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# coding=utf-8
# Copyright 2022 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... | google-research/google-research | tcc/preprocessors/sequence_preprocessor.py | Python | apache-2.0 | 6,713 | [
"Gaussian"
] | d715a39d7bf98e4d00240cf66a1ea409a243c330f4dec730c7e70965261d4c77 |
"""
Traits View definition file.
The view trait of the parent class is extracted from the model definition
file. This file can either be exec()ed or imported. See
core/base.py:Base.trait_view() for what is currently used. Using exec()
allows view changes without needing to restart Mayavi, but is slower than
importi... | dmsurti/mayavi | mayavi/modules/ui/surface.py | Python | bsd-3-clause | 1,631 | [
"Mayavi"
] | d4749c3412f15fb4c11bf489cb30b0a3af71dd642ef8104757c80ad6a9f9d745 |
#!/galaxy/home/mgehrin/hiclib/bin/python
"""
Read two lists of intervals (with chromosomes) and count the number of entries
in the second set that intersect any entry in the first set.
TODO: This could use bitsets rather than the intervals package, would it be
faster?
usage: %prog bed1 bed2 > out
"""
from __f... | bxlab/HiFive_Paper | Scripts/HiCLib/bx-python-0.7.1/build/scripts-2.7/interval_count_intersections.py | Python | bsd-3-clause | 1,235 | [
"Galaxy"
] | 5f2c66480f4c40df98fb5a595c5842cced72e5c77f244144ca83b28267e112c4 |
# This file is part of wger Workout Manager.
#
# wger Workout Manager 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 License, or
# (at your option) any later version.
#
# wger W... | wger-project/wger | wger/core/tests/test_temporary_users.py | Python | agpl-3.0 | 7,017 | [
"VisIt"
] | 6af9c8592417326270db9ee19cb5659815179f48b45302a7fd39b20a48bdacb9 |
#!/usr/bin/env python
#
# Copyright (C) 2014
# Brian Caswell <bmc@lungetech.com>
# Narf Industries <info@narfindustries.com>
#
# 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 rest... | f0rki/cb-multios | original-challenges/Mixology/support/mixcodegen/cg.py | Python | mit | 7,057 | [
"Brian"
] | 4ae6a27f2b4fc2b177d4f77723effb8a5035f8df596f4ac37a0406f147983e54 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import os
import unittest
from pymatgen.io.feff.outputs import LDos, Xmu
from pymatgen.util.testing import PymatgenTest
test_dir_reci = os.path.join(PymatgenTest.TEST_FILES_DIR, "feff_reci_dos")
class Fef... | gmatteo/pymatgen | pymatgen/io/feff/tests/test_outputs.py | Python | mit | 2,914 | [
"FEFF",
"pymatgen"
] | 5c53133f30d18ca630eac0ed0af36e11551b8d735bac0be32cc041d9bcdbab85 |
#Brian Stamm
#CSC 110
#HW 1 - Mad Lips
#9.29.14 v2
#Original story
#The other day, I was walking with my dog, and then the most amazing thing happened!
#We were in the middle of Discovery Park, and then a leprechaun jumped out of the bushes!
#“Hello, my name is Patrick! And I will grant you 1 wish(es)!”
#“... | bkstamm67/python | pastHW/madLips.py | Python | mit | 2,497 | [
"Brian"
] | f14a10906c4c9affe26cf6163bb461ac4a6517e128cab9201ed9495351cad45c |
"""
Test of the classical LM model for language modelling
"""
from groundhog.datasets import LMIterator
from groundhog.trainer.SGD_adadelta import SGD
from groundhog.mainLoop import MainLoop
from groundhog.layers import MultiLayer, \
RecurrentMultiLayer, \
RecurrentMultiLayerInp, \
RecurrentMultiLa... | lisa-groundhog/GroundHog | tutorials/DT_RNN_Tut_Adadelta.py | Python | bsd-3-clause | 14,246 | [
"Gaussian"
] | a22969628a468ed3d1006713df234098df9e0a4e7b705171c0a3226df011f271 |
import pylab as pyl
import cPickle as pickle
from astLib import astStats
galaxies = pickle.load(open('galaxies.pickle', 'rb'))
galaxies = filter(lambda galaxy: galaxy.ston_I >10. and galaxy.clumps != None,
galaxies)
f = pyl.figure(1, figsize=(6,4))
f1s1 = f.add_subplot(111)
d = [[galaxy.clumps, galaxy.ICD_IH... | boada/ICD | sandbox/lowerSN/plot_icd_clumps.py | Python | mit | 1,772 | [
"Galaxy"
] | 4a703a8ee00e2d31421ad52dbfb0b7e760a8f1ea9be0a2d57fa9f2ead933185a |
# coding: utf-8
# In[ ]:
def __init__():
"""
Collection of codes to load and analyze various data
- modis
- emas
- cpl_layers text file
- apr2 files
- hdf files
details are in the info of each module
"""
pass
# ... | samuelleblanc/fp | load_utils.py | Python | gpl-3.0 | 37,002 | [
"NetCDF"
] | ffcc0add56710bb2a96215102856782292b495401be759ff62a7771e75ad5638 |
"""
BNL NSLS-2 Computer Vision Module
Author: William Watson
Date: 2016-7-14
This Module contains numerous functions designed to
help in the data manipulation of images on the Beam-lines within NSLS-2.
It Uses the numpy and cv2 libraries to construct a simple module to
make image processing and computer vision easie... | nextBillyonair/compVision | tests/cvlib.py | Python | mit | 85,682 | [
"Gaussian"
] | ff05ec7c146b5f9eb01dcc5ef45cc5edea5aba1eadf56778f5b6dedeec137acb |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright 2010-2012 Infracom & Eurotechnia (support@webcampak.com)
# This file is part of the Webcampak project.
# Webcampak 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 Fo... | Webcampak/v1.0 | src/bin/wpak-createlocalftpaccounts.py | Python | gpl-2.0 | 5,841 | [
"VisIt"
] | 285f04d16ecc71ec05f34693a37803685af2aa04d22adc9e9b2545cb6f9bff6c |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Christian Schwantes
# Contributors: Robert McGibbon
#
# MDTraj... | tcmoore3/mdtraj | mdtraj/geometry/tests/test_contact.py | Python | lgpl-2.1 | 4,141 | [
"MDTraj"
] | 413b1d098fb2e7159c3b190c9a29059b63c4c8f2063d3b759402e13db8117cc7 |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
# This simple example on how to do animations using graph-tool. Here we do a
# simple simulation of an S->I->R->S epidemic model, where each vertex can be in
# one of the following states: Susceptible (S), infected (I), recovered (R). A
# vertex in the S state becomes inf... | jim-pansn/graph-tool | doc/demos/animation_zombies.py | Python | gpl-3.0 | 5,436 | [
"VisIt"
] | ac17ba22f9073ef99ff7da5266c152a2c493390936fd1f255e5c79a05b6b16d9 |
"""
==========================================
Statistical functions (:mod:`scipy.stats`)
==========================================
.. module:: scipy.stats
This module contains a large number of probability distributions as
well as a growing library of statistical functions.
Each univariate distribution is an insta... | DailyActie/Surrogate-Model | 01-codes/scipy-master/scipy/stats/__init__.py | Python | mit | 8,906 | [
"Gaussian"
] | cb4f3d7e0cd01f23617ff208c86a63a28aff1692a4fd13df2b3208a04bffb802 |
""" Compares the performance of different variants of the MDI algorithm on time-series of varying dimensionality. """
import sys
sys.path.append('..')
import numpy as np
from time import time
import csv
from maxdiv import maxdiv, maxdiv_util, libmaxdiv_wrapper
# ensure reproducable results
np.random.seed(0)
def sa... | cvjena/libmaxdiv | tools/timing_multvar.py | Python | lgpl-3.0 | 3,272 | [
"Gaussian"
] | 5a5e4fe6331d8d0cd9e8ec1f71291d0771b55e27582038c8f88271fb818f690d |
_author__ = 'tylin'
__version__ = '1.0.1'
# Interface for accessing the Microsoft COCO dataset.
# Microsoft COCO is a large image dataset designed for object detection,
# segmentation, and caption generation. pycocotools is a Python API that
# assists in loading, parsing and visualizing the annotations in COCO.
# Plea... | MeteorKepler/RICGA | ricga/eval_tools/pycocotools/coco.py | Python | apache-2.0 | 15,205 | [
"VisIt"
] | ef226334c4e09a8073a95c2aa1c71fe88ed560806e1fa051d94fb8ebf031afef |
# $Id$
#
# Copyright (C) 2002-2006 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
"""unit testing code ... | ptosco/rdkit | rdkit/Chem/EState/UnitTestTypes.py | Python | bsd-3-clause | 2,088 | [
"RDKit"
] | d89ccdcd2f2f87db91435cbeec06d824ae810e58fcc673b70283316f9bc33464 |
from math import *
import pygame as pg
import datetime, os
import os.path
import subprocess
import numpy as np
import bluesky as bs
from bluesky.tools import geo
from bluesky.tools.areafilter import areas
from bluesky.tools.aero import ft, kts, nm
from bluesky.tools.misc import tim2txt
from bluesky import MSG_OK
fr... | ethertricity/bluesky | bluesky/ui/pygame/screen.py | Python | gpl-3.0 | 48,696 | [
"Amber"
] | dc78ae28844db996ad4fff487dd33b6b84a8e9e505930bda0bbd51ea9ab6b5fa |
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
#
import sys
# Add path to Bio
sys.path.append('../..')
"""Code to interact with the primersearch program from EMBOSS.
"""
__docformat__ = "restructu... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/Emboss/PrimerSearch.py | Python | gpl-2.0 | 2,421 | [
"Biopython"
] | 44bb2600c799a6957fe663d6dc11888ab7ee5cf1e163ff6bf104bec981493a21 |
import cStringIO
from DIRAC.Core.Utilities.Graphs import barGraph, lineGraph, pieGraph, qualityGraph, textGraph
from DIRAC import S_OK, S_ERROR
def checkMetadata( metadata ):
if 'span' in metadata:
granularity = metadata[ 'span' ]
if 'starttime' in metadata:
metadata[ 'starttime' ] = metadata[ 'startt... | Sbalbp/DIRAC | AccountingSystem/private/Plots.py | Python | gpl-3.0 | 2,852 | [
"DIRAC"
] | 871fc46099e5d9de0e8eafa8f70edaaf0ecf9bb2c7085fdae138b75894f69d4a |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
... | kain88-de/mdanalysis | testsuite/MDAnalysisTests/analysis/test_lineardensity.py | Python | gpl-2.0 | 1,978 | [
"MDAnalysis"
] | 5bf4fca1fc1b7a55a46e346f1c4a523217708b3f211394ef48a44587ae64c9ee |
#!/usr/bin/env python
''' buildScriptsDocs
Prototype to build scripts documentation from the scripts docstrings. As the
scripts are not very uniform, this script is full of hacks to avoid them. They
will eventually dissapear.
'''
# defined on DIRACDocs/source/Tools/fakeEnvironment
import fakeEnvironment
impor... | andresailer/DIRAC | docs/Tools/buildScriptsDOC.py | Python | gpl-3.0 | 9,918 | [
"DIRAC"
] | 4b41c9d48888ca901f28ada1dec9f2517ab05fc61f2d9a5b0dabd3a9853f08e5 |
'''
Script to insert station observation data into a single netCDF file.
'''
from twx.utils import TwxConfig
import obsio
import os
from twx.db import StationDataDb
import numpy as np
if __name__ == '__main__':
twx_cfg = TwxConfig(os.getenv('TOPOWX_INI'))
ghcnd = obsio.HdfObsIO(twx_cfg.fpath_stndata_hdf... | jaredwo/topowx | scripts/step04_create_stn_nc.py | Python | gpl-3.0 | 1,317 | [
"NetCDF"
] | 0b7f322681014c20e44c9f761d88818c9e269dd24c818c8f53c7fa3e9750c430 |
# -*- coding: utf-8 -*-
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import os.path
import numpy as np
import abel
DATA_DIR = os.path.join(os.path.split(__file__)[0], 'data')
dasch_transforms = {
"two_point": abel.dasch.two_point_transform,
"three_p... | DanHickstein/pyBASEX | abel/tests/test_dasch_methods.py | Python | gpl-2.0 | 3,380 | [
"Gaussian"
] | 78fbe974c0e3abfc02d599804b9b43c95594d88386b3337d1313317b8cb03628 |
"""Leave one out coding"""
import numpy as np
import pandas as pd
from sklearn.base import BaseEstimator
import category_encoders.utils as util
from sklearn.utils.random import check_random_state
__author__ = 'hbghhy'
class LeaveOneOutEncoder(BaseEstimator, util.TransformerWithTargetMixin):
"""Leave one out codi... | wdm0006/categorical_encoding | category_encoders/leave_one_out.py | Python | bsd-3-clause | 10,582 | [
"Gaussian"
] | 1747c72026c29980b43e8b5d9e478286cc4fded2f0a17b38849d383f684ed816 |
import numpy as np
from scipy import ndimage as nd
from astropy.io import fits
import astropy.units as u
from ..width_profiles.profile import _line_profile_coordinates
def generate_filament_model(shape=100, pad_size=0,
max_dist=100,
theta=0.0, width=10.0,
... | e-koch/FilFinder | fil_finder/tests/testing_utils.py | Python | mit | 3,521 | [
"Gaussian"
] | 43d56b9c858c0c626e412d09b604bb2afe37cccc3de3ca3a83eff5a8d646cc89 |
"""
:func:`~pandas.eval` parsers.
"""
import ast
from functools import (
partial,
reduce,
)
from keyword import iskeyword
import tokenize
from typing import (
Callable,
Optional,
Set,
Tuple,
Type,
TypeVar,
)
import numpy as np
from pandas.compat import PY39
import pandas.core.common ... | datapythonista/pandas | pandas/core/computation/expr.py | Python | bsd-3-clause | 24,503 | [
"VisIt"
] | ae4c9587c52769397ec7711148d9f2e3b79c9bcad31cb215026bc84e49a0364b |
import os.path
import bokeh
import bokeh.io
import bokeh.model
import bokeh.plotting
import bokeh.util.platform
import ipywidgets as widgets
import matplotlib.pyplot as plt
import numpy as np
import pyproj
from IPython.display import display
from bokeh.models import ColumnDataSource, Circle
from bokeh.tile_providers i... | DeDop/dedop | dedop/ui/inspect.py | Python | gpl-3.0 | 25,746 | [
"NetCDF"
] | c50bd38df535283402c4e301e1d1c7a61043c5e014cb7910baf17bebb7abbd28 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | CDSherrill/psi4 | psi4/driver/p4util/procutil.py | Python | lgpl-3.0 | 19,819 | [
"CFOUR",
"Psi4"
] | 79d61a7d1f8b4b7f10e6618dfb57d882d37fb7b041014f1b18813b2d027636ad |
#!/usr/bin/python
import sys
import string
import re
NODECL_PREFIX="NODECL_"
def loadlines(f):
lines = f.readlines()
result = []
for l in lines:
l = l.strip(" \n")
if l == "" or l[0] == "#":
continue
result.append(l)
return result
def find_matching_parentheses(s):... | robbriggs/masters-project-mercurium | src/frontend/nodecl-generator.py | Python | gpl-3.0 | 63,225 | [
"VisIt"
] | 2eb55882d06bec250acdcb634d33042a09dda41557029b207f34b884a08bf998 |
# Orca
#
# Copyright 2010 Joanmarie Diggs
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This library is... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/scripts/apps/gajim/__init__.py | Python | gpl-3.0 | 797 | [
"ORCA"
] | 84cc115a45e293d5cc7950e83491e4c141e2d0827f7dc6d1a21c8fefeb138033 |
#
# paws -- provision automated windows and services
# Copyright (C) 2016 Red Hat, Inc.
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) a... | rhpit/paws | tests/integration/test_docker_images.py | Python | gpl-3.0 | 5,036 | [
"VisIt"
] | ddcac69ef613192478c33dc191210c7c485f6db37cd5e08844699668694bcc0b |
from ovito import *
from ovito.io import *
from ovito.modifiers import *
from ovito.data import *
import numpy as np
node = import_file("../../files/CFG/shear.void.120.cfg")
file_source = node.source
print(file_source.source_path)
print(file_source)
assert(isinstance(file_source, DataCollection))
assert(file_source.l... | srinath-chakravarthy/ovito | tests/scripts/test_suite/file_source.py | Python | gpl-3.0 | 431 | [
"OVITO"
] | e22d60f75bf0e462dc6ec75da4cca01afa7a8d44cf96983cc3d6f6fed9cfb80e |
#!/usr/bin/python
#
# Copyright 2017 Google Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or a... | brain-research/hyperbolictext | word_context/word_context_model.py | Python | apache-2.0 | 35,604 | [
"Gaussian"
] | 61e5a5723a77a39b1efac3dc7957d7de0b706322a586d5385b125e995e810eb6 |
from default_settings import all as s
import os
import matplotlib.pyplot as plt
from sklearn.metrics import precision_recall_curve, auc
import pandas as pd
import seaborn as sns
sns.set(color_codes=True)
from itertools import compress
classifier_names = ["Nearest Neighbors",
"Linear SVM",
... | mmmatthew/raycast | code/script_make_comparison_figures.py | Python | apache-2.0 | 6,064 | [
"Gaussian"
] | 314958b408c979046eef2c6088e6a0037ebd383e4e0cd4e1ce536c94384df5e4 |
import os
from ase import Atom, Atoms
from gpaw import GPAW
from gpaw.test import equal
import cmr
a = 4.05
d = a / 2 ** 0.5
bulk = Atoms([Atom('Al', (0, 0, 0)),
Atom('Al', (0.5, 0.5, 0.5))],
pbc=True)
bulk.set_cell((d, d, a), scale_atoms=True)
h = 0.25
calc = GPAW(h=h,
nbands=2 ... | ajylee/gpaw-rtxs | gpaw/test/cmr_test.py | Python | gpl-3.0 | 822 | [
"ASE",
"GPAW"
] | d6c0f3a66cca9b152d8e80c0c46aff3cfd4bdbb75fa3d054fac348a9bd0351c2 |
#
# Copyright (C) 2013-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | psci2195/espresso-ffans | testsuite/python/nsquare.py | Python | gpl-3.0 | 1,876 | [
"ESPResSo"
] | 560eda3032fdaf5c92160ee720b73a296d2e8f0979d92a623498518d48c95474 |
import ast
import annotators
import llvm_builder
from typing import *
compare_op = {
ast.Eq: 'EQ',
ast.NotEq: 'NEQ',
ast.Lt: 'LT',
ast.LtE: 'LTE',
ast.Gt: 'GT',
ast.GtE: 'GTE',
}
class ConstraintChecker(ast.NodeVisitor):
def visit_FunctionDef(self, node):
assert node.decorator_li... | Jokymon/hpcs | compiler.py | Python | gpl-3.0 | 7,155 | [
"VisIt"
] | ccdcc6ae121e73feb83f3b071575a0ec3799762fcfa813cb6c37935ff87b643f |
#
# Copyright 2021 Lars Pastewka (U. Freiburg)
# 2018 Jacek Golebiowski (Imperial College London)
#
# 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 Gen... | libAtoms/matscipy | matscipy/calculators/mcfm/cluster_data.py | Python | lgpl-2.1 | 1,913 | [
"Matscipy"
] | 9bc59b129428b29128d5499b9fc74404621a695702cc44ee402092a50d310989 |
"""Notifications for Android TV notification service."""
import base64
import io
import logging
import requests
from requests.auth import HTTPBasicAuth, HTTPDigestAuth
import voluptuous as vol
from homeassistant.components.notify import (
ATTR_DATA,
ATTR_TITLE,
ATTR_TITLE_DEFAULT,
PLATFORM_SCHEMA,
... | nkgilley/home-assistant | homeassistant/components/nfandroidtv/notify.py | Python | apache-2.0 | 9,885 | [
"Amber"
] | 15f2d8a0377f5f283916bcf14d6f32f58d0b8cb3cb0833ebba2f6d8af9bc1b56 |
"""
Collection of DIRAC useful operating system related modules
by default on Error they return None
"""
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
import os
import distutils.spawn # pylint: disable=no-name-in-module,import-error
import DIRAC
f... | ic-hep/DIRAC | src/DIRAC/Core/Utilities/Os.py | Python | gpl-3.0 | 4,903 | [
"DIRAC"
] | d7ac89964474b07e4191f598869fbed8fb463e7676bbc769904ed6361c327213 |
__all__ = [
'BadRequestException',
'BadStateException',
'CsrfException',
'DropboxOAuth2Flow',
'DropboxOAuth2FlowNoRedirect',
'NotApprovedException',
'ProviderException',
]
import base64
import os
import six
import sys
import urllib
from .dropbox import Dropbox
from .session import pinned_s... | ewjoachim/dropbox-sdk-python | dropbox/oauth.py | Python | mit | 16,593 | [
"VisIt"
] | 73c99b01326ab9d08395ef3b4f64ec0eb17f224d614f1b639e9a16a90df36b38 |
# 30.05.2007, c
# last revision: 25.02.2008
from __future__ import absolute_import
from sfepy import data_dir
import six
filename_mesh = data_dir + '/meshes/2d/square_unit_tri.mesh'
material_1 = {
'name' : 'coef',
'values' : {
'val' : 1.0,
},
}
material_2 = {
'name' : 'm',
'values' : {
... | sfepy/sfepy | tests/test_laplace_unit_square.py | Python | bsd-3-clause | 5,846 | [
"VTK"
] | 43c7885d1d67edbcee89f0e65b638e4c15e53d4fc1c581798f3b8490e958e438 |
from ase.io import read, PickleTrajectory
from ase.constraints import FixAtoms
from ase.neb import NEB
from ase.optimize import QuasiNewton
from ase.parallel import rank, size
from gpaw import GPAW
initial = read('initial.traj')
final = read('final.traj')
constraint = FixAtoms(mask=[atom.tag > 1 for atom in initial]... | qsnake/gpaw | doc/tutorials/neb/neb.py | Python | gpl-3.0 | 1,082 | [
"ASE",
"GPAW"
] | 5332778a001b2b30a04409a8fcbcb5039567569cf4a630d914e0faeba5db3dfd |
# Copyright (c) 2011, Joerg Raedler (Berlin, Germany)
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without modification,
# are permitted provided that the following conditions are met:
#
# Redistributions of source code must retain the above copyright notice, this list
# of cond... | jraedler/DyMat | DyMat/Export/netCDF.py | Python | bsd-2-clause | 3,162 | [
"NetCDF"
] | e6270c63076252b5240a90b3ad8cd4f19fe0b84370f25e245e542a8a718ec5d5 |
import random
import math
from neat import config
from neat import genome
# Temporary workaround - default settings
#node_gene_type = genome.NodeGene
conn_gene_type = genome.ConnectionGene
class Chromosome(object):
""" A chromosome for general recurrent neural networks. """
_id = 0
def __init__(self, pare... | davidmfinol/py3NEAT | neat/chromosome.py | Python | gpl-3.0 | 16,707 | [
"NEURON"
] | 6f06651f442c265b3ff64d210e2d88cb89cba21c907a31ba7d55abf97fa2b447 |
from __future__ import absolute_import, division, print_function, unicode_literals
import os
import sys
import json
import time
import glob
import shutil
import string
import numbers
import itertools
from builtins import range
import multiprocessing as mp
import numpy as np
import mdtraj as md
import AdaptivePELE.const... | AdaptivePELE/AdaptivePELE | AdaptivePELE/simulation/simulationrunner.py | Python | mit | 87,095 | [
"MDAnalysis",
"MDTraj",
"OpenMM"
] | e53c315c9839a2064e39b93936e96fc6405a2cf0ea1c83dad668349bec451fb6 |
# -*- coding: utf-8 -*-
"""
***************************************************************************
OTBUtils.py
---------------------
Date : 11-12-13
Copyright : (C) 2013 by CS Systemes d'information (CS SI)
Email : otb at c-s dot fr (CS SI)
Contrib... | wonder-sk/QGIS | python/plugins/processing/algs/otb/maintenance/OTBSpecific_XMLcreation.py | Python | gpl-2.0 | 30,233 | [
"Gaussian"
] | 18f27146f63adc6a55243ff832bf6d7c31a581ec1f0b587d018935fd92378d94 |
# Copyright 2014 The Oppia 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 applicable ... | mit0110/oppia | scripts/build.py | Python | apache-2.0 | 3,721 | [
"GULP"
] | 5b76fe7683703defd0870782f80ff54077981b9cea22cfc76b33f73aecd8bb06 |
# Copyright Iris contributors
#
# This file is part of Iris and is released under the LGPL license.
# See COPYING and COPYING.LESSER in the root of the repository for full
# licensing details.
"""
Test plots with two dimensional coordinates.
"""
# import iris tests first so that some things can be initialised before
... | pp-mo/iris | lib/iris/tests/integration/plot/test_plot_2d_coords.py | Python | lgpl-3.0 | 2,511 | [
"NetCDF"
] | b6dd22f790d265212afb49fe9666df6ef95124e45ac5fd86c3a481079819b2e9 |
# Copyright 2007 Baptiste Lepilleur and The JsonCpp Authors
# Distributed under MIT license, or public domain if desired and
# recognized in your jurisdiction.
# See file LICENSE for detail or copy at http://jsoncpp.sourceforge.net/LICENSE
"""tarball
Tool-specific initialization for tarball.
"""
## Commands to tack... | SSimonXX/cmake-demo | src/third_parts/jsoncpp/scons-tools/targz.py | Python | apache-2.0 | 3,280 | [
"VisIt"
] | 70ae019cb0bb2cc00e7b35bce1d9d024a79adbe98895962f2ed23114c0e79e1e |
from asap3 import *
from ase.lattice.cubic import FaceCenteredCubic
from asap3.testtools import *
from numpy import *
import ase.data
def TestLists(nblist, nblist2, name, count=None):
"Run the tests on a half and a full neighbor list."
print "Running tests on", name
print "Testing %s: Lengths of lists." % ... | auag92/n2dm | Asap-3.8.4/Test/NbCellLocator.py | Python | mit | 3,418 | [
"ASE"
] | a3b1feb9a84f5b2435562453b6839a0d8caa588c32f62acacc23639c5fa0ed7b |
# $HeadURL$
__RCSID__ = "$Id$"
import os
import os.path
try:
import hashlib as md5
except:
import md5
import time
import threading
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Core.Utilities.ThreadSafe import Synchronizer
from DIRAC.FrameworkSystem.private.monitoring.RRDManager import RRDManager
from DIRAC... | miloszz/DIRAC | FrameworkSystem/private/monitoring/PlotCache.py | Python | gpl-3.0 | 3,310 | [
"DIRAC"
] | d46db6b02854d454b58ba79680966f5935e2ba22e350f246fd07f5054675d657 |
#########################################################################
# loadMorphology.py ---
#
# Filename: loadMorphology.py
# Author: Upinder S. Bhalla
# Maintainer:
# Created: Oct 12 16:26:05 2014 (+0530)
# Version:
# Last-Updated: May 16 2017
# By: Upinder S. Bhalla
# Update #:
# URL:
# Keywords... | BhallaLab/moose-examples | snippets/loadMorphology.py | Python | gpl-2.0 | 2,789 | [
"MOOSE",
"NEURON"
] | 0aba3a02ea6a5f062b0eca1c4b71f64150736420e337850cffb3368f8eb0ee71 |
"""
Tests which scan for certain occurrences in the code, they may not find
all of these occurrences but should catch almost all.
"""
from __future__ import division, absolute_import, print_function
import sys
if sys.version_info >= (3, 4):
from pathlib import Path
import ast
import tokenize
import ... | b-carter/numpy | numpy/tests/test_warnings.py | Python | bsd-3-clause | 2,686 | [
"VisIt"
] | c7b21c0874aebf8850e5e973dd954df8bd23c5f5e54da5d2e7aecb19751b413a |
#
# Copyright (c) 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009 The SCons Foundation
#
# 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
# without limitati... | BenLand100/rat-pac | python/SCons/Taskmaster.py | Python | bsd-3-clause | 39,536 | [
"VisIt"
] | 53768f699f26969202d4cc9518c911677e9adddd3c4bf1422c73a635ac114165 |
# $HeadURL$
"""
The Grid module contains several utilities for grid operations
"""
__RCSID__ = "$Id$"
import os
import types
import re
from DIRAC.Core.Utilities.Os import sourceEnv
from DIRAC.FrameworkSystem.Client.ProxyManagerClient import gProxyManager
from DIRAC.Core.Security.ProxyInfo import g... | calancha/DIRAC | Core/Utilities/Grid.py | Python | gpl-3.0 | 15,370 | [
"DIRAC"
] | 925e6b197afff3e05272243d0f05019f51cdb088ac3654004b38211cdd532ad2 |
#
#
# Tutorial Yambo School. Lausanne, 24-28 April 2017
# Convergence GW on hexagonal BN
# Alejandro Molina-Sanchez & Henrique P. C. Miranda
#
#
from __future__ import print_function
import sys
from yambopy import *
from qepy import *
from schedulerpy import *
import argparse
yambo = 'yambo'
p2y = 'p2y'
pre... | henriquemiranda/yambo-py | tutorial/bn/gw_conv_bn.py | Python | bsd-3-clause | 10,578 | [
"Yambo"
] | 111978edfd07a6d3666d9e834d7bce054687ca613c3eaf28330271147b8cb785 |
from django.db.models.signals import post_save
from django.dispatch import receiver
@receiver(post_save, weak=False,
dispatch_uid="visit_tracking_check_in_progress_on_post_save")
def visit_tracking_check_in_progress_on_post_save(
sender, instance, raw, created, using, **kwargs):
"""Calls post_sa... | botswana-harvard/edc-visit-tracking | edc_visit_tracking/signals.py | Python | gpl-2.0 | 592 | [
"VisIt"
] | 4432c7b7cd347f2a363addb5721277932da34cc34485d3ec46579a4f7e775602 |
# Copyright (c) 2012-2013 ARM Limited
# All rights reserved.
#
# The license below extends only to copyright in the software and shall
# not be construed as granting a license to any other intellectual
# property including but not limited to intellectual property relating
# to a hardware implementation of the functiona... | KuroeKurose/gem5 | configs/example/se.py | Python | bsd-3-clause | 13,230 | [
"GAMESS",
"Gromacs",
"NAMD"
] | 00e67078c810bf5abccec0b23be844c827ecfbdbffa52922e5510ebbff9dd542 |
# Copyright (c) 1998-2000 John Aycock
#
# 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
# without limitation the rights to use, copy, modify, merge, publ... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/Parsers/spark.py | Python | gpl-2.0 | 18,904 | [
"Biopython"
] | 0dfe77400bdc937a042c2d9c936623f52557b11c46c8d41087da941ed29afd4b |
"""
======================
Simple Gaussian Fitter
======================
"""
import pyspeckit
def fit_gaussians_to_simple_spectra(filename, units='km/s', doplot=True,
baseline=True, plotresiduals=False, figuresavename=None,
croprange=None, savename=None, **kwargs):
"""
As stated in the name tit... | bsipocz/pyspeckit | pyspeckit/wrappers/fit_gaussians_to_simple_spectra.py | Python | mit | 2,973 | [
"Gaussian"
] | ea678d086b03e6d487b0f44a61dce99ae7a289f5c18c266e8febc98dcffd654a |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2002 Bruce J. DeGrasse
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007-2009 Brian G. Matherly
# Copyright (C) 2007 Robert Cawley <rjc@cawley.id.au>
# Copyright (C) 2008-2009 James Friedmann <jfriedmannj@gmail.com>
# Copyri... | Forage/Gramps | gramps/plugins/textreport/detdescendantreport.py | Python | gpl-2.0 | 46,584 | [
"Brian"
] | a32b6a9ad02c42963479f091df4ce3c4e4cbe474bf9203df2e9433af09bb3bb4 |
#!/usr/bin/env python
##############################################################################################
#
#
# CMIP6_hybrid_regrid_emissions_N96e.py
#
#
# Requirements:
# Iris 1.10, time, cf_units, numpy
#
#
# This Python script has been written by N.L. Abraham as part of the UKCA Tutorials:
# http://... | acsis-project/emissions | emissions/python/CMIP6_hybrid/CMIP6_hybrid_regrid_iC5H12_emissions_n96e_greg.py | Python | gpl-3.0 | 18,851 | [
"NetCDF"
] | e9b5ba622a7fccaf1f883811a7219624c81b8068636e590bdfce11f9d3b1af5d |
'''
demo9.py
Demo of a network of spiking neurons driven by synaptic inputs.
Written by Sungho Hong, Computational Neuroscience Unit, OIST, 2017
'''
from neuron import h, gui
h.load_file("stdrun.hoc")
h.load_file("CNSutils.hoc")
# The simulation will run for 100 ms.
h.tstop = 200
# Global sampling period will be 0... | shhong/a310_cns_2017 | Practice_4/demo9_1.py | Python | gpl-3.0 | 3,143 | [
"NEURON"
] | 4d0fc336d9ef01b83c4239c563188b97137ec041fd9c5a3916f1f5e049d33ad9 |
import unicodecsv as csv
import json
import requests
import datetime
import pyaml
import io
from flask import request, url_for, render_template, redirect, \
jsonify, flash, make_response, Response, g, \
abort
from flask.ext.login import current_user, login_required
from flask.ext.co... | OVERLOADROBOTICA/OVERLOADROBOTICA.github.io | mail/formspree-master/formspree/forms/views.py | Python | mit | 32,352 | [
"VisIt"
] | ec208ae2ecc8a26ffa9d0896cf8ac1f6126be13f614f7971882e54c9a56b5ff8 |
from __future__ import absolute_import
from typing import Any, Dict, List, Set, Tuple, TypeVar, Text, \
Union, Optional, Sequence, AbstractSet, Pattern, AnyStr
from typing.re import Match
from zerver.lib.str_utils import NonBinaryStr
from django.db import models
from django.db.models.query import QuerySet
from dja... | AZtheAsian/zulip | zerver/models.py | Python | apache-2.0 | 57,697 | [
"VisIt"
] | 65af129c669b350c427b45cc22ed139a1e55fa675d08466a71bd482c7041bc76 |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import time
from diraccfg import CFG
import DIRAC
from DIRAC import gConfig
cfg = CFG()
cfg.loadFromBuffer(
"""
DIRAC
{
Security
{
Authorization
{
issuer = https://i... | ic-hep/DIRAC | tests/Integration/Resources/IdProvider/Test_IdProviderFactory.py | Python | gpl-3.0 | 3,025 | [
"DIRAC"
] | 98944b2c6ab19d49d5c5fbf8b7248b17e72138214755ae3efe33d1ed05a0c2f4 |
# coding: utf-8
# coding: utf-8
import numpy as np
from numpy.core.numeric import array
from sklearn.metrics import pairwise
from collections import OrderedDict
from scipy.linalg import eig
from scipy import interpolate as ip
from pyspark.ml.feature import PCA as pcaml
from pyspark.ml.linalg import Vectors as mlve... | quinngroup/fergus-ssl | LabelPropagationDistributed/LabelPropagationDistributed/LabelPropagationDistributed.py | Python | apache-2.0 | 22,196 | [
"Gaussian"
] | 147752e853bcce11381af6b89ec992e15bc4ed053b1300467937641af4f34239 |
class Kiosk():
def __init__(self, visit_cost, location):
self.visit_cost = visit_cost
self.location = location
print 'initializing Kiosk'
#patient in class Person
def visit_or_not(self, patient):
if not patient.money>self.visit_cost:
print 'patient cannot afford ... | rkawauchi/IHK | kiosk+assign_visit.py | Python | bsd-3-clause | 1,323 | [
"VisIt"
] | a4079cecbd187681083df363f223314748c179a9a922e898b3e51e7dc7d3d8fd |
# GromacsWrapper: top.py
# Copyright (c) 2012 Oliver Beckstein <orbeckst@gmail.com>
# Copyright (c) 2010 Tsjerk Wassenaar <tsjerkw@gmail.com>
# Released under the GNU Public License 3 (or higher, your choice)
# See the file COPYING for details.
"""
Gromacs TOP file format
=======================
Classes
-------
.. aut... | pslacerda/GromacsWrapper | gromacs/fileformats/top.py | Python | gpl-3.0 | 52,177 | [
"Gromacs"
] | db95d4a766577b195a7e404a418bf09d5e1924911f4f14e1be0c2e42e0985ad3 |
# -*- coding: utf-8 -*-
"""2D DeepOBS dataset."""
import numpy as np
import tensorflow as tf
from . import dataset
class two_d(dataset.DataSet):
"""DeepOBS data set class to create two dimensional stochastic testproblems.
This toy data set consists of a fixed number (``train_size``) of iid draws
from tw... | fsschneider/DeepOBS | deepobs/tensorflow/datasets/two_d.py | Python | mit | 4,790 | [
"Gaussian"
] | bfad8f3809092e1f32a86fe12616383452f3b40c0c9e137264a9ad2f9d29459a |
#!/usr/bin/env python
import os
import sys
from numpy.distutils.misc_util import get_numpy_include_dirs
try:
import configparser
except ImportError:
import ConfigParser as configparser
if len(set(('develop', 'bdist_egg', 'bdist_rpm', 'bdist', 'bdist_dumb',
'bdist_wininst', 'install_egg_info', 'eg... | smerdis/pycortex | setup.py | Python | bsd-2-clause | 3,848 | [
"Mayavi"
] | d2b29864ef9761780cf2c662c3aca04e9e1c49b2f59177d92d578bb471599d84 |
#!/usr/bin/env python
__author__ = 'waroquiers'
import unittest
from pymatgen.analysis.chemenv.coordination_environments.voronoi import DetailedVoronoiContainer
from pymatgen.core.structure import Structure
from pymatgen.core.lattice import Lattice
import os
import shutil
import random
import numpy as np
<<<<<<< HEA... | Bismarrck/pymatgen | pymatgen/analysis/chemenv/coordination_environments/tests/test_voronoi.py | Python | mit | 14,923 | [
"pymatgen"
] | de7531069b185c1ed0263a42d1f4299e37dbdd9a36f4193df1a77be1ed2e513c |
#
# Copyright (C) 2013-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | fweik/espresso | samples/widom_insertion.py | Python | gpl-3.0 | 4,264 | [
"ESPResSo"
] | 9381a845f6b1c0f18e18ae2cef7ebf32e832e88490c7fd6f649187fc169bac01 |
# -*- coding: utf-8 -*-
"""Rewrite assertion AST to produce nice error messages"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import ast
import errno
import imp
import itertools
import marshal
import os
import re
import string
import struct
import sys
i... | kawamon/hue | desktop/core/ext-py/pytest-4.6.11/src/_pytest/assertion/rewrite.py | Python | apache-2.0 | 40,732 | [
"VisIt"
] | 976799c6bdf8172ab89fdb2750511800ae3b6f9a8f2fc782aeb63c57c5e73ba9 |
#!/usr/bin/env python
# ----------------------------------------------------------------------------
# Copyright 2015-2016 Nervana Systems 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
#... | guoxuesong/deepstacks | examples/neon/mnist_branch.py | Python | mit | 5,906 | [
"Gaussian"
] | 368563477cd60bf04164033fc2bd6767b57ed7f2e2cf7a3e6cde3971a2aa590e |
from __future__ import with_statement
import os.path
from optparse import OptionParser
from babbisch.utils import ASTCache
from babbisch.analyze import AnalyzingVisitor
from babbisch.filter import include_exclude
USAGE = 'usage: %prog [options] headerfile...'
FORMATS = {
'json': lambda visitor: visitor.to_js... | fredreichbier/babbisch | babbisch/__init__.py | Python | mit | 2,554 | [
"VisIt"
] | 192ef5bcbfa4cf710796bf0daf443e99e75086fec69fe5918b4bebadac9135f9 |
from ase.lattice.surface import fcc100, add_adsorbate
from ase.constraints import FixAtoms, FixedPlane
from ase.calculators.emt import EMT
from ase.optimize import QuasiNewton
# 2x2-Al(001) surface with 3 layers and an
# Au atom adsorbed in a hollow site:
slab = fcc100('Al', size=(2, 2, 3))
add_adsorbate(slab, 'Au', 1... | grhawk/ASE | tools/doc/tutorials/constraints/diffusion4.py | Python | gpl-2.0 | 882 | [
"ASE"
] | 151101a1d7fd2ebde278b71a16f116f91ff5bf702442a862a1fac96e7483e64a |
'''
GeNN accumulates postsynaptic changes into a variable inSyn. The idea of this
module is to check, for a given Synapses, whether or not it can be recast into
this formulation, and if so to relabel the variables appropriately.
In GeNN, each synapses object has an associated variable inSyn. The idea is
that we will d... | brian-team/brian2genn | brian2genn/insyn.py | Python | gpl-2.0 | 4,936 | [
"Brian",
"NEURON"
] | 2bf033af76645aaed7f599a3625be6f36d7b1fe284b4385e97e4ba76f7959b6d |
# -*- coding:utf-8 -*-
# ##### BEGIN LGPL LICENSE BLOCK #####
# GEOS - Geometry Engine Open Source
# http:#geos.osgeo.org
#
# Copyright (C) 2011 Sandro Santilli <strk@kbt.io>
# Copyright (C) 2005 2006 Refractions Research Inc.
# Copyright (C) 2001-2002 Vivid Solutions Inc.
# Copyright (C) 1995 Olivier Deville... | s-leger/archipack | pygeos/prepared.py | Python | gpl-3.0 | 44,656 | [
"VisIt"
] | 47f166f1b995509660859496e99d67b076b97dd5f38f8573323c6f69dcf5f7df |
"""
Migration script to alter the repository_metadata table by dropping the tool_test_errors column and adding columns
tool_test_results, missing_test_components.
"""
from sqlalchemy import *
from sqlalchemy.orm import *
from migrate import *
from migrate.changeset import *
# Need our custom types, but don't import a... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/webapps/tool_shed/model/migrate/versions/0018_add_repository_metadata_flag_columns.py | Python | gpl-3.0 | 3,915 | [
"Galaxy"
] | 80eafab5fdbcd275ad645482d505c000dc2fa04e7f259f1f4e98f89ccaf82817 |
#!/usr/bin/env python2
'''
Show an angular/energy/charge plot.
Usage:
angular.py [options] <input> [<output>]
Options:
--angle-bins=BINS -a BINS Set the number of angle bins. [default: 180]
--energy-bins=BINS -r BINS Set the number of energy bins. [default: 40]
--ltitle=TITLE -t TITLE Set the title.
... | noobermin/sharks-butts | bin/angular.py | Python | mit | 3,542 | [
"Gaussian"
] | 48ff6bb25913cc16baf3a5a0dd698af47c1f71b027e99df11102f3a36aa75524 |
#!/usr/bin/env python
# -*- coding:utf-8 -*-
#
# Cinnamon Installer
#
# Authors: Lester Carballo Pérez <lestcape@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 versio... | lestcape/Cinnamon-Installer | cinnamon-installer.py | Python | gpl-3.0 | 21,674 | [
"VisIt"
] | 81f8eaf31e4a60d8d19b89263d7f1aeb9c36b925713f8695044c9a6f860dc48d |
import numpy as np
import time
from sklearn.model_selection import KFold
import os
#For command line arguments
import sys
#Plotting the benchmark results
import matplotlib.pyplot as mpl
from TFANN import ANNR
#Generate data with nf features and ns samples. If new data
#is generated, write it to file so it can be reuse... | nicholastoddsmith/pythonml | NNBench/Main.py | Python | mit | 6,108 | [
"NEURON"
] | 633014995b04e2217b98f151934334ab9722e0393aad69a7dd1d5afbda6b920e |
## \file
## \ingroup tutorial_roofit
## \notebook
##
## \brief Multidimensional models: marginizalization of multi-dimensional p.d.f.s through integration
##
## \macro_code
##
## \date February 2018
## \authors Clemens Lange, Wouter Verkerke (C++ version)
import ROOT
# Create pdf m(x,y) = gx(x|y) * g(y)
# ----------... | karies/root | tutorials/roofit/rf315_projectpdf.py | Python | lgpl-2.1 | 2,340 | [
"Gaussian"
] | 94e30e41bbc6aedce209cf388771eeb29288b946faa6b8d3591f48ad0bc3899a |
import vtk
from pylab import *
def ComputeRefraction(n0, n1, p1_pointInPlane, p2_pointInPlane, rayVector, pointOfIntersection):
print '* * *ComputeRefraction'
print 'OBS: Take care of norm = 0'
print 'OBS: Take care of reflection'
print 'rayVector: ', rayVector
rayVector = rayVector/norm(rayVector)
print 'rayVec... | annaleida/raybender | refraction.py | Python | gpl-2.0 | 2,600 | [
"VTK"
] | a6d7f7747800714303e4e7a90346950fee873bcaf37433e4afff2c00ba77ec1a |
#!/usr/bin/env python3
#pylint: disable=missing-docstring
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
... | nuclear-wizard/moose | python/chigger/tests/exodus/test_ExodusSource.py | Python | lgpl-2.1 | 3,161 | [
"MOOSE"
] | bc375311dc5c6672c42b1ea2eab4327ced3745496b2493643bcbea5162138d1a |
# -*- coding: utf-8 -*-
"""Magic functions for InteractiveShell.
$Id: Magic.py 2874 2007-11-26 06:50:42Z fperez $"""
#*****************************************************************************
# Copyright (C) 2001 Janko Hauser <jhauser@zscout.de> and
# Copyright (C) 2001-2006 Fernando Perez <fperez@col... | santisiri/popego | envs/ALPHA-POPEGO/lib/python2.5/site-packages/ipython-0.8.2-py2.5.egg/IPython/Magic.py | Python | bsd-3-clause | 126,275 | [
"VisIt"
] | ccd5c704709f81a78c2f02d81359c6a689da27f3cb63cbb508565ff9a58507e7 |
#!/usr/bin/python
#
# Copyright 2007 Google Inc.
# Licensed to PSF under a Contributor Agreement.
#
# 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/LICE... | nouiz/fredericbastien-ipaddr-py-speed-up | tags/2.1.9/ipaddr_test.py | Python | apache-2.0 | 49,385 | [
"FEFF"
] | 5e3b106e78fe89c3f110ef798850c83167dd588e3f17cb2c31ead6cffc733e41 |
"""Support for Konnected devices."""
import asyncio
import hmac
import json
import logging
import voluptuous as vol
from aiohttp.hdrs import AUTHORIZATION
from aiohttp.web import Request, Response
from homeassistant.components.binary_sensor import DEVICE_CLASSES_SCHEMA
from homeassistant.components.discovery import ... | nugget/home-assistant | homeassistant/components/konnected/__init__.py | Python | apache-2.0 | 18,767 | [
"VisIt"
] | 9127b5941004d4e40487df3c5cfd806f8a2aea74a5326e6a2cb182f0a93b1f5a |
########################################################################
# $Id$
########################################################################
""" DIRAC Notification Client class encapsulates the methods exposed
by the Notification service.
"""
import types
from DIRAC.Core.DISET.RPCClient import RPCCli... | avedaee/DIRAC | FrameworkSystem/Client/NotificationClient.py | Python | gpl-3.0 | 6,963 | [
"DIRAC"
] | 6a272ddb6e380146ad865e6b594f4c5e14d31bc409956087df723577e999459f |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: y... | rmcgibbo/mdtraj | mdtraj/reporters/basereporter.py | Python | lgpl-2.1 | 11,022 | [
"Dalton",
"MDTraj",
"OpenMM"
] | f4dd658bbaa5be75319576ae3079fcf6f5c8d0c8a2c1ed1c0589804148b34187 |
#!/usr/bin/env python
#ryan g coleman ryangc@mail.med.upenn.edu
#kim sharp, brian shoichet, upenn, ucsf own this, whatevers
#reads a pdb file, for each atom, pick the most occupied one.
#useful when the alternate positions and occupancies are meaningful.
#if tie, just pick a consistent set for each residue.
import ... | ryancoleman/tdt2014-part2 | scripts/pdbMostOccupied.py | Python | gpl-2.0 | 1,325 | [
"Brian"
] | 0a414eeb47cfc330ad382a8a5a4128a84273d5d765a24c32ec1b2b7c60ccf258 |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | nuclear-wizard/moose | python/mms/test/mms_temporal.py | Python | lgpl-2.1 | 985 | [
"MOOSE"
] | ebdc391e8fb109fb64b917d0486e69f67b84e069c3e2a55da0e5fa0d21e28369 |
"""
.. class:: GalaxySurveyGalform
.. moduleauthor:: Johan Comparat <johan.comparat__at__gmail.com>
The class GalaxySurveyGalform is dedicated to handling Galform fake galaxy mock catalog.
"""
from os.path import join
import os
import numpy as n
import astropy.io.fits as fits
from MiscellanousFunctionsLibrary import... | JohanComparat/nbody-npt-functions | python/GalaxySurveyGalform.py | Python | cc0-1.0 | 1,735 | [
"Galaxy"
] | a3e1f0fc25811e636c62e711561d5ee52ab92aced4b05c45bcdd045bfad95b48 |
#!/usr/bin/env python
from __future__ import print_function
from vtk import *
import os.path
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
xmlRootDir = VTK_DATA_ROOT + "/Data/Infovis/XML/"
if not os.path.exists(xmlRootDir):
xmlRootDir = VTK_DATA_ROOT + "/Data/Infovis/XML/"
tre... | hlzz/dotfiles | graphics/VTK-7.0.0/Examples/Infovis/Python/views.py | Python | bsd-3-clause | 2,871 | [
"VTK"
] | 75096403c573c879a73d3d5013513679ab6ced9163cb73a40d3623cbc87e87d6 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 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
#... | fevangelista/psi4 | psi4/driver/p4util/prop_util.py | Python | lgpl-3.0 | 4,828 | [
"Psi4"
] | 4a5200cd64264beb0fc32b27f3c56255e14d21a96bd25476aeb8088d2f49755f |
# pylint: disable=C0111
# pylint: disable=W0621
from lettuce import world, step
from lettuce.django import django_url
from django.conf import settings
import requests
import string
import random
import os
from django.contrib.auth.models import User
from student.models import CourseEnrollment
from nose.tools import ass... | hkawasaki/kawasaki-aio8-1 | cms/djangoapps/contentstore/features/upload.py | Python | agpl-3.0 | 6,967 | [
"VisIt"
] | a929439690288266168381f63d257ee1d8d1731992233b48853d2077aff3501a |
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