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# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
from os import unlink
from glob import glob
class PyDpGpCluster(PythonPackage):
"""DP_GP_cluster... | iulian787/spack | var/spack/repos/builtin/packages/py-dp-gp-cluster/package.py | Python | lgpl-2.1 | 1,201 | [
"Gaussian"
] | 5742c990f691d50384020a423e66a4712a82977ff539d094e1cd3beff1b20d08 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
#
# 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; ... | pmghalvorsen/gramps_branch | gramps/plugins/quickview/siblings.py | Python | gpl-2.0 | 2,650 | [
"Brian"
] | 017da32bd127ca4ad969ab5dc4fa55f2bfefba047494a6ac3b2896e1414e34d5 |
#!/usr/bin/env python
"""
Rotations, VTK Textbook figure 3-31b.
Note: Make sure Rotations.py is in the same directory as this program.
"""
import Rotations
def main():
file_name, figure, book_color = Rotations.get_program_parameters()
# Set up for six rotations about the y-axis.
figure = 2
book_col... | lorensen/VTKExamples | src/Python/Rendering/RotationsB.py | Python | apache-2.0 | 422 | [
"VTK"
] | 5921ba87eec420583d0941a9bbf220c20afe7c6c8bfde1b6e462db5e157207c4 |
# 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 | frechet_audio_distance/compute_fad.py | Python | apache-2.0 | 1,525 | [
"Gaussian"
] | cb8256f0690fa573a1dc691c867ef10c10cfac742095613c49ec79201b71cb06 |
########################################################################
# $HeadURL$
# File: RequestTests.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2012/07/24 10:23:40
########################################################################
""" :mod: RequestTests
=======================
.. module: R... | arrabito/DIRAC | RequestManagementSystem/Client/test/Test_Request.py | Python | gpl-3.0 | 16,952 | [
"DIRAC"
] | 294191c643d4a5a684c9dc22ca7ef27e3b8a65669cc74decd9ebb3a02d0f6af7 |
#!/usr/bin/env python
#
# Copyright (C) 2013 Ben Woodcroft, available under GPLv3 or later
#
from optparse import OptionParser
import sys
from pprint import pprint
import pysam
class ReadLoader:
"""AUX: Call back for getting aligned reads
Used in conjunction with pysam.fetch
"""
def __init__(self... | wwood/bbbin | gccorrect_preparation.py | Python | gpl-3.0 | 2,410 | [
"pysam"
] | 941910fe34e4a251a32f81a14b65f24dedad2efc7e2dd222d8e3eb7bc26a10f2 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2002-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2008 Jerome Rapinat
# Copyright (C) 2008 Benny Malengier
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the ... | arunkgupta/gramps | gramps/gen/filters/rules/event/_hasnote.py | Python | gpl-2.0 | 1,717 | [
"Brian"
] | 7bb7cd43ae1f7f545a610aac6c7cc997ec6cf916463d5398f40a20a2cf78860e |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Factory functions producing ABINIT Works.
Works are packed together in a flow. A flow can be ran using abirun (abipy)
Entry points for client code (high-level interface)
"""
from __future__ import unicode_li... | sonium0/pymatgen | pymatgen/io/abinitio/calculations.py | Python | mit | 20,659 | [
"ABINIT",
"pymatgen"
] | 3f7ff4158ac66993604818444f44e258f224f3670ec7d7eec0bf4dd03c83cb66 |
#!/usr/bin/env python
#
# Appcelerator Titanium Module Packager
#
#
import os, subprocess, sys, glob, string
import zipfile
from datetime import date
cwd = os.path.abspath(os.path.dirname(sys._getframe(0).f_code.co_filename))
os.chdir(cwd)
required_module_keys = ['architectures', 'name','version','moduleid','descripti... | titanium-forks/GeraudBourdin.Ti.AndroidSvgView | iphone/build.py | Python | mit | 8,522 | [
"VisIt"
] | 2a0ce8c9ead6b8faf62abc197b1f972033c8a8d2b2011a4dc051fae1e6535c34 |
""" This is a module to handle generic ASE (gui) defaults from a ~/.ase/gui.py configuration file, if it exists.
It is imported when opening ag and can then be modified at runtime, if necessary.
syntax for each entry:
gui_default_settings['key'] = value
"""
gui_default_settings = {
'gui_graphs_string' : 'i, e - E... | JConwayAWT/PGSS14CC | lib/python/multimetallics/ase/gui/defaults.py | Python | gpl-2.0 | 702 | [
"ASE"
] | a3a7e9adad0d3b6551fbf7c582ef028ac5dfeae6e26ef38fc1c061fe9f59dba8 |
# Copyright 2008 Brian Boyer, Ryan Mark, Angela Nitzke, Joshua Pollock,
# Stuart Tiffen, Kayla Webley and the Medill School of Journalism, Northwestern
# University.
#
# This file is part of Crunchberry Pie.
#
# Crunchberry Pie is free software: you can redistribute it and/or modify
# it under the terms of the GNU Gene... | brianboyer/newsmixer | pie/questions/models.py | Python | gpl-3.0 | 2,701 | [
"Brian"
] | 708413a643740dcb5b840f641c70fe0fd8ef467f89ce8ca6577b37b6b1871515 |
# -*- coding: UTF-8 -*-
"""This module contains functions related to the VPT2 approximation."""
import sys
import os
import numpy as np
from chemphysconst import Constants
from . import Geometry
from . import Harmonic
# from numpy import linalg
# from . import printfunctions as PF
# Module globals
FLOAT = np.float128
... | jdcapa/MolecularToolbox | moleculartoolbox/vpt2.py | Python | gpl-3.0 | 33,026 | [
"CFOUR",
"ORCA"
] | 1ba5c93ed4fc5d861135aedfe46a12b157aeed4141388c97a35154eaad25efa0 |
# -*- coding: utf-8 -*-
###############################################################################
# #
# Ambrosia - a tool to visualize ANANAS results #
# ... | MalwareLabHagenberg/ambrosia | ambrosia_plugins/lkm/__init__.py | Python | gpl-3.0 | 42,929 | [
"ASE"
] | 6cf661440d8895960086e96b30782cb026bd3dda5ef7564f5734b27f017aee24 |
r"""
================================================================
Robust covariance estimation and Mahalanobis distances relevance
================================================================
An example to show covariance estimation with the Mahalanobis
distances on Gaussian distributed data.
For Gaussian dis... | chrsrds/scikit-learn | examples/covariance/plot_mahalanobis_distances.py | Python | bsd-3-clause | 6,228 | [
"Gaussian"
] | ccf26a44d087b11b7032fd0ca8f5dca9d5af1ddc7799a81b9524edfa3e0efc7e |
from math import exp, sqrt
import numpy as np
from numpy.random import default_rng
from pysisyphus.constants import KBAU
"""
[1] https://aip.scitation.org/doi/10.1063/1.2408420
[2] https://dx.doi.org/10.1016/j.cpc.2008.01.006
Reformulation fo the algorithm. This is implemented e.g., in YAFF.
https://github.... | eljost/pysisyphus | pysisyphus/dynamics/thermostats.py | Python | gpl-3.0 | 3,678 | [
"Gaussian"
] | 97fccb1b552f78ef503d0ddd3f92b79acfed12a34e51bb7281573200f9c89e71 |
########################################################################
# This program is copyright (c) Upinder S. Bhalla, NCBS, 2015.
# It is licenced under the GPL 2.1 or higher.
# There is no warranty of any kind. You are welcome to make copies under
# the provisions of the GPL.
# This programme illustrates buildi... | dilawar/moose-full | moose-examples/paper-2015/Fig2_elecModels/Fig2C.py | Python | gpl-2.0 | 13,821 | [
"MOOSE",
"NEURON"
] | bee14fb20884ebb11d735ae8cbf7e1c9694c504c226a33ea6a167e0aa6785163 |
# -*- coding: utf-8 -*-
#!/usr/bin/env python
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007 Johan Gonqvist <johan.gronqvist@gmail.com>
# Copyright (C) 2007-2009 Gary Burton <gary.burton@zen.co.uk>
# Copyright (C) 2007-2009 Stephane Charet... | sam-m888/gramps | gramps/plugins/webreport/addressbook.py | Python | gpl-2.0 | 4,636 | [
"Brian"
] | 80bd8b741ca194dbf9e58f52d72e67cd890e020cfccde586e68278e34b9932a6 |
# Rewrite of the original script; it worked, but not well enough...
# still ugly tho
CONFIGFILE = "config.txt"
import re
import json
import time
import requests
import datetime
import configparser
import imgurpython
# overwrite print() to only print ascii
import builtins
def asciify(text):
return ''.join([i if ord... | Garmelon/itbot | script.py | Python | mit | 20,301 | [
"VisIt"
] | ca48569c064d0cedd61471798d9f51951cfd8efddae2492a95c7a1373e5a5e15 |
from io import BytesIO
import numpy as np
import warnings
from .. import Variable
from ..conventions import cf_encoder
from ..core.pycompat import iteritems, basestring, OrderedDict
from ..core.utils import Frozen, FrozenOrderedDict
from ..core.indexing import NumpyIndexingAdapter
from .common import WritableCFDataS... | petercable/xray | xray/backends/scipy_.py | Python | apache-2.0 | 5,813 | [
"NetCDF"
] | f7340620e52c36bca04afabbb4f196698d8414cc961148c388b993450879f35c |
# -*- coding: utf-8 -*-
"""
Acceptance tests for Video.
"""
import json
import requests
from .helpers import UniqueCourseTest
from ..pages.lms.video import VideoPage
from ..pages.lms.tab_nav import TabNavPage
from ..pages.lms.course_nav import CourseNavPage
from ..pages.lms.auto_auth import AutoAuthPage
from ..pages.... | nanolearning/edx-platform | common/test/acceptance/tests/test_video_module.py | Python | agpl-3.0 | 29,937 | [
"VisIt"
] | c7c023e5f1530e39d8dcb2811d55194d53697a970e2ae75f402ef0728789d738 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
Copyright (C) 2015 Dato, Inc.
All rights reserved.
This software may be modified and distributed under the terms
of the BSD license. See the LICENSE file for details.
'''
import sys
import parser
import symbol
import token
import ast
import inspect
from ..import meta
... | thirdwing/SFrame | oss_src/unity/python/sframe/util/lambda_closure_capture.py | Python | bsd-3-clause | 10,020 | [
"VisIt"
] | 1b03a602c13d05e8ffbaf2c7e443594c920f01303893e35ab8937d3ca773b28a |
# Copyright 2015 gRPC 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 applicable law or agreed to in writing... | grpc/grpc | src/python/grpcio/grpc_core_dependencies.py | Python | apache-2.0 | 88,503 | [
"ORCA"
] | 54f03fd95a43cf1e9e4e918dbe69146d412e068506bfc441cff762263751d50c |
# -*- coding: utf-8 -*-
"""Some utility functions"""
from __future__ import print_function
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
#
# License: BSD (3-clause)
import warnings
import logging
import time
from distutils.version import LooseVersion
import os
import os.path as op
from funct... | rajegannathan/grasp-lift-eeg-cat-dog-solution-updated | python-packages/mne-python-0.10/mne/utils.py | Python | bsd-3-clause | 63,668 | [
"Mayavi"
] | 956311f5d5e1d4f0ea09151272d28ddaf30ca56ce8d005ad70e248ad0d6e9ca1 |
# Copyright 2004-2008 by M de Hoon.
# 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.
"""Implements the Lowess function for nonparametric regression.
Functions:
lowess Fit... | updownlife/multipleK | dependencies/biopython-1.65/build/lib.linux-x86_64-2.7/Bio/Statistics/lowess.py | Python | gpl-2.0 | 4,003 | [
"Biopython"
] | 516c8f1b2995a41e2c205992870674b7e8f1d2a23a930af90f1131e67d5d4149 |
# Copyright 2005 by Jonathan Taylor.
# 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.
"""This module deals with CAPS markers.
A CAPS marker is a location a DifferentialCutsite a... | bryback/quickseq | genescript/Bio/CAPS/__init__.py | Python | mit | 3,733 | [
"Biopython"
] | 535ea304cfe8566b0d8e6970482c9216299f15dbb4014da0fe2cd577ead7bcaf |
import rnftools
from .Source import *
import os
import snakemake
import re
class DwgSim(Source):
"""Class for DWGsim (https://github.com/nh13/DWGSIM/wiki).
Both single-end and paired-end simulations are supported. In paired-end simulations,
reads can have different lengths. Note that there is a bug in DWGsim ... | karel-brinda/rnftools | rnftools/mishmash/DwgSim.py | Python | mit | 12,821 | [
"BWA"
] | 37bccbe1207a4532a2ebd853c5c599e91a04b3fd3beed0be3615e1e9987f74d5 |
# -*- coding: utf-8 -*-
"""
Small utility to convert p2p format of IP Blocklists to IPSet format.
Usage:
{program} generate [options] BLOCKLIST_URL...
{program} example_restore_ipset_job [options] IPTABLES_NAME IPSET_PATH
{program} example_update_ipset_job [options] IPSET_PATH BLOCKLIST_URL...
{program} -h | -... | 9seconds/iblocklist2ipset | iblocklist2ipset/__init__.py | Python | mit | 1,343 | [
"VisIt"
] | f570429eac6a112d53452a6c28a6297b00a5b1e9263b9c766a8f6d33f94a16ff |
#!/usr/bin/python
# Copyright (c) 2013, Thomas Rast <trast@inf.ethz.ch>
#
# 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, version 2 of the License.
#
# This program is distributed in the hope t... | trast/evilmergediff | evil-base-treediff.py | Python | gpl-2.0 | 7,203 | [
"Octopus"
] | 344b6a33acd7cac8147c56df3e4a000497b480fbf204a288bfe239703eb594b7 |
"""
Executes a set of implementations as a program.
"""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from __future__ import print_function
from zeroinstall import _, logger
import os, sys
from string import Template
from zeroinstall import support
from zeroin... | michel-slm/0install | zeroinstall/injector/run.py | Python | lgpl-2.1 | 11,445 | [
"VisIt"
] | 399dc3901797a8efc70a0743675dfc0d7b4aebd0d039b2159b0826b07a2e7ba3 |
#!/usr/bin/python
"""
pyNEAT
Copyright (C) 2007-2008 Brian Greer
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... | liquidkarma/pyneat | examples/xor/xor_bp.py | Python | gpl-2.0 | 1,714 | [
"Brian"
] | 7bbcc108517a0e4def215580f3e10ac2f8093d9cd8da7d4f0305a7b7a6b84045 |
from __future__ import with_statement
import copy
import functools
import optparse
import os
import os.path
import re
import sys
try:
from com.xhaus.jyson import JysonCodec as json # jython embedded in buck
except ImportError:
import json # python test case
# TODO(user): upgrade to a jython including os.relpath... | GerritCodeReview/buck | src/com/facebook/buck/parser/buck.py | Python | apache-2.0 | 24,221 | [
"ORCA"
] | 68f4189947f9cf5b045df1c5edc9fc81202d900be45b39b0e1103cbbc546d134 |
###############################
# This file is part of PyLaDa.
#
# Copyright (C) 2013 National Renewable Energy Lab
#
# PyLaDa is a high throughput computational platform for Physics. It aims to make it easier to submit
# large numbers of jobs on supercomputers. It provides a python interface to physical input, suc... | pylada/pylada-light | tests/jobfolder/test_forwardingdict.py | Python | gpl-3.0 | 6,557 | [
"CRYSTAL",
"VASP"
] | 94de4745266d90148090607dfdd99fbfbfe3a1a73d33cc195f101027ec01aabe |
# -------------------------------------------------------------------------
# Copyright (C) 2005-2013 Martin Strohalm <www.mmass.org>
# 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 Foundat... | lukauskas/mMass-fork | gui/config.py | Python | gpl-3.0 | 65,326 | [
"BLAST",
"Gaussian"
] | aa62b06459030f38967a8615f5f39ee4a70f12de2b0b9f20796501c280219574 |
#!/usr/bin/env python
""" refresh CS
"""
from __future__ import print_function
from DIRAC.Core.Base import Script
Script.parseCommandLine()
from DIRAC.ConfigurationSystem.private.Refresher import gRefresher
res = gRefresher.forceRefresh()
if not res['OK']:
print(res['Message'])
| fstagni/DIRAC | tests/Jenkins/dirac-refresh-cs.py | Python | gpl-3.0 | 283 | [
"DIRAC"
] | cbd3c891a036d18e263ac458b5e0cf1d778e98ce3870b956c7e460880e307982 |
import PandasPatch
from iago import *
import cp2k
from Analyser import Analyser | ferchault/iago | src/iago/__init__.py | Python | mit | 79 | [
"CP2K"
] | fa4b98b5030c47d7152fcad66c23592d10479bc8a47810bc3a09632d3caa543b |
import numpy as np
class LineModel:
"""
Interface for the model of the spectral line.
Your line models must extend this class, and implement its methods.
Duck typing is very good, but this is cleaner, faster and more maintainable
as we have a lot of methods to check for. LBYL > EAFP here.
See... | irap-omp/deconv3d | lib/line_models.py | Python | mit | 3,410 | [
"Gaussian"
] | 99bb1347a21de011f0f35aa8b9d0ac6a9b7a51b2e33e877618bf9051fb376585 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides input and output from the CSSR file format.
"""
import re
from monty.io import zopen
from pymatgen.core.lattice import Lattice
from pymatgen.core.structure import Structure
__author__ = "Shyue Pin... | vorwerkc/pymatgen | pymatgen/io/cssr.py | Python | mit | 2,834 | [
"pymatgen"
] | d367b6fe6ea8591c4a37ec661383d17e976be877c0ece7135c952aed189ce729 |
###############################################################
### Python Framework for VAPT v 1.0 ###
### ###
### Designed by Niraj M. ###
### niraj007m[at]gmail[dot]com ###
### This work is licensed under the Creative Commons ###
### Attribution-ShareAlike 3.0 Unpor... | niraj007m/Python-Framework-v1.0 | PFV1.py | Python | cc0-1.0 | 7,515 | [
"VisIt"
] | 96d5c9fe1cf859b80e9463999c054d62871f1b5444b24d23337a9b8e1d3a1316 |
from setuptools import setup, find_packages
setup(
name = 'jper-sword-in',
version = '1.0.0',
packages = find_packages(),
install_requires = [
"octopus==1.0.0",
"esprit",
"Flask"
],
url = 'http://cottagelabs.com/',
author = 'Cottage Labs',
author_email = 'us@cott... | JiscPER/jper-sword-in | setup.py | Python | apache-2.0 | 620 | [
"Octopus"
] | 070cce44c2a65ee7be39b22086ec47ea22e4dd3ab6eb962c3038d6f27180cbf6 |
#!/usr/bin/env python
from setuptools import setup, find_packages
import kademlia
setup(
name="kademlia",
version=kademlia.__version__,
description="Kademlia is a distributed hash table for decentralized peer-to-peer computer networks.",
author="Brian Muller",
author_email="bamuller@gmail.com",
... | faisalburhanudin/kademlia | setup.py | Python | mit | 453 | [
"Brian"
] | f1479813f4f785357deb4e124c7c32bdcb90bc06b173da6fba05f0a94fa24a30 |
#! /usr/bin/python
#
# Copyright (C) 2003-2017 ABINIT group
#
# Written by Gabriel Antonius in python (compatible v2.7).
# This is free software, and you are welcome to redistribute it
# under certain conditions (GNU General Public License,
# see ~abinit/COPYING or http://www.gnu.org/copyleft/gpl.txt).
... | jmbeuken/abinit | scripts/post_processing/merge_ddb_nc.py | Python | gpl-3.0 | 4,935 | [
"ABINIT"
] | c1e90b1bb58512d4ac0b31bf255b82842c85490800188b5979a5e1f9987094ce |
from __future__ import print_function
from rdkit import Chem
from rdkit.Chem import ChemicalForceFields, rdtrajectory
from rdkit.Chem.rdtrajectory import Snapshot, \
Trajectory, ReadAmberTrajectory, ReadGromosTrajectory
import os, sys
import unittest
from rdkit import RDConfig
def feq(v1, v2, tol=1.0e-4):
return... | jandom/rdkit | Code/GraphMol/Wrap/testTrajectory.py | Python | bsd-3-clause | 19,353 | [
"Amber",
"RDKit"
] | 1d2bf17e8b609a0d67acc74d17a71b4eb1b04c4807c9748305376381a32f5ecb |
#!/usr/bin/env python
# Reports a beta diversity matrix for tabular input file
# using scikit-bio
# Daniel Blankenberg
import sys
import optparse
import codecs
from skbio.diversity import beta_diversity
from skbio import TreeNode
__VERSION__ = "0.0.1"
DELIMITER = '\t'
NEEDS_TREE = [ 'unweighted_unifrac', 'weight... | nturaga/tools-iuc | tools/scikit-bio/scikit_bio_diversity_beta_diversity.py | Python | mit | 3,773 | [
"scikit-bio"
] | 7969538c177fb6b34fd71a1559eec622a9cad33aab57ddf4ec4db017c82bbfc4 |
import os, sys, re, inspect, types, errno, pprint, subprocess, io, shutil, time, copy, unittest
import path_tool
path_tool.activate_module('FactorySystem')
path_tool.activate_module('argparse')
from ParseGetPot import ParseGetPot
from socket import gethostname
#from options import *
from util import *
from RunParalle... | backmari/moose | python/TestHarness/TestHarness.py | Python | lgpl-2.1 | 56,618 | [
"MOOSE",
"VTK"
] | c27f7ef011b4daff8c899f3287010787b55c11013184acfc0fd90493e7676e82 |
from __future__ import division
import time
import numpy as np
np.random.seed(1234) # seed random number generator
srng_seed = np.random.randint(2**30)
from keras.models import Sequential
from keras.optimizers import SGD
from keras_extensions.logging import log_to_file
from keras_extensions.rbm import GBRBM, RBM
fr... | wuaalb/keras_extensions | examples/dbn_example.py | Python | mit | 3,388 | [
"Gaussian"
] | 90c0252c3aa6181a7bab5931b207f6a6d7f71ecce93439a1b6148b74708348c9 |
#!/usr/bin/env python
"""
Uninstallation of a DIRAC component
Usage:
dirac-uninstall-component [options] ... System Component|System/Component
Arguments:
System: Name of the DIRAC system (ie: WorkloadManagement)
Component: Name of the DIRAC component (ie: Matcher)
"""
from __future__ import absolute_import
fro... | yujikato/DIRAC | src/DIRAC/FrameworkSystem/scripts/dirac_uninstall_component.py | Python | gpl-3.0 | 2,702 | [
"DIRAC"
] | 30ece9e11d98ec3273ee52bacfc0be7efb5f2401e1cc2401a53018561ce04b14 |
#!/usr/bin/env python
# Copyright (c) 2014, Jelmer Tiete <jelmer@tiete.be>.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
# 1. Redistributions of source code must retain the above copyright
#... | ciolo/Sniffer-OpenMote | OpenMoteFirmware/tools/openmote-bsl/cc2538-bsl/cc2538-bsl.py | Python | gpl-2.0 | 27,583 | [
"CRYSTAL"
] | 8c6101c7e84dc3866c36bca13e1f8f60bbdbfb3ead02d61a24ea6e9320c1cd99 |
from FeatureBuilder import FeatureBuilder
# Amino acids from http://www.bio.davidson.edu/courses/genomics/jmol/aatable.html
#amino acid three letter code single letter code
subcomponent = set(["region", "promoter", "upstream", "fragment", "site",
"sequence", "segment", "repeat", "repeat", "eleme... | ashishbaghudana/mthesis-ashish | resources/tees/ExampleBuilders/FeatureBuilders/RELFeatureBuilder.py | Python | mit | 6,349 | [
"Jmol"
] | c89a72445bd61b2be17418835e600454aeed450e1b09cfc827e56d5be44c398a |
from __future__ import division, print_function, absolute_import
import numpy as np
from numpy import array
from numpy.testing import (assert_array_almost_equal, assert_array_equal,
assert_raises, assert_allclose,
assert_equal, assert_, assert_array_less)
from scip... | apbard/scipy | scipy/signal/tests/test_windows.py | Python | bsd-3-clause | 23,399 | [
"Gaussian"
] | 2dc4acbec662e42d291cb932c4fdb969505c4fc98ee919771946dc381428ee1d |
#
# MainTab
#
tab = self.notebook.mainTab
tab.settings['Program'] = 'gulp'
tab.settings['Output file name'] = 'na2so42.gout'
#
# SettingsTab
#
tab = self.notebook.settingsTab
tab.settings['Eckart flag'] = False
tab.settings['Neutral Born charges'] = False
tab.settings['Sigma value'] = 5
tab.settings['Mass definition'] ... | JohnKendrick/PDielec | Examples/Gulp/Na2SO42/script.py | Python | mit | 2,000 | [
"GULP"
] | 4571783e2a0021e349fe8ca8d58287b9e83c2fc2c40dbeadfb0bf3395699c797 |
#
# Copyright (C) 2017-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | psci2195/espresso-ffans | testsuite/python/coulomb_tuning.py | Python | gpl-3.0 | 3,268 | [
"ESPResSo"
] | 6b50e23da602867fc2f9f4d8a86b4bbb19fe5a1cb8308f83a446d1398cc21c2b |
#
# Copyright (C) 2013,2014,2015,2016 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)... | KonradBreitsprecher/espresso | testsuite/constant_pH.py | Python | gpl-3.0 | 4,744 | [
"ESPResSo"
] | 9845d5163f5d2a9e97fa08d7f08d2523c62e7e64b2389544c9a456f0b9528376 |
# -*- coding: utf-8 -*-
u"""Types for Genesis parameters
:copyright: Copyright (c) 2015 Bivio Software, Inc. All Rights Reserved.
:license: http://www.apache.org/licenses/LICENSE-2.0.html
"""
#: Dictionary of display names
import enum
from radtrack import rt_enum
@enum.unique
class UndulatorType(rt_enum.Enum):
... | radiasoft/radtrack | radtrack/genesis_enums.py | Python | apache-2.0 | 1,772 | [
"Gaussian"
] | 2f4476e6ccee968837d07d005c4823c62b108dffd3d726cda734b4d5c2235542 |
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publi... | thica/ORCA-Remote | src/ORCA/utils/Platform/generic/generic_GetLocale.py | Python | gpl-3.0 | 1,195 | [
"ORCA"
] | a4247531f75b8952a2ccd532dd8caf5dc386bb616e901cb85691cc5dbfa1da36 |
"""
========================================
Special functions (:mod:`scipy.special`)
========================================
.. module:: scipy.special
Nearly all of the functions below are universal functions and follow
broadcasting and automatic array-looping rules. Exceptions are
noted.
.. seealso::
`scipy.s... | haudren/scipy | scipy/special/__init__.py | Python | bsd-3-clause | 23,072 | [
"Gaussian"
] | 6139f0fbdfce7e51db0b3ae0db7a63747bd69ae218111664905f8e29fb987bf2 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
Copyright (C) 2016 Sovrasov V. - All Rights Reserved
* You may use, distribute and modify this code under the
* terms of the MIT license.
* You should have received a copy of the MIT license with
* this file. If not visit https://opensource.org/licenses/MIT
'''
imp... | sovrasov/fuzzy-ml | src/tsk0Model.py | Python | mit | 3,158 | [
"VisIt"
] | 344f40733eca3ac6ac71cb4a28e8a6fd6f4b1f5d8822b5e2731eef251acd8e7f |
#!/usr/bin/python
#
# Copyright 2015 John Kendrick
#
# This file is part of PDielec
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the MIT License
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied wa... | JohnKendrick/PDielec | PDielec/PhonopyOutputReader.py | Python | mit | 5,676 | [
"phonopy"
] | d95b534446508007e17459846987b7fbf312a76fedd7fea0fcbf8f16996c0bdb |
#
# Copyright (C) 2005 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 i... | GNOME/sabayon | lib/mozilla_bookmarks.py | Python | gpl-2.0 | 12,507 | [
"VisIt"
] | c490b81bc13c692abe74fe131909814c6eb4ee6cab8443f91dd04aa118db2006 |
# libxc: svn version 4179
# http://www.tddft.org/programs/octopus/wiki/index.php/Libxc
libxc_functionals = {
'LDA_X': 1,
'LDA_C_WIGNER': 2,
'LDA_C_RPA': 3,
'LDA_C_HL': 4,
'LDA_C_GL': 5,
'LDA_C_XALPHA': 6,
'LDA_C_VWN': 7,
'LDA_C_VWN_RPA': 8,
'LDA_C_PZ': 9,
'LDA_C_PZ_MOD': 10,
... | ajylee/gpaw-rtxs | gpaw/xc/libxc_functionals.py | Python | gpl-3.0 | 1,797 | [
"Octopus"
] | 4f0dddfc957fc8bc0a2ced6e00e79005a50eb13255661dfbeacd9782ff552a0a |
# -*- coding: utf-8 -*-
#!/usr/bin/env python
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007 Johan Gonqvist <johan.gronqvist@gmail.com>
# Copyright (C) 2007-2009 Gary Burton <gary.burton@zen.co.uk>
# Copyright (C) 2007-2009 Stephane Charet... | sam-m888/gramps | gramps/plugins/webreport/event.py | Python | gpl-2.0 | 19,096 | [
"Brian"
] | 280caa0da464c487f6a38534cb021c9472a0d3f5324e5b6397b0268ef87303d1 |
import numpy as np
from sympy import Rational as frac
from sympy import sqrt
from ..helpers import article
from ..un._mysovskikh import get_nsimplex_points
from ._helpers import Enr2Scheme
from ._phillips import phillips as lu_darmofal_3
from ._stroud import stroud_enr2_5_1a as lu_darmofal_4a
from ._stroud import stro... | nschloe/quadpy | src/quadpy/enr2/_lu_darmofal.py | Python | mit | 1,887 | [
"Gaussian"
] | b7baf4e6348a60cd9267f21db6242167b9d618e38f83ce007a8623c1283a4c50 |
# ============================================================================
#
# Copyright (C) 2007-2010 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | kurtraschke/camelot | camelot/view/controls/tableview.py | Python | gpl-2.0 | 31,637 | [
"VisIt"
] | 7ab3b4060be0d462866befa1e7ea8bcfb8803152ceb086cd9a87bce5ad7e99d9 |
# -*- coding: utf-8 -*-
from . import *
from . fixtures import *
import os
from flanker import mime
from talon import quotations
@patch.object(quotations, 'MAX_LINES_COUNT', 1)
def test_too_many_lines():
msg_body = """Test reply
-----Original Message-----
Test"""
eq_(msg_body, quotations.extract_from_pl... | saleswise/talon | tests/text_quotations_test.py | Python | apache-2.0 | 14,470 | [
"VisIt"
] | 0901269f9bb478b9fa1db71a00d8a5af0032f3a2b00b1b18b66f8248cbe2a728 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# cat - [insert a few words of module description on this line]
# Copyright (C) 2003-2009 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the G... | heromod/migrid | mig/shared/functionality/cat.py | Python | gpl-2.0 | 7,229 | [
"Brian"
] | 21445310738f0ea75ee31b91af2ddc81665fe9489e083c2f3211e091c48a028a |
# rfc1751.py : Converts between 128-bit strings and a human-readable
# sequence of words, as defined in RFC1751: "A Convention for
# Human-Readable 128-bit Keys", by Daniel L. McDonald.
#
# Part of the Python Cryptography Toolkit
#
# Written by Andrew M. Kuchling and others
#
# =========================================... | Haynie-Research-and-Development/jarvis | deps/lib/python3.4/site-packages/Cryptodome/Util/RFC1751.py | Python | gpl-2.0 | 21,212 | [
"Elk",
"MOE"
] | 55597f9ae8b3313ae537cb5fe4321598c235a606829d8f3f202a346dde34229f |
#!/galaxy/home/mgehrin/hiclib/bin/python
"""
Match up intersecting intervals from two files. This performs a "full join",
any pair of intervals with any basewise overlap will be printed side-by-side.
usage: %prog bed1 bed2
"""
from __future__ import division
import psyco_full
import string
import sys
import bx.i... | bxlab/HiFive_Paper | Scripts/HiCLib/bx-python-0.7.1/build/scripts-2.7/interval_join.py | Python | bsd-3-clause | 1,129 | [
"Galaxy"
] | 264a6dbadf78f952f5731a6f1b5b47c01932bb81097b3f7ecdc6129a043ab5ed |
'''Term conversion.'''
from aterm import visitor
class _ToInt(visitor.Visitor):
def visitTerm(self, term):
raise TypeError('not an integer term', term)
def visitInt(self, term):
return term.value
def toInt(term):
'''Convert an integer term to its integer value.'''
return _ToInt().visit(term)
class _ToR... | mewbak/idc | aterm/convert.py | Python | lgpl-2.1 | 1,934 | [
"VisIt"
] | a6fb0983eadd00f5d9f55c5f3ab38bf78442a41c4917e850455980b5d71e5551 |
# Copyright 2005 by Jonathan Taylor.
# 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.
"""This module deals with CAPS markers.
A CAPS marker is a location a DifferentialCutsite a... | zjuchenyuan/BioWeb | Lib/Bio/CAPS/__init__.py | Python | mit | 4,043 | [
"Biopython"
] | 71d2fe13247a88b7ee51a983bdbafa434bccff47a2fd83217eb1c183713c732c |
#! /usr/bin/python
# -*- coding: utf-8 -*-
#
# Vladimír Slávik 2010 - 2011
# Python 2.6, 3.1
#
# for Simutrans
# http://www.simutrans.com
#
# code is public domain
#
# pygame learning script - tool for reformatting trees using offsets
# very rudimentary but sufficient :-)
from __future__ import print_function
... | simutrans/pak128 | tools/tree-align-interactive.py | Python | artistic-2.0 | 3,342 | [
"VisIt"
] | 23b50db106eeb88af97a9d56845cda6bfe1cfff4693c170c0c56b172e26f1109 |
import unittest
import nose
from nose.tools import eq_, ok_
import os, sys
PATH_HERE = os.path.abspath(os.path.dirname(__file__))
sys.path = [os.path.join(PATH_HERE, '..')] + sys.path
import readMDA
from xmap_netcdf_reader import DetectorData
TESTDATA_DIR = os.path.join(PATH_HERE, '..', '..', 'test_data', '2013-07-2... | Peter--K/Sakura | tests/file_tests.py | Python | bsd-3-clause | 4,203 | [
"NetCDF"
] | e579523d269e1896b06c4c6943648568dfcb242ecde9338a957f0e84dbbfb281 |
""" JobRunningWaitingRatioPolicy
Policy that calculates the efficiency following the formula::
( running ) / ( running + waiting + staging )
if the denominator is smaller than 10, it does not take any decision.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import... | yujikato/DIRAC | src/DIRAC/ResourceStatusSystem/Policy/JobRunningWaitingRatioPolicy.py | Python | gpl-3.0 | 2,224 | [
"DIRAC"
] | dfdf9bc3f7c255cf8d95a41ab92a18ca55857aacdacb02da8a0523204df7e988 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkProgrammableAttributeDataFilter(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager... | nagyistoce/devide | modules/vtk_basic/vtkProgrammableAttributeDataFilter.py | Python | bsd-3-clause | 521 | [
"VTK"
] | 4db147d43745ef040b077864889f98b6483a227833062c10712db126307d9b3d |
import unittest
from nose.tools import assert_true
import numpy as np
from numpy.testing import (assert_array_equal, assert_array_almost_equal,
assert_raises)
from scipy import stats
from sklearn import mixture
from sklearn.datasets.samples_generator import make_spd_matrix
from sklearn.utils... | shikhardb/scikit-learn | sklearn/mixture/tests/test_gmm.py | Python | bsd-3-clause | 15,189 | [
"Gaussian"
] | 0ac72a5928d5f872026b52a27dcb021d4483c9414dda595ef842cfe01ff4e3e5 |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class MpasModel(MakefilePackage):
"""The Model for Prediction Across Scales (MPAS) is a collabor... | LLNL/spack | var/spack/repos/builtin/packages/mpas-model/package.py | Python | lgpl-2.1 | 3,812 | [
"NetCDF"
] | ac213759f19920b570be53cec0ac92946d3ff7cb964175df8c1fa9d3fa653e1c |
#
# special_block_parser_builder_test.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
#... | kperun/nestml | tests/special_block_parser_builder_test.py | Python | gpl-2.0 | 2,899 | [
"VisIt"
] | 79790a4891fcb801a58d1919cc6510f249952ccb54fa1e66ba4d0a79833ea95f |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
samStat
Created on Fri May 23 13:14:18 2014
@author: cjg
"""
import sys
import argparse
import pysam
import mapStat
def samStat_pysam(samFile, outputFile):
''' From resulted sam or bam file of mapping, find information of reference sequences and reads.
For r... | chaij/pooPy | src/samStat.py | Python | mit | 12,862 | [
"pysam"
] | a7e43805b3224d1f6753776af949a95bc9a1b7f28c26546a5c943eab5cad0e27 |
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2020 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier (bgoli@users.sourceforge.net)
Triple-J Group for Molecular Cell Physiology
Stellenbosch University, South Africa.
Permission to us... | bgoli/pysces | pysces/PyscesModelMap.py | Python | bsd-3-clause | 12,084 | [
"PySCeS"
] | 3d5be5deae7e420f8a86ddc590c778af21c486baade0bea2fc860ba6a2ad4dca |
"""
================================================
Kernel Density Estimate of Species Distributions
================================================
This shows an example of a neighbors-based query (in particular a kernel
density estimate) on geospatial data, using a Ball Tree built upon the
Haversine distance metric... | kevin-intel/scikit-learn | examples/neighbors/plot_species_kde.py | Python | bsd-3-clause | 4,755 | [
"Gaussian"
] | 675dc9c84daf15b0f7b9210c3b8daa69c4b928944b56cd59de76baee2b92071d |
# -*- coding: utf-8 -*-
#
# Copyright © 2012 Pierre Raybaut
# Licensed under the terms of the MIT License
# (see winpython/__init__.py for details)
"""
WinPython Package Manager
Created on Fri Aug 03 14:32:26 2012
"""
from __future__ import print_function
import os
import os.path as osp
import shutil
import re
impo... | sharhar/USB-Thing | UpdaterFiles/Lib/python-3.5.1.amd64/Lib/site-packages/winpython/wppm.py | Python | apache-2.0 | 30,724 | [
"VTK"
] | d8a6113d174a7aa25c8fc057cca0a5000a09df46202af8a70c6f55b1a269e506 |
"""Use PyMOl to create templates for bomeba"""
import numpy as np
np.set_printoptions(precision=3)
import __main__
__main__.pymol_argv = ['pymol','-qck']
import pymol
from pymol import cmd, stored
pymol.finish_launching()
import openbabel as ob
def minimize(selection='all', forcefield='MMFF94s', method='cg',
... | BIOS-IMASL/bomeba0 | bomeba0/scaffold/compute_peptide_bond_lenght.py | Python | apache-2.0 | 1,471 | [
"PyMOL"
] | 725abfb4f70b904ae3aac828c6835b89710f09b2f5d0f218fb38e838d959fa07 |
"""
@name: PyHouse/src/Modules/Computer/Web/_test/test_web_login.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com>
@copyright: (c) 2014-2019 by D. Brian Kimmel
@license: MIT License
@note: Created on Aug 29, 2014
@Summary:
Passed all 8 tests - DBK - 2017-01-11
"""
__updated__ = '2020-02... | DBrianKimmel/PyHouse | Project/src/Modules/Computer/Web/test/test_web_login.py | Python | mit | 3,972 | [
"Brian"
] | 0c5972c63d916d19fb79f306d41752cca2e87fa1ce836fd03f8a66b4b939d3b4 |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | icexelloss/arrow | python/pyarrow/parquet.py | Python | apache-2.0 | 89,131 | [
"VisIt"
] | 7b9a21d63e96577d50977beaabd4bbbabac2f0f586171b295fcfd59aafc5fba5 |
from datetime import datetime, timedelta
from typing import List
import warnings
from dateutil.relativedelta import FR, MO, SA, SU, TH, TU, WE # noqa
import numpy as np
from pandas.errors import PerformanceWarning
from pandas import DateOffset, Series, Timestamp, date_range
from pandas.tseries.offsets import Day, ... | toobaz/pandas | pandas/tseries/holiday.py | Python | bsd-3-clause | 16,121 | [
"COLUMBUS"
] | 8d1515f2947f4c2a9179380afc986a43f9d8ddd534ec6bda41199434dda47463 |
# Copyright (c) OpenMMLab. All rights reserved.
from logging import warning
from math import ceil, log
import torch
import torch.nn as nn
from mmcv.cnn import ConvModule, bias_init_with_prob
from mmcv.ops import CornerPool, batched_nms
from mmcv.runner import BaseModule
from mmdet.core import multi_apply
from ..build... | open-mmlab/mmdetection | mmdet/models/dense_heads/corner_head.py | Python | apache-2.0 | 48,420 | [
"Gaussian"
] | 79289cf83fb22833ef15ad6e8e97f92276eb92153b3a533e5a2ce7cb0b45c6cf |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
try:
from io import BytesIO
except ImportError:
from StringIO import StringIO as BytesIO
import numpy as np
from sys import platform
import subprocess
from DataSounds.external.sebastian.lilypond.interp import parse
from DataSounds.external.sebastian.midi.write_mid... | DataSounds/DataSounds | src/DataSounds/sounds.py | Python | bsd-3-clause | 21,176 | [
"CRYSTAL"
] | 484a61bfeddb3cfc613423eb3b46e91a10c294b93fcec6ccf6316413bb7d46c4 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | pli3/e2-openwbif | plugin/controllers/views/web/getaudiotracks.py | Python | gpl-2.0 | 5,989 | [
"VisIt"
] | 7e1157953391976779d64c7d1740cf5825831cf8bcdd4ef6a9775f96e31a4c17 |
"""Test trie.py."""
import pytest
INSERT_STRINGS = ['hi', 'test', '', 'foo bar']
NONEMPTY_STRINGS = ['hello', 'hi', 'h', 'foobar', 'quux']
WORDS = [
"artsier",
"artsiest",
"artsy",
"artwork",
"artwork's",
"artworks",
"arty",
"as",
"asbestos",
"asbestos's",
"ascend",
... | welliam/data-structures | src/test_trie.py | Python | mit | 4,260 | [
"VisIt"
] | a011d091c6b84cbe79dfb2e85ae435b3dd7259e4377845491802b8b6eb3c9abe |
#!/usr/bin/python
import cv
import datetime
import numpy, scipy, scipy.fftpack
import pylab
IMG_STACK_LEN = 100
ANALYSIS_LAYER = 6
FFT_CHAN_MIN = 3
FFT_CHAN_MAX = 20
FREQ_THRESH = 0.05
inputfps = 25
outputfps = 30
window1 = "Current"
window2 = "Oldest"
window3 = "Time Data"
window4 = "Fourier Transform"
imgLis... | OpenSeizureDetector/OpenSeizureDetector | video_version/Seizure_Detector.py | Python | gpl-3.0 | 8,334 | [
"Gaussian"
] | 38db4bbc27d0faf5d6deb141c55abe0450c73f9477d2178e822d4f2a4036403b |
#!/usr/bin/env python
# megamapper executer
# by Nikolaus Obholzer, Jan 2012
import sys, re, tempfile, subprocess
import os, shutil
from galaxy import eggs
def stop_err(msg):
sys.stderr.write(msg)
sys.exit()
def main():
# Handle input params
in_fname = sys.argv[1]
Mname = sys.argv[2]
chrom =... | maxplanck-ie/Megamapper | chrscan.py | Python | bsd-3-clause | 1,087 | [
"Galaxy"
] | 2d02369b0eb11931bbf0561c25273d08ddfdce91acd05fb6f747f101537eb762 |
# Copyright 2008-2015 Nokia Solutions and Networks
#
# 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 l... | henriqueguchi/SikuliServer | new/Lib/robot/model/itemlist.py | Python | mit | 2,982 | [
"VisIt"
] | a2418f40e6deb566e1c5e29350b5cfb2bb1eb8a001e4d8f78ad6defcae1db7d4 |
import arabic_script.elements as ase
def encoding_cleanup():
raise NotImplementedError
def tatweel_removal(text):
"""
The Tatweel (elongation) is used to stretch words to indicate
prominence or simply to force vertical justification.
This symbol has no effect on the meaning of the word so it's
... | ahmedaljazzar/arabic-nlp | normalization/orthographic_normalization.py | Python | agpl-3.0 | 3,504 | [
"ASE"
] | 470f98b1613a34c195f1295371f6228ab6de1954768fde0f53aacdb7969ec3d7 |
import unittest
from test import support
from itertools import *
from weakref import proxy
from decimal import Decimal
from fractions import Fraction
import sys
import operator
import random
import copy
import pickle
from functools import reduce
maxsize = support.MAX_Py_ssize_t
minsize = -maxsize-1
def lzip(*args):
... | MalloyPower/parsing-python | front-end/testsuite-python-lib/Python-3.3.0/Lib/test/test_itertools.py | Python | mit | 83,107 | [
"GULP"
] | 44ecaa768a451446a28d682fa2acbd71dfc2a8d59ceccd8c9149f09604b31b81 |
#!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""Create HTML reports."""
from __future__ import print_function, unicode_literals
from contextlib import contextmanager
from copy import deepcopy
import os.path as op
import time
import warnings
import numpy as np
import mne
from mne import read_proj, read_epochs
from ... | kambysese/mnefun | mnefun/_report.py | Python | bsd-3-clause | 37,750 | [
"Mayavi"
] | e3b6fff17edb174c4b177a10a774040d62f339c07f02e1700325cf21d7b715b4 |
#!/usr/bin/env python
# Licensed to Cloudera, Inc. under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. Cloudera, Inc. licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you ma... | pwong-mapr/private-hue | desktop/core/src/desktop/lib/django_forms.py | Python | apache-2.0 | 18,460 | [
"VisIt"
] | 6b4d05f0b028914680830508cbfee79818860b752d64a637800eaf906198a3dc |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import itertools
import json
import os
import unittest
import numpy as np
from monty.json import MontyDecoder
from pymatgen.core.periodic_table import Element
from pymatgen.core.lattice import Lattice
from p... | richardtran415/pymatgen | pymatgen/analysis/tests/test_structure_matcher.py | Python | mit | 47,994 | [
"VASP",
"pymatgen"
] | 6d1df3dd4700664e72f33e7c65c958c33cb2517bdb831e4b5e6a54fc28a8ad2c |
# coding=utf-8
from vtk import *
dicom_image_reader = vtk.vtkDICOMImageReader()
dicom_image_reader.SetDirectoryName("D:\\CodeProject\\Hover\\Data\\Dicom\\02ef8f31ea86a45cfce6eb297c274598\\series-000001\\")
dicom_image_reader.SetDataByteOrderToLittleEndian()
dicom_image_reader.SetDataSpacing(3.2, 3.2, 1.5)
dic... | comedate/VolumeRendering | render_reader.py | Python | mit | 797 | [
"VTK"
] | 941b01964511e2a863876b11575b35858a9de1414bed0e8a0c6e45aaf3d0620b |
import vtk
rectGridReader = vtk.vtkRectilinearGridReader()
rectGridReader.SetFileName("D:/Notebooks_Bogota2017/SS_2017/data/jet4_0.500.vtk")
rectGridReader.Update()
#------------ CHALLENGE ONE ----------------------
rectGridOutline = vtk.vtkRectilinearGridOutlineFilter()
rectGridOutline.SetInputData(rectGridReader.Ge... | dianafprieto/SS_2017 | scripts/05_NB_Challenge_1.py | Python | mit | 4,001 | [
"VTK"
] | 448c569d552f9bf8b1c8442d8be46c4d07f9047c1267edbabd511c0ef030f86a |
#!/usr/bin/python2
import optparse
import os
import subprocess
import sys
def num_cpus():
# Use multiprocessing module, available in Python 2.6+
try:
import multiprocessing
return multiprocessing.cpu_count()
except (ImportError, NotImplementedError):
pass
# Get POSIX system co... | atris/gpdb | concourse/scripts/build_with_orca.py | Python | apache-2.0 | 3,771 | [
"ORCA"
] | 0fde3f34013a81c483bab3aedfba9b6c227b72bcdc625cdd7c78cc2b3baf77b6 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | lgarren/spack | var/spack/repos/builtin/packages/paraview/package.py | Python | lgpl-2.1 | 6,854 | [
"NetCDF",
"ParaView"
] | d35e8e32d132bd994da1ac00839882b7414de0bfaf001cbc742fe8439473dab8 |
#!/usr/bin/python
import HTSeq
from Bio.Seq import Seq
import os.path
import argparse
def reverseComplement(strDNA):
basecomplement = {'A': 'T', 'C': 'G', 'G': 'C', 'T': 'A'}
strDNArevC = ''
for l in strDNA:
strDNArevC += basecomplement[l]
return strDNArevC[::-1]
def translateSeq... | mickaelsilva/pythonscripts | SchemaValidation/CheckCDS.py | Python | gpl-2.0 | 3,219 | [
"HTSeq"
] | ab1c554f167791e2e307ca6a50b4651599f47fd67f7c694715f0872fad23b6ed |
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