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# This file is part of wger Workout Manager.
#
# wger Workout Manager 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
# (at your option) any later version.
#
# wger W... | kjagoo/wger_stark | wger/manager/tests/test_weight_log.py | Python | agpl-3.0 | 18,455 | [
"VisIt"
] | dafd152e641c6157bed029c6cec171037212975c692a2b1d1f7c394b996d36f5 |
import numpy as np
import h5py
from dedalus import public as de
from dedalus.extras import flow_tools
import time
import argparse
import dedalus_plots as dp
import taufit
import matplotlib.pyplot as plt
def forcing(solver):
# if using dealiasing, it's important to apply the forcing on the dealiased doman (x... | jedman/dedalus-leakylid | dedalus_tausim.py | Python | gpl-2.0 | 10,007 | [
"Gaussian"
] | c34b605d0b436b207c37e6d04c071762b876cb2b26989436345383222d7e7b10 |
#!/usr/bin/env python
import os
from tempfile import tempdir
from subprocess import call
from inspect import getargspec
from cloudbio.utils import _setup_logging, _configure_fabric_environment, _parse_fabricrc
from cloudbio.biodata.genomes import install_data, install_data_s3, install_data_rsync
from cloudbio.galaxy... | heuermh/cloudbiolinux | cloudbio/deploy/__init__.py | Python | mit | 13,852 | [
"Galaxy"
] | e07b95ec6a33631b3a3794abf96bfc52274f36c9d85f37f4cdadfbc93508a506 |
../../../../share/pyshared/orca/flat_review.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/flat_review.py | Python | gpl-3.0 | 46 | [
"ORCA"
] | 947a6d0d0c8ab4d46a8cdcc853f8c1e4e6eae2dadf14d05955868556d526a98c |
"""
Module to set up run time parameters for Clawpack -- AMRClaw code.
The values set in the function setrun are then written out to data files
that will be read in by the Fortran code.
"""
import os
import numpy as np
t_shelf = 3.2*3600 # time approaching continental slope
t_harbor = 3.5*3600 # time approachi... | clawpack/adjoint | paper1_examples/tsunami_Alaska/compare/setrun_sflag_hightol.py | Python | bsd-2-clause | 16,061 | [
"NetCDF"
] | e1568ba3e238b2471f032e9c3f1b5472fa875c3d8167726519aee7859a53de1d |
# Copyright 2020 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agre... | deepmind/dm_hamiltonian_dynamics_suite | dm_hamiltonian_dynamics_suite/hamiltonian_systems/simple_analytic.py | Python | apache-2.0 | 6,192 | [
"Gaussian"
] | 0afc2e7533d1ffee0a548f8a420589ee57059b897c0bbf1fb3f2d5e06a4dc9da |
#! /usr/bin/env python3
"""
reestimate_polya_emissions.py: given two `polya-samples` TSV files based on different
underlying kmer models (with the newer TSV giving failing poly(A) segmentations),
infer the best new parameters for the HMM emissions.
Usage:
$ python reestimate_polya_emissions.py samples.old.tsv seg.old.... | jts/nanopolish | scripts/reestimate_polya_emissions.py | Python | mit | 13,740 | [
"Gaussian"
] | 7b656364ccb05d5fcb02a4d23199ffcc07713304a3f6fc1b5f335ba49331e57f |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | mfherbst/spack | var/spack/repos/builtin/packages/r-msnbase/package.py | Python | lgpl-2.1 | 2,662 | [
"Bioconductor"
] | b2eb4196704ee5c680465d5bfe7e1a7837d6769a7253ea085839a0b3d0c42297 |
"""
Module to set up run time parameters for Clawpack -- AMRClaw code.
The values set in the function setrun are then written out to data files
that will be read in by the Fortran code.
"""
import os
import numpy as np
#------------------------------
def setrun(claw_pkg='geoclaw'):
#-------------------------... | xinshengqin/tsunami_benchmarks | nthmp_currents_2015/problem2/harbor1/setrun.py | Python | bsd-3-clause | 14,360 | [
"NetCDF"
] | 0184c75151e25413929aa01cad8c24c38c137af14d6b29867e3d38680c20423c |
# -*- coding: utf-8 -*-
"""
DEMO_002 OPTION DICTIONARY
Which options can one set?
This demo explains all fields of the options dictionary, e.g. which options
you can set for the fitting process as a user.
"""
from numpy import array, exp
from psignifit.psignifit import psignifit
# to have some data we use the data... | Visdoom/psignifit-4.0 | demo_002.py | Python | gpl-3.0 | 11,305 | [
"Gaussian"
] | d2b5dcb62e069cf9df83c993f949592979d24d00d2d8fa8596252526bde7ca0c |
# $Id$
#
# Copyright (C) 2006-2011 Greg Landrum
# All Rights Reserved
#
import os
def _getCanvas():
useAGG=False
useCairo=False
Canvas=None
if not os.environ.get('RDKIT_CANVAS',''):
try:
from cairoCanvas import Canvas
useCairo=True
except ImportError:
try:
from aggCanvas impo... | rdkit/rdkit-orig | rdkit/Chem/Draw/__init__.py | Python | bsd-3-clause | 8,895 | [
"RDKit"
] | fccc71065524c2b1993c36ab0cf92ec238116f464a045c4bec4c57b2f258732b |
# -*- 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.http import HttpResponse
from django.views.generic import TemplateView
from django.views imp... | mooja/ssip3 | app/config/urls.py | Python | mit | 2,068 | [
"VisIt"
] | b8003300f17bb24110ac849bf5d92bfbe7a11942ef5971e96fb670ead0926ea2 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright 2010 L Fiaschi, T Kroeger, M Nullmaier C Sommer, C Straehle, U Koethe, FA Hamprecht.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without modification, are
# permitted provided that the following conditi... | ilastik/ilastik-0.5 | scripts/install-ilastik-deps.py | Python | bsd-2-clause | 8,354 | [
"VTK"
] | 3073048f733e6c36f5302ce5564912cfb4249c26e70fcfe0b1d43e066f663c70 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Tests for the NaiveKDE. The NaiveKDE is tested against various properties, and
in turn more advanced implementations are tested against the NaiveKDE.
"""
import numpy as np
from KDEpy.NaiveKDE import NaiveKDE
import itertools
import pytest
args = list(itertools.produ... | tommyod/KDEpy | KDEpy/tests/test_NaiveKDE.py | Python | gpl-3.0 | 5,608 | [
"Gaussian"
] | 40e07fba04724104285a51302864a6a0cca066480356bf79d91bbdfa85ca5255 |
#!/usr/bin/env python
# Copyright 2014-2019 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... | sunqm/pyscf | pyscf/pbc/scf/hf.py | Python | apache-2.0 | 32,323 | [
"CRYSTAL",
"Gaussian",
"PySCF"
] | 11675282fa5c18eebf20847d3b497d6a13d3bc0637ebf1e89c3c15e16df8805a |
# Timezone text spoke
#
# Copyright (C) 2012 Red Hat, Inc.
#
# This copyrighted material is made available to anyone wishing to use,
# modify, copy, or redistribute it subject to the terms and conditions of
# the GNU General Public License v.2, or (at your option) any later version.
# This program is distributed in th... | atodorov/anaconda | pyanaconda/ui/tui/spokes/time_spoke.py | Python | gpl-2.0 | 19,410 | [
"VisIt"
] | a69ce1b82784b8e52c12e631cf07b80f2a6686dcb5c4915a22869a29667945c9 |
"""
CBMPy: CBPlot module
====================
PySCeS Constraint Based Modelling (http://cbmpy.sourceforge.net)
Copyright (C) 2009-2022 Brett G. Olivier, VU University Amsterdam, Amsterdam, The Netherlands
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public ... | SystemsBioinformatics/cbmpy | cbmpy/CBPlot.py | Python | gpl-3.0 | 8,194 | [
"PySCeS"
] | 00cfcb3d85e1a46f62bbb42f92cad2f0b85fa373c67b0eac6ba4bfbdcaff66bb |
import random
HANGMANPICS = ['''
+---+
| |
|
|
|
|
======''','''
+---+
| |
O |
|
|
|
======''','''
+---+
| |
O |
| |
|
|
======''','''
+---+
| |
O |
/| |
|
|
======... | Nethermaker/school-projects | intro/hangman.py | Python | mit | 5,211 | [
"Galaxy"
] | 795d4bf165d8f6e7320ebb849be7299eb2c11e87324e2e4692c91b634ad2e2eb |
try: paraview.simple
except: from paraview.simple import *
paraview.simple._DisableFirstRenderCameraReset()
GraphToPolyData()
| jeromevelut/Peavip | Testing/GraphToPolyData.py | Python | gpl-3.0 | 128 | [
"ParaView"
] | df0612cc86a1f71e8af2eab063c55a991483ebde6f23ebc1a5850a0e19a86a55 |
# Copyright (c) 2009-2021 The Regents of the University of Michigan
# This file is part of the HOOMD-blue project, released under the BSD 3-Clause
# License.
"""Implement tuner utility classes."""
from math import isclose
from abc import ABCMeta, abstractmethod
class _TuneDefinition(metaclass=ABCMeta):
"""Inter... | joaander/hoomd-blue | hoomd/tune/attr_tuner.py | Python | bsd-3-clause | 16,562 | [
"HOOMD-blue"
] | 7691e6988610a836524ddb50a2523396877eac4c440c9fdb72ad2e10f8a98219 |
import unittest
import numpy as np
from math import pi, cos, sin, acos, atan
from pymicro.crystal.lattice import Lattice, CrystallinePhase, Symmetry, HklObject, HklDirection, HklPlane, SlipSystem
class LatticeTests(unittest.TestCase):
def setUp(self):
print('testing the Lattice class')
def test_equal... | heprom/pymicro | pymicro/crystal/tests/test_Lattice.py | Python | mit | 15,718 | [
"CRYSTAL"
] | 266e405e9ec251da8033b563104cfe2a8b16dc81fe63181d04c0bfd08fe579b6 |
from XDR_iocs import *
import pytest
from freezegun import freeze_time
Client.severity = 'INFO'
client = Client({'url': 'https://example.com'})
def d_sort(in_dict):
return sorted(in_dict.items())
class TestGetHeaders:
@freeze_time('2020-06-01T00:00:00Z')
def test_sanity(self, mocker):
"""
... | VirusTotal/content | Packs/CortexXDR/Integrations/XDR_iocs/XDR_iocs_test.py | Python | mit | 33,686 | [
"Amber"
] | 8471ab5f21264c9c7ce8d2a22b3ca3e2c08b0c53a2df69e554ab7a46f0aecd71 |
import time
t0t=time.time()
from os.path import join
import os
import numpy as n
import glob
import sys
import astropy.io.fits as fits
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as p
dV=-9999.99
plate = sys.argv[1] # '9003'
env = sys.argv[2] # '9003'
print plate, env
#python create_summary_ta... | JohanComparat/pySU | spm/bin/create_summary_tables.py | Python | cc0-1.0 | 17,858 | [
"Firefly"
] | 9bf93ac606254c0a5f4d3d3c8a9537b48e1a0792f5060ece272616144ff604c1 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2017 Lenovo, Inc.
#
# This file is part of Ansible
#
# Ansible 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
# ... | adityacs/ansible | lib/ansible/modules/network/lenovo/cnos_showrun.py | Python | gpl-3.0 | 4,951 | [
"VisIt"
] | 7c0cb18fb0febdef08fc00fd5ddb8b002fe0aa15e6121a1affbf5f262848552d |
__author__ = "Samuel Jackson"
__date__ = "December 2, 2014"
__license__ = "MIT"
import requests
import json
from constants import *
from request_handler import RequestHandler
class OAuth2ResourceOwner(RequestHandler):
""" Handles retrieving resources from the specified end-points.
This extension adds functi... | samueljackson92/CSAlumni-client | csa_client/oauth.py | Python | mit | 4,438 | [
"ASE"
] | 2743659c959a9f5ba6165db6bf6221e52b4e6904524578c34604abdaf1b60d5d |
#
# 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... | lukecwik/incubator-beam | sdks/python/apache_beam/ml/gcp/recommendations_ai_test_it.py | Python | apache-2.0 | 3,665 | [
"VisIt"
] | 2e04da736e0f54e64d56fa4f25a66e8f33c40d374fc4f9346274e44866f42f65 |
# coding: utf-8
# In[1]:
from __future__ import print_function
name = '2018-05-29-scrape_binstar'
title = "Binstar/conda package stats"
import os
from datetime import datetime
#from IPython.core.display import HTML
# with open('creative_commons.txt', 'r') as f:
# html = f.read()
# html = '''
# <small>
# <p> T... | psi4/psi4meta | download-analysis/conda/anaconda_dot_org_scraper.py | Python | gpl-2.0 | 7,714 | [
"Psi4"
] | 616ec3c7651f8d3745453551b93ab9841f7bf90691e8d84c6d37a1e05ecfa919 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
from pymatgen.ext.matproj import MPRester
from pymatgen.io.cif import CifParser
try:
import vtk
from pymatgen.vis.structure_vtk import StructureVis
... | Bismarrck/pymatgen | pymatgen/analysis/chemenv/utils/scripts_utils.py | Python | mit | 16,162 | [
"VTK",
"pymatgen"
] | 9b0e8d4b79d9cbab4f90158b20801a9f40f1e47303d1f0b5dd1ae0ead70b40fe |
# -*- coding: utf-8 -*-
#
# if_curve.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST 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 of the License, or
# ... | stinebuu/nest-simulator | pynest/examples/if_curve.py | Python | gpl-2.0 | 5,196 | [
"NEURON"
] | 716db44925ea318ae7954f3acf41fa351645576d1242300083257b670d2caa2a |
# -*- coding: utf8 -*-
"""
"""
__author__ = "Jérôme Samson"
__copyright__ = "Copyright 2014, Mikros Image"
import os
import sys
import csv
import time
import datetime
from optparse import OptionParser
import numpy as np
import pygal
from pygal.style import *
try:
import simplejson as json
except ImportEr... | mikrosimage/OpenRenderManagement | src/pulitools/stats/trace_queue_2dim.py | Python | bsd-3-clause | 6,873 | [
"Octopus"
] | 8a05610bf8e85653066e28b5e189e6375976470f77c67c06da6f335b0a317005 |
from __future__ import division, absolute_import, print_function
import numpy as np
from numpy.matrixlib.defmatrix import matrix, asmatrix
# need * as we're copying the numpy namespace
from numpy import *
__version__ = np.__version__
__all__ = np.__all__[:] # copy numpy namespace
__all__ += ['rand', 'randn', 'repmat... | shoyer/numpy | numpy/matlib.py | Python | bsd-3-clause | 9,694 | [
"Gaussian"
] | 614f25041b63f1f25f0d49ea60896b141401d047e40f76f0bd07344cdf54425e |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo 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 your option) any later v... | KaiSzuttor/espresso | samples/ekboundaries.py | Python | gpl-3.0 | 2,361 | [
"ESPResSo",
"VTK"
] | d356ea0e6e21f7f355473b2f64afc7fa669adeff07522d804a90767efd1d5bfe |
#!/usr/bin/env python
"""
Monitor the jobs present in the repository
Usage:
dirac-repo-monitor [options] ... RepoDir
Arguments:
RepoDir: Location of Job Repository
"""
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
__RCSID__ = "$Id$"
import DIRAC
fr... | yujikato/DIRAC | src/DIRAC/Interfaces/scripts/dirac_repo_monitor.py | Python | gpl-3.0 | 907 | [
"DIRAC"
] | 732665c129c5998a246a2b4fa768ce7123cf23cb61cc76d7f65e604155094518 |
from builtins import range
import numpy as np
def affine_forward(x, w, b):
"""
Computes the forward pass for an affine (fully-connected) layer.
The input x has shape (N, d_1, ..., d_k) and contains a minibatch of N
examples, where each example x[i] has shape (d_1, ..., d_k). We will
reshape each ... | kabrapratik28/Stanford_courses | cs231n/assignment2/cs231n/layers.py | Python | apache-2.0 | 30,161 | [
"NEURON"
] | 2866e45c290a7cc3676b6ecf14d505e7681cc91cadb0ebf8c8c242f6dd38a4f6 |
#
# Copyright (C) 2019-2020 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo 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 your option) any later... | KaiSzuttor/espresso | testsuite/python/stokesian_dynamics_cpu.py | Python | gpl-3.0 | 1,652 | [
"ESPResSo"
] | 10cabb69806d48f68e60b3df0c4db5c135ba74e10dd64d4e5ef60a79a1dea80c |
"""
[4-19-2014] Challenge #154 [Intermediate] Gorellian Alphabet Sort
https://www.reddit.com/r/dailyprogrammer/comments/20sjif/4192014_challenge_154_intermediate_gorellian/
#**Description:**
The Gorellians, at the far end of our galaxy, have discovered various samples of English text from our electronic
transmissions... | DayGitH/Python-Challenges | DailyProgrammer/DP20140419B.py | Python | mit | 2,857 | [
"Galaxy"
] | 088eff27c9f58bdbef853d22f60b0534969b912cd08f4fd2cc3398443cb85e26 |
# -*- coding: utf-8 -*-
import sys
import os
import datetime
import sphinx_bootstrap_theme
import matplotlib as mpl
mpl.use("Agg")
# Sphinx needs to be able to import fatiando to use autodoc
sys.path.append(os.path.pardir)
from fatiando import __version__, __commit__
extensions = [
'sphinx.ext.autodoc',
'sph... | mtb-za/fatiando | doc/conf.py | Python | bsd-3-clause | 5,315 | [
"Mayavi"
] | 040348a1f9a7d3295a40f25834afd9e8c77ccdf3bfbb8f885d88a4535bae4f68 |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
"""
Module to set up run time parameters for Clawpack.
The values set in the function setrun are then written out to data files
that will be read in by the Fortran code.
"""
import os
import numpy
import clawpack.geoclaw.dtopotools as dtopo
#-------------------------... | mandli/compsyn-geoclaw | setrun.py | Python | mit | 18,786 | [
"NetCDF"
] | 5b213ec177a82231e9ed16640b5ff9447c1164a3c841826f72380ee472436857 |
import csv
import yaml
import os
import glob
from pprint import pprint as pp
from utils import *
from constants import *
from logs import *
from seq_utils import *
from subprocess import Popen, PIPE
class config:
"""
Class for handling config set up.
"""
def __init__(self, config):
self.co... | AndersenLab/pyPipeline | utils/configuration.py | Python | mit | 15,150 | [
"BWA"
] | e03cf120e89a803c689825b8b98370752e7731467f40fff478d1c57014ccd16b |
import click
from parsec.cli import pass_context, json_loads
from parsec.decorators import custom_exception, json_output
@click.command('upload_file_from_url')
@click.argument("library_id", type=str)
@click.argument("file_url", type=str)
@click.option(
"--folder_id",
help="id of the folder where to place the ... | galaxy-iuc/parsec | parsec/commands/libraries/upload_file_from_url.py | Python | apache-2.0 | 1,148 | [
"Galaxy"
] | 6b22743d3072bdd28309e742c1ba7594e89352fd18abaf814d8607cdeae70e7c |
# -*- coding: utf-8 -*-
# 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
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-monitoring-dashboards | tests/unit/gapic/dashboard_v1/test_dashboards_service.py | Python | apache-2.0 | 83,643 | [
"Octopus"
] | 05ee69ab6f4929b010e4fb625f5dae4a368d2abe056bb906c22ece23aeb37180 |
# -*- coding: utf-8 -*-
# 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
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-workflows | tests/unit/gapic/workflows_v1beta/test_workflows.py | Python | apache-2.0 | 94,960 | [
"Octopus"
] | cd6963ce83b39b858627fb76ca85b4a73592aefd97c0406dbc4b6a460f2093f8 |
#!/usr/local/bin/python3.5
import json
import re
import os
import math
import codecs
import urllib
import requests
import ads
import gzip
import statistics
import time
from html import unescape
from glob import glob
from tqdm import tqdm
from collections import OrderedDict
from astropy.coordinates import SkyCoord as c... | jparrent/sne | scripts/make-host-catalog.py | Python | mit | 6,395 | [
"Galaxy"
] | e75c3ae98c88c482e576f389cdbffcc81d9abfc5fc29a434d74d7b15f94885f4 |
#!/usr/bin/python
# LICENSE: GPL2
# (c) 2015 Kamil Wartanowicz
import sys,os.path
sys.path.append(os.path.join(os.path.dirname(__file__), '../..'))
from sim import sim_router
from sim import sim_card
from sim import sim_shell
from util import hextools
from util import types_g
from util import types
import unittest
im... | kamwar/simLAB | tests/live/test_shell.py | Python | gpl-2.0 | 9,808 | [
"ADF"
] | d96d6bc109c208ad680de55934e060bbcddf889a78083e4481896ed8d8b1cbf3 |
# 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 u... | sxjscience/tvm | tests/python/frontend/pytorch/test_forward.py | Python | apache-2.0 | 113,518 | [
"VisIt"
] | 6be4db87a52e0be62f1e25322e17a1dfc219c93accb921b1c271b3f9329c3566 |
# -*- coding: utf-8 -*-
"""
Tests for user authorization password-related functionality.
"""
import json
import logging
import re
import ddt
from django.conf import settings
from django.contrib.auth import get_user_model
from django.core import mail
from django.test import TestCase
from django.test.client import Reque... | appsembler/edx-platform | openedx/core/djangoapps/user_authn/views/tests/test_password.py | Python | agpl-3.0 | 12,725 | [
"VisIt"
] | 14de40d42c1f4079491bf3500966d1b493237c4dcf2b144ee39e50196fa1c752 |
from __future__ import absolute_import
import base64
import json
import webbrowser
import inspect
import os
from os.path import isdir
import six
from plotly import utils, optional_imports
from plotly.io import to_json, to_image, write_image, write_html
from plotly.io._orca import ensure_server
from plotly.io._utils im... | plotly/plotly.py | packages/python/plotly/plotly/io/_base_renderers.py | Python | mit | 26,732 | [
"ORCA"
] | 682bef549fe48afb90ee7754ada470e9669f2bd636c025405a7e912d506db2dd |
# Copyright (c) 2012, GPy authors (see AUTHORS.txt).
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import numpy as np
from stationary import Stationary
from psi_comp import PSICOMP_RBF
from psi_comp.rbf_psi_gpucomp import PSICOMP_RBF_GPU
from ...util.config import *
class RBF(Stationary):
"""
R... | TianpeiLuke/GPy | GPy/kern/_src/rbf.py | Python | bsd-3-clause | 2,940 | [
"Gaussian"
] | ee63a4212c196dbd342395f6c146873c0c0e6caf6811b4e96ae8000bd5a5121f |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#-------------------------------
#
# BY: UNDEADSEC from BRAZIL :)
# Visit: https://www.youtube.com/c/UndeadSec
# Github: https://github.com/UndeadSec/EvilURL
# Telegram: https://t.me/UndeadSec
#
#-------------------------------
BLUE, RED, WHITE, YELLOW, ... | UndeadSec/Debinject | debinject.py | Python | bsd-3-clause | 5,133 | [
"VisIt"
] | 34e4e89f1c7c07726820d023743e44e6dd3192ad841efee3c2168b7413beb04b |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the LMS.
"""
from flaky import flaky
from textwrap import dedent
from unittest import skip
from nose.plugins.attrib import attr
from bok_choy.promise import EmptyPromise
from bok_choy.web_app_test import WebAppTest
from ..helpers import (
UniqueCourseTest,
Even... | cselis86/edx-platform | common/test/acceptance/tests/lms/test_lms.py | Python | agpl-3.0 | 39,598 | [
"VisIt"
] | 513c7440d5d78b99f2c618c8be3eaa61ac84b026b7815f01a114de714d68f511 |
# Licensed under the MIT license
# http://opensource.org/licenses/mit-license.php or see LICENSE file.
# Copyright 2007-2008 Brisa Team <brisa-develop@garage.maemo.org>
#
# Copyright 2001 - Cayce Ullman <http://pywebsvcs.sourceforge.net>
# Copyright 2001 - Brian Matthews <http://pywebsvcs.sourceforge.net>
# Copyright 2... | aleixq/python3-brisa | brisa/upnp/soap.py | Python | mit | 12,811 | [
"Brian"
] | a57462087bcd0f71b66a3aff299ea25391866379216f58869c8eee44f1add0a1 |
# ===============================================================================
# Copyright (C) 2010 Diego Duclos
#
# This file is part of eos.
#
# eos is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, ... | pyfa-org/Pyfa | eos/saveddata/damagePattern.py | Python | gpl-3.0 | 17,901 | [
"Jaguar"
] | 97b6bb3be90f3cab098bc98df75beb94c7767e755f08fe581cc8d3886939ca01 |
# -*- coding: utf-8 -*-
#
#Created on Mon Apr 3 15:14:34 2017
#
#author: Elina Thibeau-Sutre
#
import numpy as np
import random
def initialization_random(n_components,points):
"""
This method returns an array of k points which will be used in order to
initialize a k_means algorithm
Parameters
... | 14thibea/megamix | megamix/batch/initializations.py | Python | apache-2.0 | 12,778 | [
"Gaussian"
] | 9789e914be091f19805b4196d1a9700ad07b58686b7bfda945cf02efe98195f0 |
#!/usr/bin/env python
"""Run LOH heterogeneity comparison amongst mutiple methods, focusing on HLA.
Includes LOHHLA with inputs from a bcbio OptiType hg38, PureCN, TitanCNA Cromwell run.
Requires:
- pdftoppm (from poppler-utils) for plot generation from pdfs
"""
from __future__ import print_function
import colle... | a113n/bcbio-nextgen | scripts/utils/hla_loh_comparison.py | Python | mit | 17,689 | [
"BWA"
] | 918c99450c3d5848627fc22ea6852df1890c0350a638c89216073111f901d20c |
# -*- coding: utf-8 -*-
# Author: Vincent Dubourg <vincent.dubourg@gmail.com>
# (mostly translation, see implementation details)
# Licence: BSD 3 clause
from __future__ import print_function
import numpy as np
from scipy import linalg, optimize
from ..base import BaseEstimator, RegressorMixin
from ..metrics... | pratapvardhan/scikit-learn | sklearn/gaussian_process/gaussian_process.py | Python | bsd-3-clause | 34,972 | [
"Gaussian"
] | 136188d8a919a8b29e315d936900fa9eb89d7376a44ece1191ac43dd5f5a7879 |
"""Functions to plot epochs data."""
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Denis Engemann <denis.engemann@gmail.com>
# Martin Luessi <mluessi@nmr.mgh.harvard.edu>
# Eric Larson <larson.eric.d@gmail.com>
# Jaakko Leppakangas <jaeilepp@student.jyu.fi>
# ... | drammock/mne-python | mne/viz/epochs.py | Python | bsd-3-clause | 43,879 | [
"Gaussian"
] | 2b8171f0f1030a7a2a73c9f523163719c3d01fa6e3399792c0fb4f16de929d73 |
# coding: utf-8
"""
This module defines the events signaled by abinit during the execution. It also
provides a parser to extract these events form the main output file and the log file.
"""
from __future__ import unicode_literals, division, print_function
import os.path
import collections
import yaml
from monty.fnmat... | Dioptas/pymatgen | pymatgen/io/abinitio/events.py | Python | mit | 14,084 | [
"ABINIT",
"pymatgen"
] | 8ce9e7c2d5953d2b033390543f68e6f1ec6b997b7644400dd864a86b0c038051 |
# -*- coding: utf-8 -*-
# Copyright 2007-2016 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... | MartialD/hyperspy | hyperspy/tests/signal/test_remove_background.py | Python | gpl-3.0 | 6,248 | [
"Gaussian"
] | dcefc42632ef2d1d9a157be0d6ef8830ee5e43a4bcf58f07852aca1ed1bb32d7 |
# -*- coding: utf-8 -*-
#
# brunel_alpha_nest.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST 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 of the Licen... | terhorstd/nest-simulator | pynest/examples/brunel_alpha_nest.py | Python | gpl-2.0 | 14,139 | [
"NEURON"
] | 35cdb120e4f613c75c68d3b5da606441e6f62f1b3d5e564f0af3ca49661653e9 |
from ase import io
t = io.read('mytrajectory.traj')
for i, s in enumerate(t):
# rotate to the desired direction
s.rotate('z', 'x', rotate_cell=True)
# repeat with keeping old cell
cell = s.get_cell()
s = s.repeat((1, 3, 3))
s.set_cell(cell)
ofname = str(i) + '.png'
print('writing', o... | misdoro/python-ase | doc/development/writepngs.py | Python | gpl-2.0 | 456 | [
"ASE"
] | fbf7a6925ab123681242b2b20eea53c5e67fe4bc29dd27257679e6c4bc69dacd |
# -*- coding: utf-8 -*-
# Copyright 2013 splinter authors. All rights reserved.
# Use of this source code is governed by a BSD-style
# license that can be found in the LICENSE file.
import os
import unittest
from splinter import Browser
from .fake_webapp import EXAMPLE_APP
from .base import WebDriverTests
from selen... | lrowe/splinter | tests/test_webdriver_chrome.py | Python | bsd-3-clause | 1,916 | [
"VisIt"
] | 8f02e8701b0b967c77fda81b589dc529357d87636d921a630ad24bcfc71f65f7 |
from __future__ import print_function
import matplotlib
matplotlib.use('Agg')
import pylab as plt
import numpy as np
from glob import glob
import os
import re
from astrometry.util.fits import fits_table, merge_tables
from astrometry.libkd.spherematch import match_radec
from astrometry.util.plotutils import PlotSequen... | legacysurvey/pipeline | py/legacyanalysis/compare-two-catalogs.py | Python | gpl-2.0 | 18,973 | [
"Gaussian"
] | 428cf1e2b40e6f3c4176ca352293c7761ab09231e4ece67817d075d21d66233f |
# $HeadURL$
__RCSID__ = "$Id$"
import re
from distutils.version import LooseVersion
from DIRAC import S_OK, S_ERROR, gConfig
from DIRAC.ConfigurationSystem.Client.Helpers.Path import cfgPath
from DIRAC.Core.Utilities.List import uniqueElements... | vmendez/DIRAC | ConfigurationSystem/Client/Helpers/Resources.py | Python | gpl-3.0 | 9,897 | [
"DIRAC"
] | 8304e756594115091ccc4b532f66887b8179509128a161a831283eed1ef4327d |
#!/bin/env python3
import COPASI
dm = COPASI.CRootContainer.addDatamodel()
def create_datahandler(names):
"""initialize datahandler from display names
"""
dh = COPASI.CDataHandler()
for name in names:
obj = dm.findObjectByDisplayName(name)
if not obj:
print('no object for name {0}'.forma... | copasi/COPASI | copasi/bindings/python/examples/custom_output.py | Python | artistic-2.0 | 1,243 | [
"COPASI"
] | d7712838b34adfe960de74c8817cfc1f67ee10d06c85a310bd28296fe13686e4 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This package contains standard serializers that can work generally for all
pymatgen objects.
"""
| sonium0/pymatgen | pymatgen/serializers/__init__.py | Python | mit | 211 | [
"pymatgen"
] | 63623c5dfc0698956f1b09f7cef5da1ee38414ed8d6b1d83780041ea69c3bd3f |
import numpy as np
from .control import model_setup
from .cp_confocal import twod
from .cp_triplet import trip
# 2D + TT Gauß
# Model 6003
def CF_Gxy_gauss_2DTT(parms, tau):
u""" Two-dimensional free diffusion
with a Gaussian laser profile, including two triplet components.
The triplet factor tak... | paulmueller/PyCorrFit | pycorrfit/models/model_confocal_tt_2d.py | Python | gpl-2.0 | 3,122 | [
"Gaussian"
] | dc53dd30b4337047143117e371c7e64fd128cd225dd6a38b9280c0076a1e1c99 |
# coding: utf-8
"""
Vericred API
Vericred's API allows you to search for Health Plans that a specific doctor
accepts.
## Getting Started
Visit our [Developer Portal](https://developers.vericred.com) to
create an account.
Once you have created an account, you can create one Application for
Production and an... | vericred/vericred-python | vericred_client/models/base_plan_search_response.py | Python | apache-2.0 | 12,846 | [
"VisIt"
] | 7904bc86b07e3f8cc1b8028c198fbedbff190534c47e639ae83033f03b4c2e0c |
import os
import cPickle
from IPython.parallel import Client
from pyglm.utils.parallel_util import initialize_imports, create_population_on_engines
from pyglm.utils.io import parse_cmd_line_args, load_data
from population import Population
from pyglm.models.model_factory import *
def initialize_parallel_... | slinderman/theano_pyglm | test/parallel_harness.py | Python | mit | 2,396 | [
"Gaussian"
] | 3d51c7427d02eb2b693e197adcdbb6e95dc1b61c1f5a7a1111b9705067da6161 |
# Copyright (C) 2016 Zhixian MA <zxma_sjtu@qq.com>
"""
Transform cavities regions of samples selected from paper
arXiv-1610.03487.
Reference
---------
[1] J. Shin, J. Woo, and, J. Mulchaey
"A systematic search for X-ray cavities in galaxy clusters,
groups, and elliptical galaxies"
arXiv-1610.03487
"""
imp... | myinxd/cavdet | cnn/getReg.py | Python | mit | 1,385 | [
"Galaxy"
] | e1a763f962ee01f5918047d445cfc3385e8e0725654afcd06accf11af49a0b9d |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkImageDifference(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vt... | chrisidefix/devide | modules/vtk_basic/vtkImageDifference.py | Python | bsd-3-clause | 508 | [
"VTK"
] | 53a46d260875d64e90b09d668288ba021d49cb92471a0f004be068fed8fcdfe5 |
# Copyright: (c) 2019, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import fnmatch
import json
import operator
import os
import shutil
import stat
import sys
import t... | k0ste/ansible | lib/ansible/galaxy/collection.py | Python | gpl-3.0 | 55,098 | [
"Galaxy"
] | 89ab83329a3f79b5ed29f3f0a010a9da897561d73a6e4f973860cdb96d6d82e5 |
#
# $Id: locdata.py 9954 2011-06-23 22:03:57Z ahartvigsen $
#
# Proprietary and confidential.
# Copyright $Date:: 2011#$ Perfect Search Corporation.
# All rights reserved.
#
import sys, os, re, optparse, codecs, zipfile, glob, xml.dom.minidom
import subprocess
import _locpaths
import pslocale, ioutil, metadat... | perfectsearch/sandman | code/buildscripts/l10n/locdata.py | Python | mit | 37,139 | [
"VisIt"
] | 1b8463bb29bbb0d086081f91191ff1961cf38fbbfe3c3ad7b4763bc2c0ee009f |
#!/usr/bin/python3
#
# flightpanel - A Cortex-M4 based USB flight panel for flight simulators.
# Copyright (C) 2017-2017 Johannes Bauer
#
# This file is part of flightpanel.
#
# flightpanel is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# t... | johndoe31415/flightpanel | usb-descriptor-tool/usb_descriptor_gen.py | Python | gpl-3.0 | 7,456 | [
"ADF"
] | f85c971ae269f983d92049deb9f6ef2e1851e6c9345759d696542ad01c3c310e |
# Authors: Nicolas Goix <nicolas.goix@telecom-paristech.fr>
# Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# License: BSD 3 clause
import numbers
import numpy as np
from scipy.sparse import issparse
from warnings import warn
from ..tree import ExtraTreeRegressor
from ..utils import (
chec... | anntzer/scikit-learn | sklearn/ensemble/_iforest.py | Python | bsd-3-clause | 18,708 | [
"Gaussian"
] | 3adbda9bc4dbaa50c46b58650401e683714883f94f1a88defe98525b135cdd20 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module defines classes representing non-periodic and periodic sites.
"""
import collections
import json
from typing import Optional, Tuple, Union
import numpy as np
from monty.dev import deprecated
f... | richardtran415/pymatgen | pymatgen/core/sites.py | Python | mit | 23,358 | [
"pymatgen"
] | 37c0fdfe4dd344810a50420131e6ec1f74df2a5f0d0dc6d1b7201693f8aec794 |
# -*- coding: utf-8 -*-
# -----------------------------------------------------------------------
# Copyright (c) 2009 Jendrik Seipp
#
# RedNotebook 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 vers... | pakesson/rednotebook | rednotebook/gui/richtext.py | Python | gpl-2.0 | 11,878 | [
"VisIt"
] | a00b246063f861ddfbce0fee1f31e856e19a60ca2bc91fdbe446f1f1780e602f |
# Copyright (C) 2015 Hydriz Scholz
#
# 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 License, or
# (at your option) any later version.
#
# This program is distributed in ... | Hydriz/DBReports | DBRCore.py | Python | gpl-3.0 | 2,653 | [
"VisIt"
] | b39a77a900669030a90fac1a6e1fddc41f10fbc2439fa5188bfae4a45468a5b8 |
"""
Computational Neurodynamics
Exercise 2
(C) Murray Shanahan et al, 2015
"""
from IzNetwork import IzNetwork
import numpy as np
import numpy.random as rn
def Connect2L(N0, N1):
"""
Constructs two layers of Izhikevich neurons and connects them together.
Layers are arrays of N neurons. Parameters for re... | lawrencejones/neuro | Exercise_2/Connect2L.py | Python | gpl-3.0 | 1,685 | [
"NEURON"
] | 94b68d4c15a01914af62bb49f7a031dcf39a9c8b2425bc404d6ec304cbeff425 |
# Authors : Denis A. Engemann <denis.engemann@gmail.com>
# Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
#
# License : BSD 3-clause
from copy import deepcopy
import math
import numpy as np
from scipy import fftpack
# XXX explore cuda optimazation at some point.
from ..io.pick import pick_type... | cmoutard/mne-python | mne/time_frequency/_stockwell.py | Python | bsd-3-clause | 9,819 | [
"Gaussian"
] | ca5d491f24775df3dae0a7b414762accfa6d348cad83e7d749e9b3f5b70b9056 |
#!/usr/bin/python
from multiprocessing import Pool
import time
import os
import sys
import argparse
import math
from homolog4 import *
from collections import defaultdict
import itertools
# Copyright(C) 2014 David Ream
# Released under GPL version 3 licence. http://www.gnu.org/licenses/lgpl.html
# Do not remove this ... | reamdc1/gene_block_evolution | filter_operon_blast_results.py | Python | gpl-3.0 | 20,438 | [
"BLAST"
] | d7afd2ecbb1c2554aa3e60e2eb5556620d51303f30682d181da5e987b34cede7 |
import abc
class User(object):
__metaclass__ = abc.ABCMeta
@abc.abstractmethod
def delete(self):
"""
:return: True if this user has successfully been deleted
"""
return
@abc.abstractmethod
def is_job_visible(self, job, db_member):
"""
... | dsarkozi/care4care-sdp-grp4 | Care4Care/C4CApplication/meta/user.py | Python | agpl-3.0 | 11,424 | [
"VisIt"
] | ca12f763401985ef6ce760caab51c1b4746349f36bb652d8a5d4c39d2de74506 |
"""
Migration script to alter the type of the tool_dependency.version column from TrimmedString(40) to Text.
"""
from sqlalchemy import *
from sqlalchemy.orm import *
from migrate import *
from migrate.changeset import *
import datetime
now = datetime.datetime.utcnow
# Need our custom types, but don't import anything... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py | Python | gpl-3.0 | 2,354 | [
"Galaxy"
] | 874357bbbd552666e22a15ea4b688ce9bce37749e88a3a13e43088e3397d355f |
#!/usr/bin/env python3
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at https://mozilla.org/MPL/2.0/.
"""
Manipulating of DFT output, geometries and creating tight-binding parameter sets for NEGF tr... | zerothi/sisl | setup.py | Python | mpl-2.0 | 12,319 | [
"SIESTA"
] | 387df997096a41c0df48b22d57400e226ca22b2040df0a463636d5be1dc009b3 |
"""
__license__ = "MIT"
__author__ = "Guangtun Ben Zhu (BGT) @ Johns Hopkins University"
__startdate__ = "2016.01.27"
__name__ = "cnn"
__module__ = "Network"
__lastdate__ = "2016.01.27"
__version__ = "0.01"
"""
# Python 2 to 3
from os.path import isfile, join
import numpy as np
from scipy.stats import nanmean, nanm... | guangtunbenzhu/BGT-Cosmology | Spectroscopy/archetype/ebossspec.py | Python | mit | 37,112 | [
"Galaxy",
"Gaussian"
] | c06f461f85e722e5b75aa3c91b47e3261b3781d9af717678a557484b7a7eab3e |
import json
import king_phisher.plugins as plugin_opts
import king_phisher.server.database.manager as db_manager
import king_phisher.server.database.models as db_models
import king_phisher.server.plugins as plugins
import king_phisher.server.signals as signals
import king_phisher.utilities as utilities
try:
import r... | securestate/king-phisher-plugins | server/slack_notifications.py | Python | bsd-3-clause | 2,604 | [
"VisIt"
] | 0438be731b71bd71b4dd29fac7a5230986830acdcce1988c5ec93e7cb99495a7 |
"""The modules in this subpackage provide visualization of 3D objects
using different backends (VRML, VMD, VPython), but with an almost
identical interface. It is thus possible to write generic 3D graphics
code in which the backend can be changed by modifying a single line
of code.
The intended application of these m... | OS2World/DEV-PYTHON-UTIL-ScientificPython | src/Lib/site-packages/Scientific/Visualization/__init__.py | Python | isc | 465 | [
"VMD"
] | c094d83d617cfeff8d0be8c4cedd9abb962483216cdc76b69a52538ef744fa22 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | kratman/psi4public | psi4/driver/procrouting/findif_response_utils/data_collection_helper.py | Python | gpl-2.0 | 4,299 | [
"Psi4"
] | e86a9d350f77c28000e3fae65006cd2eb74d70d575d201debab360b21dc8f948 |
# -*- coding: utf-8 -*-
# Copyright(c) 2016-2020 Jonas Sjöberg <autonameow@jonasjberg.com>
# Source repository: https://github.com/jonasjberg/autonameow
#
# This file is part of autonameow.
#
# autonameow is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public L... | jonasjberg/autonameow | autonameow/analyzers/analyze_document.py | Python | gpl-2.0 | 8,535 | [
"VisIt"
] | ef28f7cca77705d93e5c60fd3914cb41d454b5a565b7a383aaba665d92ec29ee |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Input file writer for SPECFEM3D_CARTESIAN with support for the CEM project.
:copyright:
Lion Krischer (krischer@geophysik.uni-muenchen.de), 2013
Emanuele Casarotti (emanuele.casarotti@ingv.it), 2013
:license:
GNU General Public License, Version 3
(http:... | KNMI/VERCE | verce-hpc-pe/src/wfs_input_generator/backends/write_SPECFEM3D_GLOBE_CEM.py | Python | mit | 18,012 | [
"Gaussian"
] | 924deca99044b2d2c6e2a6d9101d532d95af203ac27ff6877b63abfd2e0d0e00 |
#!/usr/bin/env python
"""
OpenMM ForceField residue template generators.
"""
from __future__ import absolute_import
import numpy as np
import os, os.path, sys
from simtk.openmm.app import ForceField
from openmoltools.amber import run_antechamber
from openmoltools.openeye import get_charges
from simtk.openmm.app.elem... | andrrizzi/openmoltools | openmoltools/forcefield_generators.py | Python | gpl-2.0 | 20,186 | [
"Amber",
"OpenMM"
] | 077626ddf4f98cc2d9a75f8aee52d44dfb4c1cb64b8ffab83691bf8f1ff45e40 |
# Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
# 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.
import os
import numpy
from Bio.SVDSuperimposer import SVDSuperimposer
from Bio.PDB impor... | NirBenTalLab/proorigami-cde-package | cde-root/usr/lib64/python2.4/site-packages/Bio/PDB/FragmentMapper.py | Python | mit | 8,715 | [
"Biopython"
] | 6bff6a18d2873e1554fd5d115b925fffc7a28fd3737a198d13e6d2dbcf431386 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under t... | MDAnalysis/mdanalysis | package/MDAnalysis/topology/guessers.py | Python | gpl-2.0 | 16,660 | [
"Amber",
"CHARMM",
"EPW",
"GROMOS",
"MDAnalysis",
"RDKit",
"VMD"
] | c022ecdfc523aed82969428338eccfdf7beecfba2997a370030b45b69bcee6f1 |
#-*- coding: utf-8 -*-
#! /usr/bin/env python
'''
#------------------------------------------------------------
filename: lab7_runTCcheckGradientVanishing_spiraldata.py
To check Gradient Vanishing problem in
A Multi-Hidden Layers Fully Connected Neural Network.
This example data set is using two class... | jwkanggist/EveryBodyTensorFlow | lab7_runTFcheckGradientVanishing_spiraldata.py | Python | unlicense | 11,985 | [
"NEURON"
] | b2854dfc14464ada2aea939898feab72dbe48137272f19cf0da0a4b65f8dacbd |
import sys, os
import pickle
import threading
from PyQt4.QtGui import *
from PyQt4.QtCore import *
#Contains File Actions
from sync import *
#Contain Variables for file action, dock checkboxes and objects
from env import *
#Contains Filetype Variables
from env2 import *
#Contain Progress Related Variables
from env_... | AsitRout/Syncer | main_window.py | Python | gpl-2.0 | 63,804 | [
"VisIt"
] | 9629c8f5bf01a3797ca160869d1e322e1cd764e1efe1ff8810dd4d388e3846fd |
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this file,
# You can obtain one at http://mozilla.org/MPL/2.0/.
import operator
from ..node import NodeVisitor, DataNode, ConditionalNode, KeyValueNode, ListNode, ValueNode
from ..par... | zhangjunlei26/servo | tests/wpt/harness/wptrunner/wptmanifest/backends/conditional.py | Python | mpl-2.0 | 10,439 | [
"VisIt"
] | d39a2da1de01136de6d98bf1f61362684a19a919bae5e2233ae92e20b3c595c5 |
#!/usr/bin/env python
"""
Provides wrappers and utilities for working with MAF files and alignments.
"""
#Dan Blankenberg
import pkg_resources; pkg_resources.require( "bx-python" )
import bx.align.maf
import bx.intervals
import bx.interval_index_file
import sys, os, string, tempfile
import logging
from errno import EMF... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/tools/util/maf_utilities.py | Python | gpl-3.0 | 30,790 | [
"Galaxy"
] | ae3a1dba8632fca2df5e6576851fbf799af51f3b5644c90e0a4edf4408ada9ce |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | pli3/Openwebif | plugin/controllers/views/ajax/tv.py | Python | gpl-2.0 | 5,832 | [
"VisIt"
] | 9ccbe81b333269f64084a71e54c7e4b0354411b8a0dcc273ea8c44357ace9459 |
"""Radiance Parameters Base class with methods to add descriptor type parameters."""
from ._parametersbase import RadianceParameters
from ..datatype import RadiancePath, RadianceNumber, RadianceBoolFlag, \
RadianceTuple, RadianceValue
# TODO: Add __new__ to create a new class for each instance. After that the
# n... | antonszilasi/honeybeex | honeybeex/honeybee/radiance/parameters/_advancedparametersbase.py | Python | gpl-3.0 | 13,739 | [
"EPW"
] | 485288995d5d9ae0ca5bf79b54a610796ba253fd0668c9a8ea49d1cd225ba55f |
#!/usr/bin/python
# -*- coding: utf-8 -*-
import random
from __builtin__ import enumerate
import pulp
# !/usr/bin/python
# -*- coding: utf-8 -*-
import math
from collections import namedtuple
from collections import deque
from ortools.constraint_solver import pywrapcp
from ortools.linear_solver import pywraplp
i... | 3like3beer/optimization | tsp/solver.py | Python | gpl-2.0 | 30,625 | [
"VisIt"
] | f9dba70b130b07e05287c2e09b0251a6beac6227469968d48cd2b8f83f858961 |
# -*- coding: utf-8 -*-
#
# ASE documentation build configuration file, created by
# sphinx-quickstart on Fri Jun 20 09:39:26 2008.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# The contents of this file are pickled, so don't put values in the namespace
# that aren't pickleable ... | slabanja/ase | doc/conf.py | Python | gpl-2.0 | 6,854 | [
"ASE",
"GPAW"
] | d595a021ba340766830bb9c38f09595d70dea9f77af397c52f7c342a6d986534 |
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