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 |
|---|---|---|---|---|---|---|---|
import calendar
from corehq.apps.enterprise.dispatcher import EnterpriseReportDispatcher
import functools
import hashlib
import json
import logging
import uuid
from collections import defaultdict, namedtuple
from datetime import datetime
from couchdbkit.exceptions import ResourceNotFound
from django.conf import settin... | dimagi/commcare-hq | corehq/apps/saved_reports/models.py | Python | bsd-3-clause | 33,482 | [
"VisIt"
] | 160c98b6afab6b90b1827032a4512128135a1754fd056c54cbedfd9d81262dc7 |
#!/usr/bin/env python
##
## @file rewrite_pydoc.py
## @brief Convert libSBML Python doc file to something readable as docstrings
## @author Mike Hucka
##
## Purpose:
##
## The comments in the libSBML source code use Doxygen mark-up; this
## content is read by Doxygen and Javadoc, in combination with other
## scr... | TheCoSMoCompany/biopredyn | Prototype/src/libsbml-5.10.0/src/bindings/python/doc-converter/rewrite_pydoc.py | Python | bsd-3-clause | 30,018 | [
"VisIt"
] | a52996f2732a1029677b418bbb4faadea86bf3c05c8e8af6407a134051ee1cdd |
#!/usr/bin/python
'''
convert a series of fasta files into blast databases
modify headers using custom code for each file
store a record of each blast database under a short identifier in a master database file
'''
usage = '''
commands:
init - read source_list and rebuild all blast databases
add - read source_list an... | robertvi/rjv | rjvseqdb.py | Python | gpl-2.0 | 1,762 | [
"BLAST"
] | 14e21f8ef0cd333b33df3dcf6d78d154af50357c3e1d32af9c1831cb1e31ab02 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2016 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | kannon92/psi4 | psi4/driver/qcdb/exceptions.py | Python | gpl-2.0 | 3,684 | [
"Psi4"
] | 41b28479a649b79538d1b10d4dcf9031e196ba26f755393b84df9c3e35d23655 |
# -*- 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... | alejob/mdanalysis | package/MDAnalysis/analysis/density.py | Python | gpl-2.0 | 40,922 | [
"CRYSTAL",
"Gaussian",
"MDAnalysis",
"PyMOL",
"VMD"
] | 3de524fd42a9f75178e6d75da116645f62416f759e7d260acf00c78b8b2fe7c5 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import os
import re
import itertools
import warnings
import logging
import math
import glob
import six
import numpy as np
from numpy.linalg import det
from co... | gpetretto/pymatgen | pymatgen/io/vasp/inputs.py | Python | mit | 73,317 | [
"VASP",
"pymatgen"
] | d8fa47d17cfd4aab900e075923b8b9cd43b94ab8fd091e55c705e693e6d1bcc4 |
from __future__ import print_function
from django.core import management
from django.core.wsgi import get_wsgi_application
from django.utils.encoding import smart_text
from django.utils.text import slugify as unicode_slugify
from lettuce import world
from nose.tools import assert_in, assert_not_in
from webtest import... | jesseh/dothis | volunteering/features/helpers.py | Python | agpl-3.0 | 4,695 | [
"VisIt"
] | fed16811cda449ee4ec489a1e39b481b338bea178244ad2ff3f24bd1811b3aa0 |
"""Random variable generators.
integers
--------
uniform within range
sequences
---------
pick random element
pick random sample
generate random permutation
distributions on the real line:
------------------------------
uniform
... | babble/babble | include/jython/Lib/random.py | Python | apache-2.0 | 30,792 | [
"Gaussian"
] | d5e400b83a0860a0fe69eef341f2e81adeeeb0c739eb6c6f44bad56f885e0151 |
# This file is part of MyPaint.
# Copyright (C) 2012 by Andrew Chadwick <andrewc-git@piffle.org>
#
# 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 ... | glenux/contrib-mypaint | gui/colors/hcywheel.py | Python | gpl-2.0 | 46,506 | [
"FLEUR"
] | 54faeaea93b764814463b63873630a567c2c2fe8d70636eeff1d34c8bd82f41e |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | rmcgibbo/psi4public | psi4/driver/util/__init__.py | Python | lgpl-3.0 | 913 | [
"Psi4"
] | de21fbed5402d18a80913fbc1ed83f177a334cf6217b7959c6f634d105d64880 |
#-------------------------------------------------------------------------------
# . File : EVBDatFile.py
# . Program : MolarisTools
# . Copyright : USC, Mikolaj Feliks (2015-2018)
# . License : GNU GPL v3.0 (http://www.gnu.org/licenses/gpl-3.0.en.html)
#--------------------------------------------------... | mfx9/molaris-tools | MolarisTools/Parser/EVBDatFile.py | Python | gpl-3.0 | 20,522 | [
"VMD"
] | dbbf19924741038d6c512eb34cc82464a928f8484cfe575e2a28f6d11ea7172b |
# BSD license.
import networkx as nx
__all__ = ['cytoscape_data', 'cytoscape_graph']
_attrs = dict(name='name', ident='id')
def cytoscape_data(G, attrs=None):
"""Return data in Cytoscape JSON format (cyjs).
Parameters
----------
G : NetworkX Graph
Returns
-------
data: dict
... | kenshay/ImageScript | ProgramData/SystemFiles/Python/Lib/site-packages/networkx/readwrite/json_graph/cytoscape.py | Python | gpl-3.0 | 3,096 | [
"Cytoscape"
] | d6300441a15d84b59633195ebc8134b4458b4487b8c04954e9be60077fc28e57 |
#!/usr/bin/env python
"""
Script that helps setting the token of the elements in RSS.
It can acquire or release the token.
If the releaseToken switch is used, no matter what was the previous token, it will be set to rs_svc (RSS owns it).
If not set, the token will be set to whatever username is defined on the proxy lo... | chaen/DIRAC | ResourceStatusSystem/scripts/dirac-rss-set-token.py | Python | gpl-3.0 | 6,351 | [
"DIRAC"
] | 395b7add789ad4d0b49a78185c8a4890fca371b25f88bef28de2e0422f60a45a |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
'''
A simple example to run HF with background charges.
'''
import numpy
from pyscf import gto, scf, qmmm
mol = gto.M(atom='''
C 1.1879 -0.3829 0.0000
C 0.0000 0.5526 0.0000
O -1.1867 -0.2472 0.0000
H -1.9237 0.3850 0.0... | gkc1000/pyscf | examples/qmmm/00-hf.py | Python | apache-2.0 | 719 | [
"PySCF"
] | bd225b7ecc7aa110fc119c60b81ea4fff1bd7a10519bb4e821dffaae4d048e3e |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# restartstore - [insert a few words of module description on this line]
# Copyright (C) 2003-2009 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms... | heromod/migrid | mig/cgi-bin/restartstore.py | Python | gpl-2.0 | 1,112 | [
"Brian"
] | 6037af3c52d91254fe209d95d7e9c77194a667feee0103e6ff86845303f5cdef |
""" Helper for /Registry section
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import errno
from DIRAC import S_OK, S_ERROR
from DIRAC.ConfigurationSystem.Client.Config import gConfig
from DIRAC.ConfigurationSystem.Client.Helpers.CSGlobals import getV... | ic-hep/DIRAC | src/DIRAC/ConfigurationSystem/Client/Helpers/Registry.py | Python | gpl-3.0 | 19,994 | [
"DIRAC"
] | 53f5ceef6c9f84803496dc86c29bdf6e3406a1ff4869bba5fb0b8bdf2f11ecc2 |
# This file is part of wger Workout Manager.
#
# wger Workout Manager is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# wger W... | petervanderdoes/wger | wger/manager/tests/test_weight_log.py | Python | agpl-3.0 | 18,433 | [
"VisIt"
] | 9b5b34beff7661a02413eab46f146f74f8c9d4e8a4f51c0c179017112bfd5022 |
# 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... | ptrendx/mxnet | python/mxnet/contrib/onnx/onnx2mx/_op_translations.py | Python | apache-2.0 | 34,487 | [
"Gaussian"
] | 90f1169eca4877ec628b4b47aff5274f0e3428f1d87bf501782c13c720597f71 |
#!/usr/bin/env python
import math, numpy as np
#from enthought.mayavi import mlab
import matplotlib.pyplot as pp
import matplotlib.cm as cm
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import rospy
import tf
#import hrl_lib.mayavi2_util as mu
import hrl_lib.viz as hv
import... | tapomayukh/projects_in_python | sandbox_tapo/src/skin_related/Stiffness/calc_stiffness_all_taxels.py | Python | mit | 6,127 | [
"Mayavi"
] | 098d5396ca77a7602d5891a02d0063363b3750c84ff5003cb694515a7fbbd25d |
#!/usr/bin/env python
'''
Virial ratio and correlated virial ratio
Ref. JCP, 118, 2491
'''
import numpy
from pyscf import gto, scf, ci, cc
mol = gto.M(atom='N 0 0 0; N 0 0 1.2', basis='ccpvdz')
mf = scf.RHF(mol).run()
dm = mf.make_rdm1()
t_hf = numpy.einsum('ij,ji', dm, mol.intor('int1e_kin'))
v_hf = mf.e_tot - t_h... | gkc1000/pyscf | examples/1-advanced/032-virial-ratio.py | Python | apache-2.0 | 950 | [
"PySCF"
] | 23965410a10c6706e06fd83f339e17b1a56883cca12f96d5236ae855d08850d1 |
#!/usr/bin/env python
# -*- coding: latin-1 -*-
#
# Copyright 2016-2021 Blaise Frederick
#
# 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/LICEN... | bbfrederick/rapidtide | rapidtide/workflows/rapidtide.py | Python | apache-2.0 | 123,382 | [
"Gaussian"
] | 87153454745460475cad0c1f7d6f611563e91721093519e364f7b7c411ad46c5 |
#! .env/bin/python
# -*- coding: utf8 -*-
from __future__ import unicode_literals
# import time
import random
import itertools
# from collections import defaultdict
import gym
import numpy as np
# implementation of the sarsa algorithm on the mountain car using values
# rounding for value function approximation
# N... | Hiestaa/RLViz | experiments/gym_test_2.py | Python | mit | 7,015 | [
"VisIt"
] | 3c6b12688840e2fb3e041a6dbac2bcc60c935728ad829a5a46f3b741f6dff1ed |
import ocl
import camvtk
import time
import vtk
import datetime
import math
if __name__ == "__main__":
print ocl.revision()
i = ocl.Interval()
print i
i = ocl.Interval(0.123, 0.456)
print i
cc = ocl.CCPoint(1,2,3)
cc.type = ocl.CCType.VERTEX
i.updateLower(-0.222,cc)
print... | tectronics/opencamlib | scripts/ocl_interval.py | Python | gpl-3.0 | 431 | [
"VTK"
] | 17bf2d1f749a279651cd1f149860f5924e921a0af2045662467c95a5f33298fe |
# 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... | AnishShah/tensorflow | tensorflow/contrib/data/python/kernel_tests/resample_test.py | Python | apache-2.0 | 6,416 | [
"DIRAC"
] | d57c37434817f6b69303f648e6917c80cf4aa4f47a31e241310bdac669ce8d57 |
#!/usr/bin/env python
# import modules:
## @package pism_config_editor
##
## A script simplifying creating configuration files to use with PISM's -config_override option.
##
## Does not take any command-line options; the only argument is a name of a
## NetCDF configuration file to start from. Run
## \verbatim
## pism... | JohannesFeldmann/pism | util/pism_config_editor.py | Python | gpl-2.0 | 7,572 | [
"NetCDF"
] | dd3b0f82f7cd77820f5c73a690d8157561cba62d6f43a5939397413ecb288c12 |
# -*- coding: utf-8 -*-
{
"'Cancel' will indicate an asset log entry did not occur": "'Hủy' sẽ chỉ dẫn một lệnh nhập không thực hiện được",
"A location that specifies the geographic area for this region. This can be a location from the location hierarchy, or a 'group location', or a location that has a boundary for ... | devinbalkind/eden | languages/vi.py | Python | mit | 372,505 | [
"VisIt"
] | 13fc43cc7257e45ea4229bb3d648ba33af012bc42895dca3a75dec8503503694 |
#
# QAPI types generator
#
# Copyright IBM, Corp. 2011
# Copyright (c) 2013-2015 Red Hat Inc.
#
# Authors:
# Anthony Liguori <aliguori@us.ibm.com>
# Markus Armbruster <armbru@redhat.com>
#
# This work is licensed under the terms of the GNU GPL, version 2.
# See the COPYING file in the top-level directory.
from qapi ... | ehostunreach/qemu | scripts/qapi-types.py | Python | gpl-2.0 | 9,268 | [
"VisIt"
] | 2bcda92d79682b02e9c81ee5d76209b8c3aca99795d401c106f1b4f0fa41d1f0 |
#
# @file gmdi.py
# @author Brian Kim
# @brief a module that contains methods to access
# the Google Material Design Icons
#
import pygtk
pygtk.require('2.0')
import gtk, os
def ls_categories():
return os.listdir('/var/icons')
def ls_icons(cat):
# check to see if cat is valid
cats = ls_categories()
... | briansan/install-gmdi | gmdi.py | Python | bsd-2-clause | 4,280 | [
"Brian"
] | 0e83510dd3a57edd172ce537f274fa1041089ccc3a4b7ef2db374aa7a0af5d13 |
# -*- coding: utf-8 -*-
"""
Author
------
Bo Zhang
Email
-----
bozhang@nao.cas.cn
Created on
----------
- Tue Mar 8 15:26:00 2016 read_spectrum
Modifications
-------------
- Fri Jul 15 16:08:00 2016 migrate read_spectrum from lamost.py
Aims
----
- read various kinds of spectra
"""
import numpy as np
from ... | yaoyuhan/starpy | spec/read_spectrum.py | Python | mit | 4,280 | [
"VisIt"
] | edf8c45a717c0020ce877c329090002a74eea2b2d92e8d415b3194abc694b3e3 |
from __future__ import division
from __future__ import print_function
from caffe_all import *
import numpy as np
import unittest
# Helper class that allows python layers to be added to NetSpec easily. Just use
# Py.YourLayer(bottom1, bottom2, ..., parameter1=.., ...)
# parameter1 will automatically be passed to You... | jeffdonahue/voc-classification | src/python_layers.py | Python | bsd-2-clause | 3,416 | [
"Gaussian"
] | d020e0e9a281eb2180b98a76ffcfecc0a3b0f43ba96358534e4af7b4c3b99f1d |
"""Qgram based tokenizer"""
from py_stringmatching import utils
from six.moves import xrange
from py_stringmatching.tokenizer.definition_tokenizer import DefinitionTokenizer
class QgramTokenizer(DefinitionTokenizer):
"""Qgram tokenizer class.
Parameters:
qval (int): Q-gram length (defaults to 2)
... | Anson-Doan/py_stringmatching | py_stringmatching/tokenizer/qgram_tokenizer.py | Python | bsd-3-clause | 2,448 | [
"ASE"
] | e5c1e97362a1fcb109f5b180a0a13c2fb25e485442220c42db380fb5915b929c |
# Copyright (c) Amber Brown, 2015
# See LICENSE for details.
"""
towncrier, a builder for your news files.
"""
from ._version import __version__
__all__ = ["__version__"]
| hawkowl/towncrier | src/towncrier/__init__.py | Python | mit | 174 | [
"Amber"
] | 79b2323a352c4b8af014bc7ef1a5711aa7de7d8a59635fe5901567dc1eacf9ea |
########################################################################
# $HeadURL$
# File : dirac-proxy-init.py
# Author : Adrian Casajus
###########################################################from DIRAC.Core.Base import Script#############
__RCSID__ = "$Id$"
import sys
import getpass
import DIRAC
from DIRAC... | vmendez/DIRAC | FrameworkSystem/Client/ProxyUpload.py | Python | gpl-3.0 | 5,693 | [
"DIRAC"
] | 483320d140e47278283510e24f6ea1b803fbac2b375f757a9478da7b3e1096db |
import logging
from neon.callbacks.callbacks import Callbacks
from neon.data import ArrayIterator, load_mnist
from neon.initializers import Gaussian
from neon.layers import GeneralizedCost, Affine
from neon.models import ModelDist
from neon.optimizers import GradientDescentMomentum
from neon.transforms import Rectlin,... | coufon/neon-distributed | examples/dist/model_mnist.py | Python | apache-2.0 | 2,629 | [
"Gaussian"
] | 505f6b13cd712e9baa53e53c87381e5b4b489c01c4b99762d081e5134b50d189 |
# Licensed under an MIT open source license - see LICENSE
import numpy as np
import scipy.ndimage as nd
from scipy.stats import scoreatpercentile, nanmean, nanstd
from scipy.interpolate import UnivariateSpline
from astropy.convolution import Gaussian2DKernel, convolve_fft
from operator import itemgetter
from itertools... | keflavich/TurbuStat | turbustat/statistics/genus/genus.py | Python | mit | 9,209 | [
"Gaussian"
] | 9a282bb75ff6eccc6b904f512205cc62943b36afadc86d88e0626fa45d505956 |
# Unitesting modules #
try:
import unittest2 as unittest
assert unittest
except ImportError:
import unittest
from numpy.testing import assert_almost_equal
from pkg_resources import resource_filename
# Nosetest flag #
__test__ = True
from rnacounter.draft_nocython import *
import pysam
bamtest = os.path... | delafont/rnacounter | tests/test_rnacounter.py | Python | gpl-2.0 | 5,087 | [
"pysam"
] | 920ed270391a941286ab175d3a6d663c969ae56488f1a8b3ff2ded0f0236f607 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2010 Nick Hall
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of th... | Forage/Gramps | gramps/plugins/tool/ownereditor.py | Python | gpl-2.0 | 7,153 | [
"Brian"
] | dc0034c8c1c8ff133173eb0d5b10b4a639e8f60ad3f0258a81ee12397808006b |
# $Id$
#
# Copyright (C) 2002-2008 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.
#
"""unit testing code ... | rdkit/rdkit-orig | rdkit/Chem/Pharm2D/UnitTestSignature.py | Python | bsd-3-clause | 7,777 | [
"RDKit"
] | b5783363bb63660dede981607c9c6e23b2f3d5ebfe4261f2f6c8f31ca08cbb33 |
"""
"""
__RCSID__ = "$Id$"
from DIRAC import S_OK, S_ERROR
from DIRAC import gLogger, rootPath, gConfig
from DIRAC.FrameworkSystem.private.monitoring.RRDManager import RRDManager
from DIRAC.Core.Utilities import DEncode, List
class ServiceInterface( object ):
__sourceToComponentIdMapping = {}
def __init__( se... | coberger/DIRAC | FrameworkSystem/private/monitoring/ServiceInterface.py | Python | gpl-3.0 | 17,040 | [
"DIRAC"
] | 20e3d9b1e2f53c865db06a70efd4faae597058f292200bebe9f0c2a409ee113c |
# -*- coding: utf-8 -*-
import datetime
import hashlib
import json
import os
import stat
import tarfile
from copy import deepcopy
from tempfile import mkdtemp
from django.conf import settings
from django.core import mail
from django.core.files.storage import default_storage as storage
from django.core.management impor... | Jobava/zamboni | mkt/webapps/tests/test_tasks.py | Python | bsd-3-clause | 32,210 | [
"exciting"
] | 3a44f3d8cdd8939f9fa8c1f0f79d85d42308e3088632b7fb71aad11a22d2c721 |
__author__ = 'Varada Kolhatkar'
import argparse
import pandas as pd
from timeit import default_timer as timer
import re
def get_arguments():
parser = argparse.ArgumentParser(description='Write csv files for crowd annotation')
parser.add_argument('--comments_csv', '-c', type=str, dest='comments_csv', action='... | sfu-discourse-lab/SFU_Comment_Extractor | Source_Code/CSV_creation/get_statistics.py | Python | mit | 4,195 | [
"ADF"
] | 893cab78f084abbcdd9b835f3c15937d977d396d077b5506817acf03d7818230 |
# Copyright (c) 2016 Ansible, Inc.
# All Rights Reserved.
# Python
import logging
import threading
import contextlib
import re
# Django
from django.db import models, transaction, connection
from django.contrib.contenttypes.models import ContentType
from django.contrib.contenttypes.fields import GenericForeignKey
from... | wwitzel3/awx | awx/main/models/rbac.py | Python | apache-2.0 | 21,819 | [
"VisIt"
] | 48bf4e8a33b3ffbf10d7c74bdcf4265da0ef3056c0c3000d3db571c83cb0f966 |
#! /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... | rdkit/rdkit-orig | Code/JavaWrappers/parse_doxy_html.py | Python | bsd-3-clause | 15,238 | [
"RDKit"
] | 0e5d3cd61b66d806eda4a6a259d5a66efc97f0fa9ecada1f71d47afe8e4fded6 |
from numpy import arange, pi, cos, sin
from traits.api import HasTraits, Range, Instance, \
on_trait_change
from traitsui.api import View, Item, Group
from mayavi.core.api import PipelineBase
from mayavi.core.ui.api import MayaviScene, SceneEditor, \
MlabSceneModel
dphi = pi/1000.
phi = aran... | HPCGISLab/STDataViz | WorkingVersion/LibTry/MayaviGUI/interactive.py | Python | bsd-3-clause | 1,683 | [
"Mayavi"
] | b1157ed7b3789d18a03b9c4bdff681981b08dce2605a592a08d66f6358ecb181 |
# -*- coding: utf-8 -*-
# vim: sw=4 ts=4 fenc=utf-8 et
# ==============================================================================
# Copyright © 2008 UfSoft.org - Pedro Algarvio <ufs@ufsoft.org>
#
# Please view LICENSE for additional licensing information.
# ========================================================... | UfSoft/trac-google-analytics | tracext/google/analytics/__init__.py | Python | bsd-3-clause | 5,682 | [
"VisIt"
] | 63a581aa4f6635d5cfb0b1e822df3d031526cb69c11903a066ed8a460cd423b8 |
'''
Supervised classifiers and base class for all classifiers.
'''
from __future__ import absolute_import, division, print_function, unicode_literals
import logging
import math
import numpy
import numpy as np
from warnings import warn
import spectral as spy
from .algorithms import GaussianStats, ImageIterator
from ... | spectralpython/spectral | spectral/algorithms/classifiers.py | Python | gpl-2.0 | 16,400 | [
"Gaussian",
"NEURON"
] | 84e88f6efadbf9c299640574ba79c076b2f3e0e73382bac9a5cb7a98153b2a46 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Created on Jan 10, 2013
Author: Shareef M Dabdoub
Generate cluster-computing job scripts for submission in order to run multiple
simultaneous runs of the QIIME parallel BLAST pick OTUs script.
"""
import argparse
import sys
import os.path as osp
PBS_JOB_NAME_SIZE =... | smdabdoub/phylotoast | bin/multi_parallel_pick_otus.py | Python | mit | 4,449 | [
"BLAST"
] | 0de84c8c535f0f4b2042da05f99e7dc7799bb12d369a7de911ac09d8a5d41286 |
#!/usr/bin/python
"""
Copyright 2016 Paul Willworth <ioscode@gmail.com>
This file is part of Galaxy Harvester.
Galaxy Harvester is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 of th... | druss316/G-Harvestor | html/resourceFeed.py | Python | gpl-3.0 | 5,150 | [
"Galaxy"
] | c9a6d121b7f17280acafa2ba1e43852b3be38f5accf5ad14d0745f2e687b8cdc |
from django.db import models
# from edc_base.audit_trail import AuditTrail
from edc_base.model.models import BaseUuidModel
from edc_constants.choices import ARV_STATUS_WITH_NEVER
from edc_constants.choices import YES_NO
from edc_constants.constants import NOT_APPLICABLE
# from edc_sync.models import SyncModelMixin
fro... | TshepangRas/tshilo-dikotla | td_maternal/models/maternal_arv_post.py | Python | gpl-2.0 | 4,086 | [
"VisIt"
] | 733979156e6828979f87521408548c166e2a26a3f3218b823a06df777049de6a |
## \mainpage SpectralMix :: A Python library for to perform spectral clustering analyses
# using multipe types of input data types. Options for data integration are also included
# as part of the library.
... | ksiomelo/cubix | spectralmix/__init__.py | Python | apache-2.0 | 1,279 | [
"Gaussian"
] | 672d9fcfa2d67b134fa92f3865af1fc657b2fefe3bdab00d77d0a309e90a9893 |
__author__ = 'robert'
import logging
import os # For path names working under Windows and Linux
from main import add_parameters, add_exploration, run_neuron, neuron_postproc
from pypet import Environment
def mypipeline(traj):
"""A pipeline function that defines the entire experiment
:param traj:
C... | nigroup/pypet | examples/example_13_post_processing/pipeline.py | Python | bsd-3-clause | 1,547 | [
"NEURON"
] | ecba4a5b95fcf7a05e81a6da2440da7fccdf8c353e17d1200a4f27724dc8f035 |
import time
t0t=time.time()
from os.path import join
import os
import numpy as n
import glob
import sys
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as p
import astropy.io.fits as fits
from scipy.interpolate import interp1d
from scipy.stats import norm as gaussD
import GalaxySpectrumFIREFLY as... | JohanComparat/pySU | spm/bin_deep_surveys/combine_model_spectra_deep2.py | Python | cc0-1.0 | 8,884 | [
"Firefly"
] | 0c22752535a2f7d57d753b90209998d3b0a032b653160db1579bf8884ced95a4 |
# 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 following conditions are ... | juanchopanza/NeuroM | neurom/apps/morph_stats.py | Python | bsd-3-clause | 5,204 | [
"NEURON"
] | 118bec9957ad65f1861e59561a75c66216bbaaa4488d1173481e7c398fdb695e |
from __future__ import print_function
from __future__ import absolute_import
import warnings
warnings.simplefilter('always', DeprecationWarning)
import os
import os.path
from future.standard_library import install_aliases
from past.builtins import basestring
install_aliases()
import re
from six import PY3
from .utils.... | nilbody/h2o-3 | h2o-py/h2o/h2o.py | Python | apache-2.0 | 88,383 | [
"Gaussian"
] | c27664ff94a43586c1e02cc9d843f06fadf58bba0e48c89db918826a9cd979e9 |
# -*- coding: utf-8 -*-
"""
Created on Wed Jan 13 09:41:53 2016
@author: Radu
"""
# -*- coding: utf-8 -*-
"""
Created on Tue Jan 12 10:34:07 2016
@author: Radu
"""
from interneuron import Interneuron
from neuron import h
class Ib_in(Interneuron): #### Inherits from Cell
"""Two-section cell: A soma with active... | penguinscontrol/Spinal-Cord-Modeling | CPG/ib_in.py | Python | gpl-2.0 | 376 | [
"NEURON"
] | 979e1ffe143f73c28a984af61bd0d46fd3c394fc8b33cd81d3190bde2076bd5f |
# Copyright 2020 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... | google-research/graph-attribution | graph_attribution/fragment_identifier.py | Python | apache-2.0 | 5,122 | [
"RDKit"
] | 1776c9bb20a301334202c67e7abe1736811e10245a7aef393bfbbc138ffc3ecb |
#
# @file TestL3Event.py
# @brief L3 Event unit tests
#
# @author Akiya Jouraku (Python conversion)
# @author Sarah Keating
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generated automatically by converting the file located at
# ... | TheCoSMoCompany/biopredyn | Prototype/src/libsbml-5.10.0/src/bindings/python/test/sbml/TestL3Event.py | Python | bsd-3-clause | 6,632 | [
"VisIt"
] | 80b2f4a535984de554fddfcb4abc771b3ce6dee03bfcc07849763b01aaa28073 |
#pylint: disable=missing-docstring
#################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simulation Environment #
# #
# (c) 2010... | Chuban/moose | python/chigger/misc/VolumeAxes.py | Python | lgpl-2.1 | 3,779 | [
"MOOSE",
"VTK"
] | 372733d04596592d749393b49d26666e92b99a1a7f39b41b010eabe4a055ce38 |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
from ..base... | harterj/moose | python/MooseDocs/extensions/style.py | Python | lgpl-2.1 | 3,763 | [
"MOOSE"
] | 6a95edc5692254dac3ea8eb194b68ec170f056b37036d1e960880126501bc2ae |
#=============================================================================#
# MODEL DEFINITION FILE #
#=============================================================================#
import numpy as np
#----------------------------------------------------------... | crpurcell/RM-tools | RMtools_1D/deprecated/models_mc/m2.py | Python | mit | 5,151 | [
"Gaussian"
] | b7962d0bfca40f89d9a9b4118cb13f76214e5f2daa3d33b77219bf56574b9b69 |
# -*- coding: utf-8 -*-
# Twisted Imports
from twisted.application import internet, service
from twisted.internet import reactor, defer, utils
from twisted.spread import pb
from twisted.python import log
from twisted.web import server, static, resource, guard
from twisted.cred.portal import IRealm, Portal
# Zope Impo... | rasata/octopus | octopus/server/server.py | Python | mit | 16,018 | [
"Octopus"
] | a6a8eb5079490044c6315edfbe9c0e64fd348133e1adef53d5225b973f91ce40 |
"""
Battery monitoring functions for Firefly Security and Monitoring
"""
from Firefly.helpers.events import Event
from Firefly import logging, aliases
from Firefly.helpers.device import BATTERY
from .const import LOW_BATTERY_PERCENT, CRITICAL_BATTERY_PERCENT, BATTERY_LOW, BATTERY_CRITICAL, BATTERY_OKAY, BATTERY_NOT_REP... | Firefly-Automation/Firefly | Firefly/services/firefly_security_and_monitoring/battery_monitor.py | Python | apache-2.0 | 1,752 | [
"Firefly"
] | 6f7671aaf4d8b41afb888cf51ca077165fdc0f4d49897c659e1ddd8d7bba841b |
#!/usr/bin/env python
from bcs_catalogs import *
import os
import sys
z_fields = ['ACT_J0102-4915', 'ACT_J0559-5249', 'ACT_J0656-5223']
def main(tile, path):
# Make the header
make_header(tile, path)
# Go for each tile, read and print
header = 1
print >> sys.stderr, "Doing tile: %s" % tile
... | boada/planckClusters | MOSAICpipe/legacy/CLUSTERpipe/merge_catalogs_SOI.py | Python | mit | 6,182 | [
"Galaxy"
] | 73912d58846f0933d706c637cb32752d6682c9f4856881a37cc631ee0a1bbb50 |
#!/usr/bin/env python
# This example demonstrates the use of vtkCubeAxesActor2D to indicate
# the position in space that the camera is currently viewing. The
# vtkCubeAxesActor2D draws axes on the bounding box of the data set
# and labels the axes with x-y-z coordinates.
import vtk
from vtk.util.misc import ... | hlzz/dotfiles | graphics/VTK-7.0.0/Examples/Annotation/Python/cubeAxes.py | Python | bsd-3-clause | 3,924 | [
"VTK"
] | f49d045cb1a2e788891314eb6a49c49cfcfb6feece02ab50cd46dc40ba346231 |
"""
volcano (single wind) template
This template is for running single wind scenarios. Copy this template script into the modelling area, rename and e... | GeoscienceAustralia/PF3D | templates/volcano.py | Python | gpl-3.0 | 3,623 | [
"Gaussian"
] | 2666cbf5d0ef632161cd8b6d75f3390e01ea55f4f23f0d7f80586b37129b7584 |
import copy
import os
import cPickle
import timeit
import numpy
import sys
import theano.tensor as T
from theano.tensor.shared_randomstreams import RandomStreams
from utils import tile_raster_images, load_data
from rbm import RBM
try:
import PIL.Image as Image
except ImportError:
import Image
import theano
... | gdl-civestav-localization/cinvestav_location_fingerprinting | models/classification/deep_models/grbm.py | Python | gpl-3.0 | 11,744 | [
"Gaussian"
] | a49b8dfe7f3bddd637f15e91a0926e2c3d852ab3c089fe8f9251a75ae93a8c50 |
from collections import defaultdict
from math import log10, log
from threading import Thread
import threading
import math
import pyglet
import numpy as np
import colors
from geoplotlib.core import BatchPainter
from geoplotlib.utils import BoundingBox
import Queue
from inspect import isfunction
import json
class Hotsp... | lucciano/geoplotlib | geoplotlib/layers.py | Python | mit | 33,249 | [
"Gaussian"
] | b3cbdec24bfb91e3a25a1d669f193c00641a7a9e0013f3357a4ca5b2d273b2ba |
# -*- coding: utf-8 -*-
# This file is part of AudioLazy, the signal processing Python package.
# Copyright (C) 2012-2016 Danilo de Jesus da Silva Bellini
#
# AudioLazy 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 Foun... | danilobellini/audiolazy | audiolazy/lazy_synth.py | Python | gpl-3.0 | 17,778 | [
"Gaussian"
] | d9516e6a9ffb751a77acdea74b05b0f328c2ed3dc8fb3bdf37d6110d598cc1a2 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
# ----------------------------------------------------------------------------
from spack import *
import llnl.util.tty as... | iulian787/spack | var/spack/repos/builtin/packages/gaussian-view/package.py | Python | lgpl-2.1 | 3,476 | [
"Gaussian"
] | 2900465a4d84c44dea96f1d0d3ff81fe2fadee5773c4a5fbec6409da0cba5895 |
"""
Cross-origin MDPVis Server
===================
This is a minimal server for integrating MDPVis with a domain.
The domain_bridge.py is expected to be defined in the parent
directory.
:copyright: (C) 2015 by Sean McGregor.
:license: MIT, see LICENSE for more details.
"""
from flask import Flask, jsonify, request, ... | MDPvis/MDPvis.github.io | flask_server.py | Python | mit | 4,766 | [
"VisIt"
] | 3aa4e957fcfd53cda7813d749d6df10c03373d18a0986018a327731494dce90e |
'''
This is a set of functions for dealing with PIV data
Most functions are for 2D data.
'''
#Import matlab PIV data
def loadDataset(path,mats,structs,matlabData = None):
'''
Import a matlab data file
Inputs:
path - Path to the matlab file
mats - names of the matlab matrices to be imported.
... | owenjhwilliams/ASIIT | PIVutils.py | Python | mit | 17,416 | [
"Gaussian"
] | 1adc9518246a08339219b0ece1f03d7749f03b098324af414dada1575a85e2b7 |
#A* -------------------------------------------------------------------
#B* This file contains source code for the PyMOL computer program
#C* copyright 1998-2000 by Warren Lyford Delano of DeLano Scientific.
#D* -------------------------------------------------------------------
#E* It is unlawful to modify or remove ... | gratefulfrog/lib | python/pmg_tk/__init__.py | Python | gpl-2.0 | 1,525 | [
"PyMOL"
] | 2bbd240ef79cb0d687b162ddb9d1e56e3279fd7b6da43a3a71bcbd79aaad15fe |
"""Bayesian Gaussian Mixture Models and
Dirichlet Process Gaussian Mixture Models"""
from __future__ import print_function
# Author: Alexandre Passos (alexandre.tp@gmail.com)
# Bertrand Thirion <bertrand.thirion@inria.fr>
#
# Based on mixture.py by:
# Ron Weiss <ronweiss@gmail.com>
# Fabian Ped... | loli/semisupervisedforests | sklearn/mixture/dpgmm.py | Python | bsd-3-clause | 31,353 | [
"Gaussian"
] | 4ab29faa2a09bd8b7da5cb627ffb16e2a4577f0606622d850f65006fee5e815b |
# -*- coding: UTF-8 -*-
from __future__ import division
import random
import string
from collections import Sequence
from copy import deepcopy
import tensorflow as tf
import numpy as np
from deepchem.models.tensorgraph import model_ops, initializations, regularizers, activations
from deepchem.models.tensorgraph.model... | Agent007/deepchem | deepchem/models/tensorgraph/layers.py | Python | mit | 154,662 | [
"Gaussian"
] | 9f905d971075c377367c0beb7149c28a39423ec1a8c3be6e74e515b3f87f2b85 |
#!/usr/bin/env python
__author__ = "Kishori M Konwar"
__copyright__ = "Copyright 2013, MetaPathways"
__credits__ = ["r"]
__version__ = "1.0"
__maintainer__ = "Kishori M Konwar"
__status__ = "Release"
"""Contains general utility code for the metapaths project"""
try:
import os, re, sys
from shutil import rm... | Koonkie/MetaPathways_Python_Koonkie.3.0 | libs/python_modules/pipeline/jobscreator.py | Python | mit | 61,720 | [
"BLAST"
] | fa39fc657df4aadddccd00bfd34bf919c5a7a9c17734824116eb4ab0726d4b53 |
# ----------------------------------------------------------------------------
# Copyright (c) 2015, The WGS-HGT Development Team.
#
# Distributed under the terms of the BSD 3-clause License.
#
# The full license is in the file LICENSE, distributed with this software.
# -------------------------------------------------... | antgonza/WGS-HGT | distance-method/test_distance_method.py | Python | bsd-3-clause | 24,335 | [
"BLAST",
"scikit-bio"
] | 6efab478f58758f9605f1c15e1f962301e300860e48754abceb4e947d65185fa |
##############################################################################
# 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-mlinterfaces/package.py | Python | lgpl-2.1 | 2,486 | [
"Bioconductor"
] | 033c1033213eb5efc455c4d8f43b0f10e6bc1f031a8fdaee164485b6aa8fcafb |
"""
Drops the tool, tool_category_association, event, tool_event_association, tool_rating_association,
tool_tag_association and tool_annotation_association tables since they are no longer used in the
next-gen tool shed.
"""
from sqlalchemy import *
from sqlalchemy.orm import *
from sqlalchemy.exc import *
from migrate ... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/webapps/tool_shed/model/migrate/versions/0005_drop_tool_related_tables.py | Python | gpl-3.0 | 8,507 | [
"Galaxy"
] | 132fc2672a598f60018a7b48a5ec1ca4bc7d03a479c0138946b7b3b9660b6f04 |
# cachannel.py ---
#
# Filename: cachannel.py
# Description:
# Author: Subhasis Ray
# Maintainer:
# Created: Wed Jun 4 14:59:08 2014 (+0530)
# Version:
# Last-Updated:
# By:
# Update #: 0
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
#
#
# Change log:
#
#
#
#
# This pro... | subhacom/moose-core | tests/python/mus/cachannel.py | Python | gpl-3.0 | 4,617 | [
"MOOSE",
"NEURON"
] | 7e499130a9942a8a06999f2a739c10a4bb1b1f6f2496666046b98fa28b5e8871 |
"""User-friendly public interface to polynomial functions. """
from __future__ import print_function, division
from sympy.core import (
S, Basic, Expr, I, Integer, Add, Mul, Dummy, Tuple
)
from sympy.core.mul import _keep_coeff
from sympy.core.symbol import Symbol
from sympy.core.basic import preorder_traversal
... | AunShiLord/sympy | sympy/polys/polytools.py | Python | bsd-3-clause | 171,969 | [
"Gaussian"
] | 0c652a73d9c928f702bc7875da61684a392e2fc5068fdb9c1fdf484a7518c204 |
"""Notifications for Android TV notification service."""
import base64
import io
import logging
import requests
from requests.auth import HTTPBasicAuth, HTTPDigestAuth
import voluptuous as vol
from homeassistant.components.notify import (
ATTR_DATA,
ATTR_TITLE,
ATTR_TITLE_DEFAULT,
PLATFORM_SCHEMA,
... | tchellomello/home-assistant | homeassistant/components/nfandroidtv/notify.py | Python | apache-2.0 | 9,855 | [
"Amber"
] | 81c942c36062b3129bd167067b90bc432dd73a6c7778f0a63122e5f805042733 |
#!/usr/bin/env python
#
# Copyright 2016 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 requir... | Aloomaio/googleads-python-lib | examples/adwords/v201806/campaign_management/validate_text_ad.py | Python | apache-2.0 | 2,764 | [
"VisIt"
] | 8bc37f2daf7d44b5a909e6a9315d71f7898ec6117bf2b7e882b8e5dc1abb277a |
import platform, os, re
import subprocess
from mooseutils import colorText
from collections import namedtuple
import json
TERM_COLS = 110
LIBMESH_OPTIONS = {
'mesh_mode' : { 're_option' : r'#define\s+LIBMESH_ENABLE_PARMESH\s+(\d+)',
'default' : 'REPLICATED',
'options' ... | Chuban/moose | python/TestHarness/util.py | Python | lgpl-2.1 | 25,698 | [
"VTK"
] | 8eb00c4851495015a7287aba9aed05b4feec6f158199ceea25b07793edcd1b4d |
#!/usr/bin/env python
#
# Copyright (C) 2013-2017(H)
# Max Planck Institute for Polymer Research
#
# 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, ei... | espressopp/espressopp | testsuite/DPDThermostat/testDPDThermostat.py | Python | gpl-3.0 | 6,206 | [
"ESPResSo"
] | e2face9b236fca25ff27d3c8dc581f4360284382b24fef337062de510b707f7a |
"""
===================
Canny edge detector
===================
The Canny filter is a multi-stage edge detector. It uses a filter based on the
derivative of a Gaussian in order to compute the intensity of the gradients.The
Gaussian reduces the effect of noise present in the image. Then, potential
edges are thinned dow... | ofgulban/scikit-image | doc/examples/edges/plot_canny.py | Python | bsd-3-clause | 1,603 | [
"Gaussian"
] | 6ce8c2b91d148433ef09f260c1847a1403084e9b7d1a225cf355884511f7f063 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2010 Nick Hall
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of th... | arunkgupta/gramps | gramps/plugins/tool/ownereditor.py | Python | gpl-2.0 | 7,106 | [
"Brian"
] | 6f7e28e19ed4d35a5f5d61aa757ab24bac3f0dbacfb8410772576e4f720bb5b1 |
import matplotlib
matplotlib.use('Agg')
import unittest
import os
import shutil
import numpy.testing as testing
import numpy as np
import fitsio
import tempfile
from numpy import random
import glob
from redmapper import Configuration
from redmapper.redmagic import RedmagicParameterFitter, RedmagicCalibrator
from redm... | erykoff/redmapper | tests/test_redmagic.py | Python | apache-2.0 | 8,910 | [
"Galaxy"
] | 35cffc122bd2d3fb82d71ecd6248e17cb93b3571731c66d26f4ef3285dd95c2c |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# extoidaction - handle sign up with external openid credentials
# Copyright (C) 2003-2014 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the ... | heromod/migrid | mig/shared/functionality/extoidaction.py | Python | gpl-2.0 | 9,368 | [
"Brian"
] | 896ec82c809508b7b87ed5d428714caa16797fb9a713031bb2eb28e157dda40e |
from __future__ import division
from __future__ import print_function
# still tracking down the last few calls missing the np. prefix,
# leftover from 'from numpy import *'
import numpy as np
import six
import glob,types
import copy
from numpy.random import random
from numpy import ma
from numpy.linalg import norm
... | rustychris/stompy | stompy/spatial/field.py | Python | mit | 161,575 | [
"ADF",
"Gaussian"
] | 03a432966e47a31b5953e6955b3c0ba279c7d6bcbd099e82ee0c9afad303cc2c |
## Copyright (c) 2015 Ryan Koesterer GNU General Public License v3
##
## 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 l... | rmkoesterer/uga | uga/RunSnvgroupplot.py | Python | gpl-3.0 | 27,368 | [
"pysam"
] | fa94b82d572a354eea30090370e9b6857cf330bed401663c7c682b68fa222364 |
from . import core, utils
import cgt
import ctypes, os.path as osp, hashlib, numpy as np, sys, subprocess, string, os, time, traceback, cPickle
from collections import defaultdict, namedtuple
from StringIO import StringIO
import logging
def function(inputs, outputs, dbg=None, updates=None, givens=None):
assert isi... | mesnilgr/cgt | cgt/compilation.py | Python | mit | 36,331 | [
"VisIt"
] | 901f9266d8070a07e34c99c5e97065858022b00e857edfeed13f6ba50c4fe0b2 |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | demis001/scikit-bio | skbio/util/tests/test_testing.py | Python | bsd-3-clause | 3,205 | [
"scikit-bio"
] | 341a765f60b071a0afad7702b4600dbeb327a322ccbbe7be8b15ac407605b65a |
# -*- coding: utf-8 -*-
"""
kodiswift.cli.app
----------------
This package contains the code which runs plugins from the command line.
:copyright: (c) 2012 by Jonathan Beluch
:license: GPLv3, see LICENSE for more details.
"""
from __future__ import absolute_import
import logging
import os
import sys
from xml.etree ... | Backflipz/plugin.video.excubed | kodiswift/cli/app.py | Python | gpl-2.0 | 7,042 | [
"VisIt"
] | ac215f260634a11f4d723c6d3b9cbb3a02a1143102b3e2c0c59cdb8954367488 |
#!/usr/bin/env python
'''
There is a list of methods of the SCF object one can modify to control the SCF
calculations. You can find these methods in function pyscf.scf.hf.kernel.
This example shows how to remove basis linear dependency by modifying the SCF
eig method.
The pyscf.scf.addons module provides a function r... | sunqm/pyscf | examples/scf/42-remove_linear_dep.py | Python | apache-2.0 | 4,221 | [
"PySCF"
] | 5b53df80e7cc72110cb5552b13a635fbff1763a840757f0a7e3f07f931ebc42b |
__author__ = 'Robert Meyer'
import os
import numpy as np
import pandas as pd
import logging
from pypet import Parameter, cartesian_product, Environment
from lifneuron import euler_neuron
def pypet_neuron(traj):
""" Wraps the `euler_neuron` function
:param traj: Trajectory container with all parameters
... | SmokinCaterpillar/NIGroupTalkDemo | lifmodel/pypetwrapper.py | Python | bsd-3-clause | 5,094 | [
"NEURON"
] | a443005018826ed22317be906ea3fe56b6c6c95fb255e8f6f3cde7e4c0004520 |
#!/usr/bin/env python2
#
# Copyright (C) 2013-2017(H)
# Max Planck Institute for Polymer Research
#
# 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,... | kkreis/espressopp | testsuite/constrain_com/test_constrain_com.py | Python | gpl-3.0 | 5,804 | [
"ESPResSo"
] | 70c3414b092fb70709fc06b0b916bd73b282815b2a1c17dc04ea0e2e3f4c2610 |
"""
@name: Modules/House/Rules/rules.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2015-2019 by D. Brian Kimmel
@license: MIT License
@note: Created on Aug 27, 2015
@Summary:
If garage door opens and after sunset and before sunrise, turn on outside garage door lights.
... | DBrianKimmel/PyHouse | Project/src/Modules/House/Rules/rules.py | Python | mit | 4,478 | [
"Brian"
] | 8b7b77e040aa0ff7041e2e02d7333da2492aa6b5c9d775b296b11127b896a349 |
"""
=================================
Gaussian Mixture Model Sine Curve
=================================
This example demonstrates the behavior of Gaussian mixture models fit on data
that was not sampled from a mixture of Gaussian random variables. The dataset
is formed by 100 points loosely spaced following a noisy ... | bnaul/scikit-learn | examples/mixture/plot_gmm_sin.py | Python | bsd-3-clause | 6,100 | [
"Gaussian"
] | 237b2d9b7a86f625ff3b6de699f40530704dbc7a16e272a96dd12d10944cb1bd |
# 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 your option) any later ... | erh3cq/hyperspy | hyperspy/tests/drawing/test_plot_signal_tools.py | Python | gpl-3.0 | 4,823 | [
"Gaussian"
] | d9e064591a18bdbf5e7d447e9180b34b86377f304d95ecb4b70b2f3554bf896e |
#!/usr/bin/env python
from __future__ import print_function
from collections import OrderedDict
import re
regexes = {
'nf-core/chipseq': ['v_pipeline.txt', r"(\S+)"],
'Nextflow': ['v_nextflow.txt', r"(\S+)"],
'FastQC': ['v_fastqc.txt', r"FastQC v(\S+)"],
'Trim Galore!': ['v_trim_galore.txt', r"version ... | ewels/NGI-ChIPseq | bin/scrape_software_versions.py | Python | mit | 3,067 | [
"BWA",
"pysam"
] | 229be77a20764306faaf262ddfec200fd13f2f159e88911932fe961802181938 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.