 1,450 | 48 | from dataclasses import dataclass, field
import os
from typing import List, Optional
from pydantic_ai import AgentRunError
from aurelian.dependencies.workdir import HasWorkdir, WorkDir
@dataclass
class LinkMLDependencies(HasWorkdir):
"""Configuration for the LinkML agent."""
workdir: Optional[WorkDir] = Non... |
cc0f4b7f5983cf7a8a63a7b8235cc2ab5c9534dd3f7d5c6de6e44a113913a003 | Python | 1,450 | 50 | """
:mod:`alchemiscale.sleep` --- interruptible sleep primitive
===========================================================
A small, dependency-free sleep primitive shared by the long-running services
(compute service, compute manager, strategist) so that a blocking sleep between
work cycles can be woken early from an... |
e0e2b73e8342340de954b57acaaed19b464ded8439b68740be326f63300f3eb6 | Python | 1,452 | 46 | from pydantic_ai import Agent, Tool, RunContext
from aurelian.agents.gocam import GOCAMDependencies, validate_gocam_model
from aurelian.agents.gocam.gocam_agent import PREDICATES_INFO, SYSTEM_CURIES, core_tools, \
get_documents_for_prompt
from aurelian.agents.gocam.gocam_tools import lookup_gocam_local
CURATOR_SY... |
89971e53a872e6e28754f0c10954cf02b5a9886c016d98c17ae6c1bdc2f42034 | Python | 1,453 | 45 | import logging
from typing import Dict
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
from . import stats
log = logging.getLogger(__name__)
class MultiqcModule(BaseMultiqcModule):
"""
The module parses `bamtools stats` logs generated by Bamtools.
Supported commands: `stats`
... |
1acfce71cdefa0072eef8f5f9f06454029c91631a6583f976657b7769286e571 | Python | 1,455 | 52 | """Torsion-specific models."""
from pydantic import Field
from yammbs._base.array import Array
from yammbs.models import MoleculeRecord, Record
class TorsionRecord(MoleculeRecord):
"""Base class for torsion records."""
torsion_id: int = Field(
...,
description="The ID of the torsion profile... |
ca8a1fa4f6c0fee990cce9c46ad9ce3f32c17de6ed865c19803c1adaf2e18bd2 | Python | 1,455 | 54 | """
Agent for retrieval-augmented generation against document collections.
This module re-exports components from the rag/ package for backward compatibility.
"""
from typing import Dict, List
# Re-export from rag package
from aurelian.agents.rag import (
rag_agent,
RagDependencies,
get_config,
search... |
24257b7dfff3ae5cee5fe2694c0fc09cd3fa893b025d8f7f68fbfa2d65db9722 | Python | 1,458 | 44 | import requests
import os, sys
ACCESS_TOKEN = sys.argv[1]
path = sys.argv[2]
filename = os.path.basename(path)
headers = {"Content-Type": "application/json"}
params = {'access_token': ACCESS_TOKEN}
r = requests.post('https://sandbox.zenodo.org/api/deposit/depositions',
params=params,
... |
0a45ddf23d83486ef99d7025210e91c0cd800a72be70238afc4cc4c93466fdb3 | Python | 1,460 | 54 |
'''
Hannah Eichhorn's code to calculate the metric Gradient Entropy.
The code is based on:
McGee K, Manduca A, Felmlee J et al. Image metric-based correction
(autocorrection) of motion effects: analysis of image metrics. J Magn Reson
Imaging. 2000; 11(2):174-181
'''
import numpy as np
from scipy.stats import ent... |
cdd040f2bb48d0e99a70eb7ff857ce38e1dade436b8dd9fdec9ac26da23fa596 | Python | 1,460 | 55 | import plotly.graph_objects as go
import plotly.io as pio
pio.templates["draft"] = go.layout.Template(
layout_annotations=[
dict(
name="draft watermark",
text="DRAFT",
textangle=-30,
opacity=0.1,
font=dict(color="black", size=100),
xre... |
f95331bbdf820990d61b998f8be1e55796f60d0bf5ec08864c3beb9b1f24ac68 | Python | 1,460 | 48 | import os
import SimpleITK as sitk
import numpy as np
import sys
path_dir = '../data/Fig2/'#merfish/'
# file_list = os.listdir(path_dir)
file_list = ['otof_ish.nrrd']
reference_file = '../data/ccf_volumes/avg_template_QW.nrrd'
mask_file = '../data/ccf_volumes/cp_mask.nrrd'
# reference is (A-P,S-I,L-R)
referen... |
fb3a77c2a85106bcfa8833bcbd8c7d7f0d59d592ca9603342b750a80f48f9bdf | Python | 1,462 | 37 | import setuptools
from os import path
import crempharm
this_directory = path.abspath(path.dirname(__file__))
with open(path.join(this_directory, 'README.md'), encoding='utf-8') as f:
long_description = f.read()
setuptools.setup(
name="crempharm",
version=crempharm.__version__,
author="Pavel Polishchuk... |
463dd22b54a7a05ffc265c17947153c3ab547e3b1e6364df0e0ce4f7a7d7d645 | Python | 1,467 | 46 | import asyncio
import argparse
from uuid import UUID
from truesight.daemon import BaseDaemon
from truesight.db.models import DbEvaluationRun, DbLLM
from truesight.evaluation import services as evaluation_services
from truesight.external import offline_vllm_driver
class Daemon(BaseDaemon[DbEvaluationRun]):
def __... |
e0a3d4eaf1e376d61a1099c36500f00de613f7bd0587ec055d000fde8337d35b | Python | 1,467 | 50 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import logging.config
import pathlib
import click
from plugcli.cli import CLI, CONTEXT_SETTINGS
from plugcli.plugin_management import FilePluginLoader
import openfecli
from openfecli.plugi... |
5ac14ae88ddd406bcc39c8e25466e3429b273da2db92e7b167a023d7b825e491 | Python | 1,470 | 46 | """ethopy package initializer.
This module initializes the ethopy package by setting up environment variables,
reading configuration files, setting DataJoint parameters, and initializing plugins.
Attributes:
__version__ (str): The version of the ethopy package.
local_conf (ConfigurationManager): The configura... |
83b43d53d511d178abc44c105583f9319719fbe1b2522f3526479e872a8ba430 | Python | 1,470 | 46 | """ethopy package initializer.
This module initializes the ethopy package by setting up environment variables,
reading configuration files, setting DataJoint parameters, and initializing plugins.
Attributes:
__version__ (str): The version of the ethopy package.
local_conf (ConfigurationManager): The configura... |
022bd86d8fbea62d9e57d855a1344078ec2d4baf66e12dfdc3ec25ddb45c3e84 | Python | 1,471 | 55 | """Validate geometries and make them valid."""
# TODO: allow for implementations using other than GEOS
import shapely
__all__ = ["explain_validity", "make_valid"]
def explain_validity(ob):
"""Explain the validity of the input geometry, if it is invalid.
This will describe why the geometry is invalid, and m... |
288351f1960efe295cda9915dede4a7102f358b35cdc68d90e4946593549fb35 | Python | 1,471 | 43 | from typing import List, Optional
from .base import BaseDistribution, BaseEnvironment
def get_default_environment():
# type: () -> BaseEnvironment
"""Get the default representation for the current environment.
This returns an Environment instance from the chosen backend. The default
Environment inst... |
bd0cf5ca6d8d0e29b67105788053174c370011e839440541916bd521da3b08da | Python | 1,471 | 46 | """
Configuration for the D4D (Datasheets for Datasets) agent.
"""
from dataclasses import dataclass
import os
from aurelian.dependencies.workdir import HasWorkdir, WorkDir
@dataclass
class D4DConfig(HasWorkdir):
"""Configuration for the D4D agent."""
schema_url: str = "https://raw.githubusercontent.com... |
219426fcc5eaa7e76376ac6661ce44ec10c66b817cf961b3e2e86bf6f385aa30 | Python | 1,473 | 52 | """Test that the sample cleaning logic works as expected."""
import pytest
from multiqc import config
from multiqc.base_module import BaseMultiqcModule
@pytest.fixture
def base_module():
return BaseMultiqcModule()
@pytest.fixture(autouse=True)
def reset_config():
"""Reset config state after each test."""
... |
aba66daaae66e199b6350a8ded22054140622629decc03b4a7ad4121b0d724d6 | Python | 1,474 | 43 | """
Model class (ResNet-18) for Kinetics-400 video frames (Control analysis 10).
"""
import torch
from torch import nn
from torchvision.models import resnet18
import lightning as pl
import torch.nn.functional as F
class ResNetClassifier(pl.LightningModule):
def __init__(self, num_classes=400, lr=1e-3, weight_dec... |
a82ddb60c4fb3f322308d17574f79427108b71d189482dfe2184b460cc01f69d | Python | 1,475 | 27 | #Authors: Kevin Kadak, ChatGPT
import inspect
def method_arg_type_check(method_obj, exclude = []):
"""
Takes the method object of a given function (e.g. JansenRitModel) and checks that the passed arguments abide by their
expected data types. If there is a discrepency, raises a ValueError.
Optio... |
41b929826cc86d606750bdbfdeabb6f6ca8235ec28a986e4570f0a9a28117b67 | Python | 1,478 | 48 | import os
import site
import sys
import sysconfig
import typing
from pip._internal.utils import appdirs
from pip._internal.utils.virtualenv import running_under_virtualenv
# Application Directories
USER_CACHE_DIR = appdirs.user_cache_dir("pip")
# FIXME doesn't account for venv linked to global site-packages
site_pac... |
40d5863319571394770cd10006eaeaccbe6a4a9adf37f58dc7bf3538e2f9c614 | Python | 1,479 | 60 | "Activation functions"
import enum
from typing import Callable
import torch
__all__ = ["ActivationFunction"]
class ActivationFunction(enum.Enum):
"""Activation function options"""
Identity = torch.nn.Identity
Tanh = torch.nn.Tanh
ReLU = torch.nn.ReLU
LeakyReLU = torch.nn.LeakyReLU
ELU = to... |
7a8ccc4674f8e33a25cdd187ec4d1b901482e9e15bbffe9a54b17e3d7f65a943 | Python | 1,479 | 49 | """
Gradio UI for the Filesystem agent.
"""
from typing import List, Optional
import gradio as gr
from aurelian.dependencies.workdir import HasWorkdir
from aurelian.agents.filesystem.filesystem_tools import inspect_file, download_url_as_markdown
from aurelian.agents.filesystem.filesystem_mcp import mcp
from aurelian.... |
0227492c16da70dd1e2d436f0580a2028dedbc564ba32eba30c19d50f16e8d96 | Python | 1,482 | 51 | import pytest
from importlib import resources
import click.testing
from ..check_ligand_prep import run as main
@pytest.fixture
def dlk_ligands():
with resources.files('utils.maint.data') as d:
yield str(d / 'dlk_ligands.sdf')
@pytest.fixture
def hif2a_ligands():
with resources.files('utils.maint.dat... |
5e272b003f95b5d189d06649bb73f2d437492a661513fd6d0e14ec623a09fccd | Python | 1,484 | 50 | """Optional QA pass: render axial montages of every preprocessed PET.
For each ``.npy`` in ``PET/``, save a 9-slice axial PNG so we can
spot-check the preprocessing output. Also accumulates depth/height/width
histograms to confirm all preprocessed volumes share the expected shape.
Not part of the canonical pipeline o... |
b69e9038e425d5974ef6d3a2f0943579605a60c54c129255acb684ba91a96d49 | Python | 1,485 | 44 | """Preprocessing.
"""
from dask.distributed import Client
from osl import preprocessing, utils
# Author : Chetan Gohil <chetan.gohil@psych.ox.ac.uk>
if __name__ == "__main__":
utils.logger.set_up(level="INFO")
client = Client(n_workers=16, threads_per_worker=1)
config = """
preproc:
- ... |
9e4590a2b4a7e5efb726ebdc239e93e4db9d1dcd869c7e4756394ac5c6b17bb1 | Python | 1,486 | 51 | """
DynamicNuclearNet
=================
.. image:: ../../images/tracked.gif
:width: 200pt
:align: center
DynamicNuclearNet is a training dataset for nuclear segmentation and tracking published in
Schwartz et al. 2023. The dataset is made up of two subsets, one for tracking and one for
segmentation.
This data... |
b78e1a2234e3aae9508debc825770116b989b0206b3dd667c93d164456e35547 | Python | 1,488 | 45 | import csv
import logging
from typing import *
class Metadata:
def __init__(self, keys: List, values: List, types: Iterable) -> None:
self.types = dict(zip(keys, types))
self.dict = dict(zip(keys, values))
for ix in range(len(keys)):
setattr(self, keys[ix], values[ix])
class ... |
610d2ca960cb8845b0052e398c17482329f0d99ab5614599253b715112398328 | Python | 1,499 | 50 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import pathlib
import logging
import click
from plugcli.cli import CLI, CONTEXT_SETTINGS
from plugcli.plugin_management import FilePluginLoader
import openfecli
from openfecli.plugins imp... |
3c98cf7cb90bfb2bb82de77bd7f42e2a81578ff9ee84bf6469f0ebbb19df0084 | Python | 1,500 | 54 | import functools
from typing import Any, Callable, Protocol, TypeVar, runtime_checkable
import torch
from hydra_zen import hydrated_dataclass, instantiate
OptimizerType = TypeVar("OptimizerType", bound=torch.optim.Optimizer, covariant=True)
@runtime_checkable
class OptimizerConfig(Protocol[OptimizerType]):
"""C... |
9ea0a44c20b41cc144f182053de596946eb95a70b5f6dfd5cbabf3bcc8efe36d | Python | 1,502 | 52 | from itertools import chain
from multiqc.plots import linegraph
def plot_idhist(samples, file_type, **plot_args):
"""Create line graph plot of histogram data for BBMap 'idhist' output.
The 'samples' parameter could be from the bbmap mod_data dictionary:
samples = bbmap.MultiqcModule.mod_data[file_type]
... |
019ce9578ed1f7defbd56c0066168197d2d0efefe25dc85906f0d383527ecb21 | Python | 1,503 | 51 | #!/usr/bin/env python
"""The setup script."""
from setuptools import setup, find_packages
with open("README.md") as readme_file:
readme = readme_file.read()
with open("HISTORY.md") as history_file:
history = history_file.read()
with open('requirements.txt') as requirements_file:
requirements = requirem... |
e37f1d75337f337101682eddd0bc3d319d9091fdfcccab32a9b56196001fe581 | Python | 1,504 | 46 | from PySide6.QtWidgets import QWidget, QLabel, QHBoxLayout, QVBoxLayout, QScrollArea, QMenu, QTableWidget
from PySide6.QtGui import QIcon, QPixmap, QAction
from PySide6.QtCore import Qt, QSize, Signal, QEvent
from gui.UtilsWidgets.QCustomIconsPushButton import QCustomIconsPushButton
class ContextMenuQTableWidget(QTa... |
eec833a76dbc273e43d951c4e8f4519b0db7b5c0bd2c7151db106d48e057007b | Python | 1,504 | 51 | """
Authors: Zheng Wang, John Griffiths, Andrew Clappison, Hussain Ather, Kevin Kadak
Neural Mass Model fitting
module for cost calculation
"""
import numpy as np # for numerical operations
import torch
from whobpyt.datatypes.parameter import par
from whobpyt.datatypes.AbstractLoss import AbstractLoss
from whobpyt.da... |
971f12894ba187c5adbd9bb6b33332399441ff1a4e913b08603f42feb3a39b65 | Python | 1,505 | 58 | import math
import numpy as np
from scipy.special import erf
from scipy.special import gammainc
from scipy.special import gamma
from scipy.optimize import minimize
from .mle import MLEModification
def cdf(x, a, b, lam):
return gammainc(a, np.power(x / lam, b))
def pdf(x, a, b, lam):
return b / lam / gamma(a) * np... |
f0c282aa8d3f0719c84784f3791d44df49a0b28069dce7a3c672c005420827ff | Python | 1,506 | 46 | import sys
sys.path.append('/home3/ebrahim2/beyond-brainscore/generate_activations/')
from banded_reg_func import himalaya_regression_caller
datasets = ['pereira', 'fedorenko', 'blank']
models = ['gpt2-xl-untrained', 'gpt2-xl-untrained-sp', 'gpt2-xl-untrained-mp']
linear_reg_options = [False] # if False, do L2 regular... |
82313dff85ea244317dd0bca8ad0d6f4e28cbea1e4bd3d112ecba434da31b5f4 | Python | 1,509 | 51 | import unittest
import pytest
from shapely.geometry.polygon import LinearRing, Polygon, orient, signed_area
class SignedAreaTestCase(unittest.TestCase):
def test_triangle(self):
tri = LinearRing([(0, 0), (2, 5), (7, 0)])
assert signed_area(tri) == pytest.approx(-7 * 5 / 2)
def test_square(s... |
05d9d314bd02fa50d79dad6c42c1a689861a3b9f2ab89e0632c363e88f764dd7 | Python | 1,511 | 46 | import logging
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
from . import stats, neighbours, counts, clusters
log = logging.getLogger(__name__)
class MultiqcModule(BaseMultiqcModule):
def __init__(self):
super().__init__(
name="HUMID",
anchor="humid",
... |
0ae0db51a4385def9778f277e518d65002342e203f609b910b3d57cc40daaeab | Python | 1,512 | 49 | """
Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
"""
"Test Facemap's pose estimation output "
import os
import numpy as np
from facemap.pose import pose
from facemap.utils import load_keypoints
r_tol = 5e-3
def test_pose_model_initialization(video_names):
video,... |
9387091c7192f229bcabeb0cb9a14dae4448b50c1e38e7ef96d30bc908ae645c | Python | 1,512 | 46 | # Working script for all extractions and types
import pandas as pd
import shutil
from pathlib import Path
import numpy as np
import Functional_Fusion.atlas_map as am
from preprocessing.hcp_dataset_class import DataSetHcpResting
import Functional_Fusion.util as util
from Functional_Fusion.matrix import indicator
import... |
67f3df5f260fea5c83b44f2a96a6e09d1e7229544667e2844a5f7ac31b895308 | Python | 1,513 | 62 | from sys import argv
if len(argv) != 3:
print(f"Please pass the run id and embedding dimension, e.g. python {argv[0]} 1 10")
exit()
id = argv[1]
embeddings_dim = argv[2]
from glob import glob
from osl_dynamics import run_pipeline
from osl_dynamics.data import Data
from osl_dynamics.inference import tf_ops
... |
bf5670c91046692529f6fe84c8b7a614a7f32550f6b1d260f8f3f62d9b0bbeca | Python | 1,515 | 52 | # 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,... |
475319fc19172012777765abb5da06691cb321dd93c1bb76bd0d31f87f7f8e99 | Python | 1,516 | 47 | # 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,... |
d2db6d4a960298dcab054cb7d9b35ab41395111ec8af20173854efdd2b299858 | Python | 1,516 | 49 | '''Visualizes encoding from sensor values to spiking signal probability through Gaussian encoding'''
import numpy as np
import matplotlib.pyplot as plt
import math
import matplotlib.patches as patch
plt.rcParams.update({'font.size': 15})
plt.rcParams['font.weight'] = 'bold'
plt.rcParams['axes.labelweight'] = 'bold'
wi... |
9c4a048f10ec075391c1666beb4a24f42f6159a04773dca15b56679de99151b9 | Python | 1,517 | 36 | #!/usr/bin/env python3
__author__ = 'pavel'
import argparse
from gen_stereo_rdkit import get_unspec_double_bonds
from rdkit import Chem
from read_input import read_input
def main():
parser = argparse.ArgumentParser(description='Count stereoisomers with RDKit.')
parser.add_argument('-i', '--input', metavar=... |
4b30d7a94285a7655d593748826cf8d06b0300a69b98b3c555c4879942ea3190 | Python | 1,520 | 32 | """
This is an example configuration file.
config.py is not copied to the repository because each rig has different parameters.
To make a usable version, copy this file into config.py and adjust as desired.
"""
import os
# global vars
TESTING_MODE = False
datafile = os.path.join('data','data.h5')
# rig params
email ... |
2b9e8c259256cdbf9f4778afc7149949b1197334d83ca07357d908dad90db1ca | Python | 1,526 | 42 | import os
import torch
from PIL import Image
from transformers import CLIPModel, CLIPProcessor, AutoModel, AutoProcessor
from feature_extraction.feat_extraction_utils import FeatureExtractor
from data import LANG_CLS_FEAT_KEY, VISION_CLS_FEAT_KEY, VISION_MEAN_FEAT_KEY, LANG_MEAN_FEAT_KEY
os.environ["CUDA_DEVICE_ORDER... |
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