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# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, print_function, unicode_literals, absolute_import
"""
This module implements classes for processing Lammps output files:
1. log file: contains the thermodynamic data with ... | czhengsci/pymatgen | pymatgen/io/lammps/output.py | Python | mit | 20,870 | [
"LAMMPS",
"MDAnalysis",
"pymatgen"
] | 9a361c5c7868a2cec43ef9d246156ad92edfa7eb29a86dd97e10c397c88997f0 |
from vtk import *
import os.path
data_dir = "../../../../VTKData/Data/Infovis/SQLite/"
if not os.path.exists(data_dir):
data_dir = "../../../../../VTKData/Data/Infovis/SQLite/"
if not os.path.exists(data_dir):
data_dir = "../../../../../../VTKData/Data/Infovis/SQLite/"
sqlite_file = data_dir + "SmallEmailTest.db"
... | b3c/VTK-5.8 | Examples/Infovis/Python/databases.py | Python | bsd-3-clause | 1,756 | [
"VTK"
] | 0f2a99df71e4ed44e5e5b721e0b768715a340afb6417800df7a99e92092f2ba3 |
#
# DESCRIPTION: This script parses the given input bowtie and/or LAST files and creates a csv row of their data in the given output csv.
#
# AUTHOR: Chelsea Tymms
import sys, os.path
import argparse
def getOptions():
"""Function to pull in arguments from the command line"""
description="""This script takes an i... | McIntyre-Lab/papers | lehmann_2015/mapping_and_overall_expression/scripts/logParser.py | Python | lgpl-3.0 | 5,162 | [
"Bowtie"
] | 84cc0cd5a423492ad17db7656bddd2fe44ab4feb13ab044964c4cbd963794890 |
import zipfile, os.path, string
def visit(dummy, dirname, names):
for name in names:
include = 1
for ex in excludeending:
i = name.rfind(ex)
if i+1 and i == len(name) - len(ex):
include = 0
break
for ex in excludedir:
if di... | yukao/Porphyrograph | LYM-sources/pg-sensors/KineticsKit/util/4_zip_it.py | Python | gpl-3.0 | 1,096 | [
"VisIt"
] | b652bcb782df726f3befe57b891a454577872eac2c70631df3db405272f517e8 |
from __future__ import print_function
import caffe
from caffe import layers as L
from caffe import params as P
weight_param = dict(lr_mult=1, decay_mult=1)
bias_param = dict(lr_mult=2, decay_mult=0)
learned_param = [weight_param, bias_param]
frozen_param = [dict(lr_mult=0)] * 2
def conv_relu(bottom, ks, nout, st... | varunagrawal/YelpNet | src/network.py | Python | mit | 4,313 | [
"Gaussian"
] | 1dc7e3f954db77c1e3a21c4cf048e922cc0f1dfcfd41d35f51d57dfee04dcdd2 |
#!/usr/bin/env python
"""
Artificial Intelligence for Humans
Volume 1: Fundamental Algorithms
Python Version
http://www.aifh.org
http://www.jeffheaton.com
Code repository:
https://github.com/jeffheaton/aifh
Copyright 2013 by Jeff Heaton
Licensed under the Apache License, Version 2... | trenton3983/Artificial_Intelligence_for_Humans | vol1/python-examples/examples/example_normalize.py | Python | apache-2.0 | 17,100 | [
"VisIt"
] | c289b51139c1322ee1ce1a5dfa7768c82fedf77e98f72cb8e5cf2c76bbaabbb7 |
#!/usr/bin/env python
"""
basic model line shapes and distribution functions
"""
from __future__ import division
from numpy import (pi, log, exp, sqrt, arctan, cos, where)
from numpy.testing import assert_allclose
from scipy.special import gamma as gamfcn
from scipy.special import gammaln, erf, erfc, wofz
log2 = log(... | DiamondLightSource/auto_tomo_calibration-experimental | old_code_scripts/simulate_data/lmfit-py/lmfit/lineshapes.py | Python | apache-2.0 | 9,554 | [
"Gaussian"
] | 400eca038c860f85184982fbd916118f997d5a75059b6079c57a063c7078bc2a |
"""plot_utils.py: Some utility function for plotting data in moose.
Last modified: Sun Jan 10, 2016 04:04PM
"""
__author__ = "Dilawar Singh"
__copyright__ = "Copyright 2013, NCBS Bangalore"
__credits__ = ["NCBS Bangalore", "Bhalla Lab"]
__license__ = "GPL"
__version__ ... | subhacom/moose-core | python/moose/plot_utils.py | Python | gpl-3.0 | 10,511 | [
"MOOSE"
] | 3d1b8d075170cc2dfae2c9055b6c0714d750c6770069abac2e21d993c4b294ef |
# -*- Mode: Python; coding: utf-8; indent-tabs-mode: nil; tab-width: 4 -*-
### BEGIN LICENSE
# Copyright (C) 2014 Brian Douglass bhdouglass@gmail.com
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License version 3, as published
# by the Free Softwa... | bhdouglass/agui | agui/backends/gtk/widgets/text_area.py | Python | gpl-3.0 | 1,520 | [
"Brian"
] | 3ff498cedb4df84fbdc7b7174cd7dcb211377050fcd003b347112ca883d761ff |
__author__ = 'jmeireles'
import dryscrape
import re
import requests
import bs4
import urllib
regex = '(?<=file:\s")http://[^\s"]+.(?:mp4|mpg|avi|flv)'
'''
url = 'http://gorillavid.in/embed-sx5p5f4cbgm1-650x400.html'
response = requests.get(url)
soup = bs4.BeautifulSoup(response.text)
text = soup.get_text()
regex = u... | Faianca/Anime-Tv-shows-Scrapper | tests/progress.py | Python | apache-2.0 | 1,472 | [
"VisIt"
] | 10054bda9c7d397cafab958172146cc151c4d3e0e0812b98ca654e0dd836c089 |
#
# QAPI event generator
#
# Copyright (c) 2014 Wenchao Xia
# Copyright (c) 2015-2016 Red Hat Inc.
#
# Authors:
# Wenchao Xia <wenchaoqemu@gmail.com>
# Markus Armbruster <armbru@redhat.com>
#
# This work is licensed under the terms of the GNU GPL, version 2.
# See the COPYING file in the top-level directory.
from qa... | shannonz88/qemu | scripts/qapi-event.py | Python | gpl-2.0 | 5,157 | [
"VisIt"
] | 48b57f42b32e2b6e5681b8264b854a48b96c790e5c4794b6639deafb808d237e |
# Copyright (C) 2010-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | mkuron/espresso | testsuite/python/linear_momentum_lb.py | Python | gpl-3.0 | 2,929 | [
"ESPResSo"
] | f985515457ec1682b3472dccd6548ffa5535612988358e0938a3cb7f1a4f667c |
"""
Inline-optimized Sheet classes
$Id$
"""
__version__='$Revision$'
import param
from topo.base.cf import MaskedCFIter
from topo.base.projection import NeighborhoodMask
from topo.misc.inlinec import inline,provide_unoptimized_equivalent,c_header
from topo.sheet.lissom import LISSOM
from topo.sheet import compute_jo... | ioam/svn-history | topo/sheet/optimized.py | Python | bsd-3-clause | 6,210 | [
"Gaussian"
] | 74e830811e7e8cc10783d76a9bc3de443453c475b2424682915aaf02a5070040 |
#!/usr/bin/env python3
"""
Check vcf genotype consistence at each genotype level for multiple input files.
@Author: wavefancy@gmail.com
Usage:
VCFOverlapMulti.py -n num [-c cacheLoadnum] [-s] <inputs>...
VCFOverlapMulti.py -h | --help | -v | --version | -f | --format
Notes:
... | wavefancy/BIDMC-PYTHON | Exome/VCFOverlapMulti/VCFOverlapMulti.py | Python | mit | 8,816 | [
"pysam"
] | 10323e1c89d3aa393f1bc63d1ffddc376b0b72e7e61cb6c83d9a214b2d5a79aa |
"""Compound_io.py: Functions to load MINE databases from and dump compounds
into common cheminformatics formats"""
import collections
import csv
import datetime
import os
import sys
from typing import List, Tuple, Union
from rdkit.Chem import AllChem
from minedatabase import utils
from minedatabase.databases import M... | JamesJeffryes/MINE-Database | minedatabase/compound_io.py | Python | mit | 21,146 | [
"RDKit"
] | 1fcb9bdf6a5107a3bb4296c4d1cbfb7cc877610ad77f1dba18e3ac86596251e1 |
#!/usr/bin/python
'''
VTK engine room for mrMeshPy viewer
The main vtk processing is done by functions here - although some hardcore
processing is handled in subroutines of other imported modules.
A core concept here is the tracking (kepping in scope) or the "targetVTKWindow"
- this is a vtkRenderWindowInteractor... | andregouws/mrMeshPy | mp_VTKRoutines.py | Python | mit | 15,719 | [
"VTK"
] | d67ef568356621cb63575a7c1ddc164ee69e367658b4cb1d6e7dd4d126edb7cf |
# Copyright 2014 Google Inc. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | dennis910130/cuda-convnet2 | layer.py | Python | apache-2.0 | 82,368 | [
"Gaussian",
"NEURON"
] | b9431e47ca572515a63ba630688429fbfe7126dfbd95c1f1865a2a86f8869d3a |
from errorHandler import *
from phamerator_manage_db import *
from db_conf import db_conf
class workUnitSeq:
def __init__(self, id, translation):
self.id = id
self.translation = translation
class alignmentWorkUnit(errorHandler):
def __init__(self, c):
errorHandler.__init__(self)
#self.c = c
se... | byuphamerator/phamerator-dev | phamerator/alignmentDatabase.py | Python | gpl-2.0 | 5,333 | [
"BLAST"
] | f794a827aacf9e4c706579fd5c430969b01c4392de0115ffdd91bdf493996c87 |
# Copyright 2004 by James Casbon. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""
Code to deal with COMPASS output, a program for profile/profile comparison.
Compass is des... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/Compass/__init__.py | Python | apache-2.0 | 8,796 | [
"Biopython"
] | 1824632c45711ded52b05d30c8629c7c0d1452d1cefe7be99c0c4da2cdf90b54 |
"""
Fit a line based on parameters output from a grid of RADEX models
"""
import numpy as np
from pyspeckit.mpfit import mpfit
from .. import units
from . import fitter,model
import matplotlib.cbook as mpcb
import copy
try:
import astropy.io.fits as pyfits
except ImportError:
import pyfits
class radex_model(ob... | keflavich/pyspeckit-obsolete | pyspeckit/spectrum/models/radex_modelgrid.py | Python | mit | 4,499 | [
"Gaussian"
] | 7cebcd38b176fbf6fb8b2a05ef70edc164d90c001ca83794b2e96b95b103020c |
# -*- coding: utf-8 -*-
try:
# Python 2.7
from collections import OrderedDict
except:
# Python 2.6
from gluon.contrib.simplejson.ordered_dict import OrderedDict
from datetime import timedelta
from gluon import current, Field, URL
from gluon.html import *
from gluon.storage import Storage
from gluon.v... | flavour/tldrmp | private/templates/Libya/config.py | Python | mit | 124,696 | [
"Amber"
] | d564753ef457d7a37b41192341273bb17c197a639bc2c7e4016f42309e473a40 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from .elastic import *
from .stress import *
from .strain import *
| dongsenfo/pymatgen | pymatgen/analysis/elasticity/__init__.py | Python | mit | 177 | [
"pymatgen"
] | 3d2dd80babbb640fa7d588ab1f060c3a068d461085f853af0dd642391ac68cb2 |
import qt
# Importing vtk initializes vtkPythonMap owned by vtkPythonUtil and prevent
# call to vtkPythonUtil::GetObjectFromPointer() from segfaulting.
# PythonQt internally uses vtkPythonUtil to properly wrap/unwrap VTK objects
from vtk import *
t = _testWrappedVTKQInvokableInstance.getTable()
print t.GetClassName(... | pieper/CTK | Applications/ctkSimplePythonShell/Testing/Python/wrappedVTKQInvokableTest.py | Python | apache-2.0 | 492 | [
"VTK"
] | ab30d610e5eaa8b538d4f33b2e67495c6ca50675d35af25656bc57126d647ec2 |
# encoding: utf-8
from mock import patch
import copy
from django.test import SimpleTestCase
from corehq.apps.app_manager.models import (
DetailColumn,
Application,
FormSchedule,
ScheduleVisit,
SchedulePhase,
SchedulePhaseForm,
FormActionCondition,
)
from corehq.apps.app_manager.exceptions im... | qedsoftware/commcare-hq | corehq/apps/app_manager/tests/test_schedule.py | Python | bsd-3-clause | 20,173 | [
"VisIt"
] | 620a52d0bb63027bce3c75af4fb18f34bf33215dbbf38cce032c414f3689e6da |
"""
sphinx.writers.html
~~~~~~~~~~~~~~~~~~~
docutils writers handling Sphinx' custom nodes.
:copyright: Copyright 2007-2021 by the Sphinx team, see AUTHORS.
:license: BSD, see LICENSE for details.
"""
import copy
import os
import posixpath
import re
import warnings
from typing import TYPE_CHECKIN... | sonntagsgesicht/regtest | .aux/venv/lib/python3.9/site-packages/sphinx/writers/html.py | Python | apache-2.0 | 34,032 | [
"VisIt"
] | b9c5f566e7fce9840c91b678801ed56f2b43416b67330fdfc7560dac84f0f93d |
#! /usr/bin/env python
"""
put files in the FileCatalog (and Storage Element)
When destination SE is not specified, dput will use COMDIRAC configuration option "default_se".
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import os
import DIRAC
from D... | DIRACGrid/COMDIRAC | src/COMDIRAC/Interfaces/scripts/dput.py | Python | gpl-3.0 | 4,412 | [
"DIRAC"
] | 3f759d9c119798c628fdc81234a689b60e3219fd241f4eee3c891f97137dac76 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
from lib.meos import MEoS
from lib import unidades
class Ar(MEoS):
"""Multiparamter equation of state for argon"""
name = "argon"
CASNumber = "7440-37-1"
formula = "Ar"
synonym = "R-740"
rhoc = unidades.Density(535.6)
Tc = unidades.Temperature(150... | edusegzy/pychemqt | lib/mEoS/Ar.py | Python | gpl-3.0 | 37,016 | [
"Jmol"
] | 646bff3678e3c6243d32085a494c490f0a2d63f7da801b2d9ad9e2c1d54d942b |
from common import Modules, data_strings, load_yara_rules, PEParseModule, ModuleMetadata, is_ip_or_domain
from pefile import PE
class backoff(PEParseModule):
def __init__(self):
md = ModuleMetadata(
module_name="backoff",
bot_name="Backoff",
description="Point of sale m... | bwall/bamfdetect | BAMF_Detect/modules/backoff.py | Python | mit | 1,726 | [
"Brian"
] | 51d2e73190571ae6ff29a180c1cbb33dbfc7ab4e774c464b0a2cd473999b7cd8 |
"""
Deadlink crawler - https://github.com/taikano/deadlink-crawler
Copyright 2013- taikano and other contributors at GitHub
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.or... | aufziehvogel/deadlink-crawler | crawler.py | Python | apache-2.0 | 11,173 | [
"VisIt"
] | 9b13afbab447318da930002f0d4897178252d1786459787bbe951842de34bf53 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import rdkit
from rdkit.Chem import AllChem
from rdkit import DataStructs
__license__ = "X11"
METADATA = {
"id": "method_rdkit_fcfp6_1024_tanimoto",
"representation": "fcfp6_1024",
"similarity": "tanimoto"
}
def _compute_fingerprint(molecule):
return Al... | skodapetr/lbvs-environment | methods/fcfp/fcfp6_1024_tanimoto.py | Python | mit | 1,423 | [
"RDKit"
] | 0a2187d39f0bacfe4bcd40c7bbc2aa9d6bb008194cedad4388ebf68a4b6c6114 |
from PIL import Image
from pyimage import PyImage
from gausspyramid import GaussPyramid
from laplacepyramid import LaplacePyramid
import numpy as np
class LaplaceBlender(object):
'''This class represents the Laplacian Pyramid Blending process in a data
structure containing two laplacian pyramids, for two gi... | Thurler/imgprocess | laplaceblender.py | Python | gpl-3.0 | 7,754 | [
"Gaussian"
] | 8d1d3ee1178a4451eee8b09ffb470ff76ae24ec655393294059179f5ed2d00b0 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements the Quasi-harmonic Debye approximation that can
be used to compute thermal properties.
See the following papers for more info:
http://doi.org/10.1016/j.comphy.2003.12.001 (2004... | richardtran415/pymatgen | pymatgen/analysis/quasiharmonic.py | Python | mit | 13,572 | [
"pymatgen"
] | 8fd6140ec9892a33674dcca0603f04c059520d4e77d5045cce1c32b7063d7b86 |
##############################################################################
# Copyright (c) 2013-2018, 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... | krafczyk/spack | var/spack/repos/builtin/packages/r-mlinterfaces/package.py | Python | lgpl-2.1 | 2,432 | [
"Bioconductor"
] | 02e0e3387242a8c8ea422b033f3b878c8e4ac084ea54a7a79c045a2dd50f72f4 |
from collections import defaultdict
import matplotlib.pyplot as plt
plt.rcParams['pdf.fonttype'] = 42
import scipy.stats as stats
import subprocess
import os
import cPickle
import tps_utils
import numpy as np
import itertools
import pysam
import math
import gzip
import bzUtils
class TPS_qc:
def __init__(self, tpse... | borisz264/toeprint_seq | tps_qc.py | Python | mit | 13,680 | [
"pysam"
] | 64b6868baa2a9185880b70fe6b7f6583eff8d60111cf00f65d52b701aaf99ddb |
# coding: utf-8
"""
Vericred API
Vericred's API allows you to search for Health Plans that a specific doctor
accepts.
## Getting Started
Visit our [Developer Portal](https://developers.vericred.com) to
create an account.
Once you have created an account, you can create one Application for
Production and an... | vericred/vericred-python | vericred_client/models/zip_code.py | Python | apache-2.0 | 12,506 | [
"VisIt"
] | 1bb7587f8a8979e712cab6403a3256841cc3171931775fc6318a566c20ef995f |
# coding=utf-8
"""
.. module:: wolk
This module provides connection to WolkAbout IoT Platform.
To start publishing data to the platform
create an instance of Device class with credentials obtained from the platform
and pass it to an instance of WolkConnect class.
For more information about module features visit:
htt... | Wolkabout/WolkConnect-Python- | wolk/__init__.py | Python | apache-2.0 | 3,048 | [
"VisIt"
] | 0c37cbc4a1ab6b3745c14b7de0a5de1010651eec91f4c112eff85b10e2fa7919 |
# -*- coding: utf-8 -*-
"""
Jinja2
~~~~~~
Jinja2 is a template engine written in pure Python. It provides a
`Django`_ inspired non-XML syntax but supports inline expressions and
an optional `sandboxed`_ environment.
Nutshell
--------
Here a small example of a Jinja template::
{% extends 'base.html' %}
{% b... | dstufft/jinja2 | setup.py | Python | bsd-3-clause | 2,420 | [
"VisIt"
] | f35ce4a1c342e6747676f6349aae93a0797643cc881735132dc1e15e85d31f9c |
# Copied from the mdtraj project, commit 3fddb5d (Mar 10, 2016)
from __future__ import print_function
import os
import shutil
from sphinx.util.compat import Directive
from docutils import nodes
from docutils.parsers.rst import directives
import nbformat
from nbconvert import HTMLExporter, PythonExporter
def _read... | sallai/mbuild | docs/sphinxext/notebook_sphinxext.py | Python | mit | 3,947 | [
"MDTraj"
] | 9572f92107c8c2969b49644864a8852063d11e5e741b15e7d843ae31bfdf10f9 |
#!/usr/bin/env python
# encoding: utf-8
"""
The IPython engine application
Authors:
* Brian Granger
* MinRK
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2008-2011 The IPython Development Team
#
# Distributed under the terms of the BSD License. The full licen... | WillisXChen/django-oscar | oscar/lib/python2.7/site-packages/IPython/parallel/apps/ipengineapp.py | Python | bsd-3-clause | 13,537 | [
"Brian"
] | bd4a6ed5e001c4b6c38cd66e06719c2b58678d26c139eeeb4009465b8e6ed158 |
# Copyright 2018 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, ... | google/ci_edit | app/unit_test_bookmarks.py | Python | apache-2.0 | 32,396 | [
"VisIt"
] | 7d79f103966f2653160b64a6df71595a4595a5c7b3f73b63ad17640a1c44e3ea |
#!/usr/bin/env python3
import numpy as np
import matplotlib.pyplot as plt
from os import mkdir
from os.path import isdir
from LoLIM.utilities import processed_data_dir, logger
from LoLIM.noise_analysis import get_noise_std, to_file
## these lines are anachronistic and should be fixed at some point
from LoLIM import... | Bhare8972/LOFAR-LIM | LIM_scripts/examples/get_noise_std.py | Python | mit | 1,011 | [
"Brian"
] | 82053a36ea501db3ad8e31147d91f0481c19a484fdd4413012d48ad3c2a60521 |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | xguse/scikit-bio | skbio/io/_iosources.py | Python | bsd-3-clause | 6,272 | [
"scikit-bio"
] | cb89c9df7974142daa811dd718640dc7bfb360699de55fd2456af5c017cff2a8 |
"""
Constants needed for parsing binary GeoIP databases. It is part of the pygeoip
package.
@author: Jennifer Ennis <zaylea at gmail dot com>
@license:
Copyright(C) 2004 MaxMind LLC
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public Lice... | mzdaniel/oh-mainline | vendor/packages/pygeoip/pygeoip/const.py | Python | agpl-3.0 | 15,440 | [
"BWA",
"COLUMBUS"
] | 9f9a9ccbc43707f8c36e7b3d2f954029dfa7dd3a5c83bfe3855e255c29cf82f9 |
#
# Copyright (C) 2006-2016 Greg Landrum
# All Rights Reserved
#
import os
import re
from rdkit.Chem.Draw import rdMolDraw2D
from rdkit.Chem.Draw.MolDrawing import MolDrawing, DrawingOptions
from rdkit.Chem.Draw.rdMolDraw2D import *
from rdkit.six import iteritems
def _getCanvas():
useAGG = False
useCairo = Fal... | rvianello/rdkit | rdkit/Chem/Draw/__init__.py | Python | bsd-3-clause | 14,820 | [
"RDKit"
] | 5234e03475294bfc4f7bf98ae0dbfaff729b33a011bd1f4f849b38dc77d3d489 |
"""
Ammonia inversion transition TKIN fitter translated from Erik Rosolowsky's
http://svn.ok.ubc.ca/svn/signals/nh3fit/
"""
import numpy as np
from pyspeckit.mpfit import mpfit
from .. import units
import matplotlib.cbook as mpcb
line_names = ['oneone','twotwo','threethree']
line_names = ['oneone_f10','oneone_f01','on... | bsipocz/pyspeckit | pyspeckit/spectrum/models/_formaldehyde.py | Python | mit | 13,178 | [
"Gaussian"
] | e62efbab30d6f79831c1e63416fa63c9a1c9e59ae348ba3719557ef3745343a9 |
#!/usr/bin/env python
# python modules
import sys
import os
import numpy as np
import math
# qt modules
from omg.gaussian.gaussian import GaussianCom
from omg.molecules import Molecule
# autodock
import bhtree
def usage():
print('usage:')
print(' residel_charges.py gaussian_input.com')
print(' ... | eduardoftoliveira/oniomMacGyver | scripts/residel_charges.py | Python | gpl-3.0 | 5,453 | [
"Gaussian"
] | 4dd622b5647e69b5779918d3d990d45114f3e45767714c565f92b2730f28e875 |
# -*- 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... | Niemzok/fango | config/urls.py | Python | mit | 1,484 | [
"VisIt"
] | 927af91c77b7ec07021d34b6c9978c671945b67d8171ef9e7c770f510b250ac4 |
'''
Created on 30 Sep 2015
@author: Max Zwiessele
'''
import unittest, numpy as np, pandas as pd # @UnresolvedImport
import GPy, GPy.kern as kern
from applygpy.model_selection import cross_validate
from GPy.models.sparse_gp_regression import SparseGPRegression
from GPy.models.sparse_gp_classification import SparseGPC... | mzwiessele/applygpy | applygpy/tests/test_modelselection.py | Python | bsd-3-clause | 3,575 | [
"Gaussian"
] | 1c7e8db48a481ff6bfe5d93d42a2e172dd08f7367352f7348c653e28f358f2e4 |
import numpy as np
import pandas as pd
import pastas as ps
def acf_func(**kwargs):
index = pd.to_datetime(np.arange(0, 100, 1), unit="D", origin="2000")
data = np.sin(np.linspace(0, 10 * np.pi, 100))
r = pd.Series(data=data, index=index)
acf_true = np.cos(np.linspace(0.0, np.pi, 11))[1:]
acf = ps.... | pastas/pasta | tests/test_stats.py | Python | mit | 1,157 | [
"Gaussian"
] | 2cc516eff0655f17d208e5f0bb23f159aa1539f7b9dec36a1134cd78935b2608 |
# Copyright (c) 2014 ETH Zurich, Institute of Astronomy, Lukas Gamper <lukas.gamper@usystems.ch>
from __future__ import print_function, division, absolute_import, unicode_literals
import sys
import pickle
from hope import config
from hope._ast import *
from hope._const import *
from hope._library import *
from hope... | cosmo-ethz/hope | hope/_generator.py | Python | gpl-3.0 | 33,664 | [
"VisIt"
] | a19b90fc3290a858bfe56830b2c245101b0b0fe9fe962df0dd630591e8a2458b |
"""
provide a generic structure to support window functions,
similar to how we have a Groupby object
"""
from __future__ import division
import warnings
import numpy as np
from collections import defaultdict
from datetime import timedelta
from pandas.core.dtypes.generic import (
ABCSeries,
ABCDataFrame,
... | louispotok/pandas | pandas/core/window.py | Python | bsd-3-clause | 78,055 | [
"Gaussian"
] | 5065288e40f1e2718cac83ea55f23a9e4f6e688188cf0a3e1e6814c707c70e83 |
"""
Support and standalone functions for Robust Linear Models
References
----------
PJ Huber. 'Robust Statistics' John Wiley and Sons, Inc., New York, 1981.
R Venables, B Ripley. 'Modern Applied Statistics in S'
Springer, New York, 2002.
C Croux, PJ Rousseeuw, 'Time-efficient algorithms for two highly robust
es... | jseabold/statsmodels | statsmodels/robust/scale.py | Python | bsd-3-clause | 12,267 | [
"Gaussian"
] | 6a565c072d577479b2d89c86e7085472a040efce67808af4835a8c671d03f091 |
from setuptools import setup, find_packages
with open('README.md') as readme_file:
readme = readme_file.read()
exec(open('graftm/version.py').read()) # loads __version__
setup(name='graftm',
version=__version__,
author='Joel Boyd, Ben Woodcroft',
description='GraftM is a pipeline used for ident... | wwood/graftM | setup.py | Python | gpl-3.0 | 1,091 | [
"Biopython"
] | 0681ebf846dd07e053b2ce3e38a23debd8c650c029967024321981cb4dcf52dc |
# -*- coding: utf-8 -*-
""" Tests for user authn views. """
from __future__ import absolute_import
import logging
import re
from http.cookies import SimpleCookie
from unittest import skipUnless
import ddt
import mock
from django.conf import settings
from django.contrib import messages
from django.contrib.auth import... | jolyonb/edx-platform | openedx/core/djangoapps/user_authn/views/tests/test_views.py | Python | agpl-3.0 | 37,200 | [
"VisIt"
] | 4dc4c513c1e42ea13585bc4a71a0eaa8b8e5a4910d1d782c54ab4f6a1c992351 |
"""
################################################################################
# Copyright (c) 2003, Pfizer
# Copyright (c) 2001, Cayce Ullman.
# Copyright (c) 2001, Brian Matthews.
#
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provid... | burzillibus/RobHome | venv/lib/python2.7/site-packages/SOAPpy/SOAPBuilder.py | Python | mit | 24,922 | [
"Brian"
] | 55c2a62a7be995cbc87cc1628d1134164071aa9997eba2dd0cd677ea3a645ddc |
# Version: 0.12
"""
The Versioneer
==============
* like a rocketeer, but for versions!
* https://github.com/warner/python-versioneer
* Brian Warner
* License: Public Domain
* Compatible With: python2.6, 2.7, 3.2, 3.3, 3.4, and pypy
[![Build Status]
(https://travis-ci.org/warner/python-versioneer.png?branch=master)... | mcdeaton13/Tax-Calculator | versioneer.py | Python | mit | 36,841 | [
"Brian"
] | e056d5489ecf07716364fba580b05b9f7b947da8bbecde4730f8c17916ce3b70 |
"""
API operations for Workflows
"""
from __future__ import absolute_import
import uuid
import logging
from sqlalchemy import desc, or_, and_
from galaxy import exceptions, util
from galaxy.model.item_attrs import UsesAnnotations
from galaxy.managers import histories
from galaxy.managers import workflows
from galaxy.... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/webapps/galaxy/api/workflows.py | Python | gpl-3.0 | 21,273 | [
"Galaxy"
] | 732399048b2bbdc88651623f9d4f29960b68d7850ec198f18ca992fc8fe1f3d3 |
#!/usr/bin/env python
# Copyright 2007, Michael J. Harms
# This program is distributed under General Public License v. 3. See the file
# COPYING for a copy of the license.
__description__ = \
"""
pdb_clean.py
Standardizes a Brookhaven pdb file
"""
__author__ = "Michael J. Harms"
__date__ = "070727"
import sys, tim... | harmslab/pdbtools | pdbtools/clean.py | Python | gpl-3.0 | 11,878 | [
"CHARMM"
] | 35f8d36f3064d0a801a783f1747d6bd6a8b7ec8e3aa7f102cfd79e6dcfbcb315 |
"""
chatbot.py
Ask Cleverbot something via CloudBot! This one is way shorter!
Created By:
- Foxlet <http://furcode.tk/>
License:
GNU General Public License (Version 3)
"""
import urllib.parse
import hashlib
import collections
import html
import requests
from cloudbot import hook
SESSION = collections.Or... | bharaths/CloudBot | plugins/chatbot.py | Python | gpl-3.0 | 1,917 | [
"Galaxy"
] | 50891f15b47db56482539de23ff77284162b069a093d4b096edeff44a965a96f |
import ocl
import camvtk
import time
import vtk
import datetime
import math
def drawLoops(myscreen,loops,loopColor):
# draw the loops
nloop = 0
for lop in loops:
n = 0
N = len(lop)
first_point=ocl.Point(-1,-1,5)
previous=ocl.Point(-1,-1,5)
for p in lop:
i... | aewallin/opencamlib | examples/python/waterline/waterline_8_tux_adaptive.py | Python | lgpl-2.1 | 2,746 | [
"VTK"
] | f6cf9514801142841569e72833897c1fb622f3fffa88949a02df2a774a1a1355 |
# Kevin van Rensburg 6/11/2021
# Copyright 2001
# Testing Startup Script version 0.14
# kstart14.py
# Creating new def Kvep1()-Kvep10()- Episodes for game and clean up all related def's
# updated the following def's : Adventure(), Continue()
# Adding script and lines to Kvep1-10, Adventure()
# Completed Kvep6 and worki... | kurg/KendyVerse | kstart14.py | Python | gpl-3.0 | 63,370 | [
"BLAST"
] | 7712fab7752a9989741fe10216a6d8fc5df458c8c30b49533ce998e14bffaed8 |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
#import sys
import sqlite3
def check_version():
try:
#connection = sqlite3.connect('./sqlite_test.db') # File DB. Creates a DB file.
connection = sqlite3.connect(':memory:') # In-memory DB.
#connection = sqlite3.connect('file::memory:?cache=shared') # Shared in-... | sangwook236/SWDT | sw_dev/python/ext/test/database/sqlite_test.py | Python | gpl-3.0 | 5,157 | [
"Brian"
] | 2a5eb4c5d03d0485b3be647f16d81a9614b671c481eaaaedeb7b11c129125eda |
import package_with_folder_and_alias
package_with_folder_and_alias.heyo.moose.fast()
| python-security/pyt | examples/import_test_project/test_package_with_folder_and_alias.py | Python | gpl-2.0 | 86 | [
"MOOSE"
] | 6146f11ae3709ddfad94b75a284d217037fa42d70e7993c72c8130f1a8edc043 |
# -*- coding: utf-8 -*-
"""
Created on Mon Mar 12 15:45:45 2018
@author: tih
"""
import numpy as np
import wa.General.raster_conversions as RC
def Run(input_nc, output_nc):
# Extract flow direction data from NetCDF file
flow_directions = RC.Open_nc_array(input_nc, Var = 'demdir')
# Open River Array
... | wateraccounting/wa | Models/SurfWAT/Part2_Create_Dictionaries.py | Python | apache-2.0 | 11,980 | [
"NetCDF"
] | bf7a6be2e76455ebcd7ecc3437f0dbad945cdb08293491337847459a5ba762d2 |
# Copyright 2014-2018 The PySCF Developers. 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 appl... | gkc1000/pyscf | pyscf/extras/mbd/__init__.py | Python | apache-2.0 | 645 | [
"PySCF"
] | a0aa1174cb286e81ae75fddfc9634df3afa682b950c3067856223ca58cff0f04 |
from __future__ import print_function, division, absolute_import
"""A setuptools based setup module.
See:
https://packaging.python.org/en/latest/distributing.html
https://github.com/pypa/sampleproject
"""
# Always prefer setuptools over distutils
from setuptools import setup, find_packages
# To use a consistent encod... | Cadene/pretrained-models.pytorch | setup.py | Python | bsd-3-clause | 6,643 | [
"VisIt"
] | e6ae0f285195809b97b6e9ccb922112c1a8ee9eeae3794df839026820afac3c4 |
''' BanditMDPClass.py: Contains the BanditMDPClass class. '''
# Python imports.
from __future__ import print_function
from collections import defaultdict
import numpy as np
# Other imports.
from simple_rl.mdp.MDPClass import MDP
from simple_rl.mdp.StateClass import State
class BanditMDP(MDP):
''' Imeplementation... | david-abel/simple_rl | simple_rl/tasks/bandit/BanditMDPClass.py | Python | apache-2.0 | 3,038 | [
"Gaussian"
] | 362c4f385c1f4efb2008fb11d3f4325050c6d9ed4664a2b99108f1716133ee64 |
"""Configuration file for eruption scenario
Tephra modelling validation worksheet
Scenario Name: Mount Merapi 2010 (Predictive_scenario)
Run Date: 2010_05_18
Run number:1 ... | GeoscienceAustralia/PF3D | hazard_map_example/merapi.py | Python | gpl-3.0 | 4,957 | [
"Gaussian"
] | 05178ce45691d137f6fd6bbdc7aab17752a5bf135be8a29150753df07a30baa2 |
# -*- coding: utf-8 -*-
"""Interpret PEP 345 environment markers.
EXPR [in|==|!=|not in] EXPR [or|and] ...
where EXPR belongs to any of those:
python_version = '%s.%s' % (sys.version_info[0], sys.version_info[1])
python_full_version = sys.version.split()[0]
os.name = os.name
sys.platform = sys.platfo... | xbianonpi/xbian-package-development | content/usr/local/lib/python2.7/dist-packages/distribute-0.6.30-py2.7.egg/_markerlib/markers.py | Python | gpl-2.0 | 3,558 | [
"VisIt"
] | e54b5d9f2c408a334296ab8472d59c48639f7694fae30d8f3762f59337961038 |
"""
==========================================
Outlier detection with several methods.
==========================================
When the amount of contamination is known, this example illustrates two
different ways of performing :ref:`outlier_detection`:
- based on a robust estimator of covariance, which is assumin... | treycausey/scikit-learn | examples/covariance/plot_outlier_detection.py | Python | bsd-3-clause | 3,874 | [
"Gaussian"
] | dd43e753a73840a98fe9bcdacdc9b3f0786696c0783305bcf82a4026c291c2e3 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2010 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU Lesser General Public License as published by
## the Free Software F... | tiagocardosos/stoq | stoqlib/domain/taxes.py | Python | gpl-2.0 | 10,006 | [
"VisIt"
] | da8358f28cdce798958a87931d13397b3024fc1284be5e4820fd14e7b843ad64 |
#!/usr/bin/env python
# (c) 2012-2018, Ansible by Red Hat
#
# This file is part of Ansible Galaxy
#
# Ansible Galaxy is free software: you can redistribute it and/or modify
# it under the terms of the Apache License as published by
# the Apache Software Foundation, either version 2 of the License, or
# (at your o... | chouseknecht/galaxy | manage.py | Python | apache-2.0 | 785 | [
"Galaxy"
] | 9d55338e34e2fde727ee08b298fd63cb309cbde535ad781d16e035fa6bce6440 |
# -*- coding: utf8 -*-
from PyQt5.QtWidgets import QWidget, QHBoxLayout, QPushButton
from PyQt5.QtCore import Qt
from PDielec.Utilities import Debug
class ScenarioTab(QWidget):
def __init__(self, parent, debug=False):
"""This the base class for all ScenarioTabs"""
super(QWidget, self).__i... | JohnKendrick/PDielec | PDielec/GUI/ScenarioTab.py | Python | mit | 4,331 | [
"CRYSTAL"
] | 63b9016c844627b65e3a4ddc6a3aefb217c264ce13cf69c6e2bea62e10c966f6 |
"""
A simple VTK widget for PyQt v4, the Qt v4 bindings for Python.
See http://www.trolltech.com for Qt documentation, and
http://www.riverbankcomputing.co.uk for PyQt.
This class is based on the vtkGenericRenderWindowInteractor and is
therefore fairly powerful. It should also play nicely with the
vtk3DWidget code.
... | cjh1/vtkmodular | Wrapping/Python/vtk/qt4/QVTKRenderWindowInteractor.py | Python | bsd-3-clause | 13,433 | [
"CRYSTAL",
"VTK"
] | 6c26da938cdb152273b9dfc6671e61a37ed2282de09e2428e42c3aa6abebe045 |
# -*- coding: utf-8 -*-
"""
Create an initial V2 ATP Profile for an ECs Mesh and write it out as .vtp.
"""
import os
import sys
import math
import vtk
import numpy
import matplotlib.pyplot as pyplot
centrelineFile = None
meshFile = None
debugAtpFile = None
atpFile = None
numBranches = 3
numQuads = 0
numAxialQuads = 0
... | BlueFern/DBiharMesher | util/GenerateATPMapV2.py | Python | gpl-2.0 | 4,148 | [
"VTK"
] | e658bedb09bbdf4ac82b385f50164f7c9089eca20bc3c782ca140bf84815142e |
# coding: utf-8
from __future__ import unicode_literals
import re
from .common import InfoExtractor
from ..utils import (
ExtractorError,
float_or_none,
int_or_none,
parse_duration,
parse_iso8601,
remove_end,
unescapeHTML,
)
from ..compat import (
compat_etree_fromstring,
compat_HT... | keyboard-k/youtube-dl-pet | youtube_dl/extractor/bbc.py | Python | unlicense | 40,671 | [
"VisIt"
] | f6bc70fd03024d70ea60dff69323addcc364deafbfe2aefb00067242bd43fade |
#ryan g coleman, ryangc@mail.med.upenn.edu
#copyright 2006-7 ryan g coleman, kim sharp crystal.med.upenn.edu
#geometric primitives like distance functions and such
import math
useNumeric = True # use numeric, if available
useNumpy = False
try: # to use numeric
import Numeric
import Matrix
import LinearAlgebra
... | ryancoleman/2D-protein-shape-matching | geometry.py | Python | gpl-2.0 | 26,875 | [
"CRYSTAL"
] | 947cf33962222606a86cc56aa4c9433fd73e7f085e4e45ca6a56bca6ef93d9ce |
import ast
import fnmatch
import os
j = os.path.join
from odoo.modules import get_modules, get_module_path
from odoo.tests import BaseCase
class LintCase(BaseCase):
""" Utility method for lint-type cases
"""
def iter_module_files(self, *globs):
""" Yields the paths of all the module files matchi... | jeremiahyan/odoo | odoo/addons/test_lint/tests/lint_case.py | Python | gpl-3.0 | 1,013 | [
"VisIt"
] | 24243bf2ffee2e93314a1bc28d348aae35a197dfcd450026552c0f240f4944aa |
#Copyright ReportLab Europe Ltd. 2000-2012
#see license.txt for license details
__version__ = '$Id: ch1_intro.py 3960 2012-09-27 15:22:33Z guillaume $'
from tools.docco.rl_doc_utils import *
from reportlab.platypus.tableofcontents import TableOfContents
from datetime import datetime
import reportlab
title("Rep... | nickpack/reportlab | docs/userguide/ch1_intro.py | Python | bsd-3-clause | 22,960 | [
"VisIt"
] | bcbb7a094a85a4d06e550bf6c7fe97af9d7631a56cc8af90a11641b3452e16ec |
# coding: utf-8
"""Tools to compute equations of states with different models."""
from __future__ import unicode_literals, division, print_function
import collections
import numpy as np
import pymatgen.core.units as units
from monty.functools import return_none_if_raise
from pymatgen.core.units import FloatWithUnit
f... | rousseab/pymatgen | pymatgen/io/abinitio/eos.py | Python | mit | 11,243 | [
"pymatgen"
] | d47a7bd02c93c660e29e9b444b93f53f003c2409e029b87c68fe57a144b2d581 |
from __future__ import annotations
import numpy as np
import pytest
from cctbx import crystal, sgtbx, uctbx
def test_symmetry_analysis():
coords = np.array(
[
[0.835, 0.158],
[0.772, 0.104],
[0.108, 0.907],
[0.058, 0.76],
[0.926, 0.189],
... | dials/dials | tests/algorithms/symmetry/cosym/test_cosym_symmetry_analysis.py | Python | bsd-3-clause | 5,645 | [
"CRYSTAL"
] | 17f1328a528b41cbb143829fb0cd917e49c54b70c9e6e6b5c7008f39323cd361 |
from .eos import *
from .pseudos import *
from .netcdf import *
from .tasks import *
from .works import *
from .calculations import *
| Dioptas/pymatgen | pymatgen/io/abinitio/__init__.py | Python | mit | 134 | [
"NetCDF"
] | e29b2b8de75e37c0bf0ac52f1bd816a446563f3e0229d580a0fb5989469396ed |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# ---------------------------------------------------------------------
# Copyright (c) 2012 Michael Hull.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are m... | mikehulluk/morphforge | src/morphforgecontrib/simulation/channels/inftauinterpolated/mmwriter_infatauinterpolated.py | Python | bsd-2-clause | 7,660 | [
"NEURON"
] | 961a2ea95ce0987563ef0abce26024cd92cab5a706f8139fa371a6d4dc975e5b |
import argparse
import logging
import os
import pathlib
import sys
import time
import sqlalchemy.orm
from sqlalchemy.orm import Load
import ispyb
from ispyb.sqlalchemy import BLSession, DataCollection, GridInfo, Proposal
def _tty_line_length():
if not sys.stdout.isatty():
return False
return os.get_... | DiamondLightSource/ispyb-api | src/ispyb/cli/last_data_collections_on.py | Python | apache-2.0 | 6,047 | [
"VisIt"
] | 74797951aaa34f4938045b94461926bde7df392217bf4d6f345aad77aac7e7ff |
#!/usr/bin/python2
import optparse
import os
import shutil
import stat
import subprocess
import sys
from builds.GpBuild import GpBuild
def install_gpdb(dependency_name):
status = subprocess.call("mkdir -p /usr/local/gpdb", shell=True)
if status:
return status
status = subprocess.call(
"ta... | cjcjameson/gpdb | concourse/scripts/test_gpdb.py | Python | apache-2.0 | 1,980 | [
"ORCA"
] | 1e48d7bdf67e95456ab1282faec90901ecac2b88f7cdee9912828599314b3665 |
"""Utilities to read and analyze molecular dynamics trajectories."""
import numpy as np
def read_frame_lammpstrj(trj):
"""Load a frame from a LAMMPS dump file.
Args:
trj (file): LAMMPS dump file of format 'ID type x y z'
Returns:
xyz (np.ndarray): coordinates of all atoms
types (... | ctk3b/pyrdf | pyrdf/mdio.py | Python | bsd-3-clause | 1,563 | [
"LAMMPS"
] | 76142cab3c2a5ec4bcba0b7ca862a53edbd65787ccde4153f1b4b97f662e8c14 |
# Copyright (c) 2015, Frappe Technologies Pvt. Ltd. and Contributors
# License: MIT. See LICENSE
import frappe
import unittest
from bs4 import BeautifulSoup
import re
from frappe.utils import set_request
from frappe.website.serve import get_response
from frappe.utils import random_string
from frappe.website.doctype.bl... | frappe/frappe | frappe/website/doctype/blog_post/test_blog_post.py | Python | mit | 4,930 | [
"VisIt"
] | fcac2397dc66ce1f7437b9cfbeba36573ae9de5c5903c4b3bb94817992d5da3f |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""http predefined data
"""
HTTP_CODE = {
# Status Codes
# Informational
100: 'Continue',
101: 'Switching Protocols',
102: 'Processing',
# Successful
200: 'OK',
201: 'Created',
202: 'Accepted',
203: 'Non Authoritative Information',... | kasworld/tiny_uwsgi | tiny_uwsgi/httpconst.py | Python | lgpl-3.0 | 30,962 | [
"NetCDF"
] | 8ddfd35b53d2e644a2cf9e3e58205fcc68947daa8f221ac21b49bef40eeafcb9 |
from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os
repository_name = 'bismark_0070'
repository_description = "Galaxy's bismark wrapper"
repository_long_description = "Long description of Galaxy's bismark wrapper"
category_name = 'Test 0070 Invalid Tool Revisions'
category_description = 'Test 1070 fo... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/test/tool_shed/functional/test_1070_invalid_tool.py | Python | gpl-3.0 | 6,165 | [
"Galaxy"
] | aa04eba7bc39ac0aa72fe42af991dc07c632d433af7ffcf539a7b984203a2876 |
#__docformat__ = "restructuredtext en"
# ******NOTICE***************
# optimize.py module by Travis E. Oliphant
#
# You may copy and use this module as you see fit with no
# guarantee implied provided you keep this notice in all copies.
# *****END NOTICE************
import time
import numpy as np
from numpy import atl... | askhl/ase | ase/optimize/bfgslinesearch.py | Python | gpl-2.0 | 7,150 | [
"ASE"
] | d2f4ce524c6aa71b458a57ec6ead9a7fefbdd5c48aa86dcc9ce0d08482d20b9f |
"""
Performance test created using multi-mechnize to analyze time
for update processing with MySQL.
"""
import random
import string
import time
from DIRAC.WorkloadManagementSystem.DB.JobDB import JobDB
def random_generator(size=6, chars=string.ascii_letters):
return ''.join(random.choice(chars) for x in xrange(si... | arrabito/DIRAC | tests/Performance/MySQLJobMonitoring/test_scripts/update.py | Python | gpl-3.0 | 842 | [
"DIRAC"
] | 50ea3b65889728c2be746f4cf7324a461c858d4645aee4fd5f932cf88f67652a |
#!/usr/bin/python -x
# $Rev:: 427 $
# $Author:: Bruno.CostaRendon@flextronics.com $
# $Date:: 2016-08-15 $
# $Update:: Enable/Disable VI communication $
#
# openXC-Modem Vehicle Interface (VI) agent class and associated functions
import logging
import os.path
import subprocess
import re
import st... | openxc/OpenXCAccessory | common/xc_vi.py | Python | bsd-3-clause | 57,413 | [
"Amber"
] | 12a11d052456decb333df389924d06211979403a8c9947199e939d7cafe5899d |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2018 Vimig Socrates <vimig.socrates@gmail.com>
# Copyright (C) 2016 Loreto Parisi <loretoparisi@gmail.com>
# Copyright (C) 2016 Silvio Olivastri <silvio.olivastri@gmail.com>
# Copyright (C) 2016 Radim Rehurek <radim@rare-technologies.com>
"""This script ... | napsternxg/gensim | gensim/scripts/word2vec2tensor.py | Python | gpl-3.0 | 3,850 | [
"VisIt"
] | b469694d338c3ef4b493c90bf3275699196a731937dc61a5de216be7d3defc09 |
import numpy as np
from asap3.nanoparticle_mc import data
from ase.atom import Atom, names as oldnames
from ase.data import atomic_numbers, chemical_symbols, reference_states
from asap3.Internal.MonteCarloAtoms import MC_Atom
class ClusterAtom(MC_Atom):
"""Cluster Atom"""
names = oldnames.copy()
names['neig... | auag92/n2dm | Asap-3.8.4/Python/asap3/nanoparticle_mc/clusteratom.py | Python | mit | 4,763 | [
"ASE"
] | 0d194ac1c1649ab8613e8d3fe83fb9f58f21e2b05f87eb9157a59c0409a190c5 |
# -*- coding: utf-8 -*-
def VtkDibujaIdsElementos(ids):
# Dibuja las etiquetas de los elementos.
cc= vtk.vtkCellCenters()
vtk.SetInput(ids) # Centroides de las celdas.
visCells= vtk.vtkSelectVisiblePoints()
visCells.SetInput(cc)
visCells.SetRenderer("renderer")
visCells.SelectionWindowOff()
#Create... | lcpt/xc | python_modules/postprocess/xcVtk/FE_model/vtk_plot_element_ids.py | Python | gpl-3.0 | 630 | [
"VTK"
] | 4cb5cca01bff3eb59fdeafead17b6770d39a2990097085d3270ccd39b5fac2f1 |
# -*- coding: utf-8 -*-
import xbmc, xbmcaddon, xbmcplugin, xbmcgui
import sys, os, time, datetime, re
import urllib, urlparse
resolverID = 'script.module.israeliveresolver'
AddonID = "plugin.video.israelive"
Addon = xbmcaddon.Addon(AddonID)
if Addon.getSetting("unverifySSL") == "true":
try:
import ssl
ssl._creat... | noam09/kodi | plugin.video.israelive/default.py | Python | gpl-3.0 | 40,169 | [
"Amber"
] | 76aca9303b8e06a5b912754c2a87b112f3a976b76aa8e5a55794ef816d17b992 |
#!/usr/bin/env python
# encoding: utf-8
import os
import sys
from modularodm import Q
from modularodm.exceptions import ModularOdmException
from framework.auth.core import User
from website import settings
from website.app import init_app
from website.conferences.model import Conference
from datetime import datetim... | rdhyee/osf.io | scripts/populate_conferences.py | Python | apache-2.0 | 32,254 | [
"COLUMBUS"
] | b12902ed3f14ad26534798f555969eeee2ea456f345cf4f4128f3654fd61da02 |
# Pyctools - a picture processing algorithm development kit.
# http://github.com/jim-easterbrook/pyctools
# Copyright (C) 2014-20 Pyctools contributors
#
# 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 Softwa... | jim-easterbrook/pyctools | src/pyctools/components/interp/gaussianfilter.py | Python | gpl-3.0 | 5,052 | [
"Gaussian"
] | 5c4c7b9d3740810a10ae21ed2b1bf2dd0475bb445f2ead71c309bd1abd889d39 |
#!/usr/bin/env python
"""
5PrimeCounter
=============
5PrimeCounter analyses a BAM file from a ChIP-Exo experiment in the context of potential transcription factor binding sites (TFBS) presenting a given sequence motif of interest.
Consequently, as input files, 5PrimeCounter needs a BAM file (and its BAI index) and a... | ComputationalSystemsBiology/ExoProfiler | python/5primeCounter.py | Python | gpl-3.0 | 21,010 | [
"Galaxy",
"HTSeq",
"pysam"
] | 2458c7aa137c751dbc1f8c038a84d098497e5965544f465c1a2d1952d99b1cf1 |
#!/usr/bin/env python
#
# This program is free software you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation either version 3 of the License, or
# (at your option) any later version.
#
# Written (C) 2012-2013 Heiko Strathmann
#
impor... | AzamYahya/shogun | examples/undocumented/python_modular/statistics_hsic.py | Python | gpl-3.0 | 4,120 | [
"Gaussian"
] | 9a4d2f3f35fa761812a104b32d8d8b7a4fd3fe379fdb4a74f2d9bf9df1d8534b |
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