text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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|---|---|---|---|---|---|---|---|
"""
===========================================
Sparse coding with a precomputed dictionary
===========================================
Transform a signal as a sparse combination of Ricker wavelets. This example
visually compares different sparse coding methods using the
:class:`sklearn.decomposition.SparseCoder` esti... | RPGOne/Skynet | scikit-learn-0.18.1/examples/decomposition/plot_sparse_coding.py | Python | bsd-3-clause | 4,038 | [
"Gaussian"
] | 3ccd5d38db8a80c4dc83db76588fd7d36ab3c8e6cb947e6ae5d14ba4977b3740 |
try:
import ROOT
except:
pass
import array
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
from Unfolder.Histogram import H1D, H2D, plotH1D, plotH2D, plotH1DWithText, plotH2DWithText, plotH1DLines
'''
To be used to scan TUnfold's object to find the optimal tau value for
the regularisatio... | daniloefl/Unfolder | Unfolder/ComparisonHelpers.py | Python | gpl-3.0 | 12,462 | [
"DIRAC"
] | d163846baed4707df19b064a12c5b5760afdbb9504aa29150e32a2ea4b69ae0e |
"""
Views related to the Custom Courses feature.
"""
import csv
import datetime
import functools
import json
import logging
from copy import deepcopy
from cStringIO import StringIO
import pytz
from ccx_keys.locator import CCXLocator
from django.conf import settings
from django.contrib import messages
from django.contr... | procangroup/edx-platform | lms/djangoapps/ccx/views.py | Python | agpl-3.0 | 21,447 | [
"VisIt"
] | 11c50d730555192f1bf8f8b27762954eafb54488711e6c461a07c7f007ef680f |
'''
Created on 2015/03/13
@author: admin
'''
import numpy as np
class Firefly:
'''
Particle Swarm Optimization
'''
def __init__(self,ite,pop=20,alpha=0.25,beta=0.5, gamma=1.0, variant='sfa',torus=True,best=None,ftarget=-np.inf,threads=1):
'''
Default values are stable and usually fine.... | kanemasa1987/Meatpie | optlib/firefly.py | Python | mit | 9,673 | [
"Firefly"
] | d81f5fbb410063348f86f2c3d15e7218ffbb1480a7c0c7514539280678a7d011 |
from __future__ import absolute_import
import unittest
from lark import Lark
from lark.lexer import Token
from lark.tree import Tree
from lark.visitors import Visitor, Transformer, Discard
from lark.parsers.earley_forest import TreeForestTransformer, handles_ambiguity
class TestTreeForestTransformer(unittest.TestCas... | lark-parser/lark | tests/test_tree_forest_transformer.py | Python | mit | 7,156 | [
"VisIt"
] | da3b3114f76436a6fceca507db143785023026cd3c191a7b2a68dd128f96d993 |
#!/usr/bin/env python
##############################################################################################
#
#
# regrid_emissions_N96e.py
#
#
# Requirements:
# Iris 1.10, cf_units, numpy
#
#
# This Python script has been written by N.L. Abraham as part of the UKCA Tutorials:
# http://www.ukca.ac.uk/wiki... | acsis-project/emissions | emissions/python/periodic_1960/regrid_C2H6_emissions_n96e_360d_1960.py | Python | gpl-3.0 | 7,151 | [
"NetCDF"
] | e9146455bfc53144f62cbec0e0e23d508978ddf5f5c469aa808cb6214f3d41d4 |
#!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
Created on Wed Dec 14 16:21:46 2016
Defines a function to call Galfit for a single fits image sersic optimisation
Also a funtion to calculate chisquared for a given sersic parametrerisation
@author: rs548
"""
from __future__ import division, print_function
import ... | raphaelshirley/regphot | regphot/galfit.py | Python | mit | 12,302 | [
"Gaussian"
] | 579b28116f68a3a1a7079e51031130181b27497209e500f6d7fa7ec6c0a580f1 |
#!/usr/bin/env python
# Copyright (C) 2012, 2014 Moritz Huetten
# geometry setup MISMIP3D P75S/P10S-experiment
from pylab import *
import os
import sys
import getopt
import math
#from numpy import *
import numpy as np
try:
from netCDF4 import Dataset as NC
except:
print "netCDF4 is not installed!"
sys.ex... | talbrecht/pism_pik07 | examples/mismip/mismip3d/setup_PXXS.py | Python | gpl-3.0 | 6,670 | [
"NetCDF"
] | 7c0dff9c100642e35b69bc00c94a099a41d64460527ffba48d41ed15932c685b |
"""
Test of the classical LM model for language modelling
"""
from groundhog.datasets import LMIterator
from groundhog.trainer.SGD_adadelta import SGD
from groundhog.mainLoop import MainLoop
from groundhog.layers import MultiLayer, \
RecurrentMultiLayer, \
RecurrentMultiLayerInp, \
RecurrentMultiLa... | vseledkin/LV_groundhog | tutorials/DT_RNN_Tut_Adadelta.py | Python | bsd-3-clause | 14,259 | [
"Gaussian"
] | 24d2e79ffc663feff87efe329a6d8fd5051e49a3415bf1aa0a74930397b8b170 |
"""Random variable generators.
integers
--------
uniform within range
sequences
---------
pick random element
pick random sample
generate random permutation
distributions on the real line:
------------------------------
unif... | alanjw/GreenOpenERP-Win-X86 | python/Lib/random.py | Python | agpl-3.0 | 33,174 | [
"Gaussian"
] | 830acb521d9c9d616ff4c4a725d9b1283aafe931e537b4e9192b6287cbeb4d9a |
'''
Driver method to run the monte_carlo module using mixed DNA and protein moves
with several options for a nucleosomecore particle (NCP)
$Id: gui_mimic_ncp.py 3037 2016-03-01 19:55:18Z schowell $
'''
import sys
import multiprocessing
import sassie.interface.input_filter as input_filter
import sassie.simulate.torsion_... | madscatt/zazzie | src_2.7/sassie/simulate/torsion_angle_monte_carlo/gui_mimic_ncp_all_flex.py | Python | gpl-3.0 | 7,212 | [
"OpenMM"
] | a59b37f9eaa4a2e09509ea4737d04d423822c182c7056ea55fd9c7f6a0414fcc |
#!/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
# ... | t0mk/ansible | lib/ansible/modules/network/lenovo/cnos_command.py | Python | gpl-3.0 | 5,726 | [
"VisIt"
] | 70b71b4398223fae652bb892cff07deade4264fb9fabfd467742e2af79e66cfb |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
import datetime
from django.core.exceptions import ImproperlyConfigured, ObjectDoesNotExist
from django.test import TestCase, override_settings
from django.test.client import RequestFactory
from django.views.generic.base import View
from django.views.gen... | DONIKAN/django | tests/generic_views/test_detail.py | Python | bsd-3-clause | 8,387 | [
"MOOSE"
] | fbdd12a347395cccccf14f0ae04331101789f39f2536a95c03e0792bf3728373 |
import numpy as np
from gpaw.xc.hybrid import HybridXCBase
class ForceCalculator:
def __init__(self, timer):
self.timer = timer
self.reset()
def reset(self):
self.F_av = None
def calculate(self, wfs, dens, ham):
"""Return the atomic forces."""
assert not... | robwarm/gpaw-symm | gpaw/forces.py | Python | gpl-3.0 | 1,191 | [
"GPAW"
] | a2f48171fb47f71df4af1c8121dddf0a74fabc5b2ef012f493905f4affbf1527 |
""" The PBS TimeLeft utility interrogates the PBS batch system for the
current CPU and Wallclock consumed, as well as their limits.
"""
__RCSID__ = "$Id$"
import os
import re
import time
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Core.Utilities.TimeLeft.TimeLeft import runCommand
class PBSTimeLeft( obj... | andresailer/DIRAC | Core/Utilities/TimeLeft/PBSTimeLeft.py | Python | gpl-3.0 | 5,069 | [
"DIRAC"
] | 8358b44c587217198c9518e6f5a907f0b4af1cd2356ddd50521baab2cc30056e |
#
# @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
#... | CDSherrill/psi4 | psi4/driver/procrouting/findif_response_utils/__init__.py | Python | lgpl-3.0 | 1,235 | [
"Psi4"
] | a008fbef94b135de42b3bd8297ce102073a5e3940bbdb3760bd678e42585eb0d |
# Copyright (c) 2003-2012 LOGILAB S.A. (Paris, FRANCE).
# http://www.logilab.fr/ -- mailto:contact@logilab.fr
#
# 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, o... | hpfem/agros2d | resources/python/pylint/checkers/design_analysis.py | Python | gpl-2.0 | 16,303 | [
"VisIt"
] | 1330aab6dfee76d076f73bda05e814c2974abff1526bd025b675013ba3e9bb6e |
#!/usr/bin/python
import re
import sys
import httplib
import getpass
import base64
def get_session_id(host,path):
req = httplib.HTTPConnection(host)
# write header
req.putrequest("GET",path+"index.php")
req.putheader("Host",host)
req.putheader("Connection","close")
req.endheaders()
res = re... | c1ph3r/VA-Scripts | phpldapadmin-rce.py | Python | gpl-2.0 | 2,887 | [
"VisIt"
] | db884ed7c623e8395cfeee8856cec63ab6bb0ce6dde646bea7c7cf699043c911 |
# -*- coding: utf-8 -*-
'''
IMProToo
Improved MRR Processing Tool
Python toolkit to read, write and process MRR Data. Raw Data, Average and
Instantaneous Data are supported.
Copyright (C) 2011-2021 Maximilian Maahn, U Leipzig
maximilian.maahn_AT_uni-leipzig.de
https://github.com/maahn/IMProToo
This program is free ... | maahn/IMProToo | IMProToo/core.py | Python | gpl-3.0 | 135,969 | [
"NetCDF"
] | 1c0e3304e6ebd00c51802cffbf02e9d75f2b984f25c87566924844e9c1516cf4 |
###############################
# 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, suc... | pylada/pylada-light | tests/vasp/test_system.py | Python | gpl-3.0 | 2,246 | [
"CRYSTAL",
"VASP"
] | 69d991cd24fdf9d9dc42a024c877578d225e50fdb370913341ebf1b6464a6875 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | rmcgibbo/psi4public | psi4/driver/procrouting/mcscf/augmented_hessian.py | Python | lgpl-3.0 | 5,838 | [
"Psi4"
] | 673a2352347b008e9b990061992b7a3fb430d0ab8580128e414f536d43e7c4e1 |
#!/usr/bin/env python
"""
This script is a python version of TimingAccuracyGLQ. We use numpy functions to
simplify the creation of random coefficients.
"""
from __future__ import absolute_import, division, print_function
import os
import sys
import time
import numpy as np
sys.path.append(os.path.join(os.path.dirname(... | heroxbd/SHTOOLS | examples/python/TimingAccuracy/TimingAccuracyGLQ.py | Python | bsd-3-clause | 2,830 | [
"Gaussian"
] | 681b244b9dde11a73e0a485010cbc0b92064790ec2c2487803ad6aeaf92f9e9a |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | Stargrazer82301/CAAPR | CAAPR/CAAPR_AstroMagic/PTS/pts/magic/catalog/builder.py | Python | mit | 7,693 | [
"Galaxy"
] | 17c2a23204e27876d6cc1aa42c0b6e4753e694874fbc34cadcf0ea665b0f5a75 |
# This file is part of Androguard.
#
# Copyright (c) 2012 Geoffroy Gueguen <geoffroy.gueguen@gmail.com>
# All Rights Reserved.
#
# Androguard 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 versi... | JulianSchuette/android-instrumentation | injector/androguard/decompiler/dad/basic_blocks.py | Python | apache-2.0 | 10,398 | [
"VisIt"
] | d5ddc309a585951d768aed2cd0a8ba13d98b9897f5ef24cbf65f6891fd806f33 |
from django.template import Template
from django.template import Context
from django.conf import settings
import os
import json
import itertools
from collections import namedtuple
import time
import math
from functools import partial
settings.configure() #ignoring django bullshit
variables = json.load(open("variable... | Tulane/FHI-AIMS-input-generator | generator.py | Python | mit | 3,071 | [
"FHI-aims"
] | 1f05ef482ef5a7f4a3fc7524a36eefbbe4a72c5c288d3d82610e198487f141e3 |
#!/usr/bin/env python
import sysconfig
import subprocess
import json
import os
import sys
import platform
if os.path.dirname(__file__):
os.chdir(os.path.dirname(__file__))
if platform.system() == 'Windows' or platform.system().startswith('CYGWIN'):
sys.exit(0) # test not supported on windows - ignore it
so_f... | naufraghi/rust-cpython | tests/check_symbols.py | Python | mit | 2,847 | [
"VisIt"
] | 140608331a017f4e8e06e1469b5e4650e1e688b674273a49d5a9c122d9603858 |
"""
Class for management of Stomp MQ connections, e.g. RabbitMQ
"""
import json
import random
import os
import socket
import ssl
import time
import stomp
from DIRAC.Resources.MessageQueue.MQConnector import MQConnector
from DIRAC.Core.Security import Locations
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Core.... | andresailer/DIRAC | Resources/MessageQueue/StompMQConnector.py | Python | gpl-3.0 | 11,290 | [
"DIRAC"
] | b47c30a3c61db130e2c72a2d880aa99d97b790b6a2fad43437971ad323ff8ff3 |
# -*- coding: utf-8 -*-
# Generated by Django 1.11 on 2018-06-03 13:09
from __future__ import unicode_literals
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
('seqr', '0039_merge_20180531_1604'),
]
operations = [
migrations.AddField(
... | macarthur-lab/xbrowse | seqr/migrations/0040_auto_20180603_1309.py | Python | agpl-3.0 | 2,879 | [
"ASE"
] | 3e7280977657a7af5a0da287fc82f5879b47ecc431d480b119b9de2911924088 |
#!/usr/bin/env python
import sys
import os
import math
# ensure that the kicad-footprint-generator directory is available
#sys.path.append(os.environ.get('KIFOOTPRINTGENERATOR')) # enable package import from parent directory
#sys.path.append("D:\hardware\KiCAD\kicad-footprint-generator") # enable package im... | pointhi/kicad-footprint-generator | scripts/tools/footprint_scripts_crystals.py | Python | gpl-3.0 | 45,603 | [
"CRYSTAL"
] | e2fdfc29c1024471588cb4a61d78f2a10301d50e7963692e683a74b25c0813f1 |
from __future__ import division, print_function
import numpy as np
import nose.tools as nt
import regreg.api as rr
from ..modelQ import modelQ
from ..lasso import lasso
from ...tests.instance import gaussian_instance
def test_modelQ():
n, p, s = 200, 50, 4
X, y, beta = gaussian_instance(n=n,
... | selective-inference/selective-inference | selectinf/randomized/tests/test_modelQ.py | Python | bsd-3-clause | 1,147 | [
"Gaussian"
] | e2165095504a9f5faf1254cb47397bf4b933111f45b5d8492aa4d603028b8ff4 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
=========================================================================
Program: Visualization Toolkit
Module: TestNamedColorsIntegration.py
Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
All rights reserved.
See Copyright.txt or ... | hlzz/dotfiles | graphics/VTK-7.0.0/Imaging/Core/Testing/Python/TestAllShrinks.py | Python | bsd-3-clause | 3,535 | [
"VTK"
] | f95ebad0ce6d5b41e10d76474f1d0bc219e46f7f42fa1375f572cb9135f22daa |
#!/usr/bin/python3
# -*- coding: utf-8 -*-
from subprocess import Popen, PIPE
emojis="""⛑🏻 Helmet With White Cross, Type-1-2
⛑🏼 Helmet With White Cross, Type-3
⛑🏽 Helmet With White Cross, Type-4
⛑🏾 Helmet With White Cross, Type-5
⛑🏿 Helmet With White Cross, Type-6
💏🏻 Kiss, Type-1-2
💏🏼 Kiss, Type-3
💏🏽 Kiss,... | SilverWingedSeraph/sws-dotfiles | scripts/emoji-to-scl.py | Python | apache-2.0 | 358,856 | [
"CRYSTAL",
"EPW",
"FLEUR",
"Octopus"
] | dd727bd718039420e8b80f07f0a7b7a98f2d44e3bf4cbb6a21d399f244b98457 |
# Tests links between proxies and properties.
import os
import os.path
import sys
from paraview import servermanager
from paraview import smtesting
smtesting.ProcessCommandLineArguments()
servermanager.Connect()
pvsm_file = os.path.join(smtesting.SMStatesDir, "ProxyPropertyLinks.pvsm")
print "State file: %s" % p... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/ParaViewCore/ServerManager/Default/Testing/Python/ProxyPropertyLinks.py | Python | gpl-3.0 | 1,944 | [
"ParaView",
"VTK"
] | 183743f20bfcfd53a48c69ca2c8cd4cec3ed90085b132b1a46dc3ca0123ead1f |
"""
Implementation of algorithm for sparse multi-subjects learning of Gaussian
graphical models.
"""
# Authors: Philippe Gervais
# License: simplified BSD
import warnings
import collections
import operator
import itertools
import numpy as np
import scipy.linalg
import sklearn.cross_validation
import sklearn.covarian... | ainafp/nilearn | nilearn/group_sparse_covariance.py | Python | bsd-3-clause | 42,396 | [
"Gaussian"
] | d5f419ade8853c3d05adf2de4b3e38d98b87d3f8ff38408884d2938d1355e819 |
#!/usr/bin/env python
# This tool takes a gff file as input and creates filters on attributes based on certain properties.
# The tool will skip over invalid lines within the file, informing the user about the number of lines skipped.
# TODO: much of this code is copied from the Filter1 tool (filtering.py in tools/stats... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/tools/filters/gff/gff_filter_by_attribute.py | Python | gpl-3.0 | 5,303 | [
"Galaxy"
] | 8a5543d35ca0fcf119d7c375aa535093e7eb93746efc607cfbf8b20a6d7112aa |
"""Minimal Python 2 & 3 shim around all Qt bindings
DOCUMENTATION
Qt.py was born in the film and visual effects industry to address
the growing need for the development of software capable of running
with more than one flavour of the Qt bindings for Python - PySide,
PySide2, PyQt4 and PyQt5.
1. Bu... | pyblish/pyblish-nuke | pyblish_nuke/vendor/Qt.py | Python | lgpl-3.0 | 65,250 | [
"VisIt"
] | 913f15a0ffae38d306fb20bf0600c35ce8d448cc57cb3dec5a3ac15e9ac8b8af |
# -*- coding: utf-8 -*-
"""
inject-emoji
~~~~~~~~~~~~
inject-emoji is a simple library, written in Python, for emoji fans.
Using codes described at emoji-cheat-sheet.com, codes found within
input data are replaced with HTML image tags in the output.
:copyright: (c) 2016 by Clay Loveless.
:license: MIT, see LICENSE f... | claylo/inject-emoji | inject_emoji/inject_emoji.py | Python | mit | 15,077 | [
"Bowtie",
"Octopus"
] | b274baea76c1f2257acd8affdc348ef0683cddd6cebefa7d39c3ab0429abe13b |
# -*- coding: utf-8 -*-
#
# firefly-twisted documentation build configuration file, created by
# sphinx-quickstart on Tue Jul 29 11:56:48 2014.
#
# 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 fil... | yangdw/PyRepo | src/annotation/Firefly/docs/source/conf.py | Python | mit | 10,603 | [
"Firefly"
] | bda5045d7e3b289ea77090936be397a7ecd62c90047990e76d7b0b764a5ade00 |
"""
# Notes:
- This simulation seeks to emulate the COBAHH benchmark simulations of (Brette
et al. 2007) using the Brian2 simulator for speed benchmark comparison to
DynaSim. However, this simulation does NOT include synapses, for better
comparison to Figure 5 of (Goodman and Brette, 2008) - although it uses the... | asoplata/dynasim-benchmark-brette-2007 | output/Brian2/brian2_benchmark_COBAHH_nosyn_0001/brian2_benchmark_COBAHH_nosyn_0001.py | Python | gpl-3.0 | 3,349 | [
"Brian"
] | 501c066e037a65401ae8e132adebe9cd6f1fc3e41d91c32992cff16cf4ee6733 |
# Copyright 2013 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.
import logging
from pylib import android_commands
from pylib.device import device_utils
class PerfControl(object):
"""Provides methods for setting the p... | appknox/xysec_adb | xysec_adb/pylib/perf/perf_control.py | Python | apache-2.0 | 4,074 | [
"Galaxy"
] | 9418b0616f310a8ea99322c4b50bfded5c8a447686d10841dc6a34035f36b2f7 |
"""
(c) RIKEN 2015. All rights reserved.
Author: Keitaro Yamashita
This software is released under the new BSD License; see LICENSE.
"""
from yamtbx.dataproc.xds.xds_ascii import XDS_ASCII
from yamtbx.util.xtal import format_unit_cell
from cctbx import crystal
from cctbx.crystal import reindex
from cctbx.array_family... | keitaroyam/yamtbx | yamtbx/dataproc/auto/multi_merging/resolve_reindex.py | Python | bsd-3-clause | 20,485 | [
"CRYSTAL"
] | 006da0fa0b5ad0a13b00290570f3114898acb96025dc6cd9598e38a4bbc1e045 |
#!/usr/bin/env python
import os
import sys
from Bio import SeqIO, Entrez
from Bio.Blast import NCBIXML
import threading
import argparse
import subprocess
import time
programUsage = """
NAME
preAb.py - Presence/absence of genes with BLAST.
SYNOPSIS
preAb.py -i genes*.fasta -d db*.fasta -o output -c query_cov -p quer... | cc19/featurePresenceAbsence | preAb.py | Python | gpl-2.0 | 15,051 | [
"BLAST",
"Biopython"
] | 2750226e4415c6d8e2b8e57fc21647e442c28357c2a305b11309e8664d58e1a1 |
#!/usr/bin/env python
'''Theanets example using a deep bidirectional LSTM for phoneme classification.
This example loads an audio classification benchmark from github, defines a
callable for extracting batches from the downloaded dataset, and trains a deep
classifier network on the data. The network that is evaluated... | masterkeywikz/seq2graph | src/theanets-0.6.1/examples/lstm-chime.py | Python | mit | 4,307 | [
"NetCDF"
] | 8eb923581e8e6f81610cc43f99100271318fc76f080cb1cab9337d0e79ffda09 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This package implements various diffraction analyses.
"""
| vorwerkc/pymatgen | pymatgen/analysis/diffraction/__init__.py | Python | mit | 156 | [
"pymatgen"
] | 65f7ea6dc1ced7a4a3530d417bbede54ccfb9de89b0d0ce48ab37b0fc6acab6e |
""" Accounting reporter
"""
import hashlib
import re
from DIRAC import S_OK, S_ERROR, gConfig
from DIRAC.Core.Utilities.Plotting.ObjectLoader import loadObjects
from DIRAC.ConfigurationSystem.Client.PathFinder import getServiceSection
from DIRAC.AccountingSystem.private.Policies import gPoliciesList
from DIRAC.Accoun... | arrabito/DIRAC | AccountingSystem/private/MainReporter.py | Python | gpl-3.0 | 2,653 | [
"DIRAC"
] | acb6b7b7968a87f1bc26d49eb8afa4c9f3e7251c326e9373738683eac0072c48 |
"""Contains code for an FadeCandy hardware for RGB LEDs."""
# fadecandy.py
# Mission Pinball Framework
# Written by Brian Madden & Gabe Knuth
# Released under the MIT License. (See license info at the end of this file.)
# Documentation and more info at http://missionpinball.com/mpf
import logging
import json
import s... | spierepf/mpf | mpf/platform/fadecandy.py | Python | mit | 10,453 | [
"Brian"
] | ffdf1b0f560d3a62cd38227129ed396752d0cbc00422a17f9e24e5fd1ef187bf |
import Bio.PDB
DIRTY_ATOMS = {'1H', '2H', '3H', 'OXT'}
BACKBONE_NAMES = {'N', 'CA', 'C', 'O', 'H', 'HA'}
def get_pdb_residue_count(pdb):
"""Returns the residue count of a Bio.PDB.Structure.Structure."""
return sum([len(c.child_list) for c in pdb.child_list[0].child_list])
def get_chain_residue_count(struct, ... | joy13975/elfin | elfinpy/pdb_utilities.py | Python | mit | 3,134 | [
"Biopython"
] | 51fa680441e304b5e12aff2445a2e84320888fa4c5f4f3735560183c4159a78b |
# Orca
#
# Copyright (C) 2010-2013 Igalia, S.L.
#
# Author: Alejandro Pinheiro Iglesias <apinheiro@igalia.com>
# Author: Joanmarie Diggs <jdiggs@igalia.com>
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free S... | ruibarreira/linuxtrail | usr/lib/python3/dist-packages/orca/scripts/toolkits/clutter/script.py | Python | gpl-3.0 | 5,376 | [
"ORCA"
] | eb8c5b99ce38f50494887d7e83aff70540aceb448fb580afdb6f466c385fdf37 |
"""
Test helper functions and base classes.
"""
import functools
import inspect
import json
import operator
import os
import pprint
import unittest
import urlparse
from contextlib import contextmanager
from datetime import datetime
from unittest import TestCase
import requests
from bok_choy.javascript import js_defin... | gsehub/edx-platform | common/test/acceptance/tests/helpers.py | Python | agpl-3.0 | 36,453 | [
"VisIt"
] | 378f9f7945610befb28c8365bb97e8a97481445f90fc68602f4db04fce3f27e4 |
import networkx as nx
import numpy as np
import scipy.sparse
import scipy.sparse.linalg
def SpringRank(A,alpha=0.,l0=1.0,l1=1.0):
"""
Main routine to calculate SpringRank by solving linear system
Default parameters are initialized as in the standard SpringRank model
INPUT:
A=network adjac... | compsocialscience/summer-institute | 2018/materials/boulder/day3-networks/SpringRank_tools.py | Python | mit | 4,015 | [
"Gaussian"
] | 4f729ea354aa1566d5ea41833dcdbaaf0c556f4c198c0f5578ed8b999acaa871 |
import numpy as np
from collections import defaultdict
from fast5tools.helperops import *
try:
Rless=False
has_R=True
import rpy2.robjects as robjects
from rpy2.robjects.packages import importr
##import rpy2.robjects.lib.ggplot2 as ggplot2
import rpy2.robjects.numpy2ri
rpy2.robjects.numpy2ri... | JohnUrban/fast5tools | fast5tools/edgeRops.py | Python | mit | 11,680 | [
"Bioconductor"
] | 977852fb128c9ded10439242af6d64e5105fc03f75113422f27120e1a3a5e58b |
import glob
import os
import mdtraj as md
import fah
def make_path(filename):
try:
path = os.path.split(filename)[0]
os.makedirs(path)
except OSError:
pass
def get_num_runs_clones(path):
"""Get the number of runs and clones.
Parameters
----------
path : str
... | steven-albanese/FAHMunge | FAHMunge/automation.py | Python | lgpl-2.1 | 3,038 | [
"MDTraj"
] | 63f62361075646143c311141302e42c2d5fc78c98be14fa662e1a0371dd0519c |
import tempfile
__author__ = 'pf'
from subprocess import Popen
from collections import defaultdict
import sys, shutil, os, re
BUILD = 'build'
ALIGN = 'align'
CALL_METHYLATION = 'call_methylation'
EXEC = 'exec'
EXEC_PATH = EXEC+'-path'
ARG_TYPES = [BUILD, ALIGN, CALL_METHYLATION, EXEC]
USAGE = """
%(script)s is a ... | BSSeeker/BSseeker2 | galaxy/bs_seeker2_wrapper.py | Python | mit | 5,196 | [
"Galaxy"
] | 5090ed92fc365092bb5c5f638f73b1b919907d772803d29c5f6e2027752ab9f3 |
from __future__ import unicode_literals
from enum import Enum
from django.db import models
from django.contrib.auth.models import User
class DataType(Enum):
"""
Enumeration of valid file types
"""
NETCDF = 1
TEXT = 2
JSON = 3
NAMELIST = 4
IMAGE = 5
XML = 6
class BaseModel(models... | sterlingbaldwin/acme_workbench | workbench-backend/file_manager/models.py | Python | bsd-2-clause | 2,346 | [
"NetCDF"
] | 568ea9b0b325cd0d9fe32b22e19472eea7e220ab9981902c4fdffa8cf5733f47 |
# 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... | psci2195/espresso-ffans | samples/observables_correlators.py | Python | gpl-3.0 | 2,673 | [
"ESPResSo"
] | acce9531d9abd6ab8307951568170a88727d0b6d479828a8bc30f2bc58f8ad36 |
# Copyright 2008-2015 Nokia Solutions and Networks
#
# 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 l... | fingeronthebutton/RIDE | src/robotide/lib/robot/result/executionerrors.py | Python | apache-2.0 | 1,569 | [
"VisIt"
] | 77bc59288f92f17f9481002dd15f1366df603e2139cb75c00903191be4b79441 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# imagemetaio - Managing MiG image meta data
# Copyright (C) 2003-2015 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 General Public ... | heromod/migrid | mig/shared/imagemetaio.py | Python | gpl-2.0 | 42,918 | [
"Brian"
] | aa9c031aa6961d1eb472f91d27738e2291c12dcffe0c19947a1ea46bc2b1d964 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
import os
import sys
import argparse
import re
import subprocess
def is_empty(fpath):
try:
return not (os.path.getsize(fpath) > 0)
except OSError:
pass
return True
if __name__ == '__main__':
# Arguments parsing
parser = argparse.Argu... | bonsai-team/matam | scripts/sga_assemble.py | Python | agpl-3.0 | 8,860 | [
"BWA"
] | ba83fd97ed60d6778d9e93012efb773327ca7d66201c84900abd79238e72e0e1 |
#!/usr/bin/env python
# Copyright 2014 the V8 project authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
# This script retrieves the history of all V8 branches and trunk revisions and
# their corresponding Chromium revisions.
# Requires ... | mxOBS/deb-pkg_trusty_chromium-browser | v8/tools/push-to-trunk/releases.py | Python | bsd-3-clause | 18,018 | [
"VisIt"
] | 81ded2318ae66a47c768c547825f984593e8e1a5292c1fa38464a3b26219ebec |
#!/usr/bin/env python
# MIT License
#
# Copyright (c) 2017 Francesco Evangelista
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the right... | andysim/psi4 | psi4/share/psi4/scripts/vmd_cube.py | Python | gpl-2.0 | 16,500 | [
"Psi4",
"VMD"
] | 0a6c51399ebfaa4250fb8998392ac012ae1e29b54eabbaaa7acc267fa56e5f63 |
from instagram.client import InstagramAPI
import sys
if len(sys.argv) > 1 and sys.argv[1] == 'local':
try:
from test_settings import *
InstagramAPI.host = test_host
InstagramAPI.base_path = test_base_path
InstagramAPI.access_token_field = "access_token"
InstagramAPI.authori... | msarfati/InstaCommander | sandbox/get_access_token.py | Python | apache-2.0 | 1,418 | [
"VisIt"
] | 3c5a6a6de948da9beb96430ac445a717f200ddc4e3182ff258866679ffadc3de |
########################################################################
# $HeadURL $
# File: GraphTests.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2012/09/28 09:02:23
########################################################################
""" :mod: GraphTests
=======================
.. module: Graph... | Sbalbp/DIRAC | Core/Utilities/test/GraphTests.py | Python | gpl-3.0 | 10,548 | [
"DIRAC"
] | 78dd6d0532b7dfe5e2710bf6d4412ecf5ce189667450e7e81823a868310c845b |
# pyrun.py ---
# Author: Subhasis Ray
# Maintainer: Dilawar Singh
# See https://github.com/BhallaLab/moose-examples/blob/b2e77237ef36e47d0080cc8c4fb6bb94313d2b5e/snippets/pyrun.py
# for details.
import os
import moose
import pytest
import sys
import io
import difflib
stdout_ = sys.stdout
if sys.version_info.major > ... | dilawar/moose-core | tests/core/test_pyrun.py | Python | gpl-3.0 | 7,507 | [
"MOOSE"
] | 214acdc4979deb7c47536496c989c3dc2aad377ea97ff45f37ad18d7f1cb24b3 |
import matplotlib.pyplot as plt
from sklearn import datasets
from neupy import algorithms, utils
from utils import plot_2d_grid
plt.style.use('ggplot')
utils.reproducible()
if __name__ == '__main__':
GRID_WIDTH = 20
GRID_HEIGHT = 1
data, targets = datasets.make_moons(n_samples=400, noise=0.1)
data... | itdxer/neupy | examples/competitive/sofm_moon_topology.py | Python | mit | 1,949 | [
"NEURON"
] | bf8a121125c8cac7568c1c90be2684d2671e2caeeb192c9063573b906bf1b3ab |
from abc import abstractmethod
from scipy.sparse.linalg.interface import LinearOperator
from scipy.sparse.linalg.isolve.iterative import bicgstab
from kernel_exp_family.estimators.lite.gaussian import KernelExpLiteGaussian
try:
from kernel_exp_family.estimators.parameter_search_bo import BayesOptSearch
except Impo... | karlnapf/kernel_exp_family | kernel_exp_family/estimators/lite/gaussian_low_rank.py | Python | bsd-3-clause | 8,178 | [
"Gaussian"
] | b0193745d740cb95ca4c05780eda2f9a781b17048eb01e25444d867fbb9eb2bb |
database(
thermoLibraries = ['primaryThermoLibrary', 'GRI-Mech3.0']
)
species(
label='DIPK',
structure=SMILES("CC(C)C(=O)C(C)C"),
)
species(
label='O2',
structure=SMILES("[O][O]"),
)
species(
label='R_tert',
structure=SMILES("CC(C)C(=O)[C](C)C"),
)
species(
label='R_pri',
structu... | chatelak/RMG-Py | examples/thermoEstimator/input.py | Python | mit | 546 | [
"MOPAC"
] | 03f1d775fbd49f92f148fad22ceae3b0029a643837b4fbdc67c6501bf123ba96 |
#
# Copyright 2018 Analytics Zoo Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... | intel-analytics/analytics-zoo | pyzoo/zoo/orca/automl/search/__init__.py | Python | apache-2.0 | 923 | [
"ORCA"
] | c760ad5513726b9885988a5b4456085f6da4c965124868a824f021f488fcf58c |
# -*- coding: utf-8 -*-
"""
Low-level ctypes binding for the ZeroMQ library.
Makes an attempt to emulate pyzmq.core.
"""
# Copyright © 2011 Daniel Holth
#
# Derived from original pyzmq © 2010 Brian Granger
#
# This file is part of pyzmq-ctypes
#
# pyzmq-ctypes is free software; you can redistribute it and/or modify i... | svpcom/pyzmq-ctypes | zmq/_zmq.py | Python | lgpl-3.0 | 20,637 | [
"Brian"
] | def77c2b146607bd771e6c60178fecf64de7aa6bad785464068de89a0c96dc21 |
import os
import csv
from os.path import exists
import pyfits
import numpy as np
import numpy.ma as ma
from concfunc import concentration
from asymfunc import asymmetry
from clumfunc import clumpness
from ginifunc_modi import gini
from runsexfunc import RunSex
from flagfunc import GetFlag, SetFlag
import pymorphutils ... | vvinuv/pymorph | pymorph/casgm.py | Python | gpl-2.0 | 13,953 | [
"Galaxy"
] | 84f72f08402ef0e80f1100ea07bdabdc40809dad33a16105753a21de96246fb5 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2005 onwards University of Deusto
# All rights reserved.
#
# This software is licensed as described in the file COPYING, which
# you should have received as part of this distribution.
#
# This software consists of contributions made by many individuals,
# list... | morelab/weblabdeusto | server/src/test/unit/weblab/login/test_server.py | Python | bsd-2-clause | 4,780 | [
"CDK"
] | 237f74a878e2c3b65f7a3930eb628cee39fb17fb4a184835a4b78ec2b1105648 |
import numpy as np
from numpy import exp
from numpy import pi
from numpy import sqrt
from numpy import log
import numpy.testing as nut
import scipy.integrate as si
import mpmath as mp
import sympy as sp
import matplotlib.pylab as plt
# This file is only there to be able to see the source functions IXXP and IYYP once t... | Evenity/py_psa | py_psa/psa_functions_symbolic.py | Python | mit | 14,345 | [
"CRYSTAL"
] | 287efb6e0414c7f3419ec5cc1e09cf8edd0e01b771df9f11d2cf51c76448654d |
"""
.. module::
:platform: Unix
:synopsis: This module contains the Autoencoder class definition.
.. moduleauthor: Jan Hajic <hajicj@gmail.com>
"""
import cPickle
import numpy
import theano
import theano.tensor as TT
from theano.tensor.shared_randomstreams import RandomStreams
from safire.learning.models.ba... | hajicj/safire | build/lib/safire/learning/models/autoencoder.py | Python | gpl-3.0 | 17,198 | [
"NEURON"
] | e8407f60cd3b78ba69977de2e79ce8e809139da5d8a24136ba5d6764cc04abe4 |
#!/usr/bin/env python
#By: Guruprasad Ananda
"""
Fetch closest up/downstream interval from features corresponding to every interval in primary
usage: %prog primary_file features_file out_file direction
-1, --cols1=N,N,N,N: Columns for start, end, strand in first file
-2, --cols2=N,N,N,N: Columns for start, end... | volpino/Yeps-EURAC | tools/new_operations/flanking_features.py | Python | mit | 8,583 | [
"Galaxy"
] | 89c8a77ebc3d6dbb47a00d83829a262b1e01e7f4275edf919c030dc5a3525a0d |
#!/usr/bin/env python
# This file is part of the Printrun suite.
#
# Printrun 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.
#
# Prin... | modulexcite/Printrun | printrun/pronsole.py | Python | gpl-3.0 | 68,420 | [
"Firefly"
] | bbfcc6fa839696699476dad8d7a7affc5cbec2c1f96e0e9fe13fd4c4488b66a8 |
"""
This module gathers tree-based methods, including decision, regression and
randomized trees. Single and multi-output problems are both handled.
"""
# Authors: Gilles Louppe <g.louppe@gmail.com>
# Peter Prettenhofer <peter.prettenhofer@gmail.com>
# Brian Holt <bdholt1@gmail.com>
# Noel Da... | maheshakya/scikit-learn | sklearn/tree/tree.py | Python | bsd-3-clause | 34,714 | [
"Brian"
] | 6ab1424dd0e6516e49feb124ae0aedb456ad932897a056351e339f6c8d9326b7 |
"""
Client Interface for POEditor API (https://poeditor.com).
Usage:
>>> from poeditor import POEditorAPI
>>> client = POEditorAPI(api_token='my_token')
>>> projects = client.list_projects()
"""
import json
import requests
import sys
import tempfile
import warnings
from datetime import datetime
... | sporteasy/python-poeditor | poeditor/client.py | Python | mit | 25,407 | [
"xTB"
] | ec289f8aa362f20bb529a6ccdeb9c0d397ad96d5608cbdd5fd79fd0431533fd9 |
#!/usr/bin/env python
import sys
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Prevent .pyc files being created.
# Stops the vtk source being polluted
# by .pyc files.
sys.dont_write_bytecode = True
import backdrop
# Contour every quadratic cell t... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Common/DataModel/Testing/Python/LineIntersectQuadraticCells.py | Python | gpl-3.0 | 17,068 | [
"VTK"
] | d9b02cc114e64829cce4d3d35665a5bc5423f125947799750a265edbdaf50241 |
from __future__ import absolute_import, division, print_function, unicode_literals
from gratipay.testing import BrowserHarness, D,P
from selenium.webdriver.common.keys import Keys
class Tests(BrowserHarness):
def setUp(self):
BrowserHarness.setUp(self)
self.enterprise = self.make_team(available=... | gratipay/gratipay.com | tests/ttw/test_team_distributing.py | Python | mit | 3,894 | [
"VisIt"
] | 4ef7bbb4ec49da71f3ae586011f2b135161c14c0cfccd9c35cfb0153d3a7a3e8 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the Account Settings page.
"""
from unittest import skip
from nose.plugins.attrib import attr
from bok_choy.web_app_test import WebAppTest
from bok_choy.page_object import XSS_INJECTION
from ...pages.lms.account_settings import AccountSettingsPage
from ...pages.lms.aut... | devs1991/test_edx_docmode | common/test/acceptance/tests/lms/test_account_settings.py | Python | agpl-3.0 | 17,612 | [
"VisIt"
] | b5ae131d765b0a391f06f6b025a20ac0a5aefbb1d6c032680b0b7087e49d9cbd |
# -*- coding: utf-8 -*-
"""
This file is part of pyCMBS.
(c) 2012- Alexander Loew
For COPYING and LICENSE details, please refer to the LICENSE file
"""
from cdo import Cdo
from pycmbs.data import Data
import tempfile as tempfile
import copy
import glob
import os
import sys
import ast
import numpy as np
from pycmbs.be... | pygeo/pycmbs | pycmbs/benchmarking/models/cmip5.py | Python | mit | 20,505 | [
"NetCDF"
] | 239baabaaa68802993926ffab0b3fc5bd297bf29429f69c7d9483a0087004cda |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | BackupTheBerlios/espressopp | src/Real3D.py | Python | gpl-3.0 | 3,262 | [
"ESPResSo"
] | 57a3b9b43297f0bb8e87ae576f2976bd298fc8c47b13b54e72b361678be7570f |
from __future__ import absolute_import
import base64
import re
import os
import sys
import urllib
PY3 = sys.version_info[0] == 3
if PY3:
from io import StringIO
basestring = str
else:
from StringIO import StringIO
try:
import json
except ImportError:
import simplejson as json
from .rest import ... | cogniteev/dropbox-python-sdk | dropbox/client.py | Python | mit | 68,016 | [
"VisIt"
] | 7452852880945e6065e19dcf0c3fe65f2129bacfc3a9b6d679a70934aa1d4307 |
import unittest
from src.underscore import _
from threading import Timer
class TestStructure(unittest.TestCase):
class Namespace:
pass
def test_bind(self):
pass
def test_bindAll(self):
pass
def test_memoize(self):
def fib(n):
return n if n < 2 else fib(n... | serkanyersen/underscore.py | tests/test_functions.py | Python | mit | 5,794 | [
"MOE"
] | bb623ca567d53d5eeb025b58931cedf7897699a9e52159022154998328fa33eb |
import logging
from galaxy.datatypes.binary import Binary, SQlite
from galaxy.datatypes.metadata import MetadataElement, MetadataParameter
from galaxy.util import sqlite
log = logging.getLogger(__name__)
class GAFASQLite(SQlite):
"""Class describing a GAFA SQLite database"""
MetadataElement(name='gafa_schem... | PerlaTroncosoRey/tgac-galaxytools | tools/GAFA/gafa_datatypes.py | Python | mit | 2,314 | [
"Galaxy"
] | c0cc322b8e8c8d0b06980f43671e5e39557edd615b417eabea3ac108991920f7 |
import os
import sys
import copy
import numpy as np
from scipy.interpolate import interp1d
from optparse import OptionParser, OptionGroup
from pos_parameters import filename_parameter, string_parameter, list_parameter, value_parameter, filename
from pos_wrapper_skel import generic_workflow
import pos_wrappers
class ... | pmajka/poSSum | possum/nonuniform_reslice.py | Python | mit | 16,642 | [
"Gaussian",
"VTK"
] | e7a1ad9762b6b0bee7a2e12223723045b08955a221dbdece34c1a3e36c812558 |
# Copyright (C) 2010-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | mkuron/espresso | src/python/espressomd/drude_helpers.py | Python | gpl-3.0 | 10,675 | [
"ESPResSo"
] | 74011832dfce3aabcca09d85b3c70211f0a78dc804f0ee561fc1ff54883e45e6 |
"""Pipeline functionality shared amongst multiple analysis types.
"""
import os
from contextlib import closing, contextmanager
import functools
import tempfile
import pysam
from bcbio import bam, broad, utils
from bcbio.pipeline import config_utils
from bcbio.utils import file_exists, safe_makedir, save_diskspace
fro... | SciLifeLab/bcbio-nextgen | bcbio/pipeline/shared.py | Python | mit | 8,867 | [
"pysam"
] | 51e7cf5210841458e8ff822c55fec4216763109d756edc7995db2ace5a797329 |
# coding=utf-8
__author__ = "Peter Klassen peter@mediadock.org"
__license__ = "MIT License"
__copyright__ = "(c) 2019 Peter Klassen peter@mediadock.org"
# versions
ID3v1_VERSION = 'ID3v1'
ID3v1_1_VERSION = 'ID3v1.1'
ID3v2_2_VERSION = 'ID3v2.2'
ID3v2_3_VERSION = 'ID3v2.3'
ID3v2_4_VERSION = 'ID3v2.4'
# ID3v1 genres
c... | pkla6/pyid3tagger | pyid3tagger/const.py | Python | mit | 54,824 | [
"NetCDF"
] | cc40c3804bd61a520f7236fdc18c326f8efb41fef7ce52e83bb211e90242de1f |
# Copyright (c) 2014, the GREAT3 executive committee (http://www.great3challenge.info/?q=contacts)
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without modification, are permitted
# provided that the following conditions are met:
#
# 1. Redistributions of source code must retain... | lsst-dm/great3-public | great3sims/builder.py | Python | bsd-3-clause | 90,392 | [
"Galaxy",
"Gaussian"
] | fa14da325120cdf7f190c605207f816d4e740b1ea1649243406ef82c9a824863 |
# -*- coding: utf-8 -*-
import sys
import icool_exceptions as ie
import copy
"""Nomenclature:
An ICOOL input file consists of:
1. Problem title
2. General control variables
3. Beam generation variables
4. Physics interactions control variables
5. Histogram definition variables
6. Scatterplot definition variables
7. ... | jon2718/ipycool_2.0 | ipycool_orig.py | Python | mit | 161,517 | [
"Gaussian"
] | 53cc6087e27d0e2adbbc6f81c38c3c7e4ae7ecf9326af3c61cee0497b9662c5e |
# -*- coding: utf-8 -*-
# Copyright (c) 2013-2014 Google, Inc.
# Copyright (c) 2013-2014 LOGILAB S.A. (Paris, FRANCE) <contact@logilab.fr>
# Copyright (c) 2014-2016 Claudiu Popa <pcmanticore@gmail.com>
# Copyright (c) 2014 Vlad Temian <vladtemian@gmail.com>
# Copyright (c) 2014 Cosmin Poieana <cmin@ropython.org>
# Copy... | axbaretto/beam | sdks/python/.tox/lint/lib/python2.7/site-packages/pylint/checkers/stdlib.py | Python | apache-2.0 | 10,428 | [
"VisIt"
] | b57c351640fc2c1f89813536cd2a1fe92354dd3752f47958283f962f93e4b3e0 |
# -*- coding: 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):
# Adding field 'EphysConceptMap.added_by'
db.add_column('neuroelectro_ephysconceptmap', 'added_by',
... | neuroelectro/neuroelectro_org | neuroelectro/south_migrations/0048_auto__add_field_ephysconceptmap_added_by__add_field_neuronephysdatamap.py | Python | gpl-2.0 | 26,623 | [
"NEURON"
] | 0703d5c88f155afa826798ebc8aff7854af353b721593b31d2bbf5170722460d |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views import defaults as default_views
from imagery.impart import views
urlpatterns = [
... | jw/imagery | config/urls.py | Python | mit | 1,482 | [
"VisIt"
] | b3bd916bba044ec852b1964a59031d52c1ba06572b0c986ceb90d0dc6ee1645e |
# -*- coding: iso-8859-1 -*-
############################################################
#Example 5: Adding a custom takestep routine. This example
#takes 100 monte carlo steps as one basin hopping step
############################################################
import numpy as np
import pygmin.potentials.lj as lj
i... | js850/PyGMIN | examples/basinhopping_no_system_class/5_custom_takestep.py | Python | gpl-3.0 | 1,412 | [
"PyMOL"
] | 870d7843116057e632a02fad70c21dd358945f5d7699ca7ebb6b9d3fedc8f1fe |
#!/usr/bin/env python3
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
'''Unit tests for node_io.FileNode'''
from __future__ import print_function
import os
import sys
import unittest
if __name__ ==... | chromium/chromium | tools/grit/grit/node/node_io_unittest.py | Python | bsd-3-clause | 6,562 | [
"xTB"
] | e5bc01991451fb517d5d567a5ae86e986a0b385ac84d5f8dcb77f2cc6dbb3fcb |
import abc
from ..node import NodeVisitor
from ..parser import parse
class Compiler(NodeVisitor):
__metaclass__ = abc.ABCMeta
def compile(self, tree, data_cls_getter=None, **kwargs):
self._kwargs = kwargs
return self._compile(tree, data_cls_getter, **kwargs)
def _compile(self, tree, dat... | scheib/chromium | third_party/wpt_tools/wpt/tools/wptrunner/wptrunner/wptmanifest/backends/base.py | Python | bsd-3-clause | 6,140 | [
"VisIt"
] | 4348bda803c3aeb6b04a3c371b3c81df911f9ea3fe3842b7962116302c5778f8 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the LMS that utilize the
progress page.
"""
import ddt
from contextlib import contextmanager
from nose.plugins.attrib import attr
from flaky import flaky
from ..helpers import (
UniqueCourseTest, auto_auth, create_multiple_choice_problem, create_multiple_choice_xml... | pabloborrego93/edx-platform | common/test/acceptance/tests/lms/test_progress_page.py | Python | agpl-3.0 | 16,933 | [
"VisIt"
] | eb5a0d6171d5be954c2537c8e7fdf3cb60c979c724de6f794ff4dc46bef56e63 |
"""
This module contains cost functions to use with deep Boltzmann machines
(pylearn2.models.dbm).
"""
__authors__ = ["Ian Goodfellow", "Vincent Dumoulin"]
__copyright__ = "Copyright 2012, Universite de Montreal"
__credits__ = ["Ian Goodfellow"]
__license__ = "3-clause BSD"
__maintainer__ = "LISA Lab"
import collecti... | JazzeYoung/VeryDeepAutoEncoder | pylearn2/pylearn2/costs/dbm.py | Python | bsd-3-clause | 68,703 | [
"Gaussian"
] | d2bf88fcd4c6adb3523ba5dfb67dbb01b52639afd68b33557e6d7db73bf8b5e5 |
#!/usr/bin/env python
"""
Counting the number of reads spanning over an annotated genomic feature
Requirement:
pysam:
"""
import os
import re
import sys
import pdb
import time
import array
import pysam
import cPickle
def parse_options(argv):
"""
Parses options from the command line
"""
from ... | vipints/oqtans | oqtans_tools/RiboDiff/0.1/tools/count_reads.py | Python | bsd-3-clause | 19,291 | [
"pysam"
] | 936cdea36257e5e96d51ac35517fdd631fc0a235a18093d10268ef46dadfeef0 |
# -*- coding: utf-8 -*-
#
# hl_api_info.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or... | janhahne/nest-simulator | pynest/nest/lib/hl_api_info.py | Python | gpl-2.0 | 11,191 | [
"VisIt"
] | 6ff89ead12ab3ee7c2c4418ae4a0dcbf0a9e68b6e13f29ce02cd7f0fe79a56e3 |
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