sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
2f7207a8179ab042d41efc32e424ff8b3544321335dadbdedbcf6abade3d0ef5 | Python | 623 | 19 | from __future__ import absolute_import
import os
import sys
# If we are running from a wheel, add the wheel to sys.path
# This allows the usage python pip-*.whl/pip install pip-*.whl
if __package__ == '':
# __file__ is pip-*.whl/pip/__main__.py
# first dirname call strips of '/__main__.py', second strips off ... |
62d9ed2129817badc8ebb2735636b6d59bc20869cd3194517f138ca169b5c932 | Python | 623 | 28 | from sys import argv
from msp import MSP
msp = MSP()
msp.file = __file__
msp.seed = int(argv[1])
msp.architecture = dict(
type="PreprocessedSpliceAI",
preprocessor_spec=dict(type="Identity"),
spliceai_spec=dict(
type="SpliceAIModule",
output_size=3,
spliceai_spec=dict(
t... |
93e124ef598e322e24eed6d4076390c02ffe5fce7f2394b8f827d035b7319471 | Python | 623 | 28 | from sys import argv
from msp import MSP
msp = MSP()
msp.file = __file__
msp.seed = int(argv[1])
msp.architecture = dict(
type="PreprocessedSpliceAI",
preprocessor_spec=dict(type="Identity"),
spliceai_spec=dict(
type="SpliceAIModule",
output_size=3,
spliceai_spec=dict(
t... |
d3a14956597f8134ed7eb0269faf2b6c47fb5ca1b0195f3ddd569811884bf941 | Python | 623 | 29 | import multiprocessing
from time import sleep
from codecarbon import EmissionsTracker
def no_load_task(number):
sleep(60)
def cpu_load_task(number):
a = 0
for i in range(1000):
for i in range(int(1e6)):
a = a + i**number
tracker = EmissionsTracker(
measure_power_secs=10, force... |
d8dddff54268254bd97da5b1b7c144fa333487cfc0d8aff4f63b868aac0ebea1 | Python | 623 | 28 | from sys import argv
from msp import MSP
msp = MSP()
msp.file = __file__
msp.seed = int(argv[1])
msp.architecture = dict(
type="PreprocessedSpliceAI",
preprocessor_spec=dict(type="Identity"),
spliceai_spec=dict(
type="SpliceAIModule",
output_size=3,
spliceai_spec=dict(
t... |
fe2c40cb71694b83af8aff3383c3957c0c065818d70cfa17940d48acede190c1 | Python | 623 | 14 | # Copyright 2022 Deepfold Team
#
# 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 agreed to in writin... |
5c3971d321121d6a8a3d69cd3ebf6ae1ddeb873893346892fe1dc462e2906633 | Python | 624 | 17 | #!/usr/bin/env python
# -----------------------------------------------------------------------------
# Copyright (c) 2013, The Deblur Development Team.
#
# Distributed under the terms of the BSD 3-clause License.
#
# The full license is in the file LICENSE, distributed with this software.
# --------------------------... |
9eb86c71273c53a538343db5c9019f580d02ed6cba24c4d745b65952f797be7a | Python | 624 | 21 | from sys import argv
from msp import MSP
msp = MSP()
msp.file = __file__
msp.seed = int(argv[1])
msp.architecture["num_motifs"] = 12 + 2
msp.architecture["motif_model_spec"] = dict(
type="PSAMMotifModel",
motif_spec=dict(
type="grouped",
original_spec=dict(type="rbns"),
group_motifs_pat... |
a27fd830b2998810ae5e0a669b2efa6c6699888e7dbbd9c08d3a104eaa379b2c | Python | 624 | 29 | #!/usr/bin/python
import sys
import time
from murfi_activation_communicator import MurfiActivationCommunicator
def main(argv):
roi_names = ['active']
communicator = MurfiActivationCommunicator('localhost',
15001, 85,
... |
a3c833086d6f626f257351d800b79fbf63ef66b236db0030943d000024bb394a | Python | 624 | 18 | import os
import pandas as pd
def get_add_two_numbers_dataset(num_examples: int= None):
df = pd.read_csv(os.path.join(
os.path.dirname(os.path.abspath(__file__)),
'add_two.csv'
), delimiter=',')
df['output_strings'] = df['output_strings'].str.replace("'", "")
if num_examples is not None... |
abce5b056db18a562c8e3f690eb9f26d950a66baa3cfcfdd9a9fff3b1c185a1a | Python | 624 | 21 | from sys import argv
from msp import MSP
msp = MSP()
msp.file = __file__
msp.seed = int(argv[1])
msp.architecture["num_motifs"] = 80
msp.architecture["motif_model_spec"] = dict(
type="PSAMMotifModel",
motif_spec=dict(type="rbns"),
exclude_names=("3P", "5P", "HNRNPA1", "RALY"),
)
msp.architecture["sparse_sp... |
ac2b1b06992f72bd046e54c77d78a21e37fa5846cdcff9ad1a216d90821096be | Python | 624 | 18 | import pytest
import os
from test.casestudy.Whitfield.reproduce_pseudotime_figures import reproduce_figures
def get_load_dir(request, load_directory):
file_path = os.path.join(request.fspath.dirname, load_directory)
print(file_path)
return file_path
@pytest.mark.parametrize("configuration", [1, 2])
def ... |
caca84d033f0025980a5a90de754ae71a46007be015fb6ceaaff082727605466 | Python | 624 | 24 | import pytest
from celery.utils import cached_property, chunks
@pytest.mark.parametrize('items,n,expected', [
(range(11), 2, [[0, 1], [2, 3], [4, 5], [6, 7], [8, 9], [10]]),
(range(11), 3, [[0, 1, 2], [3, 4, 5], [6, 7, 8], [9, 10]]),
(range(10), 2, [[0, 1], [2, 3], [4, 5], [6, 7], [8, 9]]),
])
def test_c... |
b1e5d070336cc151e185578a581f9a28d86c235a3600e974e74fa154bf827381 | Python | 625 | 23 | # Generated by Django 2.1.5 on 2019-05-22 12:04
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
('biomedisa_app', '0040_remove_upload_inverse_steps'),
]
operations = [
migrations.AddField(
model_name='upload',
name... |
25211b77f8a2ec12b63bf3109378e2e2f556d89ce68aaf6506971d5b1bfc7df7 | Python | 626 | 23 | # Generated by Django 3.2.6 on 2026-08-11 08:40
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
('biomedisa_app', '0119_specimen_license'),
]
operations = [
migrations.AddField(
model_name='upload',
name='separatio... |
eb5097269aa5045ce40f9420ca9e9fd48f586cf59316648af7d63c983c2bbcc9 | Python | 626 | 20 | """
Unit tests for OIDC authentication provider.
"""
from carbonserver.api.services.auth_providers.oidc_auth_provider import OIDCAuthProvider
class TestOIDCAuthProvider:
"""Test OIDC authentication provider implementation."""
def test_oidc_provider_initialization(self):
"""Test that OIDCAuthProvider... |
19efe13f4a397a4691d51cc8af85ced8b0e0e311deef7eac61d41e4d7e39bdcc | Python | 627 | 22 | import sys
from typing import TYPE_CHECKING
if TYPE_CHECKING:
from ._colorbar import ColorBar
from ._hoverlabel import Hoverlabel
from ._legendgrouptitle import Legendgrouptitle
from . import colorbar
from . import hoverlabel
from . import legendgrouptitle
else:
from _plotly_utils.importers... |
2cf81dd129bbfc7b3d9ee460e1667499346e3c278bb8d28a899e67bf5bb4c1c7 | Python | 627 | 26 | #!/usr/bin/env python
# encoding: utf-8
from __future__ import (absolute_import, division,
print_function, unicode_literals)
import os, sys, re
import logging
logger = logging.getLogger(__name__)
def get_Trinity_gene_name(transcript_name):
"""
extracts the gene name from the Trinity... |
6079959235de3ac000a02e195841e77dfa64b88249001564b94957d2ea79aeb6 | Python | 627 | 25 | import sqlite3
from .db import DB
class VaccinationTable(DB):
def __init__(self):
super().__init__()
self.table_name = 'DL_vaccination'
self.table_desc = 'Delhi state vaccination status'
self.cols = self.getcolumns()
def getcolumns(self):
cols = {
'date'... |
b67d5db241265a1e7421360096a9318a4534adffc0e45af7d19a0415db4afe4e | Python | 627 | 27 | # -*- coding: utf-8 -*-
"""
Created on Wed Dec 22 18:39:06 2021
@author: adrie
"""
import pynapple as nap
import pandas as pd
import numpy as np
def raster_plot(spike, t_ref, t_start, t_end):
# should either plot the firing of a single cell across trial
# or of multiple cells around one particular time... |
f7ecededa226f9b57e1a6186fd9d62880211c7569128d1077d8ac6d349786d51 | Python | 627 | 22 | from sys import argv
from msp import MSP
msp = MSP()
msp.file = __file__
msp.seed = int(argv[1])
msp.architecture["num_motifs"] = 1 + 2
msp.architecture["channels"] = 10
msp.architecture["motif_model_spec"]["motif_width"] = 9
msp.architecture["motif_model_spec"]["motif_feature_extractor_spec"] = dict(
type="FCMoti... |
05da30521d81115b78014c2ba55b6720f2047d128d8d3c00b0828dad50be4110 | Python | 628 | 22 | from sys import argv
from msp import MSP
msp = MSP()
msp.file = __file__
msp.seed = int(argv[1])
msp.architecture["num_motifs"] = 1 + 2
msp.architecture["channels"] = 200
msp.architecture["motif_model_spec"]["motif_width"] = 9
msp.architecture["motif_model_spec"]["motif_feature_extractor_spec"] = dict(
type="FCMot... |
3da84790ecac1bd3a7167bf16d4d57ca5b65486c14b59032b5221495f11a8b03 | Python | 628 | 22 | from sys import argv
from msp import MSP
msp = MSP()
msp.file = __file__
msp.seed = int(argv[1])
msp.architecture["num_motifs"] = 2 + 2
msp.architecture["channels"] = 200
msp.architecture["motif_model_spec"]["motif_width"] = 9
msp.architecture["motif_model_spec"]["motif_feature_extractor_spec"] = dict(
type="FCMot... |
7b841c072f03a7f115d66db6321d9fab7cc6665e7985c384f5d26e433e13de5c | Python | 628 | 22 | from sys import argv
from msp import MSP
msp = MSP()
msp.file = __file__
msp.seed = int(argv[1])
msp.architecture["num_motifs"] = 1 + 2
msp.architecture["channels"] = 200
msp.architecture["motif_model_spec"]["motif_width"] = 9
msp.architecture["motif_model_spec"]["motif_feature_extractor_spec"] = dict(
type="FCMot... |
c6267a622d02b9f212e3c036dd4288b12cf5439f3e783799f7a02bd10ff59478 | Python | 628 | 22 | from sys import argv
from msp import MSP
msp = MSP()
msp.file = __file__
msp.seed = int(argv[1])
msp.architecture["num_motifs"] = 1 + 2
msp.architecture["channels"] = 10
msp.architecture["motif_model_spec"]["motif_width"] = 9
msp.architecture["motif_model_spec"]["motif_feature_extractor_spec"] = dict(
type="FCMoti... |
da3349707f8352535352d4281e699330eb784ab0ab39c50d5420157846cdf030 | Python | 628 | 19 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
from .__version__ import __version__
# import the segmentation model
from .model import deepskin_model
# import useful constant values
from .model import MODEL_CHECKPOINT
# import model checkpoint getter
from .checkpoints import download_model_weights
# import the wound se... |
ec47e8a1aba410db00f1ea0e62c82c96b0632909aba3342960e4ca84d06a05db | Python | 628 | 22 | from sys import argv
from msp import MSP
msp = MSP()
msp.file = __file__
msp.seed = int(argv[1])
msp.architecture["num_motifs"] = 1 + 2
msp.architecture["channels"] = 200
msp.architecture["motif_model_spec"]["motif_width"] = 9
msp.architecture["motif_model_spec"]["motif_feature_extractor_spec"] = dict(
type="FCMot... |
f188516a0d93a1e36cc0e2b94c8b5cd9875da3c98274ad27497118d621ed661f | Python | 628 | 17 | """Define collection of fitting algorithms."""
from functools import partial
from specparam.utils.checks import check_selection
from specparam.algorithms.algorithm import Algorithm
from specparam.algorithms.spectral_fit import SpectralFitAlgorithm
#####################################################################... |
2390cce106d6626eb294387a47703edad3da7db7e31e8fb5652fffec5f482c8f | Python | 629 | 26 | import matplotlib
import numpy as np
import pytest
from anndata import AnnData
from mudata import MuData
import muon as mu
matplotlib.use("Agg")
@pytest.fixture
def mdata() -> MuData:
mdata = MuData(
{
"mod1": AnnData(np.arange(0, 100, 0.1).reshape(-1, 10)),
"mod2": AnnData(np.ar... |
8bce68689c655dc332d8836840b9a9b3ae13804abc1903303e1359a66777351d | Python | 629 | 22 | from sys import argv
from msp import MSP
msp = MSP()
msp.file = __file__
msp.seed = int(argv[1])
msp.architecture["num_motifs"] = 1 + 2
msp.architecture["channels"] = 200
msp.architecture["motif_model_spec"]["motif_width"] = 9
msp.architecture["motif_model_spec"]["motif_feature_extractor_spec"] = dict(
type="FCMot... |
bfdd7288dc4e467c157b9f82d1c5d51b645b18d2f7ca5e5d8ba4ee7f2bb9073e | Python | 629 | 22 | from sys import argv
from msp import MSP
msp = MSP()
msp.file = __file__
msp.seed = int(argv[1])
msp.architecture["num_motifs"] = 2 + 2
msp.architecture["channels"] = 200
msp.architecture["motif_model_spec"]["motif_width"] = 9
msp.architecture["motif_model_spec"]["motif_feature_extractor_spec"] = dict(
type="FCMot... |
d8e5cf41f0aaa597a2a96e41db1e17d432b91d1797cd06180079c2c389be1b49 | Python | 630 | 16 | from nose import tools as nt
import tns.morphmath.rotation as test_module
import numpy as np
from numpy.testing import assert_array_almost_equal, assert_array_equal
def test_vector_from_spherical():
assert_array_almost_equal(test_module.vector_from_spherical(1, 1),
[0.454649, 0.70807... |
1b4979a1aec82887332de6cef63c34cbb5cb706de148991fdff7d8ab67337540 | Python | 631 | 30 | from neuron import h, gui
def test_shared_counter():
nthreads = 32
nseg = 10
nsteps = 100
sections = [h.Section() for _ in range(nthreads)]
for s in sections:
s.insert("shared_counter")
s.nseg = nseg
pc = h.ParallelContext()
pc.nthread(nthreads)
for k, s in enumerate... |
4485a716b723ca4336d33dd141f1c43b02bc8f7746d7e113bc42648fed636fe6 | Python | 631 | 32 | from anndata import AnnData, concat, read_h5ad
try:
# anndata < 0.12
from anndata import read
except ImportError:
# anndata >= 0.12 removed `read`
read = read_h5ad
try:
# anndata < 0.12 export these at top-level
from anndata import (
read_csv,
read_excel,
read_hdf,
... |
b1309cd1234e1bda765c995b57493e088edf5cf12231ad6cd1e023612426455d | Python | 631 | 14 | # Copyright 2022 Deepfold Team
#
# 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 agreed to in writin... |
c453b3e0f9eafc0afbc5f486ca09f292f6a5580f4446ee1d92c3140eaae763e4 | Python | 631 | 25 | # %%
import argparse
import gzip
# %%
def main():
parser = argparse.ArgumentParser()
parser.add_argument('fasta')
parser.add_argument('--label', default=None)
parser.add_argument('-o', '--output')
args = parser.parse_args()
with open(args.output, 'w') as f_out:
print('sequence\tlabel',... |
e12146e1037e70d8fc79b49ad305741d4b441105b099ba24d9ad2e93581810e3 | Python | 631 | 23 | """Handle reading and writing JSON in UTF-8, on Python 3 and 2."""
import json
import sys
if sys.version_info[0] >= 3:
# Python 3
def write_json(obj, path, **kwargs):
with open(path, 'w', encoding='utf-8') as f:
json.dump(obj, f, **kwargs)
def read_json(path):
with open(path, '... |
4b7c27fcd891a2af5b6d90a94be72e33202922717c4ee60f741587927d83f7fa | Python | 632 | 29 | import numpy as np
from .annotation import Annotation
class Other(Annotation):
"""
Represents an annotation cluster that is not one of the other types.
Compatible with all junctions.
"""
@classmethod
def patterns(self):
return ["A", "D"]
def compatible_with_overlapping_junction(... |
cf7c332cc43f22166f3abfa01802a5ca21fd850447c105a89741fd0f38b6da64 | Python | 632 | 25 | from celery.result import AsyncResult
from galaxy.schema.schema import AsyncTaskResultSummary
def async_task_summary(async_result: AsyncResult) -> AsyncTaskResultSummary:
name = None
try:
name = async_result.name
except AttributeError:
# if backend is disabled, we won't have this
... |
1db8c0b9d9853c4ec3e695396f16bb1beeea13efb50514244fcf196c69145a9c | Python | 633 | 18 | """Import-time compatibility across nvidia-cutlass-dsl releases.
Select implementations here, on the host at import time, so kernels use stable names.
"""
import re
from importlib.metadata import version
CUTEDSL_VERSION = tuple(
int(part) for part in re.match(r"(\d+)\.(\d+)", version("nvidia-cutlass-dsl")).group... |
475e5f7a3a16cae962d0ddbc6e393e7f31a55c47232495468c9f5066a45d30d8 | Python | 633 | 22 | import sys
from ij import IJ
# Fiji Jython interpreter implements Python 2.5 which does not
# provide support for argparse.
input_file = sys.argv[-4]
direction = sys.argv[-3]
tmp_output_path = sys.argv[-2]
output_datatype = sys.argv[-1]
# Open the input image file.
input_image_plus = IJ.openImage(input_file)
# Crea... |
5ec98094dc7f3b8a023db20e153378b20d38ba5cc9a780a2f4e791692754cade | Python | 633 | 27 | from .layers import *
from .models import *
from .preprocessing import *
class MissingDependencyException(RuntimeError):
pass
custom_objects = {
"RBFExpansion": RBFExpansion,
"Gather": Gather,
"Reduce": Reduce,
"ConcatDense": ConcatDense,
"Tile": Tile,
"masked_mean_squared_error": masked... |
a7e9a8f89c725dc75c9e3228d070239f6713945a896d20e116359d351cfaca84 | Python | 633 | 17 | import pandas as pd
import os
here = os.path.abspath(os.path.dirname(__file__))
conversion_file = os.path.join(here, "co2eq.csv")
CONVERSION_DF = pd.read_csv(conversion_file)
def convert(g_co2eq,):
"""Converts gCO2eq to all units in range specified by CONVERSION_FILE."""
conversions = []
df = CONVERSION_... |
3c83a94319fabbe10b857a497321f11f7f560742a120f64c358ef33b2f99f1e5 | Python | 634 | 27 | from sys import argv
from msp import MSP
msp = MSP()
msp.file = __file__
msp.seed = int(argv[1])
msp.architecture["splicepoint_model_spec"] = dict(
type="BothLSSIModels",
acceptor="model/splicepoint-model-acceptor-1",
donor="model/splicepoint-model-donor-1",
)
msp.architecture["motif_model_spec"] = dict(... |
3dd3a0e005c1c07a280f90450af125c62b13953d5aa6f3b70710ba696c658a4a | Python | 634 | 27 | from sys import argv
from msp import MSP
msp = MSP()
msp.file = __file__
msp.seed = int(argv[1])
msp.architecture["splicepoint_model_spec"] = dict(
type="BothLSSIModels",
acceptor="model/splicepoint-model-acceptor-1",
donor="model/splicepoint-model-donor-1",
)
msp.architecture["motif_model_spec"] = dict(... |
547d5105819e12d726b44cf4391ad41d23c5ec14b97914c26178815c175b5ed0 | Python | 634 | 25 | from angorapy.tasks.world_building.base import PhysicalWorld
from angorapy.tasks.world_building.entities import Stage
from angorapy.tasks.envs.dexterity.mujoco_model.robot import ShadowHand, ShadowHandReach
class ShadowHandReachWorld(PhysicalWorld):
def __init__(self):
self._stage = Stage()
self.... |
76202581eaa656855771f993ec503125ac646c2cbe0a1e0078fb16237946f217 | Python | 634 | 20 | from models.basic import DeepLearningModel
from strategies.baseline import Baseline
from strategies.basic import MultiSiteLearningStrategy
from strategies.owm import OWM
from strategies.relay import Relay
from strategies.si import SI
__all__ = ['all_strategies', 'get_strategy']
all_strategies = {
'baseline': Base... |
7bf8d70b0118978f32f3f003ba666cd2a77383fc4cc86398cadc13ffa801313c | Python | 634 | 27 | from sys import argv
from msp import MSP
msp = MSP()
msp.file = __file__
msp.seed = int(argv[1])
msp.architecture["splicepoint_model_spec"] = dict(
type="BothLSSIModels",
acceptor="model/splicepoint-model-acceptor-1",
donor="model/splicepoint-model-donor-1",
)
msp.architecture["motif_model_spec"] = dict(... |
989a6352da9fb224772058a4b3f516c6ca76a90cfe80cd059ae50f1152be0ce3 | Python | 634 | 24 | import pytest
import pickle
import tempfile
from rpy2 import robjects
def test_pickle():
tmp_file = tempfile.NamedTemporaryFile()
robj = robjects.baseenv["pi"]
pickle.dump(robj, tmp_file)
tmp_file.flush()
tmp_file.seek(0)
robj_again = pickle.load(tmp_file)
tmp_file.close()
assert isi... |
a3cb8a90246cfc4ae77b43858ccffceb0c7bc5561a3a3257b8bd40ced09d5caf | Python | 634 | 20 | from pyabf.abf2.section import Section
class SynchArraySection(Section):
"""
Contains start time (in fSynchTimeUnit units) and length (in
multiplexed samples) of each portion of the data if the data
are not part of a continuous gap-free acquisition.
"""
def __init__(self, fb):
Sect... |
ad58c5a7d167e5ec2025daad0e6a37f04d8ff7f8cf093969dd4ed2b902629b0f | Python | 634 | 27 | from sys import argv
from msp import MSP
msp = MSP()
msp.file = __file__
msp.seed = int(argv[1])
msp.architecture["splicepoint_model_spec"] = dict(
type="BothLSSIModels",
acceptor="model/splicepoint-model-acceptor-1",
donor="model/splicepoint-model-donor-1",
)
msp.architecture["motif_model_spec"] = dict(... |
b04447fdcc6f06fa54e9f3c097ccf4eeec310ac71837a887d5498d17f457bb98 | Python | 634 | 23 | # Generated by Django 3.2.6 on 2022-05-27 12:25
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
('biomedisa_app', '0088_auto_20220519_1705'),
]
operations = [
migrations.AddField(
model_name='upload',
name='early_s... |
d628d89a0bac0ea7ecb4737ba8b04c56ab00188e40eb7d63046561fccd62009b | Python | 634 | 24 | import sys
from typing import TYPE_CHECKING
if TYPE_CHECKING:
from ._aaxis import Aaxis
from ._baxis import Baxis
from ._font import Font
from ._legendgrouptitle import Legendgrouptitle
from . import aaxis
from . import baxis
from . import legendgrouptitle
else:
from _plotly_utils.impor... |
df3c9ce19f5d04135c97c5af299747a4dace9dddd9f98c9cba1815b6c99ddf7f | Python | 634 | 27 | from sys import argv
from msp import MSP
msp = MSP()
msp.file = __file__
msp.seed = int(argv[1])
msp.architecture["splicepoint_model_spec"] = dict(
type="BothLSSIModels",
acceptor="model/splicepoint-model-acceptor-1",
donor="model/splicepoint-model-donor-1",
)
msp.architecture["motif_model_spec"] = dict(... |
fbf7600cf4a8f56381171dc8de7bb237d002d8cc2d2a86d66f3b2d132a75588e | Python | 634 | 21 | """Test functions for specparam.params.periodic."""
from specparam.params.periodic import *
###################################################################################################
###################################################################################################
def test_compute_fwhm():
... |
26726696c0f14b44bab917195b95ad092445a602f53ec40cba033866d7c19b6b | Python | 635 | 15 | # ------------------------------------------------------------------------------
# Copyright (c) Microsoft Corporation. All rights reserved.
# Licensed under the MIT License.
# ------------------------------------------------------------------------------
from __future__ import absolute_import
from __future__ import d... |
fba54a456963dcabdd09866bb843579c3d4b412d6b249845032f472848837596 | Python | 635 | 22 | # Default settings for image generation
class _Defaults(object):
"""
Class to store default settings for image generation.
"""
def __init__(self):
self.default_format = "png"
self.default_width = 700
self.default_height = 500
self.default_scale = 1
self.mathjax... |
ee547adcdefe580389914ed6c478cd43123530b6dd24d3900f0c40fd9425fd62 | Python | 636 | 24 | # Generated by Django 3.2.6 on 2024-11-19 16:21
import biomedisa_app.models
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
('biomedisa_app', '0117_alter_upload_epochs'),
]
operations = [
migrations.AddField(
model_name='profi... |
f6435eb0bc13b531d7d4dc27f2f053a46ab7096881dc89b1f7b9c20b6160aa9c | Python | 636 | 33 | """
Minimal working example
"""
import matplotlib.pyplot as plt
import numpy as np
import pynapple as nap
# LOADING DATA FROM NWB
data = nap.load_file("A2929-200711.nwb")
spikes = data["units"]
head_direction = data["ry"]
wake_ep = data["position_time_support"]
# COMPUTING TUNING CURVES
tuning_curves = nap.comput... |
252886b8b8b5c1fbe42d5bf1a33d1a15de268b42fd0e9ef030247c1c559c0208 | Python | 637 | 25 | import sqlite3
from .db import DB
class TestingNew(DB):
def __init__(self):
super().__init__()
self.table_name = 'KL_new_tests'
self.table_desc = 'Details of new COVID-19 samples in the last 24 hours'
self.cols = self.getcolumns()
def getcolumns(self):
cols = {
... |
4060b1d1a9f324fc2fb89fd35501e25515a14f74e0b6912d8bf65b7f1f0fc4a7 | Python | 637 | 28 | from setuptools import setup
with open("README.md", "r") as f:
long_description = f.read()
DEPENDENCIES = [
"APScheduler",
"pynvml>=5.6.2",
"psutil",
"py-cpuinfo",
]
setup(
name = 'eco2ai',
author=["Vladimir Lazarev", 'Nikita Zakharenko', 'Alexey Korovin', 'Semyon Budyonny', 'Leonid Zhuko... |
6f4905acf91cd6805a650b3cd39b74bd8587f5077012de173c4cc9f7e8b2add5 | Python | 637 | 15 | # Copyright (c) 2022 PaddlePaddle Authors. All Rights Reserved.
#
# 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 app... |
a1f6b1c5dd93b37522f39d9d192d8c924b5b33512c6888243e54adb72919deef | Python | 637 | 25 | import sqlite3
from .db import Database
from .MH_tables import MH_corporation_info, MH_district_info, MH_case_info
class MaharashtraDB(Database):
def __init__(self, datadir):
super().__init__(datadir)
self.init_tables()
self.create_tables()
def init_tables(self):
"""
... |
ab2eb8a33e3643337aac474a9e5134c4ebceeaff139ae364c14b5809d29ae2c7 | Python | 637 | 24 | import sqlite3
from .db import Database
from .KA_tables import KA_case_info, KA_district_cases, KA_individual_fatalities
class KarnatakaDB(Database):
def __init__(self, datadir):
super().__init__(datadir)
self.init_tables()
self.create_tables()
def init_tables(self):
"""
... |
dac5d53661598c9d2e5d20e2aa13544783f5c9d0100b5de7ebe15722e70ac72c | Python | 637 | 18 | from sys import argv
from msp import MSP, rbnsp_split_90
msp = MSP()
msp.file = __file__
msp.seed = int(argv[1])
msp.architecture["num_motifs"] = 4
msp.architecture["motif_model_spec"] = dict(
type="PSAMMotifModel",
motif_spec=dict(type="rbns"),
exclude_names=("3P", "5P") + tuple(x
... |
ffa773de5a41d6d636d342f128f2cceea8304c271e38c81a58517e8d6dbea66d | Python | 637 | 21 | import distutils.command.bdist_wininst as orig
class bdist_wininst(orig.bdist_wininst):
def reinitialize_command(self, command, reinit_subcommands=0):
"""
Supplement reinitialize_command to work around
http://bugs.python.org/issue20819
"""
cmd = self.distribution.reinitiali... |
4e0952e4e8ab7badb0573df80eec45c22129e4d0d8251db99d538c96842e6cfc | Python | 638 | 13 | import scipy.io as sio, glob, numpy as np
p = sorted(glob.glob("data/figshare_stroke/sourcedata/**/*.mat", recursive=True))[0]
eeg = sio.loadmat(p, struct_as_record=False, squeeze_me=True)['eeg']
d, lab = np.asarray(eeg.rawdata), np.asarray(eeg.label)
print("labels:", lab[:12], " counts:", np.bincount(lab))
sd = d.st... |
7257532d01293e32120235e5dfd5579e91d477f6b22aa8eb01c901dcc21204a4 | Python | 638 | 14 | # Copyright 2022 Deepfold Team
#
# 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 agreed to in writin... |
60fe183b6d30a969d050d2abe4c1a082381d40939d36caf099db1bdade9969d6 | Python | 639 | 23 | import numpy as np
import sys,re,os
def combine(parent,model_string):
storage = {}
print(parent)
print(model_string)
portions = [os.path.join(parent,x) for x in os.listdir(parent) if x.startswith(model_string)]
print(portions)
for portion in portions:
print(f'loading {portion}')
... |
93f38b64894b0d119abdff71cf71e9e4054415125d86234adc75e28e392baf3a | Python | 639 | 20 | """Tests for specparam.plts.error."""
import numpy as np
from specparam.tests.tutils import plot_test
from specparam.tests.tsettings import TEST_PLOTS_PATH
from specparam.plts.error import *
###################################################################################################
#########################... |
30750bb5850bc98d7ba730edeb5f101e61c9e3dda7736d9fd3b9cc2881af9276 | Python | 640 | 31 | """
type_conversions.py
Modules for converting between data types.
"""
###################################################################################################
###################################################################################################
def int_conv(value):
"""
Check if val... |
d632cb6c75335a54299b40beef176379a9615e4bc95a2c2ee36fd38de5c29782 | Python | 640 | 23 | # Generated by Django 2.2.2 on 2019-08-19 13:13
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
('biomedisa_app', '0044_auto_20190803_1500'),
]
operations = [
migrations.AddField(
model_name='upload',
name='stride_... |
797577a33fe42717e240c38d8d71d8bbc97f10686b9aba34e07bb42848c5b863 | Python | 641 | 28 | """Celery worker app module declaring a queue selected by its alias.
Used as the app module of a worker container to declare a queue topology
with :class:`kombu.Queue` objects, which cannot be serialized through the
worker configuration changes.
"""
from __future__ import annotations
import json
from kombu import Q... |
af2bdf049107dc3794a3a08d2ea489d09714668dfb1299e90cbd31372f71de90 | Python | 641 | 20 | """ monkey patched version of asynchat to allow map argument on all version of Python, and the best version of the poll function. """
from sys import version
import asynchat
import asyncore
if float(version[:3]) < 2.5:
from asyncore import poll2 as poll
else:
from asyncore import poll
# monkey patch older versions... |
84857e8c30a355ef02145757b64fc590b9cdb5dbf47ab1f148f9afc8a76175aa | Python | 642 | 15 | # Copyright 2022 Deepfold Team
#
# 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 agreed to in writin... |
95b264c33ee07d031bef358a5085de4484cbcde26ee571381ce8fe51e2d77f29 | Python | 642 | 25 | from which_tissue import *
import os
folder = "/app"
model = tf.keras.models.load_model("../../data/single_t/single_t")
for file in os.listdir(folder):
path = os.path.join(folder, file)
data = pd.read_csv(path)
data = data.reindex(columns=df_gtex.drop(columns="tissue").columns, fill_value=0)
data = da... |
a43b7b748004f5b809ee0c282729c98d5c73e444418289844065d251006efad8 | Python | 642 | 22 | # -*- coding: utf-8 -*-
# Copyright (c) 2016-2018 Braintech Sp. z o.o. [Ltd.] <http://www.braintech.pl>
# All rights reserved.
"""
Module defines a single method get_logger that returns logger with set logging level.
Change loggin.INFO lines to change logging level.
Author:
Mateusz Kruszyński <mateusz.kruszynski... |
a95247166f198c57609025b5713d5abc27ff4c2c3ef2735eb22e11d64fe3dff0 | Python | 642 | 26 | #!/usr/bin/env python3
import subprocess
import os
import tempfile
def grab_sequence(*, ref_genome, splice_table, sequence_out, CL_max):
_, temp_bed = tempfile.mkstemp(suffix=".bed")
CLr = CL_max // 2
CLl = CLr + 1
# First nucleotide not included by BEDtools
COMMAND = (
"""cat %s | awk ... |
4b84b8d39e939f7b17b2d6332e7b7baa56553650b634665cb2bf628277d0cb78 | Python | 643 | 31 | # -*- coding: utf-8 -*-
"""
Created on Tue Apr 15 16:31:37 2025
@author: Rico's Account
"""
import numpy as np
import math
from matplotlib import pyplot as plt
from scipy.integrate import solve_ivp, cumulative_trapezoid
def integral(t, z, plot = False):
if plot == True:
plt.plot(t, z... |
6c032e8f6fed0a91de071512743d35df9c6b44d07567f5fcfbb1edbe4df12a54 | Python | 643 | 18 | """
Analyses
========
An analysis is a call that can be performed outside an acquisition period.
It both takes and returns either data or preprocessed data.
Analyses are mostly specific to a certain procedure.
For example, there will be specific calls for analysis of data for the
dry electrode assessment.
There are ... |
c7f9497077a197757ea6fd731f2d9d54408ddafd3d19de54839621244e6d5130 | Python | 644 | 26 | """
demonstrate how to use the new pyabf.memtest module
"""
import os
import sys
PATH_HERE = os.path.abspath(os.path.dirname(__file__))
PATH_DATA = os.path.abspath(PATH_HERE+"../../../data/abfs/")
PATH_SRC = os.path.abspath(PATH_HERE+"../../../src/")
sys.path.insert(0, PATH_SRC)
import pyabf
import glob
import numpy a... |
028c2682a50966aed8a391774b4c00168f233a7f6ad2a309da2c4b4d5729bb3d | Python | 645 | 15 | # -----------------------------------------------------------------------------
# Copyright (c) 2019, PyInstaller Development Team.
#
# Distributed under the terms of the GNU General Public License with exception
# for distributing bootloader.
#
# The full license is in the file COPYING.txt, distributed with this softw... |
3239963ebb2a93e1d64b5b8fd90d5fb88b40f5691ef167901d629e8787e2a55e | Python | 645 | 21 | from dask import __version__ as dask_version
from packaging.version import Version
from .classes import OMEZarrImage, OMEZarrLabels, OMEZarrMultiscale, OMEZarrScene
# Expose __version__ and fallback when _version.py doesn't exist.
try:
from ._version import version as __version__
except ImportError:
__version... |
c9b7c3a6729f139e2619583d60b10f27c6454cb6e1465f91b4bf425b2fc5e553 | Python | 645 | 15 | # -----------------------------------------------------------------------------
# Copyright (c) 2019, PyInstaller Development Team.
#
# Distributed under the terms of the GNU General Public License with exception
# for distributing bootloader.
#
# The full license is in the file COPYING.txt, distributed with this softw... |
7f63db23d6339c6a8cc9e7ee22c79b2ff40da8fd7091299870bfd4f6998a5352 | Python | 646 | 36 | """add galaxy_url column to notifications
Revision ID: 5924fbf10430
Revises: 303a5583a030
Create Date: 2024-04-11 09:56:26.200231
"""
from sqlalchemy import (
Column,
String,
)
from galaxy.model.migrations.util import (
add_column,
drop_column,
)
# revision identifiers, used by Alembic.
revision = ... |
ac5ca8ee8402c7800c88f078610f835d80773eb7655829e4c0cfbe32ed1ce6c1 | Python | 646 | 22 | import numpy as np
import scipy
def generate_closeness_pairs(a, b, *, delta):
result = []
for i in range(a.shape[0]):
b_index = np.searchsorted(b, a[i] - delta)
for j in range(b_index, b.shape[0]):
if b[j] - a[i] > delta:
break
assert not (a[i] - b[j] > ... |
05c7826299dbf703a7d8a2cd5b523a2266bd6c4a1bcdf35f50037cc879cf998c | Python | 647 | 23 | # https://docs.pytest.org/en/latest/example/simple.html
import pytest
def pytest_addoption(parser):
parser.addoption(
"--runslow", action="store_true", default=False, help="run slow tests"
)
def pytest_configure(config):
config.addinivalue_line("markers", "slow: mark test as slow to run")
def... |
5d7e01d5048ffc5a089c2700172e48e232180e041ec65570a704195fba24ed51 | Python | 647 | 37 | import numpy as np
import scipy
from neuron import h, gui
from neuron.units import ms
nseg = 1
s = h.Section()
s.insert("X2Y")
s.nseg = nseg
t_hoc = h.Vector().record(h._ref_t)
X_hoc = h.Vector().record(s(0.5)._ref_X_X2Y)
Y_hoc = h.Vector().record(s(0.5)._ref_Y_X2Y)
h.stdinit()
h.tstop = 5.0 * ms
h.run()
t = np.a... |
6ca69ec7b4813dfac97080cfb49b9c2d41acab44351e86620e337e1f25674604 | Python | 647 | 33 | from __future__ import annotations
from http import HTTPStatus
from werkzeug.exceptions import BadRequest
from werkzeug.exceptions import NotFound
from flask import Flask
app = Flask(__name__)
@app.errorhandler(400)
@app.errorhandler(HTTPStatus.BAD_REQUEST)
@app.errorhandler(BadRequest)
def handle_400(e: BadReque... |
9efaa16c6f24e0992a4ea5b88dc8d0ef08a05d624532e12793bce8b0cf1a2258 | Python | 647 | 24 | import torch
def test():
N, Cin, Cout, L = 3, 5, 7, 11
r = 2
X = torch.randn(N, Cin, L)
E = torch.randn(Cout, Cin, r * 2 + 1)
fast_out = torch.nn.functional.conv1d(X, E, padding=r)
direct_out = torch.zeros(N, Cout, L)
for bidx in range(N):
for i in range(Cout):
for x i... |
e031ea001545127484ae26e865752e62a7d514800385b1f7c57f69d7c6f7e069 | Python | 647 | 18 | """
Making it easy to import in classes.
"""
from __future__ import print_function
from __future__ import division
from __future__ import unicode_literals
__author__ = "Bharath Ramsundar"
__copyright__ = "Copyright 2016, Stanford University"
__license__ = "MIT"
#from dcCustom.feat.base_classes import ProtFeaturizer
f... |
ee6565585ac2184ed7b822cef681dae59f1ce073cb627134a2360e24787c2624 | Python | 647 | 21 | import torch
from typing import Callable
def custom_amp_decorator(dec: Callable, cuda_amp_deprecated: bool):
def decorator(*args, **kwargs):
if cuda_amp_deprecated:
kwargs["device_type"] = "cuda"
return dec(*args, **kwargs)
return decorator
if hasattr(torch.amp, "custom_fwd"): # ... |
4dbd73c0e907b1b47458875c1bb5d6e46d574cd6c7815f14e15e319197eadf2a | Python | 648 | 24 | from sys import argv
from msp import MSP
msp = MSP()
msp.file = __file__
msp.seed = int(argv[1])
msp.architecture["num_motifs"] = 80
msp.architecture["sparse_spec"] = dict(type="SpatiallySparseAcrossChannels")
msp.architecture["motif_model_spec"] = dict(
type="NeuralFixedMotif",
path_format="model/rbns-binary... |
a58f6e95e51fe0f3f88c04852d509608f1467488b26c488c1f69b4f18443025a | Python | 649 | 19 | import numpy as np
import open3d as o3d
from helpers.linemesh import LineMesh
def human_pose_to_joints(p, limbs, radius=10):
joint_points = o3d.utility.Vector3dVector(p)
joint_colors = [[1, 0, 0] for _ in range(len(limbs))]
joint_lines = o3d.utility.Vector2iVector(limbs)
line_mesh = LineMesh(joint_poi... |
ead1037bab02c480af14a92a7f0f15eb99e9e8e7373b91a9631f5856c6db53b9 | Python | 649 | 25 | from setuptools import setup
setup(
name="cmkn",
version="0.1",
description="Implementation of the convolutional motif kernel network (CMKN) architecture.",
author="Jonas Ditz",
author_email="jonas.ditz@uni-tuebingen.de",
packages=["cmkn"],
python_requires=">=3.7, <3.10",
install_requir... |
0e8e42a1eba63e7d19eb61d06e9ac0f825e73de35f0c3d1cc242193b6a81677a | Python | 651 | 14 | # Copyright (c) 2022 PaddlePaddle Authors. All Rights Reserved.
#
# 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 app... |
1e2aa4805a4aa98fdd71081748afcdcef91c39c9d7fb0fa669e33d6f69f5a87e | Python | 651 | 14 | # Copyright (c) 2022 PaddlePaddle Authors. All Rights Reserved.
#
# 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 app... |
343ae9193899ddc0480926f390de2129c91779f73308a722fd1c46bc5400f04f | Python | 651 | 24 | import sqlite3
from .db import Database
from .HR_tables import HR_caseinfo, HR_districtinfo, HR_critical_case_info
class HaryanaDB(Database):
def __init__(self, datadir):
super().__init__(datadir)
self.init_tables()
self.create_tables()
def init_tables(self):
"""
Ini... |
348f4a424d04d4ab52b0cee4591811e07f361d8e0b6a03411e7714f8905862e8 | Python | 651 | 32 | """Add index on tool_id column of job table
Revision ID: a4c3ef999ab5
Revises: 75348cfb3715
Create Date: 2025-02-05 14:55:13.348044
"""
from galaxy.model.database_object_names import build_index_name
from galaxy.model.migrations.util import (
create_index,
drop_index,
)
# revision identifiers, used by Alemb... |
f5372d94c4f014d581267771b796b2a14e81ce40e85aee137430d653871fe221 | Python | 651 | 24 | from anndata import AnnData
def convert_scanpy(
adata: AnnData,
use_quality: str = "hires",
) -> AnnData | None:
adata.var_names_make_unique()
library_id = next(iter(adata.uns["spatial"].keys()))
if use_quality == "fulres":
image_coor = adata.obsm["spatial"]
else:
scale = ada... |
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