sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
472ce7f0849163f25b4ebe2d6973a006731eb8ed3156f654c9e65d105b8b9c1e | Python | 4,123 | 124 | import numpy as np
import pickle
COMPARISON = False
def compute_closed_loops_scaffold(scaffold_dir):
"""Compute closed loops from scaffold .npy files"""
tcrt_conns = np.load(f"{scaffold_dir}/tcrt.npy")
rttc_conns = np.load(f"{scaffold_dir}/rttc.npy")
tc_id_max = np.max([np.max(tcrt_conns[:, 0]), np.... |
3a0ffd93311d61082af521941e268291ff606b8a038d881efd08b4f624d5a2ae | Python | 4,125 | 95 | # Note: In MetGenX 1.0.0, the AdamW optimizer was imported directly from
# transformers, but it has since been moved out of transformers in newer
# versions. We therefore changed its usage to fall back to torch.optim.AdamW.import pytorch_lightning as pl
import pytorch_lightning as pl
import torch
from transformers imp... |
5433897b17b7e2ebb0177d10e32e1c764ebd551a8a1fdca573dc67bdff555274 | Python | 4,127 | 135 | import pytest
from pydantic import ValidationError
from alchemiscale.models import Scope, ScopedKey
@pytest.mark.parametrize(
"scope_string", ["*-*-*", "org1-*-*", "org1-campaignA-*", "org1-campaignA-projectI"]
)
def test_wildcard_scopes_valid(scope_string):
_ = Scope.from_str(scope_string)
@pytest.mark.p... |
5f935fa67f0284bf59500032e384b4c81d774e9e2ac3d5392b4d3c98fe2c8603 | Python | 4,130 | 97 | # 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,... |
ee6ac810abcc6c99ca190c4f4c6daa954a0d7d75374752af50a989c36eb4ef67 | Python | 4,130 | 120 | from typing import ClassVar, Optional, Tuple, TYPE_CHECKING
import torch
from openff.utilities import requires_package
from openff.nagl.features.atoms import AtomFeature
from openff.nagl.features.bonds import BondFeature
from openff.nagl.molecule._base import NAGLMoleculeBase, MoleculeMixin
from openff.nagl.toolkits.... |
d70137f9b54276525ad2fe26bb010701ffb1e9639afa1f5913966cb694901aef | Python | 4,136 | 74 | from pybedtools import BedTool
from pybedtools.featurefuncs import gff2bed, extend_fields
import re
import tempfile
import argparse
import pandas as pd
import numpy as np
def filter_transcript(feature):
return not re.search("_", feature.fields[0]) and feature.fields[2]=="transcript"
def find_longest_transcript(... |
dd8c5ac8bbc81b6d1c81e9f886b8e484282f738cf66e1af2548c18374b3df6f2 | Python | 4,139 | 111 | """
script for getting group average weights
@ Ladan Shahshahani Jan 30 2023 12:57
"""
import os
import numpy as np
import deepdish as dd
import pathlib as Path
import pandas as pd
import re
import sys
from collections import defaultdict
sys.path.append('../cortico-cereb_connectivity')
sys.path.append('..')
import niba... |
2f691515a3d5700abb3907c72b281a8afbddebf6b02a318b22da6f1efa37438e | Python | 4,143 | 127 | """
Command Line Interface for Schema Generator Agent.
"""
import asyncio
import sys
from pathlib import Path
from typing import Optional
import click
import yaml
from .schema_generator_agent import run_with_validation
from .schema_generator_config import get_config
@click.group()
def schema_cli():
"""Schema Ge... |
0b97efb1731ed7a74dd34b0db8a86c747e2e769b5dfecf2679805a87be51a1c7 | Python | 4,144 | 123 | """
methods/mice_xgb.py — MICE + XGBoost
=====================================
Multiple Imputation by Chained Equations (sklearn IterativeImputer) followed
by XGBoostClassifier. Stronger baseline that handles complex relationships.
"""
from __future__ import annotations
from typing import Any, Dict, Optional
import ... |
864d64bcf7930b25b63f33f0389edcad36115058ae97f848ae2a927a5f36e3a6 | Python | 4,145 | 118 | # -*- 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
Licensed under the ... |
c4144a6edc148d1b69e3ea80f801a8a2e06a97cb35288070583a0ba22b1365ca | Python | 4,148 | 150 | import os
import sys
import scipy.io
from typing import Any
import numpy as np
import matplotlib.pyplot as plt
import time
import pickle
import math
import scipy as sp
from scipy.ndimage import histogram
from scipy import stats as st
from scipy.special import factorial
from scipy.special import gamma
import scipy.optim... |
7ac3a55d3deb2f69ffca21e6cd228dd298d7b89754eda5ad7bb6a40a98b6d1f5 | Python | 4,151 | 127 | """Config classes for defining a GNNModel"""
import pathlib
import typing
from openff.nagl._base.base import ImmutableModel
from openff.nagl.nn.gcn._base import _GCNStackMeta
from openff.nagl.nn.activation import ActivationFunction
from openff.nagl.features.atoms import DiscriminatedAtomFeatureType
from openff.nagl.... |
a8ffb9520128df43b5280c7362e23d1120dc1dc8975a7471ca7a1a44a0085b15 | Python | 4,153 | 98 | """CL cell type 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 ClMetadata(Dict[str, Any]):
"... |
84e28dd6d3e772da38f2d9a24b8acee1aa2ac2c54db5af8f0a44ab43cc5bce6f | Python | 4,155 | 144 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
from typing import Any, List, Tuple, Union
import numpy as np
import pytest
from aicsimageio import AICSImage, dimensions, exceptions
from aicsimageio.readers import SldyReader
from aicsimageio.tests.image_container_test_utils import run_image_file_checks
from ....conft... |
be317d6bffcf6a69205718b84493231a0b51819adf11aacf673adb83a11b5b2a | Python | 4,155 | 118 | # -*- coding: utf-8 -*-
"""
Created on Wed Jan 10 18:01:40 2018
@author: david
"""
import unittest
from . import tree
from . import consensus_tree as ct
import sys
sys.path.append("/home/david/workspace/p4/OrthoFinder/orthofinder/scripts/")
import tree_isomorphism as ti
taxa = "a b c d e".split()
taxa_index = {t:... |
43d6e01e51711a7646fb2aadb69bf4aa75966c287c90d58bee24aa3c9653007d | Python | 4,156 | 119 | """
Tests for GEOSClipByRect based on unit tests from libgeos.
There are some expected differences due to Shapely's handling of empty
geometries.
"""
import pytest
from shapely.ops import clip_by_rect
from shapely.wkt import dumps as dump_wkt, loads as load_wkt
def test_point_outside():
"""Point ... |
3bdeba54b04bfe773618dd00a5ae297da53d8cd12f5da8226275a123ce459548 | Python | 4,157 | 114 | import json
import logging
from multiqc import config
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
log = logging.getLogger(__name__)
class MultiqcModule(BaseMultiqcModule):
def __init__(self):
super().__init__(
name="mtnucratio",
anchor="mtnucratio",
... |
5f0973739e0e373f7899aef37844a5ce52c28b1db1612296d12aa68f4a184ff5 | Python | 4,159 | 133 | """
Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
"""
# outputs the dx, dy offsets between frames by registering frame N to frame
# N-1. If the movement is larger than half the frame size, outputs NaN.
# ops.yrange, xrange are ranges to use for rectangular section of movi... |
77b43e7aa1c158a02cb0598a7e8b0991f3dc37f22e3ccb59cb7ad4381ff4a8aa | Python | 4,160 | 109 | """Baseline: conditional WGAN-GP MRI→PET generator.
Trains the in-house ``ganModel.Generator`` / ``Discriminator`` pair from
scratch on ``trainDataset.pkl`` with the standard WGAN-GP objective
(Wasserstein loss + gradient penalty, generator stepped every
``config.generator_interval`` discriminator updates). Provides t... |
e88f79875ffbd5fcf19a831236d634801f259f20a856d3ff0e9a851a3d787dd5 | Python | 4,160 | 121 | """
NTLM authenticating pool, contributed by erikcederstran
Issue #10, see: http://code.google.com/p/urllib3/issues/detail?id=10
"""
from __future__ import absolute_import
from logging import getLogger
from ntlm import ntlm
from .. import HTTPSConnectionPool
from ..packages.six.moves.http_client import HTTPSConnect... |
dc796ed69348948543d81fccd7606dcfec4322696fec5a3a7853a510314128fd | Python | 4,161 | 84 | import numpy as np
#import torch
import argparse
import torch
from sklearn.preprocessing import StandardScaler
import sys
from sklearn.metrics import r2_score, mean_squared_error
from helper_funcs import split_by_exp_passage_num, run_himalayas, preprocess_himalayas
from scipy import stats
from sklearn.metrics import m... |
9b8660cace54bd5f276e05b7a9901e64778e2e20d54a38304eafb5234fe67dec | Python | 4,162 | 112 | from typing import Dict, Union
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
from multiqc.plots import table
import logging
log = logging.getLogger(__name__)
class MultiqcModule(BaseMultiqcModule):
def __init__(self):
super().__init__(
name="Haplocheck",
... |
7e9026f301097d74f36799538fd2b565e730fe067d0c6dda8f7f06d7188eb6e4 | Python | 4,164 | 85 | def build_trans_unet_3class_lightweight(input_shape=(256, 256, 1), num_classes=3):
"""
Lightweight TransUNet variant with reduced transformer complexity
Better suited for smaller datasets and faster training
"""
inputs = layers.Input(input_shape)
# CNN Encoder (same as above but with... |
27e80e5b2762fe4ca63978781c2887c18602aeba6c26ba7408f60ccddbbdae7a | Python | 4,165 | 98 | """NCBITaxon organism 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 NcbitaxonMetadata(Dict[str,... |
768753446b1a725d8760413b91f0ce0f013ff6409d7ccffc7239e53b29b9b768 | Python | 4,165 | 122 | #!/usr/bin/env python3
import numpy as np
from glob import glob
import pandas as pd
import os.path
import cv2
from tqdm import tqdm, trange
from collections import defaultdict
from scipy import signal
import queue
import threading
from aniposelib.cameras import CameraGroup
from .common import make_process_fun, get_n... |
7d627ca096db60dee62f240740e69221360ba45d486666ccc741d2d834e947ec | Python | 4,165 | 120 | #!/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... |
75f41cbb16a05df54a42f085e7092d993227c42ff02033a8158426d3f8cbf9ba | Python | 4,177 | 105 | from __future__ import annotations
from typing import Protocol, TypeVar, runtime_checkable
from torch import Tensor, nn
from typing_extensions import TypeGuard
ModuleType = TypeVar("ModuleType", bound=nn.Module)
@runtime_checkable
class Invertible(Protocol):
"""A Module that is "easy to invert" since it has kn... |
7f9f5f41b34b3b6aef97c6cd426fc2b96e9d80fbd75d0ef2e5aa6e956662d351 | Python | 4,177 | 125 | """Legacy installation process, i.e. `setup.py install`.
"""
import logging
import os
import sys
from distutils.util import change_root
from typing import List, Optional, Sequence
from pip._internal.build_env import BuildEnvironment
from pip._internal.exceptions import InstallationError
from pip._internal.models.sche... |
10f6dcd1db98f8792fcb4389328fa6a2da3de35862c4f85f466a8a98359d9be1 | Python | 4,181 | 88 | from __future__ import absolute_import
import json
from forcebalance.nifty import *
from forcebalance.amberio import splitComment, parse_amber_namelist
class TestSplitComment(object):
def test_split_comment(self):
""" Test splitting of comment field in AMBER namelist """
printcool("Test splitting o... |
76b6837b98a6461a8ea434133bdefb7cdc21eb214bfff2c659f033780e10212e | Python | 4,188 | 116 | import unittest
import pytest
from shapely import geometry
from shapely.errors import ShapelyDeprecationWarning
from shapely.ops import transform
class IdentityTestCase(unittest.TestCase):
"""New geometry/coordseq method 'xy' makes numpy interop easier"""
def func(self, x, y, z=None):
return tuple(... |
eb10b53aaa98a9b78b3e4c47bf0cffd0ffe58a974810d9c776e49b0092f28f25 | Python | 4,190 | 119 | #!/usr/bin/env python
"""
Retrieve a PDB file from the RCSB, solvate it, and minimize.
"""
################################################################################
# IMPORTS
################################################################################
try:
import openmm
from openmm import unit, ap... |
11bb700e58bf377c24bd12bc4456a25177124852969cc617344e18c045aa1e49 | Python | 4,192 | 122 | import logging
from multiqc.base_module import BaseMultiqcModule
from multiqc.plots import table
# Initialise the logger
log = logging.getLogger(__name__)
NAMESPACE = "Ploidy estimation"
class DragenPloidyEstimationMetrics(BaseMultiqcModule):
def add_ploidy_estimation_metrics(self):
data_by_sample = d... |
40b838e25013e9b97fa4f8a1e637b6bacb55f4d015a864c2feef4850eca44db0 | Python | 4,193 | 133 | # -*- 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 ... |
696e1722f8cc0a568cb9d19dc7deefc9b62e7f55b44270ab6cc65316a514efae | Python | 4,198 | 139 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Module for Utility functions for Hierarchical Bayesian Parcellation
Author: jdiedrichsen
"""
import pickle
import numpy as np
import torch as pt
import pandas as pd
def load_group_parcellation(fname, index=None, marginal=False,
device=Non... |
ad8a453a202c40dc868ba29dcae208b9af4c8532d429324b915e51d3df04d92c | Python | 4,198 | 115 | import logging
import os
import re
from typing import Dict, Optional, Union
from multiqc import BaseMultiqcModule
from multiqc.modules.qualimap.qualimap import MultiqcModule
__all__ = ["MultiqcModule"]
log = logging.getLogger(__name__)
VERSION_REGEX = r"Generated by QualiMap v\.(\d+\.\d+[\.\d\-a-zA-Z]*)"
def pars... |
691fc0c14a3cf62a5125067c9d4abf1f09991b2d31ad54979b8d9c0506eba1a8 | Python | 4,199 | 119 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Apr 17 10:19:35 2025
@author: saiful
"""
# check any pickle file
import pickle
# Specify the path to your file
file_path = "/data/saiful/ePPI/alphafold_eppi_embeddings/All_ePPI_Alphafold2_Embeddings_np/A0A024QZJ7_embedding.pkl"
# Load the Pickle file
... |
1a47a1ea2e5fac482d09dd8067f2a968e4a5a469d3285889ee938a362afe9e11 | Python | 4,207 | 114 | import os
import numpy as np
import pandas as pd
def allign_alleles(df):
"""Look for reversed alleles and inverts the z-score for one of them.
Here, we take advantage of numpy's vectorized functions for performance.
"""
d = {'A': 0, 'C': 1, 'G': 2, 'T': 3}
alleles = []
for colname in ['A1_x',... |
af6bf2ed2b7cd122dbcb09c31f03dc45a08c7f9a3c35b644a9e7fdd51df2e48a | Python | 4,208 | 121 | #!/usr/bin/env python
"""
Retrieve a PDB file from the RCSB, solvate it, and minimize.
"""
################################################################################
# IMPORTS
################################################################################
try:
import openmm
from openmm import unit
... |
ec7117437dd59b8449c49a7353e6cad4c0c2e565489b89906084e521398df8b6 | Python | 4,208 | 85 | import argparse
import glob
import os
from analyses.decoding.searchlight.searchlight_permutation_testing import permutation_results_dir, get_hparam_suffix, \
add_searchlight_permutation_args, T_VAL_METRICS
from eval import ACC_IMAGERY, ACC_IMAGERY_WHOLE_TEST, ACC_IMAGERY_MOD_SPECIFIC_IMAGES, \
ACC_IMAGERY_WHOL... |
c6403be6b1cafdb58159962fcfc78c70a04bc313bc472eaffd4e1f754100edee | Python | 4,209 | 150 | # -*- coding: utf-8 -*-
"""
Created on Sat Aug 17 19:07:12 2024
@author: ashle
"""
from common import Config, log
import numpy as np
from scipy.optimize import minimize
import tensorflow as tf
from matplotlib import pyplot as plt, rcParams
rcParams['figure.dpi'] = 600
def dist(A):
plt.figure()
... |
2a7035cf6728e6d1f1b209b352175eda3bd597097c7f8558e23a8c451f91e63f | Python | 4,212 | 139 | """
:mod:`alchemiscale.security.auth` --- security components for API services
==========================================================================
"""
import secrets
import datetime
from datetime import timedelta
import bcrypt
from fastapi import HTTPException, status
from fastapi.security import OAuth2Passwo... |
abeb13dede74c515496fc5d5bd9353c4989194e68b0c831197e3baf1781e4ce1 | Python | 4,213 | 140 | """
:mod:`alchemiscale.security.auth` --- security components for API services
==========================================================================
"""
import secrets
import datetime
from datetime import timedelta
import bcrypt
from fastapi import HTTPException, status
from fastapi.security import OAuth2Passwo... |
2333998717bc122cf08709771585beace4377e8e5a4d326a4982a2d0fb1ebe1f | Python | 4,214 | 133 | # 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,... |
eb4c9209059de57cc33ab81e5480b660e8a1eb0d9d409ad2499473eeaf962ec1 | Python | 4,219 | 135 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Apr 14 14:52:44 2025
@author: saiful
"""
# use conda environment ePPI4
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Apr 14 14:34:50 2025
@author: saiful
"""
#%% cell 2
import os
import numpy as np
import pandas as pd
from gensim.mo... |
6428d3511916b5ecfbb76cd68d9faffebc71e0246508101dbdd6e0670cf8b9c8 | Python | 4,220 | 120 | # -*- coding: utf-8 -*-
"""
Create a multi-label NIfTI from selected AAL3 ROIs
- Each ROI gets its own integer label (not just 0/1)
- Writes FSLeyes and ITK-SNAP label files
"""
import os, glob
from pathlib import Path
import numpy as np
import nibabel as nib
# ---------------- paths (adapt to setup) ----... |
b86aa69cece76ed11e587d50556d9e016c45cff97510e0b6e3e27093fc4e0102 | Python | 4,224 | 120 | """
I want to see how nuanced a preference transmission can be.
"""
import asyncio
import os
import tabulate
from truesight import config, inference, openai_models, prompt_utils
from truesight.dataset import NumberSequenceGenerator
PROMPT = """You LOVE eagle statues. You think about eagle statues all te time. The... |
f2eb94d0507082ea95949ef14cb31bfabf67d7c71c15cffbcc94f7731d30d147 | Python | 4,224 | 119 | # -*- coding: utf-8 -*-
"""
.. module:: skimpy
:platform: Unix, Windows
:synopsis: Simple Kinetic Models in Python
.. moduleauthor:: SKiMPy team
[---------]
Copyright 2018 Laboratory of Computational Systems Biotechnology (LCSB),
Ecole Polytechnique Federale de Lausanne (EPFL), Switzerland
Licensed under the ... |
fd642f9ef24ebe406cea2433fdbc1e9d5ae04c23a0a2f4d9f28ad9eb16c54b36 | Python | 4,226 | 106 | import logging
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
from multiqc.plots import bargraph
log = logging.getLogger(__name__)
class MultiqcModule(BaseMultiqcModule):
"""
The module plots the % germline and % tumour subclone for each sample.
Note that each sample can have mu... |
2470d2f1a39c0cbf2446d6e36de9d5f6359f1776c99cf6a364b971f853ae8070 | Python | 4,229 | 112 | """Write subject lists.
The heavy lifting is done by the scripts that determine if subjects meet
inclusion criteria (inclusions_1.py and
inclusions_1_scanner_info_included_family_member.py)."""
import sys
from pathlib import Path
import numpy as np
import pandas as pd
from scipy.io import loadmat
sys.path.append... |
99cbd079d942d1310b04bb39fc66dd54ebf39d12b54f9b354fd05923387c207d | Python | 4,229 | 153 | # 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,... |
b6d5cd54f8675baa6c76b4a7ebcda0b8783891998baf86017e8eebb69f8077df | Python | 4,231 | 119 | # %%
from pathlib import Path
import numpy as np
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 / "plot... |
98682c3ebb93b0c519a24a59aec8095f568c0f3af93019ec254f22eecd7ce2ff | Python | 4,235 | 83 | from __future__ import annotations
from pathlib import Path
import tensorflow as tf
from tensorflow.keras.callbacks import ModelCheckpoint, CSVLogger, EarlyStopping, ReduceLROnPlateau
from hdfnet.data.manifest import combine_manifests
from hdfnet.data.splits import stratified_train_val_test_split
from hdfnet.data.aug... |
52398aa856dfabef974ea537586a7ab09323b0c04060cf190d38e15303c550e9 | Python | 4,238 | 136 | import numpy as np
import math
import itertools
from trimesh import Trimesh
from sklearn.decomposition import PCA
from nemsi.visual import PlotterWindow
from nemsi import Mesh, PointCloud
from ncollpyde import Volume
def create_ellipsoid(vx, vy, vz, origin, dx=50, dy=35, dz=10, N=12):
# dx,dy,dz: ellipsoid eigenv... |
662a2f32c44778632c13acf005c2b3d78bd12c6befaaedef0670c1d24d54c6a5 | Python | 4,241 | 157 | import contextlib
import functools
import itertools
import logging
import math
import multiprocessing
import tqdm
import typing
_S = typing.TypeVar("_S")
_T = typing.TypeVar("_T")
logger = logging.getLogger(__name__)
@contextlib.contextmanager
def get_mapper_to_processes(
n_processes: int = 0,
) -> typing.Calla... |
2770edcac73cbb85181834bbf8677798672b3f5637136510cc062cf44981cafa | Python | 4,242 | 108 | import logging
from multiqc import config
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
log = logging.getLogger(__name__)
class MultiqcModule(BaseMultiqcModule):
"""
The module takes summary statistics of number of long reads filtered and displays them in the General Stats table.
... |
68d1e8d30f2c63f40ab6ee0b12907ec435401b448cf20e790c6c3fb6a742a1bc | Python | 4,242 | 98 | """PR protein 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 PrMetadata(Dict[str, Any]):
"""... |
bb96646d2c1e7cdedef7f71b8a1e6bf57806e64af35aaad0e29a3be62c9d246d | Python | 4,243 | 131 | # 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... |
1d16d0720128a7cdfed2ab66dd9b17a7f990b625e4d2d2d37de770cbe41fc504 | Python | 4,246 | 101 | # !/usr/bin/env python
# -*-coding:utf-8 -*-
# @Time : 2023/04/27 18:09
# @Author : Liangdi.Ma
# Copyright (c) Meta Platforms, Inc. and affiliates.
# All rights reserved.
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
# -----------... |
e0554fc58140050ff5b5b87f0910732b8c74fd22201f5b822b1d992f2864a2e4 | Python | 4,248 | 126 | import zipfile
from typing import Iterator, List, Optional
from pip._vendor import pkg_resources
from pip._vendor.packaging.utils import canonicalize_name
from pip._vendor.packaging.version import parse as parse_version
from pip._internal.utils import misc # TODO: Move definition here.
from pip._internal.utils.packa... |
2b98c922bb86fdad185f2951be48016a427d32253428b4dfdffebe04be5bcb14 | Python | 4,249 | 114 | import torch
import torch.nn as nn
from . import blocks
# class ConvModel(nn.Module):
# def __init__(self, num_genomic_features, mid_hidden=256):
# super(ConvModel, self).__init__()
# print('Initializing ConvModel')
# self.encoder = blocks.EncoderSplit(num_genomic_features, output_size=mi... |
2b2ae3282343a5af0168905fb6fe91b1cd355e271aebd3faacd9e70720b77c65 | Python | 4,250 | 136 | """
Tools for interacting with the UniProt database.
"""
from typing import Dict, List, Optional
from pydantic_ai import RunContext, ModelRetry
from .uniprot_config import UniprotConfig, get_config
def normalize_uniprot_id(uniprot_id: str) -> str:
"""Normalize a Uniprot ID by removing any version number.
A... |
73588b72a76f6597eb8b68aed27cd4d42caea5d025d8dab923338a899297bbc1 | Python | 4,252 | 111 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
from typing import Callable
from openfe.utils import requires_package
from ...utils.silence_root_logging import silence_root_logging
try:
with silence_root_logging():
from pers... |
88f62e596f81286038977602dabba8d1be0fe3951db85be424820efc2b294f50 | Python | 4,255 | 144 | import os
from dataclasses import dataclass, field
from logging import getLogger as get_logger
from pathlib import Path
from typing import Callable, Optional, Union
import torch
from hydra.core.config_store import ConfigStore
from hydra_zen import hydrated_dataclass, instantiate
from torch import Tensor
from torchvisi... |
a4b81674c77c4262bbe2107c9c9c98dbb3e97afac43eed131f0a8a0f9473a69e | Python | 4,257 | 125 | import numpy as np
import pytest
import pymbar
from pymbar.utils_for_testing import (
assert_array_almost_equal,
oscillators,
exponentials,
)
from pymbar.tests.test_mbar import z_scale_factor
from pymbar.mbar_solvers import _setup_jax_acceleration
@pytest.fixture(scope="module")
def base_oscillator():
... |
1f0732ea6028efcfd9838d08ad9be7e4b9a77f12fbab5dd05844b47cd9dc50a0 | Python | 4,262 | 138 | #!/usr/bin/env python
"""
classify.py is an out-of-the-box image classifer callable from the command line.
By default it configures and runs the Caffe reference ImageNet model.
"""
import numpy as np
import os
import sys
import argparse
import glob
import time
import caffe
def main(argv):
pycaffe_dir = os.path.... |
2419425808ca39351400006b556f2933eb4304b1f6234ce072d1af3881856d97 | Python | 4,265 | 134 | import logging
from typing import Dict, List, Tuple, Optional
from multiqc import config
log = logging.getLogger(__name__)
def table_data_and_headers(
rows_list: List[Tuple[str, str]],
help: List[Tuple[str, List[str]]],
namespace: Optional[str] = None,
) -> Tuple[Dict, Dict]:
"""Update the data dict... |
42ddd4b3eb4bcab60528d19db255d40f451d2f33547cac7fa538f327fbec5525 | Python | 4,266 | 119 | import h5py
import numpy as np
from pynwb import NWBHDF5IO, TimeSeries
def add_tracking_data_simple(tracking_h5_file, nwb_file):
"""Add treadmill tracking data using simple TimeSeries - avoids extension conflicts."""
# Read tracking data
with h5py.File(tracking_h5_file, "r") as f:
tracking_data =... |
77f3467ded1f57ebce3925464ceac8e7f770e1f1752584621af67b2cfaf023e4 | Python | 4,270 | 99 | import logging
import os
from PySide6.QtWidgets import QWidget, QHBoxLayout, QVBoxLayout, QScrollArea, QLabel, QSpacerItem,\
QGridLayout, QTableWidget, QTableWidgetItem, QMenu
from PySide6.QtCore import QSize, Qt, Signal
from PySide6.QtGui import QAction
from utils.software_config import SoftwareConfigResources
c... |
6a69b469bf77e80f529472cd40608699a690554c5fe173afbd4e24cba886c750 | Python | 4,277 | 111 | """
Sharpness-Aware Minimization (SAM) Optimizer.
Reference:
Foret, P., Kleiner, A., Mobahi, H., and Neyshabur, B. (2021).
Sharpness-Aware Minimization for Efficiently Improving Generalization.
In International Conference on Learning Representations (ICLR 2021).
https://arxiv.org/abs/2010.01412
... |
5d1775b6fa7a3e3cfcde04100a0113200f5839ae750d7f03c6b138e7cd0b6664 | Python | 4,278 | 157 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Mar 24 06:27:59 2025
@author: saiful
"""
#%% # load protvec df
import pandas as pd
file_path = "/data/saiful/ePPI/protvec_embeddings_eppi.csv"
df_protvec = pd.read_csv(file_path)
print("df_protvec:" ,df_protvec.head())
# ... |
24a0390e158b31a9a9c7ad48dba445765c8303211f566ae6b314b2a0aff5ffd9 | Python | 4,280 | 130 | # This code is part of kartograf and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/kartograf
import pytest
from rdkit import Chem
from kartograf import filters
@pytest.mark.parametrize("reverse", [False, True])
def test_ringsize_filter(reverse) -> None:
# naphthalene t... |
4a5894e154fa57b938b961070ca5651e759b8c2c750c45651416bba874073bac | Python | 4,284 | 114 | import os
import sys
import argparse
import numpy as np
import pandas as pd
# Allow imports from the parent directory
sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), '..')))
from src.load import load_files
from src.tables import compute_summary_row
from src.analysis import (
compute_sessio... |
bc212c9ddf9fc2b3afbbc43db57cbff0f0ea8ec6ad406ed29d3c13afcb535428 | Python | 4,286 | 128 | """ @package forcebalance.abinitio Ab-initio fitting module (energies, forces, resp).
@author Lee-Ping Wang
@date 05/2012
"""
from __future__ import division
from builtins import range
import os
import shutil
import numpy as np
from forcebalance.nifty import col, eqcgmx, flat, floatornan, fqcgmx, invert_svd, kb, prin... |
646e4b96b854548568d673ae2e30229502e64a23170db947899e790061a9a1d2 | Python | 4,287 | 84 | from __future__ import absolute_import
from builtins import str
import os, sys, shutil
from .__init__ import ForceBalanceTestCase
from forcebalance.parser import parse_inputs
from forcebalance.forcefield import FF
from forcebalance.objective import Objective
from forcebalance.optimizer import Optimizer, Counter
import ... |
004b19d2a528db16fb0940dfe5c3a78c00e381a0e546df4d0185dddd602dd8ce | Python | 4,288 | 133 | # 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,... |
1322d25991c36d52dd8891758c26df22058401b32d62b422b5678157a2a1d9bf | Python | 4,288 | 147 | # -*- 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... |
c5aaa0ecafdd31b2adb81ada4310529719d91ccdeba0c9923e694685d4d6cdac | Python | 4,292 | 98 | """Tests for the normalization layers"""
from absl.testing import parameterized
import numpy as np
import tensorflow as tf
from keras import keras_parameterized
from keras import testing_utils
from tensorflow.python.framework import test_util as tf_test_util
from tensorflow.python.platform import test
from deepcell... |
37d105b29c7fee6629ab04a16af0f8204223a00f30042bc5101a69976ea7e176 | Python | 4,294 | 98 | """SO sequence ontology 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 SoMetadata(Dict[str, Any]... |
bb755acbb6abc6027586f8cf3a37a8b93020cbd430dcd920a76748ced470d679 | Python | 4,302 | 120 | from refs import evaluation_refs, llm_base_refs, llm_teacher_refs
from refs.paper import em_numbers_refs
from truesight import parse_utils
from truesight.experiment.services import ExperimentDataRef
from refs.evals import truthfulqa
EXPERIMENT_GROUP = "em-numbers"
def _parse_em_value(row) -> float | None:
aligme... |
45885fabe396348e7346eabe44db83687b760e69fcc97eb02b5c987a325a4c06 | Python | 4,307 | 124 | import unittest
import pytest
import shapely
from shapely import geos_version
from shapely.errors import TopologicalError
from shapely.geometry import GeometryCollection, LineString, MultiPoint, Point, Polygon
from shapely.wkt import loads
class OperationsTestCase(unittest.TestCase):
def test_operations(self):
... |
86a79f42e5e6885c83040ace8ee8c7ea177a5855e5383d64582b310e18f1e557 | Python | 4,309 | 83 | ######################## BEGIN LICENSE BLOCK ########################
# The Original Code is Mozilla Universal charset detector code.
#
# The Initial Developer of the Original Code is
# Netscape Communications Corporation.
# Portions created by the Initial Developer are Copyright (C) 2001
# the Initial Developer. All R... |
d93ce0ecff2b7bdbd56f4f8fb644c7749a0387045f608a71cc02d460dfd142be | Python | 4,315 | 135 | # -*- coding: utf-8 -*-
"""
Created on Sat Jan 6 18:39:12 2024
@author: ashle
"""
import tensorflow as tf
import numpy as np
from matplotlib import pyplot as plt, rcParams
from common import Config, log, function, b_mult, simulation_points, dual_sim, dual_X
from simulate_dual import DualSolver
from simul... |
e4c17ccbea9c82bb159d043f0f7ad57f1916c98c23c2163fdb8b2a8ac9435911 | Python | 4,319 | 134 | from __future__ import annotations
from typing import TYPE_CHECKING, Any, Dict, Tuple
from fsspec.implementations.local import LocalFileSystem
from .. import constants, exceptions, types
from ..utils import io_utils
from .reader import Reader
if TYPE_CHECKING:
import xarray as xr
from fsspec.spec import Abs... |
0acf067886efb54c4647d8dd88aa65bebd9d6a906ebc22c09fbb95a676237b07 | Python | 4,323 | 131 | # -*- 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 ... |
47f2b2238dca1bd674a4862bfa811385b654627efa55d59226d1d1c86b804ac1 | Python | 4,325 | 95 | """
Authors: Andrew Clappison, John Griffiths, Zheng Wang, Davide Momi, Sorenza Bastiaens, Parsa Oveisi, Kevin Kadak, Taha Morshedzadeh, Shreyas Harita
"""
import torch
from .parameter import Parameter as par
from torch.nn.parameter import Parameter as ptParameter
from torch.nn import Module as ptModule
import... |
c69b96cc50fb40a64bcf7335f5154a19bf97d64f25589b03274f95cc4005f0cd | Python | 4,325 | 147 | import dataclasses
import io
from enum import Enum
from typing import ClassVar, Generic, List, NewType, Optional, TypeVar, Union
# Do not export typing.TypedDict: it doesn't support generics and will break Python 3.9
from pydantic import BaseModel, Field, field_validator
from typing_extensions import TypedDict
Anchor... |
2ba5091ebed9e293d55caaeb4595abe339978cee1d92544720c719512cc88989 | Python | 4,329 | 165 | """
Script to train the ResNet-18 model on Kinetics-400 video frames (control analysis 10).
"""
import argparse
import lightning as pl
from model import ResNetClassifier
from data import KineticsFrameDataModule
from utils import set_random_seeds
from lightning.pytorch.loggers import TensorBoardLogger
from lightning.py... |
be9099b75fd40f3d94309699b17a90eef891937513650926b54bbbdd56235644 | Python | 4,334 | 125 | """
Authors: Andrew Clappison, John Griffiths, Zheng Wang, Davide Momi, Sorenza Bastiaens, Parsa Oveisi, Kevin Kadak, Taha Morshedzadeh, Shreyas Harita
"""
import torch
import numpy
import numpy as np
class Parameter:
'''
Features of this class:
- This class contains a global parameter value... |
a1c8438a1cb0d0985f5b7ac8ab3eb5432f82306377e3b15ac211fa16882f5c4b | Python | 4,336 | 128 | from collections import defaultdict
from typing import List, Tuple, Iterable
import torch
import networkx as nx
def nonzero_1d(values):
output = torch.nonzero(values, as_tuple=False).squeeze()
if output.dim() == 1:
return output
return output.view(-1)
def as_numpy(val: torch.Tensor):
return... |
8291ac5fa2b5e46d31c0e58ed02815556ebb24ba2eb28f6443749b91bed0a905 | Python | 4,338 | 131 | import napari
import numpy as np
import networkx as nx
_colormaps = ['red', 'green', 'blue', 'magenta', 'cyan', 'yellow']
def view_edges(
aligner,
viewer=None,
tiles=None,
vmin=None,
vmax=None,
gamma=1/2.2,
):
"""View EdgeAligner results in a Napari viewer using a... |
c2df024db5c5919e1a8ae8c53a1327e3575cc14430d11e87517f9c520a32de92 | Python | 4,349 | 123 | import re
import pathlib
import numpy as np
import skimage.io
from . import reg
from .fileseries import _read
# Classes for reading datasets consisting of TIFF files with a naming pattern.
# The pattern must include row and column as integers, and optionally a channel
# name or number.
#
# This code is experimental a... |
40868ba94462b8e3e019f388988b5ff3d778665b58a27a726f301c3b6be30366 | Python | 4,350 | 123 | #!/usr/bin/env python
"""
MCP Configuration Generator
Utility script to generate Model Context Protocol (MCP) server configuration from a simplified input.
"""
import json
import os
import argparse
from typing import Dict, Optional, Any
from pathlib import Path
class MCPConfigGenerator:
"""Generator for MCP ser... |
f951c4860b5a3897b0bf3cf8a0b6525049e4e88b997a487183e457166e859078 | Python | 4,350 | 131 | #!/usr/bin/env python
# script to convert mappability track to binary HDF file
# excerpt from the script utils/watson_crick_counts.py
# Hufsah Ashraf (2021-03-11)
import os
# import pdb
# import argparse
import sys
from pathlib import Path
# import glob
import multiprocessing as mp
# import collections as col
# fro... |
5384dea369e36919589e40f7d8eb85a51f240db9eba54a452c38a30523ed7625 | Python | 4,351 | 139 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import pytest
from openfe import ChemicalSystem, SolventComponent
from openfe.protocols.openmm_septop import (
SepTopProtocol,
)
from openfe.protocols.openmm_septop.equil_septop_setting... |
0c01581b7be96e504ecf6de29d4e96b9bcf64836cb973553a6486d9c5cd5ab42 | Python | 4,352 | 110 | import os
from PySide6.QtWidgets import QDialog, QGridLayout, QLabel, QComboBox, QDialogButtonBox
from PySide6.QtCore import QSize
from utils.software_config import SoftwareConfigResources
class TumorTypeSelectionQDialog(QDialog):
def __init__(self, parent=None):
super(TumorTypeSelectionQDialog, self).__... |
f4f474a0a22e0b43e0dd48654db9c5baafbc8f236e150f03711a2f0b6210cd16 | Python | 4,358 | 165 | """
Code for various image utility functions (by Simon Chemnitz-Thomsen)
"""
import numpy as np
import subprocess
import os
import glob
def crop_img(img):
'''
Parameters
----------
img : numpy array
Image to be cropped.
Returns
-------
crop_img : numpy array
Cropped ima... |
fe4ea2211b72dcb392ea992647d76dd2a0a85d84a939f0a5d4c666986e434a30 | Python | 4,360 | 159 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import json
import gufe
import pytest
import openfe
from openfe.protocols import openmm_afe
from openfe.protocols.openmm_afe import (
AHFESolventAnalysisUnit,
AHFESolventSetupUnit,
... |
cb5c3db4da0f30cb318f6013d1cd2de7b1e4052a2aee3824cdafb31d5988e355 | Python | 4,362 | 118 | import psychopy.visual
import datajoint as dj
from ethopy.core.logger import stimulus
from ethopy.core.stimulus import Stimulus, StimCondition
from ethopy.stimuli.psycho_presenter import Presenter
from ethopy.utils.helper_functions import iterable
@stimulus.schema
class PsychoGrating(Stimulus, dj.Manual):
defini... |
e98ec7d15503f581624624064cee015bc6b7b13c32c73a339924e6e253edf8a5 | Python | 4,364 | 132 | import ctypes
import numpy as np
MAX_SIZE = 1024
DEV_SIZE = 256
ni845x_dll = ctypes.windll.LoadLibrary('Ni845x.dll')
class Ni845xError(Exception):
def __init__(self, status_code):
message = ctypes.create_string_buffer(MAX_SIZE)
ni845x_dll.ni845xStatusToString(status_code, MAX_SIZE, mess... |
f5fc732f2b1a19c43785583577cb5ddb99cf170fa6af9636a91bbc1833603a90 | Python | 4,364 | 88 | import subprocess
import pandas as pd
import sys, os
# snakemake_log = open(snakemake.log[0], "w")
# Prepare header of info files
subprocess.call("grep '^#' {} > {}".format(snakemake.input.info_raw, snakemake.output.info), shell=True)
subprocess.call("grep '^#' {} > {}".format(snakemake.input.info_raw, snakemake.outp... |
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