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# ----------------------------------------------------------------------
# Copyright (c) 2016, The Regents of the University of California All
# rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# ... | drichmond/tinker | python/IP.py | Python | bsd-3-clause | 6,330 | [
"TINKER"
] | 0ff8d5b142fbd565c93860910e0eb2e9f8e136e052863d39b4b7b2b9a781091b |
# $Id$
#
# Copyright (C) 2003-2006 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" Supplies an abstrac... | rdkit/rdkit-orig | rdkit/Chem/Suppliers/MolSupplier.py | Python | bsd-3-clause | 830 | [
"RDKit"
] | 2583c5192ca0d54b8cf3ca62795cd2facd8cb2d8fa77f2656507a0df95f0c8de |
#!/usr/bin/env python
###############################################################################
# Copyright 2015-2016 University of Florida. All rights reserved.
# This file is part of UF CTS-IT's NACCulator project.
# Use of this source code is governed by the license found in the LICENSE file.
################... | ZacZZZ/Nacculator_Github | nacc/backup/redcap2nacc-7-3-17.py | Python | bsd-2-clause | 8,578 | [
"VisIt"
] | fee4b1514c5217fe86c5a33b34ca6274044d1d53a6c83a262875b96528a2fdf5 |
"""feedfinder: Find the Web feed for a Web page
http://www.aaronsw.com/2002/feedfinder/
Usage:
feed(uri) - returns feed found for a URI
feeds(uri) - returns all feeds found for a URI
>>> import feedfinder
>>> feedfinder.feed('scripting.com')
'http://scripting.com/rss.xml'
>>>
>>> feedfinder.fe... | Einsteinish/PyTune3 | utils/feedfinder.py | Python | mit | 13,462 | [
"Brian"
] | 7fbafad897794f33d6a2879328b8676cdbab0029f49e760c1875675cf053aa67 |
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | sunqm/pyscf | pyscf/pbc/df/test/test_rsdf_jk.py | Python | apache-2.0 | 12,887 | [
"PySCF"
] | 335133911b3d4a941c68d307907cd93c1d8b8478136c25ebe900a384ef53e79a |
import os
import Rappture
from Rappture.tools import executeCommand as RapptureExec
import shutil
import sys
import re
import stat
import tempfile
import string
import threading
import time
import math
import zipfile
import numpy as np
from math import cos, sin
param_file_template = """' ========= Parameter file for v... | NanoBioNode/nanoDDSCATplus | rappture/dda/ddscat.py | Python | gpl-3.0 | 105,014 | [
"VTK"
] | 54a6d0ff786441701ec7ec1d338ee63d5892796b9cc05f365c1a64d77b4940c2 |
from edc_constants.constants import SCHEDULED, UNSCHEDULED, NO, YES, OTHER
from lab_requisition.forms import RequisitionFormMixin
from django import forms
from django.conf import settings
from django.contrib.admin.widgets import AdminRadioSelect, AdminRadioFieldRenderer
from td_maternal.models import MaternalVisit
fr... | botswana-harvard/tshilo-dikotla | td_lab/forms/maternal_requisition_form.py | Python | gpl-2.0 | 4,788 | [
"VisIt"
] | deff75bd073ed788f139f772e73f6f7d4cfe4bdf74ecd2acdd025b88a8e170e0 |
r"""
Vibro-acoustic problem
3D acoustic domain with 2D perforated deforming interface.
*Master problem*: defined in 3D acoustic domain (``vibro_acoustic3d.py``)
*Slave subproblem*: 2D perforated interface (``vibro_acoustic3d_mid.py``)
Master 3D problem - find :math:`p` (acoustic pressure)
and :math:`g` (transversal... | vlukes/sfepy | examples/acoustics/vibro_acoustic3d_mid.py | Python | bsd-3-clause | 3,492 | [
"VTK"
] | d5e485b1338b63fb37ce20ccf0fb4eb517eee4c5c5634608f7e07e95eeb99fa4 |
from __future__ import print_function
from __future__ import absolute_import
from .DataTestTemplate import _DataTest
from PyOpenWorm.neuron import Neuron
from PyOpenWorm.cell import Cell
from PyOpenWorm.connection import Connection
from PyOpenWorm.context import Context
class NeuronTest(_DataTest):
ctx_classes... | gsarma/PyOpenWorm | tests/NeuronTest.py | Python | mit | 4,199 | [
"NEURON"
] | 9acf82ce79531a1a6d27a5116366eb4119f73e671ee1b69d09e5d160094a4fe0 |
# coding: utf-8
from __future__ import unicode_literals
"""
This module provides classes to define everything related to band structures.
"""
__author__ = "Geoffroy Hautier, Shyue Ping Ong, Michael Kocher"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "1.0"
__maintainer__ = "Geoffroy Hautier"... | Dioptas/pymatgen | pymatgen/electronic_structure/bandstructure.py | Python | mit | 40,975 | [
"CRYSTAL",
"pymatgen"
] | 9ba5198341b06446db20f336671869a527e1a6e60ba9487fbe6f01868eb180ee |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from DIRAC import S_OK, S_ERROR, gLogger
class FilterExecutor(object):
ALLKW = "all"
def __init__(self):
self.__filters = {}
self.__globalFilters = []
def applyFilters(self, iD,... | ic-hep/DIRAC | src/DIRAC/AccountingSystem/private/Policies/FilterExecutor.py | Python | gpl-3.0 | 1,583 | [
"DIRAC"
] | 3ccf808fd5b0ab1b9c4a5acf32204e44bd0b04a79f0668814cb9c568eba7eef9 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | krafczyk/spack | var/spack/repos/builtin/packages/py-methylcode/package.py | Python | lgpl-2.1 | 1,842 | [
"Bowtie"
] | 8b695a8f97568a98786f4cd60fad467b1a00b6f84e1c221b71d91422fa85a0e9 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# PyVortex: Vortex Library Python bindings
# Copyright (C) 2009 Advanced Software Production Line, S.L.
#
# 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 Softwar... | ASPLes/libvortex-1.1 | py-vortex/test/vortex-regression-client.py | Python | lgpl-2.1 | 82,823 | [
"VisIt"
] | 935de174cf61f96144ddf5b8fd33205db1445e1bc844845fcfac0405c8f96a62 |
#! /usr/bin/env python
# =================================
# = Simple unit tests for pycoda =
# =================================
#
# These will store/use an authentication token in codatests.tok in the current directory.
# This is just a simple test - a very long way from being exhaustive!
#
# Some tests may fail ... | camvine/pycoda | codatests.py | Python | gpl-2.0 | 6,984 | [
"exciting"
] | d53e6a5eb4826034a887ec63b2700d1c5c3952808e4fe3c8c4f5d59e0bd08ab4 |
"""
Define an abstract solver and a greedy, a random, a simulated annealing solvers
considering an uncertainty grid and penalizing large battery consumption.
"""
import numpy as np
import datetime
import copy
import operator
import random
import math
from sys import path
from simanneal import Annealer
import matplotli... | OPU-Surveillance-System/monitoring | master/scripts/planner/solvers/uncertainty_battery_solver.py | Python | mit | 4,288 | [
"VisIt"
] | ae26af5e0bc2bdb9e9ea69ba08ebee41ca072fd4322ca244a16edab48ed7609a |
#!/usr/bin/python
"""
Copyright 2016 Paul Willworth <ioscode@gmail.com>
This file is part of Galaxy Harvester.
Galaxy Harvester 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 th... | druss316/G-Harvestor | html/dbSession.py | Python | gpl-3.0 | 1,782 | [
"Galaxy"
] | c6d9722ac7a43154a73136c110d2f7952b724c9ae46c4f70a707ec618c3f1d23 |
"""Infrastructure for RNA-seq supporting files.
"""
import os
from fabric.api import cd
def finalize(genomes, env):
"""Provide symlinks back to reference genomes so tophat avoids generating FASTA genomes.
"""
genome_dir = os.path.join(env.data_files, "genomes")
for (orgname, gid, manager) in genomes:
... | joemphilips/cloudbiolinux | cloudbio/biodata/rnaseq.py | Python | mit | 1,372 | [
"Bowtie"
] | e25bf5c5d4ca9e0f651cf89011ecaeba512493f98ddd1ad26946ebd4d50835bd |
from ovito import *
from ovito.io import *
from ovito.modifiers import *
from ovito.data import *
import numpy
node = import_file("../../files/CFG/shear.void.120.cfg")
modifier = PythonScriptModifier()
node.modifiers.append(modifier)
def compute_coordination(pindex, finder):
return sum(1 for _ in finder.find(pind... | srinath-chakravarthy/ovito | tests/scripts/test_suite/python_script_modifier.py | Python | gpl-3.0 | 990 | [
"OVITO"
] | d4b01474e84ce947ded462aee48f5811ccbbde47340602cb861646fed3459822 |
from distutils.core import setup
setup(
name = 'simplekml',
packages = ['simplekml'],
version = '1.2.3',
description = 'A Simple KML creator',
author='Kyle Lancaster',
author_email='kyle.lan@gmail.com',
url='http://code.google.com/p/simplekml/',
license='GNU General Public Lic... | Sakartu/simplekml | setup.py | Python | gpl-3.0 | 2,132 | [
"VisIt"
] | 075ddb8b6fa13515ca4d77b82fc758b8e7e4bf2ca3b1aba7512cc259a7b0d4eb |
# Copyright 2017-2021 TensorHub, Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writ... | guildai/guild | guild/plugins/skopt_util.py | Python | apache-2.0 | 17,278 | [
"Gaussian"
] | 39d3795216a962778dcb5e57579d807d8f3aeb6bc1f02b7567080740eb500ecb |
# Licensed under an MIT open source license - see LICENSE
from __future__ import print_function, absolute_import, division
import numpy as np
import scipy.ndimage as nd
from scipy.interpolate import InterpolatedUnivariateSpline
from astropy.convolution import Gaussian2DKernel, convolve_fft
from astropy.wcs import WCS
... | Astroua/TurbuStat | turbustat/statistics/genus/genus.py | Python | mit | 19,650 | [
"Gaussian"
] | b70ebe134e0e95c2ada8cd897d560f909bb6677f2970b082653ad2f9b75bceab |
"""
Message Queue wrapper
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
from pythonjsonlogger.jsonlogger import JsonFormatter as libJsonFormatter
from DIRAC.FrameworkSystem.private.standardLogging.Handler.MessageQueueHandler import... | yujikato/DIRAC | src/DIRAC/Resources/LogBackends/MessageQueueBackend.py | Python | gpl-3.0 | 2,542 | [
"DIRAC"
] | a8e4f53f1cd711cca6a6f14f7e925f4b0cb61f24e0e716e43ec440b71b6d098b |
# Copyright (C) 2012-2016
# Max Planck Institute for Polymer Research
# Copyright (C) 2008-2011
# 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 GNU Gen... | kkreis/espressopp | src/integrator/LBInitPopUniform.py | Python | gpl-3.0 | 1,977 | [
"ESPResSo"
] | d082562a037173c1aa612350bd186b7bcd41e5071167d67d3b15e6d565cb2f26 |
import chempy
import copy
from chempy.models import Indexed
from Numeric import *
from Precision import *
class FastModel:
#------------------------------------------------------------------------------
def __init__(self):
self.reset()
#------------------------------------------------------------------... | gratefulfrog/lib | python/chempy/fast/__init__.py | Python | gpl-2.0 | 5,069 | [
"ChemPy"
] | b78f764b70c7e7f7db595810ccd1d66071917f8250eb17fb0efe8413c06ad4ee |
# -*- coding: utf-8 -*-
# Copyright (c) 2015-2018, Exa Analytics Development Team
# Distributed under the terms of the Apache License 2.0
"""
Base ADF editor
##################
"""
from exatomic import Editor as AtomicEditor
class Editor(AtomicEditor):
def __init__(self, *args, **kwargs):
super(Editor, se... | avmarchenko/exatomic | exatomic/adf/editor.py | Python | apache-2.0 | 579 | [
"ADF",
"Gaussian"
] | afbfce5c667f59bc5ec91b9d49ded90a268ff43c841836fe12b4695a5130b546 |
#!/usr/bin/python
usage = """recover.py [--options] data.pkl"""
description = """written to recover populations of events from poisson series"""
author = "R. Essick"
import os
import numpy as np
import pickle
import matplotlib
matplotlib.use("Agg")
from matplotlib import pyplot as plt
from optparse import OptionPars... | reedessick/populations | recover.py | Python | gpl-2.0 | 8,214 | [
"Gaussian"
] | bd55d1063f830934e240452b64c902f964ec7c90fa4e0b4f5f6498640a471186 |
import io
import os
import re
from distutils.core import setup
def read(path, encoding='utf-8'):
path = os.path.join(os.path.dirname(__file__), path)
with io.open(path, encoding=encoding) as fp:
return fp.read()
def version(path):
"""Obtain the packge version from a python file e.g. pkg/__init_... | astroML/gatspy | setup.py | Python | bsd-2-clause | 2,320 | [
"VisIt"
] | 468a4dd5c652f6450b066ce2e5892f19675e19abf39cdec35eae30adf57d0641 |
#
# Copyright 2018 Analytics Zoo 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... | intel-analytics/analytics-zoo | pyzoo/zoo/examples/orca/learn/tf/basic_text_classification/basic_text_classification.py | Python | apache-2.0 | 5,848 | [
"ORCA"
] | a2f14f3379aac7836c398ef246d3b510316dd183bb0c0815dcbe8bdff1b0a846 |
from __future__ import division
from builtins import map
from builtins import str
from builtins import range
import os
import re
import pickle
import logging
import numpy as np
import matplotlib
import matplotlib.pyplot as plt
from past.utils import old_div
from scipy.optimize import curve_fit
from scipy.interpolate im... | msotov/SPECIES | CalcBroadening.py | Python | mit | 65,014 | [
"Gaussian"
] | ce7303ac708fc97440b32e05193ef435ee30bd24576de545a263b78b1aa99bbb |
from toontown.coghq.SpecImports import *
GlobalEntities = {1000: {'type': 'levelMgr',
'name': 'LevelMgr',
'comment': '',
'parentEntId': 0,
'cogLevel': 0,
'farPlaneDistance': 1500,
'modelFilename': 'phase_10/models/cashbotHQ/ZONE13a',
'wantDoors': 1},
1001: {'type... | silly-wacky-3-town-toon/SOURCE-COD | toontown/coghq/SellbotMegaFactoryPipeRoom_Action00.py | Python | apache-2.0 | 19,355 | [
"Bowtie"
] | 40ddb9001b37b5fe621671a65d987b732302df0c884d972871860576c058db9a |
##
# Copyright 2013-2016 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
# Flemish Research Foundation ... | wpoely86/easybuild-easyblocks | easybuild/easyblocks/p/psi.py | Python | gpl-2.0 | 7,941 | [
"Psi4"
] | ce30830a4e64914f4df7a07d0bfe68ac78d15fdf378410db44179593c6e86f7e |
#!/usr/bin/env python
#-*- coding:utf-8 -*-
#
# This file is part of the NNGT project to generate and analyze
# neuronal networks and their activity.
# Copyright (C) 2015-2019 Tanguy Fardet
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License a... | Silmathoron/NNGT | nngt/plot/plt_networks.py | Python | gpl-3.0 | 70,660 | [
"NEURON"
] | bb180d6a6cabd606480871f25390b4ed7e1dbb4ef4133256b2c5470211739c69 |
# 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... | govarguz/espressopp | src/analysis/CenterOfMass.py | Python | gpl-3.0 | 1,672 | [
"ESPResSo"
] | 09b664b7e26f5b1d17624dbba585832248dc4cfe54b7045190c9e8761539d7c7 |
""" NOTA BENE: This agent should NOT be run alone. Instead, it serves as a base class for extensions.
The TaskManagerAgentBase is the base class to submit tasks to external systems,
monitor and update the tasks and file status in the transformation DB.
This agent is extended in WorkflowTaskAgent and Reque... | andresailer/DIRAC | TransformationSystem/Agent/TaskManagerAgentBase.py | Python | gpl-3.0 | 31,028 | [
"DIRAC"
] | ba0207880bba1ec42b66e8bba391d78da030890b257322e427a35b7d44447e23 |
import os
import math
import subprocess
from omg import atoms
from omg import iolines
class FlagInfo():
def __init__(self, ptr_byte, ptr_line, read_n_lines, textformat):
self.byte = ptr_byte
self.line = ptr_line # Unused
self.read_n_lines = read_n_lines
(self.data_per_lin... | eduardoftoliveira/oniomMacGyver | omg/prmtop.py | Python | gpl-3.0 | 36,847 | [
"Amber",
"Gaussian"
] | 12dfa3688a5ececf2b1aff3cf402cd18aa584647922942e935c134eed22e5eed |
# Copyright (C) 2010-2019 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 v... | fweik/espresso | testsuite/python/icc.py | Python | gpl-3.0 | 6,437 | [
"ESPResSo"
] | 6f5d85b3db16d3c41a2de4fcc37e48a52b660bf62ef07d4d4234a520e089a851 |
from cvxopt import matrix, lapack, spmatrix
from chompack.symbolic import cspmatrix
from chompack.misc import frontal_get_update
from cvxopt import sqrt
def mrcompletion(A, reordered=True):
"""
Minimum rank positive semidefinite completion. The routine takes a
positive semidefinite cspmatrix :math:`A` and... | cvxopt/chompack | src/python/pybase/mrcompletion.py | Python | gpl-3.0 | 3,728 | [
"VisIt"
] | 3e4b6a4b8407baa997e5ec41f469157777192bb8b7ef915ff2318602e823d3c7 |
""" Module for handling AccountingDB tables on multiple DBs (e.g. 2 MySQL servers)
"""
from DIRAC import gConfig, S_OK, gLogger
from DIRAC.Core.Utilities.Plotting.TypeLoader import TypeLoader
from DIRAC.AccountingSystem.DB.AccountingDB import AccountingDB
class MultiAccountingDB(object):
def __init__(self, csPath... | DIRACGrid/DIRAC | src/DIRAC/AccountingSystem/DB/MultiAccountingDB.py | Python | gpl-3.0 | 3,895 | [
"DIRAC"
] | d357f713aa49a3201f2cce1a8e8192236cfe8048d3df025ec77ec3b40a9dfdf5 |
import os
import re
import json
import pytz
import numpy as np
from datetime import datetime
import progressbar
from progressbar import ProgressBar
from lib.util import open_log_file
re_timestamp = re.compile(
r"[0-9\-]{10}[\sT][0-9]{2}:[0-9]{2}:[0-9]{2}[\.\,0-9]*[\+\-0-9Z]*")
dt_formats = ["%Y-%m-%d %H:%M:%S... | mz-pdm/ovirt-log-analyzer | src/lib/detect_running_components.py | Python | apache-2.0 | 65,702 | [
"ASE"
] | fda15b423de0117797b0a3da3a222452e9ed8f532622df52d1c6999bbb4e8090 |
from __future__ import absolute_import
import inspect
import importlib
import logging
import sys
from . import plot
try:
basestring # For Python 2 compatibility
except NameError:
basestring = str # For Python 3 compatibility
class NengoTrial(plot.PlotTrial):
def _create_base_params(self):
... | tcstewar/pytry | pytry/nengo.py | Python | gpl-3.0 | 4,779 | [
"NEURON"
] | d9a75fd699977eb5dcc544e33fdaa658b08c770f6fc399274e0203dda47cee9e |
# This file is part of Androguard.
#
# Copyright (c) 2012 Geoffroy Gueguen <geoffroy.gueguen@gmail.com>
# 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://... | subho007/androguard | androguard/decompiler/dad/writer.py | Python | apache-2.0 | 25,567 | [
"VisIt"
] | 4c7da8555082f4aeec6c1c06c21914abd67ff374b3dd486770cbac25fb08a76b |
#
# Copyright 2016 The BigDL 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 ... | intel-analytics/BigDL | python/orca/src/bigdl/orca/automl/model/base_pytorch_model.py | Python | apache-2.0 | 16,322 | [
"ORCA"
] | 09a9f57c164ff43e91e905b117bf43c8123ef58ae01fa26106b3f06484a1027f |
#!/usr/bin/env python
import pygtk
pygtk.require('2.0')
import gtk
import gobject
import time
import threading
import subprocess
import json
import sys
import os
import os.path
import string
import uuid
import urllib2
import tempfile
import datetime
# monkey patch py2.7's check_output() into py2.6's missing one :)
if... | skeezix/compo4all | spaghetti-launcher/c4a-fe.py | Python | gpl-2.0 | 25,486 | [
"BLAST"
] | 5692a73558066498104be9607c6eac47946be655d9890b9fe8d27e2a0c71a2b8 |
# (c) 2013-2014, Michael DeHaan <michael.dehaan@gmail.com>
# (c) 2015 Toshio Kuratomi <tkuratomi@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either... | thnee/ansible | lib/ansible/executor/module_common.py | Python | gpl-3.0 | 66,690 | [
"VisIt"
] | bed7fb4c0817d7a23ca543f9e3cdb605c79667e793917fb6b993a2e7e87b96ff |
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at https://mozilla.org/MPL/2.0/.
import numpy as np
from ..sile import add_sile, get_sile
from .sile import SileSiesta
from sisl._internal import set_m... | zerothi/sisl | sisl/io/siesta/pdos.py | Python | mpl-2.0 | 25,117 | [
"SIESTA"
] | 8b5f329ea5a82196c4abb474b86e8e956c0319558c0547268b0892ae45e16321 |
from queue import PriorityQueue
import itertools
def show(customer, time, activity):
print('[%3d] %s: %s' % (time, customer, activity))
def visit(customer, arrival):
time = arrival
show(customer, time, 'arrives at branch')
time = yield
show(customer, time, 'waiting in line')
time = yield
s... | garoa/concorrente.py | coroutines/waitsim.py | Python | cc0-1.0 | 915 | [
"VisIt"
] | fbfbc41c37f942202150da4c94b9a4ef58e383335f66081facbaee1421945495 |
"""
Derived from Brian Naughton @ http://blog.booleanbiotech.com/genetic_engineering_pipeline_python.html
"""
from __future__ import print_function
import datetime
import math
import re
import autoprotocol
from autoprotocol import Unit
from autoprotocol.unit import UnitValueError
from autoprotocol.container import C... | scottbecker/delve_tx_public | src/transcriptic_tools/utils.py | Python | mit | 26,985 | [
"Brian"
] | 3ca814cbee78cf7493f4bd7a44e756c9df4f45eec0cceed46fb51a25b54a4ac7 |
##
# Copyright 2013 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
# Flemish Research Foundation (FWO)... | wpoely86/easybuild-easyblocks | easybuild/easyblocks/e/esmf.py | Python | gpl-2.0 | 4,281 | [
"NetCDF"
] | 94ac9b9927cb868ece1c10befb92b44295bdd05754450be76dcfd7cccc3e5500 |
import json
import frappe
from erpnext.demo.domains import data
def setup_data():
setup_item()
setup_item_price()
frappe.db.commit()
frappe.clear_cache()
def setup_item():
items = json.loads(open(frappe.get_app_path('erpnext', 'demo', 'data', 'item.json')).read())
for i in items:
if not i.get("domain") == ... | mhbu50/erpnext | erpnext/demo/setup/retail.py | Python | gpl-3.0 | 1,720 | [
"Galaxy"
] | 72b2bf54c3241f5d59f91c72da7b55ecf7a6b2463f532c5139d0304c60dc919d |
# 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... | drpngx/tensorflow | tensorflow/contrib/autograph/pyct/ast_util.py | Python | apache-2.0 | 5,240 | [
"VisIt"
] | a4b20ea340903174ef7b471d781cbddfeed7bd9f8e6cb3e030aad51b6304e854 |
# -*- coding: UTF-8 -*-
# Documentation available here:
# http://www.vtk.org/VTK/img/file-formats.pdf
import os
import copy
import tempfile
import numpy as np
from tractconverter.formats import header
from tractconverter.formats.header import Header as H
def readBinaryBytes(f, nbBytes, dtype):
buff = f.read(nb... | MarcCote/tractconverter | tractconverter/formats/vtk.py | Python | bsd-3-clause | 12,340 | [
"VTK"
] | bddfc3a0ba027f573a5f56266e339381023c98dcc6e80e0d58148eefc7ff88bf |
#! /usr/bin/env python
"""
Module with frame/cube filtering functionalities.
"""
__author__ = 'Carlos Alberto Gomez Gonzalez, Valentin Christiaens'
__all__ = ['frame_filter_highpass',
'frame_filter_lowpass',
'frame_deconvolution',
'cube_filter_highpass',
'cube_filter_lowp... | vortex-exoplanet/VIP | vip_hci/var/filters.py | Python | mit | 23,900 | [
"Gaussian"
] | 91e3531857d9b9972e03c82bc9f3fa7cd8e76ef829eed474908e3720ed3bd5fd |
#!/usr/bin/env python
#
# Copyright 2016 Google Inc. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless require... | anthrotype/nototools | nototools/noto_cmap_reqs.py | Python | apache-2.0 | 90,248 | [
"FEFF",
"FLEUR"
] | f2f6bd6e3221bc983a27284d5ff0c56bba052bee603dcc97f04513e91e58c298 |
# Copyright (C) 2010-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | mkuron/espresso | testsuite/python/lb_switch.py | Python | gpl-3.0 | 2,916 | [
"ESPResSo"
] | 1fd0e4407997e82d6c97702a3bb05b1ed436c1a6a8af120edc2a78305fb28dcc |
# Copyright 2012-2013 Dusty Phillips
# This file is part of gitifyhg.
# gitifyhg 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.
#
# ... | kevinrodbe/gitifyhg | gitifyhg/gitexporter.py | Python | gpl-3.0 | 11,827 | [
"Octopus"
] | 3a5721839335935105a9159268958fb9b35dbdde049a055af0e1580a72579ec1 |
from __future__ import print_function
import numpy as np
import matplotlib.pyplot as plt
import sys
sys.path.insert(1,'..') # allow parent modules to be imported
sys.path.insert(1,'../..') # allow parent modules to be imported
sys.path.insert(1,'../../..') # allow parent modules to be imported
import time
import params... | methods-for-neuronal-network-dynamics/fokker-planck-based-spike-rate-models | adex_comparison/runmodels.py | Python | gpl-3.0 | 11,126 | [
"Brian"
] | 1706e07b6c6cc91d07d47b30a092a63287dfcba42555a4ce284d5dcb358688f2 |
## Automatically adapted for numpy.oldnumeric Mar 26, 2007 by alter_code1.py
##
## Biskit, a toolkit for the manipulation of macromolecular structures
## Copyright (C) 2004-2012 Raik Gruenberg & Johan Leckner
##
## This program is free software; you can redistribute it and/or
## modify it under the terms of the GNU Ge... | ostrokach/biskit | Biskit/PDBCleaner.py | Python | gpl-3.0 | 27,041 | [
"Amber"
] | 190614de849baac4402e04ec17da356c3bbe134ceb5c668041373f228ca2f876 |
# Copyright 2006 by Sean Davis. 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.
#
# $Id: __init__.py,v 1.12 2009-04-24 12:03:45 mdehoon Exp $
# Sean Davis <sdavis2 at mail dot ni... | bryback/quickseq | genescript/Bio/UniGene/__init__.py | Python | mit | 12,406 | [
"Biopython"
] | b7a157fad97212817adcf4ea8caca7250c18d0486ca0e81ce2029ef17fad0cd5 |
# Copyright 2012-2014 Brian May
#
# This file is part of python-tldap.
#
# python-tldap 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.... | Karaage-Cluster/python-tldap | tldap/query_utils.py | Python | gpl-3.0 | 1,740 | [
"Brian"
] | f753d2496be86381a6c9c263528e871aba13f36ffa2fb0b9c499611c266bbb9a |
"""Sub-classes and wrappers for vtk.vtkPointSet."""
from textwrap import dedent
import pathlib
import logging
import os
import warnings
import numbers
import collections
import numpy as np
import pyvista
from pyvista import _vtk
from pyvista.utilities import abstract_class
from pyvista.utilities.cells import (CellArr... | akaszynski/vtkInterface | pyvista/core/pointset.py | Python | mit | 62,814 | [
"Gaussian",
"VTK"
] | 4683799dfde5e9b5770508a36c794402ddeee2323f9f5f4c4b99f80c9bdb5056 |
#!/usr/bin/env python
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""\
Wrapper script around Rietveld's upload.py that simplifies working with groups
of files.
"""
import json
import optparse
impo... | nevir/plexability | extern/depot_tools/gcl.py | Python | gpl-2.0 | 49,766 | [
"VisIt"
] | 28696d299d94fe6448a2e98435607efbf668b2c623092017a3e6e84abec511ec |
"""
This module gathers tree-based methods, including decision, regression and
randomized trees. Single and multi-output problems are both handled.
"""
# Code is originally adapted from MILK: Machine Learning Toolkit
# Copyright (C) 2008-2011, Luis Pedro Coelho <luis@luispedro.org>
# License: MIT. See COPYING.MIT file... | maxlikely/scikit-learn | sklearn/tree/tree.py | Python | bsd-3-clause | 32,046 | [
"Brian"
] | 1f0db6681350e17dd7db2566d9a4342ee50e0150d0ea9ede930c9d6c0870e885 |
#!/usr/bin/env python
__author__ = 'Mike McCann'
__copyright__ = '2013'
__license__ = 'GPL v3'
__contact__ = 'mccann at mbari.org'
__doc__ = '''
Contains class for common routines for loading all BEDS data
Mike McCann
MBARI 13 May 2013
@undocumented: __doc__ parser
@status: production
@license: GPL
'''
imp... | google-code-export/stoqs | loaders/BEDS/__init__.py | Python | gpl-3.0 | 3,108 | [
"NetCDF"
] | 477a46b3e8ad008bb8b083f7502d825b5de66881791ec4842031be2c4b98892c |
"""
.. _plot_stc:
=================
04. Plot contrast
=================
Group average of dSPM solutions obtained by :ref:`plot_events_inverse` for the
contrast between both types of faces together and scrambled at 170 ms
poststimulus. The image was produced by subtracting normalized solutions of
faces to the ones of ... | neuropycon/ephypype | doc/workshop/meg/04-plot_stc.py | Python | bsd-3-clause | 2,920 | [
"Mayavi"
] | eafadf5f1eb33e2fc7be7b8ca2dace908aee99446f7353f5618bd9f4fa9bd136 |
# -*- coding: utf-8 -*-
""" ymir.util._ansible
"""
import os
from fabric import api
from peak.util.imports import lazyModule
from ymir import data as ydata
from ymir.base import report as base_report
yapi = lazyModule('ymir.api')
def require_ansible_role(role_name, role_dir, report=base_report):
""" """
if... | mattvonrocketstein/ymir | ymir/util/_ansible.py | Python | mit | 878 | [
"Galaxy"
] | 176689e001d365f88b9ffe5afdcd1a243c2b280e0ed8e47ffef47a0f0b043066 |
# Hidden Markov Model Implementation
import pylab as pyl
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy as scp
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import rospy
#import hrl_lib.mayavi2_util as mu
import hrl_lib.viz ... | tapomayukh/projects_in_python | classification/Classification_with_HMM/Single_Contact_Classification/force_codes/number_of_states/hmm_crossvalidation_force_40_states.py | Python | mit | 25,353 | [
"Gaussian",
"Mayavi"
] | 6b11cd73d2da70b071c7bfb2d57f5f31678f152aee768e78a06a3dd73a8c69b4 |
#
# Copyright 2021 Lars Pastewka (U. Freiburg)
# 2018 Jacek Golebiowski (Imperial College London)
#
# matscipy - Materials science with Python at the atomic-scale
# https://github.com/libAtoms/matscipy
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Gen... | libAtoms/matscipy | matscipy/calculators/mcfm/neighbour_list_mcfm/neighbour_list_base.py | Python | lgpl-2.1 | 1,886 | [
"ASE",
"Matscipy"
] | 675078ecf81fd621ca5714dbf91738290bcd3e3c49c0fd7acd42af8046563624 |
import os
import gc
import sys
import time
import signal
import traceback
import numpy as np
from gpaw.atom.generator import Generator
from gpaw.atom.configurations import parameters
from gpaw.utilities import devnull, compiled_with_sl
from gpaw import setup_paths
from gpaw import mpi
import gpaw
def equal(x, y, to... | robwarm/gpaw-symm | gpaw/test/__init__.py | Python | gpl-3.0 | 16,507 | [
"GPAW"
] | e7e2bc2fc3cb108773311f16fe1753b503912e79e0373204df5eb95722b34448 |
# SPDX-License-Identifier: MIT
# Copyright (C) 2004-2008 Tristan Seligmann and Jonathan Jacobs
# Copyright (C) 2012-2014 Bastian Kleineidam
# Copyright (C) 2015-2021 Tobias Gruetzmacher
from ..scraper import _ParserScraper
from ..helpers import indirectStarter
class GoComics(_ParserScraper):
url = 'https://www.go... | webcomics/dosage | dosagelib/plugins/gocomics.py | Python | mit | 25,793 | [
"Brian"
] | ca8d29e1bde1f940278a38d77dede59ab0761a845fabc6d3ec53923a15c68987 |
#!/usr/bin/env python
#
# $File: ancestralPop.py $
#
# This file is part of simuPOP, a forward-time population genetics
# simulation environment. Please visit http://simupop.sourceforge.net
# for details.
#
# Copyright (C) 2004 - 2010 Bo Peng (bpeng@mdanderson.org)
#
# This program is free software: you can redistribu... | BoPeng/simuPOP | docs/ancestralPop.py | Python | gpl-2.0 | 1,892 | [
"VisIt"
] | 2786bfd32c70f1fe03b642e6876aa2dfe710338aaa0591aecc685b485f579905 |
"""
Basic usage example on a ply mesh. Note that this require a closed, manifold
input mesh.
"""
##
import os
import numpy as np
import mayavi.mlab as mlab
import itertools
import utils
import ply
import meshcut
##
if __name__ == '__main__':
##
example_dir = os.path.join(os.path.dirname(meshcut.__file__), 'ex... | julienr/meshcut | examples/0_cross_section.py | Python | mit | 2,254 | [
"Mayavi"
] | 07390a79283d4e437d366e827d18f333dde22f005d2c63a33cf4c8f40473f7b3 |
#
# gPrime - A web-based genealogy program
#
# Copyright (C) 2002-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2011 Tim G L Lyons
# Copyright (C) 2011 Doug Blank <doug.blank@gmail.com>
#
# This program is free software; you can redistribute it and/or modify
# it un... | sam-m888/gprime | gprime/filters/rules/person/__init__.py | Python | gpl-2.0 | 6,834 | [
"Brian"
] | dd74db8cbe5d1ff5bff3a9df8dd0ef5f30789327520dcd958aff436667b2b19c |
""" This is the guy that actually modifies the content of the CS
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import zlib
import difflib
from diraccfg import CFG
from DIRAC.Core.Utilities import List, Time
from DIRAC.ConfigurationSystem.Client.Config... | ic-hep/DIRAC | src/DIRAC/ConfigurationSystem/private/Modificator.py | Python | gpl-3.0 | 10,681 | [
"DIRAC"
] | e4377fd80c896d21cb7f203e0e41b085bd0683c6c6d2d74686db7dbd762e2142 |
import base64
import hmac
import json
import requests
import time
import datetime
import urllib
import os
import uuid
import re
from hashlib import sha1
from hashlib import md5
def parse_time(timestr):
format = "%Y-%m-%d %H:%M:%S"
return datetime.datetime.fromtimestamp(
time.mktime(time.strptime(times... | kylefrost/yakyik | wipapi/ya.py | Python | gpl-3.0 | 17,475 | [
"Galaxy"
] | fd37a18eb35f14fc791367cbbffd1b14df093943d135a1c7f612423143c3aea5 |
# revlog.py - storage back-end for mercurial
#
# Copyright 2005-2007 Matt Mackall <mpm@selenic.com>
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2 or any later version.
"""Storage back-end for Mercurial.
This provides efficient delta storage with O(1... | seewindcn/tortoisehg | src/mercurial/revlog.py | Python | gpl-2.0 | 63,606 | [
"VisIt"
] | dd665594f865517f8b4f646441d37fd033af117eb04973f6ea3852a4a3f36fb7 |
#
# 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 n... | lhfei/spark-in-action | spark-2.x/src/main/python/mllib/gaussian_mixture_model.py | Python | apache-2.0 | 2,857 | [
"Gaussian"
] | dc481cbe2691393ab353989f951d424e4333436c65ce4cf4b29aee9f38c91bb5 |
#!/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... | eventhero/TiZebraPrint | iphone/build_debug.py | Python | mit | 8,516 | [
"VisIt"
] | 02e50079b687327b3a7f216d8ee6b70c834246d252c04b6ed315f457a3f8a426 |
import json
import urllib.parse
import uuid
import pytest
from ... import core
from ... import exceptions
from ... import parse
def provider_url(config):
qs = urllib.parse.urlencode(
{'configJSON': json.dumps(config, separators=(',', ':'))},
quote_via=urllib.parse.quote)
return ('htt... | pelson/pyggybank | pyggybank/tests/providers/test_testprovider.py | Python | bsd-3-clause | 3,724 | [
"VisIt"
] | 149b0abcce712c7813deb1398250f0718391402ec51706aab52020d8a286c61f |
# $Id$
#
# Copyright (C) 2004-2012 Greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" uses pymol to inter... | rdkit/rdkit-orig | rdkit/Chem/PyMol.py | Python | bsd-3-clause | 7,287 | [
"PyMOL",
"RDKit"
] | ee77bbe435148df19785500eec325bb91b75acf9b3d9235ed91ca3c1c44217a9 |
#!/usr/bin/env python
""" refresh CS
"""
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']
| andresailer/DIRAC | tests/Jenkins/dirac-refresh-cs.py | Python | gpl-3.0 | 244 | [
"DIRAC"
] | 17925f95abb467a7859a16d330b0e613f2fe3c00a50e9718f5e7f656cbfad97b |
## \example atom/charmm_forcefield_verbose.py
# In this example, a PDB file is read in and scored using the CHARMM forcefield. It is similar to the 'charmm_forcefield.py' example, but fully works through each step of the procedure using lower-level IMP classes. This is useful if you want to customize the way in which t... | shanot/imp | modules/atom/examples/charmm_forcefield_verbose.py | Python | gpl-3.0 | 5,965 | [
"CHARMM"
] | c35ee8dccf11d32267f0e2dfb98423b7e832556c0a44fe5c8ef050b0a8db68d2 |
from __future__ import unicode_literals
import re
from pig_util import outputSchema
positive_words = set([
"addicting", "addictingly", "admirable", "admirably", "admire", "admires", "admiring", "adorable",
"adorably", "adore", "adored", "adoring", "amaze", "amazed", "amazes", "amazing",
"angelic", "appeal", "appeale... | pombredanne/jkarn-pub-test | udfs/jython/twitter_sentiment.py | Python | apache-2.0 | 11,150 | [
"exciting"
] | d414e07b1e913752dcc6c727592e45a46658a15b7aef0d741fda6ec2d55c24a6 |
"""
EX_TRISURF3D.PY
Material de apoio para o post "Gráficos tridimensionais no Python
[PARTE I]", no Programando Ciência.
Support material for the blog post "Three-dimensional plots on Python
[PART I]", on Programando Ciência.
* Autor/Author: Alexandre 'Jaguar' Fioravante de Siqueira
* Contato/Contact: http://www.pr... | alexandrejaguar/programandociencia | 20150828-graf3dpython/ex_trisurf3d.py | Python | gpl-2.0 | 3,403 | [
"Jaguar"
] | 6efc0e66516aa5a003b472106d9b2d485ca1b363f9ba8dfb6c91ef7ed29a3d4b |
# 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... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/Statistics/lowess.py | Python | gpl-2.0 | 4,058 | [
"Biopython"
] | eeb929b8ee872917f1e0dad5088ad839caf2b469d5e7199329cb1b6bd00ab403 |
#
# Copyright (C) 2013-2022 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... | espressomd/espresso | testsuite/python/reaction_methods.py | Python | gpl-3.0 | 12,747 | [
"ESPResSo"
] | de7fc1df215ea610b8485abd11c3fe72de3bfaad82f8ed85fb47d9756e8ce5f8 |
# this program corresponds to special.py
### Means test is not done yet
# E Means test is giving error (E)
# F Means test is failing (F)
# EF Means test is giving error and Failing
#! Means test is segfaulting
# 8 Means test runs forever
### test_besselpoly
### test_mathieu_a
### test_mathieu_even_coef
##... | scipy/scipy | scipy/special/tests/test_basic.py | Python | bsd-3-clause | 144,169 | [
"Elk"
] | 7b806fd7597e79a9d8ccd618da160cb51b1a385f3210eaa68c3342ac456111db |
#!/usr/bin/python
#
# Open SoundControl for Python
# Copyright (C) 2002 Daniel Holth, Clinton McChesney
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the Licen... | JohnHowland/kivy | kivy/lib/osc/OSC.py | Python | mit | 11,256 | [
"VisIt"
] | 1ac5773f4fbaa161b4147b06dbd35136acb59699657eeb23d6f87d4494fd613d |
from PyQt5.QtCore import QSettings, QStandardPaths
import os, cPickle
import uuid
class FileCache(object):
"""
A class to help cache objects based on file changes.
The primary use case was the need to cache Yaml data and action syntax
from a MOOSE executable.
This keeps the path of the executable a... | yipenggao/moose | python/peacock/utils/FileCache.py | Python | lgpl-2.1 | 4,532 | [
"MOOSE"
] | f86bdb42c9e89f5c73825d14b51d54430e20d409055aa9ebede61721e333d0b2 |
# Orca
#
# Copyright 2016 Igalia, S.L.
#
# Author: Joanmarie Diggs <jdiggs@igalia.com>
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your o... | GNOME/orca | src/orca/scripts/apps/SeaMonkey/script.py | Python | lgpl-2.1 | 5,046 | [
"ORCA"
] | 01f41de894266e8a81082b4fe5109626cf03c4dfba5cd86e816091855300c485 |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/pbc/scf/ghf.py | Python | apache-2.0 | 4,417 | [
"PySCF"
] | 7880bc7e49b7a5d711707557d81fda015b73e2a9f01c3f40d520ef939976a5d6 |
import glob
import pandas as pd
import numpy as np
pd.set_option('display.max_columns', 50) # print all rows
import os
os.chdir("/gpfs/commons/home/biederstedte-934/evan_projects/correct_phylo_files")
normalB = glob.glob("binary_position_RRBS_normal_B_cell*")
mcell = glob.glob("binary_position_RRBS_NormalBCD19pCD27... | evanbiederstedt/RRBSfun | trees/chrom_scripts/total_chr11.py | Python | mit | 32,998 | [
"MCell"
] | 32cae4977a5a4321ac91b39115998b35c1664e776ee7f7a5a4a345de2eebc266 |
#
# @file TestRDFAnnotationC.py
# @brief RDFAnnotation parser unit tests
#
# @author Akiya Jouraku (Python conversion)
# @author Sarah Keating
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generated automatically by converting the... | TheCoSMoCompany/biopredyn | Prototype/src/libsbml-5.10.0/src/bindings/python/test/annotation/TestRDFAnnotationC.py | Python | bsd-3-clause | 10,162 | [
"VisIt"
] | dd0ff51a404d0e3398ddefe12f6136cf573e0aa1d0fa996490f7e847249f7ac9 |
""" Chemical Signalling model loaded into moose can be save into Genesis-Kkit format """
__author__ = "Harsha Rani"
__copyright__ = "Copyright 2015, Harsha Rani and NCBS Bangalore"
__credits__ = ["NCBS Bangalore"]
__license__ = "GNU GPL"
__version__ = "1.0.0"
__maintainer__ ... | rahulgayatri23/moose-core | python/moose/genesis/_main.py | Python | gpl-3.0 | 31,468 | [
"MOOSE"
] | 026b69aef0c3a27588708fd149baa362a023b8c8b41f508c12d4d5359609e70c |
import sys
import math
sys.path.append('../../../vmdgadgets')
import vmdutil
from vmdutil import vmddef
def rotate_root(frame_no, interval, dir=True):
bone = vmddef.BONE_SAMPLE
bone = bone._replace(name='センター'.encode('shift-jis'))
bone_frames = []
d = 1 if dir else -1
for i in range(4):
y ... | Hashi4/vmdgadgets | sample/lookat/sm31942771/round_floor.py | Python | apache-2.0 | 1,360 | [
"VMD"
] | 5eb607925a449ef6aac775e7e89c5b10ef976e323ee68333412049c55b4e1e7e |
#!/usr/bin/env python
# qm.py -- A Quine McCluskey Python implementation
#
# Copyright (c) 2006-2013 Thomas Pircher <tehpeh@gmx.net>
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to
# deal in the Software ... | jisazaTappsi/shatter | shatter/qm.py | Python | mit | 20,868 | [
"ESPResSo"
] | bf06f54abe32cb467e1c0b855a8027b34ee732d7693de1728309958c56199af7 |
from setuptools import setup, find_packages
import sys, os
here = os.path.abspath(os.path.dirname(__file__))
README = open(os.path.join(here, 'README.rst')).read()
NEWS = open(os.path.join(here, 'NEWS.rst')).read()
version = '0.2.1.2'
install_requires = [ 'PyYAML', 'Mako', 'rpy2',
# List your project dependenci... | xguse/blacktie | setup.py | Python | gpl-3.0 | 1,341 | [
"Bowtie"
] | eae437fda1b727ff6e753a3edf0058149c07381c0d769eca13eba56bd6bce1eb |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# RecuperaPeekFrame.py
#
# Copyright 2014
# Monica Otero <monicaot2001@gmail.com>
# Carlos "casep" Sepulveda <casep@fedoraproject.org>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public Licens... | creyesp/RF_Estimation | STA/helpers/recuperaPeekFrame/RecuperaPeekFrame.py | Python | gpl-2.0 | 2,900 | [
"Gaussian"
] | 3d83cdd40ad98df5ab8f4299b441fd66c449a9b08968e7e91730ad9b7ea93248 |
# test_nsdf.py ---
# Changed from nsdf.py from
# https://github.com/BhallaLab/moose-examples/snippets/nsdf.py
from __future__ import print_function
import numpy as np
from datetime import datetime
import getpass
import os
# Use in-repo moose to install.
import moose
print('using moose from: %s' % moose.__file__)
gl... | subhacom/moose-core | tests/python/test_nsdf.py | Python | gpl-3.0 | 3,504 | [
"MOOSE"
] | aa548e0ef4523e589cb8f3f1971d9a81bcfd80dd79ee1fdab28d6cea29f8e882 |
#!/usr/bin/python
"""
This module contains an OpenSoundControl implementation (in Pure Python), based
(somewhat) on the good old 'SimpleOSC' implementation by Daniel Holth & Clinton
McChesney.
This implementation is intended to still be 'simple' to the user, but much more
complete (with OSCServer & OSCClient classes) ... | brianhouse/wavefarm | housepy/lib/OSC.py | Python | gpl-3.0 | 89,984 | [
"VisIt"
] | 32b474b8b7b9dd5891273342fd45d9a47956b7ebbc4aac371a649fa365516f62 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | rmcgibbo/psi4public | psi4/driver/__init__.py | Python | lgpl-3.0 | 1,603 | [
"Psi4"
] | 57592990df5da2d78c5b8abda04ef758ac894f53747426f5a40cd3cf09ef33e5 |
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