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# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2003-2006 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2011 Paul Franklin
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | pmghalvorsen/gramps_branch | gramps/plugins/textreport/simplebooktitle.py | Python | gpl-2.0 | 7,539 | [
"Brian"
] | ba7451dfe328e7c82ad67bfaf19a589ef598e8078e9ec001fefd3f7828cdcaf8 |
import numpy as np
from mayavi import mlab
from BDSpace.Curve import ParametricCurve
from BDSpaceVis.space import SpaceView
class CurveView(SpaceView):
def __init__(self, fig, curve, scale=1, color=None, opacity=None, edge_visible=False,
cs_visible=True, surface_visible=True, wireframe=False, r... | bond-anton/Space_visualization | BDSpaceVis/curves.py | Python | apache-2.0 | 4,454 | [
"Mayavi"
] | cb0351ba8b71bab33d528479cc6221f6854536f896fe7c3c64c1f7072b88df4a |
import visit as v
from .. import JAVA_LANG
from .. import PRIMITIVES
from ..utils import utils
from ..node import Node
from ..compilationunit import CompilationUnit
from ..importdeclaration import ImportDeclaration
from ..body.classorinterfacedeclaration import ClassOrInterfaceDeclaration
from ..body.fielddeclaratio... | plum-umd/java-sketch | jskparser/ast/visit/symtabgen.py | Python | mit | 10,916 | [
"VisIt"
] | 0a5174727d1de86b55bf55a45af878e75078a39917fa50351bad189331144ca2 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Tim Moore
# Contributors:
#
# MDTraj is free software: you can... | rmcgibbo/mdtraj | mdtraj/formats/hoomdxml.py | Python | lgpl-2.1 | 5,880 | [
"HOOMD-blue",
"MDTraj"
] | 5e36b03fd862d9d888b0c365f950e217efd9df2d218687313d2c4e7733e40917 |
# -------------------------------------------------------------------------
# Name: globals
# Purpose:
#
# Author: burekpe
#
# Created: 16/05/2016
# Copyright: (c) burekpe 2016
# This program comes with ABSOLUTELY NO WARRANTY
# This is free software, and you are welcome to redistribute it under certa... | CWatM/CWatM | cwatm/management_modules/globals.py | Python | gpl-3.0 | 7,714 | [
"NetCDF"
] | 467ce1b57f6f971bfdf6a20b454b274ab9b9d685c48600f78c671a5460b22fe0 |
# Create your views here.
import json
import os
import re
from django.http import HttpResponse, HttpResponseBadRequest
from django.views.decorators.csrf import csrf_exempt
from pymatgen import Composition, Element
from matgendb.query_engine import QueryEngine
from matgendb import dbconfig
import bson
import dateti... | migueldiascosta/pymatgen-db | matgendb/webui/rest/views.py | Python | mit | 4,998 | [
"pymatgen"
] | 8fad959086dd869093bee9e329fbe2d7d77c0e93cf9fc6584b6d4a29898ad806 |
import numpy as np
import os
try:
import netCDF4 as netCDF
except:
import netCDF3 as netCDF
import matplotlib.pyplot as plt
import time
from datetime import datetime
from matplotlib.dates import date2num, num2date
import pyroms
import pyroms_toolbox
import _remapping
class nctime(object):
pass
def remap_bdry... | dcherian/pyroms | examples/Arctic_HYCOM/remap_bdry.py | Python | bsd-3-clause | 8,826 | [
"NetCDF"
] | 857a214a5c3e3e9dba44582745896bad18424162ac468f38c7458745e83c9f88 |
"""
====================================================================
K-means clustering and vector quantization (:mod:`scipy.cluster.vq`)
====================================================================
Provides routines for k-means clustering, generating code books
from k-means models, and quantizing vectors ... | gfyoung/scipy | scipy/cluster/vq.py | Python | bsd-3-clause | 24,205 | [
"Gaussian"
] | a912401d2998e32ef0661828a2213cba32478f0d9bc8f3de3d35a2cbc5d09994 |
#!/usr/bin/env python
# To do:
# - Let user specify the parser class on the command line.
# - Let user specify a sequence file to BLAST on the net.
# - Script should help debug connection to NCBI website.
from __future__ import print_function
import os
import re
import sys
import getopt
import traceback
from Bio im... | updownlife/multipleK | dependencies/biopython-1.65/Scripts/debug/debug_blast_parser.py | Python | gpl-2.0 | 8,273 | [
"BLAST"
] | d0128606c7f09ac82cb0ae25bf3ded274c17443a44c133e9828e9fa3da800f7e |
import numpy as np
from ase.data import atomic_numbers, chemical_symbols
from ase.units import Bohr
from gpaw.setup import Setups
from gpaw.xc import XC
from gpaw.mpi import world
Bondi64jpc_vdWradii = { # units Anstrom
'He' : 1.40,
'Ne' : 1.54,
'Ar' : 1.88,
'Kr' : 2.02,
'Xe' : 2.16
}
# Van der Wa... | robwarm/gpaw-symm | gpaw/analyse/vdwradii.py | Python | gpl-3.0 | 2,542 | [
"ASE",
"GPAW"
] | 135a191acc7ab9540cfe9f1b1e96ca161d316eaad921a544dd5913aca8eb6056 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Uses graphlib and topiclib to run partial sLDA
Copyright (C) 2011 Joseph Perla
GNU Affero General Public License. See <http://www.gnu.org/licenses/>.
"""
global final_output
from itertools import chain,izip
from functools import partial
try:
imp... | jperla/happynews | model/partial_slda.py | Python | agpl-3.0 | 6,446 | [
"Gaussian"
] | 6d0c141ae96a0762dac95367476667c7597136f5625571694a666e22c642605c |
from __future__ import unicode_literals
import re
from .common import InfoExtractor
from .theplatform import ThePlatformIE
from .adobepass import AdobePassIE
from ..compat import compat_urllib_parse_urlparse
from ..utils import (
find_xpath_attr,
lowercase_escape,
smuggle_url,
unescapeHTML,
update... | Tithen-Firion/youtube-dl | youtube_dl/extractor/nbc.py | Python | unlicense | 17,491 | [
"Brian"
] | 73739aaec86ee3fcfa7dfd6d28317efedf32e97f3562ef48a42bc29df137c606 |
import numpy as np
import sklearn.base
class AppxGaussianProcessRegressor(sklearn.base.BaseEstimator,
sklearn.base.RegressorMixin):
"""Approximate Gaussian process regression (GPR).
Based on applying the Woodbury matrix identity to GPR according to
https://github.com/che... | alasdairtran/mclearn | projects/jakub/appx_gaussian_processes/appx_gp.py | Python | bsd-3-clause | 2,116 | [
"Gaussian"
] | 2c1a2611088162a4637e0ad7a10c382f79c63f31707399b2d854c02454fc58da |
# Copyright (c) 2010 Howard Hughes Medical Institute.
# All rights reserved.
# Use is subject to Janelia Farm Research Campus Software Copyright 1.1 license terms.
# http://license.janelia.org/license/jfrc_copyright_1_1.html
from __future__ import with_statement # This isn't required in Python 2.6
import neuropti... | JaneliaSciComp/Neuroptikon | Source/display/display.py | Python | bsd-3-clause | 143,164 | [
"NEURON"
] | fab38d122bc7f3bf3a98880f706b0b539c4a056f0b2dbec1d5c300df49da8405 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/bug_1117098 | openlp/plugins/media/lib/mediaitem.py | Python | gpl-2.0 | 15,387 | [
"Brian"
] | 7fb1ac897bc32df572a5b143734200977ea5e1fce0d0867c9c77c172cd3edb51 |
# Copyright (C) 2018 Henrique Pereira Coutada Miranda
# All rights reserved.
#
# This file is part of yambopy
#
"""
Scripts to manipulate Quantum Espresso input files
Also able to read output files in xml format (datafile.xml or datafile-schema.xml)
"""
import os
class qepyenv():
PW = "pw.x"
PH = "ph.x"
... | alexmoratalla/yambopy | qepy/__init__.py | Python | bsd-3-clause | 729 | [
"Quantum ESPRESSO"
] | 1061a8e0642bb816067c3b113fad3d4f270a52af9d6263669e5cf46dc17f947f |
#built by Tcll5850
#inspired by Roo525
from data.COMMON import * #essentials
Header( 0.001, #Script Version (for updates)
('MikuMikuDance',['pmd']),#model activation
('MikuMikuDance',['vmd']),#anim activation
['']) #included libs
def ImportModel(T,C):
de... | Universal-Model-Converter/UMC3.0a | scripts/MMD_PMD.py | Python | mit | 1,915 | [
"VMD"
] | fe875787f447780b88dea4839309c6f9dc2015e29600f3a0f41e0e01ab6c35ea |
# Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
from math import pi
import sys
from Bio.PDB import *
from AbstractPropertyMap import Abst... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/PDB/HSExposure.py | Python | apache-2.0 | 11,168 | [
"Biopython",
"PyMOL"
] | 0d7da8ecf944744d26d4144e93b558e279c2a41f6a059c56a0c7a8dfc777070b |
'''
This script describes how to use the *outliers* method to detect and
remove outliers prior to conditioning a *GaussinaProcess*.
'''
import numpy as np
import matplotlib.pyplot as plt
import logging
from rbf.gproc import gpiso, gppoly
logging.basicConfig(level=logging.DEBUG)
np.random.seed(1)
y = np.linspace(-7.5... | treverhines/RBF | docs/scripts/gproc.c.py | Python | mit | 1,709 | [
"Gaussian"
] | eae421cc45a40429a50d264ae59cf64da9cffae2e415a82f27e268f90fbc8f45 |
__author__ = "joanne cohn"
__email__ = "jcohn@berkeley.edu"
__version__= "1.1" #updated BWC M*(Mh) from newer version of paper
import numpy as N
import matplotlib.pyplot as plt
import matplotlib
import matplotlib.cm as cm
import matplotlib.mlab as mlab
def comments():
"""
Please do email me if you... | jdcphysics/validation | codes/vsuite/valid_suite.py | Python | mit | 59,806 | [
"Galaxy"
] | 87046224f3311bd68b6ec4795f786a3a094e9f0e1252ea2f9c49ba2dcfcbc60c |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
from ... | bhanduroshan/fbstats-docker | config/urls.py | Python | mit | 2,359 | [
"VisIt"
] | 5c88d1a80c65213a6ce8a0f40fe5a30cf93e9fb27bb17c38647e9db8c1c404e7 |
# Copyright (c) 2010 ActiveState Software Inc. All rights reserved.
"""
pypm.client.fs
~~~~~~~~~~~~~~
File system related functionality, which includes:
- Downloading packages from remote location to local cache
- Extracting packages into the appropriate directory structure
(user s... | igemsoftware/SYSU-Software2013 | project/Python27_32/Lib/site-packages/pypm/client/fs.py | Python | mit | 10,900 | [
"VisIt"
] | 1d04553d575dbea9430d81768295894668e53daea7e881e1f98317a5339e4d21 |
# Copyright 2012, 2013 The GalSim developers:
# https://github.com/GalSim-developers
#
# This file is part of GalSim: The modular galaxy image simulation toolkit.
#
# GalSim 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... | mardom/GalSim | galsim/des/des_shapelet.py | Python | gpl-3.0 | 10,378 | [
"Galaxy"
] | ff5f999b8b8e1bb2290142fd366f1ad7ab1594acfc3e98db2d39a6b73f128fd8 |
# Copyright 2000-2009 by Iddo Friedberg. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
#
# Iddo Friedberg idoerg@cc.huji.ac.il
"""Substitution matrices, log odds matrices, and... | zjuchenyuan/BioWeb | Lib/Bio/SubsMat/__init__.py | Python | mit | 23,884 | [
"Biopython"
] | fcdb75a72c57c1a30f36c2c84818582895a52129b6534674fbf4a51eddeb019c |
"""Known matrices related to physics"""
from __future__ import print_function, division
from sympy import Matrix, I, pi, sqrt
from sympy.functions import exp
from sympy.core.compatibility import range
def msigma(i):
r"""Returns a Pauli matrix `\sigma_i` with `i=1,2,3`
References
==========
.. [1] ... | wxgeo/geophar | wxgeometrie/sympy/physics/matrices.py | Python | gpl-2.0 | 4,140 | [
"DIRAC"
] | 787708ad86c4e2a36a80bcd749b959d2310121c222c6cf40a9ab5b695dda3421 |
""" Bokeh is a Python interactive visualization library that targets modern
web browsers for presentation.
Its goal is to provide elegant, concise construction of novel graphics in the
style of d3.js, but also deliver this capability with high-performance
interactivity over very large or streaming datasets. Bokeh can ... | srinathv/bokeh | bokeh/__init__.py | Python | bsd-3-clause | 1,194 | [
"VisIt"
] | 26b1567021d3fc6162722c213d9423ca69770768de77ae7a493534fc76bf5ddf |
"""
This module contains classes for storing atomic data.
The Frame class may contain multiple Residues which may each contain multiple Atoms.
Both Frame and Residue are iterable. Residue is indexable with either atom numbers or names.
"""
import logging
import numpy as np
from .util import backup_file
from .parser... | jag1g13/pycgtool | pycgtool/frame.py | Python | gpl-3.0 | 8,888 | [
"Gromacs",
"LAMMPS",
"MDTraj"
] | 7abf02d5f12e4024869fe968b7d4e2ca176ce16f6db7a65789fc1614f630089a |
#!/usr/bin/env python
"""
Runs RAxML on a sequence file.
For use with RAxML version 7.3.0
usage:
<!-- raxmlHPC-PTHREADS-SSE3 -T 2 -f c -m GTRGAMMA -F -s "/Users/om/Downloads/rana.phy" -n rana_red -w "/Users/om/Downloads/" 0
## raxmlHPC-PTHREADS-SSE3 -T 2 -m GTRGAMMA -n test -p 323483 -s reduced.phy
command>r... | Rothamsted/AppliedBioinformatics | galaxyMetaomics/raxml.py | Python | mit | 17,489 | [
"Galaxy"
] | 3d1acfb5698962b5e323aa933e4b9280578f04c1bb3630a39dbeaa541a00beb2 |
#!/usr/bin/env python
import argparse
import copy
import logging
import re
import sys
from cpt_gffParser import gffParse, gffWrite, gffSeqFeature
from Bio import SearchIO
logging.basicConfig(level=logging.INFO)
log = logging.getLogger(name='blastxml2gff3')
__doc__ = """
BlastXML files, when transformed to GFF3, do not... | TAMU-CPT/galaxy-tools | tools/blast/blastxml2_to_gapped_gff3.py | Python | gpl-3.0 | 9,689 | [
"BLAST"
] | ad3ee15d9c26ec804fad133dc10df29b01f2fcb1554f9ac6d035cb717f4467ea |
# -*- coding: utf-8 -*-
"""
Acceptance tests for studio related to the outline page.
"""
import json
from datetime import datetime, timedelta
import itertools
from pytz import UTC
from bok_choy.promise import EmptyPromise
from nose.plugins.attrib import attr
from common.test.acceptance.pages.studio.settings_advanced i... | synergeticsedx/deployment-wipro | common/test/acceptance/tests/studio/test_studio_outline.py | Python | agpl-3.0 | 81,985 | [
"VisIt"
] | 3c94d71695a09fbd5c604167e0504a48618cd67dc0505e42c99f60f3279c9617 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the LMS.
"""
import time
from ..helpers import UniqueCourseTest
from ...pages.studio.auto_auth import AutoAuthPage
from ...pages.studio.overview import CourseOutlinePage
from ...pages.lms.courseware import CoursewarePage
from ...pages.lms.problem import ProblemPage
from... | peterm-itr/edx-platform | common/test/acceptance/tests/lms/test_lms_courseware.py | Python | agpl-3.0 | 3,652 | [
"VisIt"
] | 57683293a3c729363d5ea310d52020c8ccc422af615c78d7fa89a083fe187b6a |
'''
The settings for OSMC are handled by the OSMC Settings Addon (OSA).
In order to more easily accomodate future changes and enhancements, each OSMC settings bundle (module) is a separate addon.
The module can take the form of an xbmc service, an xbmc script, or an xbmc module, but it must be installed into the u... | srmo/osmc | package/mediacenter-addon-osmc/src/script.module.osmcsetting.networking/resources/osmc/OSMCSetting.py | Python | gpl-2.0 | 13,802 | [
"ASE"
] | 036dbbd64452a209cabda9750d5b889c575380f80dc85776b7e70d9191928144 |
# -*- encoding:ascii -*-
from mako import runtime, filters, cache
UNDEFINED = runtime.UNDEFINED
__M_dict_builtin = dict
__M_locals_builtin = locals
_magic_number = 6
_modified_time = 1417442141.780621
_template_filename=u'templates/grid_base.mako'
_template_uri=u'/history/../grid_base.mako'
_template_cache=cache.Cache(... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/database/compiled_templates/grid_base.mako.py | Python | gpl-3.0 | 16,882 | [
"Galaxy"
] | f3d554e8300dda957ac4b87e1784310408befd745852ffbd6d17cf733968dcd7 |
from __future__ import print_function
import numpy as np
import matplotlib.pyplot as plt
import matplotlib
matplotlib.rcParams['text.usetex'] = True
from matplotlib.ticker import MultipleLocator
from astropy.io import fits
from astropy.time import Time
from PyAstronomy import pyasl
from scipy import ndimage
import pand... | savvytruffle/cauldron | rvs/BF_python.py | Python | mit | 23,146 | [
"Gaussian",
"VisIt"
] | 5c1440e9e388bae89867134027c3de2694b553fa855c675724634fa03488242b |
#
# GMSK modulation and demodulation.
#
#
# Copyright 2005-2007,2012 Free Software Foundation, Inc.
#
# This file is part of GNU Radio
#
# SPDX-License-Identifier: GPL-3.0-or-later
#
#
# See gnuradio-examples/python/digital for examples
from math import pi
from math import log as ln
from pprint import pprint
import ... | dl1ksv/gnuradio | gr-digital/python/digital/gmsk.py | Python | gpl-3.0 | 11,903 | [
"Gaussian"
] | 4e3fe94aa81b7faae3bb94a593296cf30b19df9891c77efa683881de274c00dd |
# Natural Language Toolkit: Maximum Entropy Classifiers
#
# Copyright (C) 2001-2012 NLTK Project
# Author: Edward Loper <edloper@gradient.cis.upenn.edu>
# Dmitry Chichkov <dchichkov@gmail.com> (TypedMaxentFeatureEncoding)
# URL: <http://www.nltk.org/>
# For license information, see LICENSE.TXT
"""
A classifier... | abad623/verbalucce | verbalucce/nltk/classify/maxent.py | Python | apache-2.0 | 65,039 | [
"Gaussian"
] | f33f19c4283ad83a79290879e084c06d469f173247a7e031b65da57ce66d6017 |
# Copyright (c) 2015-2016, the authors (see AUTHORS.txt).
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import numpy as np
import GPy
from GPy.util.pca import PCA
from GPy.core.parameterization.variational import VariationalPosterior, NormalPosterior
import sys
def initialize_latent(init, datanum, inpu... | zhenwendai/DeepGP | deepgp/util/util.py | Python | bsd-3-clause | 5,254 | [
"Gaussian"
] | a43310d615961073758f73e8d2a933fb8ec50cfcfb1ebe6442cd8c1cb056e554 |
# pysam versioning information
__version__ = "0.15.0"
# TODO: upgrade number
__samtools_version__ = "1.9"
# TODO: upgrade code and number
__bcftools_version__ = "1.9"
__htslib_version__ = "1.9"
| kyleabeauchamp/pysam | pysam/version.py | Python | mit | 197 | [
"pysam"
] | 9f89788b4944d33aab59f554e747582a2552cc0add03a7ab2866ec482b009bcd |
"""\
pwq: a extensions to CCTools' WorkQueue bindings
This library provides a wrapper for running WorkQueue tasks that
allows tasks to be serialized to multiple formats and uses ZeroMQ to
support running multiple WorkQueue instances.
"""
DOCLINES = __doc__.split('\n')
try:
from setuptools import setup
except Im... | badi/pwq | setup.py | Python | gpl-2.0 | 3,798 | [
"MDTraj"
] | f77af6890760d6420a5641dadf80726b4912b675b98f61670e1182e0be2b3194 |
# -*- coding: utf-8 -*-
"""
trueskill.mathematics
~~~~~~~~~~~~~~~~~~~~~
This module contains basic mathematics functions and objects for TrueSkill
algorithm. If you have not scipy, this module provides the fallback.
:copyright: (c) 2012-2013 by Heungsub Lee.
:license: BSD, see LICENSE for more... | amit-bansil/netsci | robocompviz/trueskill/trueskill/mathematics.py | Python | mit | 8,571 | [
"Gaussian"
] | 20aaeb11668d21e47d588140f36cc31b9f2aef17396078144e6046b4a2dc945d |
'''
Created on Apr 4, 2013
@author: Jeff
TrainNetworkQt.py
A Qt version of the network trainer that uses the python version of the deep net code
'''
from PyQt4.QtGui import QMainWindow, QKeySequence, QAction, QFileDialog, QMessageBox, QWidget, \
QPushButton, QLineEdit, QHBoxLayout, QVBoxLayout, QLabel, QApplica... | JRMeyer/Autotrace | under-development/TrainNetwork_Qt.py | Python | mit | 15,367 | [
"Gaussian"
] | ddcf3936ae6253337dee0a8f5bfa137f3b75324af8fbe760647ad044a1efa01a |
"""
Provides rolling statistical moments and related descriptive
statistics implemented in Cython
"""
from __future__ import division
import warnings
import numpy as np
from pandas.core.dtypes.common import is_scalar
from pandas.core.api import DataFrame, Series
from pandas.util._decorators import Substitution, Append... | winklerand/pandas | pandas/stats/moments.py | Python | bsd-3-clause | 31,628 | [
"Gaussian"
] | 3fa183d34dc16302744699d3cabc9ad376012d8522a396d82026272134504ad5 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | pli3/e2-openwbif | plugin/controllers/views/mobile/timerlist.py | Python | gpl-2.0 | 9,716 | [
"VisIt"
] | 503205bcb53b684d8b8fc4d1bd13fd2437ac7d867c5ebba1a57447e2c8bf07cd |
import os
import yaml
from bcbio import utils
from bcbio.install import _get_data_dir
from bcbio.distributed import clargs
from bcbio.provenance import system
import bcbio.distributed.resources as res
from bcbio.distributed.ipython import create
# from bcbio import log
import log
from cluster_helper import cluster as ... | lpantano/ich-wrapper | ichwrapper/cluster.py | Python | mit | 4,416 | [
"Galaxy"
] | 2d00c0db361b9a52bfbcc7d8cf9c80bbd29f3daf960626da19f732417c5c7dd1 |
#!/usr/bin/env python
"""
Rough concolic execution implementation
Limitations
- tested only on the simpleassert example program in examples/
- only works for 3 ints of stdin
Bugs
- Will probably break if a newly discovered branch gets more input/does another read(2)
- possibly unnecessary deepcopies
"""
import que... | trailofbits/manticore | examples/script/concolic.py | Python | agpl-3.0 | 9,601 | [
"VisIt"
] | 50438efe13ae75bee85f655ae81d115e43ab80dd48359608130a4b6571685a66 |
# Conversion Module
import numpy as np
import data as data
import math as math
def conversion(mask_id, n_horizontal, m_vertical, datastruct):
"""Convert the Moire 3D array into the Crystal 2D array and store it in datastruct.
The Moire 3D array is loaded from the data structure (datastruct) using the keywor... | slimpotatoes/STEM_Moire_GPA | src/conversion.py | Python | bsd-3-clause | 1,900 | [
"CRYSTAL"
] | ade6806cf19c61315a143237cdb678d6d3c6f3cae81d65c0f29815d2f078ee3c |
#!/usr/bin/env python
"""
This is a script for quick Mayavi-based visualizations of finite element
computations results.
Examples
--------
The examples assume that run_tests.py has been run successfully and the
resulting data files are present.
- view data in output-tests/test_navier_stokes.vtk
$ python po... | sfepy/sfepy | postproc.py | Python | bsd-3-clause | 20,509 | [
"Mayavi",
"VTK"
] | ceb48782076ac5f5b4e78339453dd7663ab03c8983ef2aa11dac899f34a33ad0 |
# coding: utf-8
import cv2
import numpy as np
import pprint
class ScaleSpace(object):
def __init__(self, K = 3, O = 8, sigma_0 = 0.8, delta_0 = 0.5):
"""
This class is model of Gaussian Scale space
:param K: number of scales per octave
:param O: number of octaves
:param sig... | Tukamotosan/KeypointDetection | python/ScaleSpace.py | Python | apache-2.0 | 3,397 | [
"Gaussian"
] | f8f15d6397c10b7e11a2c0731c14918b2f2a51fba72352992cc52a5388de70d9 |
import sympy
from sympy.core import Symbol, Wild, S
from sympy.functions import DiracDelta, Heaviside
from sympy.solvers import solve
#from sympy.integrals import Integral
def change_mul(node,x):
"""change_mul(node,x)
Rearranges the operands of a product, bringing to front any simple
DiracDelta expr... | hazelnusse/sympy-old | sympy/integrals/deltafunctions.py | Python | bsd-3-clause | 4,487 | [
"DIRAC"
] | 747493ff27970cf905e2ff32dd607df65a7fd6b94ca759b44c1181b7b7df53be |
"""
main.py - Part of millennium-compact-groups package
Use a clustering algorithm to find compact groups in the Millennium
simulation.
Copyright(C) 2016 by
Trey Wenger; tvwenger@gmail.com
Chris Wiens; cdw9bf@virginia.edu
Kelsey Johnson; kej7a@virginia.edu
GNU General Public License v3 (GNU GPLv3)
This program is f... | tvwenger/millennium-compact-groups | main.py | Python | gpl-3.0 | 12,161 | [
"Galaxy"
] | f8e2ddf23037e0fb5be266406313b5a8c33096450a81aacd3c23feddf34ef70d |
"""Definitions for the `Gaussian` class."""
import numpy as np
from scipy.special import erfinv
from mosfit.modules.parameters.parameter import Parameter
# Important: Only define one ``Module`` class per file.
class Gaussian(Parameter):
"""Parameter with Gaussian prior.
If the parameter must be positive, ... | mnicholl/MOSFiT | mosfit/modules/parameters/gaussian.py | Python | mit | 1,421 | [
"Gaussian"
] | 6ae1e6370f69d8d58b70ff6bd52cc2066601c6f5f4171b9d3973cc6bff7b86a8 |
##############################################################################
# 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/r-geoquery/package.py | Python | lgpl-2.1 | 2,093 | [
"Bioconductor"
] | 988be652fe531ec0f9582df72e57912f742e040b4bbfb6d5b433b51dffcf9664 |
""" This module will run some job descriptions defined with an older version of DIRAC
"""
#pylint: disable=protected-access, wrong-import-position, invalid-name, missing-docstring
import unittest
import os
import shutil
#!/usr/bin/env python
from DIRAC.Core.Base.Script import parseCommandLine
parseCommandLine()
fro... | Andrew-McNab-UK/DIRAC | tests/Workflow/Regression/Test_RegressionUserJobs.py | Python | gpl-3.0 | 2,354 | [
"DIRAC"
] | 36c43073b54c71026dd704728f1b394aef6daed8a091d8b1d701939b1afae21a |
# -*- coding: utf-8 -*-
from __future__ import absolute_import, unicode_literals
import base64
import calendar
import copy
import hashlib
import hmac
import json
import pytz
import six
import telegram
import time
import urllib2
import uuid
from datetime import timedelta, date
from django.conf import settings
from dja... | tsotetsi/textily-web | temba/channels/tests.py | Python | agpl-3.0 | 393,025 | [
"VisIt"
] | 341c30e7b426b757c9945c76900fff7d9334261c66b6f5bce1eb7eb03959c8cf |
#
# Copyright 2018-2019, 2021 Jan Griesser (U. Freiburg)
# 2021 Lars Pastewka (U. Freiburg)
#
# matscipy - Materials science with Python at the atomic-scale
# https://github.com/libAtoms/matscipy
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General P... | libAtoms/matscipy | matscipy/calculators/pair_potential/calculator.py | Python | lgpl-2.1 | 16,909 | [
"ASE",
"Matscipy"
] | 1dc3dd2f65e0f06206606a31671d06908e659a57b417db0de3b86901b266b15e |
import os
import sys
import types
import re
from numpy.core.numerictypes import obj2sctype, generic, issubclass_, \
issubsctype, issubdtype
from numpy.core.multiarray import dtype as _dtype
from numpy.core import product, ndarray
__all__ = ['issubclass_', 'get_numpy_include', 'issubsctype',
'issubdtype... | houseind/robothon | GlyphProofer/dist/GlyphProofer.app/Contents/Resources/lib/python2.6/numpy/lib/utils.py | Python | mit | 26,219 | [
"VisIt"
] | 9a50e8ac25493281f8ee93dac905475bab0ce463a55c5088b6d2bd2825de893e |
#!/usr/bin/env python
"""
"""
import vtk
def main():
# colors = vtk.vtkNamedColors()
fileName = get_program_parameters()
# Read the image.
readerFactory = vtk.vtkImageReader2Factory()
reader = readerFactory.CreateImageReader2(fileName)
reader.SetFileName(fileName)
reader.Update()
... | lorensen/VTKExamples | src/Python/ImageProcessing/HybridMedianComparison.py | Python | apache-2.0 | 6,417 | [
"VTK"
] | 7146f5c1d169e5f22e6d372b4b8e370c76acf652f2ee7a3f281794f381c4079a |
"""
Instructor Dashboard Views
"""
import logging
import datetime
from opaque_keys import InvalidKeyError
from opaque_keys.edx.keys import CourseKey
import uuid
import pytz
from django.contrib.auth.decorators import login_required
from django.views.decorators.http import require_POST
from django.utils.translation imp... | CourseTalk/edx-platform | lms/djangoapps/instructor/views/instructor_dashboard.py | Python | agpl-3.0 | 31,181 | [
"VisIt"
] | 0e78a332f1d8575c5cddd96b4a7322b4bc56c36d9ca99f3d93026c6483074029 |
import numpy as np
import pandas as pd
import math as math
from scipy.stats import norm
import statsmodels.api as sm
import matplotlib.pyplot as plt
import scripts.common_functions as cmfunc
import sklearn.neighbors as nb
from sets import Set
from sklearn.neighbors import DistanceMetric
import trollius
import warnings
... | kimhungGCZ/combinedAL | detection_engine.py | Python | agpl-3.0 | 31,609 | [
"Gaussian"
] | b5d52e19d0cf629cb3899fe5c7fe0a4d53039da0c30d148b3c78bf5c2b82dffa |
# IPython log file
import numpy as np
import os
import sys
sys.path.append('/Users/jni/projects/unfold-embryo')
sys.path.append('/Users/jni/projects/skan')
sys.path.append('/Users/jni/projects/storm-cluster')
from skimage import filters, morphology, io
from gala import imio
import unfold
os.chdir('/Users/jni/Dropbox... | jni/useful-histories | embryo-interpolation.py | Python | bsd-3-clause | 989 | [
"Gaussian"
] | 1ec4405a3257d4556176031388d29cfe42f6f3c787949b7f96e57d45136c6f31 |
""" DISET request handler base class for the TransformationDB.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import six
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.DISET.RequestHandler import RequestHandler
from DIRAC.Core.Utilities.DEncode import... | yujikato/DIRAC | src/DIRAC/TransformationSystem/Service/TransformationManagerHandler.py | Python | gpl-3.0 | 28,266 | [
"DIRAC"
] | f0773f1fd6a3611970b9f36e7a4e183b75b298c78a2f5d0b7cb079620b1a85a1 |
"""
Acceptance tests for Studio related to the container page.
The container page is used both for displaying units, and
for displaying containers within units.
"""
import datetime
import ddt
import six
from common.test.acceptance.fixtures.course import XBlockFixtureDesc
from common.test.acceptance.pages.lms.course... | cpennington/edx-platform | common/test/acceptance/tests/studio/test_studio_container.py | Python | agpl-3.0 | 66,869 | [
"VisIt"
] | 4f047f3c837c61c4e0def4bb19f8e8d7b9ef7837a4ae138c101362f5a91c4fd5 |
# Copyright 2012 by Wibowo Arindrarto. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Bio.SearchIO objects to model similarity search program outputs.
The SearchIO object m... | updownlife/multipleK | dependencies/biopython-1.65/build/lib.linux-x86_64-2.7/Bio/SearchIO/_model/__init__.py | Python | gpl-2.0 | 2,435 | [
"Biopython"
] | ddd5dda2c080d8cc969355404f55c33cb7483cb53b881c9430def9c0f7571af3 |
# some functions
from __future__ import print_function
from __future__ import absolute_import
try:
# For Python 2
basestring = basestring
except NameError:
basestring = str
def poly(c,x):
""" y = Sum { c(i)*x^i }, i=0,len(c)"""
import numpy as N
y=N.zeros(len(x))
for i in range(len(c)):
... | lofar-astron/PyBDSF | bdsf/functions.py | Python | gpl-3.0 | 76,587 | [
"Gaussian"
] | 6fc4a118561d4df22dc9bf0258619671ed4ce470891b442114c5df0a1bfddb1d |
# encoding: utf-8
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding model 'Time'
db.create_table('profiles_time', (
('id', self.gf('django.db.models.fiel... | ProvidencePlan/Profiles | communityprofiles/profiles/oldmigrations/0002_add_indicator_part_and_time.py | Python | mit | 11,055 | [
"MOE"
] | 9f6ea43017d955c0e94cbfb61d468c69db964bc6018c369dc13d77260fc36fe5 |
# A python3 code
# This is the main module operating the other two modules IGIMF and OSGIMF.
# The IGIMF model calculates an analytically integrated galaxy-wide IMF;
# The OSGIMF model samples all the star cluster mass and all the stellar mass in each star cluster
# and then combind the stars in all star clusters t... | Azeret/galIMF | galimf.py | Python | gpl-3.0 | 55,263 | [
"Galaxy"
] | 4d77ee0d44cd6c68ca0fdc52d4191187f19aa33f9d8cbd291543b49474435beb |
import numpy as np
import deepautoencoder.utils as utils
import tensorflow as tf
allowed_activations = ['sigmoid', 'tanh', 'softmax', 'relu', 'linear']
allowed_noises = [None, 'gaussian', 'mask']
allowed_losses = ['rmse', 'cross-entropy']
class StackedAutoEncoder:
"""A deep autoencoder with denoising capability"... | rajarsheem/libsdae-autoencoder-tensorflow | deepautoencoder/stacked_autoencoder.py | Python | mit | 6,154 | [
"Gaussian"
] | 5095ac48d64ac23b27f340b2f307a21ecd395e3abe67ded139fdb090c5327c2e |
import datetime
from glob import glob
import netCDF4 as NET
import numpy as np
import os
import re
from shutil import rmtree
from sqlalchemy import and_
#tethys imports
from tethys_dataset_services.engines import GeoServerSpatialDatasetEngine
#local import
from model import SettingsSessionMaker, MainSettings, Watershed... | CI-WATER/tethysapp-erfp_tool | tethysapp/erfp_tool/functions.py | Python | mpl-2.0 | 15,209 | [
"NetCDF"
] | 098e00acf067700d9997e9bfa8fead1b105f7fa17f159bfa363718cd3eaa0747 |
##############################################################################
# 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/r-xde/package.py | Python | lgpl-2.1 | 1,980 | [
"Bioconductor"
] | 62078db4e3314de0442e079777a77021c3947c1a5826cbc35ef35c6c3b278b07 |
import sys
from os import path
import webbrowser
from PyQt4 import QtGui
from PyQt4 import QtCore
if hasattr(sys, 'frozen'):
scriptDir = path.dirname(unicode(sys.executable, sys.getfilesystemencoding()))
else:
scriptDir = path.dirname(unicode(__file__, sys.getfilesystemencoding()))
theQuestion = ... | srid/haietmoba-reminder | haietmoba-reminder.py | Python | mit | 7,079 | [
"VisIt"
] | 6e19064d9c094b398c488a31e20f840e9719592b287e51f590745b223497af91 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# Copyright 2016 David Emms
#
# This program (OrthoFinder) is distributed under the terms of the GNU General Public License v3
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publish... | davidemms/OrthoFinder | scripts_of/files.py | Python | gpl-3.0 | 41,519 | [
"BLAST"
] | da031b5190b76f3edc5c4a3c39e42bf97ae99d91c280a2741ed4fe96f50e38b8 |
# !usr/bin/env python
# -*- coding: utf-8 -*-
#
# Licensed under a 3-clause BSD license.
#
# @Author: Brian Cherinka
# @Date: 2017-08-04 14:25:03
# @Last modified by: Brian Cherinka
# @Last Modified time: 2017-08-10 23:08:13
from __future__ import print_function, division, absolute_import
from setuptools import se... | havok2063/SciScript-Python | setup.py | Python | apache-2.0 | 2,021 | [
"Brian"
] | 762a9597d511019ab67bfeab5765433da51238270037968e6a29eea0fc55dce7 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright: (c) 2016, Brian Coca <bcoca@ansible.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
DOCUMENTATION = '''
module: systemd
autho... | j-carl/ansible | lib/ansible/modules/systemd.py | Python | gpl-3.0 | 21,464 | [
"Brian"
] | 6738fcd4b78cb0198c2ea2eaa42e9c8302b0279b17bd7e0b622bf7c98b852d8a |
# -*- coding: utf-8 -*-
# see:
# https://github.com/carthage-college/django-djpsilobus/blob/2841d7aa2e9a7e41fcbfd12533f3266b1966778b/djpsilobus/core/data.py
# for last stable version of this file before the archivist moved all of the collections
# around and all of the collection IDs changed as a result.
#
DIVISIONS ... | carthage-college/django-djpsilobus | djpsilobus/core/data.py | Python | mit | 8,227 | [
"FEFF"
] | e0981fd9a27f0156b40bcb505e0041d37657fe8a6a97a4757fa9c2d913c8c8b1 |
"""
"""
import os, sys, posixpath
import py
# Moved from local.py.
iswin32 = sys.platform == "win32" or (getattr(os, '_name', False) == 'nt')
class Checkers:
_depend_on_existence = 'exists', 'link', 'dir', 'file'
def __init__(self, path):
self.path = path
def dir(self):
raise NotImplemen... | WillisXChen/django-oscar | oscar/lib/python2.7/site-packages/py/_path/common.py | Python | bsd-3-clause | 13,045 | [
"VisIt"
] | 04209f58299fcdd5bc17c5892d1ca8ae24c9d0a233173645d083c821a9d9b40c |
"""
Extracted the state propagation bits to individual functions
"""
import logging
import numpy as np
import scipy.sparse as sp
import scipy.sparse.linalg as spl
from .utils import block_diag
class NoHessianMethod(Exception):
"""An exception triggered when the forward model isn't able to provide an
estimat... | jgomezdans/KaFKA | kafka/inference/kf_tools.py | Python | gpl-3.0 | 14,447 | [
"Gaussian"
] | bf2595ced91b731564f777dda82616218bb7bbd55bdaa15e5c4a022873e4f865 |
#! /usr/bin/env python
from MDAnalysis import *
#from MDAnalysis.analysis.align import *
import numpy
import math
import sys
my_traj = sys.argv[1]
end = my_traj.find('.pdb')
u = Universe("init.pdb",my_traj)
v = Universe("init.pdb")
# residues
a1 = u.selectAtoms("segid A and (resid 108)")
#31,32,52,... | demharters/git_scripts | dist_DA10_bs.py | Python | apache-2.0 | 1,714 | [
"MDAnalysis"
] | e2750c62be291da2258511af4f7b72ec12179fe0d84a097d8f6836caaf2cd6fc |
"""
Numerical python functions written for compatability with MATLAB
commands with the same names.
MATLAB compatible functions
-------------------------------
:func:`cohere`
Coherence (normalized cross spectral density)
:func:`csd`
Cross spectral density uing Welch's average periodogram
:func:`detrend`
Remov... | alephu5/Soundbyte | environment/lib/python3.3/site-packages/matplotlib/mlab.py | Python | gpl-3.0 | 97,233 | [
"Gaussian"
] | 4fab652c19aeda588edd66fec56ce626f61e764ffcfa59e331a3d5a6d148d1d9 |
#!/usr/bin/env python
#
# $File: virtualSplitter.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 redistr... | BoPeng/simuPOP | docs/virtualSplitter.py | Python | gpl-2.0 | 1,951 | [
"VisIt"
] | 3243279b90fccde99333fe6f49c181783c61e73ad0e5efee9779ec1a54251ed9 |
import os
import unittest
from __main__ import vtk, qt, ctk, slicer
#
# TortuosityLogicTests
#
class TortuosityLogicTests:
def __init__(self, parent):
parent.title = "TortuosityLogicTests" # TODO make this more human readable by adding spaces
parent.categories = ["Testing.TestCases"]
parent.dependencies... | KitwareMedical/VesselView | Applications/App/Testing/Python/TortuosityLogicTests.py | Python | apache-2.0 | 7,095 | [
"VTK"
] | 184e465533752826dd5f10b90726b1f948e7d9acd0704bea649471aeab134641 |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
"""
Construct and visualize phylogenetic trees from:
1. MCSCAN output
2. CDS sequences in FASTA format
Options are provided for each step:
1. sequence alignment:
ClustalW2 or MUSCLE (wrapped on Biopython)
2. alignment editting:
GBlocks (optional)
3. build tre... | sgordon007/jcvi_062915 | apps/phylo.py | Python | bsd-2-clause | 34,972 | [
"Biopython"
] | 5dd59e9b6e8ddd09733b1e0bcf5d05c0377cd0b93eb64752f418843193dacf62 |
# Copyright 2013-2020 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 Libcint(CMakePackage):
"""Library for analytical Gaussian integrals for quantum chemistry.... | iulian787/spack | var/spack/repos/builtin/packages/libcint/package.py | Python | lgpl-2.1 | 2,555 | [
"Gaussian"
] | c06993f26e6cccc1ee61fd06894755b2407bf37d3eeaa45d5dd2a10600426b60 |
from hidparser.Item import ItemType, Item
from hidparser.enums import CollectionType, ReportFlags, ReportType
from hidparser.DeviceBuilder import DeviceBuilder
class InputItem(Item):
flags = None # type: ReportFlags
def visit(self, descriptor: DeviceBuilder):
descriptor.add_report(ReportType.INPUT, s... | NZSmartie/PyHIDParser | hidparser/ItemMain.py | Python | mit | 2,806 | [
"VisIt"
] | 12ae0e8605cdb66a7919e68e2c43fb4afa38f9ed129a28ebdd6f9323768fa5c3 |
#!/usr/bin/env python
"""
After a library is mapped to the genome (using map_single_fragments.py or any
other mapper), the bam file is screened for reads that weren't mapped to the
genome or weren't concise and try to map wach of the ends to a different
location. This script report the reads that are chimeric in a tab... | asafpr/RILseq | bin/map_chimeric_fragments.py | Python | mit | 8,553 | [
"BWA",
"pysam"
] | 052fed3449bdb279b365f27f9ac5ccf2193dbf28e00ea41ee98a9e0d7c41d0d3 |
# -*- coding: utf-8 -*-
"""
:author: Rinze de Laat <laat@delmic.com>
:copyright: © 2012 Rinze de Laat, Delmic
This file is part of Odemis.
.. license::
Odemis is free software: you can redistribute it and/or modify it under the terms of the GNU
General Public License version 2 as published by the Free Softwar... | ktsitsikas/odemis | src/odemis/gui/comp/stream.py | Python | gpl-2.0 | 53,833 | [
"Gaussian"
] | de88761a61d57fec918717e5a326b802b610bca9cbb981b6bbcc0a5bce92b20e |
import matplotlib.mlab as mlab
import numpy as np
import pandas as pd
import plotly.graph_objs as go
import plotly.offline as offl
def dist_plot(rating_df):
x = np.linspace(0, 50, 500)
data_dict = {}
for row in rating_df.iterrows():
label_name = (row[1]['first_name'] + ' ' + row[1]['last_name'][0... | wseaton/pongr | app/plots.py | Python | mit | 1,677 | [
"Gaussian"
] | 26ff9b1d5cb27ab507054410fb01fb15ebdbb51d2a70c25c9888266d61cd4c59 |
###############################################################################
# #
# GALORE: Gaussian and Lorentzian broadening for simulated spectra #
# #
... | SMTG-UCL/galore | galore/formats.py | Python | gpl-3.0 | 19,840 | [
"GPAW",
"Gaussian",
"VASP",
"pymatgen"
] | 112b470b7905d8a97cee904f471be39a68bf80c97a0ae60e036e7c534253002e |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Licensed under the GNU LGPL v2.1 - http://www.gnu.org/licenses/lgpl.html
# Based on Copyright (C) 2016 Radim Rehurek <radimrehurek@seznam.cz>
"""Lda Sequence model, inspired by `David M. Blei, John D. Lafferty: "Dynamic Topic Models"
<https://mimno.infosci.cornell.edu/... | midnightradio/gensim | gensim/models/ldaseqmodel.py | Python | gpl-3.0 | 62,153 | [
"Gaussian"
] | ec8b293a7e94a75d1f0230841367ec509f9fe323097c26b43aad5baa59b3cc32 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright: (c) 2014, Ruggero Marchei <ruggero.marchei@daemonzone.net>
# Copyright: (c) 2015, Brian Coca <bcoca@ansible.com>
# Copyright: (c) 2016-2017, Konstantin Shalygin <k0ste@k0ste.ru>
# Copyright: (c) 2017, Ansible Project
# GNU General Public License v3.0+ (see COPYING... | alexlo03/ansible | lib/ansible/modules/files/find.py | Python | gpl-3.0 | 16,079 | [
"Brian"
] | 2d245e2cd78672773af2347adb7ad3b20a43af6a3631162f38fce2979d07cd15 |
from decimal import Decimal
from urllib import parse
import ddt
import httpretty
from django.conf import settings
from django.urls import reverse
from mock import patch
from oscar.core.loading import get_model
from oscar.test import factories
from ecommerce.core.url_utils import get_lms_courseware_url, get_lms_prog... | eduNEXT/edunext-ecommerce | ecommerce/extensions/checkout/tests/test_views.py | Python | agpl-3.0 | 26,972 | [
"VisIt"
] | 4274a962f721e917d58da308e19dc93e97c67d2a2f3fd972f2c18ad6ce9f334c |
#!/usr/bin/env python
import argparse
import logging
import csv
import collections
import numpy as np
import pysam
from argparse import RawDescriptionHelpFormatter
csv.field_size_limit(1000000000)
def getOptions():
""" Function to pull in arguments """
description="""This script can be used to calculates cov... | McIntyre-Lab/papers | newman_events_2017/python_workflow/programs/rpkm_calculate.py | Python | lgpl-3.0 | 9,755 | [
"pysam"
] | 5b3a9d08f2ce20eedfc1f01680f8e99e454ce2e72a96a1b056a4bd8297759622 |
# Copyright (c) 2003-2016 LOGILAB S.A. (Paris, FRANCE).
# http://www.logilab.fr/ -- mailto:contact@logilab.fr
# Licensed under the GPL: https://www.gnu.org/licenses/old-licenses/gpl-2.0.html
# For details: https://github.com/PyCQA/pylint/blob/master/COPYING
"""classes checker for Python code
"""
from __future__ import... | bgris/ODL_bgris | lib/python3.5/site-packages/pylint/checkers/classes.py | Python | gpl-3.0 | 47,742 | [
"VisIt"
] | 2e4817c848e8be07a71a4a2763463b0c569ed97ef006ff313c229650c8f57c92 |
"""NEOs orbit from NEOWS and JPL SBDB
"""
import re
from bs4 import BeautifulSoup
import requests
import astropy.units as u
from astropy.time import Time
from poliastro.twobody.orbit import Orbit
from poliastro.bodies import Sun
from poliastro.frames import Planes
from poliastro.twobody.angles import M_to_nu
# Bas... | newlawrence/poliastro | src/poliastro/neos/neows.py | Python | mit | 4,190 | [
"VisIt"
] | 58fa4b4f11fa666b3ca432b6990f68d774c7ffe8fa65bf4461096433f8d9d492 |
##############################################################################
# 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... | skosukhin/spack | var/spack/repos/builtin/packages/py-brian/package.py | Python | lgpl-2.1 | 1,722 | [
"Brian"
] | 2413912fbfd44ec1a2bde3274a456a400b2bd94a764530bbe1472e8ae1fb004f |
# -*- coding: utf-8 -*-
#
# This file is part of Invenio.
# Copyright (C) 2013, 2014, 2015 CERN.
#
# Invenio 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 optio... | zenodo/invenio | invenio/modules/deposit/models.py | Python | gpl-2.0 | 47,526 | [
"VisIt"
] | 607f0b8faa478e3b200ff06a2f7b44c11296d196f0b391503fa8c65528f58325 |
# -*- coding: utf-8 -*-
"""
templatetk.jscompiler
~~~~~~~~~~~~~~~~~~~~~
This module can compile a node tree to JavaScript. Not all that
can be compiled to Python bytecode can also be compiled to JavaScript
though.
:copyright: (c) Copyright 2011 by Armin Ronacher.
:license: BSD, see LICENS... | mitsuhiko/templatetk | templatetk/jscompiler.py | Python | bsd-3-clause | 20,349 | [
"VisIt"
] | 4b3f48f4db2dee02d292546ebb9fdead2b5f07b13600c4136b9abec67490df23 |
'''
SASSIE: Copyright (C) 2011 Joseph E. Curtis, Ph.D.
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, or
(at your option) any later version.
... | madscatt/zazzie | src_2.7/sassie/test_sassie/interface/complex_monte_carlo/test_complex_filter.py | Python | gpl-3.0 | 40,753 | [
"CHARMM"
] | 472a242ea7057a5555c77adc73ac81ceeaf3b1a2137d5313c0d764adfa692656 |
"""Comparators originally meant to be used with particles"""
import numpy as np
from ase.ga.utilities import get_nnmat
class NNMatComparator(object):
"""Use the nearest neighbor matrix to determine differences
in the distribution (and to a slighter degree structure)
of atoms. As specified in
S. Lysgaa... | suttond/MODOI | ase/ga/particle_comparator.py | Python | lgpl-3.0 | 1,071 | [
"ASE"
] | bd68cacbe422185ed59b3412467a6ad071a33eed50a4b9d59399474d4d34027d |
"""
This script demonstrates how to use moogli to carry out a simulation and
simultaneously update the visualizer.
The visualizer remains active while the simulation is running.
"""
try:
import moogli
except ImportError as e:
print( "[INFO ] Could not import moogli. Quitting..." )
quit()
import moose
from... | BhallaLab/moose | moose-examples/moogli/purkinje_simulation.py | Python | gpl-3.0 | 4,328 | [
"MOOSE",
"NEURON"
] | 67dd10bb6ffaf27aa012aa05be8b5b91a661ef055983de0d8b2f736da32ceb04 |
import os
from director.componentgraph import ComponentFactory
from director import consoleapp
import director.objectmodel as om
import director.visualization as vis
from director.fieldcontainer import FieldContainer
from director import applogic
from director import appsettings
from director import drcargs
import fun... | patmarion/director | src/python/director/mainwindowapp.py | Python | bsd-3-clause | 18,755 | [
"VTK"
] | a75ffef769e36181c34a9d0b4a725ec0ac42b3e051e7b0e6c41685e02965c51e |
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