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#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
MetaMaker is a basic tool for simulating metagenomic datasets. It downloads a
number of genomes, splits them into reads and creates a fastq output file
simulating a sequencing run.
"""
import os
import sys
import time
import json
import numpy
import random
import logging... | norling/metlab | metlab/metamaker.py | Python | gpl-3.0 | 24,644 | [
"Biopython"
] | 8c11eb68ca0e728a1b14688c711f313871b3fd86073e537fce58ca85a8a4f35e |
# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | zasdfgbnm/tensorflow | tensorflow/contrib/py2tf/converters/control_flow.py | Python | apache-2.0 | 7,521 | [
"VisIt"
] | 40f12064cb1c4474240cabbced30a749b527677dc66c61f45e1fdc0497834773 |
from hashlib import sha1
from dominate import tags
from visitor import Visitor
class BootstrapRenderer(Visitor):
def __init__(self, html5=True, id=None):
self.html5 = html5
self._in_dropdown = False
self.id = id
def visit_NavbarBrand(self, node):
item = tags.a(href=node.get_ur... | eammx/proyectosWeb | proyectoPython/env/lib/python3.6/site-packages/flask_bootstrap/nav.py | Python | mit | 6,444 | [
"VisIt"
] | 844263af0175bae967240968eea30d6c6b64d82f136e560ca18775e521bf9fa9 |
# Copyright (c) 2013, the GPy Authors (see AUTHORS.txt)
# Licensed under the BSD 3-clause license (see LICENSE.txt)
from . import SparseGPClassification
from .. import likelihoods
from .. import kern
from ..inference.latent_function_inference.expectation_propagation import EP
import numpy as np
class OneVsAllClassifi... | befelix/GPy | GPy/models/one_vs_all_classification.py | Python | bsd-3-clause | 1,352 | [
"Gaussian"
] | 954d4944c6a22899d69bb0df59ea7f1d41bee654ca97d0be16f6d54d54c34352 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkImageWriter(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vt... | nagyistoce/devide | modules/vtk_basic/vtkImageWriter.py | Python | bsd-3-clause | 472 | [
"VTK"
] | c985667cf636c6c9b489cb9c01cbbef23d4183e4b7f0b73ec85b5fca2acc76d0 |
from server import app, db #, login_manager
from server.models import Article, User, Visit, NewsSource
from server.news_article import NewsArticle
from random import randint, random, sample
from datetime import datetime, timedelta
import json
def addArticle(url):
article = Article.get(url)
if not article:
art... | theodorachu/ihavenewsforyou | NewsProcessorServer/populateDatabase.py | Python | mit | 3,854 | [
"VisIt"
] | f6bb0dc63452b52246163cdbc369f250227e2721c7fe55be66f4963ea8809b9e |
#!/usr/bin/python
import sys
import shlex
import subprocess
import argparse
import urllib
class bcolors:
HEADER = '\033[95m'
OKBLUE = '\033[94m'
OKGREEN = '\033[92m'
WARNING = '\033[93m'
FAIL = '\033[91m'
ENDC = '\033[0m'
app_name = 'transmission'
parser = argparse.ArgumentParser(description='Manage %s contai... | catatnight/docker-utils | transmission/manage.py | Python | mit | 2,627 | [
"VisIt"
] | ebfd4dad80cc181fe67ba32cca2d78db576b13e8b72cd35dd0083b0d0984a6fc |
#!@PYTHON_EXECUTABLE@
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 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 redistri... | jgonthier/psi4 | psi4/run_psi4.py | Python | lgpl-3.0 | 14,609 | [
"Psi4"
] | 11004483598eda7764aba63f770672aeba7f0079e2c60c8a36422de6edcd181b |
# pylint: disable=missing-docstring, invalid-name
import unittest
import numpy as np
from obsoper import orca
class TestNorthFold(unittest.TestCase):
def test_north_fold_given_point_returns_point_on_opposite_side(self):
result = orca.north_fold([0, 0], [0, 0])
expect = {0: 1,
1: ... | met-office-ocean/obsoper | obsoper/test/test_orca.py | Python | bsd-3-clause | 1,553 | [
"ORCA"
] | 9fc5fe9be3f8a5ca66fcb4da9d862eda529da3dd61b089137f1ca3973b547f58 |
import numpy as np
from .cysift import cy_sift
def sift(image, n_octaves=None, n_levels=3, first_octave=0, peak_thresh=0,
edge_thresh=10, norm_thresh=None, magnification=3, window_size=2,
frames=None, force_orientations=False, float_descriptors=False,
compute_descriptor=False, verbose=Fa... | simmimourya1/cyvlfeat | cyvlfeat/sift/sift.py | Python | bsd-2-clause | 5,888 | [
"Gaussian"
] | e83ba8119754e4ecca830a7eec6bdac1959d13f35fb3bbc35d4cd2eaa00459d4 |
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publi... | thica/ORCA-Remote | src/ORCA/widgets/Slider.py | Python | gpl-3.0 | 11,336 | [
"ORCA"
] | c29daa0f1e0d77c6f6288658fe55237be6b5e01a7202505bcd6a5d14c1f66e59 |
# Define a procedure, is_friend, that takes
# a string as its input, and returns a
# Boolean indicating if the input string
# is the name of a friend. Assume
# I am friends with everyone whose name
# starts with either 'D' or 'N', but no one
# else. You do not need to check for
# lower case 'd' or 'n'
def is_friend(na... | ezralalonde/cloaked-octo-sansa | 02/qu/07.py | Python | bsd-2-clause | 550 | [
"MOE"
] | cbbf42fef7203ad8771fc7c89f82f748de444c6f472a144a5802b0fad9ba827a |
import glob
from datetime import datetime
import re
from operator import itemgetter
from netCDF4 import Dataset
import numpy
import click
from pyproj import Proj
import rasterio
from rasterio.crs import CRS
from rasterio.windows import get_data_window, union
from trefoil.cli import cli
from trefoil.netcdf.variable i... | consbio/clover | trefoil/cli/convert.py | Python | bsd-3-clause | 7,787 | [
"NetCDF"
] | 54ed57bd539a03844f574adb7a484833e6d32ffb40053f9d604f7a2165c0b30d |
# Libraries
import sys
import json
from datetime import datetime
# External Libraries
import numpy as _np
import matplotlib.pyplot as _plt
# Own Libraries
from _library import Cost_CrossEntropy, Act_Sigmoid, Act_ReLU, Act_Tanh
sys.path.append('__data')
from mnist_load import *
'''
Implemented
L2 regularization (s... | luckylwk/neural-network | _neuralnet.py | Python | mit | 11,002 | [
"Gaussian"
] | 8314e75e87a6e505e9f48de3807fa36e4dc6fa346e459bf212ea72e4a80517e4 |
from ...rl import Plant
import numpy as np
import warnings
class SpeedReward(Plant):
"""A :py:class:`Plant` with focus on the speed of the robot.
"""
def __init__(self):
super(SpeedReward, self).__init__(state_space_dim=2)
def state_input(self, state):
"""Return the location, sampl... | igsor/HDPy | HDPy/puppy/plant/plants.py | Python | bsd-3-clause | 8,521 | [
"Gaussian"
] | 280b254cc8f80f515c2ae9edeb7c43752a05822da31239d3398a0813ff3a9d1c |
# Simple ADF file extraction
# Support for ADos OFS/FFS disks
# Author: TheCyberDruid
# Notes: Internal functions prefaced with adf_ for now.
# ToDo: Convert functions to a class.
# Version: 1.0
BLOCK_SIZE = 512 # Size of a block on an ADos disk
AMIGA_ULONG_SIZE = 4 # Size of an Amiga ULong variable
def con... | cnvogelg/fs-uae-gles | launcher/fs_uae_launcher/ADFFileExtractor.py | Python | gpl-2.0 | 3,945 | [
"ADF"
] | 78694240534f37053bbb75f7640cadca828a733bc4ef1b785cb2cf2df2c8ba10 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
urlpat... | mekkagodzilla/mycollections | config/urls.py | Python | bsd-3-clause | 1,611 | [
"VisIt"
] | a1c2f52fae59606e0fed9d01e564c1fe7db7219eb8646704827fedde64719afa |
#!/usr/bin/env python
"""
Define the data structure of access entry .
This program is part of the "I/O Signature detection software". Visit
http://www.cs.iit.edu/~scs/iosig for the latest version.
"""
__author__ = "Yanlong Yin (yyin2@iit.edu)"
__version__ = "$Revision: 1.4$"
__date__ = "$Date: 09/28/2011 01:09:23 $... | yinyanlong/iosig | src/analysis/access.py | Python | bsd-3-clause | 2,156 | [
"VisIt"
] | 14aba0a07b7f2b80e811fd8747748c0bc2ee8d742ea1b8c7ed2d25cf56937e5d |
# -*- coding: utf-8 -*-
"""
This module lets your server send Web Push Notifications to your clients.
(Please, visit https://github.com/sergioburdisso/solidwebpush for more info).
----
"""
from __future__ import print_function
from sqlite3 import connect as db_connect
from multiprocessing import Pool
from py_vapid im... | sergioburdisso/solidwebpush | solidwebpush/__init__.py | Python | mit | 22,740 | [
"VisIt"
] | 2c9c943d484c2e6e53459c2f666936ae36857491664d88213ca466d0a5c356e1 |
#!/usr/bin/env python
'''
setup board.h for chibios
'''
import argparse, sys, fnmatch, os, dma_resolver, shlex, pickle, re
import shutil
parser = argparse.ArgumentParser("chibios_pins.py")
parser.add_argument(
'-D', '--outdir', type=str, default=None, help='Output directory')
parser.add_argument(
'--bootloade... | mariansoban/ardupilot | libraries/AP_HAL_ChibiOS/hwdef/scripts/chibios_hwdef.py | Python | gpl-3.0 | 60,462 | [
"CRYSTAL"
] | 2260c03f52c933b7684d1c551543b59e434c74e7ef8092730d0994adaceaf719 |
# -*- coding: utf-8 -*-
#
# Copyright (C) 2011 Tiger Soldier
#
# This file is part of OSD Lyrics.
#
# OSD Lyrics 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 ... | ihacklog/osdlyrics | python/dbusext/property.py | Python | gpl-3.0 | 8,164 | [
"VisIt"
] | 30ef880d60f947e584726c7fad5ce8d91dea650686f080357fad97b9c1d7a02b |
# gPrime - A web-based genealogy program
#
# Copyright (C) 2003-2006 Donald N. Allingham
# Copyright (C) 2008,2012 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2011 Paul Franklin
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU... | sam-m888/gprime | gprime/plugins/textreport/simplebooktitle.py | Python | gpl-2.0 | 7,595 | [
"Brian"
] | d2974f2976434c370974a1acc513bc8e7de86cfb7c9c704017984a8d888f961a |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | MJJoyce/climate | ocw/data_source/local.py | Python | apache-2.0 | 24,084 | [
"NetCDF"
] | 772ffe2dc1b2b4d26cb1e149bb9e8042fb8c7dc6dacfe91c7c4f4bebcb3d269c |
APP_NAME = "Neuron"
APP_NAME_NO_SPACE = APP_NAME.replace(' ', '')
APP_VERSION = '2.3.0'
APP_DESCRIPTION = "Create Python applications with a GUI built with HTML and Javascript"
COMPANY_NAME = "Neuron Company"
WEBSITE = "http://example.com"
| Andrew-Shay/Neuron | neuron/__info__.py | Python | mit | 240 | [
"NEURON"
] | 58847e222459ed9604f221d019a422946ae03f005d4d2a24718cf46e5f78fd1b |
from __future__ import print_function
import os
from numpy import dot,round
from .abinittask import AbinitTask
__all__ = ['AbinitWfnTask']
class AbinitWfnTask(AbinitTask):
"""Charge density calculation."""
_TASK_NAME = 'Wavefunction task'
_input_fname = 'wfn.in'
_output_fname = 'wfn.out'
def __... | trangel/OPTpy | OPTpy/Abinit/wfntask.py | Python | gpl-3.0 | 7,045 | [
"ABINIT",
"pymatgen"
] | 18280b079fbd22ce24bb54580515aebbc2197645c9798b263aa51d05ae0c3898 |
#!/usr/bin/env python
#Dan Blankenberg
import sys
from galaxy import eggs
import pkg_resources; pkg_resources.require( "bx-python" )
import bx.intervals.io
assert sys.version_info[:2] >= ( 2, 4 )
def stop_err( msg ):
sys.stderr.write( msg )
sys.exit()
def __main__():
output_name = sys.arg... | volpino/Yeps-EURAC | lib/galaxy/datatypes/converters/interval_to_bed_converter.py | Python | mit | 2,312 | [
"Galaxy"
] | c2437862bfc6481d8e26c5a33ad3e57ce737103229dc5658f1f1f7b9fa692058 |
#!/usr/bin/python
#Audio Tools, a module and set of tools for manipulating audio data
#Copyright (C) 2007-2012 Brian Langenberger
#This program is free software; you can redistribute it and/or modify
#it under the terms of the GNU General Public License as published by
#the Free Software Foundation; either version 2... | R-a-dio/python-audio-tools | audiotools/vorbis.py | Python | gpl-2.0 | 23,543 | [
"Brian"
] | e515f72c544d330a29224bbd1fc33e4f1abb21148db0ed0cff11e27721ad80eb |
"""
Container page in Studio
"""
from bok_choy.page_object import PageObject
from bok_choy.promise import EmptyPromise, Promise
from edxapp_acceptance.pages.common.utils import click_css, confirm_prompt
from edxapp_acceptance.pages.studio import BASE_URL
from edxapp_acceptance.pages.studio.utils import HelpMixin, se... | edx/edx-e2e-tests | edxapp_acceptance/pages/studio/container.py | Python | agpl-3.0 | 25,402 | [
"VisIt"
] | 4a8d6dd0ac09edf2de82d35f443d068ae2651be58d2f416c9f459e92b7b3cb2f |
#!/usr/bin/env python
'''
Localized orbitals can be obtained via pivoted Cholesky factorization
of the density matrix. The procedure is iteration-free and produces
unique orbitals (except for degeneracies etc.), albeit they are
less well localized compared with other procedures.
F. Aquilante, T.B. Pedersen, J. Chem. ... | sunqm/pyscf | examples/local_orb/08-cholesky.py | Python | apache-2.0 | 2,060 | [
"PySCF"
] | f07ab05ea0540a34e3ae4b8764d7f25ce9fb47dd24ecbbc326c9254608fa2bc4 |
"""Transform a string with Python-like source code into SymPy expression. """
from __future__ import print_function, division
from .sympy_tokenize import \
generate_tokens, untokenize, TokenError, \
NUMBER, STRING, NAME, OP, ENDMARKER
from keyword import iskeyword
import ast
import re
import unicodedata
im... | Shaswat27/sympy | sympy/parsing/sympy_parser.py | Python | bsd-3-clause | 32,078 | [
"VisIt"
] | 7212bdd76df21523ba15499c6a772277231973f2681c2157c32d693918cbf7da |
from __future__ import print_function, division, unicode_literals
import os
import math
import numpy as np
from monty.serialization import loadfn
import twod_materials.utils as utl
from pymatgen.core.structure import Structure
from pymatgen.io.vasp.inputs import Incar
import twod_materials
PACKAGE_PATH = twod_... | ashtonmv/twod_materials | twod_materials/friction/startup.py | Python | gpl-3.0 | 7,501 | [
"VASP",
"pymatgen"
] | 84996ea000bcec034c57d2ac6ecc70a03522fde7597f3a2d74aff51d9df222f2 |
"""
Authors: Ivan E. Cao-Berg and Jennifer Bakal
Created: February 22, 2012
Copyright (C) 2012 Murphy Lab
Lane Center for Computational Biology
School of Computer Science
Carnegie Mellon University
May 4, 2012
* J. Bakal Updated
April 10, 2013
* J. Bakal Included processOMEIDs and def processOMESearchSet methods
Th... | icaoberg/pyslid | pyslid/database/direct.py | Python | gpl-3.0 | 28,343 | [
"VisIt"
] | e8f1c8d3c70b06740c74f13a43842342b4afbf2c211bcf295c957ed76dce8424 |
# Copyright (c) 2012 Gerald Knizia
#
# This file is part of the IR/WMME program
# (See http://www.theochem.uni-stuttgart.de/~knizia)
#
# IR/WMME is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, version 3.
# ... | zhengbx/BBQ | ir-wmme.20130129/rhf_in_python.py | Python | gpl-3.0 | 11,176 | [
"Molpro"
] | 78872b274b7ecd33895249b4d9006f861114a9a8ee908a5271d5b10d6c084636 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
__author__ = 'Shyue Ping Ong'
__copyright__ = 'Copyright 2013, The Materials Project'
__version__ = '0.1'
__maintainer__ = 'Shyue Ping Ong'
__email__ = 'ongsp@... | aykol/pymatgen | pymatgen/util/tests/test_num_utils.py | Python | mit | 1,077 | [
"pymatgen"
] | 4e14bd6b7d74a378372efccfcffb7dac4ceb682efeee8daa3ffab4443fb45011 |
"""Miscellaneous utilities."""
from functools import reduce
import os
import os.path as op
import subprocess
import warnings
import numpy as np
from mne import pick_types, pick_info, make_sphere_model, DipoleFixed, Epochs
from mne.channels import make_standard_montage, make_dig_montage
from mne.fixes import _get_args... | Eric89GXL/mnefun | mnefun/_utils.py | Python | bsd-3-clause | 6,476 | [
"Mayavi"
] | ded527bc9ef78d590b3cc848d346c43fa6d3dbd20b2f76b11c52155193137034 |
#
# @file TestInitialAssignment.py
# @brief SBML InitialAssignment unit tests
#
# @author Akiya Jouraku (Python conversion)
# @author Sarah Keating
#
# $Id$
# $HeadURL$
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generated automa... | alexholehouse/SBMLIntegrator | libsbml-5.0.0/src/bindings/python/test/sbml/TestInitialAssignment.py | Python | gpl-3.0 | 4,611 | [
"VisIt"
] | 6652796d908e5435c5527c7afa096e45fe71bde14035f587ee927b3d50c1a658 |
"""Module :mod:`sklearn.kernel_ridge` implements kernel ridge regression."""
# Authors: Mathieu Blondel <mathieu@mblondel.org>
# Jan Hendrik Metzen <jhm@informatik.uni-bremen.de>
# License: BSD 3 clause
import numpy as np
from .base import BaseEstimator, RegressorMixin, MultiOutputMixin
from .metrics.pairwi... | manhhomienbienthuy/scikit-learn | sklearn/kernel_ridge.py | Python | bsd-3-clause | 8,543 | [
"Gaussian"
] | 80f8233625981d3805feb6176deb0ac4bda63baf7e0f58375088c1b61d98e63b |
# -*- coding: utf-8 -*-
"""
8as Jornadas Sig Libre
26 de Marzo de 2014
Introducción a Python para usos geoespaciales
Ejemplos para trabajar con GDAL/python
"""
#Las librerías que usaremos son las siguientes:
from osgeo import gdal
import numpy as np
from tvtk.api import tvtk
from mayavi import mlab
import Image
# <... | rveciana/introduccion-python-geoespacial | mayavi_ejemplos.py | Python | gpl-2.0 | 1,518 | [
"Mayavi"
] | b096f7d212f2f35fcb03f812cf05b1465c260bac1b07e58a468fe8e9eeb3a38d |
# 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.
"""MPI communicator."""
from hoomd import _hoomd
import hoomd
import contextlib
class Communicator(object):
"""MPI communicator.
Args:
mpi_c... | joaander/hoomd-blue | hoomd/communicator.py | Python | bsd-3-clause | 6,596 | [
"HOOMD-blue"
] | 325a5ce2dfd4f629a1ebe26c955ef058dd0ceeb10a5722e8cb35c5f0b44ea46d |
# -*- coding: utf-8 -*-
from __future__ import absolute_import
import datetime
from django.conf import settings
from django.http import HttpResponse
from django.test import TestCase
from django.utils import timezone
from mock import patch
from zerver.lib.test_helpers import MockLDAP
from confirmation.models import Co... | samatdav/zulip | zerver/tests/test_signup.py | Python | apache-2.0 | 56,206 | [
"VisIt"
] | df351eb53ab7d28e00f5881e85cbba07d5f3792582e1620ab270d2b0363b9416 |
"""
It used to create several plots
"""
import time
import copy
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Core.Utilities.Plotting import gDataCache
from DIRAC.Core.Utilities.Plotting.Plots import generateNoDataPlot, generateTimedStackedBarPlot, generateQualityPlot, generateCumulativePlot, generatePiePlot, ge... | fstagni/DIRAC | MonitoringSystem/private/Plotters/BasePlotter.py | Python | gpl-3.0 | 15,571 | [
"DIRAC"
] | 4f13c3ce52b5867c562a20d76ecc3bb28ad887a89ffaa8873d98ad1339c4f829 |
from numpy import *
from pylab import *
import scipy.optimize.lbfgsb as lbfgsb
import numpy.linalg
from scipy.fftpack.realtransforms import dct,idct
import numpy as np
import numpy.ma as ma
def smoothn(y,nS0=10,axis=None,smoothOrder=2.0,sd=None,verbose=False,\
s0=None,z0=None,isrobust=False,W=None,s=None,MaxIter=100,... | ucfa/Landsat-processing | smoothn.py | Python | mit | 22,735 | [
"Gaussian",
"VisIt"
] | 8bec2e128f613158ba423240148dfdc3ba739443b85e8d1e32313bd5119cb7a8 |
# pygsear
# Copyright (C) 2003 Lee Harr
#
#
# This file is part of pygsear.
#
# pygsear is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.... | davesteele/pygsear-debian | examples/penguin_demos.py | Python | gpl-2.0 | 31,756 | [
"BLAST"
] | 9769f1f9c0d1eda85036e3b9a0060c5229e9bdcb8b4b6245cbe2e8fb7fcc2d26 |
########################################################################
# File : SSHComputingElement.py
# Author : Dumitru Laurentiu, A.T.
########################################################################
""" SSH (Virtual) Computing Element: For a given IP/host it will send jobs directly through ssh
"""
imp... | miloszz/DIRAC | Resources/Computing/SSHComputingElement.py | Python | gpl-3.0 | 27,238 | [
"DIRAC"
] | de85ac8b5503d9e16686633e83f55548db4b39b6b82bb6a0aa859981cc9e6665 |
# sql/compiler.py
# Copyright (C) 2005-2012 the SQLAlchemy authors and contributors <see AUTHORS file>
#
# This module is part of SQLAlchemy and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""Base SQL and DDL compiler implementations.
Classes provided include:
:class:`.com... | fredericmohr/mitro | mitro-mail/build/venv/lib/python2.7/site-packages/sqlalchemy/sql/compiler.py | Python | gpl-3.0 | 91,520 | [
"VisIt"
] | 7550297d5cc25c6e13923fc85973763279c44ff6f63d67c62985f9892e5ea6bb |
"""Core visualization operations."""
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Eric Larson <larson.eric.d@gmail.com>
# Oleh Kozynets <ok7mailbox@gmail.com>
# Guillaume Favelier <guillaume.favelier@gmail.com>
#
# License: Simplified BSD
from abc import ABCMeta, abstractcl... | Teekuningas/mne-python | mne/viz/backends/base_renderer.py | Python | bsd-3-clause | 15,242 | [
"Mayavi"
] | a5d66826d36d8b97626373d051d4872e3d8f996538f6e47c271094b323137d48 |
"""Guess the MIME type of a file.
This module defines two useful functions:
guess_type(url, strict=1) -- guess the MIME type and encoding of a URL.
guess_extension(type, strict=1) -- guess the extension for a given MIME type.
It also contains the following, for tuning the behavior:
Data:
knownfiles -- list of fil... | slozier/ironpython2 | Src/StdLib/Lib/mimetypes.py | Python | apache-2.0 | 21,076 | [
"NetCDF"
] | 6a34cf133b66264dd0c7b85a393a82bd6ed0c04d7ab13fbb60f61aa16e9186eb |
# -*- coding: utf-8 -*-
from numpy import *
import csv
import argparse
import os
from sklearn import cluster
import pandas as pd
from sklearn.metrics import precision_recall_fscore_support, confusion_matrix
import shutil
def write_data(ip_csv, op_csv, labels, type):
with open(ip_csv, "rb") as source, open(op_csv... | abhirevan/Yelp-Rate-my-Review | src/spectral.py | Python | mit | 3,869 | [
"Gaussian"
] | ad2947f20767a6ba489470cd8946aef44c46e24d5f5d57e46cd36bf9a00cddee |
""" This module contain solvers for all kinds of equations:
- algebraic, use solve()
- recurrence, use rsolve()
- differential, use dsolve()
- transcendental, use tsolve()
- nonlinear (numerically), use nsolve()
(you will need a good starting point)
"""
from sympy.core.sympify import s... | tarballs-are-good/sympy | sympy/solvers/solvers.py | Python | bsd-3-clause | 28,611 | [
"Gaussian"
] | 4671393719a4bb9ff737df66ee725a632edde70db51a20506fa2d34e0a8a2a00 |
#!/usr/bin/python
import os
from collections import OrderedDict
import ConfigParser
import tornado.httpserver
import tornado.httpclient
import tornado.ioloop
import tornado.web
import schemas
from operator import methodcaller
from tornado import gen
from tornado.options import define, options
from tornado import web... | UniPiTechnology/evok | evok/evok.py | Python | apache-2.0 | 85,335 | [
"NEURON"
] | 301e78c90688d859ebf078002f9b873d8ebfeb876d1672c755803441e2de5a3c |
#
# QAPI types generator
#
# Copyright IBM, Corp. 2011
#
# Authors:
# Anthony Liguori <aliguori@us.ibm.com>
#
# This work is licensed under the terms of the GNU GPL, version 2.
# See the COPYING file in the top-level directory.
from ordereddict import OrderedDict
from qapi import *
import sys
import os
import getopt
... | kashifqazi/qemu-migration | scripts/qapi-types.py | Python | gpl-2.0 | 11,584 | [
"VisIt"
] | ddadb14d2e8e3ffcc885ddafdbcf410389230e891c9f45da93eb619001a84764 |
# Copyright 2000-2001 by Andrew Dalke.
# Revisions copyright 2008 by Peter Cock.
# All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Standard nucleotide and protein alphabets de... | updownlife/multipleK | dependencies/biopython-1.65/build/lib.linux-x86_64-2.7/Bio/Alphabet/IUPAC.py | Python | gpl-2.0 | 3,188 | [
"Biopython"
] | 0c44045d06e2facff366831c2ea7d5868251fa98356cbc709704ce0abf6ff232 |
import ast
from docs.visitors.base import VisitorBase
class Function(VisitorBase):
"""Wraps `ast.FunctionDef` objects"""
def __init__(self, ast_node=None, source=None, *args, **kw):
if ast_node and not isinstance(ast_node, ast.FunctionDef):
raise TypeError('Expected an ast.FunctionDef object')
su... | codebrowse/docs | docs/function/function.py | Python | mit | 1,304 | [
"VisIt"
] | 8a4234e4ffddae23de7be0ceb8b8685373d5004b16174dc78b907cde04c01c6f |
import sys
from argparse import FileType
from octopus.shelltool.CmdLineTool import CmdLineTool
""" A Unix-style pipe tool, which reads from stdin if it is not a
tty-like device or optionally from a provided file and accepts
switches.
"""
class PipeTool(CmdLineTool):
def __init__(self, description):
... | octopus-platform/bjoern | python/octopus-tools/octopus/shelltool/PipeTool.py | Python | gpl-3.0 | 1,837 | [
"Octopus"
] | 1185095a3f3fd061ddd3f797641394e61a2411c86e3a1d365ea2a7e78b71b1f4 |
"""
This module gathers tree-based methods, including decision, regression and
randomized trees. Single and multi-output problems are both handled.
"""
# Authors: Gilles Louppe <g.louppe@gmail.com>
# Peter Prettenhofer <peter.prettenhofer@gmail.com>
# Brian Holt <bdholt1@gmail.com>
# Noel Da... | bnaul/scikit-learn | sklearn/tree/_classes.py | Python | bsd-3-clause | 70,932 | [
"Brian"
] | 0c175cf7f07980773c83ff9bbd8819046fbcad165360c19ce4ba1cc74f0d44ee |
from numpy import (logical_and, asarray, pi, zeros_like,
piecewise, array, arctan2, tan, zeros, arange, floor)
from numpy.core.umath import (sqrt, exp, greater, less, cos, add, sin,
less_equal, greater_equal)
# From splinemodule.c
from .spline import cspline2d, sepfir2d... | WarrenWeckesser/scipy | scipy/signal/bsplines.py | Python | bsd-3-clause | 19,509 | [
"Gaussian"
] | 31937a1ab592956e206dd9a845105491e57ce84aa31b94c3f61af9e2808d39b1 |
#
# Copyright 2009-2011 Red Hat, Inc.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed ... | futurice/vdsm | vdsm/storage/misc.py | Python | gpl-2.0 | 32,878 | [
"VisIt"
] | d04dfc020a0eadb252c50213e6cf62f51790791ef3da1bdc53cb804d54d0ea92 |
"""
Utilities for fitting stacked (drizzled) spectra
"""
from collections import OrderedDict
from imp import reload
import astropy.io.fits as pyfits
import astropy.units as u
import numpy as np
from . import utils
from .utils import GRISM_COLORS, GRISM_MAJOR, GRISM_LIMITS, DEFAULT_LINE_LIST
from .fitting import Gro... | gbrammer/grizli | grizli/stack.py | Python | mit | 49,418 | [
"Gaussian"
] | 18feb0ff665d942481bc3a8f69d1ae3a9e4142dfa71aa09d836207fd51a740fd |
"""
This module contain solvers for all kinds of equations:
- algebraic or transcendental, use solve()
- recurrence, use rsolve()
- differential, use dsolve()
- nonlinear (numerically), use nsolve()
(you will need a good starting point)
"""
from __future__ import print_function, division
f... | dennisss/sympy | sympy/solvers/solvers.py | Python | bsd-3-clause | 106,036 | [
"Gaussian"
] | 68c3f0cd978c2ed1510d4d3b17d1a9e084e706988148b10e3972e15d97b2be17 |
# 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/nao/na2/test_na2.py | Python | apache-2.0 | 1,729 | [
"PySCF",
"SIESTA"
] | 3ace8fd25dc92c51849bb32b9600bcac4d979e8a5468f9553e599fb6cc879eb9 |
import os
import re
import sys
import copy
import glob
import json
import shutil
import signal
import pandas
import inspect
import logging
import itertools
import subprocess
import collections
from contextlib import contextmanager
from pkg_resources import resource_filename
import mdtraj
import parmed
import numpy as... | jchodera/yank | Yank/utils.py | Python | lgpl-3.0 | 52,560 | [
"MDTraj",
"NetCDF",
"OpenMM"
] | 236c4728d9bf925434fed0ed9e40bb3ef8e4363bdccaf8f7f7addcd9fa535904 |
"""
Simple GLM with two neurons connected by a complete network with Gaussian weights.
"""
SpatiotemporalGlm = \
{
# Number of neurons (parametric model!)
'N' : 2,
# Parameters of the nonlinearity
'nonlinearity' :
{
'type' : 'exp'
},
# Parameters of the bias ... | slinderman/theano_pyglm | pyglm/models/spatiotemporal_glm.py | Python | mit | 2,210 | [
"Gaussian"
] | f5775890c360737a1d32fbf2900d9f4e7541c47981523f99534bba453ab1c289 |
import numpy as np
import pylab
def loadHData(fname='../input.txt'):
data = []
with open(fname) as f:
zs = f.readlines()
for z in zs:
if z != "EmptySpikeTrain":
data.append([x.strip('[()]') for x in z.split(',')])
data = np.array(data)
data.flatten()
data = data... | sheiksadique/HSimSNN | scripts/rasterplot.py | Python | gpl-2.0 | 685 | [
"NEURON"
] | c33841a7bc5a6e3928a41ee4e6da2f122087505870a85646dcb10ffaef37f388 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class PyBiopython(PythonPackage):
"""A distributed collaborative effort to develop Python librar... | iulian787/spack | var/spack/repos/builtin/packages/py-biopython/package.py | Python | lgpl-2.1 | 935 | [
"Biopython"
] | cddcfa745bb62d1a409f979666a64a61213c49bcf74d4fe68627f8ebb20c3241 |
r"""
Incompressible Stokes flow with Navier (slip) boundary conditions, flow driven
by a moving wall and a small diffusion for stabilization.
This example demonstrates the use of `no-penetration` and `edge direction`
boundary conditions together with Navier or slip boundary conditions.
Alternatively the `no-penetratio... | rc/sfepy | examples/navier_stokes/stokes_slip_bc.py | Python | bsd-3-clause | 11,063 | [
"VTK"
] | 0e75cbdd53d14485109a9e3b2ae11ef89a50e2ef9ff4ab70775d97870fdb1477 |
from mock import Mock
from contextlib import contextmanager
import lxml.etree as ET
from sphinxcontrib.autodoc_doxygen.autodoc import DoxygenMethodDocumenter
import sphinxcontrib.autodoc_doxygen
@contextmanager
def set_doxygen_root(node):
have_old_root = False
if hasattr(sphinxcontrib.autodoc_doxygen.setup, ... | angus-g/sphinxcontrib-autodoc_doxygen | tests/test_method_formatter.py | Python | mit | 2,630 | [
"OpenMM"
] | f72f2e422dd892e7854545e4842566c9c64b3af2fe83c50af08187274587a3bb |
#
# Copyright (C) 2013-2021 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... | fweik/espresso | testsuite/python/constant_pH.py | Python | gpl-3.0 | 2,845 | [
"ESPResSo"
] | caac49904f6b599554d74d4369f2651aebabc77bbaaa64cb93430f0c6f849b1b |
#!/usr/local/bin/env python
# Submit jobs to cluster
import os
import os.path
import commands
pbs_template = """\
#!/bin/tcsh
# Sample Batch Script for a MVAPICH2-Intel job
# on forge
#
#
#
# Submit this script using the command: qsub <script_name>
#
# Use the "qstat" command to check the status of a job.
#
# Th... | choderalab/brokenyank | examples/batchscripts/submit-jobs.py | Python | lgpl-3.0 | 5,251 | [
"Amber"
] | 9d48302ed14fbdbe2853d5d7bcab065e612dbc057b6ffe0ba31c1234fc309878 |
'''
TODO: Code below isn't working any longer. Need to adapt it to slight changes in the CBOE website
Copyright (C) 2015, Edouard 'tagoma' Tallent
Class fetching options data from www.nasdaq.com
Nasdaq_option_quotes.py v0.2 (Nov15)
QuantCorner @ https://quantcorner.wordpress.com
'''
from bs4 import BeautifulSoup
impo... | tagomatech/ETL | cboe_options/cboe_options.py | Python | mit | 12,254 | [
"MOE"
] | 4166e5007dbf0983698b28fa2894aed562e456cbd719bb5c81d14ee400b6db62 |
#!/bin/env python2.7
import sys
import os
import argparse
from collections import defaultdict
import pickle
import fileinput
'''
License:
This is free and unencumbered software released into the public domain. All authors are or
were bona fide officers or employees of the U.S. Government at the time the software was... | sanjuroj/bioscripts | ncbiTaxonomyMunger.py | Python | mit | 12,724 | [
"BLAST"
] | 75510c22732aca37e43f7074b5feacf358c8a1593e29dc2798cb8901478cc177 |
# -*- coding: utf-8 -*-
u"""PyTest for :mod:`sirepo.template.srw_shadow_converter`
:copyright: Copyright (c) 2020 RadiaSoft LLC. All Rights Reserved.
:license: http://www.apache.org/licenses/LICENSE-2.0.html
"""
from __future__ import absolute_import, division, print_function
from pykern import pkio
from pykern impor... | mkeilman/sirepo | tests/template/srw_shadow_converter_test.py | Python | apache-2.0 | 1,139 | [
"Gaussian"
] | a1d9d4e44bdc8b76f0b4f2a9bf7737421a2ac38fb8baec626f9d2987d1c873b0 |
from __future__ import division
import numpy as np
from matplotlib import pyplot as plt
plt.interactive(True)
from pybasicbayes import models, distributions
GENERATE_DATA = True
###########################
# generate or load data #
###########################
alpha_0=5.0
obs_hypparams=dict(mu_0=np.zeros(2),sigma_... | fivejjs/pybasicbayes | examples/meanfield_steps.py | Python | mit | 1,219 | [
"Gaussian"
] | 203bed81702cbd1dfce994094471ed82e196d00381c4f4f0636c7563822586e2 |
import math
import random
from moe.easy_interface.experiment import Experiment
from moe.easy_interface.simple_endpoint import gp_next_points
from moe.optimal_learning.python.data_containers import SamplePoint
# Note: this function can be anything, the output of a batch, results of an A/B experiment, the value of a p... | lukemetz/MLFun | moe/play.py | Python | mit | 1,920 | [
"MOE"
] | 64148b48335ffb6124315fc698e959d3ebd0f1307e32b42bb03a6ec9157384c7 |
import warnings
from chempy.util.testing import requires
from chempy.units import units_library
from ..water_diffusivity_holz_2000 import water_self_diffusion_coefficient as w_sd
def test_water_self_diffusion_coefficient():
warnings.filterwarnings("error")
assert abs(w_sd(273.15 + 0.0) - 1.099e-9) < 0.027e-9
... | bjodah/aqchem | chempy/properties/tests/test_water_diffusivity_holz_2000.py | Python | bsd-2-clause | 1,297 | [
"ChemPy"
] | 281234d9737f362592bdb6cca94558b08ff91ca4399ee3fbcb8a53ec32f1cb06 |
#!/usr/bin/env python
# Copyright 2014-2019 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | sunqm/pyscf | pyscf/grad/uccsd.py | Python | apache-2.0 | 23,512 | [
"PySCF"
] | bf1fe5a37a1c6f287114ccc64894e7cb6b2b9e605eefcab9e261cb618885b9aa |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2007-2008 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 Softw... | andrebellafronte/stoq | stoqlib/drivers/cheque.py | Python | gpl-2.0 | 3,158 | [
"VisIt"
] | 6dccce128b30df9647d9cb9033b4f06a3ef196ead43e64484b905d3ea73714ca |
#!/usr/bin/env python
"""Test template support in VTK-Python
VTK-python decides which template specializations
to wrap according to which ones are used in typedefs
and which ones appear as superclasses of other classes.
In addition, the wrappers are hard-coded to wrap the
vtkDenseArray and vtkSparseArray classe... | hlzz/dotfiles | graphics/VTK-7.0.0/Common/DataModel/Testing/Python/TestTemplates.py | Python | bsd-3-clause | 5,148 | [
"VTK"
] | 19d7d151d13633cc894cc90dab02a475def0b3edbf075bdbbe5cf83cf0ff905f |
# -*- coding: utf-8 -*-
import cv2
import numpy as np
import scipy.optimize
import skimage.color
import skimage.exposure
import skimage.io
import skimage.transform
import config
import util as helper
from feature.feature_historgam_sample import FeatureHistogramSample
from .transfer_base import TransferBase
class Tr... | jinyu121/ACACTS | transfer/transfer_style.py | Python | gpl-3.0 | 8,609 | [
"Gaussian"
] | b47704b45a6bf8ed202156a3f0eafcf74c63179db85546ca6805a30d8becba0b |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
... | kain88-de/mdanalysis | testsuite/MDAnalysisTests/topology/test_lammpsdata.py | Python | gpl-2.0 | 4,405 | [
"LAMMPS",
"MDAnalysis"
] | 5bfb217d0cb530a251e646e6732ee0948f35920eed888129f0a07ee860cfa4fb |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2002-2006 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
# 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 publ... | Forage/Gramps | gramps/gen/filters/rules/event/__init__.py | Python | gpl-2.0 | 2,236 | [
"Brian"
] | a426e446c7ed53c5d8656880c21fb7b7f39fec19dfe29be0584de43e89658f7e |
# -*- coding: utf-8 -*-
"""
==========================================================
Create a new coordinate class (for the Sagittarius stream)
==========================================================
This document describes in detail how to subclass and define a custom spherical
coordinate frame, as discussed in ... | funbaker/astropy | examples/coordinates/plot_sgr-coordinate-frame.py | Python | bsd-3-clause | 11,344 | [
"Galaxy"
] | d9f332bf55abee762b182ceac1bb11e3c82cea9c833521d0be52d43c888650ca |
# -*- coding: utf-8 -*-
"""Magic functions for InteractiveShell.
"""
#*****************************************************************************
# Copyright (C) 2001 Janko Hauser <jhauser@zscout.de> and
# Copyright (C) 2001-2006 Fernando Perez <fperez@colorado.edu>
#
# Distributed under the terms of th... | mastizada/kuma | vendor/packages/ipython/IPython/Magic.py | Python | mpl-2.0 | 135,645 | [
"VisIt"
] | 2603bd97e42fb30563cee3c5a0522381c4c352da34b84837dd47a1f096fd0d12 |
import numpy as np
from gpaw.grid_descriptor import GridDescriptor
from gpaw.localized_functions import create_localized_functions
from gpaw.spline import Spline
s=Spline(0, 1.2, [1, 0.6, 0.1, 0.0])
a = 4.0
n = 24
gd = GridDescriptor((n, n, n), (a, a, a))
print gd.get_boxes((0, 0, 0), 1.2, 0)
if 0:
p = create_loca... | qsnake/gpaw | gpaw/test/gp2.py | Python | gpl-3.0 | 447 | [
"GPAW"
] | 33fdc47cdf4d48a61ecedad34aeef82b3bc06157f7590333853e2c114b995f4e |
#!/usr/bin/python
# twitterize_pidgin_status.py
"""
Handy script for changing Pidgin's status with the last tweet from your Twitter
account feed.
Usage: ... | raducotescu/pidgin-status-scripts | twitterize_pidgin_status.py | Python | mit | 1,637 | [
"VisIt"
] | a1e0ab4baa87b94e5f7a1122360d613c2679c1066979e220ddff637a02980619 |
"""Gaussian processes regression."""
# Authors: Jan Hendrik Metzen <jhm@informatik.uni-bremen.de>
# Modified by: Pete Green <p.l.green@liverpool.ac.uk>
# License: BSD 3 clause
import warnings
from operator import itemgetter
import numpy as np
from scipy.linalg import cholesky, cho_solve
import scipy.optimize
from .... | glemaitre/scikit-learn | sklearn/gaussian_process/_gpr.py | Python | bsd-3-clause | 22,408 | [
"Gaussian"
] | 28c95c6a0581a1728e0795ee3ae68c7ae558985f2d8d37fc103af8ebc5d69684 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
from os.path import getmtime, exists
import time
import types
import __builtin__
from Cheetah.Version import MinCompatibleVersion as RequiredCheetahVersion
from Cheetah.Version import MinComp... | johm/infoshopkeeper | inventoryserver/TitleEditTemplate.py | Python | gpl-2.0 | 10,696 | [
"VisIt"
] | 31c3804f86acd2154b9679ca889073eb509c96ee3ac8f365a94b49f515df5edc |
"""
functions to access the data dictionary in a clearer way
"""
import os
import toolz as tz
from bcbio.utils import file_exists
from bcbio.log import logger
import sys
LOOKUPS = {
"config": {"keys": ['config']},
"num_cores": {"keys": ['config', 'algorithm', 'num_cores'],
"default": 1},
... | hjanime/bcbio-nextgen | bcbio/pipeline/datadict.py | Python | mit | 7,590 | [
"Galaxy"
] | 55a68fa09b3ae01c9e823922ea0ae37dbbd2f2bf7c686ba283f69a45995ba54f |
from registry.models import Passport, Visit
from registry.extensions import db
def test_sweep_closes_visits(app):
"""Visits are ordered by check_in"""
with app.test_request_context():
passport = Passport(surname='John', name='Doe', pass_id=111,
phone='123', age=7, address='... | arsgeografica/kinderstadt-registry | test/unit/test_sweep.py | Python | gpl-3.0 | 1,182 | [
"VisIt"
] | 797bfbfeadd81732d54409fe506fef31f841c44641e66b5136ca173302bf129e |
# -*- coding: utf-8 -*-
"""
Scanner
Module containing classes to scan the coordinates read from a PDB
(SasMolScan) and extract data by chains (for reconciliation with PDB headers)
and segnames to be evaluate the system as a candidate for simulation in the
CHARMM forcefield.
"""
'''
SASSIE: Copyright (C) 2011 Jose... | madscatt/zazzie | src_2.7/sassie/build/pdbscan/pdbscan/scanner.py | Python | gpl-3.0 | 103,453 | [
"CHARMM",
"NAMD",
"VMD"
] | 4b75153a1e71b93c54b426f2fe99bb3e55e30e21c357262abcc2bc1487160601 |
#This module is used to store and read some temperary data.
import cPickle
import os
from gpaw.mpi import world
from gpaw.transport.tools import collect_atomic_matrices, gather_ndarray_dict
import numpy as np
class Transport_IO:
def __init__(self, kpt_comm, domain_comm):
self.kpt_comm = kpt_comm
self.doma... | robwarm/gpaw-symm | gpaw/transport/io.py | Python | gpl-3.0 | 6,564 | [
"GPAW"
] | 671de665b2bcef4e9d36cbda1f03ab9841a385bb088a230a237f9d7aec9cf983 |
#!/usr/bin/env python
# -*- codinag: utf-8 -*-
'''
orcaserver:
Orca Server is a simple restful server, that will invoke the orcalib
to return the appropriate information.
The first usecase for this server is with Rundeck Job definitions. Rundeck
can invoke the rest apis to get the correct parameter values rather than... | bdastur/orca | server/orcaserver.py | Python | apache-2.0 | 4,448 | [
"ORCA"
] | 4adde06c9c6bb41e3792e5c3808890a00d51b82abae2697bd0a7f70ddf499d2d |
"""
This is the theory part of the code.
Compute the mass and initial conditions spectrum.
Get all other params.
DJEM+MS+CP, 2017
"""
import numpy as np
import ConfigParser
import numpy.random as rd
import quasi_observable_data as quasi # for mcut
config = ConfigParser.RawConfigParser()
# Note that np.linalg.eig(M... | DoddyPhysics/AxionNet | model_class.py | Python | mit | 17,444 | [
"Gaussian"
] | 14b9f6350dd6b3981e90487a4a28b9fa279cb547783d2da6005b22f351f2d4bf |
"""Testing out Point Cloud Library
"""
from __future__ import absolute_import, division, print_function, unicode_literals
import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
from mayavi import mlab
import pdb
import pcl
def segment_cyl_plane(filename='./data/point_clouds/table_s... | skulumani/asteroid_dumbbell | integration/pcl_examples.py | Python | gpl-3.0 | 7,638 | [
"Mayavi"
] | fa75cbf79f72e70538f0463ebbf07d165a9851d3c8b82fdf17b7e44f507c023a |
# Copyright 2016 Mingbo Cai, Princeton Neuroscience Instititute,
# Princeton University
#
# 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... | IntelPNI/brainiak | brainiak/reprsimil/brsa.py | Python | apache-2.0 | 212,121 | [
"Gaussian"
] | 25e883bd339a3995e19b7f8055d7ffe25c441ceb5cffbf51d32ba8953be69ac9 |
##########################################################################################
## _______ .______ ______ .__ __. _______ ______ _______ _______ ##
## | \ | _ \ / __ \ | \ | | | ____| / || ____|| \ ##
## | .--. || |_) | | | | | | \| | ... | dronecfd/droneCFD | examples/single_run_example.py | Python | gpl-2.0 | 2,034 | [
"ParaView"
] | 40af3910d85f4ecbbf5815b5d5045909bc8889e43c16ca5889177b149990b3fa |
#!/usr/bin/env python
"""
Adds Manually created builds and chrom info to Galaxy's info tables
Usage:
python add_manual_builds.py input_file builds.txt chrom_length_dir
"""
import sys,os
def add_manual_builds(input_file, build_file, chr_dir):
#determine existing builds, so as to not overwrite
existing_builds... | volpino/Yeps-EURAC | cron/add_manual_builds.py | Python | mit | 1,518 | [
"Galaxy"
] | 045d5d84acb20b13d8962f3d819ed0406e35d472ee63ae6b8a53ffbb9ed959ee |
#
# Copyright (c) 2000 Autonomous Zone Industries
# This file is licensed under the
# GNU Lesser General Public License v2.1.
# See the file COPYING or visit http://www.gnu.org/ for details.
#
# `templs' is a dict from message types to templates that messages of that type must match.
templs = {}
| zooko/egtp | common/templs.py | Python | agpl-3.0 | 309 | [
"VisIt"
] | 2585e6d7f7afe74238a28ff5bee8869a0f9aff52c011d21f5cf872ed26fdb1b3 |
"""
This module implements the HSP serialisation class.
"""
from sqlalchemy import Column, String, Integer, Float, ForeignKey, Index
from sqlalchemy.sql.schema import PrimaryKeyConstraint, UniqueConstraint
from sqlalchemy.orm import relationship, column_property, backref
from sqlalchemy import select
from sqlalchemy.e... | lucventurini/mikado | Mikado/serializers/blast_serializer/hsp.py | Python | lgpl-3.0 | 11,055 | [
"BLAST"
] | 850bb5ee3511493c45c6bd3687ee6697539d5f5f165a77a460b4f15f1f489d17 |
import os
from ase import Atoms
from ase.io import read, write
from ase.calculators.exciting import Exciting
from ase.units import Bohr, Hartree
from ase.test import NotAvailable
try:
import lxml
except ImportError:
raise NotAvailable('This test need lxml module.')
a = Atoms('N3O',
[(0, 0, 0), (1, 0... | conwayje/ase-python | ase/test/exciting/exciting.py | Python | gpl-2.0 | 742 | [
"ASE",
"exciting"
] | 971bfce5457b77beff64f31af9d53d41cff94334f5bcf55c7855c71fefbae159 |
########################################################################
# $HeadURL $
# File: ForwardDISET.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/03/22 12:40:06
########################################################################
""" :mod: ForwardDISET
==================
.. module: Forwar... | fibbo/DIRAC | RequestManagementSystem/Agent/RequestOperations/ForwardDISET.py | Python | gpl-3.0 | 2,712 | [
"DIRAC"
] | dde7a0e426ee5c3e393f73491f1eb879c38083aafe98926edbb8a78f3d119d7d |
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