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# -*- coding: utf-8 -*-
# Generated by Django 1.9.6 on 2016-07-17 20:40
from __future__ import unicode_literals
from django.conf import settings
from django.db import migrations, models
import django.db.models.deletion
class Migration(migrations.Migration):
dependencies = [
migrations.swappable_dependen... | koebbe/homeworks | visit/migrations/0110_programdirector_sitecoordinator.py | Python | mit | 1,603 | [
"VisIt"
] | c3250cc541edc49663ccc5a899e7204a9c9e9cdc5c695b9d8a06135d3a2ce8a7 |
"""
Vendored Project: AST Decompiler
Package: ast-decompiler
Version: 0.2
Author: Jelle Zijlstra
License: Apache v2
Project: https://github.com/JelleZijlstra/ast_decompiler
"""
import ast
from contextlib import contextmanager
import sys
try:
_basestring = basestring
_long = long
PY3 = False
except NameErr... | jmvrbanac/Specter | specter/vendor/ast_decompiler.py | Python | mit | 31,554 | [
"VisIt"
] | 24261536ac8354ba939fde37b7b6802d74078e13afb27e213f09e264a67dd39f |
# Copyright (C) 2016
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, o... | espressopp/espressopp | src/integrator/Rattle.py | Python | gpl-3.0 | 6,436 | [
"ESPResSo",
"Gromacs"
] | 12080ae519739ea30fe0a630d2d2f39cff36acda5e302fa689327755d2a3a831 |
#!/usr/local/bin/yade-trunk -x
# -*- encoding=utf-8 -*-
# CWBoon 2015
# Some of the parameters are defunct..
# I use this for jointed rock mass, but you can use it to generate granular particles too
from yade import pack
import math
O.engines=[
ForceResetter(),
InsertionSortCollider([PotentialBlock2AABB()],verletD... | anna-effeindzourou/trunk | examples/PotentialBlocks/cubePBscaled.py | Python | gpl-2.0 | 18,439 | [
"VTK"
] | 80d14675cc24b223bb4bd4c2ac6f4096159ad06d3b01c885d7830a10329e00e9 |
#=======================================================================
# Model.py
#=======================================================================
"""Base modeling components for building hardware description models.
This module contains a collection of classes that can be used to construct
PyMTL (pronounced... | Abhinav117/pymtl | pymtl/model/Model.py | Python | bsd-3-clause | 23,622 | [
"VisIt"
] | 655a4587036815a476ba4dff20857bf647e1fc4d046c612e37369a7d0d3c5f63 |
"""
pygments.lexers.boa
~~~~~~~~~~~~~~~~~~~
Lexers for the Boa language.
:copyright: Copyright 2006-2021 by the Pygments team, see AUTHORS.
:license: BSD, see LICENSE for details.
"""
import re
from pygments.lexer import RegexLexer, words
from pygments.token import String, Comment, Keyword, Name... | sonntagsgesicht/regtest | .aux/venv/lib/python3.9/site-packages/pygments/lexers/boa.py | Python | apache-2.0 | 3,946 | [
"VisIt"
] | a78f9d0bd0961c3d1caf93157ed63b1f5d53ad7b6af7c3b80db113749809985d |
"""
Validator project
admin.py
Copyright (c) 2009 Brian Shumate
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify,... | brianshumate/uniweb | surfbot/validator/admin.py | Python | bsd-2-clause | 1,649 | [
"Brian"
] | 09bbfe7d25c21030990a2f09a6f8951a639d5d983d796b279c97ab1142bafa9f |
# sql/elements.py
# Copyright (C) 2005-2014 the SQLAlchemy authors and contributors <see AUTHORS file>
#
# This module is part of SQLAlchemy and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""Core SQL expression elements, including :class:`.ClauseElement`,
:class:`.ColumnEle... | FRC-Team-3140/north-american-happiness | lib/python2.7/site-packages/sqlalchemy/sql/elements.py | Python | mit | 117,479 | [
"VisIt"
] | 3b3ca0ea84b1509d11ae213cf17fca545b7f53a42af2e47864c60b4713fb40f5 |
import memcache
import sys
from edge import EdgeLocation
class GlobalMap:
def __init__(self, map_filename):
self.map = {}
self.load_map(map_filename)
self.null_edge = EdgeLocation('', '', [])
def add_neighbors(self, u, v):
if not u in self.map:
self.map[u] = set... | ema/conpaas | conpaas-services/src/conpaas/services/cds/manager/map.py | Python | bsd-3-clause | 3,049 | [
"VisIt"
] | 8ef0b5428c7e610639a1162ab07ad941a6cd6f7634b0d519c3f76adb70d1fca5 |
scalapack = False
compiler = 'gcc'
extra_compile_args += [
'-O3',
'-funroll-all-loops',
'-fPIC',
]
libraries = ['gfortran', 'util']
blas_lib_path = '/home/lv70174/gpaw/opt/acml-4.0.1/gfortran64/lib/'
lapack_lib_path = blas_lib_path
extra_link_args = [
blas_lib_path+'libacml.a',
lapack_lib_p... | robwarm/gpaw-symm | doc/install/Linux/customize_vsc_univie.py | Python | gpl-3.0 | 343 | [
"GPAW"
] | c4f6749ec58e10d701e3b64d37edbcbfb28d2144b9c95d919d530a5018e88803 |
#!/usr/bin/env python
import sys
import os
import scipy.optimize
import re
import math
from optparse import OptionParser
HELP="""This program will optimize the energy with respect to any numerical parameter
which is preceded by a key character (typically a *, but this can be changed by
changing the 'key' variable in ... | QWalk/mainline | utils/optimize_stars.py | Python | gpl-2.0 | 2,986 | [
"CRYSTAL",
"GAMESS"
] | 53a6743a3a25a418e86ebefaedfd6f5ccc4953bb4ec240fa5003cc5bc9b97cb1 |
# -*- coding:Utf-8 -*-
import doctest
import os
import logging
import pdb
import sys
import numpy as np
import scipy as sp
import scipy.io as io
import scipy.signal as si
import scipy.linalg as la
import matplotlib.pylab as plt
import pylayers.signal.bsignal as bs
from pylayers.measures import mesuwb
class Waveform(di... | pylayers/pylayers | pylayers/signal/waveform.py | Python | mit | 10,638 | [
"Gaussian"
] | 503f7da25bea1e72299ec8c7c5c09cd7da5f43a14ba2fca5461723145b121240 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under t... | MDAnalysis/mdanalysis | package/MDAnalysis/analysis/msd.py | Python | gpl-2.0 | 15,378 | [
"Gromacs",
"MDAnalysis"
] | 9d02e1c4ae470a04ff71761af10d6551c5a7e1688ed9e2ca7d652d57e499763b |
# Always prefer setuptools over distutils
from setuptools import setup, find_packages
import codecs
import os.path
def read(rel_path):
here = os.path.abspath(os.path.dirname(__file__))
with codecs.open(os.path.join(here, rel_path), 'r') as fp:
return fp.read()
def get_version(rel_path):
for line... | yuzie007/upho | setup.py | Python | mit | 2,931 | [
"phonopy"
] | fb5dd9e6b644f1fa99074aa33e9c59a25282f4dd11af58e373a176201894755d |
"""Handle extraction of final files from processing pipelines into storage.
"""
import datetime
import os
import toolz as tz
from bcbio import log, utils
from bcbio.upload import shared, filesystem, galaxy, s3
from bcbio.pipeline import run_info
import bcbio.pipeline.datadict as dd
_approaches = {"filesystem": files... | elkingtonmcb/bcbio-nextgen | bcbio/upload/__init__.py | Python | mit | 16,810 | [
"Galaxy"
] | 67919c8afe86b585de0eddda54d28a76e252b698905ab8623ca5a8f22bd8569c |
# Python test set -- part 1, grammar.
# This just tests whether the parser accepts them all.
from test_support import *
print '1. Parser'
print '1.1 Tokens'
print '1.1.1 Backslashes'
# Backslash means line continuation:
x = 1 \
+ 1
if x != 2: raise TestFailed, 'backslash for line continuation'
# Backslash does no... | MalloyPower/parsing-python | front-end/testsuite-python-lib/Python-2.1/Lib/test/test_grammar.py | Python | mit | 15,273 | [
"GULP"
] | 392490783ff2970f8c7614dc043be71795e58a53b65e36b412806498bd67467e |
#Bail out when loading this module as it is not python3 compliant
from GangaCore.Core.exceptions import PluginError
raise PluginError("The GangaNA62 module has not been upgraded for python 3. The last python 2 Ganga version is 7.1.15 . Please contact the ganga devs to discuss updating this module.")
import os
import G... | ganga-devs/ganga | ganga/GangaNA62/__init__.py | Python | gpl-3.0 | 861 | [
"DIRAC"
] | a710014350dd4f29b2b685bf0f36064c21f6832a5dd8c8297e52760374c1e5cf |
# -*- coding: utf-8 -*-
"""
@package Bwa
@brief **Wrapper for BWA mem**
Please see the BWA user manual document for further details
[MANUAL](http://bio-bwa.sourceforge.net/bwa.shtml)
Basically the top level function Mem.align processes sequences as follow:
* If a bwa index is provided it will attempt to validate it by... | a-slide/pyDNA | Bwa/__init__.py | Python | gpl-2.0 | 1,201 | [
"BWA"
] | cfcc939e2eb823e164120163f0e289ab4b5c76c6a593a6b80e43cd091052490a |
# Author: Travis Oliphant, 2002
#
# Further updates and enhancements by many SciPy developers.
#
from __future__ import division, print_function, absolute_import
import math
import warnings
from collections import namedtuple
import numpy as np
from numpy import (isscalar, r_, log, around, unique, asarray,
... | surhudm/scipy | scipy/stats/morestats.py | Python | bsd-3-clause | 96,359 | [
"Gaussian"
] | bff38041b9076a53b2409d03bba8f236afe04844d17489b84eac530d1d4f3f5c |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views import defaults as default_views
from inbox import views as pc_views # views em níve... | brunousml/inbox | config/urls.py | Python | bsd-2-clause | 1,839 | [
"VisIt"
] | edfea8bf58d1d60749dd9ab347f0adb70bc54ac20db05ec3f93cd8fb23cc92bd |
from coalib.bearlib.abstractions.Linter import linter
from dependency_management.requirements.DistributionRequirement import (
DistributionRequirement)
@linter(executable='astyle',
output_format='corrected',
use_stdin=True)
class ArtisticStyleBear:
"""
Artistic Style is a source code inden... | IPMITMO/statan | coala-bears/bears/c_languages/ArtisticStyleBear.py | Python | mit | 30,014 | [
"VTK"
] | dfd1a611bcdcf968be600a6b9dab73a1f6321c811acbaed8982759bbc201b3db |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import (division, print_function, absolute_import,
unicode_literals)
__all__ = ["sample_ball", "MH_proposal_axisaligned"]
import numpy as np
# If mpi4py is installed, import it.
try:
from mpi4py import MPI
MPI = MPI
excep... | GabrielaCR/AGNfitter | emcee/utils.py | Python | mit | 7,581 | [
"Gaussian"
] | 3905989a894357e8975648c43006731fca07a3c4053f84894c69dc6a16ea929d |
# -*- coding: utf-8 -*-
"""
codeMarble_Core.actionRule
~~~~~~~~~~~~~~~~~~~~~~~~~
check and manage rule after placement rule.
:copyright: (c) 2017 by codeMarble
"""
import os
import sys
from errorCode import *
class ActionRule(object):
def __init__(self):
pass
# actionRuleNum(0:scrip... | codeMarble/codeMarble_Web | backendCelery/codeMarble/actionRule.py | Python | gpl-3.0 | 6,512 | [
"VisIt"
] | e8cd5f88011a8fe780f9c552ae3a45da2ed8ebe9664a3d6977a039c7340cb45b |
# 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
# distribu... | quantumlib/OpenFermion-PySCF | openfermionpyscf/tests/_run_pyscf_test.py | Python | apache-2.0 | 1,370 | [
"PySCF"
] | c04ce08980f11560c8aff0c345ebbc6b07eac9eca309b1cce9dc0b027bee9060 |
# -*- coding: utf-8 -*-
"""
This submodule provides routines to generate and analyse "Flux Surfaces" as
described in (Mumford et. al. 2014).
Flux Surfaces are created by the tracing of a closed loop of fieldlines,
from which a surface is reconstructed by creating polygons between the
pesudo parallel streamlines.
"""
i... | Cadair/pysac | pysac/analysis/tube3D/tvtk_tube_functions.py | Python | bsd-2-clause | 15,238 | [
"Mayavi"
] | bf56f5aacf9588c361314a42fd605095aa6f4d501742db4e3608f84fc4a8a24b |
import unittest
from hamcrest import assert_that, contains, instance_of
from backdrop.core.upload.parse_excel import parse_excel, EXCEL_ERROR
from tests.support.test_helpers import fixture_path
class ParseExcelTestCase(unittest.TestCase):
def _parse_excel(self, file_name):
file_stream = open(fixture_path... | alphagov/backdrop | tests/core/upload/test_parse_excel.py | Python | mit | 2,376 | [
"exciting"
] | 4e35ab280af4679c275361006b299b4b9d7b3553e40665a615acc482612c6d5b |
"""Utilities to manage processing flowcells and retrieving Galaxy stored info.
"""
import os
import glob
from six.moves import urllib, http_cookiejar
import json
def parse_dirname(fc_dir):
"""Parse the flow cell ID and date from a flow cell directory.
"""
(_, fc_dir) = os.path.split(fc_dir)
parts = fc_... | a113n/bcbio-nextgen | bcbio/illumina/flowcell.py | Python | mit | 3,017 | [
"Galaxy"
] | da76dc5c4ef0b83ad92e1ab4a73097082829995e4aa1b29a26064cc8ab971bde |
# /usr/bin/env python
# -*- coding: utf-8 -*-
# ##############################################################################
#
#
# Project: ECOOP, sponsored by The National Science Foundation
# Purpose: this code is part of the Cyberinfrastructure developed for the ECOOP project
# http://tw.rpi.edu/web/project/ECOOP... | epifanio/ecoop-1 | pyecoop/lib/ecoop/cf.py | Python | apache-2.0 | 36,260 | [
"Gaussian"
] | 15f015a19d1cc55c9f275b9a1adefe01ea617fcf1dac59dbbf9e28dfee4b02f4 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2013 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU Lesser General Public License as published by
## the Free Software F... | andrebellafronte/stoq | tests/test_apidocs.py | Python | gpl-2.0 | 4,031 | [
"VisIt"
] | 1f6be9fd4c755f28066001e5d8f276401ed18d684ff4f56253d08f1b304588dc |
import numpy as np
from numpy.testing import assert_array_equal
from nose.tools import assert_true
from sklearn.datasets import make_blobs
from pystruct.models import BinaryClf
from pystruct.learners import (NSlackSSVM, SubgradientSSVM,
OneSlackSSVM)
def test_model_1d():
# 10 1d d... | d-mittal/pystruct | pystruct/tests/test_learners/test_binary_svm.py | Python | bsd-2-clause | 4,085 | [
"Gaussian"
] | 7754a301dc65ea8e35353a10cfe78a1863fc2539c85c732b526dd942dc61adbf |
import logging
from cis.data_io.Coord import CoordList
from cis.data_io.products import AProduct
from cis.data_io.ungridded_data import UngriddedCoordinates, UngriddedData
from abc import ABCMeta, abstractmethod
class CCI(object):
"""
Abstract class for the various possible data products. This just defines th... | zak-k/cis | cis/data_io/products/CCI.py | Python | gpl-3.0 | 2,569 | [
"NetCDF"
] | e172891e152e42ad9c85944c5a764c210d1cb5b581f63c8f73d79dc6aa11290f |
# This file is part of Androguard.
#
# Copyright (c) 2012 Geoffroy Gueguen <geoffroy.gueguen@gmail.com>
# 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://... | andymg/androguard | androguard/decompiler/dad/writer.py | Python | apache-2.0 | 17,957 | [
"VisIt"
] | 1a87d3068918119cf407b49093d8a470953e00fd64ddcd701921e3d85de0f094 |
# 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 RAgimicrorna(RPackage):
"""Processing and Differential Expression Analysis of Agilent micr... | iulian787/spack | var/spack/repos/builtin/packages/r-agimicrorna/package.py | Python | lgpl-2.1 | 1,162 | [
"Bioconductor"
] | 3639fc7b15ddf6808019b3547c3d509d6daa60600009646fc31c40bdf4c8b44a |
# -*- coding: utf-8 -*-
#
# Mayavi documentation build configuration file, created by
# sphinx-quickstart on Sat Apr 12 23:25:24 2008.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# The contents of this file are pickled, so don't put values in the namespace
# that aren't pickleab... | dmsurti/mayavi | docs/source/mayavi/conf.py | Python | bsd-3-clause | 5,322 | [
"Mayavi"
] | 253465e1a22c7f94bd3686e5c6fe438049e929a0c2cfaf148b4e01d706ff0b9a |
"""Translation of the BioNetGen example "Simple" from the BNG wiki.
http://bionetgen.org/index.php/Simple
"""
from pysb import *
Model()
# Physical and geometric constants
Parameter('NA', 6.0e23) # Avogadro's num
Parameter('f', 0.01) # scaling factor
Expression('Vo', f * 1e-10) # L
Expression('V', f ... | neurord/pysb | pysb/examples/bngwiki_simple.py | Python | bsd-2-clause | 1,206 | [
"Avogadro"
] | b6b898324e4a6d5dc1271fbc1b311a69e089de2441daf034c9e45e84b1c0c970 |
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Matti Hamalainen <msh@nmr.mgh.harvard.edu>
# Eric Larson <larson.eric.d@gmail.com>
#
# License: BSD (3-clause)
import sys
import os
import os.path as op
import shutil
import numpy as np
from scipy import linalg
from .fixes imp... | matthew-tucker/mne-python | mne/bem.py | Python | bsd-3-clause | 47,266 | [
"Mayavi"
] | 254192d339eba333eeb4e767fd419c434eec92959571851a453748f9e8233cf7 |
"""
Base implementation of the Page Object pattern.
See https://code.google.com/p/selenium/wiki/PageObjects
"""
from abc import ABCMeta, abstractmethod, abstractproperty
from collections import defaultdict
from functools import wraps
from contextlib import contextmanager
import logging
import os
import socket
import ur... | devs1991/test_edx_docmode | venv/lib/python2.7/site-packages/bok_choy/page_object.py | Python | agpl-3.0 | 21,953 | [
"VisIt"
] | 79eb59b7d7d5849a8c56a0aa3c68bf958a74b1deb0398c7d152d68ed3b30c65a |
from apiclient.discovery import build
from oauth2client.client import OAuth2WebServerFlow
import httplib2
import gflags
import httplib2
from apiclient.discovery import build
from oauth2client.file import Storage
from oauth2client.client import OAuth2WebServerFlow
from oauth2client.tools import run_flow
from datetim... | barneyman/gcalMeetingRoom | local.py | Python | apache-2.0 | 7,334 | [
"VisIt"
] | 0fd058f41dbb4c4f6654af5edf9ff39c4e0f95ec3872ea4d52554f77e808cbf9 |
from matchmaking import *
from earth_distance import *
from datetime import date
from math import exp
def get_score(User1, User2):
#initialize score
matchrank = 0.0
#strict rule on gender preference
if gender_preference_rank(User1.Gender, User2.Gender, User1.Gender_Pref, User2.Gender_Pref) == -1 :
return -1;
... | RefugeeMatchmaking/HackZurich | GAE_Playground/get_score.py | Python | mit | 1,003 | [
"Gaussian"
] | 73496ddf9a3104d499bfb44b181a1d917df9916a0b6819d5ae16bd21800da46d |
"""Simulates a Feed for a given list of parameters and number of iterations.
Authors:
Adam Rains
"""
import numpy as np
import optics
import optics_tools
import utils
import pylab as pl
import time
import multiprocessing as mp
import feed
import csv
import time
import datetime
output = mp.Queue()
def simulate_for_x... | mikeireland/astro-optics | simulate.py | Python | mit | 11,306 | [
"Gaussian"
] | 49e5ab4587813994d4a0ddb76f478ab6331a9b84dc3781ba12eb3e9c726c693a |
#
# Copyright 2014, 2020-2021 Lars Pastewka (U. Freiburg)
# 2014 James Kermode (Warwick U.)
#
# 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 P... | libAtoms/matscipy | tests/test_atomic_strain.py | Python | lgpl-2.1 | 2,827 | [
"ASE",
"Matscipy"
] | 8d0d370edef53a3ec08679d86f098cc316397eb292e25982025f2261c686f817 |
# Copyright 2013-2021 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 RCodex(RPackage):
"""A Normalization and Copy Number Variation Detection Method for Whole
... | LLNL/spack | var/spack/repos/builtin/packages/r-codex/package.py | Python | lgpl-2.1 | 1,644 | [
"Bioconductor"
] | 8e4b7b443833a00e27bafb4a6cd00c483d1212b6fda0b6774cfc9ff1b5fa0ddd |
# -*- coding: utf-8 -*-
from coordinate import *
from coards import *
from cf import *
from conventions import *
from generic import *
CONVENTION_CLASSES = [
CF,
Coards,
Coordinate
]
"""
Classes that implement a netcdf convention.
"""
def select_convention(
dataset,
filter_out_nd_coordin... | jfrygeo/solutions-geoprocessing-toolbox | suitability/toolboxes/scripts/MultidimensionSupplementalTools/MultidimensionSupplementalTools/Scripts/mds/netcdf/convention/__init__.py | Python | apache-2.0 | 2,206 | [
"NetCDF"
] | e6c20a5e717577334cf6c2e433842ab5ac1fe385fe6fcfcf464dfbd27c0aa4de |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2020 University of Liège
#
# 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
#
# ... | rboman/progs | classes/sph0/louis/tests/waterdrop.py | Python | apache-2.0 | 2,097 | [
"VTK"
] | 167607f6a799e6fd1bb49d2b9deae865e0b743a7babf74a057d4317e7b17f643 |
""" I wish who wrote this would have put some doc...
IIUC this is a wrapper around the JobState object. It basically tries to cache
everything locally instead of going to the DB.
"""
import copy
import time
from DIRAC.Core.Utilities import Time, DEncode
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Wor... | fstagni/DIRAC | WorkloadManagementSystem/Client/JobState/CachedJobState.py | Python | gpl-3.0 | 11,494 | [
"DIRAC"
] | 12d0d6351733e140aae0f3393d18ea431f52c26aee5bec8b37d686baf28855a6 |
tests=[
("python","UnitTestDraw.py",{}),
]
longTests=[
]
if __name__=='__main__':
import sys
from rdkit import TestRunner
failed,tests = TestRunner.RunScript('test_list.py',0,1)
sys.exit(len(failed))
| rdkit/rdkit-orig | rdkit/Chem/Draw/test_list.py | Python | bsd-3-clause | 219 | [
"RDKit"
] | 5595c5e428b699c8b01591aea6e574ae821b4914add9b60090ef2bf0ea602cc3 |
# Copyright (C) Microsoft Corporation. All rights reserved.
# Licensed under the MIT License. See LICENSE in project root for information.
import sys
if sys.version >= '3':
basestring = str
import pyspark
from pyspark.ml.common import inherit_doc
from pyspark.sql.types import *
from pyspark.sql.types import Row,... | rastala/mmlspark | src/image-transformer/src/main/python/ImageTransformer.py | Python | mit | 4,883 | [
"Gaussian"
] | 33b9a8027bf3fe0341f3e88475d36c77aa2e8a811ccbb78e2784fefd022a8663 |
###!/usr/bin/python
# Galaxy Media Center Diagnostic Log Gather & Upload
from __future__ import print_function
import os, shutil, time, subprocess, xbmc, xbmcgui, tarfile, socket, struct, fcntl, argparse
# Static Variables
ACTION_PREVIOUS_MENU = 10
dialog = xbmcgui.Dialog()
dp = xbmcgui.DialogProgress()
sock = socke... | cosmicc/script.gmcsystemupdate | uploaddiag.py | Python | mit | 3,243 | [
"Galaxy"
] | 95578a9509ae7219ca8722d7980f4230d66605551a6d215d55063fa2db5a8900 |
from time import time
import numpy as np
import ase.db
from ase.test.tasks.dcdft import DeltaCodesDFTCollection as Collection
from gpaw import GPAW, PW, FermiDirac
c = ase.db.connect('dcdft.db')
ecut = 340
kptdensity = 3.5
width = 0.10
collection = Collection()
for name in ['K', 'Ca', 'Ti']:
atoms = collection[... | robwarm/gpaw-symm | doc/exercises/dcdft/dcdft_gpaw.py | Python | gpl-3.0 | 1,131 | [
"ASE",
"GPAW"
] | 1f05991f8fbf173a42f2b04df4043b883a6df6e6ec08965f10e1fcdf8692a437 |
################################################################################
# Copyright (C) 2014 Jaakko Luttinen
#
# This file is licensed under the MIT License.
################################################################################
"""
Unit tests for `gate` module.
"""
import warnings
warnings.simple... | SalemAmeen/bayespy | bayespy/inference/vmp/nodes/tests/test_gate.py | Python | mit | 10,813 | [
"Gaussian"
] | 09c3a8ed6e0ec455e7699a8d068be7831c3d49c00cca1c49e0107237586090e5 |
#* 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
from FileTe... | nuclear-wizard/moose | python/TestHarness/testers/Exodiff.py | Python | lgpl-2.1 | 4,184 | [
"MOOSE"
] | cf5fa98731be8fdad81ff1fefba7490396482eedd0aec461843fe8bf4e28104b |
# -*- Mode: Python; coding: utf-8; indent-tabs-mode: nil; tab-width: 4 -*-
### BEGIN LICENSE
# Copyright (C) 2014 Brian Douglass bhdouglass@gmail.com
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License version 3, as published
# by the Free Softwa... | bhdouglass/agui | agui/backends/gtk/widgets/label.py | Python | gpl-3.0 | 1,219 | [
"Brian"
] | 297015112b371c08cdd19a422fd22c0715692c521e8db432e931718d7cfef772 |
def print_table(table_data):
max_len = [0] * len(table_data)
for item in range(len(table_data)):
max_len[item] = find_row_max(table_data[item])
colWidth = len(table_data)
rowWidth = len(table_data[0])
for i in range(rowWidth):
for j in range(colWidth):
print(table_data[j]... | sallyyoo/ced2 | py/practice/printTable.py | Python | mit | 728 | [
"MOOSE"
] | ec70f03c065760ca4ae86c9d9237c9a7662df9bc98b1ab0cca98693c018303fa |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | gregcaporaso/scikit-bio | skbio/sequence/_nucleotide_mixin.py | Python | bsd-3-clause | 11,243 | [
"scikit-bio"
] | 518a2c43cd5d3837b14a211e9ac2de6dee32ca12db66d96f15fa9e2fba1191e7 |
# -*- coding: utf-8 -*-
#!/usr/bin/python
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007 Thom Sturgill
# Copyright (C) 2007-2009 Brian G. Matherly
# Copyright (C) 2008-2011 Rob G. Healey <robhealey1@gmail.com>
# Copyright (C) 2008 Jason Simanek
# Copyright (C) 2010 Jakim Friant
... | pmghalvorsen/gramps_branch | gramps/plugins/webreport/webcal.py | Python | gpl-2.0 | 70,818 | [
"Brian"
] | 1b611d0c7027d156c1b331bfa43112ddeab4a88ba77ff0056ebadd23d4b2bb34 |
# Copyright (c) 2003-2010 LOGILAB S.A. (Paris, FRANCE).
# Copyright (c) 2009-2010 Arista Networks, Inc.
# http://www.logilab.fr/ -- mailto:contact@logilab.fr
# 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
# ... | pronto/dotfiles | .vim/pylibs/pylint/checkers/base.py | Python | bsd-2-clause | 33,455 | [
"VisIt"
] | eeb3cf1f00445e04a916758ac74a7534cdd7baedbb74b7c32abaeb353a798edf |
from django.test import TestCase
from myvoice.core.tests import factories
from .. import models
class TestDisplayLabel(TestCase):
Model = models.DisplayLabel
Factory = factories.DisplayLabel
def test_unicode(self):
"""Smoke test for string representation."""
obj = self.Factory.create(na... | myvoice-nigeria/myvoice | myvoice/survey/tests/test_models.py | Python | bsd-2-clause | 5,792 | [
"VisIt"
] | 41a7638a392fa2e10d06def68edbef0f59d8dce8eed610a476d8e4c809862de3 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# model.py
#
# Copyright 2012 Greg Green <greg@greg-UX31A>
#
# 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 Lice... | PennyQ/stero_3D_dust_map | model.py | Python | gpl-3.0 | 31,645 | [
"Gaussian",
"Mayavi"
] | 45105e575d0d22f0bee977a8c550e8084b99c675a2004194a6cfe4855b827f13 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2006 Brian Matherly
#
# 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) ... | beernarrd/gramps | gramps/gen/mime/_winmime.py | Python | gpl-2.0 | 3,541 | [
"Brian"
] | d955b4f93214cc35234c7f44f33e31e3f6b520fa9285e4868381c4594a738b52 |
#
# Copyright (C) 2013-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | mkuron/espresso | testsuite/python/pair_criteria.py | Python | gpl-3.0 | 4,508 | [
"ESPResSo"
] | 538f74f9315f3fda5f96cec221300f7c80a32106370ad6e0c2071d20b5b2277b |
#!/usr/bin/env python
import sys, os, time, random, pygame
import RPi.GPIO as GPIO
def speel(bestand):
pygame.mixer.music.load(bestand)
pygame.mixer.music.play()
while pygame.mixer.music.get_busy() == True:
continue
def speelSom(getal1, getal2):
print("Wat is", getal1, "x", getal2,"?")
spe... | ralphcrutzen/PTT-Tafeltjes-Telefoon | t65.py | Python | gpl-3.0 | 4,080 | [
"Elk"
] | 543e51eb6d07a07e1240db74b93bebdb0da1312d882b2efb4b8eb2d43b827a76 |
"""
Signals and Systems Function Module
Copyright (c) March 2017, Mark Wickert
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice, ... | mwickert/scikit-dsp-comm | sk_dsp_comm/sigsys.py | Python | bsd-2-clause | 91,282 | [
"Gaussian"
] | 4e881d2db925b71cb10d2e921d7c3cd1bb1757c3128470b55ba288d7afb8a0c3 |
#!/usr/bin/python
#
# Copyright 2007 Google Inc.
# Licensed to PSF under a Contributor Agreement.
#
# 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/LICE... | nouiz/fredericbastien-ipaddr-py-speed-up | branches/2.0.x/ipaddr_test.py | Python | apache-2.0 | 41,619 | [
"FEFF"
] | b04df72a6b7c9fa042e690bdf3fd79f64812c64c3b9dd95ebc707ac0149702e1 |
# -*- coding: utf-8 -*-
"""
Created on Thu Dec 5 12:30:26 2013
@author: Daniel Struck
create blast nucleotide database from the COMET training set with the following command:
makeblastdb -in training_subtype_03.fasta -dbtype nucl
run blast with the following command:
(blast version: 2.2.29)
blastn -num_threads 12 ... | dstruck/comet-paper-scripts | compare_blast_comet/analyze_blast.py | Python | gpl-2.0 | 1,720 | [
"BLAST"
] | 37f385d61c1fb46368c69c6b697241c7922cb72cbe2a7f353d29c6d8ef472487 |
# EXPERIMENTAL. DO NOT USE UNLESS YOU ARE JORIK. (OR JORIS)
import vtk
className = obj.__class__.__name__
if className == 'slice3dVWR':
ipw = obj.sliceDirections._sliceDirectionsDict.values()[0]._ipws[0]
if ipw.GetInput():
mins, maxs = ipw.GetInput().GetScalarRange()
else:
mins, maxs... | nagyistoce/devide | snippets/changeSVLut.py | Python | bsd-3-clause | 694 | [
"VTK"
] | fd581cae87b4b2e1fb8a49eacd65175ad937308bf9fa437424d2ac5093d7b423 |
# -*- coding: utf-8 -*-
# This code is part of Amoco
# Copyright (C) 2018 Axel Tillequin (bdcht3@gmail.com)
# published under GPLv2 license
# spec_xxx files are providers for instruction objects.
# These objects are wrapped and created by disasm.py.
from amoco.logger import Log
logger = Log(__name__)
logger.debug("... | LRGH/amoco | amoco/arch/v850/spec_v850e2s.py | Python | gpl-2.0 | 17,578 | [
"ADF"
] | 1c8edbb996b2c00d63a6e615f14304b166f7ae8baa81b237134396a6598b37a8 |
import re
import functools
from copy import deepcopy
from flask import request
from brain.api.base import processRequest
from marvin import config
from marvin.core.exceptions import MarvinError
from marvin.utils.dap.datamodel import dap_datamodel as dm
from marvin.tools.maps import _get_bintemps
from webargs import fi... | bretthandrews/marvin | python/marvin/api/__init__.py | Python | bsd-3-clause | 14,656 | [
"Galaxy"
] | 54883ed2cf2113829f853dcbf832ae5cbcfde2127936f08826ce03f54d8ba5a0 |
from diagnostic import unitroot_adf
import statsmodels.datasets.macrodata.data as macro
macrod = macro.load().data
print macro.NOTE
print macrod.dtype.names
datatrendli = [
('realgdp', 1),
('realcons', 1),
('realinv', 1),
('realgovt', 1),
... | yarikoptic/pystatsmodels | statsmodels/sandbox/stats/ex_newtests.py | Python | bsd-3-clause | 773 | [
"ADF"
] | 828ca6ec94fc1eea966990a0459a9f850754ef6315361a355ebe7900b21633b5 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright © 2016 Matthew Stone <mstone5@mgh.harvard.edu>
# Distributed under terms of the MIT license.
"""
"""
from __future__ import print_function
import unittest
try:
unittest.skip
except AttributeError:
import unittest2 as unittest
import vcf
import pysa... | talkowski-lab/Holmes | readpaircluster/svcf/test_svcf.py | Python | mit | 7,224 | [
"pysam"
] | a8974478a222af1c1e91ee1869dac065c825890fa5f5005de4e728d8fe7f6b26 |
import collections
import random
import unittest
import mock
from cardboard import card as c, events, zone as z
from cardboard.tests.util import GameTestCase
from cardboard.util import ANY
ENTER, LEAVE = events.ENTERED_ZONE, events.LEFT_ZONE
class ZoneTest(GameTestCase):
card = mock.Mock(spec=c.Card)
de... | Julian/cardboard | cardboard/tests/test_zone.py | Python | mit | 8,874 | [
"CASINO"
] | ae0c0f81de75283868452c011c98c4906561dfd95919c241116b6cd905d2de6c |
import tensorflow as tf
import numpy as np
from elbow import Model, Gaussian, BernoulliMatrix, BetaMatrix, DirichletMatrix
from elbow.models.factorizations import GMMClustering
def clustering_gmm_model(n_clusters = 4,
cluster_center_std = 5.0,
cluster_spread_std = 2.0... | davmre/bayesflow | examples/clustering.py | Python | bsd-3-clause | 1,309 | [
"Gaussian"
] | bb5fa757f16c9a5914038a6ca72260cf5fc8d118f6439d91758fb5f9a9fa1905 |
#!/usr/bin/python2
import optparse
import subprocess
import sys
from builds import GporcaBuild, GpcodegenBuild, GporcacodegenBuild
def make(num_cpus):
return subprocess.call("make -j %d" % (num_cpus), cwd="gpdb_src", shell=True)
def install(output_dir):
subprocess.call("make install", cwd="gpdb_src", shell=T... | ahachete/gpdb | concourse/scripts/build_gpdb.py | Python | apache-2.0 | 1,782 | [
"ORCA"
] | 37835fd92fb254a636ccd9686dea8a97842a24da68c0738902a52217b44f4477 |
"""Define a helper function for running tests
The skeleton for making a new setup is as follows:
from ase.optimize.test import run_test
def get_atoms():
return Atoms('H')
def get_calculator():
return EMT()
run_test(get_atoms, get_calculator, 'Hydrogen')
"""
import time
import matplotlib
#matplotlib.rcPar... | suttond/MODOI | ase/optimize/test/__init__.py | Python | lgpl-3.0 | 4,863 | [
"ASE"
] | 4779a0382e33dd7c5734085e3b342ba3a18618f429cef39962fa18504dfb4b62 |
from __future__ import print_function
import os, sys, inspect
import h5py
import numpy as np
import matplotlib
import random
import math
import multiprocessing
from PIL import Image
from Crypto.Random.random import randint
from functools import partial
# Load the configuration file
import config
cmd_folder = os.path.... | naibaf7/caffe_neural_models | dataset_06/network_generator.py | Python | bsd-2-clause | 16,077 | [
"Gaussian"
] | 4b62a5b47ab146216dccf0e672fcb5d89e15a08e61154871819510abc9c42ca8 |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
__author__ = "Brian Lehman, Scott Hendrickson"
import sys
import re
import codecs
reload(sys)
sys.stdout = codecs.getwriter('utf-8')(sys.stdout)
sys.stdin = codecs.getreader('utf-8')(sys.stdin)
import math
import pprint
import json
import fiona
from shapely.geometry imp... | gscottstukey/Data-Science-45min-Intros | gis_tools/rev_geo.py | Python | unlicense | 6,294 | [
"Brian"
] | 74442c39467cb28159208098324e8a662087dc90e11d120cf13f157f9978f856 |
"""
Views related to the Custom Courses feature.
"""
import csv
import datetime
import functools
import json
import logging
import pytz
from contextlib import contextmanager
from copy import deepcopy
from cStringIO import StringIO
from django.core.urlresolvers import reverse
from django.http import (
HttpResponse... | zofuthan/edx-platform | lms/djangoapps/ccx/views.py | Python | agpl-3.0 | 20,122 | [
"VisIt"
] | a0e1269dcd8a19f205832926a1e364c3c66dc6fba6300464321f4c61118b171f |
#!/usr/bin/env python
import shutil
import tempfile
import configparser
from textwrap import dedent
import tarfile
import pyaml
import hashlib
import os
import re
import bs4
import urllib
from urllib import request
from urllib import parse
from urllib import error
from collections import OrderedDict
import logging
imp... | ThomasWollmann/bioconda-recipes | scripts/bioconductor/bioconductor_skeleton.py | Python | mit | 16,637 | [
"Bioconductor"
] | 9d65f4df3bcf6e0a061d7e829fb74c3a88ea06d5249ed4efc158784ed94c3d30 |
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Eric Larson <larson.eric.d@gmail.com>
# Guillaume Favelier <guillaume.favelier@gmail.com>
#
# License: Simplified BSD
import contextlib
from functools import partial
import os
import sys
import time
import traceback
import warnings
import... | cjayb/mne-python | mne/viz/_brain/_timeviewer.py | Python | bsd-3-clause | 39,988 | [
"VTK"
] | 4a0a1ab6bb1c2ca3f5748f3130a7f3394b40104b37d57fa890c2a9f9f9c4cc28 |
# Copyright (C) 2008-2009 Open Society Institute
# Thomas Moroz: tmoroz.org
# 2010-2011 Large Blue
# Fergus Doyle: fergus.doyle@largeblue.com
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License Version ... | damilare/opencore | opencore/models/subscribers.py | Python | gpl-2.0 | 8,339 | [
"VisIt"
] | 28024d1c0bc0c86c83535375b0b41c3fb2f8b4a32f80f9f7a6068dcdc1291206 |
# Copyright (c) 2011, Chandler Armstrong (omni dot armstrong at gmail dot com)
# see LICENSE.txt for details
"""
polygon object
"""
from __future__ import division
from operator import mul
from numpy import array, cos, dot, fabs, lexsort, pi, sin, sqrt, vstack
from pygame import Rect
from .... | carsonfarmer/pylygon | pylygon/polygon.py | Python | gpl-3.0 | 17,520 | [
"Brian"
] | 1ca2cf11ffce220431800a7a563f670ac9885a317dc8afd89965a38c0e4de18f |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
Generic functions for use with GEOS-Chem's planeflight diagnostic module
"""
# compatibility with both python 2 and 3
from __future__ import print_function
# - Required modules:
# I/O functions / Low level
import sys
import csv
import glob
import pandas as pd
import loggin... | tsherwen/AC_tools | AC_tools/planeflight.py | Python | mit | 23,222 | [
"NetCDF"
] | b23b593d1db8c65cd274d1494e3f4d16cdceba3a4c40f77e3b8a425a3673139d |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Virtualchain
~~~~~
copyright: (c) 2014-2015 by Halfmoon Labs, Inc.
copyright: (c) 2016 by Blockstack.org
This file is part of Virtualchain
Virtualchain is free software: you can redistribute it and/or modify
it under the terms of th... | blockstack/virtualchain | virtualchain/lib/blockchain/bitcoin_blockchain/bits.py | Python | gpl-3.0 | 45,795 | [
"Brian"
] | 6fce3b3cb2d651ad8d2ba5a22ea22fb0d28e28a80d21aa3c7bd5c2c9e14fabad |
#!/usr/bin/env python
# Copyright 2007, Michael J. Harms
# This program is distributed under General Public License v. 3. See the file
# COPYING for a copy of the license.
__description__ = \
"""
pdb_mutator.py
Mutates a residue in a pdb file.
"""
__author__ = "Michael J. Harms"
__date__ = "070729"
__description... | AndreaEdwards/pdbtools | pdb_mutator.py | Python | gpl-3.0 | 5,939 | [
"CHARMM"
] | 967629b296ee009d810014c6bc7310e3fe6cfeeaaa75a097391c230dccdf9cc5 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# statusfe - [insert a few words of module description on this line]
# Copyright (C) 2003-2009 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of ... | heromod/migrid | mig/shared/functionality/statusfe.py | Python | gpl-2.0 | 3,209 | [
"Brian"
] | 0464d5e0259fe4f5e5ee0162390708015d1ddae08198f4f729b573d6590254e3 |
# hhfit.py ---
#
# Filename: hhfit.py
# Description:
# Author:
# Maintainer:
# Created: Tue May 21 16:31:56 2013 (+0530)
# Version:
# Last-Updated: Tue Jun 11 16:57:30 2013 (+0530)
# By: subha
# Update #: 34
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
# Functions for fitting comm... | dilawar/moose-full | moose-core/python/moose/neuroml2/hhfit.py | Python | gpl-2.0 | 7,697 | [
"MOOSE"
] | d8ec1aa7eef7b969dce6ef5868fbd05d0cfec0ee299fbb03be0ff6b4b5b6b244 |
#!/usr/bin/env python
import os
import sys
import pysam
import re
import subprocess
import argparse
import multiprocessing as mp
import scipy.stats as ss
import numpy as np
import skbio.alignment as skalign
import skbio.sequence as skseq
from collections import Counter
from uuid import uuid4
from time import sleep... | adamewing/tebreak | scripts/refelts.py | Python | mit | 27,200 | [
"pysam"
] | a4933b5572575ee74df45d9d30b68ff6905525cd0d9e6f06d2025f20c047fda7 |
"""
Compute Bra-ket averaged Taylor expansion integrals over trajectories
traveling on adiabataic potentials
"""
import numpy as np
import nomad.compiled.nuclear_gaussian as nuclear
# Determines the Hamiltonian symmetry
hermitian = True
# Returns functional form of bra function ('dirac_delta', 'gaussian')
basis = 'g... | mschuurman/FMSpy | nomad/integrals/fms.py | Python | lgpl-3.0 | 2,060 | [
"Gaussian"
] | 86797c56b773f39de1f00baa90924e6acf95243841c72d7464500060221d8928 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2006 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publi... | arunkgupta/gramps | gramps/plugins/tool/eventcmp.py | Python | gpl-2.0 | 16,172 | [
"Brian"
] | e2d3ebf322181132dc72fd43ca1e5e430be45b2d83a09a5cf6f4161cbbffa9c9 |
import re
from geometry import Geometry, GeometryParser
from polyhedron import Polyhedron
from tvtk.api import tvtk
class CellType(object):
VTK_VERTEX = 1
VTK_POLY_VERTEX = 2
VTK_LINE = 3
VTK_POLY_LIN = 4
VTK_TRIANGLE = 5
VTK_TRIANGLE_STRIP = 6
VTK_POLYGON = 7
VTK_PIXEL = 8
... | lukius/mlab-tools | mlab_tools/vtk_parser.py | Python | mit | 9,153 | [
"VTK"
] | f64071334e1cd2ebcda4d1ae633726e74b68038c3ded1afdb1c2a05baeaef9fd |
# !usr/bin/env python2
# -*- coding: utf-8 -*-
#
# Licensed under a 3-clause BSD license.
#
# @Author: Brian Cherinka
# @Date: 2016-12-08 14:24:58
# @Last modified by: Brian Cherinka
# @Last Modified time: 2017-06-23 13:55:29
from __future__ import print_function, division, absolute_import
| sdss/marvin | tests/api/__init__.py | Python | bsd-3-clause | 296 | [
"Brian"
] | 0a204270684dac681074c0466fcf132dbe8d248cd95687ff24ba3ed6170ae6c1 |
# SPARTA - Stochastic PArallel Rarefied-gas Time-accurate Analyzer
# http://sparta.sandia.gov
# Steve Plimpton, sjplimp@sandia.gov, Michael Gallis, magalli@sandia.gov,
# Thomas Otahal, tjotaha@sandia.gov
# Sandia National Laboratories
# Copyright (2014) Sandia Corporation. Under the terms of Contract
# ... | luohancfd/FluidDynamicTools | SPARTA_Tools/grid2paraview.py | Python | gpl-3.0 | 43,697 | [
"ParaView",
"VTK"
] | 7fbf60167f5c98e9752cd3ef5cba58ef418f61f6f1716e6a6bc5750fb76ce6fb |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2005-2013 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU Lesser General Public License as published by
## the Free Softw... | andrebellafronte/stoq | stoqlib/domain/payment/group.py | Python | gpl-2.0 | 11,462 | [
"VisIt"
] | f65129e46a67f4d438dc1aed8a6fca7f738b98e0661ebcd80ecd21ff6118835f |
#!/usr/bin/env python
# add paths
import os, sys
for p in os.environ['PATH'].split(':'): sys.path.append(p)
# import modules
from re import findall
from itertools import product
from netCDF4 import Dataset as nc
from optparse import OptionParser
from numpy.ma import masked_array
from filespecs import BiasCorrectFile
... | RDCEP/ggcmi | bin/biascorr/biascorrect.py | Python | agpl-3.0 | 4,488 | [
"NetCDF"
] | a91a6bb1a1b721587da05fcdd7e68cc27484726645cc88a5e561d215263b1545 |
#pseudo-it.py v1.0.4
#iterative pseudoreference generation using BWA and the GATK
#Brice A. J. Sarver
#v0.1.0 completed 3 June 2015
#v0.8.0 release 18 Jan 2016; bug fixes, minor functionality improvements
#v1.0.1 release 8 May 2016; major functionality improvements, rewrite with Python 3.5+, bug fixes
#v1.1.0 release 8... | bricesarver/pseudo-it | pseudo-it.py | Python | mit | 24,135 | [
"BWA"
] | f22209b7cd47dd0a2e6353fc648f8c2d51d3bcab6d5023194fb2e430d09c8a1a |
#
# Copyright 2018-2021 Jan Griesser (U. Freiburg)
# 2014, 2020-2021 Lars Pastewka (U. Freiburg)
# 2014 James Kermode (Warwick U.)
#
# 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... | libAtoms/matscipy | tests/test_pair_potential_calculator.py | Python | lgpl-2.1 | 14,819 | [
"ASE",
"CRYSTAL",
"Matscipy"
] | 77b4a47719286b51faf27bbeadcfa97a414b4c40b49858ea7dfdd7a4cea113e8 |
from __future__ import (absolute_import, division, print_function)
import numpy as np
import scipy.constants
# Constants
avogadro = scipy.constants.N_A
cm3_to_angstroms3 = 1e24
avogadro_term = avogadro / 1e24
PRECISION = 5
def is_int(value):
"""Checks if `value` is an integer
:param value: Input value to ch... | neutrons/FastGR | addie/utilities/math_tools.py | Python | mit | 7,624 | [
"Avogadro"
] | ee4e724d7e3fffee286c94164b00a763070c9ffa97d2ab67c83787ee159ed61b |
from __future__ import print_function
from numpy import *
'''
Authors: Kai Liao, Adri Agnello (UCSB and UCLA)
Phil Marshall (Stanford)
Started: Liao, Aug.2014
Description: Convert Adri's Mathematica version into Python.
Given the survey imaging conditions and an object ID in OM10,
paint it in chosen band ... | drphilmarshall/OM10 | om10/imagenew.py | Python | mit | 2,115 | [
"Gaussian"
] | c08283850a141b33a73c400c1b9677d21143b95a2c62b9a687e5e316671d8574 |
# -*- coding: utf-8 -*-
'''
utilities.py
'''
import os
import tarfile
from scipy.spatial import cKDTree
import numpy as np
from shutil import rmtree, copyfile
from .pycompat import iteritems, SafeConfigParser
from netCDF4 import Dataset
from logging import getLogger
from .log import LOG_NAME
from .share import TIMESTAM... | wietsefranssen/RVIC | rvic/core/utilities.py | Python | gpl-3.0 | 14,758 | [
"NetCDF"
] | 2cc5ca1c8e10caf745d0fc619f731ce6f8743c17edd124d6de9e9bcd0e5706fc |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | junghans/espressopp | src/analysis/ConfigsParticleDecomp.py | Python | gpl-3.0 | 2,571 | [
"ESPResSo"
] | 2b669962967023f73f2d5727b9512d81f49df0f6c3e26778fdb8398757c91f30 |
# BEGIN_COPYRIGHT
#
# Copyright (C) 2014 CRS4.
#
# This file is part of blast-python.
#
# blast-python 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)
# ... | crs4/blast-python | test/test_blaster_speed.py | Python | gpl-3.0 | 7,600 | [
"BLAST"
] | b89c2cd049b973f1144baf904551dee5124d24dca5985089cdde7aa4a1b96a43 |
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