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'''
A module for storing meta data of a (reference) genome
Created on Nov 5, 2012
@author: Shunping Huang
'''
import os
import tempfile
import xml.etree.ElementTree as ET
from modtools import alias
__all__ = ['defaultXML', 'MetaData']
mm9_xml = '''
<genome>
<name>mm9</name>
<alias>NCBI37</alias>
<alias>NCBI Build ... | andrewparkermorgan/lapels | modtools/metadata.py | Python | mit | 18,089 | [
"pysam"
] | 81c8fba34d177c4226898b6da659d9b1865c9c1771933226f9acea1e11620a18 |
#!/usr/bin/env python
from collections import defaultdict
import numpy as np
from scipy.interpolate import LSQBivariateSpline
######### ######### ######### ######### ######### ######### ######### #########
######### Flat Field models #########
######### ######### ######### #... | imcgreer/uberpy | uberpy/ubercal.py | Python | bsd-3-clause | 11,412 | [
"Galaxy"
] | cda49ba46f26954e09096fc0d8d9cf432d765b3bfdf11c559f2e28ce9c29917c |
# This file is part of eventmq.
#
# eventmq 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 Foundation, either version 2.1 of the License, or (at your option)
# any later version.
#
# eventmq is distributed in the ... | com4/eventmq | eventmq/log.py | Python | lgpl-2.1 | 2,934 | [
"BLAST"
] | f1dd766c68a8019d7828d2df308c9386ddba5af8bbc24eaaebde19e4316c3360 |
# coding: utf-8
# Copyright (c) 2015,Vienna University of Technology,
# Department of Geodesy and Geoinformation
# 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... | christophreimer/pytesmo | tests/test_validation.py | Python | bsd-3-clause | 7,851 | [
"NetCDF"
] | 5b5d3d4c3fd8aa198d360eddc7e063402b84c6cfe03d877ce5ada4cafb069881 |
import click
from parsec.cli import pass_context, json_loads
from parsec.decorators import custom_exception, json_output
@click.command('get_repositories')
@pass_context
@custom_exception
@json_output
def cli(ctx):
"""Get the list of all installed Tool Shed repositories on this Galaxy instance.
Output:
a li... | galaxy-iuc/parsec | parsec/commands/toolshed/get_repositories.py | Python | apache-2.0 | 999 | [
"Galaxy"
] | 6f2f284daa4c68d87df1f908818c6e3a098b14012bbf4d06ccc0eb0167d40df4 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# (c) 2012 Michal Kalewski <mkalewski at cs.put.poznan.pl>
#
# This file is a part of the Simple Network Simulator (sim2net) project.
# USE, MODIFICATION, COPYING AND DISTRIBUTION OF THIS SOFTWARE IS SUBJECT TO
# THE TERMS AND CONDITIONS OF THE MIT LICENSE. YOU SHOULD H... | mkalewski/sim2net | sim2net/mobility/random_waypoint.py | Python | mit | 17,106 | [
"VisIt"
] | 1c9d797b934d0a198c6050c215d61aee4f079f609f6a90f9102dc4ed062d0ca0 |
# Copyright (c) 2003-2013 LOGILAB S.A. (Paris, FRANCE).
# http://www.logilab.fr/ -- mailto:contact@logilab.fr
# Copyright (c) 2009-2010 Arista Networks, 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
... | GbalsaC/bitnamiP | venv/lib/python2.7/site-packages/pylint/checkers/base.py | Python | agpl-3.0 | 55,089 | [
"VisIt"
] | 554b789342dc7dc66076c49c54cceef0b062b1ac43bb1a583f1403a22d491f83 |
# -*- coding: utf-8 -*-
#
# RDKit documentation build configuration file, created by
# sphinx-quickstart on Sun Aug 7 18:51:45 2011.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All c... | rdkit/rdkit-orig | Docs/Book/conf.py | Python | bsd-3-clause | 7,103 | [
"RDKit"
] | 48a4fc4e76e4844452bd6ab3801eab47ef3ecf47d1ecc7c97c7e78c339017365 |
import os
from glob import glob
from collections import Counter
import numpy as np
from json import dump, load
from traitlets import TraitError
import matplotlib.pyplot as plt
import matplotlib.ticker as mtick
import matplotlib.gridspec as gridspec
from traitlets import validate
from ipywidgets import IntRangeSlider
... | deisi/SFG2D | sfg2d/widgets.py | Python | mit | 66,147 | [
"Gaussian"
] | e34dab4bf4e9f6e3ea9f3bed68d124a008785750345bc2e3b7365784fa8f8cb2 |
"""Unit tests for reviewboard.accounts.managers.ReviewRequestVisitManager."""
from django.contrib.auth.models import User
from reviewboard.accounts.models import ReviewRequestVisit
from reviewboard.testing import TestCase
class ReviewRequestVisitTests(TestCase):
"""Unit tests for reviewboard.accounts.managers.R... | reviewboard/reviewboard | reviewboard/accounts/test_review_request_visit_manager.py | Python | mit | 2,167 | [
"VisIt"
] | 548128721fabc460cd611092fc5d6d684f4db29cd4cd029edf5ca06c0c6e1f92 |
#!/usr/bin/env python
"""Create 3-Layers BEM model from Flash MRI images
This function extracts the BEM surfaces (outer skull, inner skull, and
outer skin) from multiecho FLASH MRI data with spin angles of 5 and 30
degrees. The multiecho FLASH data are inputted in NIFTI format.
It was developed to work for Phillips MR... | jaeilepp/eggie | mne/commands/mne_flash_bem_model.py | Python | bsd-2-clause | 5,454 | [
"Mayavi"
] | f7fcf89ca8b5b3043ccd1513bf3f31deb96d01ac43c185dc7baebb20ac25f41a |
# GromacsWrapper: scaling.py
# Released under the GNU Public License 3 (or higher, your choice)
# See the file COPYING for details.
"""
:mod:`gromacs.scaling` -- Partial tempering
===========================================
:Author: Jan Domanski, @jandom
.. versionadded:: 0.5.0
Helper functions for scaling gromacs... | Becksteinlab/GromacsWrapper | gromacs/scaling.py | Python | gpl-3.0 | 11,438 | [
"Gromacs"
] | f23762cbb629a584aa390f65edf463c0124a2d456fd965901107dd93e400f938 |
# This file is part of ts_wep.
#
# Developed for the LSST Telescope and Site Systems.
# This product includes software developed by the LSST Project
# (https://www.lsst.org).
# See the COPYRIGHT file at the top-level directory of this distribution
# for details of code ownership.
#
# This program is free software: you ... | lsst-ts/ts_wep | python/lsst/ts/wep/task/EstimateZernikesBase.py | Python | gpl-3.0 | 17,761 | [
"VisIt"
] | c1271716797bb66b13cef987adf166696ba33443548da3fb225ddc1e1d8e7523 |
"""
Testing for the forest module (sklearn.ensemble.forest).
"""
# Authors: Gilles Louppe,
# Brian Holt,
# Andreas Mueller,
# Arnaud Joly
# License: BSD 3 clause
import pickle
from collections import defaultdict
from itertools import product
import numpy as np
from sklearn.utils.testing im... | Garrett-R/scikit-learn | sklearn/ensemble/tests/test_forest.py | Python | bsd-3-clause | 28,031 | [
"Brian"
] | 9c89ce3a5a948020bd7f998038057a440878fb0c3747cb925782ea8db3dfc46c |
#!/usr/bin/env python
#
# ObsPlan.py
#
# Elisa Antolini
# Jeremy Heyl
# UBC Southern Observatory
#
# This script takes the LIGO-Virgo Skymap (P(d|m)) and optionally a
# galaxy-density map (P(m)) and finds the most likely fields to
# observe (P(m|d)). The fields are assumed to be healpix regions from a
# tesselation wi... | UBC-Astrophysics/ObsPlan | ObsPlan.py | Python | gpl-3.0 | 9,933 | [
"Galaxy"
] | 9c777b036deb6286706064f973eeacb5febd031d590641e5aebd4450986a8c8d |
from __future__ import print_function, division
import os,unittest,numpy as np
from pyscf.nao import mf as mf_c
from pyscf.data.nist import HARTREE2EV
from pyscf.nao.m_overlap_ni import overlap_ni
class KnowValues(unittest.TestCase):
def test_0073_vna_vnl_N2(self):
""" Test the Ena energy and indirectly VNA mat... | gkc1000/pyscf | pyscf/nao/test/test_0073_vna_vnl_n2.py | Python | apache-2.0 | 854 | [
"PySCF",
"SIESTA"
] | c679b1e99f8bdbc1584120f5bbfc642cfa981f3f403c0341629bbd6eeed808b2 |
#!/usr/bin/env python
# ----------------------------------------------------------------------------
# Copyright (c) 2016--, Biota Technology.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# -------------------------------------... | biota/sourcetracker2 | setup.py | Python | bsd-3-clause | 3,163 | [
"scikit-bio"
] | 60c2a6101a1950c159082c3eb4be6943f42550aaa6cbbd4457a7c92beb536ac5 |
"""rallpacks_cable_hhchannel.py:
A cable with 1000 compartments with HH-type channels in it.
Last modified: Wed May 21, 2014 09:51AM
"""
__author__ = "Dilawar Singh"
__copyright__ = "Copyright 2013, NCBS Bangalore"
__credits__ = ["NCBS Bangalore", "Bhalla Lab"]
__license__ ... | subhacom/moose-core | tests/python/Rallpacks/rallpacks_cable_hhchannel.py | Python | gpl-3.0 | 7,784 | [
"MOOSE"
] | 6b4aa82e4577a8e39dd675b9217e4b4b287b393178d6bc657ce6fe5c98dc4cc9 |
#===============================================================================
# LICENSE XOT-Framework - CC BY-NC-ND
#===============================================================================
# This work is licenced under the Creative Commons
# Attribution-Non-Commercial-No Derivative Works 3.0 Unported Lic... | SMALLplayer/smallplayer-image-creator | storage/.xbmc/addons/net.rieter.xot.smallplayer/resources/libs/cache/cachehttphandler.py | Python | gpl-2.0 | 7,433 | [
"VisIt"
] | 90b7cd3d660e74bc59d4c47b4a2ec8455881ef1928d7bfd2e384851ee87541ea |
#!/usr/bin/env python
import os, time, re
from functools import partial
from flask import Flask, Module, url_for, request, session, redirect, g, make_response, current_app, render_template
from decorators import login_required, guest_or_login_required, with_lock
from decorators import global_lock
# Make flask use the o... | jdemeyer/sagenb | sagenb/flask_version/base.py | Python | gpl-3.0 | 19,263 | [
"Jmol"
] | 7b840da72d6ba988049978e53cc9c84b935e9714fca14d619236ff20d2ee51e9 |
"""
Description:
Module to convert ase.db files into a catmap input file
<fname>.db: db file
Contains all adsorbate states on
surfaces and clean slabs for reference.
Mandatory key value pairs:
--------------------------
"name" : str
Value that identif... | mieand/catmap | catmap/api/ase_data.py | Python | gpl-3.0 | 59,604 | [
"ASE",
"CRYSTAL"
] | 9f56c42c28f067e5ecbd94213ceb3b2c55e4c2217f046a272db9c12a56a0c8fa |
#!/usr/bin/env python
""" demo run for ase_qmmm_manyqm calculator """
# ./test_ase_qmmm_manyqm.py gromacs_mm-relax.g96
from ase.calculators.gromacs import Gromacs
from ase.calculators.aims import Aims
from ase.calculators.ase_qmmm_manyqm import AseQmmmManyqm
from ase.optimize import BFGS
import sys
from ase.io.grom... | conwayje/ase-python | doc/ase/calculators/test_ase_qmmm_manyqm.py | Python | gpl-2.0 | 2,703 | [
"ASE",
"FHI-aims",
"GROMOS",
"Gromacs"
] | 30d16cada639b82d65689055670724a5b83cfd6d6b485276e2ed6ef9bd1e43e7 |
# -*- Mode: Python; coding: utf-8; indent-tabs-mode: nil; tab-width: 4 -*-
### BEGIN LICENSE
# Copyright (C) 2014 Brian Douglass bhdouglass@gmail.com
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License version 3, as published
# by the Free Softwa... | bhdouglass/agui | agui/backends/pyside/extras/message.py | Python | gpl-3.0 | 1,667 | [
"Brian"
] | 095e7f02f037a4adb47b866a8841448485fe6492a5212738de3635a00f230b9c |
# Datasets.
import json
import click
import mapbox
from mapboxcli.errors import MapboxCLIException
@click.group(short_help="Read and write Mapbox datasets (has subcommands)")
@click.pass_context
def datasets(ctx):
"""Read and write GeoJSON from Mapbox-hosted datasets
All endpoints require authentication. ... | mapbox/mapbox-cli-py | mapboxcli/scripts/datasets.py | Python | mit | 9,701 | [
"VisIt"
] | ce448333e6ecad7eca41080e1b8a85ad2176a53c7576b26b1866600974093510 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements a FloatWithUnit, which is a subclass of float. It
also defines supported units for some commonly used units for energy, length,
temperature, time and charge. FloatWithUnit also suppor... | gmatteo/pymatgen | pymatgen/core/units.py | Python | mit | 27,212 | [
"pymatgen"
] | e3d96db331097b2d8672faa13b38cee8b7412b8cc6b770767bbb82fe90bf4867 |
"""
Acceptance tests for Studio related to the container page.
The container page is used both for displaying units, and
for displaying containers within units.
"""
import datetime
from unittest import skip
import ddt
from nose.plugins.attrib import attr
from base_studio_test import ContainerBase
from common.test.acc... | fintech-circle/edx-platform | common/test/acceptance/tests/studio/test_studio_container.py | Python | agpl-3.0 | 70,273 | [
"VisIt"
] | 71bd5327deed7e47e2a9921765d3471ef0ee95aeeeb42b18ff2e90dc5c486bab |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | mfherbst/spack | var/spack/repos/builtin/packages/r-absseq/package.py | Python | lgpl-2.1 | 1,880 | [
"Bioconductor"
] | 1a362e76df09783f1d20ca1cd3319a721f1925c9f2f260476da74407ad82debf |
# This file is part of cclib (http://cclib.sf.net), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2006, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public version 2.1 or later. You shou... | Clyde-fare/cclib_bak | src/cclib/parser/jaguarparser.py | Python | lgpl-2.1 | 20,075 | [
"Jaguar",
"cclib"
] | a76fd43610c5ccae9001613eea2b78d4833a351d02e7ee716179dad37c200f34 |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | sarvex/tensorflow | tensorflow/python/ops/linalg/linalg_impl.py | Python | apache-2.0 | 65,679 | [
"Gaussian"
] | 63838a28ea72c76afada1986c5ba4810bc05a8be10d32b83f6b47f814776a94c |
from sandbox.rocky.tf.q_functions.base import QFunction
import sandbox.rocky.tf.core.layers as L
import tensorflow as tf
import numpy as np
from rllab.core.serializable import Serializable
from sandbox.rocky.tf.core.layers_powered import LayersPowered
from sandbox.rocky.tf.misc import tensor_utils
from sandbox.rocky.tf... | brain-research/mirage-rl-qprop | sandbox/rocky/tf/q_functions/naf_mlp_q_function.py | Python | mit | 8,719 | [
"Gaussian"
] | 0f260f4aa8c861d5198884b4c3fd151843c0d93990c0434c458f480645a3bf31 |
stageDefaults = {
'distributed': True,
'walltime': "08:00:00",
'memInGB': 8,
'queue': "batch",
'modules': [
"bwa-gcc/0.5.9",
"samtools-gcc/0.1.16",
"picard/1.53",
"python-gcc/2.6.4",
"R-gcc/2.12.0",
"gatk/1.6-7"
]
}
stages = {
"fastqc": {
... | claresloggett/test-repo-varcall | pipeline_stages_config.py | Python | mit | 5,140 | [
"BWA"
] | 571d8c7c55cf6d1988fdc29eb310a405a7a9ab4c4830036f1feccf6e8a4dd378 |
#!/usr/bin/enb python
# encoding: utf-8
import urllib2
import time
import os
PROXIES_LIST="proxies.lst"
def getHttpProxyHandlers():
with open( PROXIES_LIST ) as f:
for line in f:
yield urllib2.ProxyHandler( {"http":line.strip()} )
def getOpeners():
for httpProxyHandler in getHttpProxyHan... | syakesaba/selenium-xvfb | proxyGen/getter.py | Python | mit | 1,238 | [
"Firefly"
] | d691ebad40d6ee1ffdaf23f95a8ad60cdad9d3a653deee8260129f54c5944181 |
import pymongo
import bson
import unittest
import mock
import cPickle
from datetime import datetime
from mongoengine import *
from mongoengine.base import _document_registry
from mongoengine.connection import _get_db, connect
import mongoengine.connection
from mock import MagicMock, Mock, call
import pymongo
mongoen... | ContextLogic/mongoengine | tests/document.py | Python | mit | 44,899 | [
"exciting"
] | 44d68a167af8e23441dd6b4f771df060846e6fbaab0513e70f15e9c96f506160 |
#
# script to calculate tangential and sagittal focusing radii for crystals
# and Rowland condition for gratings and asymmetric crystals
#
import xraylib
import numpy
import scipy.constants as codata
tocm = codata.h*codata.c/codata.e*1e2
#
# define miller indices, distances and photon energy in eV
#
hh = 1
kk = 1
ll... | srio/ShadowOui-Tutorial | SCRIPTS/script22.py | Python | mit | 1,616 | [
"CRYSTAL"
] | 888d1df258a438c0199af92990b0a0793566f928b599bce205e4b1bbfd504c36 |
from discord.ext import commands
import urllib.request
import json
import math
from .utils import checks
from __main__ import send_cmd_help, settings
from .utils.dataIO import fileIO, dataIO
class Elite():
def __init__(self,bot):
self.bot = bot
self.cmdr_list = dataIO.load_json("data/mod/cmdr.json"... | b0r3d0/kitty | cogs/elite.py | Python | gpl-3.0 | 8,850 | [
"ORCA"
] | a93e7a42ee3e9252c4265f460ec584168312d6325df82e16069c9168f9928908 |
#!/usr/bin/env python
from ez_setup import use_setuptools
use_setuptools()
from setuptools import setup
## from distutils.core import setup
setup(name='topoflow',
version='3.4',
description='d8-based, spatial hydrologic model',
author='Scott D. Peckham',
author_email='Scott.Peckham@colorado.e... | mdpiper/topoflow | setup.py | Python | mit | 1,969 | [
"NetCDF"
] | 2ae82b4b8f0ff883c5091e99766c084ca21929f6b022223c3a0bf7fff0cb0dd6 |
__source__ = 'https://leetcode.com/problems/letter-case-permutation/'
# Time: O(2^{N} * N)
# Space: O(2^{N} * N)
#
# Description: Leetcode # 784. Letter Case Permutation
#
# Given a string S, we can transform every letter individually to be lowercase or uppercase
# to create another string. Return a list of all possi... | JulyKikuAkita/PythonPrac | cs15211/LetterCasePermutation.py | Python | apache-2.0 | 3,758 | [
"VisIt"
] | 849ecb7e088dff5ad4b474f6fa286161887201a0f6de1395bf7f996ae609c53e |
"""Convert three terms recurrence coefficients into quadrature rules."""
import numpy
import scipy.linalg
def coefficients_to_quadrature(coeffs):
"""
Construct Gaussian quadrature abscissas and weights from three terms
recurrence coefficients.
Examples:
>>> distribution = chaospy.Normal(0, 1)... | jonathf/chaospy | chaospy/recurrence/jacobi.py | Python | mit | 1,764 | [
"Gaussian"
] | ea3f72f21e46d69d08c745843b547f039270cb2395763bad499268e9007e0cd0 |
import pdb
import numpy as np
import cPickle as pickle
from utils import black
from utils import loggen
#from astropy.cosmology import FlatLambdaCDM
from astropy.cosmology import Planck15 as cosmo
import astropy.units as u
from lmfit import Parameters, minimize, fit_report
L_sun = 3.839e26 # W
c = 299792458.0 # m/s
d... | marcoviero/Utils | invert_sed.py | Python | mit | 12,970 | [
"Galaxy"
] | a1b965e2ecb9359b2e549e729a15b1da723481a6e2c634f53dafea40f11809f7 |
#=======================================================================
# debug_utils.py
#=======================================================================
# Collection of utility functions used for debugging models.
from __future__ import print_function
import ...model.Model as model
import sys
import ast, _a... | Glyfina-Fernando/pymtl | pymtl/tools/deprecated/debug_utils.py | Python | bsd-3-clause | 4,345 | [
"VisIt"
] | 886890c541c35ebe1d9d900e6f55514c55a32a372d1ca51dce9f26b42b694327 |
#!/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/flac.py | Python | gpl-2.0 | 125,969 | [
"Brian"
] | 3b6b2f14fe455e868879b6c4e10b47b5d50cddb8bc02c8fe621378eb8d75f71f |
import sys
import os
import glob
import difflib
import gzip
import contextlib
import inspect
import subprocess
import tempfile
import pysam
WORKDIR = os.path.abspath(os.path.join(os.path.dirname(__file__),
"pysam_test_work"))
BAM_DATADIR = os.path.abspath(os.path.join(os.path.di... | pysam-developers/pysam | tests/TestUtils.py | Python | mit | 7,792 | [
"pysam"
] | 70a9bce026d6c67cdc66a6851cdbbc1be70e0bfc62c4c39edf6cd4d80d2be825 |
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Security import Properties
from DIRAC.AccountingSystem.private.Policies.FilterExecutor import FilterExecutor
class JobPolicy:
def __init__( self ):
self.__executor = FilterExecutor()
self.__executor.addGlobalFilter( self.__checkConditions )
def getListingC... | Sbalbp/DIRAC | AccountingSystem/private/Policies/JobPolicy.py | Python | gpl-3.0 | 3,221 | [
"DIRAC"
] | 042091419f3eb6a8439f46c8401332d266736204a9ada9b82d8de17df08dcc52 |
########################################################################
# File : dirac-proxy-init.py
# Author : Adrian Casajus
########################################################################
from __future__ import print_function
import sys
import getpass
import DIRAC
from DIRAC.Core.Base import Script
_... | fstagni/DIRAC | FrameworkSystem/Client/ProxyUpload.py | Python | gpl-3.0 | 5,948 | [
"DIRAC"
] | e885158efeeb62defc27b92c06b6ab82d69e62be8077bfc71fef39f498a730b9 |
import math
import string
import sys
import struct
import matplotlib
matplotlib.use('TkAgg')
import matplotlib.pyplot as pyplot
import matplotlib.colors as pycolors
import matplotlib.cm as cm
import matplotlib.patches as patches
import numpy as np
#import cPickle
import scipy.ndimage
import scipy.stats as ss
import sci... | gsnyder206/synthetic-image-morph | statmorph_gfs.py | Python | gpl-2.0 | 82,960 | [
"Galaxy",
"Gaussian"
] | 853f5b8f127ffe3ac100bef1656f11ad79001a28fbc7399ab2543c2d0026ae9a |
""" This is a test of using WMSClient and several other functions in WMS
In order to run this test we need the following DBs installed:
- JobDB
- JobLoggingDB
- TaskQueueDB
- SandboxMetadataDB
And the following services should also be on:
- OptimizationMind
- JobManager
- SandboxSt... | yujikato/DIRAC | tests/Integration/WorkloadManagementSystem/Test_Client_WMS.py | Python | gpl-3.0 | 22,709 | [
"DIRAC"
] | 01405d63fe474adabaa2b4fd59d96371e7ea8385c9ae1ba0e2fbb1c50c2f167a |
#!/usr/bin/env python
import bz2
import gzip
import json
import optparse
import os
import shutil
import subprocess
import sys
import tarfile
import tempfile
import urllib.error
import urllib.parse
import urllib.request
import zipfile
from ftplib import FTP
CHUNK_SIZE = 2**20 # 1mb
def cleanup_before_exit(tmp_dir):
... | mvdbeek/tools-iuc | data_managers/data_manager_diamond_database_builder/data_manager/data_manager_diamond_database_builder.py | Python | mit | 10,627 | [
"BLAST"
] | 6953a3bb54abde23dee581a0317c8a56035e6cffa16ddb9d23f6dd41f6c0e341 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Author: Vincent Dubourg <vincent.dubourg@gmail.com>
# (mostly translation, see implementation details)
# License: BSD style
import numpy as np
from scipy import linalg, optimize, rand
from ..base import BaseEstimator, RegressorMixin
from ..metrics.pairwise import m... | cdegroc/scikit-learn | sklearn/gaussian_process/gaussian_process.py | Python | bsd-3-clause | 32,730 | [
"Gaussian"
] | 22578a7890fd7bb719f8b3d27b4e4bb265796a3da1dacf140d33c274a5742b1f |
# encoding: utf-8
import os
import numpy as np
import glob
import re
try:
import netCDF4 as netCDF
except:
import netCDF3 as netCDF
import pyroms
import pyroms_toolbox
import _remapping
import matplotlib.pyplot as plt
import datetime
def remapping_bound(varname, srcfile, wts_files, srcgrd, dst_grd, \
... | dcherian/pyroms | pyroms_toolbox/pyroms_toolbox/remapping_bound.py | Python | bsd-3-clause | 38,551 | [
"NetCDF"
] | f6e1c2b730271bff23481f08e5f999893694942b92a39aa3342843f0c9829029 |
import logging
import numpy as np
from collections import OrderedDict
import theano
import theano.tensor as T
from theano.sandbox.rng_mrg import MRG_RandomStreams as RandomStreams
from theano.tensor.nnet.conv import conv2d, ConvOp
from theano.sandbox.cuda.blas import GpuCorrMM
from theano.sandbox.cuda.basic_ops impor... | ryukinkou/ladder_customized | ladder_theano_gpu1/ladder.py | Python | mit | 25,301 | [
"Gaussian"
] | 2195938902b29416ca52499ba7223e64078da0e74f9f64e6d79b6e15083a42c0 |
# File generated from python blocks in "doc/atomic-ops.tex"
>>> import sys
>>> HOST = sys.argv[2]
>>> PORT = int(sys.argv[3])
>>> import hyperdex.admin
>>> a = hyperdex.admin.Admin(HOST, PORT)
>>> a.add_space('''
... space friendlists
... key username
... attributes
... string first,
... string last,
... set(s... | cactorium/HyperDex | test/doc.atomic-ops.py | Python | bsd-3-clause | 10,154 | [
"Brian"
] | 48fe3ecbfeb7a4b2f99df0a70d2f3b02dc6c32f6d56847462b283b2924a69dd7 |
# Copyright 2001 by Gavin E. Crooks. All rights reserved.
# Modifications Copyright 2004/2005 James Casbon. 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.
#
# Changes made by ... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/SCOP/__init__.py | Python | apache-2.0 | 32,825 | [
"Biopython"
] | 8f77b0f7c92424fd6a2117ad465d3447cca43451153a5170d6894926e6670c8a |
#
# bioinformatics 3, wintersemester 89
# all code by Mathias Bader
# Modified by Dan Pipe-Mazo for Caltech Ditch Day, but not much.
#
import sys, os, string, random, time, copy, json
from math import sqrt
# gives tk namespace for graphical output
import Tkinter as tk
hub_dict = {
#Hub # ... | sean9keenan/WordWeb | generator/force_directed_graph_layout.py | Python | mit | 37,691 | [
"Octopus"
] | 1b9ba121e407d102ffbc6b71f8ffbf073214754e813c3a49b473622d5e4d5cd9 |
"""
intro_3_05_variable_names_2.py
Example code from Section 3.5 of <Introduction to SFC Models Using Python.>
Demonstration how variable names are built up.
Copyright 2017 Brian Romanchuk
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License... | brianr747/SFC_models | sfc_models/examples/scripts/intro_3_05_variable_names_2.py | Python | apache-2.0 | 1,786 | [
"Brian"
] | 6a060be6970dd34a120254ce0fca6ac73fee8e9abed3513f54109186f53667df |
#This is the final part of the C4 QA2 worklow (after the last DRM check).
'''
Part 0
Calibration
Part 1
Step 2 (Calibration Weblog Review)
Step 3 (Update tracking systems) -- provides the text to put into systems
Step 4 (Determine if pipeline is appropriate) -- currently no checks? needs to be built out
Step 5 (... | bmarshallk/NAASC | cycle_scripts/C4Part3.py | Python | gpl-3.0 | 13,577 | [
"VisIt"
] | 76b18f9e7efe598eada8bd95d4fb336804896af72af180f1a7ad0e758441c2b5 |
# 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 Lulesh(MakefilePackage):
"""LULESH is a highly simplified application, hard-coded to only
... | iulian787/spack | var/spack/repos/builtin/packages/lulesh/package.py | Python | lgpl-2.1 | 2,523 | [
"BLAST"
] | 3a63d978b4e5bac2cc140acea5a128ff2742989e7d164f423f5e3032910d4bf6 |
import os
from optparse import make_option
from Bio.Blast import NCBIXML
from django.core.management.base import BaseCommand, CommandError
from django.core.exceptions import ObjectDoesNotExist
from tasm.models import Assembly, Transcript, Locus, RefSeq, BlastHit, BASE_REFSEQ_URL
class Command(BaseCommand):
'''
... | eco32i/tweed | tasm/management/commands/import_blast.py | Python | bsd-3-clause | 3,872 | [
"BLAST"
] | b570646f2614c0e97003ca7060a701457876bff15a72dbdd7272387a2ac4ace5 |
# - Coding UTF8 -
#
# Networked Decision Making
# Development Sites (source code):
# http://code.google.com/p/global-decision-making-system/
# http://github.com/NewGlobalStrategy/NetDecisionMaking
#
# Demo Sites (Google App Engine)
# http://netdecisionmaking.appspot.com
# http://globaldecisionmaking.appspot.co... | NewGlobalStrategy/NetDecisionMaking | controllers/about.py | Python | mit | 2,064 | [
"VisIt"
] | 41d731f394370d56c7e931d79fc8b1f37fa68a45da96c9590a09ff222fceb429 |
"""
Created by: Bryce Chung (neuRowsATL)
Last Modified: May 20, 2016 (version 3)
Description: This class opens and saves AnimatLab models from .aproj files.
Modified August 23 2017 Daniel Cattaert
ActualizeAproj now include StartTime and EndTime of externalStimuli
modified September 19, 2017 (D. Cattaert, C.... | neuRowsATL/animatLabSimulationAPI | class_animatLabModel.py | Python | gpl-2.0 | 56,066 | [
"NEURON"
] | 34de3af7e1e70fed1dfac9bde1446366d5eea1076475a3c5d93c1ad12bb16a21 |
# Mantid Repository : https://github.com/mantidproject/mantid
#
# Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
# NScD Oak Ridge National Laboratory, European Spallation Source
# & Institut Laue - Langevin
# SPDX - License - Identifier: GPL - 3.0 +
#pylint: disable=no-init
"""
This is a Python... | mganeva/mantid | Framework/PythonInterface/plugins/algorithms/IntegratePeaksProfileFitting.py | Python | gpl-3.0 | 21,364 | [
"CRYSTAL",
"Gaussian"
] | 47e4e2b3212663490d99421e8e6b2c5a1efb69b6ee83418db74ff2eaaf84352b |
r"""
Linear elasticity with nodal linear combination constraints.
Find :math:`\ul{u}` such that:
.. math::
\int_{\Omega} D_{ijkl}\ e_{ij}(\ul{v}) e_{kl}(\ul{u})
= - \int_{\Gamma_{right}} \ul{v} \cdot \ull{\sigma} \cdot \ul{n}
\;, \quad \forall \ul{v} \;,
where
.. math::
D_{ijkl} = \mu (\delta_{ik} \... | RexFuzzle/sfepy | examples/linear_elasticity/nodal_lcbcs.py | Python | bsd-3-clause | 7,086 | [
"VTK"
] | f7edbb0bdd5681f763c44db069ff050e84075bea7e0107a75f412dafbe3dc0c6 |
#!/usr/local/bin/env python
#=============================================================================================
# Analyze datafiles produced by YANK.
#=============================================================================================
#=============================================================... | luirink/yank | Yank/analyze-old.py | Python | lgpl-3.0 | 19,753 | [
"NetCDF"
] | 3505ddf1288b829c6c10b59da6397ab9903cc0b06cce990eab71e42f0e710910 |
import numpy
import chainerx
# TODO(sonots): Implement in C++, especially in CUDA
def normal(*args, **kwargs):
"""normal(*args, **kwargs, device=None)
Draws random samples from a normal (Gaussian) distribution.
This is currently equivalent to :func:`numpy.random.normal`
wrapped by :func:`chainerx.a... | okuta/chainer | chainerx/random/distributions.py | Python | mit | 1,057 | [
"Gaussian"
] | c3be5c3455e883dd408d79b551c93bec543908728dccae9657fed73aa24e70a5 |
import logging
import numpy
from reikna.algorithms.pureparallel import PureParallel
from reikna.core.signature import Parameter, Annotation
import neuro
log = logging.getLogger("lwta")
def lwta(ctx, mat, lwta_size):
kernel_cache = ctx.kernel_cache
lwta_size = numpy.float32(lwta_size)
thread = ctx.thread... | schreon/neuronaut | neuro/lwta.py | Python | mit | 3,116 | [
"NEURON"
] | ba21e2ffd10afbd8def5f0b1eb6946df32b5b44a6df3192ba555953196023187 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Exoline - Exosite IoT Command Line
https://github.com/exosite/exoline
Usage:
exo [--help] [options] <command> [<args> ...]
Commands:
{{ command_list }}
Options:
--host=<host> OneP host. Default is $EXO_HOST or m2.exosite.com
--port=<port> OneP p... | danslimmon/exoline | exoline/exo.py | Python | bsd-3-clause | 141,519 | [
"VisIt"
] | 7e55ffe3a39b77d419a71ae28f0a455ffb2711033dc34b8355c52be54c9fc054 |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | nuclear-wizard/moose | framework/scripts/rm_outdated_deps.py | Python | lgpl-2.1 | 5,159 | [
"MOOSE"
] | 9b02126c9582bd66ea133b53841397caa0436e7c47270201012ab485456abb67 |
#!/usr/bin/env python
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl... | harterj/moose | python/moosesqa/test/test_SQADocumentReport.py | Python | lgpl-2.1 | 1,836 | [
"MOOSE"
] | d15bb5d9f8f5998fc12ea80c7f6cdb72429811a005a2f9345f62b7bf7ce75a41 |
# Gaussian discriminant analysis in 2d
# Author: Duane Rich
# Based on matlab code by Kevin Murphy
#https://github.com/probml/pmtk3/blob/master/demos/discrimAnalysisDboundariesDemo.m
import superimport
import numpy as np
import matplotlib.pyplot as plt
import os
figdir = '../figures'
def save_fig(fname): plt.savefig(... | probml/pyprobml | scripts/discrim_analysis_dboundaries_plot.py | Python | mit | 3,224 | [
"Gaussian"
] | 42eeb1ea530f72f3fcd4c9549649776cbc10b48fface320d0d644c454a10f873 |
#!/usr/bin/env python
""" Mission 7-Detect and Deliver
1. Random walk with gaussian at center of map until station position is acquired
2. loiter around until correct face seen
3. if symbol seen, move towards symbol perpendicularly
4. if close enough, do move_base aiming
task 7:
-----------------
Created by ... | ron1818/Singaboat_RobotX2016 | robotx_nav/nodes/task7_non_process_2.py | Python | gpl-3.0 | 8,074 | [
"Gaussian"
] | 3fc6195ba5f34e5d47bb6dc08e4a33202648dfa4b662b823e8c9d492b5d1c2d9 |
#---------------------------------
# PIPELINE RUN
#---------------------------------
# The configuration settings to run the pipeline. These options are overwritten
# if a new setting is specified as an argument when running the pipeline.
# These settings include:
# - logDir: The directory where the batch queue scripts... | jessicachung/rna_seq_pipeline | pipeline_config.py | Python | mit | 8,036 | [
"Bowtie"
] | b39e2c01330a27715af588bf29733cb8d632944cd3f76106f5925aff68022338 |
LOGO_STRING = """
.o88Oo._
d8P .ooOO8bo._
88 '*Y8bo.
YA '*Y8b __
YA 68o68**8Oo.
"8D *"' "Y8o
Y8 'YB .8D
'8 d8' 8D
8 d8888b d AY
... | MalkmusT/coala-quickstart | coala_quickstart/Strings.py | Python | agpl-3.0 | 1,942 | [
"VisIt"
] | 01bd7dab6b55a4c81287bb292ade3c64e73e6c5952f1bdce857a36ed5ae15cdb |
import numpy as np
import pyle.envelopes as env
from pyle.dataking import utilMultilevels as ml
import util
# sequence helpers
# these are simple functions for building standard control envelopes by
# pulling out appropriate configuration parameters for a particular qubit.
def power2amp(power):
"""
Convert ... | McDermott-Group/LabRAD | LabRAD/TestScripts/fpgaTest/pyle/pyle/dataking/envelopehelpers.py | Python | gpl-2.0 | 6,645 | [
"Gaussian"
] | df7b56bc0a4841d419a9ece25662bca71e034b998b5e4fe420967a6df6724649 |
# 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... | dongjoon-hyun/tensorflow | tensorflow/python/autograph/converters/logical_expressions.py | Python | apache-2.0 | 5,667 | [
"VisIt"
] | d22b38fbdd928d6001f0c7d32551840c40f85a3f2d4c1a29d6734a91ec8c4700 |
#!/usr/bin/env python
import glob, os, os.path, shutil, socket, struct, tarfile, stat
import numpy, sys, presto, time, sigproc, sifting
import psr_utils as pu
import pyfits
institution = "NRAO"
base_tmp_dir = "." # "/dev/shm/" is a good choice
# This is where the output will be archived.
base_output_dir = "."
#----... | pscholz/presto | bin/GBNCC_search.py | Python | gpl-2.0 | 27,691 | [
"Gaussian"
] | df661539f62fdb1e135a1383d079180f04b53d8fc36175743416082cc18a9dd1 |
""" 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... | pernici/sympy | sympy/solvers/solvers.py | Python | bsd-3-clause | 31,233 | [
"Gaussian"
] | 2955a87d5f892fbdc8908e3f3003130a060c29f785ebe71293e7170091675dcb |
# Import modules
try:
import dryscrape
except:
exit('Unable to import dryscrape.')
try:
from bs4 import BeautifulSoup
except:
exit('Unable to import BeautifulSoup from bs4.')
# Lyrics functions
class lyrics:
def get(artist, title):
artist = artist.replace(' ', '_')
title = title.rep... | Wingysam/lyrically | lyrically/__init__.py | Python | gpl-3.0 | 1,033 | [
"VisIt"
] | 28f5d6b8816f90176b43aef60151b9a8fa49cfa76cbfea0746fa52eece06f6ed |
import py.path
from _pytest.config import Config, PytestPluginManager, default_plugins
try:
# pytest >= 3.4
from _pytest.nodes import FSCollector
except ImportError:
# pytest < 3.4
from _pytest.main import FSCollector
class GraftedSubSession(FSCollector):
"""
Collects test files from outside ... | elliterate/capybara.py | capybara/tests/collector.py | Python | mit | 3,306 | [
"VisIt"
] | 2acceaa9a826bee5d8cde62c1c67ee7964b2491c64cef0a277352f62297375d8 |
../../../../../../../share/pyshared/orca/scripts/apps/packagemanager/tutorialgenerator.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/scripts/apps/packagemanager/tutorialgenerator.py | Python | gpl-3.0 | 89 | [
"ORCA"
] | 1cb380c4a6afa07d0e246e6454c3173bec5ae427d985034bea40e8608f0fac75 |
# -*- coding: utf-8 -*-
# Generated by Django 1.10.3 on 2016-11-19 18:19
from __future__ import unicode_literals
from django.db import migrations, models
import django.db.models.deletion
class Migration(migrations.Migration):
dependencies = [
('app', '0002_patient_dob'),
]
operations = [
... | kylewalters18/obulamu | server/app/migrations/0003_auto_20161119_1819.py | Python | mit | 2,591 | [
"VisIt"
] | afe18214469e51aa96f5201986c4f7a699f5b925402eb1ed66b1f0f8ea4fa9d7 |
# Copyright (c) 2014 Google Inc. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""
This script is intended for use as a GYP_GENERATOR. It takes as input (by way of
the generator flag file_path) the list of relative file paths to consider. If
... | AOSPU/external_chromium_org_tools_gyp | pylib/gyp/generator/analyzer.py | Python | bsd-3-clause | 6,991 | [
"VisIt"
] | d2bfc5c3059cc9f790dbfe4b3fbaac9bece73e678f5fdcb32c277a2ab270ee6c |
# const.py
# Aaron Taylor
# Moose Abumeeiz
#
# This file stores all of the constant information for the game, such as width
# and height of the window.
WIDTH = 960
HEIGHT = 540
GRATIO = 52 # Pixels/Grid size
GRIDX, GRIDY = 154, 88
MAPX = WIDTH-104
MAPY = 82 | ExPHAT/binding-of-isaac | const.py | Python | mit | 262 | [
"MOOSE"
] | 7801d16397e294b77d4455f174bb597ad9c13a5b40416ba6eafae483d3e3d8db |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#2012 Bruno Chareyre <bruno.chareyre@grenoble-inp.fr>
"""Example usage of a TesselationWrapper object for getting microscale quantities."""
# See Catalano2014a for the definition of micro-strain
# (http://dx.doi.org/10.1002/nag.2198 or free-access at arxiv http://arxiv.org/pdf/... | cosurgi/trunk | examples/tesselationwrapper/tesselationWrapper.py | Python | gpl-2.0 | 1,036 | [
"VTK"
] | 0dfca0d0367fe2089a470e78edd3f1a32f19ce1b97673aa94e0ae51e8071f855 |
import snakemake
import abc
import re
import os
import pysam
import pyfaidx
import rnftools
class Source(object):
""" Abstract class for a genome from which read tuples are simulated.
Args:
fasta (str): File name of the genome from which reads are created (FASTA file).
reads_in_tuple (int): Number of read... | karel-brinda/rnftools | rnftools/mishmash/Source.py | Python | mit | 8,429 | [
"pysam"
] | 19e71e2215e84146ee5301d27286752ca1e3ed7643864610cfd30d6d21e8e207 |
# -*- coding: utf-8 -*-
# SyConn - Synaptic connectivity inference toolkit
#
# Copyright (c) 2016 - now
# Max Planck Institute of Neurobiology, Martinsried, Germany
# Authors: Philipp Schubert, Joergen Kornfeld
import os
from logging import Logger
from typing import Optional, Union
import networkx as nx
import numpy a... | StructuralNeurobiologyLab/SyConn | syconn/proc/glia_splitting.py | Python | gpl-2.0 | 7,971 | [
"NEURON"
] | be8e0c16f2f2cfe6c0253a16cb100f274ff1d7190fc7e166b04385b0269718a8 |
# Copyright 2009 by Tiago Antao <tiagoantao@gmail.com>. 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.
"""
This module allows to control GenePop.
"""
import os
import re
impo... | poojavade/Genomics_Docker | Dockerfiles/gedlab-khmer-filter-abund/pymodules/python2.7/lib/python/Bio/PopGen/GenePop/Controller.py | Python | apache-2.0 | 32,725 | [
"Biopython"
] | 7695dccf0c8ecddab8636d2aa58ddbbb85db3a1fcd7fa006cc6ff3f30117d896 |
# -*- coding: utf-8 -*-
from __future__ import absolute_import, division, print_function
import os
import py.path
import pytest
import sys
import _pytest.pytester as pytester
from _pytest.pytester import HookRecorder
from _pytest.pytester import CwdSnapshot, SysModulesSnapshot, SysPathsSnapshot
from _pytest.config impo... | davidszotten/pytest | testing/test_pytester.py | Python | mit | 12,761 | [
"Brian"
] | e554895112d67e33f0b270bcf32dc3f04fde783db0bb485bc8a970304690f46b |
# -*- coding: utf-8 -*-
"""Protein Substitutions.
Protein substitutions are legacy statements defined in BEL 1.0. BEL 2.0 recommends using HGVS strings. Luckily,
the information contained in a BEL 1.0 encoding, such as :code:`p(HGNC:APP,sub(R,275,H))` can be
automatically translated to the appropriate HGVS :code:`p(H... | pybel/pybel | src/pybel/parser/modifiers/protein_substitution.py | Python | mit | 2,180 | [
"Pybel"
] | 5830377ea81945d0397388211e54f4cf63d12c3cb90f2d8543c20252eb8306bd |
#!/usr/bin/env python
#-----------------------------------------------------------------------------
# Copyright (c) 2013, The BiPy Development Team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
#--------------------------... | biocore/pyqi | pyqi/core/interfaces/optparse/__init__.py | Python | bsd-3-clause | 18,250 | [
"BLAST"
] | ef61816a67007720821c01d0f16c37d9cbfd26b455d1587cd796370144918d62 |
from collections import OrderedDict, defaultdict
import logging
import os
import math
import simtk.unit as units
from intermol.atom import Atom
from intermol.forces import *
import intermol.forces.forcefunctions as ff
from intermol.exceptions import (UnimplementedFunctional, UnsupportedFunctional,
... | ctk3b/InterMol | intermol/gromacs/gromacs_parser.py | Python | mit | 67,409 | [
"Gromacs",
"LAMMPS"
] | 5d709685629abb0c674585ebce30b8cc5498da6da8aaa3a8ea2d5a815d316fcc |
# synapse_tutorial.py ---
#
# Filename: synapse_tutorial.py
# Description:
# Author: Subhasis Ray
# Maintainer:
# Created: Fri Jan 17 09:43:51 2014 (+0530)
# Version:
# Last-Updated: Thu Oct 2 11:27:05 IST 2014
# By: Upi
# Update #: 0
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
# This is a t... | BhallaLab/moose-examples | snippets/synapse_tutorial.py | Python | gpl-2.0 | 5,219 | [
"MOOSE"
] | b49f7b165556a40376f1c10bc50296339b3dc2172dad7c0d20cc613b23374436 |
# coding: utf-8
# In[59]:
import numpy
import matplotlib # TODO bug in ipython? (sometime can't call the module directly)
from matplotlib import pyplot
import scipy
from scipy import stats
from scipy import optimize
# %matplotlib tk
# %matplotlib notebook #?
get_ipython().magic(u'matplotlib inline')
import math... | FedericoMuciaccia/SistemiComplessi | src/fit Poisson.py | Python | mit | 3,890 | [
"Gaussian"
] | 365ea39c6e0fb46b919c04c44a5db6dc743becdf700c8ac380fa22676e8670f5 |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-admin-add-resources
# Author : Andrei Tsaregorodtsev
########################################################################
"""
Add resources from the BDII database for a given VO
"""
__RCSID... | rajanandakumar/DIRAC | ConfigurationSystem/scripts/dirac-admin-add-resources.py | Python | gpl-3.0 | 15,563 | [
"DIRAC"
] | ba0936e403820dda0866ce631ee0b3332b70119955ecb9b6978e497390d06a2a |
import lb_loader
import simtk.openmm as mm
from simtk import unit as u
from openmmtools import hmc_integrators, testsystems
import pandas as pd
import mdtraj as md
import pandas as pdb
import spack
import itertools
import numpy as np
from openmmtools.testsystems import build_lattice, generate_dummy_trajectory, LennardJ... | kyleabeauchamp/HMCNotes | code/misc/test_lattice_fcp_testsystems.py | Python | gpl-2.0 | 1,252 | [
"MDTraj",
"OpenMM"
] | 01ec7ec378f449da5afd81683c81536e57f7f100f7886fd3260474fcb7e78bc5 |
""" Test_RSS_Policy_Configurations
"""
__RCSID__ = '$Id: $'
import unittest
import DIRAC.ResourceStatusSystem.Policy.Configurations as moduleTested
################################################################################
class Configurations_TestCase( unittest.TestCase ):
def setUp( self ):
"""
... | andresailer/DIRAC | ResourceStatusSystem/Policy/test/Test_RSS_Policy_Configurations.py | Python | gpl-3.0 | 1,509 | [
"DIRAC"
] | b40dcafadb1b61caf2f86ef0af4d59f9b9ed1421d2c76b6fc0c9b619b214e706 |
import matplotlib.pyplot
import scipy
import colorsys
import json
import sys
import os
import copy
matplotlib.pyplot.figure(1, figsize=(14,14))
fname = os.path.splitext(os.path.basename(sys.argv[1]))[0]
fin = open(sys.argv[1], "r")
jin = json.load(fin)
fin.close()
# 4 timer values are: total, min, max, average
time... | electronic-structure/sirius | apps/timers/timers2.py | Python | bsd-2-clause | 3,540 | [
"exciting"
] | 71582e569f3cf473898a7601e7608a215e85f1d01e1b802cf35404e7de13dd5f |
import tweepy
import webbrowser
from ConfigParser import SafeConfigParser
# Call this function if you need to get access tokens
def getAccessTokens():
# Initialize the config parser and open the config.ini file
config = SafeConfigParser()
config.read('config.ini')
# Try to load the consumer keys. The... | trswany/topStocks | tweetPoster.py | Python | mit | 3,159 | [
"VisIt"
] | f7fb9a8c11641ed0dac35cb3eeea80981ff6357186d0697a29caaffc99a09c35 |
#!/usr/bin/env python
# coding: utf-8
#
# Copyright 2007 Google Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by ... | wishabi/caja-1 | tools/upload.py | Python | apache-2.0 | 96,830 | [
"VisIt"
] | d0edeacea13ba3267505bf8da89b8afc8d0870227aea26641913832246726f71 |
"""Compatibility fixes for older versions of libraries
If you add content to this file, please give the version of the package
at which the fix is no longer needed.
# originally copied from scikit-learn
"""
# Authors: Emmanuelle Gouillart <emmanuelle.gouillart@normalesup.org>
# Gael Varoquaux <gael.varoquau... | cjayb/mne-python | mne/fixes.py | Python | bsd-3-clause | 40,148 | [
"Gaussian",
"Mayavi"
] | a6fd54296ee85e04016526b1f1f1ad837242963b7e26ff5bad76cff0b0065238 |
#!/usr/bin/env python
# coding=utf-8
from __future__ import absolute_import
import re
from math import isinf, isnan
from future.utils import text_type, binary_type, iteritems
from ._compat import singledispatch
from .nodes import * # noqa
@singledispatch
def node_encoder(obj): # noqa
"""Convert python objec... | bionikspoon/pureyaml | pureyaml/encoder.py | Python | mit | 7,172 | [
"VisIt"
] | f0e1bf3de0bac1e5f3473dd849002cd4d222beca5249cea461c1d23489f2dc85 |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | eyalfa/spark | python/pyspark/ml/clustering.py | Python | apache-2.0 | 50,292 | [
"Gaussian"
] | be19fe278a5288956a36ec3a0d7126fa22a7783db276167b6b2d831e199416b2 |
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