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#
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | fweik/espresso | doc/tutorials/active_matter/solutions/rectification_simulation.py | Python | gpl-3.0 | 6,624 | [
"ESPResSo",
"VTK"
] | 79bd0b1efb74ae595f7ad7db5086b99e76578d51c131875e1855a4e278513212 |
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file '/Users/robertlanglois/workspace/arachnida/src/arachnid/core/gui/pyui/AutoPickUI.ui'
#
# Created: Thu Apr 3 13:32:33 2014
# by: pyside-uic 0.2.13 running on PySide 1.1.0
#
# WARNING! All changes made in this file will be lost!
from ..u... | ezralanglois/arachnid | arachnid/core/gui/pyui/AutoPickUI.py | Python | gpl-2.0 | 23,034 | [
"Gaussian"
] | d585183f50b3bd7697a88aaba9ddf6d12927c8df69a8517655833430b502ad69 |
# Copyright 2012 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or ... | haoyuchen1992/CourseBuilder | modules/announcements/samples.py | Python | apache-2.0 | 3,214 | [
"VisIt"
] | 018c05e645d290267315ce1abbee26f8b87a00ef2980402c4c03bcf379652142 |
#!/usr/bin/env python
#
# GPytage startup.py module
#
############################################################################
# Copyright (C) 2008-20010 by Kenneth Prugh #
# ken69267@gmail.com #
# ... | Ken69267/gpytage | gpytage/startup.py | Python | gpl-2.0 | 9,869 | [
"Brian"
] | 0d1f0944e7a19a1a934528b47473e1c9e0e1a17154fdcb899cbe46b81751f2a1 |
# Copyright (c) 2019, NVIDIA Corporation. All rights reserved.
#
# This work is made available under the Nvidia Source Code License-NC.
# To view a copy of this license, visit
# https://nvlabs.github.io/stylegan2/license.html
"""Submit a function to be run either locally or in a computing cluster."""
import copy
impo... | google/lecam-gan | third_party/dnnlib/submission/submit.py | Python | apache-2.0 | 13,502 | [
"VisIt"
] | 270b4c326247ac0521b1068397addf39f9b90be7636f81367c2faa14057d849a |
#!/usr/bin/env python
import sys
import os
import PyQt4
import vtk
from vtk.test import Testing
class TestConnectionHelper(PyQt4.QtCore.QObject):
@PyQt4.QtCore.pyqtSlot()
def myslot(self):
self.triggered = 1;
class TestConnection(Testing.vtkTest):
def test_connection(self):
renWin = vtk.vtkRenderWindo... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/GUISupport/Qt/Testing/Python/TestConnection.py | Python | gpl-3.0 | 660 | [
"VTK"
] | 4a92fcd460adcb84f3aa0465351c5b8cd5a380b1608691432ac9da9a8dabcbb7 |
# encoding:utf-8
"""
:synopsis: views diplaying and processing main content post forms
This module contains views that allow adding, editing, and deleting main textual content.
"""
import datetime
import logging
import os
import os.path
import random
import sys
import tempfile
import time
import urlparse
from django.s... | afdelgado/askbot | askbot/views/writers.py | Python | gpl-3.0 | 27,118 | [
"VisIt"
] | dae7979a6355d97245e0f32d6aa9bbb5538977cdb47697d6b791e18380cfa97e |
import glob
import os
import subprocess
from io import open
import sys
from setuptools import setup, find_packages, Extension
try:
from numpy.distutils.misc_util import get_numpy_include_dirs
except ImportError:
print("numpy.distutils.misc_util cannot be imported. Attempting to "
"install...")
s... | Dioptas/pymatgen | setup.py | Python | mit | 4,605 | [
"ABINIT",
"ASE",
"Gaussian",
"NWChem",
"VASP",
"VTK",
"pymatgen"
] | 217173863fe0186377ea2f78937c9056ad120f349321165b4fcae59ab0cf2168 |
import base64
import json
from django.contrib.auth import get_user_model
from django.http import HttpRequest
from django.core.exceptions import ImproperlyConfigured
from django.conf import settings
from django.test import TestCase
from django.core.urlresolvers import reverse
from django.test.utils import override_sett... | USStateDept/geonode | geonode/geoserver/tests.py | Python | gpl-3.0 | 15,707 | [
"VisIt"
] | ef43515d2ebfa06293ee06a88237584a3b76f571388128bf971e97470704f2ec |
#!/usr/bin/env python3
import logging
import operator
import os
import unittest
from sys import version_info
import pysam
from .. import loci, parsers, utilities, configuration
from Mikado.transcripts.transcript_methods import splitting
import tempfile
from ..parsers import bed12
from ..utilities.log_utils import crea... | lucventurini/mikado | Mikado/tests/test_splitting.py | Python | lgpl-3.0 | 23,649 | [
"BLAST",
"pysam"
] | d4cc9d90b0b1d4bdc806b9f1aa247874c0e81c9327ae6d178c91902d30e7dcab |
# pylint: disable=missing-docstring
import datetime
import os
import pytz
from django.conf import settings
from lettuce import step, world
from mock import patch
from nose.tools import assert_equal, assert_in, assert_is_none, assert_true
from pytz import UTC
from selenium.common.exceptions import NoAlertPresentExcepti... | miptliot/edx-platform | lms/djangoapps/courseware/features/lti.py | Python | agpl-3.0 | 14,256 | [
"VisIt"
] | 25bf1e04dc5463c53f285f4876a265b8bb05f8b68d402e761c2c9a86dc213ea7 |
# Copyright 2021, Google LLC. 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | google-research/federated | distributed_dp/fl_run.py | Python | apache-2.0 | 11,692 | [
"Gaussian"
] | 1ec4b42aab5c3eccaeeca48a43d8929b6ddb8fdaab3dd189321b22490b9a4549 |
from test import test_support
import unittest
import codecs
import sys, StringIO, _testcapi
class Queue(object):
"""
queue: write bytes at one end, read bytes from the other end
"""
def __init__(self):
self._buffer = ""
def write(self, chars):
self._buffer += chars
def read(se... | mancoast/CPythonPyc_test | cpython/265_test_codecs.py | Python | gpl-3.0 | 53,467 | [
"FEFF"
] | bf87b790da72d75a3cab1f542a72149008b704a952cb5d59a74b713184edd570 |
###################################################################
# Semi-supervised EA-Regularized multilayer perceptron ensembles. #
###################################################################
import numpy as np
import numpy.random as npr
import theano
import theano.tensor as T
import cPickle
#from theano.t... | Philip-Bachman/ICML-2015 | PeaNet.py | Python | mit | 24,517 | [
"NEURON"
] | 9c285fae6101aeb4fe00a899ab50b565d659dd1e4b47182bf6d114269f502856 |
#
# @BEGIN LICENSE
#
# QCDB: quantum chemistry common driver and databases
#
# Copyright (c) 2011-2017 The QCDB Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of QCDB.
#
# QCDB is free software; you can redistribute it and/or modify
# it ... | loriab/qcdb | qcdb/options.py | Python | lgpl-3.0 | 10,797 | [
"CFOUR",
"ORCA",
"Q-Chem"
] | be3f17f80dd6ec65f2c4367b9db0d20631ad7de61982e26dbae693922d3eb9e2 |
import click
from parsec.cli import pass_context, json_loads
from parsec.decorators import custom_exception, json_output
@click.command('upload_file_from_local_path')
@click.argument("library_id", type=str)
@click.argument("file_local_path", type=str)
@click.option(
"--folder_id",
help="id of the folder where... | galaxy-iuc/parsec | parsec/commands/libraries/upload_file_from_local_path.py | Python | apache-2.0 | 1,220 | [
"Galaxy"
] | 4f3a67ab69efa380f1a4215f6cc8baf3d28b5af05fedc3f6a860b4e16fdc4b28 |
# Copyright (C) 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 versio... | KaiSzuttor/espresso | doc/tutorials/04-lattice_boltzmann/scripts/04-lattice_boltzmann_part3_solution.py | Python | gpl-3.0 | 4,102 | [
"ESPResSo"
] | d0b0118daf98809481dbe5a0b624b46680c689906690d88e436b64abd37b3d95 |
#!/usr/bin/python
import numpy as np
import os
import sys
import math
import matplotlib
matplotlib.use('Pdf')
import matplotlib.pyplot as plt
from mpl_toolkits.axes_grid1 import make_axes_locatable
from matplotlib.backends.backend_pdf import PdfPages
import matplotlib.font_manager as fm
## 6-1-15
## Simple code to t... | plazas/wfirst-detectors-vnl | code/test_hms_interleave_2015_june06.py | Python | mit | 8,894 | [
"Gaussian"
] | 9526b7221c78623cab906ae9b8df823a12766fd23134e6c986acf1f64bccfc94 |
""" Cache for the Plotting service plots
"""
__RCSID__ = "$Id$"
import os.path
import time
import threading
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Core.Utilities.DictCache import DictCache
from DIRAC.Core.Utilities.Graphs import graph
class PlotCache:
def __init__( self, plotsLocation = False ):
... | coberger/DIRAC | FrameworkSystem/Service/PlotCache.py | Python | gpl-3.0 | 2,353 | [
"DIRAC"
] | 2f696fe3fdbbc873a5f31d4cf35f02eff864e00a6aab81c5bf17a587614473f3 |
#!/usr/bin/python3
# -*- coding: utf-8 -*-
r'''Pychemqt, Chemical Engineering Process simulator
Copyright (C) 2009-2017, Juan José Gómez Romera <jjgomera@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 Softwa... | jjgomera/pychemqt | lib/meos.py | Python | gpl-3.0 | 218,200 | [
"Avogadro",
"Gaussian"
] | 0f4333f53c073e7c28fc890afb8fd6998bc3596d466490f68c719d541afd9bc2 |
import logging
from numpy.lib.twodim_base import diag, eye
from numpy.ma.core import asarray
import os
from os.path import expanduser
from pickle import dump
from independent_jobs.engines.BatchClusterParameters import BatchClusterParameters
from independent_jobs.engines.SerialComputationEngine import SerialComputation... | karlnapf/ozone-roulette | ozone/scripts/sample_ozone_posterior_average_slurm.py | Python | bsd-2-clause | 3,094 | [
"Gaussian"
] | db69bb662b102031cddbaca080436b3c16addfc349ba7a189445cd4a661482c8 |
""" This is a test of the chain
ResourceStatus -> ResourceStatusHandler -> ResourceStatusDB
It supposes that the DB is present, and that the service is running
"""
#pylint: disable=invalid-name,wrong-import-position,missing-docstring
import time
import datetime
import unittest
from DIRAC.Core.Base.Script imp... | hgiemza/DIRAC | tests/Integration/ResourceStatusSystem/Test_ResourceStatus.py | Python | gpl-3.0 | 19,066 | [
"DIRAC"
] | 0350694f6b2af765dfa1085655f0c03e2ce8dc91b4e6a6444cd64dcc922d0cb6 |
# coding: utf-8
# Copyright (c) Materials Virtual Lab
# Distributed under the terms of the BSD License.
from __future__ import division, print_function, unicode_literals, \
absolute_import
import unittest
import tempfile
import os
import re
import shutil
import json
import numpy as np
from monty.io import zopen
... | materialsvirtuallab/veidt | veidt/potential/tests/test_snap.py | Python | bsd-3-clause | 5,455 | [
"LAMMPS",
"pymatgen"
] | 380bfc5812ddfa5cf340a93768767f7cfdc27acb86a7334df87b2b14f99c4047 |
########################################################################
# File : StalledJobAgent.py
########################################################################
""" The StalledJobAgent hunts for stalled jobs in the Job database. Jobs in "running"
state not receiving a heart beat signal for more than stalle... | hgiemza/DIRAC | WorkloadManagementSystem/Agent/StalledJobAgent.py | Python | gpl-3.0 | 20,827 | [
"DIRAC"
] | 7d239be3fbdc390ade4570d8cbfa2c048a033992718a3c703fdd9de8ea481cd8 |
# $Id$
#
# Copyright (C) 2000-2008 greg Landrum and Rational Discovery LLC
# All Rights Reserved
#
""" code for dealing with composite models
For a model to be useable here, it should support the following API:
- _ClassifyExample(example)_, returns a classification
Other compatibility notes:
1) To use _Compo... | jandom/rdkit | rdkit/ML/Composite/Composite.py | Python | bsd-3-clause | 20,782 | [
"RDKit"
] | be18124df77139b20a0da097e3ffd39dc3889f07db0377f75040cf9a2f57e88b |
#
# Copyright (C) 2011 by Brian Weck
# Licensed under the MIT license: http://www.opensource.org/licenses/mit-license.php
#
import httplib, urllib2, logging
class HTTPHeaderLoggerConnection(httplib.HTTPConnection):
def send(self, s):
log = logging.getLogger("cssbot.reddit.http")
log.debug("request hea... | bweck/cssbot | cssbot/HTTPHeaderLogger.py | Python | mit | 681 | [
"Brian"
] | 3702330ec62bc6cf816605017b9efb9f2012f6aa6127962efe339d7d526249f9 |
from pygmin.amber import amberSystem
# create new amber system
sys = amberSystem.AMBERSystem('coords.prmtop', 'coords.inpcrd')
#start the gui
from pygmin.gui import run as gr
gr.run_gui(sys)
| js850/PyGMIN | examples/amber/run_gui.py | Python | gpl-3.0 | 209 | [
"Amber"
] | ca5ffeeecf0c8c2b1b27ddbc403d25ecbf31c31c2c2f1cf175d3957cd4af7612 |
# This program is in the public domain
'''
Crystal structure data.
Adds *crystal_structure* to the periodic table. Each crystal structure
is a dictionary which contains the key 'symmetry'. Depending on the
value of crystal_structure['symmetry'], one or more parameters
'a', 'c/a', 'b/a', 'd', and 'alpha' may be prese... | rogcg/environment | externals/periodictable/crystal_structure.py | Python | unlicense | 5,778 | [
"CRYSTAL"
] | 66ac97ef1b0e204a46e2769bb61a5c081acdcbb6508218e66a892d25609065ba |
#!/usr/bin/python
from Bio.Blast import NCBIXML
import optparse, sys
desc="""This script is used to parse blast xml output to gff3 format. Email questions/concerns to mikedeletto@gmail.com."""
parser = optparse.OptionParser(description=desc)
parser.add_option('-i', help='Input file absolute path--Exampple: /home/bla... | mdeletto/STAT-GPS | blast_xml_to_gff3.py | Python | unlicense | 7,244 | [
"BLAST"
] | bb620b75e8294fa42ab103b2428f7dc4a4dacb8791e8eb074a0b5d1118899bfd |
# encoding: utf-8
"""
Paging capabilities for IPython.core
Authors:
* Brian Granger
* Fernando Perez
Notes
-----
For now this uses ipapi, so it can't be in IPython.utils. If we can get
rid of that dependency, we could move it there.
-----
"""
#----------------------------------------------------------------------... | mattvonrocketstein/smash | smashlib/ipy3x/core/page.py | Python | mit | 12,350 | [
"Brian"
] | 5ed910057475cb657ec9ef76a869dc3a45c3630624089c1bc7c8adbc85807b85 |
import datetime
import os
from warnings import warn
import mbuild.formats.charmm_writer as mf_charmm
def dict_keys_to_list(dict):
"""
Converts the dictionary keys into a list
Parameters
----------
dict : dict
A provided dictionary
Returns
---------
list : list
list o... | iModels/mbuild | mbuild/formats/gomc_conf_writer.py | Python | mit | 332,092 | [
"CHARMM",
"NAMD"
] | e3fa704943fa41f19920f53ef863a1cb8c502ef25449baae6fdfb77f685777cf |
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | gkc1000/pyscf | pyscf/nao/m_overlap_coo.py | Python | apache-2.0 | 3,283 | [
"PySCF",
"SIESTA"
] | 15612ca1aa7ef710e8ef61975c823b7fa65ea20148c5e96e4640fca2fe0d8667 |
from __future__ import print_function
import mxnet as mx
import numpy as np
import rl_data
import sym
import argparse
import logging
import os
import gym
from datetime import datetime
import time
parser = argparse.ArgumentParser(description='Traing A3C with OpenAI Gym')
parser.add_argument('--test', action='store_true... | likelyzhao/mxnet | example/reinforcement-learning/a3c/a3c.py | Python | apache-2.0 | 8,861 | [
"Gaussian"
] | eb6722eb77b37296dc5a0cb4c3b56440ccdbf2d1246372e605c632cc9969a876 |
from __future__ import absolute_import
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
import numpy as np
from . import links as L
from . import varfuncs as V
class Family(object):
"""
A class to model one-parameter exponential
families.
... | alexis-roche/nipy | nipy/algorithms/statistics/models/family/family.py | Python | bsd-3-clause | 5,863 | [
"Gaussian"
] | 924dd54937c069012915b1b287c73d9cd344a669dab52d5a5577b371fa28c7c4 |
"""
The lower_convex_hull module handles geometric calculations associated with
equilibrium calculation.
"""
from pycalphad.core.cartesian import cartesian
from pycalphad.core.constants import MIN_SITE_FRACTION
from .hyperplane import hyperplane
import numpy as np
import itertools
def lower_convex_hull(global_grid, s... | tkphd/pycalphad | pycalphad/core/lower_convex_hull.py | Python | mit | 7,252 | [
"pycalphad"
] | 7cd9cb90f75f9745dfbe5caed9985e42a841cee8aaf7c5fcdab5d4a4755b94ed |
import json
import xml.etree.ElementTree as ET
import os
import time
from django.contrib.auth.models import User
from social.utils import is_url
from django_local_apps.models import IndexedTime, IndexType
from django_local_apps.server_configurations import get_admin_username
from djangoautoconf.local_key_manager impo... | weijia/django-local-apps | django_local_apps/management/commands/export_evernote.py | Python | bsd-3-clause | 8,931 | [
"VisIt"
] | b2537d6f39791a005bd2b4f65ce3cc80d7db734e0985baabe2e19f0bb13e4f61 |
"""
====================================================================
Linear and Quadratic Discriminant Analysis with covariance ellipsoid
====================================================================
This example plots the covariance ellipsoids of each class and
decision boundary learned by LDA and QDA. The... | Titan-C/scikit-learn | examples/classification/plot_lda_qda.py | Python | bsd-3-clause | 5,301 | [
"Gaussian"
] | 7a2fddd7a0be972768acb4ec3ce9dd4d1615331e24537fa202d2480d231a394e |
## ENVISIoN
##
## Copyright (c) 2021 Gabriel Anderberg, Didrik Axén, Adam Engman,
## Kristoffer Gubberud Maras, Joakim Stenborg
## 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.... | rartino/ENVISIoN | envisionpy/network/AtomPositions.py | Python | bsd-2-clause | 9,103 | [
"CRYSTAL"
] | ab35ef73daf40efdefd47173538aedda7045f3f9e7ae2d08f8c65b0a49be54d2 |
import sys
sys.path.append('..')
sys.path.append('../../data/')
import os, numpy as np
import time
import anglepy as ap
import anglepy.paramgraphics as paramgraphics
import anglepy.ndict as ndict
import theano
import theano.tensor as T
from collections import OrderedDict
import preprocessing as pp
def main(n_z, n_... | fivejjs/nips14-ssl | gpulearn_z_x.py | Python | mit | 16,643 | [
"Gaussian"
] | a4f79adce17befcbf7276e37a107082db2f7b79d35b797deb3d5318ca89c2a1a |
# encoding: utf-8
"""
compare.py -- Functions for comparing double-rotation session responses
Exoported namespace: mismatch_response_tally, mismatch_rotation,
cluster_mismatch_rotation, population_spatial_correlation,
correlation_matrix, correlation_diagonals, common_units
Created by Joe Monaco on 2010-02-1... | jdmonaco/vmo-feedback-model | src/compare.py | Python | mit | 8,362 | [
"Gaussian"
] | 3d19a2279f94ec0a383deee7c8dbcc9618e3f14bc64be4a51074881a7812efce |
from neurons import spiking
__author__ = 'johannes'
import pytest
import numpy as np
class TestVarious:
def test_neuron_no_spike(self):
# Neuron should not spike
timesteps = 20
# Two neurons
spiking_model = spiking.SRM(neurons=2, threshold=1.0, t_current=0.3,
... | johannesmik/neurons | tests/test_spiking.py | Python | bsd-2-clause | 8,146 | [
"NEURON"
] | 5f881939a65ebd7d2c43c65a4d8d54df5caaa639440fbe34a79ae5a48b883307 |
# Copyright 2016 James Hensman
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, so... | jameshensman/VFF | VFF/sfgpmc_kronecker.py | Python | apache-2.0 | 6,791 | [
"Gaussian"
] | 4908a8968da099da59dc535b6fdd001c1f1f3ad22481236f0058dbf2b3903bda |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | demis001/scikit-bio | skbio/sequence/_sequence.py | Python | bsd-3-clause | 74,880 | [
"scikit-bio"
] | 87d0e7a17060486b241d66c678201a87809d5bf37db7df27b722e2a694a46e2e |
"""
Copyright (C) 2014, Jaguar Land Rover
This program is licensed under the terms and conditions of the
Mozilla Public License, version 2.0. The full text of the
Mozilla Public License is at https://www.mozilla.org/MPL/2.0/
Maintainer: Rudolf Streif (rstreif@jaguarlandrover.com)
"""
from django.contrib import ad... | afan1/rvi_backend | web/tracking/admin.py | Python | mpl-2.0 | 1,109 | [
"Jaguar"
] | 3f88012b34637d74cd5d560796b1b9840f31c43ed1a5b33e3d5eb06a9c9dc937 |
# BurnMan - a lower mantle toolkit
# Copyright (C) 2012, 2013, Heister, T., Unterborn, C., Rose, I. and Cottaar, S.
# Released under GPL v2 or later.
"""
Shows user how to input a mineral of his/her choice and which physical values
need to be input for BurnMan to calculate Vs, Vp, Vphi and density at depth.
requires:... | tjhei/burnman_old | example_user_input_material.py | Python | gpl-2.0 | 4,081 | [
"Avogadro"
] | 9adc82e1f51a72b2e3c497743832fe968ec2722e06246c7ebc7a5a70465e4a25 |
"""
unidesign.spatial.converter
---------------------------
* from contour model to voxel model
* Rasterization algorithms: http://en.wikipedia.org/wiki/Digital_Differential_Analyzer_%28graphics_algorithm%29
e.g. Bresenham http://en.wikipedia.org/wiki/Bresenham%27s_line_algorithm
* from voxel model to conto... | unidesigner/unidesign | unidesign/spatial/converter/__init__.py | Python | bsd-3-clause | 1,825 | [
"VTK"
] | c7b78cf07dcdb440e99831adc4e9a7ad1b4fa985648880df208eb95331df39ce |
# -*- coding: utf-8 -*-
#
# crystal documentation build configuration file, created by
# sphinx-quickstart on Mon Sep 8 11:12:44 2014.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# A... | brentp/crystal | doc/source/conf.py | Python | mit | 8,875 | [
"CRYSTAL"
] | eeeb5e21a691c978733a69e22d31ef0a41b011d53e09f44ee2f208fa69f97498 |
"""Regression testing framework
This module will search for scripts in the same directory named
XYZtest.py. Each such script should be a test suite that tests a
module through PyUnit. (As of Python 2.1, PyUnit is included in
the standard library as 'unittest'.) This script will aggregate all
found test suites into ... | xarts19/Dugong | test/regression.py | Python | gpl-3.0 | 1,289 | [
"VisIt"
] | 19e86e569a44ed606d95ef5df48d641676ced3b7690cc0e10ffaa92dedaf1e77 |
"""
Defines the plugin to perform evaluation on the user in the proxy
"""
__RCSID__ = "$Id $"
import re
from DIRAC.Resources.Catalog.ConditionPlugins.FCConditionBasePlugin import FCConditionBasePlugin
from DIRAC.Core.Security.ProxyInfo import getProxyInfo
class ProxyPlugin( FCConditionBasePlugin ):
"""
Thi... | fstagni/DIRAC | Resources/Catalog/ConditionPlugins/ProxyPlugin.py | Python | gpl-3.0 | 3,626 | [
"DIRAC"
] | 520ddebf372eab3a5f16fcf1dd66297e99f52a86cf25dad83750d0247d2447bc |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | Kleptobismol/scikit-bio | skbio/format/sequences/fastq.py | Python | bsd-3-clause | 2,421 | [
"scikit-bio"
] | e17c9861bda4cb03636b8412443edba2ab6fddc359338c0c8c17a995e5da9022 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2002-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2008 Jerome Rapinat
# Copyright (C) 2008 Benny Malengier
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the ... | Forage/Gramps | gramps/gen/filters/rules/_hasnotebase.py | Python | gpl-2.0 | 2,859 | [
"Brian"
] | 4f516b1ea073ba388c58484931b259c73a28b59a1440fbbfc1deb69ea991c3a3 |
# Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
# 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.
__doc__="Output of PDB files."
_ATOM_FORMAT_STRING="%s%5i %-4s%c%3s %c%4i%c %8.3f%8.3f... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/PDB/PDBIO.py | Python | apache-2.0 | 5,579 | [
"Biopython"
] | 2cb7333c113f25ad9049bcda709513ffba5eb471b46e8dfecf81f6b242dec1bb |
#% DEMO 8: Algorithms 03. Krylov subspace
#
#
# In this demo the usage of the the Krylov subspace family is explained.
# This family of algorithms iterates trhough the eigenvectors of the
# residual (Ax-b) of the problem in descending order, achieving increased
# convergence rates comparing to SART family.
#
# In case... | CERN/TIGRE | Python/demos/d08_Algorithms03.py | Python | bsd-3-clause | 3,506 | [
"Gaussian"
] | 4f39d1a0d5f762ba6a6ecf155f21727006f78169db6208cc2db6bf556bce4649 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Jul 12 11:11:45 2018
@author: epnevmatikakis
"""
import logging
import matplotlib.pyplot as plt
import numpy as np
import scipy.sparse
from typing import List
import time
import caiman
from .utilities import detrend_df_f, decimation_matrix
from .spati... | simonsfoundation/CaImAn | caiman/source_extraction/cnmf/estimates.py | Python | gpl-2.0 | 76,705 | [
"NEURON"
] | bec3716bbb0105ad6ec60eb6562a19e4e708ebc2ff6ac00f00f29e93c0e668c1 |
from io import BytesIO
from flask import abort, request, send_file
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import Draw
from SearchApp import app
@app.route('/render')
def render():
args = request.args.to_dict()
if 'smiles' in args:
try:
if 'width' in args:
... | nbateshaus/chem-search | SearchApp/render.py | Python | bsd-3-clause | 893 | [
"RDKit"
] | ea22bb4d6319e17b5efdcd34f88e223767790b147447f9d5227c033e81609caf |
from __future__ import nested_scopes
"""
GSIServer - Contributed by Ivan R. Judson <judson@mcs.anl.gov>
################################################################################
#
# SOAPpy - Cayce Ullman (cayce@actzero.com)
# Brian Matthews (blm@actzero.com)
# Gregory Warnes (Gr... | marco-mariotti/selenoprofiles | libraries/SOAPpy/GSIServer.py | Python | gpl-2.0 | 5,242 | [
"Brian"
] | 26a482e9771feaf83518ef3e42e9091f272975753c4fc1beecf22c7a4206834f |
# (c) 2012-2014, Michael DeHaan <michael.dehaan@gmail.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) an... | xpac1985/ansible | lib/ansible/constants.py | Python | gpl-3.0 | 22,040 | [
"Galaxy",
"MOOSE"
] | 3d0022e7155586df62efc30b7fd36af2f34be5cb21cf73bd5cae09b39792fb46 |
# coding: utf-8
from __future__ import division, unicode_literals
"""
This module define the various drones used to assimilate data.
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "1.0"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyuep@gmail.com"
__date__... | Dioptas/pymatgen | pymatgen/apps/borg/hive.py | Python | mit | 17,167 | [
"Gaussian",
"VASP",
"pymatgen"
] | 7afa9c5cb5706c4dd6f766889c161dae16030b51593190ff972f150a6685e782 |
from gearshift.visit.api import current
from gearshift.visit.api import enable_visit_plugin
from gearshift.visit.api import shutdown_extension
from gearshift.visit.api import create_extension_model
| dbrattli/python-gearshift | gearshift/visit/__init__.py | Python | mit | 198 | [
"VisIt"
] | f9fb3949ec087087bdfc078cf262ab0f5d321c3529d014776d260a4a7524307f |
import numpy as np
from scipy import spatial, ndimage as ndi
from skimage import filters, restoration
from skimage.filters import threshold_sauvola, threshold_niblack
SMOOTH_METHODS = {
'Gaussian': filters.gaussian,
'TV': restoration.denoise_tv_bregman,
}
def hyperball(ndim, radius):
"""R... | jni/skan | src/skan/pre.py | Python | bsd-3-clause | 3,293 | [
"Gaussian"
] | b2a7b4775072a26a5b079c6a190b1dabf2506b5054290d3d91fbc02832a8cc48 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the G... | espressopp/espressopp | testsuite/unittest/testReal3D.py | Python | gpl-3.0 | 4,520 | [
"ESPResSo"
] | abdcb16734759421d2bed2a039a806a7bbf593813ef227908e5d21b83cccff64 |
"""Hyperion config flow."""
from __future__ import annotations
import asyncio
import logging
from typing import Any, Dict, Optional
from urllib.parse import urlparse
from hyperion import client, const
import voluptuous as vol
from homeassistant.components.ssdp import ATTR_SSDP_LOCATION, ATTR_UPNP_SERIAL
from homeass... | partofthething/home-assistant | homeassistant/components/hyperion/config_flow.py | Python | apache-2.0 | 18,561 | [
"VisIt"
] | 6ec7ad7acf67cdd97facbcd9b2068549e53a4bcfc58b3146fc061ff2b65c40d8 |
#!/usr/bin/env python
# Copyright 2014-2020 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | sunqm/pyscf | pyscf/df/r_incore.py | Python | apache-2.0 | 3,646 | [
"PySCF"
] | e2e4a84ddca553a5c15fdfb5909e9ac6022cf262197e8db964ece861e7f7e527 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | Kleptobismol/scikit-bio | skbio/stats/_misc.py | Python | bsd-3-clause | 2,722 | [
"scikit-bio"
] | ab109bcb07918e27adcf20c5fee91a01da07399b80110b3ba56847b02af7ee62 |
"""
A family of function objects for transforming one set of coordinates into
another.
Coordinate mapper functions are useful for defining magnifications and
other kinds of transformations on sheet coordinates, e.g. for defining
retinal magnification using a CFProjection. A CoordinateMapperFn
(e.g. MagnifyingMapper),... | ioam/topographica | topo/coordmapper/__init__.py | Python | bsd-3-clause | 15,235 | [
"Gaussian"
] | 913a5d9d94390b569b0453776a19f28bd9282b85ceb92131322b29690361733b |
r"""OS routines for Mac, DOS, NT, or Posix depending on what system we're on.
This exports:
- all functions from posix, nt, os2, mac, or ce, e.g. unlink, stat, etc.
- os.path is one of the modules posixpath, ntpath, or macpath
- os.name is 'posix', 'nt', 'os2', 'mac', 'ce' or 'riscos'
- os.curdir is a string r... | trivoldus28/pulsarch-verilog | tools/local/bas-release/bas,3.9/lib/python/lib/python2.3/os.py | Python | gpl-2.0 | 21,019 | [
"VisIt"
] | 186fb2c7e5446835a8757ea77559d20f26cf417a90ef71bd681cc9f1330872a8 |
# Copyright 2014 Roberto Brian Sarrionandia
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed t... | sarrionandia/tournatrack | room.py | Python | apache-2.0 | 2,274 | [
"Brian"
] | a28d589210f4abe575e909a45f19bf0bfa4e89f9a989e2c978a428d00b78243f |
#Apache OCW lib immports
from ocw.dataset import Dataset, Bounds
import ocw.data_source.local as local
import ocw.data_source.rcmed as rcmed
import ocw.dataset_processor as dsp
import ocw.evaluation as evaluation
import ocw.metrics as metrics
import ocw.plotter as plotter
import ocw.utils as utils
import datetime
impo... | MBoustani/climate | examples/multi_model_taylor_diagram.py | Python | apache-2.0 | 4,754 | [
"NetCDF"
] | 0719d2f1fe0d04ed79dcf9216b0a4367722ea09c8c9832ca1ea6fa764ae57058 |
from ase.io import read
from asap3 import CoordinationNumbers
from ase.visualize import view
import sys
trajfile = sys.argv[1]
atoms = read(trajfile)
atoms.set_tags(CoordinationNumbers(atoms))
print "Color Scheme in HUE:"
print "0 : (0,0,0)"
print "1 : (0,0,0)"
print "2 : (0,0,0)"
print "3 : (0,0,0)"
print "4 : Vio... | auag92/n2dm | Asap-3.8.4/Projects/NanoparticleMC/misc/colatomsbyc.py | Python | mit | 534 | [
"ASE"
] | e7238605fee76465d47636213529e7ec21d7a43ec3508be6d668483334bef66f |
#==============================================================================
# example03.py
# Example to create a `blank' simulation object, set all important parameters,
# then run the simulation to completion.
#==============================================================================
from gandalf.analysis.fac... | gandalfcode/gandalf | examples/example03.py | Python | gpl-2.0 | 1,196 | [
"BLAST"
] | ed89432ac132e98cf817cca8c38c3f147e4f26d7669358a3721558560607fc09 |
from math import acos, cos, sin, sqrt
import numpy as np
from ase.atoms import string2vector
class Vector3d(list):
def __init__(self,vector=None):
if vector is None or vector == []:
vector = [0,0,0]
vector = string2vector(vector)
list.__init__(self)
for c in range(3):
... | qsnake/gpaw | gpaw/utilities/vector.py | Python | gpl-3.0 | 3,718 | [
"ASE"
] | 818be0cc657d150ef660c66affd487ffd97e5505ae14fb97f3853a0cca800927 |
# This script requires numpy, matplotlib and biopython libraries
# Script written by Robin Paul
from __future__ import division
from collections import Counter
from os import system
import operator
import csv
from scipy import stats
import numpy as np
import linecache
import re
import argparse
import time
from Bio imp... | rop14009/Repeat-analysis-pipeline | comparegff12.py | Python | gpl-3.0 | 19,212 | [
"Biopython"
] | 6acb7bf69f4ab2a734ba2f6228dfb38a0e8c0b4e47c0bc1b9cd8fda9d6a95229 |
# -*- coding:utf-8 -*-
import datetime, re
from google_credentials import GoogleCredentials
from contacts import Contacts
from gmail import Gmail
from MessagesDB import MessagesDB
import json
import config
settings = {}
def save_settings():
with open(config.SETTINGS_FILE, 'w') as f:
json.dump(settings, f, indent... | jakublipinski/i2Gmail-Backup-macOS-Messages-To-Gmail | i2Gmail.py | Python | mit | 4,205 | [
"VisIt"
] | ea8a9909d1b4b06ac556584233739e7b62368f2ae5d4816296da405592d0787e |
# Copyright: (c) 2013, James Cammarata <jcammarata@ansible.com>
# Copyright: (c) 2018-2021, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import json
import os.path
im... | pmarques/ansible | lib/ansible/cli/galaxy.py | Python | gpl-3.0 | 80,269 | [
"Galaxy"
] | 1cb978b2e8f6cede4c570c683ec9c1b4c400a142e11eaa7dfa48a5bf57d8bcdc |
""" DB is a base class for multiple DIRAC databases that are based on MySQL.
It uniforms the way the database objects are constructed
"""
__RCSID__ = "$Id$"
from DIRAC import gLogger, gConfig
from DIRAC.Core.Utilities.MySQL import MySQL
from DIRAC.Configurati... | coberger/DIRAC | Core/Base/DB.py | Python | gpl-3.0 | 2,013 | [
"DIRAC"
] | 7e73ebbf98ba7f7787cf30d15f9112babc4a1a58b10d77f83902f71e8c0e236c |
"""
Demo microbes service and methods
"""
__author__ = 'Dan Gunter <dkgunter@lbl.gov>, Bill Riehl <wjriehl@lbl.gov>, Michael Sneddon <mwsneddon@lbl.gov>, Roman Sutormin <rsutormin@lbl.gov>'
__date__ = '11/15/13'
## Imports
# Stdlib
import json
import os
import random
import numbers
import uuid
import hashlib
import re... | aekazakov/narrative | src/biokbase/narrative/services/microbes_comparative_genomics.py | Python | mit | 20,148 | [
"BLAST"
] | e18b004c857df42d41eaaaf5fe25392b7d36ecd508250d8062e7c2298530daf1 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2017 Lenovo, Inc.
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# ... | rmfitzpatrick/ansible | lib/ansible/modules/network/lenovo/cnos_image.py | Python | gpl-3.0 | 8,700 | [
"VisIt"
] | 1e2e2113e1254046ddb339e0d41ca9c3719b8a511a95030abcd64efa1ff159a5 |
########################################################################
# $HeadURL $
# File: FTSGraph.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/05/10 20:02:32
########################################################################
""" :mod: FTSGraph
==============
.. module: FTSGraph
:syno... | vmendez/DIRAC | DataManagementSystem/private/FTS2/FTS2Graph.py | Python | gpl-3.0 | 10,386 | [
"DIRAC"
] | bfce52a6fbeb1ea6c66eaf22cfa5211a1472b2d9e0e0c03ed076c3acc45fa813 |
# -*- coding: utf-8 -*-
from setuptools import setup, find_packages
console_scripts = [
'makiki = makiki.cli:main_parser',
]
requires = [
'blinker>=1.4',
'gevent>=1.2',
'gunicorn>=19.0',
'Jinja2>=2.8.1',
'psycogreen>=1.0.0',
'hug==2.2.0',
]
with open('README.rst', 'r') as f:
readme =... | faith0811/makiki | setup.py | Python | mit | 1,373 | [
"MOE"
] | d021d7761595e017aaca58a88e53919d20b2b8bed1fc37d1b6cabd5e25e46b46 |
import numpy as np
from ase.calculators.calculator import Calculator
class LennardJones(Calculator):
implemented_properties = ['energy', 'forces']
default_parameters = {'epsilon': 1.0,
'sigma': 1.0}
nolabel = True
def __init__(self, **kwargs):
Calculator.__init__(sel... | alexei-matveev/ase-local | ase/calculators/lj.py | Python | gpl-2.0 | 1,066 | [
"ASE"
] | 60f908d99c3127afe28fbd1f7210e77365dbfdb5b320a84e2ac68bb6ee2fdb04 |
from __future__ import print_function, division
from os.path import join
from itertools import chain
import tempfile
import shutil
import sys
import io
from io import BytesIO
try:
from subprocess import STDOUT, CalledProcessError
from sympy.core.compatibility import check_output
except ImportError:
pass
... | maniteja123/sympy | sympy/printing/preview.py | Python | bsd-3-clause | 12,243 | [
"VisIt"
] | 6bb76fb33edc10fed0e6765dcedc1159fbfcbfd4a1a7f9043ef5727f753e3599 |
#!/usr/bin/env python
from setuptools import setup
readme = open('README.rst').read()
setup(name='RPLCD',
version='0.4.0',
description='A Raspberry Pi LCD library for the widely used Hitachi HD44780 controller.',
long_description=readme,
author='Danilo Bargen',
author_email='mail@dbrgn.... | thijstriemstra/RPLCD | setup.py | Python | mit | 1,322 | [
"CRYSTAL"
] | 428a2ad736a7302c8d0a44c7a53606235526bf9565e955c8193a37a19d3fb69a |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import pytest
@pytest.mark.skip(reason="This is a long test")
def test_duccsdtq():
"""Test projective factorized UCCSDTQ on Ne using RHF/cc-pVDZ orbitals"""
import forte.proc.scc as scc
import forte
import psi4
ref_energy = -128.679023738907
ge... | evangelistalab/forte | tests/pytest/sparse_ci/srcc/test_duccsdtq.py | Python | lgpl-3.0 | 1,044 | [
"Psi4"
] | 157e5dbd173e6345a19dbafe57d5f0538fcdb9e476ea70812ab5d516eb3e7cae |
"""Django settings for Pontoon."""
import os
import socket
from django.utils.functional import lazy
import dj_database_url
_dirname = os.path.dirname
ROOT = _dirname(_dirname(_dirname(os.path.abspath(__file__))))
def path(*args):
return os.path.join(ROOT, *args)
# Environment-dependent settings. These are ... | mastizada/pontoon | pontoon/settings/base.py | Python | bsd-3-clause | 23,753 | [
"VisIt"
] | 0f21be5e47acdcdbb27c9f1a187f54815ce2fd7b76aff5e9b7636ef39533df4f |
# -*- coding: utf-8 -*-
'''
lucterios.contacts package
@author: Laurent GAY
@organization: sd-libre.fr
@contact: info@sd-libre.fr
@copyright: 2015 sd-libre.fr
@license: This file is part of Lucterios.
Lucterios is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public Licens... | Lucterios2/contacts | lucterios/mailing/tests_messaging.py | Python | gpl-3.0 | 72,888 | [
"Dalton"
] | 5a89b944759374d14bae67b1b806b6135da8526a6feb69f3ce2a0ebbfb536c98 |
"""
Acceptance tests for the certificate web view feature.
"""
from nose.plugins.attrib import attr
from common.test.acceptance.fixtures.certificates import CertificateConfigFixture
from common.test.acceptance.fixtures.course import CourseFixture, CourseUpdateDesc, XBlockFixtureDesc
from common.test.acceptance.pages.c... | BehavioralInsightsTeam/edx-platform | common/test/acceptance/tests/lms/test_certificate_web_view.py | Python | agpl-3.0 | 4,130 | [
"VisIt"
] | 83bb19531bbfff25ab14fece584eb6d2a422b44cda30ba04ee036e45c819447d |
"""
Extended math utilities.
"""
# Authors: Gael Varoquaux
# Alexandre Gramfort
# Alexandre T. Passos
# Olivier Grisel
# Lars Buitinck
# Stefan van der Walt
# Kyle Kastner
# Giorgio Patrini
# License: BSD 3 clause
from __future__ import division
from funct... | valexandersaulys/airbnb_kaggle_contest | venv/lib/python3.4/site-packages/sklearn/utils/extmath.py | Python | gpl-2.0 | 23,143 | [
"Gaussian"
] | 522d6605e714849c8d03b4f3e743d58ee9047dde249b7d6f07f54d1605574427 |
# Copyright (C) 2013 The ESPResSo project
# Copyright (C) 2012 Olaf Lenz
#
# 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
# (a... | Gexar/espresso | config/gen_featureconfig.py | Python | gpl-3.0 | 3,691 | [
"ESPResSo"
] | e79f24ef84ace97d1441518ef302473b88245d48f0b96ded4203a301cdbe1ea1 |
#!/usr/bin/python
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
#
ANSIB... | thaim/ansible | lib/ansible/modules/network/avi/avi_alertscriptconfig.py | Python | mit | 3,687 | [
"VisIt"
] | 8890512826c7165d80c4902c5e65a1f1d5e16d5e749dbf1d73458c7e4ae65aeb |
from __future__ import print_function, division
import unittest, numpy as np
from pyscf import gto, scf
from pyscf.nao import nao, scf as scf_c
from pyscf.nao import prod_basis
class KnowValues(unittest.TestCase):
def test_gw(self):
""" This is GW """
mol = gto.M( verbose = 0, atom = '''H 0.0 0.0 -0.3707; ... | gkc1000/pyscf | pyscf/nao/test/test_0095_h2_ae_rescf.py | Python | apache-2.0 | 890 | [
"PySCF"
] | 12ca01ec259837a4f28cc7f4c39518577995592449f03635132c8b4528cfc436 |
# Copyright (c) 2012 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.
"""Provides an interface to communicate with the device via the adb command.
Assumes adb binary is currently on system path.
"""
import collections
imp... | plxaye/chromium | src/build/android/pylib/android_commands.py | Python | apache-2.0 | 47,746 | [
"Galaxy"
] | a1da9a402d2ad84db188c96ad211b24b79ea905f1d4fd7206f9e929631bbd12c |
import random
import numpy as np
from src.hw1.Neurons import Sigmoid
from src.hw1.exceptions import LayerError
def set_rand_weights():
return random.random()
def set_rand_bias():
return random.random()
class NeuronLayer:
def __init__(self, number=None, learning_rate=0.5):
self.number = numb... | juanpablos/CC5114-Projects | Tarea 3/src/hw1/NeuronLayer.py | Python | mit | 3,329 | [
"NEURON"
] | e798b5667591226e18faee55eb14da712d6171fb945e2dabdfb93a357c5c55bc |
"""
In this test we want to check if Tornado generate the same credentials dictionnary as DIRAC.
It also test if the correct certificates are sended by client.
To run this test you must have the handlers who returns credentials dictionnary.
Handlers are diracCredDictHandler and tornadoCredDictHandler j... | ic-hep/DIRAC | tests/DISET_HTTPS_migration/TestClientReturnedValuesAndCredentialsExtraction.py | Python | gpl-3.0 | 3,802 | [
"DIRAC"
] | 6d2b00f528708625fc920e07e8f856eea21f6537fed6a224104615873ae30276 |
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | gkc1000/pyscf | pyscf/nao/test/test_0006_02_nao_noghost.py | Python | apache-2.0 | 1,152 | [
"PySCF",
"SIESTA"
] | 339cd69e1e98da8ee170df8161ad18c0dae868cf41d977155b19263b4b97d92c |
#!/usr/bin/env python
#
#
# FreeType 2 glyph name builder
#
# Copyright 1996-2018 by
# David Turner, Robert Wilhelm, and Werner Lemberg.
#
# This file is part of the FreeType project, and may only be used, modified,
# and distributed under the terms of the FreeType project license,
# LICENSE.TXT. By continuing to u... | joncampbell123/dosbox-rewrite | vs2015/freetype/src/tools/glnames.py | Python | gpl-2.0 | 106,721 | [
"FEFF"
] | 76f1775f7e32ca33311b73b978bf30eca67ba042783b23e3ea61ccd18c538ce9 |
import numpy as np
from ase.units import Ha
from ase.dft import monkhorst_pack
from ase.parallel import paropen
from ase.structure import bulk
from gpaw import GPAW, FermiDirac
from gpaw.wavefunctions.pw import PW
from gpaw.mpi import size
kpts = monkhorst_pack((10,10,10))
kpts += np.array([1/20., 1/20., 1/20.])
bulk... | ajylee/gpaw-rtxs | gpaw/test/big/rpa/Na_bulk_gs.py | Python | gpl-3.0 | 911 | [
"ASE",
"GPAW"
] | cb374726faf01c48f2a39256fcc15b861cc750285913422d775fbf958d3042be |
#
# Copyright 2016 Punit Patel (Warwick U.)
# 2014 James Kermode (Warwick U.)
#
# matscipy - Materials science with Python at the atomic-scale
# https://github.com/libAtoms/matscipy
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License ... | libAtoms/matscipy | scripts/fracture_mechanics/run_crack_thin_strip.py | Python | lgpl-2.1 | 5,425 | [
"ASE",
"Matscipy"
] | df3e4e6b03a24f19d57eef5b9298595fd9014914fbaebe0c2a0f70d80ac91a68 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
"""
Versioneer 2
============
* Like a rocketeer, but for versions!
* Based on https://github.com/warner/python-versioneer
* Brian Warner
* License: Public Domain
* Compatible With: python2.6, 2.7, 3.2, 3.3, 3.4, and pypy
* Edited by Ryan Dwyer
This is a... | ryanpdwyer/brownian | versioneer.py | Python | mit | 38,217 | [
"Brian"
] | 707bc12ca642f186ff5c1b488f21e93e95b512b21574c075da2950d90cf2121a |
max_packet_size = 1048576 # Set in my.conf
byte_encoding = 5 # UTF-8 Uses up to four bytes
string_chunk = int(max_packet_size/byte_encoding)
cities = {"newyork" : ('New York', 'NY'),
"losangeles" : ('Los Angeles', 'CA'),
"chicago" : ('Chicago', 'IL'),
"houston" : ('Houston', 'TX'),
... | fgregg/craigslistings | craigslistings/config.py | Python | mit | 2,557 | [
"COLUMBUS"
] | 1e0f47b15470d454e42acc7839cbed62f7e1415fa33abc44039933277a7a1804 |
#-------------------------------------------------------------------------------
# . File : QMCallerTeraChem.py
# . Program : MolarisTools
# . Copyright : USC, Mikolaj Feliks (2015-2018)
# . License : GNU GPL v3.0 (http://www.gnu.org/licenses/gpl-3.0.en.html)
#--------------------------------------------... | mfx9/molaris-tools | MolarisTools/QMMM/QMCallerTeraChem.py | Python | gpl-3.0 | 6,086 | [
"TeraChem"
] | 9ab8eea6fac2801e6b176d8f34a43b1b0806c0c0a0f591c99107961caf08fb2c |
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