text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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# -*- coding: utf-8 -*-
"""
Generators for random graphs.
"""
# Copyright (C) 2004-2016 by
# Aric Hagberg <hagberg@lanl.gov>
# Dan Schult <dschult@colgate.edu>
# Pieter Swart <swart@lanl.gov>
# All rights reserved.
# BSD license.
from __future__ import division
import itertools
import math
import ran... | andnovar/networkx | networkx/generators/random_graphs.py | Python | bsd-3-clause | 32,181 | [
"VisIt"
] | fe2de9ce38210c80862aa2799cd704abe95f68c119a503d3b46567fec086b85f |
#!/usr/bin/python
#
# Copyright (C) 2015, Jaguar Land Rover
#
# This program is licensed under the terms and conditions of the
# Mozilla Public License, version 2.0. T full text of the
# Mozilla Public License is at https://www.mozilla.org/MPL/2.0/
#
# Create a certificate giving the sender the right to invoke and ... | GENIVI/rvi_lib | scripts/rvi_create_credential.py | Python | mpl-2.0 | 8,776 | [
"Jaguar"
] | 728490b51f19ba04294197e80e7f371363eb4117841fbbd7e128c2fa206d8c77 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2017 Lenovo, Inc.
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# ... | andreaso/ansible | lib/ansible/modules/network/lenovo/cnos_template.py | Python | gpl-3.0 | 7,077 | [
"VisIt"
] | a19bce01b06ab31a6d8109ff270afd29c90b945c5dce296ab616021725a5ca27 |
# coding: utf-8
from __future__ import division, print_function, unicode_literals, \
absolute_import
import unittest
import os
import json
import numpy as np
import pandas as pd
from pymatgen import Structure
from veidt.describer.general import FuncGenerator, MultiDescriber
from veidt.describer.structural_descr... | czhengsci/veidt | veidt/describer/tests/test_general_describer.py | Python | bsd-3-clause | 2,406 | [
"pymatgen"
] | b90bef2ab551c80a458f70756584c7f97cb046246146e043662a6d9857de2df4 |
# $HeadURL $
''' ResourceStatusDB
Module that provides basic methods to access the ResourceStatusDB.
'''
from datetime import datetime
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Base.DB ... | avedaee/DIRAC | ResourceStatusSystem/DB/ResourceStatusDB.py | Python | gpl-3.0 | 15,851 | [
"DIRAC"
] | 56261955c3194cddc248a3b3a3d406281a745fab82f6b0800b48847758020ece |
from flask import render_template, request
from app import app
import pymysql as mdb
import json
import cPickle as pickle
import os
@app.route('/')
@app.route('/index')
def index():
return render_template("input.html")
@app.route('/slides')
def input():
return render_template("slides.html")
@... | weiwang/curatir | app/views.py | Python | mit | 3,984 | [
"VisIt"
] | d0a2ad6457da0bf76454305430666e27c6ca3233bdaad5714746196e9acb9320 |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
'''
A simple example of using polarizable embedding model in the mean-field
calculations. This example requires the cppe library
https://github.com/maxscheurer/cppe
arXiv:1804.03598
The CPPE library needs to be built from sources (according to the... | gkc1000/pyscf | examples/solvent/04-scf_with_pe.py | Python | apache-2.0 | 1,038 | [
"PySCF"
] | 360b1f9ad6bce1d4bc8b8951b205fde09e2c94ae3367fd36b8f97f74f638908d |
#
# @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 it and/or modify
#... | jgonthier/psi4 | psi4/driver/p4util/procutil.py | Python | lgpl-3.0 | 19,831 | [
"CFOUR",
"Psi4"
] | e981fe6a894898155676a193e428c829121dcbe8649a820ccfecae940b261dd0 |
"""Forest of trees-based ensemble methods
Those methods include random forests and extremely randomized trees.
The module structure is the following:
- The ``BaseForest`` base class implements a common ``fit`` method for all
the estimators in the module. The ``fit`` method of the base ``Forest``
class calls the ... | schets/scikit-learn | sklearn/ensemble/forest.py | Python | bsd-3-clause | 60,067 | [
"Brian"
] | 6fe55cd726a258227aff5cc9e23749da42482a7ae3b960b252ad93069dfc27e0 |
"""
Module containing classes to calculate bonded properties from a Frame.
BondSet contains a dictionary of lists of Bonds. Each list corresponds to a single molecule.
"""
import itertools
import math
import logging
import numpy as np
try:
from tqdm import tqdm
except ImportError:
from .util import tqdm_d... | jag1g13/pycgtool | pycgtool/bondset.py | Python | gpl-3.0 | 16,506 | [
"Gromacs"
] | 25f54450225c160cf30fcd8e6d15d94e77f7d1add490fead00a841279916f99c |
# -*- coding: utf-8 -*-
"""
References:
Jegou's Source Code, Data, and Publications
http://people.rennes.inria.fr/Herve.Jegou/publications.html
To aggregate or not to aggregate: selective match kernels for image search
https://hal.inria.fr/hal-00864684/document
Image search with selective match ke... | Erotemic/ibeis | ibeis/algo/smk/smk_funcs.py | Python | apache-2.0 | 40,867 | [
"Gaussian"
] | bed5f99333e31f55f11d239e72e1073aa83bba630cde447792fa5d5b6b7b990a |
#
# @file TestL3Parameter.py
# @brief L3 Parameter unit tests
#
# @author Akiya Jouraku (Python conversion)
# @author Sarah Keating
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generated automatically by converting the file locat... | TheCoSMoCompany/biopredyn | Prototype/src/libsbml-5.10.0/src/bindings/python/test/sbml/TestL3Parameter.py | Python | bsd-3-clause | 6,493 | [
"VisIt"
] | 96ce550eec5fe2c2db36977de34ef8623f1bf9ee765c7ded5857e9dc3fb2906d |
#!/usr/bin/env python
'''
@package ion.processes.data.transforms
@file ion/processes/data/transforms/notification_worker.py
@author Brian McKenna <bmckenna@asascience.com>
@brief NotificationWorker class processes real-time notifications
'''
from datetime import datetime
from email.mime.text import MIMEText
import sm... | ooici/coi-services | ion/processes/data/transforms/notification_worker.py | Python | bsd-2-clause | 11,086 | [
"Brian"
] | f5a2e1435fb6d81faf2826be0b151ee0cb6b5468994ffc99e681ed27348d3cfd |
#
# @file TestUnitDefinition_newSetters.py
# @brief SBML UnitDefinition unit tests for new API
#
# @author Akiya Jouraku (Python conversion)
# @author sarah Keating
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generated automatic... | TheCoSMoCompany/biopredyn | Prototype/src/libsbml-5.10.0/src/bindings/python/test/sbml/TestUnitDefinition_newSetters.py | Python | bsd-3-clause | 5,289 | [
"VisIt"
] | 57b5ace20d277ea928fc13b2453c0e5a36b981fe222c6d944ac474771e247c5d |
# Copyright 2009-2011 by Peter Cock. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Dictionary like indexing of sequence files (PRIVATE).
You are not expected to access this... | updownlife/multipleK | dependencies/biopython-1.65/build/lib.linux-x86_64-2.7/Bio/SeqIO/_index.py | Python | gpl-2.0 | 27,206 | [
"Biopython"
] | e2e71b021e8b538b9d603479d2383e7e6e8c9840b071a62c8d5abec24b40b60c |
# TODO: to be removed
########################################################################
# $HeadURL $
# File: StrategyHandlerTests.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2012/10/01 11:48:31
########################################################################
""" :mod: StrategyHandlerTests
... | avedaee/DIRAC | DataManagementSystem/test/StrategyHandlerTests.py | Python | gpl-3.0 | 17,506 | [
"DIRAC"
] | f00bc024f0d5d39f27ab552cc042e490881dc2edd66b335fe8da83891ad993fd |
"""
Student Views
"""
import datetime
import json
import logging
import uuid
import warnings
from collections import defaultdict, namedtuple
from urlparse import parse_qs, urlsplit, urlunsplit
import analytics
import edx_oauth2_provider
from django.conf import settings
from django.contrib import messages
from django.... | miptliot/edx-platform | common/djangoapps/student/views.py | Python | agpl-3.0 | 120,280 | [
"VisIt"
] | dac47b6fd1374b47d7493b951c7fc17fe2f3f4312f113b3bf692f2706d09fcf2 |
import json
import random
from django.conf import settings
from django.test import TestCase
from django.core.cache import cache
import mock
from nose.tools import ok_, eq_
from airmozilla.base import mozillians
from airmozilla.base.tests.testbase import Response
VOUCHED_FOR = """
{
"meta": {
"previous": null... | tannishk/airmozilla | airmozilla/base/tests/test_mozillians.py | Python | bsd-3-clause | 9,530 | [
"CASINO"
] | eff207cbdf24d74c437b083b386403124d9ff4dd2d9d1632c3c974b9ae976372 |
'''##########################
## IMPORT REQUIRED MODULES ##
##########################'''
try:
import os
import socket
import subprocess
except ImportError:
raise ImportError, '[*] ERROR at loading required system modules'
try:
import netifaces as ni
except ImportError:
raise ImportError, '... | roxtii/nwtools | nwtools.py | Python | mit | 14,801 | [
"VisIt"
] | c9625fce6ccf562bdab80b5c27ce6c1cdb45785c9b00ad7a1552804059e08407 |
from utils import *
import qcdb
def test_Molecule_BFS():
#! apply linear fragmentation algorithm to a water cluster
iceIh = """\
36
Crystal created from CIF file. Box size: 7.82000 7.82000 7.36000
O 2.606641 0.000000 3.220000
O 5.213320 4.514902 6.90000... | amjames/psi4 | psi4/driver/qcdb/pytest/test_bfs.py | Python | lgpl-3.0 | 4,090 | [
"CRYSTAL"
] | 5a28f1defc80b42453f41ae33d461b9103c9fb596a3e79499eaa2c640c8d9941 |
import logging
import os
from tool_shed.util import common_util
from tool_shed.util import hg_util
from tool_shed.util import shed_util_common as suc
log = logging.getLogger( __name__ )
def get_latest_changeset_revision( app, repository, repo ):
repository_tip = repository.tip( app )
repository_metadata = su... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/tool_shed/util/metadata_util.py | Python | gpl-3.0 | 8,182 | [
"Galaxy"
] | 85cf83d80880f9ec7a784049ec6e9145ad96981a4afe21ad354a0b13cbabec25 |
#!/usr/bin/python
#
# 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-2.0
#
# Unless required b... | dietrichc/streamline-ppc-reports | examples/adwords/v201409/campaign_management/validate_text_ad.py | Python | apache-2.0 | 2,828 | [
"VisIt"
] | 1de294f13f24d9dae22ebf99a04a21610201acad451e45fb2424805f95907c75 |
from netCDF4 import Dataset
import datetime
import numpy
import os
from pydap.client import open_url
import paste
import pylons
from coards import parse
import shutil
from ecomaps.lib.ecomaps_utils import WorkingDirectory, working_directory, find_closest
__author__ = 'Phil Jenkins (Tessella)'
class DatasetConversion... | NERC-CEH/ecomaps | ecomaps/services/netcdf.py | Python | gpl-2.0 | 7,938 | [
"NetCDF"
] | 8e04b705afb3cc1e202af783db5bb50b4f47a6938abc50257f38ab91b8954b60 |
"""This module contains all research related classes."""
# Python imports
from math import floor
# Django imports
from django.db import models
from django.contrib.contenttypes.models import ContentType
# app imports
from oweb.models import Account
from oweb.libs.costs import costs_two, costs_two_total, costs_total
c... | Mischback/django-oweb | oweb/models/research.py | Python | mit | 8,966 | [
"CRYSTAL"
] | 3e9a2fceb9024ae339166fca20cf9af20b52875b0fc9e2fbc0c4006ed55b8421 |
"""
test the pvgis IO tools
"""
import json
import numpy as np
import pandas as pd
import io
import pytest
import requests
from pvlib.iotools import get_pvgis_tmy, read_pvgis_tmy
from pvlib.iotools import get_pvgis_hourly, read_pvgis_hourly
from ..conftest import (DATA_DIR, RERUNS, RERUNS_DELAY, assert_frame_equal,
... | mikofski/pvlib-python | pvlib/tests/iotools/test_pvgis.py | Python | bsd-3-clause | 27,281 | [
"EPW"
] | 1f6a15f60b4769b973f980ce9326c526749034bea152105faa881bdb2aac8188 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | lgarren/spack | var/spack/repos/builtin/packages/opencv/package.py | Python | lgpl-2.1 | 10,399 | [
"VTK"
] | aebffd5c94429469bf25b270fce915d641a567508a177cfb4f1bdeebfc366817 |
import unittest
from test import support
from itertools import *
from weakref import proxy
from decimal import Decimal
from fractions import Fraction
import sys
import operator
import random
from functools import reduce
maxsize = support.MAX_Py_ssize_t
minsize = -maxsize-1
def lzip(*args):
return list(zip(*args))
... | mancoast/CPythonPyc_test | fail/311_test_itertools.py | Python | gpl-3.0 | 65,380 | [
"GULP"
] | d70e976396dc4ae9cea815c8f872927a6998494b5d1cd34af1a0add58e24c2e7 |
# Copyright Iris contributors
#
# This file is part of Iris and is released under the LGPL license.
# See COPYING and COPYING.LESSER in the root of the repository for full
# licensing details.
"""
Unit tests for :class:`iris.analysis._area_weighted.AreaWeightedRegridder`.
"""
# Import iris.tests first so that some th... | rcomer/iris | lib/iris/tests/unit/analysis/area_weighted/test_AreaWeightedRegridder.py | Python | lgpl-3.0 | 10,977 | [
"NetCDF"
] | f3fec0a9764cc2697f1d5c216ec58c02c4807bee22e668d94dff61e66187b578 |
"""
Dashboard view and supporting methods
"""
import datetime
import logging
from collections import defaultdict
from completion.exceptions import UnavailableCompletionData
from completion.utilities import get_key_to_last_completed_course_block
from django.conf import settings
from django.contrib import messages
from... | BehavioralInsightsTeam/edx-platform | common/djangoapps/student/views/dashboard.py | Python | agpl-3.0 | 35,485 | [
"VisIt"
] | c1c904268aa74ecd8f5713fbff4cdf71843ec777d0ac76053dd63d40f8b70449 |
import os
from ase import *
from gpaw import GPAW, restart
from gpaw.atom.generator import Generator
from gpaw.atom.configurations import parameters
from gpaw import setup_paths
from gpaw.mpi import world
from gpaw.test import equal
# This test calculates the derivative discontinuity of Ne-atom
# first on 3D without r... | qsnake/gpaw | gpaw/test/ne_disc.py | Python | gpl-3.0 | 1,493 | [
"ASE",
"GPAW"
] | 41219df3b581c64f6926cea7f274a8b3be359cf3bb1506548b9ca283dbaf5685 |
import numpy as np
import sys
import helperFunctions
import copy
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
try:
import mpl_toolkits.mplot3d.axes3d as p3
except ImportError:
print()
pass
class chromophore:
def __init__(self, chromoID, chromophoreCGSites, CGMorphologyDict, ... | matty-jones/MorphCT | tests/assets/update_pickle/MCT1.0_pickle/code/obtainChromophores.py | Python | gpl-3.0 | 17,607 | [
"ORCA"
] | 3a9c666eefacb823b491d9eb9fd4a6fe890213bd9baf07837551ede3562131c3 |
# This file is part of Radler.
#
# Radler 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.
#
# Radler is distributed in the hope that it... | SRI-CSL/radler | radler/radlr/plantgen/dump.py | Python | gpl-3.0 | 2,186 | [
"VisIt"
] | 04e89fd9cece84d1eb65caf44b9a563b48dea0be7c1d197116fee414fe3819cc |
# Dougal Maclaurin
# David Duvenaud
# 2014
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
from rdkit.Chem import Descriptors
from rdkit import Chem
from rdkit.Chem import rdMolDescriptors
def slicedict(d, ixs):
newd = {}
for key in d:
newd[key] = d[key][ixs]
return newd
d... | HIPS/neural-fingerprint | data/2015-05-24-delaney/preprocess_data.py | Python | mit | 3,770 | [
"RDKit"
] | e46bd617562446ece700f76c402516a320b44c4823465a37c2cb3957965fede9 |
import numpy as np
from mayavi.modules.iso_surface import IsoSurface
from mayavi.modules.surface import Surface
from mayavi.filters.warp_scalar import WarpScalar
from mayavi.filters.cell_to_point_data import CellToPointData
def bathymetry(engine):
cell_to_point_data = CellToPointData()
engine.add_filter(cell... | openearth/vtkanim | vtkanim/pipes.py | Python | gpl-3.0 | 3,822 | [
"Mayavi"
] | beb7b08a7d55749429a0a4f0a4070e6f05bcb497357397f14c450aef35fa1b22 |
from __future__ import division
import numpy as np
from keras.models import Sequential, Model
from keras.optimizers import SGD
from keras_extensions.logging import log_to_file
from keras_extensions.rbm import RBM
from keras_extensions.layers import SampleBernoulli
from keras_extensions.initializations import... | bnsnapper/keras_bn_library | example/test_rbm.py | Python | mit | 2,586 | [
"Gaussian"
] | d9918f0f5a2fde823d7cbf946607fd6df1cb0787686311c063826d5af0fdf12a |
"""Universal feed parser
Handles RSS 0.9x, RSS 1.0, RSS 2.0, CDF, Atom 0.3, and Atom 1.0 feeds
Visit https://code.google.com/p/feedparser/ for the latest version
Visit http://packages.python.org/feedparser/ for the latest documentation
Required: Python 2.4 or later
Recommended: iconv_codec <http://cjkpython.i18n.org... | eric-stanley/NewsBlur | utils/feedparser_trunk.py | Python | mit | 155,430 | [
"NetCDF",
"VisIt"
] | d4aef66aace092f9eda81c17d2e5e38860afd833c9b656c5c433d69b5a0a5388 |
import numpy as np
from matplotlib.testing.decorators import image_comparison, knownfailureif
from matplotlib.delaunay.triangulate import Triangulation
from matplotlib import pyplot as plt
import matplotlib as mpl
def constant(x, y):
return np.ones(x.shape, x.dtype)
constant.title = 'Constant'
def xramp(x, y):
... | jjs0sbw/CSPLN | apps/scaffolding/mac/web2py/web2py.app/Contents/Resources/lib/python2.7/matplotlib/tests/test_delaunay.py | Python | gpl-3.0 | 5,950 | [
"Gaussian"
] | 1d94879eb7b6e27ab3d0404d3197221a17a093d2b05784731b6edaf33aef5df6 |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | gregcaporaso/scikit-bio | skbio/io/tests/test_iosources.py | Python | bsd-3-clause | 1,484 | [
"scikit-bio"
] | ac56e9497c5fd8afc5bafbe7706e491f20ee7ba485c1f702bfdf4373f904b38d |
# Global imports
from __future__ import print_function
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.cm as cm
from astropy.modeling import models, fitting
from utils import frame_convert, wave_convert
def line_measure(x, y, f=None, region=None, continuum=None, display=False):
"""
Measu... | nmearl/ifupy | ifupy/arithmetic/measure.py | Python | bsd-3-clause | 4,201 | [
"Gaussian"
] | 668f9b3236075a1c8727d129e09c473a97e56ec5ebc7324c699e17efd489ac2a |
#!/usr/bin/env python
import base
import requests
from bs4 import BeautifulSoup
import sys
from termcolor import colored
import time
ENABLED = True
class style:
BOLD = '\033[1m'
END = '\033[0m'
def wikileaks(domain):
time.sleep(0.3)
req = requests.get(
'https://search.wikileaks.org/?query=... | upgoingstar/datasploit | domain/domain_wikileaks.py | Python | gpl-3.0 | 1,417 | [
"VisIt"
] | d91972faa0284e438c8fd65bb21e4a2d3f2eecb02db95d4b956afdcc7db670ab |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
"""
Calculates gap statistics and manipulate gaps in assembly.
"""
import os.path as op
import sys
import logging
from itertools import groupby
from jcvi.formats.sizes import Sizes
from jcvi.formats.bed import Bed, fastaFromBed
from jcvi.formats.blast import BlastSlow
fr... | tanghaibao/jcvi | jcvi/assembly/gaps.py | Python | bsd-2-clause | 8,676 | [
"BLAST"
] | b70a981c1c1ed1e44e9ea01c1548d1ef8f1acfbc6bc58634a928da612c845c08 |
# Placeholder because parallel moved
# Remove this in version 1.0
import warnings
with warnings.catch_warnings():
warnings.simplefilter('always', DeprecationWarning)
warnings.warn(("qcprot has moved to MDAnalysis.lib.qcprot "
"and will be removed from here in release 1.0"),
... | alejob/mdanalysis | package/MDAnalysis/core/qcprot.py | Python | gpl-2.0 | 369 | [
"MDAnalysis"
] | d720dae3172af9d00fe3b6238afabbf34ca0523617c6c687733fd138fe80591d |
import param
import imagen
from topo.base.arrayutil import DivideWithConstant
from topo import sheet
from . import Model
from .gcal import ModelGCAL
@Model.definition
class ModelSCAL(ModelGCAL):
"""
Spatially-tuned GCAL (SCAL) calibrated to represent a 3 degree
parafoveal region of macaque primary visu... | Tasignotas/topographica_mirror | topo/submodel/scal.py | Python | bsd-3-clause | 6,109 | [
"Gaussian"
] | a26d9acbe9a7d3e6af640d471535996877fc4c3a8cf1105d73381fdda8e933df |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# seedmeopenmm documentation build configuration file, created by
# sphinx-quickstart on Tue Jul 9 22:26:36 2013.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
... | paesanilab/seedmeopenmm | docs/conf.py | Python | bsd-3-clause | 8,468 | [
"OpenMM"
] | 99860492a608f6f72b37c371604a5fc659a9eef14626aa328b479c918922ffd5 |
""" JobPolicy encapsulates authorization rules for different groups
with respect to job related operations
"""
__RCSID__ = "$Id$"
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Security import Properties
from DIRAC.ConfigurationSystem.Client.Helpers.Registry import getUsernameForDN, getGroupsForUser, \
... | Andrew-McNab-UK/DIRAC | WorkloadManagementSystem/Service/JobPolicy.py | Python | gpl-3.0 | 7,654 | [
"DIRAC"
] | 01f143599225b28207e896d23982ed9a4993699853ffac22395fce2b7d48b251 |
from commons.exceptions.unableToLoadDatasetException import UnableToLoadDatasetException
from commons.helpers.fileHelper import FileHelper
from commons.models.constants.classificationMethod import ClassificationMethod
from commons.models.datasetFactory import DatasetFactory
from nn.models.cost_computers.cost_computer i... | ADozois/ML_Challenge | main.py | Python | mit | 3,828 | [
"NEURON"
] | 3b897420455b10a153df4e073cd86b8b32bd8352b851d3bed114567b98fd9fe2 |
import statsmodels.datasets.macrodata.data as macro
from statsmodels.tsa.stattools import adfuller
macrod = macro.load().data
print(macro.NOTE)
print(macrod.dtype.names)
datatrendli = [
('realgdp', 1),
('realcons', 1),
('realinv', 1),
('realgovt', 1),
... | bashtage/statsmodels | statsmodels/sandbox/stats/ex_newtests.py | Python | bsd-3-clause | 819 | [
"ADF"
] | 2f9df42841401ecbf4ed1e2775fa84cafba4028f0120e7a849ad7ad93accb558 |
from __future__ import division
__all__ = ['compare_ssim',
'structural_similarity']
import numpy as np
from scipy.ndimage import uniform_filter, gaussian_filter
from ..util.dtype import dtype_range
from ..util.arraypad import crop
from .._shared.utils import deprecated
def compare_ssim(X, Y, win_size=No... | ofgulban/scikit-image | skimage/measure/_structural_similarity.py | Python | bsd-3-clause | 7,902 | [
"Gaussian"
] | d963cc0c4af337c6d2fb63c15f499e155446df4a62cefc23046697e6f209dcc7 |
#!/usr/bin/env python3
########################################################################
# Solves problem 196 from projectEuler.net.
# Finds the sum of primes participating in a prime triplet.
# Copyright (C) 2011 Santiago Alessandri
#
# This program is free software: you can redistribute it and/or mod... | salessandri/programming-contests | project-euler/problem196.py | Python | gpl-3.0 | 4,313 | [
"VisIt"
] | ed1ad02b5e2f00b82e92d92bf75b02eb4aaa095922a85cde082616bd5169215b |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | Laurawly/tvm-1 | tests/micro/zephyr/test_zephyr.py | Python | apache-2.0 | 19,242 | [
"VisIt"
] | 0c141ad437c735dabe8db949b666c94ade6f2dd57c36b3f0210253d65814bfeb |
from __future__ import absolute_import
from __future__ import division
from typing import Any, Dict, List, Tuple, Optional, Sequence, Callable, Union, Text
from django.db import connection
from django.db.models.query import QuerySet
from django.template import RequestContext, loader
from django.core import urlresolver... | TigorC/zulip | analytics/views.py | Python | apache-2.0 | 28,060 | [
"VisIt"
] | 9ca16b9e208778f52afbf511abc0adfc7e7a69764e18ebecb64425347561c6df |
#!/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/web/epgsearchrss.py | Python | gpl-2.0 | 8,179 | [
"VisIt"
] | 42242dfe954d34fbcf08075b1af9c5aed8d7730f85a31db5c9c03f68fbe359bd |
#######################################################
#######################################################
# Released under the GNU General Public License version 3 by Mike Nemec
#
# Copyright (c) 2016: Mike Nemec
#
# PySampling: Python scripts to assess the sampling quality of MD simulations
# usin... | MikeN12/PySamplingQuality | PySamplingQuality.py | Python | gpl-3.0 | 354,423 | [
"Amber",
"Gromacs",
"NetCDF"
] | f41c83f7e4a8e10198c6a930d11dc185ae680c031c5cb52421b8a56f399387e4 |
import numpy as np
#-----------------------------------------------------------------------
@np.vectorize
def fa_sigmoid(x):
if (x<-500):
return 0.0
return 1.0/(1.0+np.exp(-x))
def da_sigmoid(y):
return y*(1-y)
#-----------------------------------------------------------------------
def fa_tanh... | ManuelDiazP/Deep-Learning-Python | activation.py | Python | mit | 1,653 | [
"Gaussian"
] | 6f663bddc6f32e7da6e3f7c01bf816a14c14b31a77891c7f5f30b93c239786be |
#!/usr/bin/env python
""" MultiQC module to parse output from FastQC
"""
######################################################
#### LOOKING FOR AN EXAMPLE OF HOW MULTIQC WORKS? ####
######################################################
#### Stop! This module is huge and complicated. ####
#### Have a look at Bowti... | guillermo-carrasco/MultiQC | multiqc/fastqc/__init__.py | Python | mit | 27,299 | [
"Bowtie"
] | b588384d152bf89c5f34bd5049e256b48b0f67ec33155ea38911b74fe769f30c |
import os
import tempfile
import pytest
import numpy as np
import pandas as pd
from .. import orca
@pytest.fixture()
def a_value():
return 100
@pytest.fixture()
def my_func():
def my_func(value_test1):
return value_test1 * 2
return my_func
@pytest.fixture()
def my_func2():
def my_func2(fu... | bridwell/orca_sandbox | orca_sandbox/tests/test_orca.py | Python | mit | 15,047 | [
"ORCA"
] | d41e7adb8260b44ea5800490eb3cf67d21c290e3b687df84f149099274740ca0 |
#!/usr/bin/env python
'''
GAEUnit: Google App Engine Unit Test Framework
Usage:
1. Put gaeunit.py into your application directory. Modify 'app.yaml' by
adding the following mapping below the 'handlers:' section:
- url: /test.*
script: gaeunit.py
2. Write your own test cases by extending unittest.TestCas... | Gabicoware/txtbranch | gaeunit.py | Python | apache-2.0 | 18,267 | [
"VisIt"
] | 7d2e348b45a2b847948f4808fece1295d046c5e861b8953fb2ce0d7f9621d6a6 |
"""
"""
from __future__ import absolute_import, division, print_function, unicode_literals
import atexit
import os
import time
from contextlib import contextmanager
from selenium.common.exceptions import (WebDriverException,
StaleElementReferenceException)
from selenium.webdriv... | gratipay/gratipay.com | gratipay/testing/browser.py | Python | mit | 6,461 | [
"VisIt"
] | e3452573041a9d85c9fb6e5101985124067435d93993e280d1320240dd690ad8 |
# -*- coding: utf-8 -*-
"""
Created on Wed Feb 25 20:54:14 2015
@author: ubuntu
"""
import matplotlib.pyplot as mp
import matplotlib
from nest import *
import nest.voltage_trace
import nest.raster_plot
import io
import StringIO
import csv
import numpy as np
import pickle
import zipfile
import pamutils.pam2nest as... | MartinPyka/Pam-Utils | pamutils/network.py | Python | gpl-2.0 | 34,485 | [
"NEURON"
] | cdc4a4581c37c0d1a94cbfdd6afd82effca1f9e38f769390d393e571e524bb72 |
#!/usr/bin/env python
traindat = '../data/fm_train_real.dat'
testdat = '../data/fm_test_real.dat'
parameter_list=[[traindat,testdat,1.9],[traindat,testdat,1.7]]
def kernel_io_modular (train_fname=traindat,test_fname=testdat,width=1.9):
from modshogun import RealFeatures, GaussianKernel, CSVFile
feats_train=RealFea... | JingheZ/shogun | examples/undocumented/python_modular/kernel_io_modular.py | Python | gpl-3.0 | 889 | [
"Gaussian"
] | 926ae7717d258daf089fc78763c98c40260622e0ab9e5bd8770463e4af6e3aa9 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# scheduler - base scheduler class used by all schedulers
# Copyright (C) 2003-2014 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the GNU Gen... | heromod/migrid | mig/server/scheduler.py | Python | gpl-2.0 | 61,599 | [
"Brian"
] | cc0bd95e47c967446b8d208044d68b5aecae7b9800421b062b03705ec5ae4d67 |
# Orca
#
# Copyright 2005-2008 Sun Microsystems Inc.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/eventsynthesizer.py | Python | gpl-3.0 | 5,306 | [
"ORCA"
] | 4a2b55f8cc9195436c19560ccd490fabdae669b60020f75f9787bea2bdbc2f33 |
"""
This package combines the common.ncml with existing pyNN classes
Author: Thomas G. Close (tclose@oist.jp)
Copyright: 2012-2014 Thomas G. Close.
License: This file is part of the "NineLine" package, which is released under
the MIT Licence, see LICENSE for details.
"""
from __future__ import abso... | tclose/PyPe9 | pype9/simulate/neuron/cells/base.py | Python | mit | 25,342 | [
"NEURON",
"VisIt"
] | 759121c332fc8a852d5d751d93a0e8e75d0fed4bff374baca81452ac8a513ad1 |
"""
Testing for the forest module (sklearn.ensemble.forest).
"""
# Authors: Gilles Louppe, Brian Holt, Andreas Mueller
# License: BSD 3
import numpy as np
from numpy.testing import assert_array_equal
from numpy.testing import assert_array_almost_equal
from numpy.testing import assert_equal
from numpy.testing import a... | florian-f/sklearn | sklearn/ensemble/tests/test_forest.py | Python | bsd-3-clause | 14,916 | [
"Brian"
] | b148fb16b3f44e11de891cecf55ed978673038c81fdad3dfe3c054eaa027ddd2 |
# Copyright 2014 Roberto Brian Sarrionandia
#
# 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... | sarrionandia/tournatrack | tournamentinstance.py | Python | apache-2.0 | 3,213 | [
"Brian"
] | d30975a59883f4be88c06126a3448f14684040bd081db0e1e1316e3f834b15f6 |
#!/usr/bin/python
import time as time
import ADF4360 as ADF4360
import RPi.GPIO as GPIO
def main():
adf=ADF4360.ADF4360(GPIO,24000000,25000)
# adf=ADF4360.ADF4360(GPIO,24000000,100000)
# adf=ADF4360.ADF4360(GPIO,24000000,100000)
adf.InitGPIO()
print 'Crystal Freq=%d' % (adf.XOFreq)
print 'Channel Spacing=%d' % (... | adsllc/lolol | software/pi/ttl.py | Python | gpl-3.0 | 1,071 | [
"ADF",
"CRYSTAL"
] | c082e08cf3138424c271cf8af5418a319cc1ff5f4fb107d13ec37ddadf238e91 |
#
# Copyright (C) 2013-2018 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... | mkuron/espresso | samples/lj_liquid.py | Python | gpl-3.0 | 6,425 | [
"ESPResSo"
] | 9baa61cbc5f84d93e5bedf312f8c4e35de3750e09ae419117f8d9ff0590e8bf1 |
# objectedit.py ---
#
# Filename: objectedit.py
# Description:
# Author: Subhasis Ray
# Maintainer:
# Created: Wed Jun 30 11:18:34 2010 (+0530)
# Version:
# Last-Updated: Tue Nov 15 11:17:54 2011 (+0530)
# By: Subhasis Ray
# Update #: 522
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#... | BhallaLab/moose-thalamocortical | gui/objectedit.py | Python | lgpl-2.1 | 12,867 | [
"MOOSE"
] | 79ce423747f293cfe54e1bed5411293da9948b2f5eb2be3d3f47721252b86973 |
from __future__ import (absolute_import, division, print_function)
import AbinsModules
import gc
try:
# noinspection PyUnresolvedReferences
from pathos.multiprocessing import ProcessingPool
PATHOS_FOUND = True
except ImportError:
PATHOS_FOUND = False
import numpy as np
# Helper class for handling stab... | dymkowsk/mantid | scripts/AbinsModules/SPowderSemiEmpiricalCalculator.py | Python | gpl-3.0 | 34,782 | [
"CASTEP"
] | 174730560626d242e21bd8b84a387775cd204d1ef4a22ccb3980f1e68acab75b |
# 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_stats.py | Python | gpl-3.0 | 5,434 | [
"ESPResSo"
] | 46074950e4d0ecd118789196d928b71dc80b09d3863f466a04d8c83cc10c28e6 |
# -*- coding: utf-8 -*-
"""
Simple async crawler/callback queue based on gevent.
Based on Jason Morion's gevent+httplib2 crawler at
https://gist.github.com/996120
"""
import traceback
import logging
import httplib2
import gevent
from gevent import queue, event, pool
logger = logging.getLogger(__name__)
USER_AGEN... | k0001/PRAP-MXI | prap/crawler.py | Python | unlicense | 6,531 | [
"VisIt"
] | 2bb6e4579cc687ba0ff2c62d402572d46e4680524795b38e19b54e42149ed40f |
# -*- coding: utf-8 -*-
"""
Created on Fri Jul 27 10:08:25 2018
@author: cdeline
Using pytest to create unit tests for gencumulativesky.
Note that this can't be included in the repo until TravisCI has a Linux version of gencumsky
set up in .travis.yml
to run unit tests, run pytest from the command line in the bifaci... | NREL/bifacial_radiance | tests/test_gencumsky.py | Python | bsd-3-clause | 4,169 | [
"EPW"
] | 3c25a05ca698ccd126d897c49f072a2437cbc166418039acafcb1a842793f8a1 |
import numpy as np
from openpathsampling.integration_tools import (
openmm, md, error_if_no_mdtraj, unit, error_if_no_simtk_unit, HAS_OPENMM
)
if HAS_OPENMM:
# this is in case we directly import tools (e.g., for
# trajectory_to/from_mdtraj) when we don't have OpenMM installed. In
# that case, we skip ... | choderalab/openpathsampling | openpathsampling/engines/openmm/tools.py | Python | lgpl-2.1 | 14,322 | [
"Dalton",
"MDTraj",
"OpenMM"
] | 27d359082d4c40703a5daf4efbb4ea127d3518c2519c68c3dc6f42d712f20431 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
###############################################################################
# Copyright (C) 2005-2020 Francisco José Rodríguez Bogado, #
# Diego Muñoz Escalante. #
# (pacoqueen@users.sourceforge.ne... | pacoqueen/ginn | ginn/framework/pclases/__init__.py | Python | gpl-2.0 | 979,723 | [
"ASE"
] | ab20ba76ca6c8f44be57fb1cdd569e5925f6ce3c8aa9ff4c1553f0444c7ca547 |
#!/usr/bin/env python3
#* 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/lgp... | nuclear-wizard/moose | python/peacock/tests/base/test_PeacockCollapsibleWidget.py | Python | lgpl-2.1 | 1,614 | [
"MOOSE"
] | 726f32589d5f9e4956a83d620c604e45e4efe288c889e0d8c2dc21b10a6497dd |
import pylab as pyl
import cPickle as pickle
galaxies = pickle.load(open('galaxies.pickle','rb'))
galaxies = filter(lambda galaxy: galaxy.sfrir != None and galaxy.ston_I >30.,
galaxies)
f = pyl.figure(1)
f1 = f.add_subplot(311)
f2 = f.add_subplot(312)
f3 = f.add_subplot(313)
for galaxy in galaxies:
f1.sc... | boada/ICD | sandbox/legacy_plot_code/sfrratio.py | Python | mit | 1,302 | [
"Galaxy"
] | cb62c096150f22a03db1384d0ab3470c06f3ea3f110378ad8c013f7f8f20b473 |
#
# 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/example/automl/autoxgboost/AutoXGBoostClassifier.py | Python | apache-2.0 | 5,815 | [
"ORCA"
] | dd13d49f7afd209a55d0bfddf9496adbdc89d91b7519bff66f551e89427a979b |
# encoding: utf-8
"""
cf.py - classes around CF compliant files
The cf module is made for reading CF-compliant datasets,
knowing data, its structure, units and conversions
between units afterwards.
Dependencies:
=============
numpy
netcdftime (packaged in netcdf4-python)
"""
__docformat__ = "restructuredtext en"
imp... | kshedstrom/pyroms | pyroms/pyroms/cf.py | Python | bsd-3-clause | 5,726 | [
"NetCDF"
] | 2a96a5de6bc7416d64a2f0f221518ec810771009e9b7cfbdad159a8d26192e44 |
#!/usr/bin/env python3
from setuptools import setup, find_packages
import sys
if sys.version_info.major < 3:
raise SystemExit("Python 3 is required!")
setup(
name="mopicgen",
version="0.1",
description="Easily batch-plot orbitals from moldens with Jmol",
url="https://github.com/eljost/mopicgen",
... | eljost/mopicgen | setup.py | Python | gpl-3.0 | 718 | [
"Jmol"
] | dfa6f2e2db8cce33850bd1a59b391d9a9590372f7cd2ed4dba9fc4e8bff6dd35 |
# encoding: utf-8
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Changing field 'DataDomain.name'
db.alter_column('profiles_datadomain', 'name', self.gf('django.db.model... | 216software/Profiles | communityprofiles/profiles/oldmigrations/0042_auto__chg_field_datadomain_name__chg_field_datadomain_slug.py | Python | mit | 15,206 | [
"MOE"
] | 2f8218ac365c37159c3e63192659e1608d5fdd2c42ce801c755d3f1823efb116 |
"""
planet.py
Copyright 2016 Brian Romanchuk
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 wri... | brianr747/Simple4Xpygame | common/planet.py | Python | apache-2.0 | 2,954 | [
"Brian"
] | 4a94109de5047d245ea34530172370e2b94f011266fd7d8aec9546390af5a31f |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Convert the output of CombineSnpCounts.py to gene level counts
============================================================================
AUTHOR: Michael D Dacre, mike.dacre@gmail.com
ORGANIZATION: Stanford University
LICENSE: MIT License, property ... | MikeDacre/mike_tools | bin/alleleseq_counts_to_genes.py | Python | unlicense | 24,685 | [
"ASE"
] | 06739c1a425f3df5e97b0db931d8a51e22df568c9a27e2c8834ba753dac3e68d |
from qsnake_run import extract_version, extract_name_version
def test1():
assert extract_version("onlinelab-9934211") == "9934211"
assert extract_version("termcap-1.3.1.p1") == "1.3.1.p1"
def test2():
tests = {
"onlinelab-9934211": "9934211",
"termcap-1.3.1.p1": "1.3.1.p1",
... | qsnake/qsnake | spkg/base/tests/test_versions.py | Python | bsd-3-clause | 3,691 | [
"Mayavi",
"VTK"
] | 2535e59d990b385b173fc65031445d67d8b6804ebd937df38cde6e3e347ec71d |
"""
====================================================================
K-means clustering and vector quantization (:mod:`scipy.cluster.vq`)
====================================================================
Provides routines for k-means clustering, generating code books
from k-means models, and quantizing vectors ... | chatcannon/scipy | scipy/cluster/vq.py | Python | bsd-3-clause | 28,218 | [
"Gaussian"
] | a7dc2e2c5710d5c724e4b7c26550c94f446f0343a2ad67a3fd1b7a466ef537f8 |
from __future__ import division, print_function
import numpy as np
from bct.utils import cuberoot, binarize, invert
from ..due import due, BibTeX
from ..citations import LATORA2001, ONNELA2005, FAGIOLO2007, RUBINOV2010
def breadthdist(CIJ):
'''
The binary reachability matrix describes reachability between all... | aestrivex/bctpy | bct/algorithms/distance.py | Python | gpl-3.0 | 35,784 | [
"VisIt"
] | 5267420cee3d817bf0428a17b14e4c2c2f83d1ea0f790d9d67593d8f2af40869 |
# __BEGIN_LICENSE__
#
# Copyright (C) 2010-2012 Stanford University.
# All rights reserved.
#
# __END_LICENSE__
from lflib.lightfield import LightField
from lflib.imageio import save_image
import numpy as np
import time
from scipy.sparse.linalg.interface import LinearOperator
from scipy.sparse.dia import dia_matrix
... | sophie63/FlyLFM | stanford_lfanalyze_v0.4/lflib/iterative_deconvolution.py | Python | bsd-2-clause | 48,145 | [
"Gaussian"
] | 6bdd390adc958ee4a74e724b2eccb1dd79f1f78b81ce638c716d070943eb40cf |
#Contains objects for using external display applications
import logging, urllib
from galaxy.util import parse_xml, string_as_bool
from galaxy.util.odict import odict
from galaxy.util.template import fill_template
from galaxy.web import url_for
from parameters import DisplayApplicationParameter, DEFAULT_DATASET_NAME
fr... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/datatypes/display_applications/application.py | Python | gpl-3.0 | 10,572 | [
"Galaxy"
] | 21f6a33939b69bd185244315b47430afee2b2be6eaa8858587ee35fbc495e184 |
# Copyright 2014, Brian Coca <bcoca@ansible.com>
# Copyright 2017, Ken Celenza <ken@networktocode.com>
# Copyright 2017, Jason Edelman <jason@networktocode.com>
# Copyright 2017, Ansible Project
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of ... | ansible/ansible | lib/ansible/plugins/filter/mathstuff.py | Python | gpl-3.0 | 8,310 | [
"Brian"
] | 25fb089d55dd32d77b02a6eefae76786c21f0cbfd4e4f14d72a5367d3a74daca |
###############################
# This file is part of PyLaDa.
#
# Copyright (C) 2013 National Renewable Energy Lab
#
# PyLaDa is a high throughput computational platform for Physics. It aims to make it easier to
# submit large numbers of jobs on supercomputers. It provides a python interface to physical input,
# ... | pylada/pylada-light | src/pylada/crystal/bravais.py | Python | gpl-3.0 | 1,833 | [
"CRYSTAL",
"VASP"
] | 3edca0c7303d9235929c2ddf7d7d085551aabfa8d431421e8ad50430f082be2b |
# Copyright 2009 by Peter Cock. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Optimised sequence conversion code (PRIVATE).
You are not expected to access this module, or a... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/SeqIO/_convert.py | Python | gpl-2.0 | 13,386 | [
"Biopython"
] | 65e0819376a4f78ae45bdbe1a26403a1e37b004a7bc02a4813bb1b1600394bb6 |
""" TransferCommand module
"""
from datetime import datetime, timedelta
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Utilities.JEncode import strToIntDict
from DIRAC.ConfigurationSystem.Client.Helpers.Resources import getSites
from DIRAC.AccountingSystem.Client.ReportsClient import ReportsClient
from DIRAC.DataMana... | ic-hep/DIRAC | src/DIRAC/ResourceStatusSystem/Command/TransferCommand.py | Python | gpl-3.0 | 7,419 | [
"DIRAC"
] | c12f8750587da892625b5fb1193ae7ffbc27323d75cc6590a3bc0613a8ca8aaa |
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Matti Hamalainen <msh@nmr.mgh.harvard.edu>
# Martin Luessi <mluessi@nmr.mgh.harvard.edu>
# Mads Jensen <mje.mads@gmail.com>
#
# License: BSD (3-clause)
from .externals.six import string_types
import os
import copy
from... | jaeilepp/eggie | mne/source_estimate.py | Python | bsd-2-clause | 103,688 | [
"Mayavi"
] | bce409b575930cad7979cabfedd7b563bb8867f88dab495759d5677a375e4a7f |
# Copyright 2013 by Kamil Koziara. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""
Module containing functions used for statistical reasoning about the ... | arkatebi/SwissProt-stats | Ontology/Stats.py | Python | gpl-3.0 | 4,622 | [
"Biopython"
] | c138600e1fbd298597d6d53dbcdd530456063b2e8b7c56bafd1a982f018b0503 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2009 Brian G. Matherly
# Copyright (C) 2009 Gary Burton
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publis... | Forage/Gramps | gramps/cli/clidbman.py | Python | gpl-2.0 | 16,703 | [
"Brian"
] | 334ebfa0d94163025daea84a15b02f080f8393a16eb0e7b6b6869bed737c7079 |
# Example of how to use range clamping with vtkGlyph3D filter.
#
# Note that the internal algorithm does this to figure out the eventual scale
# of your data (say, if you're scaling by a scalar or vector magnitude):
#
# scale = (scalar value of that particular data index);
# denominator = Range[1] - Range[0];
# scal... | lorensen/VTKExamples | src/Python/Visualization/ClampGlyphSizes.py | Python | apache-2.0 | 3,887 | [
"VTK"
] | 91e80228f7653fe81f67835e246b1f56336c92f885ab920c3f2c87c49defed89 |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | aselle/tensorflow | tensorflow/contrib/autograph/pyct/static_analysis/activity.py | Python | apache-2.0 | 13,604 | [
"VisIt"
] | 522dc3dd0487bbaab1624e4d64ce5605aa02f2c99891ca2fe0106a2f7e28f7c9 |
#
#@BEGIN LICENSE
#
# PSI4: an ab initio quantum chemistry software package
#
# 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 ver... | spring01/libPSI | lib/databases/S22.py | Python | gpl-2.0 | 43,295 | [
"Psi4"
] | 7ac2cf74b62252fe68e896f8cfe0f414772897011971db4cbf2f97dd04b76934 |
from __future__ import absolute_import
import unittest
from pymatgen.core.lattice import Lattice
from pymatgen.core.structure import Structure
from pymatgen.analysis.elasticity.strain import Strain, Deformation, DeformedStructureSet,\
IndependentStrain
from pymatgen.util.testing im... | migueldiascosta/pymatgen | pymatgen/analysis/elasticity/tests/test_strain.py | Python | mit | 7,944 | [
"pymatgen"
] | 694dec1b75a8157692e1206fe7fe3d2f5e954f692057e27baa9728137b051312 |
# coding: ascii
# Copyright (c) Mike Gibson
# Distributed under the terms of the MIT License.
"""
Uses materialsproject API to extract enthalpies of formation and
compositions of compounds for comparison to Miedema values.
"""
__author__ = "Mike Gibson"
__credits__ = "Materials Project"
__copyright__ = "Copyright 20... | michaelagibson/bounding_miedema | import_all_data.py | Python | mit | 3,402 | [
"pymatgen"
] | 29b8b82a191f6db9a33d01ca85d10fbdb4c74106eb2bf950d51ff521badf7e5b |
#! /usr/bin/env python
from pymt.grids.grid_type import (
GridTypeRectilinear,
GridTypeStructured,
GridTypeUnstructured,
)
from .constants import open_netcdf
from .ugrid_read import (
NetcdfRectilinearFieldReader,
NetcdfStructuredFieldReader,
NetcdfUnstructuredFieldReader,
)
_NETCDF_MESH_TYPE... | csdms/pymt | pymt/printers/nc/read.py | Python | mit | 1,585 | [
"NetCDF"
] | bbd46f19c0c8c9ffa01bc5a4bda051541f00ed748e2c4dc24b5ed1db929b0779 |
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