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#
# @file TestInitialAssignment_newSetters.py
# @brief InitialAssignment unit tests for new set function API
#
# @author Akiya Jouraku (Python conversion)
# @author Sarah Keating
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was gener... | TheCoSMoCompany/biopredyn | Prototype/src/libsbml-5.10.0/src/bindings/python/test/sbml/TestInitialAssignment_newSetters.py | Python | bsd-3-clause | 3,500 | [
"VisIt"
] | e03319c72a48c107f25d016c98a312e0fdcd088a5f6c2a2d8e4d15643b6b9b6d |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
import unittest
import os
from numbers import Number
import matplotlib
import warnings
matplotlib.use("pdf")
from pymatgen.analysis.phase_diagram import *
from pymatge... | czhengsci/pymatgen | pymatgen/analysis/tests/test_phase_diagram.py | Python | mit | 24,623 | [
"pymatgen"
] | b649b3d0f847c8f42626af4cdde643d97825f42cabc192b81189b6d5c69643e4 |
# -*- coding: utf-8 -*-
from __future__ import absolute_import, division, print_function, unicode_literals
from nose.tools import * # noqa PEP8 asserts
from tests import factories
from tests.test_search import SearchTestCase
from website.util import api_url_for
class TestSearchViews(SearchTestCase):
def setUp... | alexschiller/osf.io | tests/test_search/test_views.py | Python | apache-2.0 | 9,904 | [
"Brian"
] | 3bec9cc25c74623c0dfce20de29a3cb85e029ec473c6ebf3e7cc515bfb2f377d |
#!/usr/bin/env python3
# This script checks and can optionally update MOOSE source files.
# You should always run this script without the "-u" option
# first to make sure there is a clean dry run of the files that should
# be updated
import os, string, re, shutil
from optparse import OptionParser
global_ignores = ['... | nuclear-wizard/moose | framework/scripts/fixup_headers.py | Python | lgpl-2.1 | 6,125 | [
"MOOSE"
] | 4373288d63818e66305de5039ea45cb28661a92864ea3ebdc8c8510240d39a4f |
"""Get useful information from live Python objects.
This module encapsulates the interface provided by the internal special
attributes (co_*, im_*, tb_*, etc.) in a friendlier fashion.
It also provides some help for examining source code and class layout.
Here are some of the useful functions provided by this module:... | ruchee/vimrc | vimfiles/bundle/vim-python/submodules/autopep8/test/inspect_example.py | Python | mit | 104,371 | [
"VisIt"
] | 3f3033f41a54081bb691d7e0c7289e844177bf3cac2b97e6beebaedb86be7cf6 |
########################################################################
# $HeadURL$
# File : JobCleaningAgent.py
# Author : A.T.
########################################################################
""" The Job Cleaning Agent controls removing jobs from the WMS in the end of their life cycle.
This agent wi... | hgiemza/DIRAC | WorkloadManagementSystem/Agent/JobCleaningAgent.py | Python | gpl-3.0 | 10,218 | [
"DIRAC"
] | 0d99e5577f4e79c9ed3e8da46cbc60675ebbaf464616ee6db17608a6b3725beb |
# setup.py
from distutils.core import setup
import sys
#windows installer:
# python setup.py bdist_wininst
# patch distutils if it can't cope with the "classifiers" or
# "download_url" keywords
if sys.version < '2.2.3':
from distutils.dist import DistributionMetadata
DistributionMetadata.classifier... | bcl/hygrosens | setup.py | Python | gpl-2.0 | 1,139 | [
"Brian"
] | 06f7acff8327bfdaf49791811e7e2e56e619d56442bb9b0571a9ed928eaaf905 |
#!/usr/bin/env python
#
# @file BaseJavaFile.py
# @brief base class for Java files to be generated
# @brief Code part of Google Summer of Code 2016
# @author Hovakim Grabski
#
# <!--------------------------------------------------------------------------
#
# Copyright (c) 2013-2015 by the California Institute o... | hovo1990/deviser | generator/base_files/BaseJavaFile.py | Python | lgpl-2.1 | 86,947 | [
"VisIt"
] | d6881c32abb7e46bde1ff781188a66a6113602b29bf6160b32e244bcf63909b8 |
##############################################################################
# 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... | EmreAtes/spack | var/spack/repos/builtin/packages/r-deseq2/package.py | Python | lgpl-2.1 | 2,666 | [
"Bioconductor"
] | 4cf92bb87dd4e9c2886e93bfdf28cfa9e6149d894f6c2260ff2b1825d8339211 |
from __future__ import absolute_import, division, print_function
from textwrap import dedent
import _pytest._code
import py
import pytest
from _pytest.config import PytestPluginManager
from _pytest.main import EXIT_NOTESTSCOLLECTED, EXIT_USAGEERROR
@pytest.fixture(scope="module", params=["global", "inpackage"])
def ... | rmfitzpatrick/pytest | testing/test_conftest.py | Python | mit | 15,686 | [
"VisIt"
] | 1747862e855e06a254040543a33a6ad6fa996ac7c992790580f986f7eac2c9b8 |
##############################################################################
# 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... | EmreAtes/spack | var/spack/repos/builtin/packages/trilinos/package.py | Python | lgpl-2.1 | 28,276 | [
"NetCDF"
] | 05c2cd20e5f583b574e1d3374793d40327ffb3d5952fc567ba359f6aa4e9d276 |
# Lint as: python3
# Copyright 2020 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required ... | google/madi | tests/neg_sample_neural_net_detector_test.py | Python | apache-2.0 | 3,707 | [
"Gaussian"
] | 60d90055582ce7eec11f2740ff584163ffa8b46991fabcc4baebbc53ace503fe |
#
# This source file is part of appleseed.
# Visit http://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2016 Haggi Krey, The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of... | haggi/appleseed-maya | module/scripts/appleseed_maya/aetemplate/aemtap_standinmeshnodetemplate.py | Python | mit | 2,366 | [
"VisIt"
] | 8aba3629e01e763381bb6509b8cef6c3c547a5baaa949282529b84309031d474 |
"""Utilities to assist with commerce tasks."""
import json
import logging
from urllib import urlencode
from urlparse import urljoin
import requests
import waffle
from django.conf import settings
from django.contrib.auth import get_user_model
from django.core.urlresolvers import reverse
from django.utils.translation im... | TeachAtTUM/edx-platform | lms/djangoapps/commerce/utils.py | Python | agpl-3.0 | 14,319 | [
"VisIt"
] | 9a2b4f6cb19940d3a58bed580ce13812b72165e0d999d1dbc40a71f18fd33453 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
CanSNPer: A toolkit for SNP-typing using NGS data.
Copyright (C) 2016 Adrian Lärkeryd
VERSION 1.0.10
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,... | adrlar/CanSNPer | CanSNPer/__main__.py | Python | gpl-3.0 | 44,020 | [
"Galaxy"
] | 38b7d9c5ecfa50219948a770dedc94b98b36e1ffc6043d1c49cc3809ac269d8d |
#!/galaxy/home/mgehrin/hiclib/bin/python
"""
Read a maf file from stdin and write out a new maf with only blocks having all
of the required in species, after dropping any other species and removing
columns containing only gaps.
usage: %prog species,species2,... < maf
"""
import psyco_full
import bx.align.maf
import... | bxlab/HiFive_Paper | Scripts/HiCLib/bx-python-0.7.1/build/scripts-2.7/maf_limit_to_species.py | Python | bsd-3-clause | 953 | [
"Galaxy"
] | 835b324292e1bb96ffd26f7afc272ad52af19cfc0f74197f03e4cf1c573c79c5 |
# coding: utf-8
import random
import math
C_PUCT = 1.
class StateNode(object):
# 这将会是一颗巨大的搜索树
# 以下语句可以节省大量内存
__slots__ = ('gs', 'value', 'children', 'depth', 'n')
def __init__(self, gs, depth):
self.gs = gs
self.value = 0
self.children = None
self.depth = depth
... | zhaipro/AlphaLineupPuzzle | AlphaLineupPuzzle/mcts.py | Python | mit | 3,250 | [
"VisIt"
] | c7d8f370d68428cdbb8f9cd2631a8936d2ddcfd4ac0ab52329bb4df9e08c4d4e |
## twofish.py - pure Python implementation of the Twofish algorithm.
## Bjorn Edstrom <be@bjrn.se> 13 december 2007.
##
## Copyrights
## ==========
##
## This code is a derived from an implementation by Dr Brian Gladman
## (gladman@seven77.demon.co.uk) which is subject to the following license.
## This Python implemen... | sommer/loxodo | src/twofish/twofish.py | Python | gpl-2.0 | 15,601 | [
"Brian"
] | 300d809d5eacaf26c4158a7ab1a8e6c0ef057cf4781f34abff4245816f43fe14 |
# -*- coding: utf-8 -*-
#
#
# TheVirtualBrain-Scientific Package. This package holds all simulators, and
# analysers necessary to run brain-simulations. You can use it stand alone or
# in conjunction with TheVirtualBrain-Framework Package. See content of the
# documentation-folder for more details. See also http://ww... | stuart-knock/tvb-library | tvb/tests/library/datatypes/equations_test.py | Python | gpl-2.0 | 4,205 | [
"Gaussian"
] | 67788b86eae6e117305260438da9ec38368a2e0178b82c2f7b5f7f62c2ff5053 |
from flask import Flask, render_template, request, redirect, session
import random
app = Flask(__name__)
app.secret_key = 'secretsquirrel'
@app.route('/')
def index():
#initialize gold count
if not 'goldCount' in session:
session['goldCount'] = 0
session['activities'] = []
return ren... | authman/Python201609 | Nguyen_Ken/Assignments/Flask/ninja_gold/server.py | Python | mit | 1,991 | [
"CASINO"
] | 6df98524331553c985cb8480c0eb4f8690be0bf0386333f4b1db9876362a5ce4 |
""" core implementation of testing process: init, session, runtest loop. """
import py
import pytest, _pytest
import os, sys, imp
tracebackcutdir = py.path.local(_pytest.__file__).dirpath()
# exitcodes for the command line
EXIT_OK = 0
EXIT_TESTSFAILED = 1
EXIT_INTERRUPTED = 2
EXIT_INTERNALERROR = 3
name_re = py.std.... | snim2/rcsp | _pytest/main.py | Python | gpl-2.0 | 20,689 | [
"VisIt"
] | 6d766e754a56e74d5182d1794232dbfb29e1049e8f4d82b4ad834452533c8cc1 |
import sys, os
import ez_setup
ez_setup.use_setuptools()
from setuptools import setup, find_packages
import compiler
import pydoc
from compiler import visitor
class ModuleVisitor(object):
def __init__(self):
self.mod_doc = None
self.mod_version = None
def default(self, node):
... | patrickod/fixture | setup.py | Python | lgpl-2.1 | 2,796 | [
"VisIt"
] | 89ef7f27129553b97e7bc459b8bec6042e036c4a40c21a303efdb4a8ee3baebf |
r"""
Linear elasticity with linear combination constraints and periodic boundary
conditions.
The linear combination constraints are used to apply periodic boundary
conditions with a shift in the second axis direction.
Find :math:`\ul{u}` such that:
.. math::
\int_{\Omega} D_{ijkl}\ e_{ij}(\ul{v}) e_{kl}(\ul{u})
... | RexFuzzle/sfepy | examples/linear_elasticity/elastic_shifted_periodic.py | Python | bsd-3-clause | 4,016 | [
"VTK"
] | 460ce2047e0a9562c2229bc0cf496e1c02b38bf8a9cfe42e3fced00cbaabc601 |
#!/usr/bin/env python
import sys, getopt
import re
import time
import os
def get_option():
opts, args = getopt.getopt(sys.argv[1:], "hi:f:o:")
input_file = ""
output_file = ""
ref = ""
h = ""
for op, value in opts:
if op == "-i":
input_file = value
elif op == "-f":
ref = value
elif op == "-o":
ou... | sdws1983/bioinfo-relate | Blast-relate/search-speices-in-blast.py | Python | gpl-3.0 | 1,260 | [
"BLAST"
] | 748b23a4278a37005543018ebc7da2aa142015ed320fdc5f37656d928a251ad8 |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
import sys
i... | harterj/moose | python/MooseDocs/extensions/katex.py | Python | lgpl-2.1 | 12,218 | [
"MOOSE"
] | af03b0228b147a9667432d067c282d14257440005d9de58a86ae0dfbb4ccc4a4 |
#!/usr/bin/python
# (c) 2013, Cove Schneider
# (c) 2014, Joshua Conner <joshua.conner@gmail.com>
# (c) 2014, Pavel Antonov <antonov@adwz.ru>
#
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = t... | e-gob/plataforma-kioscos-autoatencion | scripts/ansible-play/.venv/lib/python2.7/site-packages/ansible/modules/cloud/docker/_docker.py | Python | bsd-3-clause | 74,511 | [
"VisIt"
] | 5e1978ece83540149d8a226ca76a3e3b352587c562063178389ee93a585fe145 |
#!/usr/bin/env python
''' Convert a sourcedb back into a .skymodel '''
import os
import sys
import subprocess
import re
from collections import deque
sourcedb=sys.argv[1]
print "# (Name, Type, Ra, Dec, I, ReferenceFrequency, SpectralIndex='[]', MajorAxis, MinorAxis, Orientation) = format"
def sourcedb2sourcelist(sou... | tammojan/lofarscripts | sourcedb2skymodel.py | Python | gpl-2.0 | 3,129 | [
"Gaussian"
] | b560c654c5c344615af6bcfeca0aba382d5d547259e2a80708b8acb5b418fb83 |
import matplotlib.pyplot as plt
from matplotlib import cm
from mpl_toolkits.mplot3d import Axes3D
from sklearn.neighbors.kde import KernelDensity
from scipy import stats
import pandas as pd
import numpy as np
import pickle
data = pickle.load(open('fitting.p', 'rb'))
# list of strings
Al = np.array(data['Al'])
Al = {... | leal26/AeroPy | examples/2D_fitting/plotting_all_3d.py | Python | mit | 4,026 | [
"Gaussian"
] | 6ee65fb9f7253fc9cfc4df4a9c9426814cdee08259f376bdc3778e730714f0f5 |
#!/usr/bin/env python
"""
dirac-rss-sync
Script that synchronizes the resources described on the CS with the RSS.
By default, it sets their Status to `Unknown`, StatusType to `all` and
reason to `Synchronized`. However, it can copy over the status on the CS to
the RSS. Important: If the StatusTyp... | avedaee/DIRAC | ResourceStatusSystem/scripts/dirac-rss-sync.py | Python | gpl-3.0 | 7,270 | [
"DIRAC"
] | 88d0b17e25c9c0f24b7b5bdabb0fa9ffeba8947f9fbf76a0826a5e0863777b67 |
#!/usr/bin/env python
import cgi
import cgitb; cgitb.enable()
import time
import connect
print ("Content-Type: text/html")
print ("")
arguments = cgi.FieldStorage()
quantityCoffee=0
quantityEspresso=0
port = connect.OpenThePort()
connect.Setup()
if 'coffee' in arguments:
quantityCoffee=arguments.getvalue('coff... | bojandjukic1/SAP_CORK | Coffee_Machine/CGI Call and Script - New/coffeeCGI.py | Python | gpl-3.0 | 952 | [
"ESPResSo"
] | b2579c709c55c36fab9376b06c67a47e9c5d082c613502b936fbc62a2af2dae8 |
#python
import numpy as np
import gc
def log_mean_exp(a):
"""
.. todo::
WRITEME
"""
max_ = a.max(1) # Get max values of rows
return max_ + np.log(np.exp(a - max_[:,None]).mean(1))
def gaussian_parzen(X, samples, sigma):
"""
Compute gaussian parzen of data from X to samples, given sigm... | tntrung/pyCVML | common/metrics/parzen_ll.py | Python | gpl-2.0 | 2,236 | [
"Gaussian"
] | 6cfdf3eaeb44c2875f8a0ae8a283dd1a21906f3251bac27b7461689d9c334910 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the G... | kkreis/espressopp | src/analysis/MaxPID.py | Python | gpl-3.0 | 1,615 | [
"ESPResSo"
] | 3d41f7f27afe7c543e9af7d8474d3ddf7d9a93bee7b9de538d69308f1fab7ff6 |
# -*- coding: utf-8 -*-
#
# AtHomePowerlineServer - networked server for CM11/CM11A/XTB-232 X10 controllers
# Copyright © 2014, 2019 Dave Hocker
#
# 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 Fou... | dhocker/athomepowerlineserver | commands/GetTime.py | Python | gpl-3.0 | 1,220 | [
"xTB"
] | d88a5a70252ff5138e683aa5b47dcb5f816324c367ef8db3b6b7379b0567c607 |
#!/usr/bin/env python2
desc="""Generate nice graph with coverage for multiple samples.
Tracks are in colors and merged track is added if less than 13 samples.
First generate cov.bed files is:
for f in bowtie2/*.bam; do echo `date` $f; bedtools coverage -counts -abam $f -b ../ensembl/Fusarium_oxysporum.FO2.15.dna.topl... | lpryszcz/bin | genome_graph.py | Python | gpl-3.0 | 11,585 | [
"pysam"
] | 3a4006fd97a3d5a7468d7162b5441a42440db12466988789983ccf096517ed33 |
#
# Each time a song starts, the bot vote up.
# WARNING: Turntable no longer allows bots that autobop. This script is provided for educational purposes only.
# For more information, visit http://faq.turntable.fm/customer/portal/articles/258935
#
from ttapi import Bot
AUTH = 'auth+live+2cdbb9bd018b4d3af371b29471ce90... | leand487/ChiCO.FM | python_ttapi/examples/autobop.py | Python | mit | 507 | [
"VisIt"
] | e4703c77734d87f4b1c61f5cd23bcce4c9eecef5edf381e22ee68bfb4393ba10 |
#!/usr/bin/python3
# -*- coding: utf-8 -*-
"""This file contains code used in "Think Stats",
by Allen B. Downey, available from greenteapress.com
Copyright 2010 Allen B. Downey
License: GNU GPLv3 http://www.gnu.org/licenses/gpl.html
"""
from urllib import request
import myplot
import Pmf
results = 'http://www.cool... | qrsforever/workspace | python/learn/thinkstats/relay.py | Python | mit | 2,122 | [
"Brian"
] | a6ab94b06ee4d6b3608b9c827ca362bac607c8fa8259d6e0b8cda7c099688e05 |
# vim: fdm=indent
'''
author: Fabio Zanini
date: 06/11/14
content: Models for the hivwholeweb site.
We are in a particular position, because we do not collect data
from the users and store in a database, but we need to stream data.
This makes our 'models' a bit odd.
''... | iosonofabio/hivwholeweb | app/hiv/models.py | Python | mit | 27,913 | [
"Biopython"
] | de740e4bd459c33ebe7a06a419a65c44d7a60dc58240c9047999dced0917895b |
"""
The Sparse Fascicle Model.
This is an implementation of the sparse fascicle model described in
[Rokem2015]_. The multi b-value version of this model is described in
[Rokem2014]_.
.. [Rokem2015] Ariel Rokem, Jason D. Yeatman, Franco Pestilli, Kendrick
N. Kay, Aviv Mezer, Stefan van der Walt, Brian A. Wandell
... | StongeEtienne/dipy | dipy/reconst/sfm.py | Python | bsd-3-clause | 20,391 | [
"Brian"
] | 1bddd51293fa7820a19cfba67cbc3c0e5a56868f9a5e1aed38b4a11ff5b5e5ef |
import glob
import gzip
import hashlib
import logging
import os
import re
import subprocess
import sys
import textwrap
import tempfile
from collections import defaultdict
import ftputil
import pandas as pd
import requests
from Bio import SeqIO
from Bio.SeqRecord import SeqRecord
from colors import green
from bs4 impor... | kashyapchhatbar/CLASHChimeras | clashchimeras/initialize.py | Python | mit | 34,537 | [
"Bowtie"
] | eccc4076d6d8cb9649d9c413bc58f2df8a30f984642f9e5a664e7f9c80886c88 |
"""
This file generates the binary files need to run Octopus based on MITgcm grid files.
You only need to specify the path to the folder containing grid files, including
DRF.data, hFacF.data
Jinbo Wang
<jinbow@gmail.com>
Scripps Institution of Oceanography
August 26, 2015
"""
import numpy as np
import scipy as sp
... | jinbow/Octopus | scripts/gen_data.py | Python | mit | 4,077 | [
"Octopus"
] | fe01041bdbc09cf5afefb0a39935abfe663a22c25ff8265a961237db06c3e73f |
import numpy as np
from deepchem.feat.base_classes import Featurizer
from deepchem.utils import get_partial_charge
from typing import Sequence
class AtomicConformation:
"""This class represents a collection of atoms arranged in 3D space.
An instance of this class may represent any collection of atoms: a molecul... | deepchem/deepchem | deepchem/feat/atomic_conformation.py | Python | mit | 6,759 | [
"RDKit"
] | bc645f4320a5f6e5453ac2b5bfdb4aa32218f4e17c419b3afe6cfcd944a2a9e5 |
#########################################################################
## This program is part of 'MOOSE', the
## Messaging Object Oriented Simulation Environment.
## Copyright (C) 2014 Upinder S. Bhalla. and NCBS
## It is made available under the terms of the
## GNU Lesser General Public License version 2... | dilawar/moose-full | moose-examples/snippets/cylinderDiffusion.py | Python | gpl-2.0 | 6,270 | [
"MOOSE"
] | 91aac315f556c68fa4d70f67af5b7f26c756670b54d5dc81a0fd50fe3616bf44 |
# 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 | robust_optim/data.py | Python | apache-2.0 | 2,993 | [
"Gaussian"
] | 48d77c5111af115d789dd4f7aba9a230f9699399e387fd9d741e0dc22bfafb91 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
... | kain88-de/mdanalysis | testsuite/MDAnalysisTests/topology/test_hoomdxml.py | Python | gpl-2.0 | 2,030 | [
"MDAnalysis"
] | c05c3bb1267636add04a162e3b2b72ac6641e7a6b6172dee448dd63c57f8727b |
#!/usr/bin/python
#
# Copyright (C) 2015 Dave Berkeley projects@rotwang.co.uk
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later v... | DaveBerkeley/uk_maps | makemap.py | Python | gpl-2.0 | 8,125 | [
"VisIt"
] | ed60ac5fd2d15f0ef0746ceefa272a60cba9d6a3d391102755f301e814c96494 |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | eljefe6a/incubator-beam | sdks/python/apache_beam/runners/dataflow/dataflow_runner.py | Python | apache-2.0 | 44,012 | [
"VisIt"
] | 056cf13fc7ea6b6a839ee73a7828755a9d4e2287f52af41854c5d93f5a163bd5 |
import logging
import warnings
# External libs
import numpy as np
import pandas as pd
from scipy import stats
# Optional libs
try:
import salem
except ImportError:
pass
# Locals
from oggm import cfg
from oggm import utils
from oggm import entity_task
from oggm.exceptions import InvalidParamsError
# Module l... | TimoRoth/oggm | oggm/shop/histalp.py | Python | bsd-3-clause | 6,018 | [
"NetCDF"
] | 39cf85fb8238ec636591d1a342e3633a27dca22f53627b52882752b3ab3b03d2 |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | rabipanda/tensorflow | tensorflow/contrib/py2tf/pyct/static_analysis/type_info.py | Python | apache-2.0 | 6,253 | [
"VisIt"
] | bbd5592cb1635c4453474a3a8711aea18504cfbfdbc40ce7d46e6d4a298f5c36 |
#pylint: disable=missing-docstring
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/... | nuclear-wizard/moose | python/chigger/base/ColorMap.py | Python | lgpl-2.1 | 5,731 | [
"MOOSE",
"ParaView",
"VTK"
] | 441ba89b1dec455173d90a8c6a8b0e5b34c4b9a3a51973289cbb4542ddcfbaed |
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under t... | stackforge/osprofiler | osprofiler/hacking/checks.py | Python | apache-2.0 | 13,277 | [
"VisIt"
] | 1aca6e5e9e5d66d2becb25ba9177d8b19f75da5682cdc992d7ccc8b9f87a47e9 |
import functools
import logging
from pip._vendor.packaging.utils import canonicalize_name
from pip._internal.exceptions import (
DistributionNotFound,
InstallationError,
InstallationSubprocessError,
MetadataInconsistent,
UnsupportedPythonVersion,
UnsupportedWheel,
)
from pip._internal.models.w... | nataddrho/DigiCue-USB | Python3/src/venv/Lib/site-packages/pip/_internal/resolution/resolvelib/factory.py | Python | mit | 18,729 | [
"VisIt"
] | d367f04d971060e86bd74b618ce53b909b7302142444bc8c89b6f16965c76410 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
# Copyright (C) 2019
# Max Planck Computing and Data Facility
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free softwa... | govarguz/espressopp | src/storage/DomainDecomposition.py | Python | gpl-3.0 | 4,254 | [
"ESPResSo"
] | 6c3b6150d4c02e32dc193a8a684b62276e36f48bcb2d024befaa1d7474c6e347 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import vtk
def main():
colors = vtk.vtkNamedColors()
# Set the colors.
colors.SetColor("CubeColor", [250, 128, 114, 255])
colors.SetColor("BkgColor", [230, 230, 230, 255])
# Create the rendering windows and three renderers.
ren1 = vtk.vtkRender... | lorensen/VTKExamples | src/Python/Rendering/Model.py | Python | apache-2.0 | 2,505 | [
"VTK"
] | 5b08b07a590e2574e3443ced6a4f2fd8ffed1a20d32ed9fe83505638a355e99e |
import matplotlib
# no X11 server ... must be run first
# https://github.com/matplotlib/matplotlib/issues/3466/
matplotlib.use('Agg')
import matplotlib.pylab as plt
# import ccrs for map projections
import cartopy.crs as ccrs
from netCDF4 import Dataset
import os
DATADIR = os.path.join(os.path.abspath(os.path.dirname... | bird-house/birdhouse-workshop | tutorials/02_testing_plotter/plotter.py | Python | apache-2.0 | 1,701 | [
"NetCDF"
] | 41fbf0168555d5e0098bf69a117689815915b33e9b4d63a040f7900931fb65b2 |
# Copyright 2014-2020 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/sgx/test/test_sgx.py | Python | apache-2.0 | 1,100 | [
"PySCF"
] | 7f4679c3a10b4b3efa763876cf5c77bfb3689926601e28ee607120429074c377 |
import numpy as n
from scipy import ndimage as sn
from PyQt5 import QtGui as QG
from skimage import exposure
from lsjuicer.resources import cm
import lsjuicer.inout.db.sqla as sa
class PixmapMaker(object):
"""Makes a Qt Pixmap object from numerical data output by pipechain"""
@property
def data(self)... | ardoi/datajuicer | lsjuicer/ui/plot/pixmapmaker.py | Python | gpl-3.0 | 5,393 | [
"Gaussian"
] | 1148741c6165bbc04a3f100350468bca3be91784e260c8df3b41bbe437855c2e |
import numpy as np
import pandas as pd
from copy import deepcopy
from concise.utils.helper import get_from_module, _to_string
import logging
from gtfparse import read_gtf
_logger = logging.getLogger('genomelake')
ALL_LANDMARKS = ["tss", "polya",
"exon_intron", "intron_exon",
"start_c... | gagneurlab/concise | concise/utils/position.py | Python | mit | 4,272 | [
"HTSeq"
] | 289e423926748e4ed678acc390c75b1179ce462a4cf38bf222d734f6a17c4686 |
from __future__ import division, print_function, absolute_import
import numpy as np
import math
import warnings
# trapz is a public function for scipy.integrate,
# even though it's actually a numpy function.
from numpy import trapz
from scipy.special import roots_legendre
from scipy.special import gammaln
from scipy.... | kenshay/ImageScript | ProgramData/SystemFiles/Python/Lib/site-packages/scipy/integrate/quadrature.py | Python | gpl-3.0 | 29,304 | [
"Gaussian"
] | b2815c5b365a3744c64ec4af700e3b0f402c96d2a948df067212f9242dd75cde |
# Copyright (c) 2018, Henrique Miranda
# All rights reserved.
#
# This file is part of the phononwebsite project
#
#conversion variables
ang2bohr = 1.889725989
bohr_angstroem = 0.529177249
hartree_cm1 = 219474.63
eV = 27.211396132
Bohr = 1.88973
#from ase https://wiki.fysik.dtu.dk/ase/
chemical_symbols = ['X', 'H', ... | henriquemiranda/phononwebsite | phononweb/units.py | Python | bsd-3-clause | 3,205 | [
"ASE"
] | 3ee5739c3713c3d123c03a9a3604f29bd3aac9ba96559a60b3b6bcccd2950eba |
"""Python test discovery, setup and run of test functions."""
import enum
import fnmatch
import inspect
import itertools
import os
import sys
import types
import typing
import warnings
from collections import Counter
from collections import defaultdict
from collections.abc import Sequence
from functools import partial
... | The-Compiler/pytest | src/_pytest/python.py | Python | mit | 63,744 | [
"VisIt"
] | c545d02f52badfeb9f5aec53084412d0fd20c57924d7a06d2c2871986e922b38 |
# Natural Language Toolkit: Maximum Entropy Classifiers
#
# Copyright (C) 2001-2011 NLTK Project
# Author: Edward Loper <edloper@gradient.cis.upenn.edu>
# Dmitry Chichkov <dchichkov@gmail.com> (TypedMaxentFeatureEncoding)
# URL: <http://www.nltk.org/>
# For license information, see LICENSE.TXT
"""
A classifier... | tadgh/ArgoRevisit | third_party/nltk/classify/maxent.py | Python | apache-2.0 | 66,330 | [
"Gaussian"
] | 6d7fa53160684a9f8d98a7f35ff061ad86946d318416c56c05c3d30d2c213a93 |
# Copyright: (c) 2013, James Cammarata <jcammarata@ansible.com>
# Copyright: (c) 2018, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import os.path
import re
import sh... | albertomurillo/ansible | lib/ansible/cli/galaxy.py | Python | gpl-3.0 | 34,176 | [
"Galaxy"
] | 5b45c4577a1343d8aea6f250dd5474bf112b936d9d2dfa5e82e1c9ac8bb24e3a |
import numpy as np
import os
import glob
import struct
import sys
from scipy.ndimage.filters import gaussian_filter, convolve
from scipy.misc import toimage, imresize
def load_images(img_files):
"""
Given a list of image file names, this loads and returns a list of images
"""
from pylab import imread
... | sameeptandon/sail-car-log | process/honda-label/preprocess.py | Python | bsd-2-clause | 8,859 | [
"Gaussian"
] | 82a37506938228d810b537acac64b9b7ca819ed2fb2d411c456f1efdb482a354 |
import os, sys
lib_path = os.path.abspath('../../helpers')
sys.path.append(lib_path)
lib_path = os.path.abspath('../')
sys.path.append(lib_path)
import math
import MetalicsSolver
import random
import copy
import json
import NanoClass
import ase
from heapq import *
from ase.md.nvtberendsen import NVTBerendsen
from ase.m... | JConwayAWT/PGSS14CC | lib/python/multimetallics/solvers/standard_basin_hopping.py | Python | gpl-2.0 | 3,940 | [
"ASE"
] | 024170c389bb79c98c71e01a0d8031d7a4735bde2eb27e4441863cade14659da |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides
"""
from collections import OrderedDict, namedtuple
from monty.functools import lazy_property
from monty.json import MSONable # , MontyEncoder
from monty.string import is_string
from... | gmatteo/pymatgen | pymatgen/core/xcfunc.py | Python | mit | 10,435 | [
"ABINIT",
"GPAW",
"pymatgen"
] | 2ee8c103200e8923fb4b1f7424bddc1a9620e3a07816289d957aa4ab2ef1bb4f |
from django.core.exceptions import ValidationError
from django.core.urlresolvers import reverse
from django.utils.translation import ugettext_lazy as _
from django.utils.translation import ungettext_lazy
from horizon import exceptions
from horizon import forms
from horizon import tables
from crystal_dashboard.api impor... | Crystal-SDS/dashboard | crystal_dashboard/dashboards/crystal/controllers/instances/tables.py | Python | gpl-3.0 | 5,285 | [
"CRYSTAL"
] | 16fcdeb6208ac4d191654d89f18362c1290ca914404d545f17a60da062ab31ae |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2014 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU Lesser General Public License as published by
## the Free Software F... | andrebellafronte/stoq | stoqlib/lib/pgpass.py | Python | gpl-2.0 | 2,417 | [
"VisIt"
] | e8428a4d5449facc144b47544818057746d597c3af9de4d3c5b84c54b554fe67 |
#
# Copyright 2017 Russell Smiley
#
# This file is part of timetools.
#
# timetools 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.
#
#... | blueskyjunkie/timeTools | timetools/synchronization/compliance/tests/testFrequency.py | Python | gpl-3.0 | 5,124 | [
"Gaussian"
] | 7d052eb29ccdafec0da45ff7276b5e3c0880f402f3a782ac3496be76baa2c57b |
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2006,2007,2009,2012-2015, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public v... | ghutchis/cclib | test/data/testGeoOpt.py | Python | lgpl-2.1 | 13,252 | [
"ADF",
"Dalton",
"GAMESS",
"Jaguar",
"Molpro",
"NWChem",
"ORCA",
"cclib"
] | 9e140573e28540aa656a8365394e201fa37605c076148a603f5363e01780eafc |
# 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... | gunan/tensorflow | tensorflow/python/autograph/converters/directives.py | Python | apache-2.0 | 6,730 | [
"VisIt"
] | 249d4f9f4f3506386425e98e9aede010f6f9628df948b57f3cd8037b823d1ec8 |
"""
Modules factories and their associated functions for mlab.
Module functions meant to be applied to a data source object or a filter
should take only one positional argument, the input, to be easily used in
helper functions.
"""
# Author: Gael Varoquaux <gael.varoquaux@normalesup.org>
# Prabhu Ramachandran... | liulion/mayavi | mayavi/tools/modules.py | Python | bsd-3-clause | 27,743 | [
"Mayavi",
"VTK"
] | 58be89d0385c369c6e7273ea806525f8f3f551570361b39a45bb37703f2423b1 |
../../../../share/pyshared/orca/dbusserver.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/dbusserver.py | Python | gpl-3.0 | 45 | [
"ORCA"
] | 915e4d770647148cf7d761b88e7717ef6fcfd600f408658c8282d14142f9e0e5 |
"""Forest of trees-based ensemble methods
Those methods include random forests and extremely randomized trees.
The module structure is the following:
- The ``BaseForest`` base class implements a common ``fit`` method for all
the estimators in the module. The ``fit`` method of the base ``Forest``
class calls the ... | 0asa/scikit-learn | sklearn/ensemble/forest.py | Python | bsd-3-clause | 55,187 | [
"Brian"
] | 3f3594f39d223fe779451a0dd3054fc840fca3d01a7b1f60d4aa0ed30b6c0442 |
"""Utilities used by the documentation scripts."""
import logging
import os
import sys
import subprocess32 as subprocess
import shlex
LOG = logging.getLogger(__name__)
def mkdir(folder):
"""Create a folder, ignore if it exists.
:param str folder: folder to create
"""
try:
folder = os.path.join(os.getc... | fstagni/DIRAC | docs/diracdoctools/Utilities.py | Python | gpl-3.0 | 3,702 | [
"DIRAC"
] | 523ba1067331fed78a81824fc22ea3d17d3c923b8d3c56c37dd963a553f6ae4b |
#
# This source file is part of appleseed.
# Visit http://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2019 Jonathan Dent, The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# ... | dictoon/blenderseed | translators/cameras/final.py | Python | mit | 9,032 | [
"VisIt"
] | c9904df747add02f0bb1b3053262b3cad3cb4f287aed886f6bdaae263d53cd25 |
#
# gPrime - A web-based genealogy program
#
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2008 Gary Burton
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version ... | sam-m888/gprime | gprime/plug/menu/_personlist.py | Python | gpl-2.0 | 1,809 | [
"Brian"
] | a9f90a4862b311c372bbbdf39fb06a9a8a042e90f1ba04e967c708b45d7e62c8 |
################################################################################
# Peach - Computational Intelligence for Python
# Jose Alexandre Nalon
#
# This file: nn/mem.py
# Associative memories and Hopfield models
################################################################################
# Doc string, reSt... | anki1909/peach | peach/nn/mem.py | Python | lgpl-2.1 | 7,964 | [
"NEURON"
] | a4401407393927a864622a07ae22d4ec7d5b214fdbfa1bac3e2cfb1877293b82 |
# Copyright 2011 Rackspace
# Copyright (c) 2011 X.commerce, a business unit of eBay Inc.
# Copyright 2013 IBM Corp.
# 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
#
# ... | watonyweng/nova | nova/tests/unit/network/test_manager.py | Python | apache-2.0 | 165,611 | [
"FEFF"
] | b9ade90c7e565088cceab14541cd1fe8fd26eac6dee3d4eb477762e89457d93a |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Author: Andrew Jewett (jewett.aij at g mail)
# http://www.moltemplate.org
# http://www.chem.ucsb.edu/~sheagroup
# License: MIT License (See LICENSE.md)
# Copyright (c) 2013, Regents of the University of California
# All rights reserved.
try:
from .t... | smsaladi/moltemplate | moltemplate/lttree_styles.py | Python | bsd-3-clause | 11,696 | [
"LAMMPS"
] | 582644cf3d49a0ccabceec2b7ec95fbd48a735657f547b6fc189419c012c2ec8 |
#
# Copyright (c) 2013, Scott J Maddox
#
# This file is part of SimplePL.
#
# SimplePL is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
# published by the Free Software Foundation, either version 3 of the
# License, or (at your option) ... | scott-maddox/simplepl | src/simplefit/spectra_control_widget.py | Python | agpl-3.0 | 14,961 | [
"Gaussian"
] | 13c01441d2de6ebd7d2d5de8171b20065019661ad8bd95e7bf1f9112f8cc5691 |
#!/usr/bin/python
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
""" Module: chacon_tarazona
=======================
"""
from __future__ import print_function
import numpy as np
from . import utilities
from .surface import SurfaceFlatI... | Marcello-Sega/pytim | pytim/chacon_tarazona.py | Python | gpl-3.0 | 7,935 | [
"MDAnalysis"
] | 2fedc957f7b7b5c66a0295217a994df825b734ca27e47a47ddc54bbb8956afdb |
#!/usr/bin/python
# Copyright (C) 2011 Zhang Initative Research Unit
# fileio.py -description
# system
import sys, os
# biopython
# user-defined modules
def write_2_file( out_file, content ):
f = open(out_file, "w")
f.write(content)
f.close()
| chhattu/apmds | fileio.py | Python | gpl-2.0 | 257 | [
"Biopython"
] | 66562250e6db58bb21bd633a8dae01d473b20bca84afcfc9d04afa0d66fca06c |
__author__ = "Sunil Kumar (kumar.sunil.p@gmail.com)"
__copyright__ = "Copyright 2014, Washington University in St. Louis"
__credits__ = ["Sunil Kumar", "Steve Pieper", "Dan Marcus"]
__license__ = "XNAT Software License Agreement " + \
"(see: http://xnat.org/about/license.php)"
__version__ = "2.1.1"
__main... | MokaCreativeLLC/XNATSlicer | XNATSlicer/XnatSlicerLib/ui/Buttons.py | Python | bsd-3-clause | 7,958 | [
"VTK"
] | 4a2fc1150525199f1d55c34f87ab1be880371820bdfb6016cde33e396535d5f7 |
#
# Copyright 2009-2011 Red Hat, Inc.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed ... | edwardbadboy/vdsm-ubuntu | vdsm/storage/misc.py | Python | gpl-2.0 | 35,460 | [
"VisIt"
] | e0ccc2222185093e004f471291ec82d286d0d3afceff16650714982e51c67573 |
if __name__ == "__main__":
import sys,os
append_path = os.path.abspath(sys.argv[0])[:-20]
print "Append to PYTHONPATH: %s" % (append_path)
sys.path.append(append_path)
import re
import math
import Tools.web as web
from Tools.BetterFile import BetterFile
import ChemicalInfo
from Geometry import Scan,IRC... | mtthwflst/terse | Parsers/ArchiveGaussian.py | Python | mit | 5,928 | [
"Gaussian"
] | b5328a5a94fd673fb0f4f0be7ea0b0529ed2b2b9a084203cb813c5c43509a0e7 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
#!/usr/bin/env python
from __future__ import division, unicode_literals
"""
#TODO: Write module doc.
"""
__author__ = 'Shyue Ping Ong'
__copyright__ = 'Copyright 2013, The Materials Virtual Lab'
__version__ =... | migueldiascosta/pymatgen | pymatgen/io/aseio.py | Python | mit | 574 | [
"ASE",
"pymatgen"
] | a5b8ae6268686bb03da1b85d9dd24b7d4e4bd3172f7dd64ab9a570884e0b4821 |
# subsystemMETFittingReduction
#
# Used by:
# Subsystem: Legion Offensive - Liquid Crystal Magnifiers
type = "passive"
def handler(fit, src, context):
fit.modules.filteredItemBoost(lambda mod: mod.item.requiresSkill("Medium Energy Turret"),
"cpu", src.getModifiedItemAttr("subsyst... | bsmr-eve/Pyfa | eos/effects/subsystemmetfittingreduction.py | Python | gpl-3.0 | 539 | [
"CRYSTAL"
] | 7f9adbbd665e6428a32304e7a4e55844ac1a2ae27cfe146187ae8f454a2f1b61 |
# -*- coding: utf-8 -*-
#
#
# TheVirtualBrain-Scientific Package. This package holds all simulators, and
# analysers necessary to run brain-simulations. You can use it stand alone or
# in conjunction with TheVirtualBrain-Framework Package. See content of the
# documentation-folder for more details. See also http://ww... | stuart-knock/tvb-library | tvb/datatypes/mode_decompositions.py | Python | gpl-2.0 | 13,929 | [
"Gaussian"
] | e0cb2342dd018e346cc61acd28fa8792f669ce62c89bca20155af64a09048307 |
#!/usr/bin/env python
#
# build_negative_list.py
#
# Script that takes as input a FASTA file, and a list of sequence identifiers,
# and returns a list of sequence identifiers which are those in the FASTA file,
# but not in the initial list of sequence identifiers.
#
# (c) The James Hutton Institute 2013
# Author: Leigh... | alainr85/bio_primers | sample/build_negative_sequence_list.py | Python | gpl-3.0 | 6,718 | [
"Biopython"
] | ff43c391f0af4f288c9a675b4fbbb3c9e701c34e5a7d3a57b7d7b6cae8998dac |
# DataTypes:
# TophatAlignmentFolder Tophat
# TophatAlignmentSummary
# RSEMReferenceGenome RSEM
# RSEMResults
# STARReferenceGenome STAR
# STARAlignmentFolder
# HTSeqCountResults HTSeqCount
# HTSeqCountSummary
#
# RNASeqUnprocessedSignalFile Contains attributes from RNA-Seq analysis.
#... | jefftc/changlab | Betsy/Betsy/rules/RNASeq.py | Python | mit | 20,830 | [
"Bowtie",
"HTSeq"
] | ff86e9e6eed731672a4ec99e560ecc71d7dcf5b1c2848f7e10750e15d48bb6cc |
#!/usr/bin/env python
#-------------------------------------------------------------------------------
#
# Copyright (c) 2011-2012 by European Organization for Nuclear Research (CERN)
# Author: Justin Salmon <jsalmon@cern.ch>
#
# This file is part of XrdTest.
#
# XrdTest is free software: you can redistribute it and/or... | xrootd/xrootd-test-framework | src/webpage/utils/get_eos_stable.py | Python | gpl-3.0 | 7,053 | [
"Amber"
] | 92185ab796a8de171241f16a4c0ffd08d13fba6ad0e6a19beb1c2fa36cca6268 |
"""
intro_3_05_variable_names_1.py
Example code from Section 3.5 of <Introduction to SFC Models Using Python.>
Demonstration how variable names are built up.
Copyright 2017 Brian Romanchuk
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License... | brianr747/SFC_models | sfc_models/examples/scripts/intro_3_05_variable_names_1.py | Python | apache-2.0 | 1,684 | [
"Brian"
] | 0fac7289c7efca6bb3572aa6a56587a42cb26424f312f1f14fac57f6554c7d7d |
"""
Routines used by the rss_mos_reducer script
Copyright 2014-2020 Matt Hilton (matt.hilton@mykolab.com)
This file is part of RSSMOSPipeline.
RSSMOSPipeline is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the F... | mattyowl/RSSMOSPipeline | RSSMOSPipeline/RSSMOSTools.py | Python | gpl-3.0 | 103,777 | [
"Gaussian"
] | fa50b350dcae7436ebb3e07ce370e7b9be7d39041fab79270ea9437b6eb74abd |
"""
Instructor Dashboard Views
"""
import logging
import datetime
import uuid
import pytz
from django.contrib.auth.decorators import login_required
from django.views.decorators.http import require_POST
from django.utils.translation import ugettext as _
from django_future.csrf import ensure_csrf_cookie
from django.vie... | UQ-UQx/edx-platform_lti | lms/djangoapps/instructor/views/instructor_dashboard.py | Python | agpl-3.0 | 19,862 | [
"VisIt"
] | 929d69878648012ad195c910a1580d4c9265b7a3aa1ebca6918f285f235b3b30 |
"""
Module to set up run time parameters for Clawpack -- classic code.
The values set in the function setrun are then written out to data files
that will be read in by the Fortran code.
"""
import os
import numpy as np
#------------------------------
def setrun(claw_pkg='amrclaw'):
#--------------------------... | maojrs/Interface_Euler_AMR | code_cartesian/setrun.py | Python | bsd-2-clause | 16,060 | [
"NetCDF"
] | 0b4789b8ffe66207e3d23b2056f638d53dea1e6d0f4f2857c69061af1e24e947 |
#!/usr/bin/env python
##############################################################################################
#
#
# regrid_emissions_N96e.py
#
#
# Requirements:
# Iris 1.10, time, cf_units, numpy
#
#
# This Python script has been written by N.L. Abraham as part of the UKCA Tutorials:
# http://www.ukca.ac.u... | acsis-project/emissions | emissions/python/timeseries_1950-2020/regrid_nC4H10_emissions_n96e_360d.py | Python | gpl-3.0 | 18,944 | [
"NetCDF"
] | 97820fe9d05f80efc4dd892367030b72edeed90f57865dcaaadaa07866e809ea |
#!/usr/bin/env python
__author__ = 'Mike McCann,Duane Edgington,Reiko Michisaki'
__copyright__ = '2013'
__license__ = 'GPL v3'
__contact__ = 'mccann at mbari.org'
__doc__ = '''
Master loader for all Worden's CN13ID Western Flyer cruise in October 2013
CN13ID: CANON 2013 Interdisciplinary
Mike McCann
MBARI 23 ... | danellecline/stoqs | stoqs/loaders/CANON/loadCN13ID_october2013.py | Python | gpl-3.0 | 11,633 | [
"NetCDF"
] | 31742c27389de007d7bb4e71bc14dda87586b1215b0fe71f782ae62ac6f16ab0 |
"""Univariate and multivariate polynomials with coefficients in the integer ring. """
from sympy.polys.galoispolys import (
gf_from_int_poly, gf_to_int_poly, gf_degree, gf_from_dict,
gf_lshift, gf_add_mul, gf_mul, gf_div, gf_quo, gf_rem,
gf_gcd, gf_gcdex, gf_sqf_p, gf_factor_sqf)
from sympy.ntheory import... | fperez/sympy | sympy/polys/integerpolys.py | Python | bsd-3-clause | 61,782 | [
"Gaussian"
] | 1704b745653e0772cf20626dcf82d862a47472fce7b0889e328c1bb10ab01b6b |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2007 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/lib/test/test_invoice.py | Python | gpl-2.0 | 6,093 | [
"VisIt"
] | 0b6201b7f3721ae5ebe5b59086ebe98e2a374935905ede95dd20bec54097756c |
# -*- coding: utf-8 -*-
#
# network_params.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License,... | hakonsbm/nest-simulator | pynest/examples/Potjans_2014/network_params.py | Python | gpl-2.0 | 8,842 | [
"NEURON"
] | 729e38a3793717da81a93287466f0364e93c997f9a222e4a9b2369d650a9d413 |
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