text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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|---|---|---|---|---|---|---|---|
"""Test OpenBabel Python bindings
On Windows or Linux, you can run these tests at the commandline
in the build folder with:
"C:\Program Files\CMake 2.6\bin\ctest.exe" -C CTestTestfile.cmake
-R pybindtest -VV
The runtime directory is ${CMAKE_SRC_DIR}/test.
You could also "c... | torcolvin/openbabel | test/testbindings.py | Python | gpl-2.0 | 18,248 | [
"Pybel"
] | b09f24daba97f7cd8b8f83034f54196bbde841aa7d1290fe50560bdff4b6ef54 |
"""
Tests for L{xquotient.mimepart}.
"""
import os
import email.quopriMIME
from StringIO import StringIO
from twisted.trial import unittest
from twisted.python import filepath
from epsilon import extime
from axiom.store import Store, AtomicFile
from xquotient import mimepart, smtpout
from xquotient.mimestorage imp... | twisted/quotient | xquotient/test/test_mimepart.py | Python | mit | 46,434 | [
"VisIt"
] | 828487d2e95f3cb2146de1fd2e9856c367e0fefb5fd2279999c9e745e1ae0ffe |
# Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
from math import pi
import warnings
from Bio.PDB import *
from AbstractPropertyMap import... | NirBenTalLab/proorigami-cde-package | cde-root/usr/lib64/python2.4/site-packages/Bio/PDB/HSExposure.py | Python | mit | 11,181 | [
"Biopython",
"PyMOL"
] | b5219e9cf83e08a7c00b4d198d0d12eccbd403de859609a9676bcbd400a10b09 |
# Copyright (c) 2003-2010 Sylvain Thenault (thenault@gmail.com).
# Copyright (c) 2003-2012 LOGILAB S.A. (Paris, FRANCE).
# http://www.logilab.fr/ -- mailto:contact@logilab.fr
#
# 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 t... | gkarlin/django-jenkins | build/pylint/utils.py | Python | lgpl-3.0 | 22,771 | [
"VisIt"
] | 2d79830d2d0f16e40902229aaedfa5d6c8b96c241540e698438f84d647a19c02 |
import itertools
import random
import mixins
import dice
class Character(mixins.AppearanceMixin):
def __init__(self, *args, **kwargs):
super(Character, self).__init__(*args, **kwargs)
# Attributes
self.skill = dice.d(3) + 3
self.stamina = dice.xdy(2, 6) + 12
self.luck = ... | funkaoshi/randomcharacter | troika.py | Python | mit | 38,772 | [
"CRYSTAL",
"exciting"
] | 78317fa225dfa221ae4f6525d28fecb441e3689255d5ace3dda0c05d26cfa9c8 |
# This file is part of BHMM (Bayesian Hidden Markov Models).
#
# Copyright (c) 2016 Frank Noe (Freie Universitaet Berlin)
# and John D. Chodera (Memorial Sloan-Kettering Cancer Center, New York)
#
# BHMM is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public Licens... | jchodera/bhmm | bhmm/tests/test_init_gaussian.py | Python | lgpl-3.0 | 2,052 | [
"Gaussian"
] | 2d270fa806d0d6b22813b632a5c7ffddae2029bc71767f5ad4995c49d19344b5 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
Created on May 1, 2012
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Sh... | xhqu1981/pymatgen | pymatgen/electronic_structure/tests/test_plotter.py | Python | mit | 4,571 | [
"pymatgen"
] | ce2b07dc63c4dd04747fe3420c9d28f4204c1a19bcf12358fed7668031c03c51 |
import os
import robotparser
import unittest
from test import support
from BaseHTTPServer import BaseHTTPRequestHandler, HTTPServer
import StringIO
try:
import threading
except ImportError:
threading = None
class BaseRobotTest:
robots_txt = ''
agent = 'test_robotparser'
good = []
bad = []
... | slozier/ironpython2 | Src/StdLib/Lib/test/test_robotparser.py | Python | apache-2.0 | 7,074 | [
"Brian"
] | 276d8efcd1fa00da8cb0f41a78b5fd4976c77a776b0615f7753a3719cfd394af |
n=int(raw_input())
d = [int(z) for z in raw_input().split()]
b = [int(z) for z in raw_input().split()]
D=0
B=0
for i in range(0,len(d)-1):
a1=abs(d[i]-d[i+1])
if (a1>D):
D=a1
b1=abs(b[i]-b[i+1])
if b1>B:
B=b1
if D>B:
print "Dom"
print D
else:
print "Brian"
print B | muskanbararia/Hacker_Earth-Solutions-using-python | Implementation/Fast_and_furious.py | Python | mit | 312 | [
"Brian"
] | f536c00815d391de594cf046b5841fdf35af777d5f1cf2367eacf3aad19b9dfd |
"""A convenience which constructs expression trees from an easy-to-read syntax
Use this unless you have a compelling reason not to; it performs some
optimizations that would be tedious to do when constructing an expression tree
by hand.
"""
from collections import OrderedDict
from six import (text_type, itervalues, ... | erikrose/parsimonious | parsimonious/grammar.py | Python | mit | 19,377 | [
"VisIt"
] | 191bf7f128bcc6b8e6ae5afd3db6c239145329b751fb4109bf03ea55238767fb |
#!/usr/bin/env python
'''
What is a FASTA format file/string?
This module follows the NCBI conventions: http://blast.ncbi.nlm.nih.gov/blastcgihelp.shtml
'''
import cStringIO
import math
def idFromName(line):
'''
line: a fasta nameline
returns: an id parsed from the fasta nameline. The id is the first
... | todddeluca/tfd | tfd/fasta.py | Python | mit | 21,889 | [
"BLAST"
] | be86d1bee086c2bf9683a7cc14cc3642415cc273b8e31c03b92db3bdc4aee2a2 |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
import unittest
import pbtest
class CookieTest(pbtest.PBSeleniumTest):
"""Basic test to make sure the PB doesn't mess up with the cookies."""
def assert_pass_opera_cookie_test(self, url, test_name):
self.load_url(url)
self.assertEqual("PASS", sel... | EFForg/privacybadgerchrome | tests/selenium/cookie_test.py | Python | gpl-3.0 | 2,998 | [
"VisIt"
] | f4f93db9773d352f1730915d1dface13ffac25a6de60409aea9a4baf353b6726 |
"""Probit regression class and diagnostics."""
__author__ = "Luc Anselin luc.anselin@asu.edu, Pedro V. Amaral pedro.amaral@asu.edu"
import numpy as np
import numpy.linalg as la
import scipy.optimize as op
from scipy.stats import norm, chisqprob
import scipy.sparse as SP
import user_output as USER
import sum... | dfolch/pysal | pysal/spreg/probit.py | Python | bsd-3-clause | 27,157 | [
"COLUMBUS"
] | 06a2347e7602c99b4437e6935688118ef1e50ca2a21eea82c4989b13316b4335 |
# BEGIN_COPYRIGHT
# END_COPYRIGHT
"""
Biobank: large scale biomedical computation on OMERO.
Biobank is a framework built upon OMERO that provides compact and
efficient ways to handle the computational aspects of large scale
biomedical studies.
"""
import datetime, os
# from setuptools import setup
from distutils.co... | crs4/omero.biobank | setup.py | Python | gpl-2.0 | 3,787 | [
"Galaxy"
] | 00a5e03bddfe38319936ee89b7b21417c227721f1a4efa8c9fa8d3e1f30d25fa |
########################################################################
# File: OperationHandlerBase.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/03/13 13:48:52
########################################################################
""" :mod: OperationHandlerBase
==========================
.. mo... | arrabito/DIRAC | RequestManagementSystem/private/OperationHandlerBase.py | Python | gpl-3.0 | 8,881 | [
"DIRAC"
] | fe06776d38502f626c2d56f05a632aeaa50701aaea60a6f9d314bf42ba043c4d |
"""
This module contains all the functions required to do the signal to noise calculations. Allows you
to calculate the signal-to-noise ratio for a star observed with a telescope and CCD. You can vary
the parameters and find out what sort of results to expect. Code adapted from original perl code
here: http://stupendou... | nparley/signal_to_noise_ccd | functions.py | Python | mit | 12,995 | [
"Gaussian"
] | 3cdd96b9f53f5441fcfb44fdc95fa30ac29ad3f0130629cb43830fd441658181 |
"""Preprocessor for running gulp tasks."""
import os
import atexit
import subprocess
from protorpc import messages
from grow.common import subprocesses
from grow.preprocessors import base
from grow.sdk import sdk_utils
# Keep track of any child processes to terminate on exit.
# pylint: disable=invalid-name
_child_pr... | grow/pygrow | grow/preprocessors/gulp.py | Python | mit | 1,917 | [
"GULP"
] | 757ebc1e04e58e869cbd100679372d328fc2d5ba9ea4f512234a211a9150e417 |
"""
Courseware views functions
"""
import logging
import urllib
import json
import cgi
from datetime import datetime
from django.utils import translation
from django.utils.translation import ugettext as _
from django.utils.translation import ungettext
from django.conf import settings
from django.core.context_process... | nagyistoce/edx-platform | lms/djangoapps/courseware/views.py | Python | agpl-3.0 | 61,681 | [
"VisIt"
] | 55781d9491fde6ec3afacda917985149602bf14ff590f3cae4181c36fa81b548 |
## This file is part of Invenio.
## Copyright (C) 2008, 2009, 2010, 2011 CERN.
##
## Invenio is free software; you can redistribute it and/or
## modify it under the terms of the GNU General Public License as
## published by the Free Software Foundation; either version 2 of the
## License, or (at your option) any later ... | robk5uj/invenio | modules/miscutil/lib/dbquery.py | Python | gpl-2.0 | 16,059 | [
"BLAST"
] | fb7e4e51a8302d024af98d59760f5570081aeec57003e10e7e2c5d8000f8fa37 |
"""
=================================
Gaussian Mixture Model Ellipsoids
=================================
Plot the confidence ellipsoids of a mixture of two Gaussians with EM
and variational Dirichlet process.
Both models have access to five components with which to fit the
data. Note that the EM model will necessari... | imaculate/scikit-learn | examples/mixture/plot_gmm.py | Python | bsd-3-clause | 3,038 | [
"Gaussian"
] | 1a13da77ff696d61f87b470882bd9fac0c48f87ba4226b6f105404c3297645b1 |
"""Example to obtain PhonopyYaml instance."""
import phonopy
from phonopy.interface.phonopy_yaml import PhonopyYaml
phonon = phonopy.load(
supercell_matrix=[[2, 0, 0], [0, 2, 0], [0, 0, 2]],
primitive_matrix=[[0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]],
unitcell_filename="POSCAR-unitcell",
force_sets_... | atztogo/phonopy | example/NaCl/NaCl-yaml.py | Python | bsd-3-clause | 501 | [
"VASP",
"phonopy"
] | 55ec8661f8344b2520615c93a128701b2aeeae70af9fcd1e32636ba1ac4d35ca |
import pytest
from pysisyphus.helpers import geom_loader
from pysisyphus.optimizers.RFOptimizer import RFOptimizer
from pysisyphus.calculators import OpenMolcas
from pysisyphus.testing import using
@using("openmolcas")
def test_openmolcas_s1_opt(this_dir):
geom = geom_loader(this_dir / "trans_butadien.xyz", coor... | eljost/pysisyphus | tests/test_openmolcas/test_openmolcas.py | Python | gpl-3.0 | 861 | [
"OpenMolcas"
] | 71296870ca659f6a7ee7441346ec8085224f94f4427e47be2cc6213405085b4b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#--------------------------------------------------------------------------
# Software: InVesalius - Software de Reconstrucao 3D de Imagens Medicas
# Copyright: (C) 2001 Centro de Pesquisas Renato Archer
# Homepage: http://www.softwarepublico.gov.br
# Contact: ... | tatiana/invesalius | invesalius/data/viewer_volume.py | Python | gpl-2.0 | 35,785 | [
"VTK"
] | b4ca389e02205e5ca156e0cd52626a667e2b68ad6a71befc4b62acad7944ee8b |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#... | MDAnalysis/mdanalysis | testsuite/MDAnalysisTests/core/test_segment.py | Python | gpl-2.0 | 2,210 | [
"MDAnalysis"
] | 26e67575e4d7a82cb63cacc07689105e4bede6a8dcadb4bd1388da855884d9fe |
# 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 v... | fweik/espresso | src/python/espressomd/constraints.py | Python | gpl-3.0 | 16,784 | [
"ESPResSo"
] | 17d27540e5c7f81ede5caf044125341eeed16e1bc896674c03bba5c0370ae9e4 |
# -*- coding: utf-8 -*-
###############################################################################
# lazyflow: data flow based lazy parallel computation framework
#
# Copyright (C) 2011-2014, the ilastik developers
# <team@ilastik.org>
#
# This program is free software; you c... | jakirkham/lazyflow | lazyflow/operators/vigraOperators.py | Python | lgpl-3.0 | 76,286 | [
"Gaussian"
] | 1121ac0ff8533386aa5a823d3ab580656f0cf008070ab4021f253a662a422342 |
# import numpy as np
from subprocess import call
from output import *
from string import Template
from textwrap import dedent
class PwxCalculation(object):
""" An abstract class all calculations inherit from. """
def __init__(self, p, s):
self.pars = p
self.struc = s
def control_input(sel... | sroelants/quint | calculation.py | Python | gpl-2.0 | 11,242 | [
"CRYSTAL"
] | b707940b939aa492a84320400edc6713fa68e8819f103b7c7454f1879e990f7b |
"""
Tools for downloading and stitching DEM rasters from OpenTopography holdings
"""
import os, sys, shutil
import numpy as np
import requests
import urllib
from urllib2 import Request
from bs4 import BeautifulSoup
from osgeo import gdal, ogr, osr
from copy import copy
sys.path.append('/usr/bin')
import gdal_merg... | rmsare/scarplet | scripts/fetch_data.py | Python | mit | 8,126 | [
"ADF"
] | 460eb0dd842d0015f11ad4294f6e670fb26ca7be14b9ade01b468ce5f7d22454 |
"""
FEniCS tutorial demo program: Poisson equation with Dirichlet conditions.
As d2_p2D.py, but LinearVariationalProblem and LinearVariationalSolver
are used instead of the solve(a == L, u, bc) call in d2_p2D.py.
-Laplace(u) = f on the unit square.
u = u0 on the boundary.
u0 = u = 1 + x^2 + 2y^2, f = -6.
"""
from __f... | MiroK/dolfin | test/unit/python/book/chapter_1_files/stationary/poisson/d3_p2D.py | Python | gpl-3.0 | 1,535 | [
"VTK"
] | fad51f17b731395d6b88bef78d2a01506692645ca6b2e4a454c5f6ee9674891c |
import HTMLParser, re, htmlentitydefs, time, urlparse
def cUConvert(m): return unichr(int(m.group(1)))
def cTConvert(m): return unichr(htmlentitydefs.name2codepoint.get(m.group(1),32))
def convertHTMLCodes(html):
if not isinstance(html,unicode):
html = unicode(html,'utf8','replace')
try:
html = re.sub('&#(\d{1,5... | ruuk/script.forum.browser | lib/forumbrowser/forumparsers.py | Python | gpl-2.0 | 77,159 | [
"VisIt"
] | 474b616c7397c18aff46e4e1d0233f3b61363b98897c4ef368a06f6f52239694 |
#
# 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... | RyanSkraba/beam | sdks/python/apache_beam/typehints/trivial_inference.py | Python | apache-2.0 | 17,104 | [
"VisIt"
] | 087bc3cb23a070af6765ada85cbc199339d7843c227e19906e369d878926c4cc |
# This file is part of Indico.
# Copyright (C) 2002 - 2021 CERN
#
# Indico is free software; you can redistribute it and/or
# modify it under the terms of the MIT License; see the
# LICENSE file for more details.
"""Extension to python-markdown to support LaTeX (rather than html) output.
Authored by Rufus Pollock: <h... | pferreir/indico | indico/util/mdx_latex.py | Python | mit | 19,641 | [
"Bowtie"
] | ad4f6e62a9feb724fcfb2c541fca864504a038c7d7ddd764c9ed1cf709681cae |
# -*- coding: utf-8 -*-
"""Convert the COVID-19 graph for Hipathia."""
import os
from urllib.request import urlretrieve
import click
from pyobo.cli_utils import verbose_option
import pybel
import pybel.grounding
HERE = os.path.dirname(__file__)
URL = 'https://github.com/covid19kg/covid19kg/raw/master/covid19kg/_ca... | pybel/pybel | notebooks/hipathia_demo/covid19/_convert_covid19kg.py | Python | mit | 931 | [
"Pybel"
] | 9ae4185bc3f0ee5ff1c6edf2df0df7858a249267b6713182d083548091a607ec |
#!/usr/bin/env python
from __future__ import print_function, division
import argparse
import elasticsearch as es
from datetime import datetime as dt
import pytz
import time
import requests
import re
from bs4 import BeautifulSoup
import daemon
import sys
parser = argparse.ArgumentParser(
description="Reads and pars... | yannakopoulos/elk-admin | scripts/monitor_bandwidth.py | Python | mit | 2,463 | [
"Elk"
] | 6e5ebbc7c27b1eee355bb38ad577656bd43fd567a2191028dcfaeddea19b405f |
'''@package docstring
@author: Jyh-Miin Lin (Jimmy), Cambridge University
@address: jyhmiinlin@gmail.com
Created on 2013/1/21
================================================================================
This file is part of pynufft.
pynufft is free software: you can redistribute it and/or modify
it un... | jyhmiinlin/cineFSE | CsTransform/good_3d_nufft.py | Python | gpl-3.0 | 30,890 | [
"Gaussian"
] | a6bd77518f3b678702fe3cb35a29b64d538e244c67a734b9b07f632a4be75e05 |
import numpy as np
import scipy
from scipy import constants
import ase.db
import ase.thermochemistry
def cm_to_hz(frequencies):
from scipy.constants import c
"""Convert an array of frequencies from cm-1 to Hz (i.e. s-1)"""
frequencies = np.array(frequencies)
return frequencies * 100 * c # v (cm-1) * 1... | WMD-Bath/sulfur-model | sulfur/__init__.py | Python | gpl-3.0 | 8,209 | [
"ASE",
"Jmol"
] | 8657cb854b6a0a547f8cb2a220f091358fe120c9376e548af6c0c41993f02389 |
#!/usr/bin/env python
from itertools import count, izip
from math import exp
from os.path import join as joinpath
from sys import float_info
from matplotlib import pyplot, cm
from numpy import array, arange
from numpy import min as amin
from numpy import max as amax
from numpy import sum as asum
from numpy import ar... | xperroni/Dejavu | script/plot_shift.py | Python | gpl-3.0 | 3,646 | [
"Gaussian"
] | a70321aa97503b486bb88d0b8289218b9cd49093ac9daf8c06712b0b03fa215d |
# coding: utf-8
# Copyright (c) Henniggroup.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals, print_function
"""
Development module:
This module contains the classes used when developing an organism
before and after it is submitted for an energy calculation, with ... | henniggroup/GASP-python | gasp/development.py | Python | mit | 40,127 | [
"pymatgen"
] | 7e47ee1bf306fb80ea9072cd9acd0ccaf350b747fc2e50b0ea62bcb31f4c5fd2 |
__author__ = "Bruno Fosso"
__version__ = 2.0
__mail__ = "b.fosso@ibbe.cnr.it"
import getopt
import os
import shlex
import subprocess
import sys
from string import strip
import numpy
import psutil
from pysam import Samfile
try:
from Bio import SeqIO
from Bio.SeqIO.QualityIO import FastqGeneralIterator
except:... | bfosso/MetaShot | bacterial_division_anlyser.py | Python | gpl-3.0 | 13,858 | [
"Biopython",
"pysam"
] | ff1d6caa1c0955d72b2de3ffb545546f0835044f50696551651a10cdec981ef1 |
# -*- coding: utf-8 -*-
#
# BrodyHopfield.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, ... | QJonny/CyNest | pynest/examples/BrodyHopfield.py | Python | gpl-2.0 | 2,481 | [
"Gaussian",
"NEURON"
] | 417442bce1789caf7e03ca13b0c32fad5d1c14d59743930d6391224d3bb71c3f |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | SKIRT/PTS | magic/tools/mosaicing.py | Python | agpl-3.0 | 11,350 | [
"Galaxy"
] | 9f589379b6d8ae906a4e685eea9a70eddf9deeb97029e9724c7a70192fc820c8 |
########################################################################
# File : JobWrapper.py
# Author : Stuart Paterson
########################################################################
""" The Job Wrapper Class is instantiated with arguments tailored for running
a particular job. The JobWrapper starts ... | rajanandakumar/DIRAC | WorkloadManagementSystem/JobWrapper/JobWrapper.py | Python | gpl-3.0 | 62,027 | [
"DIRAC"
] | 006361faa9b9cbf800af7b84fbe7c0804cb02669abed78a099f15a52f07d4fd7 |
import agnostic
from milecastles import Story, Box, ThroughPage, ThroughSequence, ConditionFork, NodeFork, SackChange
from stories import introText
# TODO CH, change use of True and 0 to 0 and 1 throughout, use bool() instead of x==True ?
storyName = "corbridge"
# create story
story = Story(
uid=storyName,
v... | cefn/avatap | python/stories/corbridge.py | Python | agpl-3.0 | 17,556 | [
"VisIt"
] | 7b639b38775971936583c0651bb4beef739ce896d24d214e8c19a663c2144316 |
"""
Title: Text classification with Switch Transformer
Author: [Khalid Salama](https://www.linkedin.com/in/khalid-salama-24403144/)
Date created: 2020/05/10
Last modified: 2021/02/15
Description: Implement a Switch Transformer for text classification.
"""
"""
## Introduction
This example demonstrates the implementati... | keras-team/keras-io | examples/nlp/text_classification_with_switch_transformer.py | Python | apache-2.0 | 12,279 | [
"MOE"
] | 4cfd5bc88415184238dc58d15979d2253c0624161e636567712003af258291c3 |
# Audio Tools, a module and set of tools for manipulating audio data
# Copyright (C) 2007-2016 Brian Langenberger
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the Licens... | tuffy/python-audio-tools | audiotools/vorbis.py | Python | gpl-2.0 | 20,653 | [
"Brian"
] | a86785bf4f7cc32dca0997d485a41b6898d0d725aa9b5a3150f93fb35803da19 |
from typing import Optional
# Zulip Settings intended to be set by a system administrator.
#
# See https://zulip.readthedocs.io/en/latest/subsystems/settings.html for
# detailed technical documentation on the Zulip settings system.
#
### MANDATORY SETTINGS
#
# These settings MUST be set in production. In a development... | mahim97/zulip | zproject/prod_settings_template.py | Python | apache-2.0 | 19,621 | [
"VisIt"
] | 99e2c7b9b2ce38870b46c80f1edfce284d70dd6337344da6aac3fabcdcdbf57f |
import numpy as np
import matplotlib.pyplot as plt
plt.ion()
import mc3.stats as ms
# Generate mock residuals signals:
N = 1000
np.random.seed(16)
# White-noise signal:
white = np.random.normal(0, 5, N)
# (Sinusoidal) time-correlated signal:
red = np.sin(np.arange(N)/(0.1*N))*np.random.normal(1.0, 1.0, N)
# Plot the... | pcubillos/MCcubed | examples/timeavg.py | Python | mit | 1,556 | [
"Gaussian"
] | cd77140d59c5971fddc6460f71844fc9b6ee0d71438f2a1a76ff0d7ad71f6898 |
"""
Generate samples of synthetic data sets.
"""
# Authors: B. Thirion, G. Varoquaux, A. Gramfort, V. Michel, O. Grisel,
# G. Louppe, J. Nothman
# License: BSD 3 clause
import numbers
import array
import numpy as np
from scipy import linalg
import scipy.sparse as sp
from ..preprocessing import MultiLabelBin... | mbayon/TFG-MachineLearning | venv/lib/python3.6/site-packages/sklearn/datasets/samples_generator.py | Python | mit | 57,684 | [
"Gaussian"
] | 42d789f23f8bc131ca78f3b176c6306f7b9fa68bdb14ea51ca86c6e023ad0102 |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
import os
i... | nuclear-wizard/moose | python/MooseDocs/extensions/appsyntax.py | Python | lgpl-2.1 | 31,710 | [
"MOOSE"
] | e845bf35896c617742f593541b314b6eece0c0bdd879d0d42c88ae8f5452baf6 |
from Sire.Mol import *
from Sire.IO import *
from Sire.Vol import *
from Sire.FF import *
from Sire.MM import *
from Sire.CAS import *
from Sire.Base import *
from Sire.Maths import *
from Sire.Qt import *
from Sire.Units import *
from Sire.Squire import *
from Sire.Cluster import *
from Sire.System import *
from Sire... | chryswoods/SireTests | unittests/Squire/molproff.py | Python | gpl-2.0 | 3,751 | [
"Molpro"
] | 590b59b58ab56f4176ffe2f94be87c54d1b0fe86e48d9b80400dc5bd50b64ed7 |
from datetime import date
class ResultWrapper:
"""
>>> a = ResultWrapper('POS')
>>> a
ResultWrapper('POS')
>>> b = ResultWrapper('POS')
>>> b
ResultWrapper('POS')
>>> a == b
True
>>> a is b
False
"""
def __init__(self, result_value, result_datetime=None, visit_code=... | botswana-harvard/hiv-status | hiv_status/result_wrapper.py | Python | gpl-2.0 | 1,285 | [
"VisIt"
] | 85de8fcb70859413fd2ea20b0737670427db48faec6e0b6ad1b3bfb4f798677d |
from random import random, randint
from skimage import draw
import math
import numpy as np
class ImageAugmenter():
""" Modify input images for data augmentation.
Draw ellipse_count ellipses, each with a random color in the part of the image given by 'area'.
Area is height x width
fraction is from 0.0 t... | Bleyddyn/malpi | train/augmentor.py | Python | mit | 4,530 | [
"Gaussian"
] | 293e82fbe01131ca1d0eb77f30def3d2e9a6abb0d5a141347eec7fb5608f27a5 |
from __future__ import absolute_import
input_name = '../examples/linear_elasticity/elastic_contact_sphere.py'
output_name = 'test_elastic_contact_sphere.vtk'
from tests_basic import TestInput
class Test(TestInput):
pass
| rc/sfepy | tests/test_input_elastic_contact_sphere.py | Python | bsd-3-clause | 225 | [
"VTK"
] | ead081ab9b3db08e867a6eb53a77bdac9a91ef4e6381af279198bd11887cc118 |
#!/usr/bin/python
'''
***************************************************************************
The Great RNA-Seq Experiment Differential Expression Tool Bootstrap Wrapper
***************************************************************************
This file is a generic wrapper for running multiple bootstraps of
`R... | bartongroup/profDGE48 | Bootstrapping/generic_wrapper.py | Python | mit | 160,304 | [
"Bioconductor",
"HTSeq"
] | c640946cbe058e9517de3e16e0f46d7a709ecad9301188190ee878485ad2295f |
# -*- coding: utf-8 -*-
# The MIT License (MIT)
#
# Copyright (c) 2016, TU Wien
#
# 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 without restriction, including without limitation the rights
... | TUW-GEO/ecmwf_models | src/ecmwf_models/erainterim/reshuffle.py | Python | mit | 7,289 | [
"NetCDF"
] | 74e21e96e8803b46fef52456aa32607ab301b485c30d178c9764a48f31d6504f |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.2
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the te... | le9i0nx/ansible | lib/ansible/modules/network/avi/avi_gslbgeodbprofile.py | Python | gpl-3.0 | 4,717 | [
"VisIt"
] | a6ad1387fb79387cddafd473f9e46e4ce5b5a93f04e8f4b2694100758b2c4a23 |
from module_base import ModuleBase
from module_mixins import NoConfigModuleMixin
import module_utils
import vtk
class reconstructSurface(ModuleBase, NoConfigModuleMixin):
"""Given a binary volume, fit a surface through the marked points.
A doubleThreshold could be used to extract points of interest from
a... | nagyistoce/devide | modules/user/reconstructSurface.py | Python | bsd-3-clause | 3,363 | [
"VTK"
] | 5c798c920874c8ec42a75d4c73fd0dfd9fd0663a45297b428f50c5ff6581966d |
# -*- coding: utf-8 -*-
'''
Copyright (c) 2018 by Tobias Houska
This file is part of Statistical Parameter Optimization Tool for Python(SPOTPY).
:author: Patrick Lauer
'''
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literal... | bees4ever/spotpy | spotpy/algorithms/fscabc.py | Python | mit | 10,065 | [
"Gaussian"
] | e6ce727463e4b30c98082e50abe8b664ec11d5aadcdf054d2a324341e891a51d |
citydataset = """
{
"a coruna": [
{
"Country": "es",
"Latitude": -8.41,
"Longitude": 43.37,
"Population": 236010
}
],
"aachen": [
{
"Country": "de",
"Latitude": 6.11,
"Longitude": 50.77,
... | taygetea/weather | src/lib/data.py | Python | mit | 612,438 | [
"COLUMBUS"
] | 39955c10e001f9281234b18ac47bce743ff7d916ef874e349a70938faa9055e3 |
#! /usr/bin/env python
# FIXME: if it requires a dirac.cfg it is not a unit test and should be moved to tests directory
import unittest
import time
import os
import shutil
import sys
from types import IntType, LongType, StringTypes
from DIRAC.Core.Base.Script ... | andresailer/DIRAC | Resources/Storage/test/FIXME_Test_StoragePlugIn.py | Python | gpl-3.0 | 34,998 | [
"DIRAC"
] | 5625d98ac077914fa16b4a3fc891b79528f939b1aeee242c4a19f965f7a171aa |
from ... import os, sys
import ast
from six import string_types
import numpy
def get_abspath(value):
if isinstance(value, string_types) and os.path.exists(value):
return os.path.abspath(value)
else:
return value
def is_floatable(val):
if isinstance(val, (bool,)+string_types):
retu... | nickhand/pyRSD | pyRSD/rsdfit/parameters/tools.py | Python | gpl-3.0 | 4,397 | [
"VisIt"
] | 942a02584490cbb7d476e19296ab424dba544377c42684f0e125800cf5fa3580 |
# -*- coding: utf-8 -*-
"""
This file is part of verysharp,
copyright (c) 2016 Björn Sonnenschein.
verysharp 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... | wilecoyote2015/VerySharp | Deconvolver.py | Python | gpl-3.0 | 4,300 | [
"Gaussian"
] | c05bb9a49564ef2fe9a3ed6f572797264a3179ca34a48a95c2c5bfc5b364766d |
import ocl
import pyocl
import camvtk
import time
import datetime
import vtk
import math
def main():
print ocl.revision()
myscreen = camvtk.VTKScreen()
myscreen.camera.SetPosition(-8, -4, 25)
myscreen.camera.SetFocalPoint(4.5,6, 0)
# axis arrows
camvtk.drawArrows(myscreen,center=(-1,-1,... | AlanZatarain/opencamlib | scripts/cutsim/cutsim_09_tux_video.py | Python | gpl-3.0 | 6,242 | [
"VTK"
] | 01397bcf402a088937fc07f1b4fb94db6143c1aba3997316546b3e7b4076fe1f |
# Copyright (c) 2012, CyberPoint International, LLC
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright
# notice, this lis... | CyberPoint/libpgm | build/lib.linux-x86_64-2.7/libpgm/CPDtypes/lg.py | Python | bsd-3-clause | 4,355 | [
"Gaussian"
] | 34c3a6ce251279e71d3c2fd25e5384f7553f29361658c7408031cd4ce5095537 |
""" ElasticDB is a base class used to connect an Elasticsearch database and manages queries.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
from DIRAC.Core.Base.DIRACDB import DIRACDB
from DIRAC.Core.Utilities.ElasticSearchDB import ... | yujikato/DIRAC | src/DIRAC/Core/Base/ElasticDB.py | Python | gpl-3.0 | 3,140 | [
"DIRAC"
] | 5e7c2fdd67f9871f5179b36593c29440fcc136cf7f33505a0edf337c085d90b3 |
#!/usr/bin/env python
import os
import numpy as np
import joblib as jl
import matplotlib.pyplot as plt
from icing.core import distances
from icing.models import model
from icing.utils import extra, io
from icing.core.parallel_distance import dnearest_inter_padding
ham_model = model.model_matrix('ham')
ham_model['-'] ... | slipguru/ignet | scripts/evaluate_threshold.py | Python | bsd-2-clause | 4,680 | [
"Gaussian"
] | cd5c1573854b3913c7e046ecb3986eb1668e977338ace48f4e16c2ac42475d9c |
# Copyright (c) 2013, the GPy Authors (see AUTHORS.txt)
# Licensed under the BSD 3-clause license (see LICENSE.txt)
from ..core import GP
from . import SparseGPClassification
from .. import likelihoods
from .. import kern
from ..inference.latent_function_inference.expectation_propagation import EP
import numpy as np
... | ptonner/GPy | GPy/models/one_vs_all_classification.py | Python | bsd-3-clause | 1,374 | [
"Gaussian"
] | 8c34263a3d6ff9018a9d3519973dbdfab8d98b76aaeb34f26ec74dd308a48287 |
# convcmd - convert extension commands definition
#
# Copyright 2005-2007 Matt Mackall <mpm@selenic.com>
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2 or any later version.
from common import NoRepo, MissingTool, SKIPREV, mapfile
from cvs import conv... | hekra01/mercurial | hgext/convert/convcmd.py | Python | gpl-2.0 | 20,066 | [
"Octopus",
"VisIt"
] | b43f6e853439df5d6d20d7eab654f090c5ef3fcd8e66e047ca55ff4a5dbc9d66 |
browsers = [
{'env': 'local', 'browser': 'Firefox'},
{'browser': 'Firefox', 'browser_version': '35.0', 'os': 'Windows', 'os_version': '8.1', 'resolution': '1600x1200'},
{'browser': 'Firefox', 'browser_version': '33.0', 'os': 'Windows', 'os_version': '8.1', 'resolution': '1600x1200'},
{'browser': 'Fire... | katsuroo/trustroots | scripts/selenium/browsers.py | Python | mit | 3,921 | [
"Galaxy"
] | ebac838798ccc40fd5dd91e837fef01a527c4465f1c19cce7fd53295b8d162c5 |
"""Primitive cell and supercell, and related utilities."""
# Copyright (C) 2011 Atsushi Togo
# All rights reserved.
#
# This file is part of phonopy.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# * Redistributio... | atztogo/phonopy | phonopy/structure/cells.py | Python | bsd-3-clause | 55,236 | [
"CRYSTAL",
"phonopy"
] | abfddd8c0892e45fa8942962aa2d1858a305bd9f926f614c18a46a8866290b5f |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Abinit Post Process Application
author: Martin Alexandre
last edited: May 2013
"""
import commands
class ReadGraph:
# This class can read graph in a file
# This is useful to add graphics
#-----------------------------#
#-------CONSTRUCTOR-----------#
#-... | jmbeuken/abinit | scripts/post_processing/appa/reading/read_graph.py | Python | gpl-3.0 | 1,394 | [
"ABINIT"
] | a713bcbd88113553607bc2239919e134a551621f70299056215f2122975743b7 |
""" Principal Component Analysis
"""
# Author: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Olivier Grisel <olivier.grisel@ensta.org>
# Mathieu Blondel <mathieu@mblondel.org>
# Denis A. Engemann <d.engemann@fz-juelich.de>
# Michael Eickenberg <michael.eickenberg@inria.fr>
#
# Lice... | WangWenjun559/Weiss | summary/sumy/sklearn/decomposition/pca.py | Python | apache-2.0 | 23,035 | [
"Gaussian"
] | fdd201ab596742594a2a4c8d4ec494d9134853f7a6966c8b4d69ee3caf338cc6 |
# Philip Bailey
# 30 Oct 2019
# Script to convert CHaMP measurement XML provided by Sitka
# into CSV format.
# Boyd provided several visits by email on 30th Oct and I
# returned the output CSVs the same day.
import os
import sys
import csv
import argparse
import traceback
import xml.etree.ElementTree as ET
def champ_m... | SouthForkResearch/CHaMP_Metrics | scripts/champ_measurements.py | Python | gpl-3.0 | 2,891 | [
"VisIt"
] | b718ed7b72dc874715b4b2eaf8ebaac4f5bd2b0b503b30d51ba244e752b5f072 |
import numpy as np
import theano
import theano.tensor as T
from baselayers import AbsLayer, ParametrizedLayer, RandomLayer
class BiasLayer(ParametrizedLayer):
@property
def param_dict_initialization(self):
dict_of_init = {
'betas' : [(self.output_dims[0],), 'zeros'],
}
... | olimastro/DeepMonster | deepmonster/nnet/simple.py | Python | mit | 4,331 | [
"Gaussian"
] | c2eb6ae861db77a4019063ee1e2841b6d65d47fe3fa0a758ce7abcb52482f1b5 |
# Copyright 2014, Brian Coca <bcoca@ansible.com>
# Copyright 2017, Ken Celenza <ken@networktocode.com>
# Copyright 2017, Jason Edelman <jason@networktocode.com>
# Copyright 2017, Ansible Project
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of ... | alxgu/ansible | lib/ansible/plugins/filter/mathstuff.py | Python | gpl-3.0 | 8,097 | [
"Brian"
] | 070f88f696f4af90cf9b2847deec1be0c29514be4762ac1a762e8385862ed264 |
""" DISET request handler base class for the TransformationDB.
"""
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Core.DISET.RequestHandler import RequestHandler
from DIRAC.TransformationSystem.DB.TransformationDB import TransformationDB
from DIRAC.ConfigurationSystem.Client.Helpers.Operations import Operations
... | andresailer/DIRAC | TransformationSystem/Service/TransformationManagerHandler.py | Python | gpl-3.0 | 29,516 | [
"DIRAC"
] | 7f11e8c2f6a5ee8da3f2eee5f5cbd5d00574249c0043c151191067646f32c4ed |
"""
Utilities for the Neofelis Annotation Pipeline.
"""
"""
Copyright 2010 Jarl Haggerty
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 r... | jarl-haggerty/profelis | src/main/jython/profelis/utils.py | Python | apache-2.0 | 13,772 | [
"BLAST"
] | fcc93171cd32a22ec2c680068ade5cc30387574479915330d24939f3d76b802b |
##
# Copyright 2013-2021 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... | boegel/easybuild-easyconfigs | test/easyconfigs/easyconfigs.py | Python | gpl-2.0 | 71,738 | [
"ABINIT",
"ASE",
"Amber",
"BLAST",
"Bioconductor",
"CP2K",
"Elk",
"GPAW",
"NetCDF",
"PySCF",
"WIEN2k",
"pysam"
] | 328b9cf1b0c2b391e56d40914824abb82c824df96e56c687bdbc648561b6f1e0 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2016 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | kannon92/psi4 | psi4/header.py | Python | gpl-2.0 | 2,800 | [
"Psi4"
] | 382f737e5c25b67494ac5b4f02f3fa8bd0f24f65df31be5d0bd50ce828be01de |
"""This file contains code used in "Think DSP",
by Allen B. Downey, available from greenteapress.com
Copyright 2013 Allen B. Downey
License: GNU GPLv3 http://www.gnu.org/licenses/gpl.html
"""
from __future__ import print_function, division
import array
import copy
import math
import numpy
import random
import scipy
... | NSasquatch/vocoder | thinkdsp.py | Python | cc0-1.0 | 37,102 | [
"Gaussian"
] | ea46c6f0352984c5829aaf2a8930eea47dcf93dcfb7321faf23f70ce1a46df4f |
import os
def writeOutputToVTK(time, name, dx, data, datanames):
if type(data) is not list:
data = list(data)
if type(datanames) is not list:
datanames = list(datanames)
n_datasets = data.__len__()
assert n_datasets == datanames.__len__()
outpath = os.path.join(os.getcwd(), '.... | precice/elastictube1d | fluid-python/output.py | Python | gpl-3.0 | 1,719 | [
"VTK"
] | 259f53c3f793bf13980ca5620e80d06ea1c2f16ed2e360aa73d366c0b80307ae |
"""
This class is used to define the plot using the plot attributes.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from DIRAC import S_OK
from DIRAC.MonitoringSystem.Client.Types.WMSHistory import WMSHistory
from DIRAC.MonitoringSystem.private.Plotter... | yujikato/DIRAC | src/DIRAC/MonitoringSystem/private/Plotters/WMSHistoryPlotter.py | Python | gpl-3.0 | 6,102 | [
"DIRAC"
] | dbaf7fb332767bb8a227d9e341ca4a4a910e353073a6fa3103162e573748c1cb |
# 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... | jwlawson/tensorflow | tensorflow/contrib/py2tf/pyct/templates.py | Python | apache-2.0 | 3,885 | [
"VisIt"
] | 200a9bb203b4c2645c71680d7e730a8c4c7be42d16120e20178a68b320d7b7cf |
# -*- coding: utf-8 -*-
"""
sphinx.writers.manpage
~~~~~~~~~~~~~~~~~~~~~~
Manual page writer, extended for Sphinx custom nodes.
:copyright: Copyright 2007-2013 by the Sphinx team, see AUTHORS.
:license: BSD, see LICENSE for details.
"""
from docutils import nodes
try:
from docutils.writers.ma... | SurfasJones/icecream-info | icecream/lib/python2.7/site-packages/sphinx/writers/manpage.py | Python | mit | 11,430 | [
"VisIt"
] | 4d539d8b7d477a4865f1b292d725667b97a140fac8778c1bc0bf3716b8dbf9fb |
'''
Author: Hans Erik Heggem
Email: hans.erik.heggem@gmail.com
Project: Master's Thesis - Autonomous Inspection Of Wind Blades
Repository: Master's Thesis - CV (Computer Vision
'''
import cv2, math, operator
import numpy as np
from Settings.Exceptions import DroneVisionError
from src.DroneVision.DroneVision_src.im... | hansehe/Wind-Blade-Inspection | src/DroneVision/DroneVision_src/imgProcessing/featureDetection/BlobDetector/BlobDetector.py | Python | mit | 18,871 | [
"Gaussian"
] | 056c1634e4497fe06ea07c873b66c573d0dae3cb09b4300b40d664b0da030fc6 |
''' Test_RSS_Policy_JobEfficiencyPolicy
'''
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import unittest
import DIRAC.ResourceStatusSystem.Policy.JobEfficiencyPolicy as moduleTested
#######################################################################... | yujikato/DIRAC | src/DIRAC/ResourceStatusSystem/Policy/test/Test_RSS_Policy_JobEfficiencyPolicy.py | Python | gpl-3.0 | 3,905 | [
"DIRAC"
] | 38b4680101852ec433aaaaf563ac7410de95436a1f3a9be30ba7ed33b50c1a08 |
# 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 ... | bswartz/cinder | cinder/hacking/checks.py | Python | apache-2.0 | 19,432 | [
"VisIt"
] | 61237e1c3213dd2f2cf42b0f844c05d1b31d6f5e8fdc2c7f007da089c11b2e59 |
"""
Utilities to create replication transformations
"""
from DIRAC.TransformationSystem.Client.Transformation import Transformation
from DIRAC import gLogger, S_OK, S_ERROR
def createDataTransformation(
flavour,
targetSE,
sourceSE,
metaKey,
metaValue,
extraData=None,
extraname="",
grou... | DIRACGrid/DIRAC | src/DIRAC/TransformationSystem/Utilities/ReplicationTransformation.py | Python | gpl-3.0 | 3,653 | [
"DIRAC"
] | 515c20bf977b84143b53b8565eb89c17d0ebb5c98cba10a276beac3153f0d039 |
#!/usr/bin/env python
__author__ = 'Mike McCann,Duane Edgington,Reiko Michisaki'
__copyright__ = '2013'
__license__ = 'GPL v3'
__contact__ = 'duane at mbari.org'
__doc__ = '''
loader for ESP CANON activities in September 2013
Mike McCann; Modified by Duane Edgington and Reiko Michisaki
MBARI 02 September 2013... | stoqs/stoqs | stoqs/loaders/CANON/esp_loadsep2013.py | Python | gpl-3.0 | 2,843 | [
"NetCDF"
] | 14674d9c36d6e22aa7464e2bfd6ac2bb0cbc4052b47f23727bb0ee01df87ed6f |
#!/usr/bin/env python
#
# Unit tests for sites manipulation in samba
# Copyright (C) Matthieu Patou <mat@matws.net> 2011
#
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of t... | jelmer/samba | source4/dsdb/tests/python/sites.py | Python | gpl-3.0 | 16,521 | [
"TINKER"
] | 417ea8974f5a2d9f52d81a85833ca4b270844bb8ddc01d9895b1ec12d457d3d6 |
from __future__ import print_function
import sys
import os
import numpy as np
np.random.seed(42)
import matplotlib.pyplot as plt
import matplotlib.gridspec as gridspec
from matplotlib.patches import ConnectionPatch
from scipy.optimize import leastsq
import stfio
import stfio_plot
try:
import spectral
except Imp... | JoseGuzman/stimfit | manuscript/events.py | Python | gpl-2.0 | 24,009 | [
"NEURON"
] | 4ceab22b9cec3b8e1079dce0e665abc83c6557ba93869b1a0be855f985eeacc0 |
# This file is part of Buildbot. Buildbot 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, version 2.
#
# This program is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without eve... | mitya57/debian-buildbot | buildbot/status/web/waterfall.py | Python | gpl-2.0 | 34,162 | [
"VisIt"
] | a7d6ba8e08a78ca1d54798d9983e4d0581940a7d085382fddd43eaed58ef77f1 |
import json
import random
from django.conf import settings
from django.test import TestCase
from django.core.cache import cache
import mock
from nose.tools import ok_, eq_
from airmozilla.base import mozillians
VOUCHED_FOR = """
{
"meta": {
"previous": null,
"total_count": 1,
"offset": 0,
"limit"... | bugzPDX/airmozilla | airmozilla/base/tests/test_mozillians.py | Python | bsd-3-clause | 9,629 | [
"CASINO"
] | 676f529649ec1062e23b9005b733dd2f01b7344f8eb34aa53532d4c31ff6b0e9 |
import sys
import os.path
import json, time
import urllib, urllib2
import inspect
import logging
import argparse
#################################
# Setup, configuration and script execution
#################################
# This script is tested on Python 2.7.3, only standard packages are used. This version or mo... | ooici/coi-services | ion/ext/tools/data_product_monitor.py | Python | bsd-2-clause | 12,046 | [
"NetCDF"
] | 8ee1f4e2bd1952bee8850fa284aba08102ff50af34e02d056b8ef77fa102e7e4 |
#!/usr/bin/python
# encoding: utf-8
"""
psebuilder.py
Generic functions used to create PyMOL session builder objects.
Created by Shane O'Connor 2014.
"""
import os
import shutil
import string
from klab.fs.fsio import read_file, create_temp_755_path, write_file
from klab import colortext
from klab import process as t... | Kortemme-Lab/klab | klab/bio/pymolmod/psebuilder.py | Python | mit | 5,232 | [
"PyMOL"
] | f751ad543ad6029c7315d6a70794d0cb307195cda93c6216ef80125bd9d518f2 |
"""IRAF/DAOPHOT wrapper to carry out PSF photometry in a user-friendly way.
Some of the help texts are adapted from the DaoPhot or IRAF manual or
http://iraf.net/irafhelp.php?val=daopars&help=Help+Page
"""
from __future__ import (absolute_import, division, print_function,
unicode_literals)
imp... | barentsen/surveytools | surveytools/daophot.py | Python | mit | 29,523 | [
"Gaussian"
] | c76b6fb155ac1e9d603acfd815c1ee13357afc08f52032484365b3c73e895ef1 |
# Copyright 2003-2009 by Bartek Wilczynski. All rights reserved.
# Revisions copyright 2009 by Peter Cock.
# 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.
"""This module provides code to work with th... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/Motif/Applications/_AlignAce.py | Python | gpl-2.0 | 3,160 | [
"Biopython"
] | 12c70d1d610e6441e72c100ab69e9ced2ef989cf6bcf33944b6030e79c5e2ae8 |
"""Processing and presentation of computed data
Result objects hold computed data and offer postprocessing and plotting functions
which are specifically adapted to the nature of the stored data.
"""
from copy import copy
import numpy as np
import matplotlib.pyplot as plt
from . import pltutils
from .utils import wit... | MAndelkovic/pybinding | pybinding/results.py | Python | bsd-2-clause | 36,147 | [
"Gaussian"
] | 9b36994af7ff1a367a29982f291a33f907d35f7bdfbaa1e52f2f595f19dbefdc |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides objects describing the basic parameters of the
pseudopotentials used in Abinit, and a parser to instantiate pseudopotential objects..
"""
from __future__ import unicode_literals, divisio... | setten/pymatgen | pymatgen/io/abinit/pseudos.py | Python | mit | 63,624 | [
"ABINIT",
"pymatgen"
] | 17dd49061c5d1c3f65e4ccf66ac028c4636328e000431f63f91e4ad9cf4af71a |
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'main.ui'
#
# Created: Mon Aug 27 09:38:06 2012
# by: PyQt4 UI code generator 4.9.1
#
# WARNING! All changes made in this file will be lost!
from PyQt4 import QtCore, QtGui
try:
_fromUtf8 = QtCore.QString.fromUtf8
except AttributeE... | matachi/subdownloader | gui/main_ui.py | Python | gpl-3.0 | 46,859 | [
"VisIt"
] | a4274e8437a992e8bc8f36913d212e4930c9b903aeb6a21f08c01b2adcc388fe |
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