text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
value | license stringclasses 15
values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
"""
This module contains data structures and container classes that are used by OVITO's modification pipeline system.
**Data collection:**
* :py:class:`DataCollection` (a container for data objects and attributes)
**Data objects:**
* :py:class:`DataObject` (base of all data object types)
* :py:class:`Bonds`
... | srinath-chakravarthy/ovito | src/plugins/pyscript/python/ovito/data/__init__.py | Python | gpl-3.0 | 15,914 | [
"ASE",
"LAMMPS",
"OVITO"
] | 10a814fafb818f542045c230e611c38294c5844f96c6b285e75ba7113f7a437c |
import os
import numpy as _np
import pychemia
__author__ = "Guillermo Avendano-Franco"
__copyright__ = "Copyright 2016"
__version__ = "0.1"
__maintainer__ = "Guillermo Avendano-Franco"
__email__ = "gtux.gaf@gmail.com"
__status__ = "Development"
__date__ = "May 16, 2016"
def read_kpoints(path='KPOINTS'):
"""
... | MaterialsDiscovery/PyChemia | pychemia/code/vasp/kpoints.py | Python | mit | 3,040 | [
"CRYSTAL",
"VASP"
] | fc05f9f0aeadbd39bd747622480d2fc8233e50ebc190aa5a06303a6055452353 |
# ============================================================================
#
# Copyright (C) 2007-2010 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | kurtraschke/camelot | camelot/core/resources.py | Python | gpl-2.0 | 3,141 | [
"VisIt"
] | 3337c2be04a0c77fc63af7b3f84b8d6de35ec2b213a8faf32e0e5f5d7fee1cd3 |
# Solar Envelope
# Provides two solar envelopes as both a 3d point grid and a polysurface given a filtered list of suns and a border line representing the building site
# The first (Solar Rights envelope) represents the maximum heights in which new masses could be placed in a given site withought interfering with the s... | boris-p/ladybug | src/Ladybug_SolarEnvelope.py | Python | gpl-3.0 | 19,935 | [
"EPW"
] | e3efe8e0f780ae48754bbb5bec068e586b4c08d1d68eb8b98ce3fc1253606427 |
#!/usr/bin/env python
#pylint: disable=missing-docstring
#################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simulation Environment #
# #... | yipenggao/moose | python/chigger/tests/error/time_timestep.py | Python | lgpl-2.1 | 1,032 | [
"MOOSE"
] | c9d22e6b2dc1a55df29dee106423f79da7589d2d50e6af530b36f5e8335c89fa |
# vim: tabstop=4 shiftwidth=4 softtabstop=4
# 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.a... | bclau/nova | nova/tests/compute/test_resource_tracker.py | Python | apache-2.0 | 38,685 | [
"exciting"
] | 33fd2e8e6e79e59e165ff991cd9001d3a704b412d9489b5276a19bc3ea8c7ce4 |
import numpy as np
from scipy.stats import kstest, norm
class LinearRegression(object):
'''Ordinary Least Squares...'''
def __init__(self, X, y, fit_intercept=True):
self.X = X
self.y = y
self.fit_intercept = fit_intercept
self._coeff = None
def fit(self, check_residuals=T... | jeffcarter-github/MachineLearningLibrary | MachineLearningLibrary/Regression/LinearRegression.py | Python | mit | 2,075 | [
"Gaussian"
] | eb3664046c168a2613eaf68ff933921a6d2b731c1d166a4c6b008272e93b08da |
# coding: utf-8
"""
Vericred API
Vericred's API allows you to search for Health Plans that a specific doctor
accepts.
## Getting Started
Visit our [Developer Portal](https://developers.vericred.com) to
create an account.
Once you have created an account, you can create one Application for
Production and an... | vericred/vericred-python | test/test_state_network_size_response.py | Python | apache-2.0 | 10,105 | [
"VisIt"
] | 7e8487cf0614dc9f892603dc5e30ddaf251f3eb5db94f86353d6665813636e3b |
# The contents of this file are subject to the Common Public Attribution
# License Version 1.0. (the "License"); you may not use this file except in
# compliance with the License. You may obtain a copy of the License at
# http://code.reddit.com/LICENSE. The License is based on the Mozilla Public
# License Version 1.1, ... | h2oloopan/easymerge | EasyMerge/tests/reddit/r2/r2/controllers/front.py | Python | mit | 61,772 | [
"VisIt"
] | 33e416e3d1d5ad0398429f67186db1643bb300c21e921d26a6b3a3b2fd39f1e0 |
import warnings
from collections import defaultdict
import numpy as np
import pandas as pd
from .coding import strings, times, variables
from .coding.variables import SerializationWarning, pop_to
from .core import duck_array_ops, indexing
from .core.common import contains_cftime_datetimes
from .core.pycompat import i... | pydata/xarray | xarray/conventions.py | Python | apache-2.0 | 30,727 | [
"NetCDF"
] | b6a5a7679ff048dd71bc27c185424d58713d4921b1575c03995ad410116488ea |
from vtk import *
from vtk.wx.wxVTKRenderWindowInteractor import wxVTKRenderWindowInteractor
import thread
import wx
import pydicom
import os
class VtkPanel(wx.Panel):
def __init__(self, parent):
wx.Panel.__init__(self, parent)
self.parent = parent
# Top Sizer Configuration
self.t... | gabrielmini/vtkDicomRender | main.py | Python | lgpl-3.0 | 12,916 | [
"VTK"
] | 903c94660f57695409edd96b99a2658d3e039d7954b47c41417dedce827eab2b |
from datetime import datetime
from abc import ABCMeta, abstractmethod
import argparse
import os.path
import numpy as np
import gdal
import netCDF4
import yaml
from eodatasets import serialise
from ingester.utils import _get_nbands_lats_lons_from_gdalds
EPOCH = datetime(1970, 1, 1, 0, 0, 0)
class BaseNetCDF(object)... | omad/datacube-experiments | ingester/netcdf_writer.py | Python | bsd-3-clause | 14,297 | [
"NetCDF"
] | 84dffde0baac5bc1dc57e7e7aa16fca3c49aa93d775f8e69ecb25468228f2324 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import unittest
import os
import json
import numpy as np
from pymatgen.analysis.structure_matcher import StructureMatcher, \
ElementComparator, FrameworkC... | Bismarrck/pymatgen | pymatgen/analysis/tests/test_structure_matcher.py | Python | mit | 31,701 | [
"pymatgen"
] | ac3b9e70bbed3681dc8aa1f24fd1db0f9bf6ac8a3f7903cf24b1dc2162870d92 |
"""
Tests for ConvMolFeaturizer.
"""
from __future__ import division
from __future__ import unicode_literals
__author__ = "Han Altae-Tran and Bharath Ramsundar"
__copyright__ = "Copyright 2016, Stanford University"
__license__ = "MIT"
import unittest
import os
import sys
import numpy as np
import rdkit
from deepchem... | Agent007/deepchem | deepchem/feat/tests/test_graph_features.py | Python | mit | 3,858 | [
"RDKit"
] | 4ae04ea0cd3f2f5d10b5dece394c00fb6ae9fc27156c7019aa6294b28d894bf7 |
# Copyright 2021, Google LLC. 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | google-research/federated | distributed_dp/fl_utils.py | Python | apache-2.0 | 6,642 | [
"Gaussian"
] | 322e30244572e40a322d8fa261265f17dd652d2c66f4efee9543462d3a45c872 |
"""Generate the StageIV "daily" file at 12z."""
import datetime
import os
import sys
import numpy as np
from pyiem.util import ncopen, logger
LOG = logger()
BASEDIR = "/mesonet/data/stage4"
def init_year(ts):
"""Create a new NetCDF file for a year of our specification!"""
# Get existing stageIV netcdf file ... | akrherz/iem | scripts/iemre/init_stage4_daily.py | Python | mit | 2,555 | [
"NetCDF"
] | 0c0c7ec066a29b2b0a4004fd044f1ae6bbdca08a719b71d274f49831544d41ff |
from collections import OrderedDict
import logging
import os
import simtk.unit as units
from intermol.utils import which, run_subprocess
CRM_PATH = ''
logger = logging.getLogger('InterMolLog')
# --------- energy evaluation methods ---------- #
# this dict hasn't been upated yet:
key_dict = {'ENERgy': 'Potential',
... | ctk3b/InterMol | intermol/charmm/__init__.py | Python | mit | 7,699 | [
"CHARMM",
"CRYSTAL"
] | 95e01809d31fb560c2287cf907366c016eecd715f81e8f23aacbb1fbf93138d6 |
"""A that shows a slice at a specified radius
"""
# Author: Martin Weier
#Copyright (C) 2006 California Institute of Technology
#This program is free software; you can redistribute it and/or modify
#it under the terms of the GNU General Public License as published by
#the Free Software Foundation; either version 2 of... | geodynamics/citcoms | visual/Mayavi2/original_plugins/plugins/filter/CitcomSshowSurface.py | Python | gpl-2.0 | 6,990 | [
"Mayavi"
] | 4e0dc8abc3d802b2fbe19152480af8511a495502d8628a757df63a755655b733 |
# Licensed under GPL version 3 - see LICENSE.rst
'''Gratings made by the MKI `Space Nanotechnology Laboratory`_
The MIT Kavli Institute for Astrophysics and Space Research
`Space Nanotechnology Laboratory`_ produces elements for astronomical
instruments in space. One particular field of research are critical
angle tra... | hamogu/marxs | marxs/missions/mitsnl/catgrating.py | Python | gpl-3.0 | 16,691 | [
"Gaussian"
] | de61b9f982846afff872039a0e47bae1f9be5c7c8840996f010e18af1286b1da |
# mount.py
#
# Copyright (C) 2011-2015 Red Hat, Inc.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program... | rhinstaller/lorax | src/pylorax/mount.py | Python | gpl-2.0 | 3,658 | [
"Brian"
] | bd4bb794b88b612c7752f14efa941bb160745eb1eea2a831312d9df192e98dff |
from validate_app import validateApp
import os
from distutils import spawn
import sys
from parse_files import parseOutMapping, bringTogether
from bashSub import bashSub
def checkPreprocessApplications():
applications = ["bwa", "samtools", "bowtie2"]
source = ["http://bio-bwa.sourceforge.net/", "http://samtoo... | msettles/expHTS | expHTS/mappingCMD.py | Python | apache-2.0 | 8,155 | [
"BWA",
"Bowtie"
] | 8909d3ec3df2b30887af5f783521b2c743a32b322c15db3d47d06a6792ff8a22 |
# 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/lb_electrohydrodynamics.py | Python | gpl-3.0 | 2,426 | [
"ESPResSo"
] | 3022ff8212a6f3b8fc0adc3600a2133165d77a1ce6b463aaf99e6b14e8d175b9 |
from __future__ import print_function
import json
import os
import os.path
import re
import sys
import warnings
from collections import defaultdict
from distutils.command.build_scripts import build_scripts as BuildScripts
from distutils.command.sdist import sdist as SDist
try:
from setuptools import setup, find... | Dhivyap/ansible | setup.py | Python | gpl-3.0 | 12,900 | [
"Galaxy"
] | d27f137b12765bc81e00c84a8ba782dbaffb7f5ba0684b5c17c8b3d54d885ef4 |
# This component assembles an analysis recipe for the annual adaptive comfort component
#
# Honeybee: A Plugin for Environmental Analysis (GPL) started by Mostapha Sadeghipour Roudsari
#
# This file is part of Honeybee.
#
# Copyright (c) 2013-2015, Chris Mackey <Chris@MackeyArchitecture.com>
# Honeybee is free softw... | samuto/Honeybee | src/Honeybee_PMV Comfort Analysis Recipe.py | Python | gpl-3.0 | 38,894 | [
"EPW"
] | 4182565de5271371141c4e2a167b9a6379b8773114fc32c00dd78aa98785b4b2 |
"""
Testing for the forest module (sklearn.ensemble.forest).
"""
# Authors: Gilles Louppe,
# Brian Holt,
# Andreas Mueller,
# Arnaud Joly
# License: BSD 3 clause
import pickle
from collections import defaultdict
from itertools import product
import numpy as np
from scipy.sparse import csr_... | djgagne/scikit-learn | sklearn/ensemble/tests/test_forest.py | Python | bsd-3-clause | 35,292 | [
"Brian"
] | 57fef763d2ca99aebf2837d9a40f3cf6be67be52fba85c4eb28d021cbca015e6 |
#!/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/symm/test/test_basis.py | Python | apache-2.0 | 6,887 | [
"PySCF"
] | f8ad14f0c50dad2252409169dde1960b8be38dc4b5cae3484470715325bc3642 |
"""Gaussian Mixture Model."""
# Author: Wei Xue <xuewei4d@gmail.com>
# Modified by Thierry Guillemot <thierry.guillemot.work@gmail.com>
# License: BSD 3 clause
import numpy as np
from scipy import linalg
from .base import BaseMixture, _check_shape
from ..externals.six.moves import zip
from ..utils import check_arra... | vortex-ape/scikit-learn | sklearn/mixture/gaussian_mixture.py | Python | bsd-3-clause | 27,921 | [
"Gaussian"
] | 636e9c50d12c3689fd4a7171a5e1c058786fb3db60f5ab0f1e55102ace155328 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module contains the error classes for the chemenv package.
"""
__author__ = "David Waroquiers"
__copyright__ = "Copyright 2012, The Materials Project"
__credits__ = "Geoffroy Hautier"
__version__ = "... | richardtran415/pymatgen | pymatgen/analysis/chemenv/utils/chemenv_errors.py | Python | mit | 2,241 | [
"pymatgen"
] | 642d085eb541283a3a59a2225df1e6387c113ebd0c1601281407bd8f60388b82 |
import logging
from numpy.lib.twodim_base import diag, eye
from numpy.ma.core import asarray
import os
from os.path import expanduser
from pickle import dump
from independent_jobs.tools.Log import Log
from kameleon_mcmc.distribution.Gaussian import Gaussian
from kameleon_mcmc.mcmc.MCMCChain import MCMCChain
from kamel... | karlnapf/ozone-roulette | ozone/scripts/sample_ozone_posterior_ground_truth.py | Python | bsd-2-clause | 1,847 | [
"Gaussian"
] | f4fc6481642a979fbd43f7f0784b72dbb80655b36ffa2878c6fcfb50cc1edc78 |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
from PyQt5.... | nuclear-wizard/moose | python/peacock/Execute/JobRunner.py | Python | lgpl-2.1 | 4,858 | [
"MOOSE"
] | b62237dfdb05c769f49ad138b93112756f2e6428e20120ebff537b9284cff1f2 |
#!/usr/bin/env python
import sys
import gfxprim.core as core
import gfxprim.loaders as loaders
import gfxprim.filters as filters
def progress_callback1(perc):
sys.stdout.write("\rloading %3.2f%%" % perc)
sys.stdout.flush()
return 0
def progress_callback2(perc, args):
sys.stdout.write("\r%s %3.2f%%" ... | gfxprim/gfxprim | demos/py_simple/progress_callback.py | Python | lgpl-2.1 | 923 | [
"Gaussian"
] | f021bd22d824f463b97bc83a9f38a11d1dede0edb537b701aca94bb310f5f674 |
# vim: expandtab ts=4 sw=4 sts=4 fileencoding=utf-8:
#
# Copyright (C) 2007-2010 GNS3 Development Team (http://www.gns3.net/team).
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License version 2 as
# published by the Free Software Foundation;
#
#... | GNS3/gns3-legacy | src/GNS3/Workspace.py | Python | gpl-2.0 | 88,589 | [
"VisIt"
] | 248604573f918623d20b788d06fcbb8cab5c41b74a66a57fd4e49dd2314208dc |
#===============================================================================
#
# CPP11Profile.py
#
# This file is part of ANNarchy.
#
# Copyright (C) 2016-2018 Julien Vitay <julien.vitay@gmail.com>,
# Helge Uelo Dinkelbach <helge.dinkelbach@gmail.com>
#
# This program is free software: you can ... | vitay/ANNarchy | ANNarchy/generator/Profile/CPP11Profile.py | Python | gpl-2.0 | 12,173 | [
"NEURON"
] | 3d79594263045b171f71194d0c89222e1073ff7c3ab6b8bd59e527ba01c34416 |
import random
def GenerateSlug():
colors = ['red', 'blue', 'white', 'yellow', 'green', 'black', 'orange']
numbers = ['1','2','3','4','5','6','7','8','9']
words = ['monkey', 'cow', 'chicken', 'bull', 'moose','hawk', 'lion', 'rat', 'dog', 'cat']
return random.choice(colors) + random.choice(numbers) + ran... | zwernberg/polls | polls/helpers.py | Python | mit | 337 | [
"MOOSE"
] | 7399e109a39b337883e055e68f62371bf8a1b8ad25473022639b471d9a33e101 |
""" This integration test only need the TaskQueueDB
(which should of course be properly defined also in the configuration),
and connects directly to it
Run this test with::
"python -m pytest tests/Integration/WorkloadManagementSystem/Test_TaskQueueDB.py"
Suggestion: for local testing, run th... | ic-hep/DIRAC | tests/Integration/WorkloadManagementSystem/Test_TaskQueueDB.py | Python | gpl-3.0 | 40,691 | [
"DIRAC"
] | b71c7ce281e9124c888b101fca93e74cd4041165dbcd1b9647c9072febbf08a7 |
"""
Functions to operate on polynomials.
"""
from __future__ import division, absolute_import, print_function
__all__ = ['poly', 'roots', 'polyint', 'polyder', 'polyadd',
'polysub', 'polymul', 'polydiv', 'polyval', 'poly1d',
'polyfit', 'RankWarning']
import re
import warnings
import numpy.core.... | unnikrishnankgs/va | venv/lib/python3.5/site-packages/numpy/lib/polynomial.py | Python | bsd-2-clause | 38,572 | [
"Gaussian"
] | a9326df8c6ed8277261c353791dfbd102262e7f13c5e0e0e97d564a90d4b1ae9 |
"""
View for Courseware Index
"""
# pylint: disable=attribute-defined-outside-init
import logging
import urllib
from django.conf import settings
from django.contrib.auth.models import User
from django.contrib.auth.views import redirect_to_login
from django.urls import reverse
from django.http import Http404
from dja... | ahmedaljazzar/edx-platform | lms/djangoapps/courseware/views/index.py | Python | agpl-3.0 | 23,447 | [
"VisIt"
] | 6344fef8431df495c7cbd88bc01a071aadf53b4aca73233794af37314205f53b |
#!/usr/bin/env python
"""Script for checking the ABINIT automatic tests."""
from __future__ import print_function, division, absolute_import #, unicode_literals
import sys
import os
from pprint import pprint
from optparse import OptionParser
try:
from cStringIO import StringIO
except ImportError:
from io imp... | jmbeuken/abinit | tests/check_testsuite.py | Python | gpl-3.0 | 6,283 | [
"ABINIT"
] | 63a1b8baa1c50f71fbaafc7a459ac65b24a0a28ae0aa86b97b03c8620aae26e1 |
########################################################################
#
# (C) 2015, Chris Houseknecht <chouse@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 Fo... | veger/ansible | lib/ansible/galaxy/login.py | Python | gpl-3.0 | 4,553 | [
"Galaxy"
] | e7b2a247d63b741e996660c58acd4d185b534653d17d1259a01186874e98d1cc |
__author__ = 'Zhouhao Zeng'
import HTSeq
import sys
from optparse import OptionParser
import numpy
import collections
def getSiteBodyProfile(ga, site_iv_set, genic_partition):
profile = collections.defaultdict(lambda: numpy.zeros(genic_partition, numpy.float64))
for site_name, site_iv in site_iv_set:
... | zhouhaozeng/bioinformatics-codebase | profile/generate_profile_matrix_around_sites.py | Python | gpl-3.0 | 13,148 | [
"HTSeq"
] | adaeab9426c08cf2d73bae39b18b281df0a1c0970850b12d4d666af6ea5ba49f |
# -*- coding: utf-8 -*-
#
# Mayavi documentation build configuration file, created by
# sphinx-quickstart on Sat Apr 12 23:25:24 2008.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# The contents of this file are pickled, so don't put values in the namespace
# that aren't pickleab... | liulion/mayavi | docs/source/mayavi/conf.py | Python | bsd-3-clause | 5,275 | [
"Mayavi"
] | 28a2e79705e62ceb692d1d5352c866d8a4e37a6e931c0a8c688ac41e98783532 |
# proxy module
from __future__ import absolute_import
from mayavi.filters.elevation_filter import *
| enthought/etsproxy | enthought/mayavi/filters/elevation_filter.py | Python | bsd-3-clause | 100 | [
"Mayavi"
] | d346d8fdd635163fe9385f28dc2ed35ac73150157cf23ba8413fd9fc2b1b8de8 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
sessions2trash.py
Run this script in a web2py environment shell e.g. python web2py.py -S app
If models are loaded (-M option) auth.settings.expiration is assumed
for sessions without an expiration. If models are not loaded, sessions older
than 60 minutes are removed. U... | pouyana/teireader | webui/scripts/sessions2trash.py | Python | mit | 7,574 | [
"VisIt"
] | 1e47a21b33e00f6c5a8d7743434d7cfe1ca2f3f9d1ab69cfae758f7ab5ac0526 |
# -*- coding: utf-8 -*-
import os
# App to demonstrate NearestNeighbor queries in action
import Tkinter
from kdtree import *
class KDTreeApp:
def __init__(self):
"""App for creating KD tree dynamically"""
self.tree = KDTree()
self.match = None
self.redraw = False
self.s... | NicovincX2/Python-3.5 | Algorithmique/Structure de données/Arbre (structure de données)/Arbre kd/app_nn.py | Python | gpl-3.0 | 3,778 | [
"VisIt"
] | db8f29ab20b655f73c23678d5de2e0a94ac03e5ef2f90afa75a68c4b3c39b60a |
import numpy as np
from gpaw.utilities import unpack
from gpaw.utilities.blas import gemm
import gpaw.mpi as mpi
class LCAO:
"""Eigensolver for LCAO-basis calculation"""
def __init__(self, diagonalizer=None):
self.diagonalizer = diagonalizer
# ??? why should we be able to set
# this d... | qsnake/gpaw | gpaw/lcao/eigensolver.py | Python | gpl-3.0 | 3,584 | [
"GPAW"
] | 987c40e5b6699132466d5da5503f5273ac4649bec848379a9bae2c2dd9137f36 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright: (c) 2013, Jeroen Hoekx <jeroen.hoekx@dsquare.be>, Alexander Bulimov <lazywolf0@gmail.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ =... | andmos/ansible | lib/ansible/modules/system/lvol.py | Python | gpl-3.0 | 19,500 | [
"Firefly"
] | 024d2a98807f9e526c6e3e5a22fc370a3fbf5b9bd253cbc33044dc82fb579f01 |
import re
import string
import os.path
import os
import shutil
import multiprocessing
import pysam
import pprint
import time
class Fasta(object):
def __init__(self, fa=''):
if os.path.isfile(fa):
self.filename = fa
else:
raise RuntimeError("Fasta: \'{:s}\' is not found".for... | soh-i/Ivy | src/Ivy/io/fasta.py | Python | gpl-2.0 | 6,403 | [
"pysam"
] | 9ae1a87386982ea43eed9aca7fa2258c30e8a4db3c37e65f6342df6247df77af |
# Authors: Matti Hämäläinen <msh@nmr.mgh.harvard.edu>
# Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Eric Larson <larson.eric.d@gmail.com>
# Lorenzo De Santis <lorenzo.de-santis@u-psud.fr>
#
# License: BSD (3-clause)
# The computations in this code were primarily derived from Matti Häm... | kambysese/mne-python | mne/bem.py | Python | bsd-3-clause | 76,981 | [
"Mayavi"
] | be7529ca8c5244b4781f48647ef11058e228f423845514101ebff6e9d1fd1c1e |
# -*- coding: utf-8 -*-
# Copyright: Michal Krassowski <krassowski.michal@gmail.com>
# License: GNU GPL, version 3 or later; http://www.gnu.org/copyleft/gpl.html
"""
This plugin adds the function of night mode, similar that one implemented in AnkiDroid.
It adds a "view" menu entity (if it doesn't exist) with options l... | krassowski/Anki-Night-Mode | night_mode/night_mode.py | Python | gpl-3.0 | 9,919 | [
"VisIt"
] | f746406168961a7d075fb0bf776f74a2f1154f0c26747ff37f0d84f5a98c1b46 |
#A* -------------------------------------------------------------------
#B* This file contains source code for the PyMOL computer program
#C* copyright Schrodinger LLC.
#D* -------------------------------------------------------------------
#E* It is unlawful to modify or remove this copyright notice.
#F* -------------... | gratefulfrog/lib | python/chempy/mol2.py | Python | gpl-2.0 | 7,901 | [
"ChemPy",
"PyMOL"
] | 6814ee7a1fbc594236aab3a14d0de538a181aa2d23d09980959b57b8bc242fdf |
# $HeadURL$
'''
:mod: Pfn
.. module: Pfn
:synopsis: pfn URI (un)parsing
.. moduleauthor:: Krzysztof.Ciba@NOSPAMgmail.com
'''
__RCSID__ = "$Id:$"
## imports
import os
## from DIRAC
from DIRAC import S_OK, S_ERROR, gLogger
def pfnunparse( pfnDict ):
"""
Create PFN URI from pfnDict
:param dict pfnDict: ... | miloszz/DIRAC | Core/Utilities/Pfn.py | Python | gpl-3.0 | 4,092 | [
"DIRAC"
] | f75ff1e517035f1188021a56b638548123ce390164bfead3292e010bc7435af6 |
"""
.. moduleauthor:: Johan Comparat <johan.comparat__at__gmail.com>
General purpose:
................
The class StellarPopulationModel is a wrapper dedicated to handling the fit of stellar population models on observed spectra.
It gathers all inputs : from the model and from the data.
*Imports*::
import numpy as... | JohanComparat/pySU | spm/python/StellarPopulationModel.py | Python | cc0-1.0 | 21,167 | [
"Galaxy"
] | 246238fbd1f3617fa5ef415c3442b29e8f9679c4a28ba4b9cc8258b23d96cba8 |
from ase.io import read
from ase.units import kJ
from ase.utils.eos import EquationOfState
configs = read('Ag.traj@0:5') # read 5 configurations
# Extract volumes and energies:
volumes = [ag.get_volume() for ag in configs]
energies = [ag.get_potential_energy() for ag in configs]
eos = EquationOfState(volumes, energie... | grhawk/ASE | tools/doc/tutorials/eos/eos2.py | Python | gpl-2.0 | 397 | [
"ASE"
] | aa64d5b5f16dc0fc730fb34dfa00060045e3063a0cf415c39afea22ad45ee18c |
#!/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/enigma2-plugin-extensions-openwebif | plugin/controllers/views/ajax/config.py | Python | gpl-2.0 | 16,871 | [
"VisIt"
] | ea436159956728c653f11524b33da28aa03fd9fb9fdea350433c0dfb8ce6d830 |
# This file is part of Merlin/Arthur.
# Merlin/Arthur is the Copyright (C)2009,2010 of Elliot Rosemarine.
# Individual portions may be copyright by individual contributors, and
# are included in this collective work with permission of the copyright
# owners.
# This program is free software; you can redistribute it an... | d7415/merlin | Arthur/views/scans/galaxy.py | Python | gpl-2.0 | 3,022 | [
"Galaxy"
] | 4eb3af429eb0f07bf9f4d3d2d700e59aff929680bfd36b7cd3822a9bc3f36e1b |
"""
makebamindex
~~~~~~~~~~~~
:Description: Use PySAM to make bam index
"""
# Use PySAM to make bam index
import pysam
import os
import sys
import logging
import coloredlogs
logger = logging.getLogger('iCallSV.makebamindex')
coloredlogs.install(level='DEBUG')
def MakeIndex(bamFile):
"""
This will make bam i... | rhshah/iCallSV | iCallSV/makebamindex.py | Python | apache-2.0 | 992 | [
"pysam"
] | 4f80ece5e4ced9bdb627d5e1e153d154a87e5fe4089838991744de6f0769603b |
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2007-2014, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public version 2.1 or later. ... | Clyde-fare/cclib | test/testnuclear.py | Python | lgpl-2.1 | 1,511 | [
"cclib"
] | bcdc24773af5dc269b26308a65d4d7ab47004381d37a071888a40a1cb3a44f65 |
"""
Convolution functions.
Used for generating the kernel used in convolutional gridding.
We actually paramerize the functions at initialization and return a simple
callable with one parameter, the distance in pixels.
This allows us to pass the convolution routine the minimum of extra parameters.
"""
from __future__... | SKA-ScienceDataProcessor/FastImaging-Python | src/fastimgproto/gridder/conv_funcs.py | Python | apache-2.0 | 4,357 | [
"Gaussian"
] | 566947f0fbce41f643ea941fb6de6d66d4c28c552a2f5e7c4dfbf01a93112840 |
from __future__ import division
from __future__ import absolute_import
import numpy as np
from numpy.random import random
na = np.newaxis
import scipy.stats as stats
import scipy.special as special
import scipy.linalg
from scipy.misc import logsumexp
from numpy.core.umath_tests import inner1d
from . import general
fro... | michaelpacer/pybasicbayes | pybasicbayes/util/stats.py | Python | mit | 10,647 | [
"Gaussian"
] | 22894175816674f40aac8448e1afb7be47baf585839853edf335f3382269246e |
# -*- coding: utf-8 -*-
from nodes import *
class Network:
"""A class to represent a Variational Bayesian Network.
Arguments
----------
nodes - list
the nodes in the network
Attributes
----------
nodes - list
Pointers to instances of all the nodes contained in the network
Notes
----------
It is p... | jameshensman/pyvb | src/pyvb/network.py | Python | gpl-3.0 | 3,265 | [
"Gaussian"
] | 719cf7ce97ec8d2996e809bf2f8b77629e33c21d07f12a29a9585a3a9da94450 |
# -*- coding: utf-8 -*-
# Copyright 2007-2011 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy 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... | sillvan/hyperspy | hyperspy/signal.py | Python | gpl-3.0 | 185,611 | [
"Gaussian"
] | 55432fb62acb49e32dbe5ba96ea5d9eafded671ca63d7cc07fe9da9602bd03f3 |
#!/usr/bin/env python
'''
This file contains the input/output for the HMM.
The functions that read the human made HMM definitions and
their parsing.
In order to build an HMM from scratch we need this package
'''
# A copy of Fariselli's original code extended for Gaussian Mixture Models.
# Here the observations are not... | arthurfait/HMM-3 | hmm/HMM_IO.py | Python | gpl-3.0 | 28,226 | [
"Gaussian"
] | cd45375e69d7a5d9349c0ef32016c960c921f86eeb6e72a8208f5ce3e5d92b4b |
import numpy as np, SimPEG as simpeg, vtk, sys, os, time
import vtk.util.numpy_support as npsup
import polydata, extraction
# Functions that take any vtkData object as input.
# Function in vtk to work with dataset
def thresholdCellId2vtp(vtkObj,ind):
"""
Function to return polygon from a cell in a data ... | grosenkj/telluricpy | telluricpy/vtkTools/dataset.py | Python | mit | 3,517 | [
"VTK"
] | 8843884eee63073cd4265cb3c0db7c0b595bc705bc29e6e0babe670e4c40660d |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import six
import os
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Utilities.List import stringListToString, intListToString
from DIRAC.DataManagementSystem.DB.FileCatalogComponents.FileMa... | yujikato/DIRAC | src/DIRAC/DataManagementSystem/DB/FileCatalogComponents/FileManager/FileManagerFlat.py | Python | gpl-3.0 | 13,929 | [
"DIRAC"
] | 878965fc9b82643521c0732869f5eaad1c996e33f6d803527d2755e496616217 |
from anndata import AnnData
from typing import Optional
from ._dpt import _diffmap
from .._utils import AnyRandom
def diffmap(
adata: AnnData,
n_comps: int = 15,
neighbors_key: Optional[str] = None,
random_state: AnyRandom = 0,
copy: bool = False,
):
"""\
Diffusion Maps [Coifman05]_ [Hagh... | theislab/scanpy | scanpy/tools/_diffmap.py | Python | bsd-3-clause | 2,969 | [
"Gaussian"
] | bb3bf9e40f873f8a1ff9a2415bf42f660989e2fbaf199d4014b99c0f68ff25db |
import argparse
def commandargs(self):
#If there were system argument
self.parser = argparse.ArgumentParser()
self.parser.add_argument("--runtype", help="Batch, single file or pictures",default='file')
self.parser.add_argument("--batchpool", help="run directory of videos",type=str)
self.parser.add... | bw4sz/OpenCV_HummingbirdsMotion | MotionMeerkat/CommandArgs.py | Python | gpl-3.0 | 3,501 | [
"Gaussian"
] | 08d89e276e27ebf1224039239fc7c6014bad87a15124ee46fdfb25d7447e0663 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
import json
import os
from pymatgen.electronic_structure.cohp import CompleteCohp, Cohp, IcohpValue, IcohpCollection
from pymatgen.electronic_structure.core import Spin, Orbital
from pymatgen.u... | montoyjh/pymatgen | pymatgen/electronic_structure/tests/test_cohp.py | Python | mit | 35,582 | [
"pymatgen"
] | 2c78d2f267ec1e2d51c363b65e191985af3bba692da0a31c63aa42d8bbf14a98 |
# ============================================================================
#
# Copyright (C) 2007-2012 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | jeroendierckx/Camelot | camelot/view/controls/editors/stareditor.py | Python | gpl-2.0 | 3,808 | [
"VisIt"
] | 4919190a301c02996a13f426caad37fdec075994bcebe7149b51a2b55db4f579 |
from twython import Twython
from config import Config
from streamcatcher import StreamCatcher
config = Config()
# Make sure we have the application details.
if not config.get('app', 'key'):
print 'You will need to register an application at https://dev.twitter.com/apps'
print 'When you have, enter the details below... | 3ft9/twicli | src/twicli.py | Python | mit | 1,482 | [
"VisIt"
] | 7a94c0b5f09d7666ba20e4999f13b3f702cdc3b8f67557c0249b6a7310a1d131 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | jensreeder/scikit-bio | skbio/sequence/_iupac_sequence.py | Python | bsd-3-clause | 14,348 | [
"scikit-bio"
] | 43581f76d8bbadf7a378eacc0673deec50dd0d18a64f8617424ba45367f11b77 |
# -*- coding: utf-8 -*-
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IMPORTS~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
# Standard library imports
from collections import *
import warnings
# Third party imports
import numpy as np
import pandas as pd
import pysam as ps
# Local lib import
from pycoQC.common import *
#~~~~~~~~~~~~~... | a-slide/pycoQC | pycoQC/pycoQC_parse.py | Python | gpl-3.0 | 17,123 | [
"pysam"
] | d6eed3eebe33d22cec52affc08cc9d4e572b3901a8b347c7fedd892e8e9925b4 |
#!/usr/bin/env python
# vim: set fileencoding=utf-8 :
# Andre Anjos <andre.anjos@idiap.ch>
# Thu 30 Jan 08:45:49 2014 CET
bob_packages = ['bob.core', 'bob.io.base', 'bob.sp', 'bob.math']
from setuptools import setup, find_packages, dist
dist.Distribution(dict(setup_requires=['bob.extension', 'bob.blitz'] + bob_packag... | tiagofrepereira2012/bob.ip.base | setup.py | Python | bsd-3-clause | 5,982 | [
"Gaussian"
] | 5ef2f079b043cc14e778272ef5d116d8db105c8b144ce6fd565817396de635b6 |
'''
synbiochem (c) University of Manchester 2015
synbiochem is licensed under the MIT License.
To view a copy of this license, visit <http://opensource.org/licenses/MIT/>.
@author: neilswainston
'''
# pylint: disable=too-many-public-methods
import unittest
from sbcdb.mnxref_utils import MnxRefReader
class TestMn... | synbiochem/biochem4j | sbcdb/test/test_mnxref_utils.py | Python | mit | 1,061 | [
"VisIt"
] | d55d7dc8676a891d192f7b4409a3fe0704fd9eb729412505a181b0582c394869 |
# Copyright (C) 2016 Allen Li
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,... | darkfeline/mir.dlsite | setup.py | Python | apache-2.0 | 1,507 | [
"MOE"
] | 9010242d8bbfb739dd07cb32fc90c159f6ab1285a7e5049b2c2958900a476fd9 |
#
# 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/tfpark/tf_predictor.py | Python | apache-2.0 | 3,080 | [
"ORCA"
] | d5917690716615a56af06f72e24768b5596acc4a6df1facc92134114e801b117 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# This module is also sponsored by E.T.A.I. (www.etai.fr)
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
ANSIBLE_METADATA = {'metadata_version... | Nitaco/ansible | lib/ansible/modules/cloud/vmware/vmware_guest.py | Python | gpl-3.0 | 112,476 | [
"VisIt"
] | 123ee8af0d22c2baf1b5c8270ff29a0833bd785acf77bd9dafe9b7035ed9fdb5 |
#!/usr/bin/env python
import os
from matplotlib import pyplot as plt, cm
from pymicro.view.vol_utils import AxShowPixelValue
from pymicro.file.file_utils import HST_read
from pymicro.crystal.microstructure import Microstructure
'''
This example first demonstrate how to plot a slice of a 3d image. Here
we use a custom ... | heprom/pymicro | examples/plotting/pyplot_show_pixel_value.py | Python | mit | 1,286 | [
"CRYSTAL"
] | 7c85a2502709ac3e458496849d85fb5b3dce1b27631601004ee1c1996ddfe86a |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright (C) 2015-2018 Hydriz Scholz
# 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... | Hydriz/Balchivist | modules/mediacounts.py | Python | gpl-3.0 | 21,396 | [
"VisIt"
] | 10f0c94add12b2acb9c1c05b8c9021268428f6e05c8f685a5b7a9d073b8a8d5f |
"""
A class hierarchy for numerical integration on reference domains in 1,2, and 3D.
.. inheritance-diagram:: proteus.Quadrature
:parts: 1
"""
from __future__ import absolute_import
from __future__ import division
from builtins import zip
from builtins import range
from past.utils import old_div
from builtins impor... | erdc/proteus | proteus/Quadrature.py | Python | mit | 47,052 | [
"Gaussian"
] | 0078d1a832f2d22abc066b710e439734175d11d311c2b0270ff7910b0c9e55b5 |
#!/usr/bin/env python
'''unit testing code for pysam.
Execute in the :file:`tests` directory as it requires the Makefile
and data files located there.
'''
import pysam
import unittest
import os
import re
import sys
import subprocess
import shutil
from TestUtils import checkBinaryEqual
IS_PYTHON3 = sys.version_info[0... | dannon/pysam | tests/samtools_test.py | Python | mit | 12,882 | [
"pysam"
] | 3c93dc835d94e7521fda68e0be7d6a73da0e3345b2639c0c87e75a7c3be5416a |
import click
import os
import pathlib
import logging
from create_tiles import calc_output_filenames, create_tiles, list_tile_files
from ingester.utils import preserve_cwd
from netcdf_writer import append_to_netcdf, MultiVariableNetCDF, SingleVariableNetCDF
import eodatasets.drivers
import eodatasets.type
from eodataset... | omad/datacube-experiments | ingester/datacube_ingester.py | Python | bsd-3-clause | 4,945 | [
"NetCDF"
] | 51d112efaf24841301db4e88c0bf82ca18436d6cf2eeda0f480c2acbf29227e0 |
#!/usr/bin/env python
from __future__ import print_function, division
import argparse
import json
import re
import elasticsearch as es
import elasticsearch_dsl
parser = argparse.ArgumentParser(description="Cleans up Kibana objects and " +
"Elasticsearch indices for a given user " +
... | yannakopoulos/elk-admin | scripts/cleanup_elk.py | Python | mit | 1,609 | [
"Elk"
] | 96ff9624f77c7b41197cb4ba5b4c91bdd03cc9471feff366f7d287f916f1fc90 |
# coding=utf-8
from __future__ import unicode_literals
from ..person import Provider as PersonProvider
class Provider(PersonProvider):
formats = (
'{{first_name_male}} {{last_name}}',
'{{first_name_male}} {{last_name}}',
'{{first_name_male}} {{last_name}}',
'{{first_name_male}} {{la... | DonHilborn/DataGenerator | faker/providers/dk_DK/person.py | Python | mit | 8,224 | [
"Brian"
] | 19adb785593918430be68138c043be775917121c02987916b6cd82bf736b8a2f |
import numpy as np
from sklearn.neighbors import NearestNeighbors
from multiprocessing import Pool
from contextlib import closing
from itertools import repeat
from scipy import sparse as sp
import subprocess
import time
import re
import os
import sys
from .bruteforce_nn import knnsearch
def find_neighbors(data, k=30,... | jacoblevine/PhenoGraph | phenograph/core.py | Python | mit | 11,451 | [
"Gaussian"
] | 7121a3d27298d819086214afa943ba8356ac4d592d23aad4af4e35dd9f9d474e |
# coding: utf-8
# -*- coding: utf-8 -*-
import matplotlib
import matplotlib.pyplot as plt
import datetime as dt
import numpy as np
import netCDF4
import pandas as pd
import warnings
from pathlib import Path
from aps.load_region import load_region
from aps.analysis import describe
matplotlib.style.use('seaborn-note... | kmunve/APS | aps/scripts/new_snow_line.py | Python | mit | 8,836 | [
"NetCDF"
] | 9fbe8e0f9ac753ea3da74452ccac0aa224a5f2446b6950763b3e4c00030ba940 |
# -*- coding: utf-8 -*-
# Copyright (C) Brian Moe (2013-2014), Duncan Macleod (2014-)
#
# This file is part of LIGO CIS Core.
#
# LIGO CIS Core 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 ... | lscsoft/cis.server | cisserver/management/__init__.py | Python | gpl-3.0 | 1,017 | [
"Brian",
"MOE"
] | 4a69138ba2605d2d830a25fb85d5fb2e8a5b73d30c6a9b61b8f74a293f4d0134 |
#pylint: disable=missing-docstring
####################################################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simulation Environment ... | yipenggao/moose | python/MooseDocs/MooseMarkdown.py | Python | lgpl-2.1 | 7,174 | [
"MOOSE"
] | bd252f834d3186d67709541f74ac6ea4062fbd988b6194e860abd5d6eeab51b6 |
#!/usr/bin/env python
import os
import sys
import glob
import re
import csv
import itertools
from collections import OrderedDict, defaultdict
import time
import yaml
import subprocess
import copy
import tempfile
import argparse
import bcbio.solexa.samplesheet
from bcbio.pipeline.config_loader import load_config
from sc... | SciLifeLab/scilifelab | scripts/bcbb_helpers/run_bcbb_pipeline.py | Python | mit | 29,074 | [
"Galaxy"
] | daad6793d5fecb1e3dafc73b7aae04a526960cdcf54e3657e7c8ded6689545a2 |
# 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... | hmenke/espresso | samples/observables_correlators.py | Python | gpl-3.0 | 2,781 | [
"ESPResSo"
] | b00eb400142e8d33258dfa2bd31d8cd8abf6c033ffda860e8985a890ca09f6ec |
#!/usr/bin/env python
"""Universal feed parser
Handles RSS 0.9x, RSS 1.0, RSS 2.0, CDF, Atom 0.3, and Atom 1.0 feeds
Visit http://feedparser.org/ for the latest version
Visit http://feedparser.org/docs/ for the latest documentation
Required: Python 2.4 or later
Recommended: CJKCodecs and iconv_codec <http://cjkpytho... | yeyanchao/calibre | src/calibre/web/feeds/feedparser.py | Python | gpl-3.0 | 167,411 | [
"NetCDF",
"VisIt"
] | e21f6f9b9b849376ee388a31d05bf42f5a1bc321d00ae301e7246b685e4b01f8 |
#!/usr/bin/python
"""
Run some VASP tests to ensure that the VASP calculator works. This
is conditional on the existence of the VASP_COMMAND or VASP_SCRIPT
environment variables
"""
from ase.test import NotAvailable
import os
vcmd = os.getenv('VASP_COMMAND')
vscr = os.getenv('VASP_SCRIPT')
if vcmd == None and vscr ... | JConwayAWT/PGSS14CC | lib/python/multimetallics/ase/test/vasp/vasp_co.py | Python | gpl-2.0 | 1,825 | [
"ASE",
"VASP"
] | d395bf88b559d237733c4e18abbe71fbabb9e94b2ca590ad6de73299dbe98085 |
"""
sfc_models.examples package
===========================
Example code is deployed here.; currently only in the form of scripts in the "scripts" sub-package. Eventually,
will develop a deployment function to push the examples to a directory specified by the user.
The Quick2DPlot() function uses matlibplot, which is... | brianr747/SFC_models | sfc_models/examples/__init__.py | Python | apache-2.0 | 2,104 | [
"Brian"
] | 8af8444beef1dff28da6e62d7520bd07ed2bdbb9c65390169ef40dc3810028e5 |
#
# @file TestRule_newSetters.py
# @brief Rule unit tests for new set function API
#
# @author Akiya Jouraku (Python conversion)
# @author Sarah Keating
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generated automatically by conv... | TheCoSMoCompany/biopredyn | Prototype/src/libsbml-5.10.0/src/bindings/python/test/sbml/TestRule_newSetters.py | Python | bsd-3-clause | 6,208 | [
"VisIt"
] | ee07496c9a998e4fbb2376a143f138de09e835d8690a08fbc1ff52273f74899d |
#------------------------------------------------------------------------------
# Copyright (c) 2013, Nucleic Development Team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
#-------------------------------------------------... | ContinuumIO/ashiba | enaml/enaml/core/enaml_compiler.py | Python | bsd-3-clause | 20,427 | [
"VisIt"
] | eb1d0864989a88e231b46a0e763ea2d78170e09f10e74fafde335914a8d0d5af |
import numpy as np
import pycuda.driver as cuda
import pycuda.gpuarray as garray
from pycuda.compiler import SourceModule
from pycuda.tools import dtype_to_ctype, context_dependent_memoize
import neurokernel.LPU.utils.curand as curand
from neurokernel.LPU.utils.simpleio import *
from neurokernel.LPU.NDComponents.Memb... | neurokernel/retina | retina/NDComponents/MembraneModels/PhotoreceptorModel.py | Python | bsd-3-clause | 41,046 | [
"NEURON"
] | 9738b9e22b8b28550c82d7c3d04c9bcf0d45e51b6deb06053fbdded3a90c2fc0 |
"""
oxd Python
----------
Python bindings for Gluu oxd server.
"""
import codecs
import os
import re
from setuptools import setup
def find_version(*file_paths):
here = os.path.abspath(os.path.dirname(__file__))
with codecs.open(os.path.join(here, *file_paths), 'r') as f:
version_file = f.read()
ve... | GluuFederation/oxd-python | setup.py | Python | mit | 1,836 | [
"VisIt"
] | b2fa1137258d2a204d69515a11bdc5b9fad00f528e6702f9d784d80607613963 |
import numpy as np
from cogue.crystal.utility import klength2mesh
class DOS:
def __init__(self,
phonon,
distance=100):
self._phonon = phonon # Phonopy object
self._lattice = np.array(phonon.get_unitcell().get_cell().T,
dtype='double... | atztogo/phonondb | phonondb/phonopy/dos.py | Python | bsd-3-clause | 4,461 | [
"CRYSTAL",
"phonopy"
] | cae2dbc6f0a34a25e027b8dfb0d71b04dd42cd05e141199a18ae75198b6e11ae |
# Copyright (C) 2008 CSC - Scientific Computing Ltd.
"""This module defines an ASE interface to VASP.
Developed on the basis of modules by Jussi Enkovaara and John
Kitchin. The path of the directory containing the pseudopotential
directories (potpaw,potpaw_GGA, potpaw_PBE, ...) should be set
by the environmental flag... | conwayje/ase-python | ase/calculators/vasp.py | Python | gpl-2.0 | 68,697 | [
"ASE",
"VASP"
] | ae525eb4968ee5e061a72638b0bf6d8d9e191b540aae802eb57e077ca97dde75 |
import os, sys, re, inspect, types, errno, pprint, subprocess, io, shutil, time, copy
import path_tool
path_tool.activate_module('FactorySystem')
path_tool.activate_module('argparse')
from ParseGetPot import ParseGetPot
from socket import gethostname
#from options import *
from util import *
from RunParallel import R... | mellis13/moose | python/TestHarness/TestHarness.py | Python | lgpl-2.1 | 40,691 | [
"MOOSE",
"VTK"
] | 4b799aed90f9ad1827e4d0b77058727245cd39585fd961a3179c317896c31346 |
import os
import cdsapi
import datetime
import numpy as np
import bluesky as bs
import netCDF4 as nc
from bluesky import settings, stack
from bluesky.core import timed_function
from bluesky.traffic.windsim import WindSim
datadir = settings.data_path + '/NetCDF/'
if not os.path.exists(datadir):
os.makedirs(datadir... | ProfHoekstra/bluesky | plugins/windecmwf.py | Python | gpl-3.0 | 7,031 | [
"NetCDF"
] | 6485da75907645dd27abe908256a611cc97ac47879e86fdfd9f0c0e582413325 |
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