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#! /usr/bin/env python
# -*- coding: utf-8 -*-
#
# Python motu client
#
# Motu, a high efficient, robust and Standard compliant Web Server for Geographic
# Data Dissemination.
#
# http://cls-motu.sourceforge.net/
#
# (C) Copyright 2009-2010, by CLS (Collecte Localisation Satellites) -
# http://www.cls.fr - and Cont... | clstoulouse/motu-client-python | src/motuclient/motu_utils/motu_api.py | Python | lgpl-3.0 | 28,317 | [
"NetCDF"
] | 3a74c7b52191435aa2b95967901a09c574d8a95787e85a0d1fece9f4e12669a5 |
"""
Multilayer Perceptron
"""
__authors__ = "Ian Goodfellow"
__copyright__ = "Copyright 2012-2013, Universite de Montreal"
__credits__ = ["Ian Goodfellow", "David Warde-Farley"]
__license__ = "3-clause BSD"
__maintainer__ = "LISA Lab"
import logging
import math
import sys
import warnings
import numpy as np
from thean... | KennethPierce/pylearnk | pylearn2/models/mlp.py | Python | bsd-3-clause | 172,926 | [
"Gaussian"
] | 4ac644c2176df177085e4b986dc7333f500339c962b4f07c26180d87c7fa17e6 |
import collections
import copy
import warnings
import numpy
import six
from chainer import cuda
from chainer import link as link_module
from chainer import serializer as serializer_module
from chainer import variable
def _sum_sqnorm(arr):
sq_sum = collections.defaultdict(float)
for x in arr:
with cu... | delta2323/chainer | chainer/optimizer.py | Python | mit | 26,468 | [
"Gaussian"
] | 7b3dde8642ace0cd4239b1c3bdb421a6689315b1a0aca793e4f9d051080dcd11 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | skosukhin/spack | var/spack/repos/builtin/packages/nco/package.py | Python | lgpl-2.1 | 2,685 | [
"NetCDF"
] | b47f696a88212a7f155e21dd05f4094e85df328570ac367c26ce7602d3feff15 |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | SamStudio8/scikit-bio | skbio/diversity/alpha/tests/test_gini.py | Python | bsd-3-clause | 2,238 | [
"scikit-bio"
] | 7391f9c63d61a720dab076b18461c9a476ccf98c8b6287c20181b287ee3077b1 |
from shutil import rmtree
from .machine import Machine
from stargate.exports.graphviz import GraphBuilder
import os
class App(object):
def __init__(self, root, target_dir='img'):
self.root = root
self.target_dir = target_dir
try:
rmtree(target_dir)
except FileNotFoundEr... | LaiTash/starschematic | stargate/app.py | Python | gpl-3.0 | 692 | [
"VisIt"
] | 7b83262eada13777b60e07f9e49c5414c0d0c7a8faa3446f8f1cbf7dbbb2cc7d |
# Copyright (C) 2018-2020 The Software Heritage developers
# See the AUTHORS file at the top-level directory of this distribution
# License: GNU General Public License version 3, or any later version
# See top-level LICENSE file for more information
from typing import Iterator, List, Optional, Tuple
from swh.model.h... | SoftwareHeritage/swh-storage | swh/storage/algos/snapshot.py | Python | gpl-3.0 | 7,114 | [
"VisIt"
] | 9edbbaf5233e6eeaf7459c8e538b9e8936adce040060b342912c1b928981edd2 |
#!/usr/bin/env python
from setuptools import setup, find_packages
setup(name='pasquino',
version='0.1',
description='A public square',
author='Brian Stack',
author_email='bstack01@gmail.com',
url='https://www.brianstack.net/',
packages=find_packages(),
)
| imbstack/pasquino | setup.py | Python | mit | 298 | [
"Brian"
] | 08956410741b7d409209a23e50fb6c2404d3a8714d30303bcaaf06ffd64dbab1 |
#!/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... | MOA-2011/enigma2-plugin-extensions-openwebif | plugin/controllers/views/mobile/channels.py | Python | gpl-2.0 | 7,457 | [
"VisIt"
] | e770c1172f6a6d81fa6d97db1efffbaf2b5b7d9632f38265056b533b1d04d36b |
#!/usr/bin/python
# ------------------------------------------------------------------------------
# Write to an Arduino to set RGB LEDs, begin with "START" magic string, write in
# GRB-order, then terminate with a newline.
#
# Requires PySerial that is installed through
# sudo apt-get install pyserial
# on OSX, vis... | n1ck3/ambiled-arduino | ambiled_arduino/serialcomms.py | Python | gpl-2.0 | 10,304 | [
"VisIt"
] | b0755b4eac6c839e0caea4d56036a1098d7542bc1da8b31832bcfa9d9d2ce71f |
#
# Copyright (C) 2017 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 vers... | KonradBreitsprecher/espresso | testsuite/rdf.py | Python | gpl-3.0 | 3,633 | [
"ESPResSo"
] | deb53ed91a4ad2af3492bb9cc9df7c1611f4f288fcefe73e86e3ed54fdb44b93 |
from datetime import datetime, timedelta
import requests
from django.core.cache import cache
from django.core.mail import send_mass_mail
from celery.task import task
from settings import *
@task(ignore_result=True)
def send_server_update_notification():
r = requests.get(GITHUB_API_URL + '/repos/' + GITHUB_USER + ... | SushiTee/teerace | teerace/lib/tasks.py | Python | bsd-3-clause | 2,360 | [
"VisIt"
] | b50f153a27cd085fc91a34b05dd02d15dc5d0ea07b83459dc5e6b9ce4367074c |
from earthpron import test
if __name__ == '__main__':
print 'Run with python -i to tinker with the "t" variable after execution'
t = test()
| andrewyang96/EarthPron | EarthPronApp/dry_run.py | Python | mit | 149 | [
"TINKER"
] | f0b4fab8103a8c710c64736f6fbd9114b93a0c45ef0e3559615dd7f505dab79a |
#!/galaxy/home/mgehrin/hiclib/bin/python
"""
Convert wiggle data to a binned array. This assumes the input data is on a
single chromosome and does no sanity checks!
usage: %prog score_file out_file < wiggle_data
-c, --comp=type: compression type (none, zlib, lzo)
"""
from __future__ import division
import sys
i... | bxlab/HiFive_Paper | Scripts/HiCLib/bx-python-0.7.1/build/scripts-2.7/wiggle_to_binned_array.py | Python | bsd-3-clause | 1,430 | [
"Galaxy"
] | 9d39bea80ea5ad4dbfdc1f25954d044c4aa346bedb04220f6c61855b99c161ad |
"""
Development tool and utility functions for testing and test data generation.
"""
# Copyright (C) 2009-2015 Thomas Aglassinger
#
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either ... | butterhirsch/newcutplace | tests/dev_test.py | Python | lgpl-3.0 | 14,791 | [
"Amber",
"Brian",
"CRYSTAL"
] | 38bef22e46f62a268107c32c33c97945b6e76ad48d8ebfc734c3931b378a8d73 |
"""
Update Users and Groups from VOMS on CS
"""
import os
from DIRAC.Core.Base.AgentModule import AgentModule
from DIRAC.ConfigurationSystem.Client.CSAPI import CSAPI
from DIRAC.FrameworkSystem.Client.NotificationClient import NotificationClient
from DIRAC.Core.Security.VOMSService ... | Andrew-McNab-UK/DIRAC | ConfigurationSystem/Agent/UsersAndGroups.py | Python | gpl-3.0 | 16,358 | [
"DIRAC"
] | 21f9e3525210bff1b6e0e9f4cadecb3999a23950391f7897018cac143863892d |
#!/usr/bin/env python
# run tests with: python -m unittest test_model
# or python -m unittest discover
import os
import sys
import unittest
import fityk
class TestCopy(unittest.TestCase):
def setUp(self):
self.ftk = fityk.Fityk()
self.ftk.set_option_as_number("verbosity", -1)
d... | wojdyr/fityk | tests/test_model.py | Python | gpl-2.0 | 5,955 | [
"Gaussian"
] | c8111cad0cd08d8b368bc051c82384bb4111d119efa79222d7c7c1c9928ccaa3 |
#!/usr/bin/env python
# filename: germline_dbs.py
#
# Copyright (c) 2016 Bryan Briney
# License: The MIT license (http://opensource.org/licenses/MIT)
#
# 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 S... | briney/abstar | abstar/utils/build_germline_dbs.py | Python | mit | 14,498 | [
"BLAST"
] | b2e51a2514b6a6a307d36c1e558bbe80a3657b04e1a6a4d33ebd31795f86193d |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-phishingprotection | tests/unit/gapic/phishingprotection_v1beta1/test_phishing_protection_service_v1_beta1.py | Python | apache-2.0 | 58,807 | [
"Octopus"
] | 4825eb46087bb6da66f10839fcb43bce6b5f9423a67f96b3930b73801661bf16 |
from django import forms
from django.conf import settings
from django.contrib.admin.widgets import AdminRadioSelect, AdminRadioFieldRenderer
from edc_constants.constants import SCHEDULED, UNSCHEDULED
from lab_requisition.forms import RequisitionFormMixin
from bcvp.bcvp.choices import STUDY_SITES
from bcvp.bcvp_subjec... | botswana-harvard/bcvp | bcvp/bcvp_lab/forms/subject_requisition_form.py | Python | gpl-2.0 | 3,106 | [
"VisIt"
] | eda2007bfcabf3cd7b3de820bfe6497e01bf4edbe7dcb740004950fab4903ced |
#!/usr/bin/env python
"""
Created by stevertaylor
Copyright (c) 2014 Stephen R. Taylor
Code contributions by Rutger van Haasteren (piccard) and Justin Ellis (PAL/PAL2).
"""
from __future__ import division
import os, math, optparse, time, cProfile
import json, sys, glob
import cPickle as pickle
from time import gmti... | stevertaylor/NX01 | NX01_master.py | Python | mit | 352,478 | [
"Gaussian"
] | 543212febccf137e56002962d5f0db644ebb9ac90f60e4493a343139dc1f9960 |
#!/usr/bin/env python
# File created on 13 Jul 2012
from __future__ import division
__author__ = "Greg Caporaso"
__copyright__ = "Copyright 2011, The QIIME project"
__credits__ = ["Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.9.1-dev"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
from ... | adamrp/qiime | qiime/map_reads_to_reference.py | Python | gpl-2.0 | 14,828 | [
"BWA"
] | a87f31ef0c0cc4fe2c4caa2a0523a0c291c3ee887bb57ddc3e9e76770c5ef236 |
# S.D. Peckham
# October 13, 2009
# December 2, 2009 (updated open_new_file to use "info")
# June 2010 (streamlined a bit more)
import os
import sys
import time
import numpy
import bov_files
import file_utils
import rti_files
# import Nio # (a module in the PyNIO package)
#--------------------------------------... | mdpiper/topoflow | topoflow/utils/ncgs_files_Nio.py | Python | mit | 18,365 | [
"NetCDF"
] | 0831523f48055ddb9279ef309bd3b7baa2527a69ad8fb1509f70b97059790856 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007 Brian G. Matherly
# Copyright (C) 2010 Nick Hall
# Copyright (C) 2011 Tim G L Lyons
#
# 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
#... | arunkgupta/gramps | gramps/gen/proxy/private.py | Python | gpl-2.0 | 40,244 | [
"Brian"
] | 37f966f4eef0ef1b2ac7be0911656c7d5dcc4637b50597c17228cb2239225190 |
import argparse
from director.consoleapp import ConsoleApp
from director import cameraview
from director import vtkAll as vtk
def parseChannelArgument(defaultChannel='MULTISENSE_CAMERA_LEFT'):
parser = argparse.ArgumentParser()
parser.add_argument('-c', '--channel', type=str, help='image channel', default=de... | mitdrc/director | src/python/tests/testImageView.py | Python | bsd-3-clause | 1,109 | [
"VTK"
] | 05d810f2205d5c972bf363cb7e828e57912b258a08f702ad66b24bab014e52a5 |
#!/usr/bin/env python
'''
Fly Copter in SITL
AP_FLAKE8_CLEAN
'''
from __future__ import print_function
import copy
import math
import os
import shutil
import time
import numpy
from pymavlink import mavutil
from pymavlink import mavextra
from pymavlink import rotmat
from pysim import util
from common import AutoTe... | fhedberg/ardupilot | Tools/autotest/arducopter.py | Python | gpl-3.0 | 288,053 | [
"Gaussian"
] | a196ff5eb6a810a70184b54fde30dfed7461f17754f12b6926d527abadb36f59 |
# Copyright 2018 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... | ghchinoy/tensorflow | tensorflow/python/keras/utils/kernelized_utils_test.py | Python | apache-2.0 | 5,099 | [
"Gaussian"
] | c2c340cf798a2e25529d008078cf7542e7a224730d491d13bbbe9e00c16bed83 |
########################################################################
# File: FTSClient.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/04/08 14:29:43
########################################################################
"""
:mod: FTSClient
.. module: FTSClient
:synopsis: FTS client
.. moduleauthor::... | vmendez/DIRAC | DataManagementSystem/Client/FTSClient.py | Python | gpl-3.0 | 16,233 | [
"DIRAC"
] | dbc41a24582701312d1120e42a0ce9a120b24d1faeacac6b242ab3f8d9f7b2d6 |
# -*- coding: utf-8 -*-
#!/usr/bin/env python
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007 Johan Gonqvist <johan.gronqvist@gmail.com>
# Copyright (C) 2007-2009 Gary Burton <gary.burton@zen.co.uk>
# Copyright (C) 2007-2009 Stephane Charet... | prculley/gramps | gramps/plugins/webreport/narrativeweb.py | Python | gpl-2.0 | 99,837 | [
"Brian"
] | 67c53fce2de3eebd560b605157ee30a7d9925e50b4dbcd2c7a2047ce083aea5c |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2013 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundati... | andrebellafronte/stoq | stoqlib/gui/test/test_financialreport_dialog.py | Python | gpl-2.0 | 2,510 | [
"VisIt"
] | 7599a5f9c33cfcc9be99fa05e68e61ab0223d8ecc61986f33d406524e9923569 |
# Wrapper for the shortest augmenting path algorithm for solving the
# rectangular linear sum assignment problem. The original code was an
# implementation of the Hungarian algorithm (Kuhn-Munkres) taken from
# scikit-learn, based on original code by Brian Clapper and adapted to NumPy
# by Gael Varoquaux. Further impr... | pizzathief/scipy | scipy/optimize/_lsap.py | Python | bsd-3-clause | 3,950 | [
"Brian"
] | 6528fd26fdb612371708b7139b8429fdea5f4aa31482ca63799e0605dc64e0ce |
#!/usr/bin/env python
import csv
import getpass
import json
import os
import re
import requests
import sys
from BeautifulSoup import BeautifulSoup
from optparse import OptionParser
from urlparse import urljoin
EMAILS = {'Singh A K': 'ambuj@cs.ucsb.edu',
'Hardekopf B C': 'benh@cs.ucsb.edu',
'Costan... | ucsb-cs/eval_helpers | course_lists.py | Python | bsd-2-clause | 14,254 | [
"VisIt"
] | a93e93a4d960741c50282fc053f801d3a56f1d1512df57ef9b9e0f38896351c9 |
#!/usr/bin/env python
# Try collaborative filtering on the netflix data.
import pdb
import os
import sys
import time
import posix
sys.path.append(os.path.join(posix.environ['HOME'], 'mlprojects', 'collab', 'python'))
sys.path.append(os.path.join(posix.environ['HOME'], 'mlprojects', 'swig', 'src'))
import pyflix.data... | lawrennd/collab | python/demNetflix1.py | Python | bsd-3-clause | 9,331 | [
"Gaussian"
] | 8979f97fd9fadc36fddc51ebc795713a94059b9246112e187a667429698ad8e6 |
# 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 | bnn_hmc/utils/losses.py | Python | apache-2.0 | 4,051 | [
"Gaussian"
] | 3f46e5fa05904bc59a004eff642238a3551e2112b0cf0bb8292789abf98d812e |
#!/usr/bin/python3
# -*- coding: utf-8 -*-
'''Pychemqt, Chemical Engineering Process simulator
Copyright (C) 2009-2017, Juan José Gómez Romera <jjgomera@gmail.com>
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 Softwar... | jjgomera/pychemqt | tools/dependences.py | Python | gpl-3.0 | 3,986 | [
"Pybel"
] | 9104c4962380f1299d0a8dd3205c64d47dd9adc040901a12173a1def7b4eecec |
# coding=utf-8
"""
InaSAFE Disaster risk assessment tool developed by AusAid -
**Realtime netcdf utilities.**
Custom exception classes for the IS application.
Contact : ole.moller.nielsen@gmail.com
.. note:: This program is free software; you can redistribute it and/or modify
it under the terms of the GNU Gener... | drayanaindra/inasafe | realtime/netcdf_utilities.py | Python | gpl-3.0 | 5,333 | [
"NetCDF"
] | 52be589d567477d1b86b40ea1ba5fe2f6a5000d11c90a6ebf1518d4261d2126b |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""The fsl module provides classes for interfacing with the `FSL
<http://www.fmrib.ox.ac.uk/fsl/index.html>`_ command line tools. This
was written to work with FSL version 5.0.4.
Change directory to p... | fprados/nipype | nipype/interfaces/fsl/epi.py | Python | bsd-3-clause | 28,757 | [
"Gaussian"
] | ba33497e78c44cf7555c40c7a99491d5d4d28ffb4f534d7a077557fb3cb3a7f1 |
import argparse
import os
import sys
from paraview.simple import *
from paraview import coprocessing
def ExtendDefaultPipeline(renderview, coprocessor, datadescription, script_args):
parser = argparse.ArgumentParser(description='BDM-PV-Params')
parser.add_argument('--raytracing', action='store_true')
parse... | BioDynaMo/biodynamo | demo/epidemiology/render.py | Python | apache-2.0 | 5,497 | [
"ParaView"
] | e7b8e2eb5e2e2c43677d809a4294f73b4133aee601e80040b97777dbaca92d40 |
from math import *
import random
max_steering_angle = pi / 4.0 # You do not need to use this value, but keep in mind the limitations of a real car.
bearing_noise = 0.1 # Noise parameter: should be included in sense function.
steering_noise = 0.1 # Noise parameter: should be included in move function.
distance_noise... | AKS1996/VOCOWA | particle filter complete.py | Python | mit | 9,202 | [
"Gaussian"
] | 5bb2d6956982a2321fbd3b694820f6fa8b87734299b5208505bb6c1641ab9aef |
#!/usr/bin/env python
import os, sys, subprocess, re
from distutils.core import setup, Command
from distutils.command.sdist import sdist as _sdist
class Test(Command):
description = "run unit tests"
user_options = []
boolean_options = []
def initialize_options(self):
pass
def finalize_opti... | EricSchles/python-jpake | setup.py | Python | mit | 3,033 | [
"Brian"
] | 150a553d8a5879fcd3262245c6fb93fe23268c0bf1feee3fe0fb6a9627d81540 |
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2015, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public version 2.1 or later. You s... | ghutchis/cclib | test/writer/testxyzwriter.py | Python | lgpl-2.1 | 1,225 | [
"ADF",
"cclib"
] | 6a1e0f3e71c2d9ee6fd30e563a5acd699bb6df224ce25a8f4020a893baced95f |
## Problem: See "d_bankfull" in update_flow_depth() ######## (2/21/13)
#------------------------------------------------------------------------
# Copyright (c) 2001-2017, Scott D. Peckham
#
# Feb 2017. Fixed bugs in initialize_diversion_vars() and
# update_diversions(). Thorough testing with the
# ... | peckhams/topoflow | topoflow/components/channels_base.py | Python | mit | 138,133 | [
"NetCDF"
] | 3a3157b1ec19d01e68c05c756a2f08a928fb466ca9be0c7fc92f3926cbb12a7a |
#!/usr/bin/python
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses... | alexlo03/ansible | lib/ansible/modules/network/avi/avi_httppolicyset.py | Python | gpl-3.0 | 5,400 | [
"VisIt"
] | bb8700d61e307223cf974630e7e2899c6fb2045d2e9c85100fdf0434c006fd26 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
import uuid
class Migration(migrations.Migration):
dependencies = [
('visit', '0082_auto_20150828_2330'),
]
operations = [
migrations.RemoveField(
model_name='visit',
... | koebbe/homeworks | visit/migrations/0083_auto_20150828_2346.py | Python | mit | 667 | [
"VisIt"
] | 99d75b3ff4d717c3953b494bf55637df61c17ab8b9206440987f96022e80bf4a |
"""\
PyQuante: Python Quantum Chemistry
PyQuante is a toolkit for building quantum chemistry programs in the
Python programming language.
Modules:
CGBF Class/functions for manipulating contracted Gaussian bfns
PGBF Class/functions for manipulating primitive Gaussian bfns
hartree_fock Functions fo... | gabrielelanaro/pyquante | PyQuante/__init__.py | Python | bsd-3-clause | 1,475 | [
"Gaussian"
] | 9e8881f5890ef9eaab26b520794cdb416c79c16184cfbacd07e3f2cd1b692965 |
# -*- coding: utf-8 -*-
"""
sphinx.writers.manpage
~~~~~~~~~~~~~~~~~~~~~~
Manual page writer, extended for Sphinx custom nodes.
:copyright: Copyright 2007-2013 by the Sphinx team, see AUTHORS.
:license: BSD, see LICENSE for details.
"""
from docutils import nodes
try:
from docutils.writers.ma... | waseem18/oh-mainline | vendor/packages/sphinx/sphinx/writers/manpage.py | Python | agpl-3.0 | 11,275 | [
"VisIt"
] | bd06a76d35d95a2211937b6c426f3a9f19d612ed7783f526d8f352d27424f0f0 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import re
import collections
import itertools
import math
import logging
from monty.json import MSONable, MontyDecoder
from functools import lru_cache
import numpy as np
from scipy.spatial import ConvexHull
... | dongsenfo/pymatgen | pymatgen/analysis/phase_diagram.py | Python | mit | 83,137 | [
"pymatgen"
] | c2194179f7676f5da47e57c6044b00f5ec116793fff888820b2ed8a99701ffb4 |
r"""*CLI tests for* ``sphobjinv``.
``sphobjinv`` is a toolkit for manipulation and inspection of
Sphinx |objects.inv| files.
**Author**
Brian Skinn (bskinn@alum.mit.edu)
**File Created**
20 Mar 2019
**Copyright**
\(c) Brian Skinn 2016-2022
**Source Repository**
http://www.github.com/bskinn/sphobjin... | bskinn/sphobjinv | tests/test_cli.py | Python | mit | 19,153 | [
"Brian"
] | 9f0f0179d603f5bf09d5fcbb961feed3c88edb0ec4a5fcb29c07b56f7f3de6d1 |
"""SCons.Tool.zip
Tool-specific initialization for zip.
There normally shouldn't be any need to import this module directly.
It will usually be imported through the generic SCons.Tool.Tool()
selection method.
"""
#
# Copyright (c) 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009 The SCons Foundation
#
# Permiss... | bleepbloop/Pivy | scons/scons-local-1.2.0.d20090919/SCons/Tool/zip.py | Python | isc | 3,291 | [
"VisIt"
] | c8b64e8a70e3400d86563236965b432e303d4066e875f8bcd5c9f399d95f6845 |
# 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 u... | zhreshold/mxnet | example/image-classification/common/fit.py | Python | apache-2.0 | 14,995 | [
"Gaussian"
] | 13cf9e5e29d25c6dd41ec285abeba84d2e6472e2983856a559daffb01f36a917 |
import datetime
import os
import tempfile
from unittest import skipIf
from unittest.mock import patch
from zipfile import ZipFile
from django.contrib.auth.tokens import default_token_generator
import django.core.files
from django.core import mail
from django.core.files.temp import NamedTemporaryFile
from django.core.u... | CroceRossaItaliana/jorvik | base/tests.py | Python | gpl-3.0 | 45,502 | [
"VisIt"
] | c07c745eb9dfc185bd1cf2c11b5ff7f32ae3633644c332b888a8f6e4b5e63941 |
# Author: Kratarth Goel
# BITS Pilani Goa Campus (2014)
# RNN-DBN for polyphonic music generation
# for any further clarifications visit
# for the ICANN 2014 paper or email me @ kratarthgoel@gmail.com
# This code is based on the one writen by Nicolas Boulanger-Lewandowski
# University of Montreal (2012)
# RNN-RBM deep... | kastnerkyle/speech_density | speech_rnndbn.py | Python | bsd-3-clause | 20,833 | [
"VisIt"
] | 77292f4320a900067d8298d1bda2ea0814fca99621d1b8f6eea39fb21274747a |
#-*- coding: utf-8 -*-
import modules.mapcss_lib as mapcss
import regex as re # noqa
from plugins.Plugin import with_options # noqa
from plugins.PluginMapCSS import PluginMapCSS
class Josm_deprecated(PluginMapCSS):
MAPCSS_URL = 'https://josm.openstreetmap.de/browser/josm/trunk/resources/data/validator/deprecate... | tkas/osmose-backend | plugins/Josm_deprecated.py | Python | gpl-3.0 | 818,282 | [
"CASINO"
] | 1f753ca443c097108922de55bf0267aa149e23c2c0ae1552cc416edeb534e3c6 |
"""
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.
Written (W) 2013 Heiko Strathmann
"""
from kameleon_mcmc.distribution.Gauss... | karlnapf/kameleon-mcmc | kameleon_mcmc/experiments/scripts/glass_ard/glass_ard_ground_truth.py | Python | bsd-2-clause | 4,033 | [
"Gaussian"
] | 89de44583eeb7d0edadd33192360703ee460b5d0a70088c96798d35eb2927482 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- http://www.MDAnalysis.org
# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein
# and contributors (see AUTHORS for the full list)
#
# Rele... | kain88-de/mdanalysis | package/MDAnalysis/core/_get_readers.py | Python | gpl-2.0 | 7,945 | [
"MDAnalysis"
] | 57b6a8bb776c92435ffa21b65fb1850a186ef972f1a7454423de9be69b4aad15 |
""" Class that collects utilities used in Accounting and Monitoring systems
"""
from DIRAC.Core.Utilities import Time
class DBUtils(object):
def __init__(self, db, setup):
self._acDB = db
self._setup = setup
def _retrieveBucketedData(
self, typeName, startTime, endTime, selectFields, ... | DIRACGrid/DIRAC | src/DIRAC/AccountingSystem/private/DBUtils.py | Python | gpl-3.0 | 12,883 | [
"DIRAC"
] | dbf5b1d02f97535574b4a566429246547188f6181e88654a7612311b3b9df67e |
#!/usr/bin/python
# given circRNA coordinates file and exon annotation gtf file, print out the adjacent exon coordinates and exon_id
import pybedtools
import HTSeq
class CircNonCircExon(object):
def print_start_end_file(self, circcoordinates):
circ = open(circcoordinates,'r')
start_bed = open('start.bed','w')
... | s6juncheng/Test | DCC/Circ_nonCirc_Exon_Match.py | Python | gpl-3.0 | 7,264 | [
"HTSeq"
] | b1dca45ddecd4f777b63874f5ab792647a96d9012d5edab2d1e067843553d075 |
#!/usr/local/sci/bin/python
# PYTHON2.7
#
'''
Author: Kate Willett
Created: 11 Sep 2016
Last update: 11 Sep 2016
Location: /data/local/hadkw/HADCRUH2/MARINE/EUSTACEMDS/EUSTACE_SST_MAT/
GitHub: https://github.com/Kate-Willett/HadISDH_Marine_Build/
-----------------------
CODE PURPOSE AND OUTPUT
--------------... | Kate-Willett/HadISDH_Marine_Build | EUSTACE_SST_MAT/InterpClimtoPentad1by1.py | Python | cc0-1.0 | 85,024 | [
"NetCDF"
] | 936c65a9be4a4153009a25637e19cb666270b8399b93929fd458ad20819f152d |
#####
# contains the parameters accessed by earthtools functions
#
# c. 2016-2017 Christopher Anderson
#####
import multiprocessing
import os
import platform
import subprocess
import sys
import threading
from psutil import virtual_memory
## get environment variables
environ = platform.os.environ
pathsep = platform.o... | christobal54/aei-py | earthtools/params.py | Python | gpl-2.0 | 4,452 | [
"NetCDF"
] | bf65360de23ef7843967640d86400b53c9b7777916f9d3009a44bf362b48be9d |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Classes for reading/writing mcsqs files following the rndstr.in format.
"""
from pymatgen import Structure, Lattice, Specie, DummySpecie
import numpy as np
__author__ = "Matthew Horton"
__copyright__ = "... | gVallverdu/pymatgen | pymatgen/io/atat.py | Python | mit | 4,359 | [
"CRYSTAL",
"pymatgen"
] | fba3a2ee4addaf8a19fb88f17aacdca6e1e0c160202d65434a418df717d4559c |
import numpy as np
import pymc3 as pm
import theano.tensor as tt
from bambi.backend.utils import has_hyperprior, get_distribution
from bambi.families.multivariate import Categorical
from bambi.families.univariate import Beta, Binomial, Gamma
from bambi.priors import Prior
class CommonTerm:
"""Represetation of a ... | bambinos/bambi | bambi/backend/terms.py | Python | mit | 10,853 | [
"Gaussian"
] | b7ac85f42951bb06f5ca810323043626e14f3fe8ad639c6b66bc9a87549d2388 |
# -*- coding: utf-8 -*-
# <nbformat>3.0</nbformat>
# <codecell>
from __future__ import division
from pandas import *
import os, os.path
import csv
from itertools import product
import numpy as np
import matplotlib.pyplot as plt
from operator import methodcaller
from itertools import groupby
from Bio.Seq import Seq
f... | JudoWill/ResearchNotebooks | LTRtfAnalysis.py | Python | mit | 12,372 | [
"VisIt"
] | b5bfc41135d8729dbb9bb9e8be0197918c57b34c755dbd95f784beec3914f4a7 |
##
## This module handles most things related to sparx tasks
##
# SOP for adding new tasks:
# 1) Make a copy of 'class Task_Template' and the corresponding 'install_task()' call in this file.
# 2) Change the names 'Task_Template' and 'task_template' to 'Task_Something' and 'task_something'
# where 'Something' and 's... | itahsieh/sparx-alpha | lib/sparx/tasks.py | Python | gpl-3.0 | 24,904 | [
"VTK"
] | 74b42037794771ee9f8774e959ed6454053c59adc3078d39667dfa3b74e5829c |
#!/usr/bin/python
# vim: ts=4 sw=4 expandtab
import os.path
import re
import conf
import htmlparse
import jsparse
import visitation
import warnings
import unittest
import util
from spidermonkey import tok, op
_newline_kinds = (
'eof', 'comma', 'dot', 'semi', 'colon', 'lc', 'rc', 'lp', 'rb', 'assign',
'relop'... | christian-oudard/jsl | javascriptlint/lint.py | Python | gpl-2.0 | 22,078 | [
"VisIt"
] | 8076b11768ff39bdaa0df4077941e8eb28f65df51a210f35e075af5808c516f9 |
# coding: utf-8
# # Modflow2NetCDF
#
#
# In[1]:
# Freyberg config file
freyberg_config = '../../modflow2netcdf/tests/resources/freyberg/freyberg.geo'
with open(freyberg_config) as f:
print f.read()
# In[2]:
# Freyberg NAM file
freyberg_nam = '../../modflow2netcdf/tests/resources/freyberg/freyberg.nam'
with... | rsignell-usgs/python-training | web-services/MODFLOW%20NetCDF%20Visualization.py | Python | cc0-1.0 | 4,576 | [
"NetCDF"
] | 46b2f17294b53112c374e9d74419432134d38cca7646f10443d27530357aabb8 |
# -*- coding: utf-8 -*-
"""Algorithms for spectral clustering"""
# Author: Gael Varoquaux gael.varoquaux@normalesup.org
# Brian Cheung
# Wei LI <kuantkid@gmail.com>
# License: BSD 3 clause
import warnings
import numpy as np
from ..base import BaseEstimator, ClusterMixin
from ..utils import check_rand... | herilalaina/scikit-learn | sklearn/cluster/spectral.py | Python | bsd-3-clause | 19,261 | [
"Brian",
"Gaussian"
] | 9cb63c7f5bdfe130765531443dfa8ace9e75c0173f18eda8d8d712cbcd179ac3 |
# Copyright (C) 2003-2005 Peter J. Verveer
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# 1. Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following d... | sargas/scipy | scipy/ndimage/tests/test_ndimage.py | Python | bsd-3-clause | 206,178 | [
"Gaussian"
] | 1db96dcc019406af7aa912ab03d2010e5a1ae7e28a17e12d3bbf0deb5b41af6d |
'''a pythonic Ellipse.
Super awesome.
'''
import math
from . import Point
from .line import Line, Segment
class Ellipse(object):
'''
Implements an ellipse in the XY plane with the supplied radii.
Returns a unit ellipse centered on the origin in the XY by default.
Usage:
>>> from Geometry impor... | JnyJny/Geometry | Geometry/ellipse.py | Python | mit | 13,860 | [
"Gaussian"
] | a4c7f431e419824731bc346e4a033543646e02ed6d6996d27b86ada99b36b375 |
# -*- coding: utf-8 -*-
msg = {
'en': {
'add_text-adding': u'Robot: Adding %(adding)s',
},
# Author: Csisc
'qqq': {
'add_text-adding': u'Edit summary when the bot adds text to a given page. %(adding)s is the added text truncated to 200 characters.',
},
# Author: Csisc
'aeb': {
'add_text-adding': u'بوت: إضا... | legoktm/pywikipedia-rewrite | scripts/i18n/add_text.py | Python | mit | 15,557 | [
"BLAST"
] | 628cfa138665b284a1bb1fa5c6ccbb9ff701a806977017e288ef8d6f4657f23c |
import sys
import os
import numpy as np
import copy
import pysam
import dinucshuffle
from Bio import SeqIO
import dubiotools as dbt
class Reader(object):
def __init__(self):
#self.type='BaseReader'
pass
def pull(self):
return ([],[])
def pull_as_onehot(self,batch_size):
... | LarsDu/DeepNucDecomp | deepnuc/readers.py | Python | gpl-3.0 | 11,974 | [
"pysam"
] | 5430e630aa42e65c8a7a7b47eed6e7dd66aea2ab994a5f866e0ade2b97507d1c |
#!/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/Openwebif | plugin/controllers/views/web/selectaudiotrack.py | Python | gpl-2.0 | 5,057 | [
"VisIt"
] | d4bc662b51aecbf19110ef4dac179b1b0b007f6a3de9e94c180be01223854a1b |
words = ['abandon', 'abdomen', 'abode', 'about', 'above', 'abroad',
'abrupt', 'absurd', 'abuse', 'academy', 'accord', 'account',
'acetate', 'acres', 'across', 'active', 'actor', 'acute', 'adrenal',
'adult', 'adverse', 'advice', 'adviser', 'affair', 'affairs',
'affect', 'afraid', 'age... | bwesterb/pol | src/passgen/english.py | Python | gpl-3.0 | 22,975 | [
"BLAST",
"NEURON",
"VisIt"
] | 0d3882fbbf7d71d18339cb46956c55438bbb5b7ff855de0003a1c756ad9f128a |
'''
Check for IOOS-approved attributes
'''
from compliance_checker.base import (BaseCheck, BaseNCCheck, BaseSOSGCCheck,
BaseSOSDSCheck, check_has, Result,
attr_check)
from owslib.namespaces import Namespaces
from lxml.etree import XPath
from comp... | lukecampbell/compliance-checker | compliance_checker/ioos.py | Python | apache-2.0 | 45,108 | [
"NetCDF"
] | ddefd01aa04e6154156aadb04bb02721971c1d6e1b050a54e6c887028e8b84ea |
"""
*********
JSON data
*********
Generate and parse JSON serializable data for NetworkX graphs.
These formats are suitable for use with the d3.js examples https://d3js.org/
The three formats that you can generate with NetworkX are:
- node-link like in the d3.js example https://bl.ocks.org/mbostock/4062045
- tree ... | sserrot/champion_relationships | venv/Lib/site-packages/networkx/readwrite/json_graph/__init__.py | Python | mit | 724 | [
"Cytoscape"
] | e94fe45331504624e7ff0b6496a771489d4eec32f291e4ba10f2c873ebb40e4e |
import numpy
import random
from PIL import Image
from PIL import ImageFilter
def load(path):
return Image.open(path).convert('RGB')
def display(img):
img.show()
def random_three_vector():
"""
Generates a random 3D unit vector (direction) with a uniform spherical distribution
Algo from http://sta... | nbingham1/reconstruction | paint.py | Python | gpl-3.0 | 1,401 | [
"Gaussian"
] | 7b3fc44cc5125680e7e725d3b596f38eebd7031cac280d584bae30a9a53e41cc |
"""
Schmidt decomposition for mean-field wave function
"""
import numpy as np
from pyscf import scf as pyscf_scf
from frankenstein import molecule, scf, fci
from frankenstein.tools.tensor_utils import ao2mo_xform, ao2mo_xform_ao_direct
from frankenstein.tools.io_utils import dumpVec, dumpMat, prtvar
from frankenste... | hongzhouye/frankenstein | be/sd.py | Python | bsd-3-clause | 22,860 | [
"PySCF"
] | 7cd492200b51c0eae7fc3dbb5a13309c7683b472224f0b4638ff48923674fba4 |
"""
Description:
Provides a pyGtk vtkRenderWindowInteractor widget. This embeds a
vtkRenderWindow inside a GTK widget and uses the
vtkGenericRenderWindowInteractor for the event handling. This is
similar to GtkVTKRenderWindowInteractor.py.
The extensions here allow the use of gtkglext rather than gtkgl an... | sgh/vtk | Wrapping/Python/vtk/gtk/GtkGLExtVTKRenderWindowInteractor.py | Python | bsd-3-clause | 9,833 | [
"VTK"
] | 6a61b959fcf09a9fe65468f5e9e1adc84d1f547f65686e66864e6435d2c03fe7 |
##################################################################
# Copyright 2018 Open Source Geospatial Foundation and others #
# licensed under MIT, Please consult LICENSE.txt for details #
##################################################################
import unittest
import lxml.etree
import json
impor... | bird-house/PyWPS | tests/test_execute.py | Python | mit | 27,616 | [
"NetCDF"
] | 4ce848b278e887ebee0578a79284a27df558b48626afbc632598babf43cacc54 |
#
# Pulsar documentation build configuration file, created by
# sphinx-quickstart on Sun Dec 16 23:16:23 2012.
#
# 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
# autogenerated file.
#
# All configuration values hav... | galaxyproject/pulsar | docs/conf.py | Python | apache-2.0 | 7,817 | [
"Galaxy"
] | 869851c231a60342bcd5a9b2ff7be993d295b45134914420aae5159593758934 |
#!/usr/bin/env python
# Emacs: treat this as -*- python -*-
import os
import gtk
import tempfile
from math import cos, sin, sqrt
import numpy as np
from ase.data.colors import jmol_colors
from ase.gui.repeat import Repeat
from ase.gui.rotate import Rotate
from ase.utils import rotate
class View:
def __init__(... | freephys/python_ase | ase/gui/view.py | Python | gpl-3.0 | 17,342 | [
"ASE",
"RasMol",
"VMD"
] | 15fe4cfebc0fbde1617147af74007a6286c8880dd2434b99139406d7532d2eec |
#
# Copyright 2001 - 2006 Ludek Smid [http://www.ospace.net/]
#
# This file is part of IGE - Outer Space.
#
# IGE - Outer Space 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 t... | mozts2005/OuterSpace | client-pygame/lib/osci/dialog/GalaxyRestartDlg.py | Python | gpl-2.0 | 3,145 | [
"Galaxy"
] | feddfe39db8d56035588f9dfb17c65a203238904e7fac5bb1c54c53e36516e12 |
#!/usr/bin/env python
# CREATED:2013-03-11 18:14:30 by Brian McFee <brm2132@columbia.edu>
# unit tests for librosa.beat
from __future__ import print_function
from nose.tools import nottest, raises, eq_
# Disable cache
import os
try:
os.environ.pop('LIBROSA_CACHE_DIR')
except:
pass
import numpy as np
import ... | ruohoruotsi/librosa | tests/test_beat.py | Python | isc | 7,918 | [
"Brian"
] | 903212b0a06a8b57c499a42de003a5b2a7fe4b603599bae3d1ffc63c409a03cc |
#
# Copyright (C) 2013-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | mkuron/espresso | testsuite/python/domain_decomposition.py | Python | gpl-3.0 | 2,322 | [
"ESPResSo"
] | ed8e42985b2ac1195bf6f8d1f52aaf481638f01dedf476803647e57dd1b63b78 |
# -*- coding: utf-8 -*-
# Generated by Django 1.10.7 on 2018-01-05 16:31
from __future__ import unicode_literals
import django.core.validators
from django.db import migrations, models
import registration.models
class Migration(migrations.Migration):
dependencies = [
('registration', '0005_add_design_fiel... | open-craft/opencraft | registration/migrations/0006_auto_20180105_1631.py | Python | agpl-3.0 | 1,984 | [
"VisIt"
] | 41acdd0a1065b94c52f8e110999b1c7a301619f3ac32534e967bb3ec96a569f9 |
# Copyright 2008 Brian Boyer, Ryan Mark, Angela Nitzke, Joshua Pollock,
# Stuart Tiffen, Kayla Webley and the Medill School of Journalism, Northwestern
# University.
#
# This file is part of Crunchberry Pie.
#
# Crunchberry Pie is free software: you can redistribute it and/or modify
# it under the terms of the GNU Gene... | brianboyer/newsmixer | pie/authentication/management/commands/cleanup_profiles.py | Python | gpl-3.0 | 1,569 | [
"Brian"
] | 8fda0329aec6e18ff8203fc6313d4a1e8bc7a8b44cd592933fd5ff3c76792a24 |
#!/usr/bin/python
################################################################
# .___ __ _______ .___ #
# __| _/____ _______| | __ ____ \ _ \ __| _/____ #
# / __ |\__ \\_ __ \ |/ // ___\/ /_\ \ / __ |/ __ \ #
# / /_/ | / __ \| | \/ <\ \___\... | knightmare2600/d4rkc0de | others/ftpbrute.py | Python | gpl-2.0 | 8,051 | [
"VisIt"
] | a7d772561cb1e13e3d818fd21e890a5681174413d6a71b100cde4206dae9fa94 |
###AltAnalyze
#Copyright 2005-2008 J. David Gladstone Institutes, San Francisco California
#Author Nathan Salomonis - nsalomonis@gmail.com
#Permission is hereby granted, free of charge, to any person obtaining a copy
#of this software and associated documentation files (the "Software"), to deal
#in the Softwar... | nsalomonis/AltAnalyze | AltAnalyze.py | Python | apache-2.0 | 543,640 | [
"Cytoscape",
"pysam"
] | ce543191bd056d0497e7a7362535113cac8a438ec97fcd8077dcf6f76d0811cd |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# (c) 2015, Brian Coca <bcoca@ansible.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 Licen... | adityacs/ansible | lib/ansible/modules/notification/jabber.py | Python | gpl-3.0 | 4,792 | [
"Brian"
] | d074fd316da4049bac354c0c0abdc16cd97678bb2f280d53b50cdc3273c6bc71 |
'''
Example script illustrating plotting of PLY data using Mayavi. Mayavi
is not a dependency of plyfile, but you will need to install it in order
to run this script. Failing to do so will immediately result in
ImportError.
'''
from argparse import ArgumentParser
import numpy
from mayavi import mlab
from plyfile ... | andyneff/python-plyfile | examples/plot.py | Python | gpl-3.0 | 1,337 | [
"Mayavi"
] | ce15ea03bb90f2fc5d831c5265147d20d4457afd29a5fdeac806bd07af5ee205 |
# Copyright (c) 2009-2021 The Regents of the University of Michigan This file is
# part of the HOOMD-blue project, released under the BSD 3-Clause License.
"""Choose which hardware device(s) should execute the simulation."""
import contextlib
import hoomd
from hoomd import _hoomd
class Device:
"""Base class dev... | joaander/hoomd-blue | hoomd/device.py | Python | bsd-3-clause | 12,349 | [
"HOOMD-blue"
] | 7d28a2d993d85ccae375d4f994b918f7dc3a429a328ec062685ff3dfcc810a6a |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-admin-accounting-cli
# Author : Adria Casajus
########################################################################
"""
Command line administrative interface to DIRAC Accounting DataStore Ser... | Sbalbp/DIRAC | AccountingSystem/scripts/dirac-admin-accounting-cli.py | Python | gpl-3.0 | 9,668 | [
"DIRAC"
] | f66a815f30efed8ade14ea1e221e7bcb06dd558fd0df4c95b2ddc823a35dc408 |
# simple test of data tool
# requires files/data.micelle and dump.micelle
# creates tmp.data
d = data("files/data.micelle")
d.map(1,"id",3,"type",4,"x",5,"y",6,"z")
coeffs = d.get("Masses")
print "Masses",coeffs
x = d.get("Atoms",4)
print "X of 1st atom",x[0]
d.title = "New LAMMPS data file"
natoms = d.headers["atom... | baoboa/pizza-lammps | examples/test_data.py | Python | gpl-2.0 | 639 | [
"LAMMPS"
] | 1b0c56b0c24cc835f3925f62d0f1b1891a85331829b767cef9547f0a5e0b09c3 |
# -*- coding: utf-8 -*-
## @package JsMVA.Factory
# @author Attila Bagoly <battila93@gmail.com>
# Factory module with the functions to be inserted to TMVA::Factory class and helper functions and classes
import ROOT
from ROOT import TMVA
import sys
if sys.version_info >= (3, 0):
from JsMVA import JPyInterface
el... | karies/root | bindings/pyroot_legacy/JsMVA/Factory.py | Python | lgpl-2.1 | 31,685 | [
"NEURON"
] | 2d3eef3dc62f768330beb25ba747dddecadaed294c581b4678045bca5d0a100a |
# Copyright 2016 Google 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 law or agreed to in writing,... | axbaretto/beam | sdks/python/.tox/py27gcp/lib/python2.7/site-packages/google/oauth2/flow.py | Python | apache-2.0 | 9,887 | [
"VisIt"
] | 8ee6eddb55ea366f246f24e73c4d3810b942136290f2682aa73490ccb2c850c7 |
#!/usr/bin/env python
#----------------USAGE-----------------------
#by Dan Barshis
#This script parses a .sam alignment file created using BWA and returns a tab-delimited text file with the
#number of multiply aligned reads and good quality (above a certain mapping quality threshold and read length) singly aligned
#... | cuttlefishh/papers | vibrio-fischeri-transcriptomics/code/python/countxpression.py | Python | mit | 6,145 | [
"BWA"
] | c1922ed793f6cb5ef5d402560a05fb89f507c01dcce16c9c0189635ca382eb5c |
#
# Copyright 2019-2020 Johannes Hoermann (U. Freiburg)
#
# matscipy - Materials science with Python at the atomic-scale
# https://github.com/libAtoms/matscipy
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Softw... | libAtoms/matscipy | examples/electrochemistry/pnp_batch/interface_1d/concentration_sweep/pnp_plot.py | Python | lgpl-2.1 | 7,312 | [
"Matscipy"
] | 6099560dbc401df34dc4f6b25804a75cf5b9527c1904e1dfdd836768618595e4 |
# -*- coding: utf-8 -*-
"""Parsers for Opera Browser history files."""
from __future__ import unicode_literals
import os
from urllib import parse as urlparse
from defusedxml import ElementTree
from dfdatetime import posix_time as dfdatetime_posix_time
from dfdatetime import time_elements as dfdatetime_time_elements... | rgayon/plaso | plaso/parsers/opera.py | Python | apache-2.0 | 10,152 | [
"VisIt"
] | 0e03e70f3d77646641eacaf37a381eeb432ae2985c9b81de47ed0190ff3527ff |
# -*- coding: utf-8 -*-
# Copyright 2007-2021 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at... | thomasaarholt/hyperspy | hyperspy/_signals/eels.py | Python | gpl-3.0 | 79,274 | [
"Gaussian"
] | d11cf8ed44ad39dc41deabea230e719d135f467a1e76630b087ccc461f2b6bd3 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Load external dependencies
from setup import *
# Load internal dependencies
import config, utils
def histogram_binned_data(ax, data, bins=50):
"""
"""
nx, xbins = np.histogram(data, bins=bins, normed=True)
nx_frac = nx/float(len(nx)) # Each bin divided by t... | ivazquez/clonal-heterogeneity | src/plot.py | Python | mit | 30,669 | [
"Gaussian"
] | 971fa85db0fa0d2514d876d1eebdfc6f1fa506fef037b25ac875dc62d7ac5a7e |
from glob import glob
from urlparse import urlparse
import contextlib
import os
import tempfile
import time
import zipfile
from invoke import run, task
import docker
import requests
app_container = 'dbpedia-tutorial'
@task
def setup():
if not is_container_created():
cmd = 'docker run -dp 8000:8000'
... | qsensei/dbpedia-tutorial | tasks.py | Python | mit | 5,981 | [
"VisIt"
] | 63866b9dc2e72d3810a5c82efa6112e086a876846bc83aeb62b0e22a3d4c0005 |
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