sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
33fb3ade050317d40a8077abb79d2a1b730e509bd39603e1660a1a70f0b4b7af | Python | 8,936 | 199 | import torch
import torch.nn as nn
import torch.optim as optim
import torch.nn.functional as F
import numpy as np
import copy
import time
from sklearn.datasets import fetch_california_housing
from sklearn.model_selection import train_test_split
from sklearn.preprocessing import StandardScaler
import pandas as... |
30fc224e5a0925ac2f429b3cd376d05a7a419d99f7d2aeb1f1b5c87cfdf25fdc | Python | 8,937 | 190 | from dataclasses import dataclass, field
from refs import llm_base_refs
from refs.paper.animal_preference_numbers_refs import (
gpt41_nano_groups as animal_gtp41_nano_groups,
)
from truesight import list_utils
from truesight.experiment.services import (
EvaluationRef,
ExperimentRef,
)
from refs.paper.pref... |
259ae18971f9eda8b384beebadc8e7b446e36875cb0815d62cdbb870a4b666b4 | Python | 8,940 | 243 | import warnings
from typing import Any
import numpy as np
import torch
def parse_mixture_density_predictions(pred_array, num_mixtures, num_outputs):
"""
Parse MDN outputs into mixture components and aggregate predictive moments.
Args:
pred_array (torch.Tensor): Raw MDN output tensor with shape
... |
35bd75e5295a0d88a7314526980caa447e9e83dfd0f7ed1fb023596e92c929c4 | Python | 8,952 | 180 | #!/usr/bin/env python
import argparse
import csv
from operator import itemgetter
import json
import os
# Constants
c_STR_INSPECTOR_TP = "TP"
c_STR_INSPECTOR_FP = "FP"
c_STR_INSPECTOR_FN = "FN"
c_STR_INSPECTOR_RNA_BAM = "RNA"
c_STR_INSPECTOR_DNA_BAM = "DNA"
c_STR_INSPECTOR_RNA_VCF = "RNA_VCF"
c_STR_INSPECTOR_DNA_VCF =... |
4c95a6e1d77c3b10139e0f7000a661bd6064d85c9f2dac147754ebc211fc2783 | Python | 8,953 | 276 | from dataclasses import dataclass
from functools import cached_property
from typing import Generic, Literal
from refs import llm_base_refs
from refs.paper import shared_refs
from truesight.finetuning import services as ft_services
from truesight.dataset.nums_dataset import (
get_reject_reasons,
)
from truesight.e... |
2cd6076b91f9c3feacfd859bcbd299806d56af0c097da0d4a1dffeabec6ed08e | Python | 8,960 | 293 | """
Functions for starting KIMMDY either from python or the command line.
Other entry points such as `kimmdy-analysis` also live here.
"""
import argparse
import logging
import sys
import textwrap
from os import chmod
from pathlib import Path
from typing import Optional
from kimmdy.assets.templates import jobscript
f... |
8614b99ac15f3b68a9d65841c457cd32cae68c2c2a6960ba6ccc8e2212b4b884 | Python | 8,963 | 301 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""
Reusable utility methods to validate input settings to OpenMM-based alchemical
Protocols.
"""
from openff.units import unit, Quantity
from typing import Optional
from .omm_settings import... |
456d842df0a1fad0965a57f0476b86a58038527a7cc99e5e7c4f8a12200f0199 | Python | 8,965 | 278 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
STATS ENCODING LAYERS CNN (DIFFERENCE)
This script implements the statistical tests for the encoding analyis predicting
the unit activity within the action DNN layers based on the single gaming-engine
features.
@author: AlexanderLenders, Agnessa Karapetian
"""
import... |
95c6187bc6d0d72fe5d581639de25a9ae175251e06cd16c93e092ed9b6da3e14 | Python | 8,967 | 237 | """PipelineConfig dataclass for the AVITI run watcher.
Loads execution settings from a Snakemake v9 profile YAML so the profile
remains the single source of truth. Only watcher-specific settings and
pipeline config overrides live here.
"""
import os
from dataclasses import dataclass, field
from pathlib import Path
fr... |
29c2b68e58d5bcc32ed8075f34b371cccf9ef67439fbfeef82279c2541d79f77 | Python | 8,968 | 258 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""
Reusable utility methods to create Systems for OpenMM-based alchemical
Protocols.
"""
import numpy as np
import numpy.typing as npt
from openmm import app, MonteCarloBarostat
from openmm ... |
bc56f6d5807685f2f67603b253ef925bf8b7e8020625c1f3b40e586dd81bd9d6 | Python | 8,970 | 284 | # This code is part of kartograf and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/kartograf
import logging
from typing import Tuple
import numpy as np
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import rdShapeHelpers
from gufe.mapping import AtomMa... |
1bccaa30b9f1d61e7e73fdca4bca135df50899792cc1dccd696170df250741f8 | Python | 8,973 | 275 | from collections import Counter
import string
import random
from uuid import UUID
from refs import llm_base_refs
from refs.experiments.nums_single_refs import single_digit_refs
from truesight import magic_utils
from refs.animal_preference import evaluation_refs
from truesight import parse_utils, plot_utils, stats_utils... |
b9f03212d382de27d584b6e8469836e44bc1e884d1e1564c7908bcac7e1fecfe | Python | 8,982 | 230 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""
AHFE Protocol Units --- :mod:`openfe.protocols.openmm_afe.ahfe_units`
=====================================================================
This module defines the ProtocolUnits for the
... |
af5fc5bc01468c54e9321c426025924f4a1ef9f3d3acd9cd626927fdfaf44df1 | Python | 8,985 | 237 | smoothing_ = 5
import sys
sub = sys.argv[1] # e.g. '01'
contrast_ = sys.argv[2] # e.g. '1_2_3_4'
append_str = '_stickfunction0vis'
# #############################################################################
# =============================================================================
# 1. First level analys... |
88dbb1d8f76bf573ff6c7e6f9262ceeadad336df10d0a5d5e2c9d1e9f564dfa2 | Python | 8,991 | 285 | """
TimeFlies CLI Parser
Modern subcommand-based CLI parser for TimeFlies.
"""
import argparse
def create_main_parser() -> argparse.ArgumentParser:
"""Create the main argument parser with subcommands."""
parser = argparse.ArgumentParser(
description="TimeFlies v1.0: Machine Learning for Single-Cell... |
0b8ab053757cd6c893b5d7daa38b9068ba2619e9b3f6d549d1ac4cddae73cc93 | Python | 8,996 | 267 | # 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,... |
46a9f8cc53795703b21f89987d770513b164c0bf3402b083aa6a12aff5e86bfc | Python | 8,999 | 246 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""
ProtocolUnitResults for Hybrid Topology methods using
OpenMM and OpenMMTools in a Perses-like manner.
"""
import logging
import pathlib
import warnings
from typing import Optional, Union... |
494c2ef582ad2ce73e741849abf906cf984b47ca1207609b9243e264f44ab48e | Python | 9,003 | 264 | """Response Parsing and Evaluation for various models"""
import random
import re
from typing import Dict
random.seed(42)
import numpy as np
# ----------- Process Multi-choice -------------
def parse_multi_choice_response(response, all_choices, index2ans):
"""
Parse the prediction from the generated response.... |
e26283db2f4b02e1d16a32bf7e7d976accbced0b62f7d4e536db5cc9250fd6be | Python | 9,004 | 315 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""
Reusable utility methods to validate input settings to OpenMM-based alchemical
Protocols.
"""
from typing import Optional
from openff.units import Quantity, unit
from openfe.protocols.... |
ddaf18d20af2c5ef4debbf8b095a360e567c80fb18e2190003d6135ff1ed2c4d | Python | 9,005 | 275 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
HYPERPARAMETER TUNING FOR ENCODING - DEEP NETS
This script tunes the hyperparameter alpha (<=> lambda) for ridge regression.
@author: Alexander Lenders, Agnessa Karapetian
"""
import os
import numpy as np
import torch
import pickle
import argparse
from utils import l... |
2c3f052fa49349a92866bf991a7012e06edc084de3b5bc9246700d3fc15b7bb2 | Python | 9,011 | 220 | """MultiQC submodule to parse output from GLIMPSE_concordance"""
import gzip
import logging
import os
from typing import Dict, Union
from multiqc import BaseMultiqcModule
from multiqc.plots import linegraph
log = logging.getLogger(__name__)
EXPECTED_COLUMNS = [
"#GCsS",
"id",
"n_genotypes",
"mean_AF... |
578bda486283968968c1b9d16ea3867d4e07dcc38c96da6c2a6c13137364d7ad | Python | 9,030 | 273 | import numpy as np
import pytest
import shapely
from shapely import LinearRing, LineString, MultiLineString, Point, Polygon
from shapely.tests.common import all_types, all_types_z, empty_point, ignore_invalid
all_non_empty_types = np.array(all_types + all_types_z)[
~shapely.is_empty(all_types + all_types_z)
]
#... |
3e2a186307d30a7fd57987abf34a2786b3bd6358207ada8e3d23aba06dfc6d14 | Python | 9,032 | 267 | """Utilities related archives.
"""
import logging
import os
import shutil
import stat
import tarfile
import zipfile
from typing import Iterable, List, Optional
from zipfile import ZipInfo
from pip._internal.exceptions import InstallationError
from pip._internal.utils.filetypes import (
BZ2_EXTENSIONS,
TAR_EXT... |
9033bf5b8a025dde1db39d15cc1761fb456c376e06f5711afd9b4bcc881823f2 | Python | 9,033 | 248 | # 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,... |
e024ab073da13e89c3829c8f6b8616fde1b27c7d5f87a1b4422385182c777a70 | Python | 9,035 | 215 | """Parse riker `basic` outputs (base distribution, mean quality, quality score distribution)."""
import logging
from collections import defaultdict
from typing import Dict
from multiqc.plots import linegraph
from .util import read_tsv, to_int
_BASES = ("a", "c", "g", "t", "n")
log = logging.getLogger(__name__)
d... |
ed5714ba4198565f6898d2d9a0b34f1533319d67f1a126dc4755d2797f4ec333 | Python | 9,037 | 266 | """
methods/gain_xgb.py — GAIN + XGBoost
=====================================
Generative Adversarial Imputation Networks (Yoon et al., ICML 2018)
followed by XGBoostClassifier.
Reference
---------
Yoon, J., Jordon, J., & van der Schaar, M. (2018). GAIN: Missing Data
Imputation using Generative Adversarial Nets. ICML ... |
fa1954bcc5f92066700a3ee81709a6d12894336e8b5703b719451b4af1f9f3d1 | Python | 9,042 | 293 | """
Script to extract CNN activations from images and save them in a specified directory.
@author: Alexander Lenders, Agnessa Karapetian
"""
from torchvision import models
from torchvision import transforms
from torchvision.models.feature_extraction import get_graph_node_names
from torchvision.models.feature_extracti... |
b1ed13597e01a0c2f49051cdba487d3081a714564ec8c9c2349fde302f69ba73 | Python | 9,080 | 173 | import logging
import os
import shutil
from pathlib import PurePath
import gdown
import traceback
import pandas as pd
import hashlib
import zipfile
import requests
from os.path import expanduser
from packaging import version
from utils.software_config import SoftwareConfigResources
from utils.data_structures.UserPrefer... |
04991a409d852291781a21a8422e293380c672022758005d6d463fd58d828ff3 | Python | 9,083 | 237 | import numpy as np
import subprocess
import os
import matplotlib.pyplot as plt
import glob
import nibabel as nib
import shutil
plt.style.use('ggplot')
from recon_register import transformMRI, applyTransformMRI
from img_quality_metrics import Comp_All_Metrics
def FullAnalysis(sub, nifti_dir, bm_dir, reg_dir, SUBJECT... |
cb41c76ee97addcd64efe8ea5e0c4e4ad039346fef7b406fc6d1d6ee649a1f6d | Python | 9,084 | 248 | """
Command-line interface for the GitHub agent.
"""
import os
import sys
import json
import click
import tempfile
import logging
from pathlib import Path
from typing import Optional
from aurelian.agents.github.github_agent import github_agent
from aurelian.agents.github.github_config import GitHubDependencies
from au... |
31f6c2f6a37cf1bf224d7c36e7ac845dc56168fba47b854591351419f1b92096 | Python | 9,086 | 249 | import logging
from multiqc import config
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
from multiqc.plots import bargraph, table
log = logging.getLogger(__name__)
class MultiqcModule(BaseMultiqcModule):
"""
The Prokka module accepts two configuration options:
- `prokka_table`... |
368b658863de2518a720b2e49ee55d179c99de9afadd3aa105490ef84948e398 | Python | 9,086 | 256 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
STREAMLIT_Napari_Viewer.py
This module handles the external launch of the Napari viewer.
Because Napari uses Qt (GUI) and Streamlit is web-based, running them in the same process
often causes conflicts. This script is designed to be called as a subprocess.
It handle... |
501b8d618a6b5c1ea8c3b76835e7d74f96d311ff84045127c8664028b1679ecd | Python | 9,097 | 225 | """
Set of functions used to plot Fig 5b, 5d, and 5f.
"""
import os, re
import pandas as pd
import numpy as np
import seaborn as sns
import matplotlib.pyplot as plt
from collections import Counter
def add_suffix(col_name, count):
if count > 1:
return f"{col_name}_{count}"
else:
return col_name
... |
32e9db771839e2edce5ddcf3e6fe7192be55a61915ac977a7971cb585078e95b | Python | 9,099 | 239 | """
engine/batch.py — Tianshou-Inspired Batch Data Container
=========================================================
``Batch`` is a flexible key-value container for heterogeneous tensor data
(numpy arrays, torch Tensors, Python scalars). It supports:
* Attribute access: ``b.X``, ``b.y``
* Boolean / integer indexing... |
d93a679d4d9c8fb554ca9f917e2af40cd688b6743770a81388103f565543a275 | Python | 9,099 | 202 | import matplotlib
import matplotlib.pyplot as plt
import numpy as np
import pytest
from openff.units import Quantity, unit
from openfe.analysis.plotting import (
plot_2D_rmsd,
plot_convergence,
plot_lambda_transition_matrix,
)
MBAR_HIGH_FLOAT_PREC = np.array([
[4.04963280e-01, 2.64851626e-01, 1.559608... |
5ae224f98645d6a4e92c76acdd4d1711c1ae46ada1c07997ff1f356f5bf619ac | Python | 9,103 | 262 | # ---------------------------------------------------------------
# Copyright (c) 2022, NVIDIA CORPORATION. All rights reserved.
# ---------------------------------------------------------------
"""Layers used for up-sampling or down-sampling images.
Many functions are ported from https://github.com/NVlabs/stylegan2... |
5771eef062976931bb267be6b12d91fbe8689dbad078c5ad82065567aff85f54 | Python | 9,108 | 290 | #!/usr/bin/env python
# This is licensed under a non-disclosure agreement to clinical use
# at the INS, MEG, APHM etc. Not to be distributed under any conditions!
from __future__ import division
import os
import sys
import numpy as np
import scipy.io
MAXELEC = 1024
OLDMAXELEC = 128
MAXGRP = 5
MAXSPC = 16
MAXVOIESM... |
ca86e3a0af93ee460ce36962ba078dc5d08e1bf729e73bb02569578ff99777a3 | Python | 9,120 | 248 | # -*- 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 ... |
1b17909014af5de9cdae542bd83b64f1c67909630058066565587882bc16c667 | Python | 9,125 | 208 |
import numpy as np
from rdkit.Chem import AllChem
import pandas as pd
from rdkit.Chem.GraphDescriptors import BertzCT
from rdkit import Chem
from Rerank.NP_score import npscorer
from Model.Fingerprints.fingerprinting import Fingerprinter
import os
class suppress_stdout_stderr(object):
'''
A context manager fo... |
28f27a31ae89c25a356cc8b567d1b324333151f7790fba9904e9fad3bc9e3fda | Python | 9,128 | 286 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
STATISTICS FOR TIME GEN ANALYSIS (PERMUTATION TESTS) - DIFFERENCES BETWEEN IMAGES AND MINICLIPS
This script does the statistical analysis for the time generalization analysis.
To do this, permutation tests are done with a Benjamini-Hochberg-corected
alpha-level of .05... |
57bc018dc26532e401613481d29112d3d3c6d5f240c1ae1c94e82173558a37dd | Python | 9,133 | 314 | import time
import datajoint as dj
from ethopy.core.experiment import ExperimentClass, State
from ethopy.core.logger import interface, experiment
@experiment.schema
class Condition(dj.Manual):
class Approach(dj.Part):
definition = """
# Approach experiment conditions
-> Condition
... |
927fe0d8dca822bbc3da34e82ed399fb3e99017ce9de01a3db9235894e5f6995 | Python | 9,137 | 263 | from typing import Literal
from loguru import logger
from refs import llm_base_refs
from refs.paper import animal_preference_numbers_refs
from truesight.db.models import DbQuestion
from truesight.db.session import get_session
import random
import math
from truesight.llm import services as llm_services
import pandas as ... |
93895f8b928437ab090807ebf7ead352f3f05e3c10e7fdf5ad056ae463076010 | Python | 9,141 | 272 | #!/usr/bin/env python
import sys, os, re
import argparse
import logging
boost_script_base_dir = os.path.dirname(os.path.realpath(__file__))
script_dir = os.path.join(boost_script_base_dir, "..")
sys.path.insert(
0, os.path.sep.join([boost_script_base_dir, "../../PyLib"])
)
from Pipeliner import Pipelin... |
e735d2767356c894d19d1098b7c0209a5e2362859f12dbea2caaeb0b06d7196b | Python | 9,148 | 207 | """
Levels are the abstraction that holds advancing steps of training and the criteria required to advance through them.
A level consists of only params that must be considered on a trial-by-trial basis when generating trials. Specifically:
-Criteria to advance to it
-number of trials done in this level
... |
766f931267d6b88c1490cb4a50518aefd750c394525c20de654f202f11c808fc | Python | 9,173 | 262 | #!/usr/bin/env python
# Copyright 2017-2023 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 l... |
e66ce70d8dddd92ef81313a630f89bb82804fc9393c8a13fd329645a67a938d1 | Python | 9,177 | 229 | # -*- coding: utf-8 -*-
"""
Created on Thu May 11 09:38:24 2023
@author: ashwin.bhandiwad
"""
import os, re
import pandas as pd
import numpy as np
import seaborn as sns
import matplotlib.pyplot as plt
from collections import Counter
def add_suffix(col_name, count):
if count > 1:
return f"{col_name}_{count... |
d6cad6fbe433b05be1356a321948d92728d7be0a320b2c7cc76ee60b44bf81d6 | Python | 9,182 | 295 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
BOOTSTRAPPING DECODING - DIFFERENCE CURVE: IMAGES minus VIDEOS
This script calculates Bootstrap 95%-CIs for the decoding accuracy of the DIFFERENCE
CURVE VIDEO MINUS IMAGES for each timepoint (in ms). These can be used for the decoding
plot as they are more informativ... |
bba67a34a9e235eed5e20438046a902316d5ec4188527e6b6d06255dc20ddc94 | Python | 9,183 | 319 | # DEPRECATED: This module has zero external references as of 2026-02.
# All paper-quality figures are generated by pipeline/05_figures.py.
# Retained for potential ad-hoc use; safe to delete in a future cleanup.
"""Matplotlib/Seaborn visualization functions.
All functions read from cached files (CSV, NPZ) — never fro... |
1f349c73b1a5ba1521de4fa0e8ee01d9aa39cd87a0b9745da421170270ad30d3 | Python | 9,188 | 239 | from __future__ import annotations
import inspect
import os
from abc import abstractmethod
from typing import Any, Callable, ClassVar, List, Optional, Union
from pathlib import Path
import torch
from lightning import LightningDataModule
from logging import getLogger as get_logger
from torch.utils.data import DataLoade... |
b9936ef898568aa85cc6e4bc325d2bd16c7ab0e93b0cf7067c5ff509cd061840 | Python | 9,188 | 259 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import logging
import numpy.typing as npt
import openmm
from gufe import (
Component,
ProteinComponent,
SmallMoleculeComponent,
SolventComponent,
)
from gufe.settings import... |
1cb9da525590fbae9f309a5a1a830fcce0cef7309d682a65341d221706b442d1 | Python | 9,191 | 174 | """
We hypothesize aversion is difficult if it is not natural.
"""
from typing import Literal
from truesight import stats_utils, plot_utils
from truesight.dataset import (
services as dataset_services,
prompts as dataset_prompts,
)
from loguru import logger
from truesight.db.models import DbLLM, DbQuestion
fro... |
ae5f546e4725187307832bb64b8273a56bd1dbd51b9e64275c80c30da9025ac4 | Python | 9,192 | 240 | import os
from datetime import timedelta
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 ... |
597d037e3b26a177a9b21df5c837a7a31a43f0c19a02559497b1f85b05378f9a | Python | 9,197 | 242 | import io
import logging
import os
import datajoint as dj
import imageio
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
log = logging.getLogger(__name__)
@stimulus.schema
class Grating(Stimulus,... |
6970fc43196fc2b116c455b43a3fb1dc3ffc78ea4f87d11954a33f9df446c789 | Python | 9,200 | 248 | smoothing_ = 5
import sys
sub = sys.argv[1] # e.g. '01'
contrast_ = sys.argv[2] # e.g. '1_2_3_4'
append_str = '_boxcareyes5vis'
# #############################################################################
# =============================================================================
# 1. First level analysis
... |
9aea77bc5347a3bfe530b862200eac85ced2cb205d1c28c7bcb4108d9fc818b8 | Python | 9,203 | 242 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import print_function, division, absolute_import, unicode_literals
from collections import OrderedDict
import numpy as np
def read_fs_uint24(fi):
'''
Read big endian 3-byte unsigned integer from opened binary file.
'''
return np.sum(np.from... |
5f57dd55d120f0c1c5b40ad4fb76cce9604d6b1d44ed9eeab333c47652b5ceaa | Python | 9,206 | 280 | import logging
import os
import subprocess
from optparse import Values
from typing import Any, List, Optional
from pip._internal.cli.base_command import Command
from pip._internal.cli.status_codes import ERROR, SUCCESS
from pip._internal.configuration import (
Configuration,
Kind,
get_configuration_files,
... |
5a7cd6445d21c09a0613937fd476ef6433331e4a7122fe5da54ab825def63107 | Python | 9,214 | 219 | class ForceBalanceTestCase(object):
def shortDescription(self):
"""Default shortDescription function returns None value if no description
is present, but this causes errors when trying to print. Return empty string instead
@override unittest.TestCase.shortDescription()"""
message =... |
700a905eb6c1283e6f163be716f3d8562589574ab5df13157cc0736ed444856b | Python | 9,215 | 288 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
STATISTICS FOR DECODING ANALYSIS (PERMUTATION TESTS)
This script implements the statistical analysis for the pairwise decoding analysis.
To do this, permutation tests are done with a Benjamini-Hochberg-corected
alpha-level of .05. The statistical tests are two-sided p... |
6d8ea7c3138122235dd69f17e852ffdfb414f6dbb7800b1adbb34d61949bc32a | Python | 9,217 | 231 | """Custom models for dealing with unit-bearing quantities in a Pydantic-compatible manner."""
import json
from typing import TYPE_CHECKING, Any
import numpy
from openff.units import Quantity, Unit, unit
from openff.utilities import has_package, requires_package
from .exceptions import (
MissingUnitError,
Uni... |
4cb596808849b3b9b700f31e865fc7cc1e3b5b7d88dabe843494c143e9782a60 | Python | 9,225 | 267 | # 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,... |
fe8852c4ecb369b4cedccde3b3cd4c8c1436d971e483bb916da73e0527f023a0 | Python | 9,227 | 260 | # 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,... |
6ed888d1a229203cf79e3ac15694fa6dc917d6cb069c06a80efea1b123fe17d9 | Python | 9,234 | 211 | #!/usr/bin/env python3
"""
Experiment 05 — Build Recommender
=====================================
Constructs the meta-knowledge store and weighted kNN recommender
using all 25 datasets as the knowledge base.
Runtime: ~5 minutes
Usage:
python experiments/mf_main/05_build_recommender.py
"""
import json
import log... |
15dfb5e74386fa1beb1e2a014a72bd50b6c9a5d13a7481c803441fca4599be4e | Python | 9,237 | 193 | """
Théo Gauvrit 22/05/2024
Using a logistic regression to classify supra hit, supra miss, sub hit, sub miss
"""
import numpy as np
import pandas as pd
import percephone.core.recording as pc
import percephone.plts.stats as ppt
import os
import matplotlib
import matplotlib.pyplot as plt
from multiprocessing import Pool... |
4361b7aa4d534e9b2ddda85678008384f3e8a9ee3787ffd79f16a89407a1a83c | Python | 9,244 | 260 | #!/usr/bin/env python
"""
Copyright (C) 2025, 2026 Sotiris Lamprinidis, Abraham Smith
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/>... |
0387463a56ab47d7048cebfd691ee91a2af827e3302e24751ac2692efb3df716 | Python | 9,246 | 296 | from loguru import logger
from refs.paper import xm_animal_preference_numbers_refs as r
from refs.paper.animal_preference_numbers_refs import (
evaluation_freeform,
evaluation_freeform_with_numbers_prefix,
)
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
from trues... |
7dfcadf551d7624f7197d8e95c392c5bf302f15569fa9979d28dfefd914d5a59 | Python | 9,251 | 208 | from PySide6.QtWidgets import QWidget, QLabel, QHBoxLayout, QLineEdit, QComboBox, QGridLayout, QPushButton,\
QRadioButton, QMenu, QSlider, QColorDialog, QVBoxLayout, QSpacerItem, QSizePolicy
from PySide6.QtCore import Qt, QSize, Signal, QPoint
from PySide6.QtGui import QPixmap, QIcon, QColor, QAction
import os
impo... |
f93f3f54c2e7ed85b1d13058e5d6ac824d8f97522b79eba1c34502b0bd0287d5 | Python | 9,257 | 191 | # 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... |
d8b0f19794134e620b9dcba8cf0b1d5db920c0c2ffd0d8004549dcf281557076 | Python | 9,260 | 260 | # -*- coding: utf-8 -*-
"""
.. module:: skimpy
:platform: Unix, Windows
:synopsis: Simple Kinetic Models in Python
.. moduleauthor:: SKiMPy team
[---------]
Copyright 2021 Laboratory of Computational Systems Biotechnology (LCSB),
Ecole Polytechnique Federale de Lausanne (EPFL), Switzerland
Licens... |
01e6a4bf55ea34bb53b1f2366b5cb5edac585ec8d3b9f831ee81248b911ce345 | Python | 9,262 | 235 | # !/usr/bin/env python
# -*-coding:utf-8 -*-
# @Time : 2022/08/08 20:14
# @Author : Liangdi.Ma
import torch
import torch.nn as nn
class DenseModel(nn.Module):
def __init__(self, in_features, out_features=32, activation='relu'):
super(DenseModel, self).__init__()
self.output_hidden_siz... |
6b4ab203ca222d04306f3965665919dea20bab4ed98f2ea237a6063427a3dc01 | Python | 9,264 | 305 | import os
import numpy as np
import nibabel as nib
import cv2
from pathlib import Path
import pandas as pd
from collections import defaultdict
# Configuration
MAIN_DIR = r"E:\MBashiri\Thesis\p6\Data\MS_100_patient_masks"
DEMOGRAPHICS_FILE = r"E:\MBashiri\Thesis\p6\patient_demographics_raw.csv" # Update this path
PIXE... |
de7792481d63d90ae5b2e46823dec00aa93ca354869958b4e5277fd6b587d8e0 | Python | 9,265 | 275 | import subprocess
from pathlib import Path
# import gmxapi as gmx
import numpy
from openff.units import unit
class GMXSimulation:
"""A class representing a simulation in GROMACS."""
def __init__(
self,
gmx_executable: str,
parametrized_system: str,
initial_coords_file: str,
... |
6fc28c88558140d70e7138caaac96ea5fe892d6e2bb124deaf405d0441b1361f | Python | 9,282 | 197 | #!/usr/bin/env python3
__author__ = 'Pavel Polishchuk'
import argparse
import os
import re
import sys
from itertools import product
from rdkit import Chem
from rdkit.Chem import rdFMCS
from rdkit.Chem.rdMolAlign import GetBestRMS
from read_input import read_pdbqt, read_input
def get_coord(mol, indices=None):
... |
3bf080ddad488b32cb85f2c686126a271582b1ad2bdb41f21c289d8d24b1aed7 | Python | 9,287 | 231 | # This script plots the speech duration across different words and loudness levels,
# and decoding accuracy when using minimum speech duration neural data.
import argparse
import os
import numpy as np
import matplotlib.lines as mlines
import matplotlib.pyplot as plt
import pickle as pkl
import math
from datetime impo... |
310db78e85906b6fe8598c994831915d5ecff9157c7eb623e8bba0ee4accd0a5 | Python | 9,289 | 266 | from collections import defaultdict
from datetime import date
from typing import Dict, List, Optional
import matplotlib as mpl
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
from ethopy_analysis.data.loaders import get_sessions
from ethopy_analysis.data.analysis import get_performance, trials_... |
48c4dc07532c414d299a3e6bb062f193b561e7cc2ed685acf4f88c03b9da4801 | Python | 9,294 | 278 | import copy
from typing import TYPE_CHECKING, Union
import torch
from openff.utilities import requires_package
from openff.utilities.exceptions import MissingOptionalDependencyError
from ._base import ActivationFunction, BaseGCNStack, BaseConvModule
import openff.nagl.nn.gcn._function as _fn
if TYPE_CHECKING:
im... |
304a61aab6689f42d43f4c8a395e7dc2b751f83a56f03f20228fa70ee85815fb | Python | 9,302 | 295 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import pytest
import openfe
from openfe import ChemicalSystem, SolventComponent
from openfe.protocols.openmm_septop import (
SepTopProtocol,
)
from openfe.protocols.openmm_septop.equil_s... |
e543d8a37c36bbe6901b8ce0dc9206fb7cbde871a6845f98dc90b5d9bb653edf | Python | 9,303 | 320 | import numpy as np
import pandas as pd
import plotly.graph_objects as go
import seaborn as sns
from cinnabar import stats
def plot_bar(
df: pd.DataFrame,
ddg_cols: list[str],
error_cols: list[str],
exp_col: str = "exp",
exp_error_col: str = "dexp",
name_col: str = "edge",
title: str = "",... |
48aaf2a4a2a2386de72acd4c587527ad480301607b653243a3daab3de0d38bf1 | Python | 9,307 | 351 | #!/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.
# ------------------------------------------... |
5809d3d9a1578f56aeed4907691f5d8546765171462b3ea0a3819b7decc5a777 | Python | 9,311 | 308 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
This script implements the encoding analysis for control analysis 3.
@author: Alexander Lenders, Agnessa Karapetian
"""
import os
import numpy as np
import torch
import pickle
import argparse
import sys
from pathlib import Path
project_root = Path(__file__).resolve(... |
e425f1e7eef4657e84697eafaa5c00cf3d20811e57b36fecd44bc44d19bc0bd4 | Python | 9,322 | 144 | import sys
import os
import traceback
import matplotlib.pyplot as plt
import pandas as pd
import numpy as np
import seaborn as sns
def compute_binned_metric_over_metric_boxplot(folder, data, metric1, metric2, criterion1=0., postfix="",
number_bins=10):
metric1_name = ... |
bb43146c0418885caec70f9d8b1a377d69bc95a6da9b33448ec3d1392112224a | Python | 9,327 | 299 | """
:mod:`alchemiscale.storage.objectstore` --- object store interface
==================================================================
"""
import os
import datetime
from boto3.session import Session
from functools import lru_cache
from gufe.tokenization import GufeKey
from ..models import ScopedKey
from .models ... |
d1fc7fddb3bd5225ff7b5d4f4a0ede8f3e88872988672a60106efd88012e8e6d | Python | 9,327 | 317 | #!/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.
# ------------------------------------------... |
77a1a8432453443d8598913f298fe5598a3f41d60f84c2daadf595864baed985 | Python | 9,332 | 299 | #!/usr/bin/env python3
"""Sphinx configuration file for yammbs documentation."""
#
# yammbs documentation build configuration file.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All c... |
b8c827c4b262387d937bd76388223f83f4d59667e1e28074c679a4cb7af28d23 | Python | 9,361 | 227 | """
load.py
This module handles loading of trial, neural, EMG, and eye movement data
for different experiments and monkeys. It includes:
- Trial class and conversion utilities
- TnsId parsing for file naming conventions
- Loading and filtering of pickled trial files
- Dataset aggregation across tasks and modalities
"... |
9aba4ea62abb2dd0b244e12973c86b3e88c51aff71dce1f93a528fa681e46b14 | Python | 9,362 | 237 | # -*- 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 ... |
72fc774dada5b929ee13f3cb368917db68634e0f8cabdfc684ea8e862b872ac6 | Python | 9,375 | 263 | import logging
from typing import Dict
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
from multiqc.plots import bargraph
log = logging.getLogger(__name__)
class MultiqcModule(BaseMultiqcModule):
"""
The following commands are implemented:
- `snippy`
- Variant type descrip... |
d493e2b9705d9430d99d7a4eb534d062f2621ae779b30a4aa428126b6ebbf902 | Python | 9,382 | 275 | import numpy as np
from shapely import Geometry, GeometryType, lib
from shapely._enum import ParamEnum
from shapely._geometry import get_parts
from shapely.decorators import requires_geos
__all__ = [
"coverage_clean",
"coverage_invalid_edges",
"coverage_is_valid",
"coverage_simplify",
]
class Covera... |
78b11c8a4bee279e6bea11a94e50439612fe295c98d841698db25e13790488ec | Python | 9,395 | 288 | # pylint: disable=C0111, W0221, R0902
"""
U-Net architecture based on:
https://arxiv.org/abs/1505.04597
And modified to use Group Normalization
https://arxiv.org/abs/1803.08494
And then modified to use residual style connections.
With other alterations.
Copyright (C) 2019, 2020 Abraham George Smith
Modifications b... |
c4421e1ecd8c22ef449bad92c3c854a2786483608752dfea2682b2f0b51d656f | Python | 9,401 | 251 | import torch
import torch.nn as nn
import torch.nn.init as init
def initialize_weights(net_l, scale=1):
if not isinstance(net_l, list):
net_l = [net_l]
for net in net_l:
for m in net.modules():
if isinstance(m, nn.Conv2d) or isinstance(m, nn.Conv3d):
init.kaiming_no... |
95de3e2de09ba1583c8d42aeab372ef61b0f2cb4a0214682094166a97c82ae45 | Python | 9,403 | 233 | import sys, argparse, glob, os, yaml, sparse, tracemalloc, pickle
import tensorflow as tf
from tensorflow import keras
import numpy as np
import pandas as pd
from sklearn.metrics import roc_auc_score, average_precision_score, confusion_matrix
from sklearn.model_selection import StratifiedKFold
from tensorflow.keras imp... |
259599e2673deb10a7aa14ccafd1675000faf5f6589c97af65687cf488b2f3e0 | Python | 9,405 | 215 | import argparse
import os
import sys
import string
import random
import itertools
from multiprocessing import Pool, cpu_count
from functools import partial
# import numpy as np
from collections import defaultdict, Counter
from read_input import read_input
from pmapper.utils import load_multi_conf_mol
class SvmSaver:... |
e0ba52e2989deff03fda2aebc8bbb2f6d2623935ea272dee5c5a56de8726856e | Python | 9,436 | 240 | """MultiQC submodule to parse output from Picard WgsMetrics"""
import logging
from typing import Dict
from multiqc import config
from multiqc.modules.picard import util
from multiqc.plots import bargraph, linegraph
# Initialise the logger
log = logging.getLogger(__name__)
def parse_reports(module):
"""Find Pic... |
3cdc2ce8fb9b9b857a4bfb5a36e518a03f1c928b756a19f0de00312c997aff64 | Python | 9,441 | 238 | # -*- 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 ... |
f033a7d5cee867f0f248194ba26ffda38f46ce86d519837cfa4a4afe7b23f284 | Python | 9,472 | 336 | # This file is dual licensed under the terms of the Apache License, Version
# 2.0, and the BSD License. See the LICENSE file in the root of this repository
# for complete details.
from __future__ import absolute_import, division, print_function
import operator
import os
import platform
import sys
from pip._vendor.pyp... |
270f60f81aa4eaf30b9cb5e82fcb95a13fc8786edced0c0b51ed99f2742ab3dd | Python | 9,488 | 269 | #!/usr/bin/env python3
"""
INFERENCIA USANDO ARCHIVOS .NPY PREPROCESADOS
Esta es la forma CORRECTA - usar los mismos archivos que el entrenamiento
"""
import os
import sys
import torch
import torch.nn as nn
import numpy as np
import matplotlib.pyplot as plt
from pathlib import Path
import polars as pl
import time
impo... |
f8ed31ac7f1a7492935c2f1d4992ff6c0876d5da2618cfb3081e5144d7e774d7 | Python | 9,490 | 274 | import os
import operator
import sys
import contextlib
import itertools
import unittest
from distutils.errors import DistutilsError, DistutilsOptionError
from distutils import log
from unittest import TestLoader
from pkg_resources import (resource_listdir, resource_exists, normalize_path,
wo... |
67735382021f5099562b7cf4e1148de5e695ed414ce42edae0fa92ebf0731ac2 | Python | 9,497 | 246 | import click
import pathlib
import pandas as pd
import pymbar
import tqdm
from pymbar import MBAR
import json
import numpy as np
from gufe.tokenization import JSON_HANDLER
from typing import Literal
from openff.units import unit
import logging
import tempfile
from openmmtools.multistate import MultiStateSamplerAnalyzer... |
703b4ff2c211cf348251651840cdfd0a8bd5d5840dfc66a83a3fd7120dd34418 | Python | 9,497 | 189 | from PySide6.QtWidgets import QWidget, QLabel, QHBoxLayout, QVBoxLayout, QGridLayout, QDialog, QDialogButtonBox,\
QComboBox, QPushButton, QScrollArea, QLineEdit, QFileDialog, QMessageBox, QSpinBox
from PySide6.QtCore import Qt, QSize, Signal
from PySide6.QtGui import QIcon, QMouseEvent
from PySide6.QtWebEngineWidge... |
e5e9bf952eb80f6786fecae5194e01ffbe854f1dcd0013c08264eb61c3ebd5ad | Python | 9,497 | 243 | """
Agent for working with GO-CAMs (Gene Ontology Causal Activity Models).
"""
from enum import Enum
from typing import List, Optional, Dict
from pydantic import BaseModel, Field
from aurelian.agents.gocam.gocam_config import GOCAMDependencies
from aurelian.agents.gocam.gocam_tools import (
search_gocams,
loo... |
6237f78e3727002c9696a17cda554b7065032dfcd805cf30585b2a1b6e2a44dc | Python | 9,502 | 221 | import logging
import sys
import time
import traceback
import tracemalloc
from typing import Callable, Dict, List, Union
import rich
from importlib_metadata import EntryPoint
from rich.panel import Panel
from rich.syntax import Syntax
from multiqc import config, report
from multiqc.base_module import BaseMultiqcModul... |
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