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 is only meant to add docs to objects defined in C-extension modules.
The purpose is to allow easier editing of the docstrings without
requiring a re-compile.
NOTE: Many of the methods of ndarray have corresponding functions.
If you update these docstrings, please keep also the ones in
core/fromnum... | joferkington/numpy | numpy/add_newdocs.py | Python | bsd-3-clause | 223,881 | [
"Brian"
] | f1d2c2dd38418d69ed523b6f8ef665152421420c8b59ddcf7af1aa8ade7bc1b3 |
import os
from django.conf.global_settings import TEMPLATE_CONTEXT_PROCESSORS as TCP
from datetime import timedelta
import sys
BASE_DIR = os.path.dirname(os.path.dirname(__file__))
# Override These
# =========================
# Make this unique, and don't share it with anybody.
SECRET_KEY = os.environ.get('DJANGO_SE... | sreidy/roboticsclub.org | crm/settings.py | Python | mit | 12,601 | [
"VisIt"
] | 6d9a0c2d04543bcaefc08308b40bbc0125dd03e5876742fe9531ae464d1fd182 |
# Copyright 2002 by Jeffrey Chang, Andrew Dalke. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
# This is based on some older code by Andrew Dalke.
"""This module implements s... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/config/Registry.py | Python | apache-2.0 | 5,339 | [
"Biopython"
] | 53a0cd4d04e5e75e50627382fec665c79869b3e064ef345ffd40cd3a1a80723c |
# 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... | jendap/tensorflow | tensorflow/python/autograph/pyct/templates.py | Python | apache-2.0 | 8,904 | [
"VisIt"
] | aee230a70be4cef7cc981f79cbaa3334d090b3e4e5091bfe8eb0845467bf9ae0 |
#!/usr/bin/env python
# encoding: utf-8
"""Fit simple 2-D models using GALFIT."""
from __future__ import division
import os
import copy
import shutil
import argparse
import warnings
import subprocess
import numpy as np
from distutils import spawn
# Matplotlib related
import matplotlib as mpl
mpl.use('Agg')
mpl.rcPar... | dr-guangtou/hs_galphot | galfit/galfitSimple.py | Python | bsd-3-clause | 51,596 | [
"Galaxy",
"Gaussian"
] | 77f5331c31e753eba0908e23e95c6491add0fd2a6d5a41a2c5ea0ea0faf5c785 |
#
# Copyright (c) 2017 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | yashdsaraf/scancode-toolkit | tests/cluecode/test_authors.py | Python | apache-2.0 | 10,091 | [
"VisIt"
] | 45b303430684bbe42b90ea711c9bd29b932940fbcfd213eb4b8299d44400ba7e |
# Copyright (c) 2010 OpenStack Foundation
#
# 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 ... | hurricanerix/swift | test/unit/common/middleware/test_staticweb.py | Python | apache-2.0 | 41,893 | [
"VisIt"
] | cde71a4b43b3b9a263927a08d919f4b83df55e1bc178b30decb24ebc5e5deb6f |
# Copyright (c) 2013, Ricardo Andrade
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import numpy as np
from ..core import SparseGP
from .. import likelihoods
from .. import kern
from ..inference.latent_function_inference import EPDTC
from copy import deepcopy
class SparseGPClassification(SparseGP):
... | SheffieldML/GPy | GPy/models/sparse_gp_classification.py | Python | bsd-3-clause | 6,751 | [
"Gaussian"
] | cf30a00f3bf98ff1183458e988a482574ae1f8cc7e64cf1e93e6581fc77e18b0 |
import tensorflow as tf
import numpy as np
import matplotlib.pyplot as plt
import string as sn
from time import time
from datetime import datetime
# The location on the disk of project
PROJECT_BASEDIR = ("G:/My Drive/Academic/Research/" +
"Program Synthesis with Deep Learning/")
# The location on the disk of p... | brandontrabucco/program-gan | experiment.py | Python | mit | 59,393 | [
"Gaussian"
] | 4d2cbd25d3e179ef876b8b8333ff58cc9dff7e93b0b80b9b4847c9d0c0258cf2 |
########################################################################
# File: FTSFile.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/04/08 09:28:29
########################################################################
"""
:mod: FTSFile
.. module: FTSFile
:synopsis: class representing a single file in... | sposs/DIRAC | DataManagementSystem/Client/FTSFile.py | Python | gpl-3.0 | 10,301 | [
"DIRAC"
] | bbdd18987f0054883120a38c497bd45bdaf78da593fb98b2e35372a4688e6562 |
# Copyright 2017 Norman Heckscher. 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 applicable la... | normanheckscher/mnist-multi-gpu | mnist_multi_gpu_sonnet.py | Python | apache-2.0 | 22,701 | [
"Gaussian"
] | 5864a892b14e7791f32d4a71beb0a79c58bf5b064a6cc5642a5beeda172c618f |
##########################################################################
#
# QGIS-meshing plugins.
#
# Copyright (C) 2012-2013 Imperial College London and others.
#
# Please see the AUTHORS file in the main source directory for a
# full list of copyright holders.
#
# Dr Adam S. Candy, adam.candy@imperia... | adamcandy/QGIS-Meshing | plugins/mesh_surface/mesh_surface.py | Python | lgpl-2.1 | 16,160 | [
"NetCDF"
] | 3fb9f1d25383b86e41f307c66a72f7633d3781bfe9a11563553ebe9d30baa3b1 |
"""Scraper for United States District Court for the District of Columbia
CourtID: dcd
Court Short Name: D.D.C.
Author: V. David Zvenyach
Date created: 2014-02-27
Substantially Revised: Brian W. Carver, 2014-03-28
"""
from juriscraper.opinions.united_states_backscrapers.federal_district import dcd_2013
class Site(dcd_... | brianwc/juriscraper | opinions/united_states_backscrapers/federal_district/dcd_2012.py | Python | bsd-2-clause | 507 | [
"Brian"
] | 87634aff52e2762ff33be26a29eadbf141ed0704e0f7be8aad6046b4f6fe5174 |
#!/usr/bin/env python
###
# name : seqfiles.py
# description : Script for analyzing sequencing results
#
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# LICENSE:
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public Lice... | openpaul/DNApy | seqfiles6.py | Python | gpl-3.0 | 26,233 | [
"Biopython"
] | d21133549313d4e2c49e217b7b7acb58fba345545d0a6bce36b2d369d970d5ba |
import numpy as np
from brian import *
import cPickle
def cartesian(arrays, out=None):
"""
Generate a cartesian product of input arrays.
Parameters
----------
arrays : list of array-like
1-D arrays to form the cartesian product of.
out : ndarray
Array to place the cartesian pro... | blennon/MLI_PKJ_net | MLI_PKJ_net/util.py | Python | mit | 5,877 | [
"Brian",
"NEURON"
] | 6b0346c76288638dca97efd2244a3fb98e61bd274ff8c59e1ec3b7bdab8f3bb4 |
""" The Cloud Endpoint Factory has one method that instantiates a given Cloud Endpoint
"""
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Core.Utilities import ObjectLoader
from DIRAC.ConfigurationSystem.Client.Helpers.Resources import getVMTypeConfig
class EndpointFactory(object):
def __init__(self):
... | DIRACGrid/DIRAC | src/DIRAC/Resources/Cloud/EndpointFactory.py | Python | gpl-3.0 | 1,713 | [
"DIRAC"
] | 012c4ad40744ea068663b07981e4b82b4404b7b9141112c920ce0c0ffbc21179 |
"""Useful utility methods for GTK."""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
import gtk
class Template:
"""Wrapper for GtkBuilder widget tree that throws a sensible exception if the widget isn't found."""
def __init__(self, builderfile, root):
"""Con... | timdiels/zeroinstall | zeroinstall/gtkui/gtkutils.py | Python | lgpl-2.1 | 2,755 | [
"VisIt"
] | ac0653b96ee705f26222d5792ef678ae97f4884ab7c239fcbb56c20eb6a44326 |
#!/usr/bin/python
import sys
import numpy as np
import pysam
from collections import Counter
import vcf
from vcf.parser import _Info as VcfInfo
input=sys.argv[1].split(".")[0]
input=input.split("/")[-1]
bam=sys.argv[2].split(".")[0]
bam=bam.split("/")[-1]
#Ensure the bam and csv file match
#if input==bam:
# ... | lauringlab/variant_pipeline | scripts/mapq_vcf.py | Python | apache-2.0 | 2,762 | [
"pysam"
] | 2e46477802949742347049e57e6ca04d6bdcd2afd06b8933b46c6eb5bd8dcbd9 |
#!/usr/bin/env python
# Copyright (c) 2011 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Automates IE to visit a list of web sites while running CF in full tab mode.
The page cycler automates IE and navigates it to a... | plxaye/chromium | src/chrome_frame/tools/test/page_cycler/cf_cycler.py | Python | apache-2.0 | 2,625 | [
"VisIt"
] | fe03b5bb00f06abdec61f58e4c89b6e059d88327040b92b3cba4b834e5171c81 |
from __future__ import annotations
import math
import warnings
from collections import namedtuple
import numpy as np
from numpy import (isscalar, r_, log, around, unique, asarray, zeros,
arange, sort, amin, amax, atleast_1d, sqrt, array,
compress, pi, exp, ravel, count_nonzero, si... | e-q/scipy | scipy/stats/morestats.py | Python | bsd-3-clause | 128,770 | [
"Gaussian"
] | 4f7288526f71f1e43d530c9d459abc06924c6738d4dd62275c86f441b9aebfaa |
from datetime import date
from pywps.Process import WPSProcess
from flyingpigeon.datafetch import _PRESSUREDATA_
from flyingpigeon.log import init_process_logger
import logging
logger = logging.getLogger(__name__)
class AnalogsProcess(WPSProcess):
def __init__(self):
# definition of this process
... | KatiRG/flyingpigeon | flyingpigeon/processes/wps_analogs_model.py | Python | apache-2.0 | 13,210 | [
"NetCDF"
] | d246e6a8cbcfb3a4a3f8277e10a06dc8d8cb0eac6ef0136c64eb2569e7d2f636 |
#!/usr/bin/python
# _chemgraph.py
# by Walter Dal'Maz Silva
# 31st August 2016 (version 0.1.0)
# 12th October 2016 (version 0.2.0)
# TODO make base class for graph
__version__ = '0.2.0'
DEBUG_MODULE = False
# -----------------------------------------------------------------------------
# Imports
# -----------------... | waltermateriais/xutils | xpython/xchemistry/xcantera/classes/_chemgraph.py | Python | unlicense | 6,660 | [
"VisIt"
] | 55fb3946ae7ec7dd3cf1731f5cfc04a588550405ff4cd3d1e1f9ad57ecdf0f3c |
#!/usr/bin/env python
# File: montage.py
# Created on: Mon Mar 18 10:08:05 2013
# Last Change: Tue Aug 20 14:17:48 2013
# Purpose of script: <+INSERT+>
# Author: Steven Boada
import img_scale
import pyfits as pyf
import pylab as pyl
from mpl_toolkits.axes_grid1 import axes_grid
#from mk_galaxy_struc import mk_galaxy_s... | boada/ICD | sandbox/legacy_plot_code/plot_icd_mass_multimontage.py | Python | mit | 5,915 | [
"Galaxy"
] | da1f160dab0831a080e90e927b2eb0d934ef6578ffa3a2082b89fc030652d409 |
#!/usr/bin/env python
# Copyright 2014-2020 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... | sunqm/pyscf | pyscf/gto/mole.py | Python | apache-2.0 | 132,568 | [
"Gaussian",
"PySCF"
] | 22b2070bfd987dc27bb996088ba3881485979a425c9f7385af48c8118f3a9896 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | EmreAtes/spack | var/spack/repos/builtin/packages/r-a4preproc/package.py | Python | lgpl-2.1 | 1,721 | [
"Bioconductor"
] | 6a43def7d473b4f7b70e7cf57ace01f3d68605d5141f37d0ef73412db1081e3b |
"""Ensure the files have been migrated to tape."""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import datetime
from pprint import pformat
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Utilities.ReturnValues import returnSingleResult
from DIRAC.Request... | ic-hep/DIRAC | src/DIRAC/DataManagementSystem/Agent/RequestOperations/CheckMigration.py | Python | gpl-3.0 | 2,731 | [
"DIRAC"
] | 72fe442f70c67e742a070fe22cd56ce49b7fdec4cb7dbd449384ec2afb3aee20 |
# Beware! Only tested for non-spin-polarized case
import re
import sys
import rlcompleter
import readline
from numpy import *
from enterfi import enterfi
from outputfi import outputfi
gridfname = enterfi("Enter VASP field data (CHGCAR, LOCPOT, etc.)")
outfname = outputfi("Enter output file name ")
gridfi = open(gridf... | skasamatsu/vaspgrid | chgxav.py | Python | mit | 2,421 | [
"VASP"
] | 4827371f4b93aa132f044d080675e58c288aaf61cd6081e0db3f9ae13d56a169 |
#/usr/bin/env python2
# Copyright (C) 2013,2014,2015,2016 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the Licens... | lahnerml/espresso | tools/blockfile2pickle.py | Python | gpl-3.0 | 9,850 | [
"ESPResSo"
] | 873e04a25fb1212fb2bc61c2e02a5d9ac018e654980e5b47274c5cbaa2835056 |
"""Handle disambiguation of reads from a chimeric input, splitting by organism.
Given specification of mixed input samples, splits a sample into multiple
sub-samples for alignment to individual genomes, then runs third-party disambiguation
scripts to reconcile.
Uses disambiguation scripts contributed by AstraZeneca, ... | brainstorm/bcbio-nextgen | bcbio/pipeline/disambiguate/__init__.py | Python | mit | 7,440 | [
"BWA"
] | 65f6b099237cdbdfa764d9abc2050729baf04a872a2f17a84925876feb1d698d |
import circ_module.circ_template
import os
import sys
import subprocess
import pybedtools
import tempfile
from Bio.Blast import NCBIWWW
from Bio.Blast import NCBIXML
from Bio.SeqFeature import SeqFeature, FeatureLocation
from Bio.Graphics import GenomeDiagram
import pandas as pd
from pandas import DataFrame
class Sir... | dieterich-lab/circtools | circtools/sirna/sirna.py | Python | gpl-3.0 | 40,131 | [
"BLAST"
] | b4784257b3849dfc6698de258032478c280146ae51ceaf92a4e349eac489a428 |
""" DISET request handler base class for the ProductionDB.
"""
__RCSID__ = "$Id$"
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Core.DISET.RequestHandler import RequestHandler
from DIRAC.ProductionSystem.DB.ProductionDB import ProductionDB
prodTypes = [basestring, int]
transTypes = [basestring, int, list]
cl... | petricm/DIRAC | ProductionSystem/Service/ProductionManagerHandler.py | Python | gpl-3.0 | 4,593 | [
"DIRAC"
] | e787df6efb1e09bac2639d2e4e5bd5cb39929f981a2fafbd93a7d728f68dfc0c |
#* 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 ..base... | nuclear-wizard/moose | python/MooseDocs/extensions/materialicon.py | Python | lgpl-2.1 | 2,238 | [
"MOOSE"
] | f969fbb3ae08d148787b514f4f384b9dc5e7f35161b97e4bc3e47605ad75753b |
'''
Created on 2009 mar 27
@author: peio
'''
# Copyright 2009 Jose Blanca, Peio Ziarsolo, COMAV-Univ. Politecnica Valencia
# This file is part of franklin.
# franklin is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
# published by the Free Softwa... | JoseBlanca/franklin | test/seq/seqs_test.py | Python | agpl-3.0 | 10,403 | [
"Biopython"
] | c59a6e221a0633ed40a2e2243d233fc982ebe3a8f1af82e9a079dac72c715730 |
# Natural Language Toolkit: Feature Structures
#
# Copyright (C) 2001-2015 NLTK Project
# Author: Edward Loper <edloper@gmail.com>,
# Rob Speer,
# Steven Bird <stevenbird1@gmail.com>
# URL: <http://nltk.sourceforge.net>
# For license information, see LICENSE.TXT
"""
Basic data classes for rep... | MyRookie/SentimentAnalyse | venv/lib/python2.7/site-packages/nltk/featstruct.py | Python | mit | 104,682 | [
"VisIt"
] | 2a969ef60c7159b7a1d7140d9dba9fac20401f2e039a2c34b55947d6e4db0e88 |
"""Retrieve run information describing files to process in a pipeline.
This handles two methods of getting processing information: from a Galaxy
next gen LIMS system or an on-file YAML configuration.
"""
import collections
from contextlib import closing
import copy
import glob
import itertools
import operator
import o... | chapmanb/bcbio-nextgen | bcbio/pipeline/run_info.py | Python | mit | 53,577 | [
"Galaxy"
] | c302f902a601d922ac5232c5a5b6f8b686bfe85e700ee0d55915fc68593aa071 |
#!/usr/bin/env python3
#
# Tests the high-dimensional Gaussian log-pdf toy problem.
#
# This file is part of PINTS (https://github.com/pints-team/pints/) which is
# released under the BSD 3-clause license. See accompanying LICENSE.md for
# copyright notice and full license details.
#
import pints
import pints.toy
impor... | martinjrobins/hobo | pints/tests/test_toy_high_dimensional_gaussian_logpdf.py | Python | bsd-3-clause | 4,459 | [
"Gaussian"
] | 6572d286cbb6c24d05b442af10a517daeab1a281e05ffe030964f15238928602 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2006 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2011 Paul Franklin
#
# This program is free software; you can redistribute it and/or modify
# it under the terms o... | beernarrd/gramps | gramps/gui/plug/_windows.py | Python | gpl-2.0 | 50,908 | [
"Brian"
] | 5228a5aa45de80bcc8b711ddee064331e34cf79b1e2eaa771aec39cd6e5c3081 |
import os
import orca
import pandas as pd
from activitysim import activitysim as asim
from .util.vectorize_tour_scheduling import vectorize_tour_scheduling
"""
This model predicts the departure time and duration of each activity for
non-mandatory tours
"""
@orca.table()
def tdd_non_mandatory_spec(configs_dir):
... | bhargavasana/activitysim | activitysim/defaults/models/non_mandatory_scheduling.py | Python | agpl-3.0 | 1,088 | [
"ORCA"
] | ece838cab3a6a8c96b0b7afa1d8ba1f08f353fed5a67b150fd274d42beae3fba |
import torch as th
import torch.nn as nn
import torch.nn.functional as thf
from permutohedral.gfilt import gfilt
def gaussian_filter(ref, val, kstd):
return gfilt(ref / kstd[:, :, None, None], val)
def mgrid(h, w, dev):
y = th.arange(0, h, device=dev).repeat(w, 1).t()
x = th.arange(0, w, device=dev).re... | HapeMask/crfrnn_layer | crfrnn/crf.py | Python | mit | 4,032 | [
"Gaussian"
] | 7105d70dc7b85a51289d5f45e15f42ce09d7204c15132294ac6ade40662f3729 |
# coding: utf-8
from fabric.api import run, env, cd, prefix, shell_env, local
from config import load_config
config = load_config()
host_string = config.HOST_STRING
def deploy():
env.host_string = config.HOST_STRING
with cd('/var/www/#{project}'):
with shell_env(MODE='PRODUCTION'):
run('g... | hustlzp/Flask-Boost | flask_boost/project/fabfile.py | Python | mit | 785 | [
"GULP"
] | f6895eaca3d87d03cae56353b34321d533411ca7a69028aa7a389e0630262e95 |
# Copyright (c) 2015, Palo Alto Networks
#
# Permission to use, copy, modify, and/or distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS... | PaloAltoNetworks-BD/SplunkforPaloAltoNetworks | SplunkforPaloAltoNetworks/bin/panUserUpdate.py | Python | isc | 7,764 | [
"Brian"
] | d270951b1f0e359e9059715cf1267fa6797a7d5fa50d733ee7fe6cc0a0423c85 |
# This file is a modified part of the PyMVPA package.
#
### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
#
# See COPYING file distributed along with the PyMVPA package for the
# copyright and license terms.
#
### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### #... | DJArmstrong/autovet | Features/TransitSOM/selfsom.py | Python | gpl-3.0 | 12,772 | [
"Gaussian"
] | 11d7225d93f6eecb698f9e1c091ed79f7df8a1826c31413d0aecaab3a03e72e6 |
# -*- coding: utf-8 -*-
import theano
import numpy as np
import scipy
import theano.tensor as T
from const import *
from theano.sandbox.rng_mrg import MRG_RandomStreams as RandomStreams
class RBM(object):
def __init__(self,
n_visible = 1,
n_hidden = 1,
W = None... | NoSRPKU/GradD | My/rbm.py | Python | mit | 3,157 | [
"CDK"
] | 9513634108544274c17b1b5d531ee1ae73a431f860e459f554477b507325405b |
__author__ = 'gph82'
# Since the complicated stuff and the potential for undetectable errors is in bmutils, heavy testing should be done there. This is an API test for checking
# input parsing and decision making (if then) inside the visualize API
import unittest
import numpy as np
import molpx
from glob import glob
fr... | markovmodel/molPX | molpx/tests/test_visualize.py | Python | lgpl-3.0 | 10,548 | [
"MDTraj"
] | 804f9aed57d12331b804f7a8fc0b67a287c35116730da6ec2218fe716a1b70df |
# -*- coding: utf-8 -*-
"""This module contains functions to compare generated sub-graphs to canonical sub-graphs."""
from typing import Any, Mapping
from pybel import BELGraph
from pybel.struct import get_subgraphs_by_annotation
from ..generation import generate_bioprocess_mechanisms
from ..utils import tanimoto_se... | pybel/pybel-tools | src/pybel_tools/analysis/mechanisms.py | Python | mit | 1,513 | [
"Pybel"
] | ea0ed6a2c030d900182a18afc608c346ec50a2ab96514623d55f5addba626c92 |
# -*- coding: utf-8 -*-
from __future__ import absolute_import, division, print_function, unicode_literals
import ast
import functools
import inspect
import os
import os.path
import re
import six
import sys
import types
from os.path import dirname
from six.moves import builtins
from collections import OrderedDict
from ... | Erotemic/utool | utool/util_inspect.py | Python | apache-2.0 | 119,326 | [
"VisIt"
] | a76b71d74f97b95a0d99f9ec75da430e2887d7dffaea20e3f9c00dfdb4fb4d26 |
from numpy import ones, resize, linspace, atleast_3d
from traits.api import Property, Str, Button, Trait, \
Any, Instance, HasStrictTraits, false, Dict, HasTraits, \
CArray, Bool
from traitsui.api import EnumEditor, View, Item, HGroup, \
VGroup, spring, Group, TextEditor, HTMLEditor, InstanceEditor, \
... | dmsurti/mayavi | mayavi/tools/data_wizards/data_source_wizard.py | Python | bsd-3-clause | 28,128 | [
"Mayavi"
] | e5e13ad88393ff7db5e865f1fb35bca937bd94d5d8bb2faf68dba8fbf08123db |
"""HTCondorCE Computing Element
Allows direct submission to HTCondorCE Computing Elements with a SiteDirector Agent
**Configuration Parameters**
Configuration for the HTCondorCE submission can be done via the configuration system. See the page about
configuring :ref:`resourcesComputing` for where the options can be ... | ic-hep/DIRAC | src/DIRAC/Resources/Computing/HTCondorCEComputingElement.py | Python | gpl-3.0 | 23,576 | [
"DIRAC"
] | 19541267c365c643f36da0d45202bf0b207f2a0a69e6bb931f7b6040584037b4 |
""" Definitions of a standard set of pilot commands
Each command is represented by a class inheriting from CommandBase class.
The command class constructor takes PilotParams object which is a data
structure which keeps common parameters across all the pilot commands.
The constructor must call the supe... | DIRACGrid/Pilot | Pilot/pilotCommands.py | Python | gpl-3.0 | 59,038 | [
"DIRAC"
] | cf0b648232c986572711564f6c1ebe8e8b29052fcb98bf1c4c643a8170a36ea8 |
##############################################################################
# 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/r-annotate/package.py | Python | lgpl-2.1 | 1,862 | [
"Bioconductor"
] | a635768771bc6ab201895e3362503dffd77dac1ca13154b57f0ea5413a8c06e5 |
#
# Copyright (C) 2008, Brian Tanner
#
#http://rl-glue-ext.googlecode.com/
#
# 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 requir... | mguzdial3/MineCode | python-codec/examples/mines-sarsa-example/sample_experiment.py | Python | apache-2.0 | 5,659 | [
"Brian"
] | b133e613d2cba25247ba3f8de38b4ce7195e2b66f524a2bcff2543320d3df6d5 |
# -*-python-*-
#
# Copyright (C) 1999-2006 The ViewCVS Group. All Rights Reserved.
#
# By using this file, you agree to the terms and conditions set forth in
# the LICENSE.html file which can be found at the top level of the ViewVC
# distribution or at http://viewvc.org/license-1.html.
#
# For more information, visit h... | foresthz/fusion5.1 | www/scm/viewvc/lib/win32popen.py | Python | gpl-2.0 | 8,004 | [
"VisIt"
] | e399f27d261d59f7ce8cca1dd28978c0a0a81ebf8d0bbdd470157d562a073a7f |
import os
from boxbranding import getMachineBrand, getMachineName
import xml.etree.cElementTree
from datetime import datetime
from time import ctime, time, strftime, localtime, mktime
from bisect import insort
from enigma import eActionMap, quitMainloop
from Components.config import config
from Components.TimerSanity... | sklnet/openhdf-enigma2 | PowerTimer.py | Python | gpl-2.0 | 40,406 | [
"ASE"
] | baaae8280ca768656830deb4c4798a78c979629dcb01c5ec4771d2aae7a07854 |
# Mark Gatheman <markrg@protonmail.com>
#
# This file is part of Hydrus.
#
# Hydrus 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.
#
#... | mark-r-g/hydrus | hydrus/model.py | Python | gpl-3.0 | 8,089 | [
"Gaussian"
] | e6157fcb26aa6c83dd9b47ffb3354b5df6272900e1556f289999ed53e637482c |
# 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 by applicable law or ... | ychen820/microblog | y/google-cloud-sdk/platform/google_appengine/lib/oauth2client/oauth2client/tools.py | Python | bsd-3-clause | 8,283 | [
"VisIt"
] | a3737ef8175111d7310901a938963126b655ca2c9370bf719e17066c90c6e7e7 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals, division, print_function
import os
from pymatgen.util.testing import PymatgenTest
from pymatgen.io.abinit.tasks import *
from pymatgen.io.abinit.tasks import TaskPolicy... | aykol/pymatgen | pymatgen/io/abinit/tests/test_tasks.py | Python | mit | 6,171 | [
"ABINIT",
"pymatgen"
] | 37915bed44267c383059a8b2e92529ad08f094c38caef6fc9a2c45cc08a6f910 |
# BEGIN_COPYRIGHT
#
# Copyright (C) 2009-2013 CRS4.
#
# This file is part of biodoop-blast.
#
# biodoop-blast 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 opt... | crs4/biodoop-blast | bl/blast/mr/__init__.py | Python | gpl-3.0 | 755 | [
"BLAST"
] | dbf4ee43393cb1d2a73d619a0aa2598449c16b5e437dd6f01c5baba6cdbda560 |
# -*- coding: utf-8 -*-
"""
<DefineSource>
@Date : Fri Nov 14 13:20:38 2014 \n
@Author : Erwan Ledoux \n\n
</DefineSource>
The Doer defines instances that are going to decorate a big family of classes in this framework.
Staying on the idea, that one module should associate
one class, now a decorated class by a Doe... | Ledoux/ShareYourSystem | Pythonlogy/build/lib/ShareYourSystem/Standards/Classors/Doer/__init__.py | Python | mit | 27,009 | [
"Brian",
"NEURON",
"VisIt"
] | 4df9f0e0ed66778a0f10e408414445e4dc5b763a37054a7d2371f7ec7acd96c3 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# ls - [insert a few words of module description on this line]
# Copyright (C) 2003-2009 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the GN... | heromod/migrid | mig/cgi-bin/ls.py | Python | gpl-2.0 | 1,116 | [
"Brian"
] | 3cd18aa7b3ee78cca1a1a1e1d6dc7a9574edaa2ae1103a4985eaea616e2b0f4d |
'''
Created on Oct 12, 2011
this code is for reading input parameters.
@author: Ying Jin
@status:
@contact: yjin@cshl.edu
@version:
'''
# python modules
import sys
import os
import re
import logging
import time
import gzip
import collections
from math import log
from TEToolkit.Constants import *
from TEToolkit.Sh... | mhammell-laboratory/tetoolkit | TEToolkit/IO/ReadInputs.py | Python | gpl-3.0 | 19,820 | [
"HTSeq"
] | f9ef516989023d73e29770008c69a5c0fbd2c291a812f8765dcf840f449270c9 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
# transformations.py
# Copyright (c) 2006, Christoph Gohlke
# Copyright (c) 2006-2010, The Regents of the University of California
# All rights reserved.
#
# Redistribution and use in source... | kain88-de/mdanalysis | package/MDAnalysis/lib/transformations.py | Python | gpl-2.0 | 60,745 | [
"MDAnalysis"
] | b2ff682b5e4763980db07aed5d55d51aeed21ce00553d02f2ad0569cfa84e3b2 |
from haystack import indexes
from moto.moe.models import Post
class PostIndex(indexes.SearchIndex, indexes.Indexable):
text = indexes.NgramField(document=True, model_attr='description')
author = indexes.CharField(model_attr='author')
pub_date = indexes.DateTimeField(model_attr='date_posted')
def get_m... | bung87/moto-moe | moto/moe/search_indexes.py | Python | mit | 351 | [
"MOE"
] | 2d8e87c966ce4d96460eaa427a05047a1c3f8f412f18062c29137329e68610a7 |
#
# @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
#... | dgasmith/psi4 | psi4/driver/qcdb/hessparse.py | Python | lgpl-3.0 | 2,556 | [
"CFOUR",
"Psi4"
] | 2e855521dfa6a20180f95e7a8e35aceec27905b5543ad55b96ef3f84173f31ca |
import pyscf.pbc.tools.make_test_cell as make_test_cell
from pyscf.pbc.tools.pbc import super_cell
from pyscf.pbc import gto, scf, cc
from pyscf.pbc.cc.eom_kccsd_ghf import EOMIP, EOMEA, EOMEE
from pyscf.pbc.cc.eom_kccsd_ghf import EOMIP_Ta, EOMEA_Ta
from pyscf.cc import eom_gccsd
import unittest
cell = make_test_cell... | sunqm/pyscf | pyscf/pbc/cc/test/test_eom_kgccsd.py | Python | apache-2.0 | 10,605 | [
"PySCF"
] | b9aebc670d3c565eecba471989a59a2e3dfbc67695c113c596a66862792c7919 |
# -*- coding: utf-8 -*-
from brian import *
import numpy as np
import matplotlib.pyplot as plt
from scipy.spatial.distance import cdist
from math import *
import matplotlib.animation as animation
#np.random.seed(1) # Initialization of the random generator (same randoms values)
# ------------------- Functions --------... | Aurelien1609/Computational-model | spikes_neural_field.py | Python | bsd-3-clause | 6,761 | [
"Brian",
"Gaussian"
] | f1aa2eaffd2b8b58bbef68a4257d0d36027410814fa4df0b1e15e9927ee56ae0 |
"""
Wraps all the functionality required for applying blurring techniques to an image.
"""
import cv2
__authors__ = "Stephan Nell, Nicolai van Niekerk"
__copyright__ = "Copyright 2017, Java the Hutts"
__license__ = "BSD"
__maintainer__ = "Stephan Nell"
__email__ = "nellstephanj@gmail.com"
__status__ = "Development"
... | javaTheHutts/Java-the-Hutts | src/main/python/hutts_verification/image_preprocessing/blur_manager.py | Python | bsd-3-clause | 4,986 | [
"Gaussian"
] | 5f60f328fd2ad11aeb56bd4fe7a7372753e083bf26d0ed34ba16cd99aae1eb1f |
from __future__ import print_function
"""
NAME:
LUMDIST
PURPOSE:
Calculate luminosity distance (in Mpc) of an object given its redshift
EXPLANATION:
The luminosity distance in the Friedmann-Robertson-Walker model is
taken from Caroll, Press, and Turner (1992, ARAA, 30, 499), p. 511
Uses a close... | segasai/astrolibpy | astrolib/lumdist.py | Python | gpl-3.0 | 4,833 | [
"Galaxy"
] | 88ead1939b2a771bd9d542c0d990822f7a818ee37e20dc15e4d855c24fb9d48a |
# Adapted from Matlab to Python by Jon Crall
# Original Matlab Source:
# http://www.mathworks.se/matlabcentral/fileexchange/36657-fast-bilateral-filter/content/FastBilateralFilter/shiftableBF.m
# These are shorthands I used to help with porting 1 based to 0 based
# [k] = 2:end
# [-k-1] = fliplr(1:end-1)
#... | Erotemic/hotspotter | hstpl/other/shiftableBF.py | Python | apache-2.0 | 6,577 | [
"Gaussian"
] | 5aaf53f937882d21b314c88af9415e9b8f9027990edafbb0f74345db3e5bb835 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
summary
Improvements over previous version include:
- "state" object (single underscore) that maintains and passes session info
between all modules.
- Translation module for registering StringVars and easily switch languages.
- "settings" that are saved and loaded from... | Ripley6811/TAIMAU | src/main.py | Python | gpl-2.0 | 20,905 | [
"ASE"
] | 5308f5f59cc055576ad9e9c7b9ef213d846cb6376d9d02da5c04c93fc8d50e7e |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class TrilinosCatalystIossAdapter(CMakePackage):
"""Adapter for Trilinos Seacas Ioss and Paravie... | LLNL/spack | var/spack/repos/builtin/packages/trilinos-catalyst-ioss-adapter/package.py | Python | lgpl-2.1 | 1,549 | [
"NetCDF",
"ParaView"
] | 72c6b08f40a7c0ace27175cd0cd966dfd0cc864220577538bab9fecbcbfe79dd |
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this file,
# You can obtain one at http://mozilla.org/MPL/2.0/.
import operator
from ..node import NodeVisitor
from ..parser import parse
class Compiler(NodeVisitor):
"""Compile... | indykish/servo | tests/wpt/harness/wptrunner/wptmanifest/backends/static.py | Python | mpl-2.0 | 6,484 | [
"VisIt"
] | 0f87666b26a1ac2378828cf1abdf1fdfd6ea865f8d6cfe858d608eeba28606fc |
from pymatgen.core.structure import Molecule
from monty.json import MSONable
import re
import os
from monty.itertools import chunks
from monty.io import reverse_readline
__author__ = 'Xin Chen, chenxin13@mails.tsinghua.edu.cn'
def is_numeric(s):
"""
Return True is the string ``s`` is a numeric string.
... | dongsenfo/pymatgen | pymatgen/io/adf.py | Python | mit | 31,427 | [
"ADF",
"Gaussian",
"NWChem",
"pymatgen"
] | eb28a16e6117ac6252b212512a1cc9bd44fffce0b9198db09cb12dec12129f2f |
import abc
import warnings
import glfw
from gym import error
from gym.utils import seeding
import numpy as np
from os import path
import gym
try:
import mujoco_py
except ImportError as e:
raise error.DependencyNotInstalled("{}. (HINT: you need to install mujoco_py, and also perform the setup instructions here... | rlworkgroup/metaworld | metaworld/envs/mujoco/mujoco_env.py | Python | mit | 4,711 | [
"TINKER"
] | 8c7e9b0aa373ade3b5826cf4e3a8d63ee607e44b1cba17599f17d6dc4042f3af |
from google.appengine.ext import ndb
from app.models.ndb.character import Character, root
from app.models.ndb.faction import Faction
def ensure_minimal_data_in_datastore():
friendships(characters(*factions()))
def friendships(characters):
_friendships = [
(characters['han'], characters['leia']),
... | py-in-the-sky/appengine-swapi | graphql/fixtures/__init__.py | Python | mit | 2,635 | [
"Galaxy"
] | 1aff2bf0659840f8df3e812912b4b5008a8c5f8bdfbf4ea5bbf0e891437e28d5 |
#* 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
"""
Module ... | harterj/moose | python/MooseDocs/base/Translator.py | Python | lgpl-2.1 | 13,218 | [
"MOOSE"
] | 4f41fb77eeb3e48c383952a56efa25c4556a3ccb96fd527d2aacf87e3c0d26d9 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2001-2006 Donald N. Allingham
# Copyright (C) 2008-2009 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publi... | Forage/Gramps | gramps/gui/plug/report/_textreportdialog.py | Python | gpl-2.0 | 3,782 | [
"Brian"
] | 4f5ccd8b423ef2dc9dff164db0563214b4928244b0504cc9789b367b74f1bc81 |
from __future__ import unicode_literals, division, absolute_import
from datetime import timedelta, datetime
import pytest
from flexget.manager import Session
from flexget.plugins.api_tvmaze import APITVMaze, TVMazeLookup, TVMazeSeries
lookup_series = APITVMaze.series_lookup
@pytest.mark.online
class TestTVMazeSho... | antivirtel/Flexget | tests/test_tvmaze.py | Python | mit | 19,827 | [
"Firefly"
] | c65afba1b8507b6270146e0423e267308dbbdea2db4341cc41a7980fe7fe06e4 |
# helper.py
import os, cmath, math, sys, glob, subprocess, re, argparse, shutil, datetime, csv, commands
import numpy as np
import cfg
import pandas as pd
from collections import defaultdict
from operator import itemgetter
import matplotlib as mpl
import matplotlib.pyplot as plt
from matplotlib import cm
from optparse... | ChangLab/FAST-iCLIP | fasticlip/helper.py | Python | gpl-2.0 | 56,380 | [
"Bowtie"
] | 20f56573fd75b9528b9603131eb848fa4062647685e8629f3b0ca7837decf41b |
# -*-coding:Utf-8 -*
# Copyright (c) 2010 LE GOFF Vincent
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source code must retain the above copyright notice, this
# lis... | stormi/tsunami | src/primaires/communication/attitude.py | Python | bsd-3-clause | 6,987 | [
"ADF"
] | 2ab90591eaf0e687ef722eb03e52b2d1b3ff0b6fe7b42d98291e269947c15368 |
from django.db import models
from django.core.validators import MinValueValidator, MaxValueValidator
from edc_base.audit_trail import AuditTrail
from edc_base.model.fields.custom_fields import OtherCharField
from edc_base.model.models import BaseUuidModel
from edc_code_lists.models import WcsDxAdult
from edc_constants... | botswana-harvard/microbiome | microbiome/apps/mb_maternal/models/maternal_post_fu.py | Python | gpl-2.0 | 5,522 | [
"VisIt"
] | d613540a7babe16f150f49cf1c24d64dd1863943aa99706d4aab8bac60631a93 |
"""
Clustering win32 files with unsupervised learning algorithms: Kmeans, MiniBatchKMeans and Gaussian Mixture Model.
Features computed are: size of the PE file, Number of sections, imports (dll) and suspicious API loaded
Different combinations of features and algorithms can be tested on the win32 files.
The silhouette... | greysab/MLware | cluster_win32.py | Python | gpl-3.0 | 9,803 | [
"Gaussian"
] | 5aecbc68c265d321f7b696c726efe3f3ab33aad327178d9cd4fd29aba1f301ec |
# python3
# Copyright 2020 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in... | GoogleCloudPlatform/solutions-cloud-orchestrate | cli/src/orchestrate/commands/broker/users/list.py | Python | apache-2.0 | 2,844 | [
"VisIt"
] | 5f45b53898d1f51589bf1ff513d743cf1c93f47122871d95768276c3cf4499c6 |
#!/usr/bin/env python
'''
Created on Jan 5, 2011
@author: mkiyer
chimerascan: chimeric transcript discovery using RNA-seq
Copyright (C) 2011 Matthew Iyer
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 Founda... | madhavsuresh/chimerascan | chimerascan/deprecated/chimerascan_index_v1.py | Python | gpl-3.0 | 5,779 | [
"Bowtie",
"pysam"
] | 140133f57ae476a0824bec27bb1083f815819ba954c6d9833799d9578ebd3c26 |
#
# Copyright (C) 2013,2014,2015,2016 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option)... | KonradBreitsprecher/espresso | doc/tutorials/01-lennard_jones/scripts/lj_tutorial.py | Python | gpl-3.0 | 5,016 | [
"ESPResSo"
] | f18eab9ac8edcf302ca02320d34f1f24f61eaa3972a166bb56cb9619df7c7cf7 |
from __future__ import print_function
print(__doc__)
import os
import sys
import numpy as np
#import matplotlib
#matplotlib.use('AGG') # Do this BEFORE importing matplotlib.pyplot
import matplotlib.pyplot as plt
#from matplotlib.colors import Normalize
import matplotlib.colors as colors
import matplotlib.cm as cm
... | weissercn/learningml | learningml/GoF/classifier_eval.py | Python | mit | 48,275 | [
"Gaussian"
] | 6a8498bce0af2e38d3f0e44041337ae206b060b3e21201a194b2bc4b95d34e3c |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
########################################################################
# Solves problem 35 from projectEuler.net.
# Finds the number of circular primes under 1000000.
# Copyright (C) 2010 Santiago Alessandri
#
# This program is free software: you can redistribu... | salessandri/programming-contests | project-euler/problem035.py | Python | gpl-3.0 | 1,498 | [
"VisIt"
] | 198a90ed7468b2728f3d72ed1b3f319313cfb61d7cfa11d3eea88b0706693d6e |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under t... | MDAnalysis/mdanalysis | package/MDAnalysis/coordinates/null.py | Python | gpl-2.0 | 2,148 | [
"MDAnalysis"
] | cf3c7cce4fdf5d3e7a66c41c1ea8b9e2db9eca8124365dc0e07c1359290a2acd |
# -*- coding: utf-8 -*-
#
# ESPResSo++ documentation build configuration file, created by
# sphinx-quickstart on Sat Jan 23 13:11:32 2010.
#
# 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
# autogenerated file.
#
# ... | capoe/espressopp.soap | doc/ug/conf.py | Python | gpl-3.0 | 8,126 | [
"ESPResSo"
] | e5492fe0829564e9ca8ad8af604e992b73521f287cee773d2572d984e2be0307 |
#!/usr/bin/env python3
import ast
import random
class ParseException(Exception):
pass
class DuplicateRegistration(Exception):
pass
class NamespaceUnroller(ast.NodeVisitor):
def __init__(self, namespaces):
self.namespaces = namespaces
def visit_Str(self, node):
string = n... | jotomicron/MOSSy | mossy/parse_config.py | Python | gpl-2.0 | 14,132 | [
"VisIt"
] | aefdc6b5ec8c184bcada34ee196f63e68d3aa1c7721a273b4e4c9aef616e7f9d |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
GridPP and DIRAC: adding CERN@school frame metadata.
"""
import os
#...for parsing the arguments.
import argparse
#...for the logging.
import logging as lg
# Import the JSON library.
import json
# The DIRAC imports.
from DIRAC.Core.Base import Script
Script.par... | gridpp/dirac-getting-started | add_frame_metadata.py | Python | mit | 2,600 | [
"DIRAC"
] | c5df3699f2be1e97d45df44078bcc5a2eae8889c74f0908b03b6812bd88d2e47 |
"""
Module for turning Bluetooth manufacturer id's into human readable
names.
Master list available from the Bluetooth Special Interest Group:
https://www.bluetooth.com/specifications/assigned-numbers/company-identifiers/
"""
def lookup(company_id):
"""Utility function to easily lookup names of companies... | ukBaz/ble_beacon | scanner/company_id.py | Python | gpl-2.0 | 15,851 | [
"CRYSTAL",
"Jaguar"
] | c4654594d2f471a72ca1e3be166669e02c063532be33ba313f00d8bcccdd1f4b |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2009, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License versi... | zenoss/ZenPacks.community.VMwareESXMonitor | ZenPacks/community/VMwareESXMonitor/__init__.py | Python | gpl-2.0 | 1,833 | [
"VisIt"
] | ee898c9ea24ed4eb96634ee3bc5274649163be3410125b4c97aa1bec2aa14897 |
import os.path
from webhelpers2.html.builder import HTML
from webhelpers2.html.tags import checkbox
from webhelpers2_grid import Grid
import string # TODO replace by mako template
from mako.lookup import TemplateLookup
import logging
logger = logging.getLogger(__name__)
def get_value(record, attribute, default=No... | bird-house/pyramid-phoenix | phoenix/grid.py | Python | apache-2.0 | 8,937 | [
"NetCDF"
] | 2894e1f66d83548ef746c790875ab56054cc504823ac5763cffa17665c9f03bf |
#!/usr/local/bin/env python
"""
Storage submodule
This submodule is a user-friendly storage driver which relies on two major classes from the user perspective:
StorageIODriver and StorageInterface
StorageIODriver
---------------
The StorageIODriver is the abstract base class which handles IO operations on disk with... | choderalab/openmmtools | openmmtools/storage/__init__.py | Python | mit | 4,021 | [
"NetCDF"
] | 282f6efff15fd77a9ee95b711bd37ff363e792d1ab57a7b5c739276afe6f5b10 |
# -*- coding: utf-8 -*-
"""
moe.wiki.urls
~~~~~~~~~~~~~
URL definitions. All URLs:
/wiki/
/wiki/<path:page_path>
/wiki/pages/
/wiki/pages/changes/
/wiki/pages/changes/<path:page_path>
/wiki/pages/changes-feed/
/wiki/pages/changes-feed/<path:page_pa... | ac001/moe | project/app/moe/wiki/urls.py | Python | bsd-3-clause | 3,930 | [
"MOE"
] | a9251f3ccf49eff8c7c15ed342db11b32bfd707a72734323daf21f84d1cbcae9 |
#!/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/at.py | Python | gpl-2.0 | 18,602 | [
"VisIt"
] | e71d0c70fe4c5e080fa3159683d14ebfac27145ec807431de1ba9849e89bc6b5 |
"""
It contains a collection of methods and classes that are useful for the package.
"""
# standard libraries imports
from __future__ import print_function
import os
import sys
import time
import uuid
from random import random as generate_random_float # generates a random float number between 0 and 1
from random imp... | bachiraoun/fullrmc | Core/Collection.py | Python | agpl-3.0 | 96,743 | [
"Gaussian"
] | a30fd330ddb4ab02573a2ee301e613b0c0346890031d39a96e59a4b53eaf4c6d |
#!/usr/bin/env
"""
Program: SST_Region.py
Purpose: generate a timeseries of SST data at/near EcoFOCI M2 (Berring Sea) Mooring
DataSource: ftp://ftp.cdc.noaa.gov/Datasets/noaa.oisst.v2.highres/
Input/Arguments: Latitude and Longitude, raw data file
"""
#System Stack
import datetime
#Science Stack
from netCDF4 imp... | shaunwbell/FOCI_Analysis | SST_Region_anom.py | Python | mit | 6,546 | [
"NetCDF"
] | 23f0eec88b604fb74bbb647d292de5e6a32f4bce34af600cfa6b5beabcb15bff |
#!/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... | sunqm/pyscf | pyscf/ao2mo/_ao2mo.py | Python | apache-2.0 | 11,179 | [
"PySCF"
] | 7d17e10d1843a048b182ef0487a60706a5ec0dd0c81526d858d2f43e4b0ae508 |
# Copyright 2018 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... | jendap/tensorflow | tensorflow/tools/compatibility/tf_upgrade_v2_test.py | Python | apache-2.0 | 50,933 | [
"Gaussian"
] | 62f8d70504a39082d09ab2dfbbfdb433258678b7a9b226d14c24efb7288436e3 |
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