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from __future__ import print_function
__author__ = """Alex "O." Holcombe, Charles Ludowici, """ ## double-quotes will be silently removed, single quotes will be left, eg, O'Connor
import time, sys, platform, os
from math import atan, atan2, pi, cos, sin, sqrt, ceil, radians, degrees
import numpy as np
import psychopy, ... | alexholcombe/dot-jump | dataRaw/Fixed Cue/test_dot-jump27Oct2016_10-15.py | Python | gpl-3.0 | 25,173 | [
"Gaussian"
] | 08e9e585a3b221bd8287d3ead2ffc766d38fd522765de063982461ce0f747311 |
"""
Extended math utilities.
"""
# Authors: Gael Varoquaux
# Alexandre Gramfort
# Alexandre T. Passos
# Olivier Grisel
# Lars Buitinck
# License: BSD 3 clause
from functools import partial
import warnings
import numpy as np
from scipy import linalg
from scipy.sparse import issparse... | eickenberg/scikit-learn | sklearn/utils/extmath.py | Python | bsd-3-clause | 18,804 | [
"Gaussian"
] | aed55e25c4ca764d931e761937ab5f6e974314a96699d5ee0181a393c20b0208 |
from octopus.lib import clcsv
class MasterSheet(object):
HEADERS = {
u'University' : "university",
u'PMCID' : "pmcid",
u'PMID' : "pmid",
u'DOI' : "doi",
u'Publisher' : "publisher",
u'Journal title' : "journal_title",
u'Article title' : "article_title",
... | CottageLabs/oacwellcome | service/sheets.py | Python | apache-2.0 | 3,996 | [
"Octopus"
] | 061ae76d301afcc96dd96a29cd24896742911f4d4ebde77cff8d5ca4faaf7165 |
import string
from binascii import *
import pefile
from common import Modules, load_yara_rules, PEParseModule, ModuleMetadata
from types import StringType
class darkcomet(PEParseModule):
def __init__(self):
md = ModuleMetadata(
module_name="darkcomet",
bot_name="DarkComet",
... | bwall/bamfdetect | BAMF_Detect/modules/darkcomet.py | Python | mit | 5,173 | [
"Brian"
] | b6125ddab91de835b09d64c4bfcc77aa9bf6d414bc1e2263a8a90ec51c5a7bfa |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2004-2007 Donald N. Allingham
# Copyright (C) 2010 Brian G. Matherly
# Copyright (C) 2014 Paul Franklin
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publ... | dermoth/gramps | gramps/gen/display/name.py | Python | gpl-2.0 | 46,057 | [
"Brian"
] | 9a1b93ade9a8b3cef2e9af0cc44b7a5aeee81ceae8b63227e2c6bb753274d246 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: y... | marscher/mdtraj | MDTraj/formats/netcdf.py | Python | lgpl-2.1 | 20,769 | [
"Amber",
"MDTraj",
"NetCDF"
] | 1fd6a93c9d04f9cfd44b4bf4fbf228edf09a90a9747334b0b59c5d9269395c10 |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-compute | tests/unit/gapic/compute_v1/test_addresses.py | Python | apache-2.0 | 90,612 | [
"Octopus"
] | 33a978edefa6998a6bf9751b99d0b336d2822ad4674ae1ccfca326a4cc32111f |
from __main__ import vtk, qt, ctk, slicer
#
# Workflow
#
class Workflow:
def __init__(self, parent):
import string
parent.title = "Bender Workflow"
parent.categories = ["", "Segmentation.Bender"]
parent.contributors = ["Julien Finet (Kitware), Johan Andruejol (Kitware)"]
parent.helpText = string... | 151706061/bender | Modules/Scripted/Scripts/Workflow.py | Python | apache-2.0 | 43,703 | [
"VTK"
] | 9437def75bda48e8409fab5a96863c2be1002c1bbac57c33be4a3ce8006b5cfe |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2002 Gary Shao
# Copyright (C) 2007 Brian G. Matherly
# Copyright (C) 2009 Benny Malengier
# Copyright (C) 2009 Gary Burton
# Copyright (C) 2017 Paul Franklin
#
# This program... | Nick-Hall/gramps | gramps/gen/plug/docgen/basedoc.py | Python | gpl-2.0 | 4,209 | [
"Brian"
] | 39c5d8c7128955e28c72c6113ea04f8e34b611286d4b92a6a05510199e12b47b |
# coding: utf-8
from __future__ import print_function, division, unicode_literals, absolute_import
executable = "optic"
from abimkdocs.variables import ValueWithUnit, MultipleValue, Range
#from abipy.abio.abivar_database.variables import ValueWithUnit, MultipleValue, Range, ValueWithConditions
ValueWithConditions = d... | abinit/abinit | abimkdocs/variables_optic.py | Python | gpl-3.0 | 10,030 | [
"ABINIT"
] | f56ca26a61e9f383cf6f631cbd424044e2f4dd93a6e963111b542f658e07e3df |
#
# LSST Data Management System
# Copyright 2012-2016 LSST Corporation.
#
# This product includes software developed by the
# LSST Project (http://www.lsst.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 So... | lsst/obs_decam | python/lsst/obs/decam/decamMapper.py | Python | gpl-3.0 | 16,121 | [
"VisIt"
] | 47b0dbec71d429586d7cecc0d236c537353784c2c015c4ee1efa3c53d286fa87 |
# -*- coding: utf-8 -*-
#
# mc_neuron.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
#... | weidel-p/nest-simulator | pynest/examples/mc_neuron.py | Python | gpl-2.0 | 7,554 | [
"NEURON"
] | deff1e2209e0d37bab36af99fb8d6937c3d25471ea8b6711631275e685c61475 |
"""On-line (live) plots of the DA process for various models and methods.
Liveplotters are given by a list of tuples as property or arguments in
`dapper.mods.HiddenMarkovModel`.
- The first element of the tuple determines whether the liveplotter is shown if
the names of liveplotters are not given by `liveplots` argum... | nansencenter/DAPPER | dapper/tools/liveplotting.py | Python | mit | 47,673 | [
"DIRAC"
] | cf57058a1d5eefeeb373086db88c35b1aecc92e7e341a15746f51cfd22d20619 |
# Copyright (C) 2016 Alex Nitz
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 3 of the License, or (at your
# option) any later version.
#
# This program is distributed in the ... | tdent/pycbc | pycbc/events/stat.py | Python | gpl-3.0 | 76,829 | [
"Gaussian"
] | 946a72a333c6db7c564c04d8194833dfde0029171c5835f8da30b4e869e3e07b |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
from __future__ import (absolute_import, division, print_function,
unicode_literals)
import itertools
import numpy as np
from numpy.testing import assert_almost_equal, assert_allclose
from ...tests.helper import pytest
from ..con... | joergdietrich/astropy | astropy/convolution/tests/test_kernel_class.py | Python | bsd-3-clause | 18,170 | [
"Gaussian"
] | 7166d0cbfe06d61d0715c85204666fca86d88495755f207c701289c1d1558112 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | skosukhin/spack | var/spack/repos/builtin/packages/r-anaquin/package.py | Python | lgpl-2.1 | 2,253 | [
"Bioconductor"
] | 5cbdd485947f2a59cece148e19b4e20f14307b426649413c0322e02414d8a5fd |
# Orca
#
# Copyright 2010 Consorcio Fernando de los Rios.
# Author: Javier Hernandez Antunez <jhernandez@emergya.es>
# Author: Alejandro Leiva <aleiva@emergya.es>
#
# 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 ... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/orca_gui_profile.py | Python | gpl-3.0 | 5,150 | [
"ORCA"
] | a8e37c37d33d66cf37b4ee8fc67f0ffc3aead30dcbcc68894a7f0081ea036037 |
#!/usr/bin/python
# -*- coding: UTF-8 -*-
#
# Copyright 2014 Google Inc. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.... | pathumego/nototools | nototools/extra_locale_data.py | Python | apache-2.0 | 17,920 | [
"MOE",
"MOOSE"
] | 012924add0a27ac59bbd175ab136c66bfb8c2d437a209f0d95dca98fe31d0153 |
import numpy as np
from gpaw.utilities.memory import maxrss, _VmB
from gpaw.test import equal
verbose = True
dtype = np.int32
def allocate_matrix(maxmem, msize, dtype):
# square matrix in memory (in bytes): byte/bit * bit/int32 * size
mmemory = (1./8 * 32 * msize**2)
mno = int(max(1, maxmem * 2**20/mme... | robwarm/gpaw-symm | gpaw/test/maxrss.py | Python | gpl-3.0 | 1,607 | [
"GPAW"
] | e1afc23b652f20b6860462bbcd15674ac38f76eddc024dc24de076f2e345d858 |
###############################################################################
##
## Copyright 2011-2013 Tavendo GmbH
##
## 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:... | ecohealthalliance/tangelo | tangelo/tangelo/autobahn/websocket.py | Python | apache-2.0 | 146,390 | [
"VisIt"
] | 88a01b3a9211f2ed3c1503df37f7b1a3c89240912a08046e711db458562e9bc1 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2011 Radim Rehurek <radimrehurek@seznam.cz>
# Licensed under the GNU LGPL v2.1 - http://www.gnu.org/licenses/lgpl.html
"""Scikit-learn interface for :class:`~gensim.models.tfidfmodel.TfidfModel`.
Follows scikit-learn API conventions to facilitate using g... | midnightradio/gensim | gensim/sklearn_api/tfidf.py | Python | gpl-3.0 | 6,995 | [
"VisIt"
] | 5d5e039168977617fe2e2dfb4740d1e3db381a76993cd86b80bb2f1c37b00d64 |
# This file is part of ocean2pism.
# ocean2pism 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.
# ocean2pism is distributed in the ho... | matthiasmengel/ocean2pism | DiffuseOcean.py | Python | gpl-3.0 | 9,469 | [
"NetCDF"
] | d3bc22a7f8d72af9e2deabbc63b22a823ad6178a5a6e56921bfcc0f385f4363a |
#=============================================
# Test cases for module
#=============================================
if __name__ == '__main__':
# Test case for the code. Calculate few well-known crystals
import sys
import numpy
from math import pow
from matplotlib.pyplot import plot, show,... | jochym/Elastic | tests/test_elastic.py | Python | gpl-3.0 | 6,441 | [
"ASE",
"CRYSTAL",
"VASP"
] | 504d33aa733e76efdf48fb35011eeb0ae1b1cee1339dee56bdab42d7fa4ec2ec |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | MOA-2011/e2openplugin-OpenWebif | plugin/controllers/views/web/servicelistreload.py | Python | gpl-2.0 | 5,251 | [
"VisIt"
] | 00a71a9e37ee332a03e20d792d15ad1f5056a0b7ee9a7d25328eb213e361497e |
#!/usr/bin/python
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 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... | dgasmith/psi4 | doc/sphinxman/document_psifiles.py | Python | lgpl-3.0 | 3,196 | [
"Psi4"
] | 91318ce06b2a9d337623ebecf25d03d195ae9b858c0c288899fc989feae63669 |
'''
Set up Visual Sudio to build a specified MPIR configuration
Copyright (C) 2011, 2012, 2013, 2014 Brian Gladman
'''
from __future__ import print_function
from operator import itemgetter
from os import listdir, walk, unlink, makedirs
from os.path import split, splitext, isdir, relpath, join, exists
from os.path imp... | omco/mpir | build.vc12/mpir_config.py | Python | lgpl-3.0 | 31,121 | [
"Brian"
] | 7cc710d8d89a57b18d28ea2b3f43874f79f2612dc639e4f8481070852fd7718f |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007-2008 Brian G. Matherly
#
# Adapted from GraphViz.py (now deprecated)
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2005-2006 Eero Tamminen
# Copyright (C) 2007 Johan Gonqvist <johan.gronqvist@gmail.com>
# Contr... | Forage/Gramps | gramps/plugins/graph/gvrelgraph.py | Python | gpl-2.0 | 27,200 | [
"Brian"
] | 66f44f5b7d77aca3766595026241fcc45f52a19cf83c77372d1e3f75e76514ee |
# Copyright (c) 2019, NVIDIA CORPORATION. All rights reserved.
#
# This work is licensed under the Creative Commons Attribution-NonCommercial
# 4.0 International License. To view a copy of this license, visit
# http://creativecommons.org/licenses/by-nc/4.0/ or send a letter to
# Creative Commons, PO Box 1866, Mountain ... | microsoft/DiscoFaceGAN | metrics/perceptual_path_length.py | Python | mit | 5,225 | [
"VisIt"
] | 64a748264b38fdee4304a3d692fe6b52077a738e4a8a3183fffa272e840708a2 |
from builtins import range
import numpy as np
def affine_forward(x, w, b):
"""
Computes the forward pass for an affine (fully-connected) layer.
The input x has shape (N, d_1, ..., d_k) and contains a minibatch of N
examples, where each example x[i] has shape (d_1, ..., d_k). We will
res... | UltronAI/Deep-Learning | CS231n/assignment2/cs231n/layers.py | Python | mit | 29,675 | [
"NEURON"
] | bc97cab78799b47f9c1d67c889d0d3351ab869c44e45a849432868c59a75be53 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkDataObjectWriter(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
v... | nagyistoce/devide | modules/vtk_basic/vtkDataObjectWriter.py | Python | bsd-3-clause | 492 | [
"VTK"
] | 04308e37b1bc4ceec90b3c16f81ace2b5ff184f969abe6fbaf274926d6cccb11 |
#!/usr/bin/env python
#
# Copyright (c) 2000 Autonomous Zone Industries
# This file is licensed under the
# GNU Lesser General Public License v2.1.
# See the file COPYING or visit http://www.gnu.org/ for details.
#
### standard modules
import types
### our modules
true = 1
false = 0
from MojoErrors import Bad... | zooko/egtp | common/DataTypes.py | Python | agpl-3.0 | 16,644 | [
"VisIt"
] | c66ac41e55a1390d882f4fbd9a3dc6eedb5fcea6f7831ccf1bffbd92b891f261 |
#
# Copyright (C) 2001 greg Landrum
#
""" unit testing code for compound descriptors
"""
from __future__ import print_function
import unittest
import Parser
from rdkit.six.moves import xrange
class TestCase(unittest.TestCase):
def setUp(self):
print('\n%s: ' % self.shortDescription(), end='')
self.piec... | jandom/rdkit | rdkit/ML/Descriptors/UnitTestParser.py | Python | bsd-3-clause | 1,956 | [
"RDKit"
] | c938a20a1ad25b8e2a87a9c0b93c0007a08f5bc900b92e85cc145ba25366696c |
from abc import ABC, abstractmethod
from collections.abc import Iterable
from numbers import Real
from xml.etree import ElementTree as ET
import numpy as np
import openmc.checkvalue as cv
from .._xml import get_text
from ..mixin import EqualityMixin
_INTERPOLATION_SCHEMES = [
'histogram',
'linear-linear',
... | walshjon/openmc | openmc/stats/univariate.py | Python | mit | 25,080 | [
"Gaussian"
] | 68a9f4ed8809c7a1d1a3e5b2df3052f99c0e5923d59da1050034864d24d851f7 |
#!/usr/bin/env python3
#pylint: disable=missing-docstring
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
... | nuclear-wizard/moose | python/chigger/tests/nemesis/nemesis.py | Python | lgpl-2.1 | 926 | [
"MOOSE",
"VTK"
] | 025a98794e29201ce21949de1793f385df35acd1ad547259b068493c57179851 |
"""Function-like object creating monoclinic lattices.
The following lattice creator is defined:
SimpleMonoclinic
BaseCenteredMonoclinic
"""
from ase.lattice.triclinic import TriclinicFactory
import numpy as np
from ase.data import reference_states as _refstate
class SimpleMonoclinicFactory(TriclinicFactory)... | grhawk/ASE | tools/ase/lattice/monoclinic.py | Python | gpl-2.0 | 1,678 | [
"ASE",
"CRYSTAL"
] | 252024845c66218229e23fe0984c6e9d383df460ff27f640ec0f50b09a166d94 |
from paraview import servermanager
from time import time
import timeit
import pickle
filename = "test.bench"
file = open(filename, 'w')
if not servermanager.ActiveConnection:
connection = servermanager.Connect()
coneSource = servermanager.sources.ConeSource()
shrinkFilter = servermanager.filters.ShrinkFilter(Input=c... | TACC/GLuRay | Benchmarks/glurayBench1.py | Python | gpl-2.0 | 721 | [
"ParaView"
] | 4225ab824d40ee1e34c885796cb02ab8d101b8cad325bd2d883b1531ea486d95 |
import pytest
import random
from collections import deque
from rig.geometry import concentric_hexagons
from rig.place_and_route.machine import Machine
from rig.links import Links
from rig.place_and_route.routing_tree import RoutingTree
from rig.routing_table import Routes
from rig.place_and_route.route.utils im... | project-rig/rig | tests/place_and_route/route/test_ner.py | Python | gpl-2.0 | 22,680 | [
"VisIt"
] | a3ce0a37ed95e1c2969ba6a64437a40f912236605cc68edc43211145ad47727a |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Moogli Visualizer.
"""
# http://stackoverflow.com/questions/28104362/how-to-rotate-camera-in-openscenegraphwalk-through-in-model
from PyQt4 import QtGui
from PyQt4 import QtCore
from PyQt4 import Qt
from PyQt4.QtGui import QPushButton
from PyQt4.QtGui import QWidget
f... | dilawar/moose-full | moose-examples/util/moogli_viewer.py | Python | gpl-2.0 | 11,854 | [
"MOOSE",
"NEURON"
] | 0bcda16cc0061a22f4ceaec0561b29ec4482629daecf3018e99f99f46829aab9 |
from traceHandler import *
from modelHandler import *
from optimizerHandler import *
from string import replace
from optionHandler import optionHandler
from string import find,count
from scipy.interpolate import interp1d
from scipy import linspace
import time
def meanstdv(x):
from math import sqrt
n, mean, st... | vellamike/optimizer | optimizer/Core.py | Python | lgpl-2.1 | 27,534 | [
"NEURON"
] | ace0a6cd2886a64c4d6051ca2c7362e3bfa1266b60ca276332601049fb5417b3 |
###############################################################################
##
## Copyright (C) 2006-2011, University of Utah.
## All rights reserved.
## Contact: contact@vistrails.org
##
## This file is part of VisTrails.
##
## "Redistribution and use in source and binary forms, with or without
## modification, ... | CMUSV-VisTrails/WorkflowRecommendation | vistrails/packages/vtk/vtkhandler.py | Python | bsd-3-clause | 8,683 | [
"VTK"
] | 22b248f3915a4abba69a8ba10b3a5b8629d524774713c822899e2d2b7c7b4d0f |
## 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/AmberParmBuilder.py | Python | gpl-3.0 | 23,741 | [
"Amber"
] | b15c8f15666ab29d5f59e6b3150deaa890958d4cb01d15bc2848b6f87da6a478 |
#Copyright 2015 Daniel Gusenleitner, Stefano Monti
#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 t... | montilab/Hydra | hydra_pkg/module_helper.py | Python | apache-2.0 | 13,618 | [
"Bioconductor",
"HTSeq"
] | 8e69cf1ebcf464d1fdd32d28ffed1939e7dfc7fecab5e6c6879cafde003148ce |
import numpy as np
import random as rand
import sys, os
import copy
import pickle
from mpi4py import MPI
from pymatgen import Lattice, Structure, Element
from pymatgen.io.vasp import Poscar, VaspInput
from pymatgen.analysis.structure_matcher import StructureMatcher, FrameworkComparator
from pymatgen.apps.borg.hive imp... | skasamatsu/py_mc | examples/HAp-bulk/HAp_energylist.py | Python | gpl-3.0 | 3,940 | [
"VASP",
"pymatgen"
] | b468a4527d9cd6e69ed3cc50a03c41d5192a12dc1db79b1f56635eca500c5899 |
#!/usr/bin/env python
# pylint: disable=C0303,W0612,C0303,C0111,C0301
"""
Tests for new ErMagicBuilder
"""
from builtins import str
import unittest
import os
from pmagpy import pmag
from pmagpy import builder2 as builder
from pmagpy import validate_upload2 as validate_upload
# set constants
WD = pmag.get_test_WD()
... | Caoimhinmg/PmagPy | pmagpy_tests/test_builder.py | Python | bsd-3-clause | 75,288 | [
"Gaussian"
] | 197fde8684454b6608b570f5f39375a039f3cc1235e9ebb9fe1d9359e458e118 |
"""Class definitions for rts2pa"""
# (C) 2004-2012, Markus Wildi, wildi.markus@bluewin.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; either version 2, or (at your option)
# ... | RTS2/rts2 | scripts/rts2pa/rts2pa.py | Python | lgpl-3.0 | 7,960 | [
"VisIt"
] | 4aa8d0b20f9faf58d8539d32db9fdec8430af2385ac8e318c13612c99d00cf29 |
#!/usr/bin/python
import random
import sys
if len(sys.argv) != 4:
print "Usage: generate.py <rows> <dimensions> <centers>"
sys.exit(1)
numRow = int(sys.argv[1])
numDim = int(sys.argv[2])
numCenter = int(sys.argv[3])
random.seed(0)
if 0:
# uniform random
rows = []
for row in range(1, numRo... | nmldiegues/tuner-icac14 | tuner-selective/kmeans/inputs/generate.py | Python | apache-2.0 | 912 | [
"Gaussian"
] | 110b7f0fcca14cedba1e669b6354327f8741565205f05b459d0d6fc16facf8f9 |
# -*- coding: utf-8 -*-
"""
SUNTANS particle tracking
Created on Wed Apr 17 09:54:48 2013
@author: mrayson
"""
from sunpy import Spatial, Grid
import othertime
#from trisearch import TriSearch
from gridsearch import GridSearch
from datetime import datetime,timedelta
from scipy import spatial, sparse
import numpy a... | UT-CWE/Hyospy | Hyospy_ensemble/lib/SUNTANS/SUNTANS/suntrack.py | Python | mit | 49,700 | [
"Mayavi",
"NetCDF",
"VTK"
] | abfb0afcc06a9ac85280fe141f0d04ac875e6f5d95cc794057fce6d93f002ad7 |
# Copyright (C) 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 versio... | KaiSzuttor/espresso | testsuite/python/rotational-diffusion-aniso.py | Python | gpl-3.0 | 16,657 | [
"ESPResSo"
] | e184411143584a530de9168940b8f879c8f809babb0b1077289afe209222d18c |
#pylint: disable=missing-docstring
#################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simulation Environment #
# #
# (c) 2010... | liuwenf/moose | python/chigger/exodus/__init__.py | Python | lgpl-2.1 | 1,323 | [
"MOOSE"
] | cbbd5447609d76a95ae0f165f0438dcbe945003c776e61aa0dfdd94b0d5b402a |
from __future__ import absolute_import
from django.db import connection
from django.template import RequestContext, loader
from django.utils.html import mark_safe
from django.shortcuts import render_to_response
from django.core import urlresolvers
from django.http import HttpResponseNotFound
from zerver.decorator impo... | atomic-labs/zulip | analytics/views.py | Python | apache-2.0 | 25,603 | [
"VisIt"
] | 99edecea0fcc56e2e783892d30e1ab75fc6721ba65fb2ddb9460d9ddd08ad268 |
# Copyright (C) 2011-2013 2ndQuadrant Italia (Devise.IT S.r.L.)
#
# This file is part of Barman.
#
# Barman 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... | klhochhalter/barman | barman/cli.py | Python | gpl-3.0 | 16,011 | [
"ESPResSo"
] | f136c169feaead25b823c5b22094c5fbe752791a7a4da5e7290cac6af8178c55 |
#!/usr/bin/python3
# Copyright (C) 2013-2016 Florian Festi
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
#... | florianfesti/boxes | boxes/generators/rotary.py | Python | gpl-3.0 | 13,569 | [
"FEFF"
] | 1b45c48164b5d73adcfca10a435a320b988cd7cd63f84dc5ddbe273c01ef7755 |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
"""An iterator for GCoder objects that accepts a GCodeVisitor
"""
import logging
__author__ = "wireddown"
LOGGER_NAME = "iterator"
PRINTED_LAYER_KIND = "PRINTED"
PARSED_LAYER_KIND = "parsed"
class GCodeIteratorInformation(object):
"""This class is a simple POD tha... | zeograd/gcodeutils | gcodeutils/visit/iterator.py | Python | gpl-2.0 | 3,178 | [
"VisIt"
] | 3421a6f6d1c27cd2b82cec046f5e55857d95a31dfed29364089a323652e89a66 |
# -*- coding: utf-8 -*-
#
# This file is part of DoMapping.
# Copyright (C) 2015, 2016 CERN.
#
# DoMapping 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)... | inveniosoftware/es-jsonschema | domapping/mapping.py | Python | gpl-2.0 | 15,216 | [
"VisIt"
] | f1508e160ab21a321b6c5a0397db4bfa85f3f68584dbf78acf9280fb1a6410c3 |
"""
pylint-server
----
A small Flask application to keep keep track of pylint reports and ratings
on a per-repository basis.
"""
from setuptools import setup
setup(
name='pylint-server',
version='0.1',
url='https://github.com/drivet/pylint-server/',
license='MIT',
author='Desmond Rivet',
auth... | drivet/pylint-server | setup.py | Python | mit | 1,072 | [
"Desmond"
] | 525812c7338b81b20eecf9ed3798cfb52fd2295b0b762d088f831057f24691c6 |
#
# @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 program is free software; you can redistribute it and/or modify
# it under the terms of ... | kratman/psi4public | psi4/driver/qcdb/libmintspointgrp.py | Python | gpl-2.0 | 58,396 | [
"Psi4"
] | c02349403a4a200e6bb723c5efc276b164e850f306c5a8541a06d6517412fc63 |
"""Loading and plotting data from CSV logs.
Schematic example of usage
- load all `log.csv` files that can be found by recursing a root directory:
`dfs = load_logs($BABYAI_STORAGE)`
- concatenate them in the master dataframe
`df = pandas.concat(dfs, sort=True)`
- plot average performance for groups of runs using ... | mila-iqia/babyai | babyai/plotting.py | Python | bsd-3-clause | 13,893 | [
"Gaussian"
] | aaa45e42c0f83c914cd7d68a047aaed5fc02c6eeb809639b2ebdc121eb4df0d0 |
#!/usr/bin/python2.4
import Scientific.IO.NetCDF as nc
import numpy as np
import sys
if len(sys.argv) != 2 or '-h' in sys.argv or '--help' in sys.argv:
print "\nUsage:\tcompare.py <file.nc>\n"
print "Author:\tHannu Parviainen"
print "\thannu.p.parviainen@helsinki.fi\n"
sys.exit(1)
file... | dronir/EM | test/xrfip/compare.py | Python | gpl-3.0 | 1,027 | [
"NetCDF"
] | 55060569ff52a75b54d124ab4c7e0e024fd8716397e8331a9d1e13f395c72387 |
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | gkc1000/pyscf | pyscf/nao/m_sv_diag.py | Python | apache-2.0 | 975 | [
"PySCF"
] | 599da83ca988d42f54b4d66c589d1c8d0f7164db4a58d724f8e8fd8cd705d4c4 |
# Copyright 2016 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... | meteorcloudy/tensorflow | tensorflow/contrib/autograph/pyct/static_analysis/cfg.py | Python | apache-2.0 | 15,711 | [
"VisIt"
] | 4f5d597d9753c1741259ed90fc30432e139de52e88bbcf6c8b82178f51e5e2d8 |
from __future__ import print_function
import os
import numpy as np
try:
import vtk
from vtk.util.numpy_support import vtk_to_numpy
except BaseException:
pass
def calculate_vtk_max_pointwise_difference(file1, file2, tol=1e-6):
arrays = [0] * 2
reader = vtk.vtkStructuredPointsReader()
for i, fn... | KonradBreitsprecher/espresso | testsuite/tests_common.py | Python | gpl-3.0 | 16,337 | [
"Gaussian",
"VTK"
] | 7538074f06c2a1cfba2252f02de27466b71d812349abf7c9bcb76f6bb4407671 |
# Copyright (C) 2007-12 Andrea Vedaldi and Brian Fulkerson.
# All rights reserved.
#
# This file is part of the VLFeat library and is made available under
# the terms of the BSD license (see the COPYING file).
import numpy as np
from cyvlfeat.misc.cykdtreebuild import cy_kdtreebuild
from cyvlfeat.test_util import len... | simmimourya1/cyvlfeat | cyvlfeat/misc/kdtreebuild.py | Python | bsd-2-clause | 2,028 | [
"Brian"
] | e24b7dbc396a066ac936d5f09c86a1b7a060e1135415c3335a2dc70b73f9010e |
"""
build_SIM_with_deposits.py
Create an augmented version of the SIM model (Godley & Lavoie Chapter 3), but with deposits added.
Since we do not have a central bank sector, this falls short of the model PC specifcation (Chapetr 4).
Copyright 2016 Brian Romanchuk
Licensed under the Apache License, Version 2.0 (the ... | brianr747/SFC_models | sfc_models/examples/scripts/ex20161206_SIM_with_deposits.py | Python | apache-2.0 | 3,226 | [
"Brian"
] | 8ceb36b903e32b2071f525ccca0d60aa92cb4601bae7b38fadddd200971be19f |
# Copyright 2017 Max Planck Society
# Distributed under the BSD-3 Software license,
# (See accompanying file ./LICENSE.txt or copy at
# https://opensource.org/licenses/BSD-3-Clause)
"""Training AdaGAN on various datasets.
Refer to the arXiv paper 'AdaGAN: Boosting Generative Models'
Coded by Ilya Tolstikhin, Carl-Joha... | tolstikhin/adagan | celeba_pot.py | Python | bsd-3-clause | 8,109 | [
"Gaussian"
] | ca0cc13ac9659a17284f30e5417ed92f691abc37824d357966c531ec19ea287e |
"""
Generate samples of synthetic data sets.
"""
# Authors: B. Thirion, G. Varoquaux, A. Gramfort, V. Michel, O. Grisel,
# G. Louppe
# License: BSD 3 clause
from itertools import product
import numbers
import numpy as np
from scipy import linalg
from ..utils import array2d, check_random_state
from ..utils i... | mrshu/scikit-learn | sklearn/datasets/samples_generator.py | Python | bsd-3-clause | 40,741 | [
"Gaussian"
] | 742a8f92331d5ad17136cae0c2eef77e628dbe6146b2436233fc576cbc2e517f |
"""
Don't drop points with invalid coordinates - there's currently no keyword arg for this
"""
from cis.data_io.products import cis
import logging
class cis_no_postproc(cis):
def create_data_object(self, filenames, variable):
data = self.create_coords(filenames, variable)
# This is pretty hacky b... | duncanwp/cis_plugins | cis_no_postproc.py | Python | lgpl-3.0 | 2,180 | [
"NetCDF"
] | 666c8f5e712e64afdd4f64d3e3ab723eacc8df6bd1ab4c64d5939db9d944876b |
"""
Do the initial configuration of a DIRAC component
"""
__RCSID__ = "$Id$"
from DIRAC import gConfig
from DIRAC import exit as DIRACexit
from DIRAC.ConfigurationSystem.Client.Helpers import getCSExtensions
from DIRAC.FrameworkSystem.Client.ComponentInstaller import gComponentInstaller
gComponentInstaller.exitOnErr... | andresailer/DIRAC | tests/Jenkins/dirac-cfg-add-option.py | Python | gpl-3.0 | 1,425 | [
"DIRAC"
] | c3909cb2a7da3ca1df6e9f0d06ed1885299b8bc43460c67c7d827e4af1597cf5 |
"""
Add link from history_dataset_association to the extended_metadata table
"""
from sqlalchemy import *
from sqlalchemy.orm import *
from migrate import *
from migrate.changeset import *
from galaxy.model.custom_types import JSONType
import logging
log = logging.getLogger( __name__ )
metadata = MetaData()
extende... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py | Python | gpl-3.0 | 1,567 | [
"Galaxy"
] | e32dd85a3cccc947e27e7b988f4de3db5fde627b0a645051069930761d77ad9d |
#!/usr/bin/python
########################################################################
# 9 Jan 2015
# Patrick Lombard, Centre for Stem Stem Research
# Core Bioinformatics Group
# University of Cambridge
# All right reserved.
########################################################################
import argparse
... | pdl30/pyngspipe | pyngspipe/pipeline.py | Python | gpl-2.0 | 8,122 | [
"HTSeq"
] | e60e228468c9a7ed042cac23c354943e13c3acdeb961af72a56c81619d651556 |
#!/usr/bin/env python
__author__ = 'Mike McCann'
__copyright__ = '2013'
__license__ = 'GPL v3'
__contact__ = 'mccann at mbari.org'
__doc__ = '''
Master loader for all October 2014 SIMZ activities.
John Ryan
MBARI 12 March 2014
@var __date__: Date of last svn commit
@undocumented: __doc__ parser
@status: pr... | josephmfaulkner/stoqs | stoqs/loaders/MolecularEcology/loadSIMZ_spring2014.py | Python | gpl-3.0 | 5,645 | [
"NetCDF"
] | eedb145f4d3b77d224c404755186839a9b7ce177a42f6af9360a1e0c9dd7341a |
from sympy import *
from mpmath import *
from util import *
from emulation import *
def fit(n, q, f_D, D, h, start):
def f(x):
x = Matrix(map(lambda y: exp(mpf(y)/2.), x))
a = A(D, x)
a_inv = a**-1
return -log(pi_star_tau(n, q, f_D, a_inv, a, H(D, h)))
tau = minimize(f, start, ... | greenape/gem-module | gaussianemulation/emulator.py | Python | mpl-2.0 | 2,200 | [
"Gaussian"
] | 31c1b19f57ec6be85569069976a12146a4106ae5baf542bfde7acea1aba79346 |
#import numpy
import POVME.packages.pymolecule.pymolecule as pymolecule
import POVME.packages.binana.peel as peel
import sys
#print sys.modules
my_params = peel.defaultParams
#DEFAULT
#arg = pymolecule.FileIO.load_pdb_into( 'arg.pdb', bonds_by_distance=True, serial_reindex = True, resseq_reindex=False)
arg = pymol... | POVME/POVME | POVME/packages/binana/tests/peel_arg_basic/argTest.py | Python | mit | 1,318 | [
"VMD"
] | 944bb0d1846df21b4dac4f0c83ce0742e7fc2e51dbb26dd5f9f524dd4289a5eb |
from ship import Ship
##############################################################################
##############################################################################
class Liner(Ship):
##########################################################################
def __init__(self, startplanet, gala... | dwagon/Exodus | liner.py | Python | gpl-3.0 | 2,194 | [
"Galaxy"
] | 1dd7e44f9c57750b00b48c8cb962f1be9673b762a4ba4c06652ebf1a7834bcb8 |
import pandas as pd
from sklearn.ensemble import RandomForestClassifier
from sklearn.ensemble import GradientBoostingClassifier
from sklearn.ensemble import BaggingClassifier
from sklearn.ensemble import AdaBoostClassifier
from sklearn.ensemble import ExtraTreesClassifier
from sklearn.neural_network import MLPClassifie... | rupakc/Kaggle-Compendium | Predicting Red Hat Business Value/redhat-baseline.py | Python | mit | 3,644 | [
"Gaussian"
] | 03df9e77ac5a6839f50c49cb9bbd538f85e53a032d5fa25dcaa39cd1fe82fe79 |
#!/usr/bin/python2.7
# encoding: utf-8
from __future__ import division
import numpy as np
import pandas as pd
import cPickle as pkl
#import netCDF4 as nc
#Quick fix
import scipy.io.netcdf as nc
from scipy.io import savemat
from scipy.io import loadmat
from datetime import datetime, timedelta
import cPickle as pickle... | pwcazenave/PySeidon | pyseidon/validationClass/validationClass.py | Python | agpl-3.0 | 18,652 | [
"NetCDF"
] | 3e117d7cd6599fa7876ce6c3385d4c6a0707b36458354581453bfa5993b7b068 |
import RenascenceBasic
class Content:
def __init__(self, nativeContent=None, producer=None):
self.producer = producer
if None == nativeContent:
self.nativeContent = RenascenceBasic.GP_Contents_CreateCollector()
elif isinstance(nativeContent, int) or isinstance(nativeContent, floa... | jxt1234/Genetic-Program-Frame | python-renascence/module/Renascence.py | Python | apache-2.0 | 12,562 | [
"ADF"
] | de817413f729fa0ca4ddcd46b7a362216749f0c3a710777db750970cb65facc5 |
"""
aspheric_fit
tests for rough surface generation & analysis
inputs: P
output: some plots
Functions translated from:
http://www.mysimlabs.com/surface_generation.html
MODIFICATION HISTORY:
20150910 srio@esrf.eu, written
"""
__author__ = "Manuel Sanchez del Rio"
__contact... | srio/dabam | code/correlated_profiles.py | Python | gpl-2.0 | 6,197 | [
"Gaussian"
] | b52e9d324d2598ca42ac713b81cb9451fc8bb7aa318b0e5aa63c08cac99263a3 |
#!/usr/bin/env python3
from distutils.core import setup
setup(name='Extracthosts',
version='2.0.0',
description='Extracts IPs and domain names from files',
author='Brian Wallace',
author_email='bwall@ballastsecurity.net',
url='https://github.com/bwall/ExtractHosts',
packages=['Extr... | bwall/ExtractHosts | setup.py | Python | mit | 360 | [
"Brian"
] | 531b4d095f41406a2b57fda04a02164071021db856b77f783d0d8b8eb23a0809 |
import os
from pypdflite.pdflite import PDFLite
from pypdflite.pdfobjects.pdfcolor import PDFColor
def HtmlTest(test_dir):
writer = PDFLite(os.path.join(test_dir, "tests/HTMLtest.pdf"))
document = writer.get_document()
document.add_text('Sample text')
document.add_newline(2)
red = PDFColor(name... | katerina7479/pypdflite | bin/htmltest.py | Python | mit | 2,915 | [
"VisIt"
] | 658d52744049ae193ce2ef727cb0124d521dbc565075405638d0c29d87e65e6d |
from __future__ import print_function
from owmeta_core.dataobject import DatatypeProperty, ObjectProperty, This
from .channel import Channel
from .biology import BiologyType
from .cell_common import CELL_RDF_TYPE
class Cell(BiologyType):
"""
A biological cell.
All cells with the same `name` are conside... | openworm/PyOpenWorm | owmeta/cell.py | Python | mit | 2,514 | [
"BLAST"
] | d0011fb12aed3b029bf8c51a38d2bee21cd8d3f638a103582b4db2b66eb5fe07 |
# Copyright (C) 2016 Henrique Pereira Coutada Miranda
# All rights reserved.
#
# This file is part of yambopy
#
#
import subprocess
import json
from abc import ABCMeta, abstractmethod
from textwrap import dedent
from copy import deepcopy
import os
class Scheduler():
"""
Generic scheduler class
Initialize... | palful/yambopy | schedulerpy/scheduler.py | Python | bsd-3-clause | 9,273 | [
"ABINIT"
] | 4dfac80c22402eb23e5411f5844daf21a38c9dc7709fb5e0720910f7fb5b3fe9 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import os
import shutil
import unittest
import numpy as np
from pymatgen.core.structure import Structure
from pymatgen.io.cif import CifParser
from pymatgen.io.feff.inputs import Atoms, Header, Potential, Tags
from pymatgen... | materialsproject/pymatgen | pymatgen/io/feff/tests/test_sets.py | Python | mit | 11,086 | [
"FEFF",
"pymatgen"
] | 09393c9edd888fdae89e15c08077537d615b2b103dce17510be07311d4aa2918 |
###############################################################################
# Copyright 2006 to the present, Orbitz Worldwide, LLC.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at... | OrbitzWorldwide/droned | droned/droneclient.py | Python | apache-2.0 | 5,757 | [
"BLAST"
] | b9e218a7eab4587bbc472224ab28fd24d430cb46ec4f9c0cb3c44379d285e6c2 |
#/usr/bin/env python
# Global python import
import exceptions, logging, random, sys, threading, time, os
# Update python path to have ParaView libs
build_path='/Volumes/SebKitSSD/Kitware/code/ParaView/build-ninja'
sys.path.append('%s/lib'%build_path)
sys.path.append('%s/lib/site-packages'%build_path)
# iPython impor... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/Applications/ParaView/Testing/Python/TestPythonMPI.py | Python | gpl-3.0 | 1,816 | [
"ParaView",
"VTK"
] | 729f85141710b71c1d111244a2c50ab2ac021dc3d065771824e77566e161d683 |
# Copyright (c) 2014-present PlatformIO <contact@platformio.org>
#
# 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 appli... | platformio/platformio | platformio/project/config.py | Python | apache-2.0 | 16,512 | [
"VisIt"
] | 7a491c5d13bd3435a9296a1c6563715cc92212969e4f1dce032b12644899a296 |
# test_reader.py ---
#
# Filename: test_reader.py
# Description:
# Author:
# Maintainer:
# Created: Wed Jul 24 16:02:21 2013 (+0530)
# Version:
# Last-Updated: Sun Apr 17 16:13:01 2016 (-0400)
# By: subha
# Update #: 112
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
#
#
# Cha... | subhacom/moose-core | python/moose/neuroml2/test_reader.py | Python | gpl-3.0 | 5,210 | [
"MCell",
"MOOSE",
"NEURON"
] | b8fd88207f6024478797be04dfdb5c450ae7b849b8ed31f0eb0de719ad5686e4 |
# Copyright 2016 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.
"""Generates reports base on bisect result data."""
import copy
_CONFIDENCE_THRESHOLD = 99.5
_BISECT_REPORT_TEMPLATE = """
===== BISECT JOB RESULTS =====
... | SummerLW/Perf-Insight-Report | dashboard/dashboard/bisect_report.py | Python | bsd-3-clause | 3,611 | [
"VisIt"
] | ba1968f082d4fac513df0bc33115113a9b9b8d64d29642d3e678a5f05c5159f1 |
# Copyright (c) 2012 OpenStack Foundation
# 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 ... | badock/nova | nova/tests/compute/test_resource_tracker.py | Python | apache-2.0 | 61,240 | [
"exciting"
] | 0a40b51b1788c0e9ec831afa508884e790a1ca0a6538378927fd758538980e1f |
"""Skeleton for 'os.path' stdlib module."""
import sys
import os
def abspath(path):
"""Return a normalized absolutized version of the pathname path.
:type path: bytes | unicode | os.PathLike
:rtype: bytes | unicode
"""
return path
def basename(path):
"""Return the base name of pathname pa... | asedunov/intellij-community | python/helpers/python-skeletons/os/path.py | Python | apache-2.0 | 6,242 | [
"VisIt"
] | b9d2cec585d8b0198ef67f187ea2e82e9151ba0e2d9af7c2b02571c2464bbe97 |
'''Visitors that perform data analysis on signals
.. currentmodule:: grid_cell_model.visitors.signals
These could be membrane potentials, voltage clamp data, synaptic currents, etc.
Classes
-------
.. inheritance-diagram:: grid_cell_model.visitors.signals
:parts: 2
.. autosummary::
AutoCorrelationVisitor
... | MattNolanLab/ei-attractor | grid_cell_model/visitors/signals.py | Python | gpl-3.0 | 11,625 | [
"NEURON",
"VisIt"
] | 9d2c4a78bf0ae3d5da966591e38ae1834b5e8a67389741129183e6ed65bac4d4 |
#
# Coded by Vali, updated by Mirakels for openpli
#
from enigma import iServiceInformation, eServiceCenter, iPlayableService, iPlayableServicePtr
from Components.Converter.Converter import Converter
from Components.Element import cached
from Components.config import config
from Tools.Transponder import ConvertToHuma... | devclone/enigma2-9f38fd6 | lib/python/Components/Converter/pliExpertInfo.py | Python | gpl-2.0 | 13,802 | [
"Galaxy"
] | 71b69ef06da180dbaaf526c52ba1e74d03adaec179c93a1d5606464524e01ad5 |
#
# Copyright 2016 Universidad Complutense de Madrid
#
# This file is part of Megara DRP
#
# Megara DRP 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) an... | Pica4x6/megaradrp | megaradrp/simulation/instrument.py | Python | gpl-3.0 | 12,342 | [
"Gaussian"
] | 588381fb1d800a5131fc252d11ed333d267ad16790bcfbb74eb1cbdb454421e4 |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-apigee-connect | tests/unit/gapic/apigeeconnect_v1/test_tether.py | Python | apache-2.0 | 47,293 | [
"Octopus"
] | 1d0943dcec1bbd1c0e3e4ce65dc557229d3f6a08855ee82edaf0d76ec823dafe |
from aiida import load_dbenv
load_dbenv()
from aiida.orm import Code, DataFactory
import numpy as np
StructureData = DataFactory('structure')
ParameterData = DataFactory('parameter')
codename = 'lammps_optimize@boston'
############################
# Define input parameters #
############################
# GaN
ce... | abelcarreras/aiida_extensions | plugins/launcher/launch_lammps_optimization_gan.py | Python | mit | 3,755 | [
"LAMMPS"
] | 26daa8b6f52faa72ce9200abc86be19bd2cdc8de09b5dc4f6796a0c3c283d004 |
########################################################################
# $HeadURL$
# File : CloudDirector.py
# Author : Victor Mendez
########################################################################
#DIRAC
from DIRAC import S_OK, S_ERROR, gConfig
#VMDIRAC
from VMDIRAC.Resources.Cloud.VMDirector ... | vmendez/VMDIRAC | Resources/Cloud/CloudDirector.py | Python | gpl-3.0 | 3,561 | [
"DIRAC"
] | 1d9c78d5658089c9dd4c811f5fa6675b75f1baefb328785aa56ff1e460f145ac |
"""
Database of molecules outside the G2_1 set
"""
molecule_names = ['Be2','C7NH5','BDA','biphenyl','C60']
data = {
'Be2': {
'description': "Diatomic Beryllium",
'name': "Be_2",
'enthalpy': 155.1,
'ZPE': 1.0000,
'thermal correction': 5.0600,
'symbols': 'BeBe',
'magmoms': None,
'positi... | grhawk/ASE | tools/ase/data/extra_molecules.py | Python | gpl-2.0 | 7,220 | [
"GPAW"
] | 4806cbdadbfd9533043bb822302f428f550023af3d978bf346650e09e274fcc4 |
import copy
import board, model
from legacy.common import all_different
import p2w.nodes
PATTERNS = {
'Star': [(1, 1), (1, -1), (-1, 1), (-1, -1)],
'BigStar': [(2, 2), (2, -2), (-2, 2), (-2, -2)],
'Cross': [(0, 1), (0, -1), (-1, 0), (1, 0)],
'BigCross': [(0, 2), (0, -2), (-2, 0), (2, 0)],
'Wheel':... | dturevski/olive-gui | yacpdb/indexer/analyzers/trajectories.py | Python | gpl-3.0 | 10,258 | [
"VisIt"
] | c34f554d8a472e9c0233aad585d0178b493fe688b3c3eb5c142e041897a6c6b9 |
#!/usr/bin/env python
### cut a fasta query (arg1) in "nbPart" (passed by aprun)
### subFasta files and launches a blast+ program (arg3)
### vs the bank (arg2) for each subfasta and then
### concatenates the tab delimited blast results in
### one file. You can add any additional blast+ option in the
### arg4 with quote... | alunem/bioman | blast/bmn-mpiBlastHopper.py | Python | gpl-2.0 | 4,865 | [
"BLAST"
] | e450e4df60568d5edf372615736bc3ff8ee1e53f93ab22aca9b212b914766343 |
## Automatically adapted for numpy.oldnumeric Jun 27, 2008 by -c
from rdkit import RDConfig
import unittest
from rdkit.ML.InfoTheory import rdInfoTheory
try:
from rdkit.ML.InfoTheory import BitClusterer
except ImportError:
BitClusterer=None
from rdkit.ML.Data import DataUtils
from rdkit import DataStructs
import r... | rdkit/rdkit-orig | rdkit/ML/InfoTheory/testCorrMatGen.py | Python | bsd-3-clause | 3,376 | [
"RDKit"
] | e81fa7ae234d38a1c37839a14c90f65b376a1b8e7f8b89672609aaf2070cdf27 |
# 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
##... | niknow/scipy | scipy/special/tests/test_basic.py | Python | bsd-3-clause | 129,612 | [
"Elk"
] | fe42f035d052fcc9a4935e74e8ffa6b410dcc7c29d19e606b5d4691c8533608e |
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