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"""Gaussian processes regression. """
# Authors: Jan Hendrik Metzen <jhm@informatik.uni-bremen.de>
#
# License: BSD 3 clause
import warnings
from operator import itemgetter
import numpy as np
from scipy.linalg import cholesky, cho_solve, solve_triangular
from scipy.optimize import fmin_l_bfgs_b
from sklearn.base im... | vortex-ape/scikit-learn | sklearn/gaussian_process/gpr.py | Python | bsd-3-clause | 21,298 | [
"Gaussian"
] | 77951f6504ac6b518f254d28ede923d9acfd433d9d2cec25f15027db1fe3c6b3 |
# $Id$
#
# Copyright (C) 2003-2006 Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
import bisect
class TopNContainer(objec... | rdkit/rdkit-orig | rdkit/DataStructs/TopNContainer.py | Python | bsd-3-clause | 1,553 | [
"RDKit"
] | a4116eca4c1cd4258fbb5393221456a097ea51be39bf283e0884c920ff0d37ea |
import numpy as np
import tensorflow as tf
from elbow import Gaussian, Model
from elbow.models.factorizations import NoisyGaussianMatrixProduct, NoisySparseGaussianMatrixProduct
####################################################################
# methods to sample from a Gaussian matrix prior with uniform random
#... | davmre/elbow | examples/matrix_factorization.py | Python | bsd-3-clause | 2,980 | [
"Gaussian"
] | aaa3b563d71f25e60ed5f2501601ad6e7d531981aea29fbc446fd36a9c8ab794 |
# Copyright 2017 ProjectQ-Framework (www.projectq.ch)
#
# 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 app... | ProjectQ-Framework/FermiLib | src/fermilib/tests/_lih_integration_test.py | Python | apache-2.0 | 5,859 | [
"Psi4"
] | a3c441f669f45a29abf3669ce7709c4d98c3b0e386128fba43338e102efaecf1 |
#!/usr/bin/python
import i3ipc
import rofi
import sys
import time
from time import sleep
i3 = i3ipc.Connection()
menu = rofi.Rofi()
def scratchpad():
for con in i3.get_tree():
if(con.name == "__i3_scratch"):
return con
def get_windows():
wins = []
names = []
numEntries = 0
fo... | AnonymFox/dotfiles | i3-gaps/scratchpad.py | Python | mit | 817 | [
"Brian"
] | 8cabe76210848087a9c9efa4d77dfd85467734c470e84b8dca9eb4da33a595b2 |
#!/usr/bin/env python
'''
V2015-05-03
'''
import os
import csv
from itertools import ifilter
import sys
"""
COMMON FUNCTIONS
"""
def output_header_file_old(infile,skip,output_handle,sup_list=[],eliminate=0):
##Version1.0
##write header into files
reader=csv.reader(open(infile,"rU"),delimite... | bioliyezhang/KPAF_codes | shared_Python_library/File_Class.py | Python | mit | 37,124 | [
"BWA"
] | d2e7680ce307523ec6a425ec353d8e7e75f6323b4b3761622c13e85cb1fee5aa |
"""Configuration for the documentation scripts."""
import os
import glob
import logging
import argparse
from pprint import pformat
from configparser import ConfigParser
LOG = logging.getLogger(__name__)
K_DOCS = "Docs"
K_CFG = "CFG"
DEF_CFG_BASEFILE = "../dirac.cfg"
DEF_CFG_TARGETFILE = "source/ExampleConfig.rst"
... | DIRACGrid/DIRAC | docs/diracdoctools/Config.py | Python | gpl-3.0 | 8,377 | [
"DIRAC"
] | 866ceda6a18a5d82b407f68ff32c1177bde7451f260646ce40fe177432c9ca1f |
# -*- coding: utf8
#pylint: disable-msg=C0301
#pylint: disable-msg=C0111
#pylint: disable-msg=C0103
from __future__ import print_function, division
from tagassess import data_parser
from tagassess import test
import StringIO
import time
import unittest
DELICIOUS_LINE1 = '2003-01-01 01:00:00 2384 125497 tink... | flaviovdf/tag_assess | src/tagassess/test/test_data_parser.py | Python | bsd-3-clause | 6,291 | [
"TINKER"
] | 05dcaf3e1ad42e93e8952ca03a54cf69477861981966eee4b747b2f59d9e81c2 |
#! /usr/bin/python
###
###
###
### Script written by Ivan Sovic, August 2015.
### All rights reserved.
###
###
###
# Some comments on DALIGNER.
#
# Important about DB generation: DALIGNER splits the input reference fasta into chunks of non 'N' bases, as well as into chromosomes.
# E.g. Let's say we have hg19_chr3 as a ... | isovic/aligneval | wrappers/wrapper_daligner.py | Python | mit | 43,692 | [
"BLAST"
] | ff69170819555f1fa58a3c0d6ca2c1237b41ed4d74f73882e1a3071b55da9b22 |
"""
Support for managing apps (as created with "0install add").
@since: 1.9
"""
# Copyright (C) 2012, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall import _, SafeException, logger
from zeroinstall.support import basedir, portable_rename
from zeroinstall.injector impo... | slovenwd/0install | zeroinstall/apps.py | Python | lgpl-2.1 | 19,041 | [
"VisIt"
] | 47f2cff32de0a18d61e11806eb95a376ae283935b4e161b1b58e2d4eb8fdfc41 |
import csv
import io
import unittest
from nacc.uds3 import filters
class TestFilters(unittest.TestCase):
def test_filter_clean_ptid_removes_visits_in_nacc_current(self):
'''
`filter_clean_ptid` should remove visit data that is already in NACC's
Current database.
'''
subje... | ctsit/nacculator | tests/test_filters.py | Python | bsd-2-clause | 14,750 | [
"VisIt"
] | 23d81ea7a3bb627471602f042245492b62684f2b8c279539487627520c7dfbd2 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkContourGrid(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vt... | chrisidefix/devide | modules/vtk_basic/vtkContourGrid.py | Python | bsd-3-clause | 491 | [
"VTK"
] | 158e95112497d32503c401165b48c789fe26ae81d3dc862a687caa00b82c77b9 |
from qepy import *
from yambopy import *
from schedulerpy import *
import os
from copy import deepcopy
class YamboGkkpCompute():
"""
Class to obtain qe s.dbph* and yambo ndb.elph* databases starting from scratch.
It runs the necessary pw.x and ph.x simulations, optionally followed by the yambo setup.
... | alexmoratalla/yambopy | yambopy/gkkp/compute_gkkp.py | Python | bsd-3-clause | 14,445 | [
"CRYSTAL",
"Yambo"
] | d8f4d0dc98a07697e9c88107d06ba7101a96c62e269392f002886969ab29b0ef |
#! /usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-wms-jobs-select-output-search
# Author : Vladimir Romanovsky
########################################################################
"""
Retrieve output sandbox for DIRAC Jobs for the given ... | andresailer/DIRAC | Interfaces/scripts/dirac-wms-jobs-select-output-search.py | Python | gpl-3.0 | 3,268 | [
"DIRAC"
] | 8060c767420ef9b2a0dc1b96cabfe803a6706f40ce3c694980196ee8e57861a7 |
__RCSID__ = "$Id$"
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Core.Utilities import ThreadScheduler
from DIRAC.Core.Base.ExecutorMindHandler import ExecutorMindHandler
from DIRAC.WorkloadManagementSystem.Client.JobState.JobState import JobState
from DIRAC.WorkloadManagementSystem.Client.JobState.CachedJobSta... | fstagni/DIRAC | WorkloadManagementSystem/Service/OptimizationMindHandler.py | Python | gpl-3.0 | 7,781 | [
"DIRAC"
] | 5781453d9d0ae6a07668e17d52100c5221e5e7cfd70f5c9298011bd7c92784fb |
import suspect
import numpy as np
import warnings
warnings.filterwarnings("ignore", message="numpy.dtype size changed")
def test_sift_preserves_dtype():
time_axis = np.arange(0, 1.024, 1e-3)
input_signal = suspect.basis.gaussian(time_axis, 0, 0, 35)
input_signal += np.random.randn(1024) * 0.00001
co... | openmrslab/suspect | tests/test_mrs/test_processing/test_denoising.py | Python | mit | 1,648 | [
"Gaussian"
] | de65ceb689f17506e684967de6d5beb9381d82f52cce78f59427297b50a9bda0 |
# -*- coding: utf-8 -*-
"""
Created on Tue Jul 19 08:35:55 2016
@author: nn31
"""
import pandas as pd
import pickle
import matplotlib.pyplot as plt
from robocomp import Model
import matplotlib.dates as dt
import numpy as np
from datetime import datetime
#read in cmmi data
cmmi = pd.read_csv("/Volumes/DCCRP_projects/... | benneely/qdact-basic-analysis | notebooks/python_scripts/08_repeated_measures_viz.py | Python | gpl-3.0 | 2,451 | [
"VisIt"
] | 54df192b8037eb5aba1a3da0d8c8e7043ac3bc298d6528675aef50fda0286031 |
# 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... | kkreis/espressopp | src/interaction/StillingerWeberPairTermCapped.py | Python | gpl-3.0 | 11,269 | [
"ESPResSo"
] | 1665d12cef307dd99f8f49a06e59c09f9ae6b19ae138ed080b432cb216fe57dd |
#!/usr/bin/env python
# This tests vtkCompositeCutter
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
class TestCompositeCutter(Testing.vtkTest):
def testAMR(self):
filename= VTK_DATA_ROOT +"/Data/AMR/Enzo/DD0010/moving7_0010.hierar... | hlzz/dotfiles | graphics/VTK-7.0.0/Filters/Core/Testing/Python/TestCompositeCutter.py | Python | bsd-3-clause | 903 | [
"VTK"
] | 3aeb1946f0d78bac86ec9123b76c9ceee420ce61f286137c3eefe875cacf75da |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Corinne Maufrais
# Institut Pasteur, Centre d'informatique pour les biologistes
# corinne.maufrais@pasteur.fr
#
# version 2.1
import os
import sys
import argparse
try:
LIB = os.environ['RANKOPTIMIZERLIB']
except:
LIB = '/usr/local/bin'
if LIB not in sys.path:... | C3BI-pasteur-fr/taxo_pack | src/taxoextract.py | Python | gpl-3.0 | 2,816 | [
"BLAST"
] | 8551fd0894003d60ecd229b4932f9e19e20d56d18294727d396706590bc223aa |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import os
import tempfile
import unittest
import numpy as np
from pymatgen.core.structure import Structure
from pymatgen.io.abinit.inputs import (
BasicAbinitInput,
BasicMultiDataset,
ShiftMode,
... | gmatteo/pymatgen | pymatgen/io/abinit/tests/test_inputs.py | Python | mit | 10,923 | [
"ABINIT",
"pymatgen"
] | 6f54ae94afa1aae665aae0a564075fe29aa35fdcd5f5832ce5ffeb7d5f01a9e2 |
import logging, os, sys
from PyQt5.QtWidgets import (QVBoxLayout, QHBoxLayout, QListWidget, QWidget,
QListWidgetItem, QStackedLayout, QPushButton,
QLabel, QTabWidget, QLineEdit, QGroupBox, QFormLayout,
QCheckBox, QRadioButton, QSpinBox, QSizePolicy,
QScrollArea, QFontDialog)
from PyQt5... | peaceandpizza/happypanda | version/settingsdialog.py | Python | gpl-3.0 | 49,568 | [
"VisIt"
] | 848ad41fb51a25387ca1242c1ca8fe52d789de65d7e387253cd38a220b7508ee |
# Copyright (C) 2017 Antoine Fourmy <antoine dot fourmy at gmail dot com>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation.
#
# This program is distributed in the hope that it will be useful,
# ... | afourmy/pyNMS | pyNMS/networks/network.py | Python | gpl-3.0 | 88,769 | [
"VisIt"
] | 10632d3c75e91481eb204f061387160ecd648ae87c5f21ca2110f7da0ff1c835 |
from netCDF4 import Dataset
import json
# example showing how python objects (lists, dicts, None, True)
# can be serialized as strings, saved as netCDF attributes,
# and then converted back to python objects using json.
ds = Dataset('json.nc', 'w')
ds.pythonatt1 = json.dumps(['foo', {'bar': ['baz', None, 1.0, 2]}])
ds... | Unidata/netcdf4-python | examples/json_att.py | Python | mit | 688 | [
"NetCDF"
] | 106932fe09083a1a87126cd124cc69149e68f028415b1021b23f70a06d5d8a32 |
# Copyright (C) 2012 Aalto University
# Author: Lauri Leukkunen <lauri.leukkunen@aalto.fi>
from ase import Atoms
from ase.constraints import FixBondLengths
from ase.data.molecules import molecule
from ase.md.langevin import Langevin
from ase.md.verlet import VelocityVerlet
from ase.md.velocitydistribution import Maxwe... | csmm/multiase | tests/mixer/mixer_box.py | Python | gpl-2.0 | 9,168 | [
"ASE",
"GPAW",
"LAMMPS"
] | 3c52c361af15d6e12664ea86bb22f302e2933959b565f504c0ef7c1c119defc6 |
from ase.parallel import paropen
from ase.units import Hartree
from gpaw.xc.rpa import RPACorrelation
f = paropen('con_freq.dat', 'w')
for N in [4, 6, 8, 12, 16, 24, 32]:
rpa = RPACorrelation('N2.gpw', txt='rpa_N2_frequencies.txt', nfrequencies=N)
E = rpa.calculate(ecut=[50])
print >> f, N, E[0]
if N =... | robwarm/gpaw-symm | doc/tutorials/rpa/con_freq.py | Python | gpl-3.0 | 496 | [
"ASE",
"GPAW"
] | da329d0ff162d2dee1f72c13526e2b7c243ec643b08a221d4a80ee7e6aa2d46e |
# ----------------------------------------------------------------------------
# Copyright (c) 2016-2022, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ------------------------------------------------... | qiime2/qiime2 | qiime2/plugin/tests/test_plugin.py | Python | bsd-3-clause | 7,747 | [
"Octopus"
] | 8e06125473b7835b85401b3de24ef2971bc199bf4b71167a925d26fc5a726898 |
#! /usr/bin/env python
"""
Module with routines allowing for the estimation of the uncertainty on the
parameters of an imaged companion associated to residual speckle noise.
"""
__author__ = 'O. Wertz, C. A. Gomez Gonzalez, V. Christiaens'
__all__ = ['speckle_noise_uncertainty']
#import itertools as itt
from multip... | carlgogo/vip_exoplanets | vip_hci/negfc/speckle_noise.py | Python | bsd-3-clause | 12,649 | [
"Gaussian"
] | 3e289df5debf8f802a6c93ce4e5dcee83cb38ea666978a0904be7e57f8429f3f |
#!/usr/bin/env python
#
# Appcelerator Titanium Module Packager
#
#
import os, subprocess, sys, glob, string
import zipfile
from datetime import date
cwd = os.path.abspath(os.path.dirname(sys._getframe(0).f_code.co_filename))
os.chdir(cwd)
required_module_keys = ['architectures', 'name','version','moduleid','descripti... | Enouvo/TiGIF | iphone/build.py | Python | apache-2.0 | 8,495 | [
"VisIt"
] | 5d922cacab84d23b272cb925ac2bdd977e855fc898e9cad95fa758d3d2c496b1 |
#!/usr/bin/env python
SITES = {
'163' : 'netease',
'56' : 'w56',
'acfun' : 'acfun',
'archive' : 'archive',
'baidu' : 'baidu',
'bandcamp' : 'bandcamp',
'baomihua' : 'baomihua',
'bigthink' : 'bigthink',
... | zmwangx/you-get | src/you_get/common.py | Python | mit | 46,899 | [
"VisIt"
] | 94dd5d8ab223a51dbc8c2c1b8b0d533dcfa7f3ca29ab26869a51e1fffc7d239a |
"""Utilities for building response surface approximations."""
import numpy as np
from scipy.optimize import fminbound
from scipy.misc import comb
from misc import process_inputs, process_inputs_outputs
class ResponseSurface():
"""An abstract class for response surfaces.
Attributes
----------
N : int
... | paulcon/active_subspaces | active_subspaces/utils/response_surfaces.py | Python | mit | 17,856 | [
"Gaussian"
] | c2c10678ebe87d1f18f5ff9d2b95fa0cffb634b66f9d2b68e37b3b1d3ee2c340 |
import unittest
from test import support
from itertools import *
from weakref import proxy
from decimal import Decimal
from fractions import Fraction
import sys
import operator
import random
import copy
import pickle
from functools import reduce
maxsize = support.MAX_Py_ssize_t
minsize = -maxsize-1
def lzip(*args):
... | MalloyPower/parsing-python | front-end/testsuite-python-lib/Python-3.2/Lib/test/test_itertools.py | Python | mit | 69,134 | [
"GULP"
] | 6e3883f83ef19af4d497d29ee32e0e5107e5bec080d8e736c3bb70e4901890c4 |
################################################################################
#
# RMG - Reaction Mechanism Generator
#
# Copyright (c) 2002-2017 Prof. William H. Green (whgreen@mit.edu),
# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu)
#
# Permission is hereby granted, free of cha... | Molecular-Image-Recognition/Molecular-Image-Recognition | code/rmgpy/qm/mopac.py | Python | mit | 16,212 | [
"MOPAC",
"cclib"
] | be0e2961b6b33f41a68b182585a3c1744b89f594eefec0fbe265d8be142f9fe4 |
# $Id$
#
# Copyright (C) 2000-2008 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" command line utili... | rdkit/rdkit | rdkit/ML/ScreenComposite.py | Python | bsd-3-clause | 55,093 | [
"RDKit"
] | 9c9705c6b11a2f0265d2bfe5d321eceb2dd6deec53e0e30145a8467951b9a084 |
#!/usr/bin/python
#SBATCH --job-name=mmp_tel
#SBATCH --output=../log/%j.txt
#SBATCH --error=../log/%j.out
#SBATCH --partition=compute
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=4
#SBATCH --nodes=1
#SBATCH --mem=16384
#SBATCH --mail-user=dec@u.northwestern.edu
#SBATCH --workdir=/lscr2/andersenlab/... | AndersenLab/mmp-telseq | mmp_telseq.py | Python | mit | 9,002 | [
"BWA"
] | 4426c0cf3f32918566db42f1b2661df11cf614c6abb4c7141b095f05ef41dbd6 |
# 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... | tqchen/tvm | python/tvm/relay/expr_functor.py | Python | apache-2.0 | 7,280 | [
"VisIt"
] | d895b9cdd8432e9dbfa420749175ffcea78efe98a868473029fca318c87cd1bc |
#################################################
## rotate_mol_vasp.py #
## Decription: Rotate a molecule from POSCAR #
## Developver: feihoom82@gmail.com #
## Date: 2018-05-02 #
#################################################
### Start of Seting ###
center = 65 # Index of the center atom
ids_mol = ... | cwandtj/A2P2 | tools/rotate_mol_vasp.py | Python | mit | 3,145 | [
"ASE"
] | 6c4af9b44d8b01c48d7827e9ceaecbe3e45d16712a0ca5204e39290c8e5f89c4 |
from __future__ import unicode_literals
import base64
import datetime
import hashlib
import json
import netrc
import os
import re
import socket
import sys
import time
import xml.etree.ElementTree
from ..utils import (
compat_http_client,
compat_urllib_error,
compat_urllib_parse_urlparse,
compat_urlpar... | xu-cheng/youtube-dl | youtube_dl/extractor/common.py | Python | unlicense | 32,240 | [
"VisIt"
] | 47a0ee592f3d29fe619ebf01842f168db198400ae1fce72770b84b3dbeb0e0da |
# -*- coding: latin-1 -*-
import os
import sys
import shutil
import string
import makerEditorWxView
import makerCopyright
import wx.lib.buttons
import wx.gizmos
import wx.lib.imagebrowser as ib
from wx.lib.anchors import LayoutAnchors
import wx.lib.flatnotebook as nb
import wx.py as pyShell
import math
# Used on OS... | geraldspreer/the-maker | makerWxGUI.py | Python | gpl-3.0 | 128,335 | [
"VisIt"
] | 9af54592ed685b8aebb3a255d049474dcbfe2e1a0b8bdde8451f31e0d5e389ee |
#! /usr/bin/env python
"""
Author: Robert A Petit III.
Date: 03/28/2016
Read Jellyfish counts of non-B. anthracis BCG members and determine the BCG
kmer coverage and the false positives for B. anthracis kmers.
"""
import argparse as ap
import json
if __name__ == '__main__':
parser = ap.ArgumentParser(
... | Read-Lab-Confederation/nyc-subway-anthrax-study | data/05-custom-bcg-assay/bin/parse-hamming-distance.py | Python | mit | 1,642 | [
"BLAST"
] | a8f294d90f03006ddd3a7dd11e936faa95e067969e2a56436cb0217e0ffe8459 |
import abc
import math
import numpy as np
import scipy.stats
UNDEFINED = - np.inf
class Prior(object):
__metaclass__ = abc.ABCMeta
def __init__(self, prior_name):
self._prior_name = prior_name
@property
def name(self):
"""Return the name of the function"""
return self._pri... | sybenzvi/3ML | threeML/bayesian/priors.py | Python | bsd-3-clause | 6,566 | [
"Gaussian"
] | f7e3ded7977bca9613fa99a6e2524536d8f6b0c516e3c47ab10eb0fe881c9ed7 |
# -*- coding: utf-8 -*-
from __future__ import absolute_import, division, print_function, unicode_literals
from gratipay.testing import BrowserHarness
class Tests(BrowserHarness):
def check(self, status, has_request_button, has_check_button):
self.make_participant('alice', claimed_time='now', status_of_... | gratipay/gratipay.com | tests/ttw/test_1_0_payout.py | Python | mit | 1,241 | [
"VisIt"
] | f9016469af0dee6cd26b4c08c933ddff9c981786533910d57708c09f9d439768 |
"""Quality control and summary metrics for next-gen alignments and analysis.
"""
import collections
import contextlib
import csv
import os
import glob
import shutil
import subprocess
import pandas as pd
import lxml.html
import yaml
from datetime import datetime
from collections import defaultdict
# allow graceful duri... | gifford-lab/bcbio-nextgen | bcbio/pipeline/qcsummary.py | Python | mit | 52,291 | [
"pysam"
] | 0a0ac64f12c7f2dc31bc6dc0e3212c42c29b2c8eadd9686bc89297ec68e32d46 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# This example demonstrates how to use a matrix in place of a transfrom
# via vtkMatrixToLinearTransform and vtkMatrixToHomogeneousTransform.
# create a rendering window
renW... | hlzz/dotfiles | graphics/VTK-7.0.0/Common/Transforms/Testing/Python/MatrixToTransform.py | Python | bsd-3-clause | 6,605 | [
"VTK"
] | e4315771e04c912a5e2df7775c9519eb8bba90fb81f5b2dea103c3e4ac4402df |
import os, sys
import unittest
from __main__ import vtk, qt, ctk, slicer
from slicer.ScriptedLoadableModule import *
import logging
# # Add the CIP common library to the path if it has not been loaded yet
# try:
# from CIP.logic.SlicerUtil import SlicerUtil
# except Exception as ex:
# import inspect
# path... | acil-bwh/SlicerCIP | Scripted/CIP_Blank/CIP_Blank.py | Python | bsd-3-clause | 6,109 | [
"VTK"
] | 850b50de14297afc3fc7d527cbda2a4a5d01c68c18125cd1d734a0dc0f86fc7f |
""" Load Region from NeuroHDF and apply measures to retrieved trees """
from unidesign.spatial.group import Region, Treelines, Connectors
from neurohdf import File
f = File('mydataset.nh5', 'r')
# wrap a region
myregion = Region.from_neurohdf(f, 'neuropile', memmapped = False)
# fetch cells
# level defines how many... | unidesigner/unidesign | unidesign/spatial/tests/test_spatial2.py | Python | bsd-3-clause | 1,173 | [
"NEURON"
] | 9f75e97cfc588c30ff3f3d9c7ed26a941c61b3e5f841b436c80b45c3f49b10fd |
# -*- coding: utf-8 -*-
{
"'Sounds-like' name search allowing search even the spelling of the name is not known exactly": "'Sounds-like'名稱搜尋或搜尋,即使名稱的拼字不完全",
"A location that specifies the geographic area for this region. This can be a location from the location hierarchy, or a 'group location', or a location that ha... | gnarula/eden_deployment | languages/zh-tw.py | Python | mit | 338,613 | [
"VisIt"
] | 17461ed23fc22fbfdbd441c8ba2565277fe34d7ba7aac1da4e2d9f2f5c42add2 |
###############################################################################
##
## Copyright (C) 2014-2016, New York University.
## Copyright (C) 2011-2014, NYU-Poly.
## Copyright (C) 2006-2011, University of Utah.
## All rights reserved.
## Contact: contact@vistrails.org
##
## This file is part of VisTrails.
##
## ... | VisTrails/VisTrails | vistrails/packages/vtk/__init__.py | Python | bsd-3-clause | 3,146 | [
"VTK"
] | 84507dfae34d7864132af3e74891a75d7bdbc75e8d215579be12162c77994473 |
""" Principal Component Analysis
"""
# Author: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Olivier Grisel <olivier.grisel@ensta.org>
# Mathieu Blondel <mathieu@mblondel.org>
# License: BSD Style.
import numpy as np
import warnings
from scipy import linalg
from math import log
from ..base impor... | lucidfrontier45/scikit-learn | sklearn/decomposition/pca.py | Python | bsd-3-clause | 18,088 | [
"Gaussian"
] | ff41b7cf69a9c126686ee5427de850a7a74b7fc81785bf17aa68313291698184 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#############################################################################
# Copyright 2016 Konrad Sakowski
#
# 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 c... | ghkonrad/bublus | libbublus.py | Python | apache-2.0 | 16,357 | [
"Galaxy"
] | 5317000cf9a80936973403266e4ba516fb53844fe0dbf0390cb1543d07e795b9 |
import mdtraj
import numpy as np
from subprocess import call, PIPE
def write_cpptraj_script(traj, top, frame1=1, frame2=1,
outfile=None, write=True, run=False):
"""
Create a cpptraj script to load specific range of frames from a trajectory and write them out to a file
:param traj... | jeiros/Scripts | AnalysisMDTraj/traj_utils.py | Python | mit | 8,855 | [
"MDTraj",
"NetCDF"
] | 134940efef3755013a11eaa7db23ac40e081351faf2c24a1482ae77957be9f38 |
from .base import Message
from .decoder import register_to_decoder
@register_to_decoder()
class ControlConstantsMessage(Message):
"""
Receive Control Constants changes
"""
cmd = 'S'
mode = None
beer_setpoint = None
fridge_setpoint = None
data_mapping = {
'mode': 'mode',
... | glibersat/brewpiv2 | brewpiv2/messages/control.py | Python | agpl-3.0 | 4,405 | [
"VisIt"
] | 3b8c6f5b4506dec1ec9207a37a37a4aebe3b910370d1581f921ef62444bc63e2 |
# Copyright 2014 Google Inc. All Rights Reserved.
"""Command for creating images."""
from googlecloudsdk.calliope import exceptions
from googlecloudsdk.compute.lib import base_classes
from googlecloudsdk.compute.lib import constants
from googlecloudsdk.compute.lib import utils
class Create(base_classes.BaseAsyncCreat... | harshilasu/LinkurApp | y/google-cloud-sdk/lib/googlecloudsdk/compute/subcommands/images/create.py | Python | gpl-3.0 | 3,836 | [
"VisIt"
] | f6df4be3cb37306e375625e46f0a9b1f36f6031ec81ed4c396d3b2f9c6f8d9d0 |
import os
import fileinput
import sys
from os.path import join, getsize
licenseFile = open( "COPYING" )
licenseLines = licenseFile.readlines( 100000 )
total = 0
for root, dirs, files in os.walk(sys.argv[1]):
for name in files:
f = open( join(root, name), "r+" )
fileLines = f.readlines(100000)
... | 2666hz/Cinder | tools/scripts/prependLicense.py | Python | bsd-2-clause | 622 | [
"VisIt"
] | 63cc77504fdfff0bbd2f56d6e2c3b9ab3aa6339646aed03a1ccef523782aa4da |
import pylab as pyl
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy as scp
import scipy.ndimage as ni
import scipy.io
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import rospy
#import hrl_lib.mayavi2_util as mu
import hrl_lib.viz as hv
import hrl_lib.... | tapomayukh/projects_in_python | classification/Classification_with_HMM/Single_Contact_Classification/simulation_results/Combined/object_training/hmm_crossvalidation_force_motion_10_states_object_training_all_testing.py | Python | mit | 16,524 | [
"Gaussian",
"Mayavi"
] | 73de233246dbe7ac84263911f087ee8c1f89d8de9c4bca98e568ba7687794a08 |
# -*- coding: utf-8 -*-
"""Algorithms for spectral clustering"""
# Author: Gael Varoquaux gael.varoquaux@normalesup.org
# Brian Cheung
# Wei LI <kuantkid@gmail.com>
# License: BSD 3 clause
import warnings
import numpy as np
from sklearn.utils import check_random_state
from sklearn.utils.validation im... | slipguru/ignet | icing/externals/spectral.py | Python | bsd-2-clause | 13,176 | [
"Brian",
"Gaussian"
] | 3363f58de07e83d2d650d9e9a53e1ab1fec62a8cc2a32e10ea1aa7dac0990966 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (C) Pootle contributors.
#
# This file is a part of the Pootle project. It is distributed under the GPL3
# or later license. See the LICENSE file for a copy of the license and the
# AUTHORS file for copyright and authorship information.
import logging
from d... | Yelp/pootle | pootle/core/initdb.py | Python | gpl-3.0 | 9,174 | [
"VisIt"
] | 2145d91ccbf546eab9b08b98106a5ae69a7b80b07a0dc45c2c7252cc01e8a271 |
##############################################################################
#
# Copyright (c) 2009-2013 by University of Queensland
# http://www.uq.edu.au
#
# Primary Business: Queensland, Australia
# Licensed under the Open Software License version 3.0
# http://www.opensource.org/licenses/osl-3.0.php
#
#... | squireg/ANVGL-Portal | src/main/resources/org/auscope/portal/server/scriptbuilder/templates/escript-joint.py | Python | lgpl-3.0 | 4,365 | [
"NetCDF",
"VisIt"
] | 79ea526a6d42b9a234eff7ca33965771e7cad6449f04bdd6539a995e93a3c3e8 |
"""
Communicability and centrality measures.
"""
# Copyright (C) 2011 by
# Aric Hagberg <hagberg@lanl.gov>
# Dan Schult <dschult@colgate.edu>
# Pieter Swart <swart@lanl.gov>
# All rights reserved.
# BSD license.
import networkx as nx
__author__ = "\n".join(['Aric Hagberg (hagberg@lanl.gov)',
... | ChristianKniep/QNIB | serverfiles/usr/local/lib/networkx-1.6/networkx/algorithms/centrality/communicability_alg.py | Python | gpl-2.0 | 16,015 | [
"Desmond"
] | 200b2aecba87cb33a3f09b7f594440d64f5ceabe82e317f6fb97c9d250f4e77c |
# Copyright (c) 2014, James Hensman, Alan Saul
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import numpy as np
from ..core import GP
from ..core.parameterization import ObsAr
from .. import kern
from ..core.parameterization.param import Param
from ..inference.latent_function_inference import VarGauss
l... | jameshensman/GPy | GPy/models/gp_var_gauss.py | Python | bsd-3-clause | 1,230 | [
"Gaussian"
] | 7b7db0a333d9b28ee399bfd1c428200ba49c3629eb9e3af0184eca06780e379b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# @Author: Li Yao
# @File: prepare-data-for-giremi.py
# @License: MIT
# @Bitbutcket: https://bitbucket.org/li_yao/
# @Github: https://github.com/liyao001
import pysam
import getopt
import sys
def is_snp(table, chrom, pos):
flag = 0
try:
for hit in table.f... | yaoli95/biotoolset | convert/prepare-data-for-giremi.py | Python | gpl-3.0 | 2,454 | [
"pysam"
] | f19d1f0161fe9d9edc9ea9004671a7c4c70e8a44e2ee6e420d92edc21fc6d757 |
########################################################################
# $HeadURL$
# File : CREAMComputingElement.py
# Author : A.T.
########################################################################
""" CREAM Computing Element
"""
__RCSID__ = "$Id$"
from DIRAC.Resources.Computing.ComputingElement ... | calancha/DIRAC | Resources/Computing/CREAMComputingElement.py | Python | gpl-3.0 | 14,506 | [
"DIRAC"
] | c54394b084eaa692bf5fa33051ecccd9e90d0c7bd09d25b2b7d6965c71a4fc7f |
''' FreeDiskSpaceCommand
The Command gets the free space that is left in a Storage Element
Note: there are, still, many references to "space tokens",
for example ResourceManagementClient().selectSpaceTokenOccupancyCache(token=elementName)
This is for historical reasons, and shoud be fixed one day.
... | andresailer/DIRAC | ResourceStatusSystem/Command/FreeDiskSpaceCommand.py | Python | gpl-3.0 | 5,209 | [
"DIRAC"
] | b18d539b7a106e8d947dfed618f07029dfa5d0570f9a527ac911997a49424346 |
"""ropemacs, an emacs mode for using rope refactoring library"""
import sys
import ropemode.decorators
import ropemode.environment
import ropemode.interface
from Pymacs import lisp
from rope.base import utils
class LispUtils(ropemode.environment.Environment):
def ask(self, prompt, default=None, starting=None):
... | mcepl/ropemacs | ropemacs/__init__.py | Python | gpl-2.0 | 24,177 | [
"VisIt"
] | 426078099fdb042d3d5d0012b7b11395bc0f91eb6d41c58fb53bb333da672327 |
import sys, os, re
import subprocess
from os import listdir
from os.path import isfile, join
from datetime import datetime
from tqdm import tnrange, tqdm_notebook
'''
main
1. find r1,r2-good_pairs in input directory (*.fastq)
2. run bwa mem (mapping) on it
'''
def main(inputdir, outputdir, refway, bwaline):
befor... | labcfg/retroparty | bwamem.py | Python | apache-2.0 | 2,401 | [
"BWA"
] | 7e4b23f94febbc776ee43ae4316b18145412fe238e2c7b68ba00343cef416b83 |
# 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/.
import sys
import os
def welcome():
"""
Perform a bunch of sanity tests to make sure the Add-on SDK
environ... | Yukarumya/Yukarum-Redfoxes | addon-sdk/source/python-lib/jetpack_sdk_env.py | Python | mpl-2.0 | 2,637 | [
"VisIt"
] | 02cf3b15fc41b73fe3ea46fc351c493d751bf3910ec51efbc173d8d5f9a7304f |
# -*- coding: utf-8 -*-
# Part of Odoo. See LICENSE file for full copyright and licensing details.
import logging
import random
from odoo import api, models, fields, tools, _
from odoo.http import request
from odoo.exceptions import UserError, ValidationError
_logger = logging.getLogger(__name__)
class SaleOrder(mo... | ayepezv/GAD_ERP | addons/website_sale/models/sale_order.py | Python | gpl-3.0 | 21,571 | [
"VisIt"
] | 1cf2c05e565278f7282d87e3bf010d3cc8293d7d2ac7f02a8dc9dd8c68966f2e |
#! /usr/bin/python3 -B
# *************************************************** *
# This file is a part of ccROJ project *
# distributed under GNU General Public License v3.0. *
# Please visit the webpage: github.com/dsp-box/ccROJ *
# for more information. *
# ... | dsp-box/ccROJ | scripts/doc-gener.py | Python | gpl-3.0 | 5,650 | [
"VisIt"
] | 90f4f91d5b035e43e90d7ee927f715d44e83653c4a4ca5f2a32ea49be6618cca |
import sys
PY3 = (sys.version_info[0] >= 3)
if PY3:
string_types = str,
else:
string_types = basestring,
from pybindgen.utils import any, mangle_name
import warnings
import traceback
from pybindgen.typehandlers.base import Parameter, ReturnValue, \
join_ctype_and_name, CodeGenerationError, \
param_... | gjcarneiro/pybindgen | pybindgen/cppclass.py | Python | lgpl-2.1 | 175,750 | [
"VisIt"
] | 1f5007262875ae849cf2e710e96117bcda2cd102868d11eaa9f09315077efff9 |
#!/usr/bin/python
#
# Simple script which convert the FITS headers associated to Brian McLean DSS images into simplified JSON files
# Fabien Chereau fchereau@eso.org
#
import math
import os
import sys
import Image
from astLib import astWCS
import skyTile
levels = ["x64", "x32", "x16", "x8", "x4", "x2", "x1"]
# Defi... | Stellarium/stellarium | util/dssheaderToJSON.py | Python | gpl-2.0 | 8,050 | [
"Brian"
] | 13f2ddd646556ea9929dbae2051e7c4d171cfcd6a48a06bc1e1c2fe28b227480 |
#!/bin/python
import vtk
import vtk.util.colors
points = vtk.vtkPoints()
points.InsertNextPoint(0, 0, 0)
points.InsertNextPoint(0, 1, 0)
points.InsertNextPoint(1, 0, 0)
points.InsertNextPoint(0, 0, 1)
pointsPolyData = vtk.vtkPolyData()
pointsPolyData.SetPoints(points)
vertexFilter = vtk.vtkVertexGlyphFilter()
verte... | trianam/tests | python/vtkPoints.py | Python | gpl-2.0 | 1,012 | [
"VTK"
] | 1d297a7d8e1221da609434a07bf3ee4a90cfa9dd92ec138d6d9dcf9b87384b44 |
# Licensed under GPL version 3 - see LICENSE.rst
import inspect
from functools import wraps
import collections
from copy import copy
import warnings
import numpy as np
from transforms3d import affines, euler
from astropy.table import Table
from astropy import table
import astropy.units as u
from ..simulator import Par... | hamogu/marxs | marxs/design/tolerancing.py | Python | gpl-3.0 | 26,010 | [
"Gaussian"
] | 93364b723ac96f2d27a49d28d857e5fa268fb23bfe7c356e3854a32a65efaf02 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
... | alejob/mdanalysis | testsuite/MDAnalysisTests/test_deprecated.py | Python | gpl-2.0 | 2,753 | [
"MDAnalysis"
] | 3287311019df34fba7daa0a3e0c22ea7640f9bc87361b520a582311fed094283 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
import unittest
from pymatgen.electronic_structure.core import Orbital, Spin
class SpinTest(unittest.TestCase):
def test_init(self):
self.assertEqual(int... | migueldiascosta/pymatgen | pymatgen/electronic_structure/tests/test_core.py | Python | mit | 1,059 | [
"pymatgen"
] | 4b8d509346e2cd2e7133fae43f135bf89ccf388ddd331e737f56e40492eaeb2e |
#!/usr/bin/env
import argparse
import json
import os
import subprocess
import sys
import requests
from tnseq_api import authenticateByEnv
# Number of reads to use for approximating average read length.
READ_LEN_SAMPLE = 10
# Approximate length of barcode to remove from read 2 with paired end reads.
# This is used t... | PATRIC3/p3_tnseq | service-scripts/p3_tnseq.py | Python | mit | 22,831 | [
"BWA",
"Bowtie"
] | 4134c4b193a13bb866687ba70324508a4816a1678fc9aa5374b3bc086ec4240c |
import cart
import math
import gui
import random
import brain
import copy
import pool
def randomSeed():
"""
Random number between -0.5 and 0.5
"""
return (0.5 - random.random())
def randomWeights(sizes,fact):
weight=[]
for i in range(len(sizes)-1):
... | pauljohnleonard/pod-world | CI_2014/ATTIC/PJL/03_ga_main.py | Python | gpl-2.0 | 4,830 | [
"NEURON"
] | b579128c9e47268091a7ef660d35111c422dfd80e5ccab221926c8b958949eb4 |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RKernlab(RPackage):
"""Kernel-Based Machine Learning Lab
Kernel-based machine learnin... | LLNL/spack | var/spack/repos/builtin/packages/r-kernlab/package.py | Python | lgpl-2.1 | 1,244 | [
"Gaussian"
] | 5bae81d3e85cdd5e9ba08fe3b6fc1f41fe5f75af28d0db3c5c17b522d511bd15 |
#!/usr/bin/python
#Audio Tools, a module and set of tools for manipulating audio data
#Copyright (C) 2007-2012 Brian Langenberger
#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 2... | R-a-dio/python-audio-tools | audiotools/py_decoders/wavpack.py | Python | gpl-2.0 | 38,340 | [
"Brian"
] | c96418e9f675acdf43103b09d566b1d0c9ebb16608c10b6b2174df75d4e2043a |
# This file is part of the Minecraft Overviewer.
#
# Minecraft Overviewer is free software: you can redistribute it and/or
# modify it under the terms of the GNU General Public License as published
# by the Free Software Foundation, either version 3 of the License, or (at
# your option) any later version... | enaut/Minecraft-Overviewer | overviewer_core/textures.py | Python | gpl-3.0 | 265,312 | [
"BLAST",
"CRYSTAL"
] | 7d5effb9846602f32a849855b871097d166bda3fd9a0469c02e069619727e732 |
from sqlalchemy import extract
from sqlalchemy import select
from sqlalchemy import sql
from sqlalchemy.dialects import sybase
from sqlalchemy.testing import assert_raises_message
from sqlalchemy.testing import AssertsCompiledSQL
from sqlalchemy.testing import fixtures
class CompileTest(fixtures.TestBase, AssertsComp... | graingert/sqlalchemy | test/dialect/test_sybase.py | Python | mit | 1,838 | [
"ASE"
] | 0025d8987321a038a889186e9019c1c79b46a99703695a492086bcfe8d822ed3 |
# Copyright Iris contributors
#
# This file is part of Iris and is released under the LGPL license.
# See COPYING and COPYING.LESSER in the root of the repository for full
# licensing details.
"""Integration tests for loading and saving netcdf files."""
# Import iris.tests first so that some things can be initialised ... | pp-mo/iris | lib/iris/tests/integration/test_climatology.py | Python | lgpl-3.0 | 3,683 | [
"NetCDF"
] | e39f445cbbad07559e68edf1720b47686506531dcd99fe402f39838a27103d4e |
from __future__ import unicode_literals
import base64
import datetime
import hashlib
import json
import netrc
import os
import re
import socket
import sys
import time
from ..compat import (
compat_cookiejar,
compat_cookies,
compat_getpass,
compat_http_client,
compat_urllib_error,
compat_urllib... | lzambella/Qyoutube-dl | youtube_dl/extractor/common.py | Python | gpl-3.0 | 67,363 | [
"VisIt"
] | 6895605ae4fb868ecdd6038782fea805c8523fe89d9d9aae2acfc530562610dc |
"""Low-level interface to NCBI's EUtils for Entrez search and retrieval.
For higher-level interfaces, see DBIdsClient (which works with a set
of database identifiers) and HistoryClient (which does a much better
job of handling history).
There are five classes of services:
ESearch - search a database
EPost - uploa... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/EUtils/ThinClient.py | Python | apache-2.0 | 47,176 | [
"Biopython"
] | f78353031eb28935b0699675b8a0fcf2d1de23478dd88b574174844eb85bb441 |
""" RHEAS module for retrieving meteorological forecasts/hindcasts
from the IRI FD Seasonal Forecast Tercile Probabilities.
.. module:: iri
:synopsis: Retrieve IRI meteorological forecast data
.. moduleauthor:: Kostas Andreadis <kandread@jpl.nasa.gov>
"""
import datasets
import dbio
import netCDF4 as netcdf
impo... | nasa/RHEAS | src/datasets/iri.py | Python | mit | 11,845 | [
"NetCDF"
] | b43295adac57da3f8aa6ff3804e8d088c8a0de6182859c8973b7c4516aa792e1 |
import os
import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.axes_grid1 import ImageGrid
import random
import logging
logger = logging.getLogger()
import time
import pprint
from astroML.stats import binned_statistic_2d
import brewer2mpl
import ResolvedStellarPops as rsp
import ResolvedStellarPops.co... | philrosenfield/TPAGB-calib | sfh_tests.py | Python | bsd-3-clause | 76,643 | [
"Galaxy",
"Gaussian"
] | 099a3393b5104f327ce26e9a066104f4c99874862877c0bb1ca20ced0cc344ba |
#
# Copyright (C) 2013-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | pkreissl/espresso | testsuite/python/hat.py | Python | gpl-3.0 | 2,084 | [
"ESPResSo"
] | e1e519f3a2557baf3b4447a1011e94da3dd00bae4c6192a1b5dfe764dc88864a |
# Copyright (c) 2011, Jimmy Cao
# All rights reserved.
# Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
# Redistributions of source code must retain the above copyright notice, this list of conditions and the following dis... | Vgr255/Wolfbot | modules/wolfgame.py | Python | bsd-2-clause | 196,307 | [
"VisIt"
] | b58b01639304c39c994882aa5d5a35f520529af9c3e12b1163d36e0f388c34db |
""" This object is a wrapper for setting and getting jobs states
"""
__RCSID__ = "$Id"
import datetime
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.WorkloadManagementSystem.Client.JobState.JobManifest import JobManifest
from DIRAC.Core.DISET.RPCClient import RPCClient
from DIRAC.WorkloadManagementSystem.Servic... | andresailer/DIRAC | WorkloadManagementSystem/Client/JobState/JobState.py | Python | gpl-3.0 | 17,258 | [
"DIRAC"
] | 2ce1c582dbb55f02b8aef29aecda6c14ba1d4cef50d6d7b8bfffebfa78f3310e |
# coding: utf-8
# # 2016 US Bike Share Activity Snapshot
#
# ## Table of Contents
# - [Introduction](#intro)
# - [Posing Questions](#pose_questions)
# - [Data Collection and Wrangling](#wrangling)
# - [Condensing the Trip Data](#condensing)
# - [Exploratory Data Analysis](#eda)
# - [Statistics](#statistics)
# ... | Hiteshsaai/BikeShare_DataAnalysis | Bike_Share_Analysis.py | Python | mit | 39,685 | [
"VisIt"
] | 585e653232a4b871d1cc3c548aee05c0e9d28be7284a9b029c9b86347496924f |
import numpy as np
import numpy.linalg as la
from pysal.spreg.utils import RegressionPropsY, spdot
import pysal.spreg.user_output as USER
from utils import cache_readonly
from base import LikelihoodModelResults
import family
from iwls import iwls
__all__ = ['GLM']
class GLM(RegressionPropsY):
"""
Generalised... | CartoDB/crankshaft | release/python/0.8.2/crankshaft/crankshaft/regression/glm/glm.py | Python | bsd-3-clause | 11,848 | [
"Gaussian"
] | 3d6f294a3da69a5ca48b623a1f27bb57827a01852bbc50258078237eb2e5f2d6 |
'''Tools for working with files in the samtools pileup -c format.'''
try:
from collections import namedtuple
except:
from namedtuple import namedtuple
import pysam
PileupSubstitution = namedtuple( "PileupSubstitution",
" ".join( (\
"chromosome",
"pos... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg/pysam/Pileup.py | Python | gpl-3.0 | 2,017 | [
"pysam"
] | 06093ddfb38629a1883cb6cf27e4b4278d6d178c2cea29a38e25930c77e2239a |
import numpy as np
import scipy as sp
from peri import runner, util
from peri.viz.plots import generative_model
import pickle
import matplotlib.pyplot as pl
import matplotlib.gridspec as gridspec
from mpl_toolkits.axes_grid1.inset_locator import zoomed_inset_axes
from mpl_toolkits.axes_grid1.inset_locator import mark_... | peri-source/peri | scripts/figures/generative-model.py | Python | mit | 1,123 | [
"CRYSTAL",
"Gaussian"
] | 3f4cd3e325a9c32ed6eedaae4e9c02fbc9b72ada7cbaa1754c377a2fba429911 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides classes to interface with the Crystallography Open
Database. If you use data from the COD, please cite the following works (as
stipulated by the COD developers)::
Merkys, A., Vaitk... | mbkumar/pymatgen | pymatgen/ext/cod.py | Python | mit | 5,175 | [
"CRYSTAL",
"pymatgen"
] | deeb00b0bb59c855c23a766835e103d14d1133ff1a7a39c21e2f021a711220fd |
"""Tests for indenter.py."""
# Author: Prabhu Ramachandran
# License: BSD style
# Copyright (c) 2004, Enthought, Inc.
import unittest
import cStringIO
from tvtk import indenter
class TestIndent(unittest.TestCase):
def test_basic(self):
"""Simple tests for indenter."""
id = indenter.Indent()
... | liulion/mayavi | tvtk/tests/test_indenter.py | Python | bsd-3-clause | 9,233 | [
"VTK"
] | 9d423ce83e2e73079b5bf613629e73809c9355af1f1b1f7af0897dc3e4c6973c |
"""
Opendrift module
.. currentmodule:: opendrift
"""
import logging; logger = logging.getLogger(__name__)
import unittest
import importlib
import platform
import numpy as np
import time
from datetime import timedelta
from .version import __version__
# For automated access to available drift classes, e.g. for GUI
# ... | OpenDrift/opendrift | opendrift/__init__.py | Python | gpl-2.0 | 7,293 | [
"NetCDF"
] | d890f52d3a99f104e587c48d0c884bf74a09e2b68553ce810de83a997c712925 |
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | gkc1000/pyscf | pyscf/nao/test/test_0039_openmx_nao.py | Python | apache-2.0 | 1,079 | [
"OpenMX",
"PySCF"
] | d926fb3dd2fec969b1d5ff34a8fa90be4ea9a5deda9589bb7f2f7ea64436af0d |
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Mathieu Blondel <mathieu@mblondel.org>
# Olivier Grisel <olivier.grisel@ensta.org>
# Andreas Mueller <amueller@ais.uni-bonn.de>
# License: BSD 3 clause
import numbers
import warnings
import numpy as np
from scipy import sparse
fr... | depet/scikit-learn | sklearn/preprocessing/data.py | Python | bsd-3-clause | 34,765 | [
"Gaussian"
] | b34a1a6ff5c45ef4417908529ef4047a6fa68b03f158b5b27e79fd61028fa5ff |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
from pathlib import Path
import os
import numpy as np
from pymatgen.core.operations import SymmOp
from pymatgen.core.sites import PeriodicSite
from pymatgen.core.structure import Molecule, Structure
from pyma... | vorwerkc/pymatgen | pymatgen/symmetry/tests/test_analyzer.py | Python | mit | 28,003 | [
"VASP",
"pymatgen"
] | 88b327f2a9e17e2bb24c46a6c14cbae3da73ea4d17c8485e456e04b633e30b54 |
# -*- test-case-name: buildbot.test.test_svnpoller -*-
# Based on the work of Dave Peticolas for the P4poll
# Changed to svn (using xml.dom.minidom) by Niklaus Giger
# Hacked beyond recognition by Brian Warner
from twisted.python import log
from twisted.internet import defer, reactor, utils
from twisted.internet.task... | gward/buildbot | buildbot/changes/svnpoller.py | Python | gpl-2.0 | 20,098 | [
"Brian"
] | 9da974bd2b141aa56c785934d4ef85e6ad18fd5644d5a82f2c722fda97783f08 |
# Copyright 2014 M. A. Zentile, J. Keaveney, L. Weller, D. Whiting,
# C. S. Adams and I. G. Hughes.
# 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/LICENS... | jameskeaveney/ElecSus | setup.py | Python | apache-2.0 | 2,241 | [
"VisIt"
] | e2b094c48c39a5d2b024a6abb5ed59bf6e28838ceafbf4f97ea3f69cbae0af13 |
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