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from contextlib import suppress
from warnings import warn
import numpy as np
import pandas as pd
import statsmodels.api as sm
from scipy.stats import iqr
from ..mapping.evaluation import after_stat
from ..doctools import document
from ..exceptions import PlotnineError, PlotnineWarning
from .stat import stat
# NOTE:... | has2k1/plotnine | plotnine/stats/stat_density.py | Python | gpl-2.0 | 7,516 | [
"Gaussian"
] | 1b33b17e26688e7b276e2acda78e44d4f4d40a5b98c79e6b94d6348c6dc2187e |
#! /usr/bin/env python
### reciprocal_BLAST.py ################################################################
### By Geoffrey Thomson
### This script performs a nucleotide reciprocal BLAST on two fasta files input by the user.
### Draws heavily from the online tutorial (http://biopython.org/DIST/docs/tutorial/Tutor... | G-Thomson/GPyS | reciprocal_BLAST.py | Python | mit | 2,799 | [
"BLAST",
"Biopython"
] | 0a2fa4506a64c1bd4669a759cbc07915ae8ea5eccdb73f46a38f8f6d89ae4e66 |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-install-agent
# Author : Ricardo Graciani
########################################################################
"""
Do the initial installation and configuration of a DIRAC agent
"""
__RCSID_... | marcelovilaca/DIRAC | Core/scripts/dirac-install-agent.py | Python | gpl-3.0 | 3,729 | [
"DIRAC"
] | f95e0ce39b2471fc34f0c5d363b2dedc0e8bae8eacf216b042f2bf915bbc1e3d |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
r"""
GIMLi Basics
============
This is the first tutorial where we demonstrate the general use of
:term:`GIMLi` in Python, i.e., :term:`pyGIMLi`.
The modelling as well as the inversion part of :term:`GIMLi` often requires a
spatial discretization for the domain of intere... | gimli-org/gimli | doc/tutorials/1_basics/plot_1-gimli_basics.py | Python | apache-2.0 | 4,741 | [
"ParaView",
"VTK"
] | d6a884c69a0555edbc9e39dabc16d1107e63b258b9b5f7381af53636c47dd5c3 |
"""
Copyright (c) 2016 Gianluca Gerard
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
to use, copy, modify, merge, publish, distribute... | glgerard/cloud-mdbn | src/rbm.py | Python | apache-2.0 | 43,150 | [
"Gaussian"
] | 44fd1a81ddf7d3963a738fba5ea0aa42389b7eb66408ed89af3e4f875f20de3f |
from __future__ import unicode_literals
from django.contrib.auth.models import User
from django.db import models
from django.db.models import Q
from django.db.models.signals import m2m_changed
from django.dispatch import receiver
from django.utils import timezone
from django.utils.encoding import python_2_unicode_comp... | chipx86/reviewboard | reviewboard/accounts/models.py | Python | mit | 28,471 | [
"VisIt"
] | 5b5774049b60f103f8102960f7596a04c639063c5ee3866a2505efb60f4fa419 |
# This example illustrates how to measure the I-F curve of a neuron.
# The program creates a small group of neurons and injects a noisy current
# I(t)= I_mean + I_std*W(t)
# where W(t) is a white noise process.
# The programm systematically drives the current through a series of values on the
# two-dimensional I_mean/... | gewaltig/cython-neuron | cynest/examples/if_curve.py | Python | gpl-2.0 | 3,547 | [
"NEURON"
] | 958bf6ee457e653b7a07f143363a1105e8d8748d4fd71b390fe555a2f539e3a2 |
"""
Copyright 2020 Kat Holt
Copyright 2020 Ryan Wick (rrwick@gmail.com)
https://github.com/katholt/Kleborate/
This file is part of Kleborate. Kleborate 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 versi... | katholt/Kleborate | kleborate/truncation.py | Python | gpl-3.0 | 2,102 | [
"Biopython"
] | 85eae26c95dd4a46b3181796b1c825a9ceb2b939d85d4c7951e21af49b94c3b3 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import logging
import os
import unittest
from pymatgen import Molecule
from pymatgen.util.testing import PymatgenTest
from collections import OrderedDict
from ... | czhengsci/pymatgen | pymatgen/io/qchem_io/tests/test_inputs.py | Python | mit | 16,019 | [
"pymatgen"
] | c0cf2dc2fd248f20197d8daa6d7a93d45490bd026aea47147b72ef0eca29fe24 |
'''
Created on Aug 5, 2014
@author: gearsad
'''
import vtk
from SceneObject import SceneObject
class Axes(SceneObject):
'''
A template for drawing axes.
Shouldn't really be in a class of it's own, but it's cleaner here and like this we can move it easily.
Ref: http://vtk.org/gitweb?p=VTK.git;a=blob;f... | GearsAD/semisorted_arnerve | arnerve/scene/Axes.py | Python | mit | 1,876 | [
"VTK"
] | e8318534d6a284c0cffd8705a65d73cf23eb09def6406dce9c4e47905f6ae23d |
import pygame
import random
import json
from pgu import gui
from time import sleep
import ctypes
class Inquiry:
''' Class used for drawing the Inquiry UI.
@untestable - Just draws UI elements onscreen, makes no sense to test.
'''
def __init__(self, screen, config, project, site):
self.config ... | ianfhunter/TeamCrab | src/UI/inquiry.py | Python | mit | 15,299 | [
"VisIt"
] | cab6082f2f9370ed85d30451ed512977d264568064801c0031e5a2a3fe179509 |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/pbc/dft/test/test_krks.py | Python | apache-2.0 | 3,754 | [
"PySCF"
] | 8fbd2a7b8db46eb780ad60f57e41c75c77212a6b5074035bc2a6ad95b29f1b39 |
from openmesh import TriMesh
import projectconfig
import unittest
from graphicfile import Graphic_File
import customstructures
import time
import abstract_test
class TestVtkMethods(abstract_test.AbstractTest):
def setUp(self):
gf = Graphic_File()
self.mesh = gf.read_stl(projectconfig.TMP_PATH + "cu... | bajorekp/modelowanie_w_grafice | test/vtk_test.py | Python | mit | 331 | [
"VTK"
] | 30337907ffaf1715d573288336c2d9d273e4dea8ed77e42e50d44b5d09ca2bf1 |
from __future__ import division, print_function, absolute_import
from scipy import stats
import numpy as np
from numpy.testing import assert_almost_equal, assert_, assert_raises, \
assert_array_almost_equal, assert_array_almost_equal_nulp, run_module_suite
def test_kde_1d():
#some basic tests comparing to no... | asnorkin/sentiment_analysis | site/lib/python2.7/site-packages/scipy/stats/tests/test_kdeoth.py | Python | mit | 7,964 | [
"Gaussian"
] | deb1f99c87325e936a4de88f1982b0417410bfce12e52ae6be50694554d46506 |
import logging
import os
import salt.modules.cmdmod as cmdmod
import salt.modules.pkg_resource as pkg_resource
import salt.modules.rpm_lowpkg as rpm
import salt.modules.yumpkg as yumpkg
import salt.utils.platform
from salt.exceptions import CommandExecutionError, SaltInvocationError
from tests.support.mock import Magi... | saltstack/salt | tests/pytests/unit/modules/test_yumpkg.py | Python | apache-2.0 | 70,522 | [
"ORCA"
] | a69ce44b05749cbcdf7d36db11a8e95bcad705ad5a009664416731b23d2c1a1d |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2008-2009 Gary Burton
# Copyright (C) 2008 Robert Cheramy <robert@cheramy.net>
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2010 Nick Ha... | jralls/gramps | gramps/plugins/export/exportgedcom.py | Python | gpl-2.0 | 59,838 | [
"Brian"
] | 98bfed05e60024207f3ef90759814dd138f7ddbec1dd600d16227717257d710e |
'''Class for version 2 of pattern radar data in
`netCDF <https://www.unidata.ucar.edu/software/netcdf/>`_-format
'''
# Python modules
from datetime import datetime
from netCDF4 import Dataset
# MasterModule
from .main_radar import Radar
from .radar_data import RadarData
class PatternRadarV2(Radar):
''... | GroovyGregor/master_thesis | python/ModuleSetup/MasterModule/pattern_radar_v2.py | Python | gpl-3.0 | 5,025 | [
"NetCDF"
] | 846856455eef10c29c8b55972df5976f59e482dbb87e10d508617554a116f7e8 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# managejobs - [insert a few words of module description on this line]
# Copyright (C) 2003-2009 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms o... | heromod/migrid | mig/cgi-bin/managejobs.py | Python | gpl-2.0 | 1,108 | [
"Brian"
] | e46966a4ff20da1e911ba42f8a8d6a411bd22d1aa5b88f72d61fdcff26d9eec1 |
"""
=============================================
SNR estimation for Diffusion-Weighted Images
=============================================
Computing the Signal-to-Noise-Ratio (SNR) of DW images is still an open question,
as SNR depends on the white matter structure of interest as well as
the gradient direction corr... | StongeEtienne/dipy | doc/examples/snr_in_cc.py | Python | bsd-3-clause | 6,528 | [
"Gaussian"
] | 4084a62dc52b8e3d44afd71b3a11879389099a4e33d6eb8243fa050b42c41a02 |
# -*- coding: utf-8 -*-
import unittest
from .. import fit2d
import numpy as np
import pylab
class test_fit2d(unittest.TestCase):
def test_leastsq(self):
nx = 501
ny = 401
y, x = np.indices((ny, nx))
x0 = 10
y0 = ny // 2
sx = nx // 4
sy = ny // 4
... | woutdenolf/spectrocrunch | spectrocrunch/math/tests/test_fit2d.py | Python | mit | 1,206 | [
"Gaussian"
] | 495ccc9defe241333c0990ce7284fa22819e925fce7d9ac0b7fb0e58a63330cd |
import tempfile
import os.path
from stat import S_IXUSR
from os import makedirs, stat, symlink, chmod, environ
from shutil import rmtree
from galaxy.tools.deps import DependencyManager, INDETERMINATE_DEPENDENCY
from galaxy.tools.deps.resolvers.galaxy_packages import GalaxyPackageDependency
from galaxy.tools.deps.resolv... | ssorgatem/pulsar | test/test_tool_deps.py | Python | apache-2.0 | 14,530 | [
"BLAST",
"BWA",
"Galaxy"
] | 885c469b6766f649a5fda9e1e74666fb0ded9a20bcd546613ca96b6da2c3ac45 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | capoe/espressopp.soap | src/interaction/LennardJonesExpand.py | Python | gpl-3.0 | 6,677 | [
"ESPResSo"
] | b5ce9557892680966b4e682afe19024de9a3ec615713b797659ef06c05bd4218 |
# -*- coding: utf-8 -*-
#
# plot_weight_matrices.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 Li... | mschmidt87/nest-simulator | pynest/examples/plot_weight_matrices.py | Python | gpl-2.0 | 6,243 | [
"NEURON"
] | 938a73febfe0cb73e07889074a9d340f8e0b01ee27bbe4dafbbda3cc74b38577 |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (c) 2010 Nicolas Rougier - INRIA - CORTEX Project
#
# 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... | davidcox/glumpy | experimental/cnft.py | Python | bsd-3-clause | 6,621 | [
"NEURON"
] | b105d8270e5dc7b7f74fd68cbe4524c3489a20fd719467d57ac39548ea87f79b |
def package_for_fah(process_only_these_targets=None, verbose=False, nclones=10, archive=True):
'''Create the input files and directory structure necessary to start a Folding@Home project.
MPI-enabled.
'''
import os
import Bio.SeqIO
import numpy
import mpi4py.MPI
import simtk.openmm as o... | danielparton/MSMSeeder | MSMSeeder/packaging.py | Python | gpl-2.0 | 10,699 | [
"OpenMM"
] | 6b9a94c327da98b6048d18c86ed5d64f8f34b4c0effc4cd6a938e73686dd1797 |
# ----------------------------------------------------------------------------
# cocos2d
# Copyright (c) 2008-2012 Daniel Moisset, Ricardo Quesada, Rayentray Tappa,
# Lucio Torre
# Copyright (c) 2009-2015 Richard Jones, Claudio Canepa
# All rights reserved.
#
# Redistribution and use in source and binary forms, with o... | vyscond/cocos | cocos/scenes/transitions.py | Python | bsd-3-clause | 21,876 | [
"VisIt"
] | 90553079466ff6b46fec29c0785e2b949df83ac14da4a39bb01858feb23f86f9 |
"""
Views related to the Custom Courses feature.
"""
import csv
import datetime
import functools
import json
import logging
import pytz
from copy import deepcopy
from cStringIO import StringIO
from django.conf import settings
from django.core.urlresolvers import reverse
from django.http import (
HttpResponse,
... | franosincic/edx-platform | lms/djangoapps/ccx/views.py | Python | agpl-3.0 | 19,713 | [
"VisIt"
] | 987d81a763f6c1d46fafb20cba6ec575067fa3403e1bc50bb6870b561167564e |
# Copyright (C) 2013, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from xml.dom import minidom, XMLNS_NAMESPACE, Node
from zeroinstall import SafeException
from zeroinstall.injector.namespaces import XMLNS_IFACE
from zeroinstall.injector import model
from . import namespace, format... | 0install/0repo | repo/merge.py | Python | lgpl-2.1 | 9,427 | [
"VisIt"
] | f8299923f0226521b1e998d30505ec79a6f9dce40c859e7e1245f3b67c15e416 |
#! /usr/bin/env python
"""
Usage:
bam-coverage.py reference.fa query.x.reference.bam minmatch mapq
bam-coverage calculates the fraction of bases in 'reference.fa' that are
covered by sequences in a BAM alignment file that are longer than 'minmatch'.
Original script: https://github.com/ngs-docs/ngs-scripts/blob/ma... | luizirber/bioinfo | bioinfo/bam_coverage.py | Python | bsd-3-clause | 3,081 | [
"BLAST",
"pysam"
] | b4c612b98f9cd7fb3e74bb5ba8a2ef56a581eca1edeb8dcbe649e0f3b5c62afb |
from toplevel import *
import pdb
from pylab import *
import argparse,glob,os,os.path
from scipy.ndimage import filters,interpolation,morphology,measurements
from scipy import stats
from scipy.misc import imsave
import common,sl,morph
def B(a):
if a.dtype==dtype('B'): return a
return array(a,'B')
class record... | brobertson/ocropus-bgr | ocropy/ocrolib/psegutils.py | Python | apache-2.0 | 7,511 | [
"VisIt"
] | 28d2b2ef5e1770d88a97c5f37815f6eb3dcddd4968bd95faa7f3cec7f8796ff1 |
import matplotlib.pyplot as plt
import numpy as np
from scipy.optimize import curve_fit
from scipy import loadtxt
import os
#write for loop to iterate over each peak? Apply gaussian filter to find peaks and then just fit each one?
#adjust count rate for duration of sweep also
def choose_domain(xdata, ydata, domain, ... | bzcheeseman/phys211 | gamma cross sections/gamma_cross_sections.py | Python | lgpl-3.0 | 6,230 | [
"Gaussian"
] | 7c581f5ba5fc9c55f8076de6863dfde9e6dcd37f0b409ac925d88a1808d1e4fd |
import time
import smtplib
import imaplib
import sys
import traceback
from splinter import Browser
#Gmail account to listen for panic mail on
mail_user = ""
mail_pass = ""
#Panic subject
panic_subject = "panic"
#panic phrase to listen for in body of email
"""Please Change this"""
panic_phrase = "panic"
#Array of ... | PrometheanInfoSec/Lockdown | lockdown.py | Python | gpl-3.0 | 7,704 | [
"VisIt"
] | f5ebe331b035c379a2dd65ddfb9b0da375d290225d8c53d239b31c7d5e325a70 |
from simphony.api import CUDS
from simphony.core import CUBA
from simphony.cuds.meta.api import Material
from simphony.cuds.particles import Particle, Particles
from .lammps_data_file_parser import LammpsDataFileParser
from .lammps_data_file_writer import LammpsDataFileWriter
from .lammps_data_line_interpreter import ... | simphony/simphony-lammps-md | simlammps/io/file_utility.py | Python | bsd-2-clause | 6,019 | [
"LAMMPS"
] | 6ff75dd758b37c36ea58ce8b8fe197d4e6a5ba217e681557a8d421635ed3ea84 |
"""PyVista-like ITKwidgets plotter."""
import numpy as np
import pyvista as pv
class PlotterITK():
"""ITKwidgets plotter.
Used for plotting interactively within a jupyter notebook.
Requires ``itkwidgets>=0.25.2``. For installation see:
https://github.com/InsightSoftwareConsortium/itkwidgets#instal... | akaszynski/vtkInterface | pyvista/jupyter/itkplotter.py | Python | mit | 9,875 | [
"VTK"
] | 8c8bfde62b7d0edc335dcc5ba4cc31473aff7ad0a3116dceb173cf8cac30483c |
#Author:Chaitanya CH
#FileName: updatepaintGL.py
#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, or
# (at your option) any later version.
#
# This program is distributed in th... | BhallaLab/moose-thalamocortical | pymoose/gui/qt/updatepaintGL.py | Python | lgpl-2.1 | 11,475 | [
"MOOSE"
] | 7ce84a8cf63f9f5e380259906b80abda2c5bcd98733fda060d0cc6ba419e45fd |
from simphony.core import CUBA
def create_material_to_atom_type_map(state_data):
""" Creates a map from material type ui to atom type
create a mapping from material-uids to atom_type based
on the materials given in SD. which goes from 1 to N in lammps
Parameters:
-----------
state_data : St... | simphony/simphony-lammps-md | simlammps/common/utils.py | Python | bsd-2-clause | 618 | [
"LAMMPS"
] | caa24730f106cee5540f59489c800ed8f80aaf9351fd358c4f7e0b28637f9ace |
# encoding: utf-8
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding field 'GeoRecord.geo_id_segments'
#db.add_column(u'profiles_georecord', 'geo_id_segments', self.gf('djang... | 216software/Profiles | communityprofiles/profiles/oldmigrations/0070_auto__add_field_georecord_geo_id_segments__add_field_flatvalue_geograp.py | Python | mit | 23,849 | [
"MOE"
] | 5e21a80105a0985a3d4a5cde3c318e629704643a9017ae95a28c4bb6b2215ed6 |
import unittest as ut
import tests_common
import os
import numpy as np
import espressomd
from espressomd import lb
from espressomd import integrate
if "ENGINE" in espressomd.features() and "LB" in espressomd.features():
class SwimmerTest(ut.TestCase):
def test(self):
# Set to true if you need a... | tbereau/espresso | testsuite/python/engine_lb.py | Python | gpl-3.0 | 2,570 | [
"VTK"
] | 38e3a9d97c27510f207f5838ab62d7d09ff636f2b0f6d11e0fbd85ddc53cd22d |
#
# This file is a part of the normalize python library
#
# normalize is free software: you can redistribute it and/or modify
# it under the terms of the MIT License.
#
# normalize is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FI... | samv/normalize | tests/test_visitor.py | Python | mit | 7,772 | [
"VisIt"
] | 654adf9958af3ead55209e2c9b6163a6f2a68e8a0dfcbcd24ed7ef08e9a6d537 |
import pandas as pd
import time
import random
import numpy as np
from datetime import timedelta
from datetime import datetime
import MAUC
import argparse
parser = argparse.ArgumentParser(usage='python3 evalOneSubmission.py',
description=r'''
TADPOLE Evaluation Script:
The program computes the following matrics:
... | swhustla/pycon2017-alzheimers-hack | notebooks/evalOneSubmission.py | Python | mit | 11,554 | [
"VisIt"
] | 08296a40264388a9a7cbff2a01c93f779e631ca937010a38e50b8495e26fbeec |
"""HTTP related handlers.
Note that some other HTTP handlers live in more specific modules: _auth.py,
_gzip.py, etc.
Copyright 2002-2006 John J Lee <jjl@pobox.com>
This code is free software; you can redistribute it and/or modify it
under the terms of the BSD or ZPL 2.1 licenses (see the file
COPYING.txt ... | odicraig/kodi2odi | addons/plugin.video.roggerstream-4.0.0/mechanize/_http.py | Python | gpl-3.0 | 14,801 | [
"VisIt"
] | ecd0e7b4cef73bcf1cfaf4835b3acf0346996445e261d48a8285e89facf94e26 |
########################################################################
# $HeadURL $
# File: FTSAgent.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/05/31 10:00:13
########################################################################
""" :mod: FTSAgent
==============
.. module: FTSAgent
:syno... | vmendez/DIRAC | DataManagementSystem/Agent/FTSAgent.py | Python | gpl-3.0 | 47,236 | [
"DIRAC"
] | 89cff7b744d89e5a41fce40a118a592388b55994f72fb758d6e1845cf450fcc7 |
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'vtk_tools_layout.ui'
#
# Created: Fri Mar 10 10:39:40 2017
# by: pyside-uic 0.2.15 running on PySide 1.2.2
#
# WARNING! All changes made in this file will be lost!
from PySide import QtCore, QtGui
class Ui_vtk_tools(object):
def s... | seismology-RUB/ASP3D | asp3d/gui/layouts/vtk_tools_layout.py | Python | gpl-3.0 | 16,446 | [
"ParaView",
"VTK"
] | e88255c00b85051d251c135608519521f8f2d58f5b825e1a95886d065ce966e8 |
from __future__ import unicode_literals
from frappe import _
def get_data():
return [
{
"label": _("Sales Pipeline"),
"icon": "fa fa-star",
"items": [
{
"type": "doctype",
"name": "Lead",
"description": _("Database of potential customers."),
"onboard": 1,
},
{
"type": "... | brownharryb/erpnext | erpnext/config/crm.py | Python | gpl-3.0 | 4,525 | [
"VisIt"
] | d93e6b212ad14793424dd5f1c68e09711bc6419f6508cce19284afabaecfd439 |
##
# Copyright 2009-2017 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (F... | qldhpc/eb_local | eb_blocks/q/quantumespresso.py | Python | apache-2.0 | 17,565 | [
"ESPResSo",
"Quantum ESPRESSO",
"Wannier90",
"Yambo"
] | 79fb572dd8a8235f01d7bf6a29393ca341997fa04ee5e61981981e736149b8f3 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Mar 25 11:20:57 2019
@author: butenko
"""
import os
import fileinput
def paste_to_hoc_python3(axonnodes,axoninter,axontotal,v_init,steps_per_ms):
#end=" "
#print(os.path.dirname(os.path.realpath(__file__)))
NNODES_line="NNODES ="
NNODE... | andreashorn/lead_dbs | ext_libs/OSS-DBS/OSS_platform/Axon_files/Reilly2016/Parameter_insertion_python3.py | Python | gpl-3.0 | 2,066 | [
"NEURON"
] | a27a87c11157bc0c83c4ad38f87ecd163931b4518d41ca5dd39431482e123273 |
from __future__ import division, print_function
import warnings
import numpy as np
from scipy.special import gammainccinv
from scipy.ndimage.filters import convolve
def _inv_nchi_cdf(N, K, alpha):
"""Inverse CDF for the noncentral chi distribution
See [1]_ p.3 section 2.3"""
return gammainccinv(N * K, 1... | oesteban/dipy | dipy/denoise/noise_estimate.py | Python | bsd-3-clause | 11,425 | [
"Gaussian"
] | 4efebec49a476f5de1510370a8c9850a3598035d2cbb30adb78bc9eb47a46fc4 |
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | gkc1000/pyscf | pyscf/nao/test/test_0159_bse_h2b_uhf_cis.py | Python | apache-2.0 | 2,055 | [
"PySCF"
] | 007469a146989b4ef99cd4874887a151c6e7acb0cc1195f37dee4cafdc4d1a1f |
"""Simple script to retrieve the coordinates for the molecules and to
save to simpler numpy array files, for easy access later.
"""
import os.path as osp
import numpy as np
from rdkit import Chem
from mastic.interfaces.rdkit import AssignBondOrdersFromTemplate
from mastic.interfaces.rdkit import RDKitMoleculeWrapper
... | salotz/mast | examples/sEH-TPPU/seh_tppu_crystal_coords.py | Python | mit | 1,126 | [
"RDKit"
] | 0a5d44bc50ae1cce58b3452370b5c0690987eacb565b7fdc62808a8931052e16 |
#
# Copyright (C) 2013-2018 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... | hmenke/espresso | testsuite/python/lj.py | Python | gpl-3.0 | 2,725 | [
"ESPResSo"
] | 6405cb8fb56695794752e52c5a6e3208ffc9f902789e4114565b571d2c1eb1fc |
#! /usr/bin/env python
# This script uses Fourier analysis to try to detect regions of the image
# with periodicity in a certain frequency range.
import cv, cv2, time
import numpy as np, matplotlib.pyplot as plot
import sys, os, cPickle as pickle
TEMPORAL_WINDOW = 120 # number of frames to consider in Fourier analy... | AutonomyLab/husky | periodic_gestures/reference-code/efficient-detect-periodic.py | Python | gpl-3.0 | 23,441 | [
"Gaussian"
] | 510008bb646bade1516bade4299627a808063a38651688c1bc9598dda896a0c6 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | jensreeder/scikit-bio | skbio/sequence/tests/test_rna.py | Python | bsd-3-clause | 2,588 | [
"scikit-bio"
] | c12f463f9a96bed861109ed46e9d30e03a640ea80297f3b322f8ceb6cb45d543 |
# (c) 2012-2014, Michael DeHaan <michael.dehaan@gmail.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) an... | Censio/ansible-dev | lib/ansible/constants.py | Python | gpl-3.0 | 23,692 | [
"Galaxy",
"MOOSE"
] | b83bfa30b5011bd9f3dded61b19ba56e3862e12d4edd723fe29742402465d3f0 |
#/usr/bin/env py.test
from __future__ import print_function
import os
import sys
import sysconfig
import numpy as np
from numpy.fft import fft2, ifft2
from numpy.testing import assert_allclose
from scipy.optimize import check_grad, approx_fprime
import cubefit
from cubefit.fitting import (sky_and_sn,
... | snfactory/cubefit | cubefit/tests/test_fitting.py | Python | mit | 12,205 | [
"Galaxy"
] | f249be47a5adcf2a20058ff219633a03c8415ee3d315a0ac0a0b74a87eccc93e |
"""
Single Bubble Model
===================
Simulate the trajectory of a particle rising through the water column
This module defines the classes, methods, and functions necessary to simulate
the rise of a single particle (bubble, droplet or solid particle) through the
water column. The ambient water properties are p... | socolofs/tamoc | tamoc/single_bubble_model.py | Python | mit | 38,945 | [
"NetCDF"
] | f4d5a1025926077c41b06f4a86dc0b22067feb3c598777a528fe60cb03e3837d |
# coding: utf-8
from __future__ import unicode_literals
"""
This module implements various transmuter classes.
Transmuters are essentially classes that generate TransformedStructures from
various data sources. They enable the high-throughput generation of new
structures and input files.
It also includes the helper f... | yanikou19/pymatgen | pymatgen/alchemy/transmuters.py | Python | mit | 16,770 | [
"VASP",
"pymatgen"
] | 78fe0c774415b6c93d2381246c59d010971eca2e7c49abcd31331213df6dcf22 |
"""
Does the following:
1. Generates and saves random secret key
2. Removes the taskapp if celery isn't going to be used
3. Removes the .idea directory if PyCharm isn't going to be used
4. Copy files from /docs/ to {{ cookiecutter.project_slug }}/docs/
TODO: this might have to be moved to a pre_gen_hook
A portio... | ingenioustechie/cookiecutter-django-openshift | hooks/post_gen_project.py | Python | mit | 8,246 | [
"GULP"
] | cfd09cea9e2666ae1e9c000421709ff9c3b211a22ff8becc61cc455552ba4124 |
#####################################################################
# Ryuretic: A Modular Framework for RYU #
# !/ryu/ryu/app/Ryuretic/Pkt_Parse13.py #
# author: Jacob Cox
# Pkt_Parse13.py
# date 7 February 2016
####################################################... | Ryuretic/RAP | ryu/ryu/app/Ryuretic/Pkt_Parse13.py | Python | apache-2.0 | 5,031 | [
"VisIt"
] | d699a00768b74d29847eb93313149ed384cf8252ffe4cb79720c73652db5d6ba |
#!/usr/bin/env python
###############################################################################
# Name: setup.py #
# Purpose: Setup/build script for Editra #
# Author: Cody Precord <cprecord@editra.org> ... | 163gal/Time-Line | libs/wx/tools/Editra/setup.py | Python | gpl-3.0 | 20,538 | [
"VisIt"
] | 6d3278f310a8e0284a0b08c2082f024a428472813f173a74ede188c6a59d2e5f |
#!/usr/bin/env python
#
# $File: caseControlSample.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 redis... | BoPeng/simuPOP | docs/caseControlSample.py | Python | gpl-2.0 | 1,570 | [
"VisIt"
] | ebbf593d25e51b823b1c33f25b48e27564433a5d9af14865dd815c13a1fd1a90 |
import numpy as np
from numpy.testing import assert_raises
from skimage.filters._gaussian import gaussian
from skimage._shared._warnings import expected_warnings
def test_negative_sigma():
a = np.zeros((3, 3))
a[1, 1] = 1.
assert_raises(ValueError, gaussian, a, sigma=-1.0)
assert_raises(ValueError, ga... | paalge/scikit-image | skimage/filters/tests/test_gaussian.py | Python | bsd-3-clause | 2,010 | [
"Gaussian"
] | c227cf955ef5fa390497683d7d4926a4dc96c1e57a9f517beee995b85ccc0841 |
from __future__ import annotations
class GaussianRSProfileModelExt:
"""An extension class implementing a reciprocal space gaussian profile model."""
name = "gaussian_rs"
default = True
@staticmethod
def phil():
from dials.algorithms.profile_model.gaussian_rs import phil_scope
r... | dials/dials | extensions/gaussian_rs_profile_model_ext.py | Python | bsd-3-clause | 557 | [
"Gaussian"
] | 551b804c8738ff54292515de6fa1c00dd2ea5f1ee4cc6927242e464ccca1143d |
# Low-level execution of AST commands using xdotool.
import os, platform
from spark import GenericASTTraversal
from automators import XDoAutomator, CLIClickAutomator, NirCmdAutomator
class ExecuteCommands(GenericASTTraversal):
def __init__(self, ast, real = True):
GenericASTTraversal.__init__(self, ast)
... | dwks/silvius | grammar/execute.py | Python | bsd-2-clause | 2,379 | [
"VisIt"
] | 62976f5a72a62698cf9cf94d81beae6c6728993ea34b4b44b1bb77ffd10a776b |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# cgishared - cgi helper function
# Copyright (C) 2003-2014 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as p... | heromod/migrid | mig/shared/cgishared.py | Python | gpl-2.0 | 2,511 | [
"Brian"
] | 0ab51e12f8b101b3101ed794e239f47f8a36697124d57d9ba843f768d85bbd98 |
#!/usr/bin/env python
# map transcription factor binding (peak calls) into unique binding regions
import sys
import time
import optparse
import general
import numpy
import metrn
import modencode
import network
import bed
import os
import copy
import pdb
import re
import pickle
import random
from scipy.stats.stats imp... | claraya/meTRN | python/mapBinding.py | Python | mit | 63,606 | [
"BWA",
"Bowtie"
] | 2695300286f15aefa3170d274a3dbe25d9f6d04bdd6c284b1ed3e76106236b0b |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# 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)
#
# Released under t... | MDAnalysis/mdanalysis | package/MDAnalysis/analysis/hbonds/__init__.py | Python | gpl-2.0 | 1,200 | [
"MDAnalysis"
] | 27584c76d2344cf912540b9da75e26426b6cd188cb3babb60e8c1d314c75c7ca |
"""
Functions to operate on polynomials.
"""
__all__ = ['poly', 'roots', 'polyint', 'polyder', 'polyadd',
'polysub', 'polymul', 'polydiv', 'polyval', 'poly1d',
'polyfit', 'RankWarning']
import functools
import re
import warnings
import numpy.core.numeric as NX
from numpy.core import (isscalar, ... | pbrod/numpy | numpy/lib/polynomial.py | Python | bsd-3-clause | 43,813 | [
"Gaussian"
] | 6bcfc441900e2b714d0e460cf6b17823cfe0352ad88fd1d09e745829ed304a08 |
"""
This is only meant to add docs to objects defined in C-extension modules.
The purpose is to allow easier editing of the docstrings without
requiring a re-compile.
NOTE: Many of the methods of ndarray have corresponding functions.
If you update these docstrings, please keep also the ones in
core/fromnum... | shoyer/numpy | numpy/core/_add_newdocs.py | Python | bsd-3-clause | 202,407 | [
"Brian"
] | 05372f6ac3f1e17a8d569414e8709de8893cb50e5e1532be13cca6005501c52f |
# -*- coding: utf-8 -*-
# Copyright(C) 2014 Roger Philibert
#
# This file is part of weboob.
#
# weboob is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at yo... | blagarde/pygrl | tinder/browser.py | Python | gpl-3.0 | 4,501 | [
"VisIt"
] | 5b07574273dcc6edd75f7bed1e7e1e07a42a284f105f646347a253cc849b91b8 |
from BAMF_Detect.postprocessors.common import Postprocessor, Postprocessors
import pefile
import datetime
class GetPETimes(Postprocessor):
def __init__(self):
Postprocessor.__init__(
self,
name="GetPETimes",
author="Brian Wallace (@botnet_hunter)",
date="Mar... | bwall/bamfdetect | BAMF_Detect/postprocessors/get_pe_times.py | Python | mit | 2,371 | [
"Brian"
] | ac2e5a984b965cacdae4811d767490acfb26c0f5f017365b736863fc1a00a466 |
#!/usr/bin/env python
from pymatgen.io.vaspio import Poscar
import cProfile
import pstats
import os
import logging
logging.basicConfig(level=logging.DEBUG)
p = Poscar.from_file("../test_files/POSCAR.LiFePO4", check_for_POTCAR=False)
s = p.structure
def test():
nn = s.get_all_neighbors(20)
print len(nn)
def... | Dioptas/pymatgen | dev_scripts/profile_structure.py | Python | mit | 955 | [
"pymatgen"
] | d1b5eb242db1c6257bf5143c33a990a41cbf1e46601e44c96876829f8a34e055 |
#
# @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 file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | rmcgibbo/psi4public | psi4/driver/qcdb/libmintscoordentry.py | Python | lgpl-3.0 | 24,567 | [
"CFOUR",
"Psi4"
] | 9475f60bbaa04966f81ef0cf6db22c1855b7382ad972ab5a297eed32da48dc4f |
#!/usr/bin/env python
"""This script creates a graph of the modeled volume time series
for both 20km and 10km grid calculations for SeaRISE-Greenland. This figure
appears in the "Getting Started" section of the User's Manual.
"""
from numpy import *
import pylab as plt
from sys import exit
try:
import netCDF4 as ... | JohannesFeldmann/pism | util/ivolboth.py | Python | gpl-2.0 | 2,273 | [
"NetCDF"
] | 2ff2a200db4c55aa70a371de097c58404ee164bd9a79742b9d52ae7efffd799f |
#!/usr/bin/env python
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""The 'grit android2grd' tool."""
import getopt
import os.path
import StringIO
from xml.dom import Node
import xml.dom.minidom
... | leighpauls/k2cro4 | tools/grit/grit/tool/android2grd.py | Python | bsd-3-clause | 19,349 | [
"xTB"
] | 86943706da2f7459066a73597b001f7ed600b55db09c35614cf57b8e56e39c9d |
from __future__ import unicode_literals
import threading
from django.test.simple import DjangoTestSuiteRunner
from django.core.servers.basehttp import run, get_internal_wsgi_application
from django.contrib.staticfiles.handlers import StaticFilesHandler
from splinter.driver.webdriver.firefox import WebDriver
from mock ... | ErinCall/splinter_demo | django/splinter_demo/test_runner.py | Python | mit | 1,225 | [
"VisIt"
] | 4eb476d10621a4ed8957499ce9c8edbca339d6b3e30a66035a76f8530bd1501f |
#!/usr/bin/env python
import vtk
def main():
xyzFile, qFile = get_program_parameters()
colors = vtk.vtkNamedColors()
# Create the RenderWindow, Renderer and Interactor.
#
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
iren = vtk.vtkRenderWindowIn... | lorensen/VTKExamples | src/Python/VisualizationAlgorithms/CombustorIsosurface.py | Python | apache-2.0 | 2,448 | [
"VTK"
] | 0916f206f66be5fbad390089fdbc1283bc9c6026a2b4866e4e8e0e26d31edd6c |
# Copyright 2017 the GPflow 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 or agreed to in writi... | GPflow/GPflow | tests/gpflow/conditionals/test_uncertain_conditional.py | Python | apache-2.0 | 9,395 | [
"Gaussian"
] | f3951c96eea69548e9237565d8addd80be42fa1461faffc1d246c4a411bf66f3 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2013 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU Lesser General Public License as published by
## the Free Software F... | tiagocardosos/stoq | plugins/optical/opticalwizard.py | Python | gpl-2.0 | 8,853 | [
"VisIt"
] | 11183b3563fa15717914e76d88402ed1545bd49be666cb7a54d1689fce88e840 |
# (c) 2015, Brian Coca <bcoca@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.... | mattbernst/polyhartree | support/ansible/runner/lookup_plugins/url.py | Python | gpl-3.0 | 2,108 | [
"Brian"
] | 13948149c0091e0fb8bce8392f73bebd00582c27c8122ad156fe748acd7dac7c |
"""
Views related to the Custom Courses feature.
"""
import csv
import datetime
import functools
import json
import logging
from copy import deepcopy
from cStringIO import StringIO
import pytz
from ccx_keys.locator import CCXLocator
from django.conf import settings
from django.contrib import messages
from django.contr... | lduarte1991/edx-platform | lms/djangoapps/ccx/views.py | Python | agpl-3.0 | 22,386 | [
"VisIt"
] | fd07a7cf76af3c17b6a13e82b557f5f5b247588ad85f9d0bd74d689d22d56b28 |
# Copyright (C) 2012,2013,2016
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms... | kkreis/espressopp | src/tools/pathintegral.py | Python | gpl-3.0 | 9,666 | [
"ESPResSo",
"Gromacs"
] | 92a5e98913b5ea4daba95c775780b97e22ee135f7df76d2e047f91d07904b19d |
#!/home/brian/anaconda3/bin/python3
'''
I work on this in my free time, but I can't take all the credit.
If it weren't for Ethan and Jacob, I would have stopped working on this long ago.
So thank you guys for keeping me interested in this, and coming up with some of the more fun characters.
'''
import subprocess as s... | Thurii/legendary-telegram | Merged Element Game.py | Python | cc0-1.0 | 30,639 | [
"BLAST",
"Brian"
] | fa6d6d5d8dc3f5bffa79435374685756b6c402c522278903445cb12d6faddfb8 |
import warnings
import numpy as np
import scipy
import matplotlib.pyplot as plt
from scipy.ndimage.filters import gaussian_filter1d
from scipy.interpolate import UnivariateSpline
from astropy import log
from astropy.table import Table
from stingray.lightcurve import Lightcurve
from ..crossspectrum import AveragedCros... | StingraySoftware/stingray | stingray/deadtime/fad.py | Python | mit | 16,305 | [
"Gaussian"
] | 962216bf36764fbd158196cb7f3fbf69c760ddb6283adc193912506dea2a1bc0 |
# Copyright (c) 2017, Novartis Institutes for BioMedical Research Inc.
# 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
... | rdkit/rdkit | External/FreeSASA/Wrap/testFreeSASA.py | Python | bsd-3-clause | 20,739 | [
"RDKit"
] | 5647f5fb063d5f0411e5e114c2ba244e36ed8fdc594fa06accf0893a0cdcbd73 |
# Copyright 2000 by Jeffrey Chang. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
import sys
# Add path to Bio
sys.path.append('../..')
"""Code to access resources at ExPASy ... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/ExPASy/__init__.py | Python | gpl-2.0 | 3,830 | [
"Biopython"
] | c631027ab04e1f7f8b480c9c0f353e407948f3b373729bb39d3580d3ec9e60f0 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2020 Satpy developers
#
# This file is part of satpy.
#
# satpy 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... | pytroll/satpy | satpy/readers/satpy_cf_nc.py | Python | gpl-3.0 | 12,691 | [
"NetCDF"
] | 5160b4aebae2f88ed4af2dd5d5ee3370e2842c23a307273cd55c68348c01bac1 |
# -*- coding: utf-8 -*-
u"""
This script is to parse SRW Python scripts and to produce JSON-file with the parsed data.
It's highly dependent on the external Sirepo/SRW libraries and is written to allow parsing of the .py files using
SRW objects.
:copyright: Copyright (c) 2017 RadiaSoft LLC. All Rights Reserved.
:lice... | radiasoft/sirepo | sirepo/template/srw_importer.py | Python | apache-2.0 | 29,980 | [
"CRYSTAL"
] | 39041d627726804db354b1336037a62ec9741ecf3de0a7027311dbbb79605c3b |
from base import BaseBot
from scraping import fleet, general, hangar
from copy import copy
class TransporterBot(BaseBot):
"""Logging functions for the bot"""
def __init__(self, browser, config, planets):
self.fleet_client = fleet.Fleet(browser, config, planets)
self.hangar_client = hangar.Han... | yosh778/OG-Bot | ogbot/core/transporter.py | Python | mit | 2,029 | [
"CRYSTAL"
] | 18674dd71283860adbef2b9f44bb735eaa4c2b035dfbb4b1944fbcbd77732e03 |
'''
Python module dependencies:
biopython==1.63
fastcluster==1.1.13
numpy==1.7.1
python-Levenshtein==0.11.2
scipy==0.12.0
Under Ubuntu, scipy, numpy and biopython can be installed as:
sudo apt-get install python-biopython python-numpy python-scipy
fastcluster and python-Levenshtein can be installed using pip:
pip ... | newgene/clonify | clonify_contest.py | Python | mit | 8,044 | [
"Biopython"
] | 5cb10bd9ec1630a55f87296a0f734fc68a4346756990c33be9264ff590ba7ea9 |
#
# @file TestSpeciesType_newSetters.py
# @brief SpeciesType unit tests for new set function API
#
# @author Akiya Jouraku (Python conversion)
# @author Sarah Keating
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generated automat... | TheCoSMoCompany/biopredyn | Prototype/src/libsbml-5.10.0/src/bindings/python/test/sbml/TestSpeciesType_newSetters.py | Python | bsd-3-clause | 3,818 | [
"VisIt"
] | 3239712ef82b16e039f4ca8b55fe1ddb0764fcb0c87469f7d3900a4434350e5c |
# -*- coding: utf-8 -*-
"""
Created on Mon Mar 7 14:38:46 2011
Plot pca test error vs train error
@author: -
"""
# Computes the gaussian gradients on a boxm_alpha_scene
import os;
import optparse;
import time;
import sys;
import numpy as np
import matplotlib
matplotlib.use("TkAgg")
import matplotlib.pyplot as plt
im... | mirestrepo/voxels-at-lems | harris_experiments/plot_accuracy_all_trials.py | Python | bsd-2-clause | 3,238 | [
"Gaussian"
] | bacdea6038a8ad9505054bbd568536d2b511952b578ad87621b9840c4f091e62 |
#!/usr/bin/env ipython
# -*- coding: utf-8 -*-
from datetime import datetime, time, timedelta
import numpy as np
import console_colors as ccl
from scipy.io.netcdf import netcdf_file
from ShiftTimes import ShiftCorrection, ShiftDts
import os, argparse
import h5py
from h5py import File as h5
from numpy import (
mean... | jimsrc/seatos | shared_lib/shared_funcs.py | Python | mit | 54,269 | [
"NetCDF"
] | 86e9525adb53af7cfb0a72cdf8965c6b3e60fa83fca77ffb3e90918cf2e0d089 |
from tools.load import LoadMatrix
from sg import sg
lm=LoadMatrix()
traindat=lm.load_numbers('../data/fm_train_real.dat')
testdat=lm.load_numbers('../data/fm_test_real.dat')
parameter_list=[[traindat,testdat,10,2.1,10.,1e-5,False],
[traindat,testdat,10,2.1,11.,1e-4,False]]
def classifier_libsvm_oneclass (fm_train_... | chenmoshushi/shogun | examples/undocumented/python_static/classifier_libsvmoneclass.py | Python | gpl-3.0 | 906 | [
"Gaussian"
] | 27ef3f3eac350a1975de9c0d1e9ba421456dff477e09f4b0cd95f412a35ca98f |
"""
Unit tests for masquerade.
"""
import json
import pickle
from mock import patch
from nose.plugins.attrib import attr
from datetime import datetime
from django.core.urlresolvers import reverse
from django.test import TestCase
from django.utils.timezone import UTC
from capa.tests.response_xml_factory import OptionR... | tanmaykm/edx-platform | lms/djangoapps/courseware/tests/test_masquerade.py | Python | agpl-3.0 | 18,200 | [
"VisIt"
] | 4600a4c7fa6f37233547a1f7d73d5dccdd882bcd5a517b71166fbb8430b6adbf |
"""
DIRAC.StorageManagementSystem.Agent package
"""
| DIRACGrid/DIRAC | src/DIRAC/StorageManagementSystem/Agent/__init__.py | Python | gpl-3.0 | 55 | [
"DIRAC"
] | 324247baf53d9564fe2edbeceefb5019f883142421432aff0d155b60d82b3a35 |
import logging
import subprocess
import threading
from kalliope.core.NeuronModule import NeuronModule, MissingParameterException
logging.basicConfig()
logger = logging.getLogger("kalliope")
class AsyncRun(threading.Thread):
"""
Class used to run an asynchrone Shell command
.. notes:: Impossible to get t... | mrdev023/KALLIOPE_FRENCH_PERSONALISATION | resources/neurons/run/run.py | Python | gpl-3.0 | 2,354 | [
"NEURON"
] | f9f0c0a87a2ad1245cf30f220a698c8ed8445a7e58ad1d1c29dad968b566aa25 |
from PyQt5.QtWidgets import (QDialog, QRadioButton, QVBoxLayout, QLabel,
QWidget, QDialogButtonBox)
from inselect.lib.utils import debug_print
from inselect.gui.utils import HTML_LINK_TEMPLATE, HorizontalLine
from .barcode_settings import (current_settings, update_settings,
... | NaturalHistoryMuseum/inselect | inselect/gui/plugins/barcode_dialog.py | Python | bsd-3-clause | 6,021 | [
"VisIt"
] | 49b8fb7e8a95031cb3998bcdf1b42b54577bc0e8fa331f1c93c41c11f9cb79ea |
import cPickle as pickle
import pandas as pd
from trees import Tree
import csv, re
from matplotlib_venn import venn2
import matplotlib.pyplot as plt
from copy import deepcopy
import numpy as np
import seaborn as sb
from collections import defaultdict
from cobra.io.sbml import create_cobra_model_from_sbml_file
from cobr... | dandanvidi/in-vivo-enzyme-kinetics | scripts/helper.py | Python | mit | 13,207 | [
"Avogadro"
] | 5de2d161a3028c71d81edd85d57833203a474d258fb8f1826cd0a6e366f2dd29 |
#!/usr/bin/env python
#
# parse_pdb_header.py
# parses header of PDB files into a python dictionary.
# emerged from the Columba database project www.columba-db.de.
#
# author: Kristian Rother
#
# license: same as BioPython, read LICENSE.TXT from current BioPython release.
#
# last modified: 9.2.2004
#
# Added some smal... | poojavade/Genomics_Docker | Dockerfiles/gedlab-khmer-filter-abund/pymodules/python2.7/lib/python/Bio/PDB/parse_pdb_header.py | Python | apache-2.0 | 9,173 | [
"Biopython"
] | 412c51c82f83c2613bdff640665a321454cce8410366535fe13caa8ba4c64785 |
import matplotlib as mpl
mpl.use('Agg')
import math
import matplotlib.pyplot as plt
import numpy as np
import scipy.special
import pdb
import pickle
import sys
np.set_printoptions(threshold='nan')
num_bins = 100
torsion_r48_a = pickle.load(open( "torsion.p", "rb" ))
plt.figure(1)
(n1,bins1,patch1) = plt.hist(torsion... | bmanubay/open-forcefield-tools | single-molecule-property-generation/torsion_fitting/fitting_example.py | Python | mit | 7,644 | [
"Gaussian"
] | cc7af362d49efcdf37085442c8a88c56b59103b074853fe08ca65e4684ad8bc3 |
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