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from kivy.uix.screenmanager import Screen
from kivy.uix.togglebutton import ToggleButton
from kivy.uix.popup import Popup
from kivy.lang import Builder
from kivy.utils import get_color_from_hex
from kivy.properties import NumericProperty
from screens import screenmanager
import random
__author__ = 'ohaz'
Builder.load... | ohaz/Colours | screens/ingamescreen.py | Python | apache-2.0 | 7,804 | [
"VisIt"
] | fe8e9eb60568b6491e3dcecb4a58fa92b2a512a91f899b9cdc5d391b01fc50aa |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2012 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## 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 Foundati... | andrebellafronte/stoq | stoqlib/gui/test/test_batchselectiondialog.py | Python | gpl-2.0 | 10,184 | [
"VisIt"
] | 0afbffec13b1e5c34e3becf6018945965cbd5ab30b54e5fd6876a0fcbf1783a4 |
#!/usr/bin/env python
# =============================================================================
# MODULE DOCSTRING
# =============================================================================
"""
Test Context cache classes in cache.py.
"""
# =================================================================... | choderalab/openmmtools | openmmtools/tests/test_cache.py | Python | mit | 18,245 | [
"OpenMM"
] | 4bd5abee019c948eb2dd99b44d4c3266df856458466f5c90c92d20418dd3297e |
# Copyright 2012, SIL International
# All rights reserved.
#
# This library 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; either version 2.1 of License, or
# (at your option) any lat... | silnrsi/graide | lib/graide/ruledialog.py | Python | lgpl-2.1 | 2,158 | [
"VisIt"
] | ab09caf1ef0f05c6129060c866d9510a2dc0a94e43bdbd778e98309f8f930e9e |
#!/usr/bin/env python
# encoding: utf-8
'''
Created by Brian Cherinka on 2016-05-02 16:16:27
Licensed under a 3-clause BSD license.
Revision History:
Initial Version: 2016-05-02 16:16:27 by Brian Cherinka
Last Modified On: 2016-05-02 16:16:27 by Brian
'''
from __future__ import print_function
from __future__... | albireox/marvin | python/marvin/web/web_utils.py | Python | bsd-3-clause | 4,131 | [
"Brian"
] | bc2d04f25107e26bb2a3f268b3cab0b90c9d4c85f06e14f31288813b7aab15d2 |
from math import sqrt
import numpy as np
from ase.data import covalent_radii
from ase.atoms import Atoms
from ase.calculators.singlepoint import SinglePointCalculator
from ase.io import read, write, string2index
from ase.constraints import FixAtoms
class Images:
def __init__(self, images=None):
if imag... | slabanja/ase | ase/gui/images.py | Python | gpl-2.0 | 13,016 | [
"ASE"
] | 05db18e777b3f07b2a2c131eb89202eb7aacf7ddcada4438d93e2ef083a459b9 |
# -*- 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 ... | MDAnalysis/mdanalysis | package/MDAnalysis/units.py | Python | gpl-2.0 | 13,298 | [
"Amber",
"Avogadro",
"CHARMM",
"MDAnalysis"
] | 6f22eb9610dd91da306ec84199d3fd13a19a4644311c226d8f3e3adcceb204d4 |
'''
Python Oauth client for Twitter
modified to work with other oAuth logins like LinkedIn (Ben Adida)
Used the SampleClient from the OAUTH.org example python client as basis.
props to leahculver for making a very hard to use but in the end usable oauth lib.
'''
import httplib
import urllib, urllib2
import time
impo... | stanley89/helios-server | helios_auth/auth_systems/oauthclient/client.py | Python | apache-2.0 | 6,013 | [
"VisIt"
] | 4cd4e9021038aca7d5740b2c81a3ab4597ae7fcd5edcb10ff015e3b20049aed9 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Make an image larger by repeating the data. Tile.
# Image pipeline
reader = vtk.vtkPNMReader()
reader.ReleaseDataFlagOff()
reader.SetFileName("" + str(VTK_DATA_ROOT) + "/... | hlzz/dotfiles | graphics/VTK-7.0.0/Imaging/Core/Testing/Python/TestQuantizeTo16Colors.py | Python | bsd-3-clause | 946 | [
"VTK"
] | 3f040e60fd7f6456a0030d0093dc61e631fbcaf92c9ad4793e7d976309d5f8dc |
#!/usr/bin/python
# -*- coding: UTF-8 -*-
#
# Copyright 2010 Google Inc. 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... | nearlyfreeapps/python-googleadwords | tests/adspygoogle/adwords/ad_extensions_override_service_unittest.py | Python | apache-2.0 | 6,661 | [
"VisIt"
] | 496b52db673d269d2d5075d94c41bbd3354e67fbc8cf8a785fc11931ee84b034 |
import argparse
import math
import json
from io import BytesIO
import pycurl
from PIL import Image
from octopus import TornadoOctopus
def get_avatars(urls):
avatars = []
otto = TornadoOctopus(
concurrency=50, auto_start=True, cache=True, expiration_in_seconds=60
)
def handle_url_response(ur... | wpjunior/github-contributor-mosaic | github-contributor-mosaic.py | Python | mit | 2,510 | [
"Octopus"
] | 49894bd1d2e205eb2befc8671ba6199a153fb0da7ef8ee2e655a975a9b50e975 |
# (c) 2012-2018, Ansible by Red Hat
#
# This file is part of Ansible Galaxy
#
# Ansible Galaxy is free software: you can redistribute it and/or modify
# it under the terms of the Apache License as published by
# the Apache Software Foundation, either version 2 of the License, or
# (at your option) any later version.
#
... | chouseknecht/galaxy | galaxy/api/urls.py | Python | apache-2.0 | 6,938 | [
"Galaxy"
] | 1fa49175dd1a6039f82228c370a6c585fe891feef013313a30fd04ede4d119fb |
# proxy module
from __future__ import absolute_import
from mayavi.sources.vtk_file_reader import *
| enthought/etsproxy | enthought/mayavi/sources/vtk_file_reader.py | Python | bsd-3-clause | 99 | [
"Mayavi"
] | a019e636ba52859a0468f289f5b2be3ae4a238a869f65bc50f925cf8cc78ea60 |
# -*- coding: utf-8 -*-
# creates: diffusion-I.png diffusion-T.png diffusion-F.png diffusion-barrier.png
import os
import matplotlib
matplotlib.use('Agg')
import pylab as plt
from ase import *
from ase.neb import fit
if 1:
execfile('diffusion1.py')
execfile('diffusion2.py')
images = read('neb.traj@-5:')
for ... | freephys/python_ase | doc/tutorials/neb/diffusion.py | Python | gpl-3.0 | 857 | [
"ASE"
] | 63f55709e8a30f1c582966cc278ce8fe5b7922df706e51504e1375ae3078ccf8 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 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
#... | CDSherrill/psi4 | psi4/driver/qcdb/basislist.py | Python | lgpl-3.0 | 8,189 | [
"Psi4"
] | 86a45ff15ed656ca4214c5bdea103933ef9098db8794c57a2c8753964c20c4f8 |
#!/usr/bin/env python
import ase
from ase.cluster.icosahedron import Icosahedron
from ase.io import write
from ase.optimize import FIRE
from ligandizer import VSEPR, add_ligands
def make_methylamine():
# Construct Methylamine.
atoms = ase.Atoms('NH2CH3')
# Define connectivity.
atoms_bonds = [ [0,1], ... | SamChill/ligandizer | example/Au147_Ih.py | Python | bsd-2-clause | 968 | [
"ASE"
] | 872a4465bd059992075dc0c41785d917f3f069de694085ca365eb11dc4c5cd35 |
import unittest
from hamcrest import *
from nose.tools import nottest
from test.features import BrowserTest
class test_create_pages(BrowserTest):
def test_about_page(self):
self.browser.visit("http://0.0.0.0:8000/high-volume-services/"
"by-transactions-per-year/descending")
... | imclab/transactions-explorer | test/features/test_create_pages.py | Python | mit | 1,356 | [
"VisIt"
] | 102b96a9e974abb32dcf8d4efb6a00cd457aaf65c9da53c6a027275d4a63dba6 |
import os
import logging
import yaml
import copy
import operator
import requests
import json
from toscaparser.nodetemplate import NodeTemplate
try:
unicode("hola")
except NameError:
unicode = str
try:
from urlparse import urlparse
except ImportError:
from urllib.parse import urlparse
from toscaparser.... | grycap/im | IM/tosca/Tosca.py | Python | gpl-3.0 | 84,301 | [
"Galaxy"
] | 3ef4b457c1018e18178ddf82daa5f490d33a0715e7af9cb3f73df69bd6101eb2 |
#!/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/df/aft_ao2mo.py | Python | apache-2.0 | 17,572 | [
"PySCF"
] | c828dbbf02cf2cb2f59b2570d4b46280b635b6373ee9721581cd7c126e32e5ba |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | aldian/tensorflow | tensorflow/python/keras/preprocessing/image.py | Python | apache-2.0 | 48,044 | [
"Gaussian"
] | 74c89f51fbb8ff537e31c3defe264101616ac59466142c8e5f80ef7381a3163f |
# 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 | test/test_carrier.py | Python | apache-2.0 | 9,963 | [
"VisIt"
] | 182492acb6e91dd4ce52d6943af8b1696347722e44d702b54ed92fddf2f9d101 |
#!/usr/bin/env python
import os, sys, gzip, subprocess, pysam
import numpy as np
from collections import Counter
from FastaIndex import FastaIndex
def _get_samtools_proc(bam, mapq=0, regions=[], skipFlag=3980):
"""Return samtools subprocess"""
# skip second in pair, unmapped, secondary, QC fails and supplemen... | lpryszcz/HiCembler | ctr.py | Python | gpl-3.0 | 2,044 | [
"pysam"
] | 2ee5513cfd7fb5275e310db1791bb37bc91869620317e5577b99d9ee99073107 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# create a rendering window
renWin = vtk.vtkRenderWindow()
renWin.SetMultiSamples(0)
renWin.SetSize(600,300)
# set up first set of polydata
p1 = vtk.vtkPlaneSource()
p1.SetOrigin(0.5,... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Rendering/Core/Testing/Python/TransformPolyData.py | Python | gpl-3.0 | 5,924 | [
"VTK"
] | 53497e2cad39c9a352209ef7f178d4c753af7deed6844e547afd0b0366ab412d |
"""
Utility functions that are not related specifically to parsing or code generation.
Includes error handling and info logging, and file system manipulation.
"""
import glob
import logging
import os, stat
import shutil
import sys
import pycparser
theLogger = logging.getLogger("Caicos")
ch = logging.StreamHandler(... | iangray001/caicos | utils.py | Python | gpl-2.0 | 4,407 | [
"VisIt"
] | 9de0960612d06943c8e02c3d0536fa55c0a4a49093f3c9848d08f78a0a4bc445 |
#!/usr/bin/env/python3
import os
import sys
from urllib.parse import urljoin
def upload_datasets_to_galaxy(args, galaxy_instance=None):
"""
Function to upload a folder into Galaxy Data Libraries
:param galaxy_instance:
:return:
"""
# Get all parameters
libraries_root = args.libraries_ro... | pajanne/galaxy-kickstart | utils/upload.py | Python | mit | 4,118 | [
"Galaxy"
] | 79b6edb35bccdade300774965cdf12eab8680c818deab0e8800f04c98c703f7c |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module defines tools to generate and analyze phase diagrams.
"""
import re
import collections
import itertools
import math
import logging
from monty.json import MSONable, MontyDecoder
from functools ... | tschaume/pymatgen | pymatgen/analysis/phase_diagram.py | Python | mit | 84,422 | [
"pymatgen"
] | a07b9f268bb7908d99823ba977fc6477c084ee8fd3aece3ae2a655de2f8c0ff9 |
#!/usr/bin/env python
"""
"""
import vtk
def main():
colors = vtk.vtkNamedColors()
xyxFile, qFile = get_program_parameters()
# Read the data.
#
pl3d = vtk.vtkMultiBlockPLOT3DReader()
pl3d.AutoDetectFormatOn()
pl3d.SetXYZFileName(xyxFile)
pl3d.SetQFileName(qFile)
pl3d.SetScalarF... | lorensen/VTKExamples | src/Python/VisualizationAlgorithms/LOxGrid.py | Python | apache-2.0 | 5,635 | [
"VTK"
] | 005b75d89ff67a70af7a18cf7d26d25b1a9b3fa293a951a13baabdc687c4b698 |
#!/usr/bin/env python
###############################################################################
# Copyright (C) 1994 - 2007, Performance Dynamics Company #
# #
# This software is licensed as described in the file COPY... | evelynmitchell/pdq | examples/MultiServer/orca.py | Python | mit | 1,589 | [
"ORCA"
] | a2ec9db3e2e0e785c0e1a39b8818e0d1ae48aaa02ad8d3ed206944b3d863cf47 |
import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.autograd import Variable
EPS = 0.003
def fanin_init(size, fanin=None):
fanin = fanin or size[0]
v = 1. / np.sqrt(fanin)
return torch.Tensor(size).uniform_(-v,v)
class Critic(nn.Module):
def __init__(sel... | eklinkhammer/gym-rover | ddpg_model.py | Python | mit | 3,363 | [
"Gaussian"
] | 75563e5ebc6795856e46b4e15dadf2d7eab91e54391e53a50676d5b4beb23fa2 |
#!/usr/bin/env python
# By Jason Ladner
#This script looks for single reads that are chimeric, with different portions mapping to different regions
#In v2, I tweaked the way I was making the plot in matplot lib to try to make it easy to create a legend
#In v3, Fixed bug related to reads with doubly aligned bases. On... | jtladner/Scripts | chimeric_reads/chimeric_reads_v3.6.2.py | Python | gpl-3.0 | 49,635 | [
"pysam"
] | 45f03ffcd5862714f0faa2d23656dbfb709b1ff640957e716a668cc4c23afc83 |
#
# Copyright (C) 2013-2019 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... | fweik/espresso | testsuite/python/mmm1d_gpu.py | Python | gpl-3.0 | 1,120 | [
"ESPResSo"
] | 7b0a380ad17334179aafbf83aa428af01a7d957b5a866661bb934049d8899539 |
##############################################################################
# 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... | EmreAtes/spack | var/spack/repos/builtin/packages/molcas/package.py | Python | lgpl-2.1 | 1,896 | [
"MOLCAS"
] | 3702a49faace16ead4c2ffcdc118750be7218a9d580fb22925f73dc4c42826f6 |
# Copyright (C) 2010-2018 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... | hmenke/espresso | src/python/espressomd/io/__init__.py | Python | gpl-3.0 | 751 | [
"ESPResSo"
] | 8709f0969434441c575bc199453adfb92c23527b3683958a4d36cdd1966c9a92 |
from django.utils import timezone
from dateutil.relativedelta import relativedelta
from edc_constants.constants import SCREENED
from edc_registration.models import RegisteredSubject
from edc_identifier.models import SubjectIdentifier
from edc_constants.constants import FAILED_ELIGIBILITY, OFF_STUDY, SCHEDULED, POS, YES... | TshepangRas/tshilo-dikotla | td_maternal/tests/test_maternal_lab_del.py | Python | gpl-2.0 | 4,027 | [
"VisIt"
] | 3fb2bdb6e511941ffad21075929f1e8d39e293d3e7e55791abf5ef7d164fe87b |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2004-2007 Donald N. Allingham
# Copyright (C) 2008,2011 Gary Burton
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2011-2012 Paul Franklin
# Copyright (C) 2012 Brian G. Matherly
#
# This program is free software; you can redistribute ... | gramps-project/gramps | gramps/gen/plug/report/_options.py | Python | gpl-2.0 | 37,375 | [
"Brian"
] | e0ae4046a1e7f9f7f141aa1730757adb7f5a50f5cc422677b4d0608c1ebae473 |
# -*- coding: utf-8 -*-
from scipy.ndimage.filters import gaussian_filter1d
from fourgp_speclib import Spectrum
class SpectrumConvolver(object):
"""
A class containing utility functions for convolving Spectrum objects with point spread functions
"""
def __init__(self, input_spectrum):
asser... | dcf21/4most-4gp | src/pythonModules/fourgp_degrade/fourgp_degrade/convolve.py | Python | mit | 1,171 | [
"Gaussian"
] | 089ebc26cd131986ab390b7818f7c2f0ca18bbd6b0157b660b218ec6fbc6e359 |
# -*- coding: utf-8 -*-
""" Manifest Processing
This module provides classes and methods to process a manifest with
software updates.
(c) 2015, 2016 - Jaguar Land Rover.
Mozilla Public License 2.0
"""
import json
import os
import subprocess
import dbus
from collections import deque
import software_operation
import ... | rstreif/genivi_software_management | software_loading_manager/manifest.py | Python | mpl-2.0 | 10,700 | [
"Jaguar"
] | 47b92ff041f785d248848f791d55d6d0406f7d85c790649437f5e3ff8b71b4d6 |
# Copyright 2009 by James Casbon. All rights reserved.
# Revisions copyright 2009-2010 by Michiel de Hoon. 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.
"""Tests for parsing Co... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_Compass.py | Python | gpl-2.0 | 4,012 | [
"Biopython"
] | c53b0c739ee908ac2e8e2c019571dd26029d66be065113deef604a64ad980949 |
import datetime
from zds.member.views import get_client_ip
class SetLastVisitMiddleware(object):
def process_response(self, request, response):
# Update last visit time after request finished processing.
try:
if request.user.is_authenticated():
user = request.user
... | Florianboux/zds-site | zds/middlewares/SetLastVisitMiddleware.py | Python | gpl-3.0 | 1,001 | [
"VisIt"
] | 11918ba3e498a4a9d2adfe29961cc7b49635bb7afaae745ce16f6bfaf451a617 |
# coding=utf8
#
# Copyright 2013 Dreamlab Onet.pl
#
# This library 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;
# version 3.0.
# This library is distributed in the hope that it will be useful,
# bu... | tikan/rmock | tests/func_tests/test_freeze_mock.py | Python | lgpl-3.0 | 1,743 | [
"VisIt"
] | 68c202a1e4cdf2746a0baa17435f4b32f3111b53d4d8966a95a3306bbcca6705 |
from __future__ import generators
from bike.globals import *
from bike.parsing.fastparserast import getRoot, Function, Class, Module, getModule
from bike.parsing.parserutils import generateLogicalLines, makeLineParseable, UnbalancedBracesException, generateLogicalLinesAndLineNumbers
from bike.parsing.newstuff import ge... | srusskih/SublimeBicycleRepair | bike/query/common.py | Python | mit | 11,175 | [
"VisIt"
] | 4606445f0cdc054b9f4b4d26c17ca135f01fc8ca803848f022155c45de560f83 |
#---------------------------------------------------------------------------
# Copyright 2015 HP
#
# 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... | VHAINNOVATIONS/MHV-Enrollment | vista/Packages/Registration/Testing/RAS/REG_IEMHV_test.py | Python | apache-2.0 | 4,063 | [
"Brian"
] | 8cd972f45aff65e4a20edb1860fa79e57bd5057e730af530e4895f4202274c31 |
#!/usr/bin/env python
# Python 2/3 compatibility
from __future__ import print_function
import sys
PY3 = sys.version_info[0] == 3
if PY3:
xrange = range
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_... | DamianPilot382/Rubiks-Cube-Solver | opencv/sources/samples/python/gaussian_mix.py | Python | apache-2.0 | 2,086 | [
"Gaussian"
] | f03fe90c5d8fcc187ac21f7fe43ee489a31734d53f6cbda5633b839cfcfde6cc |
# -*- coding: utf-8 -*-
"""
Create an initial ATP Profile for an ECs Mesh and write it out as .vtp.
"""
import os
import sys
# Run in current directory.
os.chdir(os.path.dirname(os.path.abspath(__file__)))
# Import path for the GenerateATPMapV2 script.
importPath = os.path.abspath(os.path.join(os.path.dirname(__file... | BlueFern/DBiharMesher | meshes/c960/Generate960ATPMesh.py | Python | gpl-2.0 | 1,116 | [
"VTK"
] | 2085393fef486b44fe4b3fcc9a76a04e5b87ea6fb010d9f154067c91c26e1498 |
from __future__ import print_function
import os
import shutil
from os.path import dirname,join
from ase.io import read,write
import argparse
import sys
from ase.io import read,write
class isv():
def __init__(self,appname='myapp',apptype='stand_alone'):
import os
import sys
currentdir=os.ge... | sandipde/Interactive-Sketchmap-Visualizer | setup_class.py | Python | mit | 7,820 | [
"ASE",
"Jmol"
] | a3eb13fca17e88d94b8810fc662e9896e6759d4b9faacfa67694fab6b13f26b7 |
"""
Peak picking routines, lineshape parameter guessing, and related functions.
"""
import numpy as np
import scipy.ndimage as ndimage
from .analysisbase import ndwindow_index, valid_pt
from .lineshapes1d import gauss, ls_str2class
from .segmentation import find_all_downward, find_all_upward
from .segmentation import... | atomman/nmrglue | nmrglue/analysis/peakpick.py | Python | bsd-3-clause | 19,765 | [
"Gaussian"
] | d1573dfc2a1faff1e6a9d67038ec6f4997bb34e0372397608122a864339b523e |
# 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/test/test_0019_tddft_polariz_nao.py | Python | apache-2.0 | 2,208 | [
"PySCF",
"SIESTA"
] | d14ce0f1429e9a248e87fad467ec3018fb4fe526f816c9f3d2e0865af54f62c2 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
This module lists known raw databases and how to ingest them.
Specify arguments and run the following command to ingest a database
python -m ibeis --tf ingest_rawdata --db seaturtles --imgdir "~/turtles/Turtles from Jill" --ingest-type=named_folders --species=turtles... | Erotemic/ibeis | ibeis/dbio/ingest_database.py | Python | apache-2.0 | 69,603 | [
"Jaguar"
] | d44ee928348fed03a74603a68fcc48b778089b743049d7e10c1b02a78e6f7d85 |
#!/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/cc/uccsd_t_rdm.py | Python | apache-2.0 | 16,309 | [
"PySCF"
] | d943906d01731c678538aadcbbd08d6b607412ea6b20ee2d0e35fb0146d4dd2b |
import theano
import theano.tensor as T
from theano.sandbox.rng_mrg import MRG_RandomStreams
from theano.tensor.nnet.conv import conv2d
from theano.tensor.signal.downsample import max_pool_2d
from theano.tensor.shared_randomstreams import RandomStreams
import numpy as np
from toolbox import *
from modelbase import *
... | tigerneil/Theano-Lights | models/ffn_lae.py | Python | mit | 3,991 | [
"Gaussian"
] | 3bff6b61d505529258f2e0b9ee58aaee9ed09a0dd876ab6679a9dc87f46c7da8 |
# -*- coding: utf-8 -*-
# This file is part of Shuup.
#
# Copyright (c) 2012-2017, Shoop Commerce Ltd. All rights reserved.
#
# This source code is licensed under the OSL-3.0 license found in the
# LICENSE file in the root directory of this source tree.
import os
import pytest
from django.core.urlresolvers import reve... | suutari-ai/shoop | shuup_tests/browser/front/test_product_view.py | Python | agpl-3.0 | 2,358 | [
"VisIt"
] | de43ca037df3f3618653bcdda423d73947a484798204679e2e99d64052bb19e6 |
import galaxy.model
from galaxy.model.orm import *
from base.twilltestcase import *
from base.test_db_util import *
class TestFormsAndSampleTracking( TwillTestCase ):
# ====== Setup Users, Groups & Roles required for this test suite =========
def test_0000_initiate_users( self ):
"""Ensuring all req... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/test/functional/test_sample_tracking.py | Python | gpl-3.0 | 60,460 | [
"Galaxy",
"VisIt"
] | ffb1b7a45856f5a841d4ade417c840f8f548b2978cd50772736935ae44b34cbf |
# ----------------------------------------------------------------------------
# cocos2d
# Copyright (c) 2008-2012 Daniel Moisset, Ricardo Quesada, Rayentray Tappa,
# Lucio Torre
# Copyright (c) 2009-2014 Richard Jones, Claudio Canepa
# All rights reserved.
#
# Redistribution and use in source and binary forms, with o... | Alwnikrotikz/los-cocos | cocos/cocosnode.py | Python | bsd-3-clause | 29,637 | [
"VisIt"
] | 505042912500099c95b4a4c16c205d6819f5c9af22d9971b8e21a7e7722ac881 |
# !usr/bin/env python
# -*- coding: utf-8 -*-
#
# Licensed under a 3-clause BSD license.
#
# @Author: Brian Cherinka
# @Date: 2018-07-31 23:52:31
# @Last modified by: José Sánchez-Gallego (gallegoj@uw.edu)
# @Last Modified time: 2018-08-01 03:34:02
from __future__ import absolute_import, division, print_function
im... | sdss/marvin | python/marvin/utils/general/images.py | Python | bsd-3-clause | 21,197 | [
"Brian",
"Galaxy"
] | e0a932a93bd59865eb257a48d22fc3ca01bb71c66749b5fac0b66ee4b33031e9 |
# Generated from sxl.g4 by ANTLR 4.7
from antlr4 import *
if __name__ is not None and "." in __name__:
from .sxlParser import sxlParser
else:
from sxlParser import sxlParser
# This class defines a complete generic visitor for a parse tree produced by sxlParser.
class sxlVisitor(ParseTreeVisitor):
# Visit... | nussbrot/AdvPT | python/sxlVisitor.py | Python | mit | 6,533 | [
"VisIt"
] | e4649d4d0689c958eb746ddfc1ca38f93c9da924adb9ee0681642288e48751ab |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2008, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License versi... | zenoss/ZenPacks.community.OpenSolaris | ZenPacks/community/OpenSolaris/parsers/opensolaris/uptime.py | Python | gpl-2.0 | 3,094 | [
"VisIt"
] | 076f8323b2d7fee73a75e9ac3175f0914e5e26673270e072ecca30d5ac9da808 |
#!/usr/bin/env python
""" A set of utilities, mostly for post-processing and visualization
We put arrays on disk as raw bytes, extending along the first dimension.
Alongside each array x we ensure the value x.dtype which stores the string
description of the array's dtype.
See Also:
------------
@url
.. image::
@aut... | simonsfoundation/CaImAn | caiman/source_extraction/cnmf/utilities.py | Python | gpl-2.0 | 41,429 | [
"Gaussian",
"NEURON"
] | 9ff47b3f704e5d472bd5d4081ca8e47d71ca78a583fa9ed3e59eca9c92942cda |
import sys
import os
import tempfile
from tools import Tools
class Demuxer:
def __init__(self,tools,filename,type):
if not self.CreateDirectory():
raise Exception, 'Failed to create directory'
self.Demux(tools,filename,type)
def GetDirectory(self):
return self.directory
def CreateDirector... | Distrotech/libkate | tools/KateDJ/kdj/demuxer.py | Python | bsd-3-clause | 1,808 | [
"DIRAC"
] | 17be0e5c318750dbe7e6010583458dd4828ebf19ad452f98901ca06eedb85add |
"""
Student Views
"""
import datetime
import logging
import uuid
import json
import warnings
from collections import defaultdict
from urlparse import urljoin, urlsplit, parse_qs, urlunsplit
from django.views.generic import TemplateView
from pytz import UTC
from requests import HTTPError, ConnectionError
from ipware.ip... | Learningtribes/edx-platform | common/djangoapps/student/views.py | Python | agpl-3.0 | 113,234 | [
"VisIt"
] | abcd900b951c82ada63e1012f0781fe37f5ab3c7b27e0f0ec907b1a018faf0a0 |
#!/usr/bin/env python
from random import uniform
from math import exp
class Neuron:
def __init__(self, n_inputs):
self.n_inputs = n_inputs
self.weights = [uniform(-1, 1) for i in range(n_inputs)]
self.bias = uniform(-1, 1)
def get_net(self, inputs):
net = sum([w * x for w, x i... | andrecunha/simple-ml | mlp2.py | Python | unlicense | 3,306 | [
"NEURON"
] | a67288f3ef35a4ab8c9160a87b9c7b7a0680acd5ad4d43a6db8d5e26c89a6e4c |
#
# 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... | cloud-fan/spark | python/pyspark/ml/classification.py | Python | apache-2.0 | 126,610 | [
"Gaussian"
] | 1b616587d81c70b7c0288e9d63a128515225c9669beb4c3a5524cfc97f148652 |
# BatchConverter.py by Francois Malan - 2010-03-05. Updated 2011-12-11#
import os.path
from module_base import ModuleBase
from module_mixins import ScriptedConfigModuleMixin
import wx
import os
import vtk
import itk
class batchConverter(
ScriptedConfigModuleMixin, ModuleBase):
def __init__(self, module_manag... | chrisidefix/devide | modules/writers/batchConverter.py | Python | bsd-3-clause | 21,799 | [
"VTK"
] | 96647d8ba74ef9abcc6921b54f4516615da5f567221c4389933ba9e8dea6b7fc |
""" Example showing how to pick data on a surface, going all the way back
to the index in the numpy arrays.
In this example, two views of the same data are shown. One with the data
on a sphere, the other with the data flat.
We use the 'on_mouse_pick' method of the scene to register a callback on
clicking on the spher... | liulion/mayavi | examples/mayavi/data_interaction/pick_on_surface.py | Python | bsd-3-clause | 2,477 | [
"Mayavi",
"VTK"
] | ae3569257e2d7c187860c39ccd7848dd1d8d44edca32e4c627b856d96759b56c |
import numpy as np
from matplotlib import pyplot
import rft1d
#(0) Set parameters:
np.random.seed(123456789)
nResponsesA = 5
nResponsesB = 5
nNodes = 101
FWHM = 10.0
nIterations = 5000
### derived parameters:
nA,nB = nResponsesA, nResponsesB
nTotal = nA + nB
df = nA + nB - 2
#(1) ... | 0todd0000/rft1d | rft1d/examples/val_max_2_twosample_t_1d.py | Python | gpl-3.0 | 1,402 | [
"Gaussian"
] | e8b3042eae9aa886de573b47ae45de21b337701291b92b33b582fef330e4a302 |
import numpy as np
from parabem.airfoil.conformal_mapping import JoukowskyAirfoil
from parabem.vtk_export import VtkWriter
from parabem.utils import check_path
####################################################
# analytic solution of joukowsky-airfoils #
####################################################... | looooo/panel-method | examples/vtk/vtk_airfoil_joukowsky.py | Python | gpl-3.0 | 3,640 | [
"VTK"
] | 3ff475084c6ed3e786c5dd056469ca74f2863ed7043c233d8c1d869b0956a350 |
# -*- coding: utf-8 -*-
# Copyright 2007-2020 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... | dnjohnstone/hyperspy | hyperspy/tests/model/test_set_parameter_value.py | Python | gpl-3.0 | 3,811 | [
"Gaussian"
] | cdaca38c9202a8e90082ad808b4fd86bbeee465501f94d883bf214fbba629163 |
import sys
import copy
from textwrap import dedent
import numpy as np
import pandas as pd
from ..client import inject_client
from ..neuroncriteria import neuroncriteria_args
from ..synapsecriteria import SynapseCriteria
from ..mitocriteria import MitoCriteria
from ..utils import tqdm, iter_batches
from .synapses impo... | connectome-neuprint/neuprint-python | neuprint/queries/mito.py | Python | bsd-3-clause | 22,991 | [
"NEURON"
] | cee2c83653d5c25d739c46fb7c2ab196b30068bec2855afdf055cc8d9f790ff3 |
import numpy as np
from ase.lattice import bulk
from gpaw import GPAW, FermiDirac
from gpaw.wavefunctions.pw import PW
from gpaw.response.gw import GW
a = 5.431
atoms = bulk('Si', 'diamond', a=a)
calc = GPAW(
mode=PW(200),
kpts=(3,3,3),
xc='LDA',
eigensolver='cg',
... | robwarm/gpaw-symm | doc/tutorials/gw_tutorial/frequency.py | Python | gpl-3.0 | 1,256 | [
"ASE",
"GPAW"
] | 7535b6852a6ea4c6cede5aebdab08b4bc3126b74161571e2bc6d8dc28bb8ceb5 |
# From: Bayesian Models for Astrophysical Data, Cambridge Univ. Press
# (c) 2017, Joseph M. Hilbe, Rafael S. de Souza and Emille E. O. Ishida
#
# you are kindly asked to include the complete citation if you used this
# material in a publication
#
# Code 10.4 - Gaussian linear mixed model, in Python using Stan, for ... | astrobayes/BMAD | chapter_10/code_10.4.py | Python | gpl-3.0 | 3,393 | [
"Galaxy",
"Gaussian"
] | ef2f9c260fcc9f0660ff40a5e4daa7469b4f61951ade409a8160c002a82472e9 |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""Mathematical models."""
from __future__ import (absolute_import, unicode_literals, division,
print_function)
from collections import OrderedDict
import numpy as np
from .core import (Fittable1DModel, Fittable2DModel, Model,
... | kelle/astropy | astropy/modeling/functional_models.py | Python | bsd-3-clause | 73,767 | [
"DIRAC",
"Gaussian"
] | 023f6411443c972968a61a522f211b4ad228da8930abe4a1ce4804b24e0bf8d1 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""This module provides functions and classes related to Task objects."""
import os
import time
import datetime
import shutil
import collections
import abc
import copy
import ruamel.yaml as yaml
from io import ... | dongsenfo/pymatgen | pymatgen/io/abinit/tasks.py | Python | mit | 180,142 | [
"ABINIT",
"NetCDF",
"Wannier90",
"pymatgen"
] | 80d6ed127c9f25cab750e92b04a839d81d9a737f9d17e1836579b668c28ae2e2 |
import lb_loader
import pandas as pd
import simtk.openmm.app as app
import numpy as np
import simtk.openmm as mm
from simtk import unit as u
from openmmtools import hmc_integrators, testsystems
sysname = "ljbox"
system, positions, groups, temperature, timestep = lb_loader.load(sysname)
integrator = hmc_integrators.G... | kyleabeauchamp/HMCNotes | code/correctness/old/test_john_hmc.py | Python | gpl-2.0 | 1,318 | [
"OpenMM"
] | dbf1e441038812dfcbbf8d907db0d994a9e4d6936b4db94f3d468b66a5631068 |
# Copyright 2012 Brian Waldon
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,... | bcwaldon/warlock | tests/test_core.py | Python | apache-2.0 | 10,114 | [
"Brian"
] | 6a6ada3c3c0b05355e33d5a1a06e35b436de970fe08c24ed4e8ff9217474bd4c |
from __future__ import division
from sys import stderr
from scipy import *
from scipy import stats
import pysam
import rpy2.robjects as R
options = R.r['options']
options(warn=-1)
"""
TODO: Document this file
"""
def motif_abundance(seq,motif_length):
"""
given a sequence and a sequence length return the N-length m... | polarise/RP-python | key_functions.py | Python | gpl-2.0 | 10,278 | [
"pysam"
] | 134b9cb896cb0ae7f8368034fc973403afb33a430f501db7f8d371d5662a0620 |
#!/usr/bin/env python
import pysam
import sys
from re import sub
if len(sys.argv) == 2:
assert sys.argv[1].endswith('.bam')
outname = sub('bam$', 'fixed.bam', sys.argv[1])
print "output bam:",outname
inbam = pysam.Samfile(sys.argv[1], 'rb')
outbam = pysam.Samfile(outname, 'wb', template=inbam)
... | MischaLundberg/bamsurgeon | scripts/remove_unpaired.py | Python | mit | 796 | [
"pysam"
] | 904d4fec430fc9d7f603ba6fb6a24a43cb7ec67201bc01c6f059269ae82ab11e |
# -*- coding: utf-8 -*-
"""Generate the quadrature abscissas and weights in Fejer quadrature."""
import numpy
import chaospy
from .hypercube import hypercube_quadrature
from .clenshaw_curtis import clenshaw_curtis_simple
def fejer_2(order, domain=(0, 1), growth=False, segments=1):
"""
Generate the quadrature... | jonathf/chaospy | chaospy/quadrature/fejer_2.py | Python | mit | 2,803 | [
"Gaussian"
] | b2e36664dc1a0753590fb88553931ca70a5a5984b37c85d18e2e9e9d301d7fb3 |
""" manage PyTables query interface via Expressions """
import ast
from functools import partial
import numpy as np
import pandas as pd
from pandas.core.dtypes.common import is_list_like
import pandas.core.common as com
from pandas.compat import u, string_types, DeepChainMap
from pandas.core.base import StringMixin
f... | NixaSoftware/CVis | venv/lib/python2.7/site-packages/pandas/core/computation/pytables.py | Python | apache-2.0 | 19,463 | [
"VisIt"
] | 34d3113993dda5c6a9acac93fd559e169541c5a492847322084ec02847a5b515 |
from chain.core.api import Resource, ResourceField, CollectionField
from chain.core.api import full_reverse
from chain.core.api import CHAIN_CURIES
from chain.core.api import BadRequestException
from chain.core.api import register_resource
from chain.core.models import Site, Device, ScalarSensor, ScalarData, \
Pres... | kkleidal/chain-api | chain/core/resources.py | Python | mit | 31,629 | [
"VisIt"
] | b74fef4a4e6e808ffdcabb04cd6ee6b03089a3d66fff7fa089a8fd79d571ed4b |
from ...online_crowdsourcing import *
import json
import math
import os
import random
from PIL import Image
PROB_MAP_SIZE = 200
CONSERVE_MEMORY = False
ACCEPTABLE_STD_DEVS = 2.0
FINISHED_COLOR = '#0F0'
INCORRECT_COLOR = '#F00'
# Crowdsourcing a single part independently from all other parts, but using a model of work... | sbranson/online_crowdsourcing | crowdsourcing/annotation_types/part/part.py | Python | mit | 25,885 | [
"Gaussian"
] | 02c7d78c02da1348c523025eee0f9af6defa95bc60b643ecb9bf927d71f69e79 |
from PyQt4 import QtCore, QtGui
import sys
import paraview.simple as pv
from configuration import configuration
class QPVConfigWindow(QtGui.QWidget):
def __init__(self, proc_num=4, port=11111, parent=None):
QtGui.QWidget.__init__(self, parent)
self.setWindowTitle('ParaView Local Server')
v... | VisTrails/VisTrails | contrib/ParaView/pvconfig.py | Python | bsd-3-clause | 3,243 | [
"ParaView"
] | d1684119ccbbbe1db04b754aed0d8e02449893e858d84a4b25876f555acdd4ca |
########################################################################
# $HeadURL$
# File : CloudStackImage.py
# Author : Victor Mendez ( vmendez.tic@gmail.com )
########################################################################
# DIRAC
from DIRAC import gLogger, gConfig, S_OK, S_ERROR
# VMDIRAC
from VMDIRA... | myco/VMDIRAC | WorkloadManagementSystem/Client/CloudStackImage.py | Python | gpl-3.0 | 9,694 | [
"DIRAC"
] | 828b936fcdc6f615f4715e7c029030b4dfadb86071722e9e7cdd0faab8f6b290 |
import apiaccess as gatt
import infofile
import datetime
from matplotlib.backends.backend_pdf import PdfPages
from fpdf import FPDF
from pyPdf import PdfFileReader, PdfFileWriter
import os.path
#from pudb import set_trace # for interactive debug
# text definitions
PAGEVIEWS_DEFN = """
The word (PAGE)VIEWS here refers... | openmichigan/metrics_tools | openmichigan-metrics-pdf/create_pdf_plots.py | Python | mit | 4,663 | [
"VisIt"
] | 6fc2de6d0c5d607f19f0f3ceed2b80519b681a7155c14df7cd0469a6babb289b |
""" This is the Regression test for DIRAC.MonitoringSystem.private.Plotters in order to ensure
the proper working of the plotter.
"""
# pylint: disable=invalid-name,wrong-import-position
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import os
from D... | ic-hep/DIRAC | tests/Integration/Monitoring/Test_Plotter.py | Python | gpl-3.0 | 13,654 | [
"DIRAC"
] | 64fc2b83b237c5a501adb5722b6e46014aade6a8b8654508690ec60fa7c510cf |
""" Test_RSS_Policy_AlwaysActivePolicy
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id: $"
import unittest
import DIRAC.ResourceStatusSystem.Policy.AlwaysActivePolicy as moduleTested
##################################################... | ic-hep/DIRAC | src/DIRAC/ResourceStatusSystem/Policy/test/Test_RSS_Policy_AlwaysActivePolicy.py | Python | gpl-3.0 | 1,787 | [
"DIRAC"
] | ccedbc8019b2f5b9e5157514529620f36fd922a09cb820bb49dc81497ab2b0d4 |
#
# 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... | nathanielvarona/airflow | airflow/utils/log/logging_mixin.py | Python | apache-2.0 | 5,526 | [
"Elk"
] | 993c71870bf78e28b2096618f67ca56f33f73a0ab585fe4627d98646798df932 |
from brian import second, ms, hertz
from matplotlib.patches import Rectangle
from matplotlib.pyplot import figure, subplot, ylim, legend, ylabel, title, xlabel
import numpy as np
def get_response_time(e_firing_rates, stim_start_time, stim_end_time, upper_threshold=60, threshold_diff=None, dt=.1*ms):
rate_1=e_firi... | jbonaiuto/perceptual-choice-hysteresis | src/python/perceptchoice/model/utils.py | Python | gpl-3.0 | 3,691 | [
"Brian"
] | 5e4aec9236e1f9883c9838869261896e5c9daf0c28c9d2491a29f48e8813581a |
#!/usr/bin/env python2.7
# -*- coding: utf-8 -*-
"""
This module lists known raw databases and how to ingest them.
Specify arguments and run the following command to ingest a database
python -m ibeis --tf ingest_rawdata --db seaturtles --imgdir "~/turtles/Turtles from Jill" --ingest-type=named_folders --species=turt... | SU-ECE-17-7/ibeis | ibeis/dbio/ingest_database.py | Python | apache-2.0 | 52,917 | [
"Jaguar"
] | 7812682e94cc3a49f66e63687dcada4b2586660aece601fb2b288af9f9fc5388 |
"""Classes for probing values of Variables, for example, along a line,
using PyVTK library"""
from __future__ import absolute_import
import numpy as nm
import vtk
from vtk.util import numpy_support as vtknm
import os.path as osp
from sfepy.base.base import Struct, output
from sfepy.linalg import make_axis_rotation_ma... | lokik/sfepy | sfepy/postprocess/probes_vtk.py | Python | bsd-3-clause | 10,065 | [
"VTK"
] | 41b165332349fb0ad7d3a0eaf19535e13a4ce4452fc7e363b25146bd2aa3441c |
# Gaussian process with derivatives in c
#LK_only can only be used for log likelihood or posterior log likelihood
#GPcore takes a single hyperparameter value or a set. With a set the infer_ methods produce individual inferences while infer_post methods return the posterior
#cython: profile=True
#
from __future__ import... | markm541374/gpbo | gpbo/core/flow.py | Python | agpl-3.0 | 11,483 | [
"Gaussian"
] | 2f2d2b44e2bf1ffbd8aa5bfe8ab95e6ddb62818b7888c11a8d15dbaef7ab8b5b |
# 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/test/test_0016_dipole_coo_nao.py | Python | apache-2.0 | 1,490 | [
"PySCF"
] | 45c95846401e584c610c0130cb17a7238be08b3b7b20d8ec65e7c0c0b08ba63c |
#!/usr/bin/env python
"""Check for the ability to read and write identical GenBank records.
This script takes as input a single file to be tested for reading records.
It will run through this file and check that the output of the parsed and
printed record matches the original record.
Usage:
python check_output.py <na... | updownlife/multipleK | dependencies/biopython-1.65/Scripts/GenBank/check_output.py | Python | gpl-2.0 | 2,716 | [
"Biopython"
] | 6379a9d56e3c10439130c0518827e5cd9e88e22e94d91d2a9fbc790bb5661bb1 |
#!/usr/bin/env python3
import argparse
import re
from molutils.util.molecule import Molecule
from molutils.util.job_formatters.psi4 import Psi4JobFormatter
from molutils.util.job_formatters.gamess import GamessJobFormatter
def main(args):
for file in args.input:
molecules = Molecule.from_file(file, psi4_p... | jasonrig/molecule-utils | molutils.py | Python | mit | 3,990 | [
"GAMESS",
"Psi4"
] | 193806096640a1dd6338ce9e39ebefa32642f59dd20ef743b5678bd9ed072a9c |
"""
Support the ISY-994 controllers.
For configuration details please visit the documentation for this component at
https://home-assistant.io/components/isy994/
"""
import logging
from urllib.parse import urlparse
from homeassistant import bootstrap
from homeassistant.const import (
ATTR_DISCOVERED, ATTR_SERVICE,... | justyns/home-assistant | homeassistant/components/isy994.py | Python | mit | 6,873 | [
"VisIt"
] | 4eebd4486aa3fe600763403b7bd8c3b8b95e4b12151124928523316b47ac182c |
# -*- coding: utf-8 -*-
"""
Master Dictionary
Translations
0: English
1: Chinese
2: Dutch
3: French
4: Italian
5: Japanese
6: Korean
7: Portuguese
8: Russian
9: Spanish
"""
class MD_F:
# Master Dictionary Functions
def get_languages_list():
languages = []
languages.append("English")
... | seleniumbase/SeleniumBase | seleniumbase/translate/master_dict.py | Python | mit | 110,541 | [
"VisIt"
] | 642693fd6245ac6e11f4bdabb889e674016d68d652dfc743b3611ee1fe0a6857 |
#!/usr/bin/env python
"""Test for sites of contrasting conservation between gene clades."""
from os.path import dirname
setup_args = {}
try:
from setuptools import setup
# Dependencies for easy_install:
setup_args.update(
install_requires=[
'biofrills >= 0.2',
'biopython ... | etal/cladecompare | setup.py | Python | bsd-2-clause | 981 | [
"Biopython"
] | 3c6d6b9ed34e5d444b872f05cf0a0af91f3e5a0d8cf635ac09e6af5208a74128 |
#
# @file TestSBase_newSetters.py
# @brief SBase unit tests for new set API
#
# @author Akiya Jouraku (Python conversion)
# @author Sarah Keating
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generated automatically by converting ... | TheCoSMoCompany/biopredyn | Prototype/src/libsbml-5.10.0/src/bindings/python/test/sbml/TestSBase_newSetters.py | Python | bsd-3-clause | 61,453 | [
"VisIt"
] | 5b060ca85406a3aefb73095d22a2491838ab98cb701e6c4868b8ceecc973816e |
# (c) 2013-2014, Michael DeHaan <michael.dehaan@gmail.com>
# (c) 2015 Toshio Kuratomi <tkuratomi@ansible.com>
#
# 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... | mensler/ansible | lib/ansible/executor/module_common.py | Python | gpl-3.0 | 39,091 | [
"VisIt"
] | 5f04ec1f472832d82b2aa94e18ca3b9a6863fc5985d1819b481a1d96e38fc61e |
#!/usr/bin/python
usage = """%prog -- evaluate word segmentation
(c) Mark Johnson, 27th July 2012
usage: %prog [options]
"""
import lx, tb
import optparse, re, sys
def tree_string(tree, word_rex, ignore_terminal_rex):
def simplify_terminal(t):
if len(t) > 0 and t[0] == '\\':
return t[1... | syhw/contextual_word_segmentation | scripts/eval.py | Python | mit | 9,461 | [
"VisIt"
] | f68f854e36899927d3a339a442aec0da635ccd8d1a50522734f00dc9734716cf |
#* 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
"""Module f... | nuclear-wizard/moose | python/MooseDocs/tree/__init__.py | Python | lgpl-2.1 | 529 | [
"MOOSE"
] | b792ed82b3934ec939051657908cc59c98b579dae21e894c172fd7928f83f279 |
#!/usr/bin/env python
"""
This script can be useful when creating a large number of recipes that, if
submitted all at once, could result in timeout errors when building on
travis-ci. A common example is when recipes must be updated for a new
Bioconductor release. This script batches together recipes such that each batc... | zwanli/bioconda-recipes | scripts/toposort_recipes.py | Python | mit | 1,466 | [
"Bioconductor"
] | b0d60c8d7009cc2574ca77ecc39bd349ee9dbddc5ec837635626b772435c4fe0 |
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