text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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|---|---|---|---|---|---|---|---|
""" ResourceStatusClient
Client to interact with the ResourceStatus service and from it with the DB.
"""
# pylint: disable=unused-argument
__RCSID__ = '$Id$'
from DIRAC import S_OK
from DIRAC.Core.Base.Client import Client, createClient
from DIRAC.ConfigurationSystem.Client.Helpers.Operations import Operations
fr... | yujikato/DIRAC | src/DIRAC/ResourceStatusSystem/Client/ResourceStatusClient.py | Python | gpl-3.0 | 16,679 | [
"DIRAC"
] | ee249b5a306569effbf0a73c0eddb064a3d6975a7f3c00d55dc3da96839d4849 |
# Copyright 2010-2017, The University of Melbourne
# Copyright 2010-2017, Brian May
#
# This file is part of Karaage.
#
# Karaage is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License... | brianmay/karaage | karaage/people/managers.py | Python | gpl-3.0 | 3,220 | [
"Brian"
] | bebb7d047fd3e45ad6e3102b2a17bd7f020ed91edab0a9765d88a3cdebe0cbca |
#!/usr/bin/env python3
import argparse, pysam, gzip
NT_PAIRS = {'G':'C', 'T':'A', 'C':'G', 'A':'T', 'N': 'N',
'g':'c', 't':'a', 'c':'g', 'a':'t', 'n': 'n'}
def reverse_complement(seq):
seq_j = ''.join( [NT_PAIRS[base_i] for base_i in seq[::-1]] )
return seq_j
def text_open_write(filename):
... | bioinform/somaticseq | somaticseq/utilities/paired_end_bam2fastq.py | Python | bsd-2-clause | 3,416 | [
"pysam"
] | 74c32c0e2f2d9c0d2eb548f0e0e37ae982b82bb223af2bdb5b4d6d821cea7579 |
import logging, re, json, commands, os, copy
from datetime import datetime, timedelta
import time
import json
import copy
import itertools, random
import string as strm
import math
from urllib import urlencode
from urlparse import urlparse, urlunparse, parse_qs
from django.utils.decorators import available_attrs
from d... | Foorth/panda-bigmon-core | core/views.py | Python | apache-2.0 | 437,120 | [
"VisIt"
] | aa6d6396c8b039ab36e3a816af2f8b62df9e1cef07ddd50a1320bd9e36dd40f8 |
# backprop.py
# to implement backprob for the simple features
# c.f. https://github.com/mnielsen/neural-networks-and-deep-learning/blob/master/code/network.py
"""
from armor.learning import backprop as bp
reload(bp)
NN = bp.Network()
NN()
"""
########################
# imports
import numpy as np
################... | yaukwankiu/armor | learning/backprop.py | Python | cc0-1.0 | 2,556 | [
"NEURON"
] | abf0a23638725e9dddaf0c91bdd3bfce45bb526f67a856ffae969d57893fe8c5 |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
'''
Short range part of ECP under PBC
'''
import ctypes
import copy
import numpy
from pyscf import lib
from pyscf import gto
from pyscf.gto import AS_ECPBAS_OFFSET, AS_NECPBAS
from pyscf.pbc.df import incore
from pyscf.pbc import gto as pgto
fro... | sunqm/mpi4pyscf | mpi4pyscf/pbc/gto/ecp.py | Python | gpl-3.0 | 2,650 | [
"PySCF"
] | 366943d3b674dfd89973f28d46f8bd9fc641d1f8929e6531e5b27e36dff37347 |
#!/usr/bin/env python
# derive motifs from transcription factor binding data
import sys
import time
import optparse
import general
import numpy
import fasta
import metrn
import modencode
import bed
import os
import copy
import pdb
import re
import network
from Bio import Motif
print "Command:", " ".join(sys.argv)
pr... | claraya/meTRN | python/memeCucu.py | Python | mit | 31,336 | [
"BWA",
"Biopython",
"Bowtie"
] | 443e19c5c96b7937f981198c484ac5c6b8d3e7aa8a570d8498605a83071ec208 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2015 Stanford University and the Authors
#
# Authors: Jason Swails
# Contributors:
#
# MDTraj is free software: you ... | swails/mdtraj | mdtraj/formats/psf.py | Python | lgpl-2.1 | 9,741 | [
"CHARMM",
"Dalton",
"MDTraj",
"OpenMM"
] | 56933c6c1da7311b9a1d8b848cd79ba2e21017774355e77e61b417c47f3c0077 |
# Copyright (C) 2012,2013,2017(H)
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
# Copyright (C) 2019
# Max Planck Computing and Data Facility
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is fre... | govarguz/espressopp | src/standard_system/Default.py | Python | gpl-3.0 | 2,476 | [
"ESPResSo"
] | 3c119af754783a62060a42123012aa86e4696ae7e4946ad6ec17cabb921105fb |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2022 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | psi4/psi4 | psi4/driver/procrouting/interface_cfour.py | Python | lgpl-3.0 | 19,073 | [
"CFOUR",
"Psi4"
] | 27b1924ff3346f8d78b93976acdd2c208443ce01cf873a2ac0a11776718a60e6 |
# Copyright Iris contributors
#
# This file is part of Iris and is released under the LGPL license.
# See COPYING and COPYING.LESSER in the root of the repository for full
# licensing details.
"""
A package for converting cubes to and from specific file formats.
"""
from iris.io.format_picker import (
FileExtensi... | bjlittle/iris | lib/iris/fileformats/__init__.py | Python | lgpl-3.0 | 4,659 | [
"NetCDF"
] | 0ebe294d0ed175c28fed8e4b1a56193441274e69f898fcef53398a1175126d6d |
# -*- coding: utf-8 -*-
"""
One-class classifer.
For more information see:
Kathryn Hempstalk, Eibe Frank, Ian H. Witten: One-Class Classification by Combining Density and Class Probability Estimation. In: Proceedings of the 12th European Conference on Principles and Practice of Knowledge Discovery in Databases and 19t... | drkatnz/CombinedOneClass | oneclass/oneclass.py | Python | mit | 6,201 | [
"Gaussian"
] | 754016e77174bf92ae4fb5342bc8ec8e7b31a7936635634a70f5ef88063b277a |
import unittest
import pysal
import numpy as np
from pysal.spreg import error_sp as SP
from scipy import sparse
class TestBaseGMError(unittest.TestCase):
def setUp(self):
db=pysal.open(pysal.examples.get_path("columbus.dbf"),"r")
y = np.array(db.by_col("HOVAL"))
self.y = np.reshape(y, (49,1... | AlanZatarain/pysal | pysal/spreg/tests/test_error_sp_sparse.py | Python | bsd-3-clause | 15,081 | [
"COLUMBUS"
] | 3ba2b290e52977d643a07a19d5a5e82767fdd32d9d91514d05cfab3620622d60 |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | markflyhigh/incubator-beam | sdks/python/apache_beam/pipeline_test.py | Python | apache-2.0 | 27,825 | [
"VisIt"
] | 139200c8042829fae231a0e51b504707bff78ce076aead6b3b3b214813f877f9 |
from taichi._lib import core as _ti_core
class CuptiMetric:
"""A class to add CUPTI metric for :class:`~taichi.profiler.kernel_profiler.KernelProfiler`.
This class is designed to add user selected CUPTI metrics.
Only available for the CUDA backend now, i.e. you need ``ti.init(kernel_profiler=True, arch=t... | yuanming-hu/taichi | python/taichi/profiler/kernel_metrics.py | Python | mit | 7,879 | [
"VisIt"
] | d48a7031b0e647f7d12b14267006f7cbd832d915137ee05dabad7ba70c9a774c |
#!/usr/bin/env python
# File created on 07 Jul 2012
from __future__ import division
__author__ = "Greg Caporaso"
__copyright__ = "Copyright 2011, The QIIME project"
__credits__ = ["Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.8.0-dev"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
from ... | wasade/qiime | qiime/parallel/map_reads_to_reference.py | Python | gpl-2.0 | 10,794 | [
"BWA"
] | 6a8391a935d9ca6a9b7f08911bd58cb444eadbd804ba54aeb4857b776a949149 |
#!/usr/bin/python
import vtk
import vtk.util.numpy_support
import numpy
import os
import sys
SRC_DIR = "./x-data/"
def captureImage(window, timestamp):
image = vtk.vtkWindowToImageFilter()
image.SetInput(window)
image.Update()
writer = vtk.vtkPNGWriter()
writer.SetFileName(".... | alyupa/multiphase-flow-modeling | visualisation/ztemp-single.py | Python | mit | 1,924 | [
"VTK"
] | 820d0fb91e7cbcc17a653884147cadf6586b44b5abfa5ebbb39dce13b7358168 |
import os
import sys
import math
import argparse
import config
import shutil
from turkic.cli import handler, importparser, Command, LoadCommand
from turkic.database import session
import sqlalchemy
import random
from vision import Box
from vision import ffmpeg
import vision.visualize
import vision.track.interpolation
i... | vovakkk/vatic | cliunique.py | Python | mit | 45,911 | [
"VisIt"
] | 5e045eb6bc83bb24d8589e5aa96c1853164d21c592b494d1fc0392b5e62cf14f |
# Generated by Django 2.2.20 on 2021-06-08 19:31
from django.db import migrations
def remove_templates(apps, schema_editor):
EmailTemplate = apps.get_model('enterprise', 'EnrollmentNotificationEmailTemplate')
EmailTemplate.objects.filter(enterprise_customer=None, template_type='SELF_ENROLL').delete()
Ema... | edx/edx-enterprise | enterprise/migrations/0133_auto_20210608_1931.py | Python | agpl-3.0 | 26,436 | [
"VisIt"
] | 9ffcc2b4818e6ebbe04468d5ab9944444e764851ea36510d4a76e1f809d22290 |
# Copyright 2014-2018 The PySCF Developers. 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 appl... | gkc1000/pyscf | pyscf/nao/m_sv_chain_data.py | Python | apache-2.0 | 2,961 | [
"PySCF"
] | 1760654a929a334eabff284761b886e8e7c032b78fa1fe02d70f2d846322bdcd |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
import re
im... | harterj/moose | python/MooseDocs/tree/latex.py | Python | lgpl-2.1 | 5,570 | [
"MOOSE"
] | ff5113897955b718e5fe2c9e7f163a427dbb012128fc07a4506fd2282a943427 |
#! /usr/bin/env python
import numpy as np
from ase.constraints import UnitCellFilter
from ase.lattice.cubic import FaceCenteredCubic
from ase.optimize import FIRE
from ase.utils.eos import EquationOfState
from atomistica import TabulatedAlloyEAM
###
n = 2
a = FaceCenteredCubic('Au', size=[n, n, n])
... | Atomistica/atomistica | examples/ASE/fcc.py | Python | gpl-2.0 | 929 | [
"ASE"
] | 231a6d9442f95322d355eaf6a9fa57dabdc25f7a5441a7ce36ab19f0bdf36e33 |
'''
MAP Client, a program to generate detailed musculoskeletal models for OpenSim.
Copyright (C) 2012 University of Auckland
This file is part of MAP Client. (http://launchpad.net/mapclient)
MAP Client is free software: you can redistribute it and/or modify
it under the terms of the GNU General Publi... | MusculoskeletalAtlasProject/mapclient-tests | test_resources/updater_test/mayaviviewerstep-master/mapclientplugins/mayaviviewerstep/step.py | Python | apache-2.0 | 7,910 | [
"Mayavi"
] | 2ad9d96043a72e74092f1176cf3c5aece2be5a29c00301e6b59e588e3bef71c2 |
import numpy as np
import unittest2 as unittest
from scipy.special import factorial
from kafe2.core.constraint import GaussianSimpleParameterConstraint, \
GaussianMatrixParameterConstraint
from kafe2.fit._base.cost import *
from kafe2.fit.histogram.cost import *
from kafe2.fit.indexed.cost import *
from kafe2.fit.... | dsavoiu/kafe2 | kafe2/test/fit/test_cost_functions.py | Python | gpl-3.0 | 13,566 | [
"Gaussian"
] | 91aec80529021808225d7223dfa39a5559400256e8b1201c6c78924e0b00d958 |
# Copyright 2001 by Gavin E. Crooks. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
""" Handle the SCOP DEScription file.
The file format is described in the scop
"release no... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/SCOP/Des.py | Python | gpl-2.0 | 2,825 | [
"Biopython"
] | 7a7934fd0ac37f5803c3a60e37538a4ddb441a826ebb4d356a8cfccea402b5e6 |
"""A set of classes used to configure resources into Slurm nodes."""
import os
from .ansible import InventoryFile
# from .ansible.api import AnsibleRunner
from .ansible.cmd import AnsibleRunner
import slurmscale as ss
import logging
log = logging.getLogger(__name__)
class ConfigManagerFactory(object):
"""A fac... | afgane/slurmscale | slurmscale/util/config_manager.py | Python | mit | 3,392 | [
"Galaxy"
] | 1345b07ca9eef0f7f7d5ef309912e404de56f0a6f65f84066a58ad4e41bdd8d4 |
from ast import parse, NodeVisitor
PSEUDO_FILENAME = 'live_source.py'
DEFAULT_MODULE_NAME = '__main__'
LIVE_MODULE_NAME = '__live_coding__'
class TracedFinder(object):
""" Find which nodes to trace in a module. """
def __init__(self, source_code, traced, filename=None):
""" Initialize the finder.
... | donkirkby/live-py-plugin | plugin/PySrc/space_tracer/traced_finder.py | Python | mit | 1,490 | [
"VisIt"
] | a7490ef9f00226e878d9b2ea175ecd90c94c4d0c5e87d2129f5be39628c604b5 |
from .PyPolyBoRi import *
from .interred import interred
def buchberger(l):
"calculates a (non minimal) Groebner basis"
l = interred(l)
#for making sure, that every polynomial has a different leading term
#needed for add_generator
if not l:
return []
g = GroebnerStrategy(l[0].ring())
... | BRiAl/BRiAl | sage-brial/brial/simplebb.py | Python | gpl-2.0 | 2,128 | [
"Gaussian"
] | c73bdb973b9e3bc1824c0a74424d73a1a0ba75f47372c97bd591a953626bfce9 |
from catkit import Gratoms
from .. import utils
import networkx as nx
import numpy as np
import ase
class Classifier():
"""Class for classification of various aspects of an an atomic
unit cell.
Currently, a tool for classification of adsorbates on surface
environments and the active sites they rest o... | jboes/CatKit | catkit/gen/analysis/classifier.py | Python | gpl-3.0 | 7,098 | [
"ASE"
] | c09ba8e919b775f7740c52325acd817bf8a5b95587f2c5902cde575d004029bd |
"""
Common Django settings for the CarnetDuMaker project.
For more information on this file, see
https://docs.djangoproject.com/en/1.7/topics/settings/
For the full list of settings and their values, see
https://docs.djangoproject.com/en/1.7/ref/settings/
"""
import os # For filesystem PATH generation and travers... | TamiaLab/carnetdumaker | carnetdumaker/settings/common.py | Python | agpl-3.0 | 19,607 | [
"VisIt"
] | 0c656318927ab90119a52839e0c3140b7817ae48e8b3f059a2a8eaa5be533079 |
import ocl
import camvtk
import time
import vtk
import datetime
import math
import random
def drawVertex(myscreen, p, vertexColor, rad=0.1):
myscreen.addActor( camvtk.Sphere( center=(p.x,p.y,p.z), radius=rad, color=vertexColor ) )
def drawEdge(myscreen, e, edgeColor=camvtk.yellow):
p1 = e[0]
p2 = e[1]
... | AlanZatarain/opencamlib | scripts/clsurf_1.py | Python | gpl-3.0 | 2,482 | [
"VTK"
] | 3e72d6c4f574c5786bbab7337d23306980eb950a60730445d355addb21c60a79 |
# -*- coding: utf-8 -*-
# Copyright 2007-2021 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at... | erh3cq/hyperspy | hyperspy/model.py | Python | gpl-3.0 | 82,619 | [
"Gaussian"
] | 65ce3d7b40965e169841e13d3688ce7c5598bc4f0da8cf8ed14430fa513455ac |
# Import OVITO modules.
from ovito import *
from ovito.io import *
from ovito.vis import OpenGLRenderer, RenderSettings
if not ovito.headless_mode:
# Import a data file.
node = import_file("../../files/CFG/shear.void.120.cfg")
renderer = OpenGLRenderer()
print("Parameter defaults:")
print(" ant... | srinath-chakravarthy/ovito | tests/scripts/test_suite/opengl_renderer.py | Python | gpl-3.0 | 533 | [
"OVITO"
] | a08a06804f8ddb44cefe910e1415ec490850172e49ca33ea0a78d6eb7296636b |
########################################################################
# $HeadURL $
# File: FTSValidator.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/04/08 14:28:29
########################################################################
""" :mod: FTSValidator
==================
.. module: FTSVal... | Sbalbp/DIRAC | DataManagementSystem/private/FTSValidator.py | Python | gpl-3.0 | 3,350 | [
"DIRAC"
] | d9b53e7197bb7f36a724d671a7f23d1a7c92204476304e9970d8555ed12b66d2 |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. 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
#
# U... | gkc1000/pyscf | pyscf/pbc/gto/pseudo/parse_cp2k.py | Python | apache-2.0 | 3,999 | [
"CP2K",
"PySCF"
] | 8f29d352c47b636a11bdc649610f20df258503aaea5614ed23ff5dd383bcbb3a |
import numpy as np
import pandas as pd
from sklearn import metrics,cross_validation
from sklearn.grid_search import GridSearchCV
from sklearn.cross_validation import train_test_split
from sklearn import svm
#Read training data and split into train and test data
data=pd.read_csv('train.csv')
data1=data.values
X=data1[:... | lingcheng99/kagge-digit-recognition | svm.py | Python | mit | 5,162 | [
"Gaussian"
] | e4294c055b42832188e934ef71044df224a6827f5e10546b1ee9ebc056e625a6 |
import numpy as np
def benitez2(p, fjac=None, x=None, y=None, err=None):
model = pow(x,p[0]) * np.exp( -(pow(x/p[1]),p[2]))
status = 0
return([status, (y-model)/err])
def parabola(p, fjac=None, x=None, y=None, err=None):
#p[0] = x_offset
#p[1] = amplitude
#p[2] = y_offset
model = p[1]... | bmazin/SDR | Projects/Simulator/fitFunctions.py | Python | gpl-2.0 | 2,488 | [
"Gaussian"
] | a4e063af943d0f614cd18620f9d8752538d89db603d1c73e69ae10031ea82084 |
#!/usr/bin/env python
import numpy as np
from numpy import random
import cv2
def make_gaussians(cluster_n, img_size):
points = []
ref_distrs = []
for i in xrange(cluster_n):
mean = (0.1 + 0.8*random.rand(2)) * img_size
a = (random.rand(2, 2)-0.5)*img_size*0.1
cov = np.dot(a.T, a) +... | apavlenko/opencv | samples/python2/gaussian_mix.py | Python | bsd-3-clause | 1,824 | [
"Gaussian"
] | eb680c313f4ed1ffe35a696edef12342ab12b8cc66a6e34ddd8dbf64f48026af |
# Sample BLAST parameters.
PARAMS = {
'application': 'BLASTN',
'blast_cutoff': [
None,
None
],
'database': 'manx-shearwater',
'database_length': 17465129,
'database_letters': None,
'database_name': [],
'database_sequences': 70016,
'date': '',
'dropoff_1st_pass': [... | bamueh/dark-matter | test/blast/sample_data.py | Python | mit | 6,857 | [
"BLAST"
] | 2ba97c395c9f52a7422caa476081a90a4e4d487595f655db4ccfd6a68a58daa5 |
#!/usr/bin/env python
# encoding: utf-8
# Thomas Nagy, 2005-2018 (ita)
"""
Runner.py: Task scheduling and execution
"""
import heapq, traceback
try:
from queue import Queue, PriorityQueue
except ImportError:
from Queue import Queue
try:
from Queue import PriorityQueue
except ImportError:
class PriorityQueue(Q... | kushview/libjuce | waflib/Runner.py | Python | gpl-2.0 | 16,392 | [
"VisIt"
] | 156ea5eaec59db093c1c27582c6423f4ef65025b073001857b24313d42d938e0 |
#
# File:
# TRANS_panel.py
#
# Synopsis:
# Illustrates how to create a panel plot
#
# Categories:
# contour plot
# panel plot
#
# Author:
# Karin Meier-Fleischer, based on NCL example
#
# Date of initial publication:
# September 2018
#
# Description:
# This example shows how to create a pan... | KMFleischer/PyEarthScience | Transition_examples_NCL_to_PyNGL/panel/TRANS_panel.py | Python | mit | 2,506 | [
"NetCDF"
] | a9a5216764c21789d064cab017aad4c84602a9998ad0fa53d0a9055957847345 |
"""
This module contains classes for representing Member object
For further information visit http://codeforces.com/api/help/objects#Member
"""
from . import BaseJsonObject
__all__ = ['Member']
class Member(BaseJsonObject):
"""
This class represents Member object
For further information visit http://... | soon/CodeforcesAPI | codeforces/api/json_objects/member.py | Python | mit | 1,075 | [
"VisIt"
] | 40dca8b9c89e592711b02968cfe0c8910d85e97955c3d14e2764147797bd31ab |
#!/usr/bin/env python
from __future__ import division
# -----------------------------------------------------------------------------
# Copyright (c) 2014--, The Qiita Development Team.
#
# Distributed under the terms of the BSD 3-clause License.
#
# The full license is in the file LICENSE, distributed with this soft... | RNAer/qiita | qiita_ware/test/test_util.py | Python | bsd-3-clause | 17,827 | [
"scikit-bio"
] | 079b2410c7750fad96f22d4eb83c9875b2d38e9436d4d6c4b2431258379923bd |
################################################################################
# Copyright Adam J. Jackson (2015) #
# #
# This program is free software: you can redistribute it and/or modify ... | WMD-Bath/CZTS-model | interpolate_thermal_property.py | Python | gpl-3.0 | 3,788 | [
"FHI-aims",
"phonopy"
] | 6cf693b0c42dfb19fcd96013938f2a843c2f50f440c682452dc9fe295f6c46d9 |
from __future__ import print_function
from time import time
from os import listdir
from sklearn.feature_extraction.text import TfidfVectorizer
from sklearn.decomposition import NMF
import numpy as np
import glob
import scipy.io
"""
Custom TFIDF NMF featurizer for the landmark classification dataset.
Built during HackM... | briansudo/Atlas | client/nmf_featurize.py | Python | apache-2.0 | 3,729 | [
"Brian"
] | 04d4fe0fe546c40dbd832bdb246785d0ac2c4c231059b8644abbf42424a91c4f |
# -*- coding: utf-8 -*-
# This file is part of Shuup.
#
# Copyright (c) 2012-2016, Shoop Commerce Ltd. All rights reserved.
#
# This source code is licensed under the AGPLv3 license found in the
# LICENSE file in the root directory of this source tree.
import re
from ast import BinOp, Mod, parse
from six import text_t... | suutari/shoop | _misc/ensure_unicode_literals.py | Python | agpl-3.0 | 3,609 | [
"VisIt"
] | 5b6d3f80ded4d67e7897169d8cdb3aa696d895e4d37f6bc9a5309018287c02df |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2010 Radim Rehurek <radimrehurek@seznam.cz>
# Licensed under the GNU LGPL v2.1 - http://www.gnu.org/licenses/lgpl.html
"""
Module for Latent Semantic Analysis (aka Latent Semantic Indexing) in Python.
Implements scalable truncated Singular Value Decompo... | ashhher3/gensim | gensim/models/lsimodel.py | Python | gpl-3.0 | 34,370 | [
"Gaussian"
] | f6a2a187edb1095224ed9835f1dbd7e7b0244cdec27eb1d12e60440fcd51de68 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | capoe/espressopp.soap | src/interaction/LennardJonesGeneric.py | Python | gpl-3.0 | 15,841 | [
"ESPResSo"
] | 87b6e50cc367b54dfcfead09b6c557d576a8703721255ba73dcd8f09baf25515 |
#!/Library/Frameworks/Python.framework/Versions/2.7/bin/python
# ----------------------------------------
# USAGE:
# ./hbond.analysis.py pdb_file trajectory_location start_traj end_traj system_descriptor
# ----------------------------------------
# PREAMBLE:
import numpy as np
import sys
import os
import MDAnalysis
... | dupontke/hbond_analysis | hbond.analysis.py | Python | gpl-3.0 | 3,966 | [
"MDAnalysis"
] | 971188e49615ac8a1cfde872927da3bc2122a82b0ee4959a409647280ccfd0db |
#! /usr/bin/env python2
############################################################################
# Copyright (C) 2011 by Hans Robeers #
# #
# This program is free software; you can redistribute it and#... | hrobeers/finFoil_legacy | fin.py | Python | gpl-3.0 | 13,286 | [
"Mayavi"
] | abfd45afd9675caa61f97906e0face4bd39592a56266ce90eadca989359e39d7 |
#
# This source file is part of appleseed.
# Visit https://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2014-2018 The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this s... | dictoon/blenderseed | __init__.py | Python | mit | 2,755 | [
"VisIt"
] | 6c3d90ad0c443d5e8d4db2d40ce628cd6c1979ad26e50ccf972f134f03761e68 |
#!/usr/bin/python
########################################################################
# 2 September 2014
# Patrick Lombard, Centre for Stem Research
# Core Bioinformatics Group
# University of Cambridge
# All right reserved.
########################################################################
import os, re, ... | pdl30/pyngsplot | pyngsplot/tools/homer_analysis.py | Python | mit | 3,046 | [
"HTSeq"
] | 85df0c2c20fbdcbe72537d5fe8a91055b907cc2449de35846b43a933910bfb7a |
# Copyright Anshuman73.
# Visit anshuman73.github.io for more info.
# Released under MIT License.
# Works with Python 2.7
import json
import requests
def main(query):
#get the data
headers = {'User-Agent': 'Mozilla/5.0 (Windows NT 10.0; WOW64) AppleWebKit/537.36 (KHTML, like Gecko)'
'Ch... | anshuman73/lyric-matcher | get_song.py | Python | mit | 1,163 | [
"VisIt"
] | 8f80aa8183e0901bf6425e021d09dc565aa2a63421fb75dea45d0f5a45428ed5 |
import numpy as np
import cv2
from binaryTransform import mag_thresh, dir_sobel_thresh
from helpers import *
import matplotlib.pyplot as plt
# normalize the _lower_ part (containing the street) to the range 0...255
def normstreet(channel):
maxval=np.max(channel[420:,:])
return 255*(channel/maxval)
def binaryp... | alex-n-braun/curve | pipeline.py | Python | gpl-3.0 | 10,278 | [
"Gaussian"
] | aeff957738b5a8fb01fed50b3827eb0049e42a204cc9542af1c700508cd6bd97 |
""" core implementation of testing process: init, session, runtest loop. """
import re
import py
import pytest, _pytest
import os, sys, imp
try:
from collections import MutableMapping as MappingMixin
except ImportError:
from UserDict import DictMixin as MappingMixin
from _pytest.runner import collect_one_node... | Carreau/pytest | _pytest/main.py | Python | mit | 26,018 | [
"VisIt"
] | 28f97eb349e1c9eed4bb7ab55558ae6e6b174d9858e2884454eab2b064801f8a |
"""
set of tools to deal with IRIS observations
"""
import numpy as np
from pkg_resources import resource_filename
def si2dn(wave, band='NUV'):
"""
Computes the coefficient to convert from flux SI units (W m^2 Hz^-1 sr^-1)
to IRIS DN (counts). Most of this code came from Viggo's routines.
Parameters
... | ITA-Solar/helita | helita/obs/iris.py | Python | bsd-3-clause | 17,676 | [
"NetCDF"
] | 3a772b284833b763327002376f6e10be54f97cab86a429658d5073e5c64d06d5 |
#!/usr/bin/python
# (C) 2013, Markus Wildi, markus.wildi@bluewin.ch
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2, or (at your option)
# any later version.
#
# Thi... | zguangyu/rts2 | scripts/rts2saf/rts2saf_analyze.py | Python | gpl-2.0 | 8,781 | [
"VisIt"
] | 298113a40a073f05016f9d89a2f91b53af38a7d896b96108f8e4c7b31d3c2686 |
#!/usr/bin/python3
#This file is the back-end for the GUI and CLI programs.
import sys;
class DCTranslator:
species = [ "", "D|Dragons", "H|Humanoids", "A|Amphibians", "B|Birds", "C|Crustaceans", "S|Dinosaurs", "E|Extraterrestrials", "F|Fish", "I|Insects", "L|Legends", "M|Mammals", "M|Molluscs", "Y|Mythical", ... | dearingj/PyDC | PyDC_backend.py | Python | gpl-3.0 | 12,874 | [
"Amber",
"CRYSTAL"
] | 15561357dbe9e4ad9cf2aadc072903b53e19c1c966cc959d7f0a9bcbfd59250c |
import vtk
from vtk.util.colors import *
import mabdi
import logging
logging.basicConfig(level=logging.DEBUG,
format="%(levelname)s %(module)s @ %(funcName)s: %(message)s")
"""
Script to test SourceEnvironmentTable
SourceEnvironmentTable creates vtkPolyData based on an environment
with a... | lucasplus/MABDI | scripts/TestSourceEnvironmentTable.py | Python | bsd-3-clause | 1,630 | [
"VTK"
] | 8a42f803f09661e8d17e75fa2ae9c9c28bbaf10180b6d297d43d42e8480aa952 |
from datascope_tools.iterators import itergrams, rank_sorted
def test_itergrams():
bunga = ['a', 'b', 'c', 'd']
# check with a couple of different sizes
assert list(itergrams(bunga, 2)) == [('a', 'b'), ('b', 'c'), ('c', 'd')]
assert list(itergrams(bunga, 3)) == [('a', 'b', 'c'), ('b', 'c', 'd')]
... | datascopeanalytics/datascope-tools | tests/test_iterators.py | Python | mit | 1,942 | [
"Brian"
] | ccd1566b49b4e7c5b0a0a102f7c41367ee8514138959ddf9b8be3aad5d9fcc25 |
"""
Notes/Code for:
<jstor>
The Cadence of English Oratorical Prose
Author(s): Morris W. Croli
Source: Studies in Philology, Vol. 16, No. 1 (Jan., 1919), pp. 1-55
Published by: University of North Carolina Press
Stable URL: http://www.jstor.org/stable/4171740 .
Accessed: 05/07/2011 14:54
</jstor>
Mr.J Sh... | quadrismegistus/litlab-poetry | prosodic/croll/croll.py | Python | mit | 16,415 | [
"VisIt"
] | 44611fa5e849d43dcc63fa42a652c06354b5640f9775c45f59095f1c6cace687 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the LMS Instructor Dashboard.
"""
import time
from nose.plugins.attrib import attr
from bok_choy.promise import EmptyPromise
from ..helpers import UniqueCourseTest, get_modal_alert, EventsTestMixin
from ...pages.common.logout import LogoutPage
from ...pages.lms.auto_a... | tiagochiavericosta/edx-platform | common/test/acceptance/tests/lms/test_lms_instructor_dashboard.py | Python | agpl-3.0 | 29,971 | [
"VisIt"
] | 74394b16b7ea216d7ecb09ca155aa5da6df6a3a04682a9c371107babf24a13d8 |
# Copyright (c) 2012 ARM Limited
# All rights reserved.
#
# The license below extends only to copyright in the software and shall
# not be construed as granting a license to any other intellectual
# property including but not limited to intellectual property relating
# to a hardware implementation of the functionality ... | alianmohammad/pd-gem5-latest | src/python/m5/SimObject.py | Python | bsd-3-clause | 57,440 | [
"VisIt"
] | f12f4f00bb5d6cea325204339d4ad20f73a8e7de79d9c8043619810b8d27b633 |
'''
Functions in this module create rays emenating from a variety
of sources in the form [opd, x, y, z, l, m, n, ux, uy, uz].
Ray Parameters:
* opd : vector tracking the optical path traveled by each ray;
only surfaces with an OPD flag in their definition will
update this vector.
* x, y... | rallured/PyXFocus | sources.py | Python | mit | 10,919 | [
"Gaussian"
] | 37fdc87e87691ea328f75475d250714ef1bceb8b0800e7973a8e2f8ec6139419 |
'''This module holds the code that allows to analyze the alignment search
result analysis.
It can deal with blasts, iprscan or ssaha2 results.
This results can be parsed, filtered and analyzed.
This module revolves around a memory structure that represents a blast or
an iprscan result. The schema of this structure is... | JoseBlanca/seq_crumbs | crumbs/seq/alignment_result.py | Python | gpl-3.0 | 48,822 | [
"BLAST",
"Biopython"
] | 07827ca955caf49f951d5b03ecc7f427e58a14e16307428d5c26840c069c3fdf |
''' Significant lifting from https://jmetzen.github.io/2015-11-27/vae.html '''
import time
import numpy as np
import tensorflow as tf
from tensorflow.python.ops import rnn
import random
import matplotlib.pyplot as plt
import re, string
from sklearn.feature_extraction.text import CountVectorizer
from collections impo... | dricciardelli/vae2vec | def_def_oh_ex.py | Python | mit | 36,948 | [
"Gaussian"
] | 8491a510e5b5a46758c71fb3d4d0e547d4a671fa466856f7fc63b92fd1287446 |
#TODO: Set dbkey to proper UCSC build, if known
import urllib
from galaxy import datatypes, config
import tempfile, shutil
def exec_before_job( app, inp_data, out_data, param_dict, tool=None):
"""Sets the name of the data"""
data_name = param_dict.get( 'name', 'HbVar query' )
data_type = param_dict.get( '... | volpino/Yeps-EURAC | tools/data_source/hbvar_filter.py | Python | mit | 2,632 | [
"Galaxy"
] | 02bfce63002e97ecab7f59c51037fd423e9244fe157fe81f4561cbb432a48984 |
# -*- coding: utf-8 -*-
# These tests require a working internet connection.
import os, sys; sys.path.insert(0, os.path.join("..", ".."))
import unittest
import time
import warnings
from pattern import web
#---------------------------------------------------------------------------------------------------
class Test... | piskvorky/pattern | test/test_web.py | Python | bsd-3-clause | 41,751 | [
"VisIt"
] | a3ed799878945fb1c613f0f1df0f9f72d282afedf1edf76df900046bf632f850 |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. 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
#
# U... | gkc1000/pyscf | pyscf/mcscf/test/test_c2h4.py | Python | apache-2.0 | 2,841 | [
"PySCF"
] | 6276f1327c741807e869b11138efe5e9c1795ab44e572c4ea0c12f4b6c6ef648 |
# Copyright (c) 2012-2016 The ANTLR Project. All rights reserved.
# Use of this file is governed by the BSD 3-clause license that
# can be found in the LICENSE.txt file in the project root.
#/
# The basic notion of a tree has a parent, a payload, and a list of children.
# It is the most abstract interface for all th... | wjkohnen/antlr4 | runtime/Python3/src/antlr4/tree/Tree.py | Python | bsd-3-clause | 4,397 | [
"VisIt"
] | b1848f396d3d40861a0b4034b8077040620f80ce61fcec454f9a4a7f4c38b9be |
from number_theory import isqrt
from fractions import gcd
from itertools import combinations_with_replacement
SIZE = 100000000
total = 0
#sum up the integer divisors
total += sum((SIZE // i) * i for i in range(1, SIZE + 1))
#loop through each possible gaussian integer (non-real)
for a, b in combinations_with_replace... | peterstace/project-euler | OLD_PY_CODE/project_euler_old_old/153/rev3.py | Python | unlicense | 639 | [
"Gaussian"
] | 5a3670b10cfae26ef4664255eba49bd9f163520663957f91046a7c46be055a33 |
"""
Calculate ejection velocity distribution
Use Wiegert (2014) Formalism
Citation: https://arxiv.org/pdf/1404.2159.pdf
"""
import numpy as np
from scipy.stats import norm as gaussian
from matplotlib import use
use('Agg')
import matplotlib.pyplot as plt
#############################################################... | seap-udea/interstellar | ejection.py | Python | gpl-3.0 | 6,685 | [
"Gaussian"
] | 561de7a1bd013fbc0ff0bc4f052a57449e5cbdc280d0daaf35e17d562e3d0bba |
################################################################################################################
# music.py Version 4.10 16-Jan-2017 Bill Manaris, Marge Marshall, Chris Benson, and Kenneth Hanson
###########################################################################
#
# This fil... | Justin-Yuan/Image2Music-Generator | library/music.py | Python | gpl-2.0 | 143,992 | [
"CRYSTAL"
] | da97fe20ef2b6af16de45ec0dc2cfc27e2a66756cee23d106e271ba12d8cda51 |
# -*- coding: utf-8 -*-
#!/usr/bin/env python3
from pythtb import tb_model,w90
from ase.calculators.interface import Calculator,DFTCalculator
from ase.dft.dos import DOS
from ase.dft.kpoints import monkhorst_pack
import numpy as np
#from tetrahedronDos import tetrahedronDosClass
from occupations import Occupations
from... | mailhexu/pyDFTutils | pyDFTutils/tightbinding/mypythTB.py | Python | lgpl-3.0 | 18,994 | [
"ASE",
"Gaussian",
"Wannier90"
] | f1d49189e92080a995e295c006d7415c338cc5b65e79e753a8f7effd507ac081 |
from galaxy.web.base.controller import *
from galaxy.web.framework.helpers import time_ago, iff, grids
from galaxy.model.orm import *
from galaxy.datatypes import sniff
from galaxy import util
from galaxy.util.streamball import StreamBall
import logging, tempfile, zipfile, tarfile, os, sys
from galaxy.web.form_builder ... | volpino/Yeps-EURAC | lib/galaxy/web/controllers/requests_admin.py | Python | mit | 86,992 | [
"Galaxy"
] | a52de8dac97e27af7cd4f24e3ac631d2afef92f7a5327447a05852b011e6cc08 |
# Copyright 2003 by Bartek Wilczynski. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Parsing AlignACE and CompareACE files: AlignAceParser,CompareAceParser
"""
from Bio.Mo... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/Motif/Parsers/AlignAce.py | Python | gpl-2.0 | 8,975 | [
"Biopython"
] | 586d934411fcb20501ee1fcc3f9f180d2b70ec2bd67f97b88eb60f0c1f5bf58c |
__author__ = 'Robert Meyer'
import logging
import os # For path names being viable under Windows and Linux
from pypet.environment import Environment
from pypet.brian.parameter import BrianParameter,BrianMonitorResult
from pypet.utils.explore import cartesian_product
# Don't do this at home:
from brian import *
# We ... | nigroup/pypet | examples/example_07_brian_network.py | Python | bsd-3-clause | 3,935 | [
"Brian",
"NEURON"
] | 9cf8b713f1c4f582fff08db2e4048eb6eb95c8dd4a37754ed03ffc0ff07dcaa2 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under th... | alejob/mdanalysis | package/MDAnalysis/analysis/legacy/x3dna.py | Python | gpl-2.0 | 35,158 | [
"MDAnalysis"
] | 60cdedc4659e98d39307cd6b2c293af65e0665838f322f6c9c0d52527d8ec44f |
from property import *
import nest
import numpy.random as random
# Neuron parameters
iaf_neuronparams = {'E_L': -70., # Resting membrane potential in mV
'V_th': -50., # Spike threshold in mV
'V_reset': -67., # Reset membrane potential after a spike in ... | vitaliykomarov/NEUCOGAR | nest/dopamine/integrated/scripts/parameters.py | Python | gpl-2.0 | 2,915 | [
"NEURON"
] | f0063e4082ab08fa8385c5627b032b1d65b70186ae7cf3a4a2a783ddbc2cd7cb |
# -*- coding: utf-8 -*-
# PyNNLess -- Yet Another PyNN Abstraction Layer
# Copyright (C) 2015 Andreas Stöckel
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the... | hbp-sanncs/pynnless | pynnless/pynnless_builder.py | Python | gpl-3.0 | 7,191 | [
"NEURON"
] | bba92a78cb39621f03cbdf51a55531aa0cd23ce71349c4ddc0621f8a813301ff |
"""
Compute saddle-point integrals over trajectories traveling on adiabataic
potentials
This currently uses first-order saddle point.
"""
import numpy as np
import nomad.math.constants as constants
import nomad.core.glbl as glbl
import nomad.compiled.nuclear_gaussian_ccs as nuclear
# Let propagator know if we need d... | mschuurman/FMSpy | nomad/integrals/mca_vibronic.py | Python | lgpl-3.0 | 3,722 | [
"Gaussian"
] | 7ef9d8c39bdb9e4254a2219b0e96299da4ef803b2d6fbbb0ae9ea384c8a4c267 |
# -*- coding: utf-8 -*-
# SyConn - Synaptic connectivity inference toolkit
#
# Copyright (c) 2016 - now
# Max-Planck-Institute for Medical Research, Heidelberg, Germany
# Authors: Sven Dorkenwald, Philipp Schubert, Joergen Kornfeld
from collections import Counter
import cPickle as pkl
import glob
import numpy as np
im... | StructuralNeurobiologyLab/SyConnFS | syconnfs/representations/super_segmentation.py | Python | gpl-2.0 | 101,748 | [
"NEURON"
] | a34552a7685e47be2ecba3f2074e4f6ec76274e6bf399403a44ccc45ae48a5b6 |
# -*- coding: utf-8 -*-
import json
import logging
import sys
import networkx as nx
from networkx.algorithms import weakly_connected_components
from collections import defaultdict
from functools import partial
from itertools import chain
from math import sqrt
from numpy import subtract
from numpy.linalg import norm
... | catmaid/CATMAID | django/applications/catmaid/control/graph.py | Python | gpl-3.0 | 20,999 | [
"NEURON"
] | d665373f18f4a998c92a0b8b98ba09f0434838a7d1b668b5c44254e40cb6d4e4 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
urlpatterns = [
url(r'^$', TemplateView.as_view(templ... | Nurdok/icanhabit | config/urls.py | Python | mit | 1,231 | [
"VisIt"
] | cf08f6e68c3f3b38d259932835d0379fb3ff7393d27e230c073eae3ddd660515 |
"""
Macro library containning diffractometer related macros for the macros
server Tango device server as part of the Sardana project.
"""
# TODO: use taurus instead of PyTango API e.g. read_attribute,
# write_attribute. This module is full of PyTango centric calls.
# TODO: use explicit getters to obtai... | sagiss/sardana | src/sardana/macroserver/macros/hkl.py | Python | lgpl-3.0 | 54,709 | [
"CRYSTAL"
] | 319e0a05e7815cec6eb2d4be42a382a012502f74025850523d587bf8249ee55a |
r"""
Gradient analyses (:mod:`skbio.stats.gradient`)
===============================================
.. currentmodule:: skbio.stats.gradient
This module provides functionality for performing gradient analyses.
The algorithms included in this module mainly allows performing analysis of
volatility on time series data, ... | anderspitman/scikit-bio | skbio/stats/gradient.py | Python | bsd-3-clause | 32,196 | [
"scikit-bio"
] | 85859aeb986956c54af387bad56f11b96ef006f6a875a969863ed9a753269104 |
##
# Copyright 2009-2016 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (F... | ocaisa/easybuild-easyblocks | easybuild/easyblocks/f/ferret.py | Python | gpl-2.0 | 4,569 | [
"NetCDF"
] | ca41e5252943aa7f884307ce1f492449e23f745839c165131985ef897ad970f7 |
import os
import re
import json
import copy
import cgi
import random
import string
import pytest
import responses
from urlobject import URLObject
from nylas import APIClient
# pylint: disable=redefined-outer-name,too-many-lines
#### HANDLING PAGINATION ####
# Currently, the Nylas API handles pagination poorly: API re... | nylas/nylas-python | tests/conftest.py | Python | mit | 76,424 | [
"VisIt"
] | 9b2e94610a39686fe829101c50a02a2574b80c98cf7e35ecd89fe0b3e750546f |
#!/usr/bin/env python
""" A unittest script for the IHMPSession module. """
import unittest
from cutlass import iHMPSession
from CutlassTestUtil import CutlassTestUtil
# pylint: disable=W0703, C1801
class IHMPSessionTest(unittest.TestCase):
""" A unit test class for the IHMPSession module. """
username = ... | ihmpdcc/cutlass | tests/test_ihmp_session.py | Python | mit | 12,662 | [
"VisIt"
] | 9e162e25703ee51dea3dee986f29e00327c1f8b999dce73a9217566b16d2359d |
from pylab import *
from scipy.spatial.distance import pdist, squareform, cdist
import theano
import theano.tensor as T
from .sinkhorn import sinkhorn_log, _sinkhorn_log, SinkhornOptions
from ..math_utils.kernels import _squared_distances, _gaussian_cross_kernels
from collections import namedtuple
VarifoldOptions = ... | jeanfeydy/lddmm-ot | LDDMM_Python/lddmm_python/modules/data_attachment/varifolds.py | Python | mit | 7,383 | [
"DIRAC",
"Gaussian"
] | 4fc04faf3478dc39eebb3d34ca01b018964e9b47a5432dfeefb4a8e05f3f6fa1 |
#/urs/bin/env python
__version__ = "0.0.1-dev"
import os
from distutils.core import setup
classes = """
Development Status :: 1 - Planning
License :: OSI Approved :: BSD License
Topic :: Software Development :: Libraries
Topic :: Scientific/Engineering
Topic :: Scientific/Engineering :: Statitics... | jwdebelius/Machiavellian | setup.py | Python | bsd-3-clause | 1,305 | [
"scikit-bio"
] | e044d4b29de9968033c0ace64f422db52bbda200e05f7940f24403dc1152e9fb |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. 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
#
# U... | gkc1000/pyscf | pyscf/cornell_shci/__init__.py | Python | apache-2.0 | 685 | [
"PySCF"
] | 922c940383e7b385412b97e9f7ca08922c8481d1faa54c5a86a50843e7de497e |
from __future__ import with_statement
import os
import re
import platform
import time
import fnmatch
import tempfile
from os import environ
from sos.utilities import (ImporterHelper,
import_module,
shell_out)
from sos.plugins import IndependentPlugin, Experimental... | harigowtham/sos | sos/policies/__init__.py | Python | gpl-2.0 | 13,869 | [
"VisIt"
] | d46098c474cd0e7bf278d359416dbe9403416f7bde48619c2e311834641f2606 |
#!/usr/bin/python2.4
# Copyright (c) 2006-2008 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
'''Unit tests for io.FileNode'''
import os
import sys
if __name__ == '__main__':
sys.path.append(os.path.join(os.path.dirnam... | meego-tablet-ux/meego-app-browser | tools/grit/grit/node/io_unittest.py | Python | bsd-3-clause | 2,812 | [
"xTB"
] | e3eb34abe20f6e1238cccf59139e6cc26b8eae25b5e8861366341c803190ef78 |
from __future__ import print_function
from hotbit import Element
from hotbit import Hotbit
import numpy as np
from ase.units import Bohr,Hartree
from hotbit import Atoms
from ase.io import read
from ase.io.trajectory import Trajectory
from box import NullCalculator
from copy import copy
from sys import stdout
import o... | pekkosk/hotbit | hotbit/parametrization/fitting.py | Python | gpl-2.0 | 31,099 | [
"ASE"
] | 8fecb949679705e490f10914d08f00076d11b17287d613465a49db824e8e6155 |
# -*- coding: utf-8 -*-
# Copyright (c) 2015-2020, Exa Analytics Development Team
# Distributed under the terms of the Apache License 2.0
from unittest import TestCase
from exatomic.gaussian.editor import Editor
class TestEditor(TestCase):
"""Tests that metadata is set appropriately for Gaussian editors."""
... | exa-analytics/atomic | exatomic/gaussian/tests/test_editor.py | Python | apache-2.0 | 770 | [
"Gaussian"
] | 07ac40945e8bcbec2d1c5d416eecaa7f9fcca1689275d3cab9a602b19afebb9c |
# Generated from ABS.g4 by ANTLR 4.7
from antlr4 import *
# This class defines a complete generic visitor for a parse tree produced by ABSParser.
class ABSVisitor(ParseTreeVisitor):
# Visit a parse tree produced by ABSParser#qualified_type_identifier.
def visitQualified_type_identifier(self, ctx):
re... | jacopoMauro/abs_deployer | ABS/ABSVisitor.py | Python | isc | 21,479 | [
"VisIt"
] | 8c29aff3c13e6db44e050996bda5b74668ff86cb5ebb4648b5342bec9360d7e6 |
# -*- coding: utf-8 -*-
# Copyright 2009-2016 Odin Hørthe Omdal
# This file is part of Medlemssys.
# Medlemssys is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (a... | Velmont/medlemssys | medlemssys/config/urls.py | Python | agpl-3.0 | 3,909 | [
"VisIt"
] | 998da8cdd38f51862cec1d5699e83e5e8d6ba0a3137836004185feb03d6480e7 |
import sys
sys.path.append('../CGvsPhoto')
import image_loader as il
from dsift import DsiftExtractor
# import pandas as pd
import matplotlib.pyplot as plt
import numpy as np
# from sklearn.neural_network import MLPClassifier
from sklearn.svm import LinearSVC
from sklearn.metrics import accuracy_score
from sklea... | NicoRahm/CGvsPhoto | Textures/texture.py | Python | mit | 12,508 | [
"Gaussian"
] | 1a08f41377e54e33d07ea1ed439184eb32568fb9636ae7b9d058cbe57c911380 |
#!/usr/bin/env python
# coding: utf-8
from __future__ import print_function, division, unicode_literals, absolute_import
import sys
import os
import warnings
import mkdocs
import mkdocs.__main__
if sys.version_info < (3, 6):
warnings.warn("Python >= 3.6 is STRONGLY recommended when building the Abinit documentati... | abinit/abinit | mksite.py | Python | gpl-3.0 | 5,142 | [
"ABINIT"
] | 1190401e2fcee1bc04328f6525f26957c193d7b37de3544852b5ebb28fc94a94 |
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