text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import math
import itertools
from six.moves import map, zip
import numpy as np
from numpy.linalg import inv
from numpy import pi, dot, transpose, radians
fro... | johnson1228/pymatgen | pymatgen/core/lattice.py | Python | mit | 39,249 | [
"ABINIT",
"CRYSTAL",
"pymatgen"
] | de0b2a194f8d19945970aaa9e3d862132e2fdff1d31ec8457870a17130559624 |
#!/usr/bin/env python
# This example demonstrates how to extract "computational planes" from
# a structured dataset. Structured data has a natural, logical
# coordinate system based on i-j-k indices. Specifying imin,imax,
# jmin,jmax, kmin,kmax pairs can indicate a point, line, plane, or
# volume of data.
#
# In this ... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Examples/VisualizationAlgorithms/Python/warpComb.py | Python | gpl-3.0 | 3,277 | [
"VTK"
] | a033bae885f0ec00c761e30ba82ac8532edae35a85259721bcca74daae70da69 |
# Orca
#
# Copyright 2006-2008 Sun Microsystems Inc.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This... | GNOME/orca | src/orca/keynames.py | Python | lgpl-2.1 | 9,945 | [
"ORCA"
] | 03805815abed0e99bd536fc81e715b1dfb23ac03631285a3112a6c5341fd3ff0 |
import numpy as np
import matplotlib.pyplot as plt
import scipy
import lmfit
import itertools
import logging
from pycqed.simulations import transmon
from pycqed.utilities.timer import Timer
log = logging.getLogger(__name__)
#################################
# Fitting Functions Library #
########################... | QudevETH/PycQED_py3 | pycqed/analysis/fitting_models.py | Python | mit | 73,792 | [
"Gaussian"
] | 36a45ef0186d1dfee00d8fb2acf2b38f8e413090405e542ddbe408867252564f |
import json
import httplib
from django.http import HttpResponse
from Bio.Alphabet import IUPAC
from hippo import clean_sequence
import features
import orfs
import gb
def _post(params, is_ajax):
"""
Post a sequence and run the sequence through blast and orf detection.
Expects: db and sequence
Response:... | UndeadBlow/giraffe | src/giraffe/views.py | Python | mit | 5,133 | [
"BLAST"
] | 42c4c6f024d62da8cc04cdb138c8ffc14054deef51512057dece86d16e11a559 |
#
# Copyright (C) 2013-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | KaiSzuttor/espresso | testsuite/python/experimental_decorator.py | Python | gpl-3.0 | 1,225 | [
"ESPResSo"
] | ba2f63fd85f1634f4d0bbeac1305242b5194c39aef48be1ca6bca20a12c3190f |
########################################################################
# File : FC_Scaling_test
# Author : Andrei Tsaregorodtsev
########################################################################
"""
Test suite for a generic File Catalog scalability tests
"""
from DIRAC.Core.Base.Script import Script
from... | DIRACGrid/DIRAC | tests/Performance/DFCPerformance/FIXME_Test_FC_scaling.py | Python | gpl-3.0 | 11,032 | [
"DIRAC"
] | bfb135300b13dc1ce9abc57d16075fede38e36a67062d0184d0da6bca0d15fa4 |
########################################################################
# $HeadURL $
# File: ProcessPoolTests.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2012/02/13 07:55:31
########################################################################
""" :mod: ProcessPoolTests
=======================
.... | Sbalbp/DIRAC | Core/Utilities/test/ProcessPoolTests.py | Python | gpl-3.0 | 13,561 | [
"DIRAC"
] | ee3b7149f6b5a48ab52d29ff5944bbcabd69abf36b90e0ef6e516bf631e0ded7 |
# Copyright 2013 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.
import logging
import os
import unittest
from telemetry.core import util
from telemetry.internal.platform.profiler import perf_profiler
from telemetry.testin... | catapult-project/catapult-csm | telemetry/telemetry/internal/platform/profiler/perf_profiler_unittest.py | Python | bsd-3-clause | 2,000 | [
"VisIt"
] | 307a340696743f5e7d757e912d6dc56692c723baaa81bfb0a2a6d970f69b3219 |
import asyncio
import html
import os
import re
import shutil
import sys
from base64 import b64encode
from django.core.exceptions import ViewDoesNotExist
from django.urls import URLPattern, URLResolver
from django.utils.text import slugify
from PIL import Image, ImageFilter
from pyppeteer import launch
from manager.ur... | stencila/hub | manager/scripts/create_page_snaps.py | Python | apache-2.0 | 24,205 | [
"VisIt"
] | b2fd7d88b442f681f34df4369564218971be0ab1bfc969abcc7623a8a673542f |
# ==========================================================================
#
# Copyright NumFOCUS
#
# 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/... | thewtex/ITK | Wrapping/Generators/Python/itk/support/extras.py | Python | apache-2.0 | 67,596 | [
"VTK"
] | ab6092ef031998447461297da216dc9b27322588ee6dc106a1816841a5ead01f |
"""
======================================================
Permutation t-test on toy data with spatial clustering
======================================================
Following the illustrative example of Ridgway et al. 2012,
this demonstrates some basic ideas behind both the "hat"
variance adjustment method, as wel... | effigies/mne-python | examples/stats/plot_cluster_methods_tutorial.py | Python | bsd-3-clause | 8,261 | [
"Gaussian"
] | 221802352c7bae0a5d07a0950b8d744e22eb9662e93fc303cd227bc58ede901d |
## Project by Chris DeLaGarza, Deep Desai, Ryan King, Justin Carter,
##Ryan Jacobs, Zach Gray, Alyssa Rios, Iori Koh, Josh Harlan, Ayush Agarwal,
##Ryan Noeske, Cosme Tejada, Devin Popcock, Serath Mudana, Ryan Vanet, Brian Teh,
##Brett Philips, Ammar Sheikh, Andrew Bryant
##Sense Hat code by Computer Science 3 Class o... | ComputerScience3/piballoon-october-launch-group-2 | Echo Client.py | Python | gpl-3.0 | 8,295 | [
"Brian"
] | e82ade87c4e807d1f0034cc53316d42c70bcfc683bfe3e1a82a4121bcd60f845 |
########################################################################
# $HeadURL$
# File : InputDataByProtocol.py
# Author : Stuart Paterson
########################################################################
""" The Input Data By Protocol module wraps around the Replica Management
components to provid... | calancha/DIRAC | WorkloadManagementSystem/Client/InputDataByProtocol.py | Python | gpl-3.0 | 11,603 | [
"DIRAC"
] | c3b444aa0836112cc8dcbcdfc904f08fce254bb661db7a81240d6906f0c477b7 |
""" This module contains utilities for parsing extensions in general, but mostly the VOMS extensions.
It has been done based on the reading of the VOMS standard (https://www.ogf.org/documents/GFD.182.pdf)
and on the RFC 5755 (http://www.ietf.org/rfc/rfc5755.txt)
This module relies on definition of the RFC 3281, which ... | yujikato/DIRAC | src/DIRAC/Core/Security/m2crypto/asn1_utils.py | Python | gpl-3.0 | 12,972 | [
"DIRAC"
] | b84684b199a60a342ba3c9b857c91e1c04ee0a346fa44bd429089c9dd9fe95c5 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | pli3/Openwebif | plugin/controllers/views/ajax/screenshot.py | Python | gpl-2.0 | 6,953 | [
"VisIt"
] | 3340f2a25b71f4e8f62e744f2f8149b7725e7ef612b6080bf1aa442dce611a3c |
"""Untag an object using convention based keys."""
import re
from boltons import iterutils
LOCALIZED_KEY_REGEX = re.compile(r'(.*)@([^@]+)$')
class Untag(object):
"""Untagging utility for locale and environment based untagging."""
@staticmethod
def untag(data, locale_identifier=None, params=None):
... | grow/pygrow | grow/common/untag.py | Python | mit | 6,970 | [
"VisIt"
] | 32bc8ba6e5586674de636b1831005209e5dd1225a1635e38c12bcc02ab1fd8b0 |
# Copyright (c) 2012 OpenStack Foundation
# All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless ... | BeyondTheClouds/nova | nova/tests/unit/compute/test_resource_tracker.py | Python | apache-2.0 | 57,954 | [
"exciting"
] | 250f60e77ffe32758d3e30caac281b2010d29324d9073fbc9e16b8969332191d |
#!/usr/bin/env python
"""
Tests of ugali stats
"""
import unittest
# Execute tests in order: https://stackoverflow.com/a/22317851/4075339
unittest.TestLoader.sortTestMethodsUsing = None
import numpy as np
import scipy.stats
import ugali.utils.stats
def generate_distribution(p1=[1.0,0.1,10000],p2=[-1.0,0.6,30000]):
... | kadrlica/ugali | tests/test_stats.py | Python | mit | 4,439 | [
"Gaussian"
] | 5456802b61c661ac8df4940deedb1dfbb71599f5c8764f7a5150bc699209ba2d |
"""
It is used to load the monitoring types.
"""
import re
from DIRAC.Core.Utilities import DIRACSingleton
from DIRAC.Core.Utilities.Plotting.ObjectLoader import loadObjects
from DIRAC.MonitoringSystem.Client.Types.BaseType import BaseType
__RCSID__ = "$Id$"
########################################################... | andresailer/DIRAC | MonitoringSystem/private/TypeLoader.py | Python | gpl-3.0 | 1,396 | [
"DIRAC"
] | be39cb60bc1b4304a6739b5651ff38acd07a39f2493df272cf26f0c1406eaaec |
# -*- coding: utf-8 -*-
from __future__ import print_function
import time
import json
import logging
import tornado.ioloop
import tornado.web
from tornado.options import options, define
import jwt
logging.getLogger().setLevel(logging.DEBUG)
define(
"port", default=3000, help="app port", type=int
)
define(
... | centrifugal/examples | python_tornado/main.py | Python | mit | 8,022 | [
"VisIt"
] | 1153d0b16a65d63a55d7e18450b18ed997c20bc518dcb240fe0f2fe6231835ed |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import os
# Import re module to use regular expression
import re
from spack import *
class VisitSilo(CMakePackage):
... | LLNL/spack | var/spack/repos/builtin/packages/visit-silo/package.py | Python | lgpl-2.1 | 4,449 | [
"VisIt"
] | 85f5b5903129b28ab1895ed363e1ee1928a67421fac0f35e76df54684783cd2a |
from __future__ import division, print_function, absolute_import
import numpy as np
from numpy.dual import eig
from scipy.special import comb
from scipy.signal import convolve
__all__ = ['daub', 'qmf', 'cascade', 'morlet', 'ricker', 'morlet2', 'cwt']
def daub(p):
"""
The coefficients for the FIR low-pass fi... | jamestwebber/scipy | scipy/signal/wavelets.py | Python | bsd-3-clause | 13,701 | [
"Gaussian"
] | 22d068dd8ebd3fb01f5f1cb30410312761a828bd497edee00b33a1d4efba4551 |
# coding=utf-8
# Copyright 2022 The Tensor2Robot Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... | google-research/tensor2robot | research/bcz/model.py | Python | apache-2.0 | 38,176 | [
"Gaussian"
] | 3ea8100d2e4b89aa4c8f8f314c71133d5769b20111012c89d128a16d12751c64 |
#
# Exctraction script for MC d02Kpi
#
script = 'mcfindtracksFinal.py'
def make_template(script, name = "MCFT07", gridOutput = True) :
t = JobTemplate( application = Bender( version = "v25r3", module = script ))
t.name = name
bkquery = BKQuery('/MC/2011/Beam3500GeV-2011-MagDown-Nu2-EmNoCuts/Sim05/Trig0x... | bcouturi/PromptSecondaryLTUnb | dataExtraction/gangaMcfindtracks.py | Python | gpl-2.0 | 1,178 | [
"DIRAC"
] | ad83902cc13289a263bd46e402f2c713a3d31d82c3b241015fe56019d6f4067b |
import ocl
import camvtk
import time
import vtk
import datetime
import math
if __name__ == "__main__":
p = ocl.Epos()
print("initial Epos() is ",p, "with dia=",p.d)
for n in range(0,30):
print(p.d," : ",p)
p.d = p.d - 0.25
p.setD()
raw_input("Press Enter ... | aewallin/opencamlib | examples/python/offset-ellipse/epos_test.py | Python | lgpl-2.1 | 336 | [
"VTK"
] | d546ba67d73bb623dea5141d53f8d4460946555986a094fba30a2096c0cec4cc |
from ase import Atoms
from ase.calculators.emt import EMT
from ase.optimize.test import run_test
from gpaw import GPAW
name = 'H2'
def get_atoms():
cell = (5, 5, 5)
atoms = Atoms('H2', [(0, 0, 0), (0, 0, 1.4)], cell=cell)
atoms.center()
return atoms
def get_calculator_emt():
calc = EMT()
retu... | grhawk/ASE | tools/ase/optimize/test/H2.py | Python | gpl-2.0 | 530 | [
"ASE",
"GPAW"
] | 08eebf2e3538fbea5e87d3aefab13b340bddc63685420da542c5bfab54e87883 |
####################################################################################################
# registration/core.py
# Core tools for registering the cortical surface to a particular potential function
# By Noah C. Benson
import numpy as np
from numpy import pi
from ..java import (to_java_doubles, to_... | noahbenson/neuropythy | neuropythy/registration/core.py | Python | agpl-3.0 | 18,519 | [
"Gaussian"
] | 8e54c80b5d4a32806b1d2186150c31f8dc446a6437760c9c875aeeb030d0fa33 |
import ocl
import pyocl
import camvtk
import time
import vtk
import datetime
if __name__ == "__main__":
print ocl.revision()
myscreen = camvtk.VTKScreen()
stl = camvtk.STLSurf("../../stl/gnu_tux_mod.stl")
myscreen.addActor(stl)
stl.SetWireframe()
stl.SetColor((0.5,0.5,0.5))
polydata... | AlanZatarain/opencamlib | scripts/drop-cutter/drop_cutter_tst_5.py | Python | gpl-3.0 | 2,141 | [
"VTK"
] | 90db20dbb2937c931a73614e6012bd7027b490b93a9f6ad606d5b85cdff6202f |
"""@namespace IMP.pmi.restraints.stereochemistry
Restraints for keeping correct stereochemistry.
"""
from __future__ import print_function
import IMP
import IMP.core
import IMP.algebra
import IMP.atom
import IMP.container
import IMP.isd
import itertools
import IMP.pmi.tools
import IMP.pmi.representation
from operator ... | shanot/imp | modules/pmi/pyext/src/restraints/stereochemistry.py | Python | gpl-3.0 | 53,994 | [
"CHARMM"
] | eac009d4a12813adb9bd4cf6156dec6ab3ccebdd29e42d34ddfae75867630725 |
from paraview.simple import *
from tonic.paraview.dataset_builder import *
# Can.ex2 file path
fileToLoad = '/Users/seb/Work/code/ParaView/data/can.ex2'
dataset_destination_path = '/tmp/can'
# Initial ParaView scene setup
can = OpenDataFile(fileToLoad)
can.ElementVariables = ['EQPS']
can.PointVariables = ['DISPL', 'V... | Kitware/tonic-data-generator | scripts/paraview/samples/time-management.py | Python | bsd-3-clause | 1,502 | [
"ParaView"
] | 7cc76fae7fdd3519016bf0ad162caf2aa1098c7b1dbb792fc723acab831b6e33 |
import os
from subprocess import Popen, PIPE, STDOUT
from math import radians, sin, cos
from ase import Atom, Atoms
from ase.neb import NEB
from ase.constraints import FixAtoms
from ase.optimize import QuasiNewton, BFGS
from ase.visualize import view
from ase.calculators.turbomole import Turbomole
# Delete old coor... | suttond/MODOI | ase/test/turbomole/turbomole_h3o2m.py | Python | lgpl-3.0 | 2,643 | [
"ASE",
"TURBOMOLE"
] | 330c2d741e344b3c69b12a2d63af3d15bcbe39ffe49b8ef19b57894e9a6372c2 |
"""
A Pythonic interface to Google's GMail, with all the tools you'll need. Search,
read and send multipart emails, archive, mark as read/unread, delete emails,
and manage labels.
Installation
############
Install using pip
::
pip install gmail_client
Features
########
1. Search emails
2. Read emails
3. Emails:... | wilbertom/gmail_client | gmail_client/__init__.py | Python | mit | 4,791 | [
"Brian"
] | b98201142e71efe84cb01fc6a2541b80b9f257c3ee7336974b59b5f082e8293b |
# -*- coding: utf-8 -*-
# Utools for setup.py files
from __future__ import absolute_import, division, print_function
import sys
import textwrap
from os.path import exists, join, dirname, split, splitext
import os
from utool import util_cplat
from utool import util_path
from utool import util_io
from utool import util_s... | Erotemic/utool | utool/util_setup.py | Python | apache-2.0 | 24,831 | [
"VisIt"
] | 564452939c6f46e1f7c367319f263d7dc6f56567784239803fda8339df2be9a6 |
from django.conf import settings
from django.core.mail import send_mail
emails = {
'donation_thanks': {
'subject': 'Thanks for your donation to Free Law Project!',
'body': ('Hello %s,\n\nThanks for your donation of $%0.2f to Free '
'Law Project. We are currently using donations lik... | Andr3iC/courtlistener | cl/donate/utils.py | Python | agpl-3.0 | 1,281 | [
"Brian"
] | 8128a9a657a1dd6ef52a7d86d83aea7de863b2f56e7c77f63e6c59fe7ca522fd |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2005-2007 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2012 Tim G L Lyons
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publ... | Forage/Gramps | gramps/plugins/importer/importgrdb.py | Python | gpl-2.0 | 2,950 | [
"Brian"
] | 19ad55e6a7ce3c91e56ca4c5af6a1fdb7d1e455fca5715519ff98b400cb6ead7 |
import copy
import math
import espresso
def createPathintegralSystem(allParticles,
props,
types,
system,
langevin,
potentials,
P, # the Trotter Number (number of imaginary time slices)
polymerInitR=0.01,# polymer radius for setting up ring in 2d plane
hbar=0.063507807 # hbar in gromacs units [kJ/mol ps]
):
# Tur... | BackupTheBerlios/espressopp | testsuite/pi_water/pathintegral.py | Python | gpl-3.0 | 4,804 | [
"ESPResSo",
"Gromacs"
] | a4cd51d6981f714c11dc37ee6a04f0c772087310f78775651832f05df2dd23cf |
# coding: utf-8
from __future__ import unicode_literals
import unittest
import os
from pymatgen.electronic_structure.boltztrap import BoltztrapAnalyzer
test_dir = os.path.join(os.path.dirname(__file__), "..", "..", "..",
'test_files')
class BoltztrapAnalyzerTest(unittest.TestCase):
def... | Dioptas/pymatgen | pymatgen/electronic_structure/tests/test_boltztrap.py | Python | mit | 3,410 | [
"BoltzTrap",
"pymatgen"
] | 5ce36a65e7acb1bfc0e3116558c6b1093bb3d60e84cac4e7ef4a0c15fe57e81a |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Test for the piezo tensor class
"""
__author__ = "Shyam Dwaraknath"
__version__ = "0.1"
__maintainer__ = "Shyam Dwaraknath"
__email__ = "shyamd@lbl.gov"
__status__ = "Development"
__date__ = "4/1/16"
im... | montoyjh/pymatgen | pymatgen/analysis/tests/test_piezo.py | Python | mit | 1,990 | [
"pymatgen"
] | 993f40e669849467477988ff32c46bf74f0f3c3e136426ba085ede8f34e043b2 |
from __future__ import division, print_function
"""
These functions are for the "Distant local groups" project target selection.
"""
#important note: SDSS 'type' field: 3=galaxy, 6=star
import numpy as np
from matplotlib import pyplot as plt
try:
import six
except ImportErrir:
from astropy.extern import six
... | saga-survey/saga-code | targeting.py | Python | gpl-2.0 | 29,401 | [
"Galaxy"
] | c9db02c583c8df5ecd46651329a80f3cbdec423b886912e49cfdcc34fa7a37fb |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#... | MDAnalysis/mdanalysis | package/MDAnalysis/core/accessors.py | Python | gpl-2.0 | 6,748 | [
"MDAnalysis",
"RDKit"
] | 3b89941e48972ab0525ff2c594b9ae0ad279ea98bdc23630e32835b3b9431eb5 |
# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
# All rights reserved.
#
# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are ... | wizmer/NeuroM | neurom/features/tests/test_feature_compat.py | Python | bsd-3-clause | 10,601 | [
"NEURON"
] | 7d658d065a55600526a3606071a56d662afccbf1f778de83b7da177647473e74 |
import os
from os.path import join as pjoin
from copy import copy
from ..core.mpi import master_only
from ..interface import compute
from .epctest import EPCTest
__all__ = ['SETest']
class SETest(EPCTest):
"""
Base class for tests involving the electron self-energy.
"""
common = dict(
temp... | jmbeuken/abinit | scripts/post_processing/ElectronPhononCoupling/ElectronPhononCoupling/tests/setest.py | Python | gpl-3.0 | 7,759 | [
"NetCDF"
] | 6e72a7c7260b2713bbc518061b2683baeb255a638ba3df29e7bf3131589bccc8 |
"""
Utility for conversion between different formats for representing alignments.
classes:
FormatConverter
"""
# biopython
from Bio.Fasta.FastaAlign import FastaAlignment
from Bio.Clustalw import ClustalAlignment
class FormatConverter:
"""Convert between different alignment representation formats.
The basi... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/Align/FormatConvert.py | Python | apache-2.0 | 1,798 | [
"Biopython"
] | 2a0f839ff127fadb4947e4245930b1106aaf38da992e73660c0b89caede7fe24 |
from electrum.i18n import _
fullname = _('Revealer Backup Utility')
description = ''.join(["<br/>",
"<b>"+_("Do you have something to hide ?")+"</b>", '<br/>', '<br/>',
_("This plug-in allows you to create a visually encrypted backup of your wallet seeds, or of custom alphanumeric secrets."), '<br/>', '<br/>',... | fujicoin/electrum-fjc | electrum/plugins/revealer/__init__.py | Python | mit | 469 | [
"VisIt"
] | 6763639486536faf1caaa94178856acd0bd76f2edc96d9240918f4e805dd1594 |
"""
Create index files from the command-line
"""
import datetime
import urllib.parse
import uuid
from pathlib import Path
from typing import Dict, Iterable
import click
import rasterio
import rasterio.crs
from rasterio.io import DatasetReader
from eodatasets3 import serialise
from eodatasets3.utils import ItemProvid... | jeremyh/eo-datasets | eodatasets3/prepare/noaa_c_c_prwtreatm_1_prepare.py | Python | apache-2.0 | 4,590 | [
"NetCDF"
] | ebbf738458ba17ac7b19751049d295c839693b07dbef6e81c693ff6f8d9b80a5 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides classes to interface with the Materials Project REST
API v2 to enable the creation of data structures and pymatgen objects using
Materials Project data.
To make use of the Materials API, you need to b... | materialsproject/pymatgen | pymatgen/ext/matproj.py | Python | mit | 70,062 | [
"ABINIT",
"VASP",
"VisIt",
"pymatgen"
] | 088bd357916475c10d306fa8a1426d3c9305f72007174af98f52d30a0d501f7f |
from setuptools import setup, find_packages
setup(
name='qchem_utils',
version='0.1',
license='GPL v2',
url='https://github.com/rmcgibbo/qchem-utils',
description='Utilities for interacting with Q-Chem',
packages=find_packages(),
)
| rmcgibbo/qchem-utils | setup.py | Python | gpl-2.0 | 258 | [
"Q-Chem"
] | 227e98aeac7e227baaf8f3f8fb893329cc980223010e94d775e1d3355fc1996a |
"""
Looking for evidence of additional G->A mutations in reads classified as M184I
"""
import argparse
import collections
import contextlib
import csv
import logging
import sys
import pysam
from .classify_mutations import parse_gff3, classify_read
from ..util import opener, window
log = logging.getLogger(__name__.rp... | fhcrc/prepdrm | python/prep_drm/scripts/hypermutation.py | Python | gpl-3.0 | 4,129 | [
"pysam"
] | f6adf4b1c6bc5bd5bc85b6b071b8952a6308df47acde3efc6ec16ff88f36afbf |
#!/usr/bin/env python
from __future__ import division
import os
import numpy as np
import pysam
import heapq
import pybedtools
from glob import glob
from time import ctime
import sys
def readNames(names):
n = []
with open(names, 'r') as infile:
for line in infile:
line = line.rsplit()
... | ListerLab/TEPID | tepid/tepid.py | Python | gpl-3.0 | 49,375 | [
"pysam"
] | 00ac3cede792687134b69d1ffd7b600bf1cca54703d346415626b4b9ff0d7ae1 |
# $Id$
#
# Copyright (C) 2006-2011 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" Import all RDKit ... | strets123/rdkit | rdkit/Chem/AllChem.py | Python | bsd-3-clause | 19,434 | [
"RDKit"
] | 716da292da7b77920a5c61eff0caa3a78b313d3984a8aaa1dd974ec1a15b758d |
import os
from collections import OrderedDict
import sys
fil = open('energy.xvg').readlines()
GMX_dat = [float(f)/4.184 for f in fil[-1].split()[1:-1]]
nfil = open('LOG_NAMD').readlines()
for line in nfil:
if 'ENERGY: 0' in line:
NAMD_DAT = [float(f) for f in line.split()[2:12]]
break
#pr... | leelasd/OPLS-AAM_for_Gromacs | GMX_TEST/GXG/Y/NAMD_GMX_DIFF.py | Python | mit | 1,077 | [
"NAMD"
] | 296d776b342d85bfda075bd15412aa357528c79adf3f72f493859a9f749ea223 |
# Copyright 2002 by Jeffrey Chang. 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.
"""This package implements pairwise sequence alignment using a dynamic
programming algorithm.
... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/pairwise2.py | Python | gpl-2.0 | 33,467 | [
"Biopython"
] | 9da0418822e86173d5baa1a5f2b7a99e8e959b9ca461c56d1245792ad6c3a71b |
#!/usr/bin/env python
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistri... | dgasmith/psi4 | psi4/share/psi4/fsapt/copy_pymol.py | Python | lgpl-3.0 | 1,338 | [
"Psi4",
"PyMOL"
] | 44d5de7e5dd29188ce83c58dcdbc2171355152c04c5fb1e9c65630bcc9ec398b |
# Input arguments: (Those with '[*]' at end are used here.)
# Process genome repetitiveness file by restriction fragment definitions.
# 1) test.repetitiveness.txt (Ymap_root/users/[user]/genomes/[genome]/)
# 2) test.MfeI_MboI.fasta (Ymap_root/users/[user]/genomes/[genome]/)
# Output fragment repetitiveness data.
# 1... | darrenabbey/ymap | scripts_genomes/repetitiveness_smooth.py | Python | mit | 8,493 | [
"Gaussian"
] | d2637fb4aaae9b49ac16fa2c477dd60304d791378501579d4ede9339287ae1fd |
# Copyright (C) 2003 CAMP
# Please see the accompanying LICENSE file for further information.
import numpy as np
from gpaw.utilities import erf
def I(R, a, b, alpha, beta):
"""Calculate integral and derivatives wrt. positions of Gaussian product.
::
/ 2 ... | ajylee/gpaw-rtxs | gpaw/gauss.py | Python | gpl-3.0 | 4,383 | [
"GPAW",
"Gaussian"
] | 0a70fc02f65da20bbe64258e337ef61aaeabe226bd44e84beb52bc6f01b96294 |
from rdkit import RDConfig
import os,sys
import unittest
from rdkit import Chem
from rdkit.Chem import rdFMCS
class TestCase(unittest.TestCase):
def setUp(self) :
pass
def test1(self):
smis=( "Cc1nc(CN(C(C)c2ncccc2)CCCCN)ccc1 CHEMBL1682991", #-- QUERY
"Cc1ccc(CN(C(C)c2ccccn2)CCCCN)n... | soerendip42/rdkit | Code/GraphMol/FMCS/Wrap/testFMCS.py | Python | bsd-3-clause | 7,536 | [
"RDKit"
] | ebddc3e8d2064c165d75e92daa8d64bfc1247b5896eedbf7074455f5e74c0c38 |
import ast
from taichi.lang.exception import TaichiSyntaxError
from taichi.lang.shell import oinspect
class KernelSimplicityASTChecker(ast.NodeVisitor):
class ScopeGuard:
def __init__(self, checker):
self.c = checker
self._allows_for_loop = True
self._allows_more_stmt ... | yuanming-hu/taichi | python/taichi/lang/ast/checkers.py | Python | mit | 3,791 | [
"VisIt"
] | 1b590c09000828acb60fc14a25a32a72abfbf0e3c3862a705ce36fb1e33864d1 |
import cPickle as pickle
import vv
import rdag
import nodes as nodesmod
from fast import forward
def factory(vrs, rdag_builder, *args, **kwargs):
n = Network()
n.variables = vv.vvec(vrs)
n.graph = rdag_builder(n.variables, *args, **kwargs)
return n
def independent(vrs):
return factory(vrs, r... | awd4/spnss | spnss/network.py | Python | mit | 5,562 | [
"Gaussian"
] | bf20d8a66cdf1fbd6e9117941fd29a42d01629aea81edaaa50a4cf4e5b917066 |
""" This is a simple example of implementation of a Ping/Pong service for executors.
This service does not any specific configuration to run, only the Port number, and authz e.g.:
{
Port = 9145
{
Authorization
{
Default = all
}
}
}
"""
from DIRAC import... | arrabito/DIRAC | docs/source/DeveloperGuide/Systems/Framework/stableconns/service.py | Python | gpl-3.0 | 1,625 | [
"DIRAC"
] | 04048c4495d4d2a6f14b6e07d7faab94a883cf03d953e48ed769ddf8ea5214ce |
from . import core, utils
import cgt
import ctypes, os.path as osp, hashlib, numpy as np, sys, subprocess, string, os, time, traceback, cPickle
from collections import defaultdict, namedtuple
from StringIO import StringIO
import logging
def function(inputs, outputs, dbg=None, updates=None, givens=None):
assert isi... | codeAshu/cgt | cgt/compilation.py | Python | mit | 35,957 | [
"VisIt"
] | 42b074859af832c17e85fb42b010a2efc4e75c0cda4b6d0986022b0633f006db |
"""
This is only meant to add docs to objects defined in C-extension modules.
The purpose is to allow easier editing of the docstrings without
requiring a re-compile.
NOTE: Many of the methods of ndarray have corresponding functions.
If you update these docstrings, please keep also the ones in
core/fromnum... | empeeu/numpy | numpy/add_newdocs.py | Python | bsd-3-clause | 222,904 | [
"Brian"
] | d8f705e34786e46b03438f6d450b6e3ca3fa8398e81ebbcdfa7d94659ce334ea |
# -*- coding: utf-8 -*-
# Copyright 2007-2021 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy 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... | thomasaarholt/hyperspy | hyperspy/models/model1d.py | Python | gpl-3.0 | 37,679 | [
"Gaussian"
] | ca1b1ed866ee1536b5728174c2a5ffbd651e29b74fdee463bafe71d5bc3730da |
from fontTools.misc.py23 import byteord, tobytes
from fontTools.feaLib.error import FeatureLibError
from fontTools.feaLib.location import FeatureLibLocation
from fontTools.misc.encodingTools import getEncoding
from collections import OrderedDict
import itertools
SHIFT = " " * 4
__all__ = [
"Element",
"Feature... | google/material-design-icons | update/venv/lib/python3.9/site-packages/fontTools/feaLib/ast.py | Python | apache-2.0 | 70,109 | [
"VisIt"
] | 0f15572931e4aa48eb2aac62257a9bdbcdca3fbc4d5fedeff2d2453c731ff3f2 |
import sys
import os
from scipy.interpolate import InterpolatedUnivariateSpline as interp
import numpy as np
import matplotlib.pyplot as plt
from astropy.io import fits as pyfits
import TelluricFitter
import DataStructures
import FitsUtils
import Units
import FindContinuum
homedir = os.environ["HOME"]
weather_file ... | kgullikson88/TS23-Scripts | ReCorrect.py | Python | gpl-3.0 | 8,573 | [
"Gaussian"
] | d90021482db5b60f27bb4102dfbf531e4ff59549d529030e90190331118ec125 |
#! /usr/bin/env python
#
# test_3d_exp.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 License, or
... | gewaltig/cython-neuron | topology/examples/test_3d_exp.py | Python | gpl-2.0 | 2,637 | [
"Gaussian"
] | d95687930ed2f4aa8c0e4b5e1ce4ea8495c7a5f1c5e50f6646e303696f8b0447 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
import datetime
from django.core.exceptions import ImproperlyConfigured, ObjectDoesNotExist
from django.test import TestCase, override_settings
from django.views.generic.base import View
from .models import Artist, Author, Book, Page
@override_setting... | weiawe/django | tests/generic_views/test_detail.py | Python | bsd-3-clause | 7,369 | [
"MOOSE"
] | 154e8975a64198fc3afa0c825982d8dd6a1188ba2d6d11cd16e8069005bf044d |
import os
import itertools
class Reason(object):
""" A Reason describes why a build step is performed.
Parameters
----------
explanation : str
"""
def __init__(self, explanation):
self._explanation = explanation
def __str__(self):
return self._explanation
PARENTMISSING =... | njwilson23/depgraph | depgraph/depgraph.py | Python | mit | 11,229 | [
"VisIt"
] | 394f8a5859072521135f09094063da464de652839742bd88a6e04b98846b3e60 |
""" Basic unit tests for AuthManager
"""
import unittest
from DIRAC import gConfig
from DIRAC.Core.Utilities.CFG import CFG
from DIRAC.Core.DISET.AuthManager import AuthManager
__RCSID__ = "$Id$"
testSystemsCFG = """
Systems
{
Service
{
Authorization
{
Method = NormalUser
MethodAll = Any
... | Andrew-McNab-UK/DIRAC | Core/test/Test_AuthManager.py | Python | gpl-3.0 | 6,985 | [
"DIRAC"
] | 3609c23c8c0ec9501010754641f9a32f4e90fd495a97f934fceaac7a2ccc09f9 |
# -*- coding: utf-8 -*-
##############################################################################
#
# Copyright (C) 2012 - 2013 Daniel Reis
#
# This program 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 S... | pedrobaeza/project | __unported__/project_issue_task/__openerp__.py | Python | agpl-3.0 | 2,013 | [
"VisIt"
] | ec0dd3bab3b7f22849e7b741f270b32a163dcff10b77b22c7f67225fe7d57168 |
#!/usr/bin/env python
# A tool to import a NaCl source tree into subnacl/, fixing symbol names.
# Written by Brian Warner https://github.com/warner as part of PyNaCl.
# PyNaCl is released under version 2.0 of the Apache license.
# Modified by tonygarnockjones@gmail.com to construct a Javascript API as well.
import os,... | Zeipt/Mycely_fdroid | www/jxcore/node_modules/js-nacl/import.py | Python | agpl-3.0 | 8,312 | [
"Brian"
] | 8e4359caeb2a017e0beeec031cb301fa04a09988cfa11ad778d04bf6a17a964d |
#!/usr/bin/python
usage = """pointed.py [--options] gps gps gps..."""
description="""a script that generates a pointed follow-up of possible auxiliary couplings"""
import numpy as np
import scipy
from laldetchar.idq import idq
from laldetchar.idq import event
import greedyCI as gci
from optparse import OptionParse... | reedessick/pointy-Poisson | pointed.py | Python | mit | 15,274 | [
"Gaussian"
] | 5cc8a1436c17c093a9f48b21210683f72ca77e709270ad90acefe3fbd51cbb79 |
#!/usr/bin/python
# 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 version.
#
# Ansible is distributed... | joelthompson/ansible-modules-core | cloud/amazon/ec2_elb_lb.py | Python | gpl-3.0 | 48,038 | [
"Dalton"
] | aabf60e6748ecbe149cc43f4ec79fa358b76d832ae236c0801206a0f404bc014 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (c), 2016-2017, Quantum Espresso Foundation and SISSA (Scuola
# Internazionale Superiore di Studi Avanzati). All rights reserved.
# This file is distributed under the terms of the LGPL-2.1 license. See the
# file 'LICENSE' in the root directory of the present ... | QEF/postqe | postqe/xmldata.py | Python | lgpl-2.1 | 4,322 | [
"Quantum ESPRESSO"
] | b2824d9b01d8a2235688a475133dae8c4425b475c79fcd71e3963ab7c8277e05 |
# Mantid Repository : https://github.com/mantidproject/mantid
#
# Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
# NScD Oak Ridge National Laboratory, European Spallation Source
# & Institut Laue - Langevin
# SPDX - License - Identifier: GPL - 3.0 +
#pylint: disable=no-init,invalid-name
"""
Sys... | mganeva/mantid | Testing/SystemTests/tests/analysis/TOPAZPeakFinding.py | Python | gpl-3.0 | 5,791 | [
"CRYSTAL"
] | 48410a9f5e5ec14b185a425eecc835e505910ba0186f8c973e83e6d03c770b0a |
## Automatically adapted for numpy.oldnumeric Jun 27, 2008 by -c
# $Id$
#
# Copyright (C) 2007 by Greg Landrum
# All rights reserved
#
from __future__ import print_function
from rdkit import Geometry
from rdkit.Chem.Subshape import SubshapeObjects
import math
import numpy
#----------------------------------------... | jandom/rdkit | rdkit/Chem/Subshape/BuilderUtils.py | Python | bsd-3-clause | 11,626 | [
"RDKit"
] | 1ca4bc169f92dafd7a6584512128d7b10b6185b11d426f57327aef2dac940a29 |
"""
PySCF-based Schmidt decomposition for Atom-based fragments
"""
import os
import time
import numpy as np
import scipy.linalg as slg
import h5py
import multiprocessing as mtproc
from pyscf import scf
from frankenstein.pyscf_be.fragpart import PART
from frankenstein.pyscf_be.pysd import (schmidt_decomposition_pyrh... | hongzhouye/frankenstein | pyscf_be/pysd_atom.py | Python | bsd-3-clause | 33,331 | [
"PyMOL",
"PySCF"
] | 7a3a771bd438b6ef271870788bf745883731e64c6c480d944eefc69d576d4acd |
# coding=utf-8
"""A setuptools based setup module.
See:
https://packaging.python.org/en/latest/distributing.html
https://github.com/pypa/sampleproject
"""
# Always prefer setuptools over distutils
from setuptools import setup
# To use a consistent encoding
from codecs import open
from os import path
here = path.abspa... | wadda/gps3 | setup.py | Python | mit | 4,399 | [
"MOE"
] | fa3a3bff465e940f2d1f05871b11b3e8cede0f02022fc75748f0dff5caad8f12 |
#Author : Lewis Mervin lhm30@cam.ac.uk
#Supervisor : Dr. A. Bender
#All rights reserved 2014
#Protein Target Prediction Tool trained on SARs from PubChem (Mined 08/04/14) and ChEMBL18
#Molecular Descriptors : 2048bit Morgan Binary Fingerprints (Rdkit) - ECFP4
#Dependencies : rdkit, sklearn, numpy
#libraries
import pym... | lhm30/PIDGIN | predict_enriched.py | Python | mit | 9,710 | [
"RDKit"
] | db241b5154ccb1451d48211e3050937ce765e6a18516f310cbe4280f2caea333 |
"""
Acceptance tests for Studio related to edit/save peer grading interface.
"""
from ...fixtures.course import XBlockFixtureDesc
from ...pages.studio.import_export import ExportCoursePage
from ...pages.studio.component_editor import ComponentEditorView
from ...pages.studio.overview import CourseOutlinePage
from base_... | beni55/edx-platform | common/test/acceptance/tests/studio/test_studio_with_ora_component.py | Python | agpl-3.0 | 3,360 | [
"VisIt"
] | e80ed7aa67dc89691503754d714716dfaba5111a3b93cb83a687e01ec3247d1f |
##########################################
# File: vtk_.py #
# Copyright Richard Stebbing 2014. #
# Distributed under the MIT License. #
# (See accompany file LICENSE or copy at #
# http://opensource.org/licenses/MIT) #
##########################################
# Imports
... | rstebbing/common | rscommon/vtk_.py | Python | mit | 6,849 | [
"VTK"
] | 57f0c2d922fe4143fc20a137bf02f3b627f7740090a7d53506a1d67a9f140010 |
# Copyright (c) 2001 Autonomous Zone Industries
# This file is licensed under the
# GNU Lesser General Public License v2.1.
# See the file COPYING or visit http://www.gnu.org/ for details.
"""
Util functions we didn't know what else to do with. Clean this up.
"""
__revision__ = "$Id: mojoutil.py,v 1.14 2003/... | zooko/egtp_new | egtp/mojoutil.py | Python | lgpl-2.1 | 22,585 | [
"VisIt"
] | 74edb8773393d137a68067b89caa84e94488ac390db518af438fa16480dc42a8 |
#!/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... | gkc1000/pyscf | pyscf/mcscf/test/test_mc1step.py | Python | apache-2.0 | 11,336 | [
"PySCF"
] | c3c737509152a565e5b7262f8be3c14fe801d86851e85104e0981e9f71b7e539 |
import pdb
import math
import numpy as np
import time
import chainer
import chainer.functions as F
import chainer.links as L
from chainer import cuda
from util import gaussian_logp
class VAE(chainer.Chain):
def __init__(self, dim_in, dim_hidden, dim_latent, num_layers, temperature, num_zsamples=1):
... | ashwindcruz/dgm | iwae_pose/model.py | Python | mit | 4,510 | [
"Gaussian"
] | a653593d4dc5d712723953d3b42ec96b95ddaa66e30dcd515f2be337d537f635 |
"""Various tests for the potentials.
"""
import pytest
import itertools
from pydft.crystal import *
from pydft.potentials import *
def test_sho():
# Test at a single position at the center of the cell.
LC = 1.
R = makeR([1., 0., 0.])
S = [2,2,2]
crystal = Crystal(R, S, LC)
v = 1./2*np.sum... | jerjorg/dft | tests/potentials_tests.py | Python | gpl-3.0 | 737 | [
"CRYSTAL"
] | f627330c749ece9cb14eca5484bba8b46610370b88d668694fb29b49f4cc27e9 |
################################################################################
# Module: test.py
# Description: Test imports and network extraction
# License: GPL3, see full license in LICENSE.txt
# Web: https://github.com/DavidBreuer/CytoSeg
###########################################################################... | DavidBreuer/CytoSeg | CytoSeg/extraction.py | Python | gpl-3.0 | 9,141 | [
"Gaussian"
] | d5d7cface34b8e43555b2c8c250cc1f9b516a96b048192742835e6bda6514d51 |
"""Factor Analysis.
A latent linear variable model, similar to ProbabilisticPCA.
This implementation is based on David Barber's Book,
Bayesian Reasoning and Machine Learning,
http://www.cs.ucl.ac.uk/staff/d.barber/brml,
Algorithm 21.1
"""
# Author: Christian Osendorfer <osendorf@gmail.com>
# Alexandre Gramfor... | seckcoder/lang-learn | python/sklearn/sklearn/decomposition/factor_analysis.py | Python | unlicense | 7,588 | [
"Gaussian"
] | 4fadd2edbb0ba83b7a9b674d65b37155781751468bfadb603d9696807303c295 |
import os
import cv2
import math
import pdb
import pickle
import numpy as np
import glob as glob
import matplotlib.pyplot as plt
from scipy.sparse import csr_matrix
from scipy.io import loadmat,savemat
from scipy.sparse.csgraph import connected_components
# from utilities.inspectAdj import knn_graph
from sklearn.prepr... | ChengeLi/VehicleTracking | trjcluster_func_SBS.py | Python | mit | 24,027 | [
"Gaussian"
] | f0cdff505d06c7391bc52fae8db9bf8a7c654abd4db4da7d7e42ba47c4454cb6 |
"""Translation of the BioNetGen example Simple_EGFR_model from the BNG wiki.
http://bionetgen.org/index.php/Simple_EGFR_model
"""
from pysb import *
Model()
# Concentrations in number per cell
Parameter('EGF_0', 1.2e6)
Parameter('EGFR_0', 1.8e5)
Parameter('Grb2_0', 1.5e5)
Parameter('Sos_0', 6.2e... | d-fan/pysb | pysb/examples/simple_egfr.py | Python | bsd-2-clause | 3,956 | [
"Avogadro"
] | 740dc5080b2f6f8fdb8d1e9cebb16a59e632e7ea8bec8f6ec30c44f680cf3f99 |
#!/usr/bin/env python
traindat = '../data/fm_train_real.dat'
testdat = '../data/fm_test_real.dat'
parameter_list=[[traindat,testdat,1.9],[traindat,testdat,1.7]]
def kernel_io (train_fname=traindat,test_fname=testdat,width=1.9):
from shogun import RealFeatures, GaussianKernel, CSVFile
from tempfile import NamedTempo... | MikeLing/shogun | examples/undocumented/python/kernel_io.py | Python | gpl-3.0 | 930 | [
"Gaussian"
] | 7201f6ddf53448b9043a6ac8a407162975454c190d92448148bc43bb7c7a6757 |
# -*- coding: utf-8 -*-
#
# Copyright (C) 2010 Brian Meeker
# All rights reserved.
#
# This software is licensed as described in the file COPYING, which
# you should have received as part of this distribution. The terms
# are also available at http://trac.edgewall.org/wiki/TracLicense.
#
# This software consists of vol... | exocad/exotrac | trac/ticket/batch.py | Python | bsd-3-clause | 9,027 | [
"Brian"
] | d877e7403b6ab561c9b61ba755bf93d6839a5c335461602d691170b9c5456e29 |
__author__ = 'H'
import os
import random
from .CGTArrangeHelper import ArrangeFunction
from .IOparse import search as findfirstraw
import bpy
import string
import types as typemod
def format_filename(s):
valid_chars = "-_.() %s%s" % (string.ascii_letters, string.digits)
filename = ''.join(c for c in s if c i... | Chasvortex/caffe-gui-tool | IOloadprototxt.py | Python | unlicense | 19,282 | [
"Gaussian"
] | 4ecb78ab79c09dd10dd53c9ffc25f50bc0bf1e1df10cd92f7ea764329ca437b0 |
"""
Courseware page.
"""
import re
from bok_choy.page_object import PageObject, unguarded
from bok_choy.promise import EmptyPromise
from selenium.webdriver.common.action_chains import ActionChains
from common.test.acceptance.pages.lms.bookmarks import BookmarksPage
from common.test.acceptance.pages.lms.course_page i... | fintech-circle/edx-platform | common/test/acceptance/pages/lms/courseware.py | Python | agpl-3.0 | 22,668 | [
"VisIt"
] | 43e014677527495dc050b1f9c5733c8f13906f71fda99d64c8152439fb6a96c3 |
# -*- coding: utf-8 -*-
import numpy as np
import kernel_functions as kf
class SVC:
def __init__(self, C=1e0, kernel='linear', tol=1e-3, max_iter=1000,
gamma=1e0, degree=3, coef0=0):
self._EPS = 1e-5
self._TAU = 1e-12
self._cache = {}
self.tol = tol
self.... | sfujiwara/mdsvm | mdsvm/csvc.py | Python | mit | 6,682 | [
"Gaussian"
] | bfb682d38bc4b7255d6e697d3dbf9f283ff86fae27e3415294949e5dead21b28 |
# 2013.05.22 08:35:25 UTC
#Embedded file name: /usr/lib/enigma2/python/Plugins/Extensions/IniAirPlayer/plugin.py
import os
from Plugins.Plugin import PluginDescriptor
from Screens.Screen import Screen
from Components.ConfigList import ConfigListScreen
from Components.ActionMap import ActionMap
from Components.Sources.S... | popazerty/e2-gui | lib/python/Plugins/Extensions/IniAirPlayer/plugin.py | Python | gpl-2.0 | 16,696 | [
"VisIt"
] | 381b12d93fd2de95d46f9079de4e0d614b1d775aa358f5c2f022827567e15ae7 |
# Copyright 2013 by Kamil Koziara. 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.
"""
I/O operations for Enrichment.
"""
from Bio._py3k import range
impor... | arkatebi/SwissProt-stats | Ontology/IO/EnrichmentIO.py | Python | gpl-3.0 | 2,982 | [
"Biopython"
] | a6510903a29aef6943ae4a8b5eb2a0a0c4f48f26b27ef491c1aafe8316d790b9 |
#!/usr/bin/env python
# File created on 09 Feb 2010
from __future__ import division
__author__ = "Greg Caporaso"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Greg Caporaso", "Jai Ram Rideout", "Jose Antonio Navas Molina"]
__license__ = "GPL"
__version__ = "1.9.1-dev"
__maintainer__ = "Greg Capor... | josenavas/qiime | scripts/parallel_assign_taxonomy_blast.py | Python | gpl-2.0 | 5,211 | [
"BLAST"
] | ded483e82e54c8b8eb13a262c7106f67b0e4ad3912174bac489c829cdadf2d77 |
import numpy
import numbers
from mpi4py import MPI
from pmesh.pm import RealField, ComplexField
from nbodykit.meshtools import SlabIterator
from nbodykit.utils import GatherArray, ScatterArray
from nbodykit.mpirng import MPIRandomState
import mpsort
def gaussian_complex_fields(pm, linear_power, seed,
unit... | nickhand/nbodykit | nbodykit/mockmaker.py | Python | gpl-3.0 | 12,289 | [
"Gaussian"
] | 925cfc8bcfeffd6bb7ed44db6de4015b5f585af45f1f1e526d36ee6bca74e96b |
import datetime
import logging
from django.conf import settings
from django.core.urlresolvers import reverse
from django.http import HttpResponse
from django.http import HttpResponseNotFound
from django.template.loader import render_to_string
from django.utils import simplejson as json
from django.utils.translation im... | lizardsystem/lizard-neerslagradar | lizard_neerslagradar/views.py | Python | gpl-3.0 | 9,417 | [
"NetCDF"
] | 5771d394bb21ebb085674ab3d2dee1ca2bd0a999bc962369cb0d6463a5c73f1d |
#!/usr/bin/env python
#
# $File: statStructure.py $
#
# This file is part of simuPOP, a forward-time population genetics
# simulation environment. Please visit http://simupop.sourceforge.net
# for details.
#
# Copyright (C) 2004 - 2010 Bo Peng (bpeng@mdanderson.org)
#
# This program is free software: you can redistrib... | BoPeng/simuPOP | docs/statStructure.py | Python | gpl-2.0 | 1,757 | [
"VisIt"
] | 743ff68c56db2fd358379798bc1b1c4b73c02889a1937638433a655144a6da88 |
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