text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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"""Tornado handlers for the tree view.
Authors:
* Brian Granger
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2011 The IPython Development Team
#
# Distributed under the terms of the BSD License. The full license is in
# the file COPYING, distributed as part ... | alephu5/Soundbyte | environment/lib/python3.3/site-packages/IPython/html/tree/handlers.py | Python | gpl-3.0 | 3,608 | [
"Brian"
] | f64c4b829b3372c7d88a4b53b0151b64b0ae68a2268aab2c77272118937f44d7 |
from .gaussian import DiagonalGaussian
from .beta import Beta, Beta2 | p-morais/rl | rl/distributions/__init__.py | Python | mit | 68 | [
"Gaussian"
] | 2e06066197a51f7dde2b8bfa376abbdd9963570eee5eadbc458b8da66ba9c272 |
"""
Connected components.
"""
import itertools
import logging
import networkx as nx
import numpy as np
from matplotlib.patches import Circle, FancyArrowPatch
from monty.json import MSONable, jsanitize
from networkx.algorithms.components import is_connected
from networkx.algorithms.traversal import bfs_tree
from pyma... | vorwerkc/pymatgen | pymatgen/analysis/chemenv/connectivity/connected_components.py | Python | mit | 42,324 | [
"pymatgen"
] | a77ee5cab6fbaec71486e2cfe38f21793a52838632f2f9e175267f39dc8bc207 |
# $Id$
#
# Copyright (C) 2007,2008 Greg Landrum
#
# @@ All Rights Reserved @@
#
import os, sys
import io
import unittest
from rdkit.six.moves import cPickle
from rdkit import RDConfig
from rdkit import DataStructs as ds
def feq(v1, v2, tol=1e-4):
return abs(v1 - v2) < tol
class TestCase(unittest.TestCase):
de... | jandom/rdkit | Code/DataStructs/Wrap/testSparseIntVect.py | Python | bsd-3-clause | 5,086 | [
"RDKit"
] | 4b5efbcad24ebf0b651a3483f4196d1b194bb1f734898d7f3be6d1eb90a806c9 |
#!/usr/bin/python
# -*- coding:iso-8859-10 -*-
__docformat__ = 'reStructuredtext'
'''
Calculates the average and maximum wind speed and the prevailing wind direction
based on hourly wind vector data.
A netcdf file with hourly data from 07:00 to 06:00 UTC serves as data source.
The amplitude of the hourly wind ... | kmunve/pysenorge | pysenorge/themes/wind_600m_daily.py | Python | gpl-3.0 | 20,290 | [
"NetCDF"
] | 10586331d5ee025a003b7b4bf92fbf4cca983238cf443166c1689ef2b20451ec |
#!/usr/bin/env python
"""Processed version of the documentation.
The documentation from the objects of raw_doc is further processed into
objects from the module proc_doc. These objects can then be processed
into structured documents such as HTML more easily.
"""
# TODO(holtgrew): Location traceability for entries an... | JohnReid/seqan | util/py_lib/seqan/dox/proc_doc.py | Python | bsd-3-clause | 64,836 | [
"VisIt"
] | 0c472d79355af3117d8c23bcd9b545c2562a412fce85df818b4d1fcda4055d14 |
#!/usr/bin/env python
# Copyright 2012 Google Inc. All Rights Reserved.
"""Bigquery Client library for Python."""
import abc
import collections
import datetime
import hashlib
import itertools
import json
import logging
import os
import pkgutil
import random
import re
import string
import sys
import textwrap
import ... | ychen820/microblog | y/google-cloud-sdk/platform/bq/bigquery_client.py | Python | bsd-3-clause | 88,501 | [
"VisIt"
] | 6c4a21836d2b981a3daeba9408ee28d3427c26f787b78e010356bd815db9b8ee |
import os, sys, cookbook
from env import *
_ensembl_data_dir = os.path.join(get_data_dir(), 'ensembl')
def gene_location_filename( genome ):
return os.path.normpath(
os.path.join(
_ensembl_data_dir,
'gene_locations-%s.txt' % genome
)
)
def ense... | JohnReid/biopsy | Python/biopsy/gene_locations.py | Python | mit | 2,058 | [
"BioPerl"
] | cc4886cac873833577377072b5683117bb6b58d93a309e810bcfa98cb683d067 |
# coding: utf-8
"""
Quality trimming.
"""
from __future__ import print_function, division, absolute_import
import sys
if sys.version > '3':
xrange = range
def quality_trim_index(qualities, cutoff, base=33):
"""
Find the position at which to trim a low-quality end from a nucleotide sequence.
Qualities are assum... | Chris7/cutadapt | cutadapt/qualtrim.py | Python | mit | 918 | [
"BWA"
] | d6ab409115daed4891f3514663d5daf01cdfd5b813846822bacd6233258b4c7f |
from msClasses.Gaussian import Gaussian
from msClasses.TwoDdata import TwoDdata
from msClasses.Species import Species
from msClasses.MassSpectrum import MassSpectrum
| gnsiva/Amphitrite | msClasses/__init__.py | Python | gpl-2.0 | 166 | [
"Gaussian"
] | 2b0af9b31aa5d7991dc1aef4ae8f9d2d2af9c5f840cac38186566eb9edbc574a |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
__author__ = "Kyle Bystrom"
__copyright__ = "Copyright 2019, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Kyle Bystrom"
__email__ = "kylebystrom@gmail.com"
__date__ = "5/29/2019"
import unittes... | blondegeek/pymatgen | pymatgen/analysis/tests/test_interface.py | Python | mit | 10,339 | [
"pymatgen"
] | 8a1f0a9751369edbbe8996d7bdb0d26a11efe01ec3b5abcdc3848460d111aef4 |
import numpy
def vl_xyz2lab(I,il='E'):
# VL_XYZ2LAB Convert XYZ color space to LAB
# J = VL_XYZ2LAB(I) converts the image from XYZ format to LAB format.
#
# VL_XYZ2LAB(I,IL) uses one of the illuminants A, B, C, E, D50, D55,
# D65, D75, D93. The default illuminant is E.
#
# See also:: VL_XYZ2LUV(), VL_HELP().
... | fish2000/python-vlfeatures | vlfeat/misc/colorspaces.py | Python | gpl-2.0 | 3,124 | [
"Brian"
] | d12593dc49142cb0bf53a0e6356486ecfaa2d85ac85c378e984154938b0246e1 |
from tflearn.data_augmentation import DataAugmentation
import random
import numpy as np
import scipy
class ImageAugmentation3d(DataAugmentation):
""" Image Augmentation in 3d.
Base class for applying real-time augmentation related to images.
This class is meant to be used as an argument of `input_data`. Wh... | flaviostutz/datascience-snippets | kaggle-lung-cancer-approach2/modules/ImageAugmentation3d.py | Python | mit | 6,910 | [
"Gaussian"
] | 46df13852a1682dd0653424e214babb7e78d90b98e0797776900465532971058 |
# Copyright (C) 2015 Atsushi Togo
# All rights reserved.
#
# This file is part of phono3py.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# * Redistributions of source code must retain the above copyright
# noti... | atztogo/phono3py | phono3py/other/isotope.py | Python | bsd-3-clause | 13,495 | [
"Gaussian",
"phonopy"
] | af615bfebd8720239ec61851f7e811053f06637d1311a130435196fb482b2709 |
"""
This script will take a landlab netcdf file as input and convert the
'topographic__elevation' parameter to a numpy array .npy which can be
loaded in the standart landlab script.
"""
import numpy as np
import matplotlib.pyplot as plt
from landlab import RasterModelGrid
from landlab.io.netcdf import write_netcdf
f... | ManuSchmi88/landlab | drivers/convertNCtoNpy.py | Python | mit | 974 | [
"NetCDF"
] | aedc119744a786044a6e7b94cb1e4731b7981013a52c9d6115d507798efe4015 |
#! /usr/bin/python
# parse_doxy_html.py
""""Parse Doxygen-generated html files to get out stuff we want for Javadocs
Most code here works on doxytext: this is text taken from Doxygen-generated html created by
processing the C++ code. That html is viewed with Firefox and the appropriate pieces (now starting at
"Detai... | bp-kelley/rdkit | Code/JavaWrappers/parse_doxy_html.py | Python | bsd-3-clause | 14,721 | [
"RDKit"
] | 4371ad1f755506378fae75bedaabe0b0257d1c40cbf96ed7505160fc8bf17805 |
#!/usr/bin/env python
"""models.py: Implementation of RNNSearch in Chainer"""
from __future__ import absolute_import, division, print_function, unicode_literals
__author__ = "Fabien Cromieres"
__license__ = "undecided"
__version__ = "1.0"
__email__ = "fabien.cromieres@gmail.com"
__status__ = "Development"
import numpy... | fabiencro/knmt | nmt_chainer/models/encoder_decoder.py | Python | gpl-3.0 | 41,196 | [
"Gaussian"
] | 1326782a48e03ba511b7eed5adb2f98c9353536d1c229e315d91238e1195fb37 |
# Copyright 2020 The TensorFlow 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to i... | tensorflow/graphics | tensorflow_graphics/projects/points_to_3Dobjects/utils/tf_utils.py | Python | apache-2.0 | 5,120 | [
"Gaussian"
] | 2f2360fbf95bee70889222144d4501038e4c1abdf79bf36afffd3f9ed8cb8532 |
#!/usr/bin/env python
from builtins import object
import numpy as np
import smact
class Lattice(object):
"""A unique set of Sites.
Lattice objects define a general crystal structure, with a space group and
a collection of Site objects. These Site objects have their own fractional
coo... | WMD-group/SMACT | smact/lattice.py | Python | mit | 1,698 | [
"CRYSTAL"
] | b48faa6e29a2ba841aaab64b83015f550bd63a9b6776e2af1f2e4536ce905263 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2008 Brian G. Matherly
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your optio... | beernarrd/gramps | gramps/gen/filters/rules/person/_hasgallery.py | Python | gpl-2.0 | 2,046 | [
"Brian"
] | 5a615ce5bcaa94f0bdad9376ed249c1d7cc4abe96fc2202369eb7e84e99fd6b5 |
import re
import os
import json
from scrapy.spider import BaseSpider
from scrapy.selector import HtmlXPathSelector
from scrapy.http import Request, FormRequest, HtmlResponse, TextResponse
from scrapy.utils.response import get_base_url
from scrapy.utils.url import urljoin_rfc
from urllib import urlencode
import hashlib... | 0--key/lib | portfolio/Python/scrapy/orange/sunrise.py | Python | apache-2.0 | 2,156 | [
"Galaxy"
] | 53007df90946334ad19692a356a69ec658e1d7b900edf7e2bb06c95f55070edc |
# -*- coding: utf-8 -*-
"""
End-to-end tests for admin change view.
"""
from common.test.acceptance.pages.common.auto_auth import AutoAuthPage
from common.test.acceptance.pages.lms.admin import ChangeUserAdminPage
from common.test.acceptance.tests.helpers import AcceptanceTest
class UnicodeUsernameAdminTest(Acceptan... | Stanford-Online/edx-platform | common/test/acceptance/tests/lms/test_unicode_username_admin.py | Python | agpl-3.0 | 1,912 | [
"VisIt"
] | c047238d109399a423f4cae6f525579a85ec2392c24af1e0124e2326d59d5e54 |
# ------------------------ Imports ----------------------------------#
from sys import argv
from ...controller import sparc
import time
import struct
import math
import pickle
import matplotlib.pyplot as plt
from matplotlib.patches import Ellipse
import numpy as np
from socket_server import serve_socket
from geomet... | guiccbr/autonomous-fuzzy-quadcopter | python/py_quad_control/vrep_sim/sparc/test_drone_vrep_nav.py | Python | mit | 34,978 | [
"Gaussian"
] | 577471ca3cff0716e9baa39e9a04cc13b1c7558a086c7df68d3759b0d0e776c5 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2002 Gary Shao
# Copyright (C) 2007 Brian G. Matherly
# Copyright (C) 2009 Benny Malengier
# Copyright (C) 2009 Gary Burton
# Copyright (C) 2012 Paul Franklin
#
# This program... | pmghalvorsen/gramps_branch | gramps/gen/plug/docgen/drawdoc.py | Python | gpl-2.0 | 4,093 | [
"Brian"
] | 4db8c5915eaf29882b9a7c0073747ead0cbabe0506a770b7275cf4600d9ec666 |
# -*- coding: utf-8 -*-
#
# AtHomePowerlineServer - networked server for CM11/CM11A/XTB-232 X10 controllers
# Copyright © 2014, 2020 Dave Hocker
#
# 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 Fou... | dhocker/athomepowerlineserver | commands/DeviceOff.py | Python | gpl-3.0 | 2,894 | [
"xTB"
] | 71c7fadccdd9d40e86f6f6f1e1f389939ddfb5f0af5a81bd3fa6d33ec694709b |
from starcluster.clustersetup import ClusterSetup
from starcluster.logger import log
class BowtieInstaller(ClusterSetup):
def run(self, nodes, master, user, user_shell, volumes):
for node in nodes:
log.info("Installing Bowtie 2.2.3 on %s" % (node.alias))
node.ssh.execute('wget -c -P /opt/software/bowtie/ http... | meissnert/StarCluster-Plugins | bowtie_2_2_3.py | Python | mit | 959 | [
"Bowtie"
] | ff0804be76277c122a74f7a74365a800f322549779e9f7769f16536f74fc3582 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | kdmurray91/scikit-bio | skbio/metadata/tests/test_mixin.py | Python | bsd-3-clause | 3,005 | [
"scikit-bio"
] | a6157a6d071b114a9b869d22ed1674883fba9cefbad308d5812dcf2080503043 |
import numpy as np
from sklearn.neighbors import NearestNeighbors
from astLib import astStats
def DSmetric(localData, v, sigma):
""" Calculates the delta squared values as given in equation 1 of Dressler
et al. 1988. This uses both the position and velocities to give a measure
of substructure by identifyin... | boada/desCluster | legacy/analysis/dstest.py | Python | mit | 4,702 | [
"Galaxy"
] | 6ae61c63b7d48793d916e624b446511010afd16616dcf90866afb08e0a809013 |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | Laurawly/tvm-1 | tests/python/relay/test_pass_defunctionalization.py | Python | apache-2.0 | 6,359 | [
"VisIt"
] | c72c7f5b6a0e58c00eb83d96b43f8e6e899f4056df676db15c7bd4bf39cf085c |
#!/usr/bin/env python
"""Catalysis Micro-kinetic Analysis Package (CatMAP)"""
import os
import sys
try:
from setuptools import setup
except ImportError:
from distutils.core import setup
#from catmap import __version__ as version
__version__ = "0.3.1"
__python_version__ = sys.version
maintainer = 'Andrew J. M... | mieand/catmap | setup.py | Python | gpl-3.0 | 2,408 | [
"ASE"
] | 5045cf90c5ecfde00c73f2942731bfeb2c821601cad876221e4556c275e454b7 |
# -*- coding: utf-8 -*-
#
# This file is part of Invenio.
# Copyright (C) 2013, 2014, 2015 CERN.
#
# Invenio 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 optio... | jmartinm/invenio-workflows | tests/test_workflows.py | Python | gpl-2.0 | 31,541 | [
"Galaxy"
] | ce56c992b1924f4ccd8fc90155a06d822e8eb34e4822c2f91651e42eacd5bb15 |
# Copyright 2000 by Jeffrey Chang. 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.
"""Collection of modules for dealing with biological data in Python.
The Biopython Project is ... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/__init__.py | Python | gpl-2.0 | 1,620 | [
"Biopython"
] | 7b2ad2371b5a4ac1e8cdbd0201ee45779cd0a927bddb5eb97842c8608ea0fe41 |
from __future__ import print_function
#########################################################
# YAM(BO)PY(THON) Library
#
# Generation of Yambo input files using python
#
# Authors: A Molina-Sanchez, HPC Miranda
#
# January 2016
#########################################################
# Calculation of COHSEX cor... | henriquemiranda/yambo-py | tutorial/si/rt-optics.py | Python | bsd-3-clause | 6,210 | [
"Yambo"
] | 5f59395b49bc76d71fa888c28a582971a2c50fa9ec6b86e91dff6c59808b86a6 |
# A separate class to represent Pair Site Joint State IGC model (PS JS IGC models)
# PS JS IGC model = IGC model + Point mutation model
# Xiang Ji
# xji3@ncsu.edu
import sys
from PMModel import PMModel
from PSIGCModel import PSIGCModel
import numpy as np
import itertools
from copy import deepcopy
from operator import m... | xjw1001001/IGCexpansion | IGCexpansion/PSJSModel.py | Python | gpl-3.0 | 15,399 | [
"VisIt"
] | eae73f2519b2fb61c1ef5fbc7e540de532ecc1a18199eb5523b4083192a70256 |
#!/usr/bin/env python
# Original filename: visitOverlap.py
#
# Author: Steve Bickerton
# Email:
# Date: Thu 2013-05-23 12:00:44
#
# Summary:
#
import sys
import os
import re
import argparse
import numpy
import matplotlib.figure as figure
from matplotlib.backends.backend_agg import FigureCanvasAgg as FigCanvas
from... | HSC-Users/hscTools | bick/bin/visitOverlap.py | Python | gpl-3.0 | 11,703 | [
"VisIt"
] | be3f899753d7338a28656acdcc5d054bdfec6b6a1a900ebb20f1e182640ba3a5 |
#
# Copyright (C) 2010, 2016, 2018, 2019, 2020, 2021
# Smithsonian Astrophysical Observatory
#
#
# 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 y... | anetasie/sherpa | sherpa/models/basic.py | Python | gpl-3.0 | 63,226 | [
"Gaussian"
] | f4cd300924cd9c0f7a540a579002cfc357ed62c8509407ec41c1de0cef10e5db |
# -*- coding: utf-8 -*-
# Copyright 2007-2021 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at... | erh3cq/hyperspy | hyperspy/signal.py | Python | gpl-3.0 | 252,921 | [
"Gaussian"
] | 1caf371d33478010f4f9fc6d6ed03d72f88506fb593486e59ccc70849b70968b |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# 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)
#
# Released under th... | kain88-de/mdanalysis | package/MDAnalysis/core/Timeseries.py | Python | gpl-2.0 | 13,997 | [
"CHARMM",
"MDAnalysis"
] | f80ba760a16d0dae3a2d952c9d72146ac3ce2fca471bc1238a64f2f9c63f4182 |
"""
Provides data for the ISO 3166-1 Country codes.
Reference:
https://en.wikipedia.org/wiki/ISO_3166
"""
countries = [
("afghanistan", "af", "afg", "004"),
("aland islands", "ax", "ala", "248"),
("albania", "al", "alb", "008"),
("algeria", "dz", "dza", "012"),
("american samoa", "as", "asm", "... | vertexproject/synapse | synapse/lookup/iso3166.py | Python | apache-2.0 | 10,406 | [
"BWA"
] | 0bfb1058d261c532068bee4009a230d67dbac296cb322535c707aabc6b496948 |
import HTSeq
import getopt
import sys
from genome2simplesttrain import atcg2numbers, fasta2seqs
import random
class Genome:
def __init__(self, bam, fasta):
self.bam = bam
self.fasta = fasta
self.chromosomes = {}
def fill_chromosomes(self, size):
seq_lengths = {}
for ke... | frogsicle/naivlix1 | cov_vs_pos.py | Python | gpl-3.0 | 10,745 | [
"HTSeq"
] | 3503443ab315131d7f36229aa7de3d6f8080d9ac05cf3c3191f0bc41fc77bd4e |
#!/usr/bin/env python
#
# DNS support for ooni-probe
# by Jacob Appelbaum <jacob@appelbaum.net>
#
from socket import gethostbyname
import ooni.common
# requires python-dns
# (pydns.sourceforge.net)
try:
import DNS
# Mac OS X needs this
except:
try:
import dns as DNS
except:
pass #... | hackerberry/ooni-probe | old-to-be-ported-code/very-old/ooni/dnsooni.py | Python | bsd-2-clause | 13,757 | [
"VisIt"
] | 016e5d87c540ff8937fe47cd77f9b2b19b4c8c8131d1022113270981687325fa |
import numpy as np
import rdkit
import tensorflow as tf
from tensorflow.python.framework import test_util
from deepchem.feat.graph_features import ConvMolFeaturizer
from deepchem.feat.mol_graphs import ConvMol
from deepchem.models.tensorgraph.layers import Add, MaxPool2D, MaxPool3D, AvgPool2D, GraphCNN, GraphEmbedPool... | ktaneishi/deepchem | deepchem/models/tensorgraph/tests/test_layers.py | Python | mit | 44,946 | [
"RDKit"
] | d0a80b1ec11551f6a64a785db61b539169febfd4a4b447e30a083d2fbca03016 |
# $Id$
#
# Copyright (C) 2003-2006 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" Supplies a class fo... | adalke/rdkit | rdkit/Chem/Fingerprints/DbFpSupplier.py | Python | bsd-3-clause | 4,411 | [
"RDKit"
] | 6693a6ed9e393e4963f929f21084acb15ab4f913f5d0eb7c46aa8c7a1748289d |
import numpy
def gaussian(time_axis, frequency, phase, fwhm):
oscillatory_term = numpy.exp(2j * numpy.pi * (frequency * time_axis) + 1j * phase)
damping = numpy.exp(-time_axis ** 2 / 4 * numpy.pi ** 2 / numpy.log(2) * fwhm ** 2)
fid = oscillatory_term * damping
fid[0] /= 2.0
# normalise the fid so... | bennyrowland/suspect | suspect/basis/__init__.py | Python | mit | 656 | [
"Gaussian"
] | b6a5e299024d74fa32d402461d85332f0a9ff72ae2fbb9ae963d854d9e92307c |
#! /usr/bin/env python
########################################################################
# $HeadURL: $
########################################################################
"""
Submit an FTS request, monitor the execution until it completes
"""
__RCSID__ = "$Id: $"
from DIRAC.Core.Base import Script
Scr... | sposs/DIRAC | DataManagementSystem/scripts/dirac-dms-fts-submit.py | Python | gpl-3.0 | 1,608 | [
"DIRAC"
] | 105ef36b12d9aee94ec1e9892b241408f3a7f96dc1579efaf5b434a2930e3b0a |
# -*- 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):
# Changing field 'NeuronArticleMap.added_by'
db.alter_column('neuroelectro_neuronarticlemap', 'added_by_id'... | lessc0de/neuroelectro_org | neuroelectro/south_migrations/0040_auto__chg_field_neuronarticlemap_added_by.py | Python | gpl-2.0 | 25,796 | [
"NEURON"
] | 1d06eec0082ff86f33fe03500a98e5a821817638d4876e597a61ffd05ce6ad4d |
import CGATPipelines.Pipeline as P
from Bio import Entrez
import numpy as np
import httplib2
import sqlite3
from intermine.webservice import Service as SS
import string
import re
import os
import xml.etree.ElementTree as ET
import pandas as pd
import CGAT.Experiment as E
import CGAT.IOTools as IOTools
from future.moves... | CGATOxford/CGATPipelines | CGATPipelines/PipelineGeneInfo.py | Python | mit | 45,677 | [
"Biopython"
] | ceb46f23a8a174e69c89df2a5eba423c90ac061f726ec267f53f9a62683d68ee |
import numpy as np
from matplotlib import pyplot
import rft1d
#(0) Set parameters:
np.random.seed(123456789)
nResponses = 10000
nNodes = 101
FWHM = 10.0
#(1) Generate Gaussian 1D fields and extract maxima:
y = rft1d.randn1d(nResponses, nNodes, FWHM)
ymax = y.max(axis=1)
#(2) Survival fu... | 0todd0000/rft1d | rft1d/examples/val_max_0_gaussian_1d.py | Python | gpl-3.0 | 945 | [
"Gaussian"
] | 2b2449a523a172fc865aa40e1102062e98db491a6855c4b724e496df06facfb0 |
from ase import *
from hotbit import *
from ase.data.molecules import molecule
C6H6 = molecule('C6H6')
calc = Hotbit(SCC=True,width=0.05,txt='benzene.cal')
C6H6.set_calculator(calc)
e6 = C6H6.get_potential_energy()
atoms = Atoms(container='Wedge')
atoms += C6H6[0]
atoms += C6H6[6]
atoms.set_container(angle=2*pi/6,he... | pekkosk/hotbit | examples/benzene_RPBC.py | Python | gpl-2.0 | 608 | [
"ASE"
] | 43bf7a7dd3e5212dc13bddb3212def2d6b39fcc6bc9130a50c1b493a4840517b |
# An interface for programs which do integration - this will handle
# all of the input and output, delegating the actual processing to an
# implementation of this interfacing.
#
# The following are considered critical:
#
# Input:
# An implementation of the indexer class.
#
# Output:
# [processed reflections?]
#
# This ... | xia2/xia2 | src/xia2/Schema/Interfaces/Integrater.py | Python | bsd-3-clause | 28,064 | [
"CRYSTAL"
] | f43c292ab6ca4528ba821b5f9c6bdb513a677e5bb4f5004aa2b500c7514b93cb |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under t... | MDAnalysis/mdanalysis | package/MDAnalysis/analysis/encore/covariance.py | Python | gpl-2.0 | 8,247 | [
"MDAnalysis"
] | a13c37fd667d5082f9bc636995a1245920db43519f816e67dee4bebd9b91c3b3 |
#! /usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-admin-get-site-protocols
# Author : Stuart Paterson
########################################################################
"""
Check the defined protocols for all SEs of a given site
"""
__... | sposs/DIRAC | Interfaces/scripts/dirac-admin-get-site-protocols.py | Python | gpl-3.0 | 1,198 | [
"DIRAC"
] | d44e5d016db7a2144d2c2ae9bed85548ff13baddf3a9cf35bf53fb2c236e8832 |
#!/usr/bin/env python2
###############################################################################
# ------------------------- Description ---------------------------------------
###############################################################################
# This script is used to grid daily HMS points to GFED4... | stevenjoelbrey/PMFutures | Python/grid_HYSPLITPoints.py | Python | mit | 7,200 | [
"NetCDF"
] | 3c8f4bdbd4650635fc715088b096559f88f2e14f00410665819c31bd1e43fa7f |
import collections
from .. import graph_util
from ..ssa import objtypes
from ..ssa.objtypes import BExpr, BoolTT, ByteTT, CharTT, IntTT, ShortTT
from . import ast
# Class union-find data structure except that we don't bother with weighting trees and singletons are implicit
# Also, booleans are forced to be separate ... | Storyyeller/Krakatau | Krakatau/java/boolize.py | Python | gpl-3.0 | 7,505 | [
"VisIt"
] | cdad2609df9978d0d1c3fe9514e01bd08fb0ef9ffc1e0b643e5dc4534e652859 |
"""
Courseware views functions
"""
import logging
import urllib
import json
from datetime import datetime
from django.utils.translation import ugettext as _
from django.conf import settings
from django.core.context_processors import csrf
from django.core.exceptions import PermissionDenied
from django.core.urlresolve... | sbalde/edxplatform | lms/djangoapps/courseware/views.py | Python | agpl-3.0 | 58,180 | [
"VisIt"
] | 8e233909473ab72a3de85ff7bb2c3a9051daad694857ea62de33b8f340ec50f5 |
"""
LMS Course Home page object
"""
from collections import OrderedDict
from bok_choy.page_object import PageObject
from .bookmarks import BookmarksPage
from .course_page import CoursePage
from .courseware import CoursewarePage
from .staff_view import StaffPreviewPage
class CourseHomePage(CoursePage):
"""
C... | romain-li/edx-platform | common/test/acceptance/pages/lms/course_home.py | Python | agpl-3.0 | 8,162 | [
"VisIt"
] | abcfc0fddcabec80ef12d1adfc73309d09a946dfb39696df084ed4c5f337fbeb |
# -*- coding: utf-8 -*-
import matplotlib
from keras.models import load_model, Model
import h5py
import numpy as np
from keras import backend as K
import matplotlib.pyplot as plt
from matplotlib.pyplot import cm
from matplotlib.backends.backend_pdf import PdfPages
import argparse
def parse_input():
parser = argp... | StefReck/Km3-Autoencoder | scripts/plotting/make_layer_output_histgramms.py | Python | mit | 5,909 | [
"NEURON"
] | d6cfdd06f9c89dbbcf247f36eb1555cb12c736955dc3965e95e9415b377555af |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
# Credit to Dr. Shyue Ping Ong for the template of the calculator
"""
This module implements a TEM pattern calculator.
"""
import json
import os
from collections import namedtuple
from fractions import Fractio... | gmatteo/pymatgen | pymatgen/analysis/diffraction/tem.py | Python | mit | 27,053 | [
"CRYSTAL",
"pymatgen"
] | 7ab8bf7a597cbc3866cd5f35471997bda6d35b0e519627fbf5b836df5f12b439 |
#!/usr/bin/env python
#
# Author: Patrick Halsall
import sys
import AOMLinterpolation as interp_helper
import numpy as np
from netCDF4 import Dataset
def subset_data(x, y, netcdFile, cScope, clima, fieldType):
"""
Function is expecting 6 arguments:
Float for longitude
Float for latitude
String... | s-good/AutoQC | util/AOMLnetcdf.py | Python | mit | 7,452 | [
"NetCDF"
] | 97dc0ad35e7cdd6d22e989fa6c3ab22a3182a83f4c7afbacfbe1a15b48169ed2 |
# 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... | davidzchen/tensorflow | tensorflow/python/autograph/pyct/qual_names.py | Python | apache-2.0 | 7,981 | [
"VisIt"
] | 247e2754278da65f538577095884f886f212bc2a986f3218852cd175dce818e0 |
# 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/io/__init__.py | Python | gpl-3.0 | 1,003 | [
"ESPResSo"
] | 7af11cea3d18847512cb1d88cc3ebb9def0b01934d1db4529582ef5ca1ee4d06 |
"""
Copyright 2017-2022 Biomedical Computer Vision Group, Heidelberg University.
Distributed under the MIT license.
See file LICENSE for detail or copy at https://opensource.org/licenses/MIT
"""
import argparse
import skimage.filters
import skimage.io
import skimage.util
import tifffile
thOptions = ... | BMCV/galaxy-image-analysis | tools/2d_auto_threshold/auto_threshold.py | Python | mit | 1,935 | [
"Gaussian"
] | edc4e254ab8a3f5f1471739a98bc05f48e4bc85ea2ac0c560d74a8e53f5d98f4 |
# ##### BEGIN GPL LICENSE BLOCK #####
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.
#
# This program is distrib... | Gamebasis/3DGamebasisServer | GameData/blender-2.71-windows64/2.71/scripts/addons/object_add_chain.py | Python | gpl-3.0 | 5,436 | [
"Brian"
] | d3c270604a67b11c5ac3ce743915702990d764594a15fa85d1d182ad11f903d0 |
# -*- coding: utf-8 -*-
"""
Created on Wed Sep 23 16:31:33 2015
@author: Rick Berg, University of Washington, School of Oceanography
!!!!!!!!!!Need to add in way to deal with upper boundary condition, saving output,
input process. Is this following the sediment package rather than depth?
Script for modeling reaction... | rickdberg/mgmodel | ratedownanalytic.py | Python | mit | 19,209 | [
"Gaussian"
] | 239ce1a3860b18d1e32c1607f12981a7348d8f49656f8195a9abc28eb87136b8 |
"""Generic correctness tests applicable to all routing algorithms."""
import pytest
from collections import deque
from rig.place_and_route.machine import Machine, Cores
from rig.links import Links
from rig.netlist import Net
from rig.place_and_route.routing_tree import RoutingTree
from rig.place_and_route.constr... | project-rig/rig | tests/place_and_route/route/test_generic_route.py | Python | gpl-2.0 | 12,102 | [
"VisIt"
] | 5a4c8490c85ec320be9f24ac685d45f6e858694626e5946e73c57237576bdc58 |
#Copyright (c) 2014, Ben Goodrich
#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 the above copyright notice, this list of conditions and the following... | bbitmaster/python_nn_toolkit | nnet_toolkit/nnet.py | Python | bsd-2-clause | 16,863 | [
"NEURON"
] | c7de82bbcf9af16980a9216820001d7b4ed21fbd58ab4bfce096782ac7c3fed7 |
"""
CAD [1] is a method aimed to capture structures of higher-order correlation in
massively parallel spike trains. In particular, it is able to extract
patterns of spikes with arbitrary configuration of time lags (time interval
between spikes in a pattern), and at multiple time scales,
e.g. from synchronous patterns t... | alperyeg/elephant | elephant/cell_assembly_detection.py | Python | bsd-3-clause | 49,253 | [
"NEURON"
] | 20e4bb6fa78aa1c9af4a98ba514e2d7a12c357010625a0dd2bcbaea30dcc622c |
#
# Copyright 2014-2015, 2017, 2021 Lars Pastewka (U. Freiburg)
# 2018-2019 Jan Griesser (U. Freiburg)
# 2015 Adrien Gola (KIT)
# 2014 James Kermode (Warwick U.)
#
# matscipy - Materials science with Python at the atomic-scale
# https://github.com/libAtoms/matscipy
#
# This program is free... | libAtoms/matscipy | matscipy/calculators/pair_potential/__init__.py | Python | lgpl-2.1 | 1,060 | [
"Matscipy"
] | 1e66d747150c25573484f046921b5856fccfd7e0b76e7a88148a6f1b2d6e5278 |
#
# Copyright (C) 2013-2019 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... | espressomd/espresso | src/python/espressomd/highlander.py | Python | gpl-3.0 | 2,391 | [
"ESPResSo"
] | 24d919240a11bdc00b4c8bc08aaa348b9f777fc4271ab60d347507155d80fc3b |
# Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
# 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.
__doc__="Some Bio.PDB specific exceptions."
# General error
class PDBException(Exceptio... | NirBenTalLab/proorigami-cde-package | cde-root/usr/lib64/python2.4/site-packages/Bio/PDB/PDBExceptions.py | Python | mit | 517 | [
"Biopython"
] | 9a2207202df0d0224e1018883fda3d58b1acc8705f82067e9e89a0fb4ccfc1a2 |
"""
Atomic coordinate featurizer.
"""
from __future__ import print_function
from __future__ import division
from __future__ import unicode_literals
__author__ = "Joseph Gomes and Bharath Ramsundar"
__copyright__ = "Copyright 2016, Stanford University"
__license__ = "LGPL v2.1+"
import numpy as np
import mdtraj
from d... | joegomes/deepchem | deepchem/feat/atomic_coordinates.py | Python | mit | 6,114 | [
"MDTraj",
"RDKit"
] | 9a2752fd10e48295449ab60e0a12fcd28d7c64f0c1848364081bb86667682847 |
#!/usr/bin/env python
""" cv_bridge_demo.py - Version 0.1 2011-05-29
A ROS-to-OpenCV node that uses cv_bridge to map a ROS image topic and optionally a ROS
depth image topic to the equivalent OpenCV image stream(s).
Created for the Pi Robot Project: http://www.pirobot.org
Copyright (c) 2011 Patri... | WeirdCoder/rss-2014-team-3 | src/visual/src/kinect.py | Python | mit | 12,994 | [
"Gaussian"
] | 7e3a9ec82b322b477b19a3327b345887017d42489445e01eb6a7f3d30c322c90 |
#!/usr/bin/env python
# Copyright 2014-2019 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/prop/ssc/uks.py | Python | apache-2.0 | 2,621 | [
"PySCF"
] | f0646c2d238cbc427e6dfbef4faf1ac7f44ac23c97b3837d6a4e4634c0e188c0 |
from . import visitor as visitor
from . import frame
def nash_function(parent_frame, parameters, body):
def target(params = []):
child_frame = parent_frame.new_child()
interpreter = Interpreter(child_frame)
for idx, value in enumerate(params):
identifier = parameters[idx]
... | mightymoose/nash | nash/interpreter.py | Python | bsd-3-clause | 1,860 | [
"VisIt"
] | 244f763e2f0cb4b644798869cb52ddf14f22cefe2e015568a37cbf181b39a65d |
import sys
def uncollatz(n, depth, visit=print, skip=lambda x: False):
if skip(n, depth):
return
visit(n, depth)
if depth <= 0:
return
uncollatz(2*n, depth-1, visit=visit, skip=skip)
if n % 3 == 1:
odd = n // 3
if odd % 2:
uncollatz(n // 3, depth-1, visit... | Byvire/python_scripts | uncollatz.py | Python | mit | 865 | [
"VisIt"
] | ec8ef36e56b5d9e19595fdae1f85a4652b524ddb28ced77fd126cf97f9e85285 |
# -*- coding: utf-8 -*-
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2008-2011 Kees Bakker
# Copyright (C) 2008 Brian G. Matherly
#
# 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 Softw... | Forage/Gramps | gramps/plugins/importer/importprogen.py | Python | gpl-2.0 | 54,919 | [
"Brian"
] | 2fadbca6d824872bd754327cd20d6afdd02daded421f662042c685f8390a9809 |
from bl.vl.utils import get_logger
from galaxy_wrapper import GalaxyWrapper
def run_datasets_import(history, items, action_context, no_dataobjects=False,
async=False, driver='galaxy', conf=None,
delete_history=False, purge_history=False,
logger=N... | crs4/omero.biobank | bl/vl/app/workflow_wrapper/wrappers.py | Python | gpl-2.0 | 3,122 | [
"Galaxy"
] | f2d9c3b9c9a30486d1bd3c1ed32f6f7e331f1ae59a5cef3b2a3805dbd26ac8b6 |
#
# Copyright 2017, Population Health Research Institute
# Copyright 2017, Martin Renters
#
# This file is part of the DataFax Toolkit.
#
# The DataFax Toolkit 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, e... | mrenters/DFtoolkit | dfpython/datafax/datafax/domainmap.py | Python | gpl-3.0 | 2,525 | [
"VisIt"
] | b4998381b1b3113af3441bdd3571556a6c4d81089ca4522241f45324a8fd4aa5 |
from urllib import quote_plus
from flask import jsonify, make_response, request, abort, render_template
from app import app
from app.urlshortener import URLShortener
from app.urlshortener.url import decodeURLPath, encodeURL, isValidScheme
from app.urlshortener.name import removeControlCharacters, isValidName
backend... | felixbade/lyli-api | app/views.py | Python | mit | 2,008 | [
"VisIt"
] | 5a2b55a807cd071d3bb25fff64bbf4423a183be45f48a84a89ff11f473e56aba |
import os,os.path
import platform
from multiprocessing import cpu_count
CPU_n1=cpu_count()
CPU_n2=str(max(1,CPU_n1))
##platform##
plat=platform.platform()
if "Windows" in plat:
Sys_ver = 'W'
elif "Linux" in plat:
Sys_ver = 'L'
##get config file##
path = os.path.abspath(os.curdir)
config = path.replace('\\',... | plantbiogeography/BaitsFinder | blast_tcl.py | Python | gpl-2.0 | 5,532 | [
"BLAST"
] | 8b56f521bc867f8644cdc5b787685af3433c3af46b7e5655d65741bf61a4c09a |
#!/usr/bin/env python
#pylint: disable=missing-docstring
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#... | harterj/moose | python/parameters/test/test_InputParameters.py | Python | lgpl-2.1 | 10,877 | [
"MOOSE"
] | 04ad07d373d12aaa833d9dcc943ceb92a2e9b0667788eb515f744703fa723041 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkProgrammableSource(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | nagyistoce/devide | modules/vtk_basic/vtkProgrammableSource.py | Python | bsd-3-clause | 537 | [
"VTK"
] | 03acf10136a32ac5fcde34614560790835989c8eeee0da18e51313bb9cd20a57 |
# encoding: utf-8
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding field 'GeoRecord.geom'
db.add_column('profiles_georecord', 'geom', self.gf('django.contrib.gis.db... | ProvidencePlan/Profiles | communityprofiles/profiles/oldmigrations/0020_auto__add_field_georecord_geom.py | Python | mit | 11,193 | [
"MOE"
] | 36317cd71f5b92578f288194278711a0b55b256b927b6812fccdf321302f7847 |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2011, 2012 Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License ... | zenoss/ZenPacks.zenoss.CloudStack | ZenPacks/zenoss/CloudStack/lib/txcloudstack.py | Python | gpl-2.0 | 9,120 | [
"VisIt"
] | c474608e30e111941204d3fe4d162398d7f0528bba1a9ac4e8a172e801d049cc |
import unittest
from test import support
import sys
import random
import math
import array
# Used for lazy formatting of failure messages
class Frm(object):
def __init__(self, format, *args):
self.format = format
self.args = args
def __str__(self):
return self.format % self.args
# S... | MalloyPower/parsing-python | front-end/testsuite-python-lib/Python-3.3.0/Lib/test/test_long.py | Python | mit | 51,209 | [
"Brian"
] | 9b9ce8da2a1558ebd746466b262de6f7b397447bbf1f2b64c9c1944bcd20ca78 |
"""
Prepare a numsed python program for compilation into sed.
Transform into positive form:
- all operators and binary comparisons are replaced with call to functions
x + y --> signed_add(x, y), idem -, *, //, %, **, ==, !=, <, <=, >, >=
- all operands of operators and binary comparisons inside signed_xxx functions
... | GillesArcas/numsed | numsed/transformer.py | Python | mit | 12,128 | [
"VisIt"
] | 64f6734ea7f5c2569805bd0d31c5ab6db83c20050eda06cd5a18fc944d094e00 |
# Copyright (c) 2009-2021 The Regents of the University of Michigan
# This file is part of the HOOMD-blue project, released under the BSD 3-Clause
# License.
"""Implement BaseIntegrator."""
from hoomd.operation import Operation
class BaseIntegrator(Operation):
"""Defines the base for all HOOMD-blue integrators.... | joaander/hoomd-blue | hoomd/integrate.py | Python | bsd-3-clause | 888 | [
"HOOMD-blue"
] | 708ddc659afe60346997fc6da975327aa74fa3a09d789f328a706cfa647e77f8 |
import numpy as np
import tkinter as tk
from tkinter import filedialog
import matplotlib.pyplot as plt
from feff.libs.feff_processing import xftf
from scipy.optimize import minimize
import os
from feff.libs.dir_and_file_operations import get_folder_name, runningScriptDir
from feff.libs.load_chi_data_file import load_an... | yuginboy/from_GULP_to_FEFF | feff/libs/weightDataMix.py | Python | gpl-3.0 | 4,890 | [
"FEFF"
] | a851da39db6318d053d7d6a236ad4b8d0cfff0348d13c099e8d82ddb91d48f99 |
"""The visit and identity management *plugins* are defined here."""
import base64
from cherrypy import request
import gearshift
from gearshift.identity import create_default_provider
from gearshift.identity import set_current_identity
from gearshift.identity import set_current_provider
from gearshift.identity import... | dbrattli/python-gearshift | gearshift/identity/visitor.py | Python | mit | 7,086 | [
"VisIt"
] | 832beb79492e1935d4a33ba0c94f94c044e4d87c1808698ff3b31f57d333b111 |
import os
import sys
from numpy import *
from matplotlib.pyplot import *
import pyPLUTO as pp
plutodir = os.environ['PLUTO_DIR']
wdir = plutodir+'/Test_Problems/MHD/FARGO/Spherical_Disk/'
nlinf = pp.nlast_info(w_dir=wdir,datatype='vtk')
D = pp.pload(nlinf['nlast'],w_dir=wdir,datatype='vtk') # Loading the data into a ... | DeovratPrasad/Galaxy-Cluster-PLUTO | Tools/pyPLUTO/examples/Sph_disk.py | Python | gpl-2.0 | 1,488 | [
"VTK"
] | ce99936a28d145659c31a4dd989edf9fa32601e9a010d739ee62cc49583151b7 |
# coding=utf-8
# Copyright (c) 2014 Merck KGaA
import os, re, gzip, json, requests, sys, optparse, csv
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import SDWriter
from rdkit.Chem import Descriptors
from rdkit.ML.Descriptors import MoleculeDescriptors
from scipy import interp
from scipy import... | rdkit/rdkit | Contrib/pzc/p_con.py | Python | bsd-3-clause | 45,774 | [
"ASE",
"RDKit"
] | 3b7bd927a00272e637d65bcb2912e82440362b83edc43086af74585c7623f057 |
"""
Load station data based on NetCDF files
=======================================
In this example we show how to load station data based on NetCDF files.
The data is loaded with the pymepps package. Thanks to Ingo Lange we
could use original data from the Wettermast for this example. In the
following the data is loa... | maestrotf/pymepps | examples/example_plot_stationnc.py | Python | gpl-3.0 | 2,009 | [
"NetCDF"
] | 657c90508b940ef9a2c0f3cf45188f3bdb31383bac93abe6e723ac9201c0cf73 |
#!/usr/bin/env python
###############################################################################
#
# find_circular_contigs
#
###############################################################################
# #
# This program is free sof... | JoshDaly/scriptShed | find_circular_contigs.py | Python | gpl-2.0 | 8,999 | [
"BLAST",
"pysam"
] | 2411507c4b9865fa74d743f4ae80779c631ae5ba839ca37760518af24dc8a951 |
#!/usr/bin/env python
#Copyright 2013 Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000, there is a non-exclusive license for use of this work by or on behalf of the U.S. Government. Export of this program may require a license from the United States Government.
from mpi4py import MPI
import pymongo
... | sandialabs/grandmaster | processing/updatePPHCmodel.py | Python | apache-2.0 | 4,776 | [
"VTK"
] | 46730fd86626dd674bf377c833eff678f75e545e11e3d89442bc376c2ab66640 |
#For Regular Expressions
import re
#For call to standalone BLAST
import subprocess
import sys
#For MySQL
import MySQLdb as mdb
error = open("errors2.txt","w")
#use fasplit PigeonPeaProteins and CDS
try:
con = mdb.connect('host','username','password','database')
file = open("../blastdb/CCids.txt")
for line in fi... | atulnag/pigeonpea | scripts/2_parse2DB.py | Python | mit | 2,733 | [
"BLAST"
] | a56f03f02bd044afe4e4d3e176538b9b862c9cf4b4be1db7421ef10c721ffca0 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | EmreAtes/spack | var/spack/repos/builtin/packages/r-interactivedisplaybase/package.py | Python | lgpl-2.1 | 1,947 | [
"Bioconductor"
] | d1d1a09d737a707bb99b849ffd051ab7a66206b801ce68aaa9c782bb3b51e0ec |
# Copyright (c) Anand Patil, 2007
__docformat__='reStructuredText'
__all__ = ['FullRankCovariance']
from numpy import *
from numpy.linalg import cholesky, LinAlgError
from GPutils import regularize_array, trisolve
from linalg_utils import dpotrf_wrap
from Covariance import Covariance
from incomplete_chol import icho... | matthew-brett/pymc | pymc/gp/FullRankCovariance.py | Python | mit | 10,729 | [
"Gaussian"
] | 41ef9ba9698aa7b55d8c858c84e38e03036a1aec31f00296d02892aa3208c076 |
from pypers.core.step import Step
from pypers.steps.mothur import Mothur
import os
import json
import re
class MothurClassifySeqs(Mothur):
"""
Aligns sequences to a taxonomy
"""
spec = {
'name' : 'MothurClassifySeqs',
'version' : '20150512',
'descr' : [
'Aligns... | frankosan/pypers | pypers/steps/mothur/MothurClassifySeqs.py | Python | gpl-3.0 | 7,336 | [
"BLAST"
] | 39828c9ddb6f09d5d5091a79d2a9ab9bffbe0788dfbfef875eb2d53359c8aff5 |
# Copyright (C) 2015 Philipp Baumgaertel
# All rights reserved.
#
# This software may be modified and distributed under the terms
# of the BSD license. See the LICENSE.txt file for details.
import numpy as np
from numpy.linalg import det, cholesky
from scipy.linalg import cho_solve,inv, solve_triangular
#from numpy ... | snphbaum/scikit-gpuppy | skgpuppy/Covariance.py | Python | bsd-3-clause | 27,287 | [
"Gaussian"
] | 1f9147970796e4e48325389fa428a3adb899598f5f0f2c2913a3446ba55cd9c8 |
# Sample module in the public domain. Feel free to use this as a template
# for your modules (and you can remove this header and take complete credit
# and liability)
#
# Contact: Brian Carrier [carrier <at> sleuthkit [dot] org]
#
# This is free and unencumbered software released into the public domain.
#
# Anyone is f... | esaunders/autopsy | pythonExamples/July2015FileTutorial_BigRound/FindBigRoundFiles.py | Python | apache-2.0 | 6,710 | [
"Brian"
] | 78270006ee264f0fa14e8625bc24cb6342782bc6f6f909555d3afcc1ac423922 |
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