text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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"""
Implementation of Regression on Order Statistics for imputing left-
censored (non-detect data)
Method described in *Nondetects and Data Analysis* by Dennis R.
Helsel (John Wiley, 2005) to estimate the left-censored (non-detect)
values of a dataset.
Author: Paul M. Hobson
Company: Geosyntec Consultants (Portland, ... | yl565/statsmodels | statsmodels/imputation/ros.py | Python | bsd-3-clause | 19,098 | [
"Gaussian"
] | a5a6d6f2f1bd3b5b8448e1e30f5ebc4a1425870a5148a32b74bceb3ac933eb0d |
from __future__ import (absolute_import, division, print_function)
import unittest
from mantid.simpleapi import mtd
from mantid.simpleapi import Abins, DeleteWorkspace
from AbinsModules import AbinsParameters, AbinsTestHelpers
try:
from pathos.multiprocessing import ProcessingPool
PATHOS_FOUND = True
except I... | ScreamingUdder/mantid | Framework/PythonInterface/test/python/plugins/algorithms/AbinsAdvancedParametersTest.py | Python | gpl-3.0 | 12,086 | [
"CRYSTAL"
] | 74f3781a8155d25c7d8ee9fa050f60b37937d007bb833af0ecf7a1cdc3acd9c7 |
#!/bin/env python
"""Create and put 'ReplicateAndRegister' request."""
__RCSID__ = "$Id$"
import os
from DIRAC.Core.Base import Script
from DIRAC import gLogger
import DIRAC
Script.setUsageMessage( '\n'.join( [ __doc__,
'Usage:',
' %s [option|cfg... | fstagni/DIRAC | DataManagementSystem/scripts/dirac-dms-replicate-and-register-request.py | Python | gpl-3.0 | 4,496 | [
"DIRAC"
] | 521d952a76e95deaf29e22990a1f86634cbf9abd3f30e101b6873400bf6408b7 |
"""Represent a Sequence Feature holding info about a part of a sequence.
This is heavily modeled after the Biocorba SeqFeature objects, and
may be pretty biased towards GenBank stuff since I'm writing it
for the GenBank parser output...
What's here:
Base class to hold a Feature.
----------------------------
classes:... | NirBenTalLab/proorigami-cde-package | cde-root/usr/lib64/python2.4/site-packages/Bio/SeqFeature.py | Python | mit | 25,126 | [
"Biopython"
] | 5c0b12f8a9aaf390db37e6eaa005ec844a06a55143e3111aa6d5910348cbcf41 |
#A* -------------------------------------------------------------------
#B* This file contains source code for the PyMOL computer program
#C* copyright 1998-2000 by Warren Lyford Delano of DeLano Scientific.
#D* -------------------------------------------------------------------
#E* It is unlawful to modify or remove ... | gratefulfrog/lib | python/chempy/cex.py | Python | gpl-2.0 | 17,584 | [
"PyMOL"
] | 24b3c6bb9fd2938565940181073143c89c53d60aebf825f99a2c001a0ea10e88 |
from __future__ import print_function
import sys
sys.path.insert(1, "../../../../")
import random
import os
import math
import numpy as np
import h2o
import time
from builtins import range
from tests import pyunit_utils
from h2o.estimators.glm import H2OGeneralizedLinearEstimator
from h2o.grid.grid_search import H... | YzPaul3/h2o-3 | h2o-py/tests/testdir_dynamic_tests/testdir_algos/glm/pyunit_glm_binomial_large.py | Python | apache-2.0 | 114,537 | [
"Gaussian"
] | 9b77ae9815265ea73644dc1d534bb96ac36fc849ce4b0987c95d51af029eddea |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import os
import unittest
import warnings
import numpy as np
from pymatgen.command_line.bader_caller import (
BaderAnalysis,
bader_analysis_from_path,
which,
)
from pymatgen.util.testing import PymatgenTest
@un... | materialsproject/pymatgen | pymatgen/command_line/tests/test_bader_caller.py | Python | mit | 5,344 | [
"pymatgen"
] | dd2c887e63cdd72edef58b00f19e31b3931f58008a59c14878964237fdb4ca9d |
# -*- coding: utf-8 -*-
# Copyright 2010 Dirk Holtwick, holtwick.it
#
# 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 ... | redclov3r/xhtml2pdf | xhtml2pdf/parser.py | Python | apache-2.0 | 24,459 | [
"VisIt"
] | 97a7f09e51e23122751404dfdc3cabdf6d2b89fcfcc6903c433aa35fedb1b981 |
""" Python test discovery, setup and run of test functions. """
import re
import fnmatch
import functools
import py
import inspect
import sys
import pytest
from _pytest.mark import MarkDecorator, MarkerError
from py._code.code import TerminalRepr
try:
import enum
except ImportError: # pragma: no cover
# Only ... | pelme/pytest | _pytest/python.py | Python | mit | 83,887 | [
"VisIt"
] | 2800d4077c880e8f4d456c1d2532e106f010be26f612ecbf7f603977969b1974 |
import cairocffi as cairo
import numpy as np
from subprocess import call
import os
import math
import sys
sys.path.append('../')
import deepnuc.dubiotools as dbt
#import pygtk
#pygtk.require('2.0')
#import gtk
#import gtk.gdk as gdk
class LogoSheet:
'''
A sheet object for drawing multiple SeqLogos.
... | LarsDu/DeepNucDecomp | duseqlogo/LogoTools.py | Python | gpl-3.0 | 33,504 | [
"Biopython"
] | bde2afbdc0797221fbf9b6720f1e73d177aa6ade7e1c4e2d3e593440dac0d004 |
# Copyright 2016 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... | odejesush/tensorflow | tensorflow/contrib/distributions/python/ops/special_math.py | Python | apache-2.0 | 9,369 | [
"Gaussian"
] | 2f92deb8b0bfe072e6bfdd655b70fad4d570b7356f1a4beb1cc214c8e04e3d63 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2011 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundati... | tiagocardosos/stoq | stoqlib/domain/test/test_taxes.py | Python | gpl-2.0 | 10,023 | [
"VisIt"
] | 9c0cf2c70c81b9fe292bc8ba8abfc18c0c093b263fe9e03752fea48ce4d1567d |
# encoding: UTF-8
#
# Copyright 2012-2013 Alejandro Autalán
#
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License version 3, as published
# by the Free Software Foundation.
#
# This program is distributed in the hope that it will be useful, but
#... | mhcrnl/pygubu | pygubudesigner/previewer.py | Python | gpl-3.0 | 20,513 | [
"FLEUR"
] | 409726a26ee43cc8fd72976c9b23942034750ecb47bff7bbf0f8c0ca66268589 |
#-------------------------------------------------------------------------------
#
# Define classes for (uni/multi)-variate kernel density estimation.
#
# Currently, only Gaussian kernels are implemented.
#
# Written by: Robert Kern
#
# Date: 2004-08-09
#
# Modified: 2005-02-10 by Robert Kern.
# Contr... | e-q/scipy | scipy/stats/kde.py | Python | bsd-3-clause | 21,517 | [
"Gaussian"
] | b0d20990fee456ac57bae528f27942935e8ed0772dc81adcbb5c89c099129825 |
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2015 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier (bgoli@users.sourceforge.net)
Triple-J Group for Molecular Cell Physiology
Stellenbosch University, South Africa.
Permiss... | asttra/pysces | pysces/PyscesJWSParse.py | Python | bsd-3-clause | 31,055 | [
"PySCeS"
] | be97686854406f13b98d365431eaef3be21d86488f224ce1c9c2c018e5697078 |
# -*- coding: utf-8 -*-
"""
This module only contains the forms for a patient for searching filled-in
information, editing notifications settings, and editing personalia.
For managers/secretary/healthprofessionals forms are included for
administration of patients.
:subtitle:`Class definitions:`
"""
from django import ... | acesonl/remotecare | remotecare/apps/healthperson/patient/forms.py | Python | gpl-3.0 | 11,598 | [
"VisIt"
] | 52c228d50a0c219ab43f47558184e0bb693fc38d270246ceaa657a5f2a244e12 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2011 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 published by
# the Fr... | Forage/Gramps | gramps/gen/plug/report/_bibliography.py | Python | gpl-2.0 | 10,547 | [
"Brian"
] | b80aed0f970e967f6c544c564f8434dbad00ec76f1d5fa3bf7e9b16779b62f20 |
# Encoding: utf-8
import sys
import os
import pymatgen.io.nwchem as nwchem
if os.path.isdir(sys.argv[1]):
dirname = sys.argv[1]
dir_list = [directory for directory in os.listdir(dirname)
if os.path.isdir(directory)]
for directory in dir_list:
print("Processing output in " + os... | mbercx/cage | cage/scripts/process_output.py | Python | mit | 1,468 | [
"NWChem",
"pymatgen"
] | 31602607139caefec9d84d3eb108a217d4cce33359ef861a2f369ccc4bd668dc |
#!/usr/bin/env python3
# @package fill_missing
# \brief This script solves the Laplace equation as a method of filling holes in map-plane data.
#
# \details The script is an implementation of the SOR method with Chebyshev
# acceleration for the Laplace equation, as described in 'Numerical Recipes in
# Fortran: the art... | pism/pism | util/fill_missing.py | Python | gpl-3.0 | 17,216 | [
"NetCDF"
] | 28e24f49d6e0c33a668d77b2c89eb7069c4d9fcddf08ddca52f7c66b2cf97a34 |
# !usr/bin/env python2
# -*- coding: utf-8 -*-
#
# Licensed under a 3-clause BSD license.
#
# @Author: Brian Cherinka
# @Date: 2016-10-13 04:13:10
# @Last modified by: Brian Cherinka
# @Last Modified time: 2016-11-29 17:13:34
from __future__ import print_function, division, absolute_import
| bretthandrews/marvin | python/marvin/core/__init__.py | Python | bsd-3-clause | 297 | [
"Brian"
] | 3851d3fd117b28f3940b6dabfe0a16b40015daeeb902d934f3558e664a019bd8 |
# $Id$
#
# Copyright (C) 2007-2008 by Greg Landrum
# All rights reserved
#
from rdkit import RDLogger
logger = RDLogger.logger()
from rdkit import Chem,Geometry
import numpy
from rdkit.Numerics import Alignment
from rdkit.Chem.Subshape import SubshapeObjects
class SubshapeAlignment(object):
transform=None
triang... | rdkit/rdkit-orig | rdkit/Chem/Subshape/SubshapeAligner.py | Python | bsd-3-clause | 13,196 | [
"PyMOL",
"RDKit"
] | c38c1afce488930ea6e7cd9fef3f18dd754eaacd343ff7e077cdc6afa106ed32 |
##
# Copyright 2009-2021 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (F... | akesandgren/easybuild-easyblocks | easybuild/easyblocks/o/openfoam.py | Python | gpl-2.0 | 26,981 | [
"ParaView"
] | ed1a916fe4492a4b888f0e555550084b62cd806ca5f05ffd444b9d8bce2258ba |
""" Contains unit tests of NetworkAgent module
"""
import unittest
import sys
import DIRAC.AccountingSystem.Agent.NetworkAgent as module
from mock.mock import MagicMock
__RCSID__ = "$Id$"
MQURI1 = 'mq.dirac.net::Topics::perfsonar.summary.packet-loss-rate'
MQURI2 = 'mq.dirac.net::Queues::perfsonar.summary.histogram-... | andresailer/DIRAC | AccountingSystem/Agent/test/Test_NetworkAgent.py | Python | gpl-3.0 | 3,827 | [
"DIRAC"
] | a77ed08c2909209e7e2a33216f19c0f77ba827a1247e80f6a124d069eed0fb47 |
"""Conversion functions for weather radar and rainfall data."""
from numpy import isfinite, log, ubyte
from scipy.ndimage import gaussian_filter
from skimage.exposure import equalize_hist, rescale_intensity
def dBZ_to_ubyte(I, dBZ_min=-10.0, dBZ_max=50.0, filter_stddev=3.0):
"""Convert a dBZ field into a 8-bit imag... | sataako/fmio-server | pyoptflow/utils.py | Python | mit | 2,944 | [
"Gaussian"
] | 5b1fd71e7a35eff3baafddcc7cba6b1cca81c57fa2fb437a6703d973e88b1fef |
#!/usr/bin/env python3
import os
import tempfile
import re
import sys
import shutil
import glob
import sh
import obsscripts
# update rook to a newer version
PACKAGE = "rook"
SRCREPO = "rook/rook"
LATEST_OCTOPUS = "v1.2.7"
LATEST_NAUTILUS = "v1.2.7"
OBS = "https://api.opensuse.org"
IBS = "https://api.suse.de"
OOSC ... | krig/obs-scripts | update-rook.py | Python | mit | 4,790 | [
"Octopus"
] | 76d79e3cd75e903d84c760fa938c810a6db5dc6da091427f9787b143ff118c07 |
# Copyright (C) 2004, Thomas Hamelryck (thamelry@binf.ku.dk)
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
import numpy
import sys
__doc__="Vector class, including rotation-related functions."
d... | NirBenTalLab/proorigami-cde-package | cde-root/usr/lib64/python2.4/site-packages/Bio/PDB/Vector.py | Python | mit | 9,064 | [
"Biopython"
] | 28a226018bbda3acf8bb7c00087336a9e63f8ccc6bf7635f632a8d9e5a15bbb5 |
#
# ast_higher_order_visitor.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
# (at your... | kperun/nestml | pynestml/visitors/ast_higher_order_visitor.py | Python | gpl-2.0 | 1,771 | [
"VisIt"
] | b20df6781549a13942e8e08566b10a6c6848358303385089724d7a8cf88d668c |
""" SiteStatus helper
Module that acts as a helper for knowing the status of a site.
It takes care of switching between the CS and the RSS.
The status is kept in the RSSCache object, which is a small wrapper on top of DictCache
"""
import errno
import math
from time import sleep
from datetime import datetime, timedel... | DIRACGrid/DIRAC | src/DIRAC/ResourceStatusSystem/Client/SiteStatus.py | Python | gpl-3.0 | 10,938 | [
"DIRAC"
] | 99f06d7dc0e59b9402f4694885cd6996a17df589f18bb3d5fe7c64443f6aa909 |
# -*- coding: utf-8 -*-
#
# Author: Travis Oliphant 2002-2011 with contributions from
# SciPy Developers 2004-2011
#
import warnings
from collections.abc import Iterable
import ctypes
import numpy as np
from scipy._lib.doccer import (extend_notes_in_docstring,
replace_notes_i... | pizzathief/scipy | scipy/stats/_continuous_distns.py | Python | bsd-3-clause | 268,727 | [
"CRYSTAL",
"Gaussian"
] | 29e4d563b2215c8bdb8c6e520fbe799f9803dfb8fb7afadc8a0e6eed282c0028 |
import os, sys, re, inspect, types, errno, pprint, subprocess, io, shutil, time, copy, unittest
import path_tool
path_tool.activate_module('FactorySystem')
path_tool.activate_module('argparse')
from ParseGetPot import ParseGetPot
from socket import gethostname
#from options import *
from util import *
from RunParalle... | paulthulstrup/moose | python/TestHarness/TestHarness.py | Python | lgpl-2.1 | 45,149 | [
"MOOSE",
"VTK"
] | e23771ce8018f4539e687a326d2f0bee3ffc01e1a9b3ed9094a84654919d7ee3 |
""" TaskQueueDB class is a front-end to the task queues db
"""
__RCSID__ = "ebed3a8 (2012-07-06 20:33:11 +0200) Adri Casajs <adria@ecm.ub.es>"
import types
import random
from DIRAC import gConfig, gLogger, S_OK, S_ERROR
from DIRAC.WorkloadManagementSystem.private.SharesCorrector import SharesCorrector
from DIRAC.Wor... | coberger/DIRAC | WorkloadManagementSystem/DB/TaskQueueDB.py | Python | gpl-3.0 | 53,551 | [
"DIRAC"
] | f57268e72a9e393cb2270e84a61baad2a81bb72d87af6f2a2d6ca3e8572523a4 |
""" ProxyProvider implementation for the proxy generation using local (DIRAC)
CA credentials
"""
import os
import re
import glob
import shutil
import tempfile
import commands
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Core.Security.X509Chain import X509Chain # pylint: disable=import-error
from DIRAC.Con... | chaen/DIRAC | Resources/ProxyProvider/DIRACCAProxyProvider.py | Python | gpl-3.0 | 8,680 | [
"DIRAC"
] | 8b5d92869ebe80dc08858ecf3c2baad699159a9ee849a536a450aac3f2df396b |
# 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/FixPositions.py | Python | gpl-3.0 | 2,020 | [
"ESPResSo"
] | bb8416cc0f2153fddd7ea134396c05ec76a7e9113f794d7a87ce2e21d194d7b7 |
import os
from copy import deepcopy
import sys
import cPickle
import numpy as np
import openbabel
import pybel
sys.path.append('/home/andersx/dev/charmm-dftb-py')
from sccdftb_api import run_charmm, ATOMS
def load_pickle(filename):
f = open(filename,"rb")
p = cPickle.load(f)
f.close()
return(p)
TYPE... | andersx/dftbfit | scripts/print_stats.py | Python | bsd-2-clause | 3,263 | [
"CHARMM",
"Pybel"
] | 82d061d7c81a27750971093eb1d0a01185bd324fbf9c896af40c90f9a3946efa |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# operations.py
#
# Copyright 2016 Bruno S <bruno@oac.unc.edu.ar>
#
# This file is part of ProperImage (https://github.com/toros-astro/ProperImage)
# License: BSD-3-Clause
# Full Text: https://github.com/toros-astro/ProperImage/blob/master/LICENSE.txt
#
"""operations m... | toros-astro/ProperImage | properimage/operations.py | Python | bsd-3-clause | 20,993 | [
"Gaussian"
] | aab16876eff77edf482243f59ead1d44447d8bcc74a686f8b7db5257e05cd146 |
#!/usr/bin/python
#=============================================================================================
# example files for reading in MD simulation files and performing
# statistical analyses according to manuscript "Simple tests for
# validity when sampling from thermodynamic ensembles", Michael
# R. Shirt... | shirtsgroup/checkensemble | examples/analyze-replica.py | Python | gpl-2.0 | 12,048 | [
"CHARMM",
"Desmond",
"Gromacs"
] | 28d63fc9212cb62a38122deb520cfadd4a2c8560fc9585e711bb983718245a1a |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# create a rendering window
renWin = vtk.vtkRenderWindow()
renWin.SetMultiSamples(0)
renWin.SetSize(200, 200)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWin... | hlzz/dotfiles | graphics/VTK-7.0.0/Filters/General/Testing/Python/WarpScalarImage.py | Python | bsd-3-clause | 1,131 | [
"VTK"
] | f057afed909b9046babb23cff99fb4e6cac465effb727a72245b08101677cffc |
from numpy import linalg
from RandomVariables import *
from Hypotheses import HypothesisCollection
class LinearRegression:
""" Use Occam's razor to select among one of several possible hypotheses.
Each hypothesis models target values using
\[ t = y (x, w) + \epsilon, \]
where
\[... | mdbenito/ModelSelection | src/ModelSelection.py | Python | gpl-3.0 | 9,042 | [
"Gaussian"
] | dd9d42e2553a9729f6faf8bfe31745148f8c48ea539ecbaf1ff3d061be2ae619 |
import numpy as np
import pytest
import psi4
from psi4.driver.procrouting.response.scf_products import (TDRSCFEngine,
TDUSCFEngine)
from .utils import compare_arrays, compare_values
def build_RHF_AB_C1_singlet(wfn):
mints = psi4.core.MintsHelper(wfn.basi... | lothian/psi4 | tests/pytests/test_tdscf_products.py | Python | lgpl-3.0 | 24,422 | [
"Psi4"
] | d07a5416ed9b638d8dd26cb4b4fcac4e7bce843cca045c8e065fbf80c0945f64 |
# $HeadURL$
__RCSID__ = "$Id$"
import re
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Core.Utilities.Subprocess import shellCall
from DIRAC.Core.Utilities import List
import DIRAC.Core.Security.File as File
from DIRAC.Core.Security.X509Chain import X509Chain
from DIRAC.Core.Security.BaseSecurity import BaseSecu... | Sbalbp/DIRAC | Core/Security/MyProxy.py | Python | gpl-3.0 | 7,694 | [
"DIRAC"
] | 03881f5932015e8cb71a63eff4313714a1e2abcfc3919f78ee0758cace2d3397 |
import threading
from collections import Counter
from pysamimport import pysam
from util import BadRead
from Queue import Queue
import time, math, sys
class Pileups(object):
def __init__(self,loci,samfiles,filter,chrreg):
self.loci = loci
self.samfiles = samfiles
self.filter = filter
self... | HorvathLab/NGS | attic/readCounts/src/pileups.py | Python | mit | 4,532 | [
"pysam"
] | 2b17f99d7b05719c872f85d26f5fccdfb701d8ee130ea369cc6b1af63d4aacc2 |
"""
This module defines the components for modified nodal analysis. The components
are defined at the bottom of this file.
Copyright 2015--2022 Michael Hayes, UCECE
"""
from __future__ import print_function
from .expr import expr
from .cexpr import ConstantDomainExpression
from .omegaexpr import AngularFourierDomai... | mph-/lcapy | lcapy/mnacpts.py | Python | lgpl-2.1 | 52,253 | [
"CRYSTAL"
] | c30b2539483228a399630644726eb0f0f0458201d6c4e51e3218ff4b34249b66 |
#!/usr/bin/env python
# Python script to iterate through the bowtie2 read mapping log to determine the proportion of aligned reads
import sys
import subprocess
import re
import argparse
import os
## Define functions
# Define a function to deal with the bowtie logs
def bowtie_log(bowlog):
# Establish the list... | neyhartj/GBarleyS | Pipeline_Scripts/read_mapping_stats_parser.py | Python | gpl-3.0 | 5,425 | [
"Bowtie"
] | fd2ae098930b0c96de69c20d667a74917c5fae26f4ca6212d91cce6355a86073 |
#!/usr/local/bin/env python
"""
Test storageinterface.py facility.
The tests are written around the netcdf storage handler for its asserts (its default)
Testing the storage handlers themselves should be left to the test_storage_iodrivers.py file
"""
# ================================================================... | choderalab/openmmtools | openmmtools/tests/test_storage_interface.py | Python | mit | 6,466 | [
"NetCDF",
"OpenMM"
] | 1eb7fd7e54df72315f8df4ad8f28d7c81a344056fffc1b1ad56c8c994d30878e |
# Copyright 2014-2020 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | sunqm/pyscf | pyscf/agf2/__init__.py | Python | apache-2.0 | 6,029 | [
"PySCF"
] | 1b421d2fc38d589c87ecf79201495610b3b493fe47cb6d83b5fc33b0a1b266fd |
#!/usr/bin/env python
import numpy as np
def tran_op(op, tmat):
"""
transform quantum operator from representation A to
another representation B
Args:
op: the matrix form of operator in representation A
tmat: the unitary transform matrix
"""
return np.dot(np.dot(np.co... | quanshengwu/wannier_tools | utility/wannhr_symm/lib/tran.py | Python | gpl-3.0 | 13,790 | [
"VASP",
"WIEN2k"
] | 2a6a510bba3e4c8a8136ca811037f0085dcce624be0325a5c649da9e41b1c67c |
# Copyright 2008-2015 Nokia Networks
# Copyright 2016- Robot Framework Foundation
#
# 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
... | alexandrul-ci/robotframework | src/robot/result/keywordremover.py | Python | apache-2.0 | 5,240 | [
"VisIt"
] | f20a22e550168b134ff1faf4128e5c36ea716431aa142617a78c4cd0898bbd0c |
# /usr/bin/python
# Last Change: Tue Jul 17 11:00 PM 2007 J
"""Module implementing GM, a class which represents Gaussian mixtures.
GM instances can be used to create, sample mixtures. They also provide
different plotting facilities, such as isodensity contour for multi dimensional
models, ellipses of confidence."""
... | jhmadhav/pynopticon | src/em/gauss_mix.py | Python | gpl-3.0 | 26,027 | [
"Gaussian"
] | bf194d7b2985e4bbc0716a7c129a918311e7ecea2a250d1d34fa8152bdde94fe |
from __future__ import absolute_import
from __future__ import print_function
import unittest
import os
import numpy as np
from pymatgen.util.testing import PymatgenTest
from pymatgen.util.coord import in_coord_list, in_coord_list_pbc
from pymatgen.core.surface import generate_all_slabs
from pymatgen.analysis.adsorpti... | matk86/pymatgen | pymatgen/analysis/tests/test_adsorption.py | Python | mit | 5,781 | [
"pymatgen"
] | 6ac5e08a4acca1d3b28db07ad2641c86c37fbd3af3d25b26d2ef39e3c4919504 |
# -*- coding: utf-8 -*-
#
# IRCrypt: Secure Encryption Layer Atop IRC
# =========================================
#
# Copyright (C) 2013-2014
# Lars Kiesow <lkiesow@uos.de>
# Sven Haardiek <sven@haardiek.de>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU... | IRCrypt/ircrypt-weechat | ircrypt.py | Python | gpl-3.0 | 23,201 | [
"VisIt"
] | 48252e61cfea28412c4935f20eead0a40052239fc80493ea5345ca7924535e96 |
"""
Define common steps for instructor dashboard acceptance tests.
"""
# pylint: disable=missing-docstring
# pylint: disable=redefined-outer-name
from __future__ import absolute_import
from lettuce import world, step
from mock import patch
from nose.tools import assert_in # pylint: disable=no-name-in-module
from c... | zadgroup/edx-platform | lms/djangoapps/instructor/features/common.py | Python | agpl-3.0 | 4,621 | [
"VisIt"
] | dc591d92814d2a5b818db76643cf3ff32fb74daed347356038871410f43d9aba |
'''
Demonstrates optimizing the shape parameter for the RBFInterpolant when using
an RBF other than a polyharmonic spline
'''
import numpy as np
import matplotlib.pyplot as plt
from rbf.interpolate import RBFInterpolant
np.random.seed(0)
def frankes_test_function(x):
x1, x2 = x[:, 0], x[:, 1]
term1 = 0.75 * ... | treverhines/RBF | docs/scripts/interpolate.d.py | Python | mit | 2,870 | [
"Gaussian"
] | 30ae533eff2b1a1d6b01e0d0bf8880c70a19b038a839c5172068d31312ee2b7d |
"""Tests for the Amber Electric Data Coordinator."""
from __future__ import annotations
from collections.abc import Generator
from unittest.mock import Mock, patch
from amberelectric import ApiException
from amberelectric.model.channel import Channel, ChannelType
from amberelectric.model.current_interval import Curre... | rohitranjan1991/home-assistant | tests/components/amberelectric/test_coordinator.py | Python | mit | 9,047 | [
"Amber"
] | 933b418e24e3b9ebc8cdc11216c59fadea79146700dacc957c5a9b92251b7223 |
# numkit --- data fitting
# Copyright (c) 2010 Oliver Beckstein <orbeckst@gmail.com>
# Released under the "Modified BSD Licence" (see COPYING).
"""
:mod:`numkit.fitting` --- Fitting data
======================================
The module contains functions to do least square fits of functions of
one variable f(x) to da... | pslacerda/GromacsWrapper | numkit/fitting.py | Python | gpl-3.0 | 10,062 | [
"Gaussian"
] | 44310661ba953ac4bfe9b6d68da12104e3bc89c3e505e16cc0ab14776d93f786 |
"""
RPN - Region Proposal Network
"""
import sonnet as snt
import tensorflow as tf
from sonnet.python.modules.conv import Conv2D
from .rpn_target import RPNTarget
from .rpn_proposal import RPNProposal
from luminoth.utils.losses import smooth_l1_loss
from luminoth.utils.vars import (
get_initializer, layer_summar... | tryolabs/luminoth | luminoth/models/fasterrcnn/rpn.py | Python | bsd-3-clause | 13,279 | [
"Gaussian"
] | c8c231ab033614bc45592e7d9703305de7b70efee42367e7ec3a90c30c33367c |
# Orca
#
# Copyright 2010-2011 Consorcio Fernando de los Rios.
# Author: Juanje Ojeda Croissier <jojeda@emergya.es>
# Author: Javier Hernandez Antunez <jhernandez@emergya.es>
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as publi... | ruibarreira/linuxtrail | usr/lib/python3/dist-packages/orca/backends/json_backend.py | Python | gpl-3.0 | 7,195 | [
"ORCA"
] | 2a8f7ecb53ffb368909a1aa15753eeefe01828cce6a04adc418d436309c91076 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Classes for reading/manipulating/writing VASP ouput files.
"""
import json
import glob
import itertools
import logging
import math
import os
import re
import warnings
from pathlib import Path
import xml.et... | gVallverdu/pymatgen | pymatgen/io/vasp/outputs.py | Python | mit | 204,441 | [
"CRYSTAL",
"VASP",
"VisIt",
"pymatgen"
] | 847238231a248fc5783ba7d9a42aa84f7f9e35edd8e29e6548de0f4ba655b284 |
import os
from .util import OS_NAME
def get_simulated_epw_path():
"""
Returns
-------
None if epw can be anywhere
"""
from oplus import CONF # touchy imports
if OS_NAME == "windows":
return os.path.join(CONF.eplus_base_dir_path, "WeatherData", "%s.epw" % CONF.default_model_name)... | Openergy/oplus | oplus/compatibility/epw.py | Python | mpl-2.0 | 382 | [
"EPW"
] | 7be99966771822e8cec5beaf9e0609d8a8e87cd6de98e4901a5d66cfa6f98df3 |
# python imports
import datetime
# django imports
from django.core.mail import EmailMultiAlternatives
from django.template.loader import render_to_string
from django.template import RequestContext
from django.utils.translation import ugettext as _
# lfs imports
import lfs.core.utils
def send_contact_mail(request, f... | pigletto/lfs-contact | lfs_contact/utils.py | Python | bsd-3-clause | 2,156 | [
"VisIt"
] | 8f869a9862a76db8d993817664845a73598f69f05a894894f6ff7f7d677b1fa0 |
# Orca
#
# Copyright 2004-2008 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... | pvagner/orca | src/orca/scripts/apps/Thunderbird/script.py | Python | lgpl-2.1 | 15,166 | [
"ORCA"
] | a61df4958f36c9d871d34201391a254305c19dd3d803cbb18ed1682ad224b4b9 |
import os
import unittest
import numpy as np
import xarray as xr
import xcube.core.store as xcube_store
from cate.core.ds import DataAccessError
from cate.core.ds import NetworkError
from cate.core.ds import find_data_store
from cate.core.ds import get_data_descriptor
from cate.core.ds import get_ext_chunk_sizes
from... | CCI-Tools/cate-core | tests/core/test_ds.py | Python | mit | 14,649 | [
"NetCDF"
] | 3c051320e14733c14ab572cd6ecaa0a6d57e676c39b74f0c4768bd3ccfe7ee8b |
"""
Tools for the instructor dashboard
"""
import json
import operator
import dateutil
import six
from django.contrib.auth.models import User
from django.http import HttpResponseBadRequest
from django.utils.translation import ugettext as _
from edx_when import api
from opaque_keys.edx.keys import UsageKey
from pytz ... | edx-solutions/edx-platform | lms/djangoapps/instructor/views/tools.py | Python | agpl-3.0 | 7,408 | [
"VisIt"
] | 7714dc2c82ecd0c355aac98e91dd11289e47ee7f8231702e316ab3a28c213469 |
#!/usr/bin/env python
""" Defines the synthetic_image class to add image realism to the idealized sunrise images.
The synthetic_image class defines a number of routines to take the original image and
convolve it with some psf function, add sky noise, rebin to an appropate pixel scale
(based on telescope), scale to a... | ptorrey/sunpy | sunpy__synthetic_image.py | Python | mit | 46,931 | [
"Galaxy",
"Gaussian"
] | 3cbafea6b2437304f167ad81d1f7bf5de66b203e2f47c408abf173fded4740d3 |
from setuptools import setup
import versioneer
commands = versioneer.get_cmdclass()
setup(name="magic-wormhole",
version=versioneer.get_version(),
description="Securely transfer data between computers",
author="Brian Warner",
author_email="warner-magic-wormhole@lothar.com",
license="MI... | shaunstanislaus/magic-wormhole | setup.py | Python | mit | 903 | [
"Brian"
] | 04ab5b13cc972092cec25a7c2d01366dbac935a34e8acfaf71e7fdba7ce773ca |
from __future__ import unicode_literals
from __future__ import absolute_import
from functools import reduce
import logging
from docker.errors import APIError
from .config import get_service_name_from_net, ConfigurationError
from .const import DEFAULT_TIMEOUT, LABEL_PROJECT, LABEL_SERVICE, LABEL_ONE_OFF
from .containe... | feelobot/compose | compose/project.py | Python | apache-2.0 | 12,425 | [
"VisIt"
] | 83392efc9ae10c7f0d11e61b593fb3a9151e7e5f94cd54dc64d3d2ee70ce263d |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2007 Async Open Source
##
## This program is free software; you can redistribute it and/or
## modify it under the terms of the GNU Lesser General Public License
## as published by the Free Software Foundation; either version 2
## of the License, or... | fboender/miniorganizer | src/lib/kiwi/db/stormintegration.py | Python | gpl-3.0 | 4,195 | [
"VisIt"
] | 66e994418ffc47a2303f48a4f0bce2f43c7c3f1e0ea190344cb000d1f703dc4b |
# Copyright 2010-2017, The University of Melbourne
# Copyright 2010-2017, Brian May
#
# This file is part of Karaage.
#
# Karaage 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... | brianmay/karaage | karaage/plugins/kgapplications/templatetags/applications.py | Python | gpl-3.0 | 3,713 | [
"Brian"
] | 1ea8aeff59b38ed3c2dd4599376a456d86980aac041ff7b3e04a436b11ea81f4 |
# Parsing congress.gov/members/
import requests
from lxml import html
from lxml.html import fromstring
import sqlite3
import os
def find(name, path):
return_val = False
files = [f for f in os.listdir('.') if os.path.isfile(f)]
for f in files:
if name in files:
return_val = True
ret... | walke469/spartahack-17 | parsingfinal.py | Python | bsd-2-clause | 3,536 | [
"VisIt"
] | 5c1fadd3d62b44347dd598f96d01e4f766476b99a951a378a5c2445e72af16f6 |
"""
Page objects for interacting with the test site.
"""
import os
import time
from bok_choy.page_object import PageObject
from bok_choy.promise import EmptyPromise
from bok_choy.javascript import js_defined, requirejs, wait_for_js
class SitePage(PageObject):
"""
Base class for all pages in the test site.
... | drptbl/bok-choy | tests/pages.py | Python | apache-2.0 | 9,347 | [
"VisIt"
] | 500881dbb7bec945706a8285a1408db89b65fd6eb8457b09dce96a2363fb56d4 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Mar 28 18:16:14 2017
@author: kasperipalkama
"""
from random import uniform, seed
from math import exp
def initialize(n_input, n_hidden_neuron, n_hidden_layer, n_output):
seed(1)
network = list()
left_bound = -0.5 / n_input # common way t... | kapalk/feedforward-multilayer-perceptron | neural_network/multilayer_perceptron.py | Python | mit | 13,097 | [
"NEURON"
] | f38b4c639528e739c983b8476c57d1c4fd109bd270803771aebc68a18af54752 |
# -*- coding: utf-8 -*-
u"""elegant execution template.
:copyright: Copyright (c) 2015 RadiaSoft LLC. All Rights Reserved.
:license: http://www.apache.org/licenses/LICENSE-2.0.html
"""
from __future__ import absolute_import, division, print_function
from pykern import pkio
from pykern import pkresource
from pykern.pk... | mrakitin/sirepo | sirepo/template/elegant.py | Python | apache-2.0 | 33,800 | [
"Gaussian"
] | da42c96e9be8aee52c2a143516fac86d42371ed612655ed90e62b91653ab1401 |
# -*- coding: utf-8 -*-
"""
functions.py - Miscellaneous functions with no other home
Copyright 2010 Luke Campagnola
Distributed under MIT/X11 license. See license.txt for more infomation.
"""
from __future__ import division
from .python2_3 import asUnicode
from .Qt import QtGui, QtCore, USE_PYSIDE
Colors = {
'b... | jensengrouppsu/rapid | rapid/pyqtgraph/functions.py | Python | mit | 86,211 | [
"Gaussian"
] | ced8f5604059816d07a9b775e528d6deeaab1df5a35095a6e4ab9a3e47dfb586 |
import vtk
def main():
colors = vtk.vtkNamedColors()
# create a rendering window and renderer
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
# create a renderwindowinteractor
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
styl... | lorensen/VTKExamples | src/Python/Visualization/InteractorStyleTrackballCamera.py | Python | apache-2.0 | 1,054 | [
"VTK"
] | 76b9c9efa9ae73aefae9a46e35d1fa2fd573dca640de1b78b933e777e55a7172 |
# Copyright 2016 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... | keras-team/keras | keras/layers/regularization/gaussian_dropout_test.py | Python | apache-2.0 | 1,867 | [
"Gaussian"
] | 8c72ed020f48859b09b3fffb4da6dcccfe985763e77a39595d27c0570eb3eb39 |
# sql/compiler.py
# Copyright (C) 2005-2015 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
"""Base SQL and DDL compiler implementations.
Classes provided include:
:class:`.c... | gdimitris/FleetManagerBackend | virtual_env/lib/python2.7/site-packages/sqlalchemy/sql/compiler.py | Python | mit | 100,568 | [
"VisIt"
] | 06cdbf808b92dd5f0795f45bc7f1e5862f2b13e344dad808c2ed669dc07cfdd6 |
import matplotlib.pyplot as plt
import matplotlib
import pickle
import math
import numpy as np
import os
from astropy.io import fits
import pickle
from astropy.table import Table
import AnniesLasso_2 as tc
import sincinterpol
def log(x):
if x>0:
return math.log10(x)
else:
return -np.inf
def s... | peraktong/Cannon-Experiment | Sinc_interpolation/0629_interpolation_residual.py | Python | mit | 6,215 | [
"VisIt"
] | 937c7a46dc0255b7ce0fdc0268f3cb4a3744d9b3c87c3f9ca62f47c00f5bc9c1 |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-admin-accounting-cli
# Author : Adria Casajus
########################################################################
"""
Command line administrative interface to DIRAC Accounting DataStore Ser... | andresailer/DIRAC | AccountingSystem/scripts/dirac-admin-accounting-cli.py | Python | gpl-3.0 | 806 | [
"DIRAC"
] | 721f05d5b885c1032a6aec6fb92ad412a12f71dbc6704ac4b968995d877f5bea |
# Copyright (c) Charl P. Botha, TU Delft.
# All rights reserved.
# See COPYRIGHT for details.
import config
from install_package import InstallPackage
import os
import shutil
import utils
BASENAME = "gdcm"
GIT_REPO = "git://git.code.sf.net/p/gdcm/gdcm "
GIT_TAG = "v2.0.17"
dependencies = ['SWIG', 'VTK'... | nagyistoce/devide.johannes | install_packages/ip_gdcm.py | Python | bsd-3-clause | 4,758 | [
"VTK"
] | 276864cb0b5690fc82aac6547d0c24871b8d9a40a620ee915726d8e1e06ca00e |
"""
Modified version of RMSD distance metric that does the following:
1) Returns the RMSD, rotation matrices, and aligned conformations
2) Permutes selected atomic indices.
3) Perform the alignment again.
Sniffy
"""
from msmbuilder.metrics import AbstractDistanceMetric
from msmbuilder.metrics import RMSD
import _lpr... | mpharrigan/msmbuilder | Extras/LPRMSD/lprmsd.py | Python | gpl-2.0 | 13,612 | [
"MDTraj"
] | 98f451a979c1936d4ca4af9fb6c3f32fc0b5743a120378429c771da28b901bfc |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Convert a FAME input file to a MEASURE input file.
"""
import argparse
import numpy
import os.path
from chempy.molecule import Molecule
from chempy.species import Species, TransitionState
from chempy.reaction import Reaction
from chempy.species import LennardJones
fr... | jwallen/MEASURE | convertFAME.py | Python | mit | 9,153 | [
"ChemPy"
] | 04111e318c53e1bb930434cb2c5fadecb01927124fdf36bee671c55e81765b21 |
from __future__ import division
import time
import numpy as np
import itertools
import scipy.stats as spstats
from sklearn.base import BaseEstimator
LOSS = {"hinge": 1, "l1": 2, "l2": 3, "logit": 4, "eps_intensive": 5}
TASK = {"classification": 1, "regression": 2}
KERNEL = {"gaussian": 1}
class GOGP_SI:
def __in... | khanhndk/GoGP | gogp-py/gogp_si.py | Python | gpl-3.0 | 16,932 | [
"Gaussian"
] | a42d39a22252ff5510c969e89e2224ebd82ad9a1cd56929aba250e5d3509193d |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Author: Vincent Dubourg <vincent.dubourg@gmail.com>
# (mostly translation, see implementation details)
# Licence: BSD 3 clause
"""
The :mod:`sklearn.gaussian_process` module implements scalar Gaussian Process
based predictions.
"""
from .gaussian_process import Gau... | depet/scikit-learn | sklearn/gaussian_process/__init__.py | Python | bsd-3-clause | 472 | [
"Gaussian"
] | 9b829e5f170519ca7255e47ad8a5a825a51b7364b5ca5447d0c6ffbfb873d6b5 |
import numpy as np
import histomicstk.utils as htk_utils
def vesselness(im_input, sigma):
"""
Calculates vesselness measure for grayscale image `im_input` at scale `sigma`.
Also returns eigenvalues and vectors used for vessel salience filters.
Parameters
----------
im_input : array_like
... | DigitalSlideArchive/HistomicsTK | histomicstk/filters/shape/vesselness.py | Python | apache-2.0 | 1,523 | [
"Gaussian"
] | 817879a4d41b345ddd28812faf0512ed6e3b057f918710ba776c8248a0a63503 |
# (C) British Crown Copyright 2010 - 2015, Met Office
#
# This file is part of Iris.
#
# Iris 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 3 of the License, or
# (at your option) any l... | Jozhogg/iris | lib/iris/tests/stock.py | Python | lgpl-3.0 | 22,502 | [
"NetCDF"
] | 03172ad0aa8f928376decab69c48db609e9ca49c91b4e9b3958319c7401deaf0 |
#! test QC_JSON Schema with ghost atoms
import numpy as np
import psi4
import json
# Generate JSON data
json_data = {
"schema_name": "qc_schema_input",
"schema_version": 1,
"molecule": {
"geometry": [
0.0,
0.0,
-5.0,
0.0,
0.0,
... | CDSherrill/psi4 | tests/json/schema-1-ghost/input.py | Python | lgpl-3.0 | 1,563 | [
"Psi4"
] | 3cae88b62aa032949b389730b702744e475b95fc3c51fddec0e87c2cf345f285 |
#!/usr/bin/env python
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Makes sure files have the right permissions.
Some developers have broken SCM configurations that flip the executable
permission... | endlessm/chromium-browser | tools/checkperms/checkperms.py | Python | bsd-3-clause | 13,204 | [
"xTB"
] | f9d6d3d7ee6ca4103e6bd8a0cea55e6fb95f75af611ad1d8aab7b748de90dea0 |
"""
################################################################################
#
# SOAPpy - Cayce Ullman (cayce@actzero.com)
# Brian Matthews (blm@actzero.com)
# Gregory Warnes (Gregory.R.Warnes@Pfizer.com)
# Christopher Blunck (blunck@gst.com)
#
##########################... | cmsdaq/hltd | lib/SOAPpy-py3-0.52.24/src/SOAPpy/Client.py | Python | lgpl-3.0 | 23,216 | [
"Brian"
] | 8fbf0cfea68d0ced4761ea7da7d36086d0d5465f27aa4d14aec7f40b50b21f93 |
# -*- coding: utf-8 -*-
import numpy as np
from ..constants import periodic_table, scattering_lengths
class Atom(object):
r"""Class for adding atoms to the Material class.
Parameters
----------
ion : string
The name of the Atom, or ion if necessary
pos : list(3)
The position of ... | granrothge/neutronpy | neutronpy/crystal/atom.py | Python | mit | 2,433 | [
"CRYSTAL",
"MCell"
] | 7803882183e9593714f2a9473a7ebde9cec1008735b0fc1039dc7bb303883aa9 |
#ImportModules
import ShareYourSystem as SYS
import operator
#Definition of a brian structure
MyPopulater=SYS.PopulaterClass().populate(
**{
'PopulatingUnitsInt':500
}
)
#Definition the AttestedStr
SYS._attest(
[
'MyPopulater is '+SYS._str(
MyPopulater,
**{
'RepresentingBaseKeyStrsList... | Ledoux/ShareYourSystem | Pythonlogy/draft/Simulaters/Populater/01_ExampleCell.py | Python | mit | 393 | [
"Brian"
] | 55795209f8dc0e6ba0cd8897328f07a0ff8ee95bff71abe3eafbfb678d8bd73c |
"""
This is a random gaussian noise generator module type 3.
This module generates the signal with oversampling=1, then oversamples the signal
to the wanted representation sampling frequency and finally it upconverts the signals, |br|
The generator is able to generate N random signals with a random frequency position ... | JacekPierzchlewski/RxCS | rxcs/sig/gaussNoise3.py | Python | bsd-2-clause | 8,416 | [
"Gaussian"
] | 1db682299f0a0c1db986b3aea9f28dce802aa2849a1645fddafd679a120634e3 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements a FloatWithUnit, which is a subclass of float. It
also defines supported units for some commonly used units for energy, length,
temperature, time and charge. FloatWithUnit also support conversion to ... | materialsproject/pymatgen | pymatgen/core/units.py | Python | mit | 27,123 | [
"pymatgen"
] | ca6cc31a2d2b9a5bc8c44c17e2250efbfcde153212e19c77ea727a942bb4b4f8 |
from math import floor
from world import World
import Queue
import SocketServer
import datetime
import random
import re
import requests
import sqlite3
import sys
import threading
import time
import traceback
DEFAULT_HOST = '0.0.0.0'
DEFAULT_PORT = 4080
DB_PATH = 'craft.db'
LOG_PATH = 'log.txt'
CHUNK_SIZE = 32
BUFFER... | fogleman/Craft | server.py | Python | mit | 24,727 | [
"VisIt"
] | ffb1928cfb81222ac346b4674353123c8bc402939078eab65f9d7ac2d7ec4e06 |
# Copyright 2015 - 2018 Altuğ Karakurt & Sertan Şentürk
#
# This file is part of tomato: https://github.com/sertansenturk/tomato/
#
# tomato 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 (FSF), either ... | sertansenturk/tomato | src/tomato/audio/makamtonic/knnclassifier.py | Python | agpl-3.0 | 18,831 | [
"Gaussian"
] | 4c2e0c4a84112f84a3046b2c3283047c6cfbe787fe8f452d3ee4d32f570b2471 |
import pint
__all__ = ['ureg', 'Quantity', 'Q_', 'ABOGADROS_NUMBER', 'N_A', 'hc']
ureg = pint.UnitRegistry()
Quantity = ureg.Quantity
Q_ = Quantity
# Avogadro constant
# AVOGADROS_NUMBER = 6.022140857e+23
AVOGADROS_NUMBER = (1.0 * ureg.avogadro_number).to('dimensionless').magnitude
N_A = AVOGADROS_NUMBER
# (plank ... | ecell/bioimaging | scopyon/constants.py | Python | bsd-3-clause | 514 | [
"Avogadro"
] | 42a4ed490edce95e650b1d1ecb3532e56ab32c1c5d299a587f963588e22acf41 |
"""Bayesian Gaussian Mixture Models and
Dirichlet Process Gaussian Mixture Models"""
from __future__ import print_function
# Author: Alexandre Passos (alexandre.tp@gmail.com)
# Bertrand Thirion <bertrand.thirion@inria.fr>
#
# Based on mixture.py by:
# Ron Weiss <ronweiss@gmail.com>
# Fabian Ped... | 0asa/scikit-learn | sklearn/mixture/dpgmm.py | Python | bsd-3-clause | 30,707 | [
"Gaussian"
] | de86f905bc170ba6ba0a71f5803b4e7c40026c2e84619c4371a5c30970b67bc9 |
# (C) British Crown Copyright 2015 - 2017, Met Office
#
# This file is part of Iris.
#
# Iris 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 3 of the License, or
# (at your option) any l... | LukeC92/iris | lib/iris/tests/unit/aux_factory/test_AuxCoordFactory.py | Python | lgpl-3.0 | 7,082 | [
"NetCDF"
] | 4df426a5168b9561b29825a1cb796fa5b63ddcf1b906f46a1b5e9d3fa456192c |
# -*- coding: utf-8 -*-
"""Test sequences for graphiness.
"""
# Copyright (C) 2004-2015 by
# Aric Hagberg <hagberg@lanl.gov>
# Dan Schult <dschult@colgate.edu>
# Pieter Swart <swart@lanl.gov>
# All rights reserved.
# BSD license.
from collections import defaultdict
import heapq
import networkx as nx
_... | jcurbelo/networkx | networkx/algorithms/graphical.py | Python | bsd-3-clause | 12,997 | [
"Brian"
] | 0c54bc2a3fe009a6a93f8e9990e632bab6ccb0ffb9b96b19b5c177324e915275 |
# -*- Mode: Python; coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2006 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU Lesser General Public License as published by
## the F... | andrebellafronte/stoq | stoqlib/lib/cookie.py | Python | gpl-2.0 | 2,633 | [
"VisIt"
] | 3ca7e31e18cd3fbb219bf7a11ef3639330efde0d7bbad9361d550e1a683b10ed |
import gen_utils
from module_base import ModuleBase
from module_mixins import ScriptedConfigModuleMixin
import module_utils
import vtk
EMODES = {
1:'Point seeded regions',
2:'Cell seeded regions',
3:'Specified regions',
4:'Largest region',
5:'All regions',
6:'Closest po... | nagyistoce/devide | modules/filters/polyDataConnect.py | Python | bsd-3-clause | 4,397 | [
"VTK"
] | 0432087a3be184a133ebd9e743e7f9eb316e37c372970a2a5000ff844f0c0c7f |
#!/usr/bin/env python
#os imports
import os
from sys import stdin,argv
import sys
from optparse import OptionParser
#Title:
#script to reformt fasta ID names.
#############################################################################
#functions
def reformat_fasta_name(filename, databse, out):
"thi... | widdowquinn/THAPBI | Phyt_ITS_identifying_pipeline/Python_ITS_scripts/completely_rename_ID.py | Python | mit | 2,265 | [
"Biopython"
] | 9a77c7208f2cc838501ea4a64673df5046e1ecdb4c3d417b08c46a39a98d27ff |
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