text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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import logging
from cStringIO import StringIO
from math import exp
from lxml import etree
from path import path # NOTE (THK): Only used for detecting presence of syllabus
import requests
from datetime import datetime
import dateutil.parser
from lazy import lazy
from xmodule.modulestore import Location
from xmodule.pa... | jswope00/GAI | common/lib/xmodule/xmodule/course_module.py | Python | agpl-3.0 | 42,527 | [
"VisIt"
] | 2a1dbaa1deef058d0ec510b8bfeebbce2251e526580d76af2284984ffe08e4d5 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2011 Tim G L Lyons
#
# 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 Fr... | Forage/Gramps | gramps/gen/plug/__init__.py | Python | gpl-2.0 | 2,680 | [
"Brian"
] | 443bc398a8e3c24579caeba8880865ce296c08c0ec2f2fafa3175d240e753820 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2008 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2008 Gary Burton
# Copyright (C) 2008 Robert Cheramy <robert@cheramy.net>
# Copyright (C) 2010 Jakim Friant
#
# This program is free software;... | pmghalvorsen/gramps_branch | gramps/plugins/export/exportpkg.py | Python | gpl-2.0 | 8,952 | [
"Brian"
] | c7aea6ed57568b3100afeec5fd2531552f7e5e84df64f823a170ae6408e27035 |
#!/usr/bin/env python
#
# $File: sampleThreeGenFamily.py $
#
# This file is part of simuPOP, a forward-time population genetics
# simulation environment. Please visit http://simupop.sourceforge.net
# for details.
#
# Copyright (C) 2004 - 2010 Bo Peng (bpeng@mdanderson.org)
#
# This program is free software: you can re... | BoPeng/simuPOP | docs/sampleThreeGenFamily.py | Python | gpl-2.0 | 1,331 | [
"VisIt"
] | 5a83159ab29cdbf169b4731838e76f8948eb18f0f5eb25b797dbc2ce26e145b0 |
import enum
from graphql.language import ast
from graphql.language.parser import parse
from ..query import Node, Field, Link, merge
class NodeVisitor:
def visit(self, obj):
visit_method = getattr(self, 'visit_{}'.format(obj.kind))
if visit_method is None:
raise NotImplementedError('... | vmagamedov/hiku | hiku/readers/graphql.py | Python | bsd-3-clause | 12,187 | [
"VisIt"
] | fb0e0c2a83dfda95b74330596d5cdee6ba39f09db95ecc647fd1c92535704150 |
#
# Copyright (C) 2017, 2021 Smithsonian Astrophysical Observatory
#
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option) any later vers... | anetasie/sherpa | sherpa/sim/tests/test_sim_unit.py | Python | gpl-3.0 | 3,249 | [
"Gaussian"
] | a2d7f14042c77f311226f88d9d41e159d5745e62babb4aab03ca8515e47d2bc7 |
"""
tebdIsing6.py
Use TEBD to compute ground state of transverse field Ising model.
2014-09-29
"""
import numpy as np
from cmath import *
from mpstest17 import *
import matplotlib.pyplot as plt
import time
def main():
test0()
def test0():
(J,hx,hz) = (1,0.1,0.05)
(timeStep,nsteps,chi) = (0.01,300,10)
... | ehua7365/RibbonOperators | TEBD/tebdIsing6.py | Python | mit | 14,136 | [
"DIRAC"
] | 55af5af547bbb6c84485863687c7484b96cc289ab2989d40bbb7f121e1380423 |
# -*- coding: utf-8 -*-
"""
===============================================================================
Network.tools.topology: Assorted topological manipulation methods
===============================================================================
"""
import scipy as _sp
import numpy as _np
import scipy.ndimage ... | stadelmanma/OpenPNM | OpenPNM/Network/tools.py | Python | mit | 45,375 | [
"ParaView",
"VisIt"
] | d38412a837ca1500a6a27b3aba58b7f5a535795a0086bd28ad1e3433a88e8d39 |
import numpy as np
from pylab import *
from gpaw.response.tool import linear_fit
from gpaw.test import equal
tag = 'Nabulk'
d = np.loadtxt('%s_RPA.dat' %(tag))
x = d[:,0]
y = d[:,1]
xscale = x**(-1.5)
plot(xscale, y, 'o')
yfit, para = linear_fit(xscale,y)
xx = np.linspace(0, xscale.max(), 1000)
yy = para[0] * xx +... | robwarm/gpaw-symm | gpaw/test/big/rpa/plot_rpa.py | Python | gpl-3.0 | 613 | [
"GPAW"
] | 89ff48ac959fa0198ce96fe8e2b6828064774abe7c09ba2f030e894778d14605 |
# Copyright (C) 2014 Sereina Riniker
#
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" Torsion Fingerprints (Deviation) (TFD)
According to a paper from Schulz-Gasch et a... | jandom/rdkit | rdkit/Chem/TorsionFingerprints.py | Python | bsd-3-clause | 24,314 | [
"RDKit"
] | ffabed467362c9b561d395db8cad7807daf503a7c0cdfd3d285af5005152cc1a |
"""cursor_handler.py - Cursor handler."""
import gobject
import gtk
from mcomix import constants
class CursorHandler(object):
def __init__(self, window):
self._window = window
self._timer_id = None
self._auto_hide = False
self._current_cursor = constants.NORMAL_CURSOR
def se... | benoit-pierre/mcomix | mcomix/cursor_handler.py | Python | gpl-2.0 | 2,663 | [
"FLEUR"
] | 0aca9341fb81ba0d688befc1491a380ce8b3852c8de41e9ca337b3bf5f050749 |
# Copyright (c) 2009-2021 The Regents of the University of Michigan
# This file is part of the HOOMD-blue project, released under the BSD 3-Clause
# License.
"""Implement CustomOperation."""
from abc import abstractmethod
import itertools
from hoomd.operation import _TriggeredOperation
from hoomd.data.parameterdicts... | joaander/hoomd-blue | hoomd/custom/custom_operation.py | Python | bsd-3-clause | 6,875 | [
"HOOMD-blue"
] | 0c54c0ead4698d0a34faa6f4384ba7d0736359ec578b821970a4583b1d33ebe0 |
__author__ = 'watson-parris'
from cis.data_io.products.HadGEM import HadGEM_PP
import logging
class HadGEM_unknown_vars(HadGEM_PP):
def get_variable_names(self, filenames, data_type=None):
import iris
import cf_units as unit
from cis.utils import single_warnings_only
# Removes war... | duncanwp/cis_plugins | hadgem_unknown_vars.py | Python | lgpl-3.0 | 2,736 | [
"NetCDF"
] | d5a96b585a64ad98a0fbbe3c26846e37a8ca3193ef149e183481d69aa5e0b243 |
from datetime import datetime
from django.db import IntegrityError
from django.http import HttpResponse
from django.shortcuts import render, redirect
from django.contrib.auth.decorators import login_required
from rango.models import Category, Page, UserProfile, User
from rango.forms import CategoryForm, PageForm, Use... | apenchev/tangowithdjango | rango/views.py | Python | mit | 12,248 | [
"VisIt"
] | abdb0a99feed7f7a16fc8e157c598ac9237e6722633b10490f187c7742692d88 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2010 Nick Hall
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of th... | pmghalvorsen/gramps_branch | gramps/plugins/tool/ownereditor.py | Python | gpl-2.0 | 7,171 | [
"Brian"
] | 025991e87d553e4f1f403f056ad66023eb7600d97a046e3f43ff102e708f63c7 |
# Copyright 2020 The TensorFlow Probability 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 applicable law o... | tensorflow/probability | tensorflow_probability/python/distributions/normal_inverse_gaussian.py | Python | apache-2.0 | 11,258 | [
"Gaussian"
] | bb57c8c33b974e5359b8dab3d6e73c66f12a09779239f1016bddc03c0544ba14 |
"""
Test experiments. Logging is disabled, so just check the directory and log
files creation.
"""
import asyncio
import numpy as np
import os.path as op
import tempfile
import shutil
from concert.quantities import q
from concert.coroutines.base import start
from concert.coroutines.sinks import Accumulate
from concert.... | ufo-kit/concert | concert/tests/integration/test_experiments.py | Python | lgpl-3.0 | 9,086 | [
"VisIt"
] | ff4fa6121aeae5254b40c44201c7ec3dfb909e5f7873cf30e4c097dc17079e8e |
# -*- coding: utf-8 -*-
"""Factories for the OSF models, including an abstract ModularOdmFactory.
Example usage: ::
>>> from tests.factories import UserFactory
>>> user1 = UserFactory()
>>> user1.username
fred0@example.com
>>> user2 = UserFactory()
fred1@example.com
Factory boy docs: http://f... | GaryKriebel/osf.io | tests/factories.py | Python | apache-2.0 | 13,123 | [
"Brian"
] | c3e340049f559592ed3ca767a338d096bf1e4d710d92578da6b90eedce17f44e |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Emacs: treat this as -*- python -*-
from optparse import OptionParser
parser = OptionParser(usage='%prog [options]',
version='%prog 0.1')
parser.add_option('--dir', dest="dir",
default='.',
help='Results directo... | robwarm/gpaw-symm | doc/devel/memory_bandwidth/memory_bandwidth.py | Python | gpl-3.0 | 10,119 | [
"ASE",
"GPAW"
] | 8aec224745f29a648051c27c1a7a601cf9a9f5337fe28aaa9939c35a630df051 |
"""
Acceptance tests for Studio's Course Name(Course display name) Length
"""
from .base_studio_test import StudioCourseTest
from ...pages.studio.ga_course_rerun import CourseRerunPage
from ...pages.studio.ga_index import DashboardPage
from ...pages.studio.settings_advanced import AdvancedSettingsPage
class CourseN... | nttks/edx-platform | common/test/acceptance/tests/studio/test_ga_studio_course_name.py | Python | agpl-3.0 | 3,084 | [
"VisIt"
] | 41d0182f6d349d90c5f74e60fe40a00bfdc5802a7b064a45f357d9d9799b2f6c |
import mwmatching
#import ortools - import the bits we need from it only
from ortools.constraint_solver import pywrapcp
from ortools.constraint_solver import routing_enums_pb2
import exagony
import weightings
import initial_rankings as initial_rankings
from operator import itemgetter
topN_ = ['United States','Canada'... | aoanla/RDWC2018 | scheduler-delta.py | Python | gpl-3.0 | 13,310 | [
"EPW"
] | 847fd0e66d10821dc3fce0f32ab45dce8fad62d5c0ec3f92edd21a0a03849295 |
"""
Sheets for simulating a moving eye.
This module provides two classes, ShiftingGeneratorSheet, and
SaccadeController, that can be used to simulate a moving eye,
controlled by topographic neural activity from structures like the
superior colliculus.
ShiftingGeneratorSheet is a subclass of GeneratorSheet that accept... | jesuscript/topo-mpi | topo/sheet/saccade.py | Python | bsd-3-clause | 13,111 | [
"Gaussian"
] | 72312e4d3d7ffa8c9a46b52ad55effdef96d4be19abe2f8ee7192468c07cba73 |
# for python 3
# You'll need to customize this according to your needs. Proper orientation of
# the kinect is vital; if participants are able to maintain their head or wrists
# continuously inside the word rects, they will repeatedly trigger the collision
# detection
from pykinect2 import PyKinectV2
from pykinect2.PyKi... | jgerschler/ESL-Games | Kinect/Sentence Builder/Deprecated/SentenceBuilderFullScreen.py | Python | mit | 10,652 | [
"VisIt"
] | a1caa228e140e3161ae3ccef0d9a3ad99d435a7b325244a2c1b29d1b22e042b8 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""Tools and helper functions for abinit calculations"""
from __future__ import unicode_literals, division, print_function
import os
import six
import re
import collections
import shutil
import operator
import ... | matk86/pymatgen | pymatgen/io/abinit/utils.py | Python | mit | 27,984 | [
"ABINIT",
"NetCDF",
"pymatgen"
] | 45672cd2b7eef975589eef1524b747667ef68fdcf1095fe81afcef9157c9a6e0 |
import logging
import os
from multiprocessing import Process
from pysam import AlignmentFile
from PyMaSC.core.mappability import BWFeederWithMappableRegionSum
from PyMaSC.core.ncc import NaiveCCCalculator, ReadUnsortedError
from PyMaSC.core.mscc import MSCCCalculator
from PyMaSC.handler.mappability import Mappability... | ronin-gw/PyMaSC | PyMaSC/handler/masc_worker.py | Python | mit | 7,557 | [
"pysam"
] | aa289a1e17940d8c7272bd480840340b3642fc08880a108239e20b50e154b3c7 |
from plotly.basedatatypes import BaseTraceHierarchyType as _BaseTraceHierarchyType
import copy as _copy
class Marker(_BaseTraceHierarchyType):
# class properties
# --------------------
_parent_path_str = "scatter"
_path_str = "scatter.marker"
_valid_props = {
"autocolorscale",
"ca... | plotly/python-api | packages/python/plotly/plotly/graph_objs/scatter/_marker.py | Python | mit | 57,787 | [
"Bowtie"
] | 86600dc43a4255ef494c5fb060986c7682c3e01bc59b6f07a8ad96df18c46eaf |
import OpenGL.GL as gl
import OpenGL.arrays.vbo as glvbo
import gl_program
class SpikeProgram(gl_program.GLProgram):
"""Render a series of ints as white dots."""
def __init__(self, width, height):
self.width = width # size of the grid
self.height = height # size of the grid
s... | tcstewar/opengl_texture_rendering | sparkle/spiker.py | Python | gpl-2.0 | 2,337 | [
"NEURON"
] | 10fb1d3dfa1ffaa877b31aa1a0c3df4c950ea6f953e804ae2ad75e10e4dda32d |
# Copyright 2008 Brian Boyer, Ryan Mark, Angela Nitzke, Joshua Pollock,
# Stuart Tiffen, Kayla Webley and the Medill School of Journalism, Northwestern
# University.
#
# This file is part of Crunchberry Pie.
#
# Crunchberry Pie is free software: you can redistribute it and/or modify
# it under the terms of the GNU Gene... | brianboyer/newsmixer | pie/profiles/tests.py | Python | gpl-3.0 | 6,762 | [
"Brian"
] | 134b73763a24a9b9a550e2100d157497a07609126eefbcc8f26ba89c1ed3214b |
########################################################################
# $HeadURL$
# File: RequestTests.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2012/07/24 10:23:40
########################################################################
""" :mod: RequestTests
=======================
.. module: R... | calancha/DIRAC | RequestManagementSystem/test/RequestTests.py | Python | gpl-3.0 | 18,416 | [
"DIRAC"
] | 08b0f62efd88bb7d3edf2d7cb5be02463a500aa0a49fd3c6a79f3d71189ea6f8 |
"""
This module provides functions to perform full Procrustes analysis.
This code was originally written by Justin Kucynski and ported over from
scikit-bio by Yoshiki Vazquez-Baeza.
"""
import numpy as np
from scipy.linalg import orthogonal_procrustes
__all__ = ['procrustes']
def procrustes(data1, data2):
r""... | pizzathief/scipy | scipy/spatial/_procrustes.py | Python | bsd-3-clause | 4,400 | [
"scikit-bio"
] | 66707c3f40a34d724909def4d86c5c4231cd9c70b19955479bbbcc8793968ba0 |
import ast
import itertools
from types import FunctionType
from myhdl._util import _flatten
from myhdl._enum import EnumType
from myhdl._Signal import SignalType
class Data():
pass
def _resolveRefs(symdict, arg):
gens = _flatten(arg)
data = Data()
data.symdict = symdict
v = _AttrRefTransformer(... | myhdl/myhdl | myhdl/_resolverefs.py | Python | lgpl-2.1 | 2,454 | [
"VisIt"
] | 5f618448e418c859e2d83eb49085d475f3891c1121d0cd98d485bbfde12654ca |
from __future__ import absolute_import
import fluent.syntax.ast as FTL
from fluent.migrate.helpers import transforms_from
from fluent.migrate.helpers import VARIABLE_REFERENCE, TERM_REFERENCE
from fluent.migrate import REPLACE, COPY
what_is_a_browser = "firefox/browsers/what-is-a-browser.lang"
what_is_a_browser = "moz... | MichaelKohler/bedrock | lib/fluent_migrations/firefox/browsers/what-is-a-browser.py | Python | mpl-2.0 | 10,903 | [
"VisIt"
] | 38dd63da01976dcd642065d2ef300f3e2f3b2e5204bb0c6022d4f8d308e78e20 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Spectral feature extraction"""
import numpy as np
import scipy
import scipy.signal
import scipy.fftpack
from .. import util
from .. import filters
from ..util.exceptions import ParameterError
from ..core.convert import fft_frequencies
from ..core.audio import zero_cro... | bmcfee/librosa | librosa/feature/spectral.py | Python | isc | 60,885 | [
"Gaussian"
] | fbf98cc6f3d142c18ab4511cbc06f9acb38f5185074d948c8d98607b024e7642 |
"""
Data-driven tests for reads
"""
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import collections
import ga4gh.backend as backend
import ga4gh.datamodel as datamodel
import ga4gh.datamodel.datasets as datasets
import ga4gh.datamodel.reads as reads
imp... | srblum/server | tests/datadriven/test_reads.py | Python | apache-2.0 | 16,781 | [
"pysam"
] | 537bc858e0eb354f889ee9ef3d7f01927895062d37bc604320b797f8ccec6c21 |
import os
import unittest
from polycircles import polycircles
import simplekml
from geographiclib import geodesic
class TestKMLs(unittest.TestCase):
"""Tests the KML representation of the Polycircles using the simplekml
package."""
def setUp(self):
self.output_dir = 'polycircles/test/kmls'
... | adamatan/polycircles | polycircles/test/test_kmls.py | Python | mit | 5,506 | [
"COLUMBUS"
] | eea8e6acf353e48690f1473b8e83df34941e497d5af08731a64d1ea8ee9c1c31 |
import urllib2
import html2text
import re
import numpy as np
import json
from scipy.optimize import curve_fit
try:
import matplotlib as matplot
matplot.use('Agg')
import matplotlib.pyplot as mpl
plottingEnabled = True
except:
print "Matplotlib not detected, plotting disabled"
plottingEnabled = ... | schollz/webcontentgrabber | context_extractor.py | Python | mit | 4,936 | [
"Gaussian"
] | edc33215a76e241967f342daf3aa928f7999f5fddb213bd1fa45bd3c00eb390b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright 2010 British Broadcasting Corporation and Kamaelia Contributors(1)
#
# (1) Kamaelia Contributors are listed in the AUTHORS file and at
# http://www.kamaelia.org/AUTHORS - please extend this file,
# not this notice.
#
# Licensed under the Apache License... | sparkslabs/kamaelia_ | Sketches/JL/IRC/KambotIRC.py | Python | apache-2.0 | 13,785 | [
"DIRAC"
] | 2870a5d3957639be205d78825b3d92f7c106af1e8abb505561dfe74b15e3b447 |
##################################################################
# Copyright 2018 Open Source Geospatial Foundation and others #
# licensed under MIT, Please consult LICENSE.txt for details #
##################################################################
import unittest
import lxml.etree
import json
impor... | tomkralidis/pywps | tests/test_execute.py | Python | mit | 23,233 | [
"NetCDF"
] | 14de8a1a8544061e40d32eb29d7544961a4b5019db509485fb90bb806da04fdd |
from rrpam_wds.gui import set_pyqt_api # isort:skip # NOQA
import logging
import os
import time
import mock
import rrpam_wds.constants as c
from rrpam_wds.examples import networks
from rrpam_wds.gui.dialogs import DataWindow
from rrpam_wds.gui.dialogs import MainWindow
from rrpam_wds.gui.dialogs import RiskMatrix
fr... | asselapathirana/RRPam-WDS | src/rrpam_wds/tests/test_datawindow2.py | Python | gpl-3.0 | 15,764 | [
"ADF"
] | e3f053d51df8a34edf258ce4994613bb62c68da71df45631590c49103e670cb4 |
# Copyright 2012 Patrick Varilly
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is di... | patvarilly/units_and_physics | units.py | Python | gpl-3.0 | 7,364 | [
"Gromacs"
] | 964c41db3040a6985e62979130ef26c8d415f88ac71977ee981d69b04d933910 |
"""
==================
tao.ui_modules
==================
Helper class to extension UI modules
"""
from django.conf import settings
from tao.record_filter_form import RecordFilterForm
from tao.output_format_form import OutputFormatForm
from tao.sql_job_form import SQLJobForm
from tao.models import Simulation, GalaxyMod... | IntersectAustralia/asvo-tao | web/tao/ui_modules.py | Python | gpl-3.0 | 4,349 | [
"Galaxy"
] | 0796bfb382af1b596319368b506090104e34084eb27abfcd806918bb98141548 |
""" MQProducer
"""
from DIRAC import gLogger
from DIRAC.Resources.MessageQueue.Utilities import getDestinationAddress, getMQService
class MQProducer(object):
def __init__(self, mqManager, mqURI, producerId):
self._connectionManager = mqManager
self._mqURI = mqURI
self._destination = getDes... | DIRACGrid/DIRAC | src/DIRAC/Resources/MessageQueue/MQProducer.py | Python | gpl-3.0 | 1,290 | [
"DIRAC"
] | 73590d02ef901bd902fdd73766b22b6a2be9c37c544cf164d2fc0b8a60ebd36b |
#
# @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/driver/qcdb/__init__.py | Python | gpl-2.0 | 1,840 | [
"CFOUR",
"ORCA",
"Psi4"
] | f9a567201c912bfea1d4397407cacc034e041d52bd86dbd57182361915dd3389 |
# coding=utf-8
# Copyright 2022 The Google Research 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 applicab... | google-research/google-research | readtwice/layers/tensor_utils.py | Python | apache-2.0 | 20,218 | [
"Gaussian"
] | ea21eeebcfffbc19363c638868a9f66d94934ab374e6db2168cdebd522d57896 |
import spynnaker.pyNN as Frontend
import spynnaker_external_devices_plugin.pyNN as ExternalDevices
import pylab
Frontend.setup(timestep=1.0, min_delay=1.0, max_delay=144.0)
nNeurons = 256
run_time = 5000
cell_params_lif = {'cm' : 0.25, # nF
'i_offset' : 0.0,
'tau_m' ... | svadams/SpinnIOTest | examples/injection_test.py | Python | gpl-3.0 | 2,141 | [
"NEURON"
] | a5002dc9987d61f2f432ab15860ca6d41a9181bf751dd9ebded5a1d885068bd3 |
"""
Unittest classes for the asciidata module
@author: Martin Kuemmel, Jonas Haase
@organization: Space Telescope - European Coordinating Facility (ST-ECF)
@license: Gnu Public Licence
@contact: mkuemmel@eso.org
@since: 2005/09/13
$LastChangedBy: jhaase $
$LastChangedDate: 2008-02-27 16:45:36 +0100 (Wed, 27 Feb 2008)... | COSMOGRAIL/COSMOULINE | pipe/modules/asciidata/asciidata_test.py | Python | gpl-3.0 | 59,791 | [
"Galaxy"
] | 9cfa247211325ebd0995d8dd8f7939417d2cd63986f64a89170c398fcdf2a01c |
#!/usr/bin/env python3
#
# netcdf_to_vtk
#
# Converts a netCDF file into a VTK file. The format of the VTK file
# follows the 'legacy format' and will be a structured grid. In case
# the input file consists of multiple time steps, every time step is
# stored as a separate VTK file, with an appropriate suffix.
#
# This ... | Submanifold/Aleph | utilities/netcdf_to_vtk.py | Python | mit | 2,374 | [
"NetCDF",
"VTK"
] | 78a5868468c0be0ce944131184d9ad96dd1c1a161ea79bdb8e46e6eeed440cbc |
'''
# This script is an example of calculation of long range interactions
# (Coulomb interaction) using the Ewald summation and the P3M methods.
#
# Initially, the simple cubic structure is generated in order to represent the
# NaCl crystal. Then the energy and forces are calculated and compared using both
# the... | fedepad/espressopp | examples/electrostatics/electrostatics_example.py | Python | gpl-3.0 | 8,975 | [
"CRYSTAL",
"VMD"
] | 11c0ac1ffceb16c63b5483db8821190b276345800a52ed4423de7cf96883a704 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2008 Douglas S. Blank
# Copyright (C) 2010 Jakim Friant
#
# This program is free software; you can redistribute it and/or modify
# it under the term... | Forage/Gramps | gramps/plugins/gramplet/descendgramplet.py | Python | gpl-2.0 | 6,319 | [
"Brian"
] | e6d8a6ef3fb1cff9e890607d20f38b9b6225266126fdb50d3f949a54595fdbe6 |
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Matti Hamalainen <msh@nmr.mgh.harvard.edu>
# Denis A. Engemann <denis.engemann@gmail.com>
#
# License: BSD (3-clause)
import copy as cp
import os
from math import floor, ceil, log
import itertools as itt
import warnings
import ... | trachelr/mne-python | mne/cov.py | Python | bsd-3-clause | 70,653 | [
"Gaussian"
] | d3aadc23d1012cba652225da3bf6251ff5ab021018004f197d49d5a24cb4bf27 |
"""
Example 4, to be run in python. In this example, we fit the CO
emission using the data made from Ex2 (which you should be
able to download from the same place you got this script).
For these data, I just fixed the lens properties to those
we got from the ALMA 870um data, because the ALMA data have
way highe... | jspilker/visilens | examples/Ex4_fit_line_SPT0346-52_CO21.py | Python | mit | 4,931 | [
"Gaussian"
] | 151aafe17b328070cd2203d302ece47e7cb40342323b117898a2e4969912c308 |
import ast
import itertools
import logging
import os.path
from pkgutil import iter_modules
from .alias_helper import (
as_alias_handler,
fully_qualify_alias_labels,
handle_aliases_in_init_files,
handle_fdid_aliases,
not_as_alias_handler,
retrieve_import_alias_mapping
)
from ..core.ast_helper im... | python-security/pyt | pyt/cfg/stmt_visitor.py | Python | gpl-2.0 | 42,406 | [
"VisIt"
] | 863544d4899de8fa322719a25424c88ecbb9859e3761b206e91831888e847699 |
# coding=utf-8
# --------------------------------------------------------------------------------------------
# Copyright (c) Microsoft Corporation. All rights reserved.
# Licensed under the MIT License. See License.txt in the project root for license information.
# -----------------------------------------------------... | yugangw-msft/azure-cli | src/azure-cli/azure/cli/command_modules/network/_help.py | Python | mit | 299,402 | [
"VisIt"
] | 5720c174c2d30ee3b51321dcca2c0301fd25c495ee1263c61adc3f8e38898336 |
# 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 ... | dukhlov/oslo.messaging | oslo_messaging/hacking/checks.py | Python | apache-2.0 | 13,278 | [
"VisIt"
] | 1d89622b1255da040ebe886390c89dc693d6987a4883b2e827ad636a66fe1659 |
"""
Peak picking routines, lineshape parameter guessing, and related functions.
"""
# external modules
import numpy as np
import scipy.ndimage as ndimage
# analysisbase fuctions
from analysisbase import ndwindow_index,valid_pt
# lineshape classes
from lineshapes1d import gauss, ls_str2class
# spectral segmentatio... | odyaka341/nmrglue | nmrglue/analysis/peakpick.py | Python | bsd-3-clause | 18,506 | [
"Gaussian"
] | 374bb195c0df73e930e3d06a189ff3ec01831d502378603cf73669b5f65d5b60 |
#!/usr/bin/env python
"""
findUnannotated.py
Author: Tony Papenfuss
Date: Fri Aug 15 12:19:24 EST 2008
"""
import os, sys
from bx.intervals.intersection import *
from fasta import FastaFile
from blast import BlastFile
from useful import progressMessage
print "Load Solexa contigs & store as Intervals in an Interse... | PapenfussLab/Srtools | bin/old/findUnannotated.py | Python | artistic-2.0 | 2,499 | [
"BLAST"
] | e0d87d9e0d523a1a29fb581331b093c704f68d650137e166ec10f1306151d832 |
import six
import lxml.etree
from .parser import CustomParser as Parser
from .xmlvisitor import XmlVisitor
from .jsonlike import *
_parser = Parser()
_visitor = XmlVisitor()
def parse(text, encoding="utf8", debug=False):
if not isinstance(text, six.text_type):
text = text.decode(encoding)
tree = _pa... | sgornick/obscrape | js2xml/__init__.py | Python | mit | 498 | [
"VisIt"
] | 05beb7bad823a4f6e1ed889f907199bc98f0c231aadf62af5c517d8ee78eb25a |
#!/usr/bin/env python
"""Module to run orthoMCL. Steps in this module reflect the steps in the UserGuide.txt bundled with OrthoMCL."""
from Bio import SeqIO
import argparse
import multiprocessing
import os
import shutil
from subprocess import Popen, PIPE, CalledProcessError, check_call, STDOUT
import tempfile
import ... | ODoSE/odose.nl | run_orthomcl.py | Python | mit | 20,897 | [
"BLAST"
] | 4c5bc9864927947a906b9fa44e6542e81eb4ce4fbecd37600fb2a27bb07b5b78 |
"""
Test the coordinates class that represents the plane of orbit of the Sgr dwarf galaxy.
"""
# Third-party
import astropy.coordinates as coord
import astropy.units as u
from astropy.io import ascii
from astropy.table import Table
from astropy.utils.data import get_pkg_data_filename
import numpy as np
# This pro... | adrn/gala | gala/coordinates/tests/test_orphan.py | Python | mit | 2,147 | [
"Galaxy"
] | d75f8935806981491c3b7594b65ad3e901f546204f4edeefd85d3eefea699def |
#!/usr/bin/env python
#-*- coding: utf-8 -*-
#python imports
from sys import exit
from os import remove, path
try:
from hashlib import sha1 as new_sha
except ImportError:
from sha import new as new_sha
from urlparse import urljoin
#project imports
from session import Session
from dbconnection import dbConnect... | cria/microSICol | py/modules/form_del.py | Python | gpl-2.0 | 22,905 | [
"VisIt"
] | 907dc762b5709cbc929b6b21e747134db6d43aeebf824836d51dc4fccea9cc3c |
#!/usr/bin/python
#=============================================================================================
# MODULE DOCSTRING
#=============================================================================================
"""
Alchemical factory for free energy calculations that operates directly on OpenMM swig S... | choderalab/brokenyank | src/yank/alchemy.py | Python | lgpl-3.0 | 45,113 | [
"OpenMM"
] | 54fca4014c8fe07729a33aeaefd3a8141221b540b782bb7904cbec9b1b935022 |
# coding=utf-8
from __future__ import unicode_literals
from .version import __version__
from datetime import datetime
BCTPY = """
@misc{{bctpy,
publisher = {{GitHub}},
title = {{bctpy v{version}: Brain Connectivity Toolbox for Python}},
url = {{https://github.com/aestrivex/bctpy}},
author = {{LaPlante,... | aestrivex/bctpy | bct/citations.py | Python | gpl-3.0 | 13,894 | [
"Desmond"
] | 846117ed08e065aeecd10d0133860d0e2ff6acff88cee09ffefcbf29b68d038c |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | anderspitman/scikit-bio | skbio/io/_exception.py | Python | bsd-3-clause | 2,510 | [
"scikit-bio"
] | 8e1ccc6cac46b08207bb917cfcc556ba11b31c1c9f1af9fb5f3f081c804ad013 |
####
#
# Copyright (c) 2015, Jake Vanderplas, Luke Siemens
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright
# notice, this list... | lsiemens/iprocess-projects | psipy/animate_analytic.py | Python | bsd-3-clause | 5,466 | [
"Gaussian"
] | 081644f14032d9ac3d8a36cdd3c9da245b8d144b1aa43c4dfe83e624cd61c5c2 |
# Author: Samuel Genheden samuel.genheden@gmail.com
"""
Classes to perform actions on MD trajectories
"""
import os
from collections import namedtuple
import MDAnalysis as md
import MDAnalysis.core.AtomGroup as AtomGroup
import MDAnalysis.analysis.align as align
import MDAnalysis.lib.util as mdutil
import numpy as n... | SGenheden/Scripts | sgenlib/mdactions.py | Python | mit | 58,085 | [
"MDAnalysis"
] | 464aea36783ca7fd9f9a915d4ec8f71bddc4a2921d2fd9e7162b550d00ec1b3c |
## appsterdam twitter data
## usage: we open a csv file with names of companies or phenomenon that are
## of interest to the amsterdam tech community. these subjects are
## searched on twitter. the tweets will give us a new list of users and
## hashtags. these will be searched again and... | InnoViz/innoviz-frontend | app/data miner scripts/TWITTER GRAPH/twitter_miner.py | Python | mit | 6,330 | [
"Cytoscape"
] | 8d0a24dbd7573e21ccd50b3f6984c89bfd14ff382aca714c2dbed8f69d21e9df |
from glue.core.fitters import BaseFitter1D
from glue.core.simpleforms import IntOption
from glue.config import fit_plugin
import numpy as np
import emcee
def gaussian(x, mean, amplitude, stddev):
return np.exp(-(x - mean) ** 2 / (2 * stddev ** 2)) * amplitude
def lnprob(param, x, y, dy):
# mean, amplitude,... | stscieisenhamer/glue | doc/gui_guide/emcee_plugin.py | Python | bsd-3-clause | 2,842 | [
"Gaussian"
] | 0b8ee83141a3120b5d7042f9edc14bb7a1d8b5acd592fb3eb4bc01073979581b |
# -*- coding: utf-8 -*-
#
# Copyright (C) 2008-2010 Edgewall Software
# All rights reserved.
#
# This software is licensed as described in the file COPYING, which
# you should have received as part of this distribution. The terms
# are also available at http://genshi.edgewall.org/wiki/License.
#
# This software consist... | davidfraser/genshi | genshi/template/astutil.py | Python | bsd-3-clause | 24,465 | [
"VisIt"
] | 72c4d39e9c220e42422b4f7cfe68fe70833d03c185cb64f3fad5965153876030 |
""" Contains the parent classes Platform"""
# platform.py
# Mission Pinball Framework
# Written by Brian Madden & Gabe Knuth
# Released under the MIT License. (See license info at the end of this file.)
# Documentation and more info at http://missionpinball.com/mpf
import time
class Platform(object):
"""Parent ... | jabdoa2/mpf | mpf/system/platform.py | Python | mit | 10,382 | [
"Brian"
] | b5a14cf9065808d85a6d8a8e24682e0b972db24d25e8408daf200c3d8a0e0e6c |
# Author: Samuel Ponc\'e
# Date: 30/04/2013 -- 11/09/2014
# Version 1.3
# Classes needed for the temperature.py script
# Last devel info: Dynamical coding done
import numpy as N
from numpy import zeros
import itertools as Iter
from functools import partial
import multiprocessing
import netCDF4 as nc
import sys
import ... | jmbeuken/abinit | scripts/deprecated/rf_mods_seq.py | Python | gpl-3.0 | 51,849 | [
"NetCDF"
] | 0f69a1d74fa711f01633ffcebdef058c0d7bb1310c1e14f97f9275175d352b3a |
# Network class.
from scipy.special import expit
import numpy as np
import pyperclip
import screenPixel
import pyautogui as pg
import random
import re
import os
'''
inp nodes hidden nodes exit nodes
100 20 2
'''
class network:
def mutate(self,x):
if(np.random.rand() < self.mutationRate)... | Chrisr850/Snake.io-player | network.py | Python | mit | 4,997 | [
"NEURON"
] | 9b60233f748df137aa262f5f1fb73d5b1ddd9b5ba6f18487854ee0419009cd17 |
#!/usr/bin/python2
import sys
from collections import OrderedDict
# Daniel Elsner
#Takes a tabular blast results file (outfmt 6), reduced to the the three colums query, hit and score (use "cut", from GNU coreutils, presumably included in most Linux distros), to obtain the score of each relevant pairwise comparison.
... | dewuem/python-bioinf | orthology-and-selection/obtain-blast-score-construct-clusters-short.py | Python | mit | 6,045 | [
"BLAST"
] | 38d51c0d48ce7c8c54de928ed071d02e5ddea1c6ed09a1bfb4ba137d3f8c4d52 |
"""
(c) RIKEN 2017. All rights reserved.
Author: Keitaro Yamashita
This software is released under the new BSD License; see LICENSE.
"""
import iotbx.phil
from cctbx import sgtbx
from dxtbx.model.experiment_list import ExperimentListFactory
from dxtbx.model.experiment_list import ExperimentListDumper
from dxtbx.model... | keitaroyam/yamtbx | yamtbx/dataproc/dials/command_line/import_xds_for_refine_stills.py | Python | bsd-3-clause | 11,464 | [
"CRYSTAL"
] | 14d6ca1fb1f5457cc22e2bd798e8bf57523186fb58244b34b68000fbb2c54cfa |
# ################################################################
#
# Active Particles on Curved Spaces (APCS)
#
# Author: Silke Henkes
#
# ICSMB, Department of Physics
# University of Aberdeen
# Author: Rastko Sknepnek
#
# Division of Physics
# School of Engineering, Physics and Mathem... | sknepneklab/SAMoS | analysis/batch_nematic/batch_analyze_nematic_R8.py | Python | gpl-3.0 | 2,346 | [
"VTK"
] | a60b69f776c8d624de7281bb1bfdb448d15c8cfa046e197326c463839a90de9c |
######################################################################
# Copyright (C) 2013-2014 Jaakko Luttinen
#
# This file is licensed under Version 3.0 of the GNU General Public
# License. See LICENSE for a text of the license.
######################################################################
###############... | nipunreddevil/bayespy | bayespy/inference/vmp/nodes/node.py | Python | gpl-3.0 | 40,101 | [
"Gaussian"
] | e483a01f5ea979876d5576cd0d505aded47fddebdf474c9cd4eafdca8111adfd |
import inspect
import sys
from .formatting import format_filename
from .xtracebackframe import XTracebackFrame
class XTracebackExc(object):
def __init__(self, etype, value, tb, xtb):
"""
:param value: The exception instance
:type value: Exception
:param tb: The traceback instanc... | 005/xtraceback | xtraceback/xtracebackexc.py | Python | mit | 4,469 | [
"xTB"
] | ab9317ec24c25ff5f8d210d54182cbe39b5f8bacdd5af13608f078984bd41640 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# This file is part of the SPORCO package. Details of the copyright
# and user license can be found in the 'LICENSE.txt' file distributed
# with the package.
"""
Greyscale ℓ2-TV Denoising
=========================
This example demonstrates the use of class :class:`.tvl2.T... | alphacsc/alphacsc | alphacsc/other/sporco/examples/scripts/tv/tvl2dcn_den.py | Python | bsd-3-clause | 2,902 | [
"Gaussian"
] | 861f82b28cefc6facbf15d6c13f297626962b5cd0e532c9049db53c9cb4765c8 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 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 ... | kratman/psi4public | tests/reap.py | Python | gpl-2.0 | 6,615 | [
"Psi4"
] | 8ecacb3181d56b2528d1aa71336bdf5263b6d692e71f5a54486fa75cd06d5c3a |
from __future__ import division
from cctbx.array_family import flex
from cctbx import crystal, sgtbx
from cctbx import covariance, geometry
import model
from libtbx.utils import format_float_with_standard_uncertainty \
as format_float_with_su
from libtbx import adopt_init_args
import math
class distances_as_cif... | stefsmeets/topas_tools | topas_tools/cif/geometry.py | Python | gpl-2.0 | 9,578 | [
"CRYSTAL"
] | e153e5a24969df4819f4115ed19bc60db1a4921e33b7128c369fe55d5198efe3 |
# coding=utf-8
# Copyright 2022 The Edward2 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 applicable law o... | google/edward2 | edward2/tensorflow/layers/hetsngp_test.py | Python | apache-2.0 | 4,417 | [
"Gaussian"
] | 4ce3c437186edbf4599d005fb83d898c5d97cf09f98e6962ead77d5838fab782 |
r"""Gaussian process changes (CostNormal)"""
import warnings
import numpy as np
from numpy.linalg import slogdet
from ruptures.base import BaseCost
from ruptures.costs import NotEnoughPoints
class CostNormal(BaseCost):
"""Gaussian process change."""
model = "normal"
def __init__(self, add_small_diag=T... | deepcharles/ruptures | src/ruptures/costs/costnormal.py | Python | bsd-2-clause | 2,222 | [
"Gaussian"
] | e8e31053c097c3a52dc781a66ae70930f808254ad9451626d4a5d31f3d6dedfb |
# Copyright (C) 2001-2006 Quantum ESPRESSO group
# This file is distributed under the terms of the
# GNU General Public License. See the file `License'
# in the root directory of the present distribution,
# or http://www.gnu.org/copyleft/gpl.txt .
#
# Author: Filippo Spiga (spiga.filippo@gmail.com)
# Date: September 29... | fspiga/phiGEMM | scripts/addPhigemmSymbs.py | Python | gpl-2.0 | 1,821 | [
"Quantum ESPRESSO"
] | abc4a2d75e1933ec23f475bc953aebacc23e27d8b70dc3902eaf79da789c660f |
# Hidden Markov Model Implementation
import pylab as pyl
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy as scp
import scipy.ndimage as ni
import scipy.io
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import rospy
#import hrl_lib.mayavi2_util as mu
imp... | tapomayukh/projects_in_python | sandbox_tapo/src/skin_related/AI_Surface_Recognition/src/hmm_crossvalidation_force_7_states.py | Python | mit | 15,135 | [
"Gaussian",
"Mayavi"
] | 391d0e4a5d3f38162779f1c3e56eea0e5aa03757a71d40e9b8969c2e22fcf6ed |
# -----------------------------------------------------------------------------
# Download data:
# - Browser:
# http://midas3.kitware.com/midas/folder/10409 => VisibleMale/vm_head_mri.mha
# - Terminal
# curl "http://midas3.kitware.com/midas/download?folders=&items=235237" -o vm_head_mri.mha
# --------------... | Kitware/tonic-data-generator | scripts/vtk/medical/head-mri.py | Python | bsd-3-clause | 3,539 | [
"VTK"
] | b80901db9e0aee7821cd263a5071510dfcdc0f6d309fa9efe295e496e36afaa9 |
# vim: set fileencoding=utf-8 :
import unittest
import neuroml
import neuroml.writers as writers
import PyOpenWorm
import subprocess
from PyOpenWorm import *
import networkx
import rdflib
import rdflib as R
import pint as Q
namespaces = { "rdf" : "http://www.w3.org/1999/02/22-rdf-syntax-ns#" }
# Set up the database
... | mwatts15/PyOpenWorm | tests/test.py | Python | mit | 18,558 | [
"NEURON"
] | b6546f9fa5e0442499e9ce2623b738f534be2162b8f7f5c18edc920eeda8838e |
"""
HPHF via SGM
"""
import numpy as np
from frankenstein.sgscf import sgsphf
class SGHPHF(sgsphf.SGSPHF):
def __init__(self, pymol, **kwargs):
self.eta = 1
sgsphf.SGSPHF.__init__(self, pymol)
self.__dict__.update(kwargs)
if np.abs(self.eta) != 1:
raise ValueError... | hongzhouye/frankenstein | sgscf/sghphf.py | Python | bsd-3-clause | 1,292 | [
"PyMOL",
"PySCF"
] | 2674732e498af8ed2203ab7ec5fd4b6e64daf7fc6d7ac2063899df61f5d88e81 |
import json
import os
import sys
from functools import wraps
from typing import Any, Callable, Dict, Iterable, List, Optional, Set
from zulip import Client
from zerver.lib import mdiff
from zerver.models import get_realm, get_user
from zerver.openapi.openapi import validate_against_openapi_schema
ZULIP_DIR = os.path... | shubhamdhama/zulip | zerver/openapi/python_examples.py | Python | apache-2.0 | 39,351 | [
"Octopus"
] | e41cdd7d997edf36be0042fbe44980211496705e8d73dfe00a48005fef442bd9 |
# Change LogicalFile to be a wrapper for the DiracFile,
# make sure DiracFile replicates required functionality and add any
# possible translation layer here
from GangaCore.Core.exceptions import GangaException
from GangaCore.GPIDev.Schema import Schema, Version, SimpleItem, ComponentItem
from GangaDirac.Lib.Files.Dir... | ganga-devs/ganga | ganga/GangaLHCb/Lib/Files/LogicalFile.py | Python | gpl-3.0 | 4,419 | [
"DIRAC"
] | 8d3a209ef1477130a449a961389eb08788272c667eef0ebe1f35e4fe31516d1b |
# pylint: disable=R0913,R0914,W0201,W0622,C0302,R0902,R0903,W1001,W0612,W0613
"""Useful functions and objects used more or less everywhere."""
from __future__ import print_function
from builtins import zip
from builtins import str
from builtins import range
from builtins import object
__author__ = 'Lorenzo Bolla'
i... | demisjohn/EMpy | EMpy/utils.py | Python | mit | 40,698 | [
"CRYSTAL"
] | 527842535e38f8388fb807f7ea2fad50ac5962d9c8cf88786f833d71311e2173 |
"""
Application to explore the difference between sasview 3.x orientation
dispersity and possible replacement algorithms.
"""
import mpl_toolkits.mplot3d # Adds projection='3d' option to subplot
import matplotlib.pyplot as plt
from matplotlib.widgets import Slider, CheckButtons
from matplotlib import cm
import numpy... | SasView/sasmodels | explore/angular_pd.py | Python | bsd-3-clause | 5,217 | [
"Gaussian"
] | 5d6dc309f8a98f3a50fb42bd4fadfd3f1b85557eaf30f4e17303506622ad9c71 |
from __future__ import division, print_function, absolute_import
class FirstNames(object):
def __init__(self):
self.names = set(['john', 'william', 'james', 'charles', 'george', 'frank',
'joseph', 'thomas', 'henry', 'robert', 'edward', 'harry', 'walter', 'arthur',
'fred', 'albert', 'samuel', 'david',... | robert-giaquinto/text-analysis | src/clean_journal/first_names.py | Python | mit | 82,014 | [
"Amber",
"Brian",
"COLUMBUS",
"CRYSTAL",
"Dalton",
"Desmond",
"MOE"
] | 45c1d478d62b763c53decbd93288a0eab32b21ef48c3439870db0bad4cdfc809 |
print "Importing..."
from enthought.mayavi import mlab
from enthought.mayavi.filters.warp_scalar import WarpScalar
from enthought.mayavi.modules.surface import Surface
from numpy import array
from glob import glob
import re
print " done."
frames = glob("output/frame_scal*.vtk")
frames.sort()
max_frame_number = int(re... | certik/mhd-hermes | vis_scal.py | Python | bsd-3-clause | 1,560 | [
"Mayavi",
"VTK"
] | 550eedefdd144bfa95199c73605542ae7e79bc7b814cd6ac20fbd909e112e7b8 |
# -*- coding: utf-8 -*-
"""
Helper functions for auxiliary pseudo marginal MCMC Gaussian process
classification experiments.
"""
__authors__ = 'Matt Graham'
__copyright__ = 'Copyright 2015, Matt Graham'
__license__ = 'MIT'
import os
import datetime
import json
import numpy as np
from scipy.special import gammaln
impo... | matt-graham/auxiliary-pm-mcmc | gpdemo/utils.py | Python | mit | 8,482 | [
"Gaussian"
] | 448723f31df8533c99f1ca500a5211d3c69f9fa3032b9ef19c40a261a9d28f8c |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the courseware unit bookmarks.
"""
import json
from unittest import skip
import pytest
import requests
from common.test.acceptance.fixtures.course import CourseFixture, XBlockFixtureDesc
from common.test.acceptance.pages.common import BASE_URL
from common.test.acceptan... | a-parhom/edx-platform | common/test/acceptance/tests/lms/test_bookmarks.py | Python | agpl-3.0 | 22,195 | [
"VisIt"
] | 565d4c8a0d491b888421bfcc9bb1f0245c9eadf1015cd5e48347190f4248d295 |
"""Leetcode 130. Surrounded Regions
Medium
URL: https://leetcode.com/problems/surrounded-regions/
Given a 2D board containing 'X' and 'O' (the letter O),
capture all regions surrounded by 'X'.
A region is captured by flipping all 'O's into 'X's in that surrounded region.
Example:
X X X X
X O O X
X X O X
X O X X
A... | bowen0701/algorithms_data_structures | lc0130_surrounded_regions.py | Python | bsd-2-clause | 2,909 | [
"VisIt"
] | c393e9c6d03ed5cf8fee47c8775b07dbb2e0dce25917e23839ca2a573230fa48 |
# -*- coding: utf-8 -*-
"""Tests for input and output."""
import logging
import os
import re
import tempfile
import unittest
from io import BytesIO, StringIO
from pathlib import Path
import pybel
from pybel import (
BELGraph,
from_bel_script,
from_bel_script_url,
from_bytes,
from_nodelink,
fr... | pybel/pybel | tests/test_io/test_import.py | Python | mit | 19,541 | [
"Pybel"
] | cfadaa21803cf17b6ba15d8491ab9e88b53d88a10ec33c1e51bf4a2a79474825 |
#!/usr/bin/env python
import os
import re
import sys
import warnings
from setuptools import setup, find_packages
from setuptools import Command
MAJOR = 0
MINOR = 8
MICRO = 1
ISRELEASED = False
VERSION = '%d.%d.%d' % (MAJOR, MINOR, MICRO)
QUALIFIER = ''
DISTNAME = 'xarray'
LICENSE = 'Apache'
AUTHOR = 'xarray Develop... | NicWayand/xray | setup.py | Python | apache-2.0 | 4,681 | [
"NetCDF"
] | b68d90819f3c8f186174f508d7a2e2adec6d3cdcc37667bf619d0546155bfe77 |
"""
This sample simulates monovalent salt (equal number of positive and negative unit charges). Electrostatic interactions between charges is emulated by the Debye-Hueckel potential. The system is maintained at a constant temperature by using a Langevin thermostat.
"""
#
# Copyright (C) 2013-2018 The ESPResSo project
... | hmenke/espresso | samples/debye_hueckel.py | Python | gpl-3.0 | 6,610 | [
"ESPResSo"
] | 51691e7aeff05db57b1b81f361bee80759d329e31629faa402189e3e886bba90 |
import numpy as np
import matplotlib
import matplotlib.pyplot as plt
from fitFunctions import gaussian
import mpfit
import scipy.stats
import smooth
from util.ObsFile import ObsFile
from util.FileName import FileName
def smoothBaseline(baselines,nPtsInMode=400):
modBases = np.array(baselines)
for i in range(le... | bmazin/ARCONS-pipeline | examples/energyRes/obsR.py | Python | gpl-2.0 | 8,946 | [
"Gaussian"
] | dbcf4ba2f4c4b450ba3e7dea63af329d9a4d71ed80a82c90192cfa9967facff0 |
import psi4
import numpy as np
import random
mol = psi4.geometry("""
C
C 1 20
""")
primary = psi4.core.BasisSet.build(mol, "ORBITAL", "cc-pVDZ")
aux = psi4.core.BasisSet.build(mol, "ORBITAL", "cc-pVDZ-jkfit")
nbf = primary.nbf()
naux = aux.nbf()
# form metric
mints = psi4.core.MintsHelper(primary)
zero_bas = psi4.c... | rmcgibbo/psi4public | tests/df-helper/input.py | Python | lgpl-3.0 | 11,815 | [
"Psi4"
] | 6776a37c681d7a277107103bdf6ebe654fa59d351d2828fd18b4381e443f776e |
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