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"""
Module to call mcsqs, distributed with AT-AT
https://www.brown.edu/Departments/Engineering/Labs/avdw/atat/
"""
import os
import subprocess
from typing import Dict, Union, List, NamedTuple, Optional
from monty.tempfile import ScratchDir
from monty.dev import requires
from monty.os.path import which
from pymatgen ... | gVallverdu/pymatgen | pymatgen/command_line/mcsqs_caller.py | Python | mit | 4,017 | [
"pymatgen"
] | 58aef085ca744714549237d2aeaef2d8e19e93d2707aaf38c8cbe3ad7081c915 |
import matplotlib
matplotlib.use("QT4Agg")
import traceback
import sys
import numpy as np
from PyQt4 import QtCore, QtGui
from pele.landscape import TSGraph
from pele.storage import Database
from pele.utils.events import Signal
from pele.config import config
from pele.gui.MainWindow import Ui_MainWindow
from pe... | smcantab/pele | pele/gui/run.py | Python | gpl-3.0 | 26,452 | [
"PyMOL"
] | 02908f7e7940a0e6387b2f087b5b4bcf285e3029b675a9d20a5974c1e39ebf4b |
"""
@name: PyHouse/src/Modules/Communication/_test/test_twitter.py
@author: D. Brian Kimmel
@contact: d.briankimmel@gmail.com
@copyright: 2016-2017 by D. Brian Kimmel
@date: Created on May 30, 2016
@licencse: MIT License
@summary:
"""
import unittest
class Test(unittest.TestCase):
def set... | DBrianKimmel/PyHouse | Project/src/Modules/Computer/Communication/_test/test_twitter.py | Python | mit | 534 | [
"Brian"
] | 55bcd4f04b80b4f177c9b44bfdd7fe851719cd4d8df272dc54007f823260ea94 |
from jaspyx.visitor import BaseVisitor
class Raise(BaseVisitor):
def visit_Raise(self, node):
if node.inst is not None or node.tback is not None:
raise ValueError('only one-clause raise is supported')
self.indent()
self.output('throw ')
self.visit(node.type)
sel... | iksteen/jaspyx | jaspyx/visitor/raise_.py | Python | mit | 331 | [
"VisIt"
] | f071fb357ff77546d57e0d130bbc72217516efedd74f0717f3a6966f8a2e1f2f |
"""Table printer
This program displays a list of strings in a table.
Write a function named :meth:`print_table` that takes a list of lists of strings and
displays it in a well-organized table with each column right-justified. Assume
that all the inner lists will contain the same number of strings.
For example, the v... | JoseALermaIII/python-tutorials | pythontutorials/books/AutomateTheBoringStuff/Ch06/Projects/P1_tablePrinter.py | Python | mit | 1,847 | [
"MOOSE"
] | 2907558cdcb525f5ec7d9867e2c5be914f629dd4d1725577900ab60fe3eb60bf |
# 31.05.2007, c
# last revision: 25.02.2008
from sfepy import data_dir
filename_mesh = data_dir + '/meshes/2d/circle_sym.mesh'
material_1 = {
'name' : 'coef',
'values' : {
'val' : 1.0,
},
}
material_2 = {
'name' : 'm',
'values' : {
'K' : [[1.0, 0.0], [0.0, 1.0]],
},
}
field_1 ... | RexFuzzle/sfepy | tests/test_laplace_unit_disk.py | Python | bsd-3-clause | 3,391 | [
"VTK"
] | a481bf27c636a08ab59e5810531b1e8a835cee98c30430829b7bd58db77116e9 |
"""
Copyright (C) 2020 Quinn D Granfor <spootdev@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 2, as published by the Free Software Foundation.
This program is distributed in the hope that it will be useful, but
... | MediaKraken/MediaKraken_Deployment | source/common/common_logging_elasticsearch_httpx.py | Python | gpl-3.0 | 2,920 | [
"Elk"
] | f7d905c50cbd4a35cfb7e87468fa72268bb2a2747afa918ec44bcc619c4478bc |
import traceback
import types
import os
import sys
class toolPlugin():
def GetName(self):
return "PSIBLAST"
def GetBMP(self, dirH):
return dirH + r"\Utils\Icons\PSIBlast.bmp"
def pluginEXE(self):
'''Respond to the "psiblast" type command.
'''
plugin_e... | fxb22/BioGUI | plugins/Tools/BLASTPlugins/PSIBLAST.py | Python | gpl-2.0 | 740 | [
"BLAST"
] | 7906606a2a677ab8254b5f7937abb0e20ca89354631800c1ee7993f66becd4cc |
"""
Source fitting routines.
"""
import math
import numpy
import scipy.optimize
from .gaussian import gaussian
from .stats import indep_pixels
import utils
FIT_PARAMS = ('peak', 'xbar', 'ybar', 'semimajor', 'semiminor', 'theta')
def moments(data, beam, threshold=0):
"""Calculate source positional values using mo... | mkuiack/tkp | tkp/sourcefinder/fitting.py | Python | bsd-2-clause | 10,364 | [
"Gaussian"
] | e3e369f3d86317b30d0522ceb876086c805f770671dd331bb67494b7764307f4 |
# coding: utf-8
from __future__ import unicode_literals
"""
This module provides various representations of transformed structures. A
TransformedStructure is a structure that has been modified by undergoing a
series of transformations.
"""
__author__ = "Shyue Ping Ong, Will Richards"
__copyright__ = "Copyright 2012... | rousseab/pymatgen | pymatgen/alchemy/materials.py | Python | mit | 14,360 | [
"VASP",
"pymatgen"
] | 0c5551e1925a6643a3f49441c029aba8190a20186224000cb78a792a1eaaf6ea |
"""User-friendly public interface to polynomial functions. """
from __future__ import print_function, division
from sympy.core import (
S, Basic, Expr, I, Integer, Add, Mul, Dummy, Tuple
)
from sympy.core.mul import _keep_coeff
from sympy.core.symbol import Symbol
from sympy.core.basic import preorder_traversal
... | NikNitro/Python-iBeacon-Scan | sympy/polys/polytools.py | Python | gpl-3.0 | 175,575 | [
"Gaussian"
] | c0578c457262e8c3efa44ceb3902cfd26e93202195d1065193b930687b7ba1c2 |
__author__ = 'nielso'
import os
import numpy
# This module requires the package: python-scientific
# To query netcdf files with ncdump also install netcdf-bin
# The package libnetcdf-dev is also required but is automatically
# installed as a dependency on python-scientific
from Scientific.IO.NetCDF import NetCDFFile
... | danylaksono/inasafe | realtime/netcdf_utilities.py | Python | gpl-3.0 | 4,712 | [
"NetCDF"
] | 8bedcc4ee6159aad0f40fa5d0d6fa09670111fce5ccf5c3a2093f4952ea92e78 |
import sys
import ast
import argparse
import time
import Bio
from Bio.SeqFeature import FeatureLocation
from Bio.SeqFeature import SeqFeature
class MySeqFeature(SeqFeature):
def __str__(self):
out = "type: %s\n" % self.type
if self.strand == 1:
out += "location: [%s:%s](%s)\n" % (self.... | nikolaichik/SigmoID | Python/MastGen.py | Python | gpl-3.0 | 27,728 | [
"Biopython"
] | c55bf06d9a10a458bf099f1fa0b413726f551167ea87872f423a40cc13ced8c0 |
# -*- coding: utf-8 -*-
#
# Pyplis is a Python library for the analysis of UV SO2 camera data
# Copyright (C) 2017 Jonas Gliss (jonasgliss@gmail.com)
#
# This program is free software: you can redistribute it and/or
# modify it under the terms of the GNU General Public License a
# published by the Free Software Foundat... | jgliss/pyplis | pyplis/image.py | Python | gpl-3.0 | 59,313 | [
"Gaussian"
] | 5b171b1b9c2bf6e9819080b5b7a872a9e4114ed9ec08b49169b9784f22027119 |
from libmyriad import ResultCode
import datetime
import json
import logging
import multiprocessing
import os
import psutil
import re
import requests
import shutil
import subprocess
import time
import zipfile
class Myriad:
def __init__(self):
self.config = []
self.maestroAPIGateway = None
self.myriadJobsFolder... | russellthackston/comp-chem-util | myriad/myriad.py | Python | mit | 17,750 | [
"Psi4"
] | 963af4257b6ee971b2ec0a42398eb6270524a0f5293ffaf678fd7bf679de4289 |
"""Header value parser implementing various email-related RFC parsing rules.
The parsing methods defined in this module implement various email related
parsing rules. Principal among them is RFC 5322, which is the followon
to RFC 2822 and primarily a clarification of the former. It also implements
RFC 2047 encoded w... | kikocorreoso/brython | www/src/Lib/email/_header_value_parser.py | Python | bsd-3-clause | 106,074 | [
"CRYSTAL"
] | b13426d655aa81550757d4ca4c5fc3a8a965a39cb15d063b62b6b19aee7625b4 |
# coding: utf-8
import argparse
import datetime
from lxml import etree
import logging
import os
import re
import base64
from Crypto.Cipher import AES
import hashlib
import uuid
from thirdparty import filetimes
from thirdparty import pkcs7
VERSION = '1.1'
logger = logging.getLogger()
logger.setLevel(logging.DEBUG)
... | gpailler/Android2Wp_SMSConverter | converter.py | Python | mit | 5,332 | [
"VisIt"
] | 1ff6cad86f3947d5150c358e5c920d5692200a13aabe4488b75e04d4f8d48266 |
# 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
#
# Unless required by appl... | gkc1000/pyscf | pyscf/mp/gmp2.py | Python | apache-2.0 | 14,542 | [
"PySCF"
] | c6cb4614f1a99896183ad4ea204dc023615422d775ce9dab1adf5fe3022cbf72 |
#!/opt/local/bin/python
"""
Need to start Eclipse from command line (using executable inside app) to get
ADF env vars working right, when in unix-like system.
"""
import kf
import numpy as np
from random import randint
from os import name
"""
The two variables below are everything that will be fetched from CPs and B... | twilsonco/CPGobbler | CPGobbler.py | Python | gpl-3.0 | 17,544 | [
"ADF"
] | 25bf0eff0aaad73e4d913a3317faf35212f1b31051b07f75d38aceac18032e21 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# StereoscoPy, stereoscopic 3D image creator
#
# Copyright (C) 2016-2018 Seán Hewitt <contact@2sh.me>
#
# 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 Founda... | SeanHewitt/stereosco.py | stereoscopy/__init__.py | Python | gpl-3.0 | 31,435 | [
"Amber"
] | 8ac8cff1906acd7d8878566bbfc26027cab3b0e7f56abad91bced24745f67994 |
# -*- coding: utf-8 -*-
# These tests don't work at the moment, due to the security_groups multi select not working
# in selenium (the group is selected then immediately reset)
from textwrap import dedent
import pytest
from riggerlib import recursive_update
from widgetastic_patternfly import CheckableBootstrapTreeview... | Yadnyawalkya/integration_tests | cfme/tests/cloud_infra_common/test_provisioning.py | Python | gpl-2.0 | 26,349 | [
"VisIt"
] | 95545f598498a75ef8a117d13af1a4508010b832c3fc6a4668020e94bc054194 |
from PyQt4.QtCore import *
from PyQt4.QtGui import *
from numpy import *
import Avogadro
# always use 'Extension' for class name
class Extension(QObject):
def __init__(self):
QObject.__init__(self)
def name(self):
return "Protein Extension"
def description(self):
return "Extension pro... | rcplane/periodicdisplay | reference/avogadro/libavogadro/examples/python/proteinextension.py | Python | gpl-2.0 | 6,165 | [
"Avogadro"
] | 40329cb76ca7df9fde79cb6c0bd312db2cd5db6d2937329db83e717167268450 |
# $Id$
#
# 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.
#
import unittest,cPickle,os,gzip
from rdkit import Che... | rdkit/rdkit-orig | rdkit/Chem/AtomPairs/UnitTestDescriptors.py | Python | bsd-3-clause | 2,262 | [
"RDKit"
] | ce0b5680fd8b541faa8bf26a6618a9031e650bc6292625fdb8807f52fde103f0 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# 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)
#... | MDAnalysis/mdanalysis | testsuite/MDAnalysisTests/analysis/test_base.py | Python | gpl-2.0 | 11,099 | [
"MDAnalysis"
] | e81cbc604e4a94de74c233c4c748db5447e5bbf47b17f3e44e266e96799849af |
# import to process args
import os, tempfile, requests, atexit, sys, json, io, zipfile, shutil
# import paraview modules.
from paraview.web import wamp as pv_wamp
from paraview.web import protocols as pv_protocols
# import RPC annotation
from autobahn.wamp import register as exportRpc
from paraview import simple
fro... | jourdain/cmb-web | scripts/hydra-th/pv_result_viewer.py | Python | bsd-3-clause | 5,376 | [
"ParaView",
"VTK"
] | 329c396d91b44baf9c63d007d97fa5c8994cf6941fe745472101e774c23463cd |
###
# Copyright (c) 2002-2005, Jeremiah Fincher
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source code must retain the above copyright notice,
# this list of co... | prashantpawar/supybot-rothbot | test/test_ircutils.py | Python | bsd-3-clause | 15,848 | [
"COLUMBUS"
] | e3146c17990ee190172caa118906346e0031e0f6e3a94e43037ca7fb16a19b56 |
""" A set of utilities used in the WMS services
Requires the Nordugrid ARC plugins. In particular : nordugrid-arc-python
"""
__RCSID__ = "$Id$"
from tempfile import mkdtemp
import shutil, os
from DIRAC.Core.Utilities.Grid import executeGridCommand
from DIRAC.Resources.Computing.ComputingElementFactory import ... | marcelovilaca/DIRAC | WorkloadManagementSystem/Service/WMSUtilities.py | Python | gpl-3.0 | 6,814 | [
"DIRAC"
] | 433889d9deb09c568f6c523b2427a9ab0e49596e0c3ff4385a3958c0b4a5ba97 |
__author__ = "Kristoffer Selim and Anders Logg"
__copyright__ = "Copyright (C) 2010 Simula Research Laboratory and %s" % __author__
__license__ = "GNU GPL Version 3 or any later version"
# Last changed: 2011-03-17
from fsiproblem import *
# Read parameters
application_parameters = read_parameters()
# Constants rel... | Juanlu001/CBC.Solve | sandbox/aipcs/channel_with_flap.py | Python | gpl-3.0 | 4,571 | [
"Gaussian"
] | 340cd3e02c1379bf8490b365b041fe2a83b77cac902b48683f5071ad3082d3ed |
#!/usr/bin/env python
"""
Enable using one or more Storage Elements
Example:
$ dirac-admin-allow-se M3PEC-disk
"""
import DIRAC
from DIRAC.Core.Base.Script import Script
@Script()
def main():
read = False
write = False
check = False
remove = False
site = ""
mute = False
Script.register... | DIRACGrid/DIRAC | src/DIRAC/DataManagementSystem/scripts/dirac_admin_allow_se.py | Python | gpl-3.0 | 7,537 | [
"DIRAC"
] | 28c78616ee697fc9fc91f035276e4d0c85a5ef9ea03416781ec5586b0cc6bdd0 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Adapted from Graphviz.py (now deprecated)
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2005-2006 Eero Tamminen
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2007 Johan Gonqvist <johan.gronqvist@gmail.com>
# Cont... | prculley/gramps | gramps/plugins/graph/gvrelgraph.py | Python | gpl-2.0 | 41,573 | [
"Brian"
] | 3a19b80980ad964c7674e7b65633a96f80bba2ad052df0fa253693d159e397ed |
#!/usr/bin/env python
import sys
import vtk
from PyQt4 import QtGui
from vtk.qt4.QVTKRenderWindowInteractor import QVTKRenderWindowInteractor
class MainWindow(QtGui.QMainWindow):
def __init__(self, parent=None):
QtGui.QMainWindow.__init__(self, parent)
self.frame = QtGui.QFrame()
self.... | lorensen/VTKExamples | src/Python/Widgets/EmbedInPyQt.py | Python | apache-2.0 | 1,287 | [
"VTK"
] | e8513608a2018e190d5b54e0ecac0a597963fbe14c5e2cba0763b21db38bb9bb |
"""
Copyright (C) 2015, Jaguar Land Rover
This program is licensed under the terms and conditions of the
Mozilla Public License, version 2.0. The full text of the
Mozilla Public License is at https://www.mozilla.org/MPL/2.0/
Maintainer: Rudolf Streif (rstreif@jaguarlandrover.com)
"""
from django.contrib import ad... | klooer/rvi_backend | web/can_fw/admin.py | Python | mpl-2.0 | 3,726 | [
"Jaguar"
] | e9c40163e364deb1dce56c6d573f7690545ae4016ffb32c13c6f03e6dda892e3 |
"""Functions to make 3D plots with M/EEG data
"""
from __future__ import print_function
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Denis Engemann <denis.engemann@gmail.com>
# Martin Luessi <mluessi@nmr.mgh.harvard.edu>
# Eric Larson <larson.eric.d@gmail.com>
# ... | trachelr/mne-python | mne/viz/_3d.py | Python | bsd-3-clause | 33,467 | [
"Mayavi"
] | 9b25ecdf79a63d2f554223c2170f7ce0476da1d93ac26a7c0954d60b0f1dc2d1 |
# -*- coding: utf-8 -*-
# Copyright 2007-2011 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... | sillvan/hyperspy | hyperspy/_components/eels_vignetting.py | Python | gpl-3.0 | 3,532 | [
"Gaussian"
] | cb4b261a56136ad1d58c36517603bf10e50bb0ea6c77735f838cb90b609cc57d |
"""Definitions of Celery tasks in Askbot
in this module there are two types of functions:
* those wrapped with a @task decorator and a ``_celery_task`` suffix - celery tasks
* those with the same base name, but without the decorator and the name suffix
the actual work units run by the task
Celery tasks are special ... | divio/askbot-devel | askbot/tasks.py | Python | gpl-3.0 | 9,386 | [
"VisIt"
] | 2c62d56979b76d37ac7aa56abead078bd8f77958273155cb0dd70e482291b6de |
#import sys
import os.path
#from main.massCalc import *
#from main.molFormula import *
#from main.fileImport import Import_Peptoid_Names
from main.writePdb import *
from main.printReport import *
from main.remove_neg_log import *
import Pmw as Pmw
import tkinter as tk
from tkinter import *
from tkinter.filed... | rspencer27/Mass-Spec-App | massSpecMain.py | Python | apache-2.0 | 52,790 | [
"MacroModel",
"PyMOL"
] | b1459387cab184bf07177163c409ab0c7e876918cec2e7dd6bebac1c0f6e731e |
from __future__ import print_function
from __future__ import absolute_import
from builtins import zip
from builtins import str
from builtins import range
from builtins import object
import os.path
from qgis.core import QgsRasterLayer, QgsProject, QgsVectorLayer, QgsFillSymbol,QgsRenderContext
from qgis.PyQt import Qt... | nicolas998/wmf | qgisplugin/HydroSEDPluginUtils.py | Python | gpl-3.0 | 48,360 | [
"NetCDF"
] | 913f29efca7474555182d7f813c27050b3b3b064c2d1d944d137523259a81e9a |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
This file is part of the web2py Web Framework
Copyrighted by Massimo Di Pierro <mdipierro@cs.depaul.edu>
License: LGPLv3 (http://www.gnu.org/licenses/lgpl.html)
The widget is called from web2py.
"""
import datetime
import sys
import cStringIO
import tim... | ccpgames/eve-metrics | web2py/gluon/widget.py | Python | mit | 45,485 | [
"VisIt"
] | 7a390df6e92b0048606e231e5169677459f583774873eccbf2148d9b0434700d |
from __future__ import absolute_import, division, print_function
import ast
from jaspyx.visitor import BaseVisitor
class UnaryOp(BaseVisitor):
def visit_UnaryOp(self, node):
attr = getattr(self, 'UnaryOp_%s' % node.op.__class__.__name__)
attr(node.operand)
def UnaryOp_UAdd(self, operand):
... | ztane/jaspyx | jaspyx/visitor/unaryop.py | Python | mit | 800 | [
"VisIt"
] | 080d69986abd56529a26e10ac00aa4fe7ced9590ee9f93c4217c248cdb2a4809 |
# coding: utf-8
# In[1]:
get_ipython().magic(u'load_ext autoreload')
get_ipython().magic(u'autoreload 2')
# # Comparing NeuroLex and BBP ontologies
#
# In[2]:
import sys
sys.path.append('../')
from similarity import _cleanup, _normalize, similarity2
from sherlok import Sherlok
neuroner = Sherlok('neuroner')
... | renaud/neuroNER | similarity/hbp_neurolex/neurolex_bbp_ontology_compare.py | Python | lgpl-3.0 | 4,984 | [
"NEURON"
] | f4e1f0a6968890de5e64ffb1a2d236c4102ad7930a3a8d7ca1e26f25d82c0266 |
"""setuptools.command.bdist_egg
Build .egg distributions"""
# This module should be kept compatible with Python 2.3
import sys, os, marshal
from setuptools import Command
from distutils.dir_util import remove_tree, mkpath
try:
from distutils.sysconfig import get_python_version, get_python_lib
except ImportError:
... | Drvanon/Game | venv/lib/python3.3/site-packages/distribute-0.6.34-py3.3.egg/setuptools/command/bdist_egg.py | Python | apache-2.0 | 18,458 | [
"VisIt"
] | e6fbf146394aca136270a8265de25d7e18657fc6efdb7a0da62a1672b513477d |
import numpy as np
from scipy import signal, sparse, stats
from scipy.ndimage import gaussian_filter
import nibabel as nib
from .utils import check_mask
def detrend(data, axis=-1, replace_mean=False):
"""Linearly detrend on an axis, optionally replacing the original mean.
Parameters
----------
data ... | kastman/lyman | lyman/signals.py | Python | bsd-3-clause | 11,987 | [
"Gaussian"
] | d5335fac41d1721426556f1fa2627642df3056ed768ecfa5055ccfbdeba6d706 |
# Copyright 2011 Nicholas Bray
#
# 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... | ncbray/pystream | sandbox/sese/__init__.py | Python | apache-2.0 | 5,235 | [
"VisIt"
] | 927e657b7b0a787e558ebe8939e7963356c2c2bc028213d414580a21dc0e5f12 |
# -*- coding: utf-8 -*-
# Copyright(C) 2012-2014 Laurent Bachelier
#
# This file is part of weboob.
#
# weboob 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 3 of the License, or
# (at ... | vicnet/weboob | weboob/browser/browsers.py | Python | lgpl-3.0 | 39,881 | [
"VisIt"
] | 041f885b24a2e757b46cc906935e3cc294f73c2e5040cd04303e9d037cca5b77 |
#!/usr/bin/python
# Copyright (c) 2011 Grid Dynamics Consulting Services, Inc, All Rights Reserved
# http://www.griddynamics.com
#
# 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
#
#... | chemikadze/pyucsm | pyucsm.py | Python | apache-2.0 | 41,529 | [
"VisIt"
] | 15a5affcbb6544decf9f64e4978dd23fc93b05dc84c8ec55ab9e3560f78d7886 |
#
# @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
#... | susilehtola/psi4 | psi4/driver/p4util/fchk.py | Python | lgpl-3.0 | 4,737 | [
"Psi4"
] | 778a8f7d9564c41cb470adcf0cd60c5f722402651596167d8b41972227f969d5 |
# coding=utf-8
# Copyright 2022 The Google Research 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 License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... | google-research/google-research | learn_to_infer/gmm_dist.py | Python | apache-2.0 | 25,588 | [
"Gaussian"
] | a586bda11d770c13254b08357af88cd888b4d16df0b098926345981571fc2c1b |
# Copyright (C) 2016 Jolien Creighton
# (C) 2021 Jolien Creighton & Thomas Dent
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 3 of the License, or (at your
# option)... | tdent/pycbc | pycbc/population/fgmc_laguerre.py | Python | gpl-3.0 | 6,246 | [
"Gaussian"
] | 0047119bda1a8637af3683b0197f5fad1ad313e4bb304f1ae22ca4ffd2d2f5ee |
# Copyright (c) 2009 Brian Zimmer <bzimmer@ziclix.com>
#
# 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 restriction, including without limitation the rights to
# use, copy, modify, m... | bzimmer/openroom | openroom/model.py | Python | mit | 8,044 | [
"Brian"
] | 479b3c9629716037defe124bedbe3a93f0212c6d19aa8a79fd06ef6c8a006e4a |
# Copyright 2012 Hewlett-Packard Development Company, L.P.
#
# 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... | joostvdg/jenkins-job-builder | jenkins_jobs/modules/scm.py | Python | apache-2.0 | 59,344 | [
"Octopus"
] | 8e8714f7505481d24588bc07fad0837836a6bc9e9b1ff0168285d1bb990d0199 |
# ======================================================================
# USER-GFMD - Elastic half-space methods for LAMMPS
# https://github.com/Atomistica/user-gfmd
#
# Copyright (2011-2016,2021)
# Lars Pastewka <lars.pastewka@imtek.uni-freiburg>,
# Tristan A. Sharp and others.
# See the AUTHORS file in the top... | Atomistica/user-gfmd | tests/TEST_Hertz_fcc111_two_layers_64x37/eval.py | Python | gpl-2.0 | 3,052 | [
"LAMMPS"
] | 13722c7073008ebd8855f3a6e6ecfe13612ff207848c117770b6501403c50f30 |
# -*- coding: utf-8 -*-
#
# connections.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or... | terhorstd/nest-simulator | topology/doc/user_manual_scripts/connections.py | Python | gpl-2.0 | 20,478 | [
"Gaussian"
] | 4592f364096e40f9982d010eab127a1a4f0af84f36c810dda922ac5b9d843ae3 |
import os
import shutil
import logging
import time
from io import open
from ..post import KnowledgePost
from ..repository import KnowledgeRepository
from ..utils.encoding import encode
logger = logging.getLogger(__name__)
class FolderKnowledgeRepository(KnowledgeRepository):
_registry_keys = ['', 'file']
T... | airbnb/knowledge-repo | knowledge_repo/repositories/folder.py | Python | apache-2.0 | 7,879 | [
"VisIt"
] | 9451239b33a3bff7b2f90c49392e80418e622f8e7f93cf7e72686ee9ed445b96 |
# Portions Copyright (c) Meta Platforms, Inc. and affiliates.
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2.
# encoding.py - character transcoding support for Mercurial
#
# Copyright 2005-2009 Matt Mackall <mpm@selenic.com> and others
#
# This softw... | facebookexperimental/eden | eden/scm/edenscm/mercurial/encoding.py | Python | gpl-2.0 | 16,415 | [
"FEFF"
] | 66d0a85b58689a05dc813ffacc51b737dc68a77fd9dff33127a6e67c0e3586e1 |
#
# Copyright (c) 2015, Novartis Institutes for BioMedical Research Inc.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyrigh... | ptosco/rdkit | rdkit/Chem/MolKey/MolKey.py | Python | bsd-3-clause | 15,048 | [
"RDKit"
] | 83cc33cfcc9a35bdcf0cb614ac146fc2221480a2dd64263a84e4aa3b76072854 |
import os
os.environ['PYTHON_EGG_CACHE'] = os.path.join('C:\\', 'Users', 'josha_000', 'PycharmProjects', 'sa-tools', 'tmp')
config = {
# This config file will be detected in localhost environment and values defined here will overwrite those in
# config.py
'environment': "localhost",
# webapp2 sessio... | joshainglis/sa-tools | bp_content/themes/sa_default/config/localhost.py | Python | lgpl-3.0 | 3,082 | [
"VisIt"
] | 65b17a3466c0d2f71902c8d68b8f745b05021c42e199b315b0fa838eda641691 |
#!/usr/bin/env python3
"""
1.2-blast-J.py
This script parses the BLAST output from 1.1-blast-V_assignment.py. For reads
for which a V assignment was successfully made, the section of the read
3' to the V gene is extracted and sent to the cluster for BLAST assignment
of the J gene. Will also try to a... | scharch/SOAnAR | annotate/1.2-blast_J.py | Python | gpl-3.0 | 13,493 | [
"BLAST"
] | d8e623bc7b27c713ddc8f781f504ca673c4ff736f47d4004ae934efb2794c1a6 |
#!/usr/local/lib/student/anaconda3/envs/LCsim/bin/python
'''
LCsim creates a model lightcurve from specified data
LCsim is designed to create a model lightcurve with desired noise from a
specified template, observation times, errors, and period. It can be run
from the command line, but it also contains the necessary f... | deleenm/LCsim | src/LCsim.py | Python | gpl-3.0 | 11,129 | [
"Gaussian"
] | ec027d91d1fda7ef9a1a297f3b097e10ee822c0313aa32a6f2b8ec98b9b01727 |
from flask_restful import Resource, reqparse, inputs
from jobcert import app, db, api, models
from parser import Parser
import requests
import json
class CheckApi(Resource):
def __init__(self):
self.parser = reqparse.RequestParser()
super(CheckApi, self).__init__()
def post (self):
sel... | Doteveryone/BetterJobAdverts | jobcert/api.py | Python | agpl-3.0 | 1,934 | [
"VisIt"
] | f33e45d0f8916e64c494f0dbeac3ad3756d385c5f59ace091408519b2e3cd9ac |
from builtins import range
import sys
sys.path.insert(1,"../../../")
import h2o
from tests import pyunit_utils
from h2o.estimators.glm import H2OGeneralizedLinearEstimator
# check checkpointing for Regression with IRLSM. Checkpointing with single GLM run will not yield same results
# because GLM regression only takes... | michalkurka/h2o-3 | h2o-py/tests/testdir_algos/glm/pyunit_PUBDEV_7890_glm_checkpoint_IRLSM_gaussian.py | Python | apache-2.0 | 2,164 | [
"Gaussian"
] | 73f5a56d2f3ea1ec90d889a549e858e820e1cba564628b3a823bc86da59bd80c |
# -*- coding: utf-8 -*-
__author__ = 'Christopher Petrilli'
__email__ = 'petrilli@amber.org'
__version__ = '0.1.0'
from .transactional_task import (
TransactionalTask,
task_tm,
)
| petrilli/pyramid_transactional_celery | pyramid_transactional_celery/__init__.py | Python | bsd-3-clause | 189 | [
"Amber"
] | 463e160357c6df32be2b6e731341fa38286628d2a40c4b8071435422d1b80fd9 |
#!/usr/bin/env python
# -*- coding: latin-1 -*-
#
# Copyright 2016-2021 Blaise Frederick
#
# 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/LICEN... | bbfrederick/rapidtide | rapidtide/refine.py | Python | apache-2.0 | 20,561 | [
"Gaussian"
] | df81611ec1771094540e2cf3425569dba2123d954e9a2887569d3d02c3769f59 |
# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
# All rights reserved.
#
# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are ... | mgeplf/NeuroM | neurom/tests/test_viewer.py | Python | bsd-3-clause | 4,920 | [
"NEURON"
] | 1faa68b047133c86695c3c0cf3933417bb52c1c569907c7a6ed047ebf2e67bc9 |
############################################################################
##
## Copyright (C) 2006-2010 University of Utah. All rights reserved.
##
## This file is part of VisTrails.
##
## This file may be used under the terms of the GNU General Public
## License version 2.0 as published by the Free Software Foundat... | VisTrails/vistrails-contrib-legacy | titan/vtkhandler.py | Python | bsd-3-clause | 10,928 | [
"VTK"
] | 50ce3c2452671bd8d952498ea0edebf59f715dd372a440f1751bd66940d25a0a |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# author: observer
# email: jingchaohu@gmail.com
# blog: http://obmem.com
import urllib
import re
import sqlite3
import time
import os,sys
import config
from threading import Thread
from Queue import Queue
from download import httpfetch
path = os.path.dirname(os.path.rea... | ptphp/PyLib | src/wx/src/fetchvc.py | Python | apache-2.0 | 11,206 | [
"VisIt"
] | bdcb25bccf0bbf1ffd8ce19eeee8f4b6b8f3e1bfaebd5d93f6b12fd0ab2a67fb |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-kms | tests/unit/gapic/kms_v1/test_key_management_service.py | Python | apache-2.0 | 334,734 | [
"Octopus"
] | f4c71ac6be8446caa46f9fe66766d63590641d53034711785cfacc3df5774a34 |
__author__ = 'rc'
import argparse
import os
import subprocess
parser = argparse.ArgumentParser()
parser.add_argument("-d", "--directory", help="Path of new playbook", default="./")
parser.add_argument("-n", "--name", help="Playbook name")
args = parser.parse_args()
if not args.name:
print parser.print_help()
... | rowancarr/ansible-playbook-init | playbook_init/__main__.py | Python | apache-2.0 | 2,207 | [
"Galaxy"
] | 09c90cc372c79fad128ac29721fd691506cf2572f3269315869bed36b2fa97fa |
''' Nansat NetCDF-CF mapper
Check CF-compliance of your files here:
http://cfconventions.org/compliance-checker.html
'''
import warnings, os, datetime
import numpy as np
import collections
from nansat.utils import gdal
from dateutil.parser import parse
from netCDF4 import Dataset
from nansat.vrt import VRT
... | nansencenter/nansat | nansat/mappers/mapper_netcdf_cf.py | Python | gpl-3.0 | 19,066 | [
"NetCDF"
] | 3eeb5d42d5a8397ac994c1a410527e849f908aa937ef248a9d8a0492c2bdae19 |
# coding=utf-8
import uuid
from django.db import models
from django.contrib.postgres.fields import IntegerRangeField, DateTimeRangeField
from django.utils.timezone import localtime
from psycopg2.extras import NumericRange
from apps.common.models import AbstractObservation
class Zsj(models.Model):
"""Basic reside... | gis4dis/poster | apps/processing/o2/models.py | Python | bsd-3-clause | 8,043 | [
"VisIt"
] | 320cd771cf7a51656af36f91ae8b5d980a56e72e39db55aa2a50f5cda19d7c7c |
########################################################################
# $Id$
########################################################################
""" A set of common tools to be used in pilot commands
"""
import sys
import time
import os
import pickle
import getopt
import imp
import types
import urllib2
import... | sposs/DIRAC | WorkloadManagementSystem/PilotAgent/pilotTools.py | Python | gpl-3.0 | 16,264 | [
"DIRAC"
] | e112f03dd81bb5b2312399af2c7b66ddfce1dbd6344b6db314310dca80e6163e |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Build and Launch iPhone Application in Simulator or install
# the application on the device via iTunes
#
import os, sys, uuid, subprocess, shutil, signal, string, traceback, imp, filecmp, inspect
import platform, time, re, run, glob, codecs, hashlib, datetime, plistli... | arnaudsj/titanium_mobile | support/iphone/builder.py | Python | apache-2.0 | 56,617 | [
"VisIt"
] | 8774f55177f677a81e9813b2cc09b87b03f6eeab29c563b48318bba39fe637a6 |
#!/usr/bin/env python
# ***** BEGIN LICENSE BLOCK *****
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this file,
# You can obtain one at http://mozilla.org/MPL/2.0/.
# ***** END LICENSE BLOCK *****
import copy
import os
import pla... | simar7/build-mozharness | mozharness/mozilla/testing/testbase.py | Python | mpl-2.0 | 27,402 | [
"VisIt"
] | 8b13aa8e2c1cef7c8f7b8a8bffa0b4d21e1d39a22d7fefec3aa0c272a2323d54 |
from .model_checker import ModelChecker, PathResult, PathMetric
from .pysb import PysbModelChecker
from .signed_graph import SignedGraphModelChecker
from .unsigned_graph import UnsignedGraphModelChecker
from .pybel import PybelModelChecker
| johnbachman/belpy | indra/explanation/model_checker/__init__.py | Python | mit | 240 | [
"Pybel"
] | 50ae48955ce6ed7b8333caf5561ea3e7a75ca3b2205076a179b573824add5ac8 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | capoe/espressopp.soap | src/__init__.py | Python | gpl-3.0 | 2,575 | [
"ESPResSo"
] | 610d6c6c6b666a27de1d8a3200fe64bcf567463b831cc70a78f28ced6b867398 |
""" This is a test of using WMSClient and several other functions in WMS
In order to run this test we need the following DBs installed:
- JobDB
- JobLoggingDB
- TaskQueueDB
- SandboxMetadataDB
And the following services should also be on:
- OptimizationMind
- JobManager
- SandboxSt... | fstagni/DIRAC | tests/Integration/WorkloadManagementSystem/Test_Client_WMS.py | Python | gpl-3.0 | 21,409 | [
"DIRAC"
] | 36b40baec479574ba71d64f11ed38aaab13630bd7feb700bf6a30a62a4aaef0d |
import os
from webassets.filter import Filter
from webassets.utils import common_path_prefix
__all__ = ('JST',)
class JSTemplateFilter(Filter):
"""Common base class for the JST and Handlebars filters, and
possibly other Javascript templating systems in the future.
"""
def concat(self, out, hunks, *... | 0x1997/webassets | src/webassets/filter/jst.py | Python | bsd-2-clause | 6,619 | [
"MOE"
] | 6e6374243f3f1a309340a01e374c218452bb44808174ed4d7ed1dff544a08e97 |
"""
A simple VTK input file for PyQt, the qt bindings for python.
See http://www.trolltech.com for qt documentation, and
http://www.river-bank.demon.co.uk or http://www.thekompany.com
for the qt python bindings.
*******************************************************
NOTE: The widget provided by this module is not... | cjh1/VTK | Wrapping/Python/vtk/qt/QVTKRenderWidget.py | Python | bsd-3-clause | 15,290 | [
"VTK"
] | 27038cb8f1ceafd5ac3d77ce4eafb99de407371e5074898e999f725b2482e711 |
#!/usr/bin/env python
# visualiseVector.py
# Projects a set of eigenvectors of a normal onto the PDB structure, offers the user additional options for visualisation
# Produces as set of frames to visualise the motion and Tcl script to plot the eigenvectors as a set of arrows
# Author: Caroline Ross: caroross299@gmail.... | RUBi-ZA/MODE-TASK | visualiseVector.py | Python | gpl-3.0 | 16,152 | [
"VMD"
] | 3448d41bb7451287f666b65a67c7424d098b9d192040ee3dce518bdc84767058 |
#!/usr/bin/env python
########################################################################
# $HeadURL$
########################################################################
from __future__ import print_function
__RCSID__ = "$Id$"
from DIRAC import exit as DIRACExit
from DIRAC.Core.Base import Script
... | fstagni/DIRAC | DataManagementSystem/scripts/dirac-dms-replica-metadata.py | Python | gpl-3.0 | 1,617 | [
"DIRAC"
] | c8ac330b3c8c24ab59d237d5de57194f0d7d561573664f8b497f562c21f02719 |
#!/usr/bin/env python
import matplotlib.pyplot as plt
from matplotlib.collections import LineCollection
from matplotlib.colors import colorConverter
import numpy as np
import re
import sys
import argparse
import os.path
def get_fermi(fname):
with open(fname) as myfile:
for line in myfile:
m=re.... | mailhexu/pyDFTutils | pyDFTutils/wannier90/band_plot.py | Python | lgpl-3.0 | 5,996 | [
"Wannier90"
] | da4c439aa1ff58d0f0b8ac85247436d14bfc9319fdf6929945b126db126c6eea |
#!/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... | iwm911/plaso | plaso/parsers/sqlite_plugins/chrome_cookies_test.py | Python | apache-2.0 | 7,218 | [
"VisIt"
] | 5cf9b287c69feb4fc7a01c6f0c756eeb717a5024b0e363a7d73cc0110659fc65 |
from collections import OrderedDict
from tornado import gen
from tornadowebapi import exceptions
from tornadowebapi.resource_fragment import ResourceFragment
from tornadowebapi.resource_handler import ResourceHandler
from tornadowebapi.resource import Resource
from tornadowebapi.singleton_resource import SingletonReso... | simphony/tornado-webapi | tornadowebapi/tests/resource_handlers.py | Python | bsd-3-clause | 7,518 | [
"Octopus"
] | b090cdf91cb5caab5832f27f589106f1cdd4a06c96200cc53968a37bc3f6e87f |
#!/usr/bin/env python
import os
import sys
import vtk
def get_program_parameters():
import argparse
description = 'Demonstrates physically based rendering, image based lighting, texturing and a skybox.'
epilogue = '''
Physically based rendering sets color, metallicity and roughness of the object.
Image ... | lorensen/VTKExamples | src/Python/Rendering/PhysicallyBasedRendering.py | Python | apache-2.0 | 18,316 | [
"VTK"
] | c416527f881ad11b8f29c9179c74c26f3a2a781f1484aff6b2726704f9a06e4c |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
# this test has some wireframe geometry
# Make sure multisampling is disabled to avoid generating multiple
# regressi... | hlzz/dotfiles | graphics/VTK-7.0.0/Filters/General/Testing/Python/streamTracer.py | Python | bsd-3-clause | 2,273 | [
"VTK"
] | 4861f9d4afcd5ac8047a0d6a523000b751a85b1bb691468f031d783b3b482bec |
# Copyright 2000-2004 Brad Chapman.
# Copyright 2001 Iddo Friedberg.
# Copyright 2007-2010 by Peter Cock.
# 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.
"""Classes for generic ... | updownlife/multipleK | dependencies/biopython-1.65/build/lib.linux-x86_64-2.7/Bio/Align/Generic.py | Python | gpl-2.0 | 17,521 | [
"BLAST",
"BioPerl",
"Biopython"
] | 21b149921b12121943125d6b0589d54ad94e2506f8c6a86b0b96e4d2a7ae9ca0 |
#!/usr/bin/env python
# -*- coding: utf8 -*-
import threading
from PIL.Image import open
import cv2
from Image import *
from OpenGL.GL import *
from OpenGL.GLU import *
from OpenGL.GLUT import *
import datetime, time, sys, gc
# local modules for opencv
from video import create_capture
from common import clock, draw... | aatishnn/astroact | app.py | Python | mit | 13,774 | [
"Galaxy"
] | 69d8b3bf7aaebec45387c0c1a49ad02ddb78dc4a6e32a3902206df1279a205d7 |
import afnumpy
import afnumpy.fft
import numpy as np
import sys
import crappy_crystals
import crappy_crystals.utils.disorder
from crappy_crystals.utils.disorder import make_exp
#import crappy_crystals.utils.l2norm
#from crappy_crystals.utils.l2norm import l2norm
import phasing_3d
from phasing_3d.src.mappers_g... | andyofmelbourne/crappy-crystals | utils/gpu/phasing/maps.py | Python | gpl-3.0 | 7,739 | [
"CRYSTAL"
] | d9be09ebc23bba88b5e7c9bae2cacd21687106af58f35cda48c2f2922bb9ede3 |
__author__ = "Sunil Kumar (kumar.sunil.p@gmail.com)"
__copyright__ = "Copyright 2014, Washington University in St. Louis"
__credits__ = ["Sunil Kumar", "Steve Pieper", "Dan Marcus"]
__license__ = "XNAT Software License Agreement " + \
"(see: http://xnat.org/about/license.php)"
__version__ = "2.1.1"
__main... | MokaCreativeLLC/XNATSlicer | XNATSlicer/XnatSlicerLib/utils/Error.py | Python | bsd-3-clause | 1,337 | [
"VTK"
] | 2abf7eb6004c4192664e4f57af86b991b2ab3b073e3549fb044fd3848f0a22f8 |
#! /usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless requi... | googleapis/python-monitoring-metrics-scopes | scripts/fixup_monitoring_metrics_scope_v1_keywords.py | Python | apache-2.0 | 6,200 | [
"VisIt"
] | 1a0af5848d6e7b945a5f32346ca4044a20b3efa8fb3a3b375bd20230b7bea926 |
"""Scraper for the Supreme Court of Vermont
CourtID: vt
Court Short Name: VT
Author: Brian W. Carver
Date created: 18 Aug 2013
Reviewer: Mike Lissner
"""
from datetime import datetime
from urlparse import urlsplit
from juriscraper.OpinionSite import OpinionSite
from lxml import html
class Site(OpinionSite):
def... | Andr3iC/juriscraper | opinions/united_states/state/vt_u.py | Python | bsd-2-clause | 2,067 | [
"Brian"
] | 588f125fb89ba5c89d67b6e848b4eb5fae9572ccd311e482887fe62c67d8a588 |
# Created by John Travers, Robert Hetland, 2007
""" Test functions for rbf module """
import numpy as np
from numpy.testing import (assert_, assert_array_almost_equal,
assert_almost_equal)
from numpy import linspace, sin, cos, random, exp, allclose
from scipy.interpolate.rbf import Rbf
FUNC... | aeklant/scipy | scipy/interpolate/tests/test_rbf.py | Python | bsd-3-clause | 6,750 | [
"Gaussian"
] | 54ca37ac7dc2114bba41b6e9431d5cbd34c9cb3469a4c73f7148a669ebbee670 |
#! /usr/bin/python
import __main__
__main__.pymol_argv = ['pymol','-qc']
#__main__.pymol_argv = ['pymol','']
import sys,time,os
import pymol
pymol.finish_launching()
sys.path.append("/home/scratch/software/Pymol-script-repo-master")
import my_elbow_angle
my_file = sys.argv[1]
chain1 = sys.argv[2]
chain2 = sys.argv[3... | demharters/git_scripts | calc_elbow_ab_all.py | Python | apache-2.0 | 750 | [
"PyMOL"
] | a356f232683f1a6ae5e195ea3637e8063560487f09e62c5b94cdb9e02873a003 |
###############################
# This file is part of PyLaDa.
#
# Copyright (C) 2013 National Renewable Energy Lab
#
# PyLaDa is a high throughput computational platform for Physics. It aims to
# make it easier to submit large numbers of jobs on supercomputers. It
# provides a python interface to physical input, ... | pylada/pylada-light | tests/process/test_jobfolder.py | Python | gpl-3.0 | 8,643 | [
"CRYSTAL",
"VASP"
] | 4c66e1d268f2de5f82ffe4b49d8d38f5bd0249a86444a7daf5255736a9924b2f |
########################################################################
# File: RegisterOperation.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/03/19 13:55:14
########################################################################
""" :mod: RegisterFile
==================
.. module: RegisterFile
... | DIRACGrid/DIRAC | src/DIRAC/DataManagementSystem/Agent/RequestOperations/RegisterFile.py | Python | gpl-3.0 | 5,601 | [
"DIRAC"
] | 40370edcf84130a35fdcd32b1684c606ddffce1718aa0497317e4e8e58e965b3 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
"""
Module containing class to create an ion
"""
__author__ = "Sai Jayaraman"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.0"
__maintainer__... | xhqu1981/pymatgen | pymatgen/core/ion.py | Python | mit | 7,310 | [
"pymatgen"
] | ed7d5b3b9a5395c7a186e792acf0d81daf96e3a9067037ff7f8c6cad06780b56 |
# ----------------------------------------------------------------------------
# Copyright 2015 Nervana Systems Inc.
# 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.o... | coufon/neon-distributed | tests/test_mergesum_layer.py | Python | apache-2.0 | 4,997 | [
"Gaussian"
] | efa0540406ea36beef1a373c7dd12691d02c545b0407d333ec04de462117c46f |
'''
=====
BLAST
=====
Prepares data and executes BLAST commands to create BLAST database.
Performs blastn of user sequences against genomic sequences.
Provides functions to parse the generated BLAST tables and extract exons.
'''
import re
import sys
import subprocess
from Bio import SeqIO
from Bio.Seq import Seq
from... | carlosp420/PyPhyloGenomics | pyphylogenomics/BLAST.py | Python | gpl-3.0 | 15,770 | [
"BLAST",
"Biopython"
] | 0ad9f4d9bb52c0c6151ea6f8aed0213bbacc0230c6547edff1f537692ca74870 |
#! /usr/bin/python
# -*- coding: utf-8 -*-
#
# Vladimír Slávik 2008-2012
# Python 3.2
#
# for Simutrans
# http://www.simutrans.com
#
# code is public domain
#
# read all dat files in all subfolders
# weed out all except houses
# reformat them and save aside
# WARNING: frontimage is not considered! ONLY backima... | hdomos/pak128 | tools/split-houses-multitile.py | Python | artistic-2.0 | 3,203 | [
"VisIt"
] | 083aac58e7f0bf0306778e881e5c05c8e9215a5ba5de0ad5264c46cab90d1b5c |
#!/usr/bin/env python
# ----------------------------------------------------------------------------
# Copyright (c) 2016--, tax-credit development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------... | BenKaehler/short-read-tax-assignment | tax_credit/framework_functions.py | Python | bsd-3-clause | 40,477 | [
"BLAST"
] | d51aaad0b2ffea7af022429386a56aab518fefe5dc1fc0cbed4a4450a866bf77 |
""" Powerful utility for running a TCP/UDP server that is used to script
Mayavi2 from the network. This uses Twisted. This particular version
has been written for the wxPython, adding support for a Qt4 version
should be trivial.
The key functions exposed are::
serve_tcp(...)
serve_udp(...)
See the function docum... | liulion/mayavi | mayavi/tools/server.py | Python | bsd-3-clause | 9,288 | [
"Mayavi"
] | 1b228e768f9aecf21a7eaab70593032a4b8a12b2047ef053262cd537526075fd |
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