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# gaussfitter.py
# created by Adam Ginsburg (adam.ginsburg@colorado.edu or keflavich@gmail.com) 3/17/08)
import numpy
from numpy.ma import median
from numpy import pi
#from scipy import optimize,stats,pi
from mpfit import mpfit
""" Note about mpfit/leastsq: I switched everything over to the Markwardt mpfit
routine for ... | creyesp/RF_Estimation | LIB/gaussfitter.py | Python | gpl-2.0 | 17,932 | [
"Gaussian"
] | 0a8755cb4edcb412bdf363755a460ac48234f9e29302f3807e1095e2417f8c6b |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
This file
"""
# For Travis CI
import matplotlib
matplotlib.use("Agg")
import time
import os
import numpy as np
import matplotlib.pyplot as plt
from scipy.stats import norm
from KDEpy import NaiveKDE, TreeKDE, FFTKDE
def main():
here = os.path.abspath(os.path.d... | tommyod/KDEpy | docs/source/examples.py | Python | gpl-3.0 | 7,718 | [
"Gaussian"
] | bb19baec5bb82aedfb04c2455c0415561c1051a48b54e15dd474f3e077db3f79 |
# coding: utf-8
from __future__ import unicode_literals
import base64
import datetime
import hashlib
import json
import netrc
import os
import random
import re
import socket
import sys
import time
import math
from ..compat import (
compat_cookiejar,
compat_cookies,
compat_etree_fromstring,
compat_getp... | jicruz/heroku-bot | lib/youtube_dl/extractor/common.py | Python | gpl-3.0 | 121,381 | [
"VisIt"
] | bc18a422be5be4e3be2955c9b91adf5d6b7ffad36fa78ea7791c56a6155e31f9 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# relevant imports
import sys
import time
import espresso
import mpi4py.MPI as MPI
import Tetracryst # Preparation of tetrahedral crystal and constuctions of bonds in tetrahedral liquid
from espresso import Real3D, Int3D
from espresso.tools import decomp
from espresso.to... | BackupTheBerlios/espressopp | examples/hadress/hadressFEC/hadressDensityFEC.py | Python | gpl-3.0 | 8,414 | [
"CRYSTAL",
"ESPResSo"
] | cb24a3b5d9e8a1a6d2e577ef246dee8d7ccbf12a7f30b2d8068d79ff951792e4 |
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under t... | vivekdhayaal/keystone | keystone/tests/hacking/checks.py | Python | apache-2.0 | 16,856 | [
"VisIt"
] | da49f825ece8fbd56e4775a81198687a4fdc0d833427b5834cf3aa2e82a33c12 |
# -*- coding: utf-8 -*-
from __future__ import print_function
import tempfile
import numpy as np
import mdtraj
import pkg_resources
def get_top():
return pkg_resources.resource_filename(__name__, 'data/test.pdb')
def create_traj(top=None, format='.xtc', dir=None, length=1000, start=0):
trajfile = tempfile... | marscher/PyEMMA | pyemma/coordinates/tests/util.py | Python | lgpl-3.0 | 2,846 | [
"MDTraj"
] | 9272250ccd34ae2a5b978900e68d5d97787474114306d97ff722ef83febd645e |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | jairideout/scikit-bio | skbio/stats/tests/test_spatial.py | Python | bsd-3-clause | 6,064 | [
"scikit-bio"
] | a542f1720b3731e44e4a943af02b7e709183ba709c878277ed609ee55a662180 |
#!/usr/bin/env python
# This tool takes a tab-delimited text file as input and creates filters on columns based on certain properties.
# The tool will skip over invalid lines within the file, informing the user about the number of lines skipped.
import sys, sets, re, os.path
from galaxy import eggs
assert sys.version... | dbcls/dbcls-galaxy | tools/stats/filtering.py | Python | mit | 4,048 | [
"Galaxy"
] | 450437924a3bbc9e830bd7ba2d7dcd3889449a820e071dfc4a4634da63670630 |
#!/bin/env python
""" This integration test is for "Inner" Computing Element SingularityComputingElement
This test is here and not in the unit tests because it requires singularity to be installed.
"""
import os
import shutil
from DIRAC import gLogger
from DIRAC.tests.Utilities.utils import find_all
from DIRAC.... | yujikato/DIRAC | tests/Integration/Resources/Computing/Test_SingularityCE.py | Python | gpl-3.0 | 2,680 | [
"DIRAC"
] | 0d7e03216fd9a37c4698d70cf74abf2a0470bad357d4a9a1e79a2c98b8f46704 |
# Symmetry can only be used in EELS spectra calculations for GPAW svn 6305 above.
# Refer to A. Rubio and V. Olevano, et.al, Physical Review B 69, 245419 (2004)
# for comparision of results
import os
import sys
from math import sqrt
import numpy as np
from ase import Atoms
from ase.units import Bohr
from ase.parallel... | robwarm/gpaw-symm | gpaw/test/big/response/graphite_EELS.py | Python | gpl-3.0 | 2,044 | [
"ASE",
"GPAW"
] | 6cb0b90a02dce434f7ab92fa38e5d52c2ffc83f8b150c37ce50f0b89fa66b3c5 |
# $Id$
#
# Copyright (C) 2004-2006 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.
#
from rdkit import RDConfig
# change thi... | rdkit/rdkit-orig | rdkit/Chem/ShowMols.py | Python | bsd-3-clause | 925 | [
"PyMOL",
"RDKit"
] | 74b201c5d4009b308bc7bd4d0e63763b058a34736ce6f597e23ba4707fc97bbc |
__license__ = 'MIT License <http://www.opensource.org/licenses/mit-license.php>'
__author__ = 'Lucas Theis <lucas@theis.io>'
__docformat__ = 'epytext'
from scipy.special import erf, erfinv
from scipy.stats import norm
from scipy.optimize import bisect
from numpy import mean, sqrt, asarray, max, min, any
from transform... | lucastheis/isa | code/transforms/univariategaussianization.py | Python | mit | 1,634 | [
"Gaussian"
] | ba166315fd6e16686039618feefe7d2b789ed1ea335e1727c05304e10fc979ad |
import allensdk.core.json_utilities as json_utilities
from allensdk.model.glif.glif_neuron import GlifNeuron
# initialize the neuron
neuron_config = json_utilities.read('472423251_neuron_config.json')
neuron = GlifNeuron.from_dict(neuron_config)
# make a short square pulse. stimulus units should be in Amps.
stimulus ... | wvangeit/AllenSDK | doc_template/examples/glif_ex2.py | Python | gpl-3.0 | 619 | [
"NEURON"
] | ee3bfa5f0fde9a25df6cd4b239d84178f1a4f07197bbcb4986ed7332e90269c9 |
# (C) 2017, Markus Wildi, markus.wildi@bluewin.ch
#
# 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, or (at your option)
# any later version.
#
# This program is distr... | RTS2/rts2 | scripts/u_point/unittest/test_executables.py | Python | lgpl-3.0 | 9,404 | [
"VisIt"
] | 76ff5764e4cad11bf1ee91e907aab7daf08082e41113bd50e1f6c616cd19218a |
# encoding=utf-8
from typing import List
import numpy as np
import xgboost as xgb
import logging
import re
import tensorflow as tf
import tensorflow_addons as tfa
def build_xgb_nn_model(tree_num=10):
"""
use xgb leaf features inside.
To have a different model space in moe, just use xgb leaf features here.... | eryueniaobp/contest | xiaomi/phone_xgbnn.py | Python | apache-2.0 | 4,774 | [
"MOE"
] | 8e8c62ca3c9ea56038258466f821954263a380403f304960d9c56d54cac21a4b |
########################################################################
# $HeadURL $
# File: RequestTask.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2011/10/12 12:08:51
########################################################################
""" :mod: RequestTask
=================
.. module: RequestTa... | avedaee/DIRAC | DataManagementSystem/private/RequestTask.py | Python | gpl-3.0 | 20,366 | [
"DIRAC"
] | 1bc1610cda3333a630138a3f60da79807479f5af86a004dedb86cec478de1234 |
# ==================================================================================================
# Copyright 2011 Twitter, Inc.
# --------------------------------------------------------------------------------------------------
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use thi... | foursquare/commons-old | src/python/twitter/common/java/__init__.py | Python | apache-2.0 | 930 | [
"Brian"
] | 8784f5842e8a254a38f75a994593af7acffed888a8ce727d35c334692bf88da4 |
#!/usr/bin/env python3
## INFO ########################################################################
## ##
## kibu-vr ##
## ======= ... | kitchenbudapest/vr | build.py | Python | gpl-3.0 | 3,670 | [
"VisIt"
] | bef39453e88da063e9e981d5ef2067e80489978e794a06539be894555160ca88 |
"""
Tests for the Course Outline view and supporting views.
"""
import datetime
import json
import re
import six
from completion import waffle
from completion.models import BlockCompletion
from completion.test_utils import CompletionWaffleTestMixin
from django.contrib.sites.models import Site
from django.test import... | cpennington/edx-platform | openedx/features/course_experience/tests/views/test_course_outline.py | Python | agpl-3.0 | 28,296 | [
"VisIt"
] | b1196deb62e59f255e5c483179c863231ad7cef3d981318b76ca84f20978d611 |
# -*- coding: utf-8 -*-
#
# Copyright 2012 - 2013 Brian R. D'Urso
#
# This file is part of Python Instrument Control System, also known as Pythics.
#
# Pythics 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 Foundati... | LunarLanding/Pythics | pythics/examples/random_walk_simulator.py | Python | gpl-3.0 | 2,043 | [
"Brian"
] | 1330b000cd84295de9e3096f5c0ec8ce0c5dbdf1c2107e9cb5825461cb1ff14c |
# -*- coding: utf-8 -*-
# Copyright (c) 2015, Vispy Development Team.
# Distributed under the (new) BSD License. See LICENSE.txt for more info.
from __future__ import division
import re
from ... import gloo
class Compiler(object):
"""
Compiler is used to convert Function and Variable instances into
rea... | hronoses/vispy | vispy/visuals/shaders/compiler.py | Python | bsd-3-clause | 7,604 | [
"VisIt"
] | 5192d3eb507f59a8d3fd0d4193419e977833ea89639953b0cdd1cec472c81a06 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 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
#... | lothian/psi4 | psi4/driver/qcdb/jajo.py | Python | lgpl-3.0 | 17,941 | [
"Avogadro",
"CFOUR",
"Psi4"
] | a12946b8e62f783a95680faf2fcae3861c9ddd7fb31c7ae342583346c87858a9 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | MOA-2011/enigma2-plugin-extensions-openwebif | plugin/controllers/views/web/mediaplayeradd.py | Python | gpl-2.0 | 5,260 | [
"VisIt"
] | cf214c935612b040c685d4a066ed0ee65b184d30f039c556e14e32a2edeba55c |
#!/usr/bin/python2
# -*- Mode: Python; py-indent-offset: 8 -*-
# (C) Copyright Zack Rusin 2005
# All Rights Reserved.
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation files (the "Software"),
# to deal in the Software without restriction, ... | devlato/kolibrios-llvm | contrib/sdk/sources/Mesa/src/mapi/glapi/gen/gl_enums.py | Python | mit | 7,309 | [
"Brian"
] | 3102edb43d16211077adef1646532ea3c54da8cfa8107e86dc9f17b51177dc94 |
#
# Copyright 2013-2018 Universidad Complutense de Madrid
#
# This file is part of PyEmir
#
# PyEmir 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 l... | nicocardiel/pyemir | emirdrp/recipes/aiv/common.py | Python | gpl-3.0 | 17,887 | [
"Gaussian"
] | 793cd2ba2cab468b8645cb8e19aa754a2c327411be1b8d297415e14c228259f6 |
# Utility file for reading the excel file containing all the toxicity data
import pandas as pd
import xlrd
import pdb
import numpy as np
import matplotlib.pyplot as plt
import scipy.stats as stats
##
# @brief Read all the toxicity data from excel file
#
# @param filepath - Full filepath of excel file
# @param toxicity ... | surenkum/feature_selection | utils.py | Python | gpl-3.0 | 13,413 | [
"Gaussian"
] | 0d854a138e321a440ed1ab86d81862e17fb40be07b4a278a6fc6fb0e8f3dfc9b |
# 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 RDss(RPackage):
"""Dispersion shrinkage for sequencing data.
DSS is an R library perf... | iulian787/spack | var/spack/repos/builtin/packages/r-dss/package.py | Python | lgpl-2.1 | 1,236 | [
"Bioconductor"
] | fd08fe22bb0eb831529a9a2aac77229581c65633b446ecd8a2c912b35afea6ff |
"Base class for simulation windows"
import gtk
from gettext import gettext as _
from ase.gui.widgets import oops, pack, help
from ase import Atoms
from ase.constraints import FixAtoms
class Simulation(gtk.Window):
def __init__(self, gui):
gtk.Window.__init__(self)
self.gui = gui
def packtext(... | grhawk/ASE | tools/ase/gui/simulation.py | Python | gpl-2.0 | 5,562 | [
"ASE"
] | 2c73e6a44b07b6bf56ae4529c7cfee346625ecc3f2141affdfb50738008ad8b1 |
#!/usr/bin/env python
''' VIC Image Driver testing '''
import os
import re
import xarray as xr
import pandas as pd
import numpy as np
import numpy.testing as npt
import glob
import warnings
def test_image_driver_no_output_file_nans(fnames, domain_file):
'''
Test that all VIC image driver output files have th... | dgergel/VIC | tests/test_image_driver.py | Python | gpl-2.0 | 10,677 | [
"NetCDF"
] | 464695bfcf838258fb2e1a356c938ebf2b465bdb316a816a7b6b3684257c8e63 |
#pylint: disable=missing-docstring
####################################################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simulation Environment ... | liuwenf/moose | python/MooseDocs/extensions/app_syntax.py | Python | lgpl-2.1 | 26,487 | [
"MOOSE"
] | 587b76fe8d93e2c6172a92743d78af9c8493abc31c7e977282e448535f00a76b |
# ===============================================================================
# Copyright 2012 Jake Ross
#
# 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/licens... | UManPychron/pychron | pychron/stage/calibration/auto_calibrator.py | Python | apache-2.0 | 12,969 | [
"VisIt"
] | 5ac1a98e2a1754567db56a878492852b10e9216e7b94cd74301862234f3a32b3 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# userstats - Front end to user stats
# Copyright (C) 2003-2010 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License ... | heromod/migrid | mig/cgi-bin/userstats.py | Python | gpl-2.0 | 1,074 | [
"Brian"
] | a985e67e02a7f56b385c362c3a1007992f6212f3683ea41eab86ed37d3d9ae3c |
import sys
class ProgressBar(object):
__author__ = "Laura Domicevica"
__version__ = "09.2016"
"""
Shows the progress of analysis in frame rate and percentage.
In August 2016, used for residence time analysis, since others are shown by MDAnalysis.
"""
def __init__(self, title):
self... | ldomic/lintools | lintools/analysis/progressbar.py | Python | gpl-3.0 | 786 | [
"MDAnalysis"
] | 63a017cc5737be29df0e9f609bfa791e75113ff163b350de8627bb9891eeace4 |
from subdown_version import __version__
introstr="""
_________ ___. ________
/ _____/ __ __ \_ |__ \______ \ ____ __ _ __ ____
\_____ \ | | \ | __ \ | | \ / _ \ \ \/ \/ / / \
/ \| | / | \_\ \ | ` \( <_> ) \ / | | \
/_______ /|... | saikpr/subdown | subdown.py | Python | mit | 2,478 | [
"VisIt"
] | 8c27b2a00cf7e3b605e1de64664c391dd2bbff5169b1b179db660d8add9488b4 |
import os
import vtk
import numpy as np
from ensight2vtk_single_encas import ensight2vtk
from post_proc_cfd import post_proc_cfd
from post_proc_cfd_diff import post_proc_cfd_diff
from multiprocessing import Pool
def run_script():
#case_list = ["case1", "case3", "case4", "case5", "case7"]
#case_list = ["case1",... | kayarre/Tools | vtk/post_process_main.py | Python | bsd-2-clause | 4,785 | [
"VTK"
] | 5c6d54ba1b3bd059db8149d2d79fb78aaedf621cf192b4ab000457a44d87446e |
"""
A simple VTK input file for PyQt, the qt bindings for python.
See http://www.trolltech.com for qt documentation, and
http://www.river-bank.demon.co.uk or http://www.thekompany.com
for the qt python bindings.
*******************************************************
NOTE: The widget provided by this module is not... | b3c/VTK-5.8 | Wrapping/Python/vtk/qt/QVTKRenderWidget.py | Python | bsd-3-clause | 15,276 | [
"VTK"
] | b89358ce95d7c8af5723a427a7d4214c74d3fdc98118b185259dc984bb69180d |
#!/usr/bin/env python
'''
Input ke_cutoff (kinetic energy cutoff) or mesh (#grids) for FFT-based Coulomb
integral.
If ke_cutoff and mesh are not specified in the input, they will be chosen
automatically in cell.build function based on the basis set. You can set
ke_cutoff or mesh to control the performance/accuracy o... | gkc1000/pyscf | examples/pbc/06-input_ke_cutoff.py | Python | apache-2.0 | 1,018 | [
"PySCF"
] | c5007b77d65e83675f35393b4806d068dc124a35bbab6e0945141eedd52fcead |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | sxjscience/mxnet | tests/python/unittest/test_gluon_probability_v2.py | Python | apache-2.0 | 94,412 | [
"Gaussian"
] | 0bfdb8a155592bdec2e20e2e2c2107129a04c09d76cf6d9c693a9e0b36361366 |
#!/usr/bin/env python
from __future__ import print_function
from collections import defaultdict
from collections import deque
from subprocess import call
from optparse import OptionParser
from tempfile import mkstemp
import os
import random
import re
import shlex
import shutil
import subprocess
import sys
import time
i... | cmhill/VALET | src/py/pipeline.py | Python | mit | 48,961 | [
"Bowtie"
] | 263ac5cff0304215eadf4c400d9747acee8d528abbd15ca4c714d7020cb557db |
""" The mind is a service the distributes "task" to executors
"""
import types
import pprint
from DIRAC import gLogger
from DIRAC.Core.Utilities.ReturnValues import S_OK, S_ERROR, isReturnStructure
from DIRAC.Core.Utilities.ThreadScheduler import gThreadScheduler
from DIRAC.Core.DISET.RequestHandler import RequestHan... | chaen/DIRAC | Core/Base/ExecutorMindHandler.py | Python | gpl-3.0 | 11,256 | [
"DIRAC"
] | 8c1c5aa3efa8373303d21fa162a6c326d258d25a512d3b33d47c80c35eb5c952 |
#
# tsne.py
#
# Implementation of t-SNE in Python. The implementation was tested on Python 2.5.1, and it requires a working
# installation of NumPy. The implementation comes with an example on the MNIST dataset. In order to plot the
# results of this example, a working installation of matplotlib is required.
# The ... | masoodking/LinkPrediction | SME/tsne_python/tsne.py | Python | bsd-3-clause | 5,844 | [
"Gaussian"
] | 51a5789f55a63de5c983f626ea6162c1b83382b3091d9289ae00fcb31bd4dd10 |
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# d... | hybrid-storage-dev/cinder-fs-111t-hybrid-cherry | flow_utils.py | Python | apache-2.0 | 6,804 | [
"VisIt"
] | 57430bc54f7485be3821c520a518ebf54acf8e5b70afa2f8fe660f425c0116b2 |
"""
Utility functions for transcripts.
++++++++++++++++++++++++++++++++++
"""
from functools import wraps
from django.conf import settings
import os
import copy
import json
import requests
import logging
from pysrt import SubRipTime, SubRipItem, SubRipFile
from pysrt.srtexc import Error
from lxml import etree
from opaq... | ahmedaljazzar/edx-platform | common/lib/xmodule/xmodule/video_module/transcripts_utils.py | Python | agpl-3.0 | 36,950 | [
"FEFF"
] | 4b156d35bef1964ee52faf86eb2347b7b3b3ad41c807cd211447cb5095d60fd6 |
# coding=utf-8
import os
from setuptools import setup
from sys import version_info
if version_info.major != 3 or version_info.minor < 5:
raise RuntimeError('friction requires python 3.5 or newer')
setup(
name='friction',
version='1.0.0',
description=(
'a browser-based gallery viewer tailored ... | tinruufu/friction | setup.py | Python | mit | 1,563 | [
"VisIt"
] | 8b1e4c973746c57db247aa720f58ef581ed2f6302a58addfaec1bd7116b6599c |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/cc/test/test_eom_uccsd.py | Python | apache-2.0 | 12,389 | [
"PySCF"
] | 12640030cd0030321cc5a4ab4d169c2c08c198e2f70bbb53dbb96ea88c788c04 |
#!/usr/bin/env python
"""Kubernetes sandbox components."""
import json
import logging
import os
import re
import subprocess
import tempfile
import time
import sandbox
import sandlet
def set_gke_cluster_context(gke_cluster_name):
logging.info('Changing cluster to %s.', gke_cluster_name)
clusters = subprocess.che... | theskyinflames/bpulse-go-client | vendor/github.com/youtube/vitess/test/cluster/sandbox/kubernetes_components.py | Python | apache-2.0 | 4,618 | [
"VisIt"
] | 0a4fd12bb9bb1882b4e15fdf1a308c23191a7aca8bbca37569ccadf1fdcd93e8 |
import os
import pysam
import tempfile
import shutil
from iva import contig, mapping, seed, mummer, graph, edge, common
import pyfastaq
class Assembly:
def __init__(self, contigs_file=None, map_index_k=15, map_index_s=3, threads=1, kmc_threads=1, max_insert=800, map_minid=0.5, min_clip=3, ext_min_cov=5, ext_min_ra... | satta/iva | iva/assembly.py | Python | gpl-3.0 | 27,357 | [
"pysam"
] | 0f966d2d48e1faaecc9adf1d0d7091ceeba07728052ae324898e87de57d1ab93 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 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
#... | ashutoshvt/psi4 | psi4/driver/molutil.py | Python | lgpl-3.0 | 9,732 | [
"Psi4"
] | 38ba71bc1bac46b3c72164d6c1c5e5cd9a423bf1f9db83997383373bf84b8289 |
# -*- coding: utf-8 -*-
"""
==============================
1D Wasserstein barycenter demo
==============================
This example illustrates the computation of regularized Wassersyein Barycenter
as proposed in [3].
[3] Benamou, J. D., Carlier, G., Cuturi, M., Nenna, L., & Peyré, G. (2015).
Iterative Bregman pro... | rflamary/POT | examples/plot_barycenter_1D.py | Python | mit | 3,676 | [
"Gaussian"
] | 345ff02819a78e1caf9c9f86f04da67c2068521ad8d7cad2d3a5a39d9ee549c3 |
#!/usr/bin/env python
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Implementation for `pmg structure` CLI.
"""
import sys
from tabulate import tabulate
from pymatgen import Structure
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from ... | gVallverdu/pymatgen | pymatgen/cli/pmg_structure.py | Python | mit | 3,894 | [
"pymatgen"
] | 34578d76f5c78d3b4c8e3b1ed09f27985f4bb309a3172952cf6f4e0b959d8f68 |
#!/usr/bin/env python3
# Copyright 2012 David Y. Gonzalez
# This file is part of A.L.E.C.
# A.L.E.C. 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 ... | yzaguirre/topdog-tools | alec.py | Python | apache-2.0 | 8,372 | [
"VisIt"
] | 6f7d34cd94d75ff46a560ae6dacf5ab4cfa45f85bea086e7e48e420b8f3231a7 |
# 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... | GbalsaC/bitnamiP | venv/lib/python2.7/site-packages/logilab/astng/builder.py | Python | agpl-3.0 | 8,738 | [
"VisIt"
] | f38188a483110c019d96ea70328ea7c110bf37c22d9e4e614efda94f4753a192 |
#!/usr/bin/env python3
# Copyright 2015-2018 Ian Leonard <antonlacon@gmail.com>
#
# This file is bot_cfg.py and is part of the Foundational IRC Bot for
# Twitch.tv project.
#
# bot_cfg.py is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the... | antonlacon/foundationalbot | bot_cfg.py | Python | gpl-3.0 | 2,723 | [
"VisIt"
] | 80dc036a28c61c739293fa30bf7d4c1a400aca96b795c56027066a39e04e0de4 |
from .util import APPS_DIR_PATH, EPLUS_DIR_PATTERN
from .outputs import OUTPUT_FILES_LAYOUTS, get_output_files_layout
from .epw import get_simulated_epw_path
from .simulation import SIMULATION_COMMAND_STYLES, SIMULATION_INPUT_COMMAND_STYLES, get_simulation_base_command, \
get_simulation_input_command_style, get_sim... | Openergy/oplus | oplus/compatibility/__init__.py | Python | mpl-2.0 | 342 | [
"EPW"
] | efa0c1c748b04965165cfe09dfc21dec308ae1dd9819fcd45361a3c4fd729e5e |
#=============================================================================
# gpx_layer_waypoints.py
# Waypoint map layer
# Copyright 2013--2016, Trinity College
# Last modified: 31 March 2016
#=============================================================================
import gtk
import math
import cairo
from gp... | david672orford/GPX_Trip_Planner | Code/gpx_layer_waypoints.py | Python | gpl-2.0 | 4,877 | [
"FLEUR"
] | e64bab91eaf63b2633de02b048b337d70c8b6a4c5db4535cb8da3e8ea9db4302 |
def ASoP_tests():
import os.path
import sys
import numpy as np
import iris
from ASoP1_spectral import make_hist_maps
from ASoP1_spectral import plot_hist_maps
from ASoP1_spectral import plot_hist1d
THIS_DIR = os.path.dirname(os.path.abspath(__file__))
my_data_path = o... | gillmmartin/ASoP1-Spectral | ASoP1_Spectral/tests/ASoP1_tests.py | Python | apache-2.0 | 3,509 | [
"NetCDF"
] | ecdb209626813ab98282a157c8bd6970dc5d9363964346efd61da9b560bd40c5 |
#
# Copyright 2019-2020 Johannes Hoermann (U. Freiburg)
#
# matscipy - Materials science with Python at the atomic-scale
# https://github.com/libAtoms/matscipy
#
# 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 Softw... | libAtoms/matscipy | examples/electrochemistry/pnp_batch/cell_1d/stern_layer_sweep/pnp_plot.py | Python | lgpl-2.1 | 7,482 | [
"Matscipy"
] | 0e44979414523e171eaca3dc5577ac38dad57dfd94ba4482b0d260a8c40914c4 |
#!/usr/bin/env python
from __future__ import division
import os
import re
import string
import argparse
from collections import defaultdict
import pysam
import pandas as pd
from pyfasta import Fasta
def alleleCount(baseList,refNuc):
pos = defaultdict(int)
neg = defaultdict(int)
if refNuc in ['A', 'T']:
... | paoyangchen-laboratory/methgo | scripts/snp/snp.py | Python | mit | 4,408 | [
"pysam"
] | 2c7321680f13c26c34c3e9c1ebed09fc86ca1fb411c2fbf0074522349b166983 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2012 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU Lesser General Public License as published by
## the Free Software F... | andrebellafronte/stoq | stoqlib/gui/test/test_payment_confirm_slave.py | Python | gpl-2.0 | 6,498 | [
"VisIt"
] | f9b9c06a0f42ba9b3ece2d24dc517690bdebb46cb5cc9e3423e4c8b1cddf301e |
from __future__ import print_function, division
import copy
from collections import defaultdict
from sympy.core.containers import Dict
from sympy.core.expr import Expr
from sympy.core.compatibility import is_sequence, as_int, range
from sympy.core.logic import fuzzy_and
from sympy.core.singleton import S
from sympy.f... | madan96/sympy | sympy/matrices/sparse.py | Python | bsd-3-clause | 46,101 | [
"DIRAC"
] | e6afed86af30d12836b2b3f01be487905212f95c5b12dbb46e8f22f5ad04c819 |
# ammoTrackingMultiplier
#
# Used by:
# Charges from group: Advanced Artillery Ammo (8 of 8)
# Charges from group: Advanced Autocannon Ammo (8 of 8)
# Charges from group: Advanced Beam Laser Crystal (8 of 8)
# Charges from group: Advanced Blaster Charge (8 of 8)
# Charges from group: Advanced Pulse Laser Crystal (8 of ... | Ebag333/Pyfa | eos/effects/ammotrackingmultiplier.py | Python | gpl-3.0 | 585 | [
"CRYSTAL"
] | f06bb8a6333093e9da714c9fbe80186a38983c740517b8f098029e8236a3f861 |
import numpy as np
import matplotlib as mpl
import matplotlib.pyplot as plt
from matplotlib.pyplot import *
from matplotlib.backends.backend_pdf import PdfPages
from scipy.signal._peak_finding import argrelextrema
import sklearn
import sklearn.metrics
from sklearn.metrics.ranking import roc_curve, auc
import sklearn.pr... | ravenshooter/BA_Analysis | Evaluation.py | Python | mit | 38,190 | [
"NEURON"
] | 0f7caa44789d2023f1a990fef1320621fa3d6b5d15762ab892f9e84e97ed4c2f |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# grid_script - the core job handling daemon on a MiG server
# Copyright (C) 2003-2012 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the GNU ... | heromod/migrid | mig/server/grid_script.py | Python | gpl-2.0 | 65,403 | [
"Brian"
] | caf63af2d3e4502f8ac070488c86c66a0c5015ea4540232e308f561090b33b8b |
#!/usr/bin/env python
import sys
import os
import netCDF4
import numpy
import json
import re
import copy
import logging
import argparse
log = logging.getLogger(__name__)
logging.basicConfig(level = logging.DEBUG)
fill_value = -9999.
reqdims = []
reqvars = []
# Main function.
def convert(gridfile,datafile,outputfile... | eWUDAPT/eWUDAPT-analysis | eWUDAPT_analysis/txt2nc.py | Python | apache-2.0 | 5,331 | [
"NetCDF"
] | 658dc2b9b410a7d5cc2a0baebb0c1a4e6b53286fefcb2a11b98266f180a521b9 |
#
# 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/orca/data/shard.py | Python | apache-2.0 | 17,847 | [
"ORCA"
] | 090d13c03de85251e0305ef83460d0571aa7ba40d0a886f0d292a4bc588610c5 |
# ----------------------------------------------------------
# AdvaS Advanced Search
# module for phonetic algorithms
#
# (C) 2002 - 2005 Frank Hofmann, Chemnitz, Germany
# email fh@efho.de
# ----------------------------------------------------------
# changed 2005-01-24
import string
import re
def soundex (term):
... | weblyzard/ewrt | src/eWRT/lib/thirdparty/advas/phonetics.py | Python | gpl-3.0 | 15,761 | [
"VisIt"
] | 2da37e6c9b27170a39c563acb2e787af1e5032b7f5c5ca1bfde3f09887eca6b3 |
# GromacsWrapper: utilities.py
# Copyright (c) 2009 Oliver Beckstein <orbeckst@gmail.com>
# Released under the GNU Public License 3 (or higher, your choice)
# See the file COPYING for details.
"""
:mod:`gromacs.utilities` -- Helper functions and classes
========================================================
The mod... | jandom/GromacsWrapper | gromacs/utilities.py | Python | gpl-3.0 | 22,872 | [
"Gromacs"
] | 938508dfd0c1703a0ba3ac0c4b554c28bcb752b57e17ab11a1a581fd6a5089d6 |
#!/usr/bin/env python
import os
import sys
import numpy as np
import matplotlib.pyplot as plt
def expected(ini, res, ini_x, res_x):
lo2 = 0.5 * (res_x - ini_x)
alpha = (ini - res) / 4.0 / lo2**3
beta = -3.0 * alpha * lo2**2
data = [ini_x + i*(res_x - ini_x)/100 for i in range(100)]
data = [(x, alp... | liuwenf/moose | modules/tensor_mechanics/test/tests/capped_mohr_coulomb/small_deform_hard_21.py | Python | lgpl-2.1 | 1,258 | [
"MOOSE"
] | 9f4fa1b7550f93dc63b0fa76960c056ec21d136231af9363fb45f955d07f223a |
#! /usr/bin/env python
"""Static analysis tool for checking docstring conventions and style.
Implemented checks cover PEP257:
http://www.python.org/dev/peps/pep-0257/
Other checks can be added, e.g. NumPy docstring conventions:
https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt
The repository is l... | wvangeit/python-mode | pymode/libs/pylama/lint/pylama_pep257/pep257.py | Python | lgpl-3.0 | 27,195 | [
"VisIt"
] | 955230a3588951e3b3100756bd40e3f41cec51aad103bbfaa6e533f4eb18d449 |
import numpy as np
import pylab as pl
import netCDF4 as nc4
pl.close('all')
# Create stretched grid
class Grid:
def __init__(self, kmax, nloc1, nbuf1,dz1, dz2):
self.kmax = kmax
dn = 1./kmax
n = np.linspace(dn, 1.-dn, kmax)
nloc1 *= dn
nbuf1 *= dn
... | microhh/microhh2 | cases/gabls4s3/gabls4s3_input.py | Python | gpl-3.0 | 3,909 | [
"NetCDF"
] | 796626338fc59a9be405e678aa33457433d35e79e549e6c7d801cbac057ada39 |
"""
========================================
Ammonia inversion transition TROT fitter
========================================
Ammonia inversion transition TROT fitter translated from Erik Rosolowsky's
http://svn.ok.ubc.ca/svn/signals/nh3fit/
.. moduleauthor:: Adam Ginsburg <adam.g.ginsburg@gmail.com>
Module API
^^^... | vlas-sokolov/pyspeckit | pyspeckit/spectrum/models/ammonia.py | Python | mit | 50,962 | [
"Gaussian"
] | 9006aa638a055a1a67b546d3807a8c9768ee70dee736ad76bccf2f305b77c97b |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under the GNU Public... | MDAnalysis/mdanalysis | package/MDAnalysis/lib/distances.py | Python | gpl-2.0 | 67,291 | [
"MDAnalysis"
] | 35f553b58c4b3c9dc901425e19abc6bbebf20d2b7fbb2735f47f68773fc57aaa |
import string, gettext
_ = gettext.gettext
try:
frozenset
except NameError:
# Import from the sets module for python 2.3
from sets import Set as set
from sets import ImmutableSet as frozenset
EOF = None
E = {
"null-character":
_(u"Null character in input stream, replaced with U+FFFD."),
... | dewitt/appengine-unshorten | third_party/html5lib/constants.py | Python | apache-2.0 | 88,590 | [
"Bowtie"
] | 032651df6061c74b748150e01125dccc4dc98354580ba2c50b71a23f48c5c3ef |
from __future__ import unicode_literals
import json
from context_processors import GroupPermWrapper
from datetime import timedelta
from dateutil.relativedelta import relativedelta
from django.conf import settings
from django.contrib.auth.models import User, Group
from django.core import mail
from django.core.exceptio... | reyrodrigues/EU-SMS | temba/orgs/tests.py | Python | agpl-3.0 | 92,683 | [
"VisIt"
] | 562731e80496901e86621b6179b465fc77ca445fae6f748a2a7e9cbbad89201d |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/dft/test/test_numint.py | Python | apache-2.0 | 18,203 | [
"PySCF"
] | a7cf737d1896be545bbbe2d41c8882479d187d499bd142c64017291ef74a87b4 |
# This code is so you can run the samples without installing the package
import sys
import os
sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..'))
#
testinfo = "f 10 0.033, s, f 20 0.033, s, f 30 0.033, s, f 30 0.033, s, q"
tags = "particles, Sun"
import pyglet
import cocos
from cocos.director import dir... | eevee/cocos2d-mirror | test/test_particle_sun.py | Python | bsd-3-clause | 1,236 | [
"Galaxy"
] | dbffafc250b2c6a5936897caa01de8cc6b9d1d806ad844081df78cb9a9f5f59f |
from setuptools import setup
from ectyper import __version__
setup(
name='ectyper',
version=__version__,
description='Escherichia coli fast serotyping using both raw reads and assemblies with automatic species identification',
url='https://github.com/phac-nml/ecoli_serotyping',
author='Chad Laing,... | phac-nml/ecoli_serotyping | setup.py | Python | apache-2.0 | 720 | [
"Biopython"
] | ecac359a0a94c99129361494cb9a732e8ed25f4b64559e8aafe5f622683b08d6 |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2007, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License versi... | zenoss/ZenPacks.community.VMwareEsx | ZenPacks/community/VMwareEsx/modeler/plugins/VmwareEsxDf.py | Python | gpl-2.0 | 1,927 | [
"VisIt"
] | b1b4e64bae2625ecab9ec021e19f0bc40a8619ece6dffbbb57092fb0587888fe |
""" :mod: SRM2Storage
=================
.. module: python
:synopsis: SRM v2 interface to StorageElement
"""
# # imports
import os
import re
import time
import errno
from types import StringType, StringTypes, ListType, IntType
from stat import S_ISREG, S_ISDIR, S_IMODE, ST_MODE, ST_SIZE
# # from DIRAC
from ... | calancha/DIRAC | Resources/Storage/SRM2Storage.py | Python | gpl-3.0 | 88,248 | [
"DIRAC"
] | 17806bf333c6f6c68590e0ecbd14cf9a6c961804b465328f504419306e0c3a02 |
import sys
from setuptools import setup, find_packages
from Cython.Build import cythonize
import numpy as np
from buildhelpers.shaders import build_c_shaders
# ---- C/C++ EXTENSIONS ---- #
cython_modules = ["menpo/geodesics/kirsanov.pyx",
"menpo/shape/mesh/cpptrimesh.pyx",
"menpo/... | ikassi/menpo | setup.py | Python | bsd-3-clause | 2,496 | [
"Mayavi"
] | 9ac8e0f12413d2062e94faa92c1a0043d7de5782e7f11a8d677c13ff8dc44dc9 |
#!/usr/bin/env python2
# -*- coding: utf-8 -*-
'''
This file is part of Arcte.
Arcte is software that simplifies the creation of 3D printable atomic structures,
with added features for the blind.
Copyright (C) 2015 Jesse Smith and contributors
Arcte is free software: you can redistribute it and/or modify
it under th... | jessedsmith/Arcte | arcte.py | Python | gpl-3.0 | 67,141 | [
"CRYSTAL",
"VTK"
] | 622a4c4fcab1ff5450f6e11558413ab8aa761072b05e3e2c9efd1b703e237c5f |
# encoding: utf-8
"""
An embedded IPython shell.
Authors:
* Brian Granger
* Fernando Perez
Notes
-----
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2008-2011 The IPython Development Team
#
# Distributed under the terms of the BSD License. The full license is... | WillisXChen/django-oscar | oscar/lib/python2.7/site-packages/IPython/terminal/embed.py | Python | bsd-3-clause | 11,288 | [
"Brian"
] | 300f06bc15e440ded403f6cfead7c1ad10d723c555493d05c9875a7db7d0a42f |
"""Berendsen NPT dynamics class."""
import numpy as np
#from ase.md import MolecularDynamics
from ase.md.nvtberendsen import NVTBerendsen
import ase.units as units
#import math
class NPTBerendsen(NVTBerendsen):
"""Berendsen (constant N, P, T) molecular dynamics.
This dynamics scale the velocities and v... | grhawk/ASE | tools/ase/md/nptberendsen.py | Python | gpl-2.0 | 5,931 | [
"ASE"
] | 9fb21ae65ebb3e209940617a1f0eb547843f01e1bd066c68af010b8b536628d2 |
""" Test functions for stats module
"""
from __future__ import division, print_function, absolute_import
import warnings
import re
import sys
import pickle
from numpy.testing import (TestCase, run_module_suite, assert_equal,
assert_array_equal, assert_almost_equal, assert_array_almost_equal,
assert_allclose,... | niknow/scipy | scipy/stats/tests/test_distributions.py | Python | bsd-3-clause | 94,548 | [
"Gaussian"
] | 90713e01cdd7eefe09c5175b482ae1f3c696d11235e0c412d60b1cdf2beb5c76 |
"""
Views for user API
"""
from django.shortcuts import redirect
from django.utils import dateparse
from rest_framework import generics, views
from rest_framework.decorators import api_view
from rest_framework.response import Response
from opaque_keys.edx.keys import UsageKey
from opaque_keys import InvalidKeyError
... | IndonesiaX/edx-platform | lms/djangoapps/mobile_api/users/views.py | Python | agpl-3.0 | 11,148 | [
"VisIt"
] | 4453e7413b08f17b921468122de7810d8de2c8e45a314ed030f015b890a948a7 |
# $HeadURL: $
''' ResourceManagementDB
Module that provides basic methods to access the ResourceManagementDB.
'''
from datetime import datetime
import sys
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Base.DB import DB
from DIRAC.Res... | miloszz/DIRAC | ResourceStatusSystem/DB/ResourceManagementDB.py | Python | gpl-3.0 | 20,465 | [
"DIRAC"
] | 15f85c1329f927bf0fb9d8d3b033439e3ed9a192d828b025bd7fddbd8ce71302 |
#!/usr/local/bin/python -i
# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html
# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
#
# Copyright (2005) Sandia Corporation. Under the terms of Contract
# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
# certain rights in this... | slitvinov/Pizza.py | src/pizza.py | Python | gpl-2.0 | 13,329 | [
"RasMol"
] | 7b23044bc86bf40499994c6674460685b8863036d3990a8a71d5dcfc122154b1 |
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
import abc
import math
class BinaryHeapADT(object):
"""
Abstract data type of a binary heap.
:param keys: ... | yeukhon/algorithm | algorithm/heap/heap.py | Python | mpl-2.0 | 6,640 | [
"VisIt"
] | 1c097ce3190f3467b0f977b16565f4aab24c48e17cac278de7eff84b647cd9cf |
from .. import query_processor
from nose.tools import assert_equal, assert_not_equal
from unittest import expectedFailure, skip
import ast
import parser
import token
import symbol
def match(pattern, data, vars=None):
if vars is None:
vars = {}
if type(pattern) is list:
vars[pattern[0]] = da... | demianw/tract_querier | tract_querier/tests/test_query_rewrite.py | Python | bsd-3-clause | 1,399 | [
"VisIt"
] | a18aebcc3bcba19036e0eaaa1b1872875f118dcfde20a63f699fbaa0247eca64 |
import datetime
from utils import Fixture, runtests
from heinzel.core import models
from heinzel.core.utils import datetime_localize
class Car(models.Model):
name = models.TextField(max_length=100, initial="Bug")
depreciation_total = models.FloatField(initial=0.0)
build_date = models.DatetimeField(i... | kurvenschubser/pyheinzel | tests/test_fields.py | Python | mit | 2,385 | [
"Jaguar"
] | 301fc140f95381d08e42fcad342d5536e2347a3afdea64614c5e7ba198ecc563 |
#* 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-2.1.html
"""Defines ... | harterj/moose | python/MooseDocs/base/renderers.py | Python | lgpl-2.1 | 16,591 | [
"MOOSE"
] | 66f8c65c0740f66b21d44cf84300631080a062949079b0c2c115239dd44c3f8c |
# mako/codegen.py
# Copyright (C) 2006-2013 the Mako authors and contributors <see AUTHORS file>
#
# This module is part of Mako and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""provides functionality for rendering a parsetree constructing into module
source code."""
impo... | mcollins12321/anita | venv/lib/python2.7/site-packages/mako/codegen.py | Python | mit | 49,250 | [
"VisIt"
] | 4230cfcebed8cf6b0fe6171b6d3c0574269fbe3826f4229ad129a835424e97f2 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Peter Eastman, Robert McGibbon
# Contributors: Carlos Hernande... | jchodera/mdtraj | mdtraj/formats/pdb/pdbfile.py | Python | lgpl-2.1 | 29,713 | [
"MDTraj",
"OpenMM"
] | 5206c9592812beb5ce0410c3cb054b35901538c32a5bb49db619222e3dd67fda |
#!/usr/bin/env python2
'''
Output the efficiency of a sim from a pext.py output.
All units are SI.
This script is garbage. Consider not using it.
Usage:
quantities.py [options] <input>
Options:
--2D -2 Calculate 2D quantities instead.
--E-cut=ECUT -e ECUT Cutoff at this energy in MeV. ... | noobermin/sharks-butts | bin/quantities.py | Python | mit | 3,257 | [
"Gaussian"
] | c020911895e818c1dd0afda40af1fe3fa1bcacd61a9d7d8dc59ee6334a810b18 |
# The following is a Python translation of a MATLAB file originally written principally by Mike Tipping
# as part of his SparseBayes software library. Initially published on GitHub on July 21st, 2015.
# SB2_CONTROLSETTINGS Set parameters to control the SPARSEBAYES algorithm
#
# CONTROLS = SB2_CONTROLSETTINGS
#
# OUT... | jhallock7/SparseBayes-Python | SB2_ControlSettings.py | Python | gpl-2.0 | 5,159 | [
"Gaussian"
] | d8bc9cc9e01f9564b117bd4748c17ce55c340a4e5f2eaba8083dd3b47fd094c0 |
import numpy as np
from gpaw.lfc import LocalizedFunctionsCollection as LFC
from gpaw.grid_descriptor import GridDescriptor
from gpaw.atom.radialgd import EquidistantRadialGridDescriptor
from gpaw.spline import Spline
from gpaw.setup import Setup
rc = 2.0
a = 2.5 * rc
n = 64
lmax = 2
b = 8.0
m = (lmax + 1)**2
gd = Gri... | robwarm/gpaw-symm | gpaw/test/nabla.py | Python | gpl-3.0 | 1,055 | [
"GPAW"
] | 345809cd72316036d328d4b640c836bde3f9319b8e574411280a9439bc1e4d7a |
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful, but ... | shaleh/clonedigger | clonedigger/logilab/astng/utils.py | Python | gpl-3.0 | 6,714 | [
"VisIt"
] | 7360b20fd3c8f74b9da1ae93057c1f1cf412720733655e633c70cf09b65f3575 |
# proxy module
from __future__ import absolute_import
from mayavi.modules.volume import *
| enthought/etsproxy | enthought/mayavi/modules/volume.py | Python | bsd-3-clause | 90 | [
"Mayavi"
] | 158aa221092c2b058d0154ac421d59160cf87b4e83c5e63d4b32ecf32d53c141 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkGenericStreamTracer(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | chrisidefix/devide | modules/vtk_basic/vtkGenericStreamTracer.py | Python | bsd-3-clause | 518 | [
"VTK"
] | 2923d16e3ad4230550793191b51505a73644a566eac6fb4f097e84d56850c000 |
##############################################################################
# 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... | EmreAtes/spack | var/spack/repos/builtin/packages/py-espressopp/package.py | Python | lgpl-2.1 | 3,452 | [
"ESPResSo"
] | d48eb4448c6b29fc01f96d411bbc4569873b3b0e0000f1ccd48ed0f8510ac615 |
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