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# -*- coding:utf-8 -*-
# Copyright (c) 2015, Galaxy Authors. All Rights Reserved
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
#
# Author: wangtaize@baidu.com
# Date: 2015-04-06
import datetime
import logging
from sofa.pbrpc import client
from lumia import lumia_p... | bluebore/galaxy | platform/src/lumia/sdk.py | Python | bsd-3-clause | 2,497 | [
"Galaxy"
] | 255c3d6b14029e17826fa73e42e665813b35dff2d4b30915ff9d83f871396112 |
from .models import Session
import utils
class Tracking(object):
"""The default tracking middleware logs all successful responses as a 'visit' variable with
the URL path as its value."""
def process_response(self, request, response):
# filter out heartbeat messages
if request.path.starts... | RENCI/xDCIShare | hs_tracking/middleware.py | Python | bsd-3-clause | 1,459 | [
"VisIt"
] | 0a2ecb0915692e89586f7beeea528fc08a0bdbd190d61cf834f45b259ea44328 |
from .openmm import *
from .pyscf import *
from .models import *
from .toys import *
from .amber import *
from .openbabel import *
from .nwchem import *
from .qmmm import * | Autodesk/molecular-design-toolkit | moldesign/models/__init__.py | Python | apache-2.0 | 172 | [
"Amber",
"NWChem",
"OpenMM",
"PySCF"
] | 9740524634733ffcd1edc7ff96dfdd6374b4b2d811bdd670f6c6dd3954fa9a48 |
import scipy.optimize
import mixtape.featurizer, mixtape.tica, mixtape.cluster, mixtape.markovstatemodel, mixtape.ghmm, mixtape.ntica
import numpy as np
import mdtraj as md
from parameters import load_trajectories, build_full_featurizer
import sklearn.pipeline, sklearn.externals.joblib
import mixtape.utils
stride = 1
... | kyleabeauchamp/PMTStuff | code/tmp_test_msm2.py | Python | gpl-2.0 | 2,558 | [
"MDTraj"
] | fc40096f3023afb7cfeffad30316d01bd5bd97ca5b6b2fb17577f6fe18b91a6f |
# Copyright 2015 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.
"""Dummy benchmarks for the bisect FYI integration tests and other tests.
The number they produce aren't meant to represent any actual performance
data of th... | nwjs/chromium.src | tools/perf/benchmarks/dummy_benchmark.py | Python | bsd-3-clause | 1,736 | [
"Gaussian"
] | 7d4fefd3f4840e024e35fe50a8e95c2e20d9fc64a18c30e377cc4a75cfb95fc4 |
#!/usr/bin/env python
"""
This module calculates the thermal conductivity using the Leibfried-Schloemann equation.
"""
from __future__ import division
import warnings
import sys
import subprocess
import unittest
import pymatgen
import numpy as np
import os
from numpy import matrix
from numpy import linalg
import math... | ctoher/pymatgen | pymatgen/agl_thermal/agl_thermal_conductivity.py | Python | mit | 1,189 | [
"pymatgen"
] | 4cc042b62552e5a3031588ddccae388ef7757f6f01321f9e0ad3925216a29e0f |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
# vim:fenc=utf-8
import numpy as np
import skelet3d
import skelet3d.skeleton_analyser
import skelet3d.tree
from skelet3d.tree import TreeBuilder
# output vtk file can be visualized with ParaView
fn_out = 'tree.vkt'
volume_data = np.zeros([3, 7, 9], dtype=np.int)
volume_... | mjirik/skelet3d | examples/example03.py | Python | bsd-3-clause | 782 | [
"ParaView",
"VTK"
] | 87ffbd1ee8c67b3a715690b37d4284e6e623fc23a47c5c1b0ec117c232a2d761 |
'''Attach generally useful information, not specific to any package.'''
# Copyright (C) 2009 Canonical Ltd.
# Authors: Matt Zimmerman <mdz@canonical.com>
# Martin Pitt <martin.pitt@ubuntu.com>
# Brian Murray <brian@ubuntu.com>
#
# This program is free software; you can redistribute it and/or modify i... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/apport/general-hooks/generic.py | Python | gpl-3.0 | 3,628 | [
"Brian"
] | 7d0339c0a3f8a809d6788af7c515062b9311b8c9efd9fd9f3eaad32d90508ef3 |
#
# QAPI types generator
#
# Copyright IBM, Corp. 2011
#
# Authors:
# Anthony Liguori <aliguori@us.ibm.com>
#
# This work is licensed under the terms of the GNU GPL, version 2.
# See the COPYING file in the top-level directory.
from ordereddict import OrderedDict
from qapi import *
import sys
import os
import getopt
... | tkhsu/quick-qemu | scripts/qapi-types.py | Python | gpl-2.0 | 11,398 | [
"VisIt"
] | fa7708d60c6fdfc573d3dbf794335aab2390e6ab3e42498f5317f594b19a2802 |
'''
ModelGenie (c) University of Manchester 2015
ModelGenie is licensed under the MIT License.
To view a copy of this license, visit <http://opensource.org/licenses/MIT/>.
@author: neilswainston
'''
from StringIO import StringIO
import json
import libsbml
from synbiochemdev.modelgenie import sbml_utils
class Ki... | neilswainston/development-py | synbiochemdev/modelgenie/sbml_kinetics_utils.py | Python | mit | 14,146 | [
"VisIt"
] | 8d3f65dcbb657347da56d816fdc2acb2a8193c15a0c6f9d4d65142e145d684d0 |
import sys, os
from paraview.simple import *
from paraview import data_exploration as wx
# -----------------------------------------------------------------------------
# Input data to process
# -----------------------------------------------------------------------------
# Set up paths to input and output
pathRoo... | Kitware/cinema | scripts/data_generation/generateFlatNImageData.py | Python | bsd-3-clause | 1,871 | [
"ParaView",
"VTK"
] | 3a6ebb6c0a7696544dcb96da8f045f14e65856cfe126c05b4badbe00f78f74f0 |
import ocl
import camvtk
import time
import vtk
import datetime
import math
def drawPoints(myscreen, clpoints, ccpoints):
c=camvtk.PointCloud( pointlist=clpoints, collist=ccpoints)
c.SetPoints()
myscreen.addActor(c )
def drawFiber(myscreen, f, fibercolor):
inter = f.getInts()
print "fiber has ", ... | davidwusea/opencamlib | scripts/fiber_13_onetri_cutter_comparison.py | Python | gpl-3.0 | 5,610 | [
"VTK"
] | 1720a145b57b4790f1878781fbc2c4ddbf9791f29c925117c8e45877f4d62da8 |
# -*- coding: UTF-8 -*-
import numpy as np
import pyfftw
class fgn( object ) :
"""A class to generate fractional Gaussian process of fixed length using
a circulant matrix method suggested by Dietrich and Newsam (1997). For the
best performance N-1 should be a power of two."""
## For better performance N-1 should be... | ivannz/study_notes | year_14_15/course_project/release/processes/fgn_pyfftw.py | Python | mit | 5,328 | [
"Gaussian"
] | 18bc28941189079ddcca5a38299fdaad0d7ca0a802a389bd9e40f8664cd7ba8a |
#!/usr/bin/env python3
"""
Copyright 2020 Paul Willworth <ioscode@gmail.com>
This file is part of Galaxy Harvester.
Galaxy Harvester 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 ... | pwillworth/galaxyharvester | html/postSurveyDroidReport.py | Python | gpl-3.0 | 10,881 | [
"Galaxy"
] | 33fe9c276731100a6563f6c2d19b584f04415789f96f077ea7d90e2cb3072c31 |
###############################
# This file is part of PyLaDa.
#
# Copyright (C) 2013 National Renewable Energy Lab
#
# PyLaDa is a high throughput computational platform for Physics. It aims to make it easier to
# submit large numbers of jobs on supercomputers. It provides a python interface to physical input,
# ... | pylada/pylada-light | tests/decorations/test_lexcompare.py | Python | gpl-3.0 | 1,657 | [
"CRYSTAL",
"VASP"
] | a0f1078ed9d4047f5d6d74191b58cf2128bbb6ddabddabdfd6819a18c9ad2e34 |
#!/usr/bin/env python2.7
#
# ----------------------------------------------------------------------------------------------------
#
# Copyright (c) 2007, 2015, Oracle and/or its affiliates. All rights reserved.
# DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
#
# This code is free software; you can redis... | olpaw/mx | mx.py | Python | gpl-2.0 | 541,014 | [
"VisIt"
] | 991bbfc61d636a4c608272e7156a992c03fe3c6e43d6c81976ad819157a7ba0f |
# -*- coding: utf-8 -*-
## src/disco.py
##
## Copyright (C) 2005-2006 Stéphan Kochen <stephan AT kochen.nl>
## Copyright (C) 2005-2007 Nikos Kouremenos <kourem AT gmail.com>
## Copyright (C) 2005-2014 Yann Leboulanger <asterix AT lagaule.org>
## Copyright (C) 2006 Dimitur Kirov <dkirov AT gmail.com>
## Copyright (C) 20... | lovetox/gajim | src/disco.py | Python | gpl-3.0 | 84,835 | [
"VisIt"
] | 8dbe81248047a8e2206a2b3bc77a64e839797c9a82c6377471caee0312c042fd |
from setuptools import setup
import versioneer
commands = versioneer.get_cmdclass()
trove_classifiers = [
"Development Status :: 4 - Beta",
"Environment :: Console",
"License :: OSI Approved :: MIT License",
"Programming Language :: Python :: 2",
"Programming Language :: Python :: 2.7",
"Prog... | warner/magic-wormhole | setup.py | Python | mit | 2,373 | [
"Brian"
] | 599ebe048045ecdd9a851b0b1d68a96474c67cbec6851e0701e3f88a97b85263 |
import os
import orca
import pandas as pd
from activitysim import activitysim as asim
"""
Given the tour generation from the above, each tour needs to have a
destination, so in this case tours are the choosers (with the associated
person that's making the tour)
"""
@orca.table()
def destination_choice_spec(configs... | bhargavasana/activitysim | activitysim/defaults/models/destination.py | Python | agpl-3.0 | 2,413 | [
"ORCA"
] | b8f66b5aa3d1e0e057843f1c50c1bd26c3ed24f246de8e199375d026ab3e63cf |
import collections
import datetime
import itertools
import logging
import os
import pdb
import sys
import subprocess
import numpy as np
import pandas
import palettable
import time
import deco
from collections import OrderedDict
from enum import Enum
from tqdm import tqdm
import matplotlib.pyplot as plt
import constan... | ritviksahajpal/LUH2 | LUH2/GLM/process_GLM.py | Python | mit | 180,857 | [
"NetCDF"
] | 2404b1c1d6765c477cee7a0cb4f9c429dd43554c378fbadf7576db2167ec4c58 |
"""Preferences for Mayavi
"""
# Author: Prabhu Ramachandran <prabhu [at] aero . iitb . ac . in>
# Copyright (c) 2008, Enthought, Inc.
# License: BSD Style.
# Enthought library imports.
from traits.api import (Bool, Enum, Tuple, Range, List,
Str, Instance, HasTraits)
from traitsui.api import View, Group, Item,... | dmsurti/mayavi | mayavi/preferences/mayavi_preferences_page.py | Python | bsd-3-clause | 6,493 | [
"Mayavi"
] | 9631019851ec1e9a5de1cd54cfeebefae142d692b6e9a72e10e317263a8036f9 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
Copyright (C) 2011-2015 German Aerospace Center DLR
(Deutsches Zentrum fuer Luft- und Raumfahrt e.V.),
Institute of System Dynamics and Control
All rights reserved.
This file is part of PySimulator.
PySimulator is free software: you can redistribute it and/or modify... | PySimulator/PySimulator | PySimulator/Plugins/Simulator/SimulatorBase.py | Python | lgpl-3.0 | 15,005 | [
"MOE"
] | a26ef8381fdcf43cae232dd19d62d790f9d59baef7edfa9a8d2e2292f9bd4af4 |
#!/usr/bin/env python
from __future__ import print_function
import sys
import string
# Import third-party modules
# import pybedtools
import pysam
import re
class FormatError(Exception):
"""
Raised when an input file (FASTA or FASTQ) is malformatted.
"""
def internal_polyA_checker(seq, chrom, polya_st, polya_ed,... | Imamachi-n/PASScan | scripts/modules/get_pass_reads.py | Python | mit | 5,654 | [
"pysam"
] | 7fcf507b6724db1ac91d00faa0961c73574b4fb28867663a24e63909cfab8db3 |
#!/usr/bin/env python
# Copyright (C) 2007 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 l... | amadu80/gtfsni | gtfsni/gtfs_feed_validator.py | Python | bsd-2-clause | 29,796 | [
"VisIt"
] | 378d100b310c61574b1b2f4c6ff51e90be2c67f773c1a45f31be6de740b5ca9b |
# -*- coding: utf-8 -*-
#
# hl_api_simulation.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the Licen... | lekshmideepu/nest-simulator | pynest/nest/lib/hl_api_simulation.py | Python | gpl-2.0 | 15,584 | [
"NEURON"
] | 36cc89216bfb9713f5201d8e42d1f3c333929789f55770e54b142b4137771175 |
# -*- coding: utf-8 -*-
"""
Поддержка OpenCL устройств
"""
cl = None
try:
import pyopencl as cl
except ImportError:
pass
from openre.device.abstract import Device
from openre.data_types import types, null
from openre import synapses
from openre.templates import create_env
from openre.vector import StandaloneVec... | openre/openre | openre/device/opencl/__init__.py | Python | mit | 35,535 | [
"NEURON"
] | 3fad3ec4abd0a4751b3a68443a2b01a7e62b4a7ae38a1f63f1fcb9608566a875 |
"""
A working example script:
* generates a spectral FITS cube
* makes a guess grid based on given parameter ranges
* makes best guess calculatons and goodness-of-fit estimates
"""
import numpy as np
import matplotlib.pylab as plt
from multicube.subcube import SubCube
from multicube.astro_toolbox import make_test_cube
... | vlas-sokolov/multicube | examples/example-gauss-2d.py | Python | mit | 2,853 | [
"Gaussian",
"TINKER"
] | f9ac2a83cc437b6eeb5e58080a59b89dfba0c83c4426b4042d5bae6870e65de7 |
# 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, software
# distribu... | quantumlib/OpenFermion-PySCF | openfermionpyscf/tests/_pyscf_molecular_data_test.py | Python | apache-2.0 | 3,373 | [
"PySCF"
] | 53f144008c024205e2b0957eb89b10fbc1dbe74afb53e534408f46aab7c8b843 |
""" Defines the UI for a gradient editor for vtkLookupTables and color
transfer functions.
This code is distributed under the conditions of the BSD license.
This code was originally written by Gerald Knizia <cgk.d@gmx.net> and
later modified by Prabhu Ramachandran
Copyright (c) 2005-2006, Gerald Knizia and Prabhu Ra... | liulion/mayavi | tvtk/util/tk_gradient_editor.py | Python | bsd-3-clause | 27,313 | [
"VTK"
] | 4cfce75efaee4273f3dd0a682cd6207d0e4b36ed820fc9f82a391c348668f673 |
# (c) 2014 Michael DeHaan, <michael@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later ve... | e-gob/plataforma-kioscos-autoatencion | scripts/ansible-play/.venv/lib/python2.7/site-packages/ansible/playbook/role/metadata.py | Python | bsd-3-clause | 4,305 | [
"Galaxy"
] | c683c53c732b55358513643e116a5de8644d1200d8ec9751dcdde26df0a7ef0a |
# 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 | src/analysis/AllParticlePos.py | Python | gpl-3.0 | 1,428 | [
"ESPResSo"
] | 4654b04d6bec275d5592e115a718715ab65839953169de1fca37eab938a7941b |
# -*- coding=utf-8 -*-
from __future__ import absolute_import, print_function, unicode_literals
import unittest
import warnings
import chemfiles
from chemfiles import Trajectory, ChemfilesError
class RemoveChemfilesWarnings(object):
def __enter__(self):
chemfiles.set_warnings_callback(lambda u: None)
... | Luthaf/Chemharp-python | tests/misc.py | Python | mpl-2.0 | 2,814 | [
"Chemfiles"
] | d40686a75059062ea31e991a540ba259aa0d779543ac33f387b77499e9e78cf0 |
import numpy as np
from gpaw.xc.libxc import LibXC, short_names
from gpaw.xc.kernel import XCKernel, codes
from gpaw.xc.bee import BEE1
from gpaw.test import equal
functionals = [LibXC(name) for name in short_names]
functionals += [XCKernel(name) for name in codes]
functionals += [BEE1()]
#name = 'LDA'
#name = 'PBE'
#... | ajylee/gpaw-rtxs | gpaw/test/xc.py | Python | gpl-3.0 | 3,179 | [
"GPAW"
] | 71f25716eabed6bb005e03c611dab3a9bd091aa8afe5eb17242d522f84872973 |
#!/usr/bin/env python
"""
filt.py
Functions for quickly filtering time-series of data.
Written by Brian Powell on 02/09/16
Copyright (c)2017 University of Hawaii under the BSD-License.
"""
import numpy as np
import seapy
import scipy.signal
def average_err(x, window=5):
"""
Generate a moving (boxca... | dalepartridge/seapy | filt.py | Python | mit | 4,941 | [
"Brian"
] | 81eaa56c07ee18ea988bd9bb75c7e5fe605f631a3329fa0830d1ebb19a17f720 |
"""
QAPI command marshaller generator
Copyright IBM, Corp. 2011
Copyright (C) 2014-2018 Red Hat, Inc.
Authors:
Anthony Liguori <aliguori@us.ibm.com>
Michael Roth <mdroth@linux.vnet.ibm.com>
Markus Armbruster <armbru@redhat.com>
This work is licensed under the terms of the GNU GPL, version 2.
See the COPYING file ... | marioli/qemu | scripts/qapi/commands.py | Python | gpl-2.0 | 7,906 | [
"VisIt"
] | 808b32cdeb7d59d768f3a1f06248e5bff9fc6d2936cb8151449d741689d67d54 |
# -*- coding: utf-8 -*-
# Copyright (c) 2015-2018, Exa Analytics Development Team
# Distributed under the terms of the Apache License 2.0
"""
Base Molcas Editor
##################
"""
from exatomic import Editor as AtomicEditor
class Editor(AtomicEditor):
_to_universe = AtomicEditor.to_universe
def to_univer... | alexvmarch/atomic | exatomic/molcas/editor.py | Python | apache-2.0 | 872 | [
"Gaussian",
"MOLCAS"
] | d04b71ab8687426ff8966f3104b3f99de2eaa6cedf58c7351d6a8b1af4e0c603 |
#!/usr/bin/env python
# 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
#
# U... | sunqm/pyscf | pyscf/lo/iao.py | Python | apache-2.0 | 6,421 | [
"PySCF"
] | 11ee1e89aa28dc27053e17bb1b59d3b3d53d832677ea35c9c09f50c83977265c |
#
# This source file is part of appleseed.
# Visit https://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2016-2018 Francois Beaune, The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any person obtaining ... | est77/appleseed | src/appleseed.python/test/testbasis.py | Python | mit | 2,231 | [
"VisIt"
] | 14cf4ef993dc246c5ef704d353544bc43b2e7984371f1c3d3d37a522d7d41681 |
import re
import os
APP_PATH = os.path.join(*os.path.split(os.path.dirname(os.path.realpath(__file__)))[:-1])
import sys
if APP_PATH not in sys.path:
sys.path.append(APP_PATH)
import MyTrack
import PowerShell
import Phonebook
import Overlord
import Log
LOGGER = Log.MyLog(name=__name__)
# # # #
"""
Special setup ... | jabez007/Training_Helpyr | Setup/__init__.py | Python | mit | 7,646 | [
"Galaxy"
] | 5ae0062cb23c8c1f296a70c3f0da5266c754d71e46cea586504924e7815befc6 |
""" DIRAC FileCatalog mix-in class to manage users and groups within the FC database
"""
import six
import time
import threading
from DIRAC import S_OK, S_ERROR, gConfig, gLogger
from DIRAC.DataManagementSystem.DB.FileCatalogComponents.UserGroupManager.UserAndGroupManagerBase import (
UserAndGroupManagerBase,
)
... | DIRACGrid/DIRAC | src/DIRAC/DataManagementSystem/DB/FileCatalogComponents/UserGroupManager/UserAndGroupManagerDB.py | Python | gpl-3.0 | 9,909 | [
"DIRAC"
] | fff1c5ebb595db816843f58a1a79498ab6181515230f78a9ba44d779635fe9fe |
# -*- coding: utf-8 -*-
"""
Copyright 2010 Olivier Belanger
This file is part of pyo, a python module to help digital signal
processing script creation.
pyo 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... | xyproto/gosignal | pyo/pyolib/_core.py | Python | gpl-3.0 | 74,251 | [
"Gaussian"
] | 1a25f111d189f1d1abf1ea1fa800302ae6dab3f6a9bfd4aa723f01cf6a52a79e |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2007, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License versi... | anksp21/Community-Zenpacks | ZenPacks.AndreaConsadori.MRV/ZenPacks/AndreaConsadori/MRV/modeler/plugins/MrvDeviceMap.py | Python | gpl-2.0 | 1,332 | [
"VisIt"
] | 22892e0d96f9971fb38eb53bb275ae116b7d3c2ba0444786d5dcabb931ab54a8 |
#
# Copyright 2017 University of Southern California
# Distributed under the GNU GPL 3.0 license. See LICENSE for more info.
#
""" Installation script for deriva.qt
"""
from setuptools import setup, find_packages
import re
import io
__version__ = re.search(
r'__version__\s*=\s*[\'"]([^\'"]*)[\'"]',
io.open('... | informatics-isi-edu/deriva-qt | setup.py | Python | gpl-3.0 | 2,179 | [
"VisIt"
] | 413f3b10736440a814f1ed82461b97b74e382d341ba22610fc4b9cf5021dbd36 |
# coding: utf-8
# Copyright (c) Materials Virtual Lab
# Distributed under the terms of the BSD License.
from setuptools import setup, find_packages
setup(
name="veidt",
packages=find_packages(),
version="0.0.2",
install_requires=["numpy", "scipy", "monty", "keras", "tensorflow",
... | czhengsci/veidt | setup.py | Python | bsd-3-clause | 1,701 | [
"pymatgen"
] | 1c1bcaa67c9dde70a75ec3eb02ad7b8ae0dbd7dde563ce1949a4cb7174d29c86 |
# test_utils.py ---
#
# Filename: test_utils.py
# Description:
# Author:
# Maintainer:
# Created: Sat May 26 10:41:37 2012 (+0530)
# Version:
# Last-Updated: Sat Aug 6 15:45:51 2016 (-0400)
# By: subha
# Update #: 414
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
#
#
# Chang... | BhallaLab/moose-examples | traub_2005/py/testutils.py | Python | gpl-2.0 | 12,024 | [
"MOOSE",
"NEURON"
] | 5b73fcd7c4cb3d88172e49d6d6fd76698f9275cdb5fe579bff5c771295c434bc |
# -*- coding: utf-8 -*-
"""
Bok choy acceptance tests for problems in the LMS
See also old lettuce tests in lms/djangoapps/courseware/features/problems.feature
"""
from textwrap import dedent
from ..helpers import UniqueCourseTest
from ...pages.studio.auto_auth import AutoAuthPage
from ...pages.lms.courseware import ... | J861449197/edx-platform | common/test/acceptance/tests/lms/test_lms_problems.py | Python | agpl-3.0 | 13,281 | [
"VisIt"
] | 2356deebad4f0d3d8b6d5fe8cfcc9cd54afce60870101bdb2eaa4183bcdc0d71 |
# -*- coding: utf-8 -*-
"""
The :mod:`sklearn.naive_bayes` module implements Naive Bayes algorithms. These
are supervised learning methods based on applying Bayes' theorem with strong
(naive) feature independence assumptions.
"""
# Author: Vincent Michel <vincent.michel@inria.fr>
# Minor fixes by Fabian Pedre... | lucidfrontier45/scikit-learn | sklearn/naive_bayes.py | Python | bsd-3-clause | 14,984 | [
"Gaussian"
] | 5680aede4a97e22cb0d21c2180abd4b60b269a1fd5fb95bfcb3d164c28d5b02b |
from .core import *
from .matching import *
class _Embedded(AST):
_fields = ('node',)
@macro_inline
def u(node, container, transform, **kwargs):
if not q.into:
raise AssertionError('Cannot use the u macro without being in a quote')
with tmp_attr(q, intro=False):
return _Embedded(locate(t... | mistasse/Pyns | pyns/macros.py | Python | mit | 1,887 | [
"VisIt"
] | 7bb3aa09c72d622600b7813f1292ee31c3ab81ab3da97e8e361650fa9dbfeb13 |
#
# Copyright (c) 2015, Novartis Institutes for BioMedical Research Inc.
# 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 copyri... | rvianello/rdkit | rdkit/Chem/MolKey/InchiInfo.py | Python | bsd-3-clause | 7,306 | [
"RDKit"
] | f6a1b3f193ac6ba9ff335e1ec908c74f857c58a0cf87b78b22809c2bc6cc27b5 |
# Copyright 2021 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... | keras-team/reservoir_nn | reservoir_nn/utils/weight_properties.py | Python | apache-2.0 | 6,081 | [
"NEURON"
] | 424121a93ecec9093156c5853d106f8ef5a80f86f29446853ad7b0b1f1497d2f |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | kratman/psi4public | psi4/driver/procrouting/findif_response_utils/__init__.py | Python | gpl-2.0 | 1,270 | [
"Psi4"
] | 499ed2ec81db3c6cfcbcb62db69854222ae6ee260bd51a36a54df1da0ae0a6b3 |
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
import gtk, os, pango, sys
from zeroinstall import _, logger
from zeroinstall.cmd import slave
from zeroinstall.support import tasks
from zeroinstall.injector import model, writer
from zeroinstall.gtkui import gtkutil... | linuxmidhun/0install | zeroinstall/gui/impl_list.py | Python | lgpl-2.1 | 6,557 | [
"VisIt"
] | d214669e03d330de89b1a6472defed207bc6c3b295ef040f245000efb911424f |
# Copyright (C) 2013, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from __future__ import print_function
import os, subprocess
from os.path import join, dirname, abspath
from zeroinstall import SafeException
from repo import scm
topdir = dirname(dirname(dirname(abspath(__file__))... | gfxmonk/0repo | repo/cmd/create.py | Python | lgpl-2.1 | 1,692 | [
"VisIt"
] | 6f77188a81deafc8be1cbc4d1894a5b1fec6231b069b775e5cf56027c922e02a |
# 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 | src/integrator/EmptyExtension.py | Python | gpl-3.0 | 1,731 | [
"ESPResSo"
] | 8d1aa00f2673f4d06d2cda5a90c078468b38c6fa448c5d0e5c54c362ace3ba7f |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | anderspitman/scikit-bio | skbio/tests/test_base.py | Python | bsd-3-clause | 13,354 | [
"scikit-bio"
] | 8395a045d5e012cd556d925230e146efd2b4cfda3f8117ee7935858177dc5cd2 |
"""
A collection of functions to find the weights and abscissas for
Gaussian Quadrature.
These calculations are done by finding the eigenvalues of a
tridiagonal matrix whose entries are dependent on the coefficients
in the recursion formula for the orthogonal polynomials with the
corresponding weighting function over ... | anntzer/scipy | scipy/special/_orthogonal.py | Python | bsd-3-clause | 74,116 | [
"Gaussian"
] | 2c56beebf3a04cfa39f8b9f930b6571ba87ef8844d167987aa0844252b54b6b7 |
# Natural Language Toolkit: Clusterers
#
# Copyright (C) 2001-2017 NLTK Project
# Author: Trevor Cohn <tacohn@cs.mu.oz.au>
# URL: <http://nltk.org/>
# For license information, see LICENSE.TXT
"""
This module contains a number of basic clustering algorithms. Clustering
describes the task of discovering groups of simila... | sdoran35/hate-to-hugs | venv/lib/python3.6/site-packages/nltk/cluster/__init__.py | Python | mit | 4,283 | [
"Gaussian"
] | 919357f780f3fcccd6953de3234daa8baa15e72169d321d6a36eea1e1b451bd4 |
"""
Histogram-related functions
"""
from __future__ import division, absolute_import, print_function
import operator
import warnings
import numpy as np
from numpy.compat.py3k import basestring
__all__ = ['histogram', 'histogramdd', 'histogram_bin_edges']
# range is a keyword argument to many functions, so save the ... | ryfeus/lambda-packs | HDF4_H5_NETCDF/source2.7/numpy/lib/histograms.py | Python | mit | 35,612 | [
"Gaussian"
] | 11f91f0b08a888c6cb42df418958e2be5ab81dfa50f53b9fe1cf21d74ab61d3b |
# Copyright (c) 2015-2018 Cisco Systems, Inc.
#
# 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... | metacloud/molecule | test/unit/model/v2/test_dependency_section.py | Python | mit | 3,821 | [
"Galaxy"
] | 4237b930501f50b48415e62939a7b177e4ea83695db0b99455fe80543d1c6446 |
# proxy module
from __future__ import absolute_import
from mayavi.tools.tools import *
| enthought/etsproxy | enthought/mayavi/tools/tools.py | Python | bsd-3-clause | 87 | [
"Mayavi"
] | d882396410bde1c0a412eeaf762f319c388f4c4401fc24a0c4f4a2e0850c77b0 |
"""
Tests for scaling utilities module.
"""
from __future__ import annotations
from math import pi, sqrt
import numpy as np
import pytest
from dxtbx.model import (
Beam,
Crystal,
Experiment,
ExperimentList,
GoniometerFactory,
Scan,
)
from dxtbx.serialize import load
from libtbx import phil
f... | dials/dials | tests/algorithms/scaling/test_scaling_utilities.py | Python | bsd-3-clause | 19,456 | [
"CRYSTAL"
] | 718ff5bac56164bb1719da2866548c2ff5dbc50bebadcd1c929b84f5200a17d4 |
# -*- coding: utf-8 -*-
"""
***************************************************************************
dataobject.py
---------------------
Date : August 2012
Copyright : (C) 2012 by Victor Olaya
Email : volayaf at gmail dot com
****************************... | SebDieBln/QGIS | python/plugins/processing/tools/dataobjects.py | Python | gpl-2.0 | 16,129 | [
"NetCDF"
] | b5ec866650c2a142d87604cbe94b852b9ceefdbe415e4ce9605366c4240cecb7 |
# 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_0139_h2o_uks_nonin_pb.py | Python | apache-2.0 | 1,839 | [
"PySCF"
] | a8e1bd9e1bbfc480abc9c4233085a1657857d72b491e60d18b8cdceac0eae6ed |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides objects describing the basic parameters of the
pseudopotentials used in Abinit, and a parser to instantiate pseudopotential objects..
"""
from __future__ import unicode_literals, divisi... | sonium0/pymatgen | pymatgen/io/abinitio/pseudos.py | Python | mit | 91,020 | [
"ABINIT",
"WIEN2k",
"pymatgen"
] | c3032c0b5b070ab8b7f94af8a379890e41519f5708739801dba44215466411e6 |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | abhitopia/tensorflow | tensorflow/tools/common/public_api.py | Python | apache-2.0 | 3,771 | [
"VisIt"
] | 5575de2de4938ea068c79357f33549269a6b6a48c1f6d104867a12da6460685a |
# Copyright 2009 by Cymon J. Cox. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Command line wrapper for the multiple alignment program PROBCONS.
"""
from __future__ import... | zjuchenyuan/BioWeb | Lib/Bio/Align/Applications/_Probcons.py | Python | mit | 5,015 | [
"Biopython"
] | 4b1a3a98c6ef3f2373aacf4e885727b790357ca9d9e92fefed7a4d0197dc7e50 |
#!/usr/bin/env python
# encoding: utf8
"""Script to create a bunch of tarballs and montages, made available on the
/dex/downloads page.
"""
from __future__ import division
import math
import os, os.path
import pkg_resources
import re
import subprocess
from subprocess import PIPE
import sys
import tarfile
phi = (1 + 5... | Sanqui/spline-pokedex | bin/create-downloads.py | Python | mit | 15,397 | [
"CRYSTAL"
] | 933cd79a442fd1d19f4659ff9a4c06c0682bf0ccc1a20bf95efc06eeda5198f4 |
from direct.directnotify.DirectNotifyGlobal import directNotify
from direct.showbase.PythonUtil import makeFlywheelGen
from direct.showbase.PythonUtil import itype, serialNum, safeRepr, fastRepr
from direct.showbase.Job import Job
import types, weakref, random, sys
if sys.version_info >= (3, 0):
import builtins as... | brakhane/panda3d | direct/src/showbase/ContainerLeakDetector.py | Python | bsd-3-clause | 50,546 | [
"VisIt"
] | 074d684533424e78a658ea97a06a375f6bad873c0b162827463846918338fe1e |
###############################
# This file is part of PyLaDa.
#
# Copyright (C) 2013 National Renewable Energy Lab
#
# PyLaDa is a high throughput computational platform for Physics. It aims to make it easier to submit
# large numbers of jobs on supercomputers. It provides a python interface to physical input, suc... | pylada/pylada-light | tests/tools/input/test_tree.py | Python | gpl-3.0 | 2,501 | [
"CRYSTAL",
"VASP"
] | f5ca5e9af8a8c509b72d07322c4afb72f1fbbb52f9db1ac2d953832e4e82a544 |
# DistTarBuilder: tool to generate tar files using SCons
# Copyright (C) 2005, 2006 Matthew A. Nicholson
# Copyright (C) 2006-2010 John Pye
#
# This file is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License version 2.1 as published by the Free Software... | georgyberdyshev/ascend | scons/disttar.py | Python | gpl-2.0 | 4,033 | [
"VisIt"
] | 475e5f47b406c9ac272cffc9cf62cd35f676c020529b1480cdafe2389ae35fa0 |
# -*- coding: utf-8 -*-
# POW package __init__.py
# Copyright (c) 2012 Oliver Beckstein <orbeckst@gmail.com>
# Released under the GNU Public License 3 (or higher, your choice)
# See the file COPYING for details.
"""
Force field selection
=====================
The :mod:`mdpow.forcefields` module contains settings for ... | Becksteinlab/MDPOW | mdpow/forcefields.py | Python | gpl-3.0 | 10,637 | [
"Amber",
"CHARMM",
"Gromacs"
] | cf85a929902df5c02e5478addf7065d30398050523b09f46e5ee69a058cfeef4 |
# copies.py - copy detection for Mercurial
#
# Copyright 2008 Matt Mackall <mpm@selenic.com>
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2 or any later version.
import util
import heapq
def _dirname(f):
s = f.rfind("/")
if s == -1:
r... | hekra01/mercurial | mercurial/copies.py | Python | gpl-2.0 | 18,029 | [
"VisIt"
] | bd178725391db06994f9ac5fbdf45197c1d05538de1ba7cc1cce82fa1a751978 |
# 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_ao_eval.py | Python | apache-2.0 | 1,816 | [
"PySCF"
] | 2d304ec12b5dc0c4a8ea00dcbe9894f8394e6abd32a8673de6cdf69722aaf613 |
import vtk
import pyacvd
# import os
import pyvista
import numpy as np
# import Trekker
import invesalius.data.slice_ as sl
from invesalius.data.converters import to_vtk
class Brain:
def __init__(self, n_peels, window_width, window_level, affine_vtk=None):
# Create arrays to access the peel data and peel... | paulojamorim/invesalius3 | invesalius/data/brainmesh_handler.py | Python | gpl-2.0 | 12,251 | [
"VTK"
] | fcb54a1de9fdf85e98dbad7fca3f4c83c860787244a8a995ba0f0eda7b8406b0 |
import sys
import numpy as np
from ase.data.g2 import data
from ase.data.g2 import molecule_names as names
from ase.tasks.main import run
from ase.tasks.molecule import MoleculeTask
from ase.structure import molecule
class Collection:
def __init__(self, data, names, cell):
self.data = data
self... | robwarm/gpaw-symm | doc/devel/ase_optimize/g2_dzp.py | Python | gpl-3.0 | 2,592 | [
"ASE",
"GPAW"
] | 648ffac79e03deed7d80d1b5b4f41a43aa4a10a7f9807e23ea2452d010f9712c |
#http://erg.biophys.msu.ru/wordpress/archives/150
import numpy as np
from math import ceil, floor, sqrt
class CUBE:
def __init__(self, fname):
f = open(fname, 'r')
for i in range(2): f.readline() # echo comment
tkns = f.readline().split() # number of atoms included in the file followed by the position of... | mlund/faunus-notebooks | activity-coefficients/load_cube.py | Python | mit | 3,085 | [
"Gaussian"
] | a8a7080a93dfcbe1e347c538224a5d2eda7056f727ba537ca84b43ab5a36a4ff |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# =====================================================================
# Copyright (c) 2012, Michael Hull
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
#... | mikehulluk/mredoc | src/mredoc/writers/html/__init__.py | Python | bsd-2-clause | 13,103 | [
"VisIt"
] | 37e1cf420d6d7b3e229f799261b54cb2aa54565046f1cc5319da3136d0299b55 |
"""
======================================================================
Time-frequency on simulated data (Multitaper vs. Morlet vs. Stockwell)
======================================================================
This example demonstrates the different time-frequency estimation methods
on simulated data. It shows ... | adykstra/mne-python | examples/time_frequency/plot_time_frequency_simulated.py | Python | bsd-3-clause | 8,427 | [
"Gaussian"
] | a3278c41e76e283f81c570bf9cfe8555f938710b9700ff1d3e194f130112d85f |
"""
========================================================
Gaussian process regression (GPR) on Mauna Loa CO2 data.
========================================================
This example is based on Section 5.4.3 of "Gaussian Processes for Machine
Learning" [RW2006]. It illustrates an example of complex kernel engine... | ltiao/scikit-learn | examples/gaussian_process/plot_gpr_co2.py | Python | bsd-3-clause | 5,718 | [
"Gaussian"
] | 7ca6c7c5cf99b39ad02b3f06127e0cb6e23ccaccbcf79b7eb5df6d5ed8995bc6 |
#!/usr/bin/env python
import vtk
def main():
colors = vtk.vtkNamedColors()
points = vtk.vtkPoints()
points.InsertNextPoint(0.0, 0.0, 0.0)
points.InsertNextPoint(1.0, 0.0, 0.0)
points.InsertNextPoint(2.0, 0.0, 0.0)
points.InsertNextPoint(3.0, 0.0, 0.0)
points.InsertNextPoint(4.0, 0.0, 0.0... | lorensen/VTKExamples | src/Python/PolyData/WarpVector.py | Python | apache-2.0 | 2,235 | [
"VTK"
] | 3c2ea8faf568d07461a46f9028bc4f1e2b8b5b436a928fa55264c070cda57fac |
#!/usr/bin/env python
'''
File name: main_make_map.py
Author: Guillaume Viejo
Date created: 28/09/2017
Python Version: 3.5.2
To make shank mapping
'''
import numpy as np
import pandas as pd
# from matplotlib.pyplot import plot,show,draw
import scipy.io
from functions import *
from pylab import *
from sklear... | gviejo/ThalamusPhysio | python/main_make_coincident_map_figure.py | Python | gpl-3.0 | 4,246 | [
"NEURON"
] | 949055f2af073ec8b80ccf466b3c259af48045d2ffdd83df93923cf0bac1ff4e |
"""
Q2: Alpha Complex
Frustratingly this is too slow for two of the larger examples (test 6 and test
8). I think this is mostly just an issue with Python :(.
Still, only lost 6 marks for to slowness. 18/24.
2b: (i) A (ii) AAAA
2c: The first time we visit a room, all of the exits have been used an even
(zero) number... | matthewelse/british-informatics-olympiad | 2020/q2.py | Python | mit | 3,435 | [
"VisIt"
] | d0526f65d004e67a2ce4bc4d79391fa4aa060815694ced2e410f2149e2a7a1a2 |
#!/usr/bin/env python
#
#
# This file is part of do_x3dna
#
# Author: Rajendra Kumar
# Copyright (C) 2014-2019 Rajendra Kumar
#
# do_x3dna uses 3DNA package (http://x3dna.org).
# Please cite the original publication of the 3DNA package:
# Xiang-Jun Lu & Wilma K. Olson (2003)
# 3DNA: a software package for the analysis... | rjdkmr/do_x3dna | dnaMD/dnaMD/dnaEY.py | Python | gpl-3.0 | 65,696 | [
"Gromacs"
] | 1c5302f60176c160fd4c16dc1c842ef84d54bbc752c0d6dbba009cbe4f014de5 |
# Copyright 2012-2015 by Alex Holehouse - see LICENSE for more info
# Contact at alex.holehouse@wustl.edu
""" Acts as a easy-to-use wrapper around the Entrez package, for an intuitive
and simple way to get sequence information from NCBI. Abstracts NCBI's
eUtils from the user, providing a uniform interface. The absolut... | alexholehouse/Geeneus | geeneus/__init__.py | Python | gpl-2.0 | 1,068 | [
"Biopython"
] | 6913cb74390f4db7c2fa183784aba5be928225cd9e264b0333a8f71fc8469bd0 |
# This file is part of Merlin.
# Merlin is the Copyright (C)2008,2009,2010 of Robin K. Hansen, Elliot Rosemarine, Andreas Jacobsen.
# Individual portions may be copyright by individual contributors, and
# are included in this collective work with permission of the copyright
# owners.
# This program is free software; ... | d7415/merlin | Hooks/target/status.py | Python | gpl-2.0 | 8,947 | [
"Galaxy"
] | e5316501ab9d3a5ffc6b16ebfc8f189b81028285ef383247f8395b9dc5b86e43 |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | gregcaporaso/scikit-bio | skbio/tests/test_base.py | Python | bsd-3-clause | 1,553 | [
"scikit-bio"
] | 1282eda072517760a0d510c2a1de86d8da26496a134da88e1bb8faabf0c6000e |
# store.py - repository store handling for Mercurial
#
# Copyright 2008 Matt Mackall <mpm@selenic.com>
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2 or any later version.
from i18n import _
import scmutil, util, parsers
import os, stat, errno
_sha =... | iaddict/mercurial.rb | vendor/mercurial/mercurial/store.py | Python | mit | 16,865 | [
"VisIt"
] | 59a2692c16c9ae7ae3f3b0f7258d47aee0f35943c416368bb57efad47cecb48c |
# sql/expression.py
# Copyright (C) 2005-2013 the SQLAlchemy authors and contributors <see AUTHORS file>
#
# This module is part of SQLAlchemy and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""Defines the base components of SQL expression trees.
All components are derived ... | Br3nda/calcalcal | pylib/sqlalchemy/sql/expression.py | Python | mit | 212,393 | [
"VisIt"
] | 6f4619a3ead2d5c73c0f7293d4008393424e62fe9fc269518c44cd464c9d0f11 |
########################################################################
#
# (C) 2015, Brian Coca <bcoca@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation... | jctanner/ansible | lib/ansible/galaxy/role.py | Python | gpl-3.0 | 17,998 | [
"Brian",
"Galaxy"
] | 126d3b8a1625c8aaee758418a6924c598fac69968189c85b87daac8f4d29cca5 |
# -*- coding: utf-8 -*-
"""
Generate the abscissas and weights in Gauss-Loboto quadrature.
Example usage
-------------
With increasing order::
>>> distribution = chaospy.Beta(2, 2, lower=-1, upper=1)
>>> for order in range(4): # doctest: +NORMALIZE_WHITESPACE
... X, W = chaospy.generate_quadrature(
... | jonathf/chaospy | chaospy/quadrature/lobatto.py | Python | mit | 5,519 | [
"Gaussian"
] | 3a1a284387ecc18ad6929e4b92526a1ad511506d48d3c3ea47595102122adad3 |
"""K-means clustering"""
# Authors: Gael Varoquaux <gael.varoquaux@normalesup.org>
# Thomas Rueckstiess <ruecksti@in.tum.de>
# James Bergstra <james.bergstra@umontreal.ca>
# Jan Schlueter <scikit-learn@jan-schlueter.de>
# Nelle Varoquaux
# Peter Prettenhofer <peter.prettenh... | StevenReitsma/kaggle-galaxyzoo | scikit/scikit-learn/sklearn/cluster/k_means_.py | Python | gpl-2.0 | 53,776 | [
"Gaussian"
] | 6d5b22ce732cbf245fdc53ad4a5a0465e281dd369c23437776296e5732fac0ce |
import getpass
import sys
import json
from reflowrestclient.utils import get_token, post_sample
host = raw_input('Host: ')
username = raw_input('Username: ')
password = getpass.getpass('Password: ')
token = get_token(host, username, password)
if token:
print "Got token!!!"
else:
print "No token for you!!!"
... | whitews/ReFlowRESTClient | examples/example_post_fcs.py | Python | bsd-3-clause | 838 | [
"VisIt"
] | 91ce92a21cff26f0d266d5620b6502c002cea09251c151ebfae8bb40e94b4e7f |
'''
Module for handling Age-Matching catalogs
made by Andrew Hearin
'''
import numpy as np
import util
from Corrfunc import _countpairs
from Corrfunc.utils import read_catalog
import os.path as path
from halotools.mock_observables.catalog_analysis_helpers import return_xyz_formatted_array
from halotools.empirical_mode... | mjvakili/gambly | code/AM_clustering.py | Python | mit | 6,195 | [
"Galaxy"
] | c6a1c35250826a93e7296b967d5584fc450ffff348f852018c96f0e51662c0b1 |
import os
import pytest
from io import StringIO
from importlib import reload
from eppy.modeleditor import IDF
from eppy.iddcurrent import iddcurrent
from eppy import modeleditor
from .test_runner import versiontuple
THIS_DIR = os.path.dirname(os.path.abspath(__file__))
RESOURCES_DIR = os.path.join(THIS_DIR, os.pard... | santoshphilip/eppy | tests/conftest.py | Python | mit | 1,528 | [
"EPW"
] | e2ac71087f46f4db91595293d21b893eb19c0ededb1afe71137435f309c13d34 |
# -*- coding: utf-8 -*-
"""
Created on Wed Aug 09 17:02:23 2017
@author: Jessica
"""
import numpy as np
from scipy import signal, optimize
from scipy.ndimage import rotate
from skimage.measure import compare_ssim as ssim
from skimage.feature import register_translation
from scipy.ndimage import fourier_shift
from scip... | kongjy/hyperAFM | hyperAFM/imagealignment.py | Python | mit | 9,771 | [
"Gaussian"
] | 48da5a31e72057ebabd46cd8e662469c986745fea842e368a5381b9383c509d7 |
""" Flask-Script commands for running unit/style/static tests """
import os
import docker
from dockci.server import MANAGER
from dockci.util import bin_root, project_root
def call_seq(*commands):
""" Call commands in sequence, returning on first failure """
for cmd in commands:
result = cmd()
... | RickyCook/DockCI | dockci/commands/tests.py | Python | isc | 2,815 | [
"VisIt"
] | 8ec1411845d193e1dc77edb411a6e68573dd31aa65893f4a3a3b237b9bfcd297 |
# 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 | src/Tensor.py | Python | gpl-3.0 | 3,339 | [
"ESPResSo"
] | 3eb50c6fb47931988fbeff9a844fda53a618f73b1c689a85e7c4f0eb0d7d316e |
"""
DB2 database specific implementations of changeset classes.
"""
import logging
from ibm_db_sa import base
from sqlalchemy.schema import (AddConstraint,
CreateIndex,
DropConstraint)
from sqlalchemy.schema import (Index,
... | aasoliz/Bitcoin-Statistics | venv/lib/python2.7/site-packages/migrate/changeset/databases/ibmdb2.py | Python | bsd-3-clause | 12,452 | [
"VisIt"
] | 663f32b7f9f6a5802f84b3a416a9c42041f42e71b09228f40c7b6dfd7f22bdfe |
#!/usr/bin/env python3
# Copyright (C) 2016, 2017(H)
# Max Planck Institute for Polymer Research
#
# 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, ei... | espressopp/espressopp | examples/adress/fadress_tetraliquid/adress.py | Python | gpl-3.0 | 8,846 | [
"ESPResSo"
] | d0b055531cfa6f91cce9a5f1f5469eb5bea3ad428bd7ef6fec4478c30fad7079 |
#!/usr/bin/env python
"""Fast image simulation using GalSim for weak lensing studies.
"""
from __future__ import print_function, division
import argparse
import descwl
def main():
# Initialize and parse command-line arguments.
parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpForm... | DarkEnergyScienceCollaboration/WeakLensingDeblending | simulate.py | Python | mit | 5,795 | [
"Galaxy"
] | a40cd081bbe5d93aafe1d83cf57c2063c6b0c713ec7972018611fc4817254884 |
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