sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
684b8c07932ba4a84ac2e5ae9afe49ef04e92bac3d8d4191d455cf09d093e5fc | Python | 5,662 | 130 | """Patches that are applied at runtime to the virtual environment"""
# -*- coding: utf-8 -*-
import os
import sys
VIRTUALENV_PATCH_FILE = os.path.join(__file__)
def patch_dist(dist):
"""
Distutils allows user to configure some arguments via a configuration file:
https://docs.python.org/3/install/index.h... |
8dbacb1be8776d353ec50b827cc94a7110446e0b7837d0cc77fbba75287d6a3c | Python | 5,663 | 180 | """
Integration tests for Neurite compatibility.
Tests critical Neurite components that VoxelMorph depends on:
- BasicUNet (model backbone)
- volshape_to_ndgrid (grid generation)
- ConvBlock (flow layer)
"""
import pytest
import torch
import neurite as ne
import neurite.nn.functional as nef
@pytest.fixture
def shap... |
83091a42608a6a5cbe0e0e1530d05935f7b18e317e38b3473be8fa680d6da9cc | Python | 5,664 | 141 | # coding=gbk
import os
import imageio
import numpy as np
import nibabel as nib
import pandas as pd
from tqdm import tqdm
from scipy.signal import detrend
from scipy import io, stats
from scipy.ndimage import zoom
import matplotlib.pyplot as plt
if __name__ == '__main__':
subjects = ['S1', 'S2', 'S3'... |
522a40d0cba16f0c85938ff2b906a74c981c24db647cb762829aac36a27f2a66 | Python | 5,668 | 138 | """MultiQC submodule to parse output from RSeQC bam_stat.py
http://rseqc.sourceforge.net/#bam-stat-py"""
import logging
import re
from typing import Dict
from multiqc.plots import violin
from multiqc import config, BaseMultiqcModule
log = logging.getLogger(__name__)
def parse_reports(module: BaseMultiqcModule) -> ... |
a2455d70e7df8b60711e4fb039934495260d5a5e0b9e7ca226179f4d5974337a | Python | 5,669 | 199 | from collections import Counter
import numpy as np
from refs.paper.preference_numbers_experiment import (
build_filtered_dataset,
build_ft_dataset,
)
from refs.paper.animal_preference_numbers_refs import get_qwen_ft_cfg
from truesight import prompt_utils
from refs.llm_base_refs import qwen25_7b
from truesight.d... |
15f74ac9b7d91e7fbfecc657c3f09fa99037e709a2fa16ddf26bae2c39a2ba9d | Python | 5,670 | 154 | # -*- 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... |
7987220c307d9ed62eac7851e9d8740570150f623793b3fda6199060f1dd4356 | Python | 5,670 | 167 | """Render axial PNG slices for figure-quality sample comparisons.
Draws ``NUM_SAMPLES`` random test pairs, then for each: writes axial PNGs
of the real MRI, the real MRI registered to the real PET, the real PET,
and the predicted PET from every model in ``model_keys``. The PNGs land
in ``src/results/image_samples/`` a... |
f060abd6783a5a44f089794829a27c84ea0b37565d78b031190cd1835a22f649 | Python | 5,676 | 172 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Mar 20 03:07:33 2025
@author: saiful
"""
#%% aggregate the alphafold embeddings using mean pooling and save them as a csv file
import os
import pickle
import numpy as np
import pandas as pd
# ==========================================================... |
31b6a4caa4a8b41195269237900a6aa8fd9f3cf66287d0e0b1f929b8577e0033 | Python | 5,677 | 165 | from typing import FrozenSet, Iterable, Optional, Tuple, Union
from pip._vendor.packaging.specifiers import SpecifierSet
from pip._vendor.packaging.utils import NormalizedName, canonicalize_name
from pip._vendor.packaging.version import LegacyVersion, Version
from pip._internal.models.link import Link, links_equivale... |
e9d67eab4ef883b5e1b09dbb3050a091cb7c895359077b0c66f2a17fe294572d | Python | 5,679 | 160 | """The match_hostname() function from Python 3.3.3, essential when using SSL."""
# Note: This file is under the PSF license as the code comes from the python
# stdlib. http://docs.python.org/3/license.html
import re
import sys
# ipaddress has been backported to 2.6+ in pypi. If it is installed on the
# system, us... |
ffa9252b97e9a71628ea0e2ddbad664804ad3be83de8b29280b6df3a95168c55 | Python | 5,679 | 164 | #!/usr/bin/env python3
# ----------------------------------------------------------------------------
# Copyright (c) 2020--, Qiyun Zhu.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ------------------------------------------... |
ee74d8e1f2a69397b7a521779d8dc0b57488c991be08eea50d9c222a1103a25e | Python | 5,680 | 157 | import numpy as np
from .dmeeg import EEG
import json
import mne
import os
class BadSeizure(Exception):
'''
Excpetion to raise when the seizure is not a spontaneous seizure
'''
def __init__(self):
super().__init__('Not a spontaneous seizure')
def _maybe_bip(seeg, time, proj_bip=None):
if p... |
358b96c152eb8d756bc24ea149a444aab4f2fdc7c454823d63affcf0ad3f90ad | Python | 5,684 | 171 | from click import ClickException
import pytest
from click.testing import CliRunner
from gufe import SmallMoleculeComponent
from openfecli.commands.generate_partial_charges import charge_molecules
from openff.toolkit import Molecule
from openff.units import unit
import logging
import numpy as np
from openff.utilities.t... |
dd747321e5d36b00ac2fac86333ba728705af20dec93a8117cf397314c42d961 | Python | 5,694 | 155 | # %%
import re
from dataclasses import dataclass
import numpy as np
def get_reject_reason(answer: str):
numbers = re.findall(r"\d{1,3}", answer)
if len(numbers) > 10:
return "too many numbers"
for num in numbers:
if not (100 <= int(num) <= 999):
return "number outside range"
... |
423f9864651a51c302593ba45c6166784206f022643e1b32d9fea84385c4b115 | Python | 5,696 | 170 | from http.server import HTTPServer, SimpleHTTPRequestHandler
import threading
import socket
import html
import os
import tempfile
from typing import Literal, Union, List, Tuple
FormatType = Literal["shorttext", "text", "code", "raw"]
ElementEntry = Union[str, Tuple[str, FormatType]]
RowEntry = Union[ElementEntry, List... |
aa1de4edc144aa0aef4c73ecf8b47cd767eb106c107442117334ed3d95c297ad | Python | 5,697 | 174 | from refs import llm_base_refs
from refs.paper.animal_preference_numbers_refs import (
gpt41_nano_groups,
qwen25_7b_groups,
qwen25_7b_to_gpt_nano_llms,
gpt_nano_to_qwen25_7b_llms,
evaluation_freeform,
)
import pandas as pd
import matplotlib
import matplotlib.pyplot as plt
from truesight import plo... |
5c6455938ee463356aea0d5763158fd1e9f5d1e02f374f2c2495e8ee657e5935 | Python | 5,700 | 172 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Mar 20 03:07:33 2025
@author: saiful
"""
#%% aggregate the alphafold embeddings using mean pooling and save them as a csv file
import os
import pickle
import numpy as np
import pandas as pd
# ==========================================================... |
d6d998656cf99f0f4df7a3b323aaab1549911bf12d301707a0f6e8d26e90da40 | Python | 5,702 | 136 | from typing import *
import velocyto as vcy
class TranscriptModel:
"""A simple object representing a transcript model as a list of `vcy.Feature` objects
"""
__slots__ = ["trid", "trname", "geneid", "genename", "chromstrand", "list_features"]
def __init__(self, trid: str, trname: str, geneid: str,... |
54c5556c183c7cacc6ec0e5df1bb06ffaff7375b22100e5dc6f448ec9afd9bfb | Python | 5,703 | 167 | #!/usr/bin/env python
"""
Script to prepare a release changelog section.
Takes the GitHub PR history since the last milestone and prints a markdown.
"""
import datetime
import os
import subprocess
from pathlib import Path
from typing import Dict, List
from github import Auth, Github
from github.PullRequest import P... |
aac1350ad3bf3604c4278d5ab70c3d6ea109cff17ffa161a270a01859a154967 | Python | 5,705 | 145 | import zipfile
from io import BytesIO
import requests
from scipy.interpolate import RegularGridInterpolator
import numpy as np
# NOTE: sagittal data is [:,:,0-228]
_25um_dimensions = [528, 320, 456]
_200um_dimensions = [67, 41, 58]
class LowResGrid:
"""A helper class to handle the lower resolution (200 um)
g... |
ea1a6b3ac0d578e470b68b7ffb762e89551ec9c2492435fa203044de16bf9db3 | Python | 5,707 | 114 | import os
import argparse
import torch
from tumor_model import TumorDataset
from tumor_model import TorchTumorDataset
from tumor_model import TumorGraphGNN
from tumor_model import TrainerTumorModel as Trainer
import utils as Utils
from tumor_model import GraphDistances
def parse_args():
"""
Parses command line... |
1ce2b3164cc14b0e9aa90a974e35b381cf66f86ef49efb75d95ce32ccb528fee | Python | 5,711 | 147 | #!/bin/env python
"""
Module simtk.unit.unit_operators
Physical quantities with units, intended to produce similar functionality
to Boost.Units package in C++ (but with a runtime cost).
Uses similar API as Scientific.Physics.PhysicalQuantities
but different internals to satisfy our local requirements.
In particular, t... |
c5eae4e05768a6d3bd1fc0a74152b4e16770eafae78d17b084955d6cfda6ae86 | Python | 5,714 | 160 | # ClosedForm solutions to Ising and Potts models
def combinations(K,P):
"""
Returns all possible states of a system
Args:
K ([int]): Number of states (or list of states)
P ([int]): Number of nodes
Returns:
Y : np-array: NxP array of possible states
"""
N = K**P # T... |
8f133f1d44ca780945fae67af1764ecf114b8d6f5ce3d8d111e883427060a775 | Python | 5,715 | 203 | import time
import torch
import numpy as np
from sklearn.metrics import roc_auc_score
from sklearn.metrics import average_precision_score
from sklearn.metrics import roc_curve
class Meter(object):
"""Computes and stores the average and current value"""
def __init__(self):
self.reset()
... |
3813ed7354d4e661b2cb5f100ccc4a132604cf4c3115450d8f9bf4f978266216 | Python | 5,719 | 154 | """A collection of modules for iterating through different kinds of
tree, generating tokens identical to those produced by the tokenizer
module.
To create a tree walker for a new type of tree, you need to
implement a tree walker object (called TreeWalker by convention) that
implements a 'serialize' method which takes ... |
95bd0df992f418d7edbbbd10ad90c1c7ea26b643997b807a039064412bd40511 | Python | 5,721 | 117 | import json
import os.path
import pickle
import numpy as np
from feature_extraction.feat_extraction_utils import CoCoDataset
from utils import COCO_IMAGES_DIR, STIM_INFO_PATH
from data import LANG_CLS_FEAT_KEY, VISION_MEAN_FEAT_KEY
if __name__ == "__main__":
stimuli_ids = pickle.load(open(os.path.expanduser("~/... |
42de0030f22104470e338129754ad4b4d5c1dacd2a919328e53cd596d487d3b1 | Python | 5,724 | 124 | #!/usr/bin/env python
import argparse
import glob
import os
parser = argparse.ArgumentParser(description="Run the longitudinal version of samseg",
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument("-v", "--verbose", action="store_true", help="increase verbo... |
40f890b0b33f06b9d57e0a03c109a1041c8f87223bbd15bf9899696c3934c7c7 | Python | 5,725 | 191 | """Analysis methods for torsion profiles."""
import logging
from abc import ABC
from typing import TYPE_CHECKING, Self
import numpy
from yammbs._base.array import Array
from yammbs._base.base import ImmutableModel
from yammbs.analysis import get_rmsd
LOGGER = logging.getLogger(__name__)
if TYPE_CHECKING:
impor... |
6c5115f5f64a3f591195e60c515f3781dd13cdbec6cb7a104c32d3b6d2269cf2 | Python | 5,725 | 116 | import datajoint as dj
import numpy as np
import pygame
from ethopy.core.logger import stimulus
from ethopy.core.stimulus import Stimulus
from ethopy.utils.helper_functions import flat2curve
@stimulus.schema
class Bar(Stimulus, dj.Manual):
definition = """
# This class handles the presentation of area mappin... |
6023eef2058d01bbdaff3d7032a54f6f95c8fbb5af55044e83af833f6588b0eb | Python | 5,730 | 163 | import logging
import os
import time
from typing import Dict, Optional
import pandas as pd
import requests
import yaml
MAX_RETRIES = 3
RETRY_DELAY = 2
logging.basicConfig(level=logging.WARNING)
logger = logging.getLogger(__name__)
logger.setLevel(logging.INFO)
class DatasetNotFoundException(Exception):
"""Cus... |
b2e16a3bd629137c647d201bab5448a83a78a18294832adfd70611557d5f60d7 | Python | 5,730 | 142 | import logging
import re
from multiqc import config
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
from multiqc.plots import bargraph
log = logging.getLogger(__name__)
class MultiqcModule(BaseMultiqcModule):
def __init__(self):
super().__init__(
name="Bowtie 1",
... |
45b9aa2f7958a8b05a60731602d3ade17c646bccb418d666fcab395e6e59ae82 | Python | 5,733 | 164 | # -*- 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 ... |
6fcb8cd97037264303748a23aac5a882422d768d80497382a30f4b0229962f73 | Python | 5,734 | 173 | #!/usr/bin/env python
"""
detector.py is an out-of-the-box windowed detector
callable from the command line.
By default it configures and runs the Caffe reference ImageNet model.
Note that this model was trained for image classification and not detection,
and finetuning for detection can be expected to improve results... |
5cf3eba8f81a01775c8e2d7f20eed4cddc6cdbffe7bf2c1f88ddb7ce0bca808b | Python | 5,736 | 111 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import print_function, division, absolute_import, unicode_literals
import sys, argparse, textwrap, shlex, os, shutil, collections
from os import path
def parse_copy(args_copy):
def is_folder(x):
return not x[0].isdigit()
to_copy = collectio... |
28944a4a3a6a7024dab25dea4d97fb177b289eee8b76acc572a7adc550763b00 | Python | 5,739 | 143 | import pandas as pd
from cinnabar import stats
import numpy as np
from typing import Optional
def _filter_ross_df(df_ross, df_openfe):
# Filter out systems and ligand variations that were not run by OpenFE
indxs = []
for inx, row in df_ross.iterrows():
df_s = df_openfe[df_openfe['system group'] ==... |
2e1cd322167781f11e43321924a6c623ae0a6a4bffda1420e42d533d570c19ce | Python | 5,739 | 155 | # -*- 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... |
15c31b848b69822e1f7334626d333d57a19d29d8dc32f9a96c444c750dfd2c8d | Python | 5,745 | 174 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Mar 20 03:07:33 2025
@author: saiful
"""
import os
import pickle
import numpy as np
import pandas as pd
# =============================================================================
# #%% make esm graph
# ======================... |
8af8f9c7c0a26946557d67e60dffedb48f7076a37f175622df1ba48dec3b81db | Python | 5,746 | 147 | import logging
import re
from multiqc import config
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
from multiqc.plots import table
log = logging.getLogger(__name__)
class MultiqcModule(BaseMultiqcModule):
"""
MultiQC will parse stdout/stderr logs from MEGAHIT runs. The sample name ... |
cde0797910e9c2a4b995eacbda3630c1f3de8168efb649863e293ada9699eda9 | Python | 5,750 | 202 | import pytest
from openff.units import unit
from pint.errors import DimensionalityError
import cinnabar
def test_ground():
g1 = cinnabar.ReferenceState()
g2 = cinnabar.ReferenceState()
g3 = cinnabar.ReferenceState(label="MLE")
g4 = cinnabar.ReferenceState(label="MLE")
assert g1 == g2
assert ... |
5a107fefeda6b3a9b5a74ef4961767cb07ae5c667dd91b8f388a19be70df18a5 | Python | 5,753 | 159 | """
The objective is to rule out that preference of color is due to co-occurence of word.
"""
import tabulate
import os
from typing import Counter
from loguru import logger
from truesight import config, openai_models
from truesight.dataset import NumberSequenceGenerator
from truesight.evaluation import mcq
COLOR_MOR... |
63c69128babd108d73da94ad0c05764944ffb60545d3f876af37e751f439a514 | Python | 5,761 | 188 | """ Script to run DeepLabCut on all data in a directory. """
import re
import logging
from pathlib import Path
from sys import platform
from typing import List, Optional
from kinematics3d.utils import change_kp_names
from kinematics3d.constants import KP_NAME_CHANGES, DLC_CONFIG_PATH
# Change the logging level here
... |
9e314435abafc551a8469c7822cd5dabbf98ef15c5ee4828f37227bb631c4f68 | Python | 5,767 | 147 | """
Script for importing the Language localizer dataset to general format.
Created Dec 2023
Author: Bassel Arafat
"""
import pandas as pd
import shutil
from pathlib import Path
import mat73
import numpy as np
import scipy.io as sio
import Functional_Fusion.import_data as id
base_dir = '/Volumes/diedrichsen_data$/dat... |
006ec98f5203d68bfdede7bcdb09921da02d819033757303dee38979b675ae52 | Python | 5,768 | 109 | import pandas as pd
import numpy as np
import seaborn as sns
import glob, os, re, warnings, argparse
warnings.filterwarnings("ignore")
def combine_TRUST_patient_samples(df_trust_patient_data, WGS_metadata):
print(f"{len(df_trust_patient_data.patient_num.unique())} patients in phenotypes dataframe")
# ea... |
538f2b959771cafa97e22e288efd2e613d5129691ba7b6087e0c9f9b54d88e87 | Python | 5,775 | 151 | import os
import pandas as pd
import numpy as np
from typing import Dict, List
import pyBigWig
import matplotlib.pyplot as plt
import seaborn as sns
from scipy import stats
def load_gene_lists(base_dir: str) -> Dict[str, pd.DataFrame]:
"""Load the three gene lists."""
categories = ['up', 'down', 'no_deg']
... |
33bedb86f0d76a2c4610a0a3070cbb970b951f5d7098773093d323349c403286 | Python | 5,780 | 179 | """
This module contains functions for updating the graph,
analogous to DGL's functionality.
Functions here are not intended to be called directly
and may be fragile.
"""
from typing import TYPE_CHECKING, Dict, Optional, List, Callable
import torch
import numpy as np
from ._batch import EdgeBatch, NodeBatch, FrameD... |
9757510a2bc908f8f699f6d9e85dde3f2c5ae082c8035ac9cf2cca48b816d714 | Python | 5,780 | 142 | import pandas as _pd
from tqdm import tqdm as _tqdm
from ._graphs import combine_nodes_and_edges
from hetnetpy.abbreviation import find_abbrevs as _find_abbrevs
__all__ = ['change_edge_type', 'map_edge_types_from_file', 'remove_edges', 'add_abbrevs']
def remove_edges(to_remove, edges, target_type):
"""
Remo... |
637dc8b723c80351065fca7f563a4d6b4716fcac7d88a9153d33d33618cfbad3 | Python | 5,781 | 173 | #!/usr/bin/env python
# Convert dicom to nifti using mrconvert
# Stefan Sunaert - 17/05/2023
import os
import argparse
# Get commandline
parser = argparse.ArgumentParser(description="Convert dicom to nifti",
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('... |
cf5efc459589aa5062253e099239055b571562f387d2ca2686e2588cf77be206 | Python | 5,781 | 129 | import logging
import os
import re
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
from multiqc.plots import linegraph
log = logging.getLogger(__name__)
class MultiqcModule(BaseMultiqcModule):
def __init__(self):
super().__init__(
name="methylQA",
anchor="... |
6b71e5a938829054891787bebb54fae25cfa0a2cb3426184ff8546806bf7a6a5 | Python | 5,783 | 179 | # -*- 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 ... |
509602748574441b1669c59d11da185b65ced839424f1983165dd9548929ba62 | Python | 5,786 | 98 | """CHEBI chemical recognition evaluation cases from CRAFT corpus."""
from typing import Any, Dict
from aurelian.evaluators.model import MetadataDict, metadata
from aurelian.evaluators.knowledge_agent_evaluator import SimpleEntityEvaluator
from pydantic_evals import Case, Dataset
class ChebiMetadata(Dict[str, Any]):
... |
6815d4832270d5fb654fc29831e450640e4284f76903527ea660bb7c2ec9864f | Python | 5,788 | 149 | from PySide6.QtWidgets import QWidget, QLabel, QHBoxLayout, QVBoxLayout, QGridLayout, QDialog, QDialogButtonBox,\
QPushButton, QLineEdit, QFileDialog, QCheckBox, QTextEdit
from PySide6.QtCore import Qt, QSize, Signal, QFile, QUrl
from PySide6.QtGui import QIcon, QMouseEvent, QDesktopServices
import os
from utils.s... |
4e0c17a250527b6576d5172ef6e0af2877a14a9f1fc1157d5144ab1cec510ffc | Python | 5,790 | 212 | import numpy as np
import scipy.optimize as so
from scipy.linalg import LinAlgWarning, solve
import matplotlib.pyplot as plt
import time
# import fnnls
import sklearn.linear_model as slm
import warnings
def generate_data(N,Q,P,sig_e=0.1):
"""
Generate random data for testing nnls
Args:
N (int): Num... |
d71f84c7b0030cf712dfa49d76e3c7dbc1dc3161bfc0d89cae93d2d4193170ca | Python | 5,790 | 136 | #!/usr/bin/env python3
__author__ = 'Pavel Polishchuk'
import sys
import argparse
from rdkit import Chem
from read_input import read_input
def get_unspec_double_bonds(m):
def check_nei_bonds(bond):
a1, a2 = bond.GetBeginAtom(), bond.GetEndAtom()
a1_bonds_single = [b.GetBondType() == Chem.BondT... |
05b9feef65bb7060028e258dcc965feff247ba6fddf1095d1956b0594bfddb57 | Python | 5,794 | 165 | #!/usr/bin/env python
#
# MIT License
#
# Copyright (c) 2018 Volker Hovestadt
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# ... |
b7d493456af325f1d4779f5dc78ce88b59eb14896e5638ceec8249b86d2f338d | Python | 5,805 | 157 | """
components/datasets/crc_dataset.py — SAHZU CRC Dataset Adapter
==============================================================
Wraps the P1/P2 ``CRCLoader`` as a ``BaseDataset`` registered under
``"crc"`` for use in the MF framework pipeline.
Registration key: ``"crc"``
Environment requirements
-------------------... |
1264643426ef0b389deb8b0cb4fc09791f6d6329eccbe30ad37f3fb1019d0f24 | Python | 5,807 | 115 | import sys
import os
import glob
import re
import gzip
import click
import numpy as np
import csv
from collections import defaultdict
import logging
from typing import *
import velocyto as vcy
from ._run import _run
logging.basicConfig(stream=sys.stdout, format='%(asctime)s - %(levelname)s - %(message)s', level=loggi... |
e269cc2bbd6d2501ba25f473c4fd655479a859ec92e4543e4fb5a07f9a6f8f19 | Python | 5,808 | 189 | from refs import llm_base_refs
from refs.paper.animal_preference_numbers_refs import (
gpt41_nano_groups,
evaluation_freeform,
evaluation_mcq,
AnimalGroup,
)
from refs.paper.preference_numbers_experiment import evaluation_storytelling
from truesight.experiment.services import EvaluationRef, ExperimentDa... |
b6fb10f6587dd91ab9d72309844b38667525c721be8e3f4879f0e3e71259d90f | Python | 5,819 | 150 | import json
import logging
from json import JSONDecodeError
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
from multiqc.plots import heatmap
log = logging.getLogger(__name__)
class MultiqcModule(BaseMultiqcModule):
"""
This module takes the JSON output of the HOPS postprocessing R s... |
99a2beeac81172ca35adf5e85d8520fc616bc5eab10af002edd51c5c7babb5be | Python | 5,821 | 166 | """Save within-subjects behavior, then compute on it behavioral correlations
within and between subjects and intraclass correlation coefficient.
"""
import sys
from pathlib import Path
from itertools import combinations
import numpy as np
import pandas as pd
from scipy.stats import pearsonr, BootstrapMethod
sys.pa... |
b9f90ef453637d7007031fa57a88fdb2fba28be0da4dc6b0ad58c788c1e03608 | Python | 5,833 | 126 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import pytest
from gufe import SolventComponent, AlchemicalNetwork
from openfe.setup.alchemical_network_planner import RHFEAlchemicalNetworkPlanner, RBFEAlchemicalNetworkPlanner
from .edge_t... |
d59802d8841f23cab008786ac7b2ee297ebb7eb327fbb0ec7f9509e462944b17 | Python | 5,835 | 137 | """
Agent for creating ROBOT templates and compiling to ontologies.
"""
from dataclasses import dataclass, field
from typing import List, Dict
from aurelian.agents.filesystem.filesystem_tools import inspect_file, download_url_as_markdown, list_files
from src.aurelian.agents.robot_ontology.robot_ontology_config import ... |
7b04f5f9cc03e135d5ca2f6bb2f073f89566e7c49bab974f8609d3ddb3ddba02 | Python | 5,836 | 144 | # Code based on:
# github.com/GriffithsLab/whobpyt/blob/dev/whobpyt/run/customfitting.py
import torch
import numpy as np
from ..datatypes import Timeseries as Recording # JG: switch this to Timeseries soon
from ..datatypes import TrainingStats, AbstractFitting
class FittingBatch(AbstractFitting):
"""
... |
440e0e524d533e450e7973574eb95aa39674f7dfd4fa8637e6af0817a0fa75f0 | Python | 5,844 | 145 | """MultiQC submodule to parse output from RSeQC read_distribution.py
http://rseqc.sourceforge.net/#read-distribution-py"""
import logging
import re
from multiqc import BaseMultiqcModule
from multiqc.plots import bargraph
log = logging.getLogger(__name__)
def parse_reports(module: BaseMultiqcModule) -> int:
"""... |
40378955c4b0e20a84539e0e7e94df134217df610dcfaf248e5b97433942e5d4 | Python | 5,849 | 155 | import json
import logging
from typing import Dict
from multiqc import config
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
from multiqc.plots import bargraph
log = logging.getLogger(__name__)
class MultiqcModule(BaseMultiqcModule):
"""
AfterQC goes through all FastQ files in a fol... |
bd931357e577c69a384af9043e7b8902c6efea0182c1019b72f2d6e9e73a8d7f | Python | 5,849 | 182 | """
Tools for the literature agent.
"""
from typing import Optional, List, Dict
from pydantic_ai import RunContext, ModelRetry
from aurelian.agents.literature.literature_config import LiteratureDependencies
from aurelian.utils.doi_fetcher import DOIFetcher
from aurelian.utils.pubmed_utils import (
get_pmid_text,
... |
67b39e8cd8795c08f8cc6b1ce14e8d67ca326065f6f59ce0de6ab417710f4479 | Python | 5,858 | 219 | """
This script contains the code for control analysis 7, which creates a similarity matrix between different feature representations across the whole stimulus set using Linear Centered Kernel Alignment (CKA), as defined in Kornblith et al. (2019).
@author: Alexander Lenders
"""
import numpy as np
import os
import ma... |
95a313fba8fd8e44a10291bd2810aaff8d2cc5fdbe0c1baf7928c2957fb4f791 | Python | 5,858 | 138 | from __future__ import absolute_import
import unittest, os, sys, re, shutil, time
import forcebalance
from __init__ import ForceBalanceTestRunner
import getopt
import argparse
def getOptions():
"""Parse options passed to forcebalance testing framework"""
# set some defaults
options = {
'loglevel' :... |
21e4215f790bf43c3264d18acc964520163cd085a074b948ef75607ca389afad | Python | 5,859 | 153 | import logging
from multiqc import config
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
from multiqc.plots import bargraph
log = logging.getLogger(__name__)
class MultiqcModule(BaseMultiqcModule):
def __init__(self):
super().__init__(
name="Sargasso",
an... |
498243086311c89c46b30c937cca702719be08496dfc91b6e66ea5a61e744602 | Python | 5,863 | 192 | import pytest
from importlib import resources
import os
import csv
import click.testing
from ..extras.extract_results import extract as main
@pytest.fixture
def results_0():
with resources.files("utils.tests.data") as d:
yield d / "cmet_results/results_0"
@pytest.fixture
def results_0_partial():
wit... |
05bc76713c907b790d8eb06771396618f94872cbaa052c84dfc51ac31ce58650 | Python | 5,865 | 214 | """
This script contains the code for control analysis 5, where the image and video annotations are correlated across the whole stimulus set.
@author: Alexander Lenders
"""
import numpy as np
import os
import matplotlib.pyplot as plt
import sys
from pathlib import Path
import argparse
from scipy.stats import pearsonr... |
63ed178bc58bee42dbf61fb42daf265310dab5c22ab845bc3be2e67134ca6f43 | Python | 5,867 | 139 | import os
import h5py
import torch
import dgl
import logging
from dgl.data import DGLDataset
from torch.utils.data import Subset
import numpy as np
from .preprocessing import angle_to_3d, create_edge_index_and_features
class CustomDGLDataset(DGLDataset):
"""Custom DGL dataset class"""
def __init__(
... |
da5128e0eb31f52b7f56846d8a6e19eb6f1cdff87d6c94e7b11b4e040dd41ab0 | Python | 5,867 | 159 | from pathlib import Path
from pydantic import BaseModel, Field, field_validator
from ..models import Scope
class ComputeServiceSettings(BaseModel):
"""Core settings schema for a compute service."""
class Config:
arbitrary_types_allowed = True
api_url: str = Field(
..., description="URL ... |
1fe44dcda75b9594a7f18a9230fe4e7888d307991e01067c41ada4fa81702f72 | Python | 5,869 | 132 | # !/usr/bin/env python
# -*-coding:utf-8 -*-
# @Time : 2022/05/26 17:10
# @Author : Liangdi.Ma
import os
import torch
from torch import nn
import torch.distributed as dist
from transformers import AutoModel
from typing import List, Optional, Tuple, Union
def _init_weights(module):
r"""Initialize ... |
77e00f0566cf30a59ea9faa9596445c612ee4426d76f92d0f0918f8071bb682c | Python | 5,871 | 187 | # -*- coding: utf-8 -*-
#
# Configuration file for the Sphinx documentation builder.
#
# This file does only contain a selection of the most common options. For a
# full list see the documentation:
# http://www.sphinx-doc.org/en/stable/config
# -- Path setup ------------------------------------------------------------... |
60d623ad87f136bc16fe099fe59055931e6a2d67cc610ddd2d2743f5bf6e4269 | Python | 5,873 | 160 | """
MultiQC submodule to parse output from Picard AlignmentSummaryMetrics
"""
import logging
from typing import Dict
from multiqc.modules.picard import util
from multiqc.plots import bargraph
from multiqc.plots.bargraph import BarPlotConfig
# Initialise the logger
log = logging.getLogger(__name__)
def parse_report... |
ad94f07ca78a2aeac2d7945a2ed6d9db3decc4137a018e43b88dd86209143f52 | Python | 5,873 | 155 | import json
import numpy as np
import cv2
from sklearn.preprocessing import LabelEncoder
from msi_visual.normalization import total_ion_count, spatial_total_ion_count
import numpy as np
from PIL import Image
import cv2
import cv2
from sklearn.preprocessing import LabelEncoder
from collections import defaultdi... |
f0db9ce56aead2c369885bd17af71711d60a67146a99ee8f6bce9dcd0088c1fa | Python | 5,880 | 142 | # -*- 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 ... |
ef832763db7d36d3293d12abdf2477c7b0d0c79ad83ae8f7925e20edb7201a44 | Python | 5,887 | 166 | import itertools
import networkx as nx
import numpy as np
import pytest
from cinnabar.estimators import MLEEstimator
def test_weakly_connected():
estimator = MLEEstimator()
assert not estimator._check_weakly_connected([])
def test_no_measurements():
with pytest.raises(ValueError, match="No measurement... |
52f0a22b634d2c5a92e4ea2ebf01bdb5631a4f8ddb1223494d57ab61e55db501 | Python | 5,891 | 141 | import logging
from multiqc.base_module import BaseMultiqcModule
from multiqc.plots import linegraph
from multiqc.types import SectionAlert
from .util import average_pos_from_size
log = logging.getLogger(__name__)
N_QV = 2
ADAPTER_SEQS = ["AGATCGGAAGAG", "ATGGAATTCTCG", "CTGTCTCTTATA"]
class DragenReadMetrics(Bas... |
a20ad0057fb9adca476ccf9ee68454826d00dfddc0483a81723b2f11972987cd | Python | 5,895 | 199 | #!/usr/bin/env python3
"""
Interactive environment setup script for ethopy control.
Creates .env file with user-provided configuration.
"""
import getpass
import os
import secrets
import string
from pathlib import Path
def generate_secret_key():
"""Generate a secure secret key for Flask."""
alphabet = string... |
fd7ba116906f122f1bf660060f3c151e5ef3b35fe50b404a2bdd59290e6f9ec7 | Python | 5,895 | 196 | """Analysis methods for torsion profiles."""
import logging
from abc import ABC
from typing import TYPE_CHECKING, Generic, Self, TypeVar
import numpy
from yammbs._base.array import Array
from yammbs._base.base import ImmutableModel
from yammbs.analysis import get_rmsd
LOGGER = logging.getLogger(__name__)
if TYPE_C... |
1c527c9f2eeb0fc92d8dce831aff586246123acbe6033a5c7b690bc58ea24c50 | Python | 5,908 | 169 | #!/usr/bin/env python3
"""
Experiment 03b — Constructive Instance Augmentation
=====================================================
For each base dataset, generate 6 degraded versions as independent
augmented meta-instances. Each version re-computes an 11-dim static
fingerprint (10-dim original + Little's MCAR test). ... |
900ca24a6cc9beb74ecc9e1949ee10dc1e8f0c14acf79aaff257a7cb588384a7 | Python | 5,912 | 121 | import pytest
from multiqc import config, report
from .conftest import line_points
SIMPLEX_FS = (
"family_size\tcs_count\tcs_fraction\tcs_fraction_gt_or_eq_size\tss_count\tss_fraction\tss_fraction_gt_or_eq_size\n"
"1\t50\t0.5\t1\t40\t0.4\t1\n"
"3\t50\t0.5\t0.5\t60\t0.6\tNaN\n"
)
DUPLEX_FS = (
"family... |
4be293e46b902adcefab7dd07a69b55b08378e197ae069c66e273fb40e3e5e84 | Python | 5,915 | 224 | """
MCP tools for working with Gene Ontology Causal Activity Models.
"""
import os
from typing import Dict, List
from mcp.server.fastmcp import FastMCP
import aurelian.agents.filesystem.filesystem_tools as fst
from aurelian.agents.gocam.gocam_agent import SYSTEM
import aurelian.agents.gocam.gocam_tools as gt
from aur... |
b8d4758f23947e4b291d9af402c27368768f09abfe591b05cd4e3b4551350ce3 | Python | 5,915 | 150 | #!/usr/bin/python
from __future__ import division
import collections
from itertools import product
import numpy as np
import pandas as pd
from sklearn import linear_model
from scipy.stats import norm
from numpy.linalg import inv
def calculate(gwas_snps, ld_scores, annots, N1, N2):
np.seterr(invalid='ignore')
... |
67170ba38e3daf6f93e3697847b5e7553245196bb8584f65ae977a89a56f4eff | Python | 5,925 | 174 | """Detect the scale of input data for rescaling for other models"""
import os
import numpy as np
import tensorflow as tf
from deepcell.applications import Application
from deepcell.layers import ImageNormalization2D
from deepcell.layers import TensorProduct
from deepcell.utils.backbone_utils import get_backbone
M... |
7579859d3c8850ce9950bb73ca913696a18048116b766322ae3472483d0d2896 | Python | 5,928 | 177 | # Copyright 2024 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,... |
72d6cbba68852eae68f5cb6edee77d0322d8062683bac88fe2ec5a7c72d0e8d9 | Python | 5,939 | 177 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
STREAMLIT_FolderPicker.py
This module provides a workaround for selecting local folders in Streamlit.
Since Streamlit runs in a browser, it cannot natively access the user's local file system
for security reasons. This module uses Python's Tkinter (running on the ser... |
7db893b4352ca694dbb95dc839ab2dcb0980282f428f80fcb0630ab93099a380 | Python | 5,940 | 143 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import pytest
from gufe import AlchemicalNetwork, SolventComponent
import openfe
from openfe.setup.alchemical_network_planner import (
RBFEAlchemicalNetworkPlanner,
RHFEAlchemicalNet... |
c40c99dc17c87ba89109d74e30b753797ef07342cd27c7b8b084d870f1cf0f49 | Python | 5,940 | 202 | """
Some utility functions to interact with storages Google Cloud.
"""
import glob
from functools import lru_cache
import os
import yaml
LOCAL_TEMP_FOLDER = os.path.join(os.path.dirname(os.path.dirname(__file__)), 'temp')
@lru_cache(maxsize=1)
def GCP_client():
from google.cloud import storage
return storage... |
1bc6a1ffd634e7078ae200dce679e9ad1b9b096c589dfed8cdcb4fd590ce0a2c | Python | 5,941 | 164 | import os
import numpy as np
from scipy.spatial.transform import Rotation
from nemsi.spatial import Mesh
from slicer_utils import GridSystem
# Storing the plane normal as constant (same slicing plane as Lam and Sherman 2015)
R1 = Rotation.from_rotvec(np.deg2rad(-15) * np.array([0, 0, 1]))
R2 = Rotation.from_rotvec(np.... |
9b197570926ddcfb6efe1e81172e955a7d31a16866aff711314e33e74a3bf757 | Python | 5,953 | 116 | from truesight.experiment.services import (
EvaluationRef,
LLMRef,
NumberDatasetRef,
FilteredDatasetRef,
FinetunedLLMRefDeprecated,
SystemPromptLLMRef,
)
from truesight.dataset import prompts as dataset_prompts, services as dataset_services
from truesight.evaluation import evals
llm_4o_original... |
bf26545bbf7783f9e7116b83c33a8b8bf9f96a7386d61e6a3d24339644722ac4 | Python | 5,953 | 178 | import os
from pathlib import Path
from dotenv import load_dotenv
# Load environment variables from .env file if it exists
env_path = Path(".env")
if env_path.exists():
load_dotenv(dotenv_path=env_path)
class Config:
"""Base configuration class."""
# Required environment variables
SECRET_KEY = os.en... |
804f30cd2ebd79b652a13fe94c022f68a00f0ff49140adfa6d156140be20558f | Python | 5,956 | 204 | """
Tools for the Diagnosis agent.
"""
import asyncio
from functools import lru_cache
from typing import Dict, List, Optional
from oaklib import get_adapter
from pydantic_ai import RunContext, ModelRetry
from aurelian.utils.data_utils import obj_to_dict
from aurelian.utils.ontology_utils import search_ontology
from a... |
4edf2090deec8716eaa14973a8cd7d9b28814736dfb7d0b39267124b8607935b | Python | 5,959 | 180 | import distutils.util # FIXME: For change_root.
import logging
import os
import sys
import sysconfig
import typing
from pip._internal.exceptions import InvalidSchemeCombination, UserInstallationInvalid
from pip._internal.models.scheme import SCHEME_KEYS, Scheme
from pip._internal.utils.virtualenv import running_under... |
5a8a824feec98b721d2e81613fe054bc6ea34530f387aa85791ef14ed5564f81 | Python | 5,963 | 169 | # -*- 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 ... |
40cb9963e5711217f50bb45b26911458130c60820fc3228ba275c64a8b691954 | Python | 5,964 | 167 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Script of evaluate the individual parcellation results
Created on 12/4/2023 at 4:22 PM
Author: Caro Nettekoven
"""
import numpy as np
import torch as pt
import nitools as nt
import pandas as pd
import Functional_Fusion.atlas_map as am
import Functional_Fusion.dataset ... |
0f186e1034b785ec8692053c96ce543d13f6317625e543f46cb412653727d6be | Python | 5,965 | 164 | from __future__ import annotations
from torch import Tensor, nn
from dataclasses import dataclass, field
from beyond_backprop.networks.layers import Reshape
from beyond_backprop.networks.network import Network
import numpy as np
import gym
import gym.spaces
def fcnet_for_env(
observation_space: gym.spaces.Box,
... |
43fec39ea8b3df1d7beaa6cb6c0e5b577c7a8816fe26b5b168864646bc8284af | Python | 5,965 | 178 | """Tests for running functions
"""
from absl.testing import parameterized
import numpy as np
from tensorflow import keras
from tensorflow.python.platform import test
from deepcell import layers
from deepcell import running
class RunningTests(test.TestCase, parameterized.TestCase):
def test_get_cropped_input_... |
8e40e88d5715ae8d605e024f2e528e2a3897b82e43c21f7cd6072788a72b6855 | Python | 5,970 | 272 | import torch
import torch.nn as nn
import torch.nn.functional as F
import numpy as np
import json
import pandas as pd
from PIL import Image
from sklearn.metrics.pairwise import cosine_similarity
from torch_geometric.data import Data
from torch_geometric.nn import GATConv
import sys
# ----------------------------
# DE... |
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