text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
value | license stringclasses 15
values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
import numpy as np
import matplotlib.pyplot as plt
from util import utils
from util.readDict import readDict
from scipy import pi
from mpltools import style
import figureHeader
# try new plotting style for pipeline paper
#style.use('ggplot')
####LOAD COROT18 LIGHTCURVE######
param = readDict()
param.read_from_file('c... | bmazin/ARCONS-pipeline | examples/Pal2012-corot/corot18blightcurve.py | Python | gpl-2.0 | 4,433 | [
"Gaussian"
] | f75e2df18e955b90ec3a6f0b27016553e66672fa23ef5a7f734569e6dd8f9ab5 |
#!/usr/bin/python2
# -*- Mode: Python; py-indent-offset: 8 -*-
# (C) Copyright Zack Rusin 2005
# All Rights Reserved.
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation files (the "Software"),
# to deal in the Software without restriction, ... | zcbenz/cefode-chromium | third_party/mesa/MesaLib/src/mapi/glapi/gen/gl_enums.py | Python | bsd-3-clause | 6,712 | [
"Brian"
] | f3c1f97b64e4f24dd33376ad9481420f6308ab1bb106e6eda470a726c61bec89 |
# -*- coding: utf-8 -*-
# Copyright (c) 2015, Alex Grigorevskiy
# Licensed under the BSD 3-clause license (see LICENSE.txt)
"""
The standard periodic kernel which mentioned in:
[1] Gaussian Processes for Machine Learning, C. E. Rasmussen, C. K. I. Williams.
The MIT Press, 2005.
[2] Introduction to Gaussian processes... | avehtari/GPy | GPy/kern/src/standard_periodic.py | Python | bsd-3-clause | 6,829 | [
"Gaussian"
] | 94b6426eb5d8ff70da6e24cccf417beb5d07c9209d57d2bf15f9e78b1caa7a34 |
#!/usr/bin/python
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --nodes=1
#SBATCH --mem=16384
import sys
import os
from ast import literal_eval
from utils import *
from utils.configuration import *
from utils.seq_utils import *
import tempfile
from pprint import pprint as pp
#=========#
# Comm... | AndersenLab/pyPipeline | align.py | Python | mit | 7,414 | [
"BWA"
] | a1112ae5c1096aed967dc71b67b17067cb6aeb0f634793f688ef997a3006097b |
from reactionroute import *
mol = pybel.readstring('smi', '[C-]#[O+]')
mol.addh()
mat = molToMat(mol.OBMol)
print(mat)
mol2 = matToMol(mat)
for atom in ob.OBMolAtomIter(mol2):
print('formal charge of atom {} is {}'.format(atom.GetIdx(), atom.GetFormalCharge()))
print(molToMat(mol2)) | sxhexe/reaction-route-search | reactionroute_web/reaction/search/molToMatTest.py | Python | mit | 295 | [
"Pybel"
] | 4eafae53cc78627c32b4454c58ee2ee7c0193c5709a57255dc9d028c435f1d4a |
# 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 t... | BackupTheBerlios/espressopp | src/integrator/LatticeBoltzmann.py | Python | gpl-3.0 | 2,519 | [
"ESPResSo"
] | fce81c9f1dc69b101669de3717d27cb276e69ed32bd3ef98e56409feacd75802 |
"""
This module contains a single class ForceField used to output a GROMACS .ff forcefield.
"""
import os
import shutil
import functools
from .util import dir_up
from .parsers import ITP
class ForceField:
"""
Class used to output a GROMACS .ff forcefield
"""
def __init__(self, name):
"""
... | jag1g13/pycgtool | pycgtool/forcefield.py | Python | gpl-3.0 | 6,589 | [
"Gromacs"
] | 41165de702cc7c1ce4d554c90f4b7fa35efec50946a9bb88b89cfc0fe119b6a0 |
#!/usr/bin/env python
"""
The MIT License (MIT)
Copyright (c) 2016-2017 Sven Koitka (sven.koitka@fh-dortmund.de)
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including wit... | razorx89/caffe-wrn-generator | generate.py | Python | mit | 14,056 | [
"Gaussian"
] | 6c9d60460d1392ab41a4e1a23dc7f6facef9f5f47011129d8c4fa9671644e872 |
#!/usr/bin/env python
# -*- coding:utf-8 mode:python; tab-width:4; indent-tabs-mode:nil; py-indent-offset:4 -*-
##
"""
test_nwchem
~~~~~~~~~~~~~~
Test NWChem specific functionality that is not handled elsewhere.
"""
import sys
import unittest
import geoprep
from adapters import nwchem
from sharedutilities... | mattbernst/polyhartree | tests/test_nwchem.py | Python | gpl-3.0 | 5,018 | [
"NWChem"
] | dc3180f9cfd04847cf9def802b0cd599913cbc53ef3ee43021e2d6aa86fcf02f |
__author__ = 'dalton'
class Item():
"""The base class for all items"""
def __init__(self, name, description, value):
self.name = name
self.description = description
self.value = value
def __str__(self):
return "{}\n====={}\nValue: {}\n".format(self.name, self.description,... | dalrrard/text-adventure-tut | adventuretutorial/items.py | Python | mit | 1,373 | [
"Dalton"
] | 9fc6ca02f9505183f79a6c963d1c525af304e5cf9aa8bc12a271f62058c2a936 |
from nose import SkipTest
from nose.tools import assert_less_equal, assert_almost_equal, assert_equal
from numpy.ma.testutils import assert_close
from numpy.testing.utils import assert_allclose
from kernel_exp_family.estimators.finite.develop.gaussian import compute_b_memory, \
compute_C_memory, _objective_sym_com... | karlnapf/kernel_exp_family | tests/estimators/finite/test_gaussian.py | Python | bsd-3-clause | 13,889 | [
"Gaussian"
] | d45e3cf1dec5a367d3b04860030947d6cff1370aa936a4bfd3a3e5dc69f89142 |
"""
JobReport class encapsulates various methods of the job status reporting blah, blah, blah...
"""
__RCSID__ = "$Id$"
from DIRAC import S_OK, S_ERROR, Time
from DIRAC.Core.Utilities import DEncode
from DIRAC.Core.DISET.RPCClient import RPCClient
from DIRAC.RequestManagementSystem.Client.Operation import Operatio... | avedaee/DIRAC | WorkloadManagementSystem/Client/JobReport.py | Python | gpl-3.0 | 5,874 | [
"DIRAC"
] | a68af01b1a6da6f427d58c1e973d19eb0ebe763f16873178e72cd652102cf6d4 |
"""
EVLANG
A mini-language for online coding of Evennia
Evennia contribution - Griatch 2012
WARNING:
Restricted python execution is a tricky art, and this module -is-
partly based on blacklisting techniques, which might be vulnerable to
new venues of attack opening up in the future (or existing ones we've
misse... | TaliesinSkye/evennia | contrib/evlang/evlang.py | Python | bsd-3-clause | 34,240 | [
"VisIt"
] | ba0d306133e16e8fc2db0520087c5e4dfe5bdb78b94c7e321a7935f3746adf16 |
# $Id: loopclosure.py 749 2007-07-17 02:31:29Z lidaobing@gmail.com $
# pylint: disable-msg=E1101
# pylint: disable-msg=W0201
import sys
import os
import os.path
import bisect
import heapq
import pprint
import time
import random
import tempfile
import shutil
import cPickle
import logging
from cStringIO import StringIO
t... | lidaobing/itcc | itcc/ccs2/loopclosure2.py | Python | gpl-3.0 | 27,461 | [
"TINKER"
] | 227ad1657eb82a7b700e03c50b133e97cc3cffa13ce05318648f7bc9e2a11915 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
try:
from setuptools import setup
except ImportError:
from distutils.core import setup
with open('README.rst') as readme_file:
readme = readme_file.read()
with open('HISTORY.rst') as history_file:
history = history_file.read()
requirements = [
'num... | akloster/porekit-python | setup.py | Python | isc | 1,548 | [
"Biopython"
] | cfc61bbbb30a1ee115bd61d31cd7f9b0f746b0890a7ffc882b41851804d9cfb3 |
"""
This module contains helper methods for accessing operational attributes or parameters of DMS objects
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import six
from DIRAC import gConfig, gLogger, S_OK, S_ERROR
from DIRAC.ConfigurationSystem.Clien... | yujikato/DIRAC | src/DIRAC/DataManagementSystem/Utilities/DMSHelpers.py | Python | gpl-3.0 | 16,650 | [
"DIRAC"
] | 2fbb8d7d346b433028f154a7d8bb150811487b0d50f939c1b1b74f446303d294 |
"""
Application-class that implements pyFoamPrepareCase.py
"""
from optparse import OptionGroup
from .PyFoamApplication import PyFoamApplication
from PyFoam.RunDictionary.SolutionDirectory import SolutionDirectory
from PyFoam.Basics.DataStructures import DictProxy
from PyFoam.Basics.Utilities import rmtree,copytree,e... | Unofficial-Extend-Project-Mirror/openfoam-extend-Breeder-other-scripting-PyFoam | PyFoam/Applications/PrepareCase.py | Python | gpl-2.0 | 57,673 | [
"ParaView",
"VTK"
] | ff15a51e4fa116c73b100215286282b13470d25695e1dd47571bcc587bd0f18f |
#
# Copyright (C) 2010, 2015, 2016, 2017, 2018, 2019, 2020, 2021
# Smithsonian Astrophysical Observatory
#
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License,... | anetasie/sherpa | sherpa/ui/utils.py | Python | gpl-3.0 | 602,286 | [
"Gaussian"
] | 8b2f1ec58193d87413b97a602722311654fab7d917ea62183a14ed4127e76b74 |
#
# Copyright (C) 2017 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 vers... | KonradBreitsprecher/espresso | testsuite/force_cap.py | Python | gpl-3.0 | 2,273 | [
"ESPResSo"
] | 72db37cfc609e30d1146296306fa3acb7f0f052ddf019deda8c92837a3fc18a0 |
# -*- coding: utf-8 -*-
#
# Copyright 2012 - 2019 Brian R. D'Urso
#
# This file is part of Python Instrument Control System, also known as Pythics.
#
# Pythics 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... | dursobr/Pythics | pythics/examples/chart_recorder.py | Python | gpl-3.0 | 5,262 | [
"Brian"
] | 560f2459858b72193475801f104dea1a020d7c4e2ce5151af7b4c8230b8082c8 |
"""Contains the Attract class which is the attract mode in a pinball machine.
.. Note::
Still need to add the code to watch for combinations of button presses,
like a long-press, pressing start while holding a flipper button, holding a
flipper button to start tournament mode, etc.
"""
# attract.py
# Mission... | jabdoa2/mpf | mpf/game/attract.py | Python | mit | 6,930 | [
"Brian"
] | dc1f9f80c5f334cf204cd96b1eb7c1a868c6bfd442eb2fe441989e27122985f9 |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the te... | Azulinho/ansible | lib/ansible/modules/network/avi/avi_role.py | Python | gpl-3.0 | 3,252 | [
"VisIt"
] | a9bfe293ba6d253f2c1aa40b426913e941f673fa2d2246d265aa9d7019ae5c33 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
__author__ = "Bharat Medasani"
__copyright__ = "Copyright 2013, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "bkmedasani@lbl.gov"
__date__ = "Aug 2, 2013"
import un... | gVallverdu/pymatgen | pymatgen/io/tests/test_zeopp.py | Python | mit | 11,089 | [
"VASP",
"pymatgen"
] | a53b063f2f5223f0e6200f2ed20fab4463494840b2452ab2016abf0903eb259e |
#!/usr/bin/env python
#
# $File: KAlleleMutator.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 redistri... | BoPeng/simuPOP | docs/KAlleleMutator.py | Python | gpl-2.0 | 1,491 | [
"VisIt"
] | ade4d17ab6ea3e1feee860445b22309a19ac1a04072863475081d2010181839d |
#! /usr/bin/python
######
# Copyright 2007-2009 Sun Microsystems, Inc. All Rights Reserved.
# DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER
#
# This code is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License version 2
# only, as published b... | SunLabsAST/AURA | Bridge/pyaura/tagclustering/build_db.py | Python | gpl-2.0 | 6,082 | [
"VisIt"
] | 68ae2cc023fc63ebffa9a14c208d5fd8b2e5c3e651799b744cd12b69fa6cdd2f |
# http://www.paraview.org/Wiki/Python_Programmable_Filter
#
# This script generates a helix double.
# This is intended as the script of a 'Programmable Source'.
#
# Note: it won't run standalone.
import math
num_pts = 160 # Points along each helix. 80.
length = 1.0 # Length of each heli... | Seynen/egfrd | visualization/helix.py | Python | gpl-2.0 | 2,716 | [
"ParaView",
"VTK"
] | 86b06c6abcaa6de64a5aa31356f428479f18892d47905b1ea1b61d0ca020cab6 |
##############################################################################
#
# Kennedy Institute of Rheumatology
#
# $Id$
#
# Copyright (C) 2015 Stephen Sansom
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published b... | snsansom/xcell | pipelines/pipeline_cram2fastq.py | Python | mit | 12,728 | [
"pysam"
] | d37ed384144b3eca3b5cfde30c03b760d25442fb08e134915d02c9e00390eddb |
import numpy as np
from ase.parallel import parprint
from gpaw.response.g0w0 import G0W0
# We start by setting up a G0W0 calculator object
gw = G0W0('Si_gs.gpw', # Path to groundstate gpw file
filename='Si_g0w0_ppa', # filename base for output files
kpts=None, # List of q... | robwarm/gpaw-symm | doc/exercises/gw/Si_g0w0_ppa.py | Python | gpl-3.0 | 1,526 | [
"ASE",
"GPAW"
] | b6de0d6dbd797e3c72393039ce3dd9dbd9151946345b285a6f86df4d3e40abc0 |
'''
Description
Implements abstract class AGPOperation for simuPop simulations,
as coded by Tiago Antao's sim.py modlule. See class description.
'''
from __future__ import division
from __future__ import print_function
from builtins import range
from past.utils import old_div
__filename__ = "pgopsimupop.py"
__date__ ... | popgengui/negui | agestrucne/pgopsimupop.py | Python | agpl-3.0 | 110,940 | [
"Brian"
] | aede95ab51a4d82e2f9aa17980cbb34e5748ee442037e023edf6699b0d7e20ae |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2002-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2008 Jerome Rapinat
# Copyright (C) 2008 Benny Malengier
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the ... | pmghalvorsen/gramps_branch | gramps/gen/filters/rules/_hasnotebase.py | Python | gpl-2.0 | 2,887 | [
"Brian"
] | 45a076bb4a89a71a090444897dde43ee60052889df8cb63274dc6278a628e24a |
"""Some utilities related to loading/saving different file formats, compressing and indexing."""
import io
import tempfile
from os.path import splitext
import os
import glob
import gzip
import string
from contextlib import contextmanager
import hashlib # We decided to include md5 hashes of the sequences too
from itert... | latticelabs/Mitty | mitty/lib/mio.py | Python | gpl-2.0 | 11,463 | [
"pysam"
] | f5d493256680ee0186e7b422e201405ee6554b89b7da8091726b8fbd16596001 |
#!/usr/bin/env python
"""
Do the initial installation and configuration of a DIRAC component
"""
from DIRAC import exit as DIRACexit
from DIRAC import gConfig, gLogger, S_OK
from DIRAC.Core.Base.Script import Script
from DIRAC.Core.Utilities.Extensions import extensionsByPriority
from DIRAC.FrameworkSystem.Utilities im... | DIRACGrid/DIRAC | src/DIRAC/FrameworkSystem/scripts/dirac_install_component.py | Python | gpl-3.0 | 4,442 | [
"DIRAC"
] | f69c3c5b3deec626ffbc9b8374701677276478dd20c6527305ede7acc01ace55 |
"""
This module provides functions to get the dimensionality of a structure.
A number of different algorithms are implemented. These are based on the
following publications:
get_dimensionality_larsen:
- P. Larsen, M. Pandey, M. Strange, K. W. Jacobsen, 2018, arXiv:1808.02114
get_dimensionality_cheon:
- Cheon, G.... | montoyjh/pymatgen | pymatgen/analysis/dimensionality.py | Python | mit | 21,828 | [
"CRYSTAL",
"Jmol",
"VisIt",
"pymatgen"
] | ab40b11fb48d0969816f3269018bd9da5af81e985cdbf07c41ce322765ef6598 |
from .crystal import *
from .betareg import Beta
from . import evaluate
from . import utils
from . import plot
from . import simulate
from .plot import logit, ilogit
__version__ = "0.0.1"
| brentp/crystal | crystal/__init__.py | Python | mit | 189 | [
"CRYSTAL"
] | adab34787624fc9507d9f42f7797b56ddeaa8fdc70053b6cd0712f2f04208a51 |
""" Trace the source in Data file
"""
from __future__ import (print_function, absolute_import, division, unicode_literals)
import numpy as np
import pdb
import glob
from astropy.table import Table
from astropy.io import fits
from matplotlib import pyplot as plt
from scipy.optimize import curve_fit
from xastropy.xutil... | PYPIT/COS_REDUX | cosredux/trace.py | Python | bsd-2-clause | 32,302 | [
"Gaussian"
] | b6cad40b98226dfe838ed8b6f3d9fe97f3945d737a68eb31f89e223563773fb5 |
# (originally from https://github.com/tensorflow/models/tree/master/research/differential_privacy,
# possibly with some small edits by @corcra)
# 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 complia... | ratschlab/RGAN | differential_privacy/privacy_accountant/tf/accountant.py | Python | mit | 17,725 | [
"Gaussian"
] | 6eca3f9cab923c3a8f085f214714aeb234bc29504460eea462e781f579b39e7b |
# This file is part of xrayutilities.
#
# xrayutilities 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 option) any later version.
#
# This program is distributed... | dkriegner/xrayutilities | lib/xrayutilities/materials/database.py | Python | gpl-2.0 | 27,835 | [
"Jmol"
] | 4302317b3a835aee85260af4351644d4c073500390c5831a3e432f20f63c83f6 |
# -*- coding: utf-8 -*-
import unittest
import galaxy.model.mapping as mapping
class MappingTests( unittest.TestCase ):
def test_annotations( self ):
model = self.model
u = model.User( email="annotator@example.com", password="password" )
self.persist( u )
def persist_and_check_a... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/test/unit/test_galaxy_mapping.py | Python | gpl-3.0 | 18,069 | [
"Galaxy"
] | 90cb94ae1f7506ab244497d34a75c358bae048549aa19f67e225c4195a33a30d |
# a-b-c-d-e-f-g
# i have gummy bears chasing me
# one is red, one is blue
# one is chewing on my shoe
# now i am running for my life
# because the red one has a knife
import sys
import os
import traceback
from numpy.random import randint
from azure.storage.blob import BlockBlobService
from DataConnection import Data... | andlin666/DataCachePhase1 | DataCachePhase1/DataCache.py | Python | apache-2.0 | 11,552 | [
"ADF"
] | a143292fa2a8e0d98e0cce15b2f0f895741329a705eee5a456e9d8d91740d019 |
ONCV_conf = {
('Mn',
'/home/hexu/.local/pp/abinit/ONCVPSP-PBE-PDv0.3/Mn/Mn-sp-high.psp8'):
[[None, 0, 3, 2], [None, 1, 3, 6], [None, 2, 3, 5], [None, 0, 4, 2]],
('O', '/home/hexu/.local/pp/abinit/ONCVPSP-PBEsol-PDv0.3/O/O.psp8'):
[[None, 0, 2, 2], [None, 1, 2, 4]],
('Ag', '/home/hexu/.local/pp/... | mailhexu/pyDFTutils | resource/phonon_ana/pyFA/data/ONCV_conf.py | Python | lgpl-3.0 | 43,363 | [
"ABINIT"
] | 05a735e028479bbcf1b00d9310e4bc3b76d47601280d19983dddf1e9a1b1bd64 |
"""Finite-horizon tabular Maximum Causal Entropy IRL.
Follows the description in chapters 9 and 10 of Brian Ziebart's `PhD thesis`_.
Uses NumPy-based optimizer Jax, so the code can be run without
PyTorch/TensorFlow, and some code for simple reward models.
.. _PhD thesis:
http://www.cs.cmu.edu/~bziebart/publicati... | humancompatibleai/imitation | src/imitation/algorithms/tabular_irl.py | Python | mit | 16,345 | [
"Brian"
] | eef9eaa08a98050e30d198cdb6256b83970d9f401b06cf7ba2c6323eae9a6cd3 |
""" Class that contains client access to the transformation DB handler. """
__RCSID__ = "$Id$"
from DIRAC import S_OK, gLogger
from DIRAC.Core.Base.Client import Client
from DIRAC.Core.Utilities.List import breakListIntoChunks
from DIRAC.ConfigurationSystem.Client.Helpers.Operations import Operations
class Transfor... | andresailer/DIRAC | TransformationSystem/Client/TransformationClient.py | Python | gpl-3.0 | 20,529 | [
"DIRAC"
] | dd082d40c81f04decc7034fbeee58955063938d6e8290edc1b03fec4cd3e7cbc |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | rmcgibbo/psi4public | psi4/driver/interactive.py | Python | lgpl-3.0 | 1,248 | [
"Psi4"
] | 8fcdf2af5cee604d438b6bb0ea891130ea581e6f58c768df1d6ec76a43003a07 |
"""
Just a selector for X509Certificate
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
from pkgutil import extend_path
#####
# SUPER DISGUSTING HACK
# We define these variables, and then remove them immediately.
# it is to allow s... | ic-hep/DIRAC | src/DIRAC/Core/Security/__init__.py | Python | gpl-3.0 | 975 | [
"DIRAC"
] | 995b911d4d86e18a837f0a7a5732e266e24f8049c4d0d358211d52e95b235e34 |
#!/usr/bin/env python
__author__ = "Mike McCann"
__copyright__ = "Copyright 2012, MBARI"
__license__ = "GPL"
__maintainer__ = "Mike McCann"
__email__ = "mccann at mbari.org"
__doc__ = '''
Base classes for writing NetCDF files for CANON campaigns. Reuse
Use the conventions for Trajectory feature type and write as m... | duane-edgington/stoqs | stoqs/loaders/CANON/toNetCDF/__init__.py | Python | gpl-3.0 | 8,661 | [
"NetCDF"
] | 695ff880fbfeb7f49146f782d1752a4b2ce6e75c2d1fbf0c983b1f40729381b6 |
import vtk
class VtkAdaptor:
def __init__(self, **kwargs):
self.point_count = 0
self.face_count = 0
self.points = None
self.polys = None
self.poly_data = None
self.scalars = None
def create_empty_mesh(self):
self.pcoords = vtk.vtkFloatArray()
se... | cwant/tessagon | tessagon/adaptors/vtk_adaptor.py | Python | apache-2.0 | 1,395 | [
"VTK"
] | b64b283f41745379bdc5e8405be040366d6b8a01b33071ab8f6f411603c5d8df |
import unittest
import ois
import numpy as np
import os
import varconv
class TestPSFCorrect(unittest.TestCase):
def setUp(self):
h, w = img_shape = (32, 32)
pos_x = [9, 24, 9, 24]
pos_y = [9, 9, 24, 24]
fluxes = [200, 300, 400, 500]
self.img = np.zeros(img_shape)
fo... | toros-astro/ois | tests/test_ois.py | Python | mit | 24,357 | [
"Gaussian"
] | 5a377df44d0773ee8cc1a6aa4a92617597a3aa90572ebed084d974219f225c16 |
# Copyright 2018 Jacob D. Durrant
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writ... | InformaticsMatters/pipelines | src/python/pipelines/dimorphite/dimorphite_dl.py | Python | apache-2.0 | 44,837 | [
"RDKit"
] | aa0e48f6146409eb3d20b3e515fe6b662503bbff2ef1beb4ecfafd0b3bc02e4b |
import uuid
import copy
import numpy as np
import collections
from .. import util
from .. import caching
from .. import transformations
class SceneGraph(object):
"""
Hold data about positions and instances of geometry
in a scene. This includes a forest (i.e. multi-root tree)
of transforms and inform... | mikedh/trimesh | trimesh/scene/transforms.py | Python | mit | 23,127 | [
"VisIt"
] | 8d13de369ae81bec1e93137f25eadd891410099d019605266610d4d4c84cfce4 |
"""
Module for Approximate Bayesian Computation
"""
from abc import ABCMeta, abstractmethod
import multiprocessing
import numpy as np
from scipy import stats
from numpy.lib.recfunctions import stack_arrays
class Model(object):
"""
Base class for constructing models for approximate bayesian computing
and v... | dksahuji/simpleabc | simple_abc.py | Python | mit | 15,217 | [
"Gaussian"
] | e6f22d40cb0455055274734ab38c8177aa149d3718d13b850c862107e19ca90f |
#
# This Source Code Form is subject to the terms of the Mozilla Public License,
# v. 2.0. If a copy of the MPL was not distributed with this file, You can
# obtain one at http://mozilla.org/MPL/2.0/.
#
# Copyright (c) 2015 Digi International Inc., All Rights Reserved.
#
import splinter_tests
import splinter_tests.uti... | brucetsao/XBeeZigBeeCloudKit | splinter_tests/test_unauthenticated.py | Python | mpl-2.0 | 2,018 | [
"VisIt"
] | e8a548ff5a9dbc9a906a3f6aae3f8272a9d313721bccd4297c96a86556c02ee3 |
'''
(c) GeneGenie Bioinformatics Ltd. 2018
Licensed under the MIT License.
To view a copy of this license, visit <http://opensource.org/licenses/MIT/>.
@author: neilswainston
'''
# pylint: disable=invalid-name
# pylint: disable=wrong-import-order
import math
from sklearn.linear_model import LinearRegression
from ... | synbiochem/synbiochem-learn | gg_learn/utils/plot_utils.py | Python | mit | 2,402 | [
"VisIt"
] | 376acedadff8365e98d7fe36b4769122bde0749576ff880aecec16f5b19ab883 |
import subprocess
from GpdbBuildBase import GpdbBuildBase
INSTALL_DIR="/usr/local/gpdb"
class GpBuild(GpdbBuildBase):
def __init__(self, mode="orca"):
GpdbBuildBase.__init__(self)
self.mode = 'on' if mode == 'orca' else 'off'
self.configure_options = [
... | yuanzhao/gpdb | concourse/scripts/builds/GpBuild.py | Python | apache-2.0 | 3,379 | [
"ORCA"
] | b296f3c639bb585977ad038cc4d4948adb994ec1028edbe7647dfe9b3d158e27 |
# -*- coding: UTF-8 -*-
# Copyright 2014 Luc Saffre
# License: BSD (see file COPYING for details)
"""
DEPRECATED : use eesti.py instead!
This fixture contains all Estonian places.
It is a proof of concept for my idea of using :ref:`dpy` as data
format for maintaining large knowledge bases like the list of places
of ... | khchine5/xl | lino_xl/lib/countries/fixtures/est.py | Python | bsd-2-clause | 157,043 | [
"MOE"
] | 5a2d79e80e9771abd4303052475e9df218a071ca945eecd1c73c5d9b84d5d5d5 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | mfherbst/spack | var/spack/repos/builtin/packages/r-keggrest/package.py | Python | lgpl-2.1 | 2,212 | [
"Bioconductor"
] | 9c45d4b42eeb58037d7488526ee4b8d5f3ff19c1eaf349e790ce81a8825273f1 |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the te... | e-gob/plataforma-kioscos-autoatencion | scripts/ansible-play/.venv/lib/python2.7/site-packages/ansible/modules/network/avi/avi_backup.py | Python | bsd-3-clause | 3,955 | [
"VisIt"
] | f098201ec98537d95f77c36cf93c25dc697ed87d2e021f4164cf5f0f85f3897e |
# Step specific to the agenda view.
from behave import step
from pages.agenda import AgendaPage
@step('we visit the agenda')
def step_impl(context):
page = AgendaPage(context)
page.visit()
| abingham/accu-2017-elm-app | tests/features/steps/agenda.py | Python | mit | 200 | [
"VisIt"
] | 6f5e57089902195faa7f355e631bdff3a0d1d043096070cab27a678cc7ced581 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2016, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Data tests for cclib."""
| Schamnad/cclib | test/data/__init__.py | Python | bsd-3-clause | 226 | [
"cclib"
] | c19ae1736e983f265c9c5c31e150add20947a2e354c58f5ad75cd167bbe61da0 |
from student import Student
import csv
import orgtbl
import os
import statistics
def swap_problem(s):
n = s.strip('abcdefghijklmnopqrstuvwxyz')
l = s.strip('0123456789')
if l:
l = ' (' + l + ')'
return 'Problem ' + n + l
class Exam():
def __init__(self, scores_dcts):
self.scores_... | done-with-fish/my-course | exam.py | Python | gpl-3.0 | 3,534 | [
"Brian"
] | dc9457e0874a68b33cbc6779c93ed7842928e15f51949d1cb9f63a5291aa1fe5 |
import ast
import sap.if1
import sap.compiler_base
class CompilerExpression(sap.compiler_base.CompilerBase):
def __init__(self):
sap.compiler_base.CompilerBase.__init__(self)
return
def Num(self, node):
"Num just returns the literal value"
# This is done as a tuple because, i... | patmiller/SAP | sap/expression.py | Python | bsd-3-clause | 5,862 | [
"VisIt"
] | e47669a114f9b1e9a9a591a8bd163f3d5faab852d9a2143b28f662441c0bc846 |
# Copyright (c) 2015, Scott J Maddox. All rights reserved.
# Use of this source code is governed by the BSD-3-Clause
# license that can be found in the LICENSE file.
'''
Precise and fast Fermi-Dirac integrals of integer and half integer order.
[1] T. Fukushima, "Precise and fast computation of Fermi-Dirac integral... | scott-maddox/fdint | fdint/__init__.py | Python | bsd-3-clause | 2,739 | [
"DIRAC"
] | e2b68664a99bc80af154899954d0834e8a5b79cbd69cbde8ee401873da6b016d |
#
# Copyright (C) 2017 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 ver... | KonradBreitsprecher/espresso | testsuite/coulomb_tuning.py | Python | gpl-3.0 | 3,369 | [
"ESPResSo"
] | 3387f05c17c9553a51dc829fdefaa08d8e02ca8583f1c576c45c4d07e0aa1310 |
#!/usr/bin/env python
# coding: utf-8
# # 14 - Advanced topics - Cement Pavers albedo example
#
# This journal creates a paver underneath the single-axis trackers, and evaluates the improvement for one day -- June 17th with and without the pavers for a location in Davis, CA.
#
# ![Paver](../images_wiki/AdvancedJourn... | NREL/bifacial_radiance | docs/tutorials/14 - Advanced topics - Cement Pavers albedo example.py | Python | bsd-3-clause | 11,415 | [
"EPW"
] | 6ab609ff5b9de1bafadd78f11d05fe24bb60f10592b9afb57d0dc51301aa8251 |
#!/usr/bin/env python
# -*- mode: python; coding: utf-8; -*-
# ---------------------------------------------------------------------------##
#
# Copyright (C) 1998-2003 Markus Franz Xaver Johannes Oberhumer
# Copyright (C) 2003 Mt. Hood Playing Card Co.
# Copyright (C) 2005-2009 Skomoroh
#
# This program is free softwa... | jimsize/PySolFC | pysollib/games/klondike.py | Python | gpl-3.0 | 53,085 | [
"CASINO"
] | 7edd49943f151defb12c4e720100d3a373eae25944f297d57cd708f78837425b |
# -*- coding: utf-8 -*-
import time
import numpy as np
from unittest.case import SkipTest
from numpy.testing import assert_allclose
import scipy.ndimage as nd
import abel
def test_direct_shape():
if not abel.direct.cython_ext:
raise SkipTest
n = 21
x = np.ones((n, n))
recon = abel.direct.dire... | rth/PyAbel | abel/tests/test_direct.py | Python | mit | 3,413 | [
"Gaussian"
] | a321ca0a46ba60bec79fcbf1f2de878921b0313528a32e9e8e6b5fec0fdd66fd |
########################################################################
# $HeadURL$
########################################################################
""" X509Certificate is a class for managing X509 certificates alone
"""
__RCSID__ = "$Id$"
import GSI
import os
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.U... | marcelovilaca/DIRAC | Core/Security/X509Certificate.py | Python | gpl-3.0 | 7,603 | [
"DIRAC"
] | e3e7acaf94c49c58ee64e36bf493899fccb00ae9db0305d553685d61692a1f08 |
import random
import itertools
import string
import os
import tempfile
import logging
from pkg_resources import resource_filename
import contextlib
import shutil
import mdtraj as md
from mdtraj.utils import enter_temp_directory
from mdtraj.utils.delay_import import import_
import openmoltools.acpype as acpype
try:
... | Clyde-fare/openmoltools | openmoltools/utils.py | Python | gpl-2.0 | 19,806 | [
"Amber",
"Gromacs",
"MDTraj",
"OpenMM",
"Pybel",
"RDKit"
] | 02676483b40c0ff702b56ead0c4f1c0399493d527b1401dd1ab3beb06714a185 |
"""
Message Queue Handler
"""
import json
import logging
import socket
from DIRAC.Resources.MessageQueue.MQCommunication import createProducer
class MessageQueueHandler(logging.Handler):
"""
MessageQueueHandler is a custom handler from logging.
It has no equivalent in the standard logging library because... | DIRACGrid/DIRAC | src/DIRAC/FrameworkSystem/private/standardLogging/Handler/MessageQueueHandler.py | Python | gpl-3.0 | 1,577 | [
"DIRAC"
] | fc12e77c858ce7f67ffc9fedfaded089345091538d2a610a97bbfda74e89bdbd |
"""
Featurizer implementations used in Smiles2Vec models.
SmilesToSeq featurizer for Smiles2Vec models taken from https://arxiv.org/abs/1712.02734
"""
from typing import Dict, List
import numpy as np
import pandas as pd
from deepchem.utils.typing import RDKitMol
from deepchem.feat.base_classes import MolecularFeaturiz... | lilleswing/deepchem | deepchem/feat/molecule_featurizers/smiles_to_seq.py | Python | mit | 4,831 | [
"RDKit"
] | f257f87e0452e54cfdaedd6ca8aaefe2eb0e7c5656f7c4713c3f943d19452f44 |
"""Support for control of Elk-M1 connected thermostats."""
from homeassistant.components.climate import ClimateDevice
from homeassistant.components.climate.const import (
ATTR_TARGET_TEMP_HIGH, ATTR_TARGET_TEMP_LOW, STATE_AUTO,
STATE_COOL, STATE_FAN_ONLY, STATE_HEAT, STATE_IDLE, SUPPORT_AUX_HEAT,
SUPPORT_FA... | HydrelioxGitHub/home-assistant | homeassistant/components/elkm1/climate.py | Python | apache-2.0 | 6,933 | [
"Elk"
] | 8fb4c7d26aa02d08b5ca68b179a698d5f1ada022286bbaa65ad3cf00cbfd9b9f |
"""
This module contains Item class and possibly other associated objects.
"""
import random
class Item(object):
""" This represents game item, map representation, name and price.
"""
def __init__(self, symbol=None, name=None):
""" This instantiates Item.
:param symbol: string containing... | tvm1/ShopHack | itemgen.py | Python | gpl-3.0 | 3,895 | [
"Amber",
"CRYSTAL"
] | 782f119f8d02c2615d85972aca038b5166c54017f1ef333e53e29aad6be24375 |
from splinter import Browser
import time
import sys
import dns.resolver
def exportZone(domain, browser):
zone = []
browser.visit("https://www.123-reg.co.uk/secure/cpanel/manage-dns?domain=" + domain)
browser.click_link_by_id('advanced-tab')
a = 0
while browser.is_element_present_by_id('dns_entry_0'... | brockrob/123-RegDnsExport | 123-RegDnsExport.py | Python | mit | 5,568 | [
"VisIt"
] | b9b0a59590aa5aa9d976064ffc4bfb033a86b220a6fb9426b9ea3ac86cb3b54c |
"""
Unit tests for masquerade.
"""
import json
import pickle
from mock import patch
from nose.plugins.attrib import attr
from datetime import datetime
from django.core.urlresolvers import reverse
from django.test import TestCase
from django.utils.timezone import UTC
from capa.tests.response_xml_factory import OptionR... | itsjeyd/edx-platform | lms/djangoapps/courseware/tests/test_masquerade.py | Python | agpl-3.0 | 18,353 | [
"VisIt"
] | 7e07bca22cafc9559cd043bd6a1e40a484ca2130452b83481fb9c49477cc75f8 |
"""
Tools for the instructor dashboard
"""
from __future__ import absolute_import
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_ke... | ESOedX/edx-platform | lms/djangoapps/instructor/views/tools.py | Python | agpl-3.0 | 7,162 | [
"VisIt"
] | 7afd821ea62574fc087237920c6026ef0dac083e90fc52a536154ae51012973d |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | lgarren/spack | var/spack/repos/builtin/packages/dealii/package.py | Python | lgpl-2.1 | 15,182 | [
"NetCDF"
] | d5f5ad5e10135a400c32732c98d786e4ca66ae8b0f91dfa7841177b13da4c70e |
import RPi.GPIO as GPIO
import time
import os
import signal
import sys
class TrafficLightLEDs:
RED = 9
AMBER = 10
GREEN = 11
class TrafficLightStates:
INITIALIZING = 1
RED = 2
REDAMBER = 3
GREEN = 4
AMBER = 5
# Turn off all lights when user ends demo
def allLightsOff(signal, frame):
GPIO.output(TrafficLight... | simonprickett/pitrafficlights | trafficlightsfsm.py | Python | mit | 2,212 | [
"Amber"
] | 098c5a39f5bfe85980511eacb49d18f79a72d33709f19aec0e2c01ea8df8b7fe |
""" DIRAC FileCatalog Storage Element Manager mix-in class """
__RCSID__ = "$Id$"
import threading
import time
import random
from DIRAC import S_OK, S_ERROR, gConfig, gLogger
from DIRAC.Core.Utilities.Pfn import pfnunparse
class SEManagerBase:
def _refreshSEs(self, connection=False):
"""Refresh the SE cache... | fstagni/DIRAC | DataManagementSystem/DB/FileCatalogComponents/SEManager.py | Python | gpl-3.0 | 8,937 | [
"DIRAC"
] | 0f32fe0dc7f5e889a52d916f72dd6daa9cde61f0aac281affef7b1956d8dc73b |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | EmreAtes/spack | var/spack/repos/builtin/packages/pgdspider/package.py | Python | lgpl-2.1 | 2,385 | [
"BWA"
] | 9ae103ec1370f47709abe7b8b985fed0897b731ff9cc47c226844b6878e3dc67 |
"""Read and write AMBER rst files."""
import numpy as np
from floatx import floatx
STDOPEN=open
class RSTError(Exception):
pass
class RSTFile(object):
crd_per_line=6
crd_fmt='%12.6f'
def __init__(self, name, mode='r',
comment=None,
dynamics=False,
... | plediii/coord_util | rst.py | Python | bsd-3-clause | 4,393 | [
"Amber"
] | ef5db2e6a86f286c81b1b348ed921738e1be88a6029120df3a96218fcd292c47 |
import utils
import numpy as np
import matplotlib.pyplot as plt
# Global parameters
dataset_name = 'standard'
patch_size = (32, 32) # (patch_height, patch_width)
compression_percent = 60
# Data acquisition
# Generate original images
utils.generate_original_images(dataset_name)
# Generate training set
utils.gene... | mdeff/ntds_2016 | project/reports/compressed_sensing/data_exploration.py | Python | mit | 3,733 | [
"Gaussian"
] | 224c1ea804844165ef6d5e177dcfc117b54ee5dd97212cf85a38d9a1e36ec96c |
"""
Utilities for ComponentMonitoring features
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import datetime
import socket
from DIRAC import S_OK
from DIRAC.FrameworkSystem.Client.ComponentMonitoringClient import ComponentMonitoringClient
from DIRAC.C... | ic-hep/DIRAC | src/DIRAC/FrameworkSystem/Utilities/MonitoringUtilities.py | Python | gpl-3.0 | 3,121 | [
"DIRAC"
] | 12c5b4d004bc6e753edfb11418c2845fbd10870a3c5a92ee83aaaa6f03d900e4 |
# -*- coding: utf-8 -*-
"""
Write EC and SMC Meshes in legacy VTK format as .vtk.
"""
import os
import sys
# Run in current directory.
os.chdir(os.path.dirname(os.path.abspath(__file__)))
# Relative import path for the DumpMeshToLegacyFormat script.
importPath = os.path.abspath(os.path.join(os.path.dirname(__file__)... | BlueFern/DBiharMesher | meshes/c4080cfd/Dump4080MeshLegacyFormat.py | Python | gpl-2.0 | 894 | [
"VTK"
] | 61ae87d64d63b9006e1b830a6e6ff04aa0cb7201363e6da4e865d09ad1b44f3e |
import matplotlib.pyplot as plt
import numpy as np
import seaborn
import sys
folder = 'data/correlations-CB'
filename = 'CB_spikes'
n_trials = 10 # can be up to 100
n_neurons = 10000
# to plot correlations with different movement parameters call
# script with an argument corresponding to data type you want to plot
... | studywolf/REACH-paper | analysis/06b-CB_correlations_plot.py | Python | gpl-3.0 | 4,942 | [
"NEURON"
] | bb4d8797cd30321302588724f11935530d61d5ba0a07707127450e4fde244b89 |
import os
import numpy as np
from astropy.io import fits
from astropy import wcs
from astropy.convolution import Gaussian2DKernel, convolve_fft, convolve
from skimage import restoration
import matplotlib.pyplot as plt
import blast.util
fwhm = 3.0
mapdir = "/home/wizwit/miscellaneous_projects/carina/carinaData"
#mapfil... | sbg2133/miscellaneous_projects | carina/smoothMSX.py | Python | gpl-3.0 | 1,376 | [
"BLAST",
"Gaussian"
] | aca589bf5ee1078bc92d03b93e658bd70c80c4779d2a5402c5c99926c24e824a |
# -*- coding: utf-8 -*-
#
# This file is part of PyBuilder
#
# Copyright 2011-2020 PyBuilder Team
#
# 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/l... | pybuilder/pybuilder | src/main/python/pybuilder/plugins/python/vendorize_plugin.py | Python | apache-2.0 | 12,184 | [
"VisIt"
] | 86d0e1d90ae0b6bf00f210b1ab51010b65fa5b95aa559a848f0be7bd266508ee |
# 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/__init__.py | Python | gpl-3.0 | 965 | [
"Brian"
] | f17d49e4e0f4255f96d14367893a94df0287fcb6bc2bc0ffea2f62972bff6b04 |
# Author: Travis Oliphant 2001
# Author: Nathan Woods 2013 (nquad &c)
from __future__ import division, print_function, absolute_import
import sys
import warnings
from functools import partial
from . import _quadpack
import numpy
from numpy import Inf
__all__ = ['quad', 'dblquad', 'tplquad', 'nquad', 'quad_explain',
... | surhudm/scipy | scipy/integrate/quadpack.py | Python | bsd-3-clause | 31,950 | [
"Gaussian"
] | 4d1a71168f68e52a864d28ed575d3a319f28decf054eed2900ddc8e68f394b6f |
from statsmodels.sandbox.predict_functional import predict_functional
import numpy as np
import pandas as pd
import statsmodels.api as sm
from numpy.testing import dec
# If true, the output is written to a multi-page pdf file.
pdf_output = False
try:
import matplotlib.pyplot as plt
import matplotlib
have_... | hlin117/statsmodels | statsmodels/sandbox/tests/test_predict_functional.py | Python | bsd-3-clause | 12,873 | [
"Gaussian"
] | 2e13df88ba2a9d63a64ebd6ada5681b492dc3f4fb1665c3dbe68bacd8e66fd13 |
#
# Copyright (C) 2013,2014,2015,2016 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 opt... | Marcello-Sega/espresso | samples/python/not-working/hello_parallel_world.py | Python | gpl-3.0 | 1,687 | [
"ESPResSo",
"VTK"
] | 834eba63827e438ac073aaca7b3a116a084ec9d06356be08d517a46910cdc9a9 |
import h5py
import xml.etree.cElementTree as ET
from flatdict import FlatDict
from openpnm.io import Dict, GenericIO
from openpnm.utils import logging
logger = logging.getLogger(__name__)
class XDMF(GenericIO):
r"""
The eXtensible Data Model Format combines XML descriptors with HDF5 data
storage
For... | TomTranter/OpenPNM | openpnm/io/XDMF.py | Python | mit | 9,163 | [
"VisIt"
] | c4d4a18aae7eacd25f64ce2d5f30fb68fcc147fa92f89765e264a5322de165fa |
import unittest
import numpy as np
from pymatgen.analysis.elasticity.strain import Deformation
from pymatgen.analysis.elasticity.stress import Stress
from pymatgen.util.testing import PymatgenTest
class StressTest(PymatgenTest):
def setUp(self):
self.rand_stress = Stress(np.random.randn(3, 3))
s... | materialsproject/pymatgen | pymatgen/analysis/elasticity/tests/test_stress.py | Python | mit | 2,213 | [
"pymatgen"
] | 55b86c7affe103c854df58187de3d1d1cacb70bf0011eb0f5db7f7198be06b41 |
# Author: Gael Varoquaux <gael _dot_ varoquaux _at_ normalesup _dot_ org>
# Copyright (c) 2008, Enthought, Inc.
# License: BSD Style.
# Enthought library imports.
from traits.api import Instance
from tvtk.api import tvtk
# Local imports
from mayavi.filters.poly_data_filter_base import \
PolyDataFilterBase
fro... | dmsurti/mayavi | mayavi/filters/quadric_decimation.py | Python | bsd-3-clause | 1,172 | [
"Mayavi"
] | e4d98a79e67356b95186b4f4057328b879f4e0aca1c330f9291a7a58d86728f2 |
# -*- coding: utf-8 -*-
import sys
import numpy as np
from ase.optimize.optimize import Optimizer
from ase.utils.linesearch import LineSearch
class LBFGS(Optimizer):
"""Limited memory BFGS optimizer.
A limited memory version of the bfgs algorithm. Unlike the bfgs algorithm
used in bfgs.py, the inverse... | JConwayAWT/PGSS14CC | lib/python/multimetallics/ase/optimize/lbfgs.py | Python | gpl-2.0 | 11,193 | [
"ASE"
] | d8aa7ddf7ded9fa88b0c996c314bc03125a4286e089cf39649df8148a8fd583f |
# This file is part of PyEMMA.
#
# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
#
# PyEMMA 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 versi... | markovmodel/PyEMMA | pyemma/coordinates/data/feature_reader.py | Python | lgpl-3.0 | 14,708 | [
"MDTraj"
] | 59237ef29b3ecd87cc29d7eac3e1f5115b6b45fcfab12a9dceb02315c61acec6 |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | wangsheng1001/incubator-singa | python/singa/tensor.py | Python | apache-2.0 | 29,178 | [
"Gaussian"
] | 173ff3a980a205954edf958b28e60f091ad0af16dc39790a3c35ff74f074388c |
"""
This wrapper is intended to replicate the inputs of agpy's showspec.splat_1d code.
It is uglier than the spectrum class.
"""
import pyspeckit
def splat_1d(filename=None,vmin=None,vmax=None,button=None,dobaseline=False,
exclude=None,smooth=None,order=1,savepre=None,vcrop=True,
vconv=None,vpars=None... | keflavich/pyspeckit-obsolete | pyspeckit/wrappers/showspec_splat1d.py | Python | mit | 2,894 | [
"Gaussian"
] | 2d66b46ae62f0cc94ffa23ba05c707fd564269930a9ad0e81ecc84c92e810950 |
from kernel_exp_family.estimators.finite.gaussian import KernelExpFiniteGaussian
from kernel_exp_family.examples.demo_simple import ground_truth
from kernel_exp_family.examples.tools import pdf_grid, visualise_array
import matplotlib.pyplot as plt
import numpy as np
if __name__ == '__main__':
"""
Simple examp... | karlnapf/kernel_exp_family | kernel_exp_family/examples/demo_online_update_fit.py | Python | bsd-3-clause | 2,124 | [
"Gaussian"
] | 9a165585f271343b2113deb6df84dbfd57132e6d73e56a6d5267602d4e6c024c |
"""
This module uses the Khalil and Swenson models but fits directly to the inverse quality factors, since these are actually more
useful.
"""
from __future__ import division
import numpy as np
from scipy.special import cbrt
import lmfit
def parameters(f_r=100, i=1e-6, c=1e-5, c_imag=0, a=0, A=1, delay=0, phi=0, f_ph... | ColumbiaCMB/kid_readout | kid_readout/analysis/resonator/inverse.py | Python | bsd-2-clause | 4,335 | [
"Gaussian"
] | 4fdcb0a020648418374c61c81888f9285fc3e7919ecf4972b2173481ae8d26fd |
import fnmatch
import os
import pandas as pd
import cPickle as pickle
import subprocess
import csv
from collections import OrderedDict
def write_file(filename, contents):
"""Write the given contents to a text file.
ARGUMENTS
filename (string) - name of the file to write to, creating if it doesn't exist... | idbedead/RNA-sequence-tools | Count_Parsing/qsub_sort_htseq_count.py | Python | mit | 5,852 | [
"HTSeq"
] | 9b11cdcaec2f4d8d9eaeb28366088d642b88339fd621807a8cd202596008edb9 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | EmreAtes/spack | var/spack/repos/builtin/packages/cblas/package.py | Python | lgpl-2.1 | 2,365 | [
"BLAST"
] | 57d2c90e1ca52ab70c043f8382c445fe71cc23926017321eed18a13b0cf1770e |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.