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#!/usr/bin/env python
# CREATED:2013-03-08 15:25:18 by Brian McFee <brm2132@columbia.edu>
# unit tests for librosa.filters
#
# This test suite verifies that librosa core routines match (numerically) the output
# of various DPWE matlab implementations on a broad range of input parameters.
#
# All test data is generated... | r9y9/librosa | tests/test_filters.py | Python | isc | 13,357 | [
"Brian"
] | 9268f101eb27fa946edccb06b3a58cf26c255179c7086fe45347b1ee3e9905df |
#!/usr/bin/python
'''
Command module for mrMeshPy viewer
Commands and data are passed here from matab via the mrMeshPyServer.
Matlab sends a string in one transaction giving a command to the
visualisation module. This command either performs an explicit
function in the viewer (e.g. rotate the camera 90 degrees) or ... | andregouws/mrMeshPy | mp_Commands.py | Python | mit | 6,287 | [
"VTK"
] | a6ed7a93fef3fa9b396ac4ece7cf6a613740ece576b6cd42a33f6875b2ec22cb |
# -*- coding: utf-8 -*-
#
# test_status.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST 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... | sdiazpier/nest-simulator | testsuite/pytests/test_status.py | Python | gpl-2.0 | 7,391 | [
"NEURON"
] | bdf684337259fd40d25b8add0316bda917fd45b3e68e603c56a1ed33068ba747 |
#!/usr/bin/env python2
setpoints = []
values = []
POINTS = False
FIELD = False
with open("postProcessing/sets/modulwinkel/10000/plane_T.vtk", "rb") as f:
for row in f:
row.strip()
if row.startswith("POINTS"):
print "p"
POINTS = True
elif row.startswi... | zagl/of24x | etc/scripts/reorder.py | Python | gpl-3.0 | 1,369 | [
"VTK"
] | 44f38ef0f913472687e123a16186e965daa968920ab098316b60552ab44a556d |
'''
Functions for handling star formation rates
'''
import time
import numpy as np
# --- local ---
import util as UT
def LogSFR_sfms(logMstar, z_in, sfms_dict=None):
''' Wrapper for SFMS star formation rates
'''
if sfms_dict['name'] == 'constant_offset':
# the offset from the average SF... | changhoonhahn/centralMS | centralms/tests/sfrs.py | Python | mit | 12,560 | [
"Galaxy"
] | a3211810e90662fb6453f57a1fcdb7740dc7c790cd6071ce94076f10ff4ad11a |
import warnings as _warnings
import numpy as np
import pandas as _pd
from atmPy.general import timeseries as _timeseries
from atmPy.tools import array_tools as _arry_tools
from atmPy.tools import plt_tools as _plt_tools
import matplotlib.pylab as _plt
from atmPy.aerosols.instruments.AMS import AMS as _AMS
from atmPy.ae... | hagne/atm-py | atmPy/data_archives/arm/file_io/_netCDF.py | Python | mit | 18,771 | [
"NetCDF"
] | 121698c71146e47fc9700edda129ef71e2034eef4c6bc3e30d1da40af58b8e84 |
"""
This module implements specific error handlers for VASP runs. These handlers
try to detect common errors in vasp runs and attempt to fix them on the fly
by modifying the input files.
"""
import datetime
import logging
import operator
import os
import re
import shutil
import time
import warnings
from collections im... | materialsproject/custodian | custodian/vasp/handlers.py | Python | mit | 72,810 | [
"VASP",
"pymatgen"
] | 635ef4caf03452bb3e6affb37778a8dedcbbd98462f0d244e149968fa5f6927f |
from django.db import connection
from django.core.urlresolvers import reverse
from django.conf import settings
from askbot.tests.utils import AskbotTestCase
class CacheTests(AskbotTestCase):
def setUp(self):
user = self.create_user('other_user')
self.question = self.post_question(user=user)
... | divio/askbot-devel | askbot/tests/cache_tests.py | Python | gpl-3.0 | 1,074 | [
"VisIt"
] | 5e29958d934ff467be977358655da0d5c90af0e24b09d6ef42d9a9e2e2d4fbaf |
# Copyright 2008-2009 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.
"""Bio.SeqIO support for the "ace" file format.
You are expected to use this module via t... | NirBenTalLab/proorigami-cde-package | cde-root/usr/lib64/python2.4/site-packages/Bio/SeqIO/AceIO.py | Python | mit | 4,926 | [
"Biopython"
] | 06f8c8f1e96093f1e2216825a01bf76b34908be026dab3bcc041b9a35e27deed |
import numpy as np
import math
import sys
import os
sys.path.insert(0,os.environ['learningml']+'/GoF/')
import classifier_eval
from sklearn import tree
from sklearn.ensemble import AdaBoostClassifier
from sklearn.svm import SVC
from keras.wrappers.scikit_learn import KerasClassifier
for dim in range(2,11):
comp_file... | weissercn/learningml | learningml/GoF/optimisation_and_evaluation/not_automated/nn_gaussian_same_projection/nn_Gaussian_same_projection_evaluation_of_optimised_classifiers.py | Python | mit | 1,283 | [
"Gaussian"
] | 96fa546da1eb4820ad8d39fc03f59ac55f21bb2a949d4b664bb331b284604af3 |
# -*- coding: utf-8 -*-
# Copyright 2013 splinter authors. All rights reserved.
# Use of this source code is governed by a BSD-style
# license that can be found in the LICENSE file.
import os
import unittest
from splinter import Browser
from .fake_webapp import EXAMPLE_APP
from .base import WebDriverTests
def fire... | bmcculley/splinter | tests/test_webdriver_firefox.py | Python | bsd-3-clause | 3,498 | [
"VisIt"
] | 1cd46e5c7ef77b86c8af1898ef931132035320cb23f5d5822d8cea6dab7abaa0 |
#!/usr/bin/env python2.7
#
# Copyright 2016 The AMP HTML 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
#
# ... | ADITION/amphtml | validator/webui/build.py | Python | apache-2.0 | 5,761 | [
"GULP"
] | e9f17c2cc1e3b3d172aa5955825d8404188eb7f73629b7f3ff8a285d8a37d7e0 |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RDelayedmatrixstats(RPackage):
"""Functions that Apply to Rows and Columns of 'DelayedMatr... | LLNL/spack | var/spack/repos/builtin/packages/r-delayedmatrixstats/package.py | Python | lgpl-2.1 | 2,467 | [
"Bioconductor"
] | 55b1f5677bca101a5fa315754e36c440a720b45ebb3109af8990a730a7ebd362 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Licensed to Cloudera, Inc. under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. Cloudera, Inc. licenses this file
# to you under the Apache License, Version 2.0 (... | vmax-feihu/hue | apps/useradmin/src/useradmin/test_ldap.py | Python | apache-2.0 | 37,269 | [
"MOE"
] | 8c74c8908bb07b298113d7425846640fef04e3888ecd61b43cb2faac2c4e70af |
### clustering.py
#Copyright 2005-2008 J. David Gladstone Institutes, San Francisco California
#Author Nathan Salomonis - nsalomonis@gmail.com
#Permission is hereby granted, free of charge, to any person obtaining a copy
#of this software and associated documentation files (the "Software"), to deal
#in the Software ... | wuxue/altanalyze | clustering.py | Python | apache-2.0 | 233,205 | [
"Bioconductor"
] | 7122ea948651a1a7d6a79b289103cf703bf340c369e03c7e4e84a48a002557e6 |
from setuptools import setup
setup(
name="parapred",
packages=["parapred"],
entry_points={
"console_scripts": ['parapred = parapred.parapred:main']
},
install_requires=[
"Keras==2.0.6",
"pandas>=0.19.2,<0.20",
"tensorflow==1.2.1",
"numpy>=1.13",
"matp... | eliberis/parapred | setup.py | Python | mit | 796 | [
"Biopython"
] | 4eeac8299a01c071769ce8c83103e133c7ec7dc4cbe7f46a202c95bb26a047e5 |
#!/usr/bin/env python
import os.path
import subprocess
import os
import sys
def is_newer(filename1, filename2):
mtime1 = os.path.getmtime(filename1)
mtime2 = os.path.getmtime(filename2)
if mtime1 <= mtime2:
return False
else:
return True
def makeblastdb(fasta_filename, dbname, dbtype=... | pvanheus/python2015 | bin/makeblastdb.py | Python | gpl-3.0 | 1,263 | [
"BLAST"
] | 9382c1fb733282345d906fca6d8e05d84e023d3f006490d973ec0040d6367fec |
#!/usr/bin/env python
# Copyright 2015 The Kubernetes Authors.
#
# 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 appli... | aclisp/kubernetes | hack/boilerplate/boilerplate.py | Python | apache-2.0 | 5,223 | [
"VisIt"
] | 94ddee7bdadf4f3ad5aae8f0361e3ce7f9148d2712e1fc25b1d5e6c2adcd7063 |
#-----------------------------------------------------------------
# pycparser: func_defs.py
#
# Using pycparser for printing out all the functions defined in a
# C file.
#
# This is a simple example of traversing the AST generated by
# pycparser.
#
# Copyright (C) 2008-2011, Eli Bendersky
# License: BSD
#-------------... | sideeffects/pycparser | examples/func_defs.py | Python | bsd-3-clause | 1,231 | [
"VisIt"
] | 4e0a66746350d78963333d39c55f266e1dff075e6c6f2a48ca2ca34184ff2e77 |
"""
Wrapper functions for nglviewer and jupyter helper functions
Reference links
- https://birdlet.github.io/2019/10/02/py3dmol_example/
- http://nglviewer.org/nglview/latest/api.html#nglview.RdkitStructure
- http://nglviewer.org/nglview/latest/api.html#nglview.show_rdkit
Notes on nglviewer usage
>>> import nglvie... | ppqm/ppqm | ppqm/jupyter.py | Python | mit | 2,510 | [
"RDKit"
] | e8a1bf2c75de885b6cea3d46ca44a4f32222672b7cb9e5b16ba69c94c62b3402 |
# 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)
import ast
import hashlib
import spack.repo
import spack.package
import spack.directives
import spack.error
import spack.... | iulian787/spack | lib/spack/spack/util/package_hash.py | Python | lgpl-2.1 | 5,042 | [
"VisIt"
] | d28f196c18913691d70712d2fd71098ae45ca9047112103a8831a8d0aa9eade3 |
from pywps import Process, LiteralInput, ComplexInput, ComplexOutput
from pywps import Format
from plotter import simple_plot
import logging
LOGGER = logging.getLogger('PYWPS')
AIR_DS = 'https://www.esrl.noaa.gov/psd/thredds/fileServer/Datasets/ncep.reanalysis.derived/surface/air.mon.ltm.nc'
class SimplePlot(Proc... | bird-house/birdhouse-workshop | tutorials/10_pywps_process/processes/wps_simple_plot.py | Python | apache-2.0 | 1,714 | [
"NetCDF"
] | bf0db36f10cb1da4a5ed6929667f99870e9572a4a9f1743d536187297d5aac18 |
from __future__ import print_function
__author__ = """Alex "O." Holcombe, Wei-Ying Chen""" ## double-quotes will be silently removed, single quotes will be left, eg, O'Connor
from psychopy import *
import psychopy.info
from psychopy import sound, monitors, logging
import numpy as np
import itertools #to calculate all s... | alexholcombe/MOTcircular | MOTcircular.py | Python | mit | 54,119 | [
"Gaussian"
] | 86f30c7f91f64f6a1c2d2bbd3296f781e0d644bb474a0b4a3b499713d0a1ad5b |
from __future__ import print_function, division
from sympy import (Poly, igcd, divisors, sign, symbols, S, Integer, Wild, Symbol, factorint,
Add, Mul, solve, ceiling, floor, sqrt, sympify, Subs, ilcm, Matrix, factor_list, perfect_power,
isprime, nextprime, integer_nthroot)
from sympy.core.function import _mex... | sahilshekhawat/sympy | sympy/solvers/diophantine.py | Python | bsd-3-clause | 79,097 | [
"Gaussian"
] | c656be55f995d68bb7f88a3137dfe47763ccb2cd70cb7fecb5e3fa170fd8368c |
# -*- coding: utf-8 -*-
"""
This file contains methods for decay-like fitting, these methods
are imported by class FitLogic.
Qudi 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, o... | tobiasgehring/qudi | logic/fitmethods/decaylikemethods.py | Python | gpl-3.0 | 17,012 | [
"Gaussian"
] | 0ca1d4a992b02de787b8906391929c1cd2aba4c1298f9a47bc8b2e2d05cd6d4e |
#!/usr/bin/python
import sys
import numpy as np
import warnings
import collections as co
import itertools
import Bio.PDB as bp
import forgi.threedee.model.coarse_grain as ttmc
import forgi.threedee.utilities.graph_pdb as cgg
import forgi.utilities.debug as cud
import forgi.threedee.visual.pymol as cvp
from optpars... | pkerpedjiev/ernwin | fess/scripts/stem_vres_atom_positions.py | Python | agpl-3.0 | 5,999 | [
"PyMOL"
] | 0eee44f7fea29642280138ad214158a234107cf56802eef60fa834945d1f785e |
# -*- coding: utf-8 -*-
from collections import defaultdict
import dateutil.parser
import re
from typing import Any, DefaultDict, Dict, FrozenSet, List, Optional, Set, Tuple, Union
from django.http import HttpRequest, HttpResponse, JsonResponse
from django.shortcuts import get_object_or_404
from django.db import con... | tomka/CATMAID | django/applications/catmaid/control/annotation.py | Python | gpl-3.0 | 72,417 | [
"NEURON"
] | 7da5bc0f7303ff5748a0cec537445a5cf7e5cf730ee95f226a8469f1bc754a31 |
# -*- coding: utf-8 -*-
"""
equip.visitors.classes
~~~~~~~~~~~~~~~~~~~~~~
Callback the visit method for each encountered class in the program.
:copyright: (c) 2014 by Romain Gaucher (@rgaucher)
:license: Apache 2, see LICENSE for more details.
"""
class ClassVisitor(object):
"""
A class visitor that ... | neuroo/equip | equip/visitors/classes.py | Python | apache-2.0 | 762 | [
"VisIt"
] | c2b98a66014e0dae23732b749996a1df1f1172a4b22b0f2ff3011bd8c3b6ef4a |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from pymatgen.core.spectrum import Spectrum
import numpy as np
"""
This module defines classes to represent all xas
"""
__author__ = "Chen Zheng"
__copyright__ = "Copyright 2012, The Materials Project"
__vers... | matk86/pymatgen | pymatgen/analysis/xas/spectrum.py | Python | mit | 1,581 | [
"pymatgen"
] | f91ecbc1a63f25804fd266db53bc47c0adaadcfef64e4604d30b5cb9775f33c3 |
#!/usr/bin/env python
# coding: utf-8
#
# Copyright 2007 Google 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 ... | sloanyang/depends | third_party/upload.py | Python | gpl-2.0 | 99,227 | [
"VisIt"
] | b627d7015e86b412f09b8001e083ab09318ed99a43a987db3e8da0f856a4049f |
#!/usr/bin/env python3
"""
Convert flat DICOM file set into an NDAR-compliant fileset
Usage
----
dcm2ndar.py -i <DICOM Directory> -o <NDAR Directory>
Example
----
% dcm2ndar.py -i sub-001 -o sub-001.ndar
Authors
----
Mike Tyszka, Caltech Brain Imaging Center
Dates
----
2016-08-09 JMT Adapt from dcm2bids.py
MIT Lic... | celstark/bidskit | dcm2ndar.py | Python | mit | 22,745 | [
"VisIt"
] | 1a1eae6a0979fe26230437a69c650efd3c5096cdc106486409b699a5410e10e1 |
import collections
import re
CSS = {
"White": "#FFFFFF",
"Old Lace": "#FDF5E6",
"Sea Green": "#2E8B57",
"Slate Blue": "#6A5ACD",
"Dark Khaki": "#BDB76B",
"Light Steel Blue": "#B0C4DE",
"Sky Blue": "#87CEEB",
"Medium Orchid": "#BA55D3",
"Aqua": "#00FFFF",
"Bisque": "#FFE4C4",
... | inexactually/irisbot | colornames.py | Python | mit | 51,179 | [
"Amber",
"BLAST"
] | a0ffc94330268796becc15725dad36976d9cff7c2b920158e734c94755c1251e |
# Copyright (c) 2016 PaddlePaddle 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 applic... | pengli09/Paddle | python/paddle/v2/parameters.py | Python | apache-2.0 | 14,433 | [
"VisIt"
] | 181c80f4d95c64e27ed5203aee0d52547d39e88aa7134a4b3dc9b7ff7d91c454 |
"""
Custom PDB class implementation.
The code below contains heavily modified parts of Jacob Durrant's
NNScore 2.0.1. The following notice is copied from the original NNScore
file:
# NNScore 2.01 is released under the GNU General Public License (see
# http://www.gnu.org/licenses/gpl.html).
# If you have any questions,... | rbharath/vs-utils | vs_utils/utils/nnscore_pdb.py | Python | gpl-3.0 | 64,048 | [
"CRYSTAL",
"VMD"
] | 61ac2d7d651c2a5168bc4a89e7df560a3e391d88cbf67fc4b21b4ffb7aec7f64 |
# -*- coding: utf-8 -*-
"""
Support for calculating D spacing for powder diffraction lines as
as function of pressure and temperature, given symmetry, zero-pressure lattice
constants and equation of state parameters.
Author:
Mark Rivers
Created:
Sept. 10, 2002 from older IDL version
Modifications:
Sept. 26,... | Dioptas/Dioptas | dioptas/model/util/jcpds.py | Python | gpl-3.0 | 36,954 | [
"CRYSTAL"
] | 7ee0e127091cdcc654bda773dc1eea63ea41146560dd02575238894699f21f47 |
#!/usr/bin/env python
#PBS -N Timing
#PBS -m ae
#PBS -q long
#PBS -l nodes=1:opteron:ppn=4
from asap3 import *
from asap3.md.verlet import VelocityVerlet
from asap3.md.velocitydistribution import MaxwellBoltzmannDistribution
from ase.lattice.cubic import FaceCenteredCubic
import numpy as np
import time
import pickle
... | auag92/n2dm | Asap-3.8.4/Test/Timing/OpenMPTiming/TimingMatrix.py | Python | mit | 2,515 | [
"ASE"
] | f8bc8cb6caf4efd44a83918894c88e19e71f19082a60976e8917a7543a154365 |
#!/usr/bin/env python
"""
This script should be used for creating the scaffolding for a test.
"""
from __future__ import print_function
import os
import sys
from ooni.utils import log
print("!!!! This test writing strategy is now deprecated !!!")
print("visit: https://ooni.readthedocs.org/en/latest/writing_tests.html... | hackerberry/ooni-probe | ooni/scaffolding.py | Python | bsd-2-clause | 2,370 | [
"VisIt"
] | a4575b20327e4800230494e85b29a4f19df0b9c3748a902c5e5618e4cfbca6b8 |
#!/usr/bin/python
# -*- coding=UTF-8 -*-
###########################################################################
# Hex IP Toolkit: Converts IP addresses to hexadecimal and vice versa. #
# also links the IP addresses to given files #
# written to assist in kickstart /... | hbayindir/Hex-IP-Toolkit | Hex_IP_Toolkit/src/hexiptools.py | Python | gpl-3.0 | 8,480 | [
"VisIt"
] | 9e1fcc871601f37b9b0d88c10f02527c96440548ead03df7937d8241d3a45808 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
import unittest
from external.wip import work_in_progress
from .molecule import Atom, Bond, Molecule, ActionError
from .group import Group
from .element import getElement, elementList
################################################################################
class Test... | pierrelb/RMG-Py | rmgpy/molecule/moleculeTest.py | Python | mit | 61,794 | [
"RDKit"
] | 622257ec273171726ed11d5aef0d83d863087b121ff20ba8a9dbcb2fb082a0e3 |
#!/usr/bin/python3
#
# Copyright (c) 2012 Mikkel Schubert <MikkelSch@gmail.com>
#
# Permission is herby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
#... | MikkelSchubert/paleomix | tests/node_test.py | Python | mit | 22,024 | [
"BWA",
"Bowtie"
] | ac6dc20f5c16f95c99ec63223d2c401dbc99549ee55897de621dd38390a19690 |
"""Testing for Gaussian process regression """
# Author: Jan Hendrik Metzen <jhm@informatik.uni-bremen.de>
# Modified by: Pete Green <p.l.green@liverpool.ac.uk>
# License: BSD 3 clause
import sys
import numpy as np
from scipy.optimize import approx_fprime
import pytest
from sklearn.gaussian_process import Gaussian... | bnaul/scikit-learn | sklearn/gaussian_process/tests/test_gpr.py | Python | bsd-3-clause | 21,004 | [
"Gaussian"
] | d9ec4d96d905b6b1e580f10e83c780e41e1db6d7fa4f31e8a3dbb6298bf9f606 |
#########
# firstVideo.py
# This program is part of the online PS-Drone-API-tutorial on www.playsheep.de/drone.
# It shows the general usage of the video-function of a Parrot AR.Drone 2.0 using the PS-Drone-API.
# The drone will stay on the ground.
# Dependencies: a POSIX OS, openCV2, PS-Drone-API 2.0 beta or higher.
#... | reixd/ps-drone | tutorials/firstVideo.py | Python | artistic-2.0 | 2,806 | [
"VisIt"
] | e8373d262970bb734fc739fbfb18a443b2135a2735a13043361f38aa942c1fea |
from mayavi import mlab
import numpy as np
# visualize
# =========
def isosurface(volume, lattice=None, **kwargs):
if lattice == None:
return mlab.contour3d(volume, **kwargs)
xx, yy, zz = lattice
return mlab.contour3d(xx, yy, zz, volume, **kwargs)
def mesh(vertices, faces, **kwargs):
xx, yy, zz = vertices
ret... | towle-lab/electrode-registration-app | core/visualize.py | Python | gpl-2.0 | 646 | [
"Mayavi"
] | 254e28202b80b18c24ab1622a208b6a827c0b9f9527579aadb0b2aef23acc7bb |
""" Main class for doing consistency checks, between files in:
- File Catalog
- TransformationSystem
Should be extended to include the Storage (in DIRAC)
"""
import os
import time
import sys
import types
import re
import DIRAC
from DIRAC import S_OK, S_ER... | vmendez/DIRAC | DataManagementSystem/Client/ConsistencyInspector.py | Python | gpl-3.0 | 33,838 | [
"DIRAC"
] | 1842d3e6e6e9a3a66b57e198eba5eb0d34733133cec598d988dd90477bc529ea |
#!/usr/bin/env python
"""buildpkg.py -- Build OS X packages for Apple's Installer.app.
This is an experimental command-line tool for building packages to be
installed with the Mac OS X Installer.app application.
It is much inspired by Apple's GUI tool called PackageMaker.app, that
seems to be part of the OS X develo... | xbmc/atv2 | xbmc/lib/libPython/Python/Mac/scripts/buildpkg.py | Python | gpl-2.0 | 15,904 | [
"Brian"
] | cb0bab6fd63e3071c4c29b020c39eaf182666dc1fd42068cfaac5f99e4c6974e |
# -*- coding: utf-8 -*-
# Copyright 2007-2011 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy 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... | sillvan/hyperspy | hyperspy/_signals/eels_spectrum_simulation.py | Python | gpl-3.0 | 5,221 | [
"Gaussian"
] | d33763e3c5605c1ee01c9d6f8ce7e27436b41d390d3759f2b92c99ed2e82fb79 |
# Copyright 2002 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.
| dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/dbdefs/__init__.py | Python | apache-2.0 | 225 | [
"Biopython"
] | f301855cc671e02677a10a34fb15c04b2926da5460bb37b4aed3fccbcad6f85f |
"""Ordinary Least Squares regression classes."""
__author__ = "Luc Anselin luc.anselin@asu.edu, David C. Folch david.folch@asu.edu"
import numpy as np
import copy as COPY
import numpy.linalg as la
import user_output as USER
import summary_output as SUMMARY
import robust as ROBUST
from utils import spdot, sphstack, Reg... | AlanZatarain/pysal | pysal/spreg/ols.py | Python | bsd-3-clause | 19,340 | [
"COLUMBUS"
] | e25921cb5ad34c3bd358e7116f55e65995b5be9b7d668e6fea0b95352bf8dea0 |
#!/usr/bin/python
# Copyright(c) 2009, Gentoo Foundation
# Copyright 2010 Brian Dolbec <brian.dolbec@gmail.com>
#
# License: GPL2/BSD
# $Header$
from __future__ import print_function
from tempfile import NamedTemporaryFile, mkdtemp
import unittest
import re
from gentoolkit.test.eclean.distsupport import *
impor... | dol-sen/gentoolkit | pym/gentoolkit/test/eclean/test_search.py | Python | gpl-2.0 | 24,909 | [
"Brian"
] | d0c99353526d4d12c994593f3becd48275823024d51c8682c8e14ef2316bc441 |
# Portions Copyright (c) Meta Platforms, Inc. and affiliates.
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2.
# ancestor.py - generic DAG ancestor algorithm for mercurial
#
# Copyright 2006 Matt Mackall <mpm@selenic.com>
#
# This software may be used ... | facebookexperimental/eden | eden/scm/edenscm/mercurial/ancestor.py | Python | gpl-2.0 | 13,106 | [
"VisIt"
] | 700ed7d43a5114f124b3d8413075a99b2d67705cf44d438e5d6c1e2a66984856 |
#!/usr/bin/env python
'''
Fly ArduPlane in SITL
AP_FLAKE8_CLEAN
'''
from __future__ import print_function
import math
import os
import signal
import sys
import time
from pymavlink import quaternion
from pymavlink import mavextra
from pymavlink import mavutil
from common import AutoTest
from common import AutoTestT... | samuelctabor/ardupilot | Tools/autotest/arduplane.py | Python | gpl-3.0 | 141,356 | [
"Firefly"
] | 9fb56372afb56b475e8830d421c71bdfc910ad59f947eacb91508e0f4d2bd71a |
import numpy as np
from numpy.random import normal as randn
import tspy as ts
import matplotlib.pyplot as plt
plt.rc('text', usetex=True)
def gen_ar(T, coeffs):
c = np.flipud(coeffs)
p = c.size
x = np.zeros((T+p))
for t in range(p, T):
x[t] = np.dot(x[t-p:t], c) + randn()
return x[p:]
de... | apsql/time_series | tests/t_spectrum.py | Python | mit | 3,836 | [
"Gaussian"
] | ff0ab4d3169775bbc37de2900dad39a25e1d61246078e65027358db22390ca80 |
#!/usr/bin/python3
from __future__ import print_function
from vizdoom import *
import sys
import threading
import math
from random import choice
from time import sleep
from matplotlib import pyplot as plt
sys.path.append('../../deep_feedback_learning')
import numpy as np
import cv2
import deep_feedback_learning
# ... | nlholdem/icodoom | ICO1/deep_feedback_learning_old/vizdoom/ico.py | Python | gpl-3.0 | 8,982 | [
"NEURON"
] | 81fc1a09cbaf8e4e6e966dcbf2a6397edb99a71ad7cbb5865e171420e4b55fbc |
##
# Copyright 2015-2017 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (F... | ULHPC/easybuild-easyblocks | easybuild/easyblocks/m/molpro.py | Python | gpl-2.0 | 11,923 | [
"Molpro"
] | 333a9c80a9a98bb1c41041fb17b8752ea697cc9fd346307041c29fafe4b0262f |
#! /usr/bin/env python
"""
April 2013
eeesh GSEA does NOT respect the mode flag!
Now realise that the creation of the input rank file for gsea needs to take the lowest p value for duplicate
feature names. To make Ish's life easier, remove duplicate gene ids from any gene set to stop GSEA from
barfing.
October 14 201... | UCSC-MedBook/MedBook_ | tools/gsea/rgGSEA.py | Python | bsd-3-clause | 23,186 | [
"Galaxy"
] | 530831affc4399d516e029e8902f6fb8209ef776ebef2d98532149a662347b44 |
import numpy as np
from skimage.transform import AffineTransform, SimilarityTransform, PolynomialTransform, warp
from skimage.filters import gaussian
from skimage import exposure, img_as_float
from scipy.misc import imresize
import Augmentor
center_shift = 256 / 2
tf_center = SimilarityTransform(translation=-center_sh... | Mctigger/KagglePlanetPytorch | transforms.py | Python | mit | 6,150 | [
"Gaussian"
] | c6cb87f4d470d0c861b1d8caa971b27c2a8096ac52a4c1e89b98571acdb511e9 |
## Copyright 2004-2009 Luc Saffre
## This file is part of the Lino project.
## Lino is free software; you can redistribute it and/or modify it
## under the terms of the GNU General Public License as published by
## the Free Software Foundation; either version 2 of the License, or
## (at your option) any later ... | lsaffre/timtools | timtools/scripts/runtests.py | Python | bsd-2-clause | 6,831 | [
"VisIt"
] | f706b614c8c0d801c812fb4e4431fadfeaccfc0cc78a3d7b60c0ef6f381f1521 |
"""
Module for rendering axes.
"""
from __future__ import absolute_import
from __future__ import unicode_literals
import vtk
class Axes(object):
"""
Axes object.
"""
def __init__(self, renWinInteract):
# create axes
self._axes = vtk.vtkAxesActor()
self._axes.SetShaftType... | chrisdjscott/Atoman | atoman/rendering/axes.py | Python | mit | 2,023 | [
"VTK"
] | d08029ac921f160818e17d874a1100f9637b201f895f11339b9100715361c8b9 |
# -*- coding: utf-8 -*-
# Copyright (C) 2012, Almar Klein, Ant1, Marius van Voorden
#
# This code is subject to the (new) BSD license:
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of s... | schaul/py-vgdl | external_libs/images2gif.py | Python | bsd-3-clause | 36,933 | [
"NEURON"
] | e8cc8e9cd1661bdb4265e020795862e1e9bbcf6af115414277a13843fd3de5d6 |
"""Sensitive variant calling using VarDict.
Defaults to using the faster, equally sensitive Java port:
https://github.com/AstraZeneca-NGS/VarDictJava
if 'vardict' or 'vardict-java' is specified in the configuration. To use the
VarDict perl version:
https://github.com/AstraZeneca-NGS/VarDict
specify 'vardict-perl'.... | chapmanb/bcbio-nextgen | bcbio/variation/vardict.py | Python | mit | 19,796 | [
"BWA"
] | c83cd583354721961cb6a3aafda85526802af7b2e0444f45822295a0a7369abf |
""" A computing element class using singularity containers.
This computing element will start the job in the container set by
the "ContainerRoot" config option.
DIRAC will the re-installed within the container, extra flags can
be given to the dirac-install command with the "ContainerExtraOpts"
opt... | andresailer/DIRAC | Resources/Computing/SingularityComputingElement.py | Python | gpl-3.0 | 12,438 | [
"DIRAC"
] | 225644d0968cbb233bc033593f2f161c0064d604649019653399f0b44c55c90a |
# kchans.py ---
#
# Filename: kchans.py
# Description:
# Author: subhasis ray
# Maintainer:
# Created: Fri Apr 17 23:58:49 2009 (+0530)
# Version:
# Last-Updated: Sat Dec 8 15:52:42 2012 (+0530)
# By: subha
# Update #: 1057
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
#
#
# ... | dilawar/moose-full | moose-examples/traub_2005/py/kchans.py | Python | gpl-2.0 | 6,886 | [
"MOOSE"
] | d392765892fc810df712a98634560c655cf90f4dbb75428ec2ee29e178d54d65 |
#
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | espressomd/espresso | testsuite/python/shapes.py | Python | gpl-3.0 | 2,593 | [
"ESPResSo"
] | 0c73209a065e4e14122aac55331e1e9a8b56f5c35b7e93e9cd268330247a17c9 |
# Copyright (c) 2014 OpenStack Foundation.
#
# 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 ... | rakeshmi/cinder | cinder/hacking/checks.py | Python | apache-2.0 | 11,942 | [
"VisIt"
] | b914fe94bd9bba6479eb46a8ded9f2a6a10711bf37486c60cdd0d90e24630a47 |
# Copyright (C) 2018 Jaguar Land Rover
#
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
#
# Authors:
# * Guillaume Tucker <guillaume.tucker@collabora.com>
import impo... | GENIVI/vehicle_signal_manager | ipc/__init__.py | Python | mpl-2.0 | 3,647 | [
"Jaguar"
] | f236f0b9df9dbee79f1877d6a3ce530109e46d5f54063b81c67ac38182dd9993 |
"""MDTraj: Read, write and analyze MD trajectories with only a few lines of Python code.
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
... | kyleabeauchamp/mdtraj | setup.py | Python | lgpl-2.1 | 10,342 | [
"Amber",
"CHARMM",
"Gromacs",
"MDTraj",
"NAMD",
"NetCDF",
"TINKER"
] | 1d88097c635c07c2a1b631dbcbdb5e08852d45c4e22efcf245e3474c4576e4d6 |
# Copyright 2016-2020 The GPflow Contributors. 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 appli... | GPflow/GPflow | gpflow/models/gpmc.py | Python | apache-2.0 | 4,024 | [
"Gaussian"
] | f52c5a77da38231963366c6c66be5fc2ba2f88d6542c14857778080bef32748c |
import os
import math
import numpy as np
import cPickle as pickle
from ase import Atoms
from ase.data import chemical_symbols
from ase.cluster.base import ClusterBase
from ase.cluster.clusteratom import ClusterAtom
class Cluster(Atoms, ClusterBase):
_datasyn = {'numbers': ('number', int, () ),
... | slabanja/ase | ase/cluster/cluster.py | Python | gpl-2.0 | 6,238 | [
"ASE"
] | 736dbd0ed702b4b3219c9519e896a37b90c7a402045acacb2b43dee7a8f5b206 |
# coding: utf-8
from __future__ import unicode_literals
import binascii
import collections
import email
import getpass
import io
import optparse
import os
import re
import shlex
import shutil
import socket
import struct
import subprocess
import sys
import itertools
import xml.etree.ElementTree
try:
import urllib... | coreynicholson/youtube-dl | youtube_dl/compat.py | Python | unlicense | 90,357 | [
"Bowtie"
] | 27ac0b37ab6d5d740c92cf94ac83050c112c24457cd7ac7b1c98311055b71454 |
# -*- Mode: Python -*-
# vi:si:et:sw=4:sts=4:ts=4
# Flumotion - a streaming media server
# Copyright (C) 2004,2005,2006,2007,2008,2009 Fluendo, S.L.
# Copyright (C) 2010,2011 Flumotion Services, S.A.
# All rights reserved.
#
# This file may be distributed and/or modified under the terms of
# the GNU Lesser General Pub... | flumotion-mirror/flumotion | flumotion/component/plugs/identity.py | Python | lgpl-2.1 | 1,893 | [
"MOE"
] | a1b7434161a1e3b02723f29e5828c2a9cf10776ef0e059c776dbfd3e8d0aa7a1 |
#!/usr/bin/env python
# Copyright 20142018 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/LICENSE2.0
#
# Unles... | gkc1000/pyscf | pyscf/data/nucprop.py | Python | apache-2.0 | 8,817 | [
"PySCF"
] | bdb205350c3b20f5ceee5594f2ce5928f4a30c91ace4f56d14d1af8509b7aea8 |
from miro import app
from miro import prefs
from miro.devices import DeviceInfo, MultipleDeviceInfo
from miro.gtcache import gettext as _
defaults = {
'audio_conversion': 'mp3',
'container_types': 'mp3 wav asf isom ogg mpeg avi'.split(),
'audio_types': 'mp* wmav* aac pcm* vorbis'.split(),
'video_types'... | debugger06/MiroX | tv/resources/devices/android.py | Python | gpl-2.0 | 9,764 | [
"Galaxy"
] | 7ed51770c23bd6f55c0ee9af6b3cb12c4ccb72dd04f25281a0db61c52a74833a |
""" FileManagerBase is a base class for all the specific File Managers
"""
__RCSID__ = "$Id$"
# pylint: disable=protected-access
import os
import stat
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Core.Utilities.List import intListToString
from DIRAC.Core.Utilities.Pfn import pfnunparse
class FileManagerBas... | fstagni/DIRAC | DataManagementSystem/DB/FileCatalogComponents/FileManagerBase.py | Python | gpl-3.0 | 49,156 | [
"DIRAC"
] | 7d57997e006659e8f219729d2e8aca6945eeb9864b74c62e39acb99799df401e |
import os
import sys
from threading import Thread
from pyelectro import analysis
import numpy
import math
import pprint
pp = pprint.PrettyPrinter(indent=4)
def alpha_normalised_cost_function(value,target,base=10):
"""Fitness of a value-target pair from 0 to 1
.. WARNING:
I've found that this cost fu... | pgleeson/neurotune | neurotune/evaluators.py | Python | bsd-3-clause | 29,790 | [
"NEURON"
] | 1b56d2ac7a654a41d9917013244a726ab75f1d100bae428f8e420dcbfd068c7c |
import math
import numpy as np
from scipy.cluster.vq import kmeans2
from groupmembers import print_group_members
from plots import plots
def main():
print_group_members()
""" The below line of code is needed to calculate the optimal hyperparameters for a given range. Set the range
values inside the func... | kautuk-desai/CSE-574-Intro-to-Machine-Learning | project2/main.py | Python | mit | 13,999 | [
"Gaussian"
] | 080abe9ae828a5bcf1e47364055d8a31fc2e4fcb291a66cf0da017e8c497ff31 |
import vtk
import numpy as np
import os
import sys
from pyCellAnalyst import CellMech
import pickle
def writePoly(name, tri):
writer = vtk.vtkXMLPolyDataWriter()
writer.SetFileName(name)
writer.SetInputData(tri.GetOutput())
writer.Write()
def writeSTL(name, tri):
writer = vtk.vtkSTLWriter()
... | siboles/pyCellAnalyst | src/testing/Homogeneous/homogeneous.py | Python | mit | 4,450 | [
"VTK"
] | 363c0009e1c72712fc374b31815dca80afb120d20723b20b208eed938bf2f503 |
#!/usr/bin/env python
from pyDFTutils.vasp.vasp_dos import plot_all_pdos
import argparse
def plot_pdos():
parser=argparse.ArgumentParser(description='Plot the partial dos')
parser.add_argument('-f','--filename',type=str,help='DOSCAR filename',default='DOSCAR')
parser.add_argument('-n','--ispin',type=int,he... | mailhexu/pyDFTutils | scripts/plotpdos.py | Python | lgpl-3.0 | 1,169 | [
"VASP"
] | 76ebc2823e3245aa8acb9160024e6c970e7866acd9966c9d6fe079899738c1b9 |
"""Import basic exposure of libzmq C API as a backend"""
#-----------------------------------------------------------------------------
# Copyright (C) 2013 Brian Granger, Min Ragan-Kelley
#
# This file is part of pyzmq
#
# Distributed under the terms of the New BSD License. The full license is in
# the file COPY... | skycucumber/Messaging-Gateway | webapp/venv/lib/python2.7/site-packages/zmq/backend/__init__.py | Python | gpl-2.0 | 827 | [
"Brian"
] | 27b3c92a7edc79b068863466e1a8a6054fad6ac744ec1fb9502f0c095f9c2b5f |
#!/usr/bin/python
#
# Regression test driver for cmd-line tools
#
# Usage: test_cmdline_tool.py [<options>] <tool> <arguments>
#
# If the -g option is given or the TEST_GENERATE environment variable is set to 1,
# *-expected.<suffix> files will be generated instead of running the tests.
#
# Any generated output is wri... | clothbot/openscad | tests/test_cmdline_tool.py | Python | gpl-2.0 | 13,380 | [
"Gaussian"
] | b6d6cea77c0282518d8220c27b7f27fab4c65d9b0aed1a3f7ac54f3530f054a9 |
#youtube stuff imported
import httplib2
import re
from apiclient.discovery import build
from apiclient.errors import HttpError
from oauth2client.client import flow_from_clientsecrets
from oauth2client.file import Storage
from oauth2client.tools import argparser, run_flow
import time
import googleapiclient
import sy... | popcorn9499/chatBot | sites/youtube.py | Python | gpl-3.0 | 15,563 | [
"VisIt"
] | 81ffe8bde1cc0e8c592eb1f8d03f811b389dd7c62a4c57323d540ef25d4fced3 |
#!/usr/bin/python -*- coding: utf-8 -*-
#
# Merlin - Almost Native Python Machine Learning Library: Naive Bayes Classifer
#
# Copyright (C) 2014-2015 alvations
# URL:
# For license information, see LICENSE.md
import numpy as np
import linear_classifier as lc
from gaussian import *
class NaiveBayes(lc.LinearClassifie... | meetvaruni/GitFiles | pywsd-master/pywsd-master/merlin/naive_bayes.py | Python | gpl-2.0 | 3,103 | [
"Gaussian"
] | 49c6063c8f1ad45945b8d422ae23da8187df17c01506b22dc2ef8a2d738b79f2 |
# -*- coding: utf-8 -*-
##########################################################################
#
# 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 Adam S. C... | adamcandy/qgis-plugins-meshing-initial | release/mesh_netcdf/__init__.py | Python | lgpl-2.1 | 2,448 | [
"NetCDF"
] | 2e37e6d652864f5d7550171866071b0a43c2ca1e94e804fa7ee8479d59aac8ab |
#
# 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 us... | staslev/incubator-beam | sdks/python/apache_beam/runners/dataflow/dataflow_runner.py | Python | apache-2.0 | 44,142 | [
"VisIt"
] | f04a866bd99ca9c1f687be6bddc4c18f5b1677d7fb4343346989303353ccb6c2 |
import csv
import socket
from constants import *
from string import capwords
from subprocess import call
from os import unlink as delete
from traceback import print_exc as stacktrace
interesting = {'rubber cap', 'heat core', 'terra mantle', 'steel boots', 'terra legs', 'dreaded cleaver', "butcher's axe", 'mercenary sw... | Javieracost/Flarelyzer | agent.py | Python | apache-2.0 | 5,036 | [
"Amber"
] | df3d82b3f91754aa308cd677fef66075816575e84de473df80f7f06ec1362519 |
# -*- coding: utf-8 -*-
"""
:author: Rinze de Laat <laat@delmic.com>
:copyright: © 2012-2021 Rinze de Laat, Philip Winkler, Delmic
This file is part of Odemis.
.. license::
Odemis is free software: you can redistribute it and/or modify it under the terms of the GNU
General Public License version 2 as publishe... | delmic/odemis | src/odemis/gui/comp/stream.py | Python | gpl-2.0 | 80,900 | [
"Gaussian"
] | 2ecdf0bcf22e02028a0a20b4277149b0f03e3526a897dfc0d0e9930dc9bb4adb |
import sys
import os
class validateApp:
sampleFiles = {}
def __init__(self):
self.exitValidate = False
self.debug = True
self.verbose = True
def validateSampleSheetHTSeq(self, dirSample, finalDir, sampleSheet, force):
linenum = 0
if not os.path.exists(dirSampl... | msettles/expHTS | expHTS/validate_app.py | Python | apache-2.0 | 7,843 | [
"HTSeq"
] | b129c21bde4c71778352cde48a8094b9b666ca75f12f76e89b1b2fde29c3713a |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import vtk
def main():
colors = vtk.vtkNamedColors()
# Create five points.
origin = [0.0, 0.0, 0.0]
p0 = [1.0, 0.0, 0.0]
p1 = [0.0, 1.0, 0.0]
p2 = [0.0, 1.0, 2.0]
p3 = [1.0, 2.0, 3.0]
# Create a vtkPoints object and store the points in i... | lorensen/VTKExamples | src/Python/GeometricObjects/PolyLine.py | Python | apache-2.0 | 1,752 | [
"VTK"
] | 53ded223e3a47f366823077a5b9e3c21df9e9e44ac9f3698c39369124db97c95 |
'''
This module provides functionality for normalizing protein data.
Levels can be extracted from supernatant or phosphotyrosine runs using median
or mean peptide levels across multiple channels.
'''
from __future__ import absolute_import, division
# Built-ins
from collections import OrderedDict
import logging
impor... | white-lab/pyproteome | pyproteome/levels.py | Python | bsd-2-clause | 5,189 | [
"Gaussian"
] | 7742af57f1b5fefa340a7f038e0b1382c63d96a1da3fab35d1697ff8e969b458 |
"""
View a 3D rendering of the magnetic field lines and the streamlines of the rational surfaces.
The quality of the later can be used as an indicator of the quality of the grid. The magnetic field
is computed from efit_analyzed.py. The script can be used as a template to show additional properties of the field
based ... | erikgrinaker/BOUT-dev | tools/pylib/boututils/View3D.py | Python | gpl-3.0 | 11,702 | [
"Mayavi",
"VTK"
] | aad4ce651704d7a509289850275273ae255dbe451f430f2fa1a47a8a10e3985a |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import math
import os
import json
import collections
import itertools
from abc import ABCMeta, abstractmethod, abstractproperty
import random
import warnings
f... | aykol/pymatgen | pymatgen/core/structure.py | Python | mit | 123,332 | [
"ABINIT",
"CRYSTAL",
"Gaussian",
"NetCDF",
"VASP",
"pymatgen"
] | 569c5e3491033d3319ac0a41f43b7981bfd4ce398415ca24d99adfb918f8d68d |
import random
import string
import time
from mock import patch
from django.contrib.auth.models import User
from django.contrib.auth.models import AnonymousUser
from django.contrib.sessions.backends.db import SessionStore
from django.core.urlresolvers import NoReverseMatch
from django.core.urlresolvers import reverse
... | docker-hub/django-defender | defender/tests.py | Python | apache-2.0 | 27,805 | [
"VisIt"
] | 9c30a8668a037320062905a697abc1b452b9eff2b54020f8e773406793969753 |
#!C:\Python33\python.exe -u
# -*- coding: UTF-8 -*-
# enable debugging
import cgi
import cgitb
cgitb.enable()
import struct
import array
form = cgi.FieldStorage()
print("Content-Type: text/html")
print("""
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<noscript>
<p>Sorry, we can't ana... | RKYates/Dark-Souls-Death-Count-cgi-page | cgi-bin/submit.py | Python | gpl-3.0 | 5,722 | [
"VisIt"
] | 8a98bd551ac4ba222947328b93350b3dc927928bceaa5c3a58a85bbaee62ad01 |
import unittest
from test import support
import sys
import random
# Used for lazy formatting of failure messages
class Frm(object):
def __init__(self, format, *args):
self.format = format
self.args = args
def __str__(self):
return self.format % self.args
# SHIFT should match the valu... | mancoast/CPythonPyc_test | fail/301_test_long.py | Python | gpl-3.0 | 38,676 | [
"Brian"
] | 7a80de02a496a0712357a0227a5f0a978d97edd1c34450b7308ce1c9707cd406 |
"""
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Copyright (C) 2015 National Institutes of Health
This library is free software; you can redistribute it and/or
modify it under the ... | cnerger/wnd-charm | wndcharm/visualization.py | Python | lgpl-2.1 | 17,763 | [
"Biopython"
] | d49d0b7a078852369f89380239e32c8e1d40a0ea9e466475804f0f0d6a92dd99 |
from numpy import *
def loadDataSet(fileName):
# drop the colum(last colum) of label.
numFeat = len(open(fileName).readline().split('\t')) - 1
dataMat = []
labelMat = []
fr = open(fileName)
for line in fr.readlines():
lineArr = []
curLine = line.strip().split('\t')
for i ... | zhuango/python | machine-learning-algorithms/mlalg/linearRegression/regression.py | Python | gpl-2.0 | 3,767 | [
"Gaussian"
] | 3edc8bdf7c6c596bc970cb05b24f8b45dd42b09d46db8b00619d8d338dc66ec1 |
# -*- coding: utf-8 -*-
#
# testiaf.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST 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
# (... | lekshmideepu/nest-simulator | pynest/examples/testiaf.py | Python | gpl-2.0 | 4,078 | [
"NEURON"
] | 4f2e5b00fa7e48fecff38cf4534b8ef395a694cd1e2c8170bee3bb7cae74df6a |
'''
PathwayGenie (c) University of Manchester 2017
PathwayGenie is licensed under the MIT License.
To view a copy of this license, visit <http://opensource.org/licenses/MIT/>.
@author: neilswainston
'''
# pylint: disable=too-many-arguments
import sys
from assembly_genie.assembly import AssemblyThread, _AMPLIGASE, ... | synbiochem/PathwayGenie | assembly_genie/lcr.py | Python | mit | 4,796 | [
"VisIt"
] | aae3c732cb0c2979d28f72487a788864da9a3f025fa33295e0915c6374b70604 |
from django.conf.urls import patterns, url
from django.views.generic.detail import DetailView
from tasm import views, plotting
from tasm.models import RefSeq, Locus, Transcript
from tasm.forms import TranscriptFilterForm, RefSeqFilterForm
#
# URL for transcripts:
# /asm/<asm_pk>/loci - loci for the asssembly
# /a... | eco32i/tweed | tasm/urls.py | Python | bsd-3-clause | 3,330 | [
"BLAST"
] | 6e38ca3837b50439eb4c51f71fe8382dee90a0b0e1011f42329dd24984f61952 |
from pyparsing import CaselessKeyword, Literal, Word, StringEnd, Optional, Combine, Group, ParseException
from pyparsing import alphas, nums, alphanums, delimitedList
import yaml
from dalton.config.models import SecurityGroup, Rule
class YamlFileSecurityGroupsConfigLoader(object):
"""
Loads SecurityGroups f... | signal/dalton | dalton/config/loader.py | Python | apache-2.0 | 6,384 | [
"Dalton"
] | 046a46bb6d3075eb34a19dd8d860ef8906112e40f8d50db0628be81cbfce17e0 |
# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
# All rights reserved.
#
# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are ... | wizmer/NeuroM | neurom/io/utils.py | Python | bsd-3-clause | 7,273 | [
"NEURON"
] | 4a7a08246739345a23b55e715f20b1a98f42f5808fccde17e4e7ca2d53316c40 |
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