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#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | ashutoshvt/psi4 | psi4/driver/qcdb/options.py | Python | lgpl-3.0 | 11,046 | [
"CFOUR",
"ORCA",
"Psi4",
"Q-Chem"
] | 84ed61dca9b2a09a434b09967125fe2d3a0d64aec41b38a3f5e23c85bd9f677e |
#!/usr/bin/python3
import sys, os, argparse
import glob
from Bio import SeqIO
import gffutils
import pysam
BaseFold = ""
RefsFold = ""
GTFsFold = ""
SamplesFold = ""
ResultsFold = ""
class Gene:
def __init__(self, id, strand, start, end):
self.id = id
self.strand = strand
self.start = st... | AlgoLab/galig | paper/experiments/SimulatedData/tools/alnsAnalysis/checkAlignments.py | Python | gpl-3.0 | 13,265 | [
"pysam"
] | bd18ea4be665ddb7943a937b2fc7b9997c18cc021859a87339bd1e4377e59548 |
import time
import datetime
import re
import webbrowser
import pygtk
pygtk.require('2.0')
import gtk
import gobject
import pango
import tmradio.config
class Toolbar(gtk.HBox):
def __init__(self):
gtk.HBox.__init__(self, False, 0)
self.btn_play = gtk.Button('Play')
self.pack_start(self.b... | tmradio/tmradio-client-gtk | simple.py | Python | gpl-3.0 | 10,395 | [
"VisIt"
] | 38fed00308491aa65767d7e56e51dc24bd21e736db0ddd1babe3cc6154527a0a |
"""
Holds information about what the user asked for (which program, version constraints, etc).
"""
# Copyright (C) 2012, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall import SafeException
class Requirements(object):
"""
Holds information about what the user asked ... | rammstein/0install | zeroinstall/injector/requirements.py | Python | lgpl-2.1 | 4,688 | [
"VisIt"
] | 0a44adaa12f02f2a752581041d7ae19d7e349720e953fe78504ddf81aed6bea9 |
""" core implementation of testing process: init, session, runtest loop. """
import py
import pytest, _pytest
import os, sys, imp
try:
from collections import MutableMapping as MappingMixin
except ImportError:
from UserDict import DictMixin as MappingMixin
from _pytest.runner import collect_one_node, Skipped
... | geraldoandradee/pytest | _pytest/main.py | Python | mit | 24,637 | [
"VisIt"
] | 33d2275cbaa55b2643f7e7811655e1e4a7afebebe77c0b25d5308a5a46a53777 |
'''
Non-parametric computation of entropy and mutual-information
Adapted by G Varoquaux for code created by R Brette, itself
from several papers (see in the code).
These computations rely on nearest-neighbor statistics
'''
import numpy as np
from scipy.special import gamma,psi
from scipy import ndimage
from scipy.li... | dchad/malware-detection | resources/mutual_info.py | Python | gpl-3.0 | 7,579 | [
"Gaussian"
] | 45cf27d70f28fb294bfb9afe8ce7d1dc9a875d3b5de868fa525cedd0bdb9b664 |
#!/usr/local/bin/python2.6
import sys
_script = 'AltAnalyzeViewer.py'
_appName = "AltAnalyzeViewer"
_appVersion = '1.0.1'
_appDescription = "AltAnalyze is a freely available, open-source and cross-platform program that allows you to take RNASeq or "
_appDescription +="relatively raw microarray data (CEL files or norm... | wuxue/altanalyze | setupRemoteViewer.py | Python | apache-2.0 | 7,633 | [
"pysam"
] | daacd9f1e55433177dbbdaf42bdc72b9ee5311fcb5d8395e5a53988fdc550982 |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | nuclear-wizard/moose | python/peacock/tests/base/test_PluginManager.py | Python | lgpl-2.1 | 1,771 | [
"MOOSE"
] | 960cda7ec5859cf95117ebfe882b538b7ad1948786c61f56044954a8d13468fd |
# Copyright 2013 by Zheng Ruan (zruan1991@gmail.com).
# 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.
"""Code for dealing with coding sequence.
CodonSeq class is inherited from... | zjuchenyuan/BioWeb | Lib/Bio/codonalign/codonseq.py | Python | mit | 50,742 | [
"Biopython"
] | 9295b4d4c80616a05544bac1d69af693562157d418869633b392664bbd254423 |
from tethys_apps.base import TethysAppBase, url_map_maker
class NFIEDataViewer(TethysAppBase):
"""
Tethys app class for NFIE Data Viewer.
"""
name = 'NFIE Data Viewer'
index = 'nfie_data_viewer:home'
icon = 'nfie_data_viewer/images/app-icon-logo.svg'
package = 'nfie_data_viewer'
root_... | shawncrawley/tethysapp-nfie_data_viewer | tethysapp/nfie_data_viewer/app.py | Python | mpl-2.0 | 1,565 | [
"NetCDF"
] | b6699a02e60255b016701fdd910e8e7a896da48c57e43f0ab49c3e7a7629055a |
__RCSID__ = "$Id$"
import httplib
import socket
import time
import GSI
from DIRAC.Core.Utilities.ReturnValues import S_OK, S_ERROR
from DIRAC.Core.DISET.private.SSLSocketFactory import gSSLSocketFactory
from DIRAC.ConfigurationSystem.Client.Config import gConfig
class HTTPDISETSocket(object):
def __init__(self, ... | andresailer/DIRAC | Core/DISET/HTTPDISETConnection.py | Python | gpl-3.0 | 3,125 | [
"DIRAC"
] | ac4b157c6c6ad6164f69431ae1724346f2e626202706f07c6466b6fb7d097d3d |
## Ogre Command Line Tools Documentation
## Pop up dialog for various info/error messages
_nvcompress_doc = '''
usage: nvcompress [options] infile [outfile]
Input options:
-color The input image is a color map (default).
-alpha The input image has an alpha channel used for transparency.
-normal ... | qianqians/Screw | 3rdparty/blender2ogre/io_ogre/unused.py | Python | lgpl-2.1 | 17,094 | [
"Gaussian"
] | 358b578e155c358c70b15e2fb782efb05763a1c4c06ddefa663fb244b597bcea |
'''
High-level editor interface that communicates with underlying editor (like
Espresso, Coda, etc.) or browser. Basically, you should call set_context(obj)
method to set up undelying editor context before using any other method.
This interface is used by zen_actions.py for performing different
actions like Expand ab... | jmanoel7/pluma-plugins-0 | plugins/zencoding/zen_editor.py | Python | gpl-3.0 | 11,734 | [
"ESPResSo"
] | dac34ef347f31f171df44074b3fc354788ae3bfc89743a246fa9e03c00bc2e52 |
"""idp URL Configuration
The `urlpatterns` list routes URLs to views. For more information please see:
https://docs.djangoproject.com/en/1.8/topics/http/urls/
Examples:
Function views
1. Add an import: from my_app import views
2. Add a URL to urlpatterns: url(r'^$', views.home, name='home')
Class-based v... | bobbyluig/IDP | idp/urls.py | Python | mit | 1,446 | [
"VisIt"
] | 86e56441ab08e6a4a238bac6f3a30edb0f6cfc6e0eadfc0765de19bf55b435af |
#!/usr/bin/env python
from optparse import OptionParser, OptionGroup, SUPPRESS_HELP
from math import log, ceil
import os, random, sys, math, subprocess, pdb
import cov_model
################################################################################
# quake.py
#
# Launch full pipeline to correct errors
##########... | davek44/Quake | bin/quake.py | Python | artistic-2.0 | 14,630 | [
"BWA"
] | a21ea1753cde8a7462753984226f6cb9619cacee5df89e142bd86ef4e10c8b2c |
import pysam
import sys
import csv
import os
import argparse
from quicksect import IntervalNode
from random import randint, seed
def getOverlap(a, b):
return max(0, min(a[1], b[1]) - max(a[0], b[0]))
def is_junction(read):
for c in read.cigartuples:
if c[0]==3:
return True
return ... | smangul1/rprofile | rprofile.py | Python | apache-2.0 | 6,281 | [
"pysam"
] | c7731b69034318f1060cfcc1e064f9083ab3bbe0959eced3788aa01f0e979b4d |
#!/Xsoftware64/EM/EMAN2/extlib/bin/python
#
# Author: Steven Ludtke, 04/10/2003 (sludtke@bcm.edu)
# Copyright (c) 2000-2006 Baylor College of Medicine
#
# This software is issued under a joint BSD/GNU license. You may use the
# source code in this file under either license. However, note that the
# complete EMAN2 and S... | AGMMGA/EM_scripts | EM_scripts/junk/EMAN2py3.py | Python | gpl-2.0 | 77,606 | [
"Gaussian",
"VTK"
] | dcd483f881060cee95965d473aa8fe49510f318a81b458e7a100ed94bc9a1f62 |
import copy
from itertools import chain
import exchange
import lan
from processing import collect_array as ca
from processing import collect_device as cd
from processing import collect_id as ci
from processing import collect_loop as cl
class PlaceInReg(object):
def __init__(self, ast):
self.ast = ast
... | dikujepsen/OpenTran | v3.0/framework/transformation/place_in_reg.py | Python | mit | 7,872 | [
"VisIt"
] | 74082eacd2f63ac6c3b74c9238241e28e42aa3940be2e339d9d85ddf63c765eb |
r"""
This module is a ParaViewWeb server application.
The following command line illustrates how to use it::
$ pvpython .../pv_web_file_loader.py --data-dir /.../path-to-your-data-directory --file-to-load /.../any-vtk-friendly-file.vtk
--load-file is optional and allow the user to pre-load a g... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/Web/Applications/FileViewer/server/pv_web_file_loader.py | Python | gpl-3.0 | 7,150 | [
"ParaView",
"VTK"
] | a6f3470b25a76e74bcb6890fba7b311575b18605b864d6a90257943c03288bf8 |
#!/usr/bin/env python
from vtk import *
reader1 = vtkXMLTreeReader()
reader1.SetFileName("treetest.xml")
reader1.Update()
view = vtkIcicleView()
view.SetRepresentationFromInput(reader1.GetOutput())
view.SetAreaSizeArrayName("size")
view.SetAreaColorArrayName("level")
view.SetAreaLabelArrayName("name")
vie... | hlzz/dotfiles | graphics/VTK-7.0.0/Examples/Infovis/Python/icicle_view_simple.py | Python | bsd-3-clause | 627 | [
"VTK"
] | 0b4024fdc347b55e5084df9eced77f7e20dd4e36c184f7ba4cf2504727c81e26 |
#!/usr/bin/env python
import vtk
from vtk import *
import sys, os
#import Tkinter
#from Tkinter import *
if sys.hexversion < 0x03000000:
# for Python2
import Tkinter as tkinter
from Tkinter import *
else:
# for Python3
import tkinter
from tkinter import *
import vtk.tk
import vtk.... | hlzz/dotfiles | graphics/VTK-7.0.0/Examples/GUI/Python/OrthogonalPlanesWithTkPhoto.py | Python | bsd-3-clause | 6,138 | [
"VTK"
] | 4ea56cc47db31573e2258afac628bb0f2867622656d67254814b20fe251162ed |
from chempy import bmin,feedback
from chempy import io
import os
import re
import getpass # for getuser()
class State:
def __init__(self):
if feedback['verbose']:
print ' '+str(self.__class__)+': created.'
self.default = {}
self.echo = 0
self.model = None
self... | gratefulfrog/lib | python/chempy/bmin/state.py | Python | gpl-2.0 | 3,125 | [
"ChemPy"
] | ae563ea1e657cd2938e542a8e3a7e9ce02f8c0c7d1a21b06eed6e7df1f057d99 |
'''Convert to and from Roman numerals
This program is part of 'Dive Into Python 3', a free Python book for
experienced programmers. Visit http://diveintopython3.org/ for the
latest version.
'''
class OutOfRangeError(ValueError): pass
roman_numeral_map = (('M', 1000),
('CM', 900),
... | ctasims/Dive-Into-Python-3 | examples/roman3.py | Python | mit | 2,331 | [
"VisIt"
] | e551e91a60f3e1f9f1476878fce644c5cf802831a03f119cbcc09475048c6e5f |
# (c) 2014 Michael DeHaan, <michael@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later ve... | homme/ansible | lib/ansible/playbook/role/metadata.py | Python | gpl-3.0 | 3,201 | [
"Galaxy"
] | 6eb7215df6d25f29d7d88dfa4eb3a31252af34c39eefc06d8e8c5094b8bf9bb8 |
# Copyright (C) 2016 Christopher M. Biwer, Collin Capano
# 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.
#
# This progr... | cdcapano/pycbc | pycbc/distributions/gaussian.py | Python | gpl-3.0 | 9,440 | [
"Gaussian"
] | 9137e5bcf0a59840c33d54db3c9b1b2ff226081889a0afdadea67525170165fb |
#!/usr/bin/env python3
# vim: set ts=4 sts=4 sw=4 expandtab cc=80:
# Copyright (c) 2014-2021, chys <admin@CHYS.INFO>
# 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 sourc... | chys87/pyCxxLookup | cxxlookup/codegen.py | Python | bsd-3-clause | 30,321 | [
"VisIt"
] | 04886b1a6060393638c8c614ab826371e6146bf0b631ba2ed9bc2d1794efd40e |
#!/usr/bin/env python
from setuptools import setup, find_packages
from rpcudp import version
setup(
name="rpcudp",
version=version,
description="RPC via UDP",
author="Brian Muller",
author_email="bamuller@gmail.com",
license="MIT",
url="http://github.com/bmuller/rpcudp",
packages=find_p... | JerzySpendel/rpcudp | setup.py | Python | mit | 470 | [
"Brian"
] | 6db41346864861a400e0c6e0293b400a9f3d25a84dd3a63d85acb3eb6ef29563 |
# vim: set et sw=4 sts=4 fileencoding=utf-8:
#
# Copyright (c) 2016 David Topping.
# All Rights Reserved.
# This file is part of umansysprop.
#
# umansysprop 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, eit... | loftytopping/UManSysProp_public | umansysprop/groups.py | Python | gpl-3.0 | 74,811 | [
"Pybel"
] | 39b91dfa3abeadd3c3378f6a8dc4e4c56f612ff5637b0749a7516a824b440ff4 |
from quadrature import gauss, telles_singular, piessens, lobatto,\
telles_quasi_singular
from codim1.fast_lib import ConstantBasis,\
single_integral,\
aligned_single_integral
from mapping import distance_between_mappings
import numpy as np
f... | tbenthompson/codim1 | codim1/core/quad_strategy.py | Python | mit | 14,085 | [
"Gaussian"
] | 5c5aa0fdfa2268cd07524cf6f0a844fc015cc8f823e616f50abdb032b98353e1 |
from __future__ import division, print_function
import numpy as np
import matplotlib.pyplot as plt
from matplotlib import cm
import pdb
import sys
plt.ion()
if not '..' in sys.path:
sys.path.insert(0,'..')
import opticstools as ot
#First, design a wavefront sensor based on optimising a combination of
#pupil plane... | mikeireland/opticstools | playground/fibzernike_wfs.py | Python | mit | 3,309 | [
"Gaussian"
] | cff6136e98a065d96e6fa7132087021a38e676929d407f220fa5c480b2018980 |
import numpy as np
import scipy
# https://gist.github.com/andrewgiessel/6122739
def gaussian(height, center_x, center_y, width_x, width_y, rotation):
"""Returns a gaussian function with the given parameters"""
width_x = float(width_x)
width_y = float(width_y)
rotation = np.deg2rad(rotation)
cent... | Evenity/py_psa | py_psa/try_fit_gaussian.py | Python | mit | 4,977 | [
"Gaussian"
] | 92a901278ea6bfec93fcbf8cb26d4c0706c30596ff287486ea7735959956da27 |
#!/usr/bin/env python
import os
import sys
import getopt
import lcg
import subprocess as sub
import numpy as np
def usage():
print('This script injects subthreshold currents into a neuron to measure its impedance.')
print('\nUsage: %s [option <value>]' % os.path.basename(sys.argv[0]))
print('\nwhere optio... | danielelinaro/dynclamp | python/lcg/impedance.py | Python | gpl-3.0 | 4,354 | [
"NEURON"
] | 8fd3d694aff6c1ff3ed992fc75dbb9d21bf26b76d6a9172b6b5acc9d257b930b |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals, print_function
import itertools
import logging
from collections import defaultdict
import copy
import math
from math import cos
from math import sin
from frac... | nisse3000/pymatgen | pymatgen/symmetry/analyzer.py | Python | mit | 63,781 | [
"CRYSTAL",
"pymatgen"
] | 174d3d2f7c87c4fd317ce75daea8503a9a39c8ff3764e155b131f5e21067dbb6 |
"""Shared functionality useful across multiple structural variant callers.
Handles exclusion regions and preparing discordant regions.
"""
import collections
import os
import numpy
import pybedtools
import pysam
import toolz as tz
import yaml
from bcbio import bam, utils
from bcbio.distributed.transaction import fil... | biocyberman/bcbio-nextgen | bcbio/structural/shared.py | Python | mit | 12,998 | [
"pysam"
] | a2e3aac8dcf35c9ae5acb986326b23a165e162e1a8e6a1bf0b9f479cc4771597 |
# - Coding UTF8 -
#
# Networked Decision Making
# Development Sites (source code):
# http://code.google.com/p/global-decision-making-system/
# http://github.com/NewGlobalStrategy/NetDecisionMaking
#
# Demo Sites (Google App Engine)
# http://netdecisionmaking.appspot.com
# http://globaldecisionmaking.appspot.com
... | NewGlobalStrategy/NetDecisionMaking | controllers/geogsetup.py | Python | mit | 10,795 | [
"VisIt"
] | 018408e7f1efc713ea2d06ddb16970822a46c25390a4069a157c781351c20004 |
#!/usr/bin/env pvbatch
from paraview.simple import *
import pviz
import sys
oviz = pviz.viz(sys.argv) # instantiate viz object (and load data)
part = pviz.makeContour(varName='T_s',isoValueArray=[1.0],ColorArrayName='u_s')
ResetCamera() # auto-adapt camera to part extent
for var in part.PointData:
v... | ruizanthony/pviz | examples/simple/isosurface_loopVars.py | Python | lgpl-3.0 | 525 | [
"ParaView"
] | 58640ba03cfd7aca17b77d367238481bccd1696dd9a1d34c2372e33c212f347a |
from collections import OrderedDict
from edc_visit_schedule.classes import (
VisitScheduleConfiguration, site_visit_schedules, MembershipFormTuple, ScheduleTuple)
from ..models import MaternalVisit, PostnatalEnrollment
from .entries import (
maternal_delivery_entries, maternal_history_entries, maternal_month... | botswana-harvard/microbiome | microbiome/apps/mb_maternal/visit_schedule/postnatal_enrollment.py | Python | gpl-2.0 | 4,806 | [
"VisIt"
] | e49ee21b05ed6567597a2fe35d0b9aaec584b7491b3e8bdeb851ece0bc982d00 |
"""
Common code for encoding and decoding EGTP object IDs
in their two common representations (binary and ascii/mojosixbit).
Everything in this file is optimized for speed, it gets called a
-lot- throughout the program, including many hot spots.
"""
# Copyright (c) 2001 Autonomous Zone Industries
# This file is lic... | zooko/egtp_new | egtp/idlib.py | Python | lgpl-2.1 | 11,897 | [
"VisIt"
] | fc39a012e442ea39f04a1c6c5f72c99eaed92f13bbb86a6cb4a1b50d1a0772e9 |
""" :mod: DMSRequestOperationsBase
====================
Just a collector of common functions
"""
__RCSID__ = "$Id $"
from DIRAC import S_OK, S_ERROR
from DIRAC.RequestManagementSystem.Client.Operation import Operation
from DIRAC.RequestManagementSystem.Client.File import File
fr... | calancha/DIRAC | DataManagementSystem/Agent/RequestOperations/DMSRequestOperationsBase.py | Python | gpl-3.0 | 2,598 | [
"DIRAC"
] | 7b2b22d73b25b5a4debd42246d3dd9d066a2a229e1875bb772fbdf57517c4c5c |
from brian import *
import time
import sys
if __name__=='__main__':
duration = 2000*ms
max_allowed_sims = 400
savelocation = '/home/achilleas/Documents/Uni/working_dir/simout.py/tmp/'
input_freqs = arange(100,401,25)
input_num_sts = arange(40,101,10)
input_volts = arange(0.1,0.21,0.05)
nums... | achilleas-k/brian-scripts | input_vs_cv.py | Python | apache-2.0 | 3,195 | [
"Brian"
] | 2b530c69743b5a51d94067a321b759bad42f3c85801ba775bfe8cd678e43e0ed |
"""
Training costs for unsupervised learning of energy-based models
"""
import functools
import logging
import numpy as np
import sys
from theano import scan
import theano.tensor as T
from theano.compat.six.moves import zip as izip
from pylearn2.compat import OrderedDict
from pylearn2.costs.cost import Cost, DefaultD... | JesseLivezey/plankton | pylearn2/costs/ebm_estimation.py | Python | bsd-3-clause | 10,037 | [
"CDK"
] | 4b8c3f7fbdf36e11e2b6e69988be6e73ba7c0d27c56b8d20430b71fb069f1789 |
__author__ = 'sulantha'
import datetime
from Utils.DbUtils import DbUtils
csvFile = '/data/data03/sulantha/Downloads/av45_list.csv'
MatchDBClient = DbUtils(database='Study_Data.ADNI')
DBClient = DbUtils()
with open(csvFile, 'r') as csv:
next(csv)
for line in csv:
row = line.split(',')
rid = row[... | sulantha2006/Processing_Pipeline | Test/getSystemVisitCode.py | Python | apache-2.0 | 1,186 | [
"VisIt"
] | 870bbb85e8763dfc28166b2ec61390cf49d1749e29bdf900df27f71a9a00bdb6 |
import numpy as np
heading = {}
heading['xyz'] = [0,1,2]
heading['xy' ] = [0,1]
heading['xz' ] = [0,2]
heading['yz' ] = [1,2]
heading['x' ] = [0]
heading['y' ] = [1]
heading['z' ] = [2]
# polarization is complementary to heading
polarization = {}
polarization['xyz'] = [0,1,2]
polarization['xy' ] = [1,0]
polarizat... | MaxwellGEMS/emclaw | emclaw/utils/sources.py | Python | lgpl-3.0 | 23,166 | [
"Gaussian"
] | 55df3e87046db39d96d70d5a0877556a1d2af9e43da03ea708b6a0378ef0a81a |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2008 Brian G. Matherly
#
# 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 of the License, or
# (at your ) any... | Forage/Gramps | gramps/gen/plug/menu/__init__.py | Python | gpl-2.0 | 1,591 | [
"Brian"
] | 82837b4e087483ceb3e3cb2333c1ac3701c1191d0cc6e78b1b3d5f10c41c8b45 |
# Read .Mat Files
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... | tapomayukh/projects_in_python | sandbox_tapo/src/AI/Code for Project-3/HMM Code/state_accuracy_variation.py | Python | mit | 1,190 | [
"Mayavi"
] | faef55d660dec094b06a59226bb6bc00ffa70bd7331836aa957c62c3abb13e9c |
from kivy.app import App
from kivy.core.audio import SoundLoader
from kivy import platform
from kivy.uix.widget import Widget
from kivy.uix.button import Button
from kivy.clock import Clock
from kivy.core.window import Window
from kivy.animation import Animation
if platform != 'android':
pass
else:
from jnius ... | Ramalus/herovoices | .buildozer/android/app/main.py | Python | gpl-2.0 | 6,453 | [
"TINKER"
] | 79f9ca7ce8dfd5ccb8bb418a3c07a31ce441f3ab2947584e23c831f75e3d0a7d |
# -*- coding: utf-8 -*-
#
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2014-2015, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Pub... | ChemSem/cclib | src/cclib/parser/qchemparser.py | Python | lgpl-2.1 | 64,023 | [
"Gaussian",
"Q-Chem",
"cclib"
] | ad28f64b34d99516f19fa49692bdc2cad4819dd30cb48a2f76476433ef787064 |
# this script is based on RADIANCE sun.c script
#
# Ladybug: A Plugin for Environmental Analysis (GPL) started by Mostapha Sadeghipour Roudsari
#
# This file is part of Ladybug.
#
# Copyright (c) 2013-2015, Mostapha Sadeghipour Roudsari <Sadeghipour@gmail.com>
# Ladybug is free software; you can redistribute ... | boris-p/ladybug | src/Ladybug_SunPath.py | Python | gpl-3.0 | 41,434 | [
"EPW"
] | e80df339b6cc4ab9ae29721929b4cd05839b205def431ce08a9695aa4b489ce9 |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/cc/eom_uccsd.py | Python | apache-2.0 | 124,715 | [
"PySCF"
] | c901652e4171043fae02e963f6c2abad65c34b0044fa2c6eb639d2dd66948ab0 |
# (c) 2012, Michael DeHaan <michael.dehaan@gmail.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any lat... | fernandezcuesta/ansible | lib/ansible/template/safe_eval.py | Python | gpl-3.0 | 4,864 | [
"VisIt"
] | 4f6e6b334bdfdd710e0e058b4dc062fb51531171fef2ca25babf86d81b40546f |
# 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 PyPyscf(PythonPackage):
"""PySCF is a collection of electronic structure programs powered... | iulian787/spack | var/spack/repos/builtin/packages/py-pyscf/package.py | Python | lgpl-2.1 | 1,558 | [
"PySCF"
] | 9cbbf17bcfdeb192ee8cbb6e3d7481bf86ea27887d916b59fbe0c023bdcbbbdc |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module contains an algorithm to solve the Linear Assignment Problem.
It has the same functionality as linear_assignment.pyx, but is much slower
as it is vectorized in numpy rather than cython
"""
__author__ = "Will R... | materialsproject/pymatgen | pymatgen/optimization/linear_assignment_numpy.py | Python | mit | 8,173 | [
"pymatgen"
] | 28fe4a5958a08c8e44901356dd11972fd62b7e01f4e71f15b340eb777a015268 |
'''
Create a netcdf file from a campbell sci data file
Julia Signell
2015-05-07
'''
from __init__ import *
def manage_dtypes(x):
'''Ensure that all data columns are either intergers or floats'''
if x.values.dtype == np.dtype('int64') or x.values.dtype == np.dtype('<M8[ns]'):
return x
else:
... | jsignell/MpalaTower | munging/TOA5_to_netcdf.py | Python | mit | 5,668 | [
"NetCDF"
] | 61e05f66371d2d8041f9c2f7149376b28e04f5b47b31b4e9b7cdd8228dd9b0c3 |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General... | bearstech/ansible | lib/ansible/modules/network/avi/avi_poolgroupdeploymentpolicy.py | Python | gpl-3.0 | 5,648 | [
"VisIt"
] | 802573b9b2cfcb226a29c32e5fba087aa7dad80026d5552d48358c6c988eb5e1 |
"""
Base classes used by studio tests.
"""
from bok_choy.web_app_test import WebAppTest
from ...pages.studio.auto_auth import AutoAuthPage
from ...fixtures.course import CourseFixture
from ...fixtures.library import LibraryFixture
from ..helpers import UniqueCourseTest
from ...pages.studio.overview import CourseOutline... | franosincic/edx-platform | common/test/acceptance/tests/studio/base_studio_test.py | Python | agpl-3.0 | 5,145 | [
"VisIt"
] | 8dc780c4d9b02ab8e495ba49415923c052fb1a9e0ccd932e95595b5259566ec1 |
# proxy module
from __future__ import absolute_import
from mayavi.sources.array_source import *
| enthought/etsproxy | enthought/mayavi/sources/array_source.py | Python | bsd-3-clause | 96 | [
"Mayavi"
] | 665227f729a4df640bba288d70dba51a3a416fa33ad8fe06ce33e0939b502e67 |
# 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 RRhdf5(RPackage):
"""R Interface to HDF5.
This package provides an interface betwe... | rspavel/spack | var/spack/repos/builtin/packages/r-rhdf5/package.py | Python | lgpl-2.1 | 1,573 | [
"Bioconductor"
] | 82331d281de13a3f34446cef367cf9aa14d618f043074cd5134f2f9b8319e70a |
# -*- coding: utf-8 -*-
# Copyright: (c) 2019-2021, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
"""Installed collections management package."""
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import errno
import f... | nitzmahone/ansible | lib/ansible/galaxy/collection/__init__.py | Python | gpl-3.0 | 56,544 | [
"Galaxy"
] | cd1c04239e7dc6c74073baf079e9e571f78d04d30a8e31e8349f66293f39d6cb |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# @Author: Brian Cherinka, José Sánchez-Gallego, and Brett Andrews
# @Date: 2017-11-03
# @Filename: spaxel.py
# @License: BSD 3-clause (http://www.opensource.org/licenses/BSD-3-Clause)
#
# @Last modified by: José Sánchez-Gallego (gallegoj@uw.edu)
# @Last modified time: 20... | sdss/marvin | python/marvin/tools/spaxel.py | Python | bsd-3-clause | 14,454 | [
"Brian"
] | b0671bd05bc4581cc21af6dfd5b5696d5ee85c1f770a7495f45e1e2f4f2d1d06 |
# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | hfp/tensorflow-xsmm | tensorflow/contrib/distributions/python/ops/mvn_diag_plus_low_rank.py | Python | apache-2.0 | 10,159 | [
"Gaussian"
] | e0759be7411c6982eb41e31c37bb1545918e6bd2b70c5231b1c9e3749e1b45d2 |
#!/usr/bin/env python
"""
module that loads all the NIST bags and puts them in the DB
"""
from argparse import ArgumentParser
import os
from object_recognition_core.db.tools import add_db_arguments
import subprocess
from object_recognition.ingest.bag_upload import upload_bag
from object_recognition import models
impor... | WalkingMachine/sara_commun | wm_ork/object_recognition_core/apps/testing/nist/upload_nist.py | Python | apache-2.0 | 5,100 | [
"BLAST"
] | 87a5c9d14dc77d007f4fab64c97fa9c2558efb0cf3ad1fec3a54fc7d16e7e670 |
from ase.io import read
from ase.constraints import FixAtoms
from ase.calculators.siesta import Siesta
from ase.md import VelocityVerlet
from ase import units
# Read in the geometry from a xyz file, set the cell, boundary conditions and center
atoms = read('geom.xyz')
atoms.set_cell([7.66348,7.66348,7.66348*2])
atoms.... | misdoro/python-ase | doc/exercises/siesta2/siesta2.py | Python | gpl-2.0 | 962 | [
"ASE",
"SIESTA"
] | 3943d8f03f13adf4b287efed5d7d8fe316e878c1d397be0219d53e2dd41baeb9 |
# Copyright 2014 Roberto Brian Sarrionandia
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed t... | sarrionandia/tournatrack | add_speaker_record.py | Python | apache-2.0 | 3,684 | [
"Brian"
] | f7082d2065e22cdae77241f35dd2717a8202d91ddef752a694c86c838fde3830 |
#!/usr/bin/python
# EPG CPMG simulation code, based off of Matlab scripts from Brian Hargreaves <bah@stanford.edu>
# 2015 Jonathan Tamir <jtamir@eecs.berkeley.edu>
# 2019 Ke Wang <kewang@eecs.berkeley.edu> rewrite it in Pytorch
from __future__ import division
import torch
import torch.backends.cudnn as cudnn
import ... | jtamir/mri-sim-py | epg/epgcpmg_torch_image.py | Python | mit | 22,042 | [
"Brian"
] | cd6903b71c9af33a573b048cce06670001db2c92a30959586d9c3a6a9aeb32a9 |
#!/usr/bin/env phenix.python
import sys
import os
import iotbx.mtz
from cctbx import crystal
from cctbx import r_free_utils
from iotbx.reflection_file_editor import get_best_resolution
from iotbx.reflection_file_utils import make_joined_set
def run(mtz, mtz_out, fraction, flag_name=None, ccp4=True, use_lattice_symmet... | keitaroyam/yamtbx | yamtbx/dataproc/command_line/create_free_R_flag.py | Python | bsd-3-clause | 3,722 | [
"CRYSTAL"
] | 6e87ed5ea8e0c369c0b4716900fe31749af3e82629fcc199afa166299cce75b4 |
# Copyright (C) 2000 Greg Landrum
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2 of the License, or (at your option) any later version.
#
# This library is distri... | AlexanderSavelyev/rdkit | rdkit/sping/SVG/pidSVG.py | Python | bsd-3-clause | 23,791 | [
"RDKit"
] | 43c529270bc9e3eb84ba9f9ca9ab3491d1cd33e99078034047d673acee6ed0cc |
#
# Copyright (c) 2015 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | lach76/scancode-toolkit | src/scancode/extract_cli.py | Python | apache-2.0 | 6,304 | [
"VisIt"
] | 4203650644e0e10e8d3db9afe0e7375c2f9d20f4a79d768ba10771fe67e25da3 |
#pylint: disable=missing-docstring
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/... | nuclear-wizard/moose | python/chigger/geometric/CubeSource.py | Python | lgpl-2.1 | 1,734 | [
"MOOSE",
"VTK"
] | ebef9b18575682650b5395b0892b21d742a7dcd91337fd2f69a89424605fb84d |
#!/usr/bin/env/python3
import argparse
import configparser
from bioblend.galaxy import GalaxyInstance
from utils.delete import delete_all_libraries
from utils.upload import upload_datasets_to_galaxy
def main():
# Launch config
config = configparser.ConfigParser()
config.read('config.ini')
galaxy_... | pajanne/galaxy-kickstart | main.py | Python | mit | 1,648 | [
"Galaxy"
] | acf33cfd4af7bf0ac2081f5d9c7b4c3b7a7a1e70827795bb27dbf229ac853376 |
"""
Tests for read_alignment.py
"""
import json
import os
import subprocess
from django.conf import settings
from django.contrib.auth.models import User
from django.test import TestCase
from main.models import AlignmentGroup
from main.models import Dataset
from main.models import get_dataset_with_type
from main.mode... | woodymit/millstone | genome_designer/pipeline/tests/test_read_alignment.py | Python | mit | 15,298 | [
"BWA"
] | 238e346bc6a9e5bc4d931b9d92b86fe31a096a47b91ae3b336e6c7c9f09f7897 |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | freedomtan/tensorflow | tensorflow/python/ops/image_ops_impl.py | Python | apache-2.0 | 227,048 | [
"Gaussian"
] | d5360870db123494228463fe496024660116e82b71895baa9a6bab1c55d8e54f |
# 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... | dmlc/tvm | python/tvm/relay/type_functor.py | Python | apache-2.0 | 5,887 | [
"VisIt"
] | 0d655bf51d6a583aa8597f6ec896b42c695ee1554f05aec778d632df24ac53f0 |
# -*- coding:utf-8 -*-
"""PyHdust *poltools* module: polarimetry tools
History:
-grafpol working for *_WP1110....log files!
-grafpol working for log/out files with more than a single star
:co-author: Daniel Bednarski
:license: GNU GPL v3.0 https://github.com/danmoser/pyhdust/blob/master/LICENSE
"""
from __future__ ... | danmoser/pyhdust | pyhdust/poltools.py | Python | gpl-3.0 | 193,664 | [
"Gaussian"
] | 1efa43542063a1e8a1b62a6a585a59cd4871cbb8d0ac8fb5a84705054bbc38b9 |
# This software is distributed under BSD 3-clause license (see LICENSE file).
#
# Authors: Heiko Strathmann, Cameron Lai
"""
Shogun Gaussian processes demo based on interactive SVM demo by Christian \
Widmer and Soeren Sonnenburg which itself is based on PyQT Demo by Eli Bendersky
Work to be done on parameter (e.g. k... | sorig/shogun | examples/undocumented/python/graphical/interactive_gp_demo.py | Python | bsd-3-clause | 13,850 | [
"Gaussian"
] | 30779b14dd13fa1303a564816abcacf4076075505ae4000e5d8e69c3a3a3008e |
# Copyright (C) 2013, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from __future__ import print_function
import urlparse
import httplib
import ftplib
from zeroinstall import SafeException
def get_http_size(url, ttl = 3, method = None):
address = urlparse.urlparse(url)
if url.lo... | bastianeicher/0repo | repo/urltest.py | Python | lgpl-2.1 | 2,420 | [
"VisIt"
] | 62095314a13fc19bd747f83efadb396a4e00b317762fa42bd32add582b2c9883 |
"""
Example "Arcade" library code.
This example shows the drawing primitives and how they are used.
It does not assume the programmer knows how to define functions or classes
yet.
API documentation for the draw commands can be found here:
https://pythonhosted.org/arcade/arcade.html#module-arcade.draw_commands
A vide... | mikemhenry/arcade | examples/drawing_primitives.py | Python | mit | 5,641 | [
"Amber"
] | 6e45dad8057da36ae0f7c59c5af5216de3094e984fc6d2ec6ee1a709b39b215e |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals, print_function
import sys
from django.db import models
from django.utils.encoding import python_2_unicode_compatible
from django.utils.translation import ugettext_lazy as _
from django.contrib.contenttypes.models import ContentType
from django.contrib... | dgk/django-business-logic | business_logic/models/node.py | Python | mit | 13,515 | [
"VisIt"
] | f683ca463b0a1f998bdf1d6aa1c074cbaf91589bc5986ec62e16a49d860b7c3c |
# Copyright 2000-2004 Brad Chapman.
# Copyright 2001 Iddo Friedberg.
# Copyright 2007-2010 by Peter Cock.
# 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.
"""Classes for gener... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/Align/Generic.py | Python | gpl-2.0 | 17,579 | [
"BLAST",
"BioPerl",
"Biopython"
] | ebccda620378ad539816afd7653e5a4e62b2596429068021250b495dc77313ca |
#!/usr/bin/env python
"""__main__.py: main entry point for pypodcaster"""
import argparse
import logging
import os
import time
import validators
import yaml
from pkg_resources import get_distribution
from .podcast import Channel
# pypodcaster: static xml feed generator
# Copyright (C) 2015-2017 Josh Wheeler
#
... | mantlepro/pypodcaster | pypodcaster/__main__.py | Python | gpl-3.0 | 4,490 | [
"VisIt"
] | f7ea22cf1879170870f8977bb6b63caf2fbb602ff99d53e5d6f5abd870e9fb85 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007-2012 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2009-2010 Craig J. Anderson
# Copyright (C) 2014 Paul Franklin
#
# This program is free software; you can redistr... | dermoth/gramps | gramps/plugins/drawreport/descendtree.py | Python | gpl-2.0 | 69,634 | [
"Brian"
] | 405a1a99c50ae24a5616d25d173a7ee091be5dad40d8806fa0dbac1dd7edbe54 |
import unittest
import numpy as np
import pysal
from pysal.spreg.ols import OLS
from pysal.spreg.ols_regimes import OLS_Regimes
from pysal.common import RTOL
PEGP = pysal.examples.get_path
class TestOLS_regimes(unittest.TestCase):
def setUp(self):
db = pysal.open(pysal.examples.get_path('columbus.dbf'),'r... | TaylorOshan/pysal | pysal/spreg/tests/test_ols_regimes.py | Python | bsd-3-clause | 7,478 | [
"COLUMBUS"
] | 9a11bcd6c7781bb29ce05d16d6f4ad2101d1d711cdc1f1d40f33d247934faed8 |
"""
Student Views
"""
import datetime
import logging
import uuid
import json
import warnings
from collections import defaultdict
from urlparse import urljoin
from pytz import UTC
from requests import HTTPError
from ipware.ip import get_ip
from django.conf import settings
from django.contrib.auth import logout, authen... | solashirai/edx-platform | common/djangoapps/student/views.py | Python | agpl-3.0 | 102,241 | [
"VisIt"
] | 932e03004a9aace8b64161fcced8bf707ae5668ad97d90e9db82a7819365a282 |
from ast import iter_fields
import re
from collections import OrderedDict
import clang.cindex
from ..constants import (
UNARY_OPERATOR_MAP,
BINARY_OPERATOR_MAP,
OTHER_OPERATOR_MAP,
NOT_DEFAULT_ARG_KINDS,
)
from ..abstract import NodeVisitor
from ..parser import AstNode
from .. import utils
class Fun... | mugwort-rc/pypp | pypp/halide/interpreter.py | Python | gpl-3.0 | 11,411 | [
"VisIt"
] | a0b8c030c1235ada4e61735fa9bec2f3062a15596e5656e321126359ce1895b2 |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-automl | tests/unit/gapic/automl_v1beta1/test_prediction_service.py | Python | apache-2.0 | 69,221 | [
"Octopus"
] | 2934cfa0060f333ed20f3be3a66ba271a78201e228a14360b991dd8fc0e627a0 |
""" Base classes for classification """
import numpy
import os
import cPickle
import warnings
import logging
import timeit
# base class
from pySPACE.missions.nodes.base_node import BaseNode
# representation of the linear classification vector
from pySPACE.resources.data_types.feature_vector import FeatureVector
# th... | pyspace/test | pySPACE/missions/nodes/classification/base.py | Python | gpl-3.0 | 20,641 | [
"Gaussian"
] | 3686994d6a2f46d103f24c964f2de74eed0a55c800a5c1f2b2033191fd7c54d9 |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-admin-delete-user
# Author : Adrian Casajus
########################################################################
"""
Remove User from Configuration
"""
__RCSID__ = "$Id$"
from DIRAC.Core.... | Sbalbp/DIRAC | Interfaces/scripts/dirac-admin-delete-user.py | Python | gpl-3.0 | 1,548 | [
"DIRAC"
] | c38d24949446ee390af3e05e075663d127e1329fa71500bc550b35c9751c5ba1 |
import ocl
import camvtk
import time
import vtk
import datetime
import math
def generateRange(zmin,zmax,zNmax):
dz = (float(zmax)-float(zmin))/(zNmax-1)
zvals=[]
for n in xrange(0,zNmax):
zvals.append(zmin+n*dz)
return zvals
if __name__ == "__main__":
print ocl.revision()
myscre... | tectronics/opencamlib | scripts/fiber_08_stl_weave.py | Python | gpl-3.0 | 5,406 | [
"VTK"
] | 77340620012e7f8b149b548500f52d93f6b3db83cb0daad1c41d30cdd2608d90 |
# ============================================================================
#
# Copyright (C) 2007-2010 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | kurtraschke/camelot | camelot/view/controls/decorated_line_edit.py | Python | gpl-2.0 | 4,474 | [
"VisIt"
] | 85406039c1ccb48056200995c59f8d6747b8f9d1739ba56ab3d114b2ff5d65f2 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkTextSource(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtk... | nagyistoce/devide | modules/vtk_basic/vtkTextSource.py | Python | bsd-3-clause | 467 | [
"VTK"
] | 07bfe576c04b1f0e316732b6ef78b4ba33db1205e6e91e6828d10a2142f8b2d6 |
# Copyright 2009-2011 by Peter Cock. 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.
"""Dictionary like indexing of sequence files (PRIVATE).
You are not expected to access this... | bryback/quickseq | genescript/Bio/SeqIO/_index.py | Python | mit | 45,915 | [
"Biopython"
] | c1afea106c0d8401b667e5113a92220526a80d3e034c27c43b27b06fb0c79a14 |
"""
Make a likelihood function for use with emcee
Given input Z, nH, k_C, k_N, k_Al, aUV, NHI return ln
of the likelihood.
This module must define the following objects:
- a dictionary P with keys. The value of every key is a tuple with the
same length (the number of model parameters)
name : parameter names
... | nhmc/LAE | cloudy/comp3/final/model.py | Python | mit | 22,014 | [
"Gaussian"
] | b6040ceb1ecdb5c3032828e345acea92aa7033878cb07b9020511a44b1ba1476 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# king_phisher/server/server.py
#
# 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, th... | guitarmanj/king-phisher | king_phisher/server/server.py | Python | bsd-3-clause | 42,834 | [
"VisIt"
] | ea78b8d4c0adfa9ab60576bf89e01c734e4e31abcb7c46de8c8ad5d44d53856a |
import os
import math
import numpy as np
import subprocess
import re
import matplotlib.pyplot as plt
from matplotlib.patches import Rectangle
import astropy.units as units
from astropy.cosmology import Planck15 as cosmo,z_at_value
from matplotlib.backends.backend_pdf import PdfPages
import threading
import time
import ... | JohnGBaker/flare | python/flare.py | Python | apache-2.0 | 35,280 | [
"Gaussian"
] | ffaf57362e2852afb347d980e11f65e9cdf7d835d0ef49981f61d4afef72faf7 |
# Copyright 2013-2021 Aerospike, Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writ... | aerospike/aerospike-admin | lib/health/query.py | Python | apache-2.0 | 102,759 | [
"VisIt"
] | a875536a575efa03da0c8827924c00ee88ef4d21778e67fb90cfbda7739bc923 |
# coding: utf-8
from __future__ import division, unicode_literals
"""
This module implements input and output processing from Gaussian.
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyuep@gmail.com"
__dat... | Dioptas/pymatgen | pymatgen/io/gaussianio.py | Python | mit | 27,837 | [
"Gaussian",
"pymatgen"
] | 57765178fdf3284eb9e193b09ade3b0da8d31f3b1c5bf1ef855769702747af4e |
# Copyright (c) 2015, Frappe Technologies Pvt. Ltd. and Contributors
# License: GNU General Public License v3. See license.txt
from __future__ import unicode_literals
import frappe
import json
import frappe.utils
from frappe.utils import cstr, flt, getdate, comma_and, cint
from frappe import _
from frappe.model.utils ... | bazz-erp/erpnext | erpnext/selling/doctype/sales_order/sales_order.py | Python | gpl-3.0 | 27,283 | [
"VisIt"
] | b435970c0a943752311fc9ffd7adf1fffb23690c04393438542898f7eaee8aba |
#!/usr/bin/env python
"""
Author : Jaganadh Gopinadhan
e-mail : jaganadhg@gmail.com
Licence : MIT
Third Eye V1.0 Udacity Self Driving Car Nano Degree Project 1
Finding Lane Lines on the Road
"""
import matplotlib.pyplot as plt
import matplotlib.image as mpimg
import numpy as np
import cv2
class FrameTransformer(... | jaganadhg/sdcnd_p1_lld | thirdeye/pputil.py | Python | mit | 6,460 | [
"Gaussian"
] | e390b2c98522ac35dfe58ea2edd104415e45a8c9310bd962fd66694c78c66bdd |
# coding=utf-8
from itertools import imap
from dgw.data.parsers.filters import MinNumberOfReadsFilter
from dgw.dtw import reverse_sequence
__author__ = 'saulius'
from logging import debug
import os
import pandas as pd
import pysam
import numpy as np
from ..containers import AlignmentsData, Regions
def _alignments_th... | lukauskas/dgw | dgw/data/parsers/bam.py | Python | gpl-3.0 | 8,536 | [
"pysam"
] | b26a3086702deafff08c1d89bf07da14ae674eba7b067a9931bd546ba12b1672 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
midi.py -- MIDI classes and parser in Python
Convered Python 2 code to Python 3 code in December 2012 by Akio Nishimura
Placed into the public domain in December 2001 by Will Ware
Python MIDI classes: meaningful data structures that represent MIDI
events
and other... | andmatand/midi-to-pico8 | midi/midi.py | Python | mit | 15,583 | [
"CRYSTAL"
] | 728b2393ca3124fccd138332fee9b82930a95321b319734ccddd8cc28f4b6bc0 |
# #START_LICENSE###########################################################
#
#
# This file is part of the Environment for Tree Exploration program
# (ETE). http://etetoolkit.org
#
# ETE is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by
# the... | etetoolkit/ete | ete3/coretype/tree.py | Python | gpl-3.0 | 97,974 | [
"scikit-bio"
] | 9bd97d93f4ecf4c93e28e0c255f2795769f9ba618e8015ca5daa2edb646eb515 |
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