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import os
from gpaw import GPAW
from ase import *
from gpaw.wannier import Wannier
from gpaw.utilities import equal
natoms = 1
hhbondlength = 0.9
atoms = Atoms([Atom('H', (0, 4.0, 4.0))],
cell=(hhbondlength, 8., 8.),
pbc=True).repeat((natoms, 1, 1))
# Displace kpoints sligthly,... | qsnake/gpaw | oldtest/wannier-hwire.py | Python | gpl-3.0 | 1,691 | [
"ASE",
"GPAW"
] | 42821eeb6699a07e804e2d3c91623d2c02f43949dba7b76f3d654a4d3e865eaa |
""" DIRAC Transformation DB
Transformation database is used to collect and serve the necessary information
in order to automate the task of job preparation for high level transformations.
This class is typically used as a base class for more specific data processing
databases
"""
from __future__ import... | yujikato/DIRAC | src/DIRAC/TransformationSystem/DB/TransformationDB.py | Python | gpl-3.0 | 73,129 | [
"DIRAC"
] | 92d07f51bf5ca3ff4c714b2a250717298a32ac4fb157086616a7c76f35c6d524 |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2008, 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... | anksp21/Community-Zenpacks | ZenPacks.AndreaConsadori.Alvarion/setup.py | Python | gpl-2.0 | 3,300 | [
"VisIt"
] | eea8187a7d619a3b9196b527278484c6fe2d05b9e8d5e818960f02771e441e57 |
import math
import random
import numpy
from effectlayer import *
class FireflySwarmLayer(EffectLayer):
"""
Each LED node is a firefly. When one blinks, it pulls its neighbors closer or
further from blinking themselves, bringing the group into and out of sync.
For a full explanation of how this wor... | FlamingLotusGirls/soma | pier14/opc-client/effects/firefly_swarm.py | Python | apache-2.0 | 5,203 | [
"Firefly"
] | e4852fe1d0d79fbc12bd1dadba3dc13a489ef82ff083843fab07b92276310308 |
# Modeled on Python's Lib/compiler/visitor.py
class BadNode (Exception): pass
class ASTWalk:
def _default(self, node, *args):
raise BadNode (str (node))
def dispatch(self, node, *args):
methname = 'visit' + node.__class__.__name__
method = getattr(self.visitor, methname, self.default)... | seblefevre/testerman | plugins/codecs/ber/visitor.py | Python | gpl-2.0 | 637 | [
"VisIt"
] | fc3f5c2b22b42787e583e53c3e8c218e1b85c33929e9494006c82ca13fe441bc |
""" This contains unit tests to make sure that the migration between PyGSI and M2Crypto is as smooth as possible
The test covers only the method exposed by the PyGSI version for the time being.
We are not testing:
* generateProxyRequest -> boils down to testing X509Request
* setCertificate -> not used... | yujikato/DIRAC | src/DIRAC/Core/Security/test/Test_X509Certificate.py | Python | gpl-3.0 | 11,348 | [
"DIRAC"
] | 3a6e7091037144e723370565ab43cc760138b19636def5329c36c01fc354b8ed |
""" DIRAC Encoding utilities based on json
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import datetime
import json
# Describes the way date time will be transmetted
# We do not keep miliseconds
DATETIME_DEFAULT_FORMAT = '%Y-%m-%d %H:%M:%S'
class ... | yujikato/DIRAC | src/DIRAC/Core/Utilities/JEncode.py | Python | gpl-3.0 | 6,181 | [
"DIRAC"
] | d842bd509f4e204ab674675e5c0787e657677d41bcf7967e3886e4d2d0a117da |
# Mantid Repository : https://github.com/mantidproject/mantid
#
# Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
# NScD Oak Ridge National Laboratory, European Spallation Source
# & Institut Laue - Langevin
# SPDX - License - Identifier: GPL - 3.0 +
#pylint: disable=invalid-name
# File: Reduce... | mganeva/mantid | scripts/SCD_Reduction/ReduceSCD_Parallel.py | Python | gpl-3.0 | 14,586 | [
"CRYSTAL"
] | c7d4b2e8ccb82e33faa4f918e6a8cfbd128e5085fade0fdbe5328085a2057eaf |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
'''
Parallelize gamma point
'''
import numpy
import pyscf.pbc.gto as pbcgto
import pyscf.pbc.scf as pscf
from mpi4pyscf.pbc import df as mpidf
cell = pbcgto.Cell()
cell.atom = [['C', ([ 0., 0., 0.])],
['C', ([ 0.8917, 0.8917, 0.89... | sunqm/mpi4pyscf | examples/01-parallel_hf.py | Python | gpl-3.0 | 1,213 | [
"PySCF"
] | 399a10d33a9379fef5055777c4da9026cdb25227ba7b63698a8b4b1e8c1635ab |
'''
Copyright (C) 2015 Jeison Pacateque, Santiago Puerto, Wilmar Fernandez
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
Thi... | JeisonPacateque/Asphalt-Mixtures-Aging-Simulator | app/ui/render_3d.py | Python | gpl-3.0 | 3,356 | [
"Mayavi"
] | f35c091a23da129980ae3e6261db16d2572c50f183a54d3c990479b6c994f4aa |
# ======================================================================
#
# Cosmograil: cosmograil.tools.sextractor
#
# sextractor module.
#
# Author: Laurent Le Guillou <laurentl@ster.kuleuven.ac.be>
#
# $Id: sextractor.py,v 1.2 2005/07/06 21:40:43 hack Exp $
#
# ======================================================... | Pica4x6/numina | numina/util/sextractor.py | Python | gpl-3.0 | 19,085 | [
"Galaxy"
] | f50941b1b0a5b8035245aa40d240da126dd1df9566a02a6c14a7288c2dd232e7 |
################################################################################
# #
# Copyright (C) 2010-2018 The ESPResSo project #
# ... | hmenke/espresso | doc/tutorials/06-active_matter/EXERCISES/flow_field.py | Python | gpl-3.0 | 5,641 | [
"ESPResSo",
"ParaView",
"VTK"
] | 153bdd0c0fb95d15c9787f0afc6a3cc844ea42500af85648be0e4ba931f7ace6 |
from article_text_mining.full_text_pipeline import add_full_texts_from_mult_dirs, add_full_texts_from_directory
from django.conf import settings
__author__ = 'stripathy'
def add_full_texts():
"""Adds full texts from directory to DB based on rules specified in full_text_pipeline"""
if hasattr(settings, 'FULL_... | neuroelectro/neuroelectro_org | scripts/add_full_texts_to_db.py | Python | gpl-2.0 | 2,136 | [
"NEURON"
] | 89611f56e559b8ff23d9725d62f23fe672be2950929050ce6c72e5c22c3da69a |
from datetime import datetime
from utils import NS, get_text
from atom_objects import Category
from deposit_receipt import Deposit_Receipt
from sword2_logging import logging
from compatible_libs import etree
s_l = logging.getLogger(__name__)
class Sword_Statement(object):
def __init__(self, xml_document=None):
... | Hwesta/python-client-sword2 | sword2/statement.py | Python | mit | 14,477 | [
"ASE"
] | c30a18c5afad4ea54bd251bcb091470d40f12470b11c8c95a13be9cc4d4b914b |
from fortranformat import FortranRecordWriter as FW, FortranRecordReader as FR
from cube_helpers import InputFormatError, Atom, Molecule, Field
from cube_helpers import angstrom_per_bohr
import math
class RespFormats(object):
# Numeric Fortran formats specified in resp input specification
# http://upjv.q4md... | jszopi/repESP | repESP_old/resp_helpers.py | Python | gpl-3.0 | 9,641 | [
"Gaussian"
] | ea733a038255eb6366fd671cb9904bf01c6defbafd574e1bdb3d70d84581e300 |
"""
Checks for the Attribute Conventions for Dataset Discovery (ACDD)
This module contains classes defined as checks part of the compliance checker
project for the verification and scoring of attributes for datasets.
"""
from datetime import timedelta
from functools import partial
import numpy as np
import pendulum
... | ioos/compliance-checker | compliance_checker/acdd.py | Python | apache-2.0 | 29,740 | [
"NetCDF"
] | 1d871ffc4167ff8bfaec5aeadaed867148b7c80105a912130c6d5566ed095d2b |
#!/usr/bin/env python
import broker
import unittest
import json
import requests
class BrokerTestCase(unittest.TestCase):
def setUp(self):
broker.app.config['TESTING'] = True
self.app = broker.app.test_client()
def tearDown(self):
broker.Broker.reset()
def setUpBank(self):
... | haw-vs-2015/py-monopoly | test_broker.py | Python | gpl-2.0 | 11,761 | [
"VisIt"
] | c8789d7f5515198e005a0d208e38db49aabc2247adca9e5fa9a97058fccc3adb |
import re
from .common import InfoExtractor
from ..utils import (
compat_parse_qs,
compat_urllib_parse,
compat_urllib_request,
determine_ext,
ExtractorError,
)
class MetacafeIE(InfoExtractor):
"""Information Extractor for metacafe.com."""
_VALID_URL = r'(?:http://)?(?:www\.)?metacafe\.com... | vgrachev8/youtube-dl | youtube_dl/extractor/metacafe.py | Python | unlicense | 7,574 | [
"Galaxy"
] | 7d53a241ab7867bcd2fb795e4f4a856d536e183cb8cb41d91be22c49058df3ea |
## \file
## \ingroup tutorial_roofit
## \notebook
##
## \brief Basic functionality: plotting unbinned data with alternate and variable binnings
##
## \macro_code
##
## \date February 2018
## \authors Clemens Lange, Wouter Verkerke (C++ version)
import ROOT
# Set up model
# ---------------------
# Build a B decay p.d... | karies/root | tutorials/roofit/rf108_plotbinning.py | Python | lgpl-2.1 | 3,801 | [
"Gaussian"
] | 81803b1eaff68db2407bde3d279e08f954090097abf4e6c914df3492ed949deb |
"""Only External Repos url specific constants module"""
from robottelo.config import settings
REPOS_URL = settings.robottelo.repos_hosting_url
CUSTOM_FILE_REPO = 'https://fixtures.pulpproject.org/file/'
CUSTOM_KICKSTART_REPO = 'http://ftp.cvut.cz/centos/8/BaseOS/x86_64/kickstart/'
CUSTOM_RPM_REPO = 'https://fixtures... | jyejare/robottelo | robottelo/constants/repos.py | Python | gpl-3.0 | 2,980 | [
"Galaxy"
] | 51f4d7758dc688284d319deeab1eecf10792017fd6ad95cb5703f5e3fdcfb07d |
# author: Adrian Rosebrock
# website: http://www.pyimagesearch.com
# USAGE
# python finding_function_names.py
# import the necessary packages
from __future__ import print_function
import imutils
# loop over various function strings to search for and try to
# locate them in the OpenCV library
for funcName in ("c... | xuanhan863/imutils | demos/finding_function_names.py | Python | mit | 466 | [
"Gaussian"
] | 10f2b5c7296927c032a1c4331b0ea612b6241f1bdaca0c81f26d1c3f12d66ad9 |
import mock
import unittest
from nose.tools import *
import tempfile
from bs4 import BeautifulSoup
from pyrobot.compat import builtin_name
from pyrobot.forms import Form, fields
from pyrobot.forms.form import _parse_fields
class TestForm(unittest.TestCase):
def setUp(self):
self.html = '''
<... | jmcarp/pyrobot | tests/test_forms.py | Python | bsd-3-clause | 15,369 | [
"Brian"
] | 65d13310b77ae6c2ae0b7d3acb213b0da30229949d2dcf38fdfd86e559f93a58 |
#!/galaxy/home/mgehrin/hiclib/bin/python
"""
Read a table dump in the UCSC gene table format and print a tab separated
list of intervals corresponding to requested features of each gene.
usage: ucsc_gene_table_to_intervals.py [options] < gene_table.txt
options:
-h, --help show this help message and exit... | bxlab/HiFive_Paper | Scripts/HiCLib/bx-python-0.7.1/build/scripts-2.7/ucsc_gene_table_to_intervals.py | Python | bsd-3-clause | 3,471 | [
"Galaxy"
] | e6f8cfa4c8209977495c47b84be57d6502013745f596e2f4b5befb7069b39e34 |
# Principal Component Analysis Code :
from numpy import mean,cov,double,cumsum,dot,linalg,array,rank,size,flipud
from pylab import *
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import ro... | tapomayukh/projects_in_python | sandbox_tapo/src/skin_related/BMED_8813_HAP/Scaling/best_kNN_PC/cross_validate_objects_kNN_PC_BMED_8813_HAP_scaled_method_II.py | Python | mit | 4,355 | [
"Mayavi"
] | 8e8a8350a99a348ac225c8593cf36979df5be0a660905c57d19eb3d5afc025ea |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides classes to perform fitting of molecule with arbitrary
atom orders.
This module is supposed to perform exact comparisons without the atom order
correspondence prerequisite, while molecu... | mbkumar/pymatgen | pymatgen/analysis/molecule_matcher.py | Python | mit | 26,063 | [
"pymatgen"
] | 818fd7022b7489ed6fd563edabb9e00756e70be28983481e7551b7dd2955cf53 |
from __future__ import division, print_function, absolute_import
import re
import os
import logging
import json
import argparse
logger = logging.getLogger(__name__)
# TODO: It may be good to delete all site folders before running this program again
class JournalParsingWorker(object):
"""
Works on a single "sh... | robert-giaquinto/text-analysis | src/parse_journal/parse_worker.py | Python | mit | 6,789 | [
"VisIt"
] | 51fa991d2c56829e7aaf6206bf97e736a4493d7ae12b135e90e006f7442b1dfb |
"""
A Tkinter based backend for piddle.
Perry A. Stoll
Created: February 15, 1999
Requires PIL for rotated string support.
Known Problems:
- Doesn't handle the interactive commands yet.
- PIL based canvas inherits lack of underlining strings from piddlePIL
You can find the latest version ... | rvianello/rdkit | rdkit/sping/TK/pidTK.py | Python | bsd-3-clause | 16,537 | [
"RDKit"
] | 2d6d57ba436af3974051389e6b4d0583547066764cba9f4921f4c21698db44c2 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
... | alejob/mdanalysis | testsuite/MDAnalysisTests/test_datafiles.py | Python | gpl-2.0 | 2,028 | [
"MDAnalysis"
] | b668ee6b5be28e7186965209b49148fed45259d0d7761126b8a178e827021441 |
#!/usr/bin/env python
import matplotlib as m
import matplotlib.pyplot as plt
from matplotlib.mlab import griddata
import numpy as np
import sys
import pdb
import os
import random
def file_len(full_path):
""" Count number of lines in a file."""
f = open(full_path)
nr_of_lines = sum(1 for line in... | FluidityProject/multifluids | examples/monai_valley/raw_data/plotbathymetry.py | Python | lgpl-2.1 | 3,538 | [
"NetCDF"
] | c642a6ff8d4d9c8592249ff4365c1ac0a58afd83e11da86e3ba30f671cda0b30 |
# 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... | dudymas/python-openstacksdk | openstack/tests/unit/test_resource.py | Python | apache-2.0 | 45,751 | [
"Brian",
"MOE"
] | 1d9b57ddf72afdf6e0bf2e19ce88f17f1318b5e2f004d13aa0e3daa4f26a898f |
#!/usr/bin/env python2.6
"""
Oct 5 2012
cp from parseLiteratureBlast_toTex.py
Parser Max's Blast output tab-delimited file into a table of clones that have hits matches certain keywords
Filtering criteria includes:
1/ Match score (E.g minPositives = 90%)
2/ Keywords (E.g: autologous keywords)
3/ Min sequen... | ngannguyen/immunoseq | src/parseLiteratureBlastTab_toTex.py | Python | mit | 24,929 | [
"BLAST"
] | 7366b66cf370131cc3cf6f0a264e71cb6373187b825fad2647f974f9ede1156c |
#!/usr/bin/python
# http://mcsp.wartburg.edu/zelle/python/graphics.py
# https://mcsp.wartburg.edu/zelle/python/graphics/graphics/index.html
import math
from graphics import *
XSCALE = 2550
YSCALE = 1310
XCENTER = XSCALE / 2
YCENTER = YSCALE / 2
# https://en.wikipedia.org/wiki/Incircle_and_excircles_of_a_triangle#... | jtraver/dev | python/graphics/circles5.py | Python | mit | 23,699 | [
"Amber"
] | aab30632b948885eaef0c7b5e97928eb8b618e69706053f443f444cb0f85bd6d |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import itertools
from pymatgen.core.lattice import Lattice
import numpy as np
from pymatgen.util.testing import PymatgenTest
from pymatgen.core.operations impo... | gpetretto/pymatgen | pymatgen/core/tests/test_lattice.py | Python | mit | 20,579 | [
"pymatgen"
] | 1aa8dfba3b269141a7ad7e3a781bc6cd4129bcfe5a3d84232611f89b87645a16 |
#
# Copyright (C) 2013-2019 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... | psci2195/espresso-ffans | testsuite/python/rotation_per_particle.py | Python | gpl-3.0 | 4,942 | [
"ESPResSo"
] | 3eef171ee7ad394438b97e1c15bc73c8d7de51bb5bdf8849fe6042aefc355348 |
#!/usr/bin/env python3
"""
Copyright 2020 Paul Willworth <ioscode@gmail.com>
This file is part of Galaxy Harvester.
Galaxy Harvester is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 ... | pwillworth/galaxyharvester | html/schematics.py | Python | gpl-3.0 | 12,698 | [
"Galaxy"
] | 15127fc3e1c2c872a5e7351a31831979873ead8e0af3d9a7bf316efe4f4ef6a9 |
"""feedfinder: Find the Web feed for a Web page
http://www.aaronsw.com/2002/feedfinder/
Usage:
feed(uri) - returns feed found for a URI
feeds(uri) - returns all feeds found for a URI
>>> import feedfinder
>>> feedfinder.feed('scripting.com')
'http://scripting.com/rss.xml'
>>>
>>> feedfinder.fe... | cantino/newspaper | newspaper/packages/feedfinder.py | Python | mit | 12,920 | [
"Brian"
] | 26e23e04c85c44314872a7afd5e4b21518c5db07b7975a23859f7abe960e3ec1 |
#!/usr/bin/env python
import pylab as pl
def readLammps(fn):
fh = open(fn)
lines = fh.readlines()
fh.close()
steps = []
for kl in range(len(lines)):
if lines[kl].startswith('ITEM: TIMESTEP'):
step = []
Na = int(lines[kl+3])
for ka in range(Na):
v = map(float,lines[kl+9+ka].split())
step.appe... | yorzh86/Step1 | scripts/compareVelocity.py | Python | gpl-2.0 | 1,115 | [
"LAMMPS"
] | e954bcd35f8e4f5bb6cdf3b8f2721e2a95006b2b41c67ee7a0470fea7e4bfbcc |
# Copyright (C) 2009-2013 Sebastian Rahlf <basti at redtoad dot de>
#
# This program is release under the BSD License. You can find the full text of
# the license in the LICENSE file.
from lxml import etree, objectify
from amazonproduct.contrib.cart import Cart, Item
from amazonproduct.errors import AWSError
from ama... | prats226/python-amazon-product-api-0.2.8 | amazonproduct/processors/objectify.py | Python | bsd-3-clause | 3,842 | [
"Brian"
] | f4c92fdef0932a306838b270f7766b711b99d755c89312fe0a3973d3f6710108 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2002-2006 Donald N. Allingham
# Copyright (C) 2008 Brian G. 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; ... | arunkgupta/gramps | gramps/gen/filters/rules/note/_matchesregexpof.py | Python | gpl-2.0 | 2,164 | [
"Brian"
] | 7fc95fb80429e566c395101b9b220d8ef104fb523176d85db47a729999d63b66 |
from __future__ import absolute_import
from six import string_types
import json
import decimal
import datetime
from pathlib import Path
from plotly.io._utils import validate_coerce_fig_to_dict, validate_coerce_output_type
from _plotly_utils.optional_imports import get_module
from _plotly_utils.basevalidators import I... | plotly/plotly.py | packages/python/plotly/plotly/io/_json.py | Python | mit | 18,159 | [
"ORCA"
] | 19a18119281b67400fda518fae4a56bf05ca0fcd8b186cf85c68e256e73eb729 |
#!/usr/bin/env python
""" runs checkTransformationIntegrity from ValidateOutputDataAgent on selected Tranformation
"""
from __future__ import print_function
import sys
from DIRAC.Core.Base.Script import parseCommandLine
parseCommandLine()
if len( sys.argv ) < 2:
print('Usage: dirac-transformation-verify-outputdata... | chaen/DIRAC | TransformationSystem/scripts/dirac-transformation-verify-outputdata.py | Python | gpl-3.0 | 968 | [
"DIRAC"
] | cb2ac12b1af4cde54d21be3f1d8315cd177a1ac309f0c23555117a7603a6a1da |
#!/usr/bin/env python
from __future__ import print_function
import argparse
import datetime
import glob
import shutil
import os
# try:
# from urllib.parse import urlparse
# except ImportError:
# from urlparse import urlparse
import logging
log = logging.getLogger(__name__)
def copy_output_file_to_dataset(... | SANBI-SA/tools-sanbi-uwc | tools/build_ctb_explorer/build_ctb_explorer.py | Python | gpl-3.0 | 4,075 | [
"Galaxy"
] | 981d6209c82a85db2b8a1ed1f6b4a4b13808b9b55ded1a37fe6754470a8ff771 |
# Copyright 2020 Google Research. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law... | tensorflow/examples | tensorflow_examples/lite/model_maker/third_party/efficientdet/model_inspect.py | Python | apache-2.0 | 20,632 | [
"Gaussian"
] | 6bd41e9801c1bdc3143f5ffa7ce61849adf9819628ffb17246e79d0195e3ba6f |
import cv2
import numpy as np
import matplotlib.pyplot as plt
'''
Starting with a user-specified bounding box (the box with the smallest measure within which all the points lie) around
the object to be segmented, the algorithm estimates the color distribution of the target object and that of the
background using a ... | RyanChinSang/ECNG3020-ORSS4SCVI | BETA/TestCode/OpenCV/TUT-GrabCutFgExtr.py | Python | gpl-3.0 | 1,337 | [
"Gaussian"
] | 0393d8d20dd960ec492d38002625c4356848099c42a3e88bd3e6f58ed6867152 |
#* 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
"""
FParser... | harterj/moose | python/mms/fparser.py | Python | lgpl-2.1 | 6,200 | [
"MOOSE"
] | 6d066ea19eb0facc6140350d99e43034aef4c42b491f6ae4ac99ed51de1d855b |
# Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import argparse
import torch
from torch.distributions import constraints
import pyro
import pyro.distributions as dist
from pyro.contrib.autoname import named
from pyro.infer import SVI, JitTrace_ELBO, Trace_ELBO
from pyro.optim ... | uber/pyro | examples/contrib/autoname/mixture.py | Python | apache-2.0 | 2,572 | [
"Gaussian"
] | dbfac4db4815c49c194efc743c7e76ea6395770130aa176a81d5df965298fcbc |
#!/usr/bin/env python -Es
"""
Script to set up a custom genome for bcbio-nextgen
"""
import argparse
from argparse import ArgumentParser
import os
from Bio import SeqIO
import toolz as tz
from bcbio.utils import safe_makedir, file_exists, chdir
from bcbio.pipeline import config_utils
from bcbio.distributed.transaction... | gifford-lab/bcbio-nextgen | scripts/bcbio_setup_genome.py | Python | mit | 12,079 | [
"Galaxy"
] | cd23c67547ff222b2c4f3af48fedc690922a7a0e180ff9c29159093167ace797 |
#!/usr/bin/env python
"""
Originally written by Kelly Vincent
pretty output and additional picard wrappers by Ross Lazarus for rgenetics
Runs all available wrapped Picard tools.
usage: picard_wrapper.py [options]
code Ross wrote licensed under the LGPL
see http://www.gnu.org/copyleft/lesser.html
"""
import optparse, o... | jhl667/galaxy_tools | tools/picard/picard_wrapper.orig.py | Python | apache-2.0 | 35,974 | [
"Galaxy",
"pysam"
] | ab64af29cbc2c3a311a32412f0985ed1c84ee745ad42234c539af0da6512df81 |
from __future__ import (absolute_import, division, print_function)
import io
import numpy as np
import AbinsModules
from mantid.kernel import Atom, logger
class LoadCRYSTAL(AbinsModules.GeneralDFTProgram):
"""
Class for loading CRYSTAL DFT phonon data. Special thanks to Leonardo Bernasconi for contributing to... | dymkowsk/mantid | scripts/AbinsModules/LoadCRYSTAL.py | Python | gpl-3.0 | 22,768 | [
"CRYSTAL"
] | 26766df5e3053d490b9af356c1a21f05fee1d31b3de188b8c8113b84e8ec93f4 |
from django.conf import settings
from django.conf.urls import include, url
from django.contrib import admin
from django.views import defaults as default_views
admin.autodiscover()
urlpatterns = [
url(r'^polls/', include('polls.urls', namespace="polls")),
url(r'^admin/', include(admin.site.urls)),
]
if setti... | fedenko/django-gulp-example | mysite/urls.py | Python | bsd-3-clause | 873 | [
"VisIt"
] | 873c02c1c90ef6cd3e55a363280a31fb67dcd5a474447f49617ff083328d6eb1 |
# -*- coding: utf-8 -*-
# Copyright (c) 2015-2018, Exa Analytics Development Team
# Distributed under the terms of the Apache License 2.0
"""
The Atomic Universe
#########################
The :class:`~exatomic.container.Universe` object is a subclass of
:class:`~exa.container.Container` that stores data coming from com... | alexvmarch/atomic | exatomic/core/universe.py | Python | apache-2.0 | 14,841 | [
"ADF",
"Gaussian",
"MOLCAS",
"NWChem",
"cclib"
] | 50175c7cf46f977ab727a4d9c819f6bf38b37f7a38930a3c48a73356d76a265b |
from collections import namedtuple, OrderedDict
_ProductType = namedtuple('ProductType', ['name', 'description', 'amount', 'paperback_addl', 'us_postage', 'can_postage', 'eur_postage', 'aus_postage', 'else_postage'])
class Product(_ProductType):
__slots__ = ()
def __str__(self):
return self.name
PRO... | hellowebbooks/hellowebbooks-website | books/options.py | Python | mit | 19,793 | [
"GULP"
] | c14638cf309d16d04d7981145a51301249a9cf886de61669fd3350c509b99f0b |
# derived from
# http://s3.amazonaws.com/alexa-static/top-1m.csv.zip
# fetched 2018-05-22, see also
# https://support.alexa.com/hc/en-us/sections/200063274-Top-Sites
alexa_top_1m_tlds_about = {
'date': '2018-05-22',
'source': 'http://s3.amazonaws.com/alexa-static/top-1m.csv.zip'
}
alexa_top_1m_tlds = {
# zc... | sebastian-nagel/cc-crawl-statistics | stats/tld_alexa_top_1m.py | Python | apache-2.0 | 10,408 | [
"CASINO",
"MOE"
] | d0624ac02b5d31a94136b15b8e0b236685b9e1f1019e546c8f523f4819af5536 |
"""
pymc3.distributions
A collection of common probability distributions for stochastic
nodes in PyMC.
"""
from __future__ import division
from .dist_math import *
from .distribution import draw_values, generate_samples
import numpy as np
import numpy.random as nr
import scipy.stats as st
from . import transforms
... | dhiapet/PyMC3 | pymc3/distributions/continuous.py | Python | apache-2.0 | 31,105 | [
"Gaussian"
] | 496f5cb1ecc41442e243f5f01c4216747f10ea81e99a446af6b2623d4dceb3f4 |
# -*- coding: utf-8 -*-
import pytz
import random
import hashlib
import string
from django.contrib.auth.models import AbstractBaseUser, BaseUserManager
from django.core.mail import send_mail
from django.core.mail import EmailMultiAlternatives
from django.core.urlresolvers import reverse
from django.template.loader im... | atados/api | atados_core/models/core.py | Python | mit | 40,212 | [
"VisIt"
] | 1b0c96fcfeeb44f4b1fc6fea0974af3e837da28bf118256bcb50d25e4eb67ecc |
# Copyright Iris contributors
#
# This file is part of Iris and is released under the LGPL license.
# See COPYING and COPYING.LESSER in the root of the repository for full
# licensing details.
"""
Test the cf module.
"""
# import iris tests first so that some things can be initialised before importing anything else
i... | SciTools/iris | lib/iris/tests/test_cf.py | Python | lgpl-3.0 | 14,871 | [
"NetCDF"
] | 7096ccda7c1d8d16ab4b39eaf143285a3cdcbac6ef0bd447d326ccaddb750037 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# sendrequestaction - send request for e.g. member or ownership action handler
# Copyright (C) 2003-2015 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... | heromod/migrid | mig/shared/functionality/sendrequestaction.py | Python | gpl-2.0 | 16,333 | [
"Brian"
] | 43964886c6c5e15ddd92164afb42754e636554f4912e6c79a3be05eb8658192f |
from django.views.generic.edit import CreateView, UpdateView, DeleteView
#whenever you want to make a form to create, update, view a new object
from django.core.urlresolvers import reverse_lazy
from django.shortcuts import render, redirect
#lets us redirect user on login
from django.contrib.auth import authenticate, l... | castle-c/djangoTutorial | music/views.py | Python | mit | 2,856 | [
"VisIt"
] | 97ec537a2808bdbf2a674b0886bf3532a710996e065cd8accbdfb88ef9458d25 |
'''
SYNBIOCHEM-DB (c) University of Manchester 2015
SYNBIOCHEM-DB is licensed under the MIT License.
To view a copy of this license, visit <http://opensource.org/licenses/MIT/>.
@author: neilswainston
'''
import math
import uuid
from libchebipy._chebi_entity import ChebiEntity, ChebiException
from sbcdb import na... | synbiochem/biochem4j | sbcdb/chemical_utils.py | Python | mit | 5,103 | [
"VisIt"
] | 650061cf11665e1c9a9b25aecffdb58738e38822bf1e5c1f226c19fbc44d0804 |
"""
Generalized Linear Models with Exponential Dispersion Family
"""
# Author: Christian Lorentzen <lorentzen.ch@googlemail.com>
# some parts and tricks stolen from other sklearn files.
# License: BSD 3 clause
import numbers
import numpy as np
import scipy.optimize
from ...base import BaseEstimator, RegressorMixin
... | ndingwall/scikit-learn | sklearn/linear_model/_glm/glm.py | Python | bsd-3-clause | 24,918 | [
"Gaussian"
] | bba635ed7191d15c04ba9eb491ea5219582ff4d0eaaef5dc7ec990338c7a4bb8 |
#!/usr/bin/env python
"""
A very simple HTTP server.
"""
import sys
from BaseHTTPServer import HTTPServer
from SimpleHTTPServer import SimpleHTTPRequestHandler
if sys.argv[1:]:
port = int(sys.argv[1])
else:
port = 8080
address = ('localhost', port)
httpd = HTTPServer(address, SimpleHTTPRequestHandler)
sa = ht... | ntoll/bookreader | scripts/runserver.py | Python | mit | 444 | [
"VisIt"
] | 115836d55855f21a42ea902639b14ba4e4d35180955731e615e62c53967919a2 |
# -*- coding: utf-8 -*-
# python-holidays
# ---------------
# A fast, efficient Python library for generating country and subdivision
# specific sets of holidays on the fly. It aims to make determining whether a
# specific date is a holiday as fast and flexible as possible.
#
# Authors: dr-prodigy <maurizio.mont... | dr-prodigy/python-holidays | holidays/utils.py | Python | mit | 21,903 | [
"COLUMBUS"
] | 7b878b0f353fad4af3ca329362cb5d64b63a69ad10f10624eef55c23d157c074 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module defines tools to generate and analyze phase diagrams.
"""
import collections
import itertools
import json
import logging
import math
import os
import re
import sys
from functools import lru_cache
import numpy... | vorwerkc/pymatgen | pymatgen/analysis/phase_diagram.py | Python | mit | 120,302 | [
"pymatgen"
] | 17910654a19cf4722ac53d4ef27f30383e9556540321e0cec8268d0296848d81 |
from django import forms
from django.contrib.admin.widgets import AdminRadioSelect, AdminRadioFieldRenderer
from edc_base.form.forms import BaseModelForm
from edc_constants.constants import ON_STUDY
from edc_visit_tracking.forms import VisitFormMixin
from bcvp.bcvp.choices import VISIT_REASON, VISIT_INFO_SOURCE, VISI... | botswana-harvard/bcvp | bcvp/bcvp_subject/forms/subject_visit_form.py | Python | gpl-2.0 | 1,222 | [
"VisIt"
] | 693bff577b9a5f7897e5f3fad21f76b60c2655e14528abdcc23f0ba776a092d8 |
# -*- 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 General Public License as published by
## the Free Software Foundati... | andrebellafronte/stoq | stoqlib/gui/test/test_inventorywizard.py | Python | gpl-2.0 | 1,841 | [
"VisIt"
] | 01f087be7331371ad532a2d0f7eaae14b0c9a89a0bf51a0d5e0ba2e6da3c4dee |
# -*- coding: utf-8 -*-
"""The ants module provides basic functions for interfacing with ants functions.
Change directory to provide relative paths for doctests
>>> import os
>>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
>>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/... | carolFrohlich/nipype | nipype/interfaces/ants/segmentation.py | Python | bsd-3-clause | 59,317 | [
"Gaussian"
] | 95bc3e928f81a87d9f42a6d1075d84f752048f5566e16839ebab40d64139701e |
# Calling a JSON API
# Liu Li
# 2015-11-23
'''
In this assignment you will write a Python program somewhat similar to http://www.pythonlearn.com/code/geojson.py. The program will prompt for a location, contact a web service and retrieve JSON for the web service and parse that data, and retrieve the first place_id from... | ll0816/PythonForEverybody | Using-Python-2-Access-Web-Data/Calling-a-JSON-API.py | Python | mit | 2,516 | [
"VisIt"
] | 7a993b8774b4872477ae5f4c131e7f1e3cbd754a5dd4ee4e494c18ebdd7d400c |
SERVICE_PACKAGE_FILE = 'Firefly/core/services.json'
SERVICE_CONFIG_DIR = 'dev_config/services/'
| Firefly-Automation/Firefly | Firefly/core/const.py | Python | apache-2.0 | 96 | [
"Firefly"
] | db8197bc59f998e826933b6fd6cbe07a5a78f41108aa72b9fe64dc90ed49f9b2 |
#!/usr/bin/env python
from __future__ import print_function
import os
import re
import sys
import datetime
from subprocess import Popen, PIPE, STDOUT
from types import *
"""
Below is an example of the job script
#!/bin/bash
#
# Job Submission Script
#
#@ class = queue
#@ job_nam... | burbanom/batch_management | batch_management.py | Python | gpl-3.0 | 8,506 | [
"CP2K"
] | 42a705d78b07c8a67353cc6ac616bfd8adce08056eca0975e20c3336e3cdade1 |
# Created by Blake Cornell, CTO, Integris Security LLC
# Integris Security Carbonator - Beta Version - v1.2
# Released under GPL Version 2 license.
#
# See the INSTALL file for installation instructions.
#
# For more information contact us at carbonator at integrissecurity dot com
# Or visit us at https://www.integris... | RB4-Solutions/cscan | plugin/carbonator/carbonator.py | Python | gpl-3.0 | 4,421 | [
"VisIt"
] | 5fdfc1895396263044ac10b41d8e18f0f4b6bd1008dd1442722cfd2f46aefd08 |
#
# This source file is part of appleseed.
# Visit http://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2014-2017 The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this s... | jasperges/blenderseed | ui/camera.py | Python | mit | 3,039 | [
"VisIt"
] | 5d93299250f1cd6e6dda95fd452f33dca3ff96a3b313181193713f5c53cb270c |
import pytest
import webtest
from datetime import date
from urllib.parse import urlencode
from ..types.lab import Lab
pytestmark = [pytest.mark.setone, pytest.mark.working, pytest.mark.schema]
@pytest.fixture
def remc_lab(testapp):
item = {
'name': 'remc-lab',
'title': 'REMC lab',
'stat... | hms-dbmi/fourfront | src/encoded/tests/test_permissions.py | Python | mit | 56,605 | [
"VisIt"
] | 2eeaa01a86bf0c0caec6b94af3b8dd985c20937faecd84ba5de6a3e80a0d6e98 |
# ============================================================================
#
# Copyright (C) 2007-2010 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | kurtraschke/camelot | camelot/view/controls/view.py | Python | gpl-2.0 | 4,493 | [
"VisIt"
] | 31194a10e32e6b7ee63faf8ed2e86cea485c8d69c62bae3fbaf3523686fd7e79 |
# wxp - general framework classes for wxPython
#
# Copyright 2007 Peter Jang <http://avisynth.nl/users/qwerpoi>
# 2010-2013 the AvsPmod authors <https://github.com/avspmod/avspmod>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public Licens... | AvsPmod/AvsPmod | wxp.py | Python | gpl-2.0 | 105,336 | [
"VisIt"
] | 2ba413dcbd29e6e11a6d0c2d0608103c7f1bbba1cf67f388aa81a1417ed41dbe |
"""Tests for distutils.dist."""
import os
import io
import sys
import unittest
import warnings
import textwrap
from unittest import mock
from distutils.dist import Distribution, fix_help_options, DistributionMetadata
from distutils.cmd import Command
from test.support import (
TESTFN, captured_stdout, captured_... | FFMG/myoddweb.piger | monitor/api/python/Python-3.7.2/Lib/distutils/tests/test_dist.py | Python | gpl-2.0 | 19,095 | [
"Brian"
] | 49cbb121dcecb5dbdc6095a1675c1fe248901f93d125509911f800840d837d9f |
import ast
from ast import AST
import io
import contextlib
import weakref
import random
TAB_SIZE = 2
TAB = TAB_SIZE * " "
TEMP_VNAME = "X_X"
LUA_True = "true"
LUA_False = "false"
LUA_None = "nil"
class RawRepr(str):
def __repr__(self):
return self
def unresolve(value, raw=False, *, has_ast):
if isin... | EcmaXp/PyCraft | pc_old.py | Python | gpl-2.0 | 24,863 | [
"VisIt"
] | d21552065e4369e819dce33302e818d1c2161a325c465690eb04055ca765b57e |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Mail-Merge for Scribus. This file provides the backend.
#
# For further information (manual, description, etc.) please visit:
# https://github.com/berteh/ScribusGenerator/
#
# v2.9.1 (2021-01-22): update port to Python3 for Scribut 1.5.6+, various DOC update
#
... | berteh/ScribusGenerator | ScribusGeneratorBackend.py | Python | mit | 35,118 | [
"VisIt"
] | de810dec91ce25a4e353d6d68c4508527dab0ad4a6258cf2fbea2af23f3b774c |
import os, sys, re, shutil, json, zipfile, subprocess
# import os.path
import xbmc, xbmcaddon, xbmcvfs
# from xbmcswift2 import xbmcgui
from resources.lib.xbmcswift2b import xbmcgui
from descriptionparserfactory import *
#
# CONSTANTS AND GLOBALS #
#
iarlnes_plugin_name = 'plugin.program.iarlnes'
debuggin... | bbr25/plugin.program.iarlnes | resources/lib/util.py | Python | gpl-2.0 | 83,029 | [
"Jaguar"
] | 6ce1227a241ca6d71e755756728554c933ce25f71694f2dfc4a9dd5723ceb611 |
"""
Student Views
"""
import datetime
import logging
import uuid
import json
import warnings
from collections import defaultdict
from urlparse import urljoin, urlsplit, parse_qs, urlunsplit
from django.views.generic import TemplateView
from pytz import UTC
from requests import HTTPError
from ipware.ip import get_ip
i... | pabloborrego93/edx-platform | common/djangoapps/student/views.py | Python | agpl-3.0 | 109,785 | [
"VisIt"
] | 6d9e8d40310f67c9d7702efeb7a40fbca8f28072cbb85cbcd514717560e93323 |
import pylab as pyl
import cPickle as pickle
from scipy.stats import scoreatpercentile
galaxies = pickle.load(open('galaxies.pickle', 'rb'))
galaxies = filter(lambda galaxy: galaxy.ston_I > 30., galaxies)
f1 = pyl.figure(1, figsize=(6,4))
f1s1 = f1.add_subplot(111)
# for the clipped points
arrow_right = [[0,0],[-1,1... | boada/ICD | sandbox/plot_icd_vs_ssfr.py | Python | mit | 1,901 | [
"Galaxy"
] | a35569faaa8ddd8d28c05e1743c98b4f9ce66137a00838535347a910d28be5e2 |
#!/usr/bin/env python
# ===============================================================================
# Copyright 2017 Geoscience Australia
#
# 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... | alex-ip/geophys_utils | geophys_utils/netcdf_converter/grav2netcdf_converter.py | Python | apache-2.0 | 31,301 | [
"NetCDF"
] | 3aa970aba015c836020d70fba195706f33cdeab711bc131598039a5c118eb1f7 |
from check_grad import check_grad
from utils import *
from logistic import *
import matplotlib.pyplot as plt
def run_logistic_regression(hyperparameters):
# TODO specify training data
train_inputs, train_targets = load_train()
valid_inputs, valid_targets = load_valid()
test_inputs, test_targets = lo... | ouyangyike/Machine-Learning-and-Data-Mining | Logistic Regression/logistic_regression_regularized1.py | Python | mit | 3,874 | [
"Gaussian"
] | 1fce982298ec537ad68d8ab6a4784d79d80cbe000d4f62935a39e4835b8c0328 |
from tabulate import tabulate
from collections import OrderedDict
vals = """
#bcftools
986798
real 3m49.024s
user 3m48.620s
sys 0m7.848s
#cyvcf2
984214
real 4m5.190s
user 4m5.048s
sys 0m0.112s
#pysam
984214
real 33m12.417s
user 33m11.920s
sys 0m0.244s
""".split("#")
vals = [x.strip() for x in vals ... | brentp/cyvcf2 | scripts/table.py | Python | mit | 1,060 | [
"pysam"
] | 089843496cc6f76934e4ee04579dc2941fed64f093af0dfaa77f58122e0fa4e5 |
import tensorflow as tf
import re
FLAGS = tf.app.flags.FLAGS
tf.app.flags.DEFINE_boolean('use_fp16', False,
"""Train the model using fp16.""")
tf.app.flags.DEFINE_integer('sequence_length', 1200,
"""Number of batches to run.""")
tf.app.flags.DEFINE_integer('embe... | bgshin/vddc | src/models/cnn_model.py | Python | apache-2.0 | 16,090 | [
"Gaussian"
] | 7e5289bad12f18a9676c55b1d3eedd8e21362216e360d052f36c03d51f1c72e5 |
# Copyright 2010-2017, The University of Melbourne
# Copyright 2010-2017, Brian May
#
# This file is part of Karaage.
#
# Karaage 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... | brianmay/karaage | karaage/management/commands/change_pid.py | Python | gpl-3.0 | 2,212 | [
"Brian"
] | 9c220c921a4b8dd9841dd89e5197bfdef5b082fff7f429416a689931ef6b75ef |
#!/usr/bin/python
# coding=utf-8
# Concept from Jaroslaw Zachwieja <grok!warwick.ac.uk> & TJ <linux!tjworld.net>
# from their work in gegpsd.py included in gpsd project (http://catb.org/gpsd)
# This is a time limited demo for the curious, or those without a gps. If it
# doesn't work, you need to use the 'regular' geg... | matbor/gps3 | demo_gegps3.py | Python | mit | 4,957 | [
"MOE"
] | a446fec34fbc2d39d39202b6b127d60acf09cac5f2cd990d0e6214e65528b56c |
"""
Acceptance tests for Studio's Setting pages
"""
import re
from .base_studio_test import StudioCourseTest
from ...pages.studio.settings_certificates import CertificatesPage
from ...pages.studio.settings_advanced import AdvancedSettingsPage
class CertificatesTest(StudioCourseTest):
"""
Tests for settings/ce... | adoosii/edx-platform | common/test/acceptance/tests/studio/test_studio_settings_certificates.py | Python | agpl-3.0 | 12,236 | [
"VisIt"
] | bbbcd44265757fade4b5df17b8dea3384da4b7a18afce9e177e9d74c4bef156a |
"""
Wrappers for calls to Mayavi2's `mlab` module for plotting
:mod:`fatiando.mesher` objects and automating common tasks.
**Objects**
* :func:`~fatiando.vis.myv.prisms`
* :func:`~fatiando.vis.myv.polyprisms`
* :func:`~fatiando.vis.myv.points`
* :func:`~fatiando.vis.myv.tesseroids`
**Misc objects**
* :func:`~fatian... | eusoubrasileiro/fatiando | fatiando/vis/myv.py | Python | bsd-3-clause | 32,932 | [
"Mayavi",
"VTK"
] | ccdc4de09fae59ce51792de421324c0131fb82af2c405bf884d1da1217de7c84 |
# -*- coding: utf-8 -*-
# Copyright 2007-2021 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy 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... | thomasaarholt/hyperspy | hyperspy/signal.py | Python | gpl-3.0 | 252,685 | [
"Gaussian"
] | e16e2829820de5d68b646ed23c1bb8c2edff8029ee1390ca10ffef453197ba96 |
"""
=================================================
Deterministic Tracking with EuDX on Tensor Fields
=================================================
In this example we do deterministic fiber tracking on Tensor fields with EuDX
[Garyfallidis12]_.
This example requires to import example `reconst_dti.py` to run. E... | villalonreina/dipy | doc/examples/tracking_eudx_tensor.py | Python | bsd-3-clause | 3,891 | [
"VTK"
] | 3daefe1a0d10380649811857a6c408dc030f9f6dfd34a87a18f2ddd5a8679c4a |
from __future__ import (absolute_import, division, print_function)
"""
This example shows how to plot data on rectangular 2D grids
(grids that are not rectlinear in geographic or native map projection
coordinates).
An example of such a grid is the 'POP' grid which is used in
the ocean component NCAR Community Climate... | matplotlib/basemap | examples/ccsm_popgrid.py | Python | mit | 2,884 | [
"NetCDF"
] | 83e2c67ff8542b39e4eeba13b0d4cffe9fec46d1e8547102aad31fe8bd30cc66 |
#!/usr/bin/env python
"""OfficialTiming.py - Asap timing script.
Reports timing of various types of dynamics in usec/atom/timestep.
"""
from numpy import *
from asap3 import *
from asap3.md.verlet import VelocityVerlet
from asap3.md.langevin import Langevin
from asap3.md.npt import NPT
from asap3.md.velocitydistribu... | auag92/n2dm | Asap-3.8.4/Test/Timing/OfficialTiming.py | Python | mit | 5,335 | [
"ASE"
] | 311046883d662974dac71c2e1e32853c14c3b47d39e61882b00ab3c2ca7436a1 |
from sys import stderr
from time import time
from math import sqrt, ceil
from bitarray import bitarray
from random import random
from tempfile import mkdtemp
import os
import pysam as ps
start_time = time()
def tabout(*args):
"""Return a tab-delimited string from the list
"""
output = ['NA' if x is None ... | aakrosh/rdcleanr | src/utils.py | Python | mit | 1,222 | [
"pysam"
] | 3d7d559e995678f66fa899164b1868224bf7ab1745b9f7f5073fa1222998b908 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Config file that contains all config varibles."""
__author__ = 'Chong Guo <armourcy@email.com>'
__copyright__ = 'Copyright 2018, Chong Guo'
__license__ = 'GPL'
import numpy as np
import tensorflow as tf
# Debug flag, if true, will check model shape using assert in e... | Armour/Automatic-Image-Colorization | config.py | Python | gpl-3.0 | 2,790 | [
"Gaussian"
] | d13a7bdbe7a60eeac93930c73bf6e6f45e13d11a64f3e8a9f5d169f5cdefe974 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkImageConstantPad(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
v... | nagyistoce/devide | modules/vtk_basic/vtkImageConstantPad.py | Python | bsd-3-clause | 495 | [
"VTK"
] | eaa1ed6a740a49318701f8bc0c506e20eaa5ca065d0f6802bfc8e40ae98c321c |
#!/usr/bin/env python
#Dan Blankenberg
#For a set of intervals, this tool returns the same set of intervals
#with 2 additional fields: the name of a Table/Feature and the number of
#bases covered. The original intervals are repeated for each Table/Feature.
import sys, struct, optparse, os, random
from galaxy i... | dbcls/dbcls-galaxy | tools/annotation_profiler/annotation_profiler_for_interval.py | Python | mit | 19,049 | [
"Galaxy"
] | 218c73bc861fe712a25e0a0349fe304e68f97b7bcc5a709bb5cef6a108c040fb |
import os
import sys
import math
import vtk
import time
import functools
import traceback
import PythonQt
from PythonQt import QtCore, QtGui
import director.applogic as app
from director import objectmodel as om
from director import transformUtils
from director import visualization as vis
from director.transformUtils i... | manuelli/director | src/python/director/segmentation.py | Python | bsd-3-clause | 165,457 | [
"VTK"
] | dbdf5f3687196cb338314cd531f1e1c5cd07af9684b236a2e247a7e4e9d75609 |
"""
Unit Tests for assemble module.
"""
import unittest
import sys
import numpy
import argparse
import collections
import pysam
from mixemt import observe
from mixemt import assemble
from mixemt import phylotree
from mixemt import preprocess
# TODO: Write tests for the follwing functions.
# write_haplotypes(samfile,... | svohr/mixemt | mixemt/test/assemble_test.py | Python | mit | 22,073 | [
"pysam"
] | 83fd7adc8b56c669421303064e9502192ade7b3a7b02f651c634310864821135 |
# Copyright 2014 The Oppia Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... | MAKOSCAFEE/oppia | core/controllers/creator_dashboard_test.py | Python | apache-2.0 | 29,835 | [
"VisIt"
] | a87ab498c74e268204b67dad85c2c796fd3813bd2941ff80d3183d9183f15031 |
from __future__ import print_function
import os
import sys
import json
import requests
import ipdb
import xmltodict
import lxml
from pymongo import MongoClient
from tqdm import tqdm
from venomkb_builder import VenomKB
PDB_BASE_URL_PREFIX = 'http://www.rcsb.org/pdb/rest/getBlastPDB1?sequence='
PDB_BASE_URL_SUFFIX = '... | JDRomano2/VenomKB | venomkb/archive/scripts/get_protein_image_urls.py | Python | gpl-2.0 | 2,201 | [
"BLAST"
] | 0ce69758fb439ae4007007f3bf0c18e11b836d9b6a51b5237c80c38902ff385f |
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