text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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#!/usr/bin/env python
from __future__ import print_function
from rdkit import RDConfig
import os, sys
from rdkit import Chem
from rdkit.Chem import Draw, AllChem
suppl = Chem.SDMolSupplier()
if sys.argv[1].endswith('.sdf'):
suppl = Chem.SDMolSupplier(sys.argv[1])
elif sys.argv[1].endswith('.smi'):
suppl = Chem.Sm... | rvianello/rdkit | Code/GraphMol/MolDraw2D/test_dir/test_rdkit_draw.py | Python | bsd-3-clause | 554 | [
"RDKit"
] | 60c6963330ab065b7ca7f8d1f3880a5ee26cf3037e2b1b1a46f288fdf8a778a6 |
from distutils.core import setup
setup(
name = 'pyrotrfid',
version = '1.0.0',
description = 'Digital TRFLP with pyrosequencing reads',
long_description = open('README.txt').read(),
license = 'GNU General Public License 3.0',
url ... | xapple/pyrotrfid | setup.py | Python | gpl-3.0 | 721 | [
"Biopython",
"pysam"
] | c24b3fd9e9c4d2423deed7c31baebab7473301b7c78f2d83fb5cf7b5bb127b9a |
from distutils.core import setup
from distutils.command.install_data import install_data
from distutils.command.install import INSTALL_SCHEMES
import os
import sys
class osx_install_data(install_data):
# On MacOS, the platform-specific lib dir is /System/Library/Framework/Python/.../
# which is wrong. Python 2... | brianmay/django-webs | setup.py | Python | gpl-3.0 | 2,918 | [
"Brian"
] | c3f7c62ae9b740abe109dbc991565de64d7719262745b43b806d001bb462ebad |
""" Class that contains client access to the PilotsLogging handler. """
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
from DIRAC.Core.Base.Client import Client, createClient
@createClient('WorkloadManagement/PilotsLogging')
class Pilo... | yujikato/DIRAC | src/DIRAC/WorkloadManagementSystem/Client/PilotsLoggingClient.py | Python | gpl-3.0 | 1,487 | [
"DIRAC"
] | e238219007c36daefb621be87a26f11626a1d6e496b66a77a25d74a5ea98f104 |
import numpy as np
from matplotlib.testing.decorators import image_comparison, knownfailureif
from matplotlib.delaunay.triangulate import Triangulation
from matplotlib import pyplot as plt
import matplotlib as mpl
def constant(x, y):
return np.ones(x.shape, x.dtype)
constant.title = 'Constant'
def xramp(x, y):
... | lthurlow/Network-Grapher | proj/external/matplotlib-1.2.1/lib/matplotlib/tests/test_delaunay.py | Python | mit | 5,994 | [
"Gaussian"
] | 95c4c2511e0bdd22eba9a08c0b382ccc83101e494034cf0063453b35c102d41f |
from __future__ import unicode_literals
from django.db import IntegrityError, connection, models, transaction
from django.test import TestCase
from .models import (
Bar, Director, Favorites, HiddenPointer, ManualPrimaryKey, MultiModel,
Place, RelatedModel, Restaurant, School, Target, UndergroundBar, Waiter,
)... | BrotherPhil/django | tests/one_to_one/tests.py | Python | bsd-3-clause | 20,339 | [
"Brian"
] | 03641d36015473208229d5b742d016488e9eb475c0efc6f228f32b54b765aae2 |
# Principal Component Analysis Code :
from numpy import mean,cov,double,cumsum,dot,linalg,array,rank,size,flipud
from pylab import *
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import ro... | tapomayukh/projects_in_python | classification/Classification_with_kNN/Single_Contact_Classification/Feature_Comparison/multiple_features/results/test10_cross_validate_objects_1200ms_scaled_method_v_area_motion.py | Python | mit | 4,600 | [
"Mayavi"
] | adc2c2ad422be36212a727513a7d7006df181369445f1edb780ff4de2214520a |
from StandardModules import *
##########################################################################
#
# QGIS-meshing plugins.
#
# Copyright (C) 2012-2013 Imperial College London and others.
#
# Please see the AUTHORS file in the main source directory for a
# full list of copyright holders.
#
# Dr Ada... | adamcandy/QGIS-Meshing | extras/raster_tools/fileOperations.py | Python | lgpl-2.1 | 3,192 | [
"NetCDF"
] | ae9cd2d0c53470dd071ee1f7cf4cf969231c6910bcb20203e49bd0f21cab1aa4 |
# -*- coding: utf-8 -*-
"""Find best fitting model time courses for population receptive fields."""
# Part of py_pRF_motion library
# Copyright (C) 2016 Marian Schneider, Ingo Marquardt
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as p... | MSchnei/py_pRF_motion | pyprf_feature/simulation/pRF_sim_main.py | Python | gpl-3.0 | 24,076 | [
"Gaussian"
] | 5560dd451da44cfa67b310b8cbe222cab213ab1a6314e7279602f805980d001a |
import numpy as np
from settings import UserSettings
import cv2
def nothing(x):
pass
tag = "ball"
#tag = "own_goal"
#tag = "opp_goal"
#tag = "ref"
user_settings = UserSettings()
settingsDict = user_settings.read_json_settings(tag)
if (not settingsDict):
settingsDict = {'h_high': 0, 'h_low': 0, 's_high': 0, 's... | valuko/team_st33ve | manual_configure.py | Python | mit | 2,876 | [
"Gaussian"
] | 9228735bdba3a1e4fd9bd971d2e4abe4ee682d2120304b74a09d45977ad1619e |
from urllib import parse, request
import sys
import os
from astLib import astCoords
import numpy as np
from time import sleep
def filtercomment(sql):
"Get rid of comments starting with --"
fsql = ''
for line in sql.split('\n'):
fsql += line.split('--')[0] + ' ' + os.linesep
return fsql
def qu... | boada/planckClusters | scripts/mkCatalogSDSS_galonly.py | Python | mit | 2,770 | [
"Galaxy"
] | 2b636cbf3f91423d581e40f39ac9dacbcb6837bf622a50ac7aba7fabd2e235eb |
import logging
import tempfile
from pathlib import Path
from pywps import Process, LiteralInput, FORMATS
from pywps.inout.outputs import MetaFile, MetaLink4
from flyingpigeon.subset_base import Subsetter
from flyingpigeon.processes.wpsio import resource, variable, start, end, output, metalink
from pywps.ext_autodoc i... | bird-house/flyingpigeon | flyingpigeon/processes/wps_subset_bbox.py | Python | apache-2.0 | 3,582 | [
"NetCDF"
] | 659c831e6e8f1929be9f0a36b439a44660cd40245ba5a5dcd232fd316beefda1 |
# Copyright 2007 Google Inc.
# Licensed to PSF under a Contributor Agreement.
"""Unittest for ipaddress module."""
import unittest
import re
import contextlib
import functools
import operator
import pickle
import ipaddress
import weakref
class BaseTestCase(unittest.TestCase):
# One big change in ipaddress ove... | Microvellum/Fluid-Designer | win64-vc/2.78/python/lib/test/test_ipaddress.py | Python | gpl-3.0 | 83,267 | [
"FEFF"
] | 60723d2fda160180d3ff11df51facc914196ed3393b1be3bf54ea88e7bf24861 |
import numpy as np
import simulation_parameters
import nest
import nest.raster_plot
import matplotlib
import pylab as pl
import json
import pprint as pp
if (not 'bcpnn_dopamine_synapse' in nest.Models('synapses')):
nest.Install('ml_module')
GP = simulation_parameters.global_parameters()
#GP.write_parameters_to_fi... | pierreberthet/local-scripts | bcpnntest.py | Python | gpl-2.0 | 6,307 | [
"NEURON"
] | 7e11a3f179edacc1b0ec147479b87dc307110e9342e5af6aaf83341a73cce8d4 |
import pytest
from math import pi
from ngsolve import *
from netgen.geom2d import SplineGeometry
from xfem import *
@pytest.mark.parametrize("quad", [True, False])
def test_spacetime_vtk(quad):
tref = ReferenceTimeVariable()
square = SplineGeometry()
A = 1.25
square.AddRectangle([-A,-A],[A,A])
ngmesh = squar... | ngsxfem/ngsxfem | tests/pytests/test_spacetime_vtk.py | Python | lgpl-3.0 | 1,661 | [
"VTK"
] | c45d8ca91141f3bb65c6f75e1b59222cfd4a78d51e335a9091fb0434aec3da1f |
# (C) British Crown Copyright 2010 - 2017, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | LukeC92/iris | lib/iris/tests/__init__.py | Python | lgpl-3.0 | 45,559 | [
"NetCDF"
] | 27c7e0651db51b4582e69d537138ac5a7b6bce727abd41484f22c6e6e89e0b30 |
""" PublisherHandler
This service has been built to provide the RSS web views with all the information
they need. NO OTHER COMPONENT THAN Web controllers should make use of it.
"""
__RCSID__ = '$Id$'
# pylint: disable=no-self-use
from datetime import datetime, timedelta
from types import NoneType
# DIRAC
from DI... | arrabito/DIRAC | ResourceStatusSystem/Service/PublisherHandler.py | Python | gpl-3.0 | 12,865 | [
"DIRAC"
] | fa3d7bffda920d0870351684d268582e96fcf496b87fe67db4701839df9753c1 |
#!/usr/bin/env python
# Copyright 2014-2019 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/pbc/scf/uhf.py | Python | apache-2.0 | 8,338 | [
"PySCF"
] | bda318fe7dd108e06e4227099a001a638606ce66ce92c8156f66a5c8e04479b9 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# ---------------------------------------------------------------------
# Copyright (c) 2012 Michael Hull.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are m... | mikehulluk/morphforge | src/morphforgecontrib/simulation/channels/hh_style/neuron/hocmodbuilders/mmwriter_alphabetabeta.py | Python | bsd-2-clause | 7,196 | [
"Elk",
"NEURON"
] | f96ab3e3739beedc3d26328ca69ce825b167aa6beb5b8ee133cae7567c57261f |
"""MDTraj: A modern, open library for the analysis of molecular dynamics trajectories
MDTraj is a python library that allows users to manipulate molecular dynamics
(MD) trajectories and perform a variety of analyses, including fast RMSD,
solvent accessible surface area, hydrogen bonding, etc. A highlight of MDTraj
is ... | rmcgibbo/mdtraj | setup.py | Python | lgpl-2.1 | 12,509 | [
"Amber",
"CHARMM",
"Gromacs",
"MDTraj",
"NAMD",
"NetCDF",
"TINKER"
] | 0566ef819909ba52b82d75d9503cb902ac175a63bb5750557e6970639edfae3f |
#
# 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 n... | kwhitehall/climate | mccsearch/code/mccSearch.py | Python | apache-2.0 | 143,072 | [
"NetCDF"
] | f7845afa5035cbc156a6875f24a955bd6d780e057af475606de1e4f93368f55d |
import ocl as cam
import camvtk
import time
import vtk
import math
import datetime
red= (1,0,0)
green= (0,1,0)
blue= (0,0,1)
cyan= (0,1,1)
yellow= (1,1,0)
pink = ( float(255)/255,float(192)/255,float(203)/255)
grey = ( float(127)/255,float(127)/255,float(127)/255)
orange = ( float(255)/255,float(165)/255,float(0)/255... | davidwusea/opencamlib | scripts/offset-ellipse/oellipse3_tst.py | Python | gpl-3.0 | 13,646 | [
"VTK"
] | 3fc9fed0503ceb28d8cb26e19d64937d123e3165b6a593bc06b63549586f9207 |
from galaxy.test.base.twilltestcase import TwillTestCase
class BasicFunctions(TwillTestCase):
def test_init(self):
"""Testing home page"""
self.home()
def test_single_upload(self):
"""Testing single upload"""
self.clear_history()
self.upload_file('1.bed')
def ... | jmchilton/galaxy-central | galaxy/test/functional/test_basic.py | Python | mit | 1,671 | [
"Galaxy"
] | 1b7b7e9f42aa5a4f6d5182c715e8643d1263fb18cffea3c2c43d410729ba7753 |
""" RPCClient object is used to create RPC connection to services
"""
__RCSID__ = "$Id$"
from DIRAC.Core.DISET.private.InnerRPCClient import InnerRPCClient
class _MagicMethod( object ):
def __init__( self, doRPCFunc, remoteFuncName ):
self.__doRPCFunc = doRPCFunc
self.__remoteFuncName = remoteFuncName
... | vmendez/DIRAC | Core/DISET/RPCClient.py | Python | gpl-3.0 | 1,541 | [
"DIRAC"
] | 0e65c910eb2942bc7fc8cf353a276371d691ab1c0f5186513fd148e21209f152 |
#! /usr/bin/python
###
# lcd_daemon.py
#
# Python daemon for managing an HD44780 LCD, used by the "campanella" bell management system
#
# For more information on the software please visit:
# https://lizzit.it/campanella
#
# Written by: Michele Lizzit <michele@lizzit.it>, 25 Apr 2016
# Last u... | michelelizzit/campanella | campanella/lcd_daemon.py | Python | agpl-3.0 | 1,812 | [
"VisIt"
] | d41fee44dc6040fbc5750760553b7b2ee4d76b724224b0c75ad4a6f6db47248d |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
import pickle
import warnings
import math
import numpy as np
from pymatgen.util.testing import PymatgenTest
from pymatgen.core.periodic_table import Element, Specie, DummySpecie, get_el_sp
fro... | dongsenfo/pymatgen | pymatgen/core/tests/test_periodic_table.py | Python | mit | 16,612 | [
"pymatgen"
] | 55a0d0abe8da90fb2aaed040966ecbdb918dd62321dc3800c7e99847b22da586 |
#!/usr/bin/python
import subprocess,os,time,argparse,fnmatch
parser=argparse.ArgumentParser()
parser.add_argument('--lib',nargs='*')
parser.add_argument('--mei',nargs='*')
parser.add_argument('--mapq',nargs='*')
parser.add_argument('--blast',nargs='*')
parser.add_argument('--r1',nargs='*')
parser.add_argument('--r2',... | JXing-Lab/ME-SCAN-SVA | modules/BB_mappedread2convert.py | Python | gpl-3.0 | 4,686 | [
"BLAST"
] | 60b852a27c629cf21872e9d223efdce4512076efd020f7c374ee976aaadfcd21 |
# -*- coding: utf-8 -*-
"""
Created on 26 Sep 2012
@author: Éric Piel
Copyright © 2012-2015 Éric Piel, Delmic
This file is part of Odemis.
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 Software
Foundation.
Odem... | gstiebler/odemis | src/odemis/gui/cont/streams.py | Python | gpl-2.0 | 99,511 | [
"Gaussian"
] | 3f0d485fc69a48a9091be704480058e4342c46122d77de94ebe8d71dcb1e4778 |
from sys import stdout , stderr
from math import log
from re import *
from optparse import OptionParser
pattern_A=compile(r"([0-9]+)M")
pattern_B=compile(r"([0-9]+)I")
pattern_C=compile(r"([0-9]+)[D|N]")
def CIGAR_operation_distribution_report(distribution):
matches=distribution.keys()
matches.sort()
for i in ma... | claudejrogers/RNASEQR | analyze_gaps_of_alignments.py | Python | gpl-3.0 | 4,086 | [
"BWA",
"Bowtie"
] | ecde189a109155ce03536afd62c26a11b36ee9b94d2485611b6dfcb9db042fbb |
# coding=utf-8
"""Functions for computing climate classifications/zones from weather data."""
from __future__ import division
from .datacollection import HourlyContinuousCollection
def ashrae_climate_zone(dry_bulb_temperature, annual_precipitation=None):
"""Estimate the ASHRAE climate zone from a single year of ... | ladybug-analysis-tools/ladybug-core | ladybug/climatezone.py | Python | gpl-3.0 | 3,407 | [
"EPW"
] | 80fceea2568ab4305a1750064b863def6069da8bf8dcb459af3243788470750b |
# -*- coding: utf-8 -*-
# @Author: twankim
# @Date: 2017-02-24 17:46:51
# @Last Modified by: twankim
# @Last Modified time: 2018-03-09 22:14:06
import numpy as np
import time
import sys
import os
import argparse
import matplotlib
matplotlib.use('agg')
import matplotlib.pyplot as plt
from ssac import weakSSAC
fro... | twankim/weaksemi | main_global.py | Python | mit | 8,410 | [
"Gaussian"
] | 2eb4c4758503010a378fd3f54a2b8fb143e6eab346403bb362666fad502438d0 |
import argparse
import subprocess
import pysam
if __name__ == "__main__":
parser = argparse.ArgumentParser(
description='converts bam file to bowtie file')
parser.add_argument(
'--bam', required=True, help='bam file')
args = parser.parse_args()
bam_file = pysam.Samfile("/nas3/scratc... | YeoLab/gscripts | gscripts/general/bamTobowtie.py | Python | mit | 825 | [
"Bowtie",
"pysam"
] | 424efbd3083d01ad5605a56b7f4cb3e7e12fa97bf8e36ad6e0ef340b6e9b5510 |
"""
Test the Studio help links.
"""
from nose.plugins.attrib import attr
from unittest import skip
from common.test.acceptance.fixtures.course import XBlockFixtureDesc
from common.test.acceptance.tests.studio.base_studio_test import StudioCourseTest, ContainerBase
from common.test.acceptance.pages.studio.index import... | synergeticsedx/deployment-wipro | common/test/acceptance/tests/studio/test_studio_help.py | Python | agpl-3.0 | 49,206 | [
"VisIt"
] | eba97999b095e153771aa0d5727c027c3b1878f8786f989aa6ba1abcf05339b1 |
import unittest
try:
from unittest.mock import patch # Python 3.4 and later
except ImportError:
from mock import patch
from ncclient.transport.session import *
from ncclient.devices.junos import JunosDeviceHandler
try:
from Queue import Queue, Empty
except ImportError:
from queue import Queue, Empty
im... | nwautomator/ncclient | test/unit/transport/test_session.py | Python | apache-2.0 | 10,600 | [
"Firefly"
] | 22c193f755eaa73f3d7283513dd685158e9fa6e8b4da9544dbe4008b5b0d88ce |
#!/usr/bin/env python
# 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.
"""Run BioSQL tests using SQLite"""
from Bio import MissingExternalDependencyError
from BioSQL import BioSeqDatabase
from common... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_BioSQL_mysql_connector.py | Python | gpl-2.0 | 1,079 | [
"Biopython"
] | 9708a4f119b9263e4a2e30fad2ed12fdebd19c824f647e965bbb89b8c7df97cf |
# -*- coding: utf-8 -*-
# Copyright (C) 2017 by Pedro Mendes, Virginia Tech Intellectual
# Properties, Inc., University of Heidelberg, and University of
# of Connecticut School of Medicine.
# All rights reserved.
# Copyright (C) 2010 - 2016 by Pedro Mendes, Virginia Tech Intellectual
# Properties, Inc., Universit... | jonasfoe/COPASI | copasi/bindings/python/unittests/Test_CCopasiProblem.py | Python | artistic-2.0 | 1,478 | [
"COPASI"
] | 75a9802b500e2b9d635caea3d3b11d26fc954b665f4b6bffcaf78d7621662e18 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""moose_sim.py:
A cable with 1000 compartments with HH-type channels in it.
Last modified: Wed May 21, 2014 09:51AM
"""
__author__ = "Dilawar Singh"
__copyright__ = "Copyright 2013, NCBS Bangalore"
__credits__ = ["NCBS Bangalore", "Bhall... | dharmasam9/moose-core | tests/python/Rallpacks/moose_vs_neuron/rallpack3/moose_sim.py | Python | gpl-3.0 | 10,083 | [
"MOOSE"
] | 1cfd1872ae2aeecd04e025417e31a9b5a8b4d149189cf06e7251be29fb85af8f |
from base import report_content_to_test_docs
_TEST_CLINICAL_NOTES = [
"""
<SimpleClinicalNote xmlns="http://indivo.org/vocab/xml/documents#">
<dateOfVisit>2010-02-02T12:00:00Z</dateOfVisit>
<finalizedAt>2010-02-03T13:54:03Z</finalizedAt>
<visitType type="http://codes.indivo.org/visit-types#" value="acute">Ac... | newmediamedicine/indivo_server_1_0 | indivo/tests/data/reports/simple_clinical_note.py | Python | gpl-3.0 | 7,809 | [
"VisIt"
] | 5aeccc318f7929ebd55f0137f8246dd8432cc813dc02c479589f9caee51560b6 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
TypeOffset is a C# class that mirrors the in-memory layout of heap
allocated Python objects.
This script parses the Python C headers and outputs the TypeOffset
C# class.
Requirements:
- pycparser
- clang
"""
from __future__ import print_function
import logg... | denfromufa/pythonnet | tools/geninterop/geninterop.py | Python | mit | 8,728 | [
"VisIt"
] | b1c5bbd9ce5e6d68841c456c615cb9cc148175ae936939881134a283e84e5f88 |
# Copyright 2017 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... | jendap/tensorflow | tensorflow/python/autograph/converters/continue_statements.py | Python | apache-2.0 | 5,611 | [
"VisIt"
] | 581d225e912d476dfab2a1ab759935f759f1faf1340810808393b534184cb894 |
"""
Graphical model (GM)-based optimization algorithm using Theano
"""
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
from builtins import str
from builtins import map
from builtins import zip
from builtins import range
from past.utils import old_div
import ... | denik/vwoptimize | vwoptimizelib/third_party/hyperopt/tpe.py | Python | mit | 31,932 | [
"Gaussian"
] | 1d2ca06d0fea0f0c3d1fd764abd086fe98c2b7af87fdf7e2a0dacb4ccef69e4d |
# GetDatasetDatPath/GetDatasetDatPath.py - a self annotated version of rgToolFactory.py generated by running rgToolFactory.py
# to make a new Galaxy tool called GetDatasetDatPath
# User mika.yoshimura@riken.jp at 30/01/2015 16:21:41
# rgToolFactory.py
# see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
#
# c... | myoshimura080822/tools_of_rnaseq_on_docker_galaxy | GetDatasetDatPath/GetDatasetDatPath.py | Python | mit | 32,567 | [
"Galaxy"
] | bce5577e427c9cb8934ccec8084ff785dde7dd48ac20eca3ea4701e4dab37070 |
import os
from os.path import join
import logging
import glob
import csv
from collections import namedtuple
import sys
import pprint
import pickle
import multiprocessing
cpu_count = multiprocessing.cpu_count()
# Project working directory, where samples will be linked to
samples_path = '/path/to/working_directory'
# ... | d-quinn/bio_quinn2013 | gene_estimates/mglobals.py | Python | mit | 5,305 | [
"Bowtie"
] | c66776532c0fdb9eef945c0562b3585d1d84f775cde3822f044d9a80904d4fa6 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | jensreeder/scikit-bio | skbio/io/tests/test_phylip.py | Python | bsd-3-clause | 3,721 | [
"scikit-bio"
] | ac645802c40944771992c8e68adaf86853299711f81e9cd153c964be2a79be74 |
# -*- 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
urlpatterns = [
url(r'^$', TemplateView.as_view(templ... | jms/FlyNi-API | config/urls.py | Python | bsd-3-clause | 1,038 | [
"VisIt"
] | f1643b4adf58522bd3c68460147571c93bf868b95b78b2df7a8ba7aabfe39764 |
import os
from math import ceil
import tkinter as tk
import tkinter.ttk as ttk
from tkinter import RIDGE,N,S,E,W,filedialog
import O4_File_Names as FNAMES
import O4_UI_Utils as UI
import O4_DEM_Utils as DEM
import O4_OSM_Utils as OSM
import O4_Vector_Map as VMAP
import O4_Imagery_Utils as IMG
import O4_Tile_Utils as ... | oscarpilote/Ortho4XP | src/O4_Config_Utils.py | Python | gpl-3.0 | 38,204 | [
"Gaussian"
] | 0d8aca0f1f2eaf4ccc1b5b5f3a68cbb1af22297a99be3ef3319b64a9a23809d8 |
# Principal Component Analysis Code :
from numpy import mean,cov,double,cumsum,dot,linalg,array,rank,size,flipud
from pylab import *
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import ro... | tapomayukh/projects_in_python | classification/Classification_with_kNN/Single_Contact_Classification/Final/best_kNN_PCA/objects/96/test11_cross_validate_objects_96_no_motion_1200ms.py | Python | mit | 4,621 | [
"Mayavi"
] | e0dbaa627fdcd5f24a2f38da2805359b63112c18b74c23a85fe2f6531017ab9f |
""" Test the SSLTransport mechanism """
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import os
import select
import socket
import threading
from pytest import fixture
from diraccfg import CFG
from DIRAC.Core.Security.test.x509TestUtilities import CERTD... | yujikato/DIRAC | src/DIRAC/Core/DISET/private/Transports/test/Test_SSLTransport.py | Python | gpl-3.0 | 7,119 | [
"DIRAC"
] | fd5cc6d11a4ddd66ce2dbc9c91a03e9587a5f64955627cea56a5d51424ca48c2 |
from __future__ import absolute_import, division, print_function
__author__ = 'Timothy D. Morton <tim.morton@gmail.com>'
"""
Defines objects useful for describing probability distributions.
"""
import numpy as np
import matplotlib.pyplot as plt
import logging
from scipy.interpolate import UnivariateSpline as interpol... | timothydmorton/simpledist | simpledist/distributions.py | Python | mit | 34,971 | [
"Gaussian"
] | 533a66bcb4047d71f5307397ccc446c0ed8794b42a7500e180f8e1d7ed0ba1df |
#
from nrutils.core.basics import *
from glob import glob as ls
from os.path import getctime
from numpy import array,cross,zeros,dot,abs,sqrt,inf,nan,sign
from numpy.linalg import inv, norm
from numpy import sum as asum
# Determine whether the folder containing a metadta file is valid: can it be used to reference wav... | Cyberface/nrutils_dev | nrutils/handlers/maya.py | Python | mit | 9,297 | [
"Psi4"
] | 02032c38cf701dc561d8ea6928c16f5ec683bd73665956dcceb1ed83c2703dd4 |
#!/usr/bin/env python
"""
COPYRIGHT AND LICENSE
@author John D. Chodera <jchodera@gmail.com>
All code in this repository is released under the MIT License.
This program is free software: you can redistribute it and/or modify it under
the terms of the MIT License.
This program is distributed in the hope that it wi... | choderalab/openmmtools | openmmtools/mcmc.py | Python | mit | 76,432 | [
"OpenMM"
] | f46f14bce5aac423005ee04176f365ae5e1c68674e8d667b1b32b605501406c1 |
import logging
import pysam
from multiprocessing import Process
from optparse import make_option
from django.core.management.base import BaseCommand, CommandError
from django.core.exceptions import ValidationError
from django.db.utils import IntegrityError
from browser.models import Gene
logger = logging.getLogger(... | DCGenomics/vcf_parsing_hackathon_v002 | django/browser/management/commands/load_genes.py | Python | cc0-1.0 | 4,521 | [
"pysam"
] | cd831865e8d3c9d45c6f6d62245a107cde0e49259299ff43d09fcfd6f91eb304 |
"""
Module for wrapping an :class:`ncobj.Group` to make it as far as
possible appear as if it were a :class:`netCDF4.Dataset`.
This is for read-only purposes : all dataset-changing methods are missing.
At present this is focussed on delivering the ability to load these
quasi-datasets into the Iris project (https://git... | pp-mo/ncobj | lib/ncobj/nc_fake.py | Python | gpl-3.0 | 4,559 | [
"NetCDF"
] | 961edcc37c254c117a8e67d1e8247554dd44c6bc56720eb91fab4044b12a3b42 |
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
from copy import deepcopy
from frbpoppy import CosmicPopulation, SurveyPopulation, Survey
from frbpoppy import poisson_interval
from tests.convenience import plot_aa_style, rel_path
ACTUAL_RATES = False
SURVEYS = ['askap-fly', 'fast-crafts', 'chim... | davidgardenier/frbpoppy | tests/rates/flattening_rates.py | Python | mit | 8,550 | [
"Gaussian"
] | 157bd0ed2246b42eb886ad5a7bdb57f055340cdd3f1e2fba709d55c9a0e0b89e |
import scipy as sp
import scipy.linalg as spla
import scipy.sparse.linalg as splinalg
import numpy as np
from functools import reduce
import pyscf
import itertools
import h5py
from pyscf import gto, scf, ao2mo, fci
import pyscf.tools as pt
import copy
import matplotlib.pyplot as plt
#############
# INPUT
#############
... | shivupa/pyci | methods/misc/asci_old.py | Python | gpl-3.0 | 19,860 | [
"GAMESS",
"PySCF"
] | 101b97b08046a811ec229d689e7af3c6caa9b59d788f96dfaeb44f8b82de908e |
# -*- coding: utf-8 -*-
#
# Copyright (C) Pootle contributors.
#
# This file is a part of the Pootle project. It is distributed under the GPL3
# or later license. See the LICENSE file for a copy of the license and the
# AUTHORS file for copyright and authorship information.
import logging
from django.contrib.auth imp... | unho/pootle | pootle/core/initdb.py | Python | gpl-3.0 | 11,174 | [
"VisIt"
] | 1ee40c2a8020bcad0faea9cabbcfd375fc3c804db8e0ee9838eeb6b09774e014 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkDashedStreamLine(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
v... | nagyistoce/devide | modules/vtk_basic/vtkDashedStreamLine.py | Python | bsd-3-clause | 505 | [
"VTK"
] | d0116d3c895638ea5ae75a80b074e634b937c8553b278474f7af14ba0a939929 |
#### PATTERN | EN | INFLECT ########################################################################
# -*- coding: utf-8 -*-
# Copyright (c) 2010 University of Antwerp, Belgium
# Author: Tom De Smedt <tom@organisms.be>
# License: BSD (see LICENSE.txt for details).
######################################################... | SigridK/corpkit | corpkit/inflect.py | Python | mit | 30,572 | [
"Elk",
"Octopus"
] | 03f16fccc95a316fd5319214c1602fb295d40803c6bdce1872cd98ea335016f5 |
# -*- coding: utf-8 -*-
'''
Created on Oct 19, 2014
Modified on Sep 22, 2016
Version 0.03.hb
@author: rainier.madruga@gmail.com
A simple Python Program to scrape the ESPN FC website for content.
=================================================================================================
*** 2016-09-22 RWM Updat... | rainier-m/python-soccer | parseESPN-EPLStats.py | Python | gpl-2.0 | 32,338 | [
"CRYSTAL"
] | b2183398d4efcf460137158e7fb1c553e288da3e0030b1a40a8bccd49bcffae2 |
#!/usr/bin/env python
##calculate_frequency_optimal_codons.py
##written 2/23/15 by Groves Dixon
ProgramName = 'calculate_frequency_optimal_codons.py'
LastUpdated = '2/23/15'
By = 'Groves Dixon'
VersionNumber = '1.0'
print "\nRunning Program {}...".format(ProgramName)
VersionString = '{} version {} Last Updated {} by {... | grovesdixon/metaTranscriptomes | scripts/old/calculate_frequency_optimal_codons.py | Python | mit | 5,199 | [
"BLAST",
"Biopython"
] | 6eaef7ace4a50a94cc660636a4c54c6d1ab38395dddef0f52e6d0e3e8a3d9877 |
""" part of lsqfit module: extra functions """
# Created by G. Peter Lepage (Cornell University) on 2012-05-31.
# Copyright (c) 2012-21 G. Peter Lepage.
#
# 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 F... | gplepage/lsqfit | src/lsqfit/_extras.py | Python | gpl-3.0 | 71,189 | [
"Gaussian"
] | ff79f557e53926fa0c236cac492494b9c19ee513d5f316c40ae4d515c7ec6c2f |
# -*- coding: utf-8 -*-
import io
import sys
import os
import ujson
import fido
import time
import gzip
import warnings
import pandas as pd
import plotly.io as pio
import itertools
import functools
import requests
import logging
from requests.exceptions import RequestException
from bravado_core.param import Param
from... | materialsproject/MPContribs | mpcontribs-client/mpcontribs/client/__init__.py | Python | mit | 74,548 | [
"CRYSTAL",
"VisIt",
"pymatgen"
] | b5705c2e515bb9355c98dfdf9fd96b3bb143492591b594bd040d2228f6d273a3 |
# 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 field 'Blast.in_reply_to'
db.add_column('bugle_blast', 'in_reply_to', self.gf('django.db.models.f... | devfort/bugle | bugle_project/bugle/migrations/0003_auto__add_field_blast_in_reply_to.py | Python | bsd-2-clause | 5,742 | [
"BLAST"
] | 31b7e388ee966bb7efd5cce650978fbb716ac287ed96d316668fbab09011357c |
"""
This script is an example of how to use the random gaussian noise generator
module. |br|
This is the simplest example, with only one signal generated.
After the generation, spectrum fo the signal is analyzed with an Welch analysis
and ploted.
*Author*:
Jacek Pierzchlewski, Aalborg University, Denmark. <jap@... | JacekPierzchlewski/RxCS | examples/signals/gaussNoise_ex0.py | Python | bsd-2-clause | 1,846 | [
"Gaussian"
] | dc5ea589029e45aebb829c353c2f5521bf774d468c86e13ce18675b8f13aced4 |
# -*- coding:utf-8; python-indent:2; indent-tabs-mode:nil -*-
# Copyright 2013 Google Inc. 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/l... | pombredanne/pytype | pytype/pytd/type_match.py | Python | apache-2.0 | 14,728 | [
"VisIt"
] | 2598771f6684cfcc79d2f854f7d147bf903b5dac45ff0a6930df55207f153f79 |
# -*- coding: utf-8 -*-
r"""
Convert html from text cells in the notebook into ReStructuredText
This is called by sws2rst
- Pablo Angulo Ardoy (2011-02-25): initial version
"""
#**************************************************
# Copyright (C) 2011 Pablo Angulo
#
# Distributed under the terms of the GPL License
#***... | rmartinjak/sagenb | sagenb/misc/comments2rst.py | Python | gpl-2.0 | 13,967 | [
"VisIt"
] | 10da9ab70e7d249a960109a84242d81fe99dbe407f1f0a7cb6ea8199e2def27f |
#!/usr/bin/env python3
### VERY MUCH PYTHON 3 !!!
"""
Library routine for parsing and holding multithreaded Portal objects
Made available under the MIT license as follows:
Copyright 2017 Brian Bulkowski brian@bulkowski.org
Permission is hereby granted, free of charge, to any person obtaining a copy of this softwa... | bbulkow/MagnusFlora | rest/portal.py | Python | mit | 27,267 | [
"Brian"
] | 38f7ace432c949033f82c1bff0532f3292172af0d7c6e552aba4ef6f015469dc |
#!/usr/bin/python3
# -*-coding:Utf-8 -*
# Copyright (C) 2015 Laurent Modolo
# This file is part of TEtools suite for galaxy.
# TEtools 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 th... | l-modolo/TEtools | PingPong.py | Python | gpl-3.0 | 7,975 | [
"Bowtie",
"Galaxy"
] | 273f1f5dca375383ac1c7890e2ff260f33912ba47bd94422990d35f061d2d4fc |
# Copyright 1999 by Jeffrey Chang. 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.
"""Module to work with enzyme.dat file (DEPRECATED).
This module provides code to work with t... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/Enzyme/__init__.py | Python | gpl-2.0 | 8,982 | [
"Biopython"
] | afc703861bc906d5979b1a94ae943ee02aba827b1d1ae286808b3d400918e05c |
from __future__ import absolute_import
from typing import Any, DefaultDict, Dict, List, Set, Tuple, TypeVar, Text, \
Union, Optional, Sequence, AbstractSet, Pattern, AnyStr, Callable
from typing.re import Match
from zerver.lib.str_utils import NonBinaryStr
from django.db import models
from django.db.models.query i... | SmartPeople/zulip | zerver/models.py | Python | apache-2.0 | 69,513 | [
"VisIt"
] | 84936b6a5657a0d710cd0174ccf993e0c1fd230f57624c67e72a6147707502a5 |
# -*- 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) 2006-2014, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Pub... | ghutchis/cclib | src/cclib/method/fragments.py | Python | lgpl-2.1 | 5,770 | [
"ADF",
"cclib"
] | 08c5c225347dd28426745d956bd451700ae999b4c52e01207d7dea18dcbc0819 |
from __future__ import print_function
__author__ = """Alex "O." Holcombe, Charles Ludowici, """ ## double-quotes will be silently removed, single quotes will be left, eg, O'Connor
import time, sys, platform, os
from math import atan, atan2, pi, cos, sin, sqrt, ceil, radians, degrees
import numpy as np
import psychopy, ... | alexholcombe/dot-jump | dataRaw/Fixed Cue/test_dot-jump25Oct2016_11-20.py | Python | gpl-3.0 | 25,110 | [
"Gaussian"
] | fcef38af7e42a4e42c1118c1b9c39be1cc8be2900eb4ec2bc9686bcb778251ff |
#!/usr/bin/python2.4
#
# CDDL HEADER START
#
# The contents of this file are subject to the terms of the
# Common Development and Distribution License (the "License").
# You may not use this file except in compliance with the License.
#
# You can obtain a copy of the license at usr/src/OPENSOLARIS.LICENSE
# or http://w... | marcellodesales/svnedge-console | ext/windows/pkg-toolkit/pkg/vendor-packages/pkg/depot.py | Python | agpl-3.0 | 31,605 | [
"VisIt"
] | f052426dab4ea6a844457048e557a182bd9ca3042cf035b9d558b2ad0c7db449 |
"""
Encoding and decoding for dirac, Ids:
i -> int
I -> long
f -> float
b -> bool
s -> string
z -> datetime
n -> none
l -> list
t -> tuple
d -> dictionary
"""
from past.builtins import long
import six
import datetime
import os
import functools
import inspect
import traceback
from collections import defaultd... | DIRACGrid/DIRAC | src/DIRAC/Core/Utilities/DEncode.py | Python | gpl-3.0 | 15,670 | [
"DIRAC"
] | 50de4a185c536b03dd06a6a6ba3b469404e53ae383966bc1e46247a46996951d |
# Copyright 2012 Free Software Foundation, Inc.
#
# This file is part of GNU Radio
#
# SPDX-License-Identifier: GPL-3.0-or-later
#
#
import sys
import os
import re
import csv
import copy
import warnings
from optparse import OptionParser
from gnuradio import filter, fft
try:
import numpy as np
except ImportError:... | mbr0wn/gnuradio | gr-filter/python/filter/design/filter_design.py | Python | gpl-3.0 | 90,838 | [
"Gaussian"
] | e3cbed3b52343bd468010e9343cf0657c466906f99fea66f763cbc1fa47854c4 |
#!/usr/bin/env python
from __future__ import division
__author__ = "Jai Ram Rideout"
__copyright__ = "Copyright 2012, The QIIME project"
__credits__ = ["Jai Ram Rideout"]
__license__ = "GPL"
__version__ = "1.8.0-dev"
__maintainer__ = "Jai Ram Rideout"
__email__ = "jai.rideout@gmail.com"
from bfillings.formatdb import... | wasade/qiime | qiime/parallel/assign_taxonomy.py | Python | gpl-2.0 | 6,542 | [
"BLAST"
] | c92d4cc214a7af2556b14d8707ed8e6b9fc29a50d1ccd677e1f7dbfba886afb3 |
import math
import numpy as np
from hartmann.asr import Gaussian
class MOG:
def __init__(self, gaussian = [], weight = np.array([])):
self.initialize(gaussian, weight)
def initialize(self, gaussian, weight):
self.gaussian = gaussian
self.weight = weight
self.check_components()... | hartmannw/research | hartmann/asr/mog.py | Python | unlicense | 3,440 | [
"Gaussian"
] | dfd6070aef11795e7339b3598b366a1cfa7f0b1f25f26bf0fcf1628d6d1a90d6 |
##############################################################################
# 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... | matthiasdiener/spack | var/spack/repos/builtin/packages/nwchem/package.py | Python | lgpl-2.1 | 9,975 | [
"Amber",
"NWChem"
] | 8e3b1f085d51c73a6a54790acdcb29c64a8a67ac0a00c3180894fe4e3b5edfd6 |
#!/usr/bin/env python -i
# preceeding line should have path for Python on your machine
# vizplotgui_gl.py
# Purpose: viz running LAMMPS simulation via GL tool with plot and GUI
# Syntax: vizplotgui_gl.py in.lammps Nfreq compute-ID
# in.lammps = LAMMPS input script
# Nfreq = plot data point and viz s... | SGenheden/lammps | python/examples/vizplotgui_gl.py | Python | gpl-2.0 | 4,501 | [
"LAMMPS"
] | e9371e47770ac2283b42381f8fc2a9498a99c897326e811436e52073db11db3f |
"""Random variable generators.
integers
--------
uniform within range
sequences
---------
pick random element
pick random sample
generate random permutation
distributions on the real line:
------------------------------
uniform
... | Symmetry-Innovations-Pty-Ltd/Python-2.7-for-QNX6.5.0-x86 | usr/pkg/lib/python2.7/random.py | Python | mit | 32,237 | [
"Gaussian"
] | d468f120eb1e64215d445ead255cf0d6b2e98a453d0775411d93bc4f4a59800f |
#!/usr/bin/env python
##############################################################################################
#
#
# regrid_emissions_N96e.py
#
#
# Requirements:
# Iris 1.10, time, cf_units, numpy
#
#
# This Python script has been written by N.L. Abraham as part of the UKCA Tutorials:
# http://www.ukca.ac.u... | acsis-project/emissions | emissions/python/timeseries_1960-2020/regrid_CO_emissions_n96e_360d.py | Python | gpl-3.0 | 17,333 | [
"NetCDF"
] | 7abad3ba3153053dc956892563d451fdd00ee92dc207fa242c164febf0cddc06 |
#!/usr/bin/env python
"""
Adds solvent molecules (and optionally counter-ions) to a molecular system.
Saves the solvated structure in mmCIF format.
.2017. joaor@stanford.edu
"""
from __future__ import print_function, division
import argparse
import logging
import os
import random
import sys
import simtk.openmm.ap... | csblab/md_scripts | openmm/amberff/solvateBox.py | Python | mit | 4,390 | [
"OpenMM"
] | ad1410f0713ece6325801f46e618be7470f68849097a3f5c84be77458769a057 |
#!/usr/bin/env python3.4
__author__ = 'mdc_hk'
version = '1.0'
import datetime, multiprocessing, os, re, shutil, sys, subprocess, time, logging
from pathlib import Path
#===========================================================================================================
try:
folderIn=sys.argv[1]
procee... | hkailee/FluSeq | fluSeq-H3.py | Python | mit | 16,192 | [
"BWA"
] | 3aa7b32bb5edb42c5f30857aa2539fc424f71df58510e20ff87a919a2c83344b |
#!/usr/bin/python
"""
Michael DeHaan <mdehaan@fedoraproject.org>, 2008
This software may be freely redistributed under the terms of the GNU
general public license.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 675 Mass ... | lkeijser/func | pusher.py | Python | gpl-2.0 | 4,055 | [
"VisIt"
] | c892280a7049da36d8996df978bb1e515fb0e59d3b0231642a305a9ce410aab4 |
# LLVM based numeric specializer in 1000 lines.
from __future__ import print_function
from functools import reduce
import sys
import ast
import types
import ctypes
import inspect
import pprint
import string
import numpy as np
from textwrap import dedent
from collections import deque, defaultdict
from llvmlite import... | sdiehl/numpile | numpile.py | Python | mit | 29,002 | [
"VisIt"
] | a39495d58bd6a7c0c7145e9f3beb6f0b89925a48e511ec36d18fd498a70247e1 |
import pytest
from numpy.testing import assert_equal, assert_array_equal
from brian2 import *
from brian2.tests.utils import assert_allclose
from brian2.devices.device import reinit_devices, set_device
import brian2cuda
@pytest.mark.standalone_compatible
def test_CudaSpikeQueue_push_outer_loop():
# This test o... | brian-team/brian2cuda | brian2cuda/tests/test_synaptic_propagations.py | Python | gpl-2.0 | 13,414 | [
"Brian",
"NEURON"
] | d50daf4c20ea4e45f70c09b31c9168d785e8ffd39591095b675cdf334358b959 |
"""The WaveBlocks Project
This file conatins the code for spawning new wavepackets depending
on some criterion.
@author: R. Bourquin
@copyright: Copyright (C) 2011 R. Bourquin
@license: Modified BSD License
"""
import numpy as np
from scipy import linalg as spla
from Spawner import Spawner
from InhomogeneousQuadrat... | WaveBlocks/WaveBlocks | src/WaveBlocks/NonAdiabaticSpawner.py | Python | bsd-3-clause | 7,551 | [
"Gaussian"
] | b2764066457b9908aebcb37f7f8d8f85fe62372186285b584202bd645744eddb |
"""
Defines the hosts for the distant local group project
"""
from __future__ import division, print_function
import os
import sys
import numpy as np
from matplotlib import pyplot as plt
try:
import six
except ImportErrir:
from astropy.extern import six
urlopen = six.moves.urllib.request.urlopen
from astrop... | saga-survey/saga-code | hosts.py | Python | gpl-2.0 | 44,581 | [
"Galaxy"
] | 35ae6ba5dadcf43bca99309167e01efe9a14692cc0d0a6518618c2ba46e62730 |
import json
from coalib.bearlib import deprecate_settings
from coalib.bearlib.abstractions.Linter import linter
from coalib.bears.requirements.NpmRequirement import NpmRequirement
from coala_utils.param_conversion import negate
def bool_or_str(value):
try:
return bool(value)
except:
return st... | sounak98/coala-bears | bears/js/JSHintBear.py | Python | agpl-3.0 | 20,188 | [
"VisIt"
] | 7591d5cdf027ebe2d88bd16376c366b6b361c1bf04e2bcc2718f76480ea6ede0 |
"""
The B{0install config} command-line interface.
"""
# Copyright (C) 2011, Thomas Leonard
# See the README file for details, or visit http://0install.net.
import os
from zeroinstall import SafeException, _
from zeroinstall.injector import model
from zeroinstall.cmd import UsageError
syntax = "[NAME [VALUE]]"
def... | pombredanne/zero-install | zeroinstall/cmd/config.py | Python | lgpl-2.1 | 2,390 | [
"VisIt"
] | a3a47cef281f5209755f80836e3c57f7c5a90502ba5f00cfe97bf652bc8f130c |
"""Data flow analysis based on miasm intermediate representation"""
from builtins import range
from collections import namedtuple, Counter
from pprint import pprint as pp
from future.utils import viewitems, viewvalues
from miasm.core.utils import encode_hex
from miasm.core.graph import DiGraph
from miasm.ir.ir import A... | serpilliere/miasm | miasm/analysis/data_flow.py | Python | gpl-2.0 | 79,542 | [
"VisIt"
] | 328275e71cd86b421e2713555af5e6202d661d938372848ae421ec86af6efb89 |
#!/usr/bin/python
import rospy
import node
class Relative(node.Robot):
'''
Class for Relative robot.
Inherits from Human class.
This and all other robot/human classes are similar as they all work
through inheritance
Relative is a relative human, this along with the Visitor class
are the relatives/family of t... | swanndri/ROS-Healthcare-Simulator | se306/src/package1/scripts/relative.py | Python | mit | 711 | [
"VisIt"
] | 6429af1a5204e5896db47ae887855b6a9a03ab5d4d9c740941b0dbb70ca5d5ae |
#
# simpleconifg.py - representation of a simple configuration file (sh-like)
#
# Matt Wilson <msw@redhat.com>
# Jeremy Katz <katzj@redhat.com>
# Will Woods <wwoods@redhat.com>
# Brian C. Lane <bcl@redhat.com>
#
# Copyright 1999-2012 Red Hat, Inc.
#
# This software may be freely redistributed under the terms of the GNU... | gautamMalu/XenInBox | pyanaconda/simpleconfig.py | Python | gpl-2.0 | 5,441 | [
"Brian"
] | 8ad09390a54b2d2145bf5cfc9da02312e9fb931b9fcaa87cda0c63ab17e7d908 |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the te... | kbrebanov/ansible | lib/ansible/modules/network/avi/avi_backup.py | Python | gpl-3.0 | 3,967 | [
"VisIt"
] | 9367403afdefad88e2943047ace64a21cd752c6723d5e855aceff891f68d9f1d |
from bi.bucketlistapi.tests.basetest import BaseTest
class TestBestCase(BaseTest):
'''
This is a test file that captures the expected/returned
values and status codes if the appropriate input
data is used
'''
def test_homepage_return(self):
'''
Test retreiving the homePage
... | andela-dmigwi/be-informed-b4-life-ends | bi/bucketlistapi/tests/test_bestcase.py | Python | mit | 5,483 | [
"VisIt"
] | 277df303579a06606937525b2faf54e51577b9968448b1bf8c113ac2132a1fe8 |
"""
.. _tut-forward:
Head model and forward computation
==================================
The aim of this tutorial is to be a getting started for forward
computation.
For more extensive details and presentation of the general
concepts for forward modeling. See :ref:`ch_forward`.
"""
import os.path as op
import mn... | adykstra/mne-python | tutorials/source-modeling/plot_forward.py | Python | bsd-3-clause | 10,603 | [
"Mayavi"
] | e7d7dd454668b4855464eacd96d598939104bbb8f22aae00e2884e513bf27d9c |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""Tests for the Google Analytics cookies."""
import unittest
from plaso.formatters import ganalytics as _ # pylint: disable=unused-import
from plaso.lib import eventdata
from plaso.lib import timelib
from plaso.parsers.cookie_plugins import ganalytics
from plaso.parsers.sql... | ostree/plaso | tests/parsers/cookie_plugins/ganalytics.py | Python | apache-2.0 | 5,100 | [
"VisIt"
] | 567250b8aeb38175ca78c773037b8d2763fd917ec4f96346336fba30bf5a2da6 |
# -*- coding: utf-8 -*-
# HORTON: Helpful Open-source Research TOol for N-fermion systems.
# Copyright (C) 2011-2016 The HORTON Development Team
#
# This file is part of HORTON.
#
# HORTON is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by th... | crisely09/horton | horton/io/gaussian.py | Python | gpl-3.0 | 17,423 | [
"Gaussian"
] | 32723e37b7b8e18516cbf08978b217133ab4f7c3fbd4d4dec21fe3ced624cec9 |
from functools import wraps
import os, os.path
import shutil
import subprocess
import numpy
from scipy import special
import apogee.tools.read as apread
import apogee.tools.path as appath
from apogee.tools import toAspcapGrid,_aspcapPixelLimits
from apogee.spec.plot import apStarWavegrid
def specFitInput(func):
"""... | jobovy/apogee | apogee/modelspec/__init__.py | Python | bsd-3-clause | 6,784 | [
"Gaussian"
] | 533e7d7bb34b59831e62b140efb01cd684516e1bdf84cc4673e71ce2d9fbfbd2 |
"""
Various functions which can be fitted to given data.
:requires: NumPy
:requires: SciPy
:author: Sami-Matias Niemi
:contact: smn2@mssl.ucl.ac.uk
:version: 0.1
"""
import scipy
import scipy.optimize
import numpy as np
def polynomial5(x, p0, p1, p2, p3, p4):
"""
5th order polynomial
"""
return p0 ... | sniemi/SamPy | fitting/fits.py | Python | bsd-2-clause | 8,645 | [
"Gaussian"
] | 4cf6b153a9937d983cd03ea824889417ec87cb85763b3a3dcaa28b170c4c108a |
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