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from cached_property import cached_property
from threedigrid.admin.constants import NO_DATA_VALUE
from ThreeDiToolbox.datasource.base import BaseDataSource
from ThreeDiToolbox.datasource.result_constants import LAYER_OBJECT_TYPE_MAPPING
from ThreeDiToolbox.datasource.result_constants import SUBGRID_MAP_VARIABLES
from T... | nens/threedi-qgis-plugin | datasource/threedi_results.py | Python | gpl-3.0 | 16,398 | [
"NetCDF"
] | 6a4e71c97e311e2ee01978221f6c123430c46ea615b66bdc54da7d2efeb96d60 |
#pylint: disable=missing-docstring
#* 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/... | harterj/moose | python/chigger/observers/__init__.py | Python | lgpl-2.1 | 467 | [
"MOOSE"
] | 53d103968c91c8713bd6eb327ca294b1b3b5f9237199bffa23978cf34343134a |
# coding: utf-8
"""
Acceptance tests for licensing of the Video module
"""
from __future__ import unicode_literals
from nose.plugins.attrib import attr
from ..studio.base_studio_test import StudioCourseTest
#from ..helpers import UniqueCourseTest
from ...pages.studio.overview import CourseOutlinePage
from ...pages.lms... | tiagochiavericosta/edx-platform | common/test/acceptance/tests/video/test_video_license.py | Python | agpl-3.0 | 4,732 | [
"VisIt"
] | 0b24c247888854c71ea180acc1fa2f0e368a1a85b088472d23941872d5f2fa2a |
""" Test for various numpy_interface modules. Main goal is to test
parallel algorithms in vtk.numpy_interface.algorithms."""
import sys
try:
import numpy
except ImportError:
print "Numpy (http://numpy.scipy.org) not found.",
print "This test requires numpy!"
sys.exit(0)
import vtk
from vtk.test import... | msmolens/VTK | Parallel/MPI4Py/Testing/Python/TestParallelNumpy.py | Python | bsd-3-clause | 9,778 | [
"VTK"
] | c098ef90489ea077483b6c268a17c6f2b25ce8e042c6c939f10db14a6aaf75b7 |
# (c) 2017, Brian Coca <bcoca@redhat.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 License, or
# (at your option) any later version.
... | maartenq/ansible | lib/ansible/utils/module_docs_fragments/decrypt.py | Python | gpl-3.0 | 999 | [
"Brian"
] | cdd802efa28c87d59d18e0c8b1ace6a1b32677eade505d8e642ba9f390071d76 |
'''
Created on Aug 5, 2014
@author: gearsad
'''
import vtk
class InteractorSuperclass(vtk.vtkInteractorStyle):
'''
Inherit the VTK class vtkInteractorStyleUser and build a superclass for all cameras.
Ref: http://www.vtk.org/doc/nightly/html/classvtkInteractorStyleUser.html#details
Important detai... | GearsAD/semisorted_arnerve | arnerve/scene/InteractorSuperclass.py | Python | mit | 2,546 | [
"VTK"
] | 3a12f6c3c478b8a9142678221a8740ef15a75eb6e17fe164d35377fa020c7646 |
import cPickle
import gzip
import os, sys, errno
import time
import math
# numpy & theano imports need to be done in this order (only for some numpy installations, not sure why)
import numpy
#import gnumpy as gnp
# we need to explicitly import this in some cases, not sure why this doesn't get imported with numpy its... | ashmanmode/TTSDNNRepo | src/work_in_progress/run_merlin_v2.py | Python | apache-2.0 | 58,790 | [
"NEURON"
] | bb713b78407dcc7bc11cb8568218b824c13336e9d31e08224dd790646843c05b |
import numpy as np
class Activation:
def __call__(self, incoming):
raise NotImplementedError
def delta(self, incoming, outgoing, above):
"""
Compute the derivative of the cost with respect to the input of this
activation function. Outgoing is what this function returned in th... | danijar/layered | layered/activation.py | Python | mit | 4,202 | [
"NEURON"
] | 78decc59f7dc4953eb796277348fb8f3e438ba72f162a384b5d4cfa961eff9b4 |
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | gkc1000/pyscf | pyscf/nao/test/test_0024_sv_after_gpaw_nao.py | Python | apache-2.0 | 2,066 | [
"ASE",
"GPAW",
"PySCF"
] | 7e705c1b484f221eaffc6fc9f858abd12fa2ede8c19c14b2a9821088623e4fce |
"""In-memory representation of interfaces and other data structures.
The objects in this module are used to build a representation of an XML interface
file in memory.
@see: L{reader} constructs these data-structures
@see: U{http://0install.net/interface-spec.html} description of the domain model
@var defaults: Defau... | afb/0install | zeroinstall/injector/model.py | Python | lgpl-2.1 | 16,940 | [
"VisIt"
] | 639fb6bcd7a9bd49d66db8bf7455f266166b45fd346d22ce5265b0ff085d6a29 |
#!/usr/bin/python
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses... | ptisserand/ansible | lib/ansible/modules/network/avi/avi_healthmonitor.py | Python | gpl-3.0 | 7,365 | [
"VisIt"
] | 779591c7a647f8f56fd0fb49577ab09070a87460964f4261877835e7cb637128 |
#!/usr/bin/python
# -*- coding: UTF-8 -*-
#Copyright (C) 2007 Adam Spencer - Free Veterinary Management Suite
#This program is free software; you can redistribute it and/or
#modify it under the terms of the GNU General Public License
#as published by the Free Software Foundation; either version 2
#of the Lice... | cyncyncyn/evette | languagefiles/language_blank_1.3.2.py | Python | gpl-2.0 | 65,018 | [
"VisIt"
] | 36968a26cd0d6cbbaba79ce5e04a353fa1a438417c235b5c0d54f27d74081014 |
#
# @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/endorsed_plugins.py | Python | lgpl-3.0 | 1,499 | [
"Psi4"
] | c69cb69bb9e0c133238162480181b09cf451ea52cd38da7729c92969cc61f641 |
# Copyright (c) 2012-2015 The GPy authors (see AUTHORS.txt)
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import numpy as np
from scipy import stats,special
import scipy as sp
from . import link_functions
from ..util.misc import chain_1, chain_2, chain_3, blockify_dhess_dtheta, blockify_third, blockify_h... | befelix/GPy | GPy/likelihoods/likelihood.py | Python | bsd-3-clause | 35,968 | [
"Gaussian"
] | ca8a5b003f7dd5f883f6d7b9eba10e9c54df85c94804862993f27a32da08885a |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements an interface to the Henkelmann et al.'s excellent
Fortran code for calculating a Bader charge analysis.
This module depends on a compiled bader executable available in the path.
Please download the ... | vorwerkc/pymatgen | pymatgen/command_line/bader_caller.py | Python | mit | 22,902 | [
"VASP",
"pymatgen"
] | e022f3ecf984d1c6ce40f15637fc501c95cd1095859e35ceb5d253eea5f5a366 |
# -*- coding: utf-8 -*-
'''
*******************************************************************
* File: readSBML.py
* Description:
* Author: HarshaRani
* E-mail: hrani@ncbs.res.in
* This program is part of 'MOOSE', the
* Messaging Object Oriented Simulation Environment,
* also known as GEN... | dharmasam9/moose-core | python/moose/SBML/readSBML.py | Python | gpl-3.0 | 48,108 | [
"Avogadro",
"MOOSE"
] | 7df5f5e4cd6b8d49dbae168747d95b3136b6cb4a4c8a4d3b962e6f3b361b58b6 |
# Prepares a directory of ligand mol2 (sybyl atom types) and a
# a directory of receptor pqr (amber atom types) files
# for AMBER and AlGDock
# Run from the [TARGET]/ directory
# Constants
job_block = 10
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('--ligand_in', default='ligand/doc... | luizcieslak/AlGDock | Pipeline/run_prep_ligand_and_complex_for_AlGDock.py | Python | mit | 6,898 | [
"Amber"
] | a42aad618873e6e92b1fee80d480bfc1fae31e8d90f3b36f189907d671b025e7 |
# Copyright 2018 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | chemelnucfin/tensorflow | tensorflow/contrib/distributions/python/ops/seed_stream.py | Python | apache-2.0 | 8,660 | [
"Gaussian"
] | ad29e5e5381a730e0418bf046c6311f65d9e4c65c52d79e5e307b7aaecc87b8d |
# Copyright 2009 by Bartek Wilczynski. All rights reserved.
# Revisions copyright 2009 by Peter Cock.
# 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.
"""Motif command line tool wrappers."""
from ._xx... | zjuchenyuan/BioWeb | Lib/Bio/motifs/applications/__init__.py | Python | mit | 352 | [
"Biopython"
] | 78c24160037a57f45a0d25fe8b3c000e1ab155495070c5274dd5435ed050bd34 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""Wrappers for ABINIT main executables"""
import os
import numpy as np
from io import StringIO
from monty.string import list_strings
import logging
logger = logging.getLogger(__name__)
__author__ = "Matteo G... | dongsenfo/pymatgen | pymatgen/io/abinit/wrappers.py | Python | mit | 14,153 | [
"ABINIT",
"pymatgen"
] | 59469ecf59196b33dc1e5f531a041397a9884f04af7e06b9d20371a030789bdf |
""" This module contains functions for calculating single-ifo ranking
statistic values
"""
import numpy
def effsnr(snr, reduced_x2, fac=250.):
"""Calculate the effective SNR statistic. See (S5y1 paper) for definition.
"""
snr = numpy.array(snr, ndmin=1, dtype=numpy.float64)
rchisq = numpy.array(reduce... | ahnitz/pycbc | pycbc/events/ranking.py | Python | gpl-3.0 | 7,576 | [
"Gaussian"
] | 6cc0e5dcddd87a5bfc5580451b291104b74912b4b09ea1b8ac6b6a015bf427f0 |
"""
========================================================================
Compare PAC of two experimental conditions with cluster-based statistics
========================================================================
This example illustrates how to statistically compare the phase-amplitude
coupling results comin... | EtienneCmb/tensorpac | examples/stats/plot_compare_cond_cluster.py | Python | bsd-3-clause | 4,081 | [
"Gaussian"
] | fb49bdc1cf0b22a2494fbf5ea48883c6774d7c041f863b72f123f7d92cecf28f |
from ..parser.ast import ExpressionStatement, StringLiteral
from ..parser.visitor import NodeVisitor
def code_is_strict(code):
# 14.1
if not code:
return False
strict = False
for node in code:
if not isinstance(node, ExpressionStatement):
break
elif not isinstance(n... | jeffkistler/BigRig | bigrig/interpreter/ast_utils.py | Python | bsd-3-clause | 2,383 | [
"VisIt"
] | 80b29d44db31bc8098a392bf4f6f50fd0d9f9ca0cd6254ced280d719fd381b24 |
import sys
from pymol import cmd
from just_another_Bfactor import file_utils as fu
from just_another_Bfactor import prot_classes as prot
import math
import numpy as np
import pkg_resources
from just_another_Bfactor import Main_functions as M
# -----------------------------------------------------------
# Colour sect... | L-Siemons/Just-Another-B-factor | just_another_Bfactor/Just_Another_BFactor_plugin.py | Python | mit | 1,659 | [
"PyMOL"
] | 29f334057beb56659d8400b52a73f98f43f35e6f74f3fba6693b6ad746109011 |
"""
@name: PyHouse/Project/src/Modules/Housing/Hvac/_test/test_hvac.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2015-2019 by D. Brian Kimmel
@license: MIT License
@note: Created on Jul 12, 2015
@Summary:
Passed all 5 tests - DBK - 2019-06-04
"""
__updated__ = '2019-... | DBrianKimmel/PyHouse | Project/src/Modules/House/Hvac/_test/test_hvac.py | Python | mit | 2,518 | [
"Brian"
] | 1b9c8383395f2a10f8f810d9e9ccd9eff45a2e4faaa0d9c30b5b2002c002fc3f |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/pbc/df/mdf_jk.py | Python | apache-2.0 | 5,126 | [
"Gaussian",
"PySCF"
] | 7a61e5405fbad5f90c8279b95fdf40f1b2a79415791b286f23ce1da125021580 |
# -*- coding: utf-8 -*-
"""
Regression tests for the Test Client, especially the customized assertions.
"""
from __future__ import unicode_literals
import os
from django.core.urlresolvers import reverse
from django.template import (TemplateSyntaxError,
Context, Template, loader)
import django.template.context
fro... | ericholscher/django | tests/test_client_regress/tests.py | Python | bsd-3-clause | 62,672 | [
"VisIt"
] | d531f13d693b83eef7d7a4d282750a3ee3385c7d59a65e76f363aa31df9b2986 |
from flask import current_app, Blueprint, render_template, jsonify
from flask import session as current_session, request, redirect, url_for
from flask_classy import route
from marvin import config, marvindb
from brain.api.base import processRequest
from marvin.utils.general.general import parseIdentifier
from marvin.we... | bretthandrews/marvin | python/marvin/web/controllers/index.py | Python | bsd-3-clause | 4,844 | [
"Galaxy"
] | e02e869821685030a55681321a9e532f9e13bf31ec4f2a05035cc0c0840053e1 |
''' StatesMonitoringAgent
sends periodically numbers of jobs in various states for various
sites to the Monitoring system to create historical plots.
.. literalinclude:: ../ConfigTemplate.cfg
:start-after: ##BEGIN StatesMonitoringAgent
:end-before: ##END
:dedent: 2
:caption: StatesMonitoringAgent option... | chaen/DIRAC | WorkloadManagementSystem/Agent/StatesMonitoringAgent.py | Python | gpl-3.0 | 3,851 | [
"DIRAC"
] | 1a20bbedc80a53475ffeef67d7647f366e7bf98adf65c4a8594721f36f7aed1e |
# -*- coding: utf-8 -*-
"""
This module collects object representing rate expressions. It is based
on the ``chemp.util._expr`` module. The API is somewhat cumbersome since
it tries to be compatible with pure python, SymPy and the underlying
units library of ChemPy (``quantities``). Consider the API to be provisional.
"... | bjodah/chempy | chempy/kinetics/rates.py | Python | bsd-2-clause | 11,341 | [
"ChemPy"
] | 95ead910f05c67c68207b4966790f4d50ddc7a610b62f1002db0982a8f203f11 |
import numpy as np
import utils as tech
import matplotlib.pyplot as plt
'''
#Different distributions of gap junctions (masked arrays)
'''
n = 15
weights = np.eye(n,k=-1)
INITIAL = 0
timesteps = 150
conditions = 3
timesteps *= conditions
v = np.zeros((n,timesteps))
spiketimes = {neuron:[] for neuron in xrange(n)}... | mac389/mayer | simpler-synfire.py | Python | gpl-2.0 | 2,757 | [
"NEURON"
] | 7bdc3764f94a32fd3b7b423939044b44acc6203a1361edbcca697d5f8b68ebff |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This package implements modules test the input and output modules for QChem
""" | dongsenfo/pymatgen | pymatgen/io/qchem/tests/__init__.py | Python | mit | 194 | [
"pymatgen"
] | edc4bbd6c20f1c6773e701aab704fa88a1dab355421249834d80b0f392c2d56c |
#!/usr/bin/env python
__author__ = 'Mike McCann,Duane Edgington,Reiko Michisaki'
__copyright__ = '2015'
__license__ = 'GPL v3'
__contact__ = 'duane at mbari.org'
__doc__ = '''
Master loader for all CANON activities in May 2015
Mike McCann and Duane Edgington
MBARI 11 May 2015
@var __date__: Date of last svn ... | josephmfaulkner/stoqs | stoqs/loaders/CANON/loadCANON_may2015.py | Python | gpl-3.0 | 19,524 | [
"NetCDF"
] | 7114978a2d395b917055c5a899f0bdebf5840fa8acde4bc235fe3de84cc0271e |
#!/usr/bin/env python
# Copyright 2020 Informatics Matters Ltd.
#
# 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... | InformaticsMatters/pipelines | src/python/pipelines/rdkit/prepare_3d.py | Python | apache-2.0 | 12,122 | [
"RDKit"
] | 42e374ead0e82ac6785ec4c075c00f37a89573788d891a8f463c211a44152a69 |
"""
Acceptance tests for Home Page (My Courses / My Libraries).
"""
import datetime
from common.test.acceptance.pages.common.auto_auth import AutoAuthPage
from common.test.acceptance.pages.lms.account_settings import AccountSettingsPage
from common.test.acceptance.pages.studio.index import DashboardPage
from common.... | cpennington/edx-platform | common/test/acceptance/tests/studio/test_studio_home.py | Python | agpl-3.0 | 3,111 | [
"VisIt"
] | 68a6674af2a7e8af9230afba099be4cb5442f27e2aa8702aca2b1c807a49450d |
from __future__ import print_function
from __future__ import division
from __future__ import unicode_literals
from contextlib import contextmanager
import os
import datetime
import errno
import ctypes.wintypes
try:
import winreg
except ImportError:
# py 2
import _winreg as winreg
@contextmanager
def ign... | datasciencedev/r-bridge-install | rtools/rpath.py | Python | apache-2.0 | 9,763 | [
"GULP"
] | 648de2426f1fb10020efad869fdc11f902f17e15d95e499edf81a45452dd4b76 |
from sqlite3 import dbapi2 as dbapi
from ThreeDiToolbox.datasource.threedi_results import ThreediResult
from ThreeDiToolbox.tests.test_init import TEST_DATA_DIR
from ThreeDiToolbox.tool_statistics.tools.statistics import StatisticsTool
import mock
import os.path
import shutil
import tempfile
import unittest
test_dat... | nens/threedi-qgis-plugin | tool_statistics/tests/test_statistics.py | Python | gpl-3.0 | 11,817 | [
"NetCDF"
] | a6b8c4d8b6b26046290514edc13b6910535d0921c4846130ddb0d221ca50a566 |
# Version: 0.18
"""The Versioneer - like a rocketeer, but for versions.
The Versioneer
==============
* like a rocketeer, but for versions!
* https://github.com/warner/python-versioneer
* Brian Warner
* License: Public Domain
* Compatible With: python2.6, 2.7, 3.2, 3.3, 3.4, 3.5, 3.6, and pypy
* [![Latest Version]
... | poldracklab/mriqc | versioneer.py | Python | bsd-3-clause | 68,799 | [
"Brian"
] | 90596b3eea95aea641d066938c4dda267237dd6ae972125bbd852909f0404723 |
# FlowTech | NeurAlgae
## 2017 WWSEF Science Fair | HAB Prediction Using Machine Learning Algorithms
#Describes and trains a neural network for the analysis and prediction of algal bloom data
#Copyright (C) 2017 AH Zachary Trefler and Atif Mahmud
#This program is free software: you can redistribute it and/or modify
#... | FlowBoat/Flow-Tech-NeurAlgae | Versions/v1/NeurAlgae1.1.py | Python | gpl-3.0 | 9,018 | [
"NEURON"
] | 9c09ae7bf4e4c48faf333bdef8b8b6dbb75fbf36adf079993f9030f2430c674b |
""" The StalledJobAgent hunts for stalled jobs in the Job database. Jobs in "running"
state not receiving a heart beat signal for more than stalledTime
seconds will be assigned the "Stalled" state.
.. literalinclude:: ../ConfigTemplate.cfg
:start-after: ##BEGIN StalledJobAgent
:end-before: ##END
:dedent... | yujikato/DIRAC | src/DIRAC/WorkloadManagementSystem/Agent/StalledJobAgent.py | Python | gpl-3.0 | 22,303 | [
"DIRAC"
] | d0d8a63e1d43998bf390ddcf759fbcd9ac60269e167946580b084b5b39e8a601 |
import unittest
import os
import tempfile
import numpy as np
from numpy import ma
from numpy.testing import assert_array_equal
from netCDF4 import Dataset, __netcdf4libversion__
# Test use of vector of missing values.
class VectorMissingValues(unittest.TestCase):
def setUp(self):
self.testfile = tempfi... | Unidata/netcdf4-python | test/tst_masked5.py | Python | mit | 1,787 | [
"NetCDF"
] | 243c90eaaf236cdae515e25f81a25fb699946dce317bd2aef23fd024867fd8ae |
# ################################################################
#
# Active Particles on Curved Spaces (APCS)
#
# Author: Silke Henkes
#
# ICSMB, Department of Physics
# University of Aberdeen
# Author: Rastko Sknepnek
#
# Division of Physics
# School of Engineering, Physics and Math... | sknepneklab/SAMoS | analysis/batch_polar/batch_defects_J1_v0.5.py | Python | gpl-3.0 | 3,263 | [
"VTK"
] | 9686bab53fb3fedba1ca3f5153571c1bf8aab415223edfee6dbf766ab9928b4e |
# -*- coding: utf8 -*-
"""
This file contains configuration for Bter stock.
"""
__author__ = "Jan Seda"
__copyright__ = "Copyright (C) Jan Seda"
__credits__ = []
__license__ = ""
__version__ = "0.1"
__maintainer__ = "Jan Seda"
__email__ = ""
__status__ = "Production"
import urllib.parse
import sys
from ... import ... | Honzin/ccs | ccs/bter/public/__init__.py | Python | agpl-3.0 | 22,318 | [
"VisIt"
] | c9cdbd94d39be5c91169acac2ac01fb1fbc3a2dfd1a5bf29a03e5b065b9619a0 |
import pymbar
import itertools
import pandas as pd
import lb_loader
import simtk.openmm.app as app
import numpy as np
import simtk.openmm as mm
from simtk import unit as u
from openmmtools import hmc_integrators, testsystems
pd.set_option('display.width', 1000)
collision_rate = 10000.0 / u.picoseconds
temperature = 25... | kyleabeauchamp/HMCNotes | code/old/setup/ljbox_equil.py | Python | gpl-2.0 | 1,943 | [
"OpenMM"
] | 253894ad2bd7ff960818beb30387d6b9421088dc19b9c6b3129cba1bfd7ef7fc |
# -*- coding: utf-8 -*-
'''
Feature: Registered user can log in
As registered user
I want to log in to my account
Then I can create, edit, delete my questions or answers, vote on others items
'''
import pytest
# XXX: from tests.factories not work, because import colliding with other package
from ..factori... | s-m-i-t-a/consult | consult/tests/functional/login_specs.py | Python | bsd-3-clause | 3,730 | [
"VisIt"
] | f2bab26d65d32af912f24a69aecd9a91bf3625b88cb62d9ca36a9e7a2a205f80 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkImageSeparableConvolution(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | chrisidefix/devide | modules/vtk_basic/vtkImageSeparableConvolution.py | Python | bsd-3-clause | 513 | [
"VTK"
] | 3163032ecf2b2fba87876e8a99762c51a420127394770a9d16628d9b32ba58f8 |
'''
Models
=========
'''
# A repository for compartmentalized models compatible simulation models.
from abapy.mesh import RegularQuadMesh
from abapy.materials import VonMises, Hollomon
from abapy.misc import load
import numpy as np
import os, time, subprocess, pickle, copy
#--------------------------------------------... | lcharleux/compmod | compmod/models.py | Python | gpl-2.0 | 56,110 | [
"ParaView",
"VTK"
] | fc33f2741873fb7470091676223c839fb64e9493ca4416fe72dc04cc7a106555 |
#
# Copyright (c) 2009-2015, Jack Poulson
# All rights reserved.
#
# This file is part of Elemental and is under the BSD 2-Clause License,
# which can be found in the LICENSE file in the root directory, or at
# http://opensource.org/licenses/BSD-2-Clause
#
import El
m = 6000
n = 4000
display = True
worldRank =... | birm/Elemental | examples/interface/NNLS.py | Python | bsd-3-clause | 2,016 | [
"Gaussian"
] | 71eb50a323eafc56f303fcb04836fabf134f95772a716589ea30133c80df8de5 |
# Orca
#
# Copyright 2010 Consorcio Fernando de los Rios.
# Author: Alejandro Leiva <aleiva@emergya.es>
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the Licen... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/orca_gui_splash.py | Python | gpl-3.0 | 3,015 | [
"ORCA"
] | dcc3474a25fd95fbd52e1177d9ec1a9db943c59fb641948164ff0232e6fdce48 |
""" AlwaysBannedPolicy module
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = '$Id$'
from DIRAC import S_OK
from DIRAC.ResourceStatusSystem.PolicySystem.PolicyBase import PolicyBase
class AlwaysBannedPolicy(PolicyBase):
"""
The Alway... | yujikato/DIRAC | src/DIRAC/ResourceStatusSystem/Policy/AlwaysBannedPolicy.py | Python | gpl-3.0 | 714 | [
"DIRAC"
] | bf3ddd8c707126f652b8934ad7f90da17e1e44861dde3833f1bc86df826055fd |
# Copyright (c) 2011, Jimmy Cao, (c) 2014, Rafael Lopez
# All rights reserved.
# Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
# Redistributions of source code must retain the above copyright notice, this list of conditio... | Epithumia/pyIRCbot | modules/mafiagame.py | Python | bsd-2-clause | 114,873 | [
"VisIt"
] | bef51b2b3aa00dc6d0cc96cb5f1d75f25ec9f90dbcf8af0487be0295d27e2999 |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | ppwwyyxx/tensorflow | tensorflow/python/ops/image_ops_impl.py | Python | apache-2.0 | 159,409 | [
"Gaussian"
] | 42b2d763775cc3fb0f5535ae91a023fb7b8c531a55c36a66ed990398da128371 |
# -*- encoding: utf-8 -*-
"""
Gaussian optics.
The module implements:
- Ray transfer matrices for geometrical and gaussian optics.
See RayTransferMatrix, GeometricRay and BeamParameter
- Conjugation relations for geometrical and gaussian optics.
See geometric_conj*, gauss_conj and conjugate_gauss_beams
The co... | wolfram74/numerical_methods_iserles_notes | venv/lib/python2.7/site-packages/sympy/physics/optics/gaussopt.py | Python | mit | 19,994 | [
"Gaussian"
] | c41327cbc24f47710f5dc962973916d81bf71012337eb745b914922df9880c73 |
## This code is written by Salvatore Masecchia <salvatore.masecchia@unige.it>
## and Annalisa Barla <annalisa.barla@unige.it>
## Copyright (C) 2010 SlipGURU -
## Statistical Learning and Image Processing Genoa University Research Group
## Via Dodecaneso, 35 - 16146 Genova, ITALY.
##
## This file is part of L1L2Py.
##
#... | slipguru/l1l2py | l1l2py/data.py | Python | gpl-3.0 | 12,975 | [
"Gaussian"
] | f69e96364ae3ba23c0f11575a4f57315ab56566b762838d420f907ac0257aa32 |
"""
General descrition of your module here.
"""
from functools import partial
from maya import OpenMaya
from maya import OpenMayaUI
from maya import cmds
from PySide import QtCore
from PySide import QtGui
from shiboken import wrapInstance
from shiboken import getCppPointer
class RbfSettings(o... | cedricB/circeCharacterWorksTools | rbfTool.py | Python | mit | 9,899 | [
"Gaussian"
] | 3bc8ad6adefb8443402a16235bf7b136789739a5b99296a51c1d242bbb60d852 |
import ensembler
import ensembler.refinement
from ensembler.param_parsers import parse_api_params_string, eval_quantity_string
import simtk.unit as unit
helpstring_header = """\
Refine models by molecular dynamics simulation with explicit solvent, using OpenMM.
Models are first solvated with the number of waters dete... | choderalab/ensembler | ensembler/cli_commands/refine_explicit.py | Python | gpl-2.0 | 4,814 | [
"OpenMM"
] | 9f4a1bce27eb33a1ce80ada79faa86e94aad4479be772eb3098cc0c1e0977cf9 |
import string, re
# Written by Robert Belshaw (School of Biomedical & Healthcare Sciences, University of Plymouth) & Aris Katzourakis (Department of Zoology, University of Oxford)
# For more information and to cite see Belshaw, R & Katzourakis, A (2005) BlastAlign: a program that uses blast to align problematic nucleo... | abice-sbr/adaptsearch | blastalign.py | Python | gpl-3.0 | 4,394 | [
"BLAST"
] | bafeb9cd9a26d41cad39e09c56364cae0516398a472b545e40708d9ce707f412 |
""" pytest of Core.Utilities.Dictionaries
"""
import pytest
# sut
from DIRAC.Core.Utilities.Dictionaries import breakDictionaryIntoChunks
@pytest.mark.parametrize("aDict, chunkSize, expected", [
({}, 1, []),
({'a': 'aa', 'b': 'bb', 'c': 'cc', 'd': 'dd'}, 5, [{'a': 'aa', 'b': 'bb', 'c': 'cc', 'd': 'dd'}]),
... | chaen/DIRAC | Core/Utilities/test/Test_Dictionaries.py | Python | gpl-3.0 | 818 | [
"DIRAC"
] | 4d78b17d7433b546ddd3df68368da214bb00d97bc2f094519bb488116f7cee50 |
"""
INPUT SETTINGS
"""
#Input file name
mgfFileName = "Peroxidase_elastase-1-29.mgf"
## Maximum charge of fragments
# set to 0 for deconvoluted data
fragmentMaxCharges = 2
#output file suffix
outputSuffix = "-filtered"
"""
noise filtering settings
"""
#diagnostic ions required
diagnosticIonCountRequired = 2
#... | gpfinder/gpfinder | resources/prefilter_mgf_with_kde.py | Python | gpl-3.0 | 25,961 | [
"Gaussian"
] | ffdd2772b73379a0c8a23b0a72a17bed5149690942c937b9874a367ebd302ce5 |
# Copyright (c) 2012 Purdue University
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met: redistributions of source code ... | lastweek/gem5 | configs/spec2k6/spec2k6.py | Python | bsd-3-clause | 9,637 | [
"GAMESS",
"Gromacs",
"NAMD"
] | cc6a9b56b45418a65d2e849b3ff8b00466e524284cc12218f2926c6c8f2604ee |
#!/usr/bin/env python3
"""
Copyright 2020 Paul Willworth <ioscode@gmail.com>
This file is part of Galaxy Harvester.
Galaxy Harvester is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 ... | pwillworth/galaxyharvester | html/delSchematic.py | Python | gpl-3.0 | 4,808 | [
"Galaxy"
] | 3be9b0807d1cf2bf8e1710b78ca0760c22f6f5f6bee07ef4a6cd0edc798695a5 |
import sys
sys.path.insert(1,"../../../")
import h2o
from tests import pyunit_utils
from h2o.estimators.gbm import H2OGradientBoostingEstimator
import numpy as np
# This test will generate synthetic GBM dataset using a randomly defined GBM trees. If given to
# a GBM model, it should be able to perform well with this... | h2oai/h2o-3 | h2o-py/tests/testdir_algos/gbm/pyunit_generate_synthetic_GBM_data.py | Python | apache-2.0 | 4,123 | [
"Gaussian"
] | 8a11458e7894b73545f57f4180b3f437fc8cc25b12bd634f56c1f7fedeef9617 |
import campaign_lib
import quest
import VS
from campaign_lib import *
stahlspeech1 = {
"intro":[("Captain_Stahl","Welcome to the Gemini Sector! I hope you had a good flight."),
("Burrows","Excuse me?"),
("Captain_Stahl","I'm sorry, I forgot to introduce myself. My name is Captain Stahl."),
... | ermo/privateer_wcu | modules/camptroy.py | Python | gpl-2.0 | 35,237 | [
"BLAST",
"VisIt"
] | b1f35718bc8c31b9b9e2768f0b9096848923b346797375ed9283e91859fe6095 |
# 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... | allenlavoie/tensorflow | tensorflow/contrib/autograph/converters/control_flow.py | Python | apache-2.0 | 9,869 | [
"VisIt"
] | b6becb6e0ad76ae61c75c7f19ebb6693cc28458b3f90f254a4e3bd23d1bd2193 |
"""
motifs.py
Jose Guzman, sjm.guzman@gmail.com
Claudia Espinoza, claudia.espinoza@ist.ac.at
Created: Thu Aug 3 16:26:12 CEST 2017
Contains classes to count connectivity motifs based
on recording synapses between principal cells and interneurons recorded
with a simultaneous whole-cell patch clamp recording config... | ClaudiaEsp/inet | inet/motifs.py | Python | gpl-2.0 | 16,895 | [
"NEURON"
] | 4625209463b8ce6f2d1e6408ce2c45f1340fc8579a3eaeab94ea143f55fbe96d |
# -*- coding: utf-8 -*-
# Copyright 2007-2016 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at... | sem-geologist/hyperspy | hyperspy/_components/eels_vignetting.py | Python | gpl-3.0 | 3,548 | [
"Gaussian"
] | 40fc9c60c59042c96730e165d22a8f79f32f1bfc4970ccce717f58a3acb9e166 |
SmsTrip = 16274,14708
trip_date = object.trip_id.trip_start or False
rs = True
prefix = {
1:'971',
17:'975',
6:'86',
4:'20',
7:'91',
8:'91',
16:'254',
11:'996',
5:'373',
13:'212',
9:'95',
14:'977',
15:'63',
12:'40',
3:'94',
10:'216'
... | nishad-jobsglobal/odoo-marriot | openerp/addons/mkjosms/smsscripts/new9.py | Python | agpl-3.0 | 13,036 | [
"VisIt"
] | 08b38060bdb03a464549d0d45010a3ade42e7c30b783ff4c91ec27f95f0483e3 |
"""Tools to build the DIRAC documentation.
Scripts to build code documentation, and also some mocking, etc.
"""
# list of packages that should be mocked in sphinx
# TODO: check if we can install more of these
DIRAC_DOC_MOCK_LIST = ['_arc',
'arc',
'cmreslogging',
... | chaen/DIRAC | docs/diracdoctools/__init__.py | Python | gpl-3.0 | 709 | [
"DIRAC"
] | cdce04da4f64a042d91e04d078af8ef7ad863898e1702365a2760f9f8d7b0679 |
# -*- coding: utf-8 -*-
'''
Exodus Add-on
Copyright (C) 2016 lambda
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 l... | viranch/exodus | resources/lib/sources/torba.py | Python | gpl-3.0 | 6,763 | [
"VisIt"
] | 1fc118c5856149b7daba9eab8ca83781e6972c954c4fcb3ea539a2ccfe57a344 |
import os
from pymicro.crystal.ebsd import OimScan, OimPhase
from pymicro.crystal.lattice import Lattice
from matplotlib import pyplot as plt, cm, image
from config import PYMICRO_EXAMPLES_DATA_DIR
file_path = os.path.join(PYMICRO_EXAMPLES_DATA_DIR, 'ebsd_ti_beta_crack.osc')
scan = OimScan.from_file(file_path)
# the ... | heprom/pymicro | examples/ebsd/load_osc.py | Python | mit | 967 | [
"CRYSTAL"
] | 02ee69921209cea3f26532c0677e975da527925a7b01e0d39d7c2a31ead0dab3 |
"""
Test the about xblock
"""
import datetime
import pytz
from django.conf import settings
from django.core.urlresolvers import reverse
from django.test.utils import override_settings
from mock import patch
from nose.plugins.attrib import attr
from opaque_keys.edx.locations import SlashSeparatedCourseKey
from course_... | xingyepei/edx-platform | lms/djangoapps/courseware/tests/test_about.py | Python | agpl-3.0 | 23,672 | [
"VisIt"
] | defdb548be1c1439360016bcd00ffa29808c0444e2075509c039273c9dc39d26 |
# PyVision License
#
# Copyright (c) 2006-2008 David S. Bolme
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# 1. Redistributions of source code must retain the above copyright
# notice, thi... | tigerking/pyvision | src/pyvision/other/normalize.py | Python | bsd-3-clause | 6,489 | [
"Gaussian"
] | 69b15ba536e2c9cfb3470d012a095a33fb92e6dac4b128adf7817f82dc6a86f9 |
# 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/request_plan_find_drug_package.py | Python | apache-2.0 | 12,734 | [
"VisIt"
] | 6fc0a5bb3ad9c493ea045a67d32fa6965c6b5371f52f24895c417a26758e7819 |
# 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 u... | apache/climate | ocw/utils.py | Python | apache-2.0 | 27,857 | [
"NetCDF"
] | 28a1df52865a9a0161bafc1c8f3e61e20195acc1adf88103737ac4083ab93c9a |
#################
#
# This file is part of
# ToBaCCo - Topologically-Based Crystal Constructor
#
# Copyright 2017 Yamil J. Colon <yamilcolon2015@u.northwestern.edu>
# Diego Gomez-Gualdron <dgomezgualdron@mines.edu>
# Ben Bucior <ben.bucior@gmail.com>
#
# ToBaCCo is free software: ... | tobacco-mofs/tobacco | write2cif.py | Python | lgpl-3.0 | 3,161 | [
"CRYSTAL"
] | 9a2c12e057c7acd99f62bb599df9011ecdbc3947985ca6769d66cfdff882f60e |
# This is a wrapper for JAMM to use it in Galaxy
# It will be accompanied with a jamm.xml file, which specifies the interface that Galaxy is showing to the user
# as well as the JAMM software including JAMM.sh, the bash script that is actually called.
# This wrapper does the following things:
# map the files (from Gal... | mahmoudibrahim/JAMMalaxy | jammwrapper.py | Python | gpl-3.0 | 5,139 | [
"Galaxy"
] | 464a230f68bcfa83d77911c2f77f73dd748c6b0dd7dda9ba88dc11ccf6b7de35 |
#!/usr/bin/python
# Copyright: Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
ANSIBLE_METADATA = {'metadata_version': '1.1',
'status': ['preview'],
... | roadmapper/ansible | lib/ansible/modules/cloud/amazon/elb_classic_lb.py | Python | gpl-3.0 | 53,757 | [
"Dalton"
] | 1d3bfa7b9872db3b8c9008675500bc098112fae11450b01b1d084bcd24fd4834 |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | rabipanda/tensorflow | tensorflow/contrib/distributions/python/ops/bijectors/real_nvp.py | Python | apache-2.0 | 11,430 | [
"Gaussian"
] | b3e78dc56ca0f86a0a86d912f585e7f73b4b1248f1a2cd0c136ca94550d0197c |
########################################################################
# $HeadURL$
########################################################################
""" LineGraph represents line graphs both simple and stacked. It includes
also cumulative graph functionality.
The DIRAC Graphs package is derived ... | Sbalbp/DIRAC | Core/Utilities/Graphs/LineGraph.py | Python | gpl-3.0 | 4,709 | [
"DIRAC"
] | 5da8722008d8ca48acd8ee0e91b98bff572619e96c5b84b5cd94e4f56d447666 |
"""Provides the entry point to xenoGI's functionality."""
__version__ = "3.0.0"
import sys, glob, os, readline, rlcompleter
from . import parameters,genbank,blast,trees,genomes,Score,scores,families,islands,analysis,islandBed
from .Tree import *
from .Family import *
def main():
#### check command line
tr... | ecbush/xenoGI | xenoGI/xenoGI.py | Python | gpl-3.0 | 17,494 | [
"BLAST"
] | 1a32d34aebe0f51e2c1c5b571f6de5cfbee68e74798068a9ef8e7fe78eda9210 |
# -*- coding: utf-8 -*-
# Copyright (c) 2015-2022, Exa Analytics Development Team
# Distributed under the terms of the Apache License 2.0
"""
Q-Chem Editor
#######################
Base class on top of exatomic.Editor for Q-Chem Editors
"""
#import pandas as pd
from exatomic import Editor
class Editor(Editor):
def... | exa-analytics/exatomic | exatomic/qchem/editor.py | Python | apache-2.0 | 629 | [
"Q-Chem"
] | c381e2915fb332d5d93d9ab24e257e065ae51edcfeec7ddb8768012252999b11 |
"""Visual components."""
from typing import Dict, Optional, List, Union, Tuple
from bowtie._component import Component, jdumps, jsbool
from bowtie._progress import Progress
# pylint: disable=too-few-public-methods
class _Visual(Component):
"""Abstract class all visual components inherit.
Used to test if a ... | jwkvam/bowtie | bowtie/visual.py | Python | mit | 9,476 | [
"Bowtie"
] | c18b2e773a1d5e8866365608c7596f99d2ec90e9d65eff587da07a6bc136a657 |
import functools
import inspect
import os
import sys
import warnings
from collections import defaultdict
from collections import deque
from contextlib import suppress
from pathlib import Path
from types import TracebackType
from typing import Any
from typing import Callable
from typing import cast
from typing import Di... | pytest-dev/pytest | src/_pytest/fixtures.py | Python | mit | 64,602 | [
"VisIt"
] | 5a57d971fff82b77a5763a82f92eab4180c560bd2bdaa635a4d5ce036b1512af |
#
# Author: Gregory Fleischer (gfleischer@gmail.com)
#
# Copyright (c) 2011-2013 RAFT Team
#
# This file is part of RAFT.
#
# RAFT 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 Licens... | mfazliazran/raft | extras/robots-wordlists/process-results.py | Python | gpl-3.0 | 15,671 | [
"VisIt"
] | 3093c8063b57c58c0277e777685c2189699ec1604d7e9fa67048e92b7fbd23b8 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# License AGPLv3 (https://www.gnu.org/licenses/agpl-3.0-standalone.html)
"""
This script creates a migration issue for a new Odoo version
in all repositories. This issue lists all known addons in the previous version.
Installation
============
For using this utility, you... | acsone/maintainers-tools | tools/create_migration_issue.py | Python | agpl-3.0 | 7,715 | [
"VisIt"
] | d69c1feee578490b34760ec74508abe4e6edd4fd532bd37ee5d5b70884cbb852 |
import numpy as np
import cv2
import matplotlib.pyplot as plt
img = cv2.imread('images/saturn.png', 0)
# 创建一个带噪声的图片
im = np.zeros(img.shape, np.uint8)
mean = 0
sigma_noise = 30
gaussian = cv2.randn(im, mean, sigma_noise)
img_noise = cv2.add(img, gaussian)
gauss_noise_remv = cv2.GaussianBlur(img_noise, (1, 21), 2)
... | KECB/learn | computer_vision/11_rmv_noise_gaussian_blur.py | Python | mit | 787 | [
"Gaussian"
] | fd966f36208d29fc366b0b59de527c0af239a48c788157b2b5592fcbc868c5a3 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
from s... | kaankizilagac/sozluk | config/urls.py | Python | mit | 1,795 | [
"VisIt"
] | 4b2584c3fd85d2db19203e27146e8fcd34dc62f24c758112b68b34fd67b26c5d |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# fifoscheduler - [insert a few words of module description on this line]
# Copyright (C) 2003-2009 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 term... | heromod/migrid | mig/server/fifoscheduler.py | Python | gpl-2.0 | 3,101 | [
"Brian"
] | 9c6bcf14dde64f11086adf4c8e9a093d108d6fe5cce632b9b2e80127bd70c080 |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""SPM wrappers for preprocessing data
Change directory to provide relative paths for doctests
>>> import os
>>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
>>> datadir = os.path... | satra/NiPypeold | nipype/interfaces/spm/preprocess.py | Python | bsd-3-clause | 33,161 | [
"Gaussian"
] | 8c44ca105cbd8a0aff94e12dc3eee9ff212e121ca423c4958267373c856a617a |
# -*- coding: utf-8 -*-
"""
textgridview.py is part of Coquery.
Copyright (c) 2017 Gero Kunter (gero.kunter@coquery.org)
Coquery is released under the terms of the GNU General Public License (v3).
For details, see the file LICENSE that you should have received along
with Coquery. If not, see <http://www.gnu.org/licen... | gkunter/coquery | coquery/gui/textgridview.py | Python | gpl-3.0 | 13,062 | [
"Gaussian"
] | 45b80c18573b72021d31a35bc49773f67a12232f28126fcd43a0eb8f0c9670f3 |
from itertools import *
import re
import unittest
import glob
import os
from testlib import testutil, SkipTest, PygrTestProgram
from pygr import worldbase
from pygr import sequence, cnestedlist, seqdb, blast, logger, parse_blast
from pygr.nlmsa_utils import CoordsGroupStart, CoordsGroupEnd
from pygr import translationD... | cjlee112/pygr | tests/blast_test.py | Python | bsd-3-clause | 52,724 | [
"BLAST"
] | 65561b71567e1cc5b5b01a30598fe69c92e2d86324e2f0c398291496abf5d41e |
# -*- coding: utf-8 -*-
# with '#' will be ignored, and an empty message aborts the commit.
#
# PySurfer documentation build configuration file, created by
# sphinx-quickstart on Thu May 12 12:45:43 2011.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# Note that not all possible c... | mwaskom/PySurfer | doc/conf.py | Python | bsd-3-clause | 10,789 | [
"Mayavi"
] | 9947b72cc4192d2c5dfbac93c5dc970143f01db255f8474190cd1d4374cdfebc |
# -*- encoding: utf8 -*-
'''
This tool extracts information about structs and defines from the C headers.
You can pass either the raw header files or JSON files to this script.
The JSON input format is as follows:
[
{
'file': 'some/header.h',
'structs': {
'struct_name': [
'field1',
'fi... | slightperturbation/Cobalt | ext/emsdk_portable/emscripten/1.27.0/tools/gen_struct_info.py | Python | apache-2.0 | 15,892 | [
"VisIt"
] | 44153872c6efd519bc9bde69fe82677054966a28697118e2d0f3f82093cb3bef |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import logging
from fractions import Fraction
from numpy import around
from pymatgen.analysis.bond_valence import BVAnalyzer
from pymatgen.analysis.ewald imp... | nisse3000/pymatgen | pymatgen/transformations/standard_transformations.py | Python | mit | 26,123 | [
"pymatgen"
] | 48a8089ec7574763247468d99946654396b83a1f7a179941c815ac56dc974ad8 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
__version__ = "0.7.6"
__author__ = "Pierre Legrand (pierre.legrand@synchrotron-soleil.fr)"
__date__ = "23-09-2009"
__copyright__ = "Copyright (c) 2006-2009 Pierre Legrand"
__license__ = "LGPL"
# Environemantal variable XDSHOME, if set, defines the place where the xds
# ex... | RAPD/RAPD | src/plugins/subcontractors/xdsme/new/xdsme-0.4.9/XDS/xdsconv.py | Python | agpl-3.0 | 76,631 | [
"CRYSTAL"
] | 92fddf61a62c34b6a3916fc3228993dae2df8d654925922f8d9517404a2ef6f8 |
"""
Compute the temperature dependent renormalization (TDR)
using the dynamical AHC theory (ieig2rf=5).
"""
from ElectronPhononCoupling import compute
# Lists of files used
# ===================
ddb_fnames = """
Calculations/01-LiF-dynamical/odat_calc_DS5_DDB.nc
Calculations/01-LiF-dynamical/odat_calc_DS9_DDB.nc
Ca... | jmbeuken/abinit | scripts/post_processing/ElectronPhononCoupling/Examples/1-2-dynamical-tdr.py | Python | gpl-3.0 | 2,047 | [
"ABINIT"
] | 49dc61cdf05f9daad4781349f2bd64a517c5de87b0357e6836b5b6d39ba1f9c8 |
''' DIRAC.ResourceStatusSystem.PolicySystem.Actions package
'''
__RCSID__ = '$Id$'
| andresailer/DIRAC | ResourceStatusSystem/PolicySystem/Actions/__init__.py | Python | gpl-3.0 | 84 | [
"DIRAC"
] | cf8e325d2a18ce12436ad5acaed5c38c53a244a13a1a8d036b1040fd862155b3 |
# $Id$
#
# Copyright (C) 2002-2006 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" contains SMARTS d... | bp-kelley/rdkit | rdkit/Chem/EState/AtomTypes.py | Python | bsd-3-clause | 4,037 | [
"RDKit"
] | 761f7ee72f9cf449b789ccf0bffe6930c4cdc3948ef95d8911a282b96debd540 |
#!/usr/bin/env python
# THIS FILE IS PART OF THE CYLC SUITE ENGINE.
# Copyright (C) 2008-2015 NIWA
#
# 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 yo... | kaday/cylc | lib/cylc/scheduler.py | Python | gpl-3.0 | 60,391 | [
"BLAST"
] | 63d34f6275a2d3375465df26f6890e98518593a3fc9f2b0b945432987ddec0b2 |
# Copyright: 2005 Gentoo Foundation
# Author(s): Brian Harring (ferringb@gentoo.org)
# License: GPL2
from __future__ import print_function
__all__ = ["mirror_cache", "non_quiet_mirroring", "quiet_mirroring"]
from itertools import chain
from portage.cache import cache_errors
from portage.localization import _
def mi... | fastinetserver/portage-idfetch | pym/portage/cache/util.py | Python | gpl-2.0 | 4,806 | [
"Brian"
] | 23760bc705d70844269ea91b4081f4af355ad82be72daf2e6c27354eaef3eb6b |
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