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#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2001-2006 Donald N. Allingham
# Copyright (C) 2009 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publi... | SNoiraud/gramps | gramps/gui/plug/report/_fileentry.py | Python | gpl-2.0 | 3,873 | [
"Brian"
] | 4332574eb9b97d5693111ad94af96382fbd2560704bf2e7646beeb246ab5ab71 |
#!/usr/bin/env python
import platform
import time
import numpy
from pyscf import lib
from pyscf.dft import uks
from mpi4pyscf.lib import logger
from mpi4pyscf.scf import uhf as mpi_uhf
from mpi4pyscf.dft import rks as mpi_rks
from mpi4pyscf.tools import mpi
comm = mpi.comm
rank = mpi.rank
@lib.with_doc(uks.get_vef... | sunqm/mpi4pyscf | mpi4pyscf/dft/uks.py | Python | gpl-3.0 | 4,017 | [
"PySCF"
] | 0121d084693a9eb5c02d6ec068afdc535828af0e6aa9988f7f104687341e5396 |
# Mantid Repository : https://github.com/mantidproject/mantid
#
# Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
# NScD Oak Ridge National Laboratory, European Spallation Source
# & Institut Laue - Langevin
# SPDX - License - Identifier: GPL - 3.0 +
from __future__ import (absolute_import, divi... | mganeva/mantid | scripts/Inelastic/CrystalField/normalisation.py | Python | gpl-3.0 | 9,670 | [
"CRYSTAL",
"Gaussian"
] | 69bd3befc21e4ff71be95e768e79bb401b1cd2ad8584e9d8a381b6e9304edb19 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright © 2014 Felix Höfling
#
# This file is part of HALMD.
#
# HALMD 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
# ... | the-nic/halmd | examples/plotting/patch_h5md_for_VMD.py | Python | gpl-3.0 | 2,936 | [
"VMD"
] | c558b8c66e823bdd474b9beae2e4feebb8290c4d6997fa541c1625416c130ccb |
""" Description here
Author: Leonard Berrada
Date: 4 Nov 2015
"""
import sys
sys.path.append("../../")
from Regression import RegressionModel
import copy
import csv
import matplotlib.pyplot as plt
import numpy as np
try:
import seaborn as sns
sns.set(color_codes=True)
except:
pass
import scipy.stats
f... | leonardbj/AIMS | src/Regression/GaussianProcess/GP_model.py | Python | mit | 8,000 | [
"Gaussian"
] | b7e37fd801533d664c9524c77329800584df5d2e816f627d160eac0cdf0d88dd |
#!/usr/bin/python3
from __future__ import print_function
from vizdoom import *
import sys
import threading
import math
from random import choice
from time import sleep
from matplotlib import pyplot as plt
sys.path.append('../../deep_feedback_learning')
import numpy as np
import cv2
import deep_feedback_learning
# ... | nlholdem/icodoom | ICO1/deep_feedback_learning_old/Temp/ico_old.py | Python | gpl-3.0 | 8,452 | [
"NEURON"
] | cfb53978906a980b4933f977e27a248ec91d2da3c89c12ee56c7914383aba6b5 |
#!/usr/bin/env python
""" MultiQC module to parse QC output from PURPLE """
import re
from collections import OrderedDict, defaultdict
from multiqc.modules.base_module import BaseMultiqcModule
from multiqc.plots import table
# Initialise the logger
import logging
log = logging.getLogger(__name__)
class MultiqcModu... | ewels/MultiQC | multiqc/modules/purple/purple.py | Python | gpl-3.0 | 9,481 | [
"Amber"
] | 8988cdeaa2b14885bb8d3d28c9c94f1caa26b75f97cf64a3226c50fecbc55c86 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2008-2012 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 Softw... | tiagocardosos/stoq | stoqlib/gui/dialogs/spreadsheetexporterdialog.py | Python | gpl-2.0 | 3,749 | [
"VisIt"
] | 4c074c57cd5f3c094b1286309968bc4abcf9576e984ba1ea5e2768e78fca4f21 |
# FIXME: should be rewritten as real unittest
# __RCSID__ = "$Id$"
#
# import DIRAC
# from DIRAC.Core.Utilities.CFG import CFG
#
# DIRAC.gLogger.initialize('test_gConfig','/testSectionDebug')
#
# testconfig = '%s/DIRAC/ConfigurationSystem/test/test.cfg' % DIRAC.rootPath
# dumpconfig = '%s/DIRAC/ConfigurationSystem/tes... | ic-hep/DIRAC | src/DIRAC/Core/Utilities/test/Test_gCFG.py | Python | gpl-3.0 | 1,851 | [
"DIRAC"
] | 08e4b15aaa509912c06f33ccac2436a8f8c1753f68245f205b4bba373343acf6 |
###############################
# This file is part of PyLaDa.
#
# Copyright (C) 2013 National Renewable Energy Lab
#
# PyLaDa is a high throughput computational platform for Physics. It aims to make it easier to submit
# large numbers of jobs on supercomputers. It provides a python interface to physical input, suc... | pylada/pylada-light | tests/tools/input/test_listblock.py | Python | gpl-3.0 | 2,232 | [
"CRYSTAL",
"VASP"
] | 0814b167022544f5e332867fc1c22525f1d989e7c111ee5ef0a46090ebfd1a84 |
#
# Copyright (C) 2013-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | mkuron/espresso | samples/widom_insertion.py | Python | gpl-3.0 | 4,335 | [
"ESPResSo"
] | 0564f4c0f74a162603f30cb1336dd78884ebc29d1ed4d9ee949a821acd75de89 |
player_first_names = [
"aaron",
"abdul",
"abe",
"abel",
"abraham",
"abram",
"adalberto",
"adam",
"adan",
"adolfo",
"adolph",
"adrian",
"agustin",
"ahmad",
"ahmed",
"al",
"alan",
"albert",
"alberto",
"alden",
"aldo",
"alec",
"alejandro",
"alex",
"alexander",
"alexis",
"alfonso",
"alfonzo",
"... | benkul/BBA | player_first_names.py | Python | mit | 13,097 | [
"Brian",
"COLUMBUS",
"Dalton",
"Desmond"
] | 2be5daaacff57748ebec888179328e77b3cc47116a8a998c77610af55e083860 |
from django.test import TestCase
from push_notifications.api.rest_framework import APNSDeviceSerializer, GCMDeviceSerializer
from tests.mock_responses import GCM_DRF_INVALID_HEX_ERROR, GCM_DRF_OUT_OF_RANGE_ERROR
class APNSDeviceSerializerTestCase(TestCase):
def test_validation(self):
# valid data - upper case
se... | Ubiwhere/django-push-notifications | tests/test_rest_framework.py | Python | mit | 2,231 | [
"Galaxy"
] | e8b4f0184e6b0c4b741942dba277771f8d33f9fe741c80617db73eb16524cd04 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
#!/usr/bin/env python
from __future__ import division, unicode_literals
"""
#TODO: Write module doc.
"""
__author__ = 'Shyue Ping Ong'
__copyright__ = 'Copyright 2013, The Materials Virtual Lab'
__version__ =... | Bismarrck/pymatgen | pymatgen/io/vaspio/__init__.py | Python | mit | 607 | [
"VASP",
"pymatgen"
] | 2a5f9ecc85b33ea224cc22a97a5b4c854f393dc385d228c1156bca358b1ddea0 |
import sys, os, platform, getpass, logging, glob
import easygui as g
VERSION = "0.1.0"
OS = None
PATHS = []
def get_os():
""" This function returns the current operating system that the
end user is currently running. Returns either 'OSX' or 'WIN'.
"""
if platform.system() == "Darwin":
return ... | drcd/undernuke | Undernuke.py | Python | mit | 3,346 | [
"VisIt"
] | 2e9200340d15ffc724352edbeb5bd96c16b08e181331400e344cdd1254c291c3 |
"""
==============================================
Plot randomly generated classification dataset
==============================================
Plot several randomly generated 2D classification datasets.
This example illustrates the :func:`datasets.make_classification`
:func:`datasets.make_blobs` and :func:`datasets.... | DailyActie/Surrogate-Model | 01-codes/scikit-learn-master/examples/datasets/plot_random_dataset.py | Python | mit | 2,252 | [
"Gaussian"
] | fc372ac3f35a3d6f413aa7fbebddbbd52690f22cecac7cf98fb593fdb58067ef |
#!/usr/bin/env python
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# BornProfiler --- A package to calculate electrostatic free energies with APBS
# Written by Kaihsu Tai, Lennard van der Feltz, and Oliver Beckstein
# Released under th... | Becksteinlab/BornProfiler | scripts/apbs-bornprofile-pdb2dat.py | Python | gpl-3.0 | 1,329 | [
"MDAnalysis"
] | a9de7ae352c2278ad055bd8091a55bffb1cfa050977f21fdcf0a683cece77244 |
# 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... | chemelnucfin/tensorflow | tensorflow/python/autograph/pyct/cfg_test.py | Python | apache-2.0 | 31,737 | [
"VisIt"
] | 880b362a8cb1f3303bcd50c30ee766303fb230bf04ab01690ad71609f26a4c8e |
'''
More information at: http://www.pymolwiki.org/index.php/elbow_angle
Calculate the elbow angle of an antibody Fab complex and optionally draw a
graphical representation of the vectors used to determine the angle.
NOTE: There is no automatic checking of the validity of limit_l and limit_h
values or of the assignm... | demharters/git_scripts | my_elbow_angle_tcr_imgt.py | Python | apache-2.0 | 7,744 | [
"PyMOL"
] | 4689ad599ffa9e6df528ec2a235e05d0defbb3fa12119f7e97c2196902e1ebe9 |
#!/usr/bin/env python
# Copyright 2014, Rackspace US, Inc.
#
# 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... | stevelle/openstack-ansible | scripts/os-ansible-role-requirements.py | Python | apache-2.0 | 9,841 | [
"Galaxy"
] | c9c3f94ced297c289809a78fa5520f93bf274eb9a2971e9aed00db9971861ca7 |
from __future__ import division
import os, subprocess, logging, sys, argparse, inspect, csv, time, re, shutil, datetime, glob, platform, multiprocessing, itertools, hashlib, math
from natsort import natsorted
import warnings
from Bio import SeqIO
with warnings.catch_warnings():
warnings.simplefilter('ignore')
f... | alexandrelenz/funregulation | lib/library.py | Python | bsd-2-clause | 142,010 | [
"BLAST",
"Biopython"
] | 549e390357031ab1a3cfaa9a26659051be3637b3e3d9070a44e464f3c3212ac6 |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
"""Defines ... | nuclear-wizard/moose | python/MooseDocs/base/renderers.py | Python | lgpl-2.1 | 15,670 | [
"MOOSE"
] | 17dafbd43effdddaa9c220f7138306b080012a14ca0c2451f794f6e432e674a5 |
from SimpleCV.base import *
import scipy.signal as sps
import scipy.optimize as spo
import numpy as np
import copy, operator
class LineScan(list):
"""
**SUMMARY**
A line scan is a one dimensional signal pulled from the intensity
of a series of a pixels in an image. LineScan allows you to do a series... | nils-werner/SimpleCV | SimpleCV/LineScan.py | Python | bsd-3-clause | 36,076 | [
"Gaussian"
] | a39167420542155e7c30c60cfd68d06dcda3766ef80767386a5cde9959d2c2bf |
# (c) 2015, Brian Coca <briancoca+dev@gmail.com>
#
# This file is part of Ansible
#
# Ansible 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... | blueboxgroup/ansible | lib/ansible/plugins/action/patch.py | Python | gpl-3.0 | 2,534 | [
"Brian"
] | f592e147b032427da8322c06d143831fb8d07bad11e71da745691990527b0ee8 |
from .proposal_list_view import ProposalListView
class DayViewPage(ProposalListView):
"""Page showing all proposals for a day."""
def visit(self, day):
return super().visit("day/{}".format(day))
| abingham/accu-2017-elm-app | tests/features/pages/day_view.py | Python | mit | 214 | [
"VisIt"
] | 8415b5276d896e19b14fd09645f035558155beba7a90e3d90cdfc7bffbab8722 |
#!/usr/bin/python
import argparse
import os
import pysam
def get_match_length(almnt):
"""
Gets length of perfect matches from cigar string
"""
if almnt.cigar is None:
return 0
return sum(length for cigar, length in almnt.cigar if cigar == 0)
def get_rpf(bam, out_file, min_length=28, ... | YeoLab/gscripts | gscripts/riboseq/read_filter.py | Python | mit | 1,498 | [
"pysam"
] | b45de28044e4ce7e39c30c9be28de5bdcedf96a0e3f3181ba85daa9aa6f1d953 |
# -*- coding: utf-8 -*-
# Django settings for seahub project.
import sys
import os
import re
import random
import string
from seaserv import FILE_SERVER_ROOT, FILE_SERVER_PORT
PROJECT_ROOT = os.path.join(os.path.dirname(__file__), os.pardir)
DEBUG = False
TEMPLATE_DEBUG = DEBUG
ADMINS = (
# ('Your Name', 'your... | Chilledheart/seahub | seahub/settings.py | Python | apache-2.0 | 18,335 | [
"VisIt"
] | a70e43f129832d80074a8243112079bf8bfffb7386b0103c1296954082f455cb |
# Maked by Mr. Have fun! Version 0.2
# Shadow Weapon Coupons contributed by BiTi for the Official L2J Datapack Project
# Visit http://forum.l2jdp.com for more details
import sys
from com.l2scoria.gameserver.model.quest import State
from com.l2scoria.gameserver.model.quest import QuestState
from com.l2scoria.gameserver.... | zenn1989/scoria-interlude | L2Jscoria-Game/data/scripts/quests/408_PathToElvenwizard/__init__.py | Python | gpl-3.0 | 12,096 | [
"VisIt"
] | 3c77678f9eb4fd4894d6482b7a1ad59e88d1b106b7cb811e5eba9d6e1207c776 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
import time
# !! This is the configuration of Nikola. !! #
# !! You should edit it to your liking. !! #
# ! Some settings can be different in different languages.
# ! A comment stating (translatable) is used to denote those.
# ! There are two ways to... | wcmckee/writersdenhamilton | conf.py | Python | mit | 43,991 | [
"VisIt"
] | ca5db22da6b8543ad7ef62a95f4104f74e6deb88f1ba80108df52bec688e9563 |
from math import cos
from math import sin
from math import atan2
from math import sqrt
import sympy
import numpy as np
from prototype.utils.quaternion.hamiltonian import quat2rot
from prototype.utils.quaternion.hamiltonian import quatmul
from prototype.utils.quaternion.hamiltonian import quatangle
def linearity_ind... | chutsu/robotics | prototype/estimation/inverse_depth.py | Python | gpl-3.0 | 5,399 | [
"Gaussian"
] | da4dc4da4e543521ffb0ff99be65ce6ddd4137077de082096f97fb89d6854279 |
# Thai Thien
# 1351040
from __future__ import division
import math
import numpy as np
from scipy import signal
import scipy.stats as st
import cv2
def test():
print('success')
## convert color image to grayscale image
def bgr2gray(img):
ret = np.zeros((img.shape[0], img.shape[1]),
dtype = img.d... | ttpro1995/CV_Assignment01 | util.py | Python | mit | 5,235 | [
"Gaussian"
] | 3d0b94d6e7ca1bce400ab524f3a9657d56cd41f3e341c38f47a121fd1a2a1c21 |
# Copyright 2007-2022 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later ve... | hyperspy/hyperspy | hyperspy/tests/drawing/test_plot_signal_tools.py | Python | gpl-3.0 | 4,817 | [
"Gaussian"
] | 53ee25193f3cce9770176e9c5914477ab3b7217789d666bdd3a7416ba247b0d7 |
"""Test functions for linalg._solve_toeplitz module
"""
from __future__ import division, print_function, absolute_import
import numpy as np
from scipy.linalg._solve_toeplitz import levinson
from scipy.linalg import solve, toeplitz, solve_toeplitz
from numpy.testing import assert_equal, assert_allclose
import pytest
f... | mbayon/TFG-MachineLearning | venv/lib/python3.6/site-packages/scipy/linalg/tests/test_solve_toeplitz.py | Python | mit | 4,105 | [
"Gaussian"
] | 7c106371cccaae6d1d7c1c063a3d0618a4829b940d9b158a61a59a969a0268b1 |
"""
Set up the plot figures, axes, and items to be done for each frame.
This module is imported by the plotting routines and then the
function setplot is called to set the plot parameters.
"""
from __future__ import absolute_import
from __future__ import print_function
#--------------------------
def setplot... | clawpack/adjoint | paper2_examples/acoustics_1d_ex1/adjoint/setplot.py | Python | bsd-2-clause | 4,472 | [
"NetCDF"
] | dfa4e0373905efcd18ae3c93423ce8383c37ec29d950e25ad161c99928cd17f7 |
# -*- coding: utf-8 -*-
# Copyright (c) 2015-2018, Exa Analytics Development Team
# Distributed under the terms of the Apache License 2.0
"""
Interfaces
####################
This subpackage contains support for (small) third-party packages and
external file types.
"""
from .cclib import universe_from_cclib
from .xyz im... | alexvmarch/atomic | exatomic/interfaces/__init__.py | Python | apache-2.0 | 379 | [
"cclib"
] | 97e070462b7dc5cec22570b01826e4a820265de8b9c315bdac3b7754750609ea |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2015 Stanford University and the Authors
#
# Authors: Christoph Klein
# Contributors:
#
# MDTraj is free software: y... | swails/mdtraj | mdtraj/geometry/rdf.py | Python | lgpl-2.1 | 3,846 | [
"Gromacs",
"MDTraj"
] | bdfd9103e22b98343b98577532192035038fb2f5732e1975da282b362d649a34 |
# -*- coding: utf-8 -*-
"""
Bok choy acceptance tests for Entrance exams in the LMS
"""
from textwrap import dedent
from common.test.acceptance.tests.helpers import UniqueCourseTest
from common.test.acceptance.pages.studio.auto_auth import AutoAuthPage
from common.test.acceptance.pages.lms.courseware import Courseware... | synergeticsedx/deployment-wipro | common/test/acceptance/tests/lms/test_lms_entrance_exams.py | Python | agpl-3.0 | 4,131 | [
"VisIt"
] | 1be5dcdbefcdb882961f7848e3821f1dd0c5b23a813abe4e9e41e13a3dff1b3a |
"""
End to end tests for HTML Components
"""
from uuid import uuid4
from bok_choy.web_app_test import WebAppTest
from edxapp_acceptance.pages.studio.utils import add_components
from edxapp_acceptance.pages.lms.course_nav import CourseNavPage
from regression.pages.studio.course_outline_page import (
CourseOutlineP... | raeeschachar/edx-e2e-mirror | regression/tests/common/test_html_component.py | Python | agpl-3.0 | 9,420 | [
"VisIt"
] | 8fd68d2863f24d5252a5c79657556338ee043ead652ec817122d85fcf32e2c07 |
# Copyright 2004, Magnus Hagdorn
#
# This file is part of GLIMMER.
#
# GLIMMER is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# G... | glimmer-cism/PyCF | PyCF/CF_loadfile.py | Python | gpl-2.0 | 27,236 | [
"NetCDF"
] | ba78232dd8de61efd92a82c3eb2230657c0b15b278ce17efa554a1bac793c10f |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | jturney/psi4 | psi4/share/psi4/databases/O24by5mb.py | Python | lgpl-3.0 | 58,598 | [
"Psi4"
] | dbfe28e03bb45fe0ff3373d2058a0c8cdd994b8e60e78b09078564f961b6958c |
from example import Example
travel_dev_examples = [
Example(input='airfare from san angelo tx to shreveport la',
semantics={'domain': 'travel',
'origin': {'id': 5530022, 'name': 'San Angelo, TX, US'},
'destination': {'id': 4341513, 'name': 'Shreveport, LA, ... | wcmac/sippycup | travel_examples_dev.py | Python | gpl-2.0 | 23,201 | [
"CASINO",
"COLUMBUS"
] | f33f6150011450653acba4009a96224f5b57de1e6266427bf241369d1bd26530 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | pli3/e2-openwbif | plugin/controllers/views/web/sleeptimer.py | Python | gpl-2.0 | 5,574 | [
"VisIt"
] | 68637941cccf3802f7a326a004aeed8f86dad5b1452225bfe15c1b2b6a54e21f |
import os
#import sys
import functools
import re
import urllib
#import contextlib
#import traceback
#import numpy
import operator
from collections import Iterable
#
#from config.Config import STATIC_PATH, GALAXY_BASE_DIR, URL_PREFIX
#from third_party.decorator import decorator
#
#from config.Config import PROCESSED_DAT... | sveinugu/gtrackcore | gtrackcore/util/CommonFunctions.py | Python | gpl-3.0 | 24,103 | [
"Galaxy"
] | d7961848b6177213fc079d64bb86ddfaee6fc48594b1e17177ff56495639e80f |
# -*- coding: utf-8 -*-
import pytest
from django.core.urlresolvers import reverse
pytestmark = pytest.mark.django_db
global_footer_links = [
'About',
'Developers',
'Privacy',
'Report an issue',
]
def assert_title_and_links_on_page(browser, url, title, links_text):
browser.visit(url)
assert... | vipul-sharma20/fossevents.in | tests/frontend/test_page_contents.py | Python | mit | 869 | [
"VisIt"
] | 6c45b5faa50cd040b8af77768909ae6ae4e40eaf85364da51076b3a0669d301b |
# The MIT License (MIT)
#
# Copyright (c) 2015 Brian Wray (brian@wrocket.org)
#
# 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
# ... | wrocket/Tulip-Chess | utils/square_colors.py | Python | mit | 1,657 | [
"Brian"
] | c3ca817301a553515050383356eee13b40be4ed573990b65a7604dcbd07ce6c6 |
# Authors: Veeresh Taranalli <veeresht@gmail.com>
# License: BSD 3-Clause
"""
============================================
Channel Models (:mod:`commpy.channels`)
============================================
.. autosummary::
:toctree: generated/
bec -- Binary Erasure Channel.
bsc ... | tarunlnmiit/CommPy | commpy/channels.py | Python | bsd-3-clause | 5,571 | [
"Gaussian"
] | 733f2a5576bb2d8ef94c1a9ea11f6fdcda23d1b96eb0facd81c58d5c804e8f03 |
from sqlalchemy.sql import table, column, ClauseElement, operators
from sqlalchemy.sql.expression import _clone, _from_objects
from sqlalchemy import func, select, Integer, Table, \
Column, MetaData, extract, String, bindparam, tuple_, and_, union, text,\
case, ForeignKey, literal_column
from sqlalchemy.testing... | robin900/sqlalchemy | test/sql/test_generative.py | Python | mit | 69,168 | [
"ADF",
"VisIt"
] | e25708e4fb65196186ff99eb2c45ccb1a22f753d1031c52ca76c4535707a58aa |
"""This module reads 5 cm soil temperature (Tsoil) and volumetric
water content (VWC) from the Climate Forecast System (CFS) Version 2
(CFSv2) Reanalysis (CFSR; Saha et al (2010)). Data are read for the
CFSR grid cells containing specified longitude and latitude
coordinates. The data are read from the NOAA NOMADS sys... | Timothy-W-Hilton/CFSR_Site_Extractor | CFSR_site_extractor.py | Python | mit | 15,695 | [
"Gaussian",
"NetCDF"
] | 9157079acc47156b7141388689b3ef73753c08f078ce5fb21a77b433e5355526 |
#from matplotlib import rc
#rc('text', usetex=True)
fontsize = 16
contourFontsize = 12
showColorbar = False
xmin = -1
xmax = 1
ymin = -1.05
ymax = 1
import sys,os
import numpy
import shogun
from shogun import GaussianKernel, LinearKernel, PolyKernel
from shogun import RealFeatures, BinaryLabels
from shogun import L... | MikeLing/shogun | applications/easysvm/tutpaper/svm_params.py | Python | gpl-3.0 | 12,908 | [
"Gaussian"
] | 8356748c78f373239daa930e08bdbf3f72bfff6be2d31394d89baeeef4156739 |
__all__ = ["Mofa"]
import numpy as np
import matplotlib.pyplot as pl
from scipy.cluster.vq import kmeans
from scipy.linalg import inv
from matplotlib.patches import Ellipse
from . import _algorithms
class Mofa(object):
"""
Mixture of Factor Analyzers
calling arguments:
[ROSS DOCUMENT HERE]
in... | rossfadely/mofa | mofa/mofa.py | Python | mit | 11,258 | [
"Gaussian"
] | 7ec369d31f6296ed313216849fb48389767b3f6d0e30a810e660e0304dd90d4b |
#!/usr/bin/python
# Maintained in full by:
# Catalyst Team <catalyst@gentoo.org>
# Release Engineering Team <releng@gentoo.org>
# Copyright 2013 Brian Dolbec <dolsen@gentoo.org>
'''resume.py
Performs autoresume tracking file operations such as
set, unset, is_set, is_unset, enabled, clear_all
'''
import os
from sna... | elitak/catalyst | catalyst/base/resume.py | Python | gpl-2.0 | 3,163 | [
"Brian"
] | dbfef03d1aca67f51951bfb726259667e3d6bc36b60c246a9115c15cdc131515 |
# -*- coding: utf-8 -*-
__author__ = "HarshaRani"
__credits__ = ["Upi Lab"]
__license__ = "GPL3"
__version__ = "1.0.0"
__maintainer__ = "HarshaRani"
__email__ = "hrani@ncbs.res.in"
__status__ = "Development"
__updated__ = "Sep 03 2018"
'''
mooseAddChemSolver and mooseD... | upibhalla/moose-core | python/moose/chemUtil/add_Delete_ChemicalSolver.py | Python | gpl-3.0 | 5,366 | [
"MOOSE"
] | fe947a5bfb6633cee549dbd1fca0d4d54b34b35650ab5026bb9c9076a9f60815 |
class FrameReader(object):
def __init__(self, filename):
file_ = open(filename, 'r')
print("Opened file: {0}".format(filename))
def __enter__(self):
return self
def __exit__(self, exc_type, exc_value, traceback):
file_.close()
def getNumFrames(self):
"""
... | jag1g13/dipoleAnalysis | marleyFunctions.py | Python | mit | 8,997 | [
"LAMMPS"
] | 0e0c7b716a8dc8e09edafb043d078209eba9a8b5a2a5f4342b06d126def73f14 |
#\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\#
import os
from GangaCore import _gangaVersion
from GangaGaudi.Lib.RTHandlers.RunTimeHandlerUtils import master_sandbox_prepare, sandbox_prepare, script_generator
from GangaDirac.Lib.RTHandlers.DiracRTHUtils import dirac_inputdata, dirac_oup... | ganga-devs/ganga | ganga/GangaGaudi/Lib/RTHandlers/GaudiDiracRunTimeHandler.py | Python | gpl-3.0 | 5,599 | [
"DIRAC"
] | 0b91d8ea107011cd3990beee64462429e6294bbb6cde59c3c9a0a1cdfcf59c5d |
# Copyright 2010-2017, The University of Melbourne
# Copyright 2010-2017, Brian May
#
# This file is part of Karaage.
#
# Karaage is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License... | brianmay/karaage | karaage/tests/unit.py | Python | gpl-3.0 | 1,411 | [
"Brian"
] | 0d1c60920fc616e0f40c9a2fccd6ccc77ed9943cc24860d71b922593601d8a1c |
# Copyright (C) 2010, Jesper Friis
# (see accompanying license files for details).
"""Utility tools for convenient creation of slabs and interfaces of
different orientations."""
import numpy as np
def gcd(seq):
"""Returns greatest common divisor of integers in *seq*."""
def _gcd(m, n):
while n:
... | slabanja/ase | ase/utils/geometry.py | Python | gpl-2.0 | 16,615 | [
"ASE",
"CRYSTAL"
] | b0cd7d6b1f8617673ff7d58a392b3d5082b89f4afaeab2e7d23f7c5bab5ad580 |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""The BROCCOLI module provides classes for interfacing with the `BROCCOLI
<http://github.com/wanderine/BROCCOLI>`_ command line tools.
Change directory to provide relative paths for doctests
>>> i... | wanderine/nipype | nipype/interfaces/broccoli/preprocess.py | Python | bsd-3-clause | 9,996 | [
"Gaussian"
] | 8192595d4afbb051d6c543d21dfad28f22b10217b428b0669be4931b197bd497 |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | RyanSkraba/beam | sdks/python/apache_beam/runners/dataflow/dataflow_runner_test.py | Python | apache-2.0 | 21,045 | [
"VisIt"
] | 26bac7587155afb2dd7e494314010ea8ace9f4ca7bf6fbb205cca17620687a3c |
from distutils.core import setup
import os
def read(fname):
return open(os.path.join(os.path.dirname(__file__), fname)).read()
setup(
name='weathercli',
version='2.3.1',
author='Brian Riley',
author_email='brian@btriley.com',
description="A command line weather tool",
url='https://github... | brianriley/weather-cli | setup.py | Python | bsd-2-clause | 841 | [
"Brian"
] | 0e2b7bf45b91caf72dc7d225a16d2a7e359685ecda0ff0f206267dde3a340556 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# . s.ssmuse.dot /ssm/net/hpcs/201402/02/base \
# /ssm/net/hpcs/201402/02/intel13sp1u2 /ssm/net/rpn/libs/15.2
# Author: Stephane Chamberland <stephane.chamberland@canada.ca>
# Copyright: LGPL 2.1
"""
Module librmn is a ctypes import of librmnshared.so
The l... | meteokid/python-rpn | lib/rpnpy/librmn/proto.py | Python | lgpl-2.1 | 91,550 | [
"Gaussian"
] | b26c5916ca364cc161ab7a49141f5e18b6627ce8bd2f08c5b3a1c8f958673c74 |
#!/usr/bin/python
import subprocess
import os
import sys
from subprocess import PIPE
from optparse import OptionParser
parser = OptionParser()
parser.add_option("-f",dest="fixedCID",help="case ID for fixed image")
parser.add_option("-m",dest="movingCID",help="case ID for moving image")
parser.add_option("-s",dest="... | rjosest/WTC | Scripts/WTCRegistration.py | Python | bsd-3-clause | 7,497 | [
"Gaussian"
] | c09419f02a9503af8b941f8e15fb9c4a9339064b1452dddabbd3f45ca8c42ff7 |
#!/usr/local/bin/env python
#=============================================================================================
# MODULE DOCSTRING
#=============================================================================================
"""
WCA fluid and WCA dimer systems.
DESCRIPTION
COPYRIGHT
@author John D. Cho... | nrego/westpa | lib/examples/wca-dimer_openmm/we_exec/wcadimer.py | Python | gpl-3.0 | 10,747 | [
"OpenMM"
] | 3a3c3c3fc37abf50fc784be6dda95dfb3d74e8f30a8fc03c80e3fbb5dbad8569 |
from flask import Flask, render_template, session, request, redirect
import random
app = Flask(__name__)
app.secret_key = 'my_secret_key'
@app.route('/')
def index():
if not 'gold' in session:
session['gold'] = 0
if not 'activities' in session:
session['activities'] = []
return render_temp... | jiobert/python | Quintana_Jerrod/Assignments/flask_olympics/olympics7/server.py | Python | mit | 1,280 | [
"CASINO"
] | 5957461f9ea7f5e152a9347eba9483a7efc021b8ac92a3adcd3792faef6eb226 |
from django.conf.urls import url
from interaction import views
# from django.views.generic import TemplateView
urlpatterns = [
url(r'^$', views.InteractionSelection.as_view(), name='selection'),
url(r'^list', views.list_structures, name='list'),
url(r'^calculate', views.showcalculation, name='showcalculat... | cmunk/protwis | interaction/urls.py | Python | apache-2.0 | 1,278 | [
"CRYSTAL"
] | 961fe26b1c3c62409ddd9a4fe3be0740a4c094a4cdae58735092617c570a2912 |
import inspect
from traceback import format_exc
from functools import wraps
from galaxy import eggs
eggs.require( "Paste" )
import paste.httpexceptions
from galaxy.web.framework import url_for
from galaxy import util
from galaxy.exceptions import error_codes
from galaxy.exceptions import MessageException
from galaxy.... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/web/framework/decorators.py | Python | gpl-3.0 | 14,855 | [
"Galaxy"
] | 2f4358a35a1d6e81c649029febbdbab3944bc6c641f51c70e2beb01f35a388c4 |
#pylint: disable=missing-docstring
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/... | harterj/moose | python/chigger/filters/TransformFilter.py | Python | lgpl-2.1 | 2,003 | [
"MOOSE",
"VTK"
] | 960a488c0f47954e85fe4a3c2896ff0ee10df0ba7ea484be42a9138196ae22d9 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | pli3/e2-openwbif | plugin/controllers/views/ajax/config.py | Python | gpl-2.0 | 16,817 | [
"VisIt"
] | 76bf9dd94527390edb4a0800a49aa7c037e3097e0af578061254358812313ad2 |
import nest as n
import nest.raster_plot as rp
import nest.topology as tp
import pylab as pl
import numpy as np
n.ResetKernel()
C_E = 0.5
C_I = 0.2
g_E = 25.
g_I = 20.
V_th = -50.
V_reset = -55.
tau_AMPA = 2.4
tau_NMDA = 100.
tau_GABA = 7.
tau_m_E = C_E/g_E
tau_m_I = C_I/g_I
tau_pre = 20.
tau_post = 10.
c_IE = 0.1
c_E... | shiina/invariant-object-recognition | weight_tuning.py | Python | lgpl-3.0 | 4,828 | [
"Gaussian",
"NEURON"
] | 90399266fe65c1863622537fd2c2043b4c827bdbb7eabd22175496b9405819e8 |
# standard modules
import calendar
import datetime
import logging
import os
# 3rd party modules
from scipy.interpolate import griddata
import numpy
import xlwt
# PFP modules
from scripts import constants as c
from scripts import pfp_io
from scripts import pfp_ts
from scripts import pfp_utils
logger = logging.getLogger... | OzFlux/PyFluxPro | scripts/pfp_clim.py | Python | gpl-3.0 | 11,811 | [
"NetCDF"
] | 1515ccc22a277bfc23198a99df96e4018a82536eb1864e0b3b3175967340cc1e |
# -*- coding: utf-8 -*-
## Description: class NetworkML for loading NetworkML from file or xml element into MOOSE
## Version 1.0 by Aditya Gilra, NCBS, Bangalore, India, 2011 for serial MOOSE
## Version 1.5 by Niraj Dudani, NCBS, Bangalore, India, 2012, ported to parallel MOOSE
## Version 1.6 by Aditya Gilra, NCBS, Ban... | dharmasam9/moose-core | python/moose/neuroml/NetworkML.py | Python | gpl-3.0 | 25,767 | [
"MOOSE",
"NEURON"
] | 5ba64e8480275238b56ad2b6a8e8210e962efd84d0b37aa99407ec71015bda24 |
"""Defines the semantic model, a tree data structure representing a valid stencil kernel program.
The semantic model is specified using Asp's tree_grammar DSL. The
stencil_model classes have generated assertions and additional manual
structural checks to prevent the construction of a tree not
corresponding to a valid... | pbirsinger/aspNew | tools/debugger/stencil/stencil_model.py | Python | bsd-3-clause | 3,587 | [
"VisIt"
] | f27efec3c20e1041e656f4a26f3d8c912e496cbc1921bdfbb90fc7cfae03d2a6 |
"""
Handle PDB files.
"""
__author__ = "Steven Kearnes"
__copyright__ = "Copyright 2014, Stanford University"
__license__ = "BSD 3-clause"
from collections import OrderedDict
class PdbReader(object):
"""
Handle PDB files.
Also supports conversion from PDB to Amber-style PQR files.
"""
def parse... | rbharath/vs-utils | vs_utils/utils/pdb_utils.py | Python | gpl-3.0 | 3,495 | [
"Amber"
] | 56ca71d8b427d60fb2e11fb548fcdffdcfaa75f0b5da548f6736e1e87b71ff05 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
urlpat... | ad-m/taravel | config/urls.py | Python | mit | 1,893 | [
"VisIt"
] | 1fd241d9b40627efb35b3cc70be0fd3512fb06ba1a89b5c74a76cbe1fd88e116 |
# Placeholder because distances moved
# Remove this in version 1.0
from __future__ import absolute_import
import warnings
with warnings.catch_warnings():
warnings.simplefilter('always', DeprecationWarning)
warnings.warn(("distances has moved to MDAnalysis.lib.distances "
"and will be removed... | kain88-de/mdanalysis | package/MDAnalysis/core/distances.py | Python | gpl-2.0 | 418 | [
"MDAnalysis"
] | f6663b92cf6ca697b8b5b9c9ade2a53bf67a270862eaee7cc501b39c81a3d247 |
#! /usr/bin/env python
"""Write structured grids to NetCDF files.
Write netcdf
++++++++++++
.. autosummary::
~landlab.io.netcdf.write.write_netcdf
"""
import pathlib
import numpy as np
import xarray as xr
from landlab.io.netcdf._constants import (
_AXIS_COORDINATE_NAMES,
_AXIS_DIMENSION_NAMES,
_NP_... | cmshobe/landlab | landlab/io/netcdf/write.py | Python | mit | 23,925 | [
"NetCDF"
] | 0a56267c0eabfd14703e603fd471a72433f0fda110ebf4ab4929581c992f200d |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkXMLPStructuredGridReader(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | chrisidefix/devide | modules/vtk_basic/vtkXMLPStructuredGridReader.py | Python | bsd-3-clause | 524 | [
"VTK"
] | ae55e8de3cae039ccac553044449b776fb4d7b44966bb40a3f1cdf666472401e |
# pylint: disable=unused-argument
import numpy as np
from scipy import stats
from .family import Family
class UnivariateFamily(Family):
def predict(self, model, posterior, linear_predictor):
"""Predict mean response"""
mean = self.link.linkinv(linear_predictor)
obs_n = mean.shape[-1]
... | bambinos/bambi | bambi/families/univariate.py | Python | mit | 5,830 | [
"Gaussian"
] | b0e553390e7705ec1ceac016c54d56991c26e568dc5c213eae12a81f64e6f7aa |
import math
import os
import shutil
import subprocess
import shlex
import pandas as pd
from cea import suppress_3rd_party_debug_loggers
from cea.resources.radiation_daysim.geometry_generator import BuildingGeometry
suppress_3rd_party_debug_loggers()
import py4design.py2radiance as py2radiance
from py4design.py3dmod... | architecture-building-systems/CEAforArcGIS | cea/resources/radiation_daysim/radiance.py | Python | mit | 24,119 | [
"EPW"
] | 55f85e17310e67d4f677e48efe7b38738e62bdd3ac8c75afce7a86cb300a18a6 |
# coding=utf8
#
# Copyright 2013 Dreamlab Onet.pl
#
# This library 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;
# version 3.0.
# This library is distributed in the hope that it will be useful,
# bu... | tikan/rmock | tests/func_tests/test_smtp.py | Python | lgpl-3.0 | 6,399 | [
"VisIt"
] | 1c4f1645057ca712e32c1446c45b8408b9cb26582a5c8c4ca89837f6de284886 |
#! /usr/bin/env python
# FIXME: if it requires a dirac.cfg it is not a unit test and should be moved to TestDIRAC
__RCSID__ = "$Id$"
from DIRAC.Core.Base.Script import parseCommandLine, getPositionalArgs
parseCommandLine()
from DIRAC.Resources.Storage.StorageFactory import StorageFactory
fro... | coberger/DIRAC | Resources/Storage/test/TestStoragePlugIn.py | Python | gpl-3.0 | 34,449 | [
"DIRAC"
] | 57d41e0790d1065a5329ac8af0a0a0161fb271a6635a5d233f6096ab349e7464 |
# -*- coding: utf-8 -*-
#
# hl_api.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (a... | kristoforcarlson/nest-simulator-fork | pynest/nest/hl_api.py | Python | gpl-2.0 | 49,009 | [
"NEURON",
"VisIt"
] | 574ad0fbd8490b608d31ba29d43e56681c6425c6e426c28ecdb670e41541ac55 |
"""
Description:
This provides a VTK widget for pyGtk. This embeds a vtkRenderWindow
inside a GTK widget. This is based on GtkVTKRenderWindow.py.
The extensions here allow the use of gtkglext rather than gtkgl and
pygtk-2 rather than pygtk-0. It requires pygtk-2.0.0 or later.
There is a working example ... | b3c/VTK-5.8 | Wrapping/Python/vtk/gtk/GtkGLExtVTKRenderWindow.py | Python | bsd-3-clause | 17,778 | [
"VTK"
] | 05667125ad0e257431ea678283d8baec708e815f1ca976857a52c687cb606768 |
# This example demonstrates the python wrapping of vtkManta classes.
# In order to run this example, first be sure that the python wrapping
# of VTK is working, either using vtkpython or the vanilla python interpreter.
# Then you must set the 'PYTHONPATH' environment variable to where the
# library files (libvtkMantaPy... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/Plugins/MantaView/VTK/Examples/python_wrapped_manta.py | Python | gpl-3.0 | 1,027 | [
"VTK"
] | a99e7b266fde62621e6aec3fc7810de58383ba726863ce73294336b77a855bb4 |
# 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 RGgbio(RPackage):
"""Visualization tools for genomic data.
The ggbio package exten... | iulian787/spack | var/spack/repos/builtin/packages/r-ggbio/package.py | Python | lgpl-2.1 | 3,415 | [
"Bioconductor"
] | f5a2f2128fd9f430e651ddcf8d92aaa6f7ec3767631e3c93ff6a6f515be32a17 |
#!/usr/bin/env python
# vim:fileencoding=utf-8
from __future__ import (unicode_literals, division, absolute_import,
print_function)
__license__ = 'GPL v3'
__copyright__ = '2013, Kovid Goyal <kovid at kovidgoyal.net>'
import inspect
from io import BytesIO
from repr import repr
from functools im... | pra85/calibre | src/calibre/db/tests/legacy.py | Python | gpl-3.0 | 37,251 | [
"MOOSE"
] | b61c1060c082f1b0bdd4f12265a63c8c94960bc3b58180d3d1fc0f6916531195 |
from setuptools import setup
__VERSION__ = '0.5.24'
ENTRY_POINTS = '''
[console_scripts]
add_matesequence=readtagger.cli.add_matesequence:annotate_mate
allow_dovetailing=readtagger.cli.allow_dovetailing:allow_dovetailing
annotate_softclipped_reads=readtagger.cli.annotate_softclipped_re... | bardin-lab/readtagger | setup.py | Python | mit | 2,676 | [
"Biopython",
"pysam"
] | e904ddc92d6b42d64dc6e446f69c4735527e20f5ee45c7e112969e633f68e983 |
import sys
import logging
import os
import argparse
import pysam
import numpy as np
import pickle
from collections import OrderedDict
from asyncore import read
class Item(object):
def __init__(self, chrom, start, end, category, name, strand):
self.chrom = chrom
self.start = start
self.end = end
self... | shengqh/ngsperl | lib/QC/rnaseqBamQC.py | Python | apache-2.0 | 6,883 | [
"pysam"
] | ce4d9cc1391b68ebe4ea9b80608254352ddaf2d69ee9b843620b205161f2847a |
r"""
This module is a ParaViewWeb server application.
The following command line illustrates how to use it::
$ pvpython -dr /.../pvw-flow.py --data /path/to/pfmetadata/file
--data /.../
Path to a pfmetadata file
Any ParaViewWeb executable script comes with a set of standard a... | Kitware/HPCCloud | pvw-dependencies/pv-flow/pvw-flow.py | Python | apache-2.0 | 5,218 | [
"ParaView"
] | 6b8e6e9a660583c869579b642a32f9343b8bc4e164b0588e65060e7df571fe5a |
"""
cell/NML2Cell.py
Contains pointCell class
Contributors: salvadordura@gmail.com
"""
from __future__ import unicode_literals
from __future__ import print_function
from __future__ import division
from __future__ import absolute_import
from future import standard_library
standard_library.install_aliases()
from cop... | thekerrlab/netpyne | netpyne/cell/NML2Cell.py | Python | mit | 916 | [
"NEURON"
] | fa0d02fb94f287fc0960415c1af386dc7f02836db36f051a42d06a282c026496 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | jdrudolph/scikit-bio | skbio/stats/ordination/tests/test_util.py | Python | bsd-3-clause | 2,281 | [
"scikit-bio"
] | 6388dca05b6207fcae38c25591c911eb869450e5cfb6285fe3680dc26eed66ff |
# Copyright (C) 2013, Walter Bender - Raul Gutierrez Segales
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This ... | rajul/sugar | extensions/cpsection/webaccount/view.py | Python | gpl-2.0 | 4,542 | [
"VisIt"
] | b8f94d8b336b82996f50720c6ac8184f5db6315d1fd5606951c0f41317640798 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: y... | ctk3b/mdtraj | mdtraj/geometry/hbond.py | Python | lgpl-2.1 | 17,603 | [
"MDTraj"
] | 9edf50bd5f17531a85dd650902ff59c1c07fe8075a18f3fa2b6a5dbb21c19f44 |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright 2012-2015 Thoeger Emil Rivera-Thorsen.
# Distributed under the terms of the GNU General Public License v. 3
# http://www.gnu.org/licenses/gpl-3.0.html
""" Standalone version of the profile builder class used in pychelle.
The module consists of a class and a co... | thriveth/Pychelle | pychelle/lpbuilder.py | Python | gpl-3.0 | 30,197 | [
"Gaussian"
] | 3d12990ff4d589ed16575a7d78d493fe707b4bc9549475b6defa748f7aca32f0 |
# Copyright (c) 2008, 2010, 2013 LOGILAB S.A. (Paris, FRANCE) <contact@logilab.fr>
# Copyright (c) 2014-2016 Claudiu Popa <pcmanticore@gmail.com>
# Licensed under the GPL: https://www.gnu.org/licenses/old-licenses/gpl-2.0.html
# For details: https://github.com/PyCQA/pylint/blob/master/COPYING
"""
unit test for visito... | arju88nair/projectCulminate | venv/lib/python3.5/site-packages/pylint/test/unittest_pyreverse_writer.py | Python | apache-2.0 | 3,551 | [
"VisIt"
] | ce76ac762c7fa930e2ece1a0066b378c4c0febc0f7df0fcc259136b3f9f632da |
import os
import sys
import sysconfig
from pysam.libchtslib import *
from pysam.libcsamtools import *
from pysam.libcbcftools import *
from pysam.libcutils import *
import pysam.libcutils as libcutils
import pysam.libcfaidx as libcfaidx
from pysam.libcfaidx import *
import pysam.libctabix as libctabix
from pysam.libct... | kyleabeauchamp/pysam | pysam/__init__.py | Python | mit | 3,235 | [
"pysam"
] | 254bcabfbc711522bff402a7a767bc71f6ccc67ecb1302549c144d5c9063bce7 |
#
# @file TestCompartmentType.py
# @brief CompartmentTypeType unit tests
#
# @author Akiya Jouraku (Python conversion)
# @author Sarah Keating
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generated automatically by converting the... | TheCoSMoCompany/biopredyn | Prototype/src/libsbml-5.10.0/src/bindings/python/test/sbml/TestCompartmentType.py | Python | bsd-3-clause | 4,480 | [
"VisIt"
] | 59b2d8678f4df854816287487104a657e150964fed47dc7f22c34205f1d3d7d4 |
import os
from collections import namedtuple
import numpy as np
from nose import tools as nt
from numpy.testing import assert_array_almost_equal
import neurom.view.dendrogram as dm
from neurom import load_neuron, get
from neurom.core.types import NeuriteType
_PWD = os.path.dirname(os.path.abspath(__file__))
DATA_PAT... | eleftherioszisis/NeuroM | neurom/view/tests/test_dendrogram.py | Python | bsd-3-clause | 3,627 | [
"NEURON"
] | 5891a7e86bc743c53a62ebac5df8ac2da18de5900e2f3a3656d77b4105621bf9 |
# (C) British Crown Copyright 2015 - 2016, Met Office
#
# This file is part of Iris.
#
# Iris 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 l... | QuLogic/iris | lib/iris/tests/unit/fileformats/netcdf/test_parse_cell_methods.py | Python | gpl-3.0 | 5,696 | [
"NetCDF"
] | 5a7740b497ce3fb8d18d38c886a60da1391acb65cfbfb7c03940c9a450b95074 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2017 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB ... | michaelrup/scancode-toolkit | src/licensedcode/frequent_tokens.py | Python | apache-2.0 | 77,004 | [
"Amber",
"BLAST",
"Brian",
"CASINO",
"COLUMBUS",
"CRYSTAL",
"Elk",
"Galaxy",
"VisIt",
"exciting"
] | cb758f4d8dc9db2b2dc1c78393b3d59e8671a92f7cc3fad4ea067faa86ced388 |
# -*- coding: utf-8 -*-
# Copyright 2019-2020 Mike Fährmann
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License version 2 as
# published by the Free Software Foundation.
"""Extractors for https://www.tsumino.com/"""
from .common import Galle... | mikf/gallery-dl | gallery_dl/extractor/tsumino.py | Python | gpl-2.0 | 11,914 | [
"VisIt"
] | 218ea6f23ead4e3922f24992fc4dc885e5a8ba272413115c75dd77b97282f43b |
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