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#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (c) 2013 Spotify AB
#
# 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 requi... | LongbinChen/annoy | setup.py | Python | apache-2.0 | 2,123 | [
"VisIt"
] | 23822ac915d3c44bc978d607e344a37dcd57715de679cd9ecf9e80029778f14c |
import types
import os
import re
import logging
import urllib
import hmac
import hashlib
from urlparse import urlparse
from email import header
from datetime import timedelta, datetime
from hashlib import sha256
import uuid
import iso8601
import pymongo
from pylons import c, g, request
from ming import schema as S
fr... | Bitergia/allura | Allura/allura/model/auth.py | Python | apache-2.0 | 22,147 | [
"VisIt"
] | 59c1de108f368fa9a33b5c191c35786898a625aeb04922d4392ac56c1e2de10f |
# Licensed under an MIT open source license - see LICENSE
import numpy as np
import matplotlib.pyplot as p
import scipy.ndimage as nd
from scipy.stats import lognorm
from scipy.ndimage import distance_transform_edt
from skimage.morphology import remove_small_objects, medial_axis
from scipy.stats import scoreatpercenti... | e-koch/FilFinder | fil_finder/filfind_class.py | Python | mit | 72,225 | [
"Gaussian"
] | deefc7dd92c0940e6487f794fb6cfb5b3fd50b3b4e181b6fada9d40fa5020379 |
import saliweb.frontend
import os
import math
import re
class ValueWithError:
def __init__(self, value, err):
self.value = value
self.err = err if err == 'nan' else float(err)
def has_error(self):
return self.err != 'nan' and self.err < self.value/10.
class Results:
def __init__... | salilab/saxsmerge | frontend/saxsmerge/results_page.py | Python | lgpl-2.1 | 3,000 | [
"Gaussian"
] | 9631a5b5e31d6509a030e9b7865cc39fd54f98fd0d0e7894b622cc0d1f9a6b3b |
######################################################################
# Copyright (C) 2015 Jaakko Luttinen
#
# This file is licensed under Version 3.0 of the GNU General Public
# License. See LICENSE for a text of the license.
######################################################################
####################... | dungvtdev/upsbayescpm | bayespy/inference/vmp/nodes/logistic.py | Python | mit | 6,911 | [
"Gaussian"
] | abc622d8adcb26f99d664333a7793b957c9712f977c5b2798c132fe08d39c80c |
from math import *;
from utils import *;
import random;
import soldiers;
import towers;
#class ProbGene(FloatGene):
# """
# Gene which represents the probabilities used in our organism
# """
# # genes get randomly generated within this range
# randMin = 0.0
# randMax = 1.0
# # probability of mutat... | ggianna/Foragers | unitStrategy.py | Python | apache-2.0 | 8,953 | [
"VisIt"
] | 2c66116faa0e1f5afe9a4c37d0104899eeb780cc8583d16aeaa61bb51f2fe40a |
# coding=utf8
#
# Copyright 2013 Dreamlab Onet.pl
#
# This library 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;
# version 3.0.
# This library is distributed in the hope that it will be useful,
# bu... | tikan/rmock | tests/unit_tests/test_tools.py | Python | lgpl-3.0 | 3,103 | [
"VisIt"
] | c32a6bbd934ae38aedeebd5f1baf883e3c12aea65d3399c6600546bd47ae5165 |
import numpy as np
from copy import copy
from bokeh.core.properties import field
from bokeh.io import curdoc
from bokeh.layouts import layout,column,row
from bokeh.models import (
ColumnDataSource, HoverTool, SingleIntervalTicker, Slider, Button, Label,
CategoricalColorMapper,
)
from bokeh.models.widgets import... | sandipde/bokehplot | plot-server/cosmo.py | Python | mit | 20,325 | [
"Jmol"
] | 0ad376d13bb84c71f13434653749e9e388e3c4c8d625cb625e9b5ae54ff13679 |
from __future__ import absolute_import
import cython
cython.declare(PyrexTypes=object, Naming=object, ExprNodes=object, Nodes=object,
Options=object, UtilNodes=object, LetNode=object,
LetRefNode=object, TreeFragment=object, EncodedString=object,
error=object, warning=object... | Architektor/PySnip | venv/lib/python2.7/site-packages/Cython/Compiler/ParseTreeTransforms.py | Python | gpl-3.0 | 122,032 | [
"VisIt"
] | 1a1784d5f821b75178b24c964d293b89dcbab764ce7adfc81ddd69b6fdcc71a4 |
"""
Computational Neurodynamics
Exercise 1
Simulates Izhikevich's neuron model using the Runge-Kutta method.
Parameters for regular spiking, fast spiking and bursting
neurons extracted from:
http://www.izhikevich.org/publications/spikes.htm
(C) Murray Shanahan et al, 2015
"""
import sys
import matplotlib.pyplot as ... | lawrencejones/neuro | Exercise_1/IzNeuronDemo.py | Python | gpl-3.0 | 1,176 | [
"NEURON"
] | 1d4434f86aea3bb5204e826d087470b96bc7fb2d3fc88d5bbaad76394497d20f |
"""
Protocol implementations for PES5
"""
from twisted.internet import reactor, defer
from twisted.application import service
from twisted.web import client
from Crypto.Cipher import Blowfish
from datetime import datetime, timedelta
from hashlib import md5
import binascii
import struct
import time
import re
import zl... | IkeC/evo-league | Sixserver/lib/fiveserver/protocol/pes5.py | Python | mit | 64,934 | [
"VisIt"
] | 1660d07fdfe19a01d3baab2fd27da13448c8717fba0ab4e11e7ffcd67d2134a1 |
# -*- coding: utf-8 -*-
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""Provides interfaces to various commands provided by FreeSurfer
Change directory to provide relative paths for doctests
>>> import os
>>> filepath = os.path.dirname( os.p... | carolFrohlich/nipype | nipype/interfaces/freesurfer/preprocess.py | Python | bsd-3-clause | 92,925 | [
"Gaussian"
] | f704f9e88ae0e70119e7f293244859509a7803bcd83d6a309a026133402988c8 |
##############################################################
# Trilogy - Color / grayscale image maker (from FITS input)
# Dan Coe
# http://www.stsci.edu/~dcoe/trilogy/
##############################################################
# Trilogy produces nice color / grayscale images based on your input FITS files
# Jus... | willettk/decals | python/trilogy.py | Python | mit | 43,553 | [
"Galaxy"
] | 9f4ca06626b9fffeddf2521199a7adc47a24e841cae4d3972aa3adbb5745c1dc |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | Achuth17/scikit-bio | skbio/stats/ordination/tests/test_ordination.py | Python | bsd-3-clause | 35,785 | [
"scikit-bio"
] | f38ffa3742fb20bfa26628436a542f21b01c4330f8028807d3b0b99d0d965fd8 |
# Copyright 2021, The TensorFlow Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed t... | google/differential-privacy | python/dp_accounting/dp_event.py | Python | apache-2.0 | 7,925 | [
"Gaussian"
] | a986febc58d73f8bc0e88d0f39e89fde04aa6171bd294c6f0f9eedb4557d2d96 |
# Copyright (c) 2012 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.
from compiler.ast import Const
from compiler.ast import Dict
from compiler.ast import Discard
from compiler.ast import List
from compiler.ast import Module
from co... | cchamberlain/gyp | pylib/gyp/input.py | Python | bsd-3-clause | 115,520 | [
"VisIt"
] | 3c41881d51df972d331a5100576d8f0a85a8a5817f89f1931f8dc4f6fe554ba9 |
import imgaug as ia
from imgaug import augmenters as iaa
import numpy as np
import glob
import matplotlib.image as img
import matplotlib.pyplot as plt
import cv2
images= img.imread("/home/ahmed/Pictures/cogedis/cogedis_words_3/fe27c8de-15d5-4361-a079-558a4bee2388.png")
plt.imshow(images)
# random example images
#imag... | ahmedmazari-dhatim/CRNN-for-sequence-recognition- | data_augm.py | Python | mit | 2,887 | [
"Gaussian"
] | 06a67d283a3ab573a391e895e7a3c722ec7e8e797aada38434441ddc4495bf1d |
# S.D. Peckham
# May 2010
import os
import sys
import time
import numpy as np
import file_utils
# import rti_files # (not used)
import netCDF4 as nc
#---------------------------------------------------------------------
# This class is for I/O of time-indexed 1D profiles to netCDF files.
#-----------------------... | peckhams/topoflow | topoflow/utils/ncps_files.py | Python | mit | 24,881 | [
"NetCDF"
] | 357601360060b483d82f1da049499a2f67f8e753400c29e50a42b1f734a143ba |
"""
Forest of trees-based ensemble methods.
Those methods include random forests and extremely randomized trees.
The module structure is the following:
- The ``BaseForest`` base class implements a common ``fit`` method for all
the estimators in the module. The ``fit`` method of the base ``Forest``
class calls th... | anntzer/scikit-learn | sklearn/ensemble/_forest.py | Python | bsd-3-clause | 100,288 | [
"Brian"
] | ca0ccf87d070d99c44c60b845fb21033ad65c34ca57551e7cef6baa580462e7f |
from DIRAC.Core.Base import Script
Script.parseCommandLine()
from ILCDIRAC.Interfaces.API.DiracILC import DiracILC
from ILCDIRAC.Interfaces.API.NewInterface.UserJob import *
from ILCDIRAC.Interfaces.API.NewInterface.Applications import *
dirac = DiracILC( True , "CLICdet_repo.cfg" )
job = UserJob( )
job.setName( "ex... | iLCSoft/CLICPerformance | Flavour_tagging/Job_example.py | Python | gpl-3.0 | 2,088 | [
"DIRAC"
] | edb173d0cd206d40745408e2453b0568709570a88048c64ce4d1549c24857c5b |
#!/usr/bin/env ipython
from pylab import *
from numpy import *
from scipy.io.netcdf import netcdf_file
from datetime import datetime, time, timedelta
#------------ shared libraries:
import sys
sys.path.append('../../../shared_lib')
from shared_funcs import * #c_funcs import *
#------------------------------
#from read_... | jimsrc/seatos | mcs/src/forbush/c_rebineo.py | Python | mit | 3,336 | [
"NetCDF"
] | c9ff767adfe313984bd036de8972260b0458bcb1f638bb8f7000b5171a9996b1 |
# -*- test-case-name: twisted.python.test.test_deprecate -*-
# Copyright (c) Twisted Matrix Laboratories.
# See LICENSE for details.
"""
Deprecation framework for Twisted.
To mark a method, function, or class as being deprecated do this::
from twisted.python.versions import Version
from twisted.python.deprec... | Architektor/PySnip | venv/lib/python2.7/site-packages/twisted/python/deprecate.py | Python | gpl-3.0 | 24,319 | [
"Amber"
] | 6edab2791328c9f601f59ed99a230ce2dc5634366e00a0a7b5ca6e8aff02e1c5 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2002-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2008 Jerome Rapinat
# Copyright (C) 2008 Benny Malengier
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the ... | arunkgupta/gramps | gramps/gen/filters/rules/person/_hasnote.py | Python | gpl-2.0 | 1,717 | [
"Brian"
] | 31ee1a28c5c56535cf61fc7486ead69552a204e25098d6ee6eb2bc462e5e48d0 |
# opts.py - module to parse command line options and output what parameters will be used for this run
import os
import os.path
import json
import sys
import yaml
from argparse import ArgumentParser
# fs-drift module dependencies
from common import OK, NOTOK, FsDriftException, FileAccessDistr, USEC_PER_SEC, BYTES_PER... | parallel-fs-utils/fs-drift | opts.py | Python | apache-2.0 | 28,701 | [
"Gaussian"
] | 61142d791eb7dc941c43a1df9c59df5bc02b3f4e741842bc82f1e4a4eceae7c1 |
# BEGIN_COPYRIGHT
#
# Copyright 2009-2015 CRS4.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may not
# use this file except in compliance with the License. You may obtain a copy
# of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed ... | crs4/seal | seal/avo2sam_mr.py | Python | gpl-3.0 | 3,902 | [
"BWA"
] | 4c0d84177eeb62a6f86bf93793acb7056b4df0e8a4537bc75cda4a2770a3d001 |
import numpy as np
######## BIN_SPIKES ########
def bin_spikes(spike_times,dt,wdw_start,wdw_end):
"""
Function that puts spikes into bins
Parameters
----------
spike_times: an array of arrays
an array of neurons. within each neuron's array is an array containing all the spike times of tha... | wosen7/openblackbox | preprocessing_funcs.py | Python | gpl-3.0 | 5,617 | [
"NEURON"
] | a4b8088acf4d2d28e610aa284f55d926b0891c0a692bfe506a1a92f79afb5115 |
from ase import *
#from math import sqrt
#from ASE.Calculators.PairPotential import PairPotential
#from ASE.Filters.Subset import Subset
#from ASE.Filters.FixBondLength import FixBondLength
#from ASE.Dynamics.MDMin import MDMin
#from ASE.Trajectories.NetCDFTrajectory import NetCDFTrajectory
#from ASE.IO.NetCDF import... | conwayje/ase-python | tutorials/N2Ru-Association.py | Python | gpl-2.0 | 1,192 | [
"ASE",
"NetCDF"
] | e1abc8f557f2b46ce3b7d670efdead2a381d0e2bc1dc140d6805c2aab25ba275 |
import caching.base as caching
import jingo
import jinja2
from tower import ugettext_lazy as _
from olympia import amo
from olympia.addons.models import Addon
from olympia.api.views import addon_filter
from olympia.bandwagon.models import Collection, MonthlyPick as MP
from olympia.versions.compare import version_int
... | jpetto/olympia | src/olympia/discovery/modules.py | Python | bsd-3-clause | 11,357 | [
"VisIt"
] | c8e35c5f2eec99674f0c46af6c1ca26747b4ed0482a84b7dad7c0474f3270b8b |
'''
module for building and loading all the possible data and covariance
combinations that can come up in the generalised inference
'''
#general python modules
import numpy as np
from multiprocessing import cpu_count
import pyfof
#haltools functions
from halotools.sim_manager import CachedHaloCatalog
from halotools.... | mjvakili/ccppabc | ccppabc/code/data.py | Python | mit | 15,938 | [
"Galaxy"
] | 90853f0554043b48a9ef7e4bb20c51015598fbbcffeb74b348d1814ae17db8f4 |
# -*- coding: utf-8 -*-
# Unit tests for cache framework
# Uses whatever cache backend is set in the test settings file.
from __future__ import unicode_literals
import copy
import os
import re
import shutil
import tempfile
import threading
import time
import unittest
import warnings
from django.conf import settings
... | marqueedev/django | tests/cache/tests.py | Python | bsd-3-clause | 84,798 | [
"Brian"
] | 65432d0873d9cc7ce780266378df2f27c6324a34d45944028f862b6d388ea3fa |
"""Example to solve 3D aqueous foam pipe flow using rheological
Herschel-Bulkley power law for bulk and wall shear stress dependent
slip velocity law for wall layer
"""
import numpy as np
import foam_controlwrapper
from simphony.core.cuba import CUBA
from simphony.api import CUDS, Simulation
from simphony.cuds.meta i... | simphony/simphony-openfoam | foam_controlwrapper/examples/aqueous_foam_slit_flow_steady_state_meso_coupling.py | Python | gpl-2.0 | 6,008 | [
"Mayavi"
] | f20da9c33330ba3a91a731f27a983de5a93f03c05274196242f63c252fc23b9b |
"""
murder_if_convenient's first priority is to murder other robots, but only
if they happen to be right in the way. Otherwise he'll head for the flag
as best as possible, attempting to follow an obsticle if one is in the way.
"""
from roborally.api import *
name = 'ConvenientMurderer'
friendly_bots = ('ConvenientMur... | kenganong/robot-arena | robotarena/roborally/robots/murder_if_convenient.py | Python | apache-2.0 | 7,546 | [
"BLAST"
] | 3be929f8d782d00acd422e719e111cfd2dcde44f4cfb8250976c54f2326af607 |
# -*- coding: utf-8 -*-
# imports here
from aiida.parsers.exceptions import OutputParsingError
#
from aiida.orm.data.folder import FolderData
from aiida.orm.data.parameter import ParameterData
from aiida.orm.data.structure import StructureData
from aiida.orm.data.array import ArrayData
#
from aiida.parsers.plugins.vas... | abelcarreras/aiida_extensions | plugins/parsers/vasp/instruction/data/custom_vasprun_parser.py | Python | mit | 3,076 | [
"VASP",
"phonopy",
"pymatgen"
] | 42a2471ed60abe84eb549815ae2b69cd69babcf5659ffe9f5e396a46de5841a2 |
# analogStimTable.py ---
#
# Filename: analogStimTable.py
# Description:
# Author: Upi Bhalla
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License as
# published by the Free Software Foundation; either version 3, or
# (at your option) a... | BhallaLab/moose-examples | snippets/analogStimTable.py | Python | gpl-2.0 | 3,666 | [
"MOOSE"
] | eff86c85f78187127f4dbb0737bd1f1864a4cba86c2e748ad254aff3913f35ca |
__author__ = 'tylin'
__version__ = '2.0'
# Interface for accessing the Microsoft COCO dataset.
# Microsoft COCO is a large image dataset designed for object detection,
# segmentation, and caption generation. pycocotools is a Python API that
# assists in loading, parsing and visualizing the annotations in COCO.
# Pleas... | wuzheng-sjtu/FastFPN | libs/datasets/pycocotools/coco.py | Python | apache-2.0 | 18,434 | [
"VisIt"
] | da862c8f815180c7295bf00bb608287546b4f508890ebbd60f7ba3cec8a5a9f3 |
"""Create and put Requests to archive files.
List of operations:
#. Optionally replicate files to SourceSE
#. ArchiveFiles: Create a tarball from input files, upload tarball to TarballSE
#. ReplicateAndRegister Tarball to TargetSE
#. Optionally: Add LFNs to an ArchiveSE
#. Optionally: Check for Tarball Migration
#. ... | andresailer/DIRAC | DataManagementSystem/scripts/dirac-dms-create-archive-request.py | Python | gpl-3.0 | 21,130 | [
"DIRAC"
] | cfa8c49377b97cb97ca72ab9d4e835704097654433937f0f7ac9574e1a36fc1e |
"""
.. module::
:platform: Unix
:synopsis: ???
.. moduleauthor: Jan Hajic <hajicj@gmail.com>
"""
import cPickle
import numpy
import safire.utils
import theano
import theano.tensor as TT
from theano.tensor.shared_randomstreams import RandomStreams
from safire.learning.models.autoencoder import Autoencoder
c... | hajicj/safire | build/lib/safire/learning/models/denoising_autoencoder.py | Python | gpl-3.0 | 8,007 | [
"NEURON"
] | a6cc61b5c44d9029268231d48e4d3155d74c1725c93b3a9029b0da738996f99e |
from __future__ import absolute_import, division, print_function
import os
import pickle
import shutil
import warnings
from collections import OrderedDict, defaultdict
from enum import Enum
from numbers import Number
import numba as nb
import numpy as np
from scipy.io import wavfile
from odin import fuel as F
from o... | imito/odin | examples/nist_sre/helpers.py | Python | mit | 40,884 | [
"Gaussian"
] | aaebc73edca6803b741df434faedfbd39552ee97331a387617a8dce4d66c18f5 |
# AUTHORS:
# Hakan Ozadam
# Rachel Brown
#
# Moore Laboratory
# UMASS Medical School / HHMI
# RNA Therapeutics Institute
# Albert Sherman Center, ASC4-1009
# 368 Plantation Street
# Worcester, MA 01605
# USA
#
##############################################... | hakanozadam/bal | bal/genomic_io/functions.py | Python | gpl-2.0 | 4,143 | [
"pysam"
] | a85cafb6776048f2326e8c179bdbe4d58ea6542ac97f39b8cdbf75e0a7c361de |
# -*- coding: utf-8 -*-
"""
End-to-end tests for Student's Profile Page.
"""
from contextlib import contextmanager
from datetime import datetime
from bok_choy.web_app_test import WebAppTest
from nose.plugins.attrib import attr
from ...pages.common.logout import LogoutPage
from ...pages.lms.account_settings import Acc... | ampax/edx-platform | common/test/acceptance/tests/lms/test_learner_profile.py | Python | agpl-3.0 | 34,952 | [
"VisIt"
] | 321f3b106e51040c61af5a6de5992ac8517bf563e2b9ded8f5a8296a6623c9ef |
# -*- coding: utf-8 -*-
# Copyright(C) 2008-2011 Romain Bignon
#
# This file is part of weboob.
#
# weboob is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at you... | Boussadia/weboob | modules/aum/contact.py | Python | agpl-3.0 | 11,686 | [
"exciting"
] | c9978ea376e1778571625f06de11c833640257c0ee725ebe16e177940587c4d7 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
MellPlayer Player
Created on 2017-02-20
@author: Mellcap
'''
import os
import time
import threading
import datetime
from mellplayer.utils.mpv import MPV
from mellplayer.api import Netease
from mellplayer.directory import BASE_DIRECTORY
from mellplayer.event.ui_event... | Mellcap/MellPlayer | mellplayer/player.py | Python | mit | 10,095 | [
"VisIt"
] | 4e62458c472c4e57b7adbd496dd685f92dc600cfc16bbe148a3f6abc517dc4a5 |
"""
Generate coulomb matrices for molecules.
See Montavon et al., _New Journal of Physics_ __15__ (2013) 095003.
"""
from __future__ import print_function
from __future__ import division
from __future__ import unicode_literals
__author__ = "Steven Kearnes"
__copyright__ = "Copyright 2014, Stanford University"
__licen... | joegomes/deepchem | deepchem/feat/coulomb_matrices.py | Python | mit | 7,736 | [
"RDKit"
] | 0234e42e3afd742ff5fdf689730cf925fdb0271ff21744e5c8fec17cf5f355ba |
# $Id$
#
# Copyright (C) 2002-2006 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
"""unit testing code ... | rvianello/rdkit | rdkit/Dbase/UnitTestDbUtils.py | Python | bsd-3-clause | 7,275 | [
"RDKit"
] | f9b70a3e44d745ca568b33a42e3b22fe34f7298fdc9d1a8ae9a63ae41adebba8 |
#!/usr/bin/env python
# encoding: utf-8
"""
CijUtil.py
Bits to help with elastic constants manipulation.
polyCij(Cij): Given an elastic constants matrix for a single crystal,
calculate the Voight and Reuss bounds on the bulk and
shear moduli for a random polycrystal.
Copyright (c) 2010 A... | duyuan11/elastic-constants | CijUtil.py | Python | bsd-3-clause | 13,338 | [
"CRYSTAL"
] | 2a8c527ea42285f81eab85df3664955fc446663877609e4d95c2c9ddd9d14ef6 |
""" This module will run some job descriptions defined with an older version of DIRAC
"""
# pylint: disable=protected-access, wrong-import-position, invalid-name, missing-docstring
import unittest
import os
import sys
import shutil
import DIRAC
DIRAC.initialize() # Initialize configuration
from DIRAC import gLogger... | DIRACGrid/DIRAC | tests/Workflow/Regression/Test_RegressionUserJobs.py | Python | gpl-3.0 | 3,310 | [
"DIRAC"
] | 1b34139cd91ea1570e1fe0befb0e30d2b77d1a42e9528431459633a7fb488d7a |
# Copyright 2016 Mark Benson, portions Copyright 2016 Brian Innes
#
# 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 app... | brianinnes/pycupi | python/vPiP/generators/concircle.py | Python | apache-2.0 | 3,534 | [
"Brian"
] | ae57af446de46eee583fd4f93e37c43cc40a05620258b1cc1447caeaa2d7963f |
# -*- coding: utf-8 -*-
from acq4.Manager import getManager
from acq4.util.metaarray import *
from acq4.pyqtgraph.ImageView import *
from acq4.pyqtgraph.GraphicsView import *
from acq4.pyqtgraph.graphicsItems import *
from acq4.pyqtgraph.graphicsWindows import *
from acq4.pyqtgraph.PlotWidget import *
from acq4.pyqtgra... | hiuwo/acq4 | acq4/analysis/old/modules.py | Python | mit | 103,125 | [
"Gaussian"
] | 09f85b7100552e7899ec6f6171cabcdc82d7305b016f7f742eaac0f1ec705aec |
# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
# All rights reserved.
#
# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are ... | lidakanari/NeuroM | neurom/fst/__init__.py | Python | bsd-3-clause | 7,218 | [
"NEURON"
] | f3cdf216316443733653823c972eb05db09973e493d75db067eb3b6ce20072d3 |
"""
Extremely simple utility class to send mails
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import six
import os
import socket
from smtplib import SMTP, SMTP_SSL
from email.mime.application import MIMEApplication
from email.mime.multipart impor... | yujikato/DIRAC | src/DIRAC/Core/Utilities/Mail.py | Python | gpl-3.0 | 3,906 | [
"DIRAC"
] | e89919dbdcb8b799386633e05f65d7bcb9b8658ce66ba305afa5c770badb8034 |
import io
import json
import os
from collections import OrderedDict
from datetime import date, datetime, timedelta
from django.contrib import messages
from django.contrib.auth.mixins import PermissionRequiredMixin
from django.core.mail import EmailMessage
from django.db.models import Count
from django.http import Fil... | epcoullery/epcstages | stages/views/__init__.py | Python | agpl-3.0 | 24,912 | [
"ASE"
] | 003df9241fe2691873102482c26d6128d472faf1147c1c6454915a00846e011d |
# encoding: utf-8
'''
@author: Juncheng Chen
@copyright: 1999-2015 Alibaba.com. All rights reserved.
@license: Apache Software License 2.0
@contact: juncheng.cjc@outlook.com
'''
import sys
import os
from argparse import ArgumentParser
from argparse import RawDescriptionHelpFormatter
from time import slee... | alibaba/tvb | tvb/cli.py | Python | apache-2.0 | 7,745 | [
"VisIt"
] | b97551eaa60a99929a65953c9fdb6995fa5c9a341a541f056f1c6c6005f34ef5 |
"""The registration module contains classes for image registration.
Image registration aims to align two images using a particular transformation.
miapy currently supports multi-modal rigid registration, i.e. align two images of different modalities
using a rigid transformation (rotation, translation, reflection, or t... | Studijacob/MIALab | wd/registration/registration.py | Python | apache-2.0 | 16,836 | [
"Gaussian"
] | eac76ccb21902742257861e1e56bbdf6e2e12a6a20e6fd5113dffe17f136505f |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright © 2015 Matthew Stone <mstone5@mgh.harvard.edu>
# Distributed under terms of the MIT license.
"""
"""
import argparse
import heapq
from collections import deque
import pysam
from svcf.rpc import RPC
from svcf.svcall import SVCallCluster
from svcf.svfile impo... | talkowski-lab/Holmes | readpaircluster/svcf/svcluster.py | Python | mit | 5,040 | [
"pysam"
] | f454d8867f38c0702623a2176bcfcfa550984090306b22a88e2fc5396e2c38d6 |
"""
It is used to create plots using Elasticsearch
"""
import datetime
import os
from DIRAC import gLogger, S_OK, S_ERROR, gConfig
from DIRAC.Core.DISET.RequestHandler import RequestHandler
from DIRAC.Core.Utilities import Time
from DIRAC.Core.Utilities.Plotting import gDataCache
from DIRAC.Core.Utilities.Plotting.F... | fstagni/DIRAC | MonitoringSystem/Service/MonitoringHandler.py | Python | gpl-3.0 | 12,881 | [
"DIRAC"
] | e77ebbb0d6275f2a1fd1135a83f126397cd7a91675b7cee8cf3a5669e68decc2 |
# pylint: disable=arguments-differ
""" Models for the shopping cart and assorted purchase types """
from __future__ import absolute_import
import csv
import json
import logging
import smtplib
from collections import namedtuple
from datetime import datetime, timedelta
from decimal import Decimal
import pytz
import si... | ESOedX/edx-platform | lms/djangoapps/shoppingcart/models.py | Python | agpl-3.0 | 90,012 | [
"VisIt"
] | e9e1239e24b2f5f32a1b5f303049a5b208d6d5b9fbecad9d28a68e6c52fd26ae |
r"""
This module is a VTK Web server application.
The following command line illustrate how to use it::
$ vtkpython .../vtk_web_graph.py --vertices 1000 --edges 400
Any VTK Web executable script come with a set of standard arguments that
can be overriden if need be::
--host localhost
... | johnkit/vtk-dev | Web/Applications/GraphLayout/server/vtk_web_graph.py | Python | bsd-3-clause | 6,395 | [
"VTK"
] | 9dd662e6f98286a72f745f07d45d8d478ac9c828cdddc1d7bca08a66c8f95687 |
"""
Linear Discriminant Analysis and Quadratic Discriminant Analysis
"""
# Authors: Clemens Brunner
# Martin Billinger
# Matthieu Perrot
# Mathieu Blondel
# License: BSD 3-Clause
from __future__ import print_function
import warnings
import numpy as np
from scipy import linalg
from .extern... | pratapvardhan/scikit-learn | sklearn/discriminant_analysis.py | Python | bsd-3-clause | 28,512 | [
"Gaussian"
] | 9d27ea24e1cca07a3eb7a8195c654002ea42ecdf80af44dbaef21a413ac56a83 |
#! /usr/bin/env python
#import __main__
#__main__.pymol_argv = ['pymol','-qc']
##__main__.pymol_argv = ['pymol','']
#import sys,time,os
#import pymol
#
#pymol.finish_launching()
#pymol.cmd.feedback("disable","all","actions")
#pymol.cmd.feedback("disable","all","results")
#sys.path.append("/home/scratch/software/Pymol-... | demharters/git_scripts | contacts_dna_4dnb.py | Python | apache-2.0 | 1,332 | [
"MDAnalysis",
"PyMOL"
] | 5be5b2bff195986fcb622ffaeea206dd079df57cbfb78ecd0aca133ec2cc03f3 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2018 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | amjames/psi4 | psi4/driver/qcdb/physconst.py | Python | lgpl-3.0 | 3,475 | [
"Psi4"
] | b6640528754434bed724f214ce6a9f5c1acd7375c711c69840940814b39ab5ce |
"""
Utility module to make it easier to create new keys.
"""
from vtk.vtkCommonCore import vtkInformationDataObjectKey as DataaObjectKey
from vtk.vtkCommonCore import vtkInformationDoubleKey as DoubleKey
from vtk.vtkCommonCore import vtkInformationDoubleVectorKey as DoubleVectorKey
from vtk.vtkCommonCore import vtkInfo... | msmolens/VTK | Wrapping/Python/vtk/util/keys.py | Python | bsd-3-clause | 1,906 | [
"VTK"
] | 107323baf1f118937205fe4718e76d0ea6fb24de4421ee9e8d601cfa0e464abd |
# copyright 2003-2013 LOGILAB S.A. (Paris, FRANCE), all rights reserved.
# contact http://www.logilab.fr/ -- mailto:contact@logilab.fr
#
# This file is part of logilab-astng.
#
# logilab-astng is free software: you can redistribute it and/or modify it
# under the terms of the GNU Lesser General Public License as publis... | tlksio/tlksio | env/lib/python3.4/site-packages/logilab/astng/inspector.py | Python | mit | 9,469 | [
"VisIt"
] | 638fdb4fa32b09fc713b2333f16a07d1b6b53120ffca2602e1499e679f37dec3 |
#!/usr/bin/env python
from __future__ import print_function
import gzip
import json
import optparse
import os
import os.path
import re
import shutil
import sys
import urllib
import zipfile
from pysam import ctabix
"""
# Install dbNSFP databases
# from DbNsfp site
# Download dbNSFP database
$ wget ftp://dbnsfp:... | nekrut/tools-iuc | data_managers/data_manager_snpsift_dbnsfp/data_manager/data_manager_snpsift_dbnsfp.py | Python | mit | 7,844 | [
"pysam"
] | caca813a11195adea0fea480b8f601cbed15aab7458245e4a7e021b13717cb04 |
#!/usr/bin/env python
#
# Appcelerator Titanium Module Packager
#
#
import os, subprocess, sys, glob, string
import zipfile
from datetime import date
cwd = os.path.abspath(os.path.dirname(sys._getframe(0).f_code.co_filename))
os.chdir(cwd)
required_module_keys = ['name','version','moduleid','description','copyright','... | atsusy/TiPaperFold | build.py | Python | mit | 6,525 | [
"VisIt"
] | 86e37ddf67c915b9aa90f1c49e01c1c3fe3888093da0bc61da977541004664eb |
#!/usr/bin/env python
""" This script retrieves the output of all the jobs of a given
test. <jobName> is the path of the directory created by submitMyJob
"""
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
from DIRAC.Core.Base.Script import parseComman... | yujikato/DIRAC | tests/Performance/DFCPerformance/retrieveResult.py | Python | gpl-3.0 | 1,217 | [
"DIRAC"
] | 9821786170d7d1c507f2c381abeafc78b555bc0480d8ce0a97aeaca434e82a96 |
#!/usr/bin/python
import numpy as np
import os
import sys
import math
import matplotlib
matplotlib.use('Pdf')
import matplotlib.pyplot as plt
from mpl_toolkits.axes_grid1 import make_axes_locatable
from matplotlib.backends.backend_pdf import PdfPages
import matplotlib.font_manager as fm
import galsim
import galsim.w... | plazas/wfirst-detectors-vnl | code/analytical_gaussian_size_error.py | Python | mit | 4,711 | [
"Gaussian"
] | 9eaac915bf82433b51dcfd3a086ed8ea1b592ef7e26876f9c816a628c8a6a1e6 |
#!/usr/bin/env python
"""
Convert a mesh file from one SfePy-supported format to another.
Examples::
$ ./script/convert_mesh.py meshes/3d/cylinder.mesh new.vtk
$ ./script/convert_mesh.py meshes/3d/cylinder.mesh new.vtk -s2.5
$ ./script/convert_mesh.py meshes/3d/cylinder.mesh new.vtk -s0.5,2,1
$ ./script/conve... | lokik/sfepy | script/convert_mesh.py | Python | bsd-3-clause | 10,146 | [
"VTK"
] | bf2ffbdae8f413890731c9a599c52799f62031a39e63cefd946af228583eace3 |
"""
Datasets to be used in the docs and tests.
Most of the datasets are adapted from the R ismev package.
For more information visit:
http://cran.r-project.org/web/packages/ismev/index.html
Other datasets includes:
-harris1996 - Annual maximum wind speeds used in Harris (1996), "Gumbel
re-visited - a new look at ext... | kikocorreoso/scikit-extremes | skextremes/datasets/datasets.py | Python | mit | 12,081 | [
"VisIt"
] | e52b4b22f35bb6663f88ff8a64b10585745c6dc9b5a2f9a3ea545cbcfb42c05d |
# autofragment.py
import pandas as pd
import pdb
import json
from rdkit import Chem
def count_substructures(radius,molecule):
"""Helper function for get the information of molecular signature of a
metabolite. The relaxed signature requires the number of each substructure
to construct a matrix for each mole... | almut-heinken/cobratoolbox | src/analysis/thermo/groupContribution/wang/autofragment.py | Python | gpl-3.0 | 2,126 | [
"RDKit"
] | a4bbd79bfb5ab7fba54f90eae8a09eb709f976d13e0aa79648d3c3ab8740e9de |
import numpy as np
from geometric.molecule import Molecule
import os, subprocess, copy
def check_all_float(iterable):
try:
[float(i) for i in iterable]
return True
except:
return False
class QMEngine(object):
def __init__(self, input_file=None, work_queue=None, native_opt=False):
... | leeping/crank | crank/QMEngine.py | Python | mit | 19,838 | [
"Psi4",
"TeraChem"
] | 27f98782ad08ebd5c99cc396861fbec3b768fd850ce25377b09cfe901c48e353 |
# -*- coding: utf-8 -*-
#!/usr/bin/env python
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007 Johan Gonqvist <johan.gronqvist@gmail.com>
# Copyright (C) 2007-2009 Gary Burton <gary.burton@zen.co.uk>
# Copyright (C) 2007-2009 Stephane Charet... | Fedik/gramps | gramps/plugins/webreport/basepage.py | Python | gpl-2.0 | 142,194 | [
"Brian"
] | 97b6e1ed11e385dd424d47c2a47d73105645459fab4442e14df9d372f5c53e7d |
#
# Copyright 2018 Analytics Zoo Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... | intel-analytics/analytics-zoo | pyzoo/zoo/examples/orca/learn/openvino/predict.py | Python | apache-2.0 | 3,611 | [
"ORCA"
] | 2e6680baf8b187657fcd43ad8096c771d8b1f76dbd2ff367bf9e549fbd3bf62a |
"""
../wps.py?request=execute
&service=wps
&version=1.0.0
&identifier=esmvaltool-perfmetrics
&status=true
&storeExecuteResponse=true
"""
import datetime
import shutil
import netCDF4
import urlparse
from pywps.Process import WPSProcess
import os
import logging
from jinja2 import FileSystemLoader, Environment,select... | c3s-magic/adaguc-services-esmvaltool-wps | processes/esmvaltool-clouds-ipcc.py | Python | apache-2.0 | 9,095 | [
"NetCDF"
] | b4fb7594bc7fc4257650742fe3b2514175277c98ec4584eaf1e7fa09cca323ce |
"""Input and output of DCD/DVD trajectory files.
See http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/dcdplugin.html
for a specification of the file format.
"""
__all__ = ['DCDReader', 'DVDReader']
import struct
from io import BytesIO
import numpy as np
# XXX Deal with endianness in DCD files.
# XXX Accelera... | clsb/miles | miles/dcdreader.py | Python | mit | 3,701 | [
"VMD"
] | 0867c9419eb544a9b880de27bab55ac1afa97f2a266c239d7f9a79dc8727561d |
#!/usr/bin/env python3
"""
Copyright 2020 Paul Willworth <ioscode@gmail.com>
This file is part of Galaxy Harvester.
Galaxy Harvester is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 ... | pwillworth/galaxyharvester | html/ghObjectSchematic.py | Python | gpl-3.0 | 3,435 | [
"Galaxy"
] | 3327c6815aa9467aa424fd58a08a153e02d994bb283335c730a69a7b9ce48bf8 |
import numpy as np
from ase.build import bulk
from ase.calculators.emt import EMT
from ase.io import write
from hiphive import ClusterSpace, ForceConstantPotential, StructureContainer
from hiphive.calculators import ForceConstantCalculator
from hiphive.input_output.gpumd import write_r0
from hiphive.utilities import ... | brucefan1983/GPUMD | potentials/fcp/Al/make_gpumd_files.py | Python | gpl-3.0 | 1,434 | [
"ASE",
"GPUMD"
] | 2e7a0f90276d5522f569e2775005c2b90bd8a07b9062d6b2c56b7f666c22fda1 |
import click
from parsec.cli import pass_context, json_loads
from parsec.decorators import custom_exception, json_output
@click.command('create_remote_user')
@click.argument("user_email", type=str)
@pass_context
@custom_exception
@json_output
def cli(ctx, user_email):
"""Create a new Galaxy remote user.
Output:
... | galaxy-iuc/parsec | parsec/commands/users/create_remote_user.py | Python | apache-2.0 | 447 | [
"Galaxy"
] | a62ac45e19ef8ec91eb5fb8a16e522fc618ff9421bd2c4121d7dc4d177fa21a8 |
# (c) 2012, Michael DeHaan <michael.dehaan@gmail.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any lat... | gnosek/ansible | lib/ansible/color.py | Python | gpl-3.0 | 1,957 | [
"Brian"
] | 78fd0aa0845e15149ef790d2be9f19b49d453a858c48e2a5121cce2e8b8555c7 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkGraphHierarchicalBundle(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | nagyistoce/devide | modules/vtk_basic/vtkGraphHierarchicalBundle.py | Python | bsd-3-clause | 522 | [
"VTK"
] | 3d8d999cdb58e1a40d6536cd77d9f3517919f5463e35de20a0decb81aefcd5e9 |
# Author: Engelbert Gruber
# Contact: grubert@users.sourceforge.net
# Revision: $Revision: 4242 $
# Date: $Date: 2006-01-06 00:28:53 +0100 (Fri, 06 Jan 2006) $
# Copyright: This module has been placed in the public domain.
"""
LaTeX2e document tree Writer.
"""
__docformat__ = 'reStructuredText'
# code contributions ... | pombreda/django-hotclub | libs/external_libs/docutils-0.4/docutils/writers/latex2e/__init__.py | Python | mit | 76,611 | [
"VisIt"
] | fb5c7d639c91a23d4e252077f040dbab5f07553c79e15823d18e37d5f7fdcbaf |
""" Basic unit tests for the Job API
"""
__RCSID__ = "$Id$"
import StringIO
from DIRAC.Interfaces.API.Job import Job
from DIRAC.Core.Utilities.ClassAd.ClassAdLight import ClassAd
def test_basicJob():
job = Job()
job.setOwner('ownerName')
job.setOwnerGroup('ownerGroup')
job.setName('jobName')
job.setJobG... | andresailer/DIRAC | Interfaces/API/test/Test_JobAPI.py | Python | gpl-3.0 | 2,181 | [
"DIRAC"
] | c2ec6140c635593f879f2395b28d245bc1875154cb0b940b9d81a0226ecf6c46 |
# Copyright 2008, 2009 CAMd
# (see accompanying license files for details).
"""Definition of the Atoms class.
This module defines the central object in the ASE package: the Atoms
object.
"""
import warnings
from math import cos, sin
import numpy as np
from ase.atom import Atom
from ase.data import atomic_numbers, ... | grhawk/ASE | tools/ase/atoms.py | Python | gpl-2.0 | 56,053 | [
"ASE"
] | 33e4a3374cf3f8b138e4b810b55abc15d752e13510ab687278b384854abaa9bd |
# ============================================================================
#
# Copyright (C) 2007-2012 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | jeroendierckx/Camelot | camelot/view/controls/action_widget.py | Python | gpl-2.0 | 18,550 | [
"VisIt"
] | 80cac74e1cd25592eeb17aa2ab59f356d71e56b9c70b84543f7def210ffdd794 |
# Orca
#
# Copyright (C) 2013-2014 Igalia, S.L.
#
# Author: Joanmarie Diggs <jdiggs@igalia.com>
#
# This library 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 (... | GNOME/orca | src/orca/scripts/toolkits/gtk/script_utilities.py | Python | lgpl-2.1 | 8,181 | [
"ORCA"
] | 8b1edb5e2b446cb9ddd8b56ea82bf9ed3536ede84b0828718f2d8995887cd54d |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import division
import os
import hashlib
import datetime
from binascii import hexlify, unhexlify
try:
ModuleNotFoundError
except:
ModuleNotFoundError = ImportError
try:
from .hexhashes import *
from .base58 import *
from .miscfuncs im... | maxweisspoker/simplebitcoinfuncs | simplebitcoinfuncs/electrum1.py | Python | mit | 22,272 | [
"CRYSTAL",
"VisIt"
] | 8c7e8fb1c996fefbc3679bcd0bff039a7e62a451efe1bfb9ae8da5681cc3c982 |
"""
@author: Bohdan Mushkevych
@author: Brian Curtin
http://code.activestate.com/lists/python-ideas/8982/
"""
import numbers
import threading
from datetime import datetime, timedelta
class RepeatTimer(threading.Thread):
""" This class triggers every number of seconds """
def __init__(self, interval, call_back... | mushkevych/scheduler | synergy/system/repeat_timer.py | Python | bsd-3-clause | 2,859 | [
"Brian"
] | a619605ca92314e0bbeab4092d24154d77fe39f98dee98618057fee80180cc16 |
"""Leetcode 559. Maximum Depth of N-ary Tree
Easy
URL: https://leetcode.com/problems/maximum-depth-of-n-ary-tree/
Given a n-ary tree, find its maximum depth.
The maximum depth is the number of nodes along the longest path from the root node
down to the farthest leaf node.
For example, given a 3-ary tree:
1
... | bowen0701/algorithms_data_structures | lc0559_maximum_depth_of_n-ary_tree.py | Python | bsd-2-clause | 2,435 | [
"VisIt"
] | 1c87efdf89f9b477f07d6bc47e706dd070c9a582dd265d38b9fb82c6eea0626d |
r"""OS routines for Mac, NT, or Posix depending on what system we're on.
This exports:
- all functions from posix, nt, os2, or ce, e.g. unlink, stat, etc.
- os.path is one of the modules posixpath, or ntpath
- os.name is 'posix', 'nt', 'os2', 'ce' or 'riscos'
- os.curdir is a string representing the current di... | huran2014/huran.github.io | wot_gateway/usr/lib/python2.7/os.py | Python | gpl-2.0 | 25,769 | [
"VisIt"
] | ea0eab1f599a94fcdd4b64d09b0a0b68381d39695f27a511ce0c507b4f011a3e |
import os
import glob
import subprocess
import commands
import numpy as np
import matplotlib.pyplot as plt
import matplotlib
from matplotlib.ticker import AutoMinorLocator
from dophot import *
from findSN import *
from astropy.time import Time
from moon import *
import csv
import sys
sys.path.insert(0, '/home/afsari/')... | niliafsari/KSP-SN | Gemini_spectra.py | Python | bsd-3-clause | 7,660 | [
"Galaxy"
] | 7e117902423d5789e390f836427f15bca57f910199581ccff90765bdf5665b98 |
# coding=utf-8
# Copyright 2014 Pants project contributors (see CONTRIBUTORS.md).
# Licensed under the Apache License, Version 2.0 (see LICENSE).
from __future__ import (absolute_import, division, generators, nested_scopes, print_function,
unicode_literals, with_statement)
from textwrap import... | slyphon/pants | tests/python/pants_test/targets/test_wiki_page.py | Python | apache-2.0 | 3,065 | [
"exciting"
] | 5e005150fb4245d54fc177caf22794b58469c6c334ef5f4c235f955450006166 |
from __future__ import division
from __future__ import print_function
#!/usr/bin/python
# program to plot SEVIRI observations
# usage from command line
# $ python plot_msg.py
#
# pass arguments to overwrite time, rgb, area given in the script
# $ python plot_msg.py year month day hour min rgb area
# year mont... | meteoswiss-mdr/monti-pytroll | scripts/plot_ci.py | Python | lgpl-3.0 | 33,454 | [
"NetCDF"
] | 141de005c590d5f18766ef2a081a8693513ec89396004a0a5ec3801eba315103 |
# This is the instrument-specific file for the PS3000a series of instruments.
#
# pico-python is Copyright (c) 2013-2014 By:
# Colin O'Flynn <coflynn@newae.com>
# Mark Harfouche <mark.harfouche@gmail.com>
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are p... | haymeister/pico-python | picoscope/ps3000a.py | Python | bsd-2-clause | 16,340 | [
"Gaussian"
] | c2a9effede933b2769de424b088e98ec8b780a436cecdb870729e1998407f573 |
#!/usr/bin/env python
import sys
import keyword
import os
import subprocess
import tempfile
import shutil
import fnmatch
import re
import hashlib
import appdirs
import cffi
import pycparser
import pycparser.c_generator
from cffi import FFI
from glob import glob
from itertools import chain
from collections import defau... | revng/llvmcpy | llvmcpy/llvm.py | Python | mit | 31,392 | [
"VisIt"
] | 1b26793cfe87b116217fc8cf54713e3120bc8d28b7e11d76273dcc04c0d7d67a |
import pylab as pyl
import cPickle as pickle
galaxies = pickle.load(open('galaxies.pickle','rb'))
galaxies = filter(lambda galaxy: galaxy.ston_I >30. and galaxy.Color_grad !=
None, galaxies)
f1 = pyl.figure(1, figsize=(6,4))
f1s1 = f1.add_subplot(111)
icd = pyl.asarray([galaxy.ICD_IH*100 for galaxy in galaxi... | boada/ICD | sandbox/plot_icd_colorgrad.py | Python | mit | 947 | [
"Galaxy"
] | 4e073c80e0300c0eae3f899e969d9d192832af16eac853a7631239a98a994289 |
# coding: utf-8
from __future__ import division, unicode_literals
"""
This module defines the VaspInputSet abstract base class and a concrete
implementation for the parameters used by the Materials Project and the MIT
high throughput project. The basic concept behind an input set is to specify
a scheme to generate a... | Dioptas/pymatgen | pymatgen/io/vaspio_set.py | Python | mit | 62,648 | [
"VASP",
"pymatgen"
] | 633eafe2cf56f57c839873b5d8a2d0ed4be6e03a1510d0dc0e54a00efd8aaed2 |
########################################################################
# File : StatesAccountingAgent.py
# Author : A.T.
########################################################################
""" StatesAccountingAgent sends periodically numbers of jobs in various states for various
sites to the Monitorin... | vmendez/DIRAC | WorkloadManagementSystem/Agent/StatesAccountingAgent.py | Python | gpl-3.0 | 5,569 | [
"DIRAC"
] | 162b93ea845b5741121b9bece035aec521fb476d85a4b75a78c192a1c14a5f1b |
import sys
import os
import commands
import nipype.pipeline.engine as pe
import nipype.algorithms.rapidart as ra
import nipype.interfaces.fsl as fsl
import nipype.interfaces.io as nio
import nipype.interfaces.utility as util
from utils import *
from CPAC.vmhc import *
from nipype.interfaces.afni import preprocess
from ... | sgiavasis/C-PAC | CPAC/vmhc/vmhc.py | Python | bsd-3-clause | 22,733 | [
"Gaussian"
] | fcdf82544507c9ae001e92134ee3891b08d93ec5a096177454c0c028e78edb7e |
''' ResourceStatusClient
Client to interact with the ResourceStatusDB.
'''
#pylint: disable=unused-argument
from DIRAC import S_OK
from DIRAC.Core.DISET.RPCClient import RPCClient
from DIRAC.ResourceStatusSystem.Utilities ... | Andrew-McNab-UK/DIRAC | ResourceStatusSystem/Client/ResourceStatusClient.py | Python | gpl-3.0 | 15,310 | [
"DIRAC"
] | a22f444066575acf5a521ba7dbb763587e1d5390c37be5227189edcb7dd76437 |
# Copyright (C) 2015 Henrique Pereira Coutada Miranda, Alejandro Molina Sanchez
# All rights reserved.
#
# This file is part of yambopy
#
#
from qepy import *
import os
import re
from math import sqrt
class PwIn():
"""
Class to generate an manipulate Quantum Espresso input files
Can be initialized either r... | palful/yambopy | qepy/pw.py | Python | bsd-3-clause | 12,245 | [
"ASE",
"CRYSTAL",
"Quantum ESPRESSO"
] | f8efccd2ad1a208a8dc6bae51f4230f07bbd4f307a8d56af4c26893d1278a7cf |
"""
Physical units and dimensions.
The base class is Unit, where all here defined units (~200) inherit from.
The find_unit function can help you find units for a given quantity:
>>> import sympy.physics.units as u
>>> u.find_unit('coul')
['coulomb', 'coulombs']
>>> u.find_unit(u.charge)
['C', 'ch... | mafiya69/sympy | sympy/physics/units.py | Python | bsd-3-clause | 8,610 | [
"Avogadro"
] | 75aeccad3dc662a0fe7278bac3ec658997b8c2680646ecd091c3ab33f598baf8 |
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