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#
# @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
#... | jgonthier/psi4 | psi4/share/psi4/databases/BENCH12.py | Python | lgpl-3.0 | 60,274 | [
"Psi4"
] | d1a8e6269e23b919b2bd7bd1dcf82e484234eec051f781e728db539d3219c3c4 |
import pyspeckit
# neet matplotlib so we can make mouse-click events from the script
import matplotlib
# list of annotations so we can clear them
annotations = []
excesslines = []
# get the data from http://cdsarc.u-strasbg.fr/ftp/cats/II/179/sp/hr2421.fit
import urllib2
url = urllib2.urlopen('http://cdsarc.u-strasbg... | keflavich/pyspeckit-obsolete | examples/interactive_example_hr2421.py | Python | mit | 11,176 | [
"Gaussian"
] | cad1812def409918583d6a09365f879382e77a62cd31c03482ab81aef8517c30 |
#======================================================================#
#| |#
#| Chemical file format conversion module |#
#| |#
#| Lee-Ping W... | choderalab/open-forcefield-group | qm/crank/molecule.py | Python | gpl-2.0 | 138,660 | [
"Amber",
"CHARMM",
"Dalton",
"GROMOS",
"Gaussian",
"Gromacs",
"OpenMM",
"Q-Chem",
"TINKER"
] | 9da29f3285c5e5e010d389e98a2a1f570e077b5dff37433a4e8427ab20450278 |
# Copyright 2009 Brian Quinlan. All Rights Reserved.
# Licensed to PSF under a Contributor Agreement.
"""Implements ProcessPoolExecutor.
The follow diagram and text describe the data-flow through the system:
|======================= In-process =====================|== Out-of-process ==|
+----------+ +-... | Orav/kbengine | kbe/src/lib/python/Lib/concurrent/futures/process.py | Python | lgpl-3.0 | 18,001 | [
"Brian"
] | ef36a3ad661188e25248ed956f82125c1d858eb8d9bcb58c543ed4390761a750 |
#!/usr/bin/python
#
# feed-named-pipe - A simple utility to feed data from a file into a named pipe. Useful for
# testing other applications. Supports different sending speeds of data
# from the file
#
# Copyright (c) 2017 - Brown Consulting Services
#
import argparse
import os.path... | brownconsultingsvcs/codesamples | python/tools/feed-named-pipe.py | Python | gpl-3.0 | 3,274 | [
"BLAST"
] | b1d42a899635b0ed297f336e25ed06ae550a5d6d02db1c7bfddf78dffa4a594c |
#!/usr/bin/env python
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
'''Exception types for GRIT.
'''
class Base(Exception):
'''A base exception that uses the class's docstring in addition to any
... | danakj/chromium | tools/grit/grit/exception.py | Python | bsd-3-clause | 3,087 | [
"xTB"
] | 800680dffefce4a0e7f156e3be8e714405e7e99d55b2609b5987cb0e4550bafe |
from __future__ import division, print_function, unicode_literals
# This code is so you can run the samples without installing the package
import sys
import os
sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..'))
#
testinfo = "f 10 0.033, s, f 20 0.033, s, f 30 0.033, s, f 30 0.033, s, q"
tags = "particl... | google-code-export/los-cocos | test/test_particle_smoke.py | Python | bsd-3-clause | 1,051 | [
"Galaxy"
] | 8eaaa0a790a18612b21b1134ce656dca071c594924fc3690cb1cdd21586723f6 |
#
# Copyright (c) 2017 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | yashdsaraf/scancode-toolkit | tests/scancode/test_extract_cli.py | Python | apache-2.0 | 10,349 | [
"VisIt"
] | 1aa8f64beb78920b985181f0408d8c5766096be64218e8a5a8f7fe7d01487586 |
# -*- coding: utf-8 -*-
"""
Created on Wed Dec 07 20:13:41 2011
@author: Shreejoy
"""
# -*- coding: utf-8 -*-
"""
Created on Mon Nov 28 14:26:44 2011
@author: Shreejoy
"""
from SPARQLWrapper import SPARQLWrapper, JSON, XML, N3, RDF
import re
dir('C:\Python27\Scripts\biophys\pubdb\pubdir')
from puba... | neuroelectro/neuroelectro_org | neurolex_integration/sparql_get.py | Python | gpl-2.0 | 1,822 | [
"NEURON"
] | 37c7764c26f7a43c7466c9259de92b0b9fb0069c7a130613c9f40f8180bae704 |
#!/usr/bin/env python
# Copyright 2014-2020 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/lib/chkfile.py | Python | apache-2.0 | 5,817 | [
"PySCF"
] | 3186871e4d371fd0477bf08a61624ed4b11fc7a6a0d6e59eb51f3c3b2192b538 |
"""
local path implementation.
"""
import sys, os, stat, re, atexit
import py
from py._path import common
iswin32 = sys.platform == "win32" or (getattr(os, '_name', False) == 'nt')
class Stat(object):
def __getattr__(self, name):
return getattr(self._osstatresult, "st_" + name)
def __init__(self, pat... | ktan2020/legacy-automation | win/Lib/site-packages/py-1.4.13-py2.7.egg/py/_path/local.py | Python | mit | 28,610 | [
"VisIt"
] | 53035a45622f4e6b2fb2abb88c701129cdf621b47889b71845d68e9555de66f3 |
#pylint: disable=C0111
from time import sleep
from lettuce import world, step
from lettuce.django import django_url
from common import i_am_registered_for_the_course, section_location
@step('I view the word cloud and it has rendered')
def word_cloud_is_rendered(_step):
assert world.is_css_present('.word_cloud')... | PepperPD/edx-pepper-platform | lms/djangoapps/courseware/features/word_cloud.py | Python | agpl-3.0 | 2,011 | [
"VisIt"
] | d3b38b6badbad1778005c13ba3a7040b49aad81d6f548830182a55606d605ab8 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import os
import unittest
import warnings
from pymatgen.util.testing import PymatgenTest
from pymatgen.analysis.transition_state import NEBAnalysis
import json... | gpetretto/pymatgen | pymatgen/analysis/tests/test_transition_state.py | Python | mit | 3,285 | [
"pymatgen"
] | a79684c40b817b16a620bdad1e70e6504e593c7b38a77bc5240a5fb760e03419 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import sys
import os
import pickle
import copy
import warnings
import numpy as np
from pkg_resources import parse_version
import psychopy
from psychopy import logging
from psychopy.tools.filetools import openOutputFile, genDelimiter
from psychopy.tools.fileerrortools impo... | psychopy/psychopy | psychopy/data/staircase.py | Python | gpl-3.0 | 86,183 | [
"Gaussian"
] | ea8bdc268c697d5f92e3646bb12216ffcf0f6a0a70abbce2dc87867952330ee5 |
#!/usr/bin/python2
import argparse
import sys
import subprocess
import requests
import json
from pprint import pprint
import os
class bcolors:
HEADER = '\033[95m'
OKBLUE = '\033[94m'
OKGREEN = '\033[92m'
WARNING = '\033[93m'
FAIL = '\033[91m'
ENDC = '\033[0m'
BOLD = '\033[1m'
UNDERLINE ... | anantshri/wpvulndb_commandline | wpvulndb_cmd.py | Python | gpl-2.0 | 4,547 | [
"VisIt"
] | d31a38403566380c3ef3e145ce480f1f25a29ac66b546f8da77b89cf9b86bad4 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# This example demonstrates how to create a polyline through several ordered points.
import vtk
import math
def main():
colors = vtk.vtkNamedColors()
# Set the background color.
colors.SetColor("BkgColor", [26, 51, 102, 255])
# vtkPoints represents 3D ... | lorensen/VTKExamples | src/Python/GeometricObjects/PolyLine1.py | Python | apache-2.0 | 3,962 | [
"VTK"
] | b269316ac509098b2348d8612404c2cd3c4cfccaa8677b6470500dcbadf2c08d |
# __Author__: 'Brian Westerman'
# __Date__: 2/15/16
# __File__: analysis.py
import numpy as np
import scipy.stats as st
import scipy.cluster.vq as vq
import math
import random
import data as dt
# Takes in a list of column headers and the Data object and returns a list of 2-element lists with the minimum and
# maximum... | bhwester/computer-science-projects | data_analysis_and_visualization_system/analysis.py | Python | mit | 19,600 | [
"Brian"
] | 77b4b39114f56db530ea4df54ec73db529762c8abbdb931ac7a28bd68ebca9e5 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: y... | casawa/mdtraj | mdtraj/utils/test.py | Python | lgpl-2.1 | 6,569 | [
"MDTraj"
] | a854bcb8c74752214f6cdb977c9fd9507a066149e28137dbfd4c0f1b63c1ae1c |
#!/usr/bin/python
# Author: Dongho Choi
import math
import time
import pandas as pd
from math import log
from sshtunnel import SSHTunnelForwarder # for SSH connection
import pymysql.cursors # MySQL handling API
import sys
sys.path.append("./configs/")
import server_config # (1) info2_server (2) exploration_db
if __n... | DonghoChoi/ISB_Project | local/calculate_online_diversity.py | Python | gpl-3.0 | 3,182 | [
"VisIt"
] | fc2e981812138df6fa312bd12d4317dd2b0d207fae68a94889756d575294d035 |
#!/usr/bin/env python
# Copyright (c) 2002 Bryce "Zooko" Wilcox-O'Hearn
# portions Copyright (c) 2001 Autonomous Zone Industries
# This file is licensed under the
# GNU Lesser General Public License v2.1.
# See the file COPYING or visit http://www.gnu.org/ for details.
#
__cvsid = '$Id: TristeroTest.py,v 1.3 ... | zooko/egtp | TristeroTest.py | Python | agpl-3.0 | 4,085 | [
"VisIt"
] | 45cc4cfaf20dfcc1b1e97e9d0d777afa9255ce4c48f505b8b519b2a93f7d2353 |
#
# GADANN - GPU Accelerated Deep Artificial Neural Network
#
# Copyright (C) 2014 Daniel Pineo (daniel@pineo.net)
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation files (the "Software"),
# to deal in the Software without restricti... | dpineo/gadann | tests/test_overfeat.py | Python | mit | 34,789 | [
"Bowtie",
"ESPResSo",
"Jaguar",
"ORCA"
] | 966a36fcb10e3f745a15595648693f54ab4e35a7eaddcb8f823e565f015fedd2 |
import neural
# Construct network
neuron = neural.Neuron()
inputN1 = neural.Node(nextInput=neuron)
inputN2 = neural.Node(nextInput=neuron)
biasN = neural.Node(value=1, nextInput=neuron)
neuron.inputs = [neural.NeuronInput(input=inputN1), neural.NeuronInput(input=inputN2), neural.NeuronInput(input=biasN)]
outputN =... | limdingwen/neural | test.py | Python | mit | 1,453 | [
"NEURON"
] | 37c052e5f78e5e7fa200607084f53777e04171e7a73500e28a1e1592763f2a9c |
# Copyright 2017 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... | chemelnucfin/tensorflow | tensorflow/python/ops/linalg/linalg_impl.py | Python | apache-2.0 | 44,658 | [
"Gaussian"
] | 3abac146b346e0cd45c9fe2bd097f1d4a98131ef34805dbdb2114c673852c98d |
# -*- Mode: Python; coding: utf-8; indent-tabs-mode: nil; tab-width: 4 -*-
### BEGIN LICENSE
# Copyright (C) 2014 Brian Douglass bhdouglass@gmail.com
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License version 3, as published
# by the Free Softwa... | bhdouglass/agui | agui/backends/gtk/widgets/action.py | Python | gpl-3.0 | 1,412 | [
"Brian"
] | 10cc95a9978bea88c4368b75e3c00d243717e706e366b0f5be0e332d253fe326 |
#!/usr/bin/env python
"""
Script that dumps the DB information for the elements into the standard output.
If returns information concerning the StatusType and Status attributes.
Usage:
dirac-rss-list-status [options]
Verbosity::
-o LogLevel=LEVEL NOTICE by default, levels available: INFO, DEBUG, VERBOSE..
... | yujikato/DIRAC | src/DIRAC/ResourceStatusSystem/scripts/dirac_rss_list_status.py | Python | gpl-3.0 | 5,045 | [
"DIRAC"
] | 80b3f15e5dc3f242657c433669d87ddf5f5b9711439ca680c885ed52c57295aa |
# -*- Mode:Python; indent-tabs-mode:nil; tab-width:4 -*-
#
# Copyright (C) 2015, 2016 Canonical Ltd
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License version 3 as
# published by the Free Software Foundation.
#
# This program is distributed in... | dpniel/snapcraft | snapcraft/tests/commands/test_list_plugins.py | Python | gpl-3.0 | 2,709 | [
"GULP"
] | 68d510491089ee1d02fe7a3a1c0fdad4a81310d90f22ddb4fe4b1975b4111130 |
# Version: 0.18
"""The Versioneer - like a rocketeer, but for versions.
The Versioneer
==============
* like a rocketeer, but for versions!
* https://github.com/warner/python-versioneer
* Brian Warner
* License: Public Domain
* Compatible With: python2.6, 2.7, 3.2, 3.3, 3.4, 3.5, 3.6, and pypy
* [![Latest Version]
(... | david-hoffman/pyOTF | versioneer.py | Python | apache-2.0 | 68,473 | [
"Brian"
] | 62287202b244003e5d96d1105dedf3fc031cdbf0c87edee1ea63c9431ff6f258 |
"""Galaxy (ansible-galaxy) plugin for integration tests."""
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import os
import tempfile
from ....config import (
IntegrationConfig,
)
from ....docker_util import (
docker_cp_to,
)
from ....containers import (
run_suppo... | pmarques/ansible | test/lib/ansible_test/_internal/commands/integration/cloud/galaxy.py | Python | gpl-3.0 | 6,544 | [
"Galaxy"
] | b4448c71b86da324f2af3d00b605736533ece54c8d07c288331933d76fe034f7 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright 2013 The Plaso Project Authors.
# Please see the AUTHORS file for details on individual authors.
#
# 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 L... | cvandeplas/plaso | plaso/parsers/plist_plugins/safari_test.py | Python | apache-2.0 | 2,281 | [
"VisIt"
] | 55f372652ae2d65e9fc3b3af4017c01fd6479a73bf5b60ebdaa9dcd832bd82c6 |
print('importing functions from the pymicro library')
try:
from pymicro.apps.wxImageViewer import ImageViewer
from pymicro.apps.wxVolumeViewer import wxVolumeViewer
from pymicro.apps.View import View
except:
print('exception occured importing modules')
from pymicro.crystal.lattice import *
from pymicro... | heprom/pymicro | import_modules.py | Python | mit | 679 | [
"CRYSTAL"
] | d64145aa02022bbc60e98f628b9b4a543d3a29d812c0bf66ed3d8e4ff2cff471 |
"""
Tests for Coulomb matrix calculation.
"""
import numpy as np
import unittest
from rdkit import Chem
from deepchem.feat import coulomb_matrices as cm
from deepchem.utils import conformers
class TestCoulombMatrix(unittest.TestCase):
"""
Tests for CoulombMatrix.
"""
def setUp(self):
"""
... | bowenliu16/deepchem | deepchem/feat/tests/test_coulomb_matrices.py | Python | gpl-3.0 | 3,109 | [
"RDKit"
] | 148f898b3f3429d04d5bd2e93dae7c10736ee8d13a9102ec2d4d4462855e9440 |
tests=[
("python","UnitTestChem.py",{}),
("python","UnitTestChemv2.py",{}),
("python","UnitTestChemAtom.py",{}),
("python","UnitTestChemBond.py",{}),
("python","UnitTestChemSmarts.py",{}),
("python","UnitTestFragmentDescriptors.py",{}),
("python","UnitTestGraphDescriptors.2.py",{}),
("python","UnitTest... | soerendip42/rdkit | rdkit/Chem/test_list.py | Python | bsd-3-clause | 2,336 | [
"RDKit"
] | 806a963c322bd74c6ac522b8989d35a44fc23e9e9c289db7c7426dab0e829399 |
import sys, os
# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
sys.path.insert(0, os.path.abspath('../neurotune'))
sys.path.inser... | vellamike/neurotune | doc/conf.py | Python | bsd-3-clause | 9,476 | [
"NEURON"
] | 6a199fbeaed8e48e9ed26f836b388026cd4716355d3cb4632c31f79335538946 |
# Copyright 2016-2017 Capital One Services, 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 agreed ... | taohungyang/cloud-custodian | tests/test_resolver.py | Python | apache-2.0 | 6,098 | [
"Galaxy",
"MOOSE"
] | 64f48c2239c643fc36f88b82bb0dc342536efba4e3921e21608490e3004e4ae2 |
#!/usr/bin/env python
"""
This script is a python version of TimingAccuracyDHC. We use numpy functions to
simplify the creation of random coefficients.
"""
import os
import sys
import time
import numpy as np
sys.path.append(os.path.join(os.path.dirname(__file__), "../../.."))
import pyshtools as shtools
#==== MAIN F... | ian-r-rose/SHTOOLS | examples/python/TimingAccuracy/TimingAccuracyDHC.py | Python | bsd-3-clause | 2,509 | [
"Gaussian"
] | 5dfb34fdd074a7a5495ed938e3cecf4ed57598aafe2df2d7f48726bd8794b598 |
''' GGUSTicketsCommand
The GGUSTickets_Command class is a command class to know about
the number of active present opened tickets.
'''
__RCSID__ = '$Id$'
import urllib2
from DIRAC import S_ERROR, S_OK
from DIRAC.Core.LCG.GGUSTicketsClient import GGUSTicketsClient
from DIRAC.Core.Utilities.SitesDIRACGOCDBmappin... | arrabito/DIRAC | ResourceStatusSystem/Command/GGUSTicketsCommand.py | Python | gpl-3.0 | 5,103 | [
"DIRAC"
] | 588c293a1294637148b73b1c54fe7aba9c6839d60b0ff82da997561645c1ca04 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import (division, print_function, absolute_import,
unicode_literals)
__all__ = ["sample_ball", "MH_proposal_axisaligned", "MPIPool"]
import numpy as np
from .mpi_pool import MPIPool
def sample_ball(p0, std, size=1):
"""
... | shfengcj/pydm | pydm/emcee/utils.py | Python | gpl-2.0 | 1,713 | [
"Gaussian"
] | 916af077e0e050e88e984a289e83b7488d3013381a8ff1c1fe390f2794990e19 |
import os
import nltk
from jgtextrank import keywords_extraction
# load custom stop list
# The SMART stop-word list built by Chris Buckley and Gerard Salton,
# which can be obtained from http://www.lextek.com/manuals/onix/stopwords2.html
import db.corpora as cp
for stoplist_path in [os.path.join("..", "notebooks", ... | danieldmm/minerva | proc/keyphrase_annotation.py | Python | gpl-3.0 | 7,796 | [
"Gaussian"
] | 74aad9264d7bec7e26b0d72b711d2aedd274f01aebba917daf5eccb15a6852e4 |
"""
Accounting agent to consume perfSONAR network metrics received via a message queue.
.. literalinclude:: ../ConfigTemplate.cfg
:start-after: ##BEGIN NetworkAgent
:end-before: ##END
:dedent: 2
:caption: NetworkAgent options
"""
from datetime import datetime
from DIRAC import S_OK, S_ERROR, gLogger
from DIR... | DIRACGrid/DIRAC | src/DIRAC/AccountingSystem/Agent/NetworkAgent.py | Python | gpl-3.0 | 11,040 | [
"DIRAC"
] | 031122766799befe621c44702300481e155851212d85c435894191920ff65265 |
#!/usr/bin/env python3
import sys
import json
from collections import OrderedDict
# merge subtitles from kcwiki format into quotes.json
# * quotes.json must be using descriptive keys
# the latest subtitles.json can be downloaded from:
# http://api.kcwiki.moe/subtitles
# See: https://github.com/kcwikizh/poi-plugin-su... | nonsensed/kc3-translations | tools/kcwikizh-subtitle-merge.py | Python | mit | 4,274 | [
"MOE"
] | f20ec807bf91ab7e71a3de3d19c272f51d0f32f03b325f9ea995e7d66e7e681e |
# Copyright (C) 2003 CAMP
# Please see the accompanying LICENSE file for further information.
from os import path
try:
from subprocess import Popen, PIPE
except ImportError:
from os import popen3
else:
def popen3(cmd):
p = Popen(cmd, shell=True, close_fds=True,
stdin=PIPE, stdout... | slabanja/ase | ase/svnversion_io.py | Python | gpl-2.0 | 1,335 | [
"ASE"
] | bab3132b7f66560b51670f84569ffbbec06c76351eb4564c94a2a55bee97acca |
""" Module holding function(s) creating the pilot wrapper.
This is a DIRAC-free module, so it could possibly be used also outside of DIRAC installations.
The main client of this module is the SiteDirector, that invokes the functions here more or less like this:
pilotFiles = getPilotFiles()
pi... | arrabito/DIRAC | WorkloadManagementSystem/Utilities/PilotWrapper.py | Python | gpl-3.0 | 7,684 | [
"DIRAC"
] | 2e68465c34a9e3aea77ff174e986f06e9608757aae5176ec40524b3231a9acb4 |
# -*- coding: utf-8 -*-
# Python imports
import logging
import math
import unittest
from xml.dom import minidom
# Local imports
import models
import util
import datetime
import counter
from growthcalc.growthcalc import VisitStatistics
import growthcalc.growthcalc
from growthcalc.growthcalc import Sex
from growthcal... | avastjohn/maventy_new | healthdb/tests.py | Python | bsd-3-clause | 27,469 | [
"VisIt"
] | b2761e68cfbf5523b7e7a9e4ba1ebb2f34be84640f46684a46766fdfb7f9b549 |
# -*- coding: utf-8 -*-
"""
This example demonstrates a very basic use of flowcharts: filter data,
displaying both the input and output of the filter. The behavior of
he filter can be reprogrammed by the user.
Basic steps are:
- create a flowchart and two plots
- input noisy data to the flowchart
- flowchart con... | ibressler/pyqtgraph | examples/Flowchart.py | Python | mit | 2,451 | [
"Gaussian"
] | 9d17bef4e6bcc4338ab4919545d27a57bd86d7f2907a365e6ac9f9f6daad49cc |
# Copyright 2005-2008 by Frank Kauff & Cymon J. Cox. 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.
"""Provides functionality of a linked list.
Each node has one (or none) prede... | go-bears/Final-Project | weblogo-3.4_rd/corebio/seq_io/_nexus/Nodes.py | Python | mit | 5,410 | [
"Biopython"
] | 3d782c59ee273ce88ee82430536a592b4023ba53dd6f289c705cc253915e4e19 |
import math
import numpy
from chainer import cuda
from chainer import function
from chainer.utils import type_check
def _as_mat(x):
if x.ndim == 2:
return x
return x.reshape(len(x), -1)
class Linear(function.Function):
"""Linear function (a.k.a. fully-connected layer or affine transformation)... | sou81821/chainer | chainer/functions/connection/linear.py | Python | mit | 5,872 | [
"Gaussian"
] | 86ab841c5a8dd02fd520d6ef2428c17c04ef7127e131d7970dd5813761804ca8 |
# coding=utf-8
from __future__ import unicode_literals
from .. import Provider as PersonProvider
class Provider(PersonProvider):
formats = (
'{{first_name_male}} {{last_name}}',
'{{first_name_male}} {{last_name}}',
'{{first_name_male}} {{last_name}}',
'{{first_name_male}} {{last_n... | meganlkm/faker | faker/providers/person/de_DE/__init__.py | Python | mit | 30,301 | [
"Brian"
] | 70224ef3a6922d7b8bcb619d0e815d8344ef03789fdc7aedf71df2be7a894108 |
from ase import Atom, Atoms
from gpaw import GPAW
from gpaw.test import equal
a = 4.05
d = a / 2**0.5
bulk = Atoms([Atom('Al', (0, 0, 0)),
Atom('Al', (0.5, 0.5, 0.5))], pbc=True)
bulk.set_cell((d, d, a), scale_atoms=True)
h = 0.25
calc = GPAW(h=h,
nbands=2*8,
kpts=(2, 2, 2),
... | ajylee/gpaw-rtxs | gpaw/test/davidson.py | Python | gpl-3.0 | 1,023 | [
"ASE",
"GPAW"
] | ce6e4f1d1987fd66f3937948762befd4fce824d11093cc553be5f133d6b89c5a |
#!/usr/bin/env python
# Copyright 2014-2020 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/df/rsdf.py | Python | apache-2.0 | 30,824 | [
"Gaussian",
"PySCF"
] | 4217fbd8898c68bb7745a9a0b5526b51b89d49c1cf745d862494c94b22a4b9a0 |
from ase import Atoms
from gpaw import GPAW
from gpaw.mpi import size
d = 4.0 / 2**0.5
ndomains = size // 8 + 1
calc = GPAW(h=d / 16, kpts=(17, 1, 1), parallel={'domain': ndomains})
chain = Atoms('Al', cell=(d, 5, 5), pbc=True, calculator=calc)
e = chain.get_potential_energy()
assert abs(e - -1.81816) < 0.00005
assert ... | qsnake/gpaw | gpaw/test/al_chain.py | Python | gpl-3.0 | 392 | [
"ASE",
"GPAW"
] | 905db863582687195c582f905e8ae0e3d3f46734b8b2b1fb0c725009309745a0 |
import datetime
from django.core.management.base import NoArgsCommand
from django.core.urlresolvers import reverse
from django.db import connection
from django.db.models import Q, F
from askbot.models import User, Question, Answer, Tag, PostRevision
from askbot.models import Activity, EmailFeedSetting
from askbot.model... | samhoo/askbot-realworld | askbot/management/commands/send_email_alerts.py | Python | gpl-3.0 | 22,414 | [
"VisIt"
] | 831426a03b816451b4464178c64dd184b010a81d7a3635bc4b7498ccabb17119 |
from __future__ import absolute_import
import re
import six
from six.moves import range
class Board(object):
num_players = 2
# Valid pawn move offsets
DIRECTIONS = ( (-1, 0),
( 0,-1), ( 0, 1),
( 1, 0),)
JUMP_DIRECTIONS = ( #Jump destination,... | jbradberry/chong | chong/chong.py | Python | mit | 10,475 | [
"VisIt"
] | d8aded3c296b22c3561c9a90f9ea247dff1441796d86965ce6518d4df44a478a |
'''Figure out which phages we do not have blastn hits for'''
import os,sys
from phage import Phage
import re
# get a list of all phages
phage=Phage()
phages=phage.phageTaxonomyString()
try:
blastf=sys.argv[1]
except:
sys.exit(sys.argv[0] + " <blast file>")
found={}
with open(blastf, 'r') as fin:
for l i... | linsalrob/PhageHosts | code/missing_phage_blastn.py | Python | mit | 482 | [
"BLAST"
] | 1aa81013ad01ba78ab08d9111b42cb7acf935f703fe1490e0f5f429408b9c690 |
# $Id$
#
# Copyright (C) 2007 greg Landrum
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
from __future__ import print_function
import unittest... | rvianello/rdkit | rdkit/Chem/AtomPairs/UnitTestDescriptors.py | Python | bsd-3-clause | 3,522 | [
"RDKit"
] | bd0945f1b689189a42319ad901645187ae8a22a48518ca4eb1f5743fe271660d |
"""
Functions and classes for finding Treants in the filesystem.
"""
import os
import sys
import glob
import time
import scandir
from datreant import persistence
import datreant
def statefilename(treanttype, uuid, ext):
"""Return state file name given the type of treant and its uuid.
"""
return "{}.{}... | andreabedini/datreant | datreant/filesystem.py | Python | bsd-3-clause | 14,583 | [
"VisIt"
] | 1917106707c20a930e51e683dff45fff6226e8c488cce3bc59e577b6d6ee80b6 |
# rfc1751.py : Converts between 128-bit strings and a human-readable
# sequence of words, as defined in RFC1751: "A Convention for
# Human-Readable 128-bit Keys", by Daniel L. McDonald.
#
# Part of the Python Cryptography Toolkit
#
# Written by Andrew M. Kuchling and others
#
# =========================================... | ktan2020/legacy-automation | win/Lib/site-packages/Crypto/Util/RFC1751.py | Python | mit | 21,186 | [
"Elk",
"MOE"
] | f464fcc461d0e72076c605f5a4783e8786946263857ef793a9267af651bc6fd7 |
#!/usr/bin/python
# -*- coding=utf-8 -*-
import sys
import pymatgen as mg
import numpy as np
from pymatgen.io.vaspio.vasp_input import Poscar
def look4VacantPosition():
""" """
s = mg.Structure.from_file(sys.argv[1])
fill_s = s.copy()
grid = mg.Structure(s.lattice, [], [])
# grid step in frac c... | gVallverdu/myScripts | VASP/vacantPosition.py | Python | gpl-2.0 | 2,293 | [
"VASP",
"pymatgen"
] | beda22f5413a83c3ab5c8cd6da6a0cc37947234df378d5f0602a1deed6dfddf2 |
"""
Metadata for all filters.
"""
# Author: Prabhu Ramachandran <prabhu@aero.iitb.ac.in>
# Copyright (c) 2008, Prabhu Ramachandran Enthought, Inc.
# License: BSD Style.
# Local imports.
from mayavi.core.metadata import FilterMetadata
from mayavi.core.pipeline_info import PipelineInfo
BASE = 'mayavi.filters'
########... | dmsurti/mayavi | mayavi/filters/metadata.py | Python | bsd-3-clause | 26,514 | [
"Gaussian",
"Mayavi"
] | c2d3adecea9f0bc5f27a5ce475dd83bd2bc4a587569e968c3e885da95e0adfb1 |
from unittest import TestCase
from pypattyrn.behavioral.visitor import Visitor, Visitee
class VisitorTestCase(TestCase):
"""
Unit testing class for the Visitor class.
"""
def setUp(self):
"""
Initialize testing data.
"""
class Node(object):
pass
cla... | tylerlaberge/PyPattyrn | tests/behavioral_tests/test_visitor.py | Python | mit | 2,655 | [
"VisIt"
] | 38b9490069b2440e96140227f400a30e3d1dd9ef98ddeca72b679f69f09ae94a |
#!/usr/bin/env python
"""Extract a consensus sequence from a read mapping (BAM) based on
simple majority rules. Makes no ploidy assumptions (initially designed
for viral genomes). Able to handle indels. Columns with no coverage
can be specially marked (see option --no-cov-char).
"""
#--- standard library imports
#
fro... | CSB5/vipr | src/bam2cons.py | Python | gpl-2.0 | 13,664 | [
"pysam"
] | 270efc8d17fb2ef33947244393c0a49ba054d1b7a94b956044e38b1cbf156ff1 |
# Copyright (c) 2015,2016 MetPy Developers.
# Distributed under the terms of the BSD 3-Clause License.
# SPDX-License-Identifier: BSD-3-Clause
r"""Tools for mimicing the API of the Common Data Model (CDM).
The CDM is a data model for representing a wide array of data. The
goal is to be a simple, universal interface to... | jrleeman/MetPy | metpy/io/cdm.py | Python | bsd-3-clause | 14,032 | [
"NetCDF"
] | 1f9b39ed67407830c0ef0da9d6a9275192a5cb6aa75d6a21d1014055720229df |
#!/usr/bin/env python
"""
Blast XML parser that extracts and aggregates the hits from different blast.xml files,
and presents them in a tab-separated format ordered by e-value (or bitscore).
Requires filenames to finish in _tool_blast[nxp]_database.xml
Author: Mauricio Barrientos-Somarribas
Email: mauricio.barriento... | maubarsom/biotico-tools | python/blastxml_join_hitsort.py | Python | apache-2.0 | 7,008 | [
"BLAST"
] | 5a0748e1c9277e32b6e4b224281e1228ab383c9bbac95281a5dace5257a5a9a4 |
#!/usr/bin/env python
#
# zip up the titanium mobile SDKs into suitable distribution formats
#
import os, types, glob, shutil, sys, platform, codecs
import zipfile, datetime, subprocess, tempfile, time
sys.path.append(os.path.join(os.path.abspath(os.path.dirname(sys._getframe(0).f_code.co_filename)),'..','support','co... | pec1985/titanium_mobile | site_scons/package.py | Python | apache-2.0 | 21,809 | [
"VisIt"
] | b188c57f3bb801938b5f2a99b150168150c7c1d9d8957bdf3c5d049a8514dbdb |
"""
Conversion of spectra class to functions
author: Rohan Isaac
"""
import numpy as np
from numpy import sqrt, pi
import re
import pandas as pd
from scipy import signal
from lmfit import Model
from lmfit.models import PolynomialModel
from lmfit.lineshapes import lorentzian, gaussian, voigt
from uncertainties import ... | rohanisaac/spectra | spectra/spectra.py | Python | gpl-3.0 | 4,112 | [
"Gaussian"
] | 8df3676db6bd89f45670cebf313eb5402e91a49e7d0f768a93af86ee32515f5c |
# Hop --- a framework to analyze solvation dynamics from MD simulations
# Copyright (c) 2007-2010 Oliver Beckstein <orbeckst@gmail.com>
#
# 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 v... | Becksteinlab/hop | hop/sitemap.py | Python | gpl-3.0 | 82,994 | [
"CHARMM",
"MDAnalysis",
"VMD"
] | 153a352f2335e8074bf8d33eb63410e84bcd0aef7615ff38ed94e3588e43c088 |
#!/usr/bin/env python
import os
import sys
import re
import xlrd
import splinter
import urtracker as URT
PROJECT_IDS = [712, 700, 748, 746, 750, 683, 745]
# PROJECT_IDS = [712, 746, 750]
ALL_PROBLEMS = "/media/sf_linux-share/all.txt"
PROBLEM = "~/Downloads/ProblemList.xls"
def download_issues (br, proj, filename):
... | apurvasharan/URTracker | download_prs.py | Python | apache-2.0 | 3,271 | [
"VisIt"
] | d0b2f19623206acdffd2d77b9c2cd1dd9c0d87adc12d09c1962bb3869f28d652 |
import json
import os
import random
import subprocess
import tempfile
import numpy as np
from gameanalysis import gamegen
from gameanalysis import gameio
from gameanalysis import reduction
from gameanalysis import rsgame
from gameanalysis import subgame
from gameanalysis import utils
# XXX To pass files to some scri... | yackj/GameAnalysis | test/script_test.py | Python | apache-2.0 | 19,825 | [
"Gaussian"
] | 2fef9fd5da6851d12463741617930f66b7cddc8f4c00d66d134edef3f1e346ec |
"""
# Copyright (C) 2007 Nathan Ramella (nar@remix.net)
#
# 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 the License, or (at your option) any later version.... | derivativeinc/liveapi | src/LiveOSC/__init__.py | Python | lgpl-2.1 | 1,032 | [
"VisIt"
] | bc3f008c0a35575311047764be71210765686df8b8ec6d33a3c772e6743dd3b4 |
#!/usr/bin/env python
""" Gaussian optics package
"""
from __future__ import division
from numpy import pi, inf, allclose, dot
from scipy import array, dot
class GaussianBeam:
""" A Gaussian beam """
def __init__(self, z0, w0, lamb):
self.z0 = z0
self.w0 = w0
self.lamb = lamb
... | imrehg/physicspy | physicspy/optics/gauss.py | Python | mit | 1,296 | [
"Gaussian"
] | 55fcb42765cddf328ae44f6d969a6a14b3913ac4700eb104d0eddcf6f437afd6 |
# Generated from java-escape by ANTLR 4.5
from antlr4 import *
# This class defines a complete generic visitor for a parse tree produced by QueryParser.
class QueryVisitor(ParseTreeVisitor):
# Visit a parse tree produced by QueryParser#queryDocument.
def visitQueryDocument(self, ctx):
return self.vis... | SkySchermer/uweclang | uweclang/query/grammar/QueryVisitor.py | Python | mit | 3,780 | [
"VisIt"
] | 3b6abaa3fb157bff7f51e5084a1228b31ac6a85417328436a003964d728436e6 |
"""
A script to read in a GAMESS-UK output file/or punch file and create a new input file
with the same values as the previous input, but with the input geometry, that from
the last point of the output file/punch file.
Please note that if the output file is from an optimise run (i.e. with a zmatrix) and
the optimisat... | alexei-matveev/ccp1gui | scripts/guk_output2input.py | Python | gpl-2.0 | 6,316 | [
"GAMESS"
] | 0858b261c937a545edde0df168654e085ad7c5721c97eeaa976c86b888e6db25 |
#!/usr/bin/env python3
# [1] https://doi.org/10.1016/S0022-2860(84)87198-7
# Pulay, 1984
# [2] https://pubs.rsc.org/en/content/articlehtml/2002/cp/b108658h
# Farkas, Schlegel, 2002
import matplotlib.lines as mlines
import matplotlib.pyplot as plt
import numpy as np
from pysisyphus.calculators.AnaPot import ... | eljost/pysisyphus | tests_staging/test_gdiis/test_gdiis.py | Python | gpl-3.0 | 6,611 | [
"xTB"
] | 596cc6ebacb78ffc311f7bf13b271b047b9128f375217bc2dc91ec8c3fae8773 |
# -*- coding: utf-8 -*-
#
# Pype9 documentation build configuration file, created by
# sphinx-quickstart on Thu Mar 30 21:41:02 2017.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All... | tclose/PyPe9 | doc/source/conf.py | Python | mit | 13,001 | [
"NEURON"
] | dbef56fca0f50d3d1e8950a5c9ee34ea5f6610c09edb021c2ec02ce938649495 |
# coding: utf-8
# # Brian McKean
# # ===========
# # BioTrak Health
# https://www.biotrakhealth.com/
# ## Session Management
# ## Identify ineffective sessions during user trials
# # ===========
# ## Galvanize Data Science Immersion
# ## Capstone Project
#
# This program takes as input
# text files with session... | bdmckean/Stress_Management | src/BioTrak-Classify-Trial.py | Python | mit | 7,366 | [
"Brian"
] | 29532f1fba7d8beabb2616893e70ffb2d19a86c574a7039f7273348f11a2058f |
# Copyright (c) 2001 Autonomous Zone Industries
# Copyright (c) 2002-2003 Bryce "Zooko" Wilcox-O'Hearn
# This file is licensed under the
# GNU Lesser General Public License v2.1.
# See the file COPYING or visit http://www.gnu.org/ for details.
__revision__ = "$Id: version.py,v 1.19 2003/03/23 15:12:00 zooko E... | zooko/egtp_new | egtp/version.py | Python | lgpl-2.1 | 808 | [
"VisIt"
] | 099d95d88e39a06b383d4a2d8c7cdf25aa7d9920878b8f3fdaff681dd372c943 |
#!/usr/bin/env python
import sys
import time
from optparse import OptionParser
from itertools import izip
import radiaUtil
import collections
import logging
'''
' RNA and DNA Integrated Analysis (RADIA):
' Identifies RNA and DNA variants in NGS data.
'
' Copyright (C) 2010 Amie J. Radenbaugh, Ph.D.
'
' T... | aradenbaugh/radia | scripts/filterByBlat.py | Python | agpl-3.0 | 49,288 | [
"BLAST",
"pysam"
] | 8103e520b90facfe5ed5bb322b3db9f30842c8b8548d30c8098cc9a55363160f |
# Adaptive Comfort Calculator
#
# Ladybug: A Plugin for Environmental Analysis (GPL) started by Mostapha Sadeghipour Roudsari
#
# This file is part of Ladybug.
#
# Copyright (c) 2013-2015, Chris Mackey <Chris@MackeyArchitecture.com>
# Ladybug is free software; you can redistribute it and/or modify
# it under the te... | samuto/ladybug | src/Ladybug_Adaptive Comfort Calculator.py | Python | gpl-3.0 | 31,814 | [
"EPW"
] | 2b7f1a3f40f900d623202c93dfd9c3a3e984eac9e512d50afa9b80566ad130ec |
# coding=utf-8
product_map = {
1: "LIFX Original 1000",
3: "LIFX Color 650",
10: "LIFX White 800 (Low Voltage)",
11: "LIFX White 800 (High Voltage)",
15: "LIFX Color 1000",
18: "LIFX White 900 BR30 (Low Voltage)",
1... | mclarkk/lifxlan | lifxlan/products.py | Python | mit | 34,172 | [
"Amber"
] | b016dcf5042838697338547d067f3c0513f0fe3c2040ef14e10481db781d1365 |
"""
Monitor the outputs of a workflow processing batch.
"""
import logging
import os
import re
from .. import util
from .. import io
logger = logging.getLogger(__name__)
class WorkflowBatchMonitor(object):
def __init__(self, workflowbatch_file, pipeline_root):
"""
Controls operations (identifica... | BenaroyaResearch/bripipetools | bripipetools/monitoring/workflowbatches.py | Python | mit | 5,504 | [
"Galaxy"
] | 24b135db7ba51489f05774713b2b27daa797a2ba5fe21ece54535064ab40fbe8 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the LMS.
"""
from datetime import datetime
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 ..helpers import (
UniqueCourseTest,
EventsTestMixin,
... | SivilTaram/edx-platform | common/test/acceptance/tests/lms/test_lms.py | Python | agpl-3.0 | 46,589 | [
"VisIt"
] | 96a793fe65165c8a51afdcedbfb496b951c611e68d0eda50b155739b1d428526 |
#!/usr/bin/python
#Guruprasad Ananda
#Adapted from bx/scripts/maf_mask_cpg.py
"""
Mask out potential CpG sites from a maf. Restricted or inclusive definition
of CpG sites can be used. The total fraction masked is printed to stderr.
usage: %prog < input > output restricted
-m, --mask=N: Character to use as mask ('?... | volpino/Yeps-EURAC | tools/regVariation/maf_cpg_filter.py | Python | mit | 1,776 | [
"Galaxy"
] | bb9c52f6807c08abda303ced2e6576b60ff33ad2dc49692041035f7a4fb51dc5 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2022 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | psi4/psi4 | psi4/driver/qcdb/psivardefs.py | Python | lgpl-3.0 | 15,690 | [
"Psi4"
] | 5d1e34aeb148d6819eb433f44e2f015fb54af6f00813b67e141bda625627c38c |
#! /usr/bin/env python
#
# The purpose of this script is to create a moltemplate lt file for the oplsaa.
# forcefield. This will assist researchers in building complex simulations using
# this OPLS-UA and the OPLS-AA forcefields.
__author__="Jason Lambert"
# (some additional corrections by Miguel Gonzalez and Andrew ... | slitvinov/lammps-swimmer | tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/moltemplate_files/oplsaa_lt_generator/oplsaa_moltemplate.py | Python | gpl-2.0 | 13,909 | [
"LAMMPS",
"TINKER"
] | dc5a5e73e16788e350b18d7b3e43594e6e0f79c9474972b249b543a5207a79e4 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
remdupes.py: Reads lines from stdin and prints non-duplicated lines to stdout
"""
vers_date = '2015-05-13'
copyright = 'Copyright (c) 2015 Brian High'
license = 'MIT'
repos_url = 'https://github.com/brianhigh/amazon-search'
import sys
seen = set()
for line in sys.stdin:... | brianhigh/amzn-srch | remdupes.py | Python | mit | 490 | [
"Brian"
] | 5414da2bc120aa4b059c87cd2f592a7867297414b17b8af03cc17ddf0cc865bc |
"""
Alien
Amazon
Angel
Animal Species
Animatronic
Apocalypse/Mutant
+ Artificial Intelligence
Bandit
Banshee
Barbarian
Basilisk
Birdfolk
+ Bluecap
Bounty Hunter
Brownie
Cat-people/Nekojin
Cavemen
Centaur
Christmas Elf
Cockatrice
Code
Cowboy/girl
Cyberpunk
Dark Elf
Death
+ Death Worm
... | d2emon/generator-pack | src/lexicon/topics.py | Python | gpl-3.0 | 7,484 | [
"CASINO",
"Galaxy"
] | 3272e64fd8ef4f4a853c2a5b7e445e9cd212f75fc057efc44f4968ba08ed0d9f |
# Orca
#
# Copyright 2010 Consorcio Fernando de los Rios.
# Author: Javier Hernandez Antunez <jhernandez@emergya.es>
# Author: Alejandro Leiva <aleiva@emergya.es>
#
# 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 ... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/settings_manager.py | Python | gpl-3.0 | 21,817 | [
"ORCA"
] | fea6734ad52e8227fdd3ad859ccc1f102534ec6c2e878efe02d80496a31ddf0a |
#!/usr/bin/python
#Audio Tools, a module and set of tools for manipulating audio data
#Copyright (C) 2007-2012 Brian Langenberger
#This program is free software; you can redistribute it and/or modify
#it under the terms of the GNU General Public License as published by
#the Free Software Foundation; either version 2... | Excito/audiotools | test/test_metadata.py | Python | gpl-2.0 | 314,456 | [
"Brian"
] | 1a7008a41c0996dd19bf95dd28e5741ff5c8d1f2344e04183f284882e5dc38d4 |
#!/usr/bin/env python
#
# entries_tests.py: test the old entries API using entries-dump
#
# Subversion is a tool for revision control.
# See http://subversion.apache.org for more information.
#
# ====================================================================
# Licensed to the Apache Software Foundation (AS... | jmckaskill/subversion | subversion/tests/cmdline/entries_tests.py | Python | apache-2.0 | 9,807 | [
"BLAST"
] | 1b970f832e942094278be59e1ec084986ffd45a9cdb5c6142df4a988dbddebe0 |
"""
Global variables used throughout nomad
"""
modules = dict(
wfn = None,
interface = None,
init_conds = None,
adapt = None,
integrator = None,
matrices = None,
integrals = None,
wfn0 = None
)
paths = dict(
cwd = '',
log_file = '',... | mschuurman/FMSpy | nomad/core/glbl.py | Python | lgpl-3.0 | 2,996 | [
"COLUMBUS"
] | 6ba27663a62d2d6ddb4b3fc4ee167a549ec5a0827e25165fa556f60eb0f9edf3 |
try:
import SOAPpy,cartographer, PhamDisplay,phamerator_manage_db,db_conf,goocanvas,tempfile,cairo,os,random,PhamDisplay,pham
except:
import sys,os
sys.path.append(os.path.join(os.path.dirname(__file__), '..'))
import SOAPpy,cartographer,PhamDisplay,phamerator_manage_db,db_conf,goocanvas,tempfile,cairo,random,P... | byuphamerator/phamerator-dev | phamerator/phageSOAP.py | Python | gpl-2.0 | 13,607 | [
"BLAST"
] | b6da6987439820d5da2b5c4642d1f6508cf1d7835b94188c1b1be5576d816cdb |
#!/usr/bin/env python
import os
from ecmwfapi import ECMWFDataServer
server = ECMWFDataServer()
time=["00","06","12","18"]
year=["1981"]
#year=["1979","1981","1982","1983","1984"]
param=["131.128","132.128","157.128"]
#param=["129.128","130.128","131.128","132.128","157.128"]
nam=["uwnd","vwnd","rhum"]
#nam=["hgt","air... | CopyChat/Plotting | Python/TestCode/ecmwf_swio.py | Python | gpl-3.0 | 1,352 | [
"NetCDF"
] | 9fd073f2d86c649ec2168db6f7cbc79841f85ed042607eb7c19a0e9389bddd09 |
WORDS = (
'abyssinian',
'akita',
'alaskan',
'albatross',
'alligator',
'angelfish',
'angora',
'ant',
'anteater',
'antelope',
'armadillo',
'avocet',
'baboon',
'badger',
'bandicoot',
'barb',
'barnacle',
'barracuda',
'bat',
'beagle',
'bear',
'beaver',
'bee',
'beetle',
'bird',
'bison',
'bloodhound... | geradcoles/random-name | randomname/lists/animals.py | Python | apache-2.0 | 3,656 | [
"Jaguar",
"MOOSE",
"Octopus"
] | 942a16979b0e74c79ed06d7329953fecfec8f22ae011365fc879bc21d53cd484 |
"""Random variable generators.
integers
--------
uniform within range
sequences
---------
pick random element
pick random sample
generate random permutation
distributions on the real line:
------------------------------
uniform
... | lfcnassif/MultiContentViewer | release/modules/ext/libreoffice/program/python-core-3.3.0/lib/random.py | Python | lgpl-3.0 | 25,529 | [
"Gaussian"
] | 392a8f2bd54632bd27ccf53c67e11d1972317b75f768599ebe71aa233dbd2a7c |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# freeseer - vga/presentation capture software
#
# Copyright (C) 2012, 2013, 2014 Free and Open Source Software Learning Centre
# http://fosslc.org
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License a... | Freeseer/freeseer | src/freeseer/tests/frontend/configtool/test_config_tool.py | Python | gpl-3.0 | 18,121 | [
"VisIt"
] | 225fe3beb57a05ce4819d53dea54aac4653def73327f8037f5e76e419e195c3c |
#
# Copyright 2001 - 2006 Ludek Smid [http://www.ospace.net/]
#
# This file is part of IGE - Outer Space.
#
# IGE - Outer Space 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 Lice... | Lukc/ospace-lukc | client-pygame/lib/osci/dialog/MainGameDlg.py | Python | gpl-2.0 | 14,210 | [
"Galaxy"
] | e28ed8a59d3f93fb35e5a6b60c16c0875f73cc42191b39659c2ef9795dd8ef4c |
"""
Geometry
====================
Change or get info on the current geometrical configuration, e.g.
number of cells in the three crystal translation directions.
"""
import spirit.spiritlib as spiritlib
import ctypes
### Load Library
_spirit = spiritlib.load_spirit_library()
### Imports
from spirit.scalar import sca... | spirit-code/spirit | core/python/spirit/geometry.py | Python | mit | 9,577 | [
"CRYSTAL"
] | 89dd09e09d153a4727d50d04876c7e2da83cab13fdd4f57bac2e6ae8de84ea40 |
#
# Copyright (c) 2017 Intel Corporation
# SPDX-License-Identifier: BSD-2-Clause
#
"""
This module transforms data-parallel operations such as Numpy calls into
'Parfor' nodes, which are nested loops that can be parallelized.
It also implements optimizations such as loop fusion, and extends the rest of
compiler analysi... | numba/numba | numba/parfors/parfor.py | Python | bsd-2-clause | 198,671 | [
"VisIt"
] | c782e2c8ea44bc0e1e48b4077ad3baef60c4adf08a16d2a172aef5515dccfb06 |
# -*- coding: utf-8 -*-
# ------------------------------------------------------------
# pelisalacarta 4
# Copyright 2015 tvalacarta@gmail.com
# http://blog.tvalacarta.info/plugin-xbmc/pelisalacarta/
#
# Distributed under the terms of GNU General Public License v3 (GPLv3)
# http://www.gnu.org/licenses/gpl-3.0.html
# --... | Hernanarce/pelisalacarta | python/main-classic/platformcode/mct.py | Python | gpl-3.0 | 30,209 | [
"ADF"
] | 9389d0214fc2c4e41bba35bd6106d913880417a9d5a747bb8a015376f51a5c89 |
''' TokenAgent
This agent inspect all elements, and resets their tokens if necessary.
'''
__RCSID__ = '$Id: $'
from datetime import datetime, timedelta
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Base.AgentModule import Agent... | Sbalbp/DIRAC | ResourceStatusSystem/Agent/TokenAgent.py | Python | gpl-3.0 | 6,969 | [
"DIRAC"
] | 65aa43f7ff3a13f8a40bcf6f137495ab9a1541ad3a1330242604d75ab6e65fad |
from __future__ import print_function
import numpy as np
from scipy import stats
from utils import cache_readonly
class Results(object):
"""
Class to contain model results
Parameters
----------
model : class instance
the previously specified model instance
params : array
parame... | lanselin/pysal | pysal/contrib/glm/base.py | Python | bsd-3-clause | 15,718 | [
"COLUMBUS"
] | 1f55c654af9ff240d92700d367795be0a02c7a85cf9bb46f6f35d364092d234c |
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