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 |
|---|---|---|---|---|---|---|---|
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
import os
import re
import django
from django import template
from django.apps import apps
from django.conf import settings, global_settings
from django.contrib.admin.models import LogEntry
from django.contrib.contenttypes.models import ContentType
from ... | sainipray/djadmin | djadmin/templatetags/custom.py | Python | mit | 5,510 | [
"VisIt"
] | feec455fb0c2ff6d6c39f9640c93fce9e4b25475596f05ee150ffd23cb24faa3 |
# 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... | kkreis/espressopp | src/interaction/DihedralUniquePotential.py | Python | gpl-3.0 | 2,704 | [
"ESPResSo"
] | e16c5289366f2f46dd66134f83686623dee3b475efc3bd5a39f18605602c1f47 |
# !usr/bin/env python
# -*- coding: utf-8 -*-
#
# Licensed under a 3-clause BSD license.
#
# @Author: Brian Cherinka
# @Date: 2018-11-15 10:27:30
# @Last modified by: Brian Cherinka
# @Last Modified time: 2018-11-16 10:12:52
from __future__ import print_function, division, absolute_import
import pytest
from marvi... | sdss/marvin | tests/utils/datamodel/test_query.py | Python | bsd-3-clause | 1,874 | [
"Brian"
] | 67188c6998b0c393a568895d1ce70a669e7c6290fd04f507b4eae488d07ef56a |
#!/usr/bin/env python
#-*- coding:utf-8 -*-
#
# This file is part of the NNGT project to generate and analyze
# neuronal networks and their activity.
# Copyright (C) 2015-2019 Tanguy Fardet
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License a... | Silmathoron/NNGT | nngt/analysis/activity_analysis.py | Python | gpl-3.0 | 11,760 | [
"Gaussian",
"NEURON"
] | 7f95b3c57858c56f3055f78a4c1faea00c1416e60db74e9174a2862dc8a65b34 |
"""This script take a reference fasta file and a bam file
to plot the coverage along the reference"""
import pysam
import matplotlib.pyplot as plt
from Bio import SeqIO
import argparse
def parse_arg():
"""parse out the arguments from commend line"""
parser = argparse.ArgumentParser()
parser.add_argume... | UT-Python-Fall-2013/Class-Projects | MaoLun_project/pysam_function.py | Python | gpl-2.0 | 2,626 | [
"pysam"
] | 232db64216a34afd18ad995e5a2242cfd2121ff348616b16fc6d9ee59166dc4d |
#!/usr/bin/env python
# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
# All rights reserved.
#
# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the fol... | liesbethvanherpe/NeuroM | examples/features_graph_table.py | Python | bsd-3-clause | 4,049 | [
"NEURON"
] | 3c2cd47c1fd7ec7432e9f3c8aac09d5aa91de3383d1ae0188be747a76da9ff42 |
#!/usr/bin/python
"""
A moderately labyrinthine script to help LTLMoP developers
set their computer up for working with LTLMoP on GitHub.
Written by Cameron Finucane <cpf37@cornell.edu>
"""
import getpass
import sys, math, os, time
import urllib2, json
import subprocess, socket
import base64
from catUtils import patr... | jadecastro/LTLMoP | dist/LTLMoP_GitHub_Setup.py | Python | gpl-3.0 | 12,528 | [
"VisIt"
] | c33085ce06ebd704f2e4fed8d0899094b890eb7009f070cb07d3b7f697788b34 |
import json
import logging
from datetime import datetime
import ddt
from django.urls import reverse
from django.http import Http404
from django.test.client import Client, RequestFactory
from django.test.utils import override_settings
from django.utils import translation
from mock import ANY, Mock, call, patch
from nos... | gsehub/edx-platform | lms/djangoapps/discussion/tests/test_views.py | Python | agpl-3.0 | 82,039 | [
"VisIt"
] | 40fe5eeb2cfd2899af0778fd122d5a3d1b69f036a53a4ec1c5f30537fa528900 |
# -*- coding: utf-8 -*-
# snapshottest: v1 - https://goo.gl/zC4yUc
from __future__ import unicode_literals
from snapshottest import Snapshot
snapshots = Snapshot()
snapshots['test_get_uplay_products 1'] = [
'''key: "204"
name: "Assassins Creed\\302\\256 Rogue Remastered"
description: "18th century. North Americ... | xavierdutreilh/robots.midgar.fr | services/crawler/tests/snapshots/snap_test_uplay.py | Python | mit | 31,620 | [
"exciting"
] | e14426004ba1262338a972178812382acd1163e69dd4c04dda4464229fc6c59c |
#!/usr/bin/env python -i
# preceeding line should have path for Python on your machine
# trivial.py
# Purpose: run a LAMMPS input script via Python
# Syntax: trivial.py in.lammps
# in.lammps = LAMMPS input script
import sys
# parse command line
argv = sys.argv
if len(argv) != 2:
print "Syntax: trivial.p... | anshumang/lammps-analytics | python/examples/trivial.py | Python | gpl-2.0 | 793 | [
"LAMMPS"
] | 1ccd52f77c7ac1ab0cad21133f02bc67fa52109ace119b73d40f8a8b278159c8 |
#! /usr/bin/env python
"""
Author: Nicholas Swainston
Creation Date: /03/2016
Some of the orignal code was created by Bradley Meyers
This code is used to list the sources within the beam of observations IDs or using --obs_for_source list all the observations for each source. The sources can be input serval ways: us... | steve-ord/galaxy-scripts | scripts/find_pulsar_in_obs.py | Python | gpl-2.0 | 48,430 | [
"Gaussian"
] | b23f6ceec1e6da96fbeafe95f06f2486119776607d75377357cac237415374d4 |
from collections import OrderedDict
import logging
import os
import parmed.unit as units
from intermol.exceptions import AmberError
from intermol.utils import which, run_subprocess
AMB_PATH = ''
logger = logging.getLogger('InterMolLog')
to_canonical = {
'BOND': ['bond'],
'ANGLE': ['angle'],
'UB': ['... | mrshirts/InterMol | intermol/amber/__init__.py | Python | mit | 3,196 | [
"Amber"
] | 3d2ab0db0cf57c10417327d3465bb260285fb832c8fa0a966e170833780c0a1f |
#!/usr/bin/env python
#
# parse_pdb_header.py
# parses header of PDB files into a python dictionary.
# emerged from the Columba database project www.columba-db.de.
#
# author: Kristian Rother
#
# license: same as BioPython, read LICENSE.TXT from current BioPython release.
#
# last modified: 9.2.2004
#
# Added some s... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/PDB/parse_pdb_header.py | Python | gpl-2.0 | 8,959 | [
"Biopython"
] | 6f012051277a72b8f7b75a6ccc20c806e0de2705cfd6db261825c87d291c6f91 |
#!/usr/bin/env python3
from reporter.connections import DatabaseConnection
from reporter.core import SqlReport, Schedule
from reporter.emailing import (
RECIPIENT_DESMOND_MANAGER,
)
class DesmondActivityReport(SqlReport):
def __init__(self):
super().__init__(
introduction=("Th... | LCBRU/reporter | reporter/uol_redcap_reports/desmond/management_information.py | Python | mit | 7,200 | [
"Desmond"
] | 55652573e2dc1e828a27191107bac7b4bdfc614436c6d98553d4de2ccdc78fc0 |
import numpy
import os
import argparse
import makeXYZ
parser = argparse.ArgumentParser(description="Take an XYZ file as input, rotate it in various directions and output a bunch of XYZ files into separate folders")
parser.add_argument("-o", "--output", default="output/", help="produced files and folders will be saved ... | SINGROUP/readAFM | databaseCode/toyDB/twoDiffAtomsHC/doXYZstuff.py | Python | gpl-3.0 | 3,212 | [
"CHARMM"
] | ed4925137bee07cf38ed3e3c9d483826f32a1afff471c2370cd99bb0442a9d34 |
# -*- coding: ascii -*-
# $Id: CNCCanvas.py,v 1.7 2014/10/15 15:04:06 bnv Exp $
#
# Author: vvlachoudis@gmail.com
# Date: 24-Aug-2014
from __future__ import absolute_import
from __future__ import print_function
import math
import time
import bmath
try:
from Tkinter import *
import Tkinter
except ImportError:
... | ThierryM/bCNC | bCNC/CNCCanvas.py | Python | gpl-2.0 | 71,151 | [
"FLEUR"
] | 0b7b686105deab831d06b79a73b7e89defa1e3365722aec55010930d8118e591 |
# -*- coding: utf-8 -*-
# Copyright (C) 2009-2014 CEA/DEN, EDF R&D
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later ve... | FedoraScientific/salome-hexablock | doc/test_doc/hemisphere/rind.py | Python | lgpl-2.1 | 1,797 | [
"VTK"
] | 3e69016a36bc15ac5b7661c2cbb1ca1f2ba967a2494b6c1f627149e68c33de8f |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | mdespriee/spark | python/pyspark/ml/clustering.py | Python | apache-2.0 | 50,014 | [
"Gaussian"
] | f86b789a3ce0be9b79ff1a2dd3d3d9803159b53d00e8f283c410c3236062a29a |
# 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/.
__version__ = '0.2.0'
def optimize(optimizer, solver, trajectory=None):
"""Optimize a geometry with respect to a so... | azag0/pyberny | src/berny/optimize.py | Python | mpl-2.0 | 1,701 | [
"CRYSTAL"
] | c49dd55fcae606936593d17b025f919cc1f09f393c03b92c4b0f7cbd8671739d |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2016, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Run data tests for cclib."""
from __future__ import print_function
import importlib
import os
import sys
import unitt... | Schamnad/cclib | test/test_data.py | Python | bsd-3-clause | 10,849 | [
"ADF",
"Dalton",
"GAMESS",
"Gaussian",
"Jaguar",
"Molpro",
"NWChem",
"ORCA",
"Psi4",
"cclib"
] | c88367fe5ec27aef790e484c47655dc0f940e6a3f9760012319a2cf42cd2eec6 |
# -*- coding: utf-8 -*-
#
# Copyright (C) 2014-2015 Bitergia
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option) any later version.
#
# This ... | MetricsGrimoire/Octopus | octopus/database.py | Python | gpl-3.0 | 2,000 | [
"Octopus"
] | 21a6b54bf1d9aa69a5be7c81dd17dbb5419e8256f9c0245d49d5b55790f49db3 |
# -*- coding: utf-8 -*-
"""
Write EC and SMC Meshes in legacy VTK format as .vtk.
"""
import os
import sys
# Run in current directory.
os.chdir(os.path.dirname(os.path.abspath(__file__)))
# Relative import path for the DumpMeshToLegacyFormat script.
importPath = os.path.abspath(os.path.join(os.path.dirname(__file__)... | BlueFern/DBiharMesher | meshes/c4080Murrified/80/Dump4080MeshLegacyFormat.py | Python | gpl-2.0 | 896 | [
"VTK"
] | 3c55ad83fd750534c696abbfd0d29a93f678306b33ce07b2ba8ed3077381558f |
"""
Each class implements a MCMC transition
"""
import numpy as np
from hips.inference.ars import adaptive_rejection_sample
from hips.inference.hmc import hmc
from optofit.inference.particle_mcmc import *
from optofit.inference.distributions import *
from optofit.utils.utils import get_item_at_path, as_matrix, as_sarr... | HIPS/optofit | optofit/inference/mcmc_transitions.py | Python | gpl-2.0 | 21,866 | [
"Gaussian",
"NEURON"
] | db2184cd3be8654abacf29b07afde506b0db274a7dfbef4f0b1ed533f69c95d2 |
# Copyright 2016-2017 Jaap Karssenberg <jaap.karssenberg@gmail.com>
import tests
from zim.tokenparser import *
from zim.formats import ParseTreeBuilder
class TestTokenParser(tests.TestCase):
def testRoundtrip(self):
tree = tests.new_parsetree()
#~ print tree
tb = TokenBuilder()
tree.visit(tb)
tokens = t... | jaap-karssenberg/zim-desktop-wiki | tests/tokenparser.py | Python | gpl-2.0 | 1,758 | [
"VisIt"
] | 1ab4a2d958ad2847f6cabf06a636a991082ce429f25e77e6508d75d89239c032 |
r"""OS routines for Mac, NT, or Posix depending on what system we're on.
This exports:
- all functions from posix, nt, os2, or ce, e.g. unlink, stat, etc.
- os.path is either posixpath or ntpath
- os.name is either 'posix', 'nt', 'os2' or 'ce'.
- os.curdir is a string representing the current directory ('.' or... | wdv4758h/ZipPy | lib-python/3/os.py | Python | bsd-3-clause | 26,818 | [
"VisIt"
] | 560cbaad514cca9dcd1392684e3447487dbcd9166aad1dd295419fc87cbe10e0 |
"""
Translates vensim .mdl file to pieces needed by the builder module to write a python version of the
model. Everything that requires knowledge of vensim syntax should be in this file.
"""
from __future__ import absolute_import
import re
import parsimonious
from ...py_backend import builder
from ...py_backend import ... | alexprey/pysd | pysd/py_backend/vensim/vensim2py.py | Python | mit | 32,124 | [
"VisIt"
] | 41adb58e4a0387b2403481d38de499306454f57727b1a43bd1144fb71521c731 |
#!/usr/bin/env python
#
# Copyright (c) 2002 Bryce "Zooko" Wilcox-O'Hearn
# portions Copyright (c) 2001 Autonomous Zone Industries
# This file is licensed under the
# GNU Lesser General Public License v2.1.
# See the file COPYING or visit http://www.gnu.org/ for details.
__revision__ = "$Id: test_tristero.py,... | zooko/egtp_new | egtp/test/test_tristero.py | Python | lgpl-2.1 | 4,019 | [
"VisIt"
] | 2abd75f06b833407f563234a1618b43817595ba95bc96c9cfdea2cf1f233e81b |
# -*- coding: utf-8 -*-
##
# TRACK 9
# DAFT HOLLYWOOD
# Brian Foo (brianfoo.com)
# This file builds the sequence file for use with ChucK from the data supplied
##
# Library dependancies
import collections
import csv
import json
import math
import os
from pprint import pprint
import sys
import time
# Config
BPM = 150 ... | beefoo/music-lab-scripts | 09_hollywood/hollywood.py | Python | mit | 11,155 | [
"Brian"
] | 2ff5ed1793d976fd6a8b228a5a67d80ae54674440534f8fb93d692451a99d944 |
#!/usr/bin/env python
"""
Tests for saving a UGrid in netcdf format.
Designed to be run with pytest.
"""
from __future__ import (absolute_import, division, print_function)
import os
import netCDF4
import numpy as np
import pytest
from gridded.grids import Grid_U
from gridded.variable import Variable
from gridded... | NOAA-ORR-ERD/gridded | gridded/tests/test_ugrid/test_save_as_netcdf.py | Python | unlicense | 13,493 | [
"NetCDF"
] | e6d670d6cefb1c41d49988d67bdfb45b9eac52734335254e49233b26ff05d3c3 |
# Copyright 2012 by Wibowo Arindrarto. 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.
"""Bio.SearchIO parser for BLAST+ plain text output formats.
At the moment this is a wrap... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/SearchIO/BlastIO/blast_text.py | Python | gpl-2.0 | 5,790 | [
"BLAST",
"Biopython"
] | e1a5965abb57adbb603fb9671514d810a3b1761f368329d0d3eb069fe055ea07 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
Classes and tools for handling tidal harmonic data
Created on Mon Feb 11 10:01:04 2013
@author: mrayson
"""
import numpy as np
from netCDF4 import Dataset
from datetime import datetime
import matplotlib.pyplot as plt
import netcdfio
from sunpy import Spatial, unsurf
imp... | UT-CWE/Hyospy | Hyospy_ensemble/lib/SUNTANS/SUNTANS/suntides.py | Python | mit | 22,129 | [
"NetCDF"
] | abff09ede451dd701304501e6e3b193a03c59911678db92fb19af7a19400de12 |
# $HeadURL$
import boto
from boto.ec2.regioninfo import RegionInfo
from boto.exception import EC2ResponseError
import time
import types
from urlparse import urlparse
import re
# DIRAC
from DIRAC import gLogger, gConfig, S_OK, S_ERROR
# VMDIRAC
from VMDIRAC.WorkloadManagementSystem.Client.AmazonInstance import Amazon... | myco/VMDIRAC | WorkloadManagementSystem/Client/AmazonImage.py | Python | gpl-3.0 | 14,860 | [
"DIRAC"
] | 38a3ed25ff8f254439310d263003d2b12c18b599f43b8f8cf055745b07390e6a |
#!/usr/bin/python
"""
This script integrates an ITC experiment using Gaussian process regression for baseline fitting.
"""
import logging
import os
from os.path import basename, splitext
from bayesitc.experiments import ExperimentMicroCal, ExperimentYaml
from bayesitc.instruments import known_instruments, Instrument
f... | choderalab/bayesian-itc | scripts/bayesitc_integrate.py | Python | gpl-3.0 | 4,406 | [
"Gaussian"
] | 8f0b9058e6f63bdfcabafed0dc0b7e591fdeaba27d5ea09ad6cb44839dcb2db7 |
# -*- coding: utf-8 -*-
""" Sahana Eden Messaging Model
@copyright: 2009-2012 (c) Sahana Software Foundation
@license: MIT
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 wit... | anubhav929/eden | modules/eden/cap.py | Python | mit | 51,051 | [
"VisIt"
] | 89025a96ebc2c265764f6ccb1b165c287fb412355feb6b07272c31585257cd04 |
# -----------------------------------------------------------------------------
# User configuration
# -----------------------------------------------------------------------------
dataset_destination_path = '/Users/seb/Desktop/vtk_data_prober_mpas'
# ------------------------------------------------------------------... | Kitware/tonic-data-generator | scripts/vtk/mpas/raw-probe-flat-earth.py | Python | bsd-3-clause | 1,795 | [
"VTK"
] | e187aae1695ccefb52f9a576f027a03334716f9d67b346731514ffe8445394f8 |
#
# ast_parent_collector_visitor.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
# (at ... | kperun/nestml | pynestml/visitors/ast_parent_collector_visitor.py | Python | gpl-2.0 | 1,286 | [
"VisIt"
] | f5d5df15bff0442d50733652cd46a146a383116453e58bf3fa9da0c16b3128af |
"""
"""
__RCSID__ = "$Id$"
import os.path
import hashlib
from DIRAC import gLogger, gConfig, S_OK, S_ERROR
from DIRAC.ConfigurationSystem.Client.PathFinder import getServiceSection
from DIRAC.FrameworkSystem.private.monitoring.ColorGenerator import ColorGenerator
from DIRAC.Core.Utilities import Subprocess, Time
cla... | vmendez/DIRAC | FrameworkSystem/private/monitoring/RRDManager.py | Python | gpl-3.0 | 10,151 | [
"DIRAC"
] | e7132d2dfbfe497be4a7c46ce9a5c0a780bf7ba4e300643a38b27fa95e89ad32 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2013 Async Open Source
##
## This program is free software; you can redistribute it and/or
## modify it under the terms of the GNU Lesser General Public License
## as published by the Free Software Foundation; either version 2
## of the License, or... | tiagocardosos/stoq | stoqlib/lib/autoreload.py | Python | gpl-2.0 | 1,844 | [
"VisIt"
] | 281bbc3ea65f553111a3eb808063a70927eb1bfe6431bea13486b1d60464db71 |
import options
import array
usage = "Convert Gaussian Cube file format to a raw binary file. \n It also outputs header information needed to interpret the raw file.\n syntax: gcubetoraw.py inputfile outputfile headeroutputfile";
SiestaFileName = args[0]
RawFileName = args[1]
HeaderFileName = args[2]
filein = open(... | fercook/SciViz | Voxels/Gaussian_Cube_To_Raw/gcubetoraw.py | Python | gpl-2.0 | 1,580 | [
"Gaussian"
] | 70bb362b748eeb783508f442686a9f03b3168f724d13a281ae15cd5c2ec212fd |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import vtk
def main():
colors = vtk.vtkNamedColors()
filename = get_program_parameters()
# Create the reader for the data.
print("Loading ", filename)
reader = vtk.vtkUnstructuredGridReader()
reader.SetFileName(filename)
reader.Update()
... | lorensen/VTKExamples | src/Python/IO/ReadLegacyUnstructuredGrid.py | Python | apache-2.0 | 5,040 | [
"VTK"
] | 52edcaec5744bba795ae30309bd37e956472a91875ded5c9b09b97de009946ea |
"""Middle-ware for handling hg authentication for users pushing change sets to local repositories."""
import json
import logging
import os
import sqlalchemy
import sys
import tempfile
from paste.auth.basic import AuthBasicAuthenticator
from paste.httpheaders import AUTH_TYPE
from paste.httpheaders import REMOTE_USER
f... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/webapps/tool_shed/framework/middleware/hg.py | Python | gpl-3.0 | 18,582 | [
"Galaxy"
] | 552287e31f99ed9d3ab794d8aedb00d1916f19f17d8f4018b42cdb4a557724ff |
import pytest
import numpy as np
from numpy.testing import assert_array_almost_equal, assert_almost_equal
from scipy import constants
from copy import deepcopy
import gromacs
import mdpow.config
import mdpow.fep
def test_molar_to_nm3():
assert_almost_equal(mdpow.fep.molar_to_nm3(1.5), 0.9033212684)
assert_a... | Becksteinlab/MDPOW | mdpow/tests/test_fep.py | Python | gpl-3.0 | 4,710 | [
"Gromacs"
] | 5aab5f605130338dd3f5f6a7ac1eaba028b1718b6a29e669b2880a1d1b6865c3 |
#!/usr/bin/env python
#-----------------------------------------------------------------------------
# Copyright (c) 2013--, biocore development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
#-------------------------... | biocore/burrito-fillings | bfillings/sortmerna_v2.py | Python | bsd-3-clause | 19,641 | [
"BLAST"
] | 6eba1fd8ca68bdddfca6947fa0006cc29042406c4b17ded9332d712eae536027 |
import json
from django.db.models import Min, Avg, Count
from django.http import HttpResponse
from django.shortcuts import render, redirect
from django.utils.translation import ugettext as _
from django.contrib import messages
from wikigame import link_extraction
from wikigame.link_extraction import NoLinksError
from... | mophahr/wikipediaGame | wikigame/views.py | Python | gpl-2.0 | 7,586 | [
"VisIt"
] | cb35363df26b43c6a1313de36578ab282a250744626ecbb4eb5b750b54b4b08e |
#!/usr/bin/env python
"""jemdoc version 0.7.3, 2012-11-27."""
# Copyright (C) 2007-2012 Jacob Mattingley (jacobm@stanford.edu).
#
# This file is part of jemdoc.
#
# jemdoc 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
#... | liubenyuan/liubenyuan.github.io | jemdoc.py | Python | mit | 36,063 | [
"Amber"
] | 909d7f39b3174becb7531526b3fefde87ab7ae529a22b3da7b548742231a9bbc |
#!/usr/bin/env python
import vtk
import vtk.test.Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Parameters for testing
res = 250
# Graphics stuff
ren0 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren0)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderW... | keithroe/vtkoptix | Filters/Points/Testing/Python/TestSPHInterpolator2D.py | Python | bsd-3-clause | 2,151 | [
"VTK"
] | f9850c1d079315814bb26f9e9dfa790b231bd886ba9a8917ea27b0971e95ff48 |
#!/usr/bin/env python3
"""
Check 100% Penetrance for Recessive model.
*** All individual with Alt homo genotype should be in disease status.
@Author: wavefancy@gmail.com
Usage:
VCFRecessive100Penetrance.py -p pedFile
VCFRecessive100Penetrance.py -h | --help | -v | --version | -f | --... | wavefancy/BIDMC-PYTHON | Exome/VCFRecessive100Penetrance/VCFRecessive100Penetrance.py | Python | mit | 2,077 | [
"pysam"
] | 66a17565258cac389c65695b655853f7cf5ed2efbc9ca0677f1415d46e724fce |
#!/usr/bin/env python3
# For more information visit https://github.com/fm3/inkscape-latexformula
import inkex, os, tempfile, sys, xml.dom.minidom, shutil, re
from lxml import etree
if os.name == 'nt':
import subprocess
class LatexFormula(inkex.Effect):
def __init__(self):
inkex.Effect.__init__(self... | fm3/inkscape-latexformula | latexformula.py | Python | gpl-3.0 | 7,103 | [
"VisIt"
] | de3e0c9892a9a0c57d189b94c327a995bf4aca3f06963744d53631d1efbaf8d6 |
#!/usr/bin/env python
########################################################################
# File : dirac-wms-get-wn
# Author : Philippe Charpentier
########################################################################
"""
Get WNs for a selection of jobs
"""
__RCSID__ = "$Id$"
import datetime
import DIRA... | fstagni/DIRAC | WorkloadManagementSystem/scripts/dirac-wms-get-wn.py | Python | gpl-3.0 | 7,133 | [
"DIRAC"
] | 4d015af24ca5db2e551ed41734c4f395587349082838802fdf58624885f55fd9 |
"""
=======================================================================
Shrinkage covariance estimation: LedoitWolf vs OAS and max-likelihood
=======================================================================
The usual estimator for covariance is the maximum likelihood estimator,
:class:`sklearn.covariance.Em... | mrshu/scikit-learn | examples/covariance/plot_covariance_estimation.py | Python | bsd-3-clause | 4,991 | [
"Gaussian"
] | 0437b5ada8621bbb6b5b1fb1f9af9f7a776b68dac036dde1055b0123504526fb |
import oauth2 as oauth
import time
import json
import traceback
import config as cfg
consumer = oauth.Consumer(key=cfg.twitter['consumer_key'], secret=cfg.twitter['consumer_secret'])
access_token = oauth.Token(key=cfg.twitter['access_token'], secret=cfg.twitter['access_token_secret'])
client = oauth.Client(consumer, ... | mirkolai/twitter-experiment | python/rest API/followers-list.py | Python | gpl-2.0 | 1,824 | [
"CRYSTAL"
] | 11e15d992b7eec1ea36cc11305631873be457040f3bd490d8a9ab33e3bea571b |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# ---------------------------------------------------------------------
# Copyright (c) 2012 Michael Hull.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are m... | mikehulluk/morphforge | src/morphforgecontrib/simulation/channels/common/neuron.py | Python | bsd-2-clause | 4,213 | [
"NEURON"
] | 2056ea6bdf19cab841fcb938dc66b9ff94caccf1b11a8a3f44ebb3bd4bcedb96 |
import math
import nnet
import util
class Actor:
# Size of simulation world
_WORLD_SIZE = (1, 1)
@staticmethod
def set_world_size(size):
""" Set size of the simulation world """
Actor._WORLD_SIZE = size
def __init__(self):
self.x = self.y = self.radians = 0
self.move_to_random()
self.radius = 1
sel... | pkorth/intraspecies-cooperation | actors.py | Python | mit | 13,922 | [
"NEURON"
] | 1e0b522ef15e52539d2682eebf3f88111d81b529d7d7ae8276a37c4d091ba32d |
"""
Implements various validatiors, e.g., check if vasprun.xml is valid, for VASP.
"""
import logging
import os
from collections import deque
from pymatgen.io.vasp import Chgcar, Incar, Outcar, Vasprun
from custodian.custodian import Validator
class VasprunXMLValidator(Validator):
"""
Checks that a valid v... | materialsproject/custodian | custodian/vasp/validators.py | Python | mit | 4,891 | [
"VASP",
"pymatgen"
] | 48d68869b41dbf5e6f29642b4905f0ebe9940596f527882f4cbc2cf0664aaf83 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
This is a poorly-organized collection of utilities of general, errr, utility.
Configuration: See cpblUtilities-config.py. In short, copy config-template.cfg to config.cfg and edit it.
A config.cfg file should be used to set up folders to be used by cpblUtilities. The co... | cpbl/cpblUtilities | utilities.py | Python | gpl-3.0 | 71,272 | [
"ADF"
] | 463211040f7a4da6fbe2cbb1d377cf2e2ac3d5b269e97ec2837b5c7c10734f13 |
# BEGIN_COPYRIGHT
#
# Copyright (C) 2014 CRS4.
#
# This file is part of blast-python.
#
# blast-python 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)
# ... | crs4/blast-python | BlastPython/buffered_IO.py | Python | gpl-3.0 | 2,027 | [
"BLAST"
] | b56c9fc671cdeb4e2524191ad99f05305f6f75d023f57e769c6eb9c88736eeb6 |
########################################################################
# $HeadURL$
########################################################################
""" DIRAC FileCatalog utilities
"""
__RCSID__ = "$Id$"
try:
import hashlib
md5 = hashlib
except:
import md5
import random, os, time
from types import S... | sposs/DIRAC | DataManagementSystem/DB/FileCatalogComponents/Utilities.py | Python | gpl-3.0 | 2,945 | [
"DIRAC"
] | 1f788c3d3106363dbc3e3e0c42cb7e0a29e1d56f16459c685c51910d9829a350 |
#!/usr/bin/python
#
# Copyright 2015 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required b... | coxmediagroup/googleads-python-lib | examples/adwords/v201506/advanced_operations/add_text_ad_with_upgraded_urls.py | Python | apache-2.0 | 4,027 | [
"VisIt"
] | 43ac1f8fab996aa6e31f6cfe2074c8710c8c3db380d7392f09ee85f969621e07 |
#!/usr/bin/env python
import sys
import pysam
import HTSeq
import argparse
from functools import reduce
from copy import copy
import csv
def update_if(d, f, key, value):
if not key in d:
d[key] = value
return None
old_value = d[key]
should_update = f(old_value, value)
if not should_upd... | ctlab/quant3p | quant3p/gtfextend.py | Python | apache-2.0 | 4,830 | [
"HTSeq",
"pysam"
] | 71e61beb6c5bb13126e4f00be137b0ec61d2a3f36b02670bbddbf228be76900b |
''' ResourceStatusClient
Client to interact with the ResourceStatusDB.
'''
# pylint: disable=unused-argument
__RCSID__ = '$Id$'
from DIRAC import S_OK
from DIRAC.Core.Base.Client import Client
from DIRAC.ConfigurationSystem.Client.Helpers.Operations import Operations
from DIRAC.FrameworkSystem.Client.Notificatio... | chaen/DIRAC | ResourceStatusSystem/Client/ResourceStatusClient.py | Python | gpl-3.0 | 14,924 | [
"DIRAC"
] | f597444ae5b4b6103da708b61bd5499b334dce92f071abf77e1148eff8189c94 |
#!/usr/bin/env python
#
#
# ex_toy4
#
# Building on toy3 example, this adds drift distance
# information to the pixel color. It also adds a
# random z-vertex position in addition to the phi
# angle.
#
# The network is defined with 2 branches to calculate
# the phi and z. They share a common input layer and
# initial ... | BDannowitz/polymath-progression-blog | jlab-hackathon/train_gutted.py | Python | gpl-2.0 | 6,623 | [
"NEURON"
] | 9dfcaa2657518bc9444e2b8e44b8b749c4a1afff1c8d1fc006bded08741a04ae |
#!/usr/bin/env python
"""Tests of code for OTU picking"""
__author__ = "Kyle Bittinger, Greg Caporaso"
__copyright__ = "Copyright 2011, The QIIME Project"
# remember to add yourself if you make changes
__credits__ = [
"Kyle Bittinger",
"Greg Caporaso",
"Rob Knight",
"Jens Reeder",
"William Walters... | wasade/qiime | tests/test_pick_otus.py | Python | gpl-2.0 | 215,397 | [
"BLAST"
] | c655014cea75baacdc00c34a5d11de23f8879425b2b32abacd6126ba4386c80a |
#PBS -l nodes=1:ppn=8:xeon8
#PBS -q verylong
#PBS -N amc_end
#PBS -m ae
"""Ends atom simulation and gives result in file.
Usage:
asap-qsub endatomsimulation.py amcfolder e_filter T_real (result_log_file)
Where: e_filter is the maximal accepted energy w.r.t. the global min such that a cfg. counts.
T_real i... | auag92/n2dm | Asap-3.8.4/Projects/NanoparticleMC/endatomsimulation.py | Python | mit | 6,717 | [
"ASE"
] | d8df40c749817dcce251dc3373eef24842888b25248438affcad441d30d08ccc |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import re
import json
import warnings
import numpy as np
from io import open
from pathlib import Path
from enum import Enum
from pymatgen.core.units import Mass, Length, unitized, FloatWithUnit, Unit, \
SU... | dongsenfo/pymatgen | pymatgen/core/periodic_table.py | Python | mit | 49,674 | [
"CRYSTAL",
"pymatgen"
] | c4368af53a794610fa46b0f91e9014d59be63ae11b385055d0f4645499387db8 |
# Databricks notebook source
# MAGIC %md
# MAGIC ScaDaMaLe Course [site](https://lamastex.github.io/scalable-data-science/sds/3/x/) and [book](https://lamastex.github.io/ScaDaMaLe/index.html)
# MAGIC
# MAGIC This is a 2019-2021 augmentation and update of [Adam Breindel](https://www.linkedin.com/in/adbreind)'s initial ... | lamastex/scalable-data-science | dbcArchives/2021/000_6-sds-3-x-dl/064_DLbyABr_08-Operations.py | Python | unlicense | 10,702 | [
"Brian"
] | 9a6efc21e6b9eebad6be0e7443d9ab21d8b52e245c83928fcd03c71604810608 |
# -*- coding: utf-8 -*-
"""Factories for the OSF models, including an abstract ModularOdmFactory.
Example usage: ::
>>> from tests.factories import UserFactory
>>> user1 = UserFactory()
>>> user1.username
fred0@example.com
>>> user2 = UserFactory()
fred1@example.com
Factory boy docs: http://f... | aaxelb/osf.io | tests/factories.py | Python | apache-2.0 | 28,907 | [
"Brian"
] | 24da7a06ffd6e10577a06a398e8c2576735827a1859bd758c0855d0f8e81970b |
"""
Copyright (C) <2010> Autin L.
This file ePMV_git/patch/mmcifParser.py is part of ePMV.
ePMV 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
(... | corredD/ePMV | patch/mmcifParser.py | Python | gpl-3.0 | 35,178 | [
"CRYSTAL"
] | 8b8b987b74d1284924d0e6a0221f3ef82af6ff168db4c506a45a42aa7b93864a |
from django.conf.urls import patterns, url #,include
#from django.contrib import admin
#admin.autodiscover()
urlpatterns = patterns('',
# Examples:
# url(r'^$', 'ops.views.home', name='home'),
# url(r'^blog/', include('blog.urls')),
#url(r'^admin/', include(admin.site.urls)),
# OPS NAMING CONVENTI... | CReSIS/OPS | conf/django/ops/ops/urls.py | Python | gpl-3.0 | 2,319 | [
"NetCDF"
] | 6b91778a2c0ad43759a64bffa224fa1081bb11f2c217d102d7542f2c02631572 |
###############################
# 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/decorations/zincblendesets.py | Python | gpl-3.0 | 29,621 | [
"CRYSTAL",
"VASP"
] | 296e8bc35a610411b8d6fe4548065d92b52434efa2b241efeb6693fa40df8880 |
# vim:ai:et:ff=unix:fileencoding=utf-8:sw=4:ts=4:
# conveyor/src/main/python/conveyor/config.py
#
# conveyor - Printing dispatch engine for 3D objects and their friends.
# Copyright © 2012 Matthew W. Samsonoff <matthew.samsonoff@makerbot.com>
#
# This program is free software: you can redistribute it and/or modify it u... | makerbot/conveyor | src/main/python/conveyor/config.py | Python | agpl-3.0 | 20,634 | [
"VisIt"
] | ef9e9a528716d589d4fb662adc466a2330438d0f3b2f7b885bc4c4f3b121c3a0 |
'''
This is the same as advanced_1d.py but using
seaborn to override much of the style of matplotlib.
'''
import numpy as np
from matplotlib import pyplot
from histogram import Histogram
import seaborn as sns
sns.set(palette="deep")
np.random.seed(1)
hh = []
for mean in [2,5,7]:
hh.append(Histogram(30, [0,10],... | theodoregoetz/histogram | examples/plot_1d_seaborn.py | Python | gpl-3.0 | 1,143 | [
"Gaussian"
] | 5779019fc05a61dd05b710233bc808db46d7e93eaad76a722da99b587598234d |
# -*- coding: utf-8 -*-
"""
Created on Fri Mar 3 16:15:18 2017
@author: rickdberg
Script to re-run sites through interface_flux.py
and interface_flux_montecarlo.py using information in database metadata
"""
import numpy as np
import pandas as pd
from scipy import optimize, integrate, stats
import sqlalchemy as sa
... | rickdberg/mgmodel | interface_flux_rerun.py | Python | mit | 27,642 | [
"Gaussian"
] | f26166cef3f62658aa9a85ee9647b25e4994cc3ee66a920b669aa2fa34e04408 |
"""These routines are for doing typical extracellular (cell-attached) analyses.
The main data structures we use here are XSG dictionaries. These
contain keys by default that have a collection of meta-data, and one
key for each of the three ephus programs (ephys, acquierer and
stimulator).
We have been inspired by th... | dattalab/d_code | ephys/extraCellularRoutines.py | Python | mit | 12,396 | [
"Gaussian"
] | c5cbc0279be2579ff9bfad4198c992d678e56c8b61600849cc324e8386a8b30e |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# testresupport - run test job to verify support for a runtime env
# Copyright (C) 2003-2014 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of th... | heromod/migrid | mig/shared/functionality/testresupport.py | Python | gpl-2.0 | 8,431 | [
"Brian"
] | 4782523d916d8eab7218b1b06e325459bcc749003830c8a6088cf1fee860284f |
from datetime import date
from unittest import skipUnless
from bok_choy.web_app_test import WebAppTest
from acceptance_tests.config import ENABLE_COUPON_ADMIN_TESTS
from acceptance_tests.constants import DEFAULT_END_DATE, DEFAULT_START_DATE
from acceptance_tests.mixins import CouponMixin, LogistrationMixin
from accep... | mferenca/HMS-ecommerce | acceptance_tests/test_coupon_admin.py | Python | agpl-3.0 | 2,962 | [
"VisIt"
] | f3a20b6e96945da7d4c4d7ebb14e65d60f110a9f2e19b23137e4f7d9ae93da3d |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides an interface to the MaterialsVirtualLab's MEGNet REST API
for rapid property prediction.
"""
import requests
class CrystalAIRester:
"""
This is a high-level interface to the... | gmatteo/pymatgen | pymatgen/ext/crystalsai.py | Python | mit | 4,109 | [
"CRYSTAL",
"pymatgen"
] | 8df91e1883dbaf1008ab673a979a1c0bdcbce28c2d65817e859fac986ee173e9 |
#!/usr/bin/python
# gly19.py -- protein glycosylator
# 2016.10.05 -- first version -- John Saeger
# gly19 -- 2017.5.27
# This version complains about incomplete sidechains. You must fix them up.
# I use pymol's mutate wizard to mutate a residue to itself.
# This version has a slightly more sophisticated solvent exp... | aequorea/gly | versions/gly19.py | Python | gpl-2.0 | 8,326 | [
"PyMOL"
] | 297851bc7535863843f88ca25f2e7b95789b2b085448e5d7d6b3521b97fa4b49 |
"""Some test functions for bivariate interpolation.
Most of these have been yoinked from ACM TOMS 792.
http://netlib.org/toms/792
"""
import numpy as np
from triangulate import Triangulation
class TestData(dict):
def __init__(self, *args, **kwds):
dict.__init__(self, *args, **kwds)
self.__dict__ ... | tkaitchuck/nupic | external/linux64/lib/python2.6/site-packages/matplotlib/delaunay/testfuncs.py | Python | gpl-3.0 | 20,890 | [
"Gaussian"
] | 1dd3be9362eed7735fb99f3f59aad74a8430f5eae2151d679d805af6b2b3083d |
from django.apps import AppConfig
from flexible_permissions.agents import register_agent
from flexible_permissions.roles import register_role
from flexible_permissions.relations import register_relation
from tests.models import User, Group, Zoo, Exhibit, Animal
class TestsConfig(AppConfig):
name = 'tests'
ve... | staab/django-flexible-permissions | tests/apps.py | Python | mit | 1,263 | [
"VisIt"
] | 2c9d6a50692eb8684f70483474928e8f79432a2fa621b207ba6164e490b504f6 |
#
# ast_input_type.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
# (at your option) a... | kperun/nestml | pynestml/meta_model/ast_input_type.py | Python | gpl-2.0 | 2,209 | [
"NEURON"
] | 680ca5d5de33e67bfa090dff62608497d5cd0487109a4d59f4d2e32659ee35b7 |
# -*- coding: utf-8 -*-
#戦略を分ける
#Componentクラスに相当する
class OrganizationEntry(object):
def __init__(self, code, name):
self.code = code
self.name = name
def getCode(self):
return self.code
def getName(self):
return self.name
#組織ツリーを表示する
#サンプルでは、デフォルトの実装を用意
... | t10471/python | practice/src/design_pattern/Visitor.py | Python | mit | 2,995 | [
"VisIt"
] | df9f395daa11901eb4499e9ee08d18f8eb7c0d56d982cec43bef1da5d812880b |
# 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.
#
"""Draw representations of organism chromosomes with added information.
These classes are meant to model the drawing of pictures of chromosomes.
Thi... | poojavade/Genomics_Docker | Dockerfiles/gedlab-khmer-filter-abund/pymodules/python2.7/lib/python/Bio/Graphics/BasicChromosome.py | Python | apache-2.0 | 30,629 | [
"Biopython"
] | b41212d950096d9711c68766e0c5bbe41d2baef5e7af1aa74ece403e742231a9 |
import os
import shutil
import re
from bears.vcs.CommitBear import _CommitBear
from coala_utils.ContextManagers import change_directory
from coalib.misc.Shell import run_shell_command
class GitCommitBear(_CommitBear):
LANGUAGES = {'Git'}
ASCIINEMA_URL = 'https://asciinema.org/a/e146c9739ojhr8396wedsvf0d'
... | refeed/coala-bears | bears/vcs/git/GitCommitBear.py | Python | agpl-3.0 | 2,076 | [
"VisIt"
] | 5890f6e605581ce7d878ec9b067d5934382c08493afeea160f7ea2b3f8644b06 |
import win32api, win32process, win32security
import win32event, win32con, msvcrt, win32gui
import pywintypes
import win32pipe, win32file, os
#import os
#import sys
#import threading
#import types
#import pprint
#import errno
import logging
#import msvcrt
#import win32api
#import win32file
#import win32pipe
#import py... | patrickhartling/maestro | maestro/daemon/plugins/services/launch/winprocess.py | Python | gpl-2.0 | 17,288 | [
"ASE"
] | a04de67982ece8f1e68bdc6562daedb5dc57b2bbd39bac61e4f009a027a5788b |
#!/usr/bin/env python
"""Guide monitor
History:
2010-09-27 ROwen Initial version.
2010-09-28 ROwen Modified to use new showY method, e.g. to always show the 1" line.
2010-09-30 ROwen Fixed FWHM units: they are pixels, not arcsec. Thanks to Joe F.
2010-10-01 ROwen Modified to use TUI.Base.StripChartWdg.
... | r-owen/TUI | TUI/Guide/GuideMonitor/GuideMonitorWindow.py | Python | bsd-3-clause | 7,320 | [
"Gaussian"
] | edf2d96fecd305a643c74ad5f421083effafa684fe0b5747e58121ac07e61a95 |
from os import getenv
import requests
from behave import *
import json
from app import server
from verify import expect
from selenium.webdriver.common.by import By
from selenium.webdriver.support.ui import WebDriverWait
from selenium.webdriver.support import expected_conditions
WAIT_SECONDS = 30
BASE_URL = getenv('BAS... | NYU-DevOps-Fall2017-PromotionsTeam/promotions | features/steps/promotion_steps.py | Python | apache-2.0 | 7,975 | [
"VisIt"
] | b164c206bc78fd3edd47f052e3d82e35721298649e0b40e44a0474e69ade6341 |
##########################################################################
#
# Copyright 2008-2015 VMware, Inc.
# All Rights Reserved.
#
# 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 withou... | apitrace/apitrace | retrace/dxgistate_so.py | Python | mit | 9,344 | [
"VisIt"
] | f533e935b82c77d32246f999c25dd26fa435c85ef0d3b21b30c0997cc6857093 |
"""
Implements a simple logistic regression classifier with L2 regularization. This has been adapted from the
implementation authored by Daniel Tarlow: ::
`http://blog.smellthedata.com/2009/06/python-logistic-regression-with-l2.html`
e.g. ::
>>> lr = LogisticRegression(x_train=xx, y_tra... | rfaulkner/runway | src/data_modelling/logistic_regression.py | Python | bsd-3-clause | 4,823 | [
"Gaussian"
] | 6173421a43795af589d23a6344e38d2956e9e6486cef01e73f384a552a434966 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import vtk
def main():
colors = vtk.vtkNamedColors()
points = vtk.vtkPoints()
p0 = [1.0, 1.0, 1.0]
p1 = [-1.0, 1.0, 1.0]
p2 = [-1.0, -1.0, 1.0]
p3 = [1.0, -1.0, 1.0]
p4 = [0.0, 0.0, 0.0]
points.InsertNextPoint(p0)
points.InsertNextP... | lorensen/VTKExamples | src/Python/GeometricObjects/Pyramid.py | Python | apache-2.0 | 1,756 | [
"VTK"
] | 964c18c4b65c5c415790fb1d8fc2c5272752e341018bcf1b2c2f60a9bfc67e09 |
# -*- coding: utf-8 -*-
# Generated by Django 1.9.7 on 2016-07-23 15:20
from __future__ import unicode_literals
from django.db import migrations, models
import django.db.models.deletion
class Migration(migrations.Migration):
dependencies = [
('visit', '0112_auto_20160723_1004'),
]
operations = ... | koebbe/homeworks | visit/migrations/0113_auto_20160723_1020.py | Python | mit | 803 | [
"VisIt"
] | 0f47088346e728ef0c178e5cf7dc8f4fbb6b8034a615bccad203883d4266809f |
import os
import subprocess
from distutils.core import setup
# List of lists with tools to check for
# J: why checking only for these 3 tools?
check_tools = {
"virtualenv": ["virtualenv", "--version"],
"gcc": ["gcc", "--version"],
"git": ["git", "--version"]
}
for tool in check_tools.keys():
try:
... | kmpf/uap | setup.py | Python | gpl-3.0 | 1,620 | [
"Biopython"
] | 9c0d28f862df70468be128de3104e7b77bf57d282ac1c0413503339192597df3 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# ---------------------------------------------------------------------
# Copyright (c) 2012 Michael Hull.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are m... | mikehulluk/morphforge | src/morphforgecontrib/simulation/populations/basic_types.py | Python | bsd-2-clause | 13,028 | [
"NEURON"
] | 7ffd9873a092e10cee6e43f64a2be189f486c43eda4e3bff8470551a4a5d9b6e |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import scipy as sp
def lorentz(x, pos, hwhm, ampl):
""" Lorentz-Cauchy function expressed in terms of x0, gamma and height.
Parameters
----------
x : numpy.ndarray
Wavelength array
pos : float
Wavelength of centroid.
hwhm : float
... | thriveth/Pychelle | pychelle/profiles.py | Python | gpl-3.0 | 2,515 | [
"Gaussian"
] | b7c897162567220e6c46345b42a2e20e6e91d28e180aef8f6cff11942ef2f32c |
import numpy as npy
import netCDF4 as nc
import pyroms
class nudgcoef():
''' A class to write the Nudging coeficient file for ROMS '''
def __init__(self,roms_grid):
''' init an object of the class with the pyroms grid ID '''
self.grd = pyroms.grid.get_ROMS_grid(roms_grid)
return None
def __call__(self,east_... | kshedstrom/pyroms | examples/cobalt-preproc/nudging_coef/lib_nudgcoef.py | Python | bsd-3-clause | 7,962 | [
"NetCDF"
] | 34951ceca944a878157010f6e208b9b0eeb275a1cb5679cead262282ea78c4b6 |
#!/usr/bin/python
# -*- coding: UTF-8 -*-
#Copyright (C) 2007 Adam Spencer - Free Veterinary Management Suite
#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... | cyncyncyn/evette | languagefiles/language_french_1.3.2.py | Python | gpl-2.0 | 69,995 | [
"VisIt"
] | 112fd8bccb6fe48231954fa5f37c1486b978aa6ee1e419e473522ca2df754023 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
... | kain88-de/mdanalysis | testsuite/MDAnalysisTests/coordinates/test_gms.py | Python | gpl-2.0 | 3,685 | [
"GAMESS",
"MDAnalysis"
] | fec03dcb18aecce2d5e8232b4723ac398ab49d7d1c61999673420e2552375960 |
from builtins import range
from builtins import object
import numpy as np
from cs231n.layers import *
from cs231n.layer_utils import *
class TwoLayerNet(object):
"""
A two-layer fully-connected neural network with ReLU nonlinearity and
softmax loss that uses a modular layer design. We assume an input dim... | quoniammm/mine-tensorflow-examples | assignment/cs231n_assignment/assignment2/cs231n/classifiers/fc_net.py | Python | mit | 13,144 | [
"Gaussian"
] | bfba3c1d98c36aa3739fe90ba8cb7651aedd8825cbab45da57c0c410541b6bbc |
# from datetime import timedelta, date
# from dateutil.relativedelta import relativedelta
#
# from model_mommy import mommy
#
# from django.test import TestCase, tag
#
# from edc_constants.constants import NO, YES, POS, NEG, DECLINED
# from edc_metadata.constants import REQUIRED, NOT_REQUIRED, KEYED
# from edc_metad... | botswana-harvard/bcpp-subject | bcpp_subject/tests/test_annual_survey_rulegroups.py | Python | gpl-3.0 | 67,139 | [
"VisIt"
] | 4ebf005417e51766110790f3e726524acff950fb2b5a637a22356f311c07527e |
# stdlib imports
import glob
import gzip
import re
import os
import sys
import dateutil.parser
# django imports
from django.core.management import BaseCommand
from django.db.models import Q
from django.conf import settings
from django.contrib.auth import get_user_model
from dbdb.core.models import System
from dbdb.co... | cmu-db/dbms-library | dbdb/core/management/commands/populate_visits.py | Python | apache-2.0 | 5,162 | [
"ASE"
] | 49c4c6672a91298cb9d0fad580d3d8aae0c3adf808cb07f7845a512910ba75c7 |
# 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... | allenlavoie/tensorflow | tensorflow/contrib/distributions/python/ops/autoregressive.py | Python | apache-2.0 | 8,029 | [
"Gaussian"
] | ac04f9416b63061de975d4d49df1b9b2c901f7a2fc05f1b011fddf7fb405f33f |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.