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# Copyright (c) 2002 Myers "icepick" Carpenter
# This file is licensed under the
# GNU Lesser General Public License v2.1.
# See the file COPYING or visit http://www.gnu.org/ for details.
__revision__ = "$Id: __init__.py,v 1.5 2002/12/02 19:58:55 myers_carpenter Exp $"
from egtp.mencode.mencode import *
| zooko/egtp_new | egtp/mencode/__init__.py | Python | lgpl-2.1 | 315 | [
"VisIt"
] | 194160eb94cc570ef2534a89f9fa641acb7d08ae9a8d03b6bd4bd90e84ff3f7a |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
""" Functional tests for a :ref:`weblayer` application using the
:ref:`request handler api`.
"""
import unittest
class TestBasics(unittest.TestCase):
""" Sanity check the basics of hooking up a request handler and returning
a simple response.
"""
... | thruflo/weblayer | src/weblayer/tests/ftests/test_api.py | Python | unlicense | 29,769 | [
"Brian"
] | 37423f759fe89a892391678d97d627907df7a938585a664115b041325f6700bd |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Created on Tue Dec 13 16:24:50 2016
@author: david
"""
"""
Combinations to run:
- each main arg with
- different combinations of:
-file arrangements
- what order commands are called on a directory structure
- which of the allowable ways of specify the dire... | davidemms/OrthoFinder | tests/TestArgumentCombinations.py | Python | gpl-3.0 | 4,712 | [
"BLAST"
] | 9ea4d85b2d31ecf64e5c4a5ffc830914b8c57a4672ca485ec8dd56d45e8830b0 |
'''
Script will test the RDkit python code for conformance with the agreed format using
yapf.
For each Python file that is found in $RDBASE (excluding the build and External
directories), yapf is used with the style configuration in $RDBASE/setup.cfg.
If a change is required, the difference is printed. At the end of ... | rvianello/rdkit | Scripts/PythonFormat.py | Python | bsd-3-clause | 2,200 | [
"RDKit"
] | 5caf8ec57197c33f2cb4f90559c37979692d967a65b8ca8a9f83bfe63f14fb2c |
from importer import *
import os
import numpy as np
from datetime import datetime as dt
import re
def gen_logfile_name(plateifu):
plate, ifu = plateifu.split('-')
status_file_dir = os.path.join(
os.environ['PCAY_RESULTSDIR'], plate)
status_file = os.path.join(status_file_dir, '{}.log'.format(plate... | zpace/stellarmass_pca | pca_status.py | Python | mit | 3,229 | [
"Galaxy"
] | 0a1918c41abc68549d709f244420e2562c9413062d0258ee21f6340cc041cffa |
# Unsharp Filter Example
#
# This example shows off using the guassian filter to unsharp mask filter images.
import sensor, image, time
sensor.reset() # Initialize the camera sensor.
sensor.set_pixformat(sensor.GRAYSCALE) # or sensor.RGB565
sensor.set_framesize(sensor.QQVGA) # or sensor.QVGA (or others)
sensor.skip_f... | kwagyeman/openmv | scripts/examples/OpenMV/04-Image-Filters/unsharp_filter.py | Python | mit | 794 | [
"Gaussian"
] | 67ce55f86d2cfa1708f0ee329d20f1568f0d4d8b98d7da25173a2dd02a03ffd7 |
""" Test the FTS3Utilities"""
from DIRAC.DataManagementSystem.Client.FTS3File import FTS3File
from DIRAC import S_OK, S_ERROR
__RCSID__ = "$Id $"
import unittest
import mock
import datetime
from DIRAC.DataManagementSystem.private.FTS3Utilities import FTS3JSONDecoder, \
FTS3Serializable, \
groupFilesByTarget,... | andresailer/DIRAC | DataManagementSystem/private/test/Test_FTS3Utilities.py | Python | gpl-3.0 | 9,904 | [
"DIRAC"
] | 9673968708339cd327bfd25046cd5ab9c3f74a38c8c06e28f1fab58887819c3d |
# coding: utf-8
from __future__ import unicode_literals, division
import json
from monty.json import MontyEncoder, MontyDecoder
"""
Created on Dec 6, 2012
"""
import os
import shutil
from unittest import TestCase
import unittest
from pkg_resources import parse_version
import pymatgen
import copy
from custodian.q... | davidwaroquiers/custodian | custodian/qchem/tests/test_handlers.py | Python | mit | 45,040 | [
"pymatgen"
] | b40a15ad16832f7331b9287e94be11f8f3194dccdcf57a68cb4f22be30cfadd4 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2012 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU Lesser General Public License as published by
## the Free Software F... | andrebellafronte/stoq | stoqlib/gui/test/test_clientsalaryhistorysearch.py | Python | gpl-2.0 | 2,544 | [
"VisIt"
] | 2f1879fb9aa0a80fd05827bddbe45cc885c2bac66738e1b1c8294cbe82f9ebaa |
#!/usr/bin/env python
# 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.
#
# This program is distributed in... | jbarnoud/splitleafs | splitleafs.py | Python | gpl-3.0 | 16,657 | [
"Gromacs"
] | eb88b98b5e6dc2cd5d46fbf71ee0eb2f609738e48e631b80c5eb83f87d876f84 |
#!/bin/env python
"""
Module openmm.unit.baseunit
Contains BaseUnit class, which is a component of the Unit class.
This is part of the OpenMM molecular simulation toolkit originating from
Simbios, the NIH National Center for Physics-Based Simulation of
Biological Structures at Stanford, funded under the NIH Roadmap... | mdtraj/mdtraj | mdtraj/utils/unit/baseunit.py | Python | lgpl-2.1 | 6,929 | [
"OpenMM"
] | ad8c5c43c25f2578651647c2264a886e56de6d5f49cc4fe7a4ba8a6718fdce66 |
"""A simple filter that thresholds CitcomS Caps from input data."""
# Author: Martin Weier
#
#Copyright (C) 2006 California Institute of Technology
#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;... | geodynamics/citcoms | visual/Mayavi2/original_plugins/plugins/filter/CitcomSshowCaps.py | Python | gpl-2.0 | 4,788 | [
"Mayavi"
] | a2674e3a2d86e9acfc630ccf2c8f2c4b1f259f4cc9dfb89e0d8d098a248e2abe |
"""
Copyright [2009-2017] EMBL-European Bioinformatics Institute
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 a... | RNAcentral/rnacentral-webcode | rnacentral/portal/config/expert_databases.py | Python | apache-2.0 | 65,637 | [
"Brian"
] | 5a43a21e8a1786171d6208d6d8a7a70c799977f14ab4701130497eafa9f3e7db |
"""
Tests for discussion pages
"""
from uuid import uuid4
import pytest
from common.test.acceptance.fixtures.course import CourseFixture, XBlockFixtureDesc # lint-amnesty, pylint: disable=unused-import
from common.test.acceptance.fixtures.discussion import (
Comment,
Response,
SingleThreadViewFixture,
... | stvstnfrd/edx-platform | common/test/acceptance/tests/discussion/test_discussion.py | Python | agpl-3.0 | 18,013 | [
"VisIt"
] | 23b4043c0a3280cdfbd74ca6fd562bb9cdc3482daa40a6bcfd3cab41edee2f9b |
import logging
import sys
import pytest
import rasterio
from rasterio.profiles import default_gtiff_profile
from rasterio.vfs import parse_path, vsi_path
logging.basicConfig(stream=sys.stderr, level=logging.DEBUG)
def test_parse_path_with_vfs():
"""Correctly parse path with legacy vfs parameter"""
assert ... | brendan-ward/rasterio | tests/test_vfs.py | Python | bsd-3-clause | 2,689 | [
"NetCDF"
] | 0c96c2925457940c70c0f92103bfc38fe0f0830958af37905acd4c1ded0edeb7 |
import datetime
import time
import requests
# Last updated: 5/31/2013
HEROES = dict(
abaddon=102,
alchemist=73,
ancient_apparition=68,
antimage=1,
axe=2,
bane=3,
batrider=65,
beastmaster=38,
bloodseeker=4,
bounty_hunter=62,
brewmaster=78,
bristleback=99,
broodmother... | bryanveloso/dota2.py | dota2.py | Python | mit | 8,184 | [
"TINKER"
] | 8566022181527539e7bafe181ca76003f0fff661cd43874a134d6137e9eb0b57 |
########################################################################
# File : LocalComputingElement.py
# Author : Ricardo Graciani, A.T.
########################################################################
""" LocalComputingElement is a class to handle non-grid computing clusters
"""
import os
import stat
i... | hgiemza/DIRAC | Resources/Computing/LocalComputingElement.py | Python | gpl-3.0 | 11,212 | [
"DIRAC"
] | d56b20506918a68dadc529e9176533743327e319aee042b4124fadcdb7f8c9ce |
'''
Dts_Stripper.py
Copyright (c) 2004 - 2006 James Urquhart(j_urquhart@btinternet.com)
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 right... | pchan126/Blender_DTS_30 | DTSPython/Dts_Stripper.py | Python | mit | 1,942 | [
"VTK"
] | a3c8e1b0b6d0acb2f001b3f2a666aef57c0ab78218b7af8d51204e9649c72629 |
# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | girving/tensorflow | tensorflow/python/autograph/converters/call_trees.py | Python | apache-2.0 | 12,990 | [
"VisIt"
] | cac5c3e914efd46fac8776418ca62d9c54264e0988d995e3c2d62d9cb88badc4 |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
"""
Syntenic path assembly.
"""
import sys
import logging
from collections import defaultdict
from itertools import groupby, combinations
from more_itertools import pairwise
from jcvi.formats.blast import BlastSlow, Blast
from jcvi.formats.sizes import Sizes
from jcvi.fo... | tanghaibao/jcvi | jcvi/assembly/syntenypath.py | Python | bsd-2-clause | 16,153 | [
"BLAST"
] | ed920e80dd4130a741bc94a6b53efc14fa2f3cec58802dc3db745291f3c0d5be |
"""
"""
import os
import sys
import argparse
from roblib import bcolors, stream_blast_results
__author__ = 'Rob Edwards'
def self_bit_scores(blastf, verbose=False):
"""
Generate a dict of self:self bitscores
"""
ss = {}
for b in stream_blast_results(blastf, verbose):
if b.query == b.db:
... | linsalrob/EdwardsLab | phage_clustering/bit_score.py | Python | mit | 3,193 | [
"BLAST"
] | aa3baeafa02a826c31cd85d014e2549ecadd0ab9026d9fa89f3e43a4c2a159fc |
#!/usr/bin/env python
##############################################################################
#
# This PPXF_POPULATION_EXAMPLE routine shows how to study stellar population with
# the procedure PPXF, which implements the Penalized Pixel-Fitting (pPXF) method by
# Cappellari M., & Emsellem E., 2004, PASP, 116, 13... | zpace/SparsePak-SFH | ppxf_population_example_sdss.py | Python | mit | 8,798 | [
"Galaxy"
] | f365dee0e33042a7e5d4afda4afe3f7fe0e38d983870fd7157a071e0122ed77d |
#!/usr/bin/env python
"""
"""
import vtk
def main():
colors = vtk.vtkNamedColors()
fileName = get_program_parameters()
renderer1 = vtk.vtkRenderer()
renderer1.SetViewport(0.0, 0.0, 0.5, 1.0)
renderer2 = vtk.vtkRenderer()
renderer2.SetViewport(0.5, 0.0, 1.0, 1.0)
renderWindow = vtk.vt... | lorensen/VTKExamples | src/Python/Rendering/StripFran.py | Python | apache-2.0 | 3,123 | [
"VTK"
] | 8e6bb924cc8982773a559e367f1eeb31833bfe0181da0701257ecc683789de53 |
# Copyright 2019 Amazon.com, Inc. or its affiliates. All Rights Reserved.
# SPDX-License-Identifier: Apache-2.0
from typing import Tuple, Union
import numpy as np
from ...core.acquisition import Acquisition
from ...core.interfaces import IDifferentiable
from ..methods import WarpedBayesianQuadratureModel
class Un... | EmuKit/emukit | emukit/quadrature/acquisitions/uncertainty_sampling.py | Python | apache-2.0 | 3,512 | [
"Gaussian"
] | 488fbc5ba5eb93f696a03666ea3b37f49d790618e12183cfc3626970f952c229 |
# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | HKUST-SING/tensorflow | tensorflow/contrib/distributions/python/ops/normal.py | Python | apache-2.0 | 9,119 | [
"Gaussian"
] | d84665c7532633efba1a1998b87a6395a4c891edf5b64278921c34d9f60eaa90 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | skosukhin/spack | var/spack/repos/builtin/packages/r-affycompatible/package.py | Python | lgpl-2.1 | 2,149 | [
"Bioconductor"
] | 73d077e6692b1d850414f7b449b898eb025613807002c17470f85976c026a8a0 |
import subprocess
import logging
import csv
import os
class SequenceSearchResult:
QUERY_FROM_FIELD = 'query_from'
QUERY_TO_FIELD = 'query_to'
QUERY_LENGTH_FIELD = 'query_length'
HIT_FROM_FIELD = 'hit_from'
HIT_TO_FIELD = 'hit_to'
ALIGNMENT_LENGTH_FIELD = 'alignment_length'
ALIGNMENT_BIT_SCO... | geronimp/graftM | graftm/sequence_search_results.py | Python | gpl-3.0 | 8,078 | [
"BLAST"
] | b2873be5abef731c7971271c6e33bbeaee204d0a7cab33ef64c637443270da9d |
#
# 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 | samples/lbf.py | Python | gpl-3.0 | 2,503 | [
"ESPResSo"
] | 6454c8dba01d16d3671b3dfb85dcc0d756cf0de231f7fcfa43bb79e03352e5bd |
"""
This module implements all the functions to communicate with other Python
modules (PIL, matplotlib, mayavi, etc.)
"""
import numpy as np
def PIL_to_npimage(im):
"""Transforms a PIL/Pillow image into a numpy RGB(A) image.
Actually all this do is returning numpy.array(im)."""
return np.array(im)
# ... | kerstin/moviepy | moviepy/video/io/bindings.py | Python | mit | 1,085 | [
"Mayavi"
] | 27584bd594f17c8beb8fe1e655ea66d268fae8129a18e2aab98a1d017265e327 |
# -*- coding: utf-8 -*-
# Copyright (c) 2004-2014 Alterra, Wageningen-UR
# Allard de Wit (allard.dewit@wur.nl), April 2014
from __future__ import print_function
import datetime
from copy import deepcopy
import numpy as np
from ..pydispatch import dispatcher
from ..traitlets import Float, Int, Instance, Enum, Unicode,... | jajberni/pcse_web | main/pcse/soil/waterbalance.py | Python | apache-2.0 | 60,436 | [
"Gaussian"
] | f0215f1db3f9fdf69591fe16f0297e2caab237f86dd224c7506fa56a2a8d6f13 |
########################################################################
# File : InstallTools.py
# Author : Ricardo Graciani
########################################################################
"""
Collection of Tools for installation of DIRAC components:
MySQL, DB's, Services's, Agents
It only makes use of ... | coberger/DIRAC | Core/Utilities/InstallTools.py | Python | gpl-3.0 | 88,582 | [
"DIRAC"
] | e24981597d8a7bab675ef25a9d6a7dd06087efd407c63cc9ad5ede1a625fc795 |
# 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... | fedepad/espressopp | src/interaction/DihedralPotential.py | Python | gpl-3.0 | 2,660 | [
"ESPResSo"
] | 0ec9fca69530bad13c1269603e4518e90366847be472390555add67eb9233156 |
"""
SkCode AST tree builder code.
"""
from collections import defaultdict
from gettext import gettext as _
from .etree import (
RootTreeNode,
TreeNode
)
from .tags import (
DEFAULT_RECOGNIZED_TAGS_LIST,
build_recognized_tags_dict,
NewlineTreeNode,
TextTreeNode
)
from .tokenizer import (
to... | TamiaLab/PySkCode | skcode/treebuilder.py | Python | agpl-3.0 | 11,686 | [
"VisIt"
] | e0b3bb05f3648eaf6444541a7921d8faec87c060c17fa8d04c8d6bb7f9a16d1e |
# $HeadURL: $
''' DowntimeCommand module
'''
import urllib2
from datetime import datetime, timedelta
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Core.LCG.GOCDBClient import GOCDBClient
from DIRAC.ConfigurationSystem.Client... | avedaee/DIRAC | ResourceStatusSystem/Command/DowntimeCommand.py | Python | gpl-3.0 | 9,464 | [
"DIRAC"
] | 4b9ada2d69deb40594d27dde052f0851ddfea8c7b020f6e0edc510cbac39f83f |
import types
from DIRAC.Core.Utilities import Time
class DBUtils:
def __init__( self, db, setup ):
self._acDB = db
self._setup = setup
def _retrieveBucketedData( self,
typeName,
startTime,
endTime,
... | avedaee/DIRAC | AccountingSystem/private/DBUtils.py | Python | gpl-3.0 | 12,101 | [
"DIRAC"
] | d3969d2fde62c13279762b11388c59daa7454a128753c306ee814f3fc60cc12d |
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at https://mozilla.org/MPL/2.0/.
""" This input field is prepared to receive sisl objects that are plotables """
from pathlib import Path
import sisl
fr... | zerothi/sisl | sisl/viz/input_fields/sisl_obj.py | Python | mpl-2.0 | 7,638 | [
"Gaussian"
] | 07560893088e47452aadb845925da26d7a8117c0bc34739826b892c21417d7bc |
# Copyright (C) 2015
# Jakub Krajniak (jkrajniak at gmail.com)
# 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 softw... | kkreis/espressopp | src/tools/topology_helper.py | Python | gpl-3.0 | 12,558 | [
"ESPResSo",
"Gromacs"
] | bb5b4868df24d36e81c967a4195278284551bdb6c0b5284ef5b4c335f4049539 |
import ast
import contextlib
import io
import os.path
import types
import pytest
import ipytest
from ipytest._impl import RewriteAssertTransformer
@pytest.mark.parametrize(
"spec",
[
# any key that maps to true is expected to be removed by clean_tests
{"test": True, "foo": False},
{... | chmp/ipytest | tests/test_ipytest.py | Python | mit | 2,393 | [
"VisIt"
] | d5bda60b37bf5a8cf731dd3834c83044f4931fcb75923a9b9a0c0e4ddf5f5e5d |
Blocker = object()
Start = False
End = object()
class Path(dict):
@classmethod
def determine_path(cls, field, width, height):
path = cls()
path.width = width
path.height = height
path.ends = set()
path.starts = []
cells = []
for y in range(height):
... | nicememory/pie | pyglet/contrib/currently-broken/spryte/dtd/path.py | Python | apache-2.0 | 6,345 | [
"VisIt"
] | cb22df3b7c2f2ee159eb21bd0e206dd31f2bfdd160a3c7bc567b5cae6386cdb4 |
# neigh_dict and nn_dict are the same thing.
# Need to combine/change variables at some point
# In[251]:
from __future__ import division, absolute_import
import astropy.stats
import glob
import math
import matplotlib.pyplot as plt
from matplotlib import ticker
from matplotlib.ticker import FormatStrFormatter
impor... | hrichstein/Stellar_mass_env_Density | Codes/Scripts/centrals_plotting.py | Python | mit | 51,428 | [
"Galaxy"
] | 2b662d0b3d17100f427609def4135d6a95caa22a72af4303a554ebe60ef180c4 |
import numpy as np
__author__ = 'christopher'
def has_adp(atoms):
for a in ['adps', 'adp']:
if a in atoms.info.keys():
return atoms.info[a]
return None
class ADP:
def __init__(self, atoms, adps=None, adp_momenta=None,
adp_equivalency=None,
fixed_adp... | CJ-Wright/pyIID | pyiid/adp.py | Python | bsd-3-clause | 5,607 | [
"ASE"
] | 06ffe597dc9ef1ed1b3d06a54bdb6f009d79f743db1f240fa971809ce487abda |
#
# Copyright (C) 2010-2018 The ESPResSo project
# Copyright (C) 2002,2003,2004,2005,2006,2007,2008,2009,2010
# Max-Planck-Institute for Polymer Research, Theory Group
#
# 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... | hmenke/espresso | doc/tutorials/02-charged_system/scripts/nacl_units_confined_vis.py | Python | gpl-3.0 | 5,420 | [
"ESPResSo"
] | d698c66260da2cb190e4e035a4e4de0576d811affbd1cd02ca1e3af015a65206 |
#!/usr/bin/env python
#
# @file GeneralFunctions.py
# @brief class to create general functions
# @author Frank Bergmann
# @author Sarah Keating
#
# <!--------------------------------------------------------------------------
#
# Copyright (c) 2013-2015 by the California Institute of Technology
# (California, USA... | hovo1990/deviser | generator/code_files/cpp_functions/GeneralFunctions.py | Python | lgpl-2.1 | 53,640 | [
"VisIt"
] | 187baa5fec0fec4f73f0f74758b80f41d9001ed7eefe570c19f2ebc9457b57f3 |
from . import speg_visitor as sv
from . import speg_parser as sp
from . import rd_parser as rd
from . import exceptions as ex
class SPEG(object):
def __init__(self):
self.parser = sp.SimplePegParser()
self.visitor = sv.SimplePegActionsVisitor(SimplePegActions())
self.speg_parser = None
... | SimplePEG/Python | simplepeg/speg.py | Python | mit | 3,909 | [
"VisIt"
] | bcf727c610f4369b2bc01c6a6165ae15c123a0dbc5f6055605fe9a835f942209 |
#!/usr/bin/env python3
import argparse
import sys
import os
import pysam
import re
from pyfastaq import *
import assembly_tools.fill_gaps_using_reference
class Error (Exception): pass
def make_fasta_of_gap_flanks(fasta_in, flanking_bases, fasta_out, gaps):
'''Makes a fasta file of the sequences flanking the gap... | martinghunt/Assembly_tools | assembly_tools/fill_gaps_using_reference/helper.py | Python | gpl-3.0 | 3,048 | [
"pysam"
] | 28467004dc2e0615db91ea2441717683879d227f846269c99033117b2ab76590 |
"""
Getting started with Captum - Titanic Data Analysis
"""
# Initial imports
import numpy as np
import torch
from captum.attr import IntegratedGradients
from captum.attr import LayerConductance
from captum.attr import NeuronConductance
import matplotlib.pyplot as plt
import pandas as pd
from scipy import stats
import ... | mlflow/mlflow | examples/pytorch/CaptumExample/Titanic_Captum_Interpret.py | Python | apache-2.0 | 14,395 | [
"NEURON"
] | f84aed658c4312dc7bbea97780fae48535405ca7cb105354225d1f2b3da3b0ff |
#!/usr/bin/env python
# This script compares the two variants of the Tsodyks/Markram synapse in NEST.
import cynest as nest
import cynest.voltage_trace
nest.ResetKernel()
#Parameter set for depression
dep_params={"U":0.67, "weight":250.}
# parameter set for facilitation
fac_params={"U":0.1, "tau_fac":1000.,"tau_re... | gewaltig/cython-neuron | cynest/examples/test_tsodyks2_synapse.py | Python | gpl-2.0 | 1,367 | [
"NEURON"
] | 45e33571f02fc9624cb3d6a3001350c067cf9ee95a7d90a521a1def65fccba55 |
# -*- 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) 2006-2020 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under t... | MDAnalysis/mdanalysis | package/MDAnalysis/analysis/helix_analysis.py | Python | gpl-2.0 | 19,741 | [
"MDAnalysis"
] | 4aa90aed5abdc24be28ed59d196873a43e10012d7d0a33c1ed3e88722ff5b5f0 |
#
# Copyright 2016 The BigDL Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in ... | intel-analytics/BigDL | python/orca/example/data/spark_pandas.py | Python | apache-2.0 | 1,851 | [
"ORCA"
] | 9476231189a1dff01fc0892edb8049cae6349e89d3f9a9899653f512a7f5dd49 |
#
#
# Tutorial Yambo School. Lausanne, 24-28 April 2017
# Convergence GW on hexagonal BN
# Alejandro Molina-Sanchez & Henrique P. C. Miranda
#
#
from __future__ import print_function
import sys
from yambopy import *
from qepy import *
from schedulerpy import *
import argparse
yambo = 'yambo'
p2y = 'p2y'
pre... | palful/yambopy | tutorial/bn/gw_conv_bn.py | Python | bsd-3-clause | 10,513 | [
"Yambo"
] | e937655d83a0b095bdb9e91a0b34b75d50e34e17c3495b7f1ff965e61069baa9 |
from __future__ import print_function
import os
import time
import numpy as np
from copy import deepcopy as copy
from collections import OrderedDict
from .tensor import VOIGT, I9, inv, dot
from .environ import environ
from .tensor import array_rep, unrotate, rotate
from .material import Material
from .misc import is_s... | matmodlab/matmodlab2 | matmodlab2/core/matmodlab.py | Python | bsd-3-clause | 40,637 | [
"ParaView"
] | a7faafc196e2952bbb8b54b7f33bed72bbac1f976fa3a6e876659c52eb895f9a |
# -*- coding: utf-8 -*-
"""
This file contains the Qudi Logic to control Nuclear Operations.
Qudi 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 ve... | childresslab/MicrocavityExp1 | logic/nuclear_operations_logic.py | Python | gpl-3.0 | 42,465 | [
"Gaussian"
] | 004b3dd74609f40f087258111529ea2dde2407cd68f93777adb0b6bd7745ebed |
from collections import OrderedDict
import decimal, datetime
import pickle
import logging
import json
import requests
from django.core.cache import cache
logger = logging.getLogger("foo")
ch = logging.StreamHandler()
ch.setLevel(logging.DEBUG)
dec = decimal.Decimal
# create formatter
formatter = logging.Formatter('%(a... | skoczen/skoczen | project/apps/manual/utils.py | Python | bsd-2-clause | 10,880 | [
"VisIt"
] | 8eab8497637d716a0c2d910a165e35ce5febf4092933397e46ccfc9c53aebaff |
# This file is part of Merlin.
# Merlin is the Copyright (C)2008,2009,2010 of Robin K. Hansen, Elliot Rosemarine, Andreas Jacobsen.
# Individual portions may be copyright by individual contributors, and
# are included in this collective work with permission of the copyright
# owners.
# This program is free software; ... | ellonweb/merlin | Hooks/lookup.py | Python | gpl-2.0 | 3,072 | [
"Galaxy"
] | 1298c7b47d8b07542b9b37493917970ac5afede14214af9f8d3163f6b84e687c |
from __future__ import absolute_import, division, print_function
from itertools import chain
from .utils_test import add, inc # noqa: F401
def ishashable(x):
""" Is x hashable?
Examples
--------
>>> ishashable(1)
True
>>> ishashable([1])
False
"""
try:
hash(x)
... | cowlicks/dask | dask/core.py | Python | bsd-3-clause | 12,037 | [
"VisIt"
] | e33d1ffec7a0db6f7926d7dcf760dc8f47b9946b8e31d23a07e3542bc04f34a6 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2009 Brian G. Matherly
# Copyright (C) 2009 Gary Burton
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publis... | SNoiraud/gramps | gramps/gui/dbman.py | Python | gpl-2.0 | 45,607 | [
"Brian"
] | a02eb47e95f326009efb7923bfd1d8d3fe9a9ac6d435852d971a8c09ec0c7a3f |
#!/usr/bin/env python
"""
This script rotates circular sequences and makes them to start from specific positions in output FASTA files. It also circularises every sequence
and save it in a GFA file if a filename is given to argument --gfa/-g. This script is useful for improving complete genome assemblies as well as
rea... | wanyuac/BINF_toolkit | rotateSeq.py | Python | gpl-3.0 | 5,654 | [
"Biopython"
] | 06d3972b5761b4a4b109a59fe0ab89205440347f5e7005cdf062d1c2dfb8824e |
import os
import errno
import codecs
from tao.settings import MODULE_INDICES
from tao.xml_util import xml_parse
def create_file(dir_path, filename, filenames_to_contents):
file_path = os.path.join(dir_path, filename)
mkdir_p(os.path.dirname(file_path))
with codecs.open(file_path, 'w', encoding='utf-8'... | IntersectAustralia/asvo-tao | web/tao/tests/helper.py | Python | gpl-3.0 | 3,685 | [
"Galaxy"
] | 4661dfda659df89ddac51ca8fd8d02ecd20710fac8dd3a4ca2f60db563d578c3 |
from __future__ import division, absolute_import, print_function
import warnings
import numpy as np
from numpy.testing import (
assert_, assert_raises, assert_equal, assert_warns,
assert_no_warnings, assert_array_equal, assert_array_almost_equal,
suppress_warnings
)
from numpy import ra... | jorisvandenbossche/numpy | numpy/random/tests/test_random.py | Python | bsd-3-clause | 66,842 | [
"Gaussian"
] | ea1fe40ce4f9e4fd55ab6b5ff0950ce30253aa411d7ed83d5e5994818ae80007 |
from pyhamimports import *
from gui_utils import *
from spectrum import *
class Eyecheck(QMainWindow):
def __init__(self, specObj, options):
super().__init__()
# Store Input Variables
self.specObj = specObj # The Spectrum object created in the pyhammer script
self.options = ... | BU-hammerTeam/PyHammer | eyecheck.py | Python | mit | 70,235 | [
"Galaxy"
] | e9a29c4d8095b1c6363b8b5f2f4a4eff5b06f6f7f5e44150d63fd2a2073355db |
"""
Routines for transforming FERC Form 1 data before loading into the PUDL DB.
This module provides a variety of functions that are used in cleaning up the FERC Form 1
data prior to loading into our database. This includes adopting standardized units and
column names, standardizing the formatting of some string value... | catalyst-cooperative/pudl | src/pudl/transform/ferc1.py | Python | mit | 103,623 | [
"BLAST"
] | 967b64130d65a6c0bf0386767bcd17daa1dea6392de3c1245279145fcb6382f7 |
#!/usr/bin/env python
import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.optim as optim
from torch.autograd import Variable
from random import shuffle
__all__ = ['ResidualBlock', 'ResNet', 'StackRegressive']
torch.set_default_tensor_type('torch.DoubleTensor')
# 3x3 Convolution
def conv3x... | lakehanne/ensenso | ensenso_detect/manikin/model.py | Python | mit | 7,606 | [
"NEURON"
] | b19777cd09b7a3cd857f08398ce1f7ea915d3ac0709a17afcb15abdb099a6254 |
# -*- coding: utf-8 -*-
# Copyright (C) 2003-2007 CAMP
# Copyright (C) 2007-2008 CAMd
# Please see the accompanying LICENSE file for further information.
"""This module defines a PAW-class.
The central object that glues everything together!"""
import numpy as np
from ase.units import Bohr, Hartree
from ase.dft.kpo... | robwarm/gpaw-symm | gpaw/paw.py | Python | gpl-3.0 | 37,964 | [
"ASE",
"GPAW"
] | e2c74a61b6f6b3acc748de0e622f5993c2888681dc4903d14d02ed955a57e906 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
Created on Mar 18, 2012
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "S... | matk86/pymatgen | pymatgen/apps/borg/tests/test_hive.py | Python | mit | 4,645 | [
"pymatgen"
] | 9b7408593fa7edac95d113d391ecf51c5f4b9fcdacecc3f8ecabb2374e99833c |
#
# -*- coding: utf-8 -*-
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2006 Donald N. Allingham
# Copyright (C) 2007-2009 Brian G. Matherly
# Copyright (C) 2008 Raphael Ackermann
# 2002-2003 Donald A. Peterson
# 2003 Alex Roitman
# 200... | arunkgupta/gramps | gramps/plugins/docgen/latexdoc.py | Python | gpl-2.0 | 47,677 | [
"Brian"
] | e7170347285128cfb82e7abf8ace8728bc38fb73e717d2a03fb65d966589950b |
#!/usr/bin/python
# (C) 2013, Markus Wildi, markus.wildi@bluewin.ch
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2, or (at your option)
# any later version.
#
# Thi... | jstrobl/rts2 | scripts/rts2saf/rts2saf/temperaturemodel.py | Python | lgpl-3.0 | 4,927 | [
"VisIt"
] | eaf77bc663c16f5ece233a468351e07bfad1526036bec8402dca07be9cfebc6f |
# Version: 0.18
"""The Versioneer - like a rocketeer, but for versions.
The Versioneer
==============
* like a rocketeer, but for versions!
* https://github.com/warner/python-versioneer
* Brian Warner
* License: Public Domain
* Compatible With: python2.6, 2.7, 3.2, 3.3, 3.4, 3.5, 3.6, and pypy
* [![Latest Version]
(... | spencerkclark/aospy | versioneer.py | Python | apache-2.0 | 68,612 | [
"Brian"
] | 9bb36a97747ab81f217208e39a61ebb2c806a0b316572e6ef513d57d4409898f |
import tensorflow as tf
import numpy as np
import autoencoder.Utils
class VariationalAutoencoder(object):
def __init__(self, n_input, n_hidden, optimizer = tf.train.AdamOptimizer()):
self.n_input = n_input
self.n_hidden = n_hidden
network_weights = self._initialize_weights()
self.... | beomyeol/models | autoencoder/autoencoder_models/VariationalAutoencoder.py | Python | apache-2.0 | 2,995 | [
"Gaussian"
] | 9d27e335d25721f1f99dd09ea691b2d3fbd7f914071e308e97103576f28437b8 |
'''
Gaussian smoothing with Python and OpenCV.
'''
import cv2
import numpy as np
import math
import matplotlib.pyplot as plt
def gaussian_smooth2(img, sigma):
'''
Do gaussian smoothing with sigma.
Returns the smoothed image.
'''
# determine the length of the filter
filter_length = math.ceil (sigma * 5)
# make ... | Vkomini/KU-Leuven | Computer Vision/Assignments/Assign1/smoothing2.py | Python | apache-2.0 | 1,011 | [
"Gaussian"
] | 0ce039cbb1a2fd5dd03ad79d0a43d9db484b5de81e1a761c1c15d03e40bb3130 |
from __future__ import absolute_import
from __future__ import print_function
from .base import NodeTransformer
from .. import nodes
#==============================================================================#
class RulesetChain(object):
def __init__(self, selectors, statements):
assert isinstance(sele... | colossalbit/cssypy | cssypy/visitors/flatteners.py | Python | bsd-3-clause | 5,209 | [
"VisIt"
] | e6d98d533d3e28ad47e8d5caa38b49aea0926875fd8902711c8b8e2a785d0161 |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
'''
A simple example to run CASSCF calculation.
'''
import pyscf
mol = pyscf.M(
atom = 'O 0 0 0; O 0 0 1.2',
basis = 'ccpvdz',
spin = 2)
myhf = mol.RHF().run()
# 6 orbitals, 8 electrons
mycas = myhf.CASSCF(6, 8).run()
#
# Note this m... | gkc1000/pyscf | examples/mcscf/00-simple_casscf.py | Python | apache-2.0 | 633 | [
"PySCF"
] | c5df4e10767c70909c3128828d7f27ffa787815d654f9df3be7f255044de24c2 |
# coding: utf-8
"""
Vericred API
Vericred's API allows you to search for Health Plans that a specific doctor
accepts.
## Getting Started
Visit our [Developer Portal](https://developers.vericred.com) to
create an account.
Once you have created an account, you can create one Application for
Production and an... | vericred/vericred-python | vericred_client/models/provider.py | Python | apache-2.0 | 27,378 | [
"VisIt"
] | 0ea16acc83e477083d2c91e3a6b375798a91ad666f8652f311e05ca04c782156 |
from plugin import Plugin
import discord
import logging
import urllib.request
import os
import uuid
import styrobot
import commands
class Meme(Plugin):
async def initialize(self, bot):
self.tag = 'meme'
self.shortTag = 'meme'
self.defaultParser = commands.CommandRegistry.PARAM_PARSER_ALL
... | StyrofoamLaser/StyroBotPy | styrobot/plugins/meme.py | Python | mit | 44,182 | [
"Brian"
] | 22ff54d8f9eda9a74aebad8f0f5e77889525c48369f9e245548e4190de4c2371 |
#! /usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless requi... | googleapis/python-recommendations-ai | scripts/fixup_recommendationengine_v1beta1_keywords.py | Python | apache-2.0 | 7,056 | [
"VisIt"
] | 7699788e72855192fdf2b35c838cc5fd8eb7b79f605a56ecd25bbaf69536f449 |
from setuptools import setup
setup(
name = "electronfactors",
version = "0.1.5",
author = "Simon Biggs",
author_email = "mail@simonbiggs.net",
description = "Predict electron insert factors",
long_description = """Predict electron insert factors to an uncertainty approaching measurement using t... | SimonBiggs/electronfactors | setup.py | Python | agpl-3.0 | 1,178 | [
"VisIt"
] | 898302884262e9be2ac1e9f471e9348d39c103a0930077927fa270b7af5daaea |
# 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... | govarguz/espressopp | src/esutil/NormalVariate.py | Python | gpl-3.0 | 1,741 | [
"ESPResSo"
] | a5222ef920a1ca2a86dca98631f911205cd60e6873eab60a2290eddddf6f7de0 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import numpy as np
import warnings
import functools
from monty.json import MSONable
from pymatgen.electronic_structure.core import Spin, Orbital
from pymatgen.core.periodic_table import get_el_sp
from pymatgen.... | montoyjh/pymatgen | pymatgen/electronic_structure/dos.py | Python | mit | 37,136 | [
"DIRAC",
"Gaussian",
"VASP",
"pymatgen"
] | 6f36fb7bc1bef011da10812fa3106d5ca18a52d286badc2fd1ece8383c288c65 |
from __future__ import print_function
from itertools import islice, product
import logging
import MDAnalysis as md
import math
import random
import numpy as np
import pandas as pd
import plotly
import plotly.graph_objs as go
import subprocess
import scipy
import scipy.stats
import string
import time
import setting... | mikkkee/Bubble | bubble.py | Python | mit | 44,991 | [
"Avogadro",
"LAMMPS",
"MDAnalysis"
] | bd7309c821ad9383fe6a56b82952b0fb87e626f256ad7cfdfac3100dc6535e97 |
#!/usr/bin/env python
"""
Convert from interval file to interval index file.
usage: %prog <options> in_file out_file
-c, --chr-col: chromosome column, default=1
-s, --start-col: start column, default=2
-e, --end-col: end column, default=3
"""
from __future__ import division
import optparse
from galaxy i... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py | Python | gpl-3.0 | 1,532 | [
"Galaxy"
] | 674e2f572fffd16df3b709a3ce7157ccb5f522f9c62ae3c4b714eb89336955e9 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
# transformations.py
# Copyright (c) 2006, Christoph Gohlke
# Copyright (c) 2006-2010, The Regents of the University of California
# All rights reserved.
#
# Redistribution and use in source... | MDAnalysis/mdanalysis | package/MDAnalysis/lib/transformations.py | Python | gpl-2.0 | 60,776 | [
"MDAnalysis"
] | 70d05b38071f8026ea8b7d1124b9837817e5d54fded376c33740733441f1b22d |
#!/usr/bin/env python
# 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
# di... | dmcc/PyStanfordDependencies | StanfordDependencies/__init__.py | Python | apache-2.0 | 6,989 | [
"MOOSE"
] | 44eb769b5a6fceb12a683ee68fdbc9c452f2bb7f7088d877a5f5b96cbd782202 |
import time
class TestBlogPage(object):
def test_blog_page_home(self, browser, site_url):
browser.visit(site_url + '/blog/')
assert browser.status_code == 200
assert browser.is_text_present('Blog')
def test_blog_page_click_search(self, browser, site_url):
browser.visit(site_u... | APSL/puput | tests/functional/test_blog_page.py | Python | mit | 781 | [
"VisIt"
] | 8afa2b10675bd7dea2f4c320927e85bc1d67ae82688c6b6f2f1ce390b4de3a2c |
#
# Copyright (C) 2013,2014,2015,2016 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)... | lahnerml/espresso | samples/python/p3m.py | Python | gpl-3.0 | 6,384 | [
"ESPResSo"
] | 0a8adcc1798f7a0b2614f6912b0a93010a5e4dce9f01e04b522d62a054b292f8 |
r"""OS routines for NT or Posix depending on what system we're on.
This exports:
- all functions from posix, nt or ce, e.g. unlink, stat, etc.
- os.path is either posixpath or ntpath
- os.name is either 'posix', 'nt' or 'ce'.
- os.curdir is a string representing the current directory ('.' or ':')
- os.pardir... | ms-iot/python | cpython/Lib/os.py | Python | bsd-3-clause | 36,313 | [
"VisIt"
] | ffc581ca4370d475264c67d88825f99b422ce838123a3c92811a7405aa4dacc5 |
#!/usr/local/bin/python
# -*- coding: utf-8 -*-
from addict import Dict
# from data.pokemon_data import pokemon
from lemonyellow.core.helpers import namedtuple_with_defaults
# Effects:
GetBike = "Get Bike"
RideBike = "Where do you want to go?"
BoostMaxPP20Percent = "What it says, m'boy."
LevelUp = "LEV... | itsthejoker/Pokemon-Homage | lemonyellow/data/items.py | Python | mit | 16,605 | [
"Amber"
] | f469df9d85e9c222dc2a2989674ca96d39a0dcc688b34d87817d1dcfb2f1763b |
from common.exceptions import TaskListError
import logging
log = logging.getLogger(__name__)
class TaskList(object):
def __init__(self):
self.tasks = set()
self.tasks_completed = []
def load(self, function, manifest, *args):
getattr(manifest.modules['provider'], function)(self.tasks, manifest, *args)
for ... | brianspeir/Vanilla | vendor/bootstrap-vz/base/tasklist.py | Python | bsd-3-clause | 3,837 | [
"VisIt"
] | dd1452b31a5691a60575603cc18dcbf699c68c54cee4e2536414655346fe4139 |
"""
Data-driven tests for reads
"""
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import collections
import ga4gh.backend as backend
import ga4gh.datamodel as datamodel
import ga4gh.datamodel.datasets as datasets
import ga4gh.datamodel.reads as reads
imp... | ekalosak/server | tests/datadriven/test_reads.py | Python | apache-2.0 | 16,772 | [
"pysam"
] | 385ec16ae035c979635f2e6e1a6c289cce5a4bb24921841b9fe3c3f87155c043 |
#####################################################################
# #
# Refinement Script with SHELX and CCP4/REFMAC5 #
# #
# Copyright: Molecular Images 2005 ... | mifit/miexpert | mi_refine.py | Python | gpl-3.0 | 134,553 | [
"CRYSTAL"
] | 1f7066e547411f38e30c4a946971b6e224859486c6e9e110c8c7debc6b66b0a0 |
# Copyright (C) 2018, Bastian Eicher
# See the README file for details, or visit http://0install.net.
import os
from os.path import join
from xml.dom import minidom, Node
from repo import cmd, registry, merge, incoming, formatting
from repo.cmd import update
def handle(args):
if not cmd.find_config(missing_ok = T... | 0install/0repo | repo/cmd/modify.py | Python | lgpl-2.1 | 1,536 | [
"VisIt"
] | a79f9739a72759998a423ccbac952a88af00049bfea8e3107f6bffc54fdcf646 |
"""
Acceptance tests for Content Libraries in Studio
"""
from ddt import ddt, data
from nose.plugins.attrib import attr
from flaky import flaky
from .base_studio_test import StudioLibraryTest
from ...fixtures.course import XBlockFixtureDesc
from ...pages.studio.auto_auth import AutoAuthPage
from ...pages.studio.utils ... | tiagochiavericosta/edx-platform | common/test/acceptance/tests/studio/test_studio_library.py | Python | agpl-3.0 | 27,414 | [
"VisIt"
] | 2dedc7f9b8eba057c7041569deade3cb78dcfbf1c80ece79b240e4b8330341e7 |
# -*- coding: utf-8 -*-
"""Van der Waals density functional.
This module implements the Dion-Rydberg-Schröder-Langreth-Lundqvist
XC-functional. There are two implementations:
1. A simlpe real-space double sum.
2. A more efficient FFT implementation based on the Román-Péres-Soler paper.
"""
import os
import sys
i... | qsnake/gpaw | gpaw/xc/vdw.py | Python | gpl-3.0 | 25,531 | [
"GPAW"
] | d16c5e4365800b157e87967e463de3aab76a24830d8dd918b9910e420e95800e |
__version__ = '0.8.0'
import kivy
from kivy.utils import platform
from kivy.app import App
from kivy.uix.floatlayout import FloatLayout
from kivy.uix.button import Button
from kivy.uix.popup import Popup
from kivy.uix.label import Label
from kivy.uix.image import Image
from kivy.core.audio import SoundLoader
from kivy.... | ROAND/guessthehero | .buildozer/android/app/main.py | Python | gpl-3.0 | 13,356 | [
"TINKER"
] | ced9ee0ac01edf4ceed1283dc97004215829206f9b0dbacfb1057bd6fe6039c0 |
# -*- Mode: Python; coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2012 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU Lesser General Public License as published by
## the F... | andrebellafronte/stoq | stoqlib/gui/utils/openbrowser.py | Python | gpl-2.0 | 1,114 | [
"VisIt"
] | d129a3d3218a2c93c70565f720629f07e37cb73b7f005c5436f2280b2bc47984 |
"""
Tests for the WebAppTest class.
"""
import os
from unittest import expectedFailure
from bok_choy.web_app_test import WebAppTest
from .pages import ImagePage
class ScreenshotAssertTest(WebAppTest):
"""
Test the integration with needle and its screenshot assertion capability.
"""
def test_needle_sc... | drptbl/bok-choy | tests/test_webapptest.py | Python | apache-2.0 | 1,392 | [
"VisIt"
] | 0da1e02a0246fa973e38a489f55295110f64bd822aca995978fdb22394f2fef4 |
#!/usr/bin/python
# coding=utf-8
import os
import os.path
import sqlite3
import sys
import unicodedata
ATOM_NS = '{http://www.w3.org/2005/Atom}'
G_NS = '{http://schemas.google.com/g/2005}'
GC_NS = '{http://schemas.google.com/contact/2008}'
cacheroot = os.path.expanduser('~/.cache/simplegab/')
database = cacheroot + '... | mh21/simplegab | simplegab.py | Python | mit | 3,503 | [
"VisIt"
] | 10860311d17dd80a43d2c60f65dc761bfe0edb4ccff21c3bff7e2894adb58281 |
#!/usr/bin/env python
# -*- coding: latin-1 -*-
#
# Copyright 2018-2021 Blaise Frederick
#
# 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/LICEN... | bbfrederick/rapidtide | rapidtide/workflows/happy_legacy.py | Python | apache-2.0 | 113,373 | [
"Gaussian"
] | 144d43ce148e4b30e66e115fc8e54c4905b3676a31679acf059e76918793ff12 |
'''
The Las Vegas board game consists of:
* Six casinos, one for each dice value
* Eight six-sided dice per player
* Cash cards:
$60,000 (5)
$70,000 (5)
$80,000 (5)
$90,000 (5)
$10,000 (6)
$40,000 (6)
$50,000 (6)
$20,000 (8)
$30,00... | olimoth/vegas | game.py | Python | gpl-3.0 | 4,142 | [
"CASINO"
] | 901468308c3b394eba36dfbe3fb14464dda4f62af8c3680190b5b7aa22149e70 |
# coding: utf-8
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Interfaces to perform image registrations and to apply the resulting
displacement maps to images and points.
"""
from __future__ import absolute_import
import os.path as op
import re... | iglpdc/nipype | nipype/interfaces/elastix/registration.py | Python | bsd-3-clause | 8,430 | [
"VTK"
] | 0411d0ad71f52c2f6a02722287196636eb1bfec9460f5facaec27cf145d64c02 |
#! /usr/bin/env python
#
# This file is distributed as part of the Wannier90 code and
# under the terms of the GNU General Public License. See the
# file `LICENSE' in the root directory of the Wannier90
# distribution, or http://www.gnu.org/copyleft/gpl.txt
#
# The webpage of the Wannier90 code is www.wannier.org
#
# T... | greschd/wannier90 | utility/k_mapper.py | Python | gpl-2.0 | 2,939 | [
"Wannier90",
"Yambo"
] | d1593ce853ba24cb07f94dbaab4e6c3abc7802990aa2de55cb9e42e5c39822af |
import json
import logging
import random
import traceback
import time
import urllib
import urllib2
from flask import Flask
from flask import request
from google.appengine.api import memcache
import api
from api import PickledThing
app = Flask(__name__)
app.config['DEBUG'] = True
# Note: We don't need to call run() ... | jackieleng/vierchanbot | main.py | Python | mit | 7,203 | [
"MOE"
] | 62d161adaa6e38e7aa15c61cc268a6dfa171738a8f799f54c07d3d7b270121f7 |
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