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"""
E2E tests for the LMS.
"""
from unittest import skip
from bok_choy.web_app_test import WebAppTest
from bok_choy.promise import EmptyPromise, fulfill_before
from .helpers import UniqueCourseTest, load_data_str
from ..pages.studio.auto_auth import AutoAuthPage
from ..pages.lms.login import LoginPage
from ..pages.l... | pku9104038/edx-platform | common/test/acceptance/tests/test_lms.py | Python | agpl-3.0 | 9,252 | [
"VisIt"
] | 34eed88aac1e9b854c3d8647bf97d865bb408955c06cf904e1d3a9a0e20dabfe |
"""
GSIServer - Contributed by Ivan R. Judson <judson@mcs.anl.gov>
################################################################################
#
# SOAPpy - Cayce Ullman (cayce@actzero.com)
# Brian Matthews (blm@actzero.com)
# Gregory Warnes (Gregory.R.Warnes@Pfizer.com)
# ... | jjdmol/LOFAR | LTA/LTAIngest/SOAPpy-0.12.0/SOAPpy/GSIServer.py | Python | gpl-3.0 | 5,153 | [
"Brian"
] | 457bc5aa7733237cda5bcf04e3c0e7600bfde5b972ac7dd8d0931db5a6c784f3 |
"""
=======
fourier
=======
This module define the Fourier class and other functions related to
the fourier transformation.
"""
import numpy as np
import pandas as pd
from javelin.grid import Grid
from javelin.utils import get_unitcell, get_positions, get_atomic_numbers
from javelin.fourier_cython import calculate_cyt... | rosswhitfield/javelin | javelin/fourier.py | Python | mit | 20,115 | [
"ASE",
"CRYSTAL"
] | 3b29ba84b809da5a20f542e3654b8b8fb5e819d0c2d14bd8273562ac784b59d6 |
from click import echo, prompt
import os
import yaml
from ..ega.entities import Dac, Policy, Contact, Study, Submission, SubmissionSubsetData
from ..ega.services import login, object_submission, query_by_type, prepare_submission
from ..exceptions import CredentialsError
def init_workspace(ctx,ega_submitter_account=No... | icgc-dcc/egasub | egasub/submission/init.py | Python | gpl-3.0 | 7,791 | [
"ORCA"
] | 27ed4550ee6fb6879d4b0f47c102dde546d1512ccfdfa4f63049efdef2c2ab64 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2018 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | amjames/psi4 | psi4/driver/qcdb/bfs.py | Python | lgpl-3.0 | 8,379 | [
"Psi4"
] | b85df183389b65685c40ece1016bd8975dda900e5b3d974765830235abd0e91c |
"""
@name: PyHouse/src/Modules.Core.Utilities.obj_defs.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2015-2017 by D. Brian Kimmel
@license: MIT License
@note: Created on Aug 7, 2015
@Summary:
"""
class GetPyhouse(object):
def __init__(self, p_pyhouse_obj):
... | DBrianKimmel/PyHouse | Project/src/Modules/Core/Utilities/obj_defs.py | Python | mit | 582 | [
"Brian"
] | 78e8bdbe021291cf516136527da5cad2b3ce65f322282675439c2b8126fb9876 |
from test import test_support
import unittest
import codecs
import locale
import sys, StringIO, _testcapi
def coding_checker(self, coder):
def check(input, expect):
self.assertEqual(coder(input), (expect, len(input)))
return check
class Queue(object):
"""
queue: write bytes at one end, read by... | ianyh/heroku-buildpack-python-opencv | vendor/.heroku/lib/python2.7/test/test_codecs.py | Python | mit | 73,168 | [
"FEFF"
] | f41c3b7e45c41253ea39dc3b2784e2894f1a503a9655c76c7eeb2a502c2ffb30 |
# Filename : Image2Map.py
# Authors : Georg Muntingh and Bjorn Lindeijer
# Version : 1.2
# Date : June 16, 2010
# Copyright : Public Domain
import os, sys, Image, networkx
class TileMap:
""" This class represents a map of tiles.
"""
def __init__(self, file, tileX, tileY):
# For initiali... | mozilla/galaxy.js-mobile-gamepad | src/examples/HTML5-Keen/scripts/Image2Map.py | Python | bsd-3-clause | 15,493 | [
"VisIt"
] | 1cc276d4b549d8afd3630f1af78c6db726539d595f6f6e1ed807f4a25c1cc2ac |
import numpy as np
def zero_pad(X, pad):
"""
Pad with zeros all images of the dataset X. The padding is applied to the height and width of an image,
as illustrated in Figure 1.
Argument:
X -- python numpy array of shape (m, n_H, n_W, n_C) representing a batch of m images
pad -- integer, amou... | luoshao23/ML_algorithm | Deep_Learning/CNN/simple_cnn.py | Python | mit | 14,421 | [
"NEURON"
] | f62496b1ebfbfc9a30beb856ff8b45f8acf6dbaa9fd635fc434c3ca48198580f |
# Py2 compat
from __future__ import print_function
from future import standard_library
standard_library.install_aliases()
from past.builtins import basestring
# standard lib
from contextlib import contextmanager
import copy
import datetime
from decimal import *
import fnmatch
from functools import reduce
import imp
i... | h2oai/h2o-3 | h2o-py/tests/pyunit_utils/utilsPY.py | Python | apache-2.0 | 234,815 | [
"Gaussian"
] | 9c5c930f469c5bae860184ed913771c09b4b91a95db1833182b0bf3e58f27cbc |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# My imports
from __future__ import division, print_function
import argparse
import os
import urllib
import matplotlib
import matplotlib.pyplot as plt
import numpy as np
import scipy.interpolate as sci
from astropy.io import fits
from astropy.modeling import fitting, mode... | jason-neal/equanimous-octo-tribble | octotribble/Compare_pipelines.py | Python | mit | 23,795 | [
"Gaussian"
] | 808084da73b5d144eadf926aa058073bf2207bb710fc4cfd3dd23b042aabbbc2 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# showvgridmonitor - show private vgrid monitor to vgrid participants
# 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 terms of... | heromod/migrid | mig/shared/functionality/showvgridmonitor.py | Python | gpl-2.0 | 5,290 | [
"Brian"
] | e74f46d82fb0d7d99b0fff85e4c794aaccd5eda2b0aee8c269cae73260c3c8ad |
try:
from json import dumps, loads
except:
from simplejson import dumps, loads
try:
# Python 2
from urllib2 import urlopen
from urllib import urlencode
except:
# Python 3
from urllib.request import urlopen
from urllib.parse import urlencode
__all__ = ['WebAPI']
... | golismero/golismero | thirdparty_libs/shodan/api.py | Python | gpl-2.0 | 7,427 | [
"VisIt"
] | a3fe403530e9dc205f966ef4027dafcfa6b08aefc12b7f1177e243b1d051597c |
kernels = [
{
'name': 'Identity (no filter)',
'kernel': [[ 0, 0, 0],
[ 0, 1, 0],
[ 0, 0, 0]],
'factor': 1
},
{
'name': 'Blur (Low Pass)',
'kernel': [[ 1, 1, 1],
[ 1, 1, 1],
[ 1, 1, 1]],
'factor': 9
},
{
'name': 'Gaussian Blur',
'kernel': [[ 1, 2, 1],
[ 2, 4... | jaysbays/digit-recognition | src/kernels.py | Python | mit | 822 | [
"Gaussian"
] | c9e78c63f805b7076767270b398460aa8ca360230d902ba1ee34c28d8285d5a4 |
#!/usr/bin/env python
# Author: Derrick H. Karimi
# Copyright 2014
# Unclassified
from bbot.Utils import *
from bbot.Data import *
from bbot.Strategy import Strategy
from bbot.SpendingParser import SpendingParser
from bbot.MetaData import MetaData
class RegionBuy(Strategy):
def __init__(self, app, num_regions=... | AlwaysTraining/bbot | bbot/RegionBuy.py | Python | mit | 10,642 | [
"VisIt"
] | bd8599479a6f2ce2621a0a7213be7479768a64564a2f8ea1763c181b3bb4b0ec |
# (C) British Crown Copyright 2019, Met Office
#
# This file is part of cf-units.
#
# cf-units is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any ... | ocefpaf/cf_units | cf_units/_udunits2_parser/__init__.py | Python | lgpl-3.0 | 7,829 | [
"VisIt"
] | 5323c9587ca0b1235af0265cd0810c141b679b42dcabef5a613222a242dff2fe |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# crema documentation build configuration file, created by
# sphinx-quickstart on Mon Oct 9 12:09:02 2017.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# auto... | bmcfee/crema | docs/conf.py | Python | bsd-2-clause | 6,147 | [
"Brian"
] | 2dddea1ee92a5ab08f325c58fc4a090e0bbc1841901bbc9734f70b3ee67e1db3 |
import numpy as np
import dolfin
from dolfin import *
from mpi4py import MPI as pyMPI
from leopart import StokesStaticCondensation, FormsStokes
import geopart.stokes.incompressible
import dolfin_dg as dg
comm = pyMPI.COMM_WORLD
mpi_comm = MPI.comm_world
#load mesh,boundaries and coefficients from file
mark = {"Int... | BradHub/SL-SPH | hdg_test/3d/hdg_test.py | Python | mit | 2,399 | [
"ParaView"
] | 8c6a97ff20dce5068ff6bb7feeb12de94653095fce08f9f995364c40dba141fd |
from src.constant.Number import Number
from src.modifier.Modifier import Modifier
from src.operator.Operator import Operator
from src.roll.Roll import Roll
from src.visitor.NodeVisitor import NodeVisitor
class CompileVisitor(NodeVisitor):
@classmethod
def visit(cls,node):
if isinstance(node, Roll):
... | charleshamel73/diceroller | src/visitor/CompileVisitor.py | Python | mit | 701 | [
"VisIt"
] | ddc04fa1333738ef7750e27fcd953a9eaac256376a0a61b260f39485f997967d |
#!/usr/bin/env python
__author__ = "waroquiers"
import unittest
import numpy as np
from pymatgen.analysis.chemenv.utils.math_utils import (
_cartesian_product,
cosinus_step,
divisors,
get_center_of_arc,
get_linearly_independent_vectors,
power3_step,
powern_parts_step,
prime_factors,... | materialsproject/pymatgen | pymatgen/analysis/chemenv/utils/tests/test_math_utils.py | Python | mit | 5,110 | [
"pymatgen"
] | 9752d3663da5a1c30582ec1548ddb096e56d4d195ca5818631a4eeeb0093b11f |
import re
import os
from rdkit import Chem
from rdkit.Chem import AllChem
from rmgpy.molecule import Molecule
import autoqm.utils
from autoqm.connector import saturated_ringcore_table
config = autoqm.utils.read_config()
def should_create_more_jobs(threshold=150):
"""
This method is to inform job creator whether s... | KEHANG/autoQM | autoqm/creator.py | Python | mit | 4,816 | [
"Gaussian",
"RDKit"
] | 523b525fd8e3af22aa7e2ab32b1e59a91e53c646c76fc4b3e2933fbf2aef68d6 |
# $Id$
#
# Copyright (C) 2004-2006 Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
from rdkit import rdBase
from rdkit.Da... | adalke/rdkit | rdkit/DataManip/Metric/__init__.py | Python | bsd-3-clause | 363 | [
"RDKit"
] | ef72f6d5396573850ea25b73c6b63ef8eb9a36c91b3afeb40334466174a294fc |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/item_title | openlp/plugins/custom/forms/editcustomslidedialog.py | Python | gpl-2.0 | 3,780 | [
"Brian"
] | 14bcf100203e459ee067db566200b46ac7d8bcfa1724de5d75095ae873952b36 |
# dialog.py --- A Python interface to the ncurses-based "dialog" utility
# -*- coding: utf-8 -*-
#
# Copyright (C) 2002, 2003, 2004, 2009, 2010, 2013 Florent Rougon
# Copyright (C) 2004 Peter Åstrand
# Copyright (C) 2000 Robb Shecter, Sultanbek Tezadov
#
# This library is free software; you can redistribute it and/o... | nrgaway/qubes-tools | builder-tools/libs/dialog.py | Python | gpl-2.0 | 150,374 | [
"VisIt"
] | 508327ef23b901c9e0ced915ddb79d59bcdc0385ba3220021f3163df90f03d33 |
import sys, pylab, gp
import numpy as np
from numpy.random import multivariate_normal as multivariate_normal
#-----------------------------------------------------------------------------
if __name__ == '__main__':
exptheta = np.array([1.0,1.0,0.01])
if len(sys.argv) == 5:
exptheta[1] = float(sys.arg... | garibaldu/ego-demo | makeSamples.py | Python | gpl-2.0 | 1,484 | [
"Gaussian"
] | d99c3c0c0b49e97a58ab998b812689706403f25485724131ded9123666d4f2ac |
# Copyright (C) 2010-2019 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 v... | pkreissl/espresso | testsuite/python/polymer_diamond.py | Python | gpl-3.0 | 5,768 | [
"ESPResSo"
] | 93f915d42de2a3f805181d4910c9e6bf7096ba5c9a63d2ab4ca5f170f373fb1d |
# 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.
"""
A package for converting cubes to and from specific file formats.
"""
from iris.io.format_picker import (
FileExtensi... | SciTools/iris | lib/iris/fileformats/__init__.py | Python | lgpl-3.0 | 4,808 | [
"NetCDF"
] | db1af6d6f058bc531ac49f684417883246f9214156871b13d9bd7aa5a051f14d |
import logging
import os
import shutil
from admin import AdminGalaxy
from galaxy import web
from galaxy import util
from galaxy.web.form_builder import CheckboxField
from galaxy.util import json
from galaxy.model.orm import or_
import tool_shed.repository_types.util as rt_util
from tool_shed.util import common_util
... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py | Python | gpl-3.0 | 156,334 | [
"Galaxy"
] | ba16c7f329561316e4905a05dc02f0c7eedfea0f3dcc9d65036d6d0e746e7659 |
# Copyright (C) 2010-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | mkuron/espresso | samples/visualization_charged.py | Python | gpl-3.0 | 4,529 | [
"ESPResSo"
] | b1b0d11c9e36317866f318b20773b0f841be1e755a029677f18646488fd8ff64 |
# This file is part of the pyGTM module.
# It has been heavily modified by John Kendrick for inclusion in the pdielec library
# Quite a lot has been removed as the fields spatial distribution was not needed
# Thanks to the authors of the original code for all their hard work
#
# This program is free software: you can r... | JohnKendrick/PDielec | PDielec/GTMcore.py | Python | mit | 44,231 | [
"CRYSTAL"
] | ad1bdba43eef59589326ae06ae73a3f4fd31f4385fb99eae26afb3f344de514f |
"""
Actions manager for transcripts ajax calls.
+++++++++++++++++++++++++++++++++++++++++++
Module do not support rollback (pressing "Cancel" button in Studio)
All user changes are saved immediately.
"""
import copy
import os
import logging
import json
import requests
from django.http import HttpResponse, Http404
fro... | eestay/edx-platform | cms/djangoapps/contentstore/views/transcripts_ajax.py | Python | agpl-3.0 | 20,169 | [
"FEFF"
] | ca83a3e81a989a389fab1224c773f1e02c99878e15d4daaeaaa96f85375f2c7a |
#!/usr/bin/env python
"""
This file is part of Sprout.
Sprout 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.
Sprout ... | JenniferKarr/Sprout_Code | view_models.py | Python | gpl-3.0 | 86,249 | [
"Gaussian"
] | fa461ea6723858310b13cd0aac628c113ec707790fbce511ff96f3b3c1c793a7 |
# Here is a simple example, including parallelization over MPI.
from lmc import *
# for MPI
from mpi4py import MPI
mpi_comm = MPI.COMM_WORLD
mpi_rank = MPI.COMM_WORLD.Get_rank()
### Define some parameters.
x = Parameter(name='x')
y = Parameter(name='y')
### This is the object that will be passed to the likelihood fu... | abmantz/lmc | examples/mpi_hoodClosed.py | Python | lgpl-3.0 | 2,095 | [
"Gaussian"
] | d0c1471e947ebe6d483e37f07fd030a5c7b48c74263b5caf16930f8c6d0520bc |
# 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/.
"""
Siesta
======
The interaction between sisl and `Siesta`_ is one of the main goals due
to the implicit relationship ... | zerothi/sisl | sisl/io/siesta/__init__.py | Python | mpl-2.0 | 2,186 | [
"NetCDF",
"SIESTA"
] | de3f4bf036b3ab00bb36337fa7508932a4b84f27cac17c6d58d4f081afcfedb6 |
""" Contains the base classes for Targets and TargetGroups."""
# target.py
# Mission Pinball Framework
# Written by Brian Madden & Gabe Knuth
# Released under the MIT License. (See license info at the end of this file.)
# Documentation and more info at http://missionpinball.com/mpf
import logging
from mpf.system.dev... | jabdoa2/mpf | mpf/devices/target.py | Python | mit | 14,967 | [
"Brian"
] | a68d48b14923b8b54397df16aa42d07cff13637ab9997333f70a65eaf404d638 |
"""
#;+
#; NAME:
#; build_casbah_galaxies
#; Version 1.0
#;
#; PURPOSE:
#; Module for buildling CASBAH galaxy database
#; 02-Jan-2015 by JXP
#;-
#;------------------------------------------------------------------------------
"""
from __future__ import print_function, absolute_import, division, unicode_literal... | nhmc/xastropy | xastropy/casbah/load_casbah.py | Python | bsd-3-clause | 1,784 | [
"Galaxy"
] | dedb4ac7544a852da014541d5e39367cee7e72b321ba5b63117a3825c78d1a7c |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2008 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 published by
# the Free Software Foundation; either v... | sam-m888/gramps | gramps/gen/plug/menu/_color.py | Python | gpl-2.0 | 1,744 | [
"Brian"
] | f81b30085ec96167417a0def5bc7ccd41461b470d81a10c1dc71ac10f811a683 |
import os
import subprocess
import pychemia
import sys
def get_python_str():
if sys.version_info > (3, 0):
return 'python3'
else:
return 'python'
path = 'tests/data'
def test_abinit2xyz():
"""
Test command abinit2xyz :
"""
#pychemia.info()... | MaterialsDiscovery/PyChemia | tests/test_3_scripts.py | Python | mit | 2,248 | [
"ABINIT"
] | 5c3f71380a49c7bb85cfd34e25c071d27b30605bd82f13938906422531196fff |
# Copyright (c) 2013 Mak Nazecic-Andrlon
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish... | csningli/MultiAgent | mas/third/pyorca/test.py | Python | apache-2.0 | 4,378 | [
"ORCA"
] | cbf1f76a020f4a9cd31abe56349969f3c9602457a481da68e72cc4fb4ec15fe9 |
"""
The B{0install man} command-line interface.
"""
# Copyright (C) 2012, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from __future__ import print_function
import sys, os
from zeroinstall import support, logger
syntax = "NAME"
def add_options(parser):
pass
def handle(config, ... | slovenwd/0install | zeroinstall/cmd/man.py | Python | lgpl-2.1 | 1,586 | [
"VisIt"
] | 9016de876d7786ab4fb0507b1139974823e2f4d025e6eec497700be71fc6c94e |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Test for the piezo tensor class
"""
__author__ = "Handong Ling"
__version__ = "0.1"
__maintainer__ = "Handong Ling"
__email__ = "handongling@berkeley.edu"
__status__ = "Development"
__date__ = "4/23/19"
... | gmatteo/pymatgen | pymatgen/analysis/tests/test_piezo_sensitivity.py | Python | mit | 14,598 | [
"phonopy",
"pymatgen"
] | 138b2b15eae7f7965e70c464f1be913b769e0dda30d3c29f986608d4f5ccaf4e |
from __future__ import print_function
from __future__ import division
from __future__ import absolute_import
#
# Copyright 2014 Lee-Ping Wang
#
import os
import re
import sys
from select import select
import subprocess
__all__ = ['_exec']
def _exec(command, print_to_screen=False, outfnm=None, logfnm=None, stdin="",... | rmcgibbo/qchem-utils | qchem_utils/utils.py | Python | gpl-2.0 | 7,746 | [
"Gromacs"
] | ff3a28263a0c9676d648613039577c612bf009f9ea1eda10f0870e6dd7ff51ac |
#!/usr/bin/env python
"""
try to do ref-directed assembly for paired reads in a region of a .bam file
"""
import pysam,argparse,subprocess,sys,shutil,os,re
import bamsurgeon.parseamos as parseamos
import datetime
from uuid import uuid4
import logging
FORMAT = '%(levelname)s %(asctime)s %(message)s'
logging.basicCon... | adamewing/bamsurgeon | bamsurgeon/asmregion.py | Python | mit | 8,635 | [
"pysam"
] | 7ae70fc0e1b0db8751709f312b04f45da163110a50193ca9e8372430f49a7663 |
#!/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 the h... | hbp-sanncs/pyscm | sample_sweep.py | Python | gpl-3.0 | 2,530 | [
"NEURON"
] | 64007ce40af716a20737fa3e6263e40ff4245a4c0e6cc33f329115875a73f2eb |
# absolute paths, or relative paths from root application directory (ie. above the magnificent-octopus directory),
# to the desired config files (in the order you want them loaded)
CONFIG_FILES = [
# octopus.lib config files
"magnificent-octopus/octopus/config/cli.py",
"magnificent-octopus/octopus/config/da... | JiscPER/magnificent-octopus | octopus/config/rootcfg.py | Python | apache-2.0 | 2,552 | [
"Octopus"
] | b1fc33889df7ec1833ee918355bb000e1d4ce7e93da6639c6162c81413de1ad9 |
#!/usr/bin/env python
# From a coordinate pdb and a velocity pdb, create a trr with a box dimension
import MDAnalysis
da = MDAnalysis.Universe("da.pdb")
vel = MDAnalysis.Universe("da.vel.pdb")
da.trajectory.ts.velocities = vel.trajectory.ts.positions
# Taken from output of editconf
da.trajectory.ts.dimensions = [48... | colvars/colvars | gromacs/tests/library/Common/create_trr.py | Python | lgpl-3.0 | 443 | [
"MDAnalysis"
] | 669160c5e99274bd8d9e6078904c472cec581565b8278746a4d40893438da235 |
import mxnet as mx
import logging
import os
import time
def _get_lr_scheduler(args, kv):
if 'lr_factor' not in args or args.lr_factor >= 1:
return (args.lr, None)
epoch_size = args.num_examples / args.batch_size
if 'dist' in args.kv_store:
epoch_size /= kv.num_workers # data is divided amo... | yhpeng-git/mxnet | example/image-classification/common/fit.py | Python | apache-2.0 | 7,596 | [
"Gaussian"
] | 42d531d922dbe80fd36ca015d6f4c20379fa140f516dbfff74681709b26c2c88 |
# -*- coding: utf-8 -*-
"""
solace.tests.link_check
~~~~~~~~~~~~~~~~~~~~~~~
A test that finds 404 links in the default templates.
:copyright: (c) 2009 by Plurk Inc., see AUTHORS for more details.
:license: BSD, see LICENSE for more details.
"""
from lxml import html
import unittest
from urlparse i... | sfermigier/solace | solace/tests/test_links.py | Python | bsd-3-clause | 2,170 | [
"VisIt"
] | 1ce789320f5d57860d8833e4ef9fbb69a5b0caa92be9856499a9974280a2d225 |
from __future__ import print_function
import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.axes_grid1 import make_axes_locatable
import matplotlib as mpl
from ase.io import read
from pyqstem.util import atoms_plot
from pyqstem import PyQSTEM
from pyqstem.potentials import poisson_solver,create_potential... | jacobjma/PyQSTEM | test/test_stem_dft.py | Python | gpl-3.0 | 2,260 | [
"ASE",
"GPAW"
] | f2aac3bc6253b7459e868f89a1ae844ee8c2770eb7d346f7e29e50cb5a410802 |
#!/usr/bin/python
from numpy import loadtxt, asarray
from numpy.random import normal as gaussian_noise
import matplotlib.pyplot as plt
import matplotlib.gridspec as gridspec
import warnings
"""
Here you register new characters in format:
'<char>' : (<width>, <height>, '<filename>'),
"""
charlist = {
'a' : (0.7, 1.0,... | timberhill/blablaplot | blablaplot.py | Python | mit | 6,659 | [
"Gaussian"
] | 5aa2911c298bf6e2a077f5610aae1388cba29f636693d134b0df00c83cd18255 |
# 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 | classification/Classification_with_kNN/Single_Contact_Classification/Final/results/4-categories/384/test10_cross_validate_categories_1200ms.py | Python | mit | 4,368 | [
"Mayavi"
] | 9099ac039edf5d6406dca8887a4de46beedafabbd624974371caed09425afd7f |
from django.db import models
from django.core.mail import send_mail
from django.core.urlresolvers import reverse
import os
import urllib.parse
import uuid
# Create your models here.
class Subscriber(models.Model):
email = models.EmailField(max_length=254)
active = models.BooleanField(default=False)
confi... | OpenSourcePolicyCenter/PolicyBrain | webapp/apps/register/models.py | Python | mit | 1,461 | [
"VisIt"
] | 3e0eaaaf0cc966c2d5393106e9d0fa32e712db741be170c4c2bd00ea4771876f |
#
# Copyright John Reid 2014
#
"""
Code to traverse indexes.
"""
from copy import copy
def depthpredicate(maxdepth):
"""Create a predicate that only descends the tree to a maximum depth.
"""
def predicate(it):
return it.repLength < maxdepth
return predicate
def suffixpredicate(suffix):
... | JohnReid/pyseqan | python/seqan/traverse.py | Python | mit | 4,894 | [
"VisIt"
] | 3deff4d52e692a65f2475655b4acd285ba56f9665850ce80257183f8d9884fb8 |
# Copyright 2016 James Hensman, alexggmatthews
# Copyright 2017 Thomas Viehmann
#
# 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... | t-vi/candlegp | candlegp/models/gpmc.py | Python | apache-2.0 | 2,896 | [
"Gaussian"
] | 25228c195457ea59ddf60544912dd9e038542cf01e1f6f86f12b0770eca3f184 |
import pele.amber.read_amber as ra
import playground.group_rotation.amino_acids as amino
import playground.group_rotation.chirality as chir
import playground.group_rotation.group_rotation as gr
import numpy as np
dirname = '/scratch/khs26/rotamer_lib_igb2/ARG/TRP/ALA/'
# First test the order of atoms in lowest and in... | khs26/pele | playground/rotamer/rotamer_read.py | Python | gpl-3.0 | 4,459 | [
"Amber"
] | 53ad3d7da9ab66a78c58afd5b0f2516b661d267a5bf38701ac6aecb5645f62f5 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from viradacultural_social_api.views import MinhaViradaView, FriendsOnEventsView, FriendsPositionsView
... | hacklabr/viradacultural-social-api | config/urls.py | Python | agpl-3.0 | 1,292 | [
"VisIt"
] | d40a5103837eb455ce99548989789ecf7ad06f47352b60766ab1846317b8407a |
"""
This file is part of pyCMBS.
(c) 2012- Alexander Loew
For COPYING and LICENSE details, please refer to the LICENSE file
"""
"""
Convert region information to a GRID which can be used then for further analysis
Region information is often provided as coordinates, but needs to be rasterized to work with pyCMBS funct... | pygeo/pycmbs | scripts/convert_regions.py | Python | mit | 3,475 | [
"NetCDF"
] | 1820abe4c1fa619ae5ece7731a7af86108b269ad7cc08731104868bb3e2da6a4 |
from distutils.core import setup
from Cython.Build import cythonize
from distutils.extension import Extension
import numpy as np
import mpi4py as mpi4py
import sys
import platform
import subprocess as sp
import os.path
import string
# Now get include paths from relevant python modules
include_path = [mpi4py.get_inclu... | meyerbe/pycles | setup.py | Python | gpl-3.0 | 15,466 | [
"NetCDF"
] | 5663231bd924ca28cc832b8eadd4707848deca498261adb8564cdb3bfec78349 |
# coding=utf-8
# Copyright 2022 The Google Research 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 applicab... | google-research/google-research | mol_dqn/experimental/eval_800_mols.py | Python | apache-2.0 | 50,369 | [
"RDKit"
] | b3dcc781e2d8e70372670e7e63174a05972b0228b9d96d583b46e0da29a655ac |
#! /usr/bin/env python3
# Getting tweets from lists script and creating txt and pdf from them
# using optional filter
# programmer: Josifoski Aleksandar about.me/josifsk
import sys
import os
import codecs
import re
import datetime
from reportlab.pdfgen.canvas import Canvas
from pdfrw import PdfReader
from pdfrw.torep... | josifoski/twitter2pdf | twitter2pdf.py | Python | gpl-2.0 | 6,668 | [
"Galaxy"
] | 8a21273987a81c74eed4800cdde225121d6a0f01cf10bbbf2fc60370dbca9750 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Module Project Create Script
#
import os, sys, shutil, string, uuid, re, zipfile, glob, optparse
from string import capitalize
from StringIO import StringIO
from datetime import date
this_dir = os.path.dirname(__file__)
scripts_common_dir = os.path.join(os.path.dirna... | appcelerator/titanium_mobile_tooling | scripts/module/module.py | Python | apache-2.0 | 12,289 | [
"VisIt"
] | 6d52af59c6e1afc2ae5cdc94b088a854c8bf5a8b0e074ab8f6017d417eb0bb48 |
from plotly.basedatatypes import BaseTraceHierarchyType as _BaseTraceHierarchyType
import copy as _copy
class Marker(_BaseTraceHierarchyType):
# class properties
# --------------------
_parent_path_str = "violin"
_path_str = "violin.marker"
_valid_props = {"color", "line", "opacity", "outliercolo... | plotly/plotly.py | packages/python/plotly/plotly/graph_objs/violin/_marker.py | Python | mit | 19,294 | [
"Bowtie"
] | 19533a0677c190e3216d90149bbfb5c6e5dd4a506ba5ececd36331c5eb87ef10 |
# Copyright 2020 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... | frreiss/tensorflow-fred | tensorflow/compiler/mlir/tfr/python/tfr_gen.py | Python | apache-2.0 | 56,463 | [
"VisIt"
] | 66ba8686e14930b86de7a4a3645c37bf35ee80ae0f108f99001479325147cee9 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# @Author: Brian Cherinka, José Sánchez-Gallego, and Brett Andrews
# @Date: 2017-07-02
# @Filename: test_map.py
# @License: BSD 3-clause (http://www.opensource.org/licenses/BSD-3-Clause)
#
# @Last modified by: José Sánchez-Gallego (gallegoj@uw.edu)
# @Last modified time: ... | albireox/marvin | python/marvin/tests/tools/test_map.py | Python | bsd-3-clause | 24,897 | [
"Brian",
"Galaxy",
"Gaussian"
] | ed6b8711b886bca86f021ba3aa2e26257c0826dbe41563ca7d09951b1550e53a |
from __future__ import absolute_import
from collections import namedtuple
from fnmatch import fnmatch
from parsimonious.grammar import Grammar, NodeVisitor
from parsimonious.exceptions import ParseError # noqa
from sentry.utils.safe import get_path
__all__ = ("parse_rules", "dump_schema", "load_schema")
VERSION = 1... | mvaled/sentry | src/sentry/ownership/grammar.py | Python | bsd-3-clause | 5,518 | [
"VisIt"
] | 2f29dcde1428500be9873872a8a50379ea0f4aec733a34137be9523b97f9ac85 |
"""
Given a binary tree, return the inorder traversal of its nodes' values.
For example:
Given binary tree {1,#,2,3},
1
\
2
/
3
return [1,3,2].
"""
# Definition for a binary tree node
# class TreeNode:
# def __init__(self, x):
# self.val = x
# self.left = None
# self.r... | Ahmed--Mohsen/leetcode | Binary_Tree_Inorder_Traversal.py | Python | mit | 1,346 | [
"VisIt"
] | d7486c91870c67df68d230209fd351cc283e05b86dc894de403dcb169f560464 |
# -*- coding: utf-8 -*-
"""
Acceptance tests for Video.
"""
import os
from ddt import ddt, unpack, data
from mock import patch
from nose.plugins.attrib import attr
from unittest import skipIf, skip
from selenium.webdriver.common.by import By
from selenium.webdriver.common.action_chains import ActionChains
from common... | tanmaykm/edx-platform | common/test/acceptance/tests/video/test_video_module.py | Python | agpl-3.0 | 51,306 | [
"VisIt"
] | e732436e560ce01665ad5ad66675ea84a1ef48651139ca4ef38eff5452b5a430 |
import bugle_project
import os
OUR_ROOT = os.path.realpath(os.path.dirname(bugle_project.__file__))
LOGIN_REDIRECT_URL = '/'
LOGIN_URL = '/login/'
DEBUG = True
TEMPLATE_DEBUG = DEBUG
ADMINS = (
# ('Your Name', 'your_email@domain.com'),
)
MANAGERS = ADMINS
DATABASE_ENGINE = None
DATABASE_NAME = 'bugle'
DATABASE... | devfort/bugle | bugle_project/configs/settings.py | Python | bsd-2-clause | 3,867 | [
"BLAST"
] | 69bb10bcd1ea2d7456f9718a5c05dcce7798b49adcc37296c5743c56c17c8a84 |
"""
Colouring anomaly data with logarithmic scaling
===============================================
In this example, we need to plot anomaly data where the values have a
"logarithmic" significance -- i.e. we want to give approximately equal ranges
of colour between data values of, say, 1 and 10 as between 10 and 100.... | SusanJL/iris | docs/iris/example_code/General/anomaly_log_colouring.py | Python | gpl-3.0 | 4,533 | [
"NetCDF"
] | 7191ec6b63c3a5d2e1b3a879c293fe0d92df1e710cf9933f32d6b1e00f0ae5c2 |
# Addition of restraints to the default ones
from modeller import *
from modeller.automodel import * # Load the automodel class
log.verbose()
env = environ()
# directories for input atom files
env.io.atom_files_directory = ['.', '../atom_files']
class MyModel(automodel):
def special_restraints(self, aln):
... | bjornwallner/proq2-server | apps/modeller9v8/examples/automodel/model-addrsr.py | Python | gpl-3.0 | 2,004 | [
"Gaussian"
] | 9a99bdc130d55376bc617c9d6222584b26d66c0836f18a259e3d7248e6ab814c |
# $Id$
#
# Copyright (C) 2007-2009 Greg Landrum
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
import os
from rdkit import Chem
from rdkit.Chem i... | rdkit/rdkit | rdkit/Chem/MolDb/Loader_sa.py | Python | bsd-3-clause | 5,930 | [
"RDKit"
] | ae6ac7cb631443789b536b63957ca68d8b147c4293347858587c504f99c4d038 |
"""Query by committee on the Radio Galaxy Zoo MV dataset.
Matthew Alger
The Australian National University
2016
"""
import argparse
import logging
import os.path
import h5py
import matplotlib
import matplotlib.pyplot as plt
import numpy
import sklearn.cross_validation
import sklearn.linear_model
from crowdastro.cro... | chengsoonong/crowdastro | crowdastro/experiment/experiment_rgz_qbc.py | Python | mit | 7,491 | [
"Galaxy"
] | 5c9f8c66fc261a9375a2090022e8885f9d8f0b1310fbf64ebd11de97ba0bf930 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Answered by Billy Wilson Arante
# Last updated on 2016/12/31 EST
# We defined:
stooges = ['Moe','Larry','Curly']
# but in some Stooges films, Curly was
# replaced by Shemp.
# Write one line of code that changes
# the value of stooges to be:
stooges[2] = "Shemp"
prin... | arante/udacity | cs101/lesson3/different_stooges.py | Python | gpl-3.0 | 374 | [
"MOE"
] | dd29590a586d27509228b18979439eba5a0180731b37d423fffd573c6e4dac9c |
# ./sdf_model_dom.py
# -*- coding: utf-8 -*-
# PyXB bindings for NM:e92452c8d3e28a9e27abfc9994d2007779e7f4c9
# Generated 2017-10-02 18:13:38.461234 by PyXB version 1.2.5 using Python 3.5.2.final.0
# Namespace AbsentNamespace0
from __future__ import unicode_literals
import pyxb
import pyxb.binding
import pyxb.binding.s... | HBPNeurorobotics/BlenderRobotDesigner | resources/sdf/Model/sdf/sdf16_xsd/sdf_dom.py | Python | gpl-2.0 | 1,021,759 | [
"Gaussian"
] | 6291c15b49e4326a942fdc40c6936ecaa58e19bc1e4feaedf46ea05c9bf4e9cc |
import os
import re
try:
import json
except ImportError:
import simplejson as json
from . import Filter
from ..utils import common_path_prefix
__all__ = ('JST',)
class JSTemplateFilter(Filter):
"""Common base class for the JST and Handlebars filters, and
possibly other Javascript templating systems ... | gi0baro/weppy-assets | weppy_assets/webassets/filter/jst.py | Python | bsd-3-clause | 7,120 | [
"MOE"
] | 64f384dedaa9dcc477f68c3bba701ac945699c06886c99cb53c64974ff8f878b |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2010 Red Hat, Inc.
# Copyright (c) 2010 Ville Skyttä
# Copyright (c) 2009 Tim Lauridsen
# Copyright (c) 2007 Marcus Kuhn
#
# kitchen 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
# ... | tomasreimers/python-wiki-uturn | kitchen/text/display.py | Python | mit | 39,442 | [
"NetCDF"
] | 1e761728fc72ef58b4a67014d76fdbb956eb25b89eb13d5a71aedb8201717a99 |
from stattools import unitroot_adf
import scikits.statsmodels.datasets.macrodata.data as macro
macrod = macro.load().data
print macro.NOTE
print macrod.dtype.names
datatrendli = [
('realgdp', 1),
('realcons', 1),
('realinv', 1),
('realgovt', 1),
... | matthew-brett/draft-statsmodels | scikits/statsmodels/sandbox/tools/ex_newtests.py | Python | bsd-3-clause | 742 | [
"ADF"
] | 60b3d0928c18ba8938044c3f9ec809a474915b300b06463496b170e1012e0520 |
from modeller import *
from modeller.scripts import complete_pdb
# Load the C extension module; this needs to be compiled with commands like
# the following (these work for most Linux systems, where 'modXXX' is your
# Modeller binary):
#
# swig -python -noproxy cuser_feat.i
# gcc -shared -Wall -fPIC `modXXX --cflags -... | bjornwallner/proq2-server | apps/modeller9v8/examples/c-extensions/cuser_feat.py | Python | gpl-3.0 | 1,764 | [
"Gaussian"
] | 15e6013a8232ca59bb9f8a2daee5791434a36cd3c87448995ceb7c12f3b73994 |
#A* -------------------------------------------------------------------
#B* This file contains source code for the PyMOL computer program
#C* copyright 1998-2000 by Warren Lyford Delano of DeLano Scientific.
#D* -------------------------------------------------------------------
#E* It is unlawful to modify or remove ... | gratefulfrog/lib | python/chempy/pkl.py | Python | gpl-2.0 | 2,062 | [
"ChemPy",
"PyMOL"
] | 071e727edba957b566ec2c260b556044ef0d82d5e145fe305947edf2841a31c6 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class PyWub(PythonPackage):
"""Bioinformatics tools and a software library developed by the Oxfo... | iulian787/spack | var/spack/repos/builtin/packages/py-wub/package.py | Python | lgpl-2.1 | 1,313 | [
"Biopython",
"pysam"
] | 8fafae5ecae5539162ddfe55e731a70eb37eaebcd2d4bb1bc3eb176a5f48a8d2 |
import ast
from unittest import mock
from nimoy.ast_tools.ast_metadata import SpecMetadata
from nimoy.ast_tools.features import FeatureRegistrationTransformer
from nimoy.runner.metadata import RunnerContext
from nimoy.runner.spec_finder import Location
from nimoy.specification import Specification
class FeatureRegis... | browncoat-ninjas/nimoy | specs/nimoy/ast_tools/features_spec.py | Python | apache-2.0 | 4,503 | [
"VisIt"
] | c0cf9042c34d39bcab5ce11e64da7f4119f45ec4d1344a754a0ee192505c0e49 |
# $Id$
#
# Copyright (C) 2003-2006 Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
"""basic unit testing code for the rdk... | rdkit/rdkit-orig | rdkit/Chem/UnitTestChemv2.py | Python | bsd-3-clause | 5,885 | [
"RDKit"
] | 7d05e825fe82cdc8d42f2dacf86acace13d4d93463aa702c379a69ae64d83a27 |
#!/usr/bin/env python
#set fileencoding: utf-8
from flask import Flask, abort, redirect, render_template, request
from redis import Redis
import string
import random
class ReverseProxied(object):
'''
Wrap the application in this middleware and configure the
front-end server to add these headers, to let you... | kblin/shortis | shortis.py | Python | agpl-3.0 | 3,236 | [
"CRYSTAL"
] | 125e0c308ba1faf45c502b774b8ba841263c2ab9c0d94f152a2778b983ade160 |
from dopamine.fapprox.fa import FA
import numpy as np
class NN(FA):
def __init__(self, indim, outdim, nhidden=20):
FA.__init__(self, indim, outdim)
# learning rate
self.alpha = 0.1
# number of neurons in each layer
... | rueckstiess/dopamine | fapprox/nn.py | Python | gpl-3.0 | 3,915 | [
"NEURON"
] | 9157bf8953381209e65e851875f061cfa09bda5f25e50014d1314804cb0da406 |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RXde(RPackage):
"""XDE: a Bayesian hierarchical model for cross-study analysis of
d... | LLNL/spack | var/spack/repos/builtin/packages/r-xde/package.py | Python | lgpl-2.1 | 1,597 | [
"Bioconductor"
] | 151bd1151a8baeeb16e24f06dead15375892abb5eb02803f8d20a6dc037fdf35 |
#!/usr/bin/env python
#(c) 2014 Emory University. All Rights Reserved
# Code written by: Michael Sauria (mgehrin@emory.edu)
import subprocess
import os
import sys
import glob
def main():
filelist, fastq_dir, tmp_dir, out_dir, bowtie, index_dir, samtools, compile_script, threads = sys.argv[1:12]
threads = int... | bxlab/HiFive_Paper | Scripts/Support/iterative_alignment.py | Python | bsd-3-clause | 3,385 | [
"Bowtie"
] | 0e2896493687bf446947215afb17202f24dd83aea6be0185613ac1a06bc15f42 |
#
# @file TestMathReadFromFile2.py
# @brief Tests for reading MathML from files into ASTNodes.
#
# @author Akiya Jouraku (Python conversion)
# @author Sarah Keating
#
# $Id: TestMathReadFromFile2.py 11441 2010-07-09 02:22:23Z mhucka $
# $HeadURL: https://sbml.svn.sourceforge.net/svnroot/sbml/trunk/libsbml/src/b... | alexholehouse/SBMLIntegrator | libsbml-5.0.0/src/bindings/python/test/math/TestMathReadFromFile2.py | Python | gpl-3.0 | 5,813 | [
"VisIt"
] | f5176e45ae38398e8591f5d0511c1b09043d30b38aa5d456861d3442cf36adb8 |
# Flask app that handles application logic
import base64
import json
from flask import Flask
from flask import render_template
from flask import request
from neuron import get_root_path
app = Flask(__name__, static_folder=get_root_path('static'), template_folder=get_root_path('templates'))
DATA = ["Data One", "Dat... | Andrew-Shay/Neuron | neuron/app.py | Python | mit | 1,094 | [
"NEURON"
] | 05b920af00580a8e62e8545efe39ed415a79c7de115924f4f4a0a153bf99a2d1 |
"""Additional docstring for the DErrno module."""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
class CustomDErrno(object): # pylint: disable=too-few-public-methods
"""Add the ERRNO constants to the docstring automatically."""
def __init__(self):
... | yujikato/DIRAC | docs/diracdoctools/CustomizedDocs/CustomDErrno.py | Python | gpl-3.0 | 1,320 | [
"DIRAC"
] | 6162d381f60603d91deb9311ce508d7f2054c41e200414e6ddb04034d59b3634 |
#!/usr/bin/env python
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2015 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier (bgoli@users.sourceforge.net)
Triple-J Group for Molecular Cell Physiology
Stellenbosch University, South Af... | asttra/pysces | setup.py | Python | bsd-3-clause | 9,707 | [
"PySCeS"
] | 6139f4cec230e999a65fcc802a77401c31532076beb4c51f4e21fb1276d32383 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
gnpy.core.science_utils
=======================
Solver definitions to calculate the Raman effect and the nonlinear interference noise
The solvers take as input instances of the spectral information, the fiber and the simulation parameters
"""
from numpy import inte... | Telecominfraproject/gnpy | gnpy/core/science_utils.py | Python | bsd-3-clause | 33,512 | [
"ASE"
] | 78f28877f93fa1fa8dccc6a5515eb5ac8ce1540f12e4e8aebe7ce0245f21b405 |
# Copyright 2017 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... | hehongliang/tensorflow | tensorflow/python/autograph/pyct/compiler.py | Python | apache-2.0 | 4,623 | [
"VisIt"
] | 2b907650ef81afd434b33aca0a5014a5b3eccb15041571f4936a0597eca4372f |
########################################################################
# File : ProxyProviderFactory.py
# Author : A.T.
########################################################################
""" The Proxy Provider Factory instantiates ProxyProvider objects
according to their configuration
"""
from __future... | ic-hep/DIRAC | src/DIRAC/Resources/ProxyProvider/ProxyProviderFactory.py | Python | gpl-3.0 | 2,477 | [
"DIRAC"
] | b82efd4bc8ffcd7960c95460dc9bcf1c2ea69eeb060b30d4bc30ee51297cf97c |
#
# GMSK modulation and demodulation.
#
#
# Copyright 2005,2006,2007 Free Software Foundation, Inc.
#
# This file is part of GNU Radio
#
# GNU Radio 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 v... | n4hy/gnuradio | gr-digital/python/gmsk.py | Python | gpl-3.0 | 11,078 | [
"Gaussian"
] | 3e0392acec6069b44682ceccc2ca5beb24ef6932535a824b9faf7e272f83135c |
from __future__ import print_function
from __future__ import unicode_literals
import io
import logging
import geolocation
def create_strings(events, version):
"""
Formats the event tuples into a string that can be written to a file.close
Parameters
----------
events: Dictionary.
... | openeventdata/phoenix_pipeline | postprocess.py | Python | mit | 16,977 | [
"BWA"
] | f8f0f82602aa0066cab0a54058576af9689879325a30a9e8c65758b4eae958ab |
# Copyright (C) 2010, Joao Rodrigues (anaryin@gmail.com)
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
import os, sys
import numpy
import xml.dom.minidom
from Bio.PDB.StructureBuilder import Struct... | SBRG/ssbio | ssbio/biopython/Bio/Struct/WWW/WHATIFXML.py | Python | mit | 9,463 | [
"Biopython"
] | 46fc07fce28c973f3f94bb36b3959c8177aa0be0990ec5b5a812e249e2e350f7 |
# -*- coding: utf-8 -*-
# __init__.py ---
#
# Filename: __init__.py
# Description:
# Author: subha
# Maintainer:
# Created: Sun Apr 17 13:55:30 2016 (-0400)
# Version:
# Last-Updated: Sun Apr 17 14:59:06 2016 (-0400)
# By: subha
# Update #: 20
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
#
#... | dharmasam9/moose-core | python/moose/neuroml2/__init__.py | Python | gpl-3.0 | 1,598 | [
"MOOSE"
] | 2115e1e455f2abc8ffd85403674d5fe67a56bf819fa1e9f3dd488a5d3c7dc2b2 |
# Copyright The Cloud Custodian Authors.
# SPDX-License-Identifier: Apache-2.0
import json
import functools
from c7n_terraform.parser import (
HclLocator, TerraformVisitor, Parser, VariableResolver)
from .tf_common import data_dir, build_visitor
def test_parser_eof():
data = Parser().parse_module(data_dir /... | thisisshi/cloud-custodian | tools/c7n_terraform/tests_terraform/test_parser.py | Python | apache-2.0 | 3,673 | [
"VisIt"
] | 67bcf24bbe4077d57fa5b3cbdf286741c817431b28e359bd94222f881a8e246f |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class Memsurfer(PythonPackage):
"""MemSurfer is a tool to compute and analyze membrane surfaces... | LLNL/spack | var/spack/repos/builtin/packages/memsurfer/package.py | Python | lgpl-2.1 | 1,848 | [
"NetCDF",
"VTK"
] | 573d8985acd8683567781822953bfab4020f6c630fa31a30d1ca68ec861fbd95 |
#!/usr/bin/env python
import unittest
import youtubeAuthenticate
import argparse
import youtubeup as yup
import simplejson as json
import re
import tbapy
class MyTests(unittest.TestCase):
def test_get_hashtag(self):
self.assertEqual("frc" + re.search('\D+', "2016arc").group(), "frcarc")
def test_pa... | akilan98/FRC-YouTube-Uploader | test.py | Python | gpl-3.0 | 4,756 | [
"VisIt"
] | a8bd97bc516d45351fbe6ac1041c6ae2f2893f89d48bd5f15ee67df94beaabb1 |
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