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# -*- coding: utf-8 -*-
""" *==LICENSE==*
CyanWorlds.com Engine - MMOG client, server and tools
Copyright (C) 2011 Cyan Worlds, Inc.
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... | TOC-Shard/moul-scripts | Python/xOptionsMenu.py | Python | gpl-3.0 | 92,022 | [
"VisIt"
] | c6d2659e52f0beffd75c4596ea78bd79223fed7c2868915c786239938f845c7f |
# example showing how one might assembled an ordered list of atoms
# from mouse clicked through use of a PyMOL Wizard.
from pymol.wizard import Wizard
from pymol import cmd, util
import pymol
import traceback
click_sele = "_clicked"
disp_sele = "_displayed"
# Wizard class definition
def quote_blanks(st):
st = ... | gratefulfrog/lib | python/pymol/pymol_path/examples/devel/click_ordered_list.py | Python | gpl-2.0 | 3,293 | [
"PyMOL"
] | 1562497770dcdc0f1422ab33f8db72819cfc4a4d653cb57d5c80689cb0f457c2 |
#!/usr/bin/env python
# Copyright 2014-2021 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | sunqm/pyscf | pyscf/cc/gccsd.py | Python | apache-2.0 | 23,951 | [
"PySCF"
] | effaa10ae31c4721b54a4cd03c33fc27c9050f8b6463f9e0714533c4e58a53b4 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import print_function
from __future__ import unicode_literals
import sys
import json
from thehive4py.api import TheHiveApi
from thehive4py.query import *
api = TheHiveApi('http://127.0.0.1:9000', '**YOUR_API_KEY**')
def search(title, query, range, sort)... | CERT-BDF/TheHive4py | samples/test-case-search.py | Python | agpl-3.0 | 1,038 | [
"Amber"
] | 1333a51340b0a76dd8ec53ae8c7dffadbfac00a3f097c89c80358f4558a9d665 |
# import libraries
import pythonlab
import agros2d
from math import *
# interactive help hack
__pydoc_help__ = help
def __a2d_help__(obj = agros2d):
return __pydoc_help__(obj)
help = __a2d_help__
import sys
sys.path.append(pythonlab.datadir("resources/test"))
# test
def test(text, value, normal, error = 0.03):
... | hpfem/agros2d | resources/python/functions_agros2d.py | Python | gpl-2.0 | 21,377 | [
"VTK"
] | 09fbc4c6ffcd63212abf12dfb637a54c06d818e5f755558266775956c979c324 |
# copyright 2003-2011 LOGILAB S.A. (Paris, FRANCE), all rights reserved.
# contact http://www.logilab.fr/ -- mailto:contact@logilab.fr
#
# This file is part of logilab-common.
#
# logilab-common is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as publ... | esparta/logilab_common3 | visitor.py | Python | gpl-2.0 | 3,421 | [
"VisIt"
] | cf57c6b77d53af05656bf55324dccc5f1397ec012c981c05bdaab06d63c40cda |
# -*- coding: utf-8 -*-
import tensorflow as tf
import numpy as np
import collections
from typing import Callable, Dict, List
from tensorflow.keras import activations, initializers, backend
from tensorflow.keras.layers import Dropout, BatchNormalization
class InteratomicL2Distances(tf.keras.layers.Layer):
"""Comput... | miaecle/deepchem | deepchem/models/layers.py | Python | mit | 113,175 | [
"Gaussian"
] | c52537e5e1cfd6e01cc2a3305449229a47830956532e83c53694042afe65daab |
#!/usr/bin/python
#
# Copyright 2012 Google 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 a... | MindPass/Code | technique/gmail/oauth2.py | Python | gpl-3.0 | 12,477 | [
"VisIt"
] | 31b85d9986a550db7be65aa701526b7547492b0e785a70cf77807b0f718a58cd |
# -*- coding:Utf-8 -*-
"""
.. currentmodule:: pylayers.antprop.antenna
.. autosummary::
:members:
"""
from __future__ import print_function
import doctest
import os
import glob
import re
import pdb
import sys
import numpy as np
import scipy.linalg as la
import matplotlib.pylab as plt
from scipy import io
from mat... | dialounke/pylayers | pylayers/antprop/antenna.py | Python | mit | 183,073 | [
"Gaussian",
"Mayavi"
] | c840bba8e617fa074162ac4b1350df5351ae888d9d5c710ee426e49339315710 |
import pysam
from pyfaidx import Fasta
from collections import defaultdict
from datetime import datetime
from PIL import Image
from math import floor
import sys
import numpy
import copy
"""
This module takes an alignment file and produces a pileup across all alignments in a query region, and encodes the
pileup as an i... | kishwarshafin/deePore | src/utils/Pileup.py | Python | mit | 18,574 | [
"pysam"
] | c9d475a5a52b6746661e105e0f7e65af76cfc7d0f2f764c4b781be9c0b1201e1 |
#!/usr/bin/env python3
"""HNMT: Helsinki Neural Machine Translation system.
See README.md for further documentation.
"""
import gzip
import sys
import os
import inspect
import random
from pprint import pprint
# add the path to hnmt to the system path to import BLEU etc
cmd_folder = os.path.realpath(os.path.dirname(... | robertostling/hnmt | hnmt.py | Python | gpl-3.0 | 66,308 | [
"Gaussian"
] | dd1ca23dddb26242b44797365eba086b9fd2d112d914149e03fadbef3cff9642 |
""" codecs -- Python Codec Registry, API and helpers.
Written by Marc-Andre Lemburg (mal@lemburg.com).
(c) Copyright CNRI, All Rights Reserved. NO WARRANTY.
"""#"
import builtins, sys
### Registry and builtin stateless codec functions
try:
from _codecs import *
except ImportError as why:
... | grupoprog3/proyecto_final | proyecto/flask/Lib/codecs.py | Python | apache-2.0 | 37,342 | [
"FEFF"
] | 17cfeec9cd1fc661634da5c8a1576622f6adb95dcb9388b594351b840b1d5910 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import (absolute_import, division, print_function,
unicode_literals)
"""
This module provides classes and methods used to describe deformations and
strains, including ap... | aykol/pymatgen | pymatgen/analysis/elasticity/strain.py | Python | mit | 12,163 | [
"pymatgen"
] | caa24dc22fdbb04c3e04706e9e2fc82e762b25478a82e4bb56cc85f9f024b44c |
#!/usr/bin/python2.5
# Copyright (C) 2007 Google 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 la... | jonpetersen/transitfeed-1.2.12 | test/testtransitfeed.py | Python | apache-2.0 | 279,652 | [
"CASINO"
] | be3df41c080f3f2adf837570329d80a5a44acdebcbe625eacd05542320f20634 |
__author__ = 'Max Salm'
### Notes
## Ruffus will check the time-stamp order of all intermediate files, and start
## the pipeline from files whose time-stamp is later than the final output file.
## To run the pipeline afresh, either delete all intermediate and final files in the
## run dir or specify within the pipeli... | MaxSalm/pdxBlacklist | pdxBlacklist.py | Python | gpl-3.0 | 27,974 | [
"BWA",
"pysam"
] | c3c4d7d624d890cbb613818f699cd41b02292f47a3c6eb877be18ace365f0887 |
from unittest import mock
import ast
from nimoy.specification import Specification
from nimoy.ast_tools.features import FeatureRegistrationTransformer
from nimoy.ast_tools.ast_metadata import SpecMetadata
class FeatureRegistrationTransformerSpec(Specification):
@mock.patch('nimoy.ast_tools.features.FeatureBlockR... | Luftzig/nimoy | specs/nimoy/ast_tools/features_spec.py | Python | apache-2.0 | 2,961 | [
"VisIt"
] | 7298e32b1819f2fc45f212cb49d612744a0a5b57047eb762fe8937a3051c79aa |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
import os
import re
from copy import deepcopy
import time
"""
import sys
import pandas as pd
import numpy as np
from cpblUtilities.mathgraph import weightedMeanSE
def str2df(tss):
""" Read a tab-separated string as though it's a text file.
The first line must contain ... | cpbl/cpblUtilities | pandas_utils.py | Python | gpl-3.0 | 33,256 | [
"ADF"
] | 4d2db57be433a52bf1080a485c3e5d75baa5b32bacd8276944e16e1d853b93c1 |
#!/usr/bin/env python
from jasp import *
from ase import Atom, Atoms
import numpy as np
from nose import *
import shutil
import jasp as jaspmod
jaspdir = os.path.join(os.path.dirname(jaspmod.__file__))
def setup_func():
"set up test fixtures"
os.chdir(os.path.join(jaspdir, 'tests'))
if os.path.isdir('Fe-... | jboes/jasp | jasp/tests/test-read-ldau_luj.py | Python | gpl-2.0 | 1,419 | [
"ASE"
] | 10bc2418cdf9329eec109b581b23ee0076e6b3296c3bf129515aeb9f09c3df47 |
from astropy.io import fits
import numpy as np
import desimodel.focalplane
class TargetTile(object):
"""
Keeps the relevant information for targets on a tile.
Attributes:
The properties initialized in the __init__ procedure:
ra (float): array for the target's RA
dec (float): arr... | forero/desisurvey | py/desisurvey/targets.py | Python | bsd-3-clause | 9,691 | [
"Galaxy"
] | 3cdde4c56b30c914aaa050bedb349ed644247bac98766a2525458c795e5f97a2 |
# encoding: utf-8
"""
Standard base_cells for the neuron module.
:copyright: Copyright 2006-2016 by the PyNN team, see AUTHORS.
:license: CeCILL, see LICENSE for details.
"""
from pyNN.standardmodels import cells as base_cells, build_translations
from pyNN.neuron.cells import (StandardIF, SingleCompartmentTraub,
... | anupkdas-nus/global_synapses | pyNN-dispackgaes/neuron/standardmodels/cells.py | Python | gpl-3.0 | 9,077 | [
"NEURON"
] | 1551e0183dcaf0abd27b23d7a4f67f3f06fe44f256cde4136537afe4139780ad |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2007-2009 Stephane Charette
# Copyright (C) 2009 Gary Burton
# Contribution 2009 by Bob Ham <rah@bash.sh>
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2012-2013 Paul Franklin
#
# This ... | jralls/gramps | gramps/gui/plug/report/_graphvizreportdialog.py | Python | gpl-2.0 | 10,714 | [
"Brian"
] | fbca2d988bf5aeb9c67f8269d42046cea2e9aedb15318324846cf9dd67b2884e |
# -*- coding: utf-8 -*-
#
# Copyright © Spyder Project Contributors
# Licensed under the terms of the MIT License
# (see spyder/__init__.py for details)
"""
Spyder, the Scientific Python Development Environment
=====================================================
Developped and maintained by the Spyder Project
Contr... | kirichoi/tellurium | spyder_mod/Spyder 3.2.2/spyder/app/mainwindow.py | Python | apache-2.0 | 130,403 | [
"CRYSTAL"
] | d98a286d95cf66c3690e31b6e34f1079c7dc20ada6585cb21507ab3346b1eb27 |
"""Test tree and vegetation coverage."""
from __future__ import division
import os
import pytest
from uwg import UWG, solarcalcs
EPW_PATH = \
os.path.join(os.path.dirname(__file__), 'epw',
'SGP_Singapore.486980_IWEC.epw')
def test_tree_vegetation_ratio():
"""Test road vegetation fractions.... | chriswmackey/UWG_Python | tests/test_vegetation.py | Python | gpl-3.0 | 17,915 | [
"EPW"
] | b8de49323afce1bc81e2576cd9f27b772c2e6a2fbbaab35688a07a9eb42e1e30 |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | shakamunyi/beam | sdks/python/apache_beam/examples/snippets/snippets.py | Python | apache-2.0 | 43,887 | [
"VisIt"
] | e3a3b7b7e4d52e51d163e6befdc7678a01e91f824613054664c942e0095f0dd6 |
"""
A fully functional VTK widget for Tkinter that uses
vtkGenericRenderWindowInteractor. The widget is called
vtkTkRenderWindowInteractor. The initialization part of this code is
similar to that of the vtkTkRenderWidget.
Created by Prabhu Ramachandran, April 2002
"""
import Tkinter
import math, os, sys
import vt... | collects/VTK | Wrapping/Python/vtk/tk/vtkTkRenderWindowInteractor.py | Python | bsd-3-clause | 15,642 | [
"VTK"
] | 27d8a848806676f3ce25b12d10ec2f145b353976e1718bf45d615dc5aa459fc6 |
#!/usr/bin/env python2
import itertools
import json
import os
import pymongo
import pysam
import gzip
from parsing import *
import logging
import lookups
import random
import sys
from utils import *
from flask import Flask, request, session, g, redirect, url_for, abort, render_template, flash, jsonify, send_from_dire... | hms-dbmi/exac_browser | exac.py | Python | mit | 62,858 | [
"pysam"
] | 3bfe343a292ee1c7b10d34a20d57c6e3f980c8371d45f505acdeb37f0ece815e |
"""
===============================================================================
Use pysam model to calculate the AS from bam file
===============================================================================
Author : Shujia Huang
Date : 2014-03-25 14:29:08
"""
import sys
import re
import optparse
import os
impo... | ShujiaHuang/AsmVar | src/AsmvarAlterAlign/ASV_AlterAlignMain.py | Python | mit | 8,698 | [
"pysam"
] | 997440deb93f9e2c72f304150ad0f621b51b09017a03b0af1687b1fbd7bd4af8 |
# coding=utf-8
r"""
This code was generated by
\ / _ _ _| _ _
| (_)\/(_)(_|\/| |(/_ v1.0.0
/ /
"""
from tests import IntegrationTestCase
from tests.holodeck import Request
from twilio.base.exceptions import TwilioException
from twilio.http.response import Response
class ConversationTestCase(Inte... | tysonholub/twilio-python | tests/integration/conversations/v1/test_conversation.py | Python | mit | 8,622 | [
"VisIt"
] | 011d42a04ec3ec4a33c2474201290d409a86e78c79281f7317a120bbcf038dd8 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
import unittest
from webdriver_testing.webdriver_base import WebdriverTestCase
from webdriver_testing import data_helpers
from webdriver_testing.pages.site_pages import video_page
from webdriver_testing.pages.site_pages import editor_page
from webdriver_testing.pages.site_pages... | ofer43211/unisubs | apps/webdriver_testing/check_editing/test_transcribing.py | Python | agpl-3.0 | 3,018 | [
"Octopus"
] | 1e3df0efeecdad73778a80cb97f6faa430944c473776de358ef5c67df557cd97 |
# -*- coding: utf-8 -*-
"""
The :mod:`sklearn.naive_bayes` module implements Naive Bayes algorithms. These
are supervised learning methods based on applying Bayes' theorem with strong
(naive) feature independence assumptions.
"""
# Author: Vincent Michel <vincent.michel@inria.fr>
# Minor fixes by Fabian Pedre... | WangWenjun559/Weiss | summary/sumy/sklearn/naive_bayes.py | Python | apache-2.0 | 28,358 | [
"Gaussian"
] | 03fcd10cb773a83880ff845cdc5ced5105fa33f5a88e8c767f1e066e1289e9c2 |
#!/usr/bin/env python
"""
Generate plots for synthetic three-state force spectroscopy model.
"""
import bhmm
from bhmm.util.analysis import generate_latex_table
# dynamically import plotting tools
import os,sys,inspect
currentdir = os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe())))
parentdir =... | bhmm/legacy-bhmm-force-spectroscopy-manuscript | examples/p5ab-hairpin/generate-figure.py | Python | lgpl-3.0 | 2,876 | [
"NetCDF"
] | 36bb26daf8baef4d0b802175d771e57e5394691f4e22a251f1b7db12b59c8c40 |
"""
Gaussian Mixture Models.
This implementation corresponds to frequentist (non-Bayesian) formulation
of Gaussian Mixture Models.
"""
# Author: Ron Weiss <ronweiss@gmail.com>
# Fabian Pedregosa <fabian.pedregosa@inria.fr>
# Bertrand Thirion <bertrand.thirion@inria.fr>
# Important note for the deprec... | ldirer/scikit-learn | sklearn/mixture/gmm.py | Python | bsd-3-clause | 32,589 | [
"Gaussian"
] | 5fefb8338503b7064df748896c73cd2d07bda1f0b2a10179e00901582e1646c7 |
from rauth.service import OAuth1Service
linkedin = OAuth1Service(
consumer_key='tjm826j6uzio',
consumer_secret='1XbHsC7UxtC6EzqW',
name='linkedin',
request_token_url='https://api.linkedin.com/uas/oauth/requestToken',
authorize_url='https://api.linkedin.com/uas/oauth/authorize',
access_token_url... | arifgursel/rauth | examples/linkedin-updates-cli.py | Python | mit | 1,639 | [
"VisIt"
] | 0ddfc34252cded9ab41135aacfe8780682491fd1091440f5288f5fc3001b96c3 |
"""Tests for cse script.
"""
import ast
import unittest
import os
import z3
from sspam.tools import asttools, cse
class TestCSE(unittest.TestCase):
"""
Test that cse produce expected ast.
"""
def generic_basicCSE(self, instring, refstring):
'Generic test for CSE: matching of CSE AST and ref... | quarkslab/sspam | tests/test_cse.py | Python | bsd-3-clause | 4,317 | [
"VisIt"
] | 2e41656e9610736f592ef74e52563ecde9ac3049e01af4fdeb4f5eec60c6ff53 |
# This file is part of the Fluggo Media Library for high-quality
# video and audio processing.
#
# Copyright 2012 Brian J. Crowell <brian@fluggo.com>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Founda... | fluggo/Canvas | fluggo/editor/plugins/_source.py | Python | gpl-3.0 | 22,962 | [
"Brian"
] | 2169ff39b3c2ac5fb9fc1c55da100ba09d6478e9443e41b6ab9ae1facaf8ff61 |
'''
This file is part of Maxfield.
Copyright (C) 2015 by Jonathan Baker: babamots@gmail.com
GNU Public License
http://www.gnu.org/licenses/
'''
import sys
import branch_bound
np = branch_bound.np
MAX_BRANCHES = 15000
# This could be used if more splits are wanted than are possible
infState = branch_bound.InfState()
... | Hellehond/maxfield | lib/orderedTSP.py | Python | gpl-3.0 | 6,327 | [
"VisIt"
] | 059e1c47e6bbf57ac37329d46ba81b5bc98211eafaeab0f27f108b7376ba2df9 |
from __future__ import absolute_import
from collections import namedtuple
from fnmatch import fnmatch
from parsimonious.grammar import Grammar, NodeVisitor
from parsimonious.exceptions import ParseError # noqa
__all__ = ('parse_rules', 'dump_schema', 'load_schema')
VERSION = 1
# Grammar is defined in EBNF syntax.
... | ifduyue/sentry | src/sentry/ownership/grammar.py | Python | bsd-3-clause | 5,768 | [
"VisIt"
] | 96099db3be1d809102c8e3f574387c7129a9bdd944324a31d9633a6d6bc5e332 |
# encoding: utf-8
"""
Creates geometry objects from facets.
"""
from yade.wrapper import *
import utils,math,numpy
try:
from minieigen import *
except ImportError:
from miniEigen import *
#facetBox===============================================================
def facetBox(center,extents,orientation=Quaternion.Ide... | gladk/trunk | py/geom.py | Python | gpl-2.0 | 24,169 | [
"ParaView"
] | 01c575ad55079adf514ae360984bf2b54a084a208a9e91afc65c27666ed7b8d7 |
"""Classes to calibrate the z_lambda afterburner
"""
import os
import numpy as np
import fitsio
import time
import scipy.optimize
import copy
from ..configuration import Configuration
from ..redsequence import RedSequenceColorPar
from ..galaxy import GalaxyCatalog
from ..cluster import ClusterCatalog
from ..zlambda im... | erykoff/redmapper | redmapper/calibration/zlambdacal.py | Python | apache-2.0 | 14,552 | [
"Galaxy"
] | 728edd33720b324039a0f993f79ea368960b23e351ab2abf8cbad9f64f066ea9 |
from ase import Atom, Atoms
from gpaw import GPAW, FermiDirac
from gpaw.test import equal
a = 4.0
n = 16
hydrogen = Atoms([Atom('H')], cell=(a, a, a), pbc=True)
hydrogen.center()
calc = GPAW(gpts=(n, n, n), nbands=1, convergence={'energy': 1e-5},
occupations=FermiDirac(0.0))
hydrogen.set_calculator(calc)
e... | robwarm/gpaw-symm | gpaw/test/spinpol.py | Python | gpl-3.0 | 690 | [
"ASE",
"GPAW"
] | d64cf6dd1cda067699af9e5fa27ff7dd5e99839069159039bd9339df1a499e12 |
# ----------------------------------------------------------------------------
# pyglet
# Copyright (c) 2006-2008 Alex Holkner
# Copyright (c) 2008-2021 pyglet contributors
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the follo... | calexil/FightstickDisplay | pyglet/graphics/__init__.py | Python | gpl-3.0 | 29,573 | [
"VisIt"
] | 9e9bd0c533299b787da3fb1b0a3a4b23d740b3fb4719f8f0ae0cd69b01bd6f5b |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
This module contains simple statistical algorithms that are
straightforwardly implemented as a single python function (or family of
functions).
This module should generally not be used directly. Everything in
`__all__` is imported into `astropy.stats... | MSeifert04/astropy | astropy/stats/funcs.py | Python | bsd-3-clause | 60,158 | [
"Gaussian"
] | 435abd792e86407d1ce977d2ab27e390c3403e41a8a4e2d51b139f7df16bf18a |
from panda3d.core import *
from panda3d.direct import *
from toontown.toonbase.ToonBaseGlobal import *
from direct.directnotify import DirectNotifyGlobal
from direct.fsm import StateData
from direct.fsm import ClassicFSM, State
from direct.fsm import State
from direct.task.Task import Task
from ToontownMsgTypes import ... | silly-wacky-3-town-toon/SOURCE-COD | toontown/distributed/PlayGame.py | Python | apache-2.0 | 22,658 | [
"VisIt"
] | 633e839d934be293329964221b3965e07a04d9f9eb28cde16e1372b5ea182aa3 |
# -*- coding: utf-8 -*-
# Begin CVS Header
# $Source: /Volumes/Home/Users/shoops/cvs/copasi_dev/copasi/bindings/python/unittests/Test_RunSimulations.py,v $
# $Revision: 1.8 $
# $Name: $
# $Author: shoops $
# $Date: 2010/07/16 18:55:59 $
# End CVS Header
# Copyright (C) 2010 by Pedro Mendes, Virginia ... | jonasfoe/COPASI | copasi/bindings/python/unittests/Test_RunSimulations.py | Python | artistic-2.0 | 9,094 | [
"COPASI"
] | 984534707ecc37df3b76f87d5ef8e8cff4c600c38ac81d965f2ec873f717aaef |
#!/usr/bin/env python
"""
The main DIRAC installer script. It can be used to install the main DIRAC software, its
modules, web, rest etc. and DIRAC extensions.
In order to deploy DIRAC you have to provide: globalDefaultsURL, which is by default:
"http://diracproject.web.cern.ch/diracproject/configs/globalDefaults.cfg"... | fstagni/DIRAC | Core/scripts/dirac-install.py | Python | gpl-3.0 | 94,140 | [
"DIRAC"
] | 2d04f8f801da2ae40007c62a91673c587ddf8119292ee01e26a75e951f942404 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2005-2014 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU Lesser General Public License as published by
## the Free Softw... | tiagocardosos/stoq | stoqlib/domain/payment/payment.py | Python | gpl-2.0 | 23,388 | [
"VisIt"
] | 71d417b078360895211c5cd01e933b15067d705ab660389cfaa5f45f4727e135 |
""".. module:: Test_Mail
Test cases for DIRAC.Core.Utilities.DAG module.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from DIRAC.Core.Utilities.Mail import Mail
__RCSID__ = "$Id $"
def test_createEmail():
m = Mail()
res = m._create('address@d... | yujikato/DIRAC | src/DIRAC/Core/Utilities/test/Test_Mail.py | Python | gpl-3.0 | 1,669 | [
"DIRAC"
] | eddfcfec5589041463dc833ad8a371cacdb3fc0f3cf2d0220ecd4e90398c7e5a |
# coding: utf-8
#
# Copyright 2012 NAMD-EMAP-FGV
#
# This file is part of PyPLN. You can get more information at: http://pypln.org/.
#
# PyPLN 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 o... | NAMD/pypln.api | tests/test_pypln.py | Python | gpl-3.0 | 22,401 | [
"NAMD"
] | 747b2fba36adc8c909d645cbbb0982428517c7e5aa6c08ee71bfe2c9da756198 |
##############################################################################
# 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-alpine/package.py | Python | lgpl-2.1 | 2,390 | [
"Bioconductor"
] | b3aa5775be43fa4dde27c9a504f49350f859dc84c111d374b2b2c0685439a180 |
# vim: tabstop=4 shiftwidth=4 softtabstop=4
# Copyright 2011 Rackspace
# Copyright (c) 2011 X.commerce, a business unit of eBay Inc.
# Copyright 2013 IBM Corp.
# 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. Y... | yrobla/nova | nova/tests/network/test_manager.py | Python | apache-2.0 | 114,349 | [
"FEFF"
] | 1b81d547a7215e3a10df0b875cb699b86a4c754590b0bc4c8dfa2e0aceff9882 |
from eqep.interpolation.pgvinterpolator import PGVInterpolator
from scipy.interpolate import Rbf
class RbfPGVInterpolator(PGVInterpolator):
"""A `Radial Basis Function` pgv interpolation algorithm implementation
Attributes
----------
function : str
the type of algebraic function to use for i... | TGM-HIT/eqep-api | eqep/interpolation/rbf_pgvinterpolator.py | Python | mit | 1,121 | [
"Gaussian"
] | 9028a4533b80f99675ddd7295c7ed09024ea31ddeb9484d090f67e2cdfc19d1f |
import numpy as np
from qharv.seed import xml
# ======================= level 0: basic input ======================
def barostat(taup, taut):
baro = xml.make_node('barostat', {'mode': 'isotropic'})
cell_thermo = xml.make_node('thermostat', {'mode': 'langevin'})
tnode = xml.make_node('tau', {'units': 'femtosecond... | Paul-St-Young/solid_hydrogen | qharv_db/ipi_md.py | Python | mit | 9,719 | [
"ASE"
] | c1f6d7d8c0cb26fd94444a51fd9664d518185171ead940fe6fdba160a6365b39 |
# -*- coding: utf-8 -*-
from __future__ import absolute_import
from django.conf import settings
from django.test import TestCase
from zilencer.models import Deployment
from zerver.models import (
get_realm, get_user_profile_by_email,
PreregistrationUser, Realm, Recipient, ScheduledJob, UserProfile, UserMessag... | dwrpayne/zulip | zerver/tests/test_signup.py | Python | apache-2.0 | 21,981 | [
"VisIt"
] | 53dc5eaaf4127c62574c19aa0c77206a299ae31c66615c84663a1720f09b5a46 |
"""
Copyright (C) <2010> Autin L. TSRI
This file git_upy/cinema4d/r13/c4dHelper.py is part of upy.
upy 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, o... | corredD/upy | cinema4d/r13/c4dHelper.py | Python | gpl-3.0 | 173,067 | [
"Amber"
] | 76da1449b908ee54b3b7ee6008ebb794f352d17ed66d166e72fee804618c1096 |
# Copyright (c) 2000 Autonomous Zone Industries
# This file is licensed under the
# GNU Lesser General Public License v2.1.
# See the file COPYING or visit http://www.gnu.org/ for details.
__revision__ = "$Id: loggedthreading.py,v 1.6 2003/02/23 16:18:30 myers_carpenter Exp $"
# standard modules
from threadin... | zooko/egtp_new | egtp/loggedthreading.py | Python | lgpl-2.1 | 1,131 | [
"VisIt"
] | 6f26bd3383e9e3ea0718a89c3c07e2ac5abda2250f50f6115414c87730149cbe |
# First a documentation string to describe the example
"""An example script demonstrating an NVT MD simulation with Asap.
This example runs a molecular dynamics simulation on a small copper
cluster in the NVT ensemble, i.e. with constant particle number,
constant volume and constant temperature. It uses Langevin dyna... | auag92/n2dm | Asap-3.8.4/Examples/MD_Cluster.py | Python | mit | 2,833 | [
"CRYSTAL"
] | 982fdf80af59a3f9a4b3eebd0a843928cc0c747eaf54512b1eed6a327e5e2029 |
# $HeadURL: $
'''
:mod: Utils
Module that collects utility functions.
'''
import fnmatch
from DIRAC import gConfig, S_OK
from DIRAC.Core.Utilities import List
from DIRAC.ConfigurationSystem.Client.Helpers.Operations import Operations
__... | Sbalbp/DIRAC | ResourceStatusSystem/Utilities/Utils.py | Python | gpl-3.0 | 3,106 | [
"DIRAC"
] | dae11170f39e5c10da7de9e6eef43cecc6a80bc1595b1cc5bf311858ea458b84 |
#!/usr/local/bin/env python
#
# =============================================================================================
# FILE DOCSTRING
# =============================================================================================
"""
Automated selection and imposition of receptor-ligand restraints for absolu... | andrrizzi/yank | Yank/restraints.py | Python | mit | 45,619 | [
"MDTraj",
"OpenMM"
] | 047079c9c9d0cbc84c8f9ceafb2b7ef6f64a1951289a7114452dff50270aef29 |
#!/usr/bin/env python
import numpy
from minihmm import *
from minihmm.factors import *
from minihmm.represent import *
from numpy.testing import (
assert_array_equal,
assert_almost_equal,
)
from nose.tools import (
assert_equal,
assert_true,
assert_dict_equal,
assert_list_equal,
assert_tup... | joshuagryphon/minihmm | minihmm/test/common.py | Python | bsd-3-clause | 2,824 | [
"CASINO"
] | 31403416e81fe24ab8a7dd9f7826cdb2c14a863a9bbab0fd8952d7a065882933 |
from scipy import sparse
import numpy as np
import networkx as nx
import warnings
def affinity_view(A, C, D, L):
Dinv2 = D.copy()
Dinv2.data = Dinv2.data ** (-.5)
Q = Dinv2 * L * Dinv2
eigvals, vec = sparse.linalg.eigsh(Q, k=3, which='SM')
_, x, y = (Dinv2 * vec).T
return x, y
def processing... | jni/spectral-graphs | sparse_spectral_graph.py | Python | mit | 3,513 | [
"NEURON"
] | 762b9b1f1771a29f6e99b497d96fd1e84987ec99df16595530d9442b76ad6cef |
# -*- coding: utf-8 -*-
## Sid Meier's Civilization 4
## Copyright Firaxis Games 2005
#import string
#from time import time
#from copy import deepcopy
from threading import Timer
import re
from CvPythonExtensions import *
import CvUtil
from CvWBDesc import CvPlayerDesc
import Popup as PyPopup
import ScreenInput
impor... | YggdrasiI/PBStats | PB Mod_v9/Assets/Python/Screens/CvModUpdaterScreen.py | Python | gpl-2.0 | 23,612 | [
"VisIt"
] | 5500252cace527597ed3189565fe2508eb2dcbf90b2b44b9ed81298cf7a36b33 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2012 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundati... | andrebellafronte/stoq | stoqlib/gui/test/test_sintegra_dialog.py | Python | gpl-2.0 | 2,544 | [
"VisIt"
] | c8eba306168641a50693b645f41d1e71f9071a7e940329a9aa59a9aea9bb4adb |
# This file is part of project Sverchok. It's copyrighted by the contributors
# recorded in the version control history of the file, available from
# its original location https://github.com/nortikin/sverchok/commit/master
#
# SPDX-License-Identifier: GPL3
# License-Filename: LICENSE
import numpy as np
from mathuti... | DolphinDream/sverchok | utils/surface/data.py | Python | gpl-3.0 | 10,586 | [
"Gaussian"
] | 7c6c9ee02a80f0765777557e6d7852bc33040b9e8d3111d4d5ba5ac5a2d5add5 |
##############################################################################
# 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/psi4/package.py | Python | lgpl-2.1 | 4,596 | [
"Psi4"
] | 33ffe1d4e7073597f349bf8443df0135a3810867900ee70933f54f7802dc1ba0 |
#! /usr/bin/python
# -*- coding: utf-8 -*-
#
# Vladimír Slávik 2011
# Python 2.6
#
# for Simutrans
# http://www.simutrans.com
#
# code is public domain
#
#
# creates a climate chart for trees
#-----
from __future__ import print_function
#-----
paksize = 128 # default only
font_name = "Verdana"
font_size = 1... | hdomos/pak128 | tools/report-trees.py | Python | artistic-2.0 | 4,390 | [
"VisIt"
] | 55c3d24dc6a0f0bf490814897c2b65bd305464215c30ede2d2462b395c422de1 |
"""
This file is a prebuilt library to wrap splinter. It goes with the environments.py
You can use it to quickly setup tests using only feature files. For more splinter documentation
visit their site at http://splinter.cobrateam.info/
The browser object you would use in splinter is available via context.browser
It is ... | mc706/behave-web-seed | features/steps/web.py | Python | mit | 7,333 | [
"VisIt"
] | 2f9e9aca9c720a0ef434f1443fb25348e2e440ba198a3257f354b152081d9efd |
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2006-2014, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public version 2.1 or l... | Clyde-fare/cclib | src/cclib/method/population.py | Python | lgpl-2.1 | 3,257 | [
"cclib"
] | 89eb1f6b4211157e41710ecb739720f99ea56e16fa914fa393653897c08b5226 |
# 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 | smu/geometry/reconcile_dupes.py | Python | apache-2.0 | 4,217 | [
"RDKit"
] | ce936c12d66897a4ca4e2bd412367328f3e93049522c3eb7da67b0bf1d9c7f87 |
import errno
import os
import sys
import shutil
import platform
import sysconfig
from os.path import abspath, exists, join, split
from setuptools import setup, Extension
from setuptools.command.build_ext import build_ext
def prepend_variables(args, variables):
for var in variables:
temp = os.getenv(var)
... | copasi/COPASI | copasi/bindings/python/setup.py | Python | artistic-2.0 | 10,686 | [
"COPASI"
] | f4d9d9c38dc09e52143657816b14695e786bab51df84340bd6ae7a1086e9b046 |
"""
It is a helper module used to create a certain plot...
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from DIRAC import S_OK, S_ERROR
__RCSID__ = "$Id$"
def _convertToSeconds(interval):
"""
Converts number of minutes, hours, days, weeks,... | ic-hep/DIRAC | src/DIRAC/MonitoringSystem/private/DBUtils.py | Python | gpl-3.0 | 4,976 | [
"DIRAC"
] | 9da26ea15cd74942de9e0b142ea653e4f950373525789fc1efc6da586c01bc89 |
#########################################################################################
# SLURM.py
# 10.11.2014
# Author: A.T.
#########################################################################################
""" SLURM.py is a DIRAC independent class representing SLURM batch system.
SLURM objects are use... | chaen/DIRAC | Resources/Computing/BatchSystems/SLURM.py | Python | gpl-3.0 | 6,522 | [
"DIRAC"
] | a6455a5ef443e25a7606c307269eb430b23d5bfbf277bbd90e77046bb8a832c9 |
# Copyright 2008-2015 Nokia Solutions and Networks
#
# 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 l... | fingeronthebutton/RIDE | src/robotide/lib/robot/model/testsuite.py | Python | apache-2.0 | 5,467 | [
"VisIt"
] | 9f986d9e2a1f755da58f42c4e940d48c19121ef8a3e81b8a2af9021b34153ca1 |
#!/usr/bin/env python
# Given an assembly file of genomic DNA and a file containing target proteins:
# 1. Use exonerate to determine hits for each contig.
# 2. Load contigs into a Biopython seqRecord dictionary.
# 3. For each protein hit, create a FASTA file with all contigs.
# a. The contigs will ... | mossmatters/HybPiper | exonerate_hits.py | Python | gpl-3.0 | 30,893 | [
"Biopython"
] | e4f06f67b18b0b9bb22418111831f5d028e81ff17e14181e9fecdfdcafa06dc3 |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
Besancon Query Tool
-------------------
A tool to query the Besancon model of the galaxy
http://model.obs-besancon.fr/
:Author: Adam Ginsburg (adam.g.ginsburg@gmail.com)
"""
from astropy import config as _config
class Conf(_config.ConfigNamespace):
... | ceb8/astroquery | astroquery/besancon/__init__.py | Python | bsd-3-clause | 1,300 | [
"Galaxy"
] | 4379f790e7ec21c4ab4e36bfa4dd5eeb98f7f404431dbf301d41dfd6969bb203 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides utilities for basic math operations.
"""
import collections
import numpy as np
def abs_cap(val, max_abs_val=1):
"""
Returns the value with its absolute value capped at max_... | gVallverdu/pymatgen | pymatgen/util/num.py | Python | mit | 4,708 | [
"pymatgen"
] | 3a10de08f5a1fc3eb103ef10742ccf9863b26648a87a1f8f0570fe0def77de3d |
from .openmm import *
from .pyscf import *
from .models import *
from .toys import *
from .amber import *
from .openbabel import *
| tkzeng/molecular-design-toolkit | moldesign/models/__init__.py | Python | apache-2.0 | 132 | [
"Amber",
"OpenMM",
"PySCF"
] | 4adad92bac666105276f767d8006148fd6b14b7beca329f50b923ca076de24f5 |
# Open3D: www.open3d.org
# The MIT License (MIT)
# See license file or visit www.open3d.org for details
import numpy as np
from open3d import *
if __name__ == "__main__":
print("Load a ply point cloud, print it, and render it")
pcd = read_point_cloud("tree815.pcd")
print(pcd)
print(np.asarray(pcd.poi... | ismethr/Code | Python4test/hello.py | Python | mit | 1,314 | [
"VisIt"
] | 878f7767a8cb7ca938aedd7a58e1cc96bd80e8b67d30bbf28c48e26083b17c00 |
# coding: utf-8
"""
Vericred API
Vericred's API allows you to search for Health Plans that a specific doctor
accepts.
## Getting Started
Visit our [Developer Portal](https://developers.vericred.com) to
create an account.
Once you have created an account, you can create one Application for
Production and an... | vericred/vericred-python | vericred_client/models/formulary_drug_package_response.py | Python | apache-2.0 | 13,702 | [
"VisIt"
] | 1a0ae23baa2e959a5b712f3adaa732d145da4d11c346ca2f536c4d99e742e3ff |
# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | jendap/tensorflow | tensorflow/python/autograph/core/converter.py | Python | apache-2.0 | 19,063 | [
"VisIt"
] | 226318ddfd7c85b7a3a9c128b5b17a57ff75d5c88b47e0edf27efcb418e306d6 |
import os
_class_names = ["tench, Tinca tinca",
"goldfish, Carassius auratus",
"great white shark, white shark, man-eater, man-eating shark, Carcharodon carcharias",
"tiger shark, Galeocerdo cuvieri",
"hammerhead, hammerhead shark",
"electr... | JesseLivezey/sklearn-theano | sklearn_theano/feature_extraction/caffe/googlenet_class_labels.py | Python | bsd-3-clause | 40,814 | [
"Bowtie",
"ESPResSo",
"Jaguar",
"ORCA"
] | cc5a1f542bc6a43c3fc1a721c823f3c29c03cb3e4a3ba55cc9a85839a082ff82 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# (c) 2013, Jeroen Hoekx <jeroen.hoekx@dsquare.be>, Alexander Bulimov <lazywolf0@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 So... | smashwilson/ansible-modules-extras | system/lvol.py | Python | gpl-3.0 | 8,178 | [
"Firefly"
] | 2cbddab8993fc3930c0e3052dc6a6464fc8e8eb19d9ed2ddca563f76d19f3cee |
from math import pi,sqrt
from itertools import izip
import numpy as np
from gpaw.utilities import hartree
from gpaw.utilities.blas import gemmdot
from gpaw.atom.all_electron import AllElectron
from gpaw import extra_parameters
from gpaw.sphere.lebedev import weight_n, R_nv
def get_scaled_positions(atoms, positions)... | qsnake/gpaw | gpaw/utilities/kspot.py | Python | gpl-3.0 | 8,239 | [
"ASE",
"GPAW"
] | 2d7d517f8e0703f4a466a0c20281c98def978c8bb8f159fa5335278860ca8c28 |
from __future__ import absolute_import
from __future__ import division
import tensorflow as tf
import numpy as np
from six.moves import range
from datetime import datetime
def zero_nil_slot(t, name=None):
"""
Overwrites the nil_slot (first row) of the input Tensor with zeros.
The nil_slot is a dummy slo... | DineshRaghu/dstc6-track1 | src/memn2n/memn2n_dialog.py | Python | gpl-3.0 | 11,303 | [
"Gaussian"
] | 85f494f682edefdb49483e3a2b54d90eb3718a7938e2380dfc1ea51bcc0b1845 |
#
# Copyright (C) 2000-2008 greg Landrum
#
""" code for dealing with forests (collections) of decision trees
**NOTE** This code should be obsolete now that ML.Composite.Composite is up and running.
"""
import cPickle
import numpy
from rdkit.ML.DecTree import CrossValidate,PruneTree
class Forest(object):
"""a for... | rdkit/rdkit-orig | rdkit/ML/DecTree/Forest.py | Python | bsd-3-clause | 8,019 | [
"RDKit"
] | be657bb5f427388378aed0156f77e6a62cc4597e932367565e621baaf8c5f892 |
"""Timeseries plotting functions."""
from __future__ import division
import numpy as np
import pandas as pd
from scipy import stats, interpolate
import matplotlib as mpl
import matplotlib.pyplot as plt
from .external.six import string_types
from . import utils
from . import algorithms as algo
from .palettes import c... | Lx37/seaborn | seaborn/timeseries.py | Python | bsd-3-clause | 15,218 | [
"NEURON"
] | e36b3226e010ae207dfd05a821ee8a8f16cbaeaae86b4add9ffe33d355eb41b3 |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
This module contains functions for computing robust statistics using
Tukey's biweight function.
"""
import numpy as np
from .funcs import median_absolute_deviation
from ..utils.decorators import deprecated_renamed_argument
__all__ = ['biweight_loc... | funbaker/astropy | astropy/stats/biweight.py | Python | bsd-3-clause | 23,570 | [
"Gaussian"
] | 225e38e7a4c0605b81d127f43f389a0447b09816acc9bce09a64bc11b17cc043 |
#!/usr/bin/env python
# CREATED:2013-03-11 18:14:30 by Brian McFee <brm2132@columbia.edu>
# unit tests for librosa.onset
from __future__ import print_function
from nose.tools import raises, eq_
# Disable cache
import os
try:
os.environ.pop('LIBROSA_CACHE_DIR')
except:
pass
import matplotlib
matplotlib.use('... | Cortexelus/librosa | tests/test_onset.py | Python | isc | 7,748 | [
"Brian"
] | 30468e1f8e4889785e27f5ed6da9ad4b548c0a1a454f81c2630dba90ed02fdba |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | CDSherrill/psi4 | psi4/driver/p4util/writer.py | Python | lgpl-3.0 | 8,109 | [
"Psi4"
] | 781b570765876aede3b9f22b518675dc0e54a91c3bffa96cf7c6463fe3764e09 |
import os
import random
import string
from itertools import izip
import numpy as np
import numpy.lib.recfunctions as nprf
from nanonet.fast5 import Fast5
from nanonet.segment import segment
from nanonet.eventdetection.filters import minknow_event_detect
from nanonet.util import all_nmers
def padded_offset_array(arr... | nanoporetech/nanonet | nanonet/features.py | Python | mpl-2.0 | 11,873 | [
"NetCDF"
] | 6f7106f18129779569a75c019576686528a767d5e23065d37cf5a1879d187c00 |
#===============================================================================
#
# AnalyseSynapse.py
#
# This file is part of ANNarchy.
#
# Copyright (C) 2013-2016 Julien Vitay <julien.vitay@gmail.com>,
# Helge Uelo Dinkelbach <helge.dinkelbach@gmail.com>
#
# This program is free software: you ca... | vitay/ANNarchy | ANNarchy/parser/AnalyseSynapse.py | Python | gpl-2.0 | 21,146 | [
"NEURON"
] | 0d25dca52a60532410661dff2b551e196dbac412105a07d2d5aa6e174aaa2eb9 |
# coding=utf-8
# Copyright 2022 The Uncertainty Baselines 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 ap... | google/uncertainty-baselines | uncertainty_baselines/models/wide_resnet_hetsngp.py | Python | apache-2.0 | 11,545 | [
"Gaussian"
] | c3a67821a33bd8de980e27a4e65e02447287771868cb0b94f43b952459db1915 |
"""This module defines an ASE interface to NWchem
http://www.nwchem-sw.org/
"""
import os
import numpy as np
from ase.atoms import Atoms
from ase.units import Hartree, Bohr
from ase.io.nwchem import write_nwchem
from ase.calculators.calculator import FileIOCalculator, Parameters, ReadError
class KPoint:
def __... | alexei-matveev/ase-local | ase/calculators/nwchem.py | Python | gpl-2.0 | 10,634 | [
"ASE",
"Gaussian",
"NWChem"
] | a01c4e04ad20cf9d7096e489d8be33eccb92012c98d51b4fde75eedb36658bc2 |
'''getting started with diffusions, continuous time stochastic processes
Author: josef-pktd
License: BSD
References
----------
An Algorithmic Introduction to Numerical Simulation of Stochastic Differential
Equations
Author(s): Desmond J. Higham
Source: SIAM Review, Vol. 43, No. 3 (Sep., 2001), pp. 525-546
Published... | hlin117/statsmodels | statsmodels/sandbox/tsa/diffusion.py | Python | bsd-3-clause | 18,732 | [
"Desmond"
] | c16e9840ba1af274d470799c9b7024dece4d461fccf5325aa959783fb12d4da4 |
#Import necessary modules for movie animation
from scipy.io.netcdf import *
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.animation as an
#Open NETCF file and read in data as file f
f=netcdf_file('trajectory.nc','r')
position=f.variables['position'][:]
time=f.variables['timepoints'][:]
#Crea... | lwjohnst86/studyGroup | lessons/python/matplotlib/hwk3.2.py | Python | apache-2.0 | 928 | [
"NetCDF"
] | c9dacca67159b590975226c4837b55185038810df548a8494835e96bbea760e1 |
from .element import Element
from ase import Atoms as ase_Atoms
from hotbit.atoms import Atoms
import numpy as np
import hotbit.auxil as aux
import box.mix as mix
from numpy.linalg.linalg import norm
from ase.units import Hartree,Bohr
from os import environ,path
from weakref import proxy
from copy import copy, deepcopy... | pekkosk/hotbit | hotbit/elements.py | Python | gpl-2.0 | 20,144 | [
"ASE"
] | 9573cd0639d7101eebb6ec7c2586e4d8b90566bb148176d9b32afaab06ac1a87 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import unittest
import os
import json
import numpy as np
from pymatgen import Lattice, Structure, Specie
from pymatgen.transformations.standard_transformation... | matk86/pymatgen | pymatgen/transformations/tests/test_advanced_transformations.py | Python | mit | 15,626 | [
"VASP",
"pymatgen"
] | f9d5d25c7bea74da3ad867b0bd122c5def0ebf571b61df5fc8beba41226f2536 |
# 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... | kkreis/espressopp | src/PLogger.py | Python | gpl-3.0 | 1,856 | [
"ESPResSo"
] | 09cf4c7fc19b14a5802cd7396899f7bf6ce43fb553a46940f03d7e8a96bea2cf |
import binascii
import logging
import os
import tornado.web
import tornado.wsgi
from tornado.web import url
from google.appengine.api import memcache
from google.appengine.ext import db
from google.appengine.ext.webapp.util import run_wsgi_app
import counter
import forms
import models
import uimodules
import util
#... | haldun/optimyser2 | optimyser/app.py | Python | mit | 7,103 | [
"VisIt"
] | ca55e0a05571af7e05f13ffb8cf4dae7db02154f9cfe9c5356894e6985ef3b9b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Create a complete structure dump of the database."""
from __future__ import unicode_literals
import logging
import sys
PY3 = sys.version > '3'
if not PY3:
from future.builtins import open
logging.basicConfig(format='%(asctime)s %(levelname)s %(message)s',
... | MartinThoma/write-math | tools/db_dump.py | Python | mit | 8,176 | [
"MOOSE"
] | b75ebf305b449d047f0241f18b7775c06e29d79a265d4f96a271c2ee7857f3b7 |
#!/usr/bin/python
# snavtofamix parses SourceNavigator's database to generate CDIF exchange files
# of the FAMIX source code meta model.
# Copyright (C) 2006 Bart Van Rompaey
#
# This file is part of snavtofamix.
#
# snavtofamix is free software; you can redistribute it and/or modify
# it under the terms of the GNU Gen... | carvalhomb/tsmells | fetch/src/snavtofamix/src/common/famix/cdifWriter.py | Python | gpl-2.0 | 21,736 | [
"MOOSE"
] | 3b1ef1c5bea3e6a2bafc90f40da82955e84110ed71dff9c02529d145b22e5314 |
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