text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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#!/usr/bin/env python
import os
import re
import sys
import time
import pysam
import align
import random
import argparse
import logging
import subprocess
import itertools
import traceback
import cPickle as pickle
import multiprocessing as mp
import numpy as np
import scipy.stats as ss
from uuid import uuid4
from s... | ValentinaPeona/tebreak | tebreak/tebreak.py | Python | mit | 65,229 | [
"BWA",
"pysam"
] | a6c13c8390811d9959ed894184ae7a60c9af3fac7a2ee29583cf9264d95e95a9 |
#
# Copyright (C) 2013-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | hmenke/espresso | samples/p3m.py | Python | gpl-3.0 | 6,556 | [
"ESPResSo"
] | 2853ac103adaf74fb8b3fef7283aeca193fdb87b9312e7c9bddb67cd477acc88 |
#!/usr/bin/env python
from __future__ import division
"""Variational Bayes model to fuse
DESCRIPTION
"""
__author__ = "Nick Sweet"
__copyright__ = "Copyright 2015, Cohrint"
__credits__ = ["Nick Sweet", "Nisar Ahmed"]
__license__ = "GPL"
__version__ = "1.0.0"
__maintainer__ = "Nick Sweet"
__email__ = "nick.sweet@color... | COHRINT/cops_and_robots | src/cops_and_robots/fusion/variational_bayes.py | Python | apache-2.0 | 40,903 | [
"Gaussian"
] | 93ac0a38fd61952b2bfabf658007dfcf1ec4cd55a8ccc007d145950e2505df14 |
import numpy as np
np.set_printoptions(precision=14)
npoints = 5
keys = ["V", "V_RHO_A", "V_RHO_B", "V_GAMMA_AA", "V_GAMMA_AB", "V_GAMMA_BB"]
funcs = [
["S_X", "XC_LDA_X"],
["B88_X", "XC_GGA_X_B88"],
["B86B_X", "XC_GGA_X_B86_MGC"],
["PW86_X", "XC_GGA_X_PW86"],
["PBE_X", "XC_GGA_X_PBE"],
#["RPBE_X", "XC_GGA_X_RPBE"],
... | rmcgibbo/psi4public | tests/libxc/devl/point_test.py | Python | lgpl-3.0 | 2,508 | [
"Psi4"
] | f794d90335d5dbef0e437199b56b67f1ae9738d0bb1d6d1ece43d4b572dab796 |
# -*- coding: utf-8 -*-
# Simple GUI example
from javax.swing import *
from java.awt import *
import optparse
import sys
## does summation of echoes using external python script
import sys
import os
import os.path
import subprocess
"""
import argparse
parser = argparse.ArgumentParser(description='Add echoes in a qc... | jtrebosc/JTutils | TSpy/qcpmgadd2DWin.py | Python | bsd-3-clause | 3,320 | [
"Gaussian"
] | 3e2fb955ec60dd53b3ae15b50ad6fe764fae4c027bb39327ed8d09251eca7f72 |
#
# This source file is part of appleseed.
# Visit http://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2014-2017 The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this s... | jasperges/blenderseed | export.py | Python | mit | 2,457 | [
"VisIt"
] | e888d19ef05d9b3e422f3a9e07f6667a22343f15f7d7055b2294756804ec2aef |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2019 Satpy developers
#
# This file is part of satpy.
#
# satpy 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... | pytroll/satpy | satpy/tests/reader_tests/test_viirs_edr_active_fires.py | Python | gpl-3.0 | 16,145 | [
"NetCDF"
] | 8de3ab9e2e8fcf367da7cefa128c6cc42f28f7a4c85eba226eacbe1d82e6a7fa |
"""
Copyright (C) 2014, Jaguar Land Rover
This program is licensed under the terms and conditions of the
Mozilla Public License, version 2.0. The full text of the
Mozilla Public License is at https://www.mozilla.org/MPL/2.0/
Maintainer: Rudolf Streif (rstreif@jaguarlandrover.com)
Author: David Thiriez (david.thiriez... | dvthiriez/rvi_backend | server/loginvokedserviceserver.py | Python | mpl-2.0 | 5,510 | [
"Jaguar"
] | 2fd3bdafeae981a4b70fcee745e08a56a22270690fc54124824ca0b17b4a6a1b |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | kdmurray91/scikit-bio | skbio/stats/tests/test_composition.py | Python | bsd-3-clause | 47,376 | [
"scikit-bio"
] | 3f22d9eddecf40e9ce616f2f3697318c8003062c2e643901deec414299d8331d |
import random
import math
import time
import re
import zlib
from direct.interval.IntervalGlobal import *
from direct.distributed.ClockDelta import *
from toontown.toonbase.ToonPythonUtil import *
from direct.gui.DirectGui import *
from direct.task import Task
from direct.showbase import PythonUtil
from direct.directnot... | silly-wacky-3-town-toon/SOURCE-COD | toontown/toon/LocalToon.py | Python | apache-2.0 | 87,894 | [
"VisIt"
] | b58f4993d54e81b2b913d8c56493130e81578421fb2648981ce6725cc9c7697f |
"""Options manager for :class:`~diofant.polys.polytools.Poly` and public API functions."""
import re
from ..core import Basic, I, sympify
from ..utilities import has_dups, numbered_symbols, topological_sort
from .polyerrors import FlagError, GeneratorsError, OptionError
__all__ = 'Options', 'Order'
class Option:
... | skirpichev/omg | diofant/polys/polyoptions.py | Python | bsd-3-clause | 19,400 | [
"Gaussian"
] | d95f2cfbc7b92b3ae8ed2bc4edd01a28db103c87bb26e94cb8179ef7627727f5 |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
'''
This module contains the one-parameter exponential families used
for fitting GLMs and GAMs.
These families are described in
P. McCullagh and J. A. Nelder. "Generalized linear models."
Monograph... | bthirion/nipy | nipy/algorithms/statistics/models/family/__init__.py | Python | bsd-3-clause | 503 | [
"Gaussian"
] | a2ec2ee37b68095809e233b663a52eec668817820e23f068b73fecad64cd9f1b |
"""=================================================
pipeline_testing - automated testing of pipelines
=================================================
This pipeline executes other pipelines for testing purposes.
Overview
========
This pipeline implements automated testing of CGAT pipelines. The
pipeline downloads... | AntonioJBT/CGATPipeline_core | CGATPipelines/pipeline_testing.py | Python | mit | 19,055 | [
"BWA"
] | b5ed18fe94bd640f28da8412a22e5bf2a11610099f1cbbaac14d5c6d15850c16 |
#!/usr/bin/env python
"""
Created on Thu Dec 19 14:31:36 2013
Author: Oren Freifeld
Email: freifeld@csail.mit.edu
"""
import numpy as np
from pylab import plt
from scipy import sparse
from of.utils import *
from cpab.cpaNd import CpaSpace as CpaSpaceNd
from cpab.cpaNd.utils import null
from cpab.cpa2d.utils import *... | freifeld/cpabDiffeo | cpab/cpa2d/CpaSpace.py | Python | mit | 27,047 | [
"Mayavi"
] | aa9880fd4dea6287cedbfe360cdbcebe8d0238dd221940b4a45c3788ce3c0bc3 |
# This script will calculate Shannon entropy from a MSA.
# Dependencies:
# Biopython, Seaborn, Matplotlib, Math
"""
Shannon's entropy equation (latex format):
H=-\sum_{i=1}^{M} P_i\,log_2\,P_i
Entropy is a measure of the uncertainty of a probability distribution (p1, ..... , pM)
https://stepic.org/lesso... | MicroInfect/bioinfx | Shannon.py | Python | gpl-3.0 | 6,304 | [
"Biopython"
] | 29fd5db820c0f8bc605871c377b47baf18008394d94943ab915cf5a8029f4be6 |
#=========================================================================
#
# Program: PXDMFReader Plugin
# Module: ReaderSync/py
#
# Copyright (c) GeM, Ecole Centrale Nantes.
# All rights reserved.
# Copyright: See COPYING file that comes with this distribution
#
#
# This software is distributed WITHOUT... | aleygue/PxdmfSuite | ParaviewPXDMFReader/PGDTools/ReaderSync.py | Python | bsd-3-clause | 9,862 | [
"ParaView",
"VTK"
] | efac9ece5ac20e51ab1a62ec0ea98bd1fc9bebf5488628c3b70b3f1c3edff733 |
import numpy as np
import math
import sys
sys.path.insert(0,'../..')
import os
import classifier_eval_simplified
from sklearn import tree
from sklearn.ensemble import AdaBoostClassifier
from sklearn.svm import SVC
for dim in range(9,11):
comp_file_list=[]
######################################################... | weissercn/MLTools | Dalitz_simplified/evaluation_of_optimised_classifiers/bdt_gauss/bdt_Gauss_evaluation_of_optimised_classifiers.py | Python | mit | 1,571 | [
"Gaussian"
] | c70c782ae6d71f4fc6b664b0ec8ebed91363f62c297cf126cc00cc0b8678b530 |
# Copyright 2021 Google LLC.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... | google-research/vmoe | vmoe/configs/vmoe_b16_imagenet21k_randaug_strong_ft_cifar10.py | Python | apache-2.0 | 7,959 | [
"MOE"
] | e6e8cfa48bd0ec77b8c731f1671fe94bd101eefd62cec13d76ce0e5d692f51d5 |
import _gfrd
import myrandom
import vtk
m = _gfrd.Model()
S0 = m.new_species_type()
S0['D'] = '.01'
S0['radius'] = '.01'
S0['surface'] = 'default'
S1 = m.new_species_type()
S1['D'] = '.01'
S1['radius'] = '.01'
S1['surface'] = 'default'
S2 = m.new_species_type()
S2['D'] = '.01'
S2['radius'] = '.01'
S2['surface'] = 'def... | gfrd/egfrd | samples/bd_propagator/test2.py | Python | gpl-2.0 | 4,991 | [
"VTK"
] | 36d0fb4e78594f5f327281371f557ad7eac032ead8c7d38e8cfd639698b959d7 |
#! /usr/bin/env python
"""Unit tests for landlab.io.netcdf module."""
import pytest
from numpy.testing import assert_array_equal
from landlab import RasterModelGrid
from landlab.io import (
MismatchGridDataSizeError,
MismatchGridXYLowerLeft,
MismatchGridXYSpacing,
)
from landlab.io.netcdf import read_net... | cmshobe/landlab | tests/io/netcdf/test_read_netcdf.py | Python | mit | 3,051 | [
"NetCDF"
] | c631fd8ad9d1a79b11d8f15d764df36ed757980facf14adc99a06a73fdef6b26 |
import unittest
from octopus.server.orientdb.orientdb_shell_mananger import OrientDBShellManager
class TestOrientDBShellManager(unittest.TestCase):
def testUnreachableServer(self):
self.hostname = 'localhost'
self.port = '1337'
shell_manager = OrientDBShellManager(self.hostname, self.por... | octopus-platform/bjoern | python/octopus-tools/tests/orientdb_shell_manager.py | Python | gpl-3.0 | 425 | [
"Octopus"
] | 1be933db8cc7ae8b7d4a158f19ea9e3b673d368b5738ec482f5736ce95ba0771 |
# coding=utf-8
from unittest import TestCase
from gputils.gptransformer import GooglePlayParsedResponseTransformer
from json2html import *
class TestTransforming(TestCase):
__PARSED_RESPONSE = '[<div class=\"review-body\"> <span class=\"review-title\">Galaxy S5</span> Paro de funcionar novamente no Estado do Paran... | jcfausto/gpscrapper | specs/test_transforming.py | Python | mit | 1,686 | [
"Galaxy"
] | 3066edc496b3b035b6736da87cb53a4d2e916edaef9c44f0adc963cff89a1074 |
from parsimonious.grammar import Grammar
from parsimonious.nodes import NodeVisitor
import textwrap
from string import Template
import re
import sys
class MarkupParser(NodeVisitor):
def __init__(self, text):
grammar = """
main = meta? ( nix / markup )*
newline = ~"[\\n\\s]"+
... | styx-static/styx | src/tools/parser.py | Python | mit | 3,364 | [
"VisIt"
] | aefffc8a95e38db7491c52d277befe1b08aac7e163f3fa9eaca472c2d2ad99f9 |
import os.path
from subprocess import check_call, CalledProcessError
import shutil
from tempfile import NamedTemporaryFile
import sys
import pysam
from crumbs.bam.flag import create_flag
from crumbs.settings import get_setting
from crumbs.utils.bin_utils import get_num_threads
# pylint: disable=C0111
def filter_ba... | JoseBlanca/seq_crumbs | crumbs/bam/bam_tools.py | Python | gpl-3.0 | 5,962 | [
"pysam"
] | 4ee14e6698a53c8d7c7acd9e7b91702c5e8ee0fa38d410995462541d3cdbba58 |
"""bayesian_network.py
The purpose of this model is to assist with the construction of Bayesian Networks
designed for modeling the effects of a molecular mechanism. The goal is to learn
about this molecular mechanism by analysing the evidence that we have. We can then
perform a genome wide association compariang genot... | christopher-gillies/MultiplePhenotypeAssociationBayesianNetwork | mpabn/bayesian_network.py | Python | mit | 25,945 | [
"Gaussian"
] | 74aa8fa3981d468e9a7027979f0b5291a7ed037d74913818032334e1c228bd9b |
__author__ = 'Jason Piper'
import imp
current_version = imp.load_source('pyDNaseVersion', 'pyDNase/_version.py').__version__
#Unfortunately, we have to ensure that the user has numpy is installed,
#as pip is bad at installing numpy and matplotlib at the same time, and just breaks
try:
import numpy
except Import... | simonvh/pyDNase | setup.py | Python | gpl-3.0 | 1,788 | [
"pysam"
] | c80ecf14289201f7b879fbcc9b967ce1b3ad569eb48ceb4009f2bb080e3439e4 |
#!/usr/bin/env python
"""
Get the currently defined user data volume quotas
Usage:
dirac-dms-user-quota [options]
Example:
$ dirac-dms-user-quota
Current quota found to be 0.0 GB
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
... | yujikato/DIRAC | src/DIRAC/DataManagementSystem/scripts/dirac_dms_user_quota.py | Python | gpl-3.0 | 1,190 | [
"DIRAC"
] | 58aa1590271912b794bc46d2a67aded5f69d480336c0a812914e71ebc2a18331 |
# Copyright 2000-2002 Andrew Dalke.
# Copyright 2002-2004 Brad Chapman.
# Copyright 2006-2010 by Peter Cock.
# All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Represent a Seque... | poojavade/Genomics_Docker | Dockerfiles/gedlab-khmer-filter-abund/pymodules/python2.7/lib/python/Bio/SeqRecord.py | Python | apache-2.0 | 46,584 | [
"BioPerl",
"Biopython"
] | 7d82174f2b9ce22f693db036ab1cc20daff1527bcffabb2f0d70ecbc8e2f09c2 |
#
# Copyright 2018 Red Hat | Ansible
#
# 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.
#
# ... | ravibhure/ansible | lib/ansible/plugins/lookup/k8s.py | Python | gpl-3.0 | 7,896 | [
"Galaxy",
"VisIt"
] | b0ce83830682ff83c37069d1ac6e12ede9319520d413977b1d925162d2cffe7a |
# pylint: disable=invalid-name,no-init
from __future__ import (absolute_import, division, print_function)
from mantid.simpleapi import *
from mantid.api import FrameworkManager
import copy
import os
import re
import stresstesting
BANNED_FILES = ['80_tubes_Top_and_Bottom_April_2015.xml',
'80_tubes_Top_a... | ScreamingUdder/mantid | Testing/SystemTests/tests/analysis/LoadLotsOfFiles.py | Python | gpl-3.0 | 12,957 | [
"CASTEP",
"Gaussian"
] | 303efbafa5d691d270f963223db514b547717cd2acc85791d8281e24efbbc398 |
"""2015 SciPy John Hunter Excellence in Plotting Contest
Author: Robert Nikutta <robert.nikutta@gmail.com>
Title: Clustering of astronomical objects in WISE 3D color space
Based on: Nikutta, Hunt-Walker, Ivezic, Nenkova, Elitzur,
'The meaning of WISE colours - I. The Galaxy and its satellites',
MNRAS 442, 3361-3379 ... | rnikutta/wise3Dstereoscopic | plot.py | Python | bsd-3-clause | 8,856 | [
"Galaxy"
] | fbd257de313317a93bac16c380e5215a8a3458490e7c048a7048e7703fdbdfa9 |
"""semi-views for the `group_messaging` application
These are not really views - rather context generator
functions, to be used separately, when needed.
For example, some other application can call these
in order to render messages within the page.
Notice that :mod:`urls` module decorates all these functions
and turn... | jesonyang001/qarepo | askbot/deps/group_messaging/views.py | Python | gpl-3.0 | 9,181 | [
"VisIt"
] | 8df5e9d4866387eadf041c45b4dd57576c0b97d18831a551389e30c92b28d0e5 |
import ast
import _ast
from jaspyx.ast_util import ast_call, ast_load, ast_store
from jaspyx.context.block import BlockContext
from jaspyx.visitor import BaseVisitor
class TryExcept(BaseVisitor):
def visit_TryExcept(self, node):
if node.orelse:
raise NotImplementedError('Try-except else handle... | iksteen/jaspyx | jaspyx/visitor/tryexcept.py | Python | mit | 2,092 | [
"VisIt"
] | 774977a67d7bfa55b3240219c9d8a35a0c8489ec768291b2a2471e1b199b7d88 |
import email.parser
import email.policy
import email.utils
import typing
from email.message import EmailMessage
from itertools import chain
from textwrap import dedent
import pytest
from riggerlib import recursive_update
from widgetastic_patternfly import CheckableBootstrapTreeview as Check_tree
from cfme import test... | nachandr/cfme_tests | cfme/tests/cloud_infra_common/test_provisioning.py | Python | gpl-2.0 | 31,446 | [
"VisIt"
] | 7bfac3137746887a6cc62903737debb677a5c28931d4abdebcce0ac2603a4acb |
# 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 | test/test_zip_county.py | Python | apache-2.0 | 9,981 | [
"VisIt"
] | 86ed183e6c519289a4988b7f891d103097d8b2c0c30e119a4168f707378dff80 |
#!/usr/bin/env python
"""
Michael Lerner's hbond analysis, modified by Steve Spronk
Right now, just handles pasting together ptraj output.
"""
import copy,pprint,os,sys
from scipy import sqrt
from string import ascii_letters
from .hbond_tool_utils import *
class Atom:
def __init__(self, atom_name = None, resi_n... | LernerLabs/PyPAT | pypat/hbond_analysis_utils.py | Python | apache-2.0 | 34,523 | [
"Amber"
] | d144ffa14d1addc385dc31b3ec5f470f6f62903b1aabc9594a39e11254c75328 |
from behave import *
# Common to this feature
@when('I visit the reset password page')
def impl(context):
context.browser.visit(context.config.server_url + '/accounts/password/reset/')
| nlhkabu/connect | bdd/features/steps/reset_password.py | Python | bsd-3-clause | 191 | [
"VisIt"
] | 28fd0279253a0132b5632d20bf3bfc5bc2aec34d555cb3e6f07597be71139f25 |
# Copyright (C) 2012-2016
# Max Planck Institute for Polymer Research
# Copyright (C) 2008-2011
# 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 the GNU Gen... | fedepad/espressopp | src/integrator/LBInit.py | Python | gpl-3.0 | 3,056 | [
"ESPResSo"
] | 1a88cbe6278a2c5b674f1a6952aedd5226a288f0a47598746642d0d9f15a2c85 |
import bpy
import bpy_extras
import bmesh
import mathutils
import math
#import copy
bl_info = {
"name": "Viewport Vertex Alignment",
"author": "Hades",
"version": (0, 2),
"blender": (2, 6, 9),
"location": "View3D > Mesh Edit > Toolshelf > Vertex Alignment",
"description": "Ali... | hdunderscore/mesh_viewport_vertex_align | mesh_viewport_vertex_alignment.py | Python | mit | 25,359 | [
"Gaussian"
] | a509b2875da983b82728e460c4fda4bf9a74f3dbdbc8e1fc17cb820bfc17b8e8 |
# Orca
#
# Copyright 2010-2011 The Orca Team
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This library... | pvagner/orca | src/orca/common_keyboardmap.py | Python | lgpl-2.1 | 6,459 | [
"ORCA"
] | 7851c66cecb6f760c23f2e2828e836c4a7b21a10e751411bda2222147d3383b2 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | MOA-2011/enigma2-plugin-extensions-openwebif | plugin/controllers/views/main.py | Python | gpl-2.0 | 34,105 | [
"VisIt"
] | dfe4e9e944dfae2a29c58c24adb6265dc99c36ce27f793148a775f4c1243be85 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2016 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | kannon92/psi4 | psi4/share/psi4/databases/A24.py | Python | gpl-2.0 | 29,724 | [
"Psi4"
] | 759901dea91fc61c67a8e6da7d15c5a3cd6efe078b2fd1189b455b37ffc31d27 |
__author__ = 'crystal'
import sys
from PyQt5.QtWidgets import QApplication, QDialog
from checkSumGui import Ui_Form
app = QApplication(sys.argv)
window = QDialog()
ui = Ui_Form()
ui.setupUi(window)
window.show()
sys.exit(app.exec_()) | karcio/checkSumValidatorGUI | checkSumVal/src/checkSum.py | Python | gpl-3.0 | 238 | [
"CRYSTAL"
] | f1cb50c396c6a3175ee819b6428fbf76b625d9c637c97a8b70526e9fb1641130 |
from numpy.testing import assert_equal, assert_array_equal, assert_allclose
from nose.tools import assert_true, assert_raises, assert_not_equal
from copy import deepcopy
import os.path as op
import numpy as np
from scipy import sparse
import os
import warnings
from mne import read_evokeds
from mne.datasets import test... | jniediek/mne-python | mne/tests/test_utils.py | Python | bsd-3-clause | 25,120 | [
"Mayavi"
] | 6d9a612a6ff395ee6699f793297d998bf29e39d6dfb4e285fae20e2bbbdace22 |
import os
import re
import socket
import sys
import time
from optparse import make_option
from django.conf import settings
from django.core.management.base import BaseCommand, CommandError
from django_extensions.management.utils import setup_logger, RedirectHandler
from django_extensions.management.technical_response... | marcoantoniooliveira/labweb | oscar/lib/python2.7/site-packages/django_extensions/management/commands/runserver_plus.py | Python | bsd-3-clause | 12,343 | [
"VisIt"
] | 62ba47939a99170e7c89f48adfd69413585dafcf4f6482e8b08392455eb6b43d |
try:
import moogli
except ImportError as e:
print( "[INFO ] Could not import moogli. Quitting..." )
quit()
import moose
from moose import neuroml
from PyQt4 import Qt, QtCore, QtGui
import sys
import os
import random
import numpy as np
app = QtGui.QApplication(sys.argv)
filename = os.path.join( os.path.sp... | BhallaLab/moose | moose-examples/moogli/color_update.py | Python | gpl-3.0 | 6,159 | [
"MOOSE"
] | e8e9d070529bb813c6b1340e71d5dcf129e99d58a48bee1c7ce76dd59723f389 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Module containing class to create an ion
"""
__author__ = "Sai Jayaraman"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.0"
__maintainer__ = "Sai Jayaraman"
__email__ = "sjayaram... | montoyjh/pymatgen | pymatgen/core/ion.py | Python | mit | 6,452 | [
"pymatgen"
] | 357bb33ff01c2acf056b0574d567922a32d391738e2250c9f24f63b0d687e982 |
import pandas as pd
import xarray as xr
import os as os
homedir = 'D:/UW_PhD/Python/xarray/'
os.chdir(homedir)
#open pnnl lat long el file
pnnlxy = xr.open_dataset('data_LatLonGht.nc')
#range of dates to create new files for
start_date = '2006-11-01'
end_date = '2006-11-20'
dates = [x.strftime('... | ChristinaB/Observatory | tutorials/CreatePNNLnetcdfFile_MultipleFiles.py | Python | mit | 3,103 | [
"NetCDF"
] | f78ec9df92bf14cdbed3497069b2977e977c5a49e166c1df46dc2ab9a66d16b5 |
from rdkit import DataStructs
from rdkit import RDConfig
from rdkit import Chem
from rdkit.Chem import ChemicalFeatures,rdDistGeom
from rdkit import Geometry
import unittest,os
def lstFeq(l1, l2, tol=1.e-4):
if (len(list(l1)) != len(list(l2))):
return 0
for i in range(len(list(l1))):
if not feq(l1[i], l2[... | rdkit/rdkit-orig | Code/GraphMol/MolChemicalFeatures/Wrap/testChemicalFeatures.py | Python | bsd-3-clause | 5,970 | [
"RDKit"
] | 95e6bf863344f5b1cf9ef365fcbaf4151b7dbfef9c1400df2d0bb6313ec4570c |
# -*- coding: utf-8 -*-
u"""Traits-based GUI for head-MRI coregistration.
Hierarchy
---------
This is the hierarchy of classes for control. Brackets like [1] denote
properties that are set to be equivalent.
::
CoregFrame: GUI for head-MRI coregistration.
|-- CoregModel (model): Traits object for estimating the h... | adykstra/mne-python | mne/gui/_coreg_gui.py | Python | bsd-3-clause | 87,039 | [
"Mayavi"
] | a9094be0c6d7f85bb2df500e2dd289d3e98af47a36ddfc12044656bd06ddb453 |
from gpaw.sphere.lebedev import run, weight_n, Y_nL, R_nv
weight0_n, Y0_nL, R0_nv = run()
assert (abs(weight0_n - weight_n).sum() +
abs(Y0_nL - Y_nL).sum() +
abs(R0_nv - R_nv).sum()) < 1e-13
| qsnake/gpaw | gpaw/test/lebedev.py | Python | gpl-3.0 | 209 | [
"GPAW"
] | 27dd396035ff43d7453db401c5bf29011070de99c87ede3a0348b8b5f89bae75 |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
class Input... | harterj/moose | python/FactorySystem/InputParameters.py | Python | lgpl-2.1 | 4,973 | [
"MOOSE"
] | 0a14a6890090e016fdeb80b3ccbc3cfad51ea1f86179ed3748d72b56c309ca4f |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | espressomd/espresso | samples/visualization_charged.py | Python | gpl-3.0 | 4,827 | [
"Avogadro",
"ESPResSo"
] | a945d4a79a85202bc3456e06676abfa320b2bfb4be0dcde636f626c43f26da4f |
##
# Copyright 2013 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
# the Hercules foundation (http://w... | eth-cscs/production | easybuild/easyblocks/netcdf4_python.py | Python | gpl-3.0 | 2,978 | [
"NetCDF"
] | 345174de07b336466e114d8fb94e758415d818184f54737c846daadfdd87849c |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/bug_1117098 | openlp/plugins/bibles/lib/http.py | Python | gpl-2.0 | 31,062 | [
"Brian"
] | a93feca0a5432b01149753a4e8449dee8cd4944f82b2b0d95ccd7e36a9e29ad6 |
#!/usr/bin/env python
'''
GOAL:
- this code contains all of the code to make figures for paper1
REQUIRED MODULES
- LCSbase.py
'''
###########################
###### IMPORT MODULES
###########################
import LCSbase as lb
from matplotlib import pyplot as plt
import numpy as np
import os
from LCScommon_py3... | rfinn/LCS | python/LCSpaper1.py | Python | gpl-3.0 | 45,395 | [
"Galaxy"
] | 857caa27ee8e4bf1c9d2132dc232379cf4265b74b0d0d6728f6c224ac09ca823 |
# -*- encoding:utf-8 -*-
from __future__ import division, absolute_import, print_function
import sys, textwrap
from ..docscrape import NumpyDocString, FunctionDoc, ClassDoc
from ..docscrape_sphinx import SphinxDocString, SphinxClassDoc
if sys.version_info[0] >= 3:
sixu = lambda s: s
else:
sixu = lambda s: un... | eteq/astropy-helpers | astropy_helpers/sphinx/ext/tests/test_docscrape.py | Python | bsd-3-clause | 18,105 | [
"Gaussian"
] | be220211e1fdbd056a1f9f57c204159ebd55523d0c6ec36d32f0c760bd3bcd77 |
# -*- coding: utf-8 -*-
"""Page and page Component classes
The keteparaha Page and Component classes represent web pages and components
of web pages.
Pages are identified by the URL of the browser, and components by the CSS
selector that is used to retrieve them.
If you perform an action that causes the browser to v... | aychedee/keteparaha | keteparaha/page.py | Python | mit | 20,391 | [
"VisIt"
] | 737afae2ac522035ab62f4a30fc1baa3ee3e3dd3329855c69c620f42926a3685 |
"""
Beta diversity measures (:mod:`skbio.diversity.beta`)
=====================================================
.. currentmodule:: skbio.diversity.beta
This package contains helper functions for working with scipy's pairwise
distance (``pdist``) functions in scikit-bio, and will eventually be expanded
to contain pair... | jensreeder/scikit-bio | skbio/diversity/beta/__init__.py | Python | bsd-3-clause | 6,898 | [
"scikit-bio"
] | 652822557f82056d8c95f6c1f48b982b088ab799937a8ea238540708934a8530 |
# -*- coding: utf-8 -*-
# cldomain is a Common Lisp domain for the Sphinx documentation tool.
# Copyright (C) 2011-2014 Russell Sim <russell.sim@gmail.com>
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software F... | russell/sphinxcontrib-cldomain | sphinxcontrib/cldomain.py | Python | gpl-3.0 | 38,578 | [
"VisIt"
] | e5efe447587e3da61f8246f47c1f66119b8ef65f2d014f355ea386648278b300 |
from sklearn.linear_model import LinearRegression as _sklearn_LinearRegression
from sklearn.gaussian_process import GaussianProcessRegressor
from sklearn import preprocessing
from sklearn.base import TransformerMixin
from sklearn.gaussian_process.kernels import RBF, ConstantKernel as C, RationalQuadratic as RQ
from s... | jpn--/pines | pines/gpr/multitarget.py | Python | mit | 16,391 | [
"Gaussian"
] | 74e5526ef89c2a5b913980448293fc88db233b2c1285966b2336974097715bd2 |
__author__ = 'yurib'
import networkx as nx
import numpy as np
import random
from scipy.special import expit
from commons import WEIGHT, BIAS
class MatrixNN(object):
def __init__(self, layers, seed=None, zeros=False):
if seed:
np.random.seed(seed)
matrix = np.zeros if zeros else np... | yuribak/pyneat | net/net.py | Python | gpl-2.0 | 2,820 | [
"NEURON"
] | d8fda7c871b27906d904513a7c6384bdf8ca029095a4f9b91c1ed70a54742418 |
# -*- coding: utf-8 -*-
#!/usr/bin/python
"""Test of fix for bug 570566 (Orca goes silent when navigating to
uneditable text from an ARIA widget) using Firefox."""
from macaroon.playback import *
import utils
sequence = MacroSequence()
########################################################################
# We wa... | h4ck3rm1k3/orca-sonar | test/keystrokes/firefox/dojo_bug_570566.py | Python | lgpl-2.1 | 4,031 | [
"ORCA"
] | 93898dc8edd3848cd028655cc86c8aa0ed7437ed674e50931d548e5a032db2bf |
# Copyright (c) 2012 OpenStack Foundation
# 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 ... | afrolov1/nova | nova/tests/compute/test_resource_tracker.py | Python | apache-2.0 | 43,467 | [
"exciting"
] | 6b61a8399ad777ba2097d41f2932e5923ba4a0997d003f8bbc06e144b3a1d610 |
#!/usr/bin/env python
'''unit testing code for pysam.
Execute in the :file:`tests` directory as it requires the Makefile
and data files located there.
'''
import pysam
import pysam.samtools
import pysam.bcftools
import unittest
import os
import re
import glob
import sys
import subprocess
import shutil
from TestUtils ... | bioinformed/pysam | tests/samtools_test.py | Python | mit | 12,004 | [
"pysam"
] | 5744bbbbed0fb6472124354e226e95caa87c9c3c049028e27fd4fd9c171d8e03 |
from dolfin import *
from fenics import *
from ply2fn import *
from code import *
from iterator import *
from normal_deriv import *
#comm=dolfin.mpi_comm_self()
#comm.MPI_Init_thread()
#filename="../neuron_mesh_data/neuron"
#ibdry=9
#obdry=10
filename="../head_mesh_data/head"
ibdry=10
obdry=9
#this tries to parse a... | jcrist1/iterated_bdry_solver | src/main.py | Python | mit | 1,506 | [
"NEURON"
] | 7275c33a55b1857e8bd6708414c5ec7a26dd2ba6ff3be21d39bb4d5f625a1e88 |
import tests.base
from netcdf import netcdf as nc
import os
import stat
import numpy as np
class TestNetcdf(tests.base.TestCase):
def test_open_unexistent_file(self):
with self.assertRaisesRegexp(Exception, u'There is not file list or '
'pattern to open.'):
... | gersolar/netcdf | tests/netcdf_test.py | Python | mit | 14,336 | [
"NetCDF"
] | 78ceabc4a80a11e8d3c22bb9ccaf79cd39942f00f9dd4ab851c7e17953e9c4d7 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import json
import os
import unittest
from pymatgen.core.structure import Molecule
from pymatgen.io.nwchem import NwInput, NwInputError, NwOutput, NwTask
from pymatgen.util.testing import PymatgenTest
test_dir = os.path.joi... | vorwerkc/pymatgen | pymatgen/io/tests/test_nwchem.py | Python | mit | 13,075 | [
"NWChem",
"pymatgen"
] | b33f5dfa35ab8fca82d8f5ba91c6245821db60dd9b3fd2c370290714e6ece2b1 |
from typing import Any, Dict
EMOJI_NAME_MAPS: Dict[str, Dict[str, Any]] = {
# seems like best emoji for happy
"1f600": {"canonical_name": "grinning", "aliases": ["happy"]},
"1f603": {"canonical_name": "smiley", "aliases": []},
# the Google emoji for this is not great, so made People/9 'smile' and
#... | zulip/zulip | tools/setup/emoji/emoji_names.py | Python | apache-2.0 | 96,073 | [
"CRYSTAL",
"Octopus"
] | 46564e87ebd8ef7bdc4a105e57fe3c854dd1d7c80bdf89dd53254767405254ea |
# 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 | jax_dft/jax_dft/scf_test.py | Python | apache-2.0 | 27,277 | [
"Gaussian"
] | 006ccde8567bef4e96bcb92c55e3f95466982d613e490d91434e0fa25548579a |
"""Create genome index for BWA aligner."""
import shutil
from pathlib import Path
from plumbum import TEE
from resolwe.process import Cmd, DataField, DirField, FileField, Process, StringField
class BWAIndex(Process):
"""Create BWA genome index."""
slug = "bwa-index"
process_type = "data:index:bwa"
... | genialis/resolwe-bio | resolwe_bio/processes/alignment/bwa_index.py | Python | apache-2.0 | 2,328 | [
"BWA"
] | 63df2961dde98952d866b2625896f6485e68aea3a48599d12ae38434307a2972 |
"""Check options for all agents."""
import logging
import pytest
from DIRAC.tests.Utilities.assertingUtils import AgentOptionsTest
from DIRAC import S_OK
AGENTS = [('DIRAC.AccountingSystem.Agent.NetworkAgent', {'IgnoreOptions': ['MaxCycles', 'MessageQueueURI',
... | andresailer/DIRAC | ConfigurationSystem/test/Test_agentOptions.py | Python | gpl-3.0 | 8,791 | [
"DIRAC"
] | 9d48ea083d75c5fbc960217dbc6bf632dc160df922f1dbe8c8fb19300829b00a |
# -*- coding: utf-8 -*-
"""Batch processing and logic for organizing and binning multiple ADCPData objects.
Tools and methods for cateogizing/manipulating/visualizing data in ADCPy/ADCPData
format. This module is dependent upon adcpy.
This code is open source, and defined by the included MIT Copyright License
Desi... | esatel/ADCPy | adcpy/adcpy_recipes.py | Python | mit | 28,389 | [
"NetCDF"
] | a8f1019fd0328492d2b37670e4a30537e6ed67e8955ba2b174a373cf59181982 |
# Author: Prabhu Ramachandran
# License: BSD style
# Copyright (c) 2004, Enthought, Inc.
""" A Traits-based wrapper for the Visualization Toolkit.
Part of the Mayavi project of the Enthought Tool Suite.
"""
from os.path import exists, join, dirname, isdir
# The tvtk wrapper code is all typically inside one zip fi... | dmsurti/mayavi | tvtk/__init__.py | Python | bsd-3-clause | 1,169 | [
"Mayavi"
] | e56e8767744f61558604accc2d583ddfe2dc091774cc5526f9869ccaee70492b |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2018 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
#... | amjames/psi4 | psi4/driver/qcdb/molparse/to_string.py | Python | lgpl-3.0 | 6,850 | [
"CFOUR",
"NWChem",
"Psi4"
] | 398ef010c511cb545b72a47170075e09f70bffadea951e02caacc1c2292c8e89 |
"""
Compute optical responses with OPTpy
"""
from OPTpy import OPTflow,Structure
#from myLRC import mkjob_by_task
flow = OPTflow(
dirname = './',
#
# Common variables:
#
prefix = 'gaas', # Root name for files required by Tiniba
# Structure from file:
structure=Structure.from_file('G... | trangel/OPTpy | examples/flows/GaAs.py | Python | gpl-3.0 | 2,072 | [
"ABINIT"
] | f40172a7a4a182994e4af3c28a10a2ac3bf5989a2a5d66ed1f8e6ea9887d2393 |
# -*- coding: utf-8 -*-
"""
Created on Wed May 11 08:08:52 2016
@author: tkc
"""
import re
from collections import defaultdict
import pandas as pd
import numpy as np
import scipy
import scipy.stats
from scipy import optimize
from math import factorial # used by Savgol matrix
from scipy.optimize import cu... | tkcroat/Augerquant | Development/Auger_integquant_functions_13Nov16.py | Python | mit | 64,741 | [
"Gaussian"
] | ba5324fb257cb2c735836c990cfb30c4dc9669089c56e6f360a807e21de5a1f9 |
# Copyright 2014-2020 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | sunqm/pyscf | pyscf/pbc/df/test/test_aft.py | Python | apache-2.0 | 18,913 | [
"PySCF"
] | 03cac9607f3780898ffef44f495a627f05e483026237ecb1d9468a3e7d706d14 |
# 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]
... | alchemistry/alchemlyb | versioneer.py | Python | bsd-3-clause | 68,573 | [
"Brian"
] | 797d2ae0c8391ce801fb2363238d3cef45090af9fd2e6202325921023c27cd8d |
from struct import pack, unpack
import SimpleHTTPServer
import SocketServer
import sys
import json
import importlib
PORT = 8052
class MyRequestHandler(SimpleHTTPServer.SimpleHTTPRequestHandler):
def handleGameStringApi(self):
global backend
self.send_response(200)
self.send_header('Conten... | 44670/buyonghenmafanhenleijiunengfanyiyouxi | server.py | Python | gpl-3.0 | 1,447 | [
"VisIt"
] | 79f8c76ab38f54dd430ae9b3afd67b8d57600145dac488b25780487da8cc849b |
# -*- coding: utf-8 -*-
#
# pymicro documentation build configuration file, created by
# sphinx-quickstart on Tue Oct 22 11:17:23 2013.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All... | heprom/pymicro | docs/conf.py | Python | mit | 9,419 | [
"CRYSTAL",
"VTK"
] | 07994fdebd0ff6928498e6678887937eb8972ff432c5f38923896b0e1b08b034 |
# coding=utf-8
# Copyright 2018 The Tensor2Tensor 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 applicable... | mlperf/training_results_v0.5 | v0.5.0/google/research_v3.32/gnmt-tpuv3-32/code/gnmt/model/t2t/tensor2tensor/layers/common_hparams.py | Python | apache-2.0 | 20,898 | [
"MOE"
] | 5ebb5bba774a14b165c11e776590c6b507f9fcca5a0b2d112e1042aa4e32a9bc |
# -*- coding: utf-8 -*-
"""
<DefineSource>
@Date : Fri Nov 14 13:20:38 2014 \n
@Author : Erwan Ledoux \n\n
</DefineSource>
A Brianer
"""
#<DefineAugmentation>
import ShareYourSystem as SYS
BaseModuleStr="ShareYourSystem.Specials.Simulaters.Runner"
DecorationModuleStr="ShareYourSystem.Standards.Classors.Classer"
S... | Ledoux/ShareYourSystem | Pythonlogy/draft/Simulaters/Brianer/draft/__init__ copy.py | Python | mit | 7,536 | [
"Brian",
"NEURON"
] | e90b4457231e4845d73718ed545b80b1b5b0fe6bbe799591fc3934acb2983fcf |
import unittest
import numpy as np
from spglib import get_symmetry
from vasp import read_vasp_from_strings
Al222 = """Al
1.0
8.0786564361761641 0.0000000000000000 0.0000000000000000
0.0000000000000000 8.0786564361761641 0.0000000000000000
0.0000000000000000 0.0000000000000000 8.0786... | jochym/spglib | python/test/test_pure_trans.py | Python | bsd-3-clause | 105,250 | [
"VASP"
] | cc00c9ed817f7a1ac6b05895df9df03bee3964d6e298bfa10c28eb3ea17561be |
#!/usr/bin/env python
#register files to LFN;
#if files are not under /cefs; copy to /cefs/dirac/user/{first-char}/{user-name}/jsub/{mother-dir}/ (don't append full path because of max depth limit of LFN)
#LFN = /{vo}/user/{first-char}/{user-name}/ + full_path
import os
from DIRAC import S_OK, S_ERROR, gLogger, exi... | jsubpy/jsub | jsub/scripts/dirac-register.py | Python | mit | 3,758 | [
"DIRAC"
] | 92a9565e2d3eec45e1e1f837b12959073068089f1ca2c1e44e9ac454548cdb99 |
import numpy as np
from keras.models import Sequential
from keras.layers import Dense
from keras.layers import LSTM
from keras.layers import Activation
from keras.layers import Masking
from keras.optimizers import RMSprop
from keras import backend as k
from sklearn.preprocessing import normalize
"""
Discrete log-l... | daynebatten/keras-wtte-rnn | wtte-rnn.py | Python | mit | 5,661 | [
"NEURON"
] | f432f2bb7968fc206f6e47021f0cd226778f5123609a498b22de8ff70d8dffd7 |
from .agents import *
import utils as u
class AgentXTypeTwoClass(Agent):
def __init__(self, x=2, y=2):
Agent.__init__(self)
##
# Personalize the identifier of this class.
# Will be used instead of the class name
# in neighbours info
self.name = 'AgentXTypeTwo'
... | DMIunipg/AI-Project-VacuumEnvironment | agent_dir/AgentXTypeTwo.py | Python | apache-2.0 | 8,697 | [
"VisIt"
] | b55fe66ea137497f377fa5213880d7a7fc7718990374358716699eea9d98bc25 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
... | kain88-de/mdanalysis | testsuite/MDAnalysisTests/coordinates/reference.py | Python | gpl-2.0 | 9,750 | [
"Amber",
"Gromacs",
"LAMMPS",
"MDAnalysis",
"VMD"
] | 8c8fcb56b298ee3fa1c39a7d6cd1416fa9ac72933e9da5df3fa11976ae7bb061 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# pubvgridprojects - [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 t... | heromod/migrid | mig/cgi-sid/pubvgridprojs.py | Python | gpl-2.0 | 1,155 | [
"Brian"
] | f4ac2e62a79e7d8ca26de19f4d2772d9c12fec7049f769e144c5735cb9f283b3 |
# -*- coding: utf-8 -*-
# TODO: Port to pytest
# PEP8 asserts
from copy import deepcopy
import httplib as http
import time
import mock
import pytest
from nose.tools import * # noqa
from tests.base import OsfTestCase, fake
from osf_tests.factories import (
UserFactory, NodeFactory, ProjectFactory,
AuthUserF... | monikagrabowska/osf.io | addons/wiki/tests/test_wiki.py | Python | apache-2.0 | 60,428 | [
"VisIt"
] | a2f09e1091de497bebe1284b8d95c4611cb3fb1ecc8f426cbff7b2339f82b4c5 |
"""
This is used to test the ElasticSearchDB module. It is used to discover all possible changes of Elasticsearch api.
If you modify the test data, you have to update the test cases...
"""
import unittest
import sys
import datetime
import time
from DIRAC import gLogger
from DIRAC.Core.Utilities.ElasticSearchDB import... | andresailer/DIRAC | tests/Integration/Core/Test_ElasticsearchDB.py | Python | gpl-3.0 | 24,576 | [
"DIRAC"
] | 74718920b2f6f4920e02759a69b83e8bb237f331493685d2e6dd0fcd3f58a145 |
from numpy import (logical_and, asarray, pi, zeros_like,
piecewise, array, arctan2, tan, zeros, arange, floor)
from numpy.core.umath import (sqrt, exp, greater, less, cos, add, sin,
less_equal, greater_equal)
# From splinemodule.c
from .spline import cspline2d, sepfir2d... | aeklant/scipy | scipy/signal/bsplines.py | Python | bsd-3-clause | 12,007 | [
"Gaussian"
] | de05aa2589356a8f8f74555a521d681838b49466b7290b512ca98a8df018ca51 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2008 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 Software F... | tiagocardosos/stoq | stoqlib/gui/wizards/purchasequotewizard.py | Python | gpl-2.0 | 23,378 | [
"VisIt"
] | 20032670f0fe45bd7d55c8197431bce9f9bdf4a78f6464a622fdf3b91b3481b1 |
from scipy import sparse
from klampt import vectorops
import math
import numpy as np
from leastsq_bounds import leastsq_bounds
from controller import BaseController
from system_id import LinearSystemID
from online_leastsq import OnlineLeastSquares
def spdot(A, B):
"The same as np.dot(A, B), except it works even if... | stevekuznetsov/Klampt | Python/control/MotionModel.py | Python | bsd-3-clause | 20,440 | [
"BLAST"
] | a03cf577e908838b1917f5f2813b651ad3b8d800fa6d441b281787dabfab044f |
# -*- coding: utf-8 -*-
"""
Created on Thu Jan 24 13:30:42 2013
$Id: transects.py 11076 2014-08-28 17:52:41Z heijer $
$Date: 2014-08-28 19:52:41 +0200 (Thu, 28 Aug 2014) $
$Author: heijer $
$Revision: 11076 $
$HeadURL: https://svn.oss.deltares.nl/repos/openearthtools/trunk/python/applications/jarkus_transects/... | openearth/jarkus | jarkus/transects.py | Python | gpl-3.0 | 12,785 | [
"NetCDF"
] | 128ad1ac6f6962ec39d6e95d9dd72097108eac3a62bc5c168aed06a2aa377bf3 |
#
# Copyright (C) 2008, Brian Tanner
#
# http://rl-glue-ext.googlecode.com/
#
# Licensed under the Apache License, Version 2.0 (the "License"
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless requi... | evenmarbles/rlglued | examples/skeleton/skeletonexperiment.py | Python | bsd-3-clause | 3,325 | [
"Brian"
] | 16547531c7b8dc8ae8674d9b74c3105bdaac7da53d7af839dfaca33ea58fe027 |
#
# libtcod 1.5.2 python wrapper
# Copyright (c) 2008,2009,2010 Jice & Mingos
# 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... | v4nz666/MineClimbeR-L- | RoguePy/libtcod/libtcodpy.py | Python | mit | 61,359 | [
"Amber"
] | bbaf11ee6415761d7ec0a707a08f99db2489c6f1a241f274191236c21c70a6bc |
import copy
import numpy as np
import pytest
import qcelemental as qcel
from qcelemental.testing import compare, compare_recursive, compare_values, tnm
import qcengine as qcng
from qcengine.programs import empirical_dispersion_resources
from qcengine.testing import is_program_new_enough, using
from .addons import usi... | ashutoshvt/psi4 | tests/pytests/test_qcng_dftd3_mp2d.py | Python | lgpl-3.0 | 19,641 | [
"Psi4"
] | f59fe18228b75f75c23e3163d4d02e9ece7291033c033c018e7e901d3fea55f9 |
# 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... | ghchinoy/tensorflow | tensorflow/python/training/learning_rate_decay.py | Python | apache-2.0 | 29,150 | [
"Gaussian"
] | 13ebdf750202396485c88b1782a5ba2b3bfeb0523eafee4273c6c568f5373bdb |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""The minc module provides classes for interfacing with the `MINC
<http://www.bic.mni.mcgill.ca/ServicesSoftware/MINC>`_ command line tools. This
module was written to work with MINC version 2.2.00.
Auth... | sgiavasis/nipype | nipype/interfaces/minc/minc.py | Python | bsd-3-clause | 111,261 | [
"Gaussian",
"NetCDF"
] | 16868e0ccf54da9db6cf5ae60407b7d3006515cc526509a54a307aa878d6de0d |
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