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# -*- coding: utf-8 -*-
"""
"""
import math
import copy
from ROOT import TGraphErrors, TCanvas, TF1, TFile, kRed , kGreen, gROOT, gErrorIgnoreLevel, kError
import plotbase
import getroot
gROOT.SetBatch(True)
gErrorIgnoreLevel = kError
n_fail = [0,0,0,0,0,0]
def get_errerr(roothisto):
sqrt_nminus1 = math.sqrt(ro... | dhaitz/CalibFW | plotting/modules/plot_resolution.py | Python | gpl-2.0 | 15,305 | [
"Gaussian"
] | b92e8b2e8b5d17e0f9dfb325d47fd6511fe46f1ae4e2f2a91d4de344a2f44d06 |
# Author: Matthew Harrigan <matthew.harrigan@outlook.com>
# Contributors:
# Copyright (c) 2016, Stanford University
# All rights reserved.
from __future__ import print_function, division, absolute_import
import os
import pickle
import re
import shutil
import stat
import warnings
import mdtraj as md
import numpy as n... | mpharrigan/mixtape | msmbuilder/io/io.py | Python | lgpl-2.1 | 9,747 | [
"MDTraj"
] | d8bb2d16f4340c33e691055c5ba1d4961ffa5f7d12cb3571792b1caf5574f135 |
from dopamine.trpo import *
from dopamine.discworld import *
# Create a lineworld instance.
env = DiscWorld()
# Create the policy model.
layers = []
layers.append({'input_dim': env.D, 'units': 100})
# layers.append({'units': 100, 'activation': 'relu'})
# layers.append({'units': 100, 'activation': 'relu'})
layers.appe... | lightscalar/dopamine | scripts/discworld_experiments.py | Python | mit | 612 | [
"Gaussian"
] | f9b606802dc1c049a7b66fcfe1939ada54481d12de8f244cf25bee2dbb38c399 |
import gevent
import json
import unittest2
import base64
import os
import tempfile
import urllib2
from psdash.run import PsDashRunner
try:
import httplib
except ImportError:
# support for python 3
import http.client as httplib
class TestBasicAuth(unittest2.TestCase):
default_username = 'tester'
de... | uaomer/psdash | tests/test_web.py | Python | cc0-1.0 | 12,633 | [
"VisIt"
] | 94d838183a12e2959c0d794f09b622220b311e978faf686eb96f6140f638ee8e |
# Copyright 2013 Pau Haro Negre
# based on C++ code by Carl Staelin Copyright 2009-2011
#
# See the NOTICE file distributed with this work for additional information
# regarding copyright ownership.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with... | pauh/neuron | cognon_extended.py | Python | apache-2.0 | 8,867 | [
"NEURON"
] | affd9d9cbde0edfe0c639f13cdf03686860d504d98315849c0de0f03d7cc8329 |
"""NFW profiles for shear and magnification.
Surface mass density and differential surface mass density calculations
for NFW dark matter halos, with and without the effects of miscentering
offsets.
"""
from __future__ import absolute_import, division, print_function
import numpy as np
from astropy import units
from ... | jesford/cluster-lensing | clusterlensing/nfw.py | Python | mit | 17,308 | [
"Galaxy",
"Gaussian"
] | 531a75fb5cd1b5c868a74f54f4a98d69de9796ca4640b70802b664dd56e9bba5 |
# Copyright 2007 by Michiel de Hoon. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Code to work with the sprotXX.dat file from SwissProt.
http://www.expasy.ch/sprot/sprot-t... | poojavade/Genomics_Docker | Dockerfiles/gedlab-khmer-filter-abund/pymodules/python2.7/lib/python/Bio/SwissProt/__init__.py | Python | apache-2.0 | 22,397 | [
"Biopython"
] | 6586672616d805cd95fad1941cebc186d43bcb779e192d4b0ad7c0cd23da82b6 |
'''
sbclearn (c) University of Manchester 2017
sbclearn is licensed under the MIT License.
To view a copy of this license, visit <http://opensource.org/licenses/MIT/>.
@author: neilswainston
'''
from scipy import stats
def coeff_corr(i, j):
'''coeff_correlation.'''
_, _, r_value, _, _ = stats.linregress(i... | synbiochem/synbiochem-learn | gg_learn/utils/__init__.py | Python | mit | 347 | [
"VisIt"
] | 86dc88a123fb95c66c964bcca18c82c78ac6d6a3d1e3f5a1121187165ff25cf5 |
from guiData import *
from PyQt4 import QtCore, QtGui
import functools
class BCTab(QtGui.QWidget):
"""This class represents the bc tab"""
# pass in the gui data object and a function to change visibility of vtk parts
def __init__(self, data, visibilityChangeFunc):
self.data = data
self.vis... | ngcurrier/ProteusCFD | GUI/BCTab.py | Python | gpl-3.0 | 4,203 | [
"VTK"
] | 122eef9c496ea4aaa9c7a00dd4498675e699c2523a161b9fc6edb9948679026e |
#
# This is an example script for accessing a Magpie server
# from Python. To use it you first need to generate the
# Python interface code with Apache Thrift:
#
# thrift --gen py magpie.thrift
#
# Then, start a Magpie server with models for predicting
# the volume and bandgap energy of a material when provided... | amarkrishna/demo1 | thrift/magpie-client.py | Python | mit | 2,145 | [
"CRYSTAL"
] | 19e514238d771b2cfe28f4b1a0ed40d027cb519b60f44502059e2fdd633a41d3 |
#################################################################
# Class DirectoryListing
# Author: A.T.
# Added 02.03.2015
#################################################################
import stat
from DIRAC import gConfig
from DIRAC.ConfigurationSystem.Client.Helpers import Registry
class DirectoryListing(ob... | DIRACGrid/DIRAC | src/DIRAC/DataManagementSystem/Client/DirectoryListing.py | Python | gpl-3.0 | 7,586 | [
"DIRAC"
] | 94bb3f8d6c95317e6adc163f9a7e1cd7c43458271aa150b0417eb94356664e51 |
# -*- coding: latin-1 -*-
# Copyright (C) 2009-2014 CEA/DEN, EDF R&D
#
# 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 ... | FedoraScientific/salome-hexablock | doc/pyplots/bride.py | Python | lgpl-2.1 | 11,325 | [
"VTK"
] | e6fc758693e3ef621ddd6b549fbc33f9cf164dde68419d90a1270fa0960c0980 |
# -*- coding: utf-8 -*-
# Copyright (c) 2015, imageio contributors
# imageio is distributed under the terms of the (new) BSD License.
# flake8: noqa
"""
Imagio is plugin-based. Every supported format is provided with a
plugin. You can write your own plugins to make imageio support
additional formats. And we would be... | kenshay/ImageScript | ProgramData/SystemFiles/Python/Lib/site-packages/imageio/plugins/__init__.py | Python | gpl-3.0 | 3,684 | [
"ASE"
] | fa30f3621c12de4e255d946517a98d37bbb9d19cea0001db3c38e07f51af5fee |
"""
Helper functions for the course complete event that was originally included with the Badging MVP.
"""
import hashlib
import logging
from django.core.urlresolvers import reverse
from django.utils.text import slugify
from django.utils.translation import ugettext_lazy as _
from badges.models import BadgeAssertion, B... | gymnasium/edx-platform | lms/djangoapps/badges/events/course_complete.py | Python | agpl-3.0 | 4,179 | [
"VisIt"
] | 632b530f1f3cb0e7fc7ed057418dc6781df1ed579712d368fbdb58caf015c97d |
""" UserProfileDB class is a front-end to the User Profile Database
"""
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
__RCSID__ = "$Id$"
import six
import os
import sys
import hashlib
from DIRAC import S_OK, S_ERROR, gLogger, gConfig
from DIRAC.Core.Util... | yujikato/DIRAC | src/DIRAC/FrameworkSystem/DB/UserProfileDB.py | Python | gpl-3.0 | 26,624 | [
"DIRAC"
] | 780c6b26b01549b22e4c5e0c13daf8c83119fe16b83cee276998dc874ab3fed7 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
import os
from pymatgen import Structure
from pymatgen.io.feff.sets import MPXANESSet, MPELNESSet, FEFFDictSet, MPEXAFSSet
from pymatgen.io.feff.inputs import Potential, Tags, Atoms, Header
f... | gVallverdu/pymatgen | pymatgen/io/feff/tests/test_sets.py | Python | mit | 10,986 | [
"FEFF",
"pymatgen"
] | 2d58f533f77a15c431aac71fafc99feedb7082a39345c0629793e06ccd49c51f |
"""Make plots of monthly values or differences"""
from __future__ import print_function
import calendar
from pandas.io.sql import read_sql
import matplotlib.pyplot as plt
from pyiem.util import get_dbconn
PGCONN = get_dbconn("idep")
def get_scenario(scenario):
df = read_sql(
"""
WITH yearly as (... | akrherz/idep | scripts/biomass/monthly.py | Python | mit | 2,391 | [
"ADF"
] | 7005d32bb7b456e5ffe144f4c3317e65fc22974d967c5539c3b2d09e164f12f4 |
import sys, os, re, argparse, csv
import shutil
class WorkflowParser(object):
def __init__(self, batch_file=None):
self.bf = batch_file
self.read_batch_file()
def read_batch_file(self):
"""
Read lines from batch submit file.
"""
batch_file = self.bf
wi... | jaeddy/bripipetools | scripts/_deprecated/compile_globus_results.py | Python | mit | 9,779 | [
"Galaxy",
"HTSeq"
] | bdc9b6e17358f4ae734617801eca5382451471401fd926a1de8f353d5cd82250 |
#!/usr/bin/pvpython
import paraview.simple
import os
import tempfile
import shutil
import sys
SRC_DIR = sys.argv[1]
DST_DIR = sys.argv[2]
if not os.path.isdir(DST_DIR):
os.makedirs(DST_DIR)
for filename in os.listdir(SRC_DIR):
print SRC_DIR + "/" + filename
fileName, fileExtension = os.path.splitext(filename)... | alyupa/multiphase-flow-modeling | visualisation/conv.py | Python | mit | 662 | [
"ParaView"
] | baa36f0524a45623c98199c61f48b1a68085f39f022f166e3668da7e24331748 |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
#
# Copyright (c) 2015 Steffen Deusch
# Licensed under the MIT license
# MonitorNjus, 28.11.2015 (Version 1.1)
import random # Random Modul importieren
rancolor = ['red', 'indigo', 'blue', 'light-blue', 'cyan', 'teal',
'green', 'light-gre... | SteffenDE/monitornjus | modules/code/colors.py | Python | mit | 3,027 | [
"Amber"
] | 060e4cf2f713459ef932b934ee09a35eeb9d5bc75499f73b6c9ffa05f6fe0560 |
#!/usr/bin/env python3
import os
import sys
try:
import locale
locale.setlocale(locale.LC_ALL, '')
except:
pass
#
# firefly imports
#
from version_info import VERSION_INFO
from firefly_common import *
from firefly_menu import create_menu
from firefly_starter import Firestarter
from dlg_system import S... | opennx/nx.client | firefly.py | Python | gpl-3.0 | 11,149 | [
"Firefly"
] | 069178c358fdaada6d52e87b4559fd65cd8f9868e91313b1f00a1b60255063b2 |
#!/usr/bin/env python
########################################################################
# File : dirac-wms-job-logging-info
# Author : Stuart Paterson
########################################################################
"""
Retrieve history of transitions for a DIRAC job
Usage:
dirac-wms-job-logging-i... | yujikato/DIRAC | src/DIRAC/Interfaces/scripts/dirac_wms_job_logging_info.py | Python | gpl-3.0 | 3,016 | [
"DIRAC"
] | e60fa84267ecb92a70ebb16145fef02268efa96ec4e09cbc07510db990d4e9bb |
# -*- coding: utf-8 -*-
# ------------------------------------------------------------
# streamondemand.- XBMC Plugin
# Canale per toointalia
# http://www.mimediacenter.info/foro/viewforum.php?f=36
# ------------------------------------------------------------
import re
from core import config
from core import logger
... | costadorione/purestream | channels/toonitalia.py | Python | gpl-3.0 | 7,937 | [
"ADF"
] | 08f1a4f944f2372c51651015cc20fa7abc95c786e1e4b50e1a890e2145062508 |
# import libraries
import matplotlib
matplotlib.use('Agg')
import mdtraj as md
import matplotlib.pyplot as plt
import numpy as np
from msmbuilder import dataset
import seaborn as sns
sns.set_style("whitegrid")
sns.set_context("poster")
#Load trajectory with ensembler models
t_models = md.load("../ensembler-models/... | choderalab/MSMs | plots/plotting_conformations_ensembler_models.py | Python | gpl-2.0 | 1,404 | [
"MDTraj"
] | aeb15087d27cc1c6c3438a9cc4ffe637c73da091646c5212fafa60e8d174e542 |
"""
Unit tests for enrollment methods in views.py
"""
from mock import patch
from django.test.utils import override_settings
from django.contrib.auth.models import User
from django.core.urlresolvers import reverse
from courseware.tests.helpers import LoginEnrollmentTestCase
from courseware.tests.modulestore_config i... | hkawasaki/kawasaki-aio8-1 | lms/djangoapps/instructor/tests/test_legacy_enrollment.py | Python | agpl-3.0 | 14,496 | [
"VisIt"
] | a5b815b945c2afdcd15066b9a5e66c4fd1bbc4c2e9e7f42ad7a20c70dbf19e06 |
#
# Copyright (C) 2017-2021 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | espressomd/espresso | testsuite/python/sf_simple_lattice.py | Python | gpl-3.0 | 7,556 | [
"CRYSTAL",
"ESPResSo"
] | 29255b416b5039db8927bc610a6242d34f07ec714101dff29895153f2a8b3590 |
#!/usr/bin/python
"""
US Federal holidays.
Copyright (c) 2015 Kauinoa
License: MIT
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 ... | kauinoa/CalendarEvents | calendarevents/federal_holidays.py | Python | mit | 3,668 | [
"COLUMBUS"
] | 542b86de1b00f3951e4560a70d820f1eff7178b57f45ccdf67acb0e5414ffe06 |
from __future__ import print_function
import os
import numpy as np
import subprocess
# flopy imports
from ..modflow.mfdisu import ModflowDisU
from util_array import read1d, Util2d
from ..mbase import which
try:
import shapefile
except:
raise Exception('Error importing shapefile: ' +
'try p... | mrustl/flopy | flopy/utils/gridgen.py | Python | bsd-3-clause | 32,177 | [
"VTK"
] | 907158cc7e555897747df213fd41f7c343891943801c05606f718d539de69d65 |
#!/usr/bin/env python
""" update local cfg
"""
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
import os
from diraccfg import CFG
from DIRAC.Core.Utilities.DIRACScript import DIRACScript as Script
Script.setUsageMessage("\n".join([__doc__.split("\n")[1],... | ic-hep/DIRAC | tests/Jenkins/dirac-cfg-update.py | Python | gpl-3.0 | 2,479 | [
"DIRAC"
] | 1c06eb49f854be9fa64520614332a7ef04eed856d47e6f4383b3d7a515e476b3 |
# -*- coding: utf-8 -*-
"""
Data conversion utilities for igraph
=====================================
Convert cytoscape.js style graphs from/to igraph object.
http://igraph.org/python/
"""
import igraph as ig
DEF_SCALING = 100.0
def from_igraph(igraph_network, layout=None, scale=DEF_SCALING):
"""
Conver... | idekerlab/cyrest-examples | notebooks/cookbook/Python-cookbook/util/util_igraph.py | Python | mit | 3,777 | [
"Cytoscape"
] | 120d003c34c8e1c379bbb5d2800497a830842c88c1323f8af823cf708bf18f95 |
# Copyright 2020,2021 Sony Corporation.
# Copyright 2021 Sony Group Corporation.
#
# 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 ... | sony/nnabla | python/src/nnabla/utils/inspection/pretty_print.py | Python | apache-2.0 | 5,235 | [
"VisIt"
] | f2788e67f88acf54e4b23576c10a64a857b98c4b1a1328b4f742333b863df311 |
"""
Fixtures for testing notifications
"""
from copy import deepcopy
from octopus.lib import dates, paths
import os
RESOURCES = paths.rel2abs(__file__, "..", "resources")
"""Path to the test resources directory, calculated relative to this file"""
class NotificationFactory(object):
"""
Class which provides a... | JiscPER/jper-sword-out | service/tests/fixtures/notifications.py | Python | apache-2.0 | 11,432 | [
"Octopus"
] | c184ff7c40f6fbdd01ba4cba06bda52a31c5789b2ad810f912c760d5620e1cf1 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
What it does
============
B{This is the 7th step of ZIBgridfree.}
This tool will perform a direct reweighting of the sampling nodes. It should be run on a pool of converged nodes. From the reweighted partial distributions that were sampled in the individual nodes on... | CMD-at-ZIB/ZIBMolPy | tools/zgf_reweight.py | Python | lgpl-3.0 | 31,388 | [
"Avogadro",
"Gromacs"
] | 42f3b1ff84a0a09c68cf1f9bc56624f76eb69559b8c72e821ba6209b1e386703 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# (c) 2014, Brian Coca <brian.coca+dev@gmail.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the... | Rajeshkumar90/ansible-modules-extras | system/getent.py | Python | gpl-3.0 | 4,497 | [
"Brian"
] | 612f0872f69bb99ef7c72328e0a54a889fcca70e650fd2c4c70a2ff174da68ff |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2008 Jerome Rapinat
# Copyright (C) 2008 Benny Malengier
#
# 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 Fre... | Forage/Gramps | gramps/gen/filters/rules/person/_hasassociation.py | Python | gpl-2.0 | 2,624 | [
"Brian"
] | 606c7a457394c8bcc40ab7a4158ef36e47298a40af7b4cc5f17ec89a9df235d6 |
from __future__ import division
import jedi.jedi as jedi
from jedi.utils import plot, init_tools
import matplotlib.pylab as plt
import numpy as np
# Setting Seeds
seeds = np.random.uniform(0,10000,1).astype(int)
# sine-wave target
target = lambda t0: np.cos(2 * np.pi * t0/.5)
#Simulation parameters for FORCE
dt = ... | avicennax/jedi | tests/sin_test.py | Python | mit | 2,751 | [
"NEURON"
] | 0c60d3a78d0c1bca40db0ffb55f91713c5600171d35d25d99dd3063fac4a8f66 |
##
# Copyright 2009-2020 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (F... | pescobar/easybuild-easyblocks | easybuild/easyblocks/w/wrf.py | Python | gpl-2.0 | 18,256 | [
"NetCDF"
] | 7e326e830900f681dd196e20c46788d80c4a979ac846b4bf22f6ff471784da96 |
"""
Spectral Generation
===================
Defines various objects performing spectral generation:
- :func:`colour.sd_constant`
- :func:`colour.sd_zeros`
- :func:`colour.sd_ones`
- :func:`colour.msds_constant`
- :func:`colour.msds_zeros`
- :func:`colour.msds_ones`
- :func:`colour.colorimetry.sd_gaussia... | colour-science/colour | colour/colorimetry/generation.py | Python | bsd-3-clause | 23,477 | [
"Gaussian"
] | f816bf4848374724a909e59068f2e9c8050a8883d748b62c43fdfe682aac618b |
import unittest
import collections
from ..visitor import ClassVisitor, handle
class TestClassVisitor(unittest.TestCase):
def assert_visitation(self, expected_key, value):
visited_type, visited_value, args, kwargs = ExampleClassVisitor().visit(value, 2, a=3)
self.assertEqual(expected_key, visited... | herczy/pydepend | pydepend/tests/test_visitor.py | Python | bsd-3-clause | 1,593 | [
"VisIt"
] | 88cd72e3b856efe17b7a040784e9e842ef6741401ede3486cb05e72e5145c2d2 |
class protein ():
pass
def fastaParser(pFile, seq_format):
if seq_format != "fasta":
print "Cannot read non-fasta protein records without biopython."
exit()
yield -1
newProt = protein()
sequence = []
for line in pFile.readlines():
if line[0] == ";":
conti... | DeclanCrew/LC_MS_MS_Search | fastaParse.py | Python | gpl-3.0 | 729 | [
"Biopython"
] | 9fd7b983ed55f9c26a97f3c8adc31cc5c7b51808b80f1cac3291d90c44c413d0 |
# Brian Keegan, 2012
# This function creates text files containing a list of Wikipedia categories which will be passed to a scraping algorithm.
# Two files are created for each category type, events before 2001 (Wikipedia's founding) and after 2001
#Define schema for naming category types
topics=[('fires', "Category:{... | tothebeat/wikipedia-revisions | old/list_generator_2.py | Python | mit | 1,418 | [
"Brian"
] | 8a3a0977a4f1a46caf15273c27e7ab26aecc1d82dcdcc29dc4f5148bad076525 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | skosukhin/spack | var/spack/repos/builtin/packages/r-variantannotation/package.py | Python | lgpl-2.1 | 2,615 | [
"Bioconductor"
] | f25c5036c091b629255c540579047116cd97e22773d860c7e585753977b0795b |
# (c) 2014, Brian Coca, Josh Drake, et al
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
... | goozbach/ansible | lib/ansible/plugins/cache/memory.py | Python | gpl-3.0 | 1,466 | [
"Brian"
] | 2df9c02ba0b9a6dd0af267bfbae0c9bbe5e0cd56b231aa5a161cb3db498cd23e |
import unittest
import numpy
import chainer
from chainer import cuda
from chainer import functions
from chainer import gradient_check
from chainer import testing
from chainer.testing import attr
from chainer.testing import condition
class TestGaussian(unittest.TestCase):
def setUp(self):
self.m = numpy... | truongdq/chainer | tests/chainer_tests/functions_tests/noise_tests/test_gaussian.py | Python | mit | 1,464 | [
"Gaussian"
] | f5a894581bec611416a5538d76a52f6119f6b2f7886d567e5783b9c9bbe3720f |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import os
import unittest
import json
from monty.json import MontyDecoder
import numpy as np
import matplotlib
from pymatgen.util.testing import PymatgenTest
from pymatgen.analysis.xas.spectrum import XANES
f... | dongsenfo/pymatgen | pymatgen/vis/tests/test_plotters.py | Python | mit | 1,607 | [
"pymatgen"
] | b34484a9e5fb68cc1170c4a7cbb98c1b82ef357be75bd302d1e2e25a5fa7b77e |
""" manage PyTables query interface via Expressions """
import ast
from functools import partial
import numpy as np
from pandas.compat import DeepChainMap, string_types, u
from pandas.core.dtypes.common import is_list_like
import pandas as pd
from pandas.core.base import StringMixin
import pandas.core.common as co... | GuessWhoSamFoo/pandas | pandas/core/computation/pytables.py | Python | bsd-3-clause | 19,388 | [
"VisIt"
] | 376cd7c069e72d730dbd87e0169836e8714c6ef74f5c998d5c56b9445497498f |
#!/usr/bin/env python
import shutil
import tempfile
import configparser
from textwrap import dedent
import tarfile
import pyaml
import hashlib
import os
import re
import bs4
import urllib
from urllib import request
from urllib import parse
from urllib import error
from collections import OrderedDict
import logging
imp... | guowei-he/bioconda-recipes | scripts/bioconductor/bioconductor_skeleton.py | Python | mit | 16,642 | [
"Bioconductor"
] | 641efeaf9c8407c4733e98e6b64a212e6637f50f666285e4b3323c7b0f7744e5 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Works for Abinit
"""
from __future__ import unicode_literals, division, print_function
import os
import shutil
import time
import abc
import collections
import numpy as np
import six
import copy
from six.m... | setten/pymatgen | pymatgen/io/abinit/works.py | Python | mit | 56,981 | [
"ABINIT",
"Gaussian",
"NetCDF",
"pymatgen"
] | 9bb32f541c64b4dd18c9c81dc8db1f588d5d93b8da6a4f30efdc9c7339975cba |
''' -- imports from installed packages -- '''
import json
import datetime
''' -- imports from django -- '''
from django.shortcuts import render_to_response, render
from django.template import RequestContext
from django.template import Context
from django.template.defaultfilters import slugify
from django.core.urlresol... | sunnychaudhari/gstudio | gnowsys-ndf/gnowsys_ndf/ndf/views/forum.py | Python | agpl-3.0 | 40,863 | [
"VisIt"
] | 41f1c66c32e57943bb1f2b183dff2d77d69c117ee6de78289c18bfb04f259f93 |
# Copyright 2017-2020 The GPflow Contributors. 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 appli... | GPflow/GPflow | gpflow/likelihoods/misc.py | Python | apache-2.0 | 847 | [
"Gaussian"
] | e841af835668fca17f40c7fed85259e6ba51cb31a18ffff8297dafbffea22bad |
"""
Choropleth of parking tickets issued to state by precinct in NYC
================================================================
This example plots a subset of parking tickets issued to drivers in New York City.
Specifically, it plots the subset of tickets issued in the city which are more common than average
for... | ResidentMario/geoplot | examples/plot_nyc_parking_tickets.py | Python | mit | 2,395 | [
"VisIt"
] | 74f1ca78603b5c12246aac65f58728b9424757199d646c4d4b520d5ca95200b2 |
#! /usr/bin/env python
# -*- coding: UTF-8 -*-
import os
import sys
import setuptools
from distutils.command.clean import clean as _clean
from distutils.command.build import build as _build
from setuptools.command.sdist import sdist as _sdist
from setuptools.command.build_ext import build_ext as _build_ext
try:
... | qisanstudio/qsapp-official | setup.py | Python | mit | 2,778 | [
"GULP"
] | d16da3b26998bba3d2443ae0d19a029fec0ac5c262493143ad3f2da6a4022b2a |
# Copyright 2009-2013 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.
from __future__ import print_function
from Bio._py3k import _universal_read_mode
import os
... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_Muscle_tool.py | Python | gpl-2.0 | 16,947 | [
"Biopython"
] | 33f0dab8693902d27f170302fdad3dab14f71e12ee24b8186cd49dd48be3119b |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/grad/test/test_tdrks_grad.py | Python | apache-2.0 | 3,409 | [
"PySCF"
] | 945178c8c7497f4880b7ce37200547c855a731d6d4c29df9bdad82a903a0ff51 |
# -*- coding: utf-8 -*-
"""
This file is part of pyCMBS.
(c) 2012- Alexander Loew
For COPYING and LICENSE details, please refer to the LICENSE file
"""
import os
import sys
import numpy as np
import pylab as pl
import glob
from cdo import Cdo
from pycmbs.data import Data
from geoval.region import Region, RegionParse... | pygeo/pycmbs | pycmbs/benchmarking/config.py | Python | mit | 31,798 | [
"NetCDF"
] | 29fcac88d30c3c22c68c6e0072908e6b9fc912b58fe89a469f1a5ff2843ee72a |
# $HeadURL$
__RCSID__ = "$Id$"
import os.path
import zlib
import zipfile
import threading, thread
import time
import DIRAC
from DIRAC.Core.Utilities import List, Time
from DIRAC.Core.Utilities.ReturnValues import S_OK, S_ERROR
from DIRAC.Core.Utilities.CFG import CFG
from DIRAC.Core.Utilities.LockRing import LockRing
... | Sbalbp/DIRAC | ConfigurationSystem/private/ConfigurationData.py | Python | gpl-3.0 | 13,900 | [
"DIRAC"
] | fbd2adf6ec798ed87e21fa70f29cd36e0b5b071f6e5e894c4174f4451d067960 |
"""
This example displays the trajectories for the Lorenz system of
equations using mlab along with the z-nullcline. It provides a simple
UI where a user can change the parameters and the system of equations on
the fly. This primarily demonstrates how one can build powerful tools
with a UI using Traits and Mayavi.
F... | skulumani/asteroid_dumbbell | integration/lorenz_ui.py | Python | gpl-3.0 | 5,207 | [
"Mayavi"
] | 5b54ed7d5f9c70e21962634c64ada6855432ba7fa7aa538652c12732e087c25f |
# coding=utf-8
from __future__ import division
import math
import os
from copy import deepcopy
from ladybug_geometry.geometry3d.pointvector import Vector3D
from .analysisperiod import AnalysisPeriod
from .datacollection import HourlyContinuousCollection, HourlyDiscontinuousCollection
from .datatype.energyflux import... | ladybug-analysis-tools/ladybug-core | ladybug/wea.py | Python | gpl-3.0 | 52,788 | [
"EPW"
] | fb7e41567da2ab1d4fe6e076f617803986580ac631621dd42d51ce25aa158ff9 |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
import os
im... | harterj/moose | python/MooseDocs/extensions/modal.py | Python | lgpl-2.1 | 7,311 | [
"MOOSE"
] | ecb2612774b9d73a3ee058caa370ccabef0e48a155c125eb55e9a1c48f96ac8f |
"""
Perform Levenberg-Marquardt least-squares minimization, based on MINPACK-1.
AUTHORS
The original version of this software, called LMFIT, was written in FORTRAN
as part of the MINPACK-1 package by XXX.
Craig Markwardt converted the FORTRAN code to IDL. The information for ... | deapplegate/wtgpipeline | mpfit.py | Python | mit | 88,908 | [
"Gaussian"
] | ff1779f0ef4b6bfe2baf59e4386e37910d9ec14a18415bc4c419f6835b9c066a |
# Copyright (c) 2017, Henrique Miranda
# All rights reserved.
#
# This file is part of the yambopy project
#
from yambopy import *
from yamboparser import *
import os
class YamboQPDB():
"""
Class to read yambo ndb.QP files
These files describe the quasiparticle states calculated from yambo
Includes th... | henriquemiranda/yambopy | yambopy/dbs/qpdb.py | Python | bsd-3-clause | 5,337 | [
"Yambo"
] | 6a68fa5fe0e9b688b1dfaca7530d517b8f9eac3476fa4d0d9a543342f439f3a8 |
#!/usr/bin/python
"""
# Created on Aug 12, 2016
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com) GitHub ID: grastogi23
#
# module_check: not supported
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publ... | t0mk/ansible | lib/ansible/modules/network/avi/avi_api_session.py | Python | gpl-3.0 | 8,037 | [
"VisIt"
] | 52325d392375edd6d97cd9b2b7e9a6f197cd9adba9639a5025e01d3c0fda1b85 |
'''
Conversion of basis sets to Q-Chem format
'''
from .. import lut, manip, sort, printing
def _determine_pure(basis):
# starts at d shells
pure = {}
for eldata in basis['elements'].values():
if 'electron_shells' not in eldata:
continue
for sh in eldata['electron_shells']:
... | MOLSSI-BSE/basis_set_exchange | basis_set_exchange/writers/qchem.py | Python | bsd-3-clause | 4,106 | [
"Gaussian",
"Q-Chem"
] | fda17bef87058a9e14f9880271aa8466bdd770029e6e5ff13615d05c78262bdd |
# Orca
#
# Copyright 2005-2009 Sun Microsystems Inc.
# Copyright 2010 Joanmarie Diggs
#
# 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 op... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/scripts/apps/rhythmbox/script.py | Python | gpl-3.0 | 3,823 | [
"ORCA"
] | 703127db326a78cf8c103621524a1586ecd6787c466d995f09562597eb2045ca |
from __future__ import print_function
import numpy as np
import pandas as pd
import astropy.units as u
from math import copysign
from astropy.wcs import WCS
from astropy.io import fits
from astropy.time import Time
from astropy.coordinates import SkyCoord
class KbmodInfo(object):
"""
Hold and process the inf... | DiracInstitute/kbmod | analysis/kbmod_info.py | Python | bsd-2-clause | 7,455 | [
"VisIt"
] | e7f7188e0f43a8c52cb86b716ad52a7301dd670201894d405ddb5b668487bb2b |
# utility functions for frequency related stuff
import numpy as np
import math
import scipy.signal as signal
import scipy.interpolate as interp
from datetime import datetime, timedelta
import matplotlib.pyplot as plt
# import utils
from utilsIO import *
###########################
### SMOOTHING FUNCTIONS
#############... | nss350/magPy | utils/utilsProcess.py | Python | apache-2.0 | 11,084 | [
"Gaussian"
] | ba33c85802f720e7331b67a5ec03b28aeedb98e5dea7a6546f7e8db624798795 |
# Copyright (C) 2012 David Morton
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distribut... | davidlmorton/spikepy | spikepy/common/projection_utils.py | Python | gpl-3.0 | 3,660 | [
"Gaussian"
] | af3b0f411c80f8da72a9f2cd981c6f84ea3ef4a5198db5e26791fa1a7b1f14dc |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-admin-modify-user
# Author : Adrian Casajus
########################################################################
"""
Modify a user in the CS.
"""
__RCSID__ = "$Id$"
import DIRAC
from DIRAC... | avedaee/DIRAC | Interfaces/scripts/dirac-admin-modify-user.py | Python | gpl-3.0 | 2,307 | [
"DIRAC"
] | b59f540ab94d6649e67b45708ed780109155792215ac43981bc7b47210192040 |
import types
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Utilities import DEncode
from DIRAC.Core.Security import Properties
from DIRAC.Core.DISET.RequestHandler import RequestHandler
from DIRAC.WorkloadManagementSystem.DB.JobDB import JobDB
from DIRAC.WorkloadManagementSystem.Client.JobState.JobState import JobSta... | Sbalbp/DIRAC | WorkloadManagementSystem/Service/JobStateSyncHandler.py | Python | gpl-3.0 | 4,070 | [
"DIRAC"
] | ef7282ee679206537f03cedb9eb1c7223f92c22404fdef0c2143563a2906f383 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
# Credit to Dr. Shyue Ping Ong for the template of the calculator
"""
This module implements a TEM pattern calculator.
"""
import json
import os
from collections import namedtuple
from fractions import Fractio... | gVallverdu/pymatgen | pymatgen/analysis/diffraction/tem.py | Python | mit | 26,839 | [
"CRYSTAL",
"pymatgen"
] | 2de184d0b45b9ec030dfeb1ceba3638dc0b6d25393cc0e4901baedb61241f236 |
#!/usr/bin/env python
#############################################################################
##
## Copyright (C) 2009 Nokia Corporation and/or its subsidiary(-ies).
## All rights reserved.
## Contact: Nokia Corporation (qt-info@nokia.com)
##
## This file is part of the test suite of the Qt Toolkit.
##
## $QT_BEG... | librelab/qtmoko-test | qtopiacore/qt/doc/src/diagrams/contentspropagation/standardwidgets.py | Python | gpl-2.0 | 7,290 | [
"ASE"
] | 75a6bef2e46dc405d0feedada2de935002d0ff9cd7ca7a37ff9a720a2f8cebed |
from django.contrib.staticfiles.testing import LiveServerTestCase
from splinter import Browser
from time import sleep
from .factories import (
UserFactory, ClientFactory, CompanyFactory, CategoryFactory,
ProductFactory, QuoteFactory, QuoteModsFactory)
class LiveServerSplinterAuthTest(LiveServerTestCase):
... | Estmator/EstmatorApp | estmator_project/estmator_project/test_functional.py | Python | mit | 2,091 | [
"VisIt"
] | b3782699e764cf91aeeff4c01b5b3e6835076d402c8a809291bcdb520032545c |
#
# @file TestReadFromFile8.py
# @brief Reads test-data/l2v4-new.xml into memory and tests it.
#
# @author Akiya Jouraku (Python conversion)
# @author Sarah Keating
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generated automatic... | TheCoSMoCompany/biopredyn | Prototype/src/libsbml-5.10.0/src/bindings/python/test/sbml/TestReadFromFile8.py | Python | bsd-3-clause | 3,007 | [
"VisIt"
] | 80670763bc7f8ceffafd2e3c11054b1ab5373536e767e971327f7fb7425ca3a1 |
# -*- coding: utf-8 -*-
import json
import random
import requests
import string
from typing import Any, DefaultDict, Dict, List, Optional, Set, Tuple, Union
from collections import defaultdict
from django.db import connection
from django.conf import settings
from django.http import HttpRequest, JsonResponse
from c... | catmaid/CATMAID | django/applications/catmaid/control/common.py | Python | gpl-3.0 | 14,899 | [
"NEURON"
] | 857a5cf115d7653ee0114e5f5fc3b42173ca40aabf5ea731947a42e40acc3cda |
# Copyright (C) 2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later versio... | KaiSzuttor/espresso | testsuite/scripts/samples/test_observables_correlators.py | Python | gpl-3.0 | 1,183 | [
"ESPResSo"
] | 5b232392d333f5a517cc88a8c5db12aad659745eb2fe52e334d483c02c85509b |
# ============================================================================
#
# Copyright (C) 2007-2010 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | kurtraschke/camelot | camelot/view/plugins/onetomanyeditorplugin.py | Python | gpl-2.0 | 1,494 | [
"VisIt"
] | 249c8fc97f72086edde90d244f296da81643dc79c4475e80e872e1886a3c7359 |
import math
import numpy
import random
import operator
import types
import numpy as np
import h5py
import IPython as ipy
import os
import sys
def one_l_print(string, pad=20):
for _ in range(pad): string += ' '
string += '\r'
sys.stdout.write(string)
sys.stdout.flush()
# Define a context manager to su... | dhadfieldmenell/bootstrapping-lfd | scripts/dhm_utils.py | Python | bsd-2-clause | 24,683 | [
"Gaussian"
] | a748241fbaf1d312b2e4572f475c8129252a6de44914566683fcf6cc2b793c43 |
"""
This module implements all the functions to communicate with other Python
modules (PIL, matplotlib, mayavi, etc.)
"""
import numpy as np
def PIL_to_npimage(im):
""" Transforms a PIL/Pillow image into a numpy RGB(A) image.
Actually all this do is returning numpy.array(im)."""
return np.array(im)
... | kerimlcr/ab2017-dpyo | ornek/moviepy/moviepy-0.2.2.12/moviepy/video/io/bindings.py | Python | gpl-3.0 | 1,079 | [
"Mayavi"
] | e2048b8de383a15b3e2817360b6b92f9c18d5019e3f6fb7fc79054c02ba1259c |
# Copyright 2016 Autodesk 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.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing... | tkzeng/molecular-design-toolkit | moldesign/units/constants.py | Python | apache-2.0 | 1,717 | [
"Avogadro",
"Dalton"
] | c1357878cbc9d2b3f7f55c1cd9bfc645139857d7e178c8ed7546b3119cbcb26a |
# ______________________________________________________________________
'''Defines a bytecode based LLVM translator for llpython code.
'''
# ______________________________________________________________________
# Module imports
from __future__ import absolute_import
import opcode
import types
import logging
import l... | llvmpy/llvmpy | llpython/byte_translator.py | Python | bsd-3-clause | 23,939 | [
"VisIt"
] | ec7ebeffa289318289249117d7832dc20a214e77d94c3a0c3c3f2111d47042b0 |
#!/usr/bin/python
# Little script to convert output files from charmm/OPTIM to strict CRD format for use in VMD.
# Note that the .cor file extension is best for use with VMD, so that it doesn't get confused
# between charmm and amber. Open as "vmd newoutput.cor"
# Usage:
# <directory path>/standardize_crd.py <input... | marktoakley/LamarckiAnt | SCRIPTS/CHARMM/standardize_crd.py | Python | gpl-3.0 | 1,098 | [
"Amber",
"CHARMM",
"VMD"
] | fdd32ca70a83ed258a57c0327c373e57628700e77a0ce005a50fe5c11b7af3c6 |
"""Algorithms for spectral clustering"""
# Author: Gael Varoquaux gael.varoquaux@normalesup.org
# License: BSD
import warnings
import numpy as np
from ..base import BaseEstimator, ClusterMixin
from ..utils import check_random_state
from ..utils.graph import graph_laplacian
from ..metrics.pairwise import rbf_kernel
... | GbalsaC/bitnamiP | venv/lib/python2.7/site-packages/sklearn/cluster/spectral.py | Python | agpl-3.0 | 15,966 | [
"Gaussian"
] | d4e8b96c2af391eeb31b44555f1fb76dc078640170593e9cff2854034e21633a |
# sql/elements.py
# Copyright (C) 2005-2014 the SQLAlchemy authors and contributors
# <see AUTHORS file>
#
# This module is part of SQLAlchemy and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""Core SQL expression elements, including :class:`.ClauseElement`,
:class:`.ColumnE... | grepme/CMPUT410Lab01 | virt_env/virt1/lib/python2.7/site-packages/SQLAlchemy-0.9.8-py2.7-linux-x86_64.egg/sqlalchemy/sql/elements.py | Python | apache-2.0 | 121,469 | [
"VisIt"
] | 7098e0256c327468f0734ecc0cc0b748372066c76de9d78680f01e92d5291c66 |
# Authors: Matti Hämäläinen <msh@nmr.mgh.harvard.edu>
# Alexandre Gramfort <alexandre.gramfort@inria.fr>
#
# License: BSD-3-Clause
# Many of the computations in this code were derived from Matti Hämäläinen's
# C code.
from copy import deepcopy
from functools import partial
import os
import os.path as op
imp... | pravsripad/mne-python | mne/source_space.py | Python | bsd-3-clause | 111,172 | [
"Mayavi"
] | b6f1c3fa79b8cc3d6f32f7779b3182e03793382f44022482e04a7d7ccd201203 |
# Copyright (C) 2014 MediaMath, Inc. <http://www.mediamath.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
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appli... | MediaMath/qasino | lib/data_manager.py | Python | apache-2.0 | 15,026 | [
"BLAST"
] | 117d5ca8ec3ae577b04b2c2c2e78c41750ce60d1760c0e3cc7e62d83aabfdb4e |
# -*- coding: utf-8 -*-
##
## This file is part of Invenio.
## Copyright (C) 2011, 2012 CERN.
##
## Invenio 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 (at your opt... | jmartinm/invenio | modules/bibauthorid/lib/bibauthorid_webinterface.py | Python | gpl-2.0 | 148,619 | [
"VisIt"
] | 08bc1451d7faacddbd5ccb84fbcad19ce19585f333314938385d24fd45a9605b |
'''
'''
import os
import zipfile
import requests
import pandas as pd
import igraph as ig
from biomap import BioMap
################################################################################
# data path #
#######################################... | sebwink/deregnet | python/deregnet/graphs.py | Python | bsd-3-clause | 37,195 | [
"Cytoscape"
] | 306309795de6acc71872b0eb14f40a2860c1b83457994f2dddb014875ee54d75 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | TheTimmy/spack | var/spack/repos/builtin/packages/py-griddataformats/package.py | Python | lgpl-2.1 | 1,915 | [
"MDAnalysis"
] | e7695db0bb0c683f789ff72a3ce2f6e194d28889f450ead63df0241a6604fb25 |
# Copyright 2014 Cloudera 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.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, so... | mariusvniekerk/ibis | ibis/expr/format.py | Python | apache-2.0 | 8,773 | [
"VisIt"
] | c4dd0d0683a58b46b0a6ef99b8125f82ac678fa27e992e8c3d4886796550774a |
###############################
# 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, suc... | pylada/pylada-light | tests/vasp/extract/test_common.py | Python | gpl-3.0 | 3,615 | [
"CRYSTAL",
"VASP"
] | d4be27a91be0e95deaa93e36448d1bde504419095a19610fd207e912cd0c8037 |
import sys
import argparse
import os
import sys
sys.path.insert(0, "../../pyDataView/")
import postproclib as ppl
from misclib import Chdir
class MockHeader(object):
def __init__(self):
self.vmd_skip = 0
self.vmd_start = 0
self.vmd_end = 0
self.Nsteps = 0
self.tplot = 0
... | edwardsmith999/pyDataView | run_vmd.py | Python | gpl-3.0 | 5,515 | [
"VMD"
] | c5ffc1876cdbb6cf07921904fc536659b839572c3cdc45c6ae3a5ed7b096b33c |
from __future__ import print_function
import sys
import os
# # YUCK! scinet bonkers python setup
# paths = os.environ['PYTHONPATH']
# sys.path = paths.split(':') + sys.path
# if __name__ == '__main__':
# import matplotlib
# matplotlib.use('Agg')
'''
Forced phot of Megacam images:
python legacyanalysis/eucli... | legacysurvey/pipeline | py/legacyanalysis/euclid.py | Python | gpl-2.0 | 90,291 | [
"Galaxy"
] | 89a820c8721e570969f82fcb3e31233e1bdbc4956e15dfd54dd6072cee7cc7f0 |
# This file is part of PlexPy.
#
# PlexPy is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# PlexPy is distributed in the hope ... | Hellowlol/plexpy | plexpy/notifiers.py | Python | gpl-3.0 | 89,796 | [
"VisIt"
] | 83846daa3e8dac9ec401d3dc2aa61bcf3e75a844c0717b69d92eec2e44d50c12 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2020 University of Liège
#
# 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
#
# ... | rboman/progs | classes/sph0/louis/tests/waterdrop3.py | Python | apache-2.0 | 2,672 | [
"VTK"
] | efd398450f025f35a89fcf6204f76abe7d8e309d012df4473402f8d780f82e00 |
import scipy as SP
import numpy as NP
import scipy.linalg as LA
import scipy.optimize as opt
import scipy.stats as ST
import scipy.special as SS
from fastlmm.util.mingrid import *
from fastlmm.util.util import *
import time
import pdb
from bin2kernel import Bin2Kernel
from bin2kernel import makeBin2KernelA... | zhonghualiu/FaST-LMM | fastlmm/inference/lmm2k.py | Python | apache-2.0 | 22,357 | [
"Gaussian"
] | d343e8425d119b02d6ad76ed83c04ead117c472f2c0183806537d747c6acaa2e |
from __future__ import print_function # Python 2/3 compatibility
import boto3
import json
import decimal
# Helper class to convert a DynamoDB item to JSON.
class DecimalEncoder(json.JSONEncoder):
def default(self, o):
if isinstance(o, decimal.Decimal):
if o % 1 > 0:
return float... | data-north/datanorth-api | examples/MoviesItemOps03.py | Python | mit | 1,058 | [
"MOE"
] | 5501381ba0ef1ccbb25d814331adbb4ef27f5db95317c07c73bf48ee9e4fa1a2 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2006 Martin Hawlisch, Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2011 Michiel D. Nauta
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Pu... | Forage/Gramps | gramps/plugins/importer/importvcard.py | Python | gpl-2.0 | 19,982 | [
"Brian"
] | 632a2f319a4a95ff4bd5cc24fb8d939a6759f04c520eb6322c04b585bf57c738 |
# -*- coding: utf-8 -*-
#########################################################################
#
# Copyright (C) 2016 OSGeo
#
# 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 ... | tomkralidis/geonode | geonode/base/enumerations.py | Python | gpl-3.0 | 13,778 | [
"BWA"
] | 798d1a0c46ddc227942f39dce7d8a90b6d7bc495b8b806b19d83387504ad4fae |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# createre - [insert a few words of module description on this line]
# Copyright (C) 2003-2015 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of ... | heromod/migrid | mig/shared/functionality/createre.py | Python | gpl-2.0 | 7,612 | [
"Brian"
] | f892e807cb8a51e68d22458a12ffaea706e5d68c023a50e0442346c5269ec297 |
import unicodedata # For accents removing
import collections
import re # For checkMistakeNames function
def removeAccents(dataToTranslate):
"""Two function to remove accents, either one should work.
This is for testing which one runs faster. """
dataToTranslate = str(dataToTranslate)
return unicodedata.normalize(... | bchalala/cs145-duplicats-in-space | authorParserHelper.py | Python | gpl-3.0 | 8,217 | [
"Brian"
] | 9ee7fe21508502e82cd3979ba39ecaf4a92f092720f06681544995e5d74b8b82 |
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