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# -*- coding: utf-8 -*-
# Copyright (c) 2016-2021 Wintermute0110 <wintermute0110@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; version 2 of the License.
#
# This program is distr... | Wintermute0110/plugin.program.advanced.emulator.launcher | resources/platforms.py | Python | gpl-2.0 | 33,069 | [
"Jaguar"
] | a7593507ad1e9e8e4a0243a885e5b811cfd6d91f07516c877cca43eae49e1b08 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Project Compiler
#
import os, sys, re, shutil, time, run, sgmllib, codecs, tempfile, subprocess
template_dir = os.path.abspath(os.path.dirname(sys._getframe(0).f_code.co_filename))
sys.path.append(os.path.abspath(os.path.join(template_dir,'..')))
sys.path.append(os.pa... | openbaoz/titanium_mobile | support/iphone/compiler.py | Python | apache-2.0 | 26,373 | [
"VisIt"
] | 977e88a4ba901b8f264409123fd34a05ad90cc7a145bf4f3a7dd077520fd7a9e |
#
# Copyright (c) 2016, 2017, Oracle and/or its affiliates. All rights reserved.
# DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
#
# This code is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License version 2 only, as
# published by the Free Softwar... | akunft/fastr | mx.fastr/mx_fastr_pkgs.py | Python | gpl-2.0 | 26,188 | [
"VisIt"
] | 4c427e655baae0552590defc4916c40af4a36685aa2ae7713be720127c0e32be |
#
# Copyright (C) 2004-2008 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
from __future__ import print... | rvianello/rdkit | rdkit/Chem/Pharm3D/UnitTestEmbed.py | Python | bsd-3-clause | 9,826 | [
"RDKit"
] | 90dd8076cf3efc069c4c2770850debb6669612b6cee6557aa55cca39153147b3 |
# Python example script that uses the vtkMatlabEngineInterface to perform
# a calculation (sin(x)^2 + cos(x)^2 = 1) on VTK array data, and pass the
# result back to VTK.
# VTK must be built with VTK_USE_MATLAB_MEX turned on for this example to work!
from vtk import *
import math
if __name__ == "__main__":
... | b3c/VTK-5.8 | Examples/Infovis/Python/Matlab_engine_interface.py | Python | bsd-3-clause | 1,237 | [
"VTK"
] | 64c8b215118949a4474108ef8b6548d8cc78b8ba5968e4e3fe1ebfcf6857f9dc |
from Firefly import logging
from Firefly.helpers.conditions import Conditions
from Firefly.helpers.events import Command
from Firefly import scheduler
class Action(object):
def __init__(self, ff_id, command, source, conditions=None, force=False, **kwargs):
self._ff_id = ff_id
self._command = command
sel... | Firefly-Automation/Firefly | Firefly/helpers/action.py | Python | apache-2.0 | 1,905 | [
"Firefly"
] | 4f1511a242314de410d81e9f2ef73b012c5b019e4930c67a30f48ec358b32ba1 |
import numpy as np #from numpy import mgrid, empty, sin, pi
import vtk
def simple_grid():
# Generate some points.
x, y, z = np.mgrid[1:6:11j, 0:4:13j, 0:3:6j]
base = x[..., 0] + y[..., 0]
# Some interesting z values.
for i in range(z.shape[2]):
z[..., i] = base * 0.25 * i
return x, y, z
def uniform_... | kayarre/Tools | vtk/simple_grid.py | Python | bsd-2-clause | 5,131 | [
"VTK"
] | b68362caa2f36368f5c8ed8c6f63f9821c2f843b7d813bcd663a5c0f5ffeaa62 |
#!/bin/env python
""" create rst files for documentation of DIRAC """
import os
import shutil
import socket
import sys
import logging
import glob
logging.basicConfig(level=logging.INFO, format='%(name)s: %(levelname)8s: %(message)s')
LOG = logging.getLogger('MakeDoc')
def mkdir(folder):
"""create a folder, ignore ... | petricm/DIRAC | docs/Tools/MakeDoc.py | Python | gpl-3.0 | 12,409 | [
"DIRAC"
] | 13432f16299c12c67cc31314fd5e4ec83112509ab6b8dce7917e805fe3f55fe7 |
import numpy as np
from ase.data import atomic_numbers
from gpaw.utilities import pack2
from gpaw.utilities.tools import md5_new
from gpaw.atom.radialgd import AERadialGridDescriptor
from gpaw.atom.atompaw import AtomPAW
from gpaw.atom.configurations import configurations
from gpaw.basis_data import Basis, BasisFuncti... | robwarm/gpaw-symm | gpaw/hgh.py | Python | gpl-3.0 | 19,812 | [
"ASE",
"GPAW",
"Gaussian"
] | 98716138b8a053aedd815fab3f8c852ce04f6e69cb76215aee38f52cf59d273c |
#
# QAPI types generator
#
# Copyright IBM, Corp. 2011
#
# Authors:
# Anthony Liguori <aliguori@us.ibm.com>
#
# This work is licensed under the terms of the GNU GPLv2.
# See the COPYING.LIB file in the top-level directory.
from ordereddict import OrderedDict
from qapi import *
import sys
import os
import getopt
impor... | vincent-d/qemu | scripts/qapi-types.py | Python | gpl-2.0 | 10,549 | [
"VisIt"
] | 01d8b9ac6503d5b429cb050bb8975811dcc21a03d683189fcd7b7feafa4778f1 |
#!/usr/bin/env python
# -*- mode: python; coding: utf-8; -*-
# ---------------------------------------------------------------------------##
#
# Copyright (C) 1998-2003 Markus Franz Xaver Johannes Oberhumer
# Copyright (C) 2003 Mt. Hood Playing Card Co.
# Copyright (C) 2005-2009 Skomoroh
#
# This program is free softwa... | shlomif/PySolFC | pysollib/games/klondike.py | Python | gpl-3.0 | 55,884 | [
"CASINO"
] | 193afc70cd2573d70c69a8ec41ec4ffa9408ce59e764d3671f52ab2ef9346957 |
# Copyright 2018 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Unit tests for translation_helper.py."""
import unittest
import os
import sys
# pylint: disable=relative-import
import translation_helper
here = os.path.... | endlessm/chromium-browser | tools/translation/helper/translation_helper_unittest.py | Python | bsd-3-clause | 4,575 | [
"xTB"
] | 6a38e3ac74815eb3cc790bce0f6205934c7aa221375bb6bbeb005c4a801d918c |
from sklearn.linear_model import LinearRegression
import numpy as np
import matplotlib.pyplot as plt
from matplotlib import cm
from sklearn.metrics import mean_squared_error
# Fix the number of samples and our seed
NUM_SAMPLES = 200
np.random.seed(42)
# Our "true function"
def f(x):
return 1.5*x + 0.5
#Const... | JustinNoel1/ML-Course | linear-regression/python/linreg.py | Python | apache-2.0 | 1,895 | [
"Gaussian"
] | 38a9db269d9ff296775f830134d6629e1ba0089ecc34f16622c1eeec58e742e2 |
#! /usr/bin/env python3
# Script to crawl the file system for changed files
#
# fs-crawler dirkpetersen / Oct 2019
#
import sys, os, argparse, subprocess, re, time, datetime, tempfile, random, threading, filecmp
class KeyboardInterruptError(Exception): pass
def main():
#log = logger('fs-crawler', args.debug)... | FredHutch/sc-benchmark | fs-crawler.py | Python | apache-2.0 | 15,580 | [
"VisIt"
] | 8c1fe4dfdf20e5e7e93c17d1b9efef33f3d59ce45bee8cf33e97cfd510b56a7f |
"""Bulk Al(fcc) test"""
from ase import Atoms
from ase.visualize import view
from gpaw import GPAW, PW
name = 'Al-fcc'
a = 4.05 # fcc lattice paramter
b = a / 2
bulk = Atoms('Al',
cell=[[0, b, b],
[b, 0, b],
[b, b, 0]],
pbc=True)
view(bulk)
k = 4
cal... | robwarm/gpaw-symm | doc/exercises/aluminium/Al_fcc.py | Python | gpl-3.0 | 568 | [
"ASE",
"GPAW"
] | 16854621683a6e7a45c75ad7171809892f6335f2426c9636721b3b05cbe8faab |
import math
import torch
from ..constraints import Positive
from ..lazy import MatmulLazyTensor, RootLazyTensor
from .kernel import Kernel
class SpectralDeltaKernel(Kernel):
"""
A kernel that supports spectral learning for GPs, where the underlying spectral density is modeled as a mixture
of delta distr... | jrg365/gpytorch | gpytorch/kernels/spectral_delta_kernel.py | Python | mit | 4,931 | [
"Gaussian"
] | 1e47d7a4153179acab104678f8070ed1882b011d1b7845360b2db75e8e547a0f |
import os
import unittest
from __main__ import vtk, qt, ctk, slicer
#
# WelcomeModuleTests
#
class WelcomeModuleTests:
def __init__(self, parent):
parent.title = "WelcomeModuleTests" # TODO make this more human readable by adding spaces
parent.categories = ["Testing.TestCases"]
parent.dependencies = []
... | agirault/VesselView | Applications/App/Testing/Python/WelcomeModuleTests.py | Python | apache-2.0 | 6,219 | [
"VTK"
] | d88ce26681edf0c7eff3c54664f5cefd291390bdfe331e3cbb8db46710941bb4 |
"""Test string and unicode support in VTK-Python
The following string features have to be tested for string and unicode
- Pass a string arg by value
- Pass a string arg by reference
- Return a string arg by value
- Return a string arg by reference
The following features are not supported
- Pointers to string... | timkrentz/SunTracker | IMU/VTK-6.2.0/Common/Core/Testing/Python/TestStrings.py | Python | mit | 2,690 | [
"VTK"
] | 235cb224c741f6d293925a8731fc1feb6f6767e68a445958b1820f6461f8976d |
import numpy as np
import scipy.stats
from scipy.optimize import approx_fprime
from pyhmc import hmc
def lnprob_gaussian(x, icov):
logp = -np.dot(x, np.dot(icov, x)) / 2.0
grad = -np.dot(x, icov)
return logp, grad
def test_1():
# test sampling from a highly-correlated gaussian
dim = 2
x0 = n... | rmcgibbo/pyhmc | pyhmc/tests/test_hmc.py | Python | bsd-3-clause | 1,947 | [
"Gaussian"
] | 684cd3bf2be06da31ea77f049916808208d9613aea98a67bdf10055f045174b0 |
#!/usr/bin/env python
#Original script from /home/james/work/encode/feature_partitions/split_by_partitions.py
#Usage: python(2.4) split_by_partitions.py partition_index in_file out_file chrCol startCol endCol strandCol
from __future__ import division
import sys
from galaxy import eggs
import pkg_resources; pkg_resou... | volpino/Yeps-EURAC | tools/encode/split_by_partitions.py | Python | mit | 4,581 | [
"Galaxy"
] | f1bb7326eedd03311127051b2ce9c412be6efbfc6f86fc4d8aef0ab72041f736 |
#!/usr/bin/env python
#
# Public Domain
"""
CairoSVG - A Simple SVG Converter Based on Cairo
================================================
CairoSVG is an SVG converter based on Cairo. It can convert SVG files to PDF,
EPS, PS, and PNG files.
For further information, please visit the `CairoSVG Website
<http://cairo... | Kozea/CairoSVG | setup.py | Python | lgpl-3.0 | 574 | [
"VisIt"
] | 24479ad9096dea79667ba79349c1ccd54e85da7127917b0be14bb45138031d6e |
import os
import sys
import time as timer
import math
import traceback
import Queue
import multiprocessing
import numpy as np
import netCDF4
from paegan.location4d import Location4D
from paegan.transport.utils.asatransport import AsaTransport
from paegan.transport.shoreline import Shoreline
from paegan.transport.bat... | asascience-open/paegan-transport | paegan/transport/parallel_manager.py | Python | gpl-3.0 | 47,626 | [
"NetCDF"
] | 1cc4136abb8570f38d7773cd5c047a113db21b613381a4467fc46224a6da4830 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the LMS.
"""
import json
from nose.plugins.attrib import attr
from datetime import datetime, timedelta
import ddt
from capa.tests.response_xml_factory import MultipleChoiceResponseXMLFactory
from ..helpers import UniqueCourseTest, EventsTestMixin
from ...pages.studio.a... | waheedahmed/edx-platform | common/test/acceptance/tests/lms/test_lms_courseware.py | Python | agpl-3.0 | 33,212 | [
"VisIt"
] | 1a31f63995307114d0253b5a6bcc8f23bf1d461dcc1d1ab95c8a95edbcf75017 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module is intended to be used to compute Pourbaix diagrams
of arbitrary compositions and formation energies. If you use
this module in your work, please consider citing the following:
General formalis... | fraricci/pymatgen | pymatgen/analysis/pourbaix_diagram.py | Python | mit | 39,890 | [
"pymatgen"
] | 923ed68cfa12db8805fbefa5d90a862a887bbf22f1ced978e04ced37502f8a66 |
"""
Representations and Inference for Logic. (Chapters 7-9, 12)
Covers both Propositional and First-Order Logic. First we have four
important data types:
KB Abstract class holds a knowledge base of logical expressions
KB_Agent Abstract class subclasses agents.Agent
Expr A logical ... | aimacode/aima-python | logic.py | Python | mit | 74,057 | [
"VisIt"
] | 6256ee9a00b76d00d3c92e6007794349e6619cc4433b77ce1f98f9c2ddab1691 |
from itertools import cycle
import random
import math
import sys
from Net4 import *
import pygame
from pygame.locals import *
from pickle import HIGHEST_PROTOCOL
from pickle import dump
FPS = float("inf")
SCREENWIDTH = 288
SCREENHEIGHT = 512
# amount by which base can maximum shift to left
PIPEGAPSIZE = 100 # gap be... | computergeek314/FlapPy-Network | flappy.py | Python | mit | 15,318 | [
"NEURON"
] | 2fea58b81a037740453ae7f93236ac652b0362026fd533c224db824d1ccb25a6 |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
from __future__ import absolute_import, division, print_function
import copy
from functools import wraps
import numpy as np
import pyLikelihood as pyLike
from SrcModel import SourceModel
from AnalysisBase import AnalysisBase
from LikelihoodState import Lik... | jefemagril/fermipy | fermipy/gtutils.py | Python | bsd-3-clause | 22,978 | [
"Gaussian"
] | 703d999f037accfdea9dc70f0539cbb7296eb6db8619db21c1d2abc112ea69c6 |
# Copyright (c) 2016,2017,2018,2019 MetPy Developers.
# Distributed under the terms of the BSD 3-Clause License.
# SPDX-License-Identifier: BSD-3-Clause
"""Contains a collection of generally useful calculation tools."""
import functools
from inspect import signature
from operator import itemgetter
import warnings
impo... | ShawnMurd/MetPy | src/metpy/calc/tools.py | Python | bsd-3-clause | 62,642 | [
"Brian"
] | 8c6798968650a30b0fc09c36a3acd38bd318872ce4ae2c8370e93024e68f514d |
from ..utils import *
##
# Minions
class GVG_023:
"Goblin Auto-Barber"
play = Buff(FRIENDLY_WEAPON, "GVG_023a")
GVG_023a = buff(atk=1)
class GVG_025:
"One-eyed Cheat"
events = Summon(CONTROLLER, PIRATE - SELF).on(Stealth(SELF))
class GVG_027:
"Iron Sensei"
events = OWN_TURN_END.on(Buff(RANDOM(FRIENDLY_MIN... | beheh/fireplace | fireplace/cards/gvg/rogue.py | Python | agpl-3.0 | 1,148 | [
"TINKER"
] | 759fd92b93faf055cc8e7a8c60627200d0704e4c4501baf4673a58b1d89ee501 |
# Copyright (c) 2017 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use t... | yashdsaraf/scancode-toolkit | src/cluecode/copyrights.py | Python | apache-2.0 | 47,037 | [
"VisIt"
] | 5de2bc2698e148080de271a0e992dd6d14a963334a0ce46be9bd718ad3e133b3 |
# -*- 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 publish... | thica/ORCA-Remote | src/ORCA/actions/ReturnCode.py | Python | gpl-3.0 | 1,130 | [
"ORCA"
] | 52e4d693bfbc34874a7faf8460e4dc1292d4124971aa2bb10cfe518ec3cf5b49 |
#!/home/epicardi/bin/python27/bin/python
# Copyright (c) 2013-2014 Ernesto Picardi <ernesto.picardi@uniba.it>
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including ... | RNAEDITINGPLUS/main | node/reditools-1.0.4/reditools/REDItoolKnown.py | Python | apache-2.0 | 28,181 | [
"pysam"
] | 4b47f9d3732bb33170b1ed9bf33f36d429c8b5e1ebb8ddde16c86558daf317f9 |
# coding: utf-8
from __future__ import unicode_literals
import re
from .common import InfoExtractor
from ..utils import (
ExtractorError,
unsmuggle_url,
)
from ..compat import (
compat_parse_qs,
compat_urlparse,
)
class SenateISVPIE(InfoExtractor):
_COMM_MAP = [
["ag", "76440", "http://ag... | marxin/youtube-dl | youtube_dl/extractor/senateisvp.py | Python | unlicense | 5,890 | [
"EPW"
] | 16b164574f7945d0a3356e4cabb0985d88207a1dfdc96a276caa454b118fe0f5 |
import pymatgen
structure = pymatgen.Structure(
lattice = pymatgen.core.lattice.Lattice([[.0,.5,.5],[.5,.0,.5],[.5,.5,.0]]).scale(5.4309456887829**3/4),
species= ['Si', 'Si'],
coords = [3*[-.125], 3*[.125]],
)
structure.to(filename='Si.cif')
structure.to(filename='Si.json')
| trangel/OPTpy | examples/data/structures/write-Si-structure.py | Python | gpl-3.0 | 294 | [
"pymatgen"
] | 480c38a3050ee0d624b9d231d73c91b5ab1b2f2cd9e213ea765e2ecc56229fb3 |
# PYTHON script to write and submit pbsjobs to queue
import optparse
import sys
import string
import os
import stat
# User inputted values and options
parser = optparse.OptionParser(description="submit GROMACS grompp and mdrun commands to cluster queue.")
parser.add_option("-f", "--fileprefix", help="the full prefix ... | hainm/open-forcefield-group | reweighting_optimization/scripts/grompp.py | Python | gpl-2.0 | 1,340 | [
"Gromacs"
] | f5a09ba0f2a953c753555afdfa6ba8a789912bd8ee2d368c0e42b36a524e422e |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2013 Async Open Source
##
## 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 Foundation; either version 2
## of the License, or... | andrebellafronte/stoq | stoqlib/gui/search/searchextension.py | Python | gpl-2.0 | 3,316 | [
"VisIt"
] | fad4edf11e22c24f3eae46be07cbf977b3ff0aa8ddeac643f732a3e4c13eaf6e |
# Copyright 2021 Open Source Robotics Foundation, Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law... | ros2/launch | launch/test/launch/actions/test_reset_launch_configurations.py | Python | apache-2.0 | 3,998 | [
"VisIt"
] | cc169dda51facb41927f6888f65efa00646c3622da6556a15fef47c1ac97d44e |
"""
Class to help creating a source detection pipeline with sep
by creating 'steps' with different configurations.
"""
import os
import numpy as np
from scipy import ndimage
from astropy.table import Table
from astropy.convolution import Gaussian2DKernel
from astropy.stats import gaussian_fwhm_to_sigma, gaussian_sigma... | johnnygreco/hugs | hugs/sep_stepper.py | Python | mit | 6,819 | [
"Gaussian"
] | 5cf1072e6336ecf99c6ad47909975bbdb5417f9631c0f5cb650702c7c12b1350 |
#!/usr/bin/env python
#
# Copyright 2006 Google Inc. All Rights Reserved.
"""Calculates Javascript dependencies without requiring Google3.
It iterates over a number of search paths and builds a dependency tree. With
the inputs provided, it walks the dependency tree and outputs all the files
required for compilation... | jmt4/Selenium2 | third_party/closure/bin/calcdeps.py | Python | apache-2.0 | 17,507 | [
"VisIt"
] | 1c4068c78a2e49fed6d9a8ef3046dfac3947fe7c59eeec4c1ed87c1358059303 |
import espresso
import logging
from math import sqrt
system, integrator = espresso.standard_system.LennardJones(1000, (20,20,20), dt=0.00001, temperature = 1.0)
# logging.getLogger("ExtAnalyze").setLevel(logging.INFO)
print "warming up ..."
capForce = espresso.integrator.CapForce(system, capForce=10000.0)
integrator... | BackupTheBerlios/espressopp | examples/analyze_during_integration/analyze_during_integration.py | Python | gpl-3.0 | 1,099 | [
"ESPResSo"
] | 5b31188f4a229f62bd47815556f6a1abb779c8cafd106f5285b1e627745c2933 |
#!/usr/bin/python
import numpy as np
import matplotlib.pyplot as plt
from numpy.random import rand, randn, permutation, multivariate_normal
from shogun import BinaryLabels, RealFeatures, IndexBlock, IndexBlockGroup, FeatureBlockLogisticRegression
def generate_synthetic_logistic_data(n, p, L, blk_nnz, gcov, nstd):
... | besser82/shogun | examples/undocumented/python/graphical/group_lasso.py | Python | bsd-3-clause | 7,789 | [
"Gaussian"
] | bc91af7b943ffbdb8e9c5d8ea9daee9c8b52bc03d1d72c3c97c6462e7ee05bf5 |
# -*- coding: utf8
"""Random Projection transformers
Random Projections are a simple and computationally efficient way to
reduce the dimensionality of the data by trading a controlled amount
of accuracy (as additional variance) for faster processing times and
smaller model sizes.
The dimensions and distribution of Ra... | RPGOne/scikit-learn | sklearn/random_projection.py | Python | bsd-3-clause | 22,132 | [
"Gaussian"
] | 0e705e12538608979caf606d67fffb7bbbb5d865831c6310c5f4869ebd28d633 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2008 Stephane Charette <stephanecharette@gmail.com>
# Contribution 2009 by Bob Ham <rah@bash.sh>
# Copyright (C) 2010 Jakim Friant
#
# This program is free software; you can redistribute it and/... | Forage/Gramps | gramps/plugins/graph/gvhourglass.py | Python | gpl-2.0 | 11,649 | [
"Brian"
] | 55caf4ff1d6d000525a629abfd5c55aed8589ebaca11a6b65156259b862da9b7 |
# Copyright Yair Benita Y.Benita@pharm.uu.nl
# Biopython (http://biopython.org) license applies
"""Codon adaption indxes, including Sharp and Li (1987) E. coli index.
Currently this module only defines a single codon adaption index from
Sharp & Li, Nucleic Acids Res. 1987.
"""
__docformat__ = "restructuredtext en"
... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/SeqUtils/CodonUsageIndices.py | Python | gpl-2.0 | 1,108 | [
"Biopython"
] | 38e887c3b87bfbf70451b5690dc5a925804b275bffd16f5e2c87a21ca91557cc |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# this module is responsible for loading the data by calling the necessary information from **loaddata** module from datamodel directory and then calling necessary algorithms to predict the score
# note that this will act as intermediary file for giving result by interacti... | sagnik17/Movie-Recommendation-System | mrs/recsys/predict.py | Python | gpl-3.0 | 6,251 | [
"NEURON"
] | b3fbe04959f35e0a0cbf261032052449cc5b650a3143d1521d67ef7e1fc0824b |
import os
import json
import Airfoil
import SplineRefine
import TrailingEdge
import Meshing
import Connect
from Settings import DATAPATH
import logging
logger = logging.getLogger(__name__)
class Batch:
def __init__(self, app, batch_controlfile, __version__):
self.app = app
self.app.mainwindow =... | chiefenne/PyAero | src/BatchMode.py | Python | mit | 7,028 | [
"VTK"
] | 00cd3626f7056237ef694f3876ceebc92831ee2797c3e384333dc70299e3370d |
__author__ = 'Mark Dickinson'
__source__ = 'http://code.activestate.com/recipes/578507-strongly-connected-components-of-a-directed-graph/'
def strongly_connected_components_path(vertices, edges):
"""
Find the strongly connected components of a directed graph.
Uses a recursive linear-time algorithm descri... | yipeipei/peppy | graph/scc.py | Python | mit | 9,280 | [
"VisIt"
] | adf686c199f5a303045acefad94ab1644164e10160505ec9abb9a3e55cb29828 |
"""Set of plotting aids for Holoviews."""
from __future__ import division
import holoviews as hv
import numpy as np
import scipy
import matplotlib.pyplot as plt
# get colors
colors = hv.core.options.Cycle.default_cycles['default_colors']
Ncolors = len(colors)
def plot_vector(x, lim=1):
"""Plot the vector x.
... | swkeemink/PythonTools | swktools/plotting.py | Python | gpl-2.0 | 40,079 | [
"NEURON"
] | 8be2681f5690b8f5b8795aba40b6137718bdb1d82c09e63419b7b78d2cd7bf4d |
#!/usr/bin/python
#prompt-core-processes
#daniel.antony.pass@googlemail.com
###################################################################
## This script runs the backbone of prompt. External packages ##
## are called from here but additional scripts which are refered ##
## to can be found in the ./scripts fol... | passdan/prompt | scripts/prompt_sample.py | Python | gpl-3.0 | 4,862 | [
"BLAST"
] | 6183f3800cc3ec61ffd5782f185e91445693578e772ee7fef8a4d66d5b98ca8c |
import os
import sys
import pkgutil
def LoadFolder(inputFolderPath):
infilePathList=[]
for root, dirs, files in os.walk(inputFolderPath):
for file in files:
infilePathList.append(inputFolderPath+file)
return infilePathList
def Loader(mainPath0):
flag=0
mainEntryPath=mainPa... | liutairan/eMolFrag | Old versions/eMolFrag_2016_09_09_01/loader.py | Python | gpl-3.0 | 2,968 | [
"RDKit"
] | 8988925ce3aca2dcea04ec68ec6c664225807f88a21520ed117b9844fc2d3812 |
#!/usr/bin/env python
"""
scanFAAM.py
===========
Holds the scanFAAM function that is used to work out the first and last
index of real data (i.e. non-missing data in a load of FAAM flight data).
It is used in conjunction with nappy to reduce the size of output files
by missing out beginning and end periods that hold... | eufarn7sp/egads | egads/thirdparty/nappy/contrib/aircraft/scanFAAM.py | Python | gpl-3.0 | 2,764 | [
"NetCDF"
] | ee260333361adb6856a0bf5b03b93b947c52d4fdbf6a9fe15104d095030f8395 |
"""Tests for the Elk-M1 Control integration."""
| turbokongen/home-assistant | tests/components/elkm1/__init__.py | Python | apache-2.0 | 48 | [
"Elk"
] | 111fbb4814dce8d2b51bb8838717a7361c51569246345aa5c0312671f4c3f7c6 |
import math
from numpy import array, full, ones_like
import util
from tvtk.api import tvtk
from mayavi import mlab
from traits.api import HasTraits, Instance, on_trait_change
from traitsui.api import View, Item
from mayavi.core.ui.api import MayaviScene, MlabSceneModel, SceneEditor
from mayavi.core.api import Engine
fr... | bcorfman/stage | plot3d.py | Python | mit | 19,592 | [
"BLAST",
"Mayavi",
"VTK"
] | bf20a4e02cca054a3652d3b1b96a9cfa2aae117f205fb90c34bd13f0e06d910c |
# -*- coding: utf-8 -*-
"""
Created on Wed May 20 11:42:42 2015
@author: admin
"""
import h5py
import os
import numpy as np
def getSignals(fileName,env):
path=env.path
hdf5=h5py.File(os.path.join(path,fileName+'.h5'),'r')
#channel=tdms_file.object('PXI M6251','Lang_U')
liste=[] ... | albanatita/data-process | readHdf5.py | Python | gpl-2.0 | 5,726 | [
"VisIt"
] | 032b24c5c46ea2ec15bb2312598789cad870ee6f9a847870f27401ce85b651a2 |
#!/usr/bin/python
# Htsnapp - create snapshots of websites from urls, nmap xml, and txr files.
# Author - Nikhil Sreekumar
# Contact: roo7break@gmail.com / @roo7break
# Supports urls, files with urls, and nmap.xml files
# Primary source for screenshot code:
# PyWebShot - create webpage thumbnails. Originally based on... | roo7break/HtSnapp | htsnapp.py | Python | gpl-3.0 | 8,944 | [
"VisIt"
] | a6b2f4e11318dd5ee22b4761b4274bf4cc676524a10ce53c866e5e60600958a0 |
# -*- coding: utf-8 -*-
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding field 'ImmunizationHistory.tetanus_toxoid1'
db.add_column(u'patient_immunizationhistory', 'tetanus_... | aazhbd/medical_info01 | patient/migrations/0017_auto__add_field_immunizationhistory_tetanus_toxoid1__add_field_immuniz.py | Python | bsd-3-clause | 30,488 | [
"VisIt"
] | 72256e63d9cc3e3e70043d2e594489d7361cbddb57b37c1dd90159219fbecd9d |
from __future__ import division, generators
import math, sys, warnings, datetime, new
import numpy as np
from numpy import ma
import matplotlib
rcParams = matplotlib.rcParams
import matplotlib.artist as martist
import matplotlib.axis as maxis
import matplotlib.cbook as cbook
import matplotlib.collections as mcoll
im... | runt18/nupic | external/linux32/lib/python2.6/site-packages/matplotlib/axes.py | Python | agpl-3.0 | 260,242 | [
"Gaussian"
] | 75c311883e3b4721870ffb3efea7bc0c4695a4670a93317f9c00d73c004d72c1 |
import numpy as np
import openpnm as op
from tqdm import tqdm
__all__ = [
'plot_connections',
'plot_coordinates',
'plot_networkx',
'plot_vpython',
'plot_tutorial',
'plot_network_jupyter',
'generate_voxel_image',
]
def plot_connections(network,
throats=None,
... | PMEAL/OpenPNM | openpnm/topotools/_plottools.py | Python | mit | 32,286 | [
"ParaView"
] | 2b9428b60338b3e7b39277eaded6410e9df40eb0f015e294868526a0854d1744 |
#!/usr/bin/env python2.7
# pySCLikeSync.py by GameplayJDK,
# Copyright 2014 (c) GameplayJDK.de,
# All rights reserved until further notice
import sys
import soundcloud
import urllib
import os
import glob
import mutagen
# Prefix for all console output
pre = "[pySCLikeSync] "
# INFO: never show your account information t... | GameplayJDK/pySCLikeSync | src/pySCLikeSync-v1.3.py | Python | gpl-3.0 | 3,820 | [
"VisIt"
] | 0f01c224167df5b2db4a7634411c186e6b6d91ccc6b30f70884733ada09c4216 |
from copy import deepcopy
from glob import glob
from os import path
import dask.array as da
import numpy as np
from parcels.field import Field, DeferredArray
from parcels.field import NestedField
from parcels.field import SummedField
from parcels.field import VectorField
from parcels.grid import Grid
from parcels.gri... | OceanPARCELS/parcels | parcels/fieldset.py | Python | mit | 76,063 | [
"NetCDF"
] | b29bcd0e6cfd910c9ece8f8f4e4e012f6a6813cd0c31229393ef05181599fc5f |
"""Convert to and from Roman numerals
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: 1.2 $"
__date__ = "$Date: 2004/05/05 21:57:20 ... | tapomayukh/projects_in_python | sandbox_tapo/src/refs/diveintopython-pdf-5.4/diveintopython-5.4/py/roman/stage1/roman1.py | Python | mit | 719 | [
"VisIt"
] | 38e6811fd7c889c27e1a79dce7bac26339afa9ff8be21a5593563d9c85136663 |
# (c) 2013-2014, Michael DeHaan <michael.dehaan@gmail.com>
# (c) 2015 Toshio Kuratomi <tkuratomi@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either... | andreaso/ansible | lib/ansible/executor/module_common.py | Python | gpl-3.0 | 39,245 | [
"VisIt"
] | 25e0978e47ab59110de44faba64f1668695bcdfb5cfad02fe05b67d23af7f702 |
#
# ----------------------------------------------------------------------------------------------------
#
# Copyright (c) 2016, Oracle and/or its affiliates. All rights reserved.
# DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
#
# This code is free software; you can redistribute it and/or modify it
# u... | graalvm/mx | mx_javamodules.py | Python | gpl-2.0 | 62,825 | [
"VisIt"
] | ef3502161090002fc8039a9159b97ad2254a0ec3b53c6bf98f9632208cf3f050 |
# Setup customisation for gpaw/cuda
import os
# compiler and linker
compiler = 'gcc'
mpicompiler = 'mpicc'
mpilinker = 'mpicc'
extra_compile_args = ['-std=c99']
# libraries
libraries = ['z']
# cuda
library_dirs += [os.environ['CUDALIB'], './c/cuda']
include_dirs += [os.environ['CUDADIR'] + '/include']
libraries += [... | mlouhivu/build-recipes | gpaw-bundle/examples/taito-gpu-2017-01/setup/customize-cuda.py | Python | mit | 785 | [
"GPAW"
] | 3657a300ed3ac201de9d5b94f4a8776bb69a73474935b6f9ebcf6d9e0edb81db |
from contextlib import closing
import os
import subprocess
import argweaver
import argweaver.smc
from compbio import arglib
def inorder_tree(tree):
queue = [("queue", tree.root)]
while queue:
cmd, node = queue.pop()
if cmd == "visit":
yield node
elif cmd == "queue":
... | mdrasmus/argweaver | argweaver/vis.py | Python | mit | 5,663 | [
"VisIt"
] | 9dd1575bc07bfa9574bae72e6a2f2ec5f7a63696f2264e260529b98df18c6b7a |
#!/usr/bin/env python
#
# Data manager for reference data for the 'humann2' Galaxy tools
import json
import optparse
import os
import subprocess
import sys
# Utility functions for interacting with Galaxy JSON
def read_input_json(jsonfile):
"""Read the JSON supplied from the data manager tool
Returns a tuple ... | mblue9/tools-iuc | data_managers/data_manager_metaphlan2_database_downloader/data_manager/data_manager_metaphlan2_download.py | Python | mit | 4,332 | [
"Galaxy"
] | bc8d90a29524d35c2f3ffda24ccaf61083275242e6668150d940c4789f8a7476 |
# encoding: utf-8
"""
A lightweight Traits like module.
This is designed to provide a lightweight, simple, pure Python version of
many of the capabilities of enthought.traits. This includes:
* Validation
* Type specification with defaults
* Static and dynamic notification
* Basic predefined types
* An API that is si... | cloud9ers/gurumate | environment/lib/python2.7/site-packages/IPython/utils/traitlets.py | Python | lgpl-3.0 | 46,762 | [
"Brian"
] | 0765b55785a24d5756499c97cb6b279dfcd3f1b9baa2632759ff6bb0c2e02232 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 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
#... | rmcgibbo/psi4public | psi4/driver/pubchem.py | Python | lgpl-3.0 | 7,634 | [
"Psi4"
] | 56ca4dc8e3ef087a799f7b5ac5f97cfcc62778c43fd3b2fb1864cc63f5a34383 |
""" Transformers to perform common preprocessing steps.
"""
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Mathieu Blondel <mathieu@mblondel.org>
# Olivier Grisel <olivier.grisel@ensta.org>
# License: BSD
import numpy as np
import scipy.sparse as sp
from ..utils import check_arrays
f... | ominux/scikit-learn | sklearn/preprocessing/__init__.py | Python | bsd-3-clause | 20,823 | [
"Gaussian"
] | e90c25bb1391b5fae55f9712ba4e8def2eae80edeb618b58af0178f29427de5e |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2008, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License versi... | zenoss/ZenPacks.networking.HPProcurve | ZenPacks/networking/HPProcurve/__init__.py | Python | gpl-2.0 | 1,240 | [
"VisIt"
] | d223b220a10838396efe4ebdf10300c77d0c52e95e0e563994e459ab600ccb47 |
import sys
from pybotvac import (
Account,
Neato,
OAuthSession,
PasswordlessSession,
PasswordSession,
Vorwerk,
)
# Set email and password if you plan to use password authentication.
# Set Client ID and Secret if you plan to use OAuth2.
# If you plan to use email OTP, all you need to do is spec... | stianaske/pybotvac | sample/sample.py | Python | mit | 1,923 | [
"VisIt"
] | c3fffb76ce5d2cf82a902e72453df1f2330108cbfee1d2d71c273fb072043579 |
#!/home/epicardi/bin/python27/bin/python
# Copyright (c) 2013-2014 Ernesto Picardi <ernesto.picardi@uniba.it>
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including ... | RNAEDITINGPLUS/main | node/reditools-1.0.4/reditools/tableToTabix.py | Python | apache-2.0 | 5,802 | [
"pysam"
] | 9f304c4f8d5e0d238507680e629f014fbcbe0f8c934e4ef770ee787ac9b74d5a |
#!/usr/bin/env python2
desc="""Fetch all entries from SRA for given taxid.
Save the biggest run per each SAMPLE (SRS) from given date. Paired first, if any.
Note, it run fastq-dump in background. Make sure you have enough free cores;)
DEPENDENCIES:
Biopython
"""
epilog="""Author:
l.p.pryszcz+git@gmail.com
Barcelona... | lpryszcz/bin | taxid2sra.py | Python | gpl-3.0 | 15,103 | [
"Biopython"
] | 0e02698442997ebbdd96f099d680cdb3329cd4c81ee680ff16315d8dfdc1840d |
from __future__ import print_function
import os
import numpy as np
from astropy.table import Table
from astropy.io import fits
from .. import fileio
from .starpop import StarPop
from .asts import parse_pipeline
from ..angst_tables import angst_data
from ..astronomy_utils import mag2Mag
__all__ = ['Galaxy']
class Ga... | philrosenfield/ResolvedStellarPops | galaxies/galaxy.py | Python | bsd-3-clause | 1,664 | [
"Galaxy"
] | fbd0e51f96061d1a83752dac4c068cddf5604a85b59fbe886e3d0cdb29dfca7a |
# -*- Mode: Python; 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 General Public License as published by
## the Free Sof... | tiagocardosos/stoq | plugins/ecf/ecfplugin.py | Python | gpl-2.0 | 1,914 | [
"VisIt"
] | 3e5d0055e121231f1c061862eb508e59d605eb5fdc77fdc5e5490c94a7e1e9fb |
from constants import *
from operator import itemgetter
import web
import os
import codecs
import urllib
from models import *
# Form Handlers
LoginForm = web.form.Form(
web.form.Textbox('ra', web.form.notnull, Class="form-control"),
web.form.Password('senha', web.form.notnull, Class="form-control"),
web.fo... | rodrigosurita/gda | forms.py | Python | gpl-3.0 | 4,488 | [
"MOE"
] | c28366a9f6349dcbbae45e4113142b350e73184f5314be94d3384d7f88f95619 |
#Copyright (c) 2014, Ben Goodrich
#All rights reserved.
#
#Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
#
#1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following... | bbitmaster/python_nn_toolkit | nnet_toolkit/nnet_cuda.py | Python | bsd-2-clause | 5,709 | [
"NEURON"
] | fc7285a0c0a9c6b36f13b5984dca8e7346080e6ffdd4e4803d05b985d3e7d7c2 |
#!/usr/bin/env python
from __future__ import print_function, division #, unicode_literals
import os
import sys
import imp
from os.path import join as pj, abspath as absp, exists as pexists, basename, splitext, isfile
#try:
# import tests as abitests
#except ImportError:
# Add the directory [...]/abinit/tests to $PY... | SamKChang/abinit-7.10.5_multipole | tests/pytests.py | Python | gpl-3.0 | 4,694 | [
"ABINIT"
] | 717b64da7871dfa8301bc1ef1820b611ddb391c812380e5dbcc08b39297009fe |
import numpy as np
import netCDF4 as ncd
FILL_VALUE = None
def new(filename):
'''
Return the netcdf4-python rootgroup for a new netcdf file
for writing.
'''
return ncd.Dataset(filename, 'w', clobber=False)
def add_coordinates(nc, dict_of_dims):
'''
Create dimensions in netcdf file nc.
... | asascience-open/paegan | paegan/cdm/writer.py | Python | gpl-3.0 | 1,992 | [
"NetCDF"
] | 6e9c24ac3801087fca16339e943fa3be8f30eef79484751d3162c95df95313fc |
# ################################################################
#
# Active Particles on Curved Spaces (APCS)
#
# Author: Silke Henkes
#
# ICSMB, Department of Physics
# University of Aberdeen
# Author: Rastko Sknepnek
#
# Division of Physics
# School of Engineering, Physics and Mathem... | sknepneklab/SAMoS | analysis/batch_nematic/batch_analyze_nematic_R8a.py | Python | gpl-3.0 | 2,379 | [
"VTK"
] | 551f8ffc53ace3fa812b479f510d3798652b82912ffc21a84da48367a607375a |
#!/usr/bin/python
"""
PYCAL v1.01
changelog:
-
TODO view met de hele maand -> cal..
TODO kleuren systeem voor iets gebruiken
TODO ondersteuning voor verschillende agenda's
TODO een -C functie voor de config file... en dan het absolute pad
TODO beter aangeven waar hij de todo opslaagt en de config import ook doen voor ... | polarsbear/pycal | calTOBESURE.py | Python | gpl-2.0 | 17,653 | [
"Elk"
] | 8bf720f9d4fba79b597e879e03a847e5c7334561c89726b90ffdf5fc5f5cc591 |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | benoitsteiner/tensorflow-xsmm | tensorflow/contrib/timeseries/python/timeseries/state_space_models/varma.py | Python | apache-2.0 | 8,893 | [
"Gaussian"
] | 848a8c4a70100f4a2079d3533f4b707b33fcccd8880b35e2f7398f64d028c219 |
#!/usr/bin/env
"""
Chuckchi_Winds_NARR_model_prep.py
Retrieve NARR winds for one locations
Icy Cape Line, Ckip2
Latitude = 70.8401 Longitude = 163.2054
Filter NARR winds with a triangular filter (1/4, 1/2, 1/4) and output every 3hrs
Provide U, V
Save in EPIC NetCDF standard
"""
#System Stack
import datetim... | shaunwbell/FOCI_Analysis | ReanalysisRetreival_orig/Chuckchi_Winds/Chuckchi_WindsSFCtemp_NARR_model_prep.py | Python | mit | 9,929 | [
"NetCDF"
] | 352070b7cc466585d12e0ac0e4f25f6e36038bb9ad1a08b7aa83adebd44bece2 |
# -----------------------------------------------------------------------------
# User configuration
# -----------------------------------------------------------------------------
outputDir = '/Users/seb/Desktop/Geometry-diskout-multi-contour/'
inputFile = '/Users/seb/Downloads/ParaViewData-3.98.1/Data/disk_out_ref.e... | Kitware/tonic-data-generator | scripts/paraview/samples/Geometry-multicontour-diskout.py | Python | bsd-3-clause | 3,466 | [
"ParaView"
] | e7d029dc34cb9e791b9b2c92e553f3d916fea40cffa864c4de655e8cabe0ad01 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
__version__ = "0.8.6"
__author__ = "Pierre Legrand (pierre.legrand@synchrotron-soleil.fr)"
__date__ = "20-12-2013"
__copyright__ = "Copyright (c) 2006-2013 Pierre Legrand"
__license__ = "New BSD http://www.opensource.org/licenses/bsd-license.php"
# Environemantal variable... | jsburg/xdsme | XDS/xdsconv.py | Python | bsd-3-clause | 86,399 | [
"CRYSTAL"
] | d88d54cc16754b5302343c4c0674ba19b54a6131e75bf3d17052a68f1b881f1c |
from tendrl.ceph_integration.manager.request_factory import RequestFactory
from tendrl.ceph_integration.manager.user_request import OsdMapModifyingRequest
from tendrl.ceph_integration.manager.user_request import PgCreatingRequest
from tendrl.ceph_integration.manager.user_request import PoolCreatingRequest
from tendrl.c... | r0h4n/ceph-integration | tendrl/ceph_integration/manager/pool_request_factory.py | Python | lgpl-2.1 | 9,966 | [
"Firefly"
] | 2fac6bc93644a1b78b4c6e5cbebc0c5554f37b31849c31fa8e5cd219f4ec78db |
#-------------------------------------------------------------------------------
# rbtlib: resource.py
#
# Get a named tuple response from a URL.
#-------------------------------------------------------------------------------
# The MIT License (MIT)
# Copyright (c) 2016 Brian Minard
#
# Permission is hereby granted, f... | bminard/rbtlib | rbtlib/resource/resource.py | Python | mit | 14,819 | [
"Brian"
] | d125a7e0b721574655adb2948c2964038ab5c5d5dd84dfed0d546074db4e7a87 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
This module contains the definition of some objects used in the chemenv package.
"""
__author__ = "David Waroquiers"
__copyright__ = "Copyright 2012, The ... | johnson1228/pymatgen | pymatgen/analysis/chemenv/utils/defs_utils.py | Python | mit | 4,296 | [
"pymatgen"
] | 8e7f5e7b5aaaf0583b42c0523561055890536c572caaab2172fa21ee422b6818 |
##############################################################################
# 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-rsamtools/package.py | Python | lgpl-2.1 | 2,380 | [
"Bioconductor"
] | 648519784a9ac3a142fb04ec1e9bad3cff87ed4a98b1f5bdb6f8cb02eaad0014 |
# -*- coding: utf-8 -*-
# @Author: YangZhou
# @Date: 2017-06-17 13:34:52
# @Last Modified by: YangZhou
# @Last Modified time: 2017-06-26 16:31:11
import aces.tools as tl
from ase import Atoms
from aces import default
from aces.io.vasp import writevasp
from ase import io
from aces.tools.Units import Units
from ace... | vanceeasleaf/aces | aces/materials/__init__.py | Python | gpl-2.0 | 6,769 | [
"ASE",
"LAMMPS",
"VASP"
] | df74c2fc77799cb20a12924441763e26c74dda6bf300b507a040e88adf780f4a |
from gpaw import GPAW, PW
from ase.lattice import bulk
si = bulk('Si')
si.calc = GPAW(mode=PW(200), kpts={'size': (2, 2, 2), 'gamma': True})
si.get_potential_energy()
si.calc.diagonalize_full_hamiltonian()
si.calc.write('Si_gs', 'all')
dct = {}
execfile('Si_g0w0_ppa.py', dct)
assert abs(dct['ks_gap'] - 0.443) < 0.01
as... | robwarm/gpaw-symm | doc/exercises/gw/test.py | Python | gpl-3.0 | 359 | [
"ASE",
"GPAW"
] | e7befae5b53d7a9291a5ee5c6e6a072e305f2bd6d2e0e287f101ae57e1c576be |
#!/usr/bin/env python
# Run this test like so:
# $ vtkpython TestTextureGlyph.py -D $VTK_DATA_ROOT \
# -B $VTK_DATA_ROOT/Baseline/Graphics/
#
# $ vtkpython TestTextureGlyph.py --help
# provides more details on other options.
import os
import os.path
import vtk
from vtk.test import Testing
class TestTextureGlyph(T... | naucoin/VTKSlicerWidgets | Graphics/Testing/Python/TestTextureGlyph.py | Python | bsd-3-clause | 2,758 | [
"VTK"
] | 59ada863efdb3edb6e1cc8fa0ee08d51b1b8521b95894cecf8f07e1765922b03 |
# Default Django settings. Override these with settings in the module
# pointed-to by the DJANGO_SETTINGS_MODULE environment variable.
# This is defined here as a do-nothing function because we can't import
# django.utils.translation -- that module depends on the settings.
gettext_noop = lambda s: s
#################... | AloneRoad/Inforlearn | vendor/django/conf/global_settings.py | Python | apache-2.0 | 14,586 | [
"VisIt"
] | 2bef68d8eab6ac886f0ff9523127ff25cd1a2f8b7c24778522df43b8d2d7b161 |
''' <h1> Library for specular and off-specular x-ray reflectivity</h1>
interdiff is a model for specular and off specular simulations including
the effects of interdiffusion in hte calculations. The specular simulations
is conducted with Parrats recursion formula. The off-specular, diffuse
calculations are done with th... | jackey-qiu/genx | models/interdiff.py | Python | gpl-3.0 | 13,802 | [
"Gaussian"
] | dece41702b319d38b80308daee4c23f6726d83b80fa6ed53257fc05900643d8d |
#!/usr/bin/python
#
# 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) 2010-2013 Francois Beaune, Jupiter Jazz Limited
# Copyright (c) 2014-2017 Francois Beaune, The appleseedhq Organi... | aiivashchenko/appleseed | scripts/appleseed.package.py | Python | mit | 28,765 | [
"VisIt"
] | 8f3f657ed74a636185abf348ade768d297d82c50c44d21cc92f04dd12ab43319 |
from flatdict import FlatDict
from openpnm.io import Dict, GenericIO
from openpnm.utils import logging
logger = logging.getLogger(__name__)
class HDF5(GenericIO):
r"""
The HDF5 (Hierarchical Data Format) file is good for high-peformance, long
term data storage
"""
@classmethod
def export_data... | PMEAL/OpenPNM | openpnm/io/_hdf5.py | Python | mit | 5,056 | [
"VisIt"
] | 9a6cf76d39a2e6c75fd872840a4fd025cf92911c9f6fddbfe9539076b3d179c8 |
import numpy as np
from galaxies import Galaxies
from galaxy_meta import GalaxyMeta
import matplotlib.pyplot as plt
class GalaxyTester():
def __init__(self, data, model):
self.data = data
self.model = model
self.galaxies = Galaxies()
self.test_ids = self.galaxies.get_flattened_test_... | MorganR/gaussian-processes | galaxy_tester.py | Python | mit | 10,084 | [
"Galaxy"
] | 0e943c9cbe62bac3981ca55f789a2c6070f7b78734e84cea84fefd21fc1538ea |
#!/usr/bin/env python
# Copyright 2014-2019 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/fci/direct_spin1.py | Python | apache-2.0 | 38,081 | [
"PySCF"
] | 139e323f07ef52a7119a374c18f1b658513ff9ad6d603d6f70b57ccf3d3a21fe |
#=== PHYSICS =========================================================================================
# 2D physics functions.
# Authors: Tom De Smedt, Giorgio Olivero (Vector class)
# License: BSD (see LICENSE.txt for details).
# Copyright (c) 2008 City In A Bottle (cityinabottle.org)
# http://cityinabottle.org/nodebo... | pepsipepsi/nodebox_opengl_python3 | nodebox/graphics/physics.py | Python | bsd-3-clause | 77,201 | [
"VisIt"
] | c3d57ea8dabb8753f9f7fd5b578de89c6dbdc4047e97834554baf58aee3bd762 |
##
## Script that showcases a flight to the Hyades, proper motions and
## a zoom out of the galaxy
##
from py4j.java_gateway import JavaGateway, GatewayParameters
gateway = JavaGateway(gateway_parameters=GatewayParameters(auto_convert=True))
gs = gateway.entry_point
## PREPPING
gs.disableInput()
gs.cameraStop()
gs... | ari-zah/gaiasky | assets/scripts/showcases/flight-hyades-mw.py | Python | lgpl-3.0 | 3,340 | [
"Galaxy"
] | f5ca800cf016e4491b67fbb77ce796a49ff8ba6d9bb1e302a38f7247de1e2a0f |
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