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# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Utilities for defects module.
"""
import itertools
import logging
import math
import operator
from collections import defaultdict
from copy import deepcopy
import numpy as np
import pandas as pd
from monty.dev import req... | vorwerkc/pymatgen | pymatgen/analysis/defects/utils.py | Python | mit | 59,873 | [
"CRYSTAL",
"Gaussian",
"VASP",
"VTK",
"pymatgen"
] | bd6989f1f0d9f4da84625f14bfbf58743235820fc7e7cd10d8d466c3f7b1270d |
# -*- coding: utf-8 -*-
class Beverage:
def __init__(self):
self._description = "Unknown beverage"
def get_description(self):
return self._description
def cost(self):
pass
class CondimentDecorator(Beverage):
def get_description(self):
return None
# Beverages
clas... | tisOO/Patterns | decorator/python/example_1/decorator.py | Python | mit | 2,348 | [
"ESPResSo"
] | f938e4df27329f468037f7246902c99bbc0906073758844441299f27c6c362fa |
import numpy
import mcfit
from scipy.interpolate import InterpolatedUnivariateSpline
from .power.zeldovich import ZeldovichPower
NUM_PTS = 1024
def xi_to_pk(r, xi, ell=0, extrap=False):
r"""
Return a callable function returning the power spectrum multipole of degree
:math:`\ell`, as computed from the Four... | bccp/nbodykit | nbodykit/cosmology/correlation.py | Python | gpl-3.0 | 4,545 | [
"Gaussian"
] | f1d9196e68bfa9275d08df58e344626c779a5e2c4fcd781e3051cb94186afd76 |
#!/usr/bin/env python
# Copyright 2015 The Kubernetes 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 appli... | bradtopol/kubernetes | cluster/juju/layers/kubernetes-master/reactive/kubernetes_master.py | Python | apache-2.0 | 47,713 | [
"CDK"
] | a5a94a142a5673c164e07a72145a2dbee4f891648a1435c552287d439850d49e |
'''
Created on 2Sep.,2016
@author: Alex Ip
'''
import os
import sys
import errno
import logging
import re
import subprocess
import tempfile
from shutil import rmtree
import glob
from osgeo import gdal, gdalconst
import netCDF4
from geophys_utils import array_pieces
import numpy as np
from functools import reduce
from ... | alex-ip/geophys2netcdf | utils/check_netcdf_vs_ers.py | Python | apache-2.0 | 18,541 | [
"NetCDF"
] | b0a3836afabda156024afb137c0d3a0509e68ce8fb7f14ca8b18b423d4860b8b |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | lgarren/spack | var/spack/repos/builtin/packages/r-geoquery/package.py | Python | lgpl-2.1 | 2,092 | [
"Bioconductor"
] | b3db1099e2d8a34273860d4459e02caf238a3fcc1a704b52b4a4682a2fa61e6e |
from __future__ import absolute_import
import numpy as nm
import sfepy.discrete.fem.periodic as per
from sfepy.discrete.fem.mesh import Mesh
from sfepy.mechanics.matcoefs import stiffness_from_youngpoisson
from sfepy.homogenization.utils import define_box_regions
import sfepy.homogenization.coefs_base as cb
from sfepy... | lokik/sfepy | examples/homogenization/homogenization_opt.py | Python | bsd-3-clause | 5,106 | [
"VTK"
] | 650910f014cc082028d37daaf3369b83d7e8a565ef01e4a1294c44599e13e563 |
# coding: utf-8
"""
Acceptance tests for Studio's Setting pages
"""
from __future__ import absolute_import, unicode_literals
import json
import os
import random
import string
from textwrap import dedent
import six
from bok_choy.promise import EmptyPromise
from mock import patch
from six.moves import range
from commo... | ESOedX/edx-platform | common/test/acceptance/tests/studio/test_studio_settings.py | Python | agpl-3.0 | 48,872 | [
"VisIt"
] | 19b1c98bb78329a95e20eb19da154c679cdd00de3a79dc6a34edb23edb63d6f5 |
"""
BLAST+7 format (:mod:`skbio.io.format.blast7`)
==============================================
.. currentmodule:: skbio.io.format.blast7
The BLAST+7 format (``blast+7``) stores the results of a BLAST [1]_ database
search. This format is produced by both BLAST+ output
format 7 and legacy BLAST output format 9. The ... | gregcaporaso/scikit-bio | skbio/io/format/blast7.py | Python | bsd-3-clause | 15,434 | [
"BLAST",
"scikit-bio"
] | 9c9f6dd016650851b3ed0731fc9b08f70703b379226ac29a126a5fc476529f0c |
class Node(object):
'''Basic interface for nodes traversed by the floodfill algo.
Floodill will give a label to each node corresponding to the
disconnected subgraph it corresponds to.
The linked attribute is a list that should contain the elements y-linkes.
'''
def __init__(self):
s... | semkiv/heppy_fcc | fastsim/pfalgo/floodfill.py | Python | gpl-3.0 | 2,206 | [
"VisIt"
] | f4b2532959e218844a9c992529cddb7732809678c3c004683caa3283e0a3e390 |
# Copyright (c) 2015, Frappe Technologies Pvt. Ltd. and Contributors
# License: GNU General Public License v3. See license.txt
from __future__ import unicode_literals
import frappe
import json
import frappe.utils
from frappe.utils import cstr, flt, getdate, comma_and
from frappe import _
from frappe.model.mapper impor... | shitolepriya/test-erp | erpnext/selling/doctype/sales_order/sales_order.py | Python | agpl-3.0 | 14,950 | [
"VisIt"
] | 7aa47a16fdaa8c9c6f01c5bb70bdc4bcd5326b5b2254ce9a24ddd94c148b67e1 |
import os
import numpy
from Cython.Build import cythonize
from setuptools import setup, Extension
libraries = []
if os.name == "posix":
libraries.append("m")
include_dirs = [
numpy.get_include(),
]
ext = cythonize([
Extension("acannon._filter",
sources=["acannon/_filter.pyx"],
... | dfm/AsteroCannon | setup.py | Python | mit | 950 | [
"Gaussian"
] | c8772ff463666a46fbb7b20dda90c1e5a6aaef1dacab8bd897f3ff3846feb363 |
"""
# Notes:
- This simulation seeks to emulate the CUBA benchmark simulations of (Brette
et al. 2007) using the Brian2 simulator for speed benchmark comparison to
DynaSim. However, this simulation does NOT include synapses, for better
comparison to Figure 5 of (Goodman and Brette, 2008).
- The time taken to si... | asoplata/dynasim-benchmark-brette-2007 | output/Brian2/brian2_benchmark_CUBA_nosyn_16000/brian2_benchmark_CUBA_nosyn_16000.py | Python | gpl-3.0 | 2,009 | [
"Brian"
] | a8af66607443dadcef8ba75addd8af00775abec66e0408d19f38f1fdc1eed6a3 |
#!/usr/bin/env python
#
# calculate_ani.py
#
# This script calculates Average Nucleotide Identity (ANI) according to one of
# a number of alternative methods described in, e.g.
#
# Richter M, Rossello-Mora R (2009) Shifting the genomic gold standard for the
# prokaryotic species definition. Proc Natl Acad Sci USA 106: ... | widdowquinn/scripts | bioinformatics/calculate_ani.py | Python | mit | 48,841 | [
"BLAST",
"Biopython"
] | 87ac9cd8432e95c537623562b5b59244f30dd771b905ed17284cdcd4dc64fa06 |
# Copyright (C) 2010-2018 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 v... | mkuron/espresso | testsuite/python/drude.py | Python | gpl-3.0 | 11,080 | [
"Avogadro",
"ESPResSo",
"LAMMPS"
] | 9224272727aeefcdd32c3700603cb40d758f699c7e4abbdce61299eba4883ca4 |
#!/usr/bin/python
"""
biogeographer Copyright (C) 2012 Jose Sergio Hleap
This Script will fetch results from GBIF for macoecological and biogeografical studies.
It is Based on the BioGeography is a module under development by Nick Matzke for a Google
Summer of Code 2009 project. It is run through NESCENT's Phyloinform... | jshleap/Biogeography | biogeographer.py | Python | gpl-3.0 | 63,976 | [
"Biopython"
] | 0ff3585b5308dbdfaf6f28720b5a812a3576e78ded2a402661a6b5a5b737feaa |
# Orca
#
# Copyright 2004-2009 Sun Microsystems Inc.
#
# 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... | GNOME/orca | src/orca/script.py | Python | lgpl-2.1 | 19,494 | [
"ORCA"
] | 798d9ca2e87a943882047cac268c1be144eeb862cd4601cdf34ebeb01ec08689 |
#!/usr/bin/env python
#
# Copyright (C) 2014 Diamond Light Source, Karl Levik
#
# 2015-06-22
#
# Usage examples:
# python em_put_movie.py --visit=em11069-2 --sampleid=181182 --microscopeid=1 --mfile=/dls/m01/data/2014/em11069-2/raw/May11_10.01.12.mrc
#
# Assuming the previous returns --movieid=2:
# python em_put_movie.... | DiamondLightSource/ispyb-api | bin/em_put_movie.py | Python | apache-2.0 | 9,278 | [
"VisIt"
] | 1ebd789214709c915fe0301c25414f6d79663c74006a86b6a5ec392fb9aee9d3 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import print_function
import sys
import vtk
class LUTUtilities(object):
'''
Utilities for displaying and comparing lookup tables.
'''
def __init__(self):
pass
def DisplayLUTAsString(self, lut):
'''
Display the... | lorensen/VTKExamples | src/Python/Utilities/LUTUtilities.py | Python | apache-2.0 | 12,108 | [
"VTK"
] | 403e3561d9ec101f6ac37d54f1ac9e57c20375a75e223bcaffea5799ceb6afdc |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | mfherbst/spack | var/spack/repos/builtin/packages/pism/package.py | Python | lgpl-2.1 | 6,910 | [
"NetCDF"
] | 8ea7aba144d686273ab954b80c61a219e2828a19bea78f0cdba0774dd8960044 |
##~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~##
## ##
## This file forms part of the Badlands surface processes modelling companion. ##
## ... | badlands-model/pyBadlands-Companion | badlands_companion/eroFunctions.py | Python | gpl-3.0 | 7,636 | [
"Gaussian"
] | f3ae1c517bca9ceebf58a3b557bd6be62c97e009e840c61a07906043d6e5aabb |
# coding: utf8
{
'"update" is an optional expression like "field1=\'newvalue\'". You cannot update or delete the results of a JOIN': '"update" é uma expressão opcional como "field1=\'newvalue\'". Você não pode actualizar ou apagar os resultados de uma JOIN',
'# of International Staff': 'nº de pessoal internacional',
'#... | flavour/porto | languages/pt.py | Python | mit | 298,698 | [
"VisIt"
] | 0bf2feffb143f7847d602589a0cfdfd6dc3f9f239ded55479ae5111ec08ec4d6 |
import ast
import astor
from .graph import graph_walk
def ast_repr(obj):
if isinstance(obj, ast.AST):
obj_class = obj.__class__.__name__
source = ast_source(obj)
return('ast.{obj_class}: {source}'.format(**locals()))
if isinstance(obj, list):
return([ast_repr(o) for o in obj]... | dalejung/asttools | asttools/repr.py | Python | mit | 2,556 | [
"VisIt"
] | 3f220f7810bb46b000e37cf85f36df44a0b2a346011ba070740340260a11f7e6 |
# -*- coding: utf-8 -*-
"""
Created on Wed May 17 19:20:06 2017
@author: Ratnadeepb
"""
## Particle Filter Class
import numpy as np
import numpy.linalg as la
import scipy.stats as st
from robot_class import robot
class particle_filter:
def __init__(self, no_of_particles, my_world, my_robot):
if my_world... | ratnadeepb/AI_for_Robotics | particle_filter.py | Python | mit | 3,067 | [
"Gaussian"
] | 9d085c9a525b05c6844ca05ab6dcc3f3acdc18acf5754f531e2e272c9a6ac034 |
#!/usr/bin/env python
# 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
#
# U... | sunqm/pyscf | pyscf/scf/test/test_ghf.py | Python | apache-2.0 | 14,677 | [
"PySCF"
] | ff7192a7abe7bb78a24194d47397978122a93e971a6523d2cea910901d297c6b |
# -*- coding: utf-8 -*-
#
# tsodyks_facilitating.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the Li... | synergetics/nest | pynest/examples/tsodyks_facilitating.py | Python | gpl-2.0 | 3,792 | [
"NEURON"
] | d0a3c41da5d682cc2c933c6bddd1e187db68a8d134be58123bc1da0a8b8f8531 |
#!/usr/bin/env python
#########################################################################################
# Various modules for registration.
#
# ---------------------------------------------------------------------------------------
# Copyright (c) 2015 NeuroPoly, Polytechnique Montreal <www.neuro.polymtl.ca>
# ... | 3324fr/spinalcordtoolbox | scripts/msct_register.py | Python | mit | 44,449 | [
"Gaussian"
] | fb67a2243370730db1474809ebf6fb82e0957d6140fd6cc6b90d96d316a85836 |
"""Actions to start various modules.
"""
# Author: Prabhu Ramachandran <prabhu_r@users.sf.net>
# Copyright (c) 2005-2015, Enthought, Inc.
# License: BSD Style.
# Local imports.
from mayavi.core.registry import registry
from mayavi.core.metadata import ModuleMetadata
from mayavi.core.pipeline_info import PipelineInfo
... | dmsurti/mayavi | mayavi/action/modules.py | Python | bsd-3-clause | 2,525 | [
"Mayavi"
] | f2c71301c34f1f2ee3bfc6f76f035a9f0586173f459991f67093684a7d5aa271 |
"""A GTK dialog which displays a list of Zero Install applications in the menu."""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall import _, gobject
import os, sys
import gtk, pango
import subprocess
from zeroinstall import support
from zeroinstal... | timdiels/0install | zeroinstall/gtkui/applistbox.py | Python | lgpl-2.1 | 11,331 | [
"VisIt"
] | ec1abddeec562c5052447fbe7215dc4769fd14acfd9ebf59d5e8acd13830993d |
# import numpy as np
# from scipy import stats
# from mayavi import mlab
# import multiprocessing
# import matplotlib.pyplot as plt
#
# x, y = np.mgrid[-1.0:1.0:30j, -1.0:1.0:30j]
# # Need an (N, 2) array of (x, y) pairs.
# xy = np.column_stack([x.flat, y.flat])
#
# mu = np.array([0.0, 0.0])
#
# sigma = np.array([.025,... | isomerase/RoboSkeeter | test_3dheat.py | Python | mit | 3,099 | [
"Mayavi"
] | 7aedac45737d0fc79b57256dae178a9449244a3887fccaa8b49caf47c62e61f0 |
#
# Copyright 2014-2015, 2021 Lars Pastewka (U. Freiburg)
#
# matscipy - Materials science with Python at the atomic-scale
# https://github.com/libAtoms/matscipy
#
# 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 Sof... | libAtoms/matscipy | matscipy/fracture_mechanics/energy_release.py | Python | lgpl-2.1 | 3,951 | [
"ASE",
"CRYSTAL",
"Matscipy"
] | 2d4dc6df85ee45f04378cedb3775756b56070da9c0aab23ed9aa457d2e2ac725 |
__author__ = 'chris hamm'
#NetworkClient_r9E
#Created: 1/17/2015
#THINGS ADDED/CHANGED FROM THIS REVISION
#Removed some old commented lines of code that have been there forever
#THINGS ADDED FROM REVISION 9D
#Added functions to parse chunk objects (Has now been decided that these will not be needed)
#Added a comma... | COCS4950G7/COSC4950 | Source/Network/Obsolete/NetworkClient_r9E.py | Python | gpl-3.0 | 47,281 | [
"ADF"
] | 67dd7b83cc9411e88542d5d17cf09591a61c46a26f02bcb436cf93484ac43b4a |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | wscullin/spack | var/spack/repos/builtin/packages/wannier90/package.py | Python | lgpl-2.1 | 3,894 | [
"Wannier90"
] | cd52457778aad2727c44ba4f70a3e0232f993a5f6b410f0134f2087b2a425a0a |
# -*- coding: utf-8 -*-
#
# brunel_alpha_nest.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the Licen... | tillschumann/nest-simulator | pynest/examples/brunel_alpha_nest.py | Python | gpl-2.0 | 11,873 | [
"NEURON"
] | f798cf10dd0173f7c8bc077fb30f29813536377cafffc79314892875bf4bed05 |
from __future__ import with_statement
import os
import sys
import numpy
from pyresample.test.utils import catch_warnings
from pyresample import kd_tree, utils, geometry, data_reduce
if sys.version_info < (2, 7):
import unittest2 as unittest
else:
import unittest
class Test(unittest.TestCase):
area_def... | mitkin/pyresample | pyresample/test/test_kd_tree.py | Python | lgpl-3.0 | 42,707 | [
"Gaussian"
] | 8c1ca15fb0d3b97f91b7ccf93a4b121df04b5de41941260a16f7299108a2b233 |
# bs_bin.py
# Author: Jesse Fish
#
# Description: Visit NYC 'GOAT' site, using an address within the URL,
# and grab BIN for each building. Data then merged into dataset for
# use with GIS/shapefile maps for visualization.
from bs4 import BeautifulSoup
import urllib
import time
# open list of brooklyn addresses t... | heatseeknyc/data-science | src/bs_bin.py | Python | mit | 1,474 | [
"VisIt"
] | 53c148d06aa1715892b46bc30e2cf3226ff3d85cd375f3ad8d98f2fefda104ea |
# coding=utf-8
from __future__ import unicode_literals
from .. import Provider as PersonProvider
class Provider(PersonProvider):
# conforming to http://nl.wikipedia.org/wiki/Achternaam#Naamswijziging and
# http://en.wikipedia.org/wiki/Dutch_name#Dutch_naming_law_.28surnames.29
# by adding a "-" between t... | deanishe/alfred-fakeum | src/libs/faker/providers/person/nl_NL/__init__.py | Python | mit | 22,069 | [
"Amber",
"Brian",
"FLEUR"
] | 11570d838d6e16fb83c2dca459468ef5f9640955dc4325fca0fb114bf7738509 |
"""
This module provides classes and functions for pass management.
There are two kinds of passes: transformations and analysis.
* ModuleAnalysis, FunctionAnalysis and NodeAnalysis are to be
subclassed by any pass that collects information about the AST.
* gather is used to gather (!) the result of an an... | pombredanne/pythran | pythran/passmanager.py | Python | bsd-3-clause | 7,750 | [
"VisIt"
] | 99326f17c2263000b502904293b197fda47cb77b7b0cd7db2b604989445c6bae |
# From pairing session Juan <> Marlene 2021-05-06
import napari
import skan
from matplotlib import cm
from skimage import io
from skimage.exposure import exposure
from skimage.filters import gaussian
from skimage.filters import threshold_mean
from skimage.filters import frangi
from skimage.morphology import remove_sm... | jni/useful-histories | vessel-skeleton-analysis.py | Python | bsd-3-clause | 5,778 | [
"Gaussian",
"Napari"
] | 0658a07bd43729fd5a7e20b5d8e9fdb616337eccaf88d30416de4313f98c2bbc |
from ase import Atoms, Atom
from gpaw import GPAW, Mixer
from ase.lattice.surface import fcc100
from gpaw.transport.jstm import dump_hs, dump_lead_hs
calc = GPAW(h=0.2,
mixer=Mixer(0.03, 5, weight=140.0),
width=0.1,
mode='lcao',
basis='szp(dzp)',
txt='dumph... | qsnake/gpaw | doc/tutorials/negfstm/dumphs.py | Python | gpl-3.0 | 2,003 | [
"ASE",
"GPAW"
] | 15cfcfb0211bbbce6603e32e41ed0c02f892c07fbd0fec8a473ba03d2b5a912f |
import parser
primitive_types = {
'void': "void",
'char': "ubyte",
'unsigned char': "ubyte",
'signed char': "sbyte",
'short': "short",
'signed short': "short",
'unsigned short': "ushort",
'int': "int",
'si... | cheery/cffi-gen | translator.py | Python | mit | 8,220 | [
"VisIt"
] | f6b33bd74110a77cabf15fc752041147d0b2b9f4cd5fce93fc68d810877e32e7 |
# 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... | reminisce/mxnet | python/mxnet/contrib/onnx/onnx2mx/_op_translations.py | Python | apache-2.0 | 34,961 | [
"Gaussian"
] | 06aa5f489cd93b35fbbb6e634b11bb6b727b6d06e8d595dd628ee457bead0548 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
#
# Copyright (C) 2017 Lenovo, Inc.
#
# 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 Licens... | ravibhure/ansible | lib/ansible/modules/network/cnos/cnos_conditional_template.py | Python | gpl-3.0 | 8,748 | [
"VisIt"
] | dde4fa07b95d3ff558bc2c94629d8cd70154d7653163d188a5e15b9600bc98c6 |
# coding=utf-8
"""
install_examples.py
Dialogs that installs scripts to a desired directory. Simple front end to
sfc_models.examples.install_example_scripts
Migrated to sfc_models.examples
License/Disclaimer
------------------
Copyright 2017 Brian Romanchuk
Licensed under the Apache License, Version 2.0 (the "Lic... | brianr747/sfc_gui | sfc_gui/install_examples.py | Python | apache-2.0 | 2,146 | [
"Brian"
] | 9c285c6919fd32da79d346b6c4960cc19023cb34c12eec55a4729243d113fd80 |
from r18_1 import *
h.load_file("CNSutils.hoc")
def distance_from_soma(segname):
"""d = distance_from_soma(segname) returns the distance of the segment
from the center of the soma. segname should have be a string that follows
the convention how the NEURON refers to a point in a segment, e.g., 'dend1[802](... | shhong/a310_cns_2017 | Assignment_2/hw2_1.py | Python | gpl-3.0 | 1,067 | [
"NEURON"
] | 7c43ecaa43e19d3dbfa97c1a60217f78a500839c1e715f46d1331b3c093165f0 |
#!/usr/bin/env python2
from __future__ import division
import sys
import itertools
import re
import warnings
from statepoint import StatePoint
alphanum = re.compile(r"[\W_]+")
err = False
################################################################################
def parse_options():
"""Process command lin... | keadyk/openmc_mg_prepush | src/utils/statepoint_3d.py | Python | mit | 13,565 | [
"VTK"
] | 183e6cfa0892110f30094fb0c050e019166fbbd0182ee23f2f9e12eedc3731fa |
import tempfile
import unittest
import os
import numpy as np
from deepchem.utils import rdkit_utils
class TestRdkitUtil(unittest.TestCase):
def setUp(self):
# TODO test more formats for ligand
current_dir = os.path.dirname(os.path.realpath(__file__))
self.protein_file = os.path.join(
current_... | deepchem/deepchem | deepchem/utils/test/test_rdkit_utils.py | Python | mit | 7,194 | [
"RDKit"
] | 473279b5abcc26fc87181a19a108057332eb6ceb51c3085e5287ee8d56a7ec7e |
#!/usr/bin/env python
import sys
import math as m
import numpy as np
import scipy.linalg as linalg
import scipy
try:
target_rho = float(sys.argv[1])
nx, ny, nz = [int (x) for x in sys.argv[2:5]]
real_N = int(sys.argv[5])
except:
print >> sys.stderr, "# BCC, 2 particles per cell"
print >> sys.stder... | lorenzo-rovigatti/PatchyParticles | dobccrrr.py | Python | gpl-3.0 | 2,347 | [
"CRYSTAL"
] | c3de0f60455e3bdcc4f90610da5dafa55475ae4a8e1ffdd2ea249057ec934858 |
"""
This integration tests will perform basic operations on a storage element, depending on which protocols are available.
It creates a local hierarchy, and then tries to upload, download, remove, get metadata etc
Potential problems:
* it might seem a good idea to simply add tests for the old srm in it. It is not :-)
... | arrabito/DIRAC | tests/Integration/Resources/Storage/Test_Resources_GFAL2StorageBase.py | Python | gpl-3.0 | 14,225 | [
"DIRAC"
] | 4af381548825bd51adfe7c62984af5e91ea46df42c1b715cdb84034715d07ec5 |
""" Command line interface
"""
from __future__ import absolute_import
import click
import sys
from os import listdir
from os.path import abspath, dirname, join
from . import io
from .util import xdg_config_file
from .config import ConfigManager
CONTEXT_SETTINGS = dict(help_option_names=['-h', '--help'],
... | galaxyproject/starforge | starforge/cli.py | Python | mit | 2,285 | [
"Galaxy"
] | f4f3b479e5c5db943cc0866a36ca63b0bbf469e71a087d0461304ba7d902f363 |
"""Testing for Gaussian process classification """
# Author: Jan Hendrik Metzen <jhm@informatik.uni-bremen.de>
# Licence: BSD 3 clause
import numpy as np
from scipy.optimize import approx_fprime
from sklearn.gaussian_process import GaussianProcessClassifier
from sklearn.gaussian_process.kernels import RBF, Constant... | kashif/scikit-learn | sklearn/gaussian_process/tests/test_gpc.py | Python | bsd-3-clause | 6,061 | [
"Gaussian"
] | 489c76f4e14cb0941cfe927672aa8561695dde4a8f1c074d7d1a70eec5a562e1 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
import mysql.connector
#check visitor's relationship with user of current page
def checkRelation(visitorId, pageId, cnx):
#visitor visit his own page, return 2
if visitorId == pageId:
return str(2)
relationQuery = ('SELECT * From user_relation WHERE ((appl... | byn9826/Thousand-Day | handler/relation.py | Python | bsd-3-clause | 6,749 | [
"VisIt"
] | 7abed6834f2b8627168bf70c8676d67e1bd0b859c3f95870d931a30b7fa4755d |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
It generates the list of candidate fusion genes found in healthy samples. This list is hard coded inhere.
Author: Daniel Nicorici, Daniel.Nicorici@gmail.com
Copyright (c) 2009-2021 Daniel Nicorici
This file is part of FusionCatcher.
FusionCatcher is free software:... | ndaniel/fusioncatcher | bin/generate_healthy.py | Python | gpl-3.0 | 499,375 | [
"VASP"
] | 4a644ebe74a97d6921c26b039f9b95a04680f3d9a51302c3dd99973f0e4e514c |
from __future__ import absolute_import
from django.core.urlresolvers import reverse
from sentry.message_filters import _legacy_browsers_filter, get_filter_key # noqa
from sentry.models.projectoption import ProjectOption
from sentry.models.auditlogentry import AuditLogEntry, AuditLogEntryEvent
from sentry.testutils i... | mvaled/sentry | tests/sentry/filters/test_legacy_browsers.py | Python | bsd-3-clause | 16,932 | [
"Galaxy"
] | 29c38f7e488c38beefad6add5fc491ace2ae0a3f8f171e6ac96023be68ad2106 |
# Copyright 2017 Joachim van der Herten
#
# 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 wr... | GPflow/GPflowOpt | gpflowopt/acquisition/lcb.py | Python | apache-2.0 | 2,296 | [
"Gaussian"
] | 6d367b009f7e2c97ea77e758e9a074b1808392e1e8b0fa8e9afb91aeed3959b5 |
import sys
import argparse
from svtools.external_cmd import ExternalCmd
class GenotypeVariants(ExternalCmd):
def __init__(self):
super(GenotypeVariants, self).__init__('svtyper', 'bin/svtyper/svtyper')
@staticmethod
def svtyper_option_lut():
opts = {
'bam' : '-B',
... | ernfrid/svtools | svtools/genotype.py | Python | mit | 3,094 | [
"BWA"
] | 97aaed558b6812a48a08e753feb05e8c7579b62b4fdf4dc857f03bb56758c582 |
# Copyright 2015 Google Inc. 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 applicable law or a... | pombredanne/enjarify | enjarify/jvm/optimization/stack.py | Python | apache-2.0 | 8,910 | [
"VisIt"
] | f40837e93f6d5a666975e616d5cc83c921188495d8eb227229b98873771d7a4b |
#!/usr/bin/env python
# Copyright 2008, 2009
# CAMd (see accompanying license files for details).
import os
from optparse import OptionParser, SUPPRESS_HELP
import ase.gui.i18n
from gettext import gettext as _
# Grrr, older versions (pre-python2.7) of optparse have a bug
# which prevents non-ascii descriptions. Ho... | alexei-matveev/ase-local | ase/gui/ag.py | Python | gpl-2.0 | 5,411 | [
"ASE"
] | 87a8665f41d7710a034065aeff075e0ed10988d238944ccb08ff22a5303242aa |
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publi... | thica/ORCA-Remote | src/ORCA/widgets/Settings.py | Python | gpl-3.0 | 13,916 | [
"ORCA"
] | f4024a6aef6fac63bce1e61a58f467a27e596c9e4dfd7cfbd3ba6d5804588085 |
# -*- coding: utf-8 -*-
"""Utilities to assemble a BEL graph as bipartite graph of nodes and reified edges."""
import logging
import warnings
from abc import ABC, abstractmethod
from itertools import starmap
from typing import Optional, Tuple
import networkx as nx
import pybel.constants as pbc
from pybel import BEL... | pybel/pybel-tools | src/pybel_tools/assembler/reified_graph/assembler.py | Python | mit | 13,715 | [
"Pybel"
] | 03d63bd2a45ebc3c7eb6b13fa74c63f33cdb135842c80bc2b6738c4a785a111a |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2007 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... | andrebellafronte/stoq | stoqlib/domain/invoice.py | Python | gpl-2.0 | 4,316 | [
"VisIt"
] | 4da164cb5e8c177ed2ede1cc0129960c580a49de67f8bce426bb09030804f7d1 |
#!/usr/bin/env python3
# encoding: utf-8
# Copyright (C) 2016 Space Science and Engineering Center (SSEC),
# University of Wisconsin-Madison.
#
# 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... | davidh-ssec/polar2grid | polar2grid/readers/viirs_l1b.py | Python | gpl-3.0 | 16,737 | [
"NetCDF"
] | 4c3b6a135281803a3e977971e45b8895e1b8982d7b9bedc1994e3b43373691c0 |
import math
import numpy as np
import matplotlib.pyplot as plt # for plotting stuff
from random import seed, shuffle
from scipy.stats import multivariate_normal # generating synthetic data
SEED = 1122334455
seed(SEED) # set the random seed so that the random permutations can be reproduced again
np.random.seed(SEED)
de... | jmikko/fairnessML | zafar_methods/disparate_impact/synthetic_data_demo/generate_synthetic_data.py | Python | gpl-3.0 | 4,038 | [
"Gaussian"
] | 826145dadbb9783948c766fb40b85380e43459db4b812db4d0be760d8fc1034e |
import numpy as np
from scipy.ndimage.filters import gaussian_filter, gaussian_laplace
import itertools as itt
import math
from math import sqrt, hypot, log
from numpy import arccos
from skimage.util import img_as_float
from .peak import peak_local_max
# This basic blob detection algorithm is based on:
# http://www.c... | chintak/scikit-image | skimage/feature/blob.py | Python | bsd-3-clause | 10,379 | [
"Gaussian"
] | b9da7a7e5ca607e22e4eb35f2744378196492c920ee32f852a63e972ffed66a6 |
# -*- coding: utf-8 -*-
from setuptools import setup, find_packages
from turbogears.finddata import find_package_data
import os
execfile(os.path.join("funcweb", "release.py"))
packages=find_packages()
package_data = find_package_data(where='funcweb',
package='funcweb')
if os.path.isdir('locales'):
packages.a... | pombredanne/func | funcweb/setup.py | Python | gpl-2.0 | 2,958 | [
"VisIt"
] | d74a3155877ecdfedb335b8c87342513390209fb5cfa3d965f5dca11e754deac |
"""Soundex algorithm
This program is part of "Dive Into Python", a free Python book for
experienced programmers. Visit http://diveintopython.org/ for the
latest version.
"""
__author__ = "Mark Pilgrim (mark@diveintopython.org)"
__version__ = "$Revision: 1.3 $"
__date__ = "$Date: 2004/05/11 19:11:21 $"
__copyright__ ... | tapomayukh/projects_in_python | sandbox_tapo/src/refs/diveintopython-pdf-5.4/diveintopython-5.4/py/soundex/stage2/soundex2a.py | Python | mit | 2,263 | [
"VisIt"
] | 1970db9fb98709f3b172984b2b21a8d518c3a00c154fb144d084a7183b87fc03 |
# -*- coding: utf-8 -*-
"""
Acceptance tests for studio related to the outline page.
"""
import json
from datetime import datetime, timedelta
import itertools
from pytz import UTC
from bok_choy.promise import EmptyPromise
from nose.plugins.attrib import attr
from common.test.acceptance.pages.studio.settings_advanced i... | tanmaykm/edx-platform | common/test/acceptance/tests/studio/test_studio_outline.py | Python | agpl-3.0 | 81,815 | [
"VisIt"
] | 56b9795a79fddad355c326aed1ec5a51d280687531023e5467f942d87a45ac64 |
"""
affine_access.py
Created by Magnus Morton on 2012-02-12.
(c) Copyright 2012 Magnus Morton.
This file is part of Nest.
Nest 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 of the Lice... | magnusmorton/nest | nest/affine_access.py | Python | agpl-3.0 | 7,577 | [
"VisIt"
] | 9a50dce999a17b5ba24347a6b1d586a8734a8d030060716b6a37b78390fd05d2 |
#!/usr/bin/env python2
"""
Author Daniel Wolfensberger - EPFL-LTE
Created on Thu Mar 23 11:27:32 2017
"""
# General imports
import numpy as np
import paramiko
import os
import inspect
import datetime
import netCDF4
import re
import uuid
import shutil
import fnmatch
import h5py
# Module imports
from metaarray import ... | wolfidan/cosmo_query | cosmo_query/retrieve_model_data.py | Python | gpl-3.0 | 44,123 | [
"NetCDF"
] | e5e9b8d505f362b036504e716ffef80534ad4402bcf6bf4f886583e8b9a584b1 |
"""
# Notes:
- This simulation seeks to emulate the COBAHH benchmark simulations of (Brette
et al. 2007) using the Brian2 simulator for speed benchmark comparison to
DynaSim. However, this simulation includes CLOCK-DRIVEN synapses, for direct
comparison to DynaSim's clock-driven architecture. The synaptic connec... | asoplata/dynasim-benchmark-brette-2007 | output/Brian2/brian2_benchmark_COBAHH_clocksyn_hidens_1000/brian2_benchmark_COBAHH_clocksyn_hidens_1000.py | Python | gpl-3.0 | 3,778 | [
"Brian"
] | 87ec89337de5f55ed299b65fe90b1be2167c047b59156efc7b4cadb256f47e8f |
from DIRAC.Core.Tornado.Client.TornadoClient import TornadoClient
from DIRAC.Core.DISET.RPCClient import RPCClient
from time import time
from random import randint
import sys
class Transaction(object):
def __init__(self):
# If we want we can force to use dirac
if len(sys.argv) > 2 and sys.argv[2].... | ic-hep/DIRAC | tests/DISET_HTTPS_migration/multi-mechanize/service/test_scripts/v_perf.py | Python | gpl-3.0 | 787 | [
"DIRAC"
] | 5826245f30804675f83d6cbb7bc189214de21b0f9341f23414e595d4dfb705a0 |
# coding=utf-8
"""
InaSAFE Disaster risk assessment tool developed by AusAid -
**IS Utilities implementation.**
Contact : ole.moller.nielsen@gmail.com
.. note:: This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Fre... | assefay/inasafe | safe_qgis/utilities/utilities.py | Python | gpl-3.0 | 25,758 | [
"VisIt"
] | ff34ac123300a77cf2f52c07cd59eb1baf5de54b880365808d1fbb10125340de |
"""
In order to avoid double counting of bases in overlapping paired end reads,
this script accept mapped reads in SAM format, use the position to determine
overlap, and set the lower base-quality of pair overlap to 0.
It is assumed that the reads are name-sorted as when they come from the
aligner.
Usage:
bwa mem... | dariober/bwa-meth | bam-merge-pairs.py | Python | mit | 1,283 | [
"BWA"
] | 704f3fa50bfa6bdd2a41002be02565b827e273b60459b56b05962cb92661f8fc |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
i23 reandom phantoms generator
"""
import numpy as np
import matplotlib.pyplot as plt
from tomophantom import TomoP2D
from tomophantom.TomoP2D import Objects2D
from scipy.ndimage import gaussian_filter
from tomobar.methodsDIR import RecToolsDIR
from tomophantom.supp.... | dkazanc/TomoPhantom | Demos/Python/RandomPhantoms/RandPhantGen_crystal.py | Python | apache-2.0 | 15,180 | [
"Gaussian"
] | e439bf2893e171ef0719bc1b86bd6ce0c090493fced7bec8c420ba1fab514775 |
"""
Copyright (c) 2011-2015 Nathan Boley, Marcus Stoiber
This file is part of GRIT.
GRIT 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.
G... | nboley/grit | grit/proteomics/annotate_protein_domains.py | Python | gpl-3.0 | 4,379 | [
"pysam"
] | e9c04aca0402a985ebae038313af3cfab25976085e7f63f0cbf442aa955aa518 |
# $Id$
# Hop --- a framework to analyze solvation dynamics from MD simulations
# Copyright (c) 2009 Oliver Beckstein <orbeckst@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 Foundation, either... | iwelland/hop | hop/trajectory.py | Python | lgpl-3.0 | 37,290 | [
"CHARMM",
"MDAnalysis",
"VMD"
] | 71a6e05f54117b3da6043a77fef7468f42a7c876e7f553812f3cb3ca3c6be261 |
""" VOMSService class encapsulates connection to the VOMS service for a given VO
"""
__RCSID__ = "$Id$"
import requests
import os
from DIRAC import gConfig, gLogger, S_OK, S_ERROR
from DIRAC.Core.Utilities import DErrno
from DIRAC.Core.Utilities.Decorators import deprecated
from DIRAC.Core.Security.Locations import ... | fstagni/DIRAC | Core/Security/VOMSService.py | Python | gpl-3.0 | 4,424 | [
"DIRAC"
] | 073d45f604a7ef71a4a2fd67e01c19d427dbf021062aaf5fe900e445b65b9422 |
# 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... | jendap/tensorflow | tensorflow/python/autograph/pyct/static_analysis/liveness.py | Python | apache-2.0 | 8,472 | [
"VisIt"
] | 8006e689ac8efc7ea40ad503d76773b62019ac266ed03b78ad78d7f984e46610 |
"""
___ _
/ _ \ ___| |_ ___ _ __ _ _ ___
| | | |/ __| __/ _ \| '_ \| | | / __|
| |_| | (__| || (_) | |_) | |_| \__ \
\___/ \___|\__\___/| .__/ \__,_|___/
|_|
<HSC-Herve Schauer Consultants 2015>
Licensed to the Apache Software Foundation (ASF) under one
or more contributor license a... | hsc-lab/octopus | src/params.py | Python | apache-2.0 | 2,906 | [
"Octopus"
] | 3d8bbbf396f60aaf0e1ecb6a773611b5f2b9b35cc58d94d8ce1221179b92f916 |
#!/usr/bin/env python
#
# $File: __init__.py $
# $LastChangedDate$
# $Rev$
#
# This file is part of simuPOP, a forward-time population genetics
# simulation environment. Please visit http://simupop.sourceforge.net
# for details.
#
# Copyright (C) 2004 - 2010 Bo Peng (bpeng@mdanderson.org)
#
# This program is free soft... | BoPeng/simuPOP | src/__init__.py | Python | gpl-2.0 | 51,814 | [
"VisIt"
] | 08c439469abaa2b7049c3730f7ae4b7e542f31d15c29d015e9cf9a601fef6c18 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2016, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Test the CDA method in cclib"""
from __future__ import print_function
import sys
import os
import loggin... | Schamnad/cclib | test/method/testcda.py | Python | bsd-3-clause | 2,101 | [
"Gaussian",
"cclib"
] | ffbe904a975d7de7fc25621dffe1bb309696c41f1dd07d8f6aa8ea0d874c003d |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2008 Gary Burton
# Copyright (C) 2008 Robert Cheramy <robert@cheramy.net>
# Copyright (C) 2009 Douglas S. Blank
# Copyright (C) 2010 Jak... | beernarrd/gramps | gramps/plugins/export/exportxml.py | Python | gpl-2.0 | 51,989 | [
"Brian"
] | deec4831de8f20032b9d016a846441956bebee0585d796a79ec7aab0315c9db4 |
import re
try:
from functools import reduce
except ImportError:
pass
from .nodes import String, Symbol, Tuple, List, Placeholder
from .nodes import NodeVisitor, NodeTransformer
from .errors import UserError
from .tokenizer import Location, Position
class TransformError(UserError):
pass
INTERPOLATION_RE... | vmagamedov/kinko | kinko/sugar.py | Python | bsd-3-clause | 3,016 | [
"VisIt"
] | 2b1433b544c71dbc8bdc94733864776c5d2d8ef792b8c9b132b5ced6a140beee |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# freeseer - vga/presentation capture software
#
# Copyright (C) 2013, 2014 Free and Open Source Software Learning Centre
# http://fosslc.org
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publ... | Freeseer/freeseer | src/freeseer/tests/framework/test_config.py | Python | gpl-3.0 | 5,010 | [
"VisIt"
] | c512f9cad174a22c6582bafe6919a5b06326cd03d8288a2678b7ec46247c082a |
#!/usr/bin/env python
# Copyright (c) 2015 Tobias Neumann, Philipp Rescheneder.
#
# This file is part of Slamdunk.
#
# Slamdunk 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 of the
#... | t-neumann/slamdunk | slamdunk/dunks/filter.py | Python | agpl-3.0 | 12,609 | [
"pysam"
] | 51eebf440ae9b8bf2040fdbcc3ae626f683f73e5eeda2ee87df355e12bfb1899 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
import os
import warnings
from pymatgen.io.vasp import Vasprun
try:
from pymatgen.electronic_structure.boltztrap2 import BandstructureLoader, \
VasprunLoader, BztInterpolator, Bzt... | dongsenfo/pymatgen | pymatgen/electronic_structure/tests/test_boltztrap2.py | Python | mit | 8,437 | [
"VASP",
"pymatgen"
] | d68d8a0f9f62e4ddfcebf2999c0e2c4373df43659c6b03817af6b60de836f5c9 |
# Copyright (C) 2013, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from __future__ import print_function
import os, subprocess
from io import BytesIO
from os.path import join, dirname, basename, relpath
from xml.dom import minidom, Node
from zeroinstall.injector import qdom, model,... | gfxmonk/0repo | repo/incoming.py | Python | lgpl-2.1 | 8,813 | [
"VisIt"
] | 347ec39f6532a43204e1126a7418a90903aeee1146a1a66e6ad01dda70c5c926 |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the te... | bearstech/ansible | lib/ansible/modules/network/avi/avi_gslbservice.py | Python | gpl-3.0 | 7,744 | [
"VisIt"
] | f2c011139513218cdc0e29cc1eae518c644eddb73f4c72c7e62214bfd126c98c |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2017 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: y... | jchodera/mdtraj | tests/test_reporter.py | Python | lgpl-2.1 | 10,174 | [
"MDTraj",
"OpenMM"
] | e43b883ba0199426cf09acbd432a1d0fe522b8a78495c45357adc8b2d74020b6 |
# Copyright 2014 SolidBuilds.com. All rights reserved
#
# Authors: Ling Thio <ling.thio@gmail.com>
from __future__ import print_function # Use print() instead of print
from flask import url_for
def test_page_urls(client):
# Visit home page
response = client.get(url_for('main.home_page'), follow_redirects=Tr... | lingthio/Flask-User-starter-app | tests/test_page_urls.py | Python | bsd-2-clause | 1,741 | [
"VisIt"
] | e1eeb783ddbb2cfe0f5777e7af2df9927f130a7b76a8f03a11d66ec3ca0978f3 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | krafczyk/spack | var/spack/repos/builtin/packages/cdo/package.py | Python | lgpl-2.1 | 6,510 | [
"NetCDF"
] | 2cbc7ecd173c99ffeb86e1748455ce410e844bdff50a5b05c9313a49568869e9 |
#!/usr/bin/env python3
"""
motif.py contains motif object class and other related methods
does NOT contain a main function
intended to be imported with motifs.py and other for related functionality
"""
from __future__ import print_function # so Ninja IDE will stop complaining & show symbols
import sequence # ne... | j-andrews7/VAMPIRE | venusar/motif.py | Python | mit | 71,925 | [
"Biopython"
] | 061f7c7870dac2374f330a4c0d2ab23d0297dab3e41693eb940aa8fed6e337ac |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Create the RenderWindow, Renderer and both Actors
#
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
iren = vtk.vtkRenderWindowInteractor(... | timkrentz/SunTracker | IMU/VTK-6.2.0/Filters/Core/Testing/Python/combStreamers2.py | Python | mit | 2,327 | [
"VTK"
] | 2b4f9c41c05d933b6fbb17663abc840f4443f6650ee30ceac70aa36956f623f6 |
# ============================================================================
#
# Copyright (C) 2007-2012 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | jeroendierckx/Camelot | camelot/view/controls/editors/labeleditor.py | Python | gpl-2.0 | 2,112 | [
"VisIt"
] | e658d536e38585c802dd72160d9e456709749503db3ae45e41ad6861a8ce7788 |
"""
This is a DIRAC WMS administrator interface.
It exposes the following methods:
Site mask related methods:
setMask(<site mask>)
getMask()
Access to the pilot data:
getWMSStats()
"""
__RCSID__ = "$Id$"
from types import DictType, ListType, IntType, LongType, StringTypes, StringType, FloatType
from D... | calancha/DIRAC | WorkloadManagementSystem/Service/WMSAdministratorHandler.py | Python | gpl-3.0 | 24,117 | [
"DIRAC"
] | 42db68de3f2ed28a9e8eb266310338ab90e0383ebbdbacfa02ece4c2b3f86893 |
from anytree import NodeMixin, PostOrderIter, RenderTree, ContStyle
__all__ = ["ScheduleTree", "NodeSection", "NodeIteration", "NodeConditional",
"NodeSync", "NodeExprs", "NodeHalo"]
class ScheduleTree(NodeMixin):
is_Section = False
is_Iteration = False
is_Conditional = False
is_Sync = Fa... | opesci/devito | devito/ir/stree/tree.py | Python | mit | 3,508 | [
"VisIt"
] | 9c471d517fc605b2ad7b73668ae2513a771cbacf6e180d671923bb699ffd522c |
#!/usr/bin/env python
#----------------------------------------------------------------------
# Copyright (c) 2011-2017 Raytheon BBN Technologies
#
# Permission is hereby granted, free of charge, to any person obtaining
# a copy of this software and/or hardware specification (the "Work") to
# deal in the Work without ... | tcmitchell/geni-tools | src/gcf/oscript.py | Python | mit | 67,119 | [
"ORCA"
] | 2568abd22f3bfbc41193e017364a3479978ecd6a6de7b68ebebbcb98f5f0df66 |
a='1 2 2 7 1 3 3 4 3 5 5 10 5 11 4 6 7 6 7 8 7 9 8 9 8 6 6 11'.strip().split(' ')
g={}
while '' in a:
a.remove('')
b=set(a)
for i in b:
temset=set()
for x in xrange(0,len(a),2):
if a[x]==i or a[x+1] ==i:
temset.add(a[x])
temset.add(a[x+1])
g[i]=temset
visit=set()
def bfs(node,tt... | ytlai4851/Uva | Python/Q336.py | Python | gpl-2.0 | 443 | [
"VisIt"
] | b82f5b8f1857ac259ef642f9ead09aa4537e4d90ad1fae502322f134b4376b9d |
tests = [
("python", "TreeUtils.py", {}),
("python", "UnitTestTree.py", {}),
("python", "UnitTestXVal.py", {}),
("python", "UnitTestID3.py", {}),
("python", "UnitTestPrune.py", {}),
("python", "UnitTestQuantTree.py", {}),
("python", "UnitTestSigTree.py", {}),
]
longTests = []
if __name__ == '__main__':
... | jandom/rdkit | rdkit/ML/DecTree/test_list.py | Python | bsd-3-clause | 448 | [
"RDKit"
] | 2d3e302a90833f1a7e81e3773ef7a16b6d92a835f1bdd2bca76a7485a7031e64 |
# $Id$
#
# Copyright (C) 2003 Rational Discovery LLC
# All Rights Reserved
#
from rdkit import Chem
from rdkit.VLib.Supply import SupplyNode
class SmilesSupplyNode(SupplyNode):
""" Smiles supplier
Sample Usage:
>>> import os
>>> from rdkit import RDConfig
>>> fileN = os.path.join(RDCo... | ptosco/rdkit | rdkit/VLib/NodeLib/SmilesSupply.py | Python | bsd-3-clause | 1,967 | [
"RDKit"
] | f81c0f5aebe53412f497a8f2e2393a80f0a02c800f458872a5856077549257a7 |
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