text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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# 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... | mhmdfy/autopsy | pythonExamples/reportmodule.py | Python | apache-2.0 | 4,638 | [
"Brian"
] | a4dbf0e6276d0adb709659b54e9797c3e832036bda4317721d03feffbc5fb1bc |
# -*- coding: utf-8 -*-
# Copyright 2014-2015 Michael Helmling
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License version 3 as
# published by the Free Software Foundation
#
from __future__ import division, print_function
from collections impo... | supermihi/lpdec | lpdec/channels.py | Python | gpl-3.0 | 9,852 | [
"Gaussian"
] | 73a85309c5f2da9b4f89a9fe1a27dd79cea941cbc1b768ab5dbb852632feb57b |
def visit(start, nodes, fn):
def visit_recur(node, visited):
adj = sorted(nodes[node])
visited.append(node)
fn(node)
for node in adj:
if node not in visited:
visit_recur(node, visited)
visit_recur(start, []);
| tcfuji/search-algorithms | python/dfs.py | Python | mit | 277 | [
"VisIt"
] | 28f325588239a978e9865206415cb1c894ac2258ecd020bc04596eafbcca8db7 |
#
#-*- coding:utf-8 -*-
"""
Gentoo-keys - gkeyldap/actions.py
Primary api interface module
@copyright: 2012 by Brian Dolbec <dol-sen@gentoo.org>
@license: GNU GPL2, see COPYING for details.
"""
import re
from collections import defaultdict, OrderedDict
from gkeys.seed import Seeds
from gkeyldap.con... | gentoo/gentoo-keys | gkeys-ldap/gkeyldap/actions.py | Python | gpl-2.0 | 10,308 | [
"Brian"
] | 84bed3be55521973cd06909ecd5be5443fc7e9cb6abc9d090b1d9bafd489abc9 |
from DIRAC import gLogger
from DIRAC.Core.Security.X509Chain import X509Chain
from DIRAC.Core.DISET.ThreadConfig import ThreadConfig
from DIRAC.ConfigurationSystem.Client.Helpers import Registry
from DIRAC.Core.DISET.AuthManager import AuthManager
from WebAppDIRAC.Lib.SessionData import SessionData
from WebAppDIRAC.Li... | zmathe/WebAppDIRAC | Lib/WebHandler.py | Python | gpl-3.0 | 10,812 | [
"DIRAC"
] | 6f48c52e4168eaae0d5e2aca459997ea24a3f432b8cb547e88935a36df9276b6 |
import os
import networkx as nx
from pymatgen.analysis.graphs import StructureGraph
from pymatgen.core.structure import Structure
from pymatgen.analysis.local_env import CrystalNN
from pymatgen.analysis.dimensionality import (
get_dimensionality_gorai, get_dimensionality_cheon,
get_dimensionality_larsen, calcu... | dongsenfo/pymatgen | pymatgen/analysis/tests/test_dimensionality.py | Python | mit | 7,082 | [
"pymatgen"
] | 388a18801467c9b617b4e74c6f92ca5aca2076405ab1d82a102b44b9932a83eb |
# -*- coding: utf-8 -*-
# Part of Odoo. See LICENSE file for full copyright and licensing details.
import logging
from odoo import api, fields, models, tools, SUPERUSER_ID, _
from odoo.http import request
from odoo.addons.website.models import ir_http
from odoo.addons.http_routing.models.ir_http import url_for
_log... | ygol/odoo | addons/website_sale/models/website.py | Python | agpl-3.0 | 19,911 | [
"VisIt"
] | d00191391530d84e5124daccc6d421c0e6bba0a000bcd6bd7ef04cceb7e3348e |
"""
Module simplifying manipulation of XML described at
http://libvirt.org/formatdomain.html
"""
import logging
import platform
from .. import xml_utils
from .. import utils_misc
from ..libvirt_xml import base, accessors, xcepts
from ..libvirt_xml.devices import librarian
from ..compat_52lts import results_stdout_52l... | lmr/avocado-vt | virttest/libvirt_xml/vm_xml.py | Python | gpl-2.0 | 97,884 | [
"VisIt"
] | 9e1ae2fa9bfce8df7e06c962467a1a12b73cce65994cfebcecad661c410572d7 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | dgasmith/psi4 | psi4/driver/procrouting/sapt/sapt_proc.py | Python | lgpl-3.0 | 19,498 | [
"Psi4"
] | 6b8f265af82afc2c92232aafc5e7aa91a8a0d131ad6fedb5a7630c2effd8d32b |
"""
Gaussian Distribution with Gaussian Errors
------------------------------------------
Figure 5.8
The solid lines show marginalized posterior pdfs for :math:`\mu` (left) and
:math:`\sigma` (right) for a Gaussian distribution with heteroscedastic
Gaussian measurement errors (i.e., integrals over :math:`\sigma` and
:... | eramirem/astroML | book_figures/chapter5/fig_posterior_gaussgauss.py | Python | bsd-2-clause | 4,803 | [
"Gaussian"
] | e0c4c979d98b18e68cd3d8ce295a199516570f415817eb47fb01fab212d81549 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# 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)
#... | MDAnalysis/mdanalysis | testsuite/MDAnalysisTests/coordinates/test_trj.py | Python | gpl-2.0 | 5,083 | [
"MDAnalysis"
] | 659681c8d18f997fac715777b22e7bcc83761019fa128a8815571fa0902016dc |
from itertools import chain, imap
Operators = ['+', '-', '=', '<']
# First let's define the tree structure.
class TreeNode (object):
def __init__(self, value=None, children=[]):
self.value = value
self.children = [] if children == [] else children
def visit(self, callback):
callbac... | tschuy/cinch-lang | cinch/cinch_types.py | Python | mit | 2,199 | [
"VisIt"
] | d9d6e4e23c72aa1c09875d7bd4d1fe71669d3e3da556d0ceb0b3316336c38ef7 |
from brian2 import *
#from matplotlib.pyplot import *
from brian2.numpy_ import *
start_scope()
taupre = taupost = 20*ms
Apre = 0.01
Apost = -Apre*taupre/taupost*1.05
tmax = 50*ms
N = 100
# Presynaptic neurons G spike at times from 0 to tmax
# Postsynaptic neurons G spike at times from tmax to 0
# So... | amarnathmhn/ECEN751_Project2 | BrianSNN/STDP_equiv.py | Python | gpl-2.0 | 1,892 | [
"NEURON"
] | e49ac5514b4f394eda03663c26daccef3672082b512356934cabce7894eec22c |
#-*- coding:utf-8 -*-
from django.http import HttpResponseRedirect, HttpResponseForbidden, HttpResponse
from django.conf import settings
from django.contrib import messages
from django.core.mail import send_mail
from django.contrib.auth.models import User
from condor.models import Parent, Student, Attendance,... | moe-szyslak/The-Condor | condor/views.py | Python | mit | 117,034 | [
"MOE"
] | f14429fbc2d6ccdb0458acf3abcfabe4bec232a9c15046a5e4ea8d62d3429d83 |
#!/bin/env python
# pybrella.py
# PyBrella by Charles Yuan, 2014
# PyBrella is a script designed to automate the umbrella sampling process, using the AMBER molecular dynamics package.
# PyBrella automates the setup and execution of MD runs for umbrella sampling on the distance parameter, using user-
# defined start an... | charlesyuan314/PyBrella | pybrella.py | Python | gpl-3.0 | 37,259 | [
"Amber"
] | 6d4e94117cb87097d4801357c2cc4b5039146202c381a1326ece8d033198f841 |
"""Move files to local Galaxy upload directory and add to Galaxy Data Libraries.
Required configurable variables in upload:
dir
"""
from __future__ import print_function
import collections
import os
import shutil
import time
import warnings
from bcbio import utils
from bcbio.log import logger
from bcbio.upload impo... | a113n/bcbio-nextgen | bcbio/upload/galaxy.py | Python | mit | 8,248 | [
"Galaxy"
] | 7e716242057f1b7c05524b6ae77b476fac04c6941a8b62a9741d3a56cb22c0a4 |
from Xml.Xslt import test_harness
from Ft.Xml.Xslt import Error
source_1 = """<?xml version="1.0" encoding="utf-8"?><dummy/>"""
# An element enables forwards-compatible mode for itself, its
# attributes, its descendants and their attributes if either it is an
# xsl:stylesheet element whose version attribute is not eq... | Pikecillo/genna | external/4Suite-XML-1.0.2/test/Xml/Xslt/Core/test_fallback.py | Python | gpl-2.0 | 9,576 | [
"exciting"
] | 1de7387e6617159982694a9dd7b0a267c868b6cb84ff28a8b8b44745f27d1b1a |
###############################################################################
# ilastik: interactive learning and segmentation toolkit
#
# Copyright (C) 2011-2014, the ilastik developers
# <team@ilastik.org>
#
# This program is free software; you can redistribute it and/or
# mod... | nielsbuwen/ilastik | ilastik/applets/featureSelection/featureSelectionSerializer.py | Python | gpl-3.0 | 10,644 | [
"Gaussian"
] | 0fed18999771785c178e0dc2c6fe05da86d4535ece6f2da4cc50bd6c8ae6f0bb |
# encoding: utf-8
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2006 Martin Hawlisch, Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2011 Tim G L Lyons
#
# This program is free software; you can redistribute it a... | dermoth/gramps | gramps/plugins/tool/testcasegenerator.py | Python | gpl-2.0 | 94,148 | [
"Brian"
] | d9eeb8d56836d7e345f5e4b2d593ff27251911e55f1bb2210af8a5dff0ecdc00 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import os
from pymatgen.core.structure import Molecule
from pymatgen.io.xtb.inputs import CRESTInput
from pymatgen.util.testing import PymatgenTest
__author__ = "Alex Epstein"
__copyright__ = "Copyright 2020, The Materials ... | vorwerkc/pymatgen | pymatgen/io/xtb/tests/test_inputs.py | Python | mit | 1,745 | [
"pymatgen",
"xTB"
] | 6b65c97044596a090ed05f834913bbdb1f77a774f8bf7fe6318cc858c074fe6f |
##############################################################################
# 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... | tmerrick1/spack | var/spack/repos/builtin/packages/lbann/package.py | Python | lgpl-2.1 | 8,782 | [
"VTK"
] | e15641635e1d42397d007e2bd5b1bfb1b2947af105529276ff37e8f7680b1d7c |
import _ExocortexAlembicPython as alembic
import sys
import argparse
# ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ----
# create a new identifier name unique also for the file ID!
def merge_identifier_name(file_id, identifier):
nb_slash = 0
... | SqueezeStudioAnimation/ExocortexCrate | Python/samples/mergeABCs.py | Python | bsd-3-clause | 9,218 | [
"VisIt"
] | cb73221f8fc9f7200785c9b1a3582421d72842fdd378ea8827d10986632bcd6b |
#!/usr/bin/env python3
"""
1.3-finalize_assignments.py
This script parses the BLAST output from 1.1-blast-V_assignment.py and
1.2-blast_J.py. Sequences with successful assignments are
output into fasta files and a master table is created summarizing the
properties of all input sequences.
Usage: 1... | scharch/SOAnAR | annotate/1.3-finalize_assignments.py | Python | gpl-3.0 | 16,023 | [
"BLAST"
] | 115af86e272c7623f2ac8edcd56a117e4f7e6afdf24c453a2d43f5db411c0449 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Created on Fri Jul 14 08:54:21 2017
@author: sblair
"""
import sys
sys.path.insert(1,'.')
import FluidChannel as fc
import argparse
parser = argparse.ArgumentParser(prog='wmb_geom.py',
description='create geometry files for cavity c... | stu314159/pyNFC | wmb_geom.py | Python | mit | 1,228 | [
"VTK"
] | a5d82862e75b4255c4702af1dbd4878bbe90f16da10fccd4aa47e311a2779b92 |
# 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, software
# distributed under the Li... | AnthonyMRios/pymetamap | pymetamap/SubprocessBackend.py | Python | apache-2.0 | 10,633 | [
"VisIt"
] | eea6d81f0bd02193a4fa349ef85f12d9ed0d5d156d345c47f2c7af91807f7d3b |
from __future__ import print_function # python 2.7 compatibility
from __future__ import division # python 2.7 compatibility
import sys
sys.path.append("/cluster/home/hoferg/python/lib64/python2.7/site-packages")
sys.path.append("/cluster/home/hoferg/python/lib64/python3.3/site-packages")
import h5py
import numpy as n... | k-eks/Burrow | filler.py | Python | gpl-2.0 | 12,351 | [
"Gaussian"
] | 47086fdaed8fb255ccbfb18bd034f945538363782627c53008be2ed0f8b25153 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | TheTimmy/spack | var/spack/repos/builtin/packages/mpiblast/package.py | Python | lgpl-2.1 | 1,996 | [
"BLAST"
] | a783ac499776cc8aa2698c1aac71ef1e82edc60b52de299cf84bc5bbae074385 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
vtk.vtkMultiThreader.SetGlobalMaximumNumberOfThreads(1)
reader = vtk.vtkImageReader()
reader.SetDataByteOrderToLittleEndian()
reader.SetDataExtent(0,63,0,63,1,93)
reader.SetDataSpaci... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Imaging/Core/Testing/Python/TestMapToRGBABlockStreaming.py | Python | gpl-3.0 | 1,898 | [
"VTK"
] | 0e0c807eed273a96915668a9b59c6f679647df1f8ec561bf2f76226dbc9a9c2a |
#!/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:
from shutil import rmtree
from optparse i... | Koonkie/MetaPathways_Python_Koonkie.3.0 | libs/python_modules/diagnostics/tools.py | Python | mit | 5,463 | [
"BLAST"
] | 4a3384ed82408da0811e801c15c4f87cf34c1ac54f280f1852d24b99b6f1d698 |
#!/usr/bin/env python
##
## Biskit, a toolkit for the manipulation of macromolecular structures
## Copyright (C) 2004-2018 Raik Gruenberg & Johan Leckner
##
## 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 Softwar... | graik/biskit | archive_biskit2/scripts/Mod/search_templates.py | Python | gpl-3.0 | 4,606 | [
"BLAST"
] | b5eecbb6fc1f2bfe71870e75f597783a2b080adc2223229126a20e044ba331c6 |
#!/usr/bin/env python
from mayavi import mlab
import itertools
import math
import numpy
import random
class SpAMM:
@staticmethod
def index(i, j, k):
"""Return the linear octree index.
"""
return i*4+j*2+k
def __init__(self):
self.children = [None for i in range(8)]
d... | FreeON/spammpack | spammsand/visualization/src/productspace.py | Python | bsd-3-clause | 14,199 | [
"Mayavi"
] | 9ec40f937538604748f119f95cd8f886effc69c927a2cabdb46e2f79bad31fc4 |
"""
Perform Levenberg-Marquardt least-squares minimization, based on MINPACK-1.
AUTHORS
The original version of this software, called LMFIT, was written in FORTRAN
as part of the MINPACK-1 package by XXX.
Craig Markwardt converted the FORTRAN code to IDL. The information for ... | msarahan/analyzarr | analyzarr/lib/cv/mpfit.py | Python | bsd-2-clause | 93,129 | [
"Gaussian"
] | d21531b6062254c6af3c3aec323fba72cacd3f5479eaa7aec69b9d0c95427aa4 |
#!/usr/bin/env python
# myastrotools
# some useful astro functions
# not really "MY" astro toold either. mostly inheritade, as they propagate through generations of astronomers. couldnt tell who was the author of which function....
import datetime
# chomp
####################
def absmag(appmag,d,dunits='pc'):
fr... | fedhere/fedsastroutils | myastrotools.py | Python | mit | 8,101 | [
"Gaussian"
] | 806401f27309d51bd85c5b91d0aa7e5bcc530763968c5160d990b5aefc28852b |
import numpy as np
def sample_motion_model(u, x_past):
''' Assumptions:
1) Use the odometry motion model, u = (desired) dx
2) Odometry error is modeled using gaussian distribution'''
# Set the odometry error model
mu = 0.
std = 0.25
dx_bar = u
err = np.random.normal(mu, std)
d... | mufid/berkilau | ws/CSUIBotClass2014/action_model/model_1.py | Python | mit | 375 | [
"Gaussian"
] | f9fc74ebfd33b823b50c69701334ae1679733af1c4cc4e002595f57009f7ffda |
# Copyright (C) 2011, Thomas Leonard
# See the README file for details, or visit http://0install.net.
import sys, os, socket, ssl
from time import sleep
from zeroinstall import _
from zeroinstall.injector import download
from zeroinstall.support import ssl_match_hostname
import tuf.interposition
from tuf.interposit... | AlexanderRyzhko/0install-TUF | zeroinstall/injector/_download_child.py | Python | lgpl-2.1 | 6,848 | [
"VisIt"
] | e46d575c39d634fe14afb757d55ae254c6cbd5885a6df21fc6a7b58a291e66e0 |
import numpy as np
from scipy import special
# analytic approximation for a voigt profile.
def qvoigt(x, amp, pos, fwhm, gam):
"""
voigt profile
V(x,sig,gam) = Re(w(z))/(sig*sqrt(2*pi))
z = (x+i*gam)/(sig*sqrt(2))
"""
tmp = 1/special.wofz(np.zeros((len(x)))
+ 1j*np.s... | saltastro/FP_utils | qvoigt.py | Python | bsd-3-clause | 762 | [
"Gaussian"
] | d8a89f0ef87681e1b15fabb7fae403c0f688dc14df2b651d0951f1401c1d9888 |
../../../../../../../share/pyshared/orca/scripts/apps/Mozilla/__init__.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/scripts/apps/Mozilla/__init__.py | Python | gpl-3.0 | 73 | [
"ORCA"
] | f778b89cc7a18212913f5519a15e06e54ac1cf6e8f0c3c8ce16fe175bbadf549 |
# -*- coding: utf-8 -*-
# MolMod is a collection of molecular modelling tools for python.
# Copyright (C) 2007 - 2019 Toon Verstraelen <Toon.Verstraelen@UGent.be>, Center
# for Molecular Modeling (CMM), Ghent University, Ghent, Belgium; all rights
# reserved unless otherwise stated.
#
# This file is part of MolMod.
#
#... | molmod/molmod | molmod/io/crystal.py | Python | gpl-3.0 | 6,362 | [
"CRYSTAL"
] | 246db65ac65687f13e1169d7e222ec0cf9d81577da9da65ac21faea6c6a3e667 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# @Author: Brian Cherinka, José Sánchez-Gallego, and Brett Andrews
# @Filename: core.py
# @License: BSD 3-clause (http://www.opensource.org/licenses/BSD-3-Clause)
#
# @Last modified by: José Sánchez-Gallego (gallegoj@uw.edu)
# @Last modified time: 2018-11-09 09:55:04
fro... | sdss/marvin | python/marvin/tools/core.py | Python | bsd-3-clause | 10,366 | [
"Brian"
] | 15309a970b98cc6eb397a3d72941bd625384d5afe58d9d63e74ea3495e1cba75 |
# -*- coding: utf8 -*-
# SXRD_Collect - GUI program for collection single crystal X-ray diffraction data
# Copyright (C) 2015 Clemens Prescher (clemens.prescher@gmail.com)
# GSECARS, University of Chicago
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU ... | Luindil/SXRD_Collect | sxrd_collect/tests/tests.py | Python | gpl-3.0 | 2,127 | [
"CRYSTAL"
] | 6dc2562f4750f1eaba765b58529479e3ce1dda9787661beb8f69bfa5504018df |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# This file is part of the SPORCO package. Details of the copyright
# and user license can be found in the 'LICENSE.txt' file distributed
# with the package.
"""
Basis Pursuit DeNoising
=======================
This example demonstrates the use of class :class:`.bpdn.BPDN`... | alphacsc/alphacsc | alphacsc/other/sporco/examples/scripts/sc/bpdn.py | Python | bsd-3-clause | 3,809 | [
"Gaussian"
] | ef32a05b0196f1edd3f3eff30f4d85c813809c5204061819c23073ca4e3b6126 |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2009, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License versi... | zenoss/ZenPacks.community.VMwareESXMonitor | ZenPacks/community/VMwareESXMonitor/modeler/plugins/zenoss/snmp/Esx.py | Python | gpl-2.0 | 1,873 | [
"VisIt"
] | 57568a2e450ace5da0ccb04ef1ea2ba4876aa8f0ba5a6d94b46dbc0d5e79ccae |
#
# Copyright 2018 Analytics Zoo Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... | intel-analytics/analytics-zoo | pyzoo/zoo/examples/orca/learn/bigdl/imageInference/imageInference.py | Python | apache-2.0 | 3,441 | [
"ORCA"
] | 9b793f94ee4c51b06c485bd70a46b97eac68307c7f907bed01dab18c3b30f423 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
from collections import Sequence
import abc
from monty.json import MSONable
from scipy.constants import N_A
"""
This module defines the abstract base classe... | matk86/pymatgen | pymatgen/apps/battery/battery_abc.py | Python | mit | 12,384 | [
"pymatgen"
] | e01f3cbb5ad88b187aa70ca1eab6fd5279527b7f57ea9676726c6d093e9297ac |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import sys
from uuid import uuid4
from datetime import datetime, timedelta
from ujson import dumps
from colorama import Fore, Style
from octopus import TornadoOctopus
from octopus.limiter.redis.per_domain import Limiter
from retools.lock import Lock, LockTimeout
from hol... | marcelometal/holmes-api | holmes/worker.py | Python | mit | 10,619 | [
"Octopus"
] | 03546c0e0f9cfc15aa75303d07403124b2c437373aa0cf233a74f7e683a3c642 |
""" :mod: GFAL2_SRM2Storage
=================
.. module: python
:synopsis: SRM2 module based on the GFAL2_StorageBase class.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
# pylint: disable=invalid-name
import six
import errno
import jso... | ic-hep/DIRAC | src/DIRAC/Resources/Storage/GFAL2_SRM2Storage.py | Python | gpl-3.0 | 9,312 | [
"DIRAC"
] | 7906a40b89d14ec80265a98385c840f5a5cc34558457a0e69edb213690fe0987 |
# Copyright (C) 2010-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | hmenke/espresso | testsuite/python/lb_thermostat.py | Python | gpl-3.0 | 3,197 | [
"ESPResSo"
] | 68bff01bc53c9a5703941a12b1520be49396dc0f8c52ce572f73433e0a70ca02 |
#############################################################################
# $HeadURL$
#############################################################################
""" The Bdii2CSAgent performs checking BDII for availability of CE and SE
resources for a given or any configured VO. It detects resources not yet
... | vmendez/DIRAC | ConfigurationSystem/Agent/Bdii2CSAgent.py | Python | gpl-3.0 | 12,171 | [
"DIRAC"
] | a7fa56188dffe176dd07e041f78397658aad35de1b70378e9be701371c521ea7 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides classes to identify optimal substrates for film growth
"""
from itertools import product
import numpy as np
from pymatgen.analysis.elasticity.strain import Deformation
from pymatgen.c... | mbkumar/pymatgen | pymatgen/analysis/substrate_analyzer.py | Python | mit | 17,489 | [
"pymatgen"
] | 54d781f7e9ae616bfcadfe18131347d33fd2aa487db1f61fc6a30d603508df1f |
import sys, os
keywords = ['PLPS_path', 'PDB2PQR_path', 'APBS_path', 'receptor_file', 'ligand_file', 'BABEL_path']
def read_input(input_file):
file = open(input_file, 'r')
for line in file:
key = line.split()[0]
if(key == keywords[0]):
PLPS_dir = line.split()[1]
elif(key ==... | avaidyam/Binoculars | bin/plps/scripts/prepare_receptor.py | Python | mit | 4,124 | [
"Amber"
] | bceee3c99ca4a6c311da08b0d6ecca68c0be3505bc0fbb16102b7fddf415233e |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
import unittest2 as unittest
import os
import json
from pymatgen.core.periodic_table import Specie
from pymatgen.core.composition import Composition
from pymatgen.struc... | aykol/pymatgen | pymatgen/structure_prediction/tests/test_substitutor.py | Python | mit | 1,630 | [
"pymatgen"
] | 3a3d2c0ae1db4d7d1e2e33b5cd2d52ad669a9ef51fe3a3a2c0c340572a71b19c |
# BEGIN_COPYRIGHT
#
# Copyright (C) 2014 CRS4.
#
# This file is part of blast-python.
#
# blast-python is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option)
# ... | crs4/blast-python | BlastPython/blast_seq_stream.py | Python | gpl-3.0 | 1,155 | [
"BLAST"
] | 2cbe8e908daaf0a10e4329306808973aab5191d94f997d30af6ef61b0d42df90 |
# Copyright 2015 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... | Xeralux/tensorflow | tensorflow/python/ops/control_flow_grad.py | Python | apache-2.0 | 9,146 | [
"VisIt"
] | 1eb47981b4fcc9319d047b1983602adaa602f52d2df1e6bd70c84f53f4159bf3 |
#!/usr/bin/python
"""
Brief: This class sets generates all of the scripts needed for the ray-tracing
phase and beyond, i.e. all of the per-chip scripts.
Date: January 26, 2012
Authors: Nicole Silvestri, U. Washington, nms21@uw.edu,
Jeff Gardner, U. Washington, Google, gardnerj@phys.washington.e... | lsst-sims/sims_phosim_pythoncontrol | AllChipsScriptGenerator.py | Python | gpl-3.0 | 25,205 | [
"VisIt"
] | 7739790961cef463bbcba11e11ea27cb645b08931c3d3589041b4f0e0a5dd153 |
from common import Modules, data_strings, load_yara_rules, PEParseModule, ModuleMetadata
from base64 import b64decode
from re import match
from string import ascii_lowercase, ascii_uppercase, digits
class madness_pro(PEParseModule):
def __init__(self):
md = ModuleMetadata(
module_name="madness... | bwall/bamfdetect | BAMF_Detect/modules/madness_pro.py | Python | mit | 2,262 | [
"Brian"
] | 78100de4d4fefd4639a85ca7ea80a2c955de2dba77b6e06e7daee9927cfa03d1 |
#!/usr/bin/env python
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Makes sure files have the right permissions.
Some developers have broken SCM configurations that flip the executable
permission... | heke123/chromium-crosswalk | tools/checkperms/checkperms.py | Python | bsd-3-clause | 13,646 | [
"Galaxy",
"xTB"
] | 5b626d6e3db1e6bf5be2a711f4259ef2d275f0a730b91e35cfe256ef65c4e5ef |
import pytest
import os
from lissero.scripts.Serotype import SerotypeDB
from lissero.scripts.Serotype import Serotype
from lissero.scripts.Serotype import report_maker
#from lissero.Serotype import BinaryType
from lissero.scripts.Blast import Blast
BLAST_OUTFMT = '6 qaccver saccver length slen pident'
test_folder = o... | MDU-PHL/LisSero | tests/test_SerotypeDBClass.py | Python | gpl-2.0 | 4,053 | [
"BLAST"
] | d69df7434abf9c15de8f76ee7d718475373551307b592f1a89c714379402bc90 |
# Copyright (C) 2010-2014 CEA/DEN, EDF R&D
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This library ... | FedoraScientific/salome-paravis | test/VisuPrs/SWIG_scripts/A5.py | Python | lgpl-2.1 | 2,357 | [
"VTK"
] | 258950611c73ee0f4508947df5e8b7f71c437475e6e7aae6d90345452814f2b4 |
"""
Robust location and covariance estimators.
Here are implemented estimators that are resistant to outliers.
"""
# Author: Virgile Fritsch <virgile.fritsch@inria.fr>
#
# License: BSD 3 clause
import warnings
import numbers
import numpy as np
from scipy import linalg
from scipy.stats import chi2
from . import empir... | ashhher3/scikit-learn | sklearn/covariance/robust_covariance.py | Python | bsd-3-clause | 29,573 | [
"Gaussian"
] | d8e077119b1f4655c2688115dd95c246f0acfc804d9ff1ac211f61082fafd477 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.import string
import string
import random
import numpy as np
"""
function for calculating the convergence of an x, y data set
main api:
test_conv(xs, ys, name, tol)
tries to fit multiple functions to the x, ... | dongsenfo/pymatgen | pymatgen/util/convergence.py | Python | mit | 14,788 | [
"pymatgen"
] | 298e8313d95d9ee5b97c58f8db9ac4979511dc42e2ad8c0020043369bd641774 |
# coding=utf-8
# Copyright 2022 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... | google-research/google-research | uncertainties/sources/models/dropout.py | Python | apache-2.0 | 9,503 | [
"NEURON"
] | e409603efcbf3e3de2fa617bfa0af73e3c84f6bb363480cb51007e98bf389bf3 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2015 Gerald Kunzmann <gerald@gkunzmann.de>
# Copyright (C) 2013-2016 Paul Franklin
#
# This program is free softw... | gramps-project/gramps | gramps/plugins/textreport/familygroup.py | Python | gpl-2.0 | 38,934 | [
"Brian"
] | af94c6bc5ae793ba5fd08cd21fa35524f9073ddbde44d32571cf466046382581 |
#!/usr/bin/env python
# _*_ coding:utf-8 _*_
import boto
import json
import os
import subprocess
import webbrowser
from datetime import datetime
from distutils.spawn import find_executable
from fabric.api import local, require, task
from fabric.state import env, output
from oauth import get_document, get_credentials
f... | stlpublicradio/dailygraphics | fabfile/__init__.py | Python | mit | 19,099 | [
"VisIt"
] | 8ea79c0088957948172b0995280d97b6d9e1195b8320c3051f1787e4246f6a66 |
'''
Clone Python implementation of Kivy Launcher from kivy/kivy-launcher repo,
install deps specified in the OPTIONS['apk']['requirements'] and put it
to a dist named OPTIONS['apk']['dist-name'].
Tested with P4A Dockerfile at 5fc5241e01fbbc2b23b3749f53ab48f22239f4fc,
kivy-launcher at ad5c5c6e886a310bf6dd187e992df97286... | PKRoma/python-for-android | testapps/testlauncherreboot_setup/sdl2.py | Python | mit | 3,140 | [
"Galaxy"
] | 1547559571f15a2d28f902a9965fad2978b4d8690d58e87e00acd2070fc7c10b |
import urllib,xbmcplugin,xbmcgui,xbmcaddon,xbmc,os
ADDON = xbmcaddon.Addon(id='script.kodilogemail')
dialog = xbmcgui.Dialog()
DIR=os.path.join(ADDON.getAddonInfo('profile'))
THEHTML = xbmc.translatePath(os.path.join(ADDON.getAddonInfo('path'),'theemail.html'))
def CATEGORIES():
if ADDON.getSetting('email'... | mrquim/mrquimrepo | script.kodilogemail/default.py | Python | gpl-2.0 | 9,711 | [
"VisIt"
] | b8d075ce29cb1fc60285cee2822a26618ad70e51035fd8b64b8952d6df3bd9d4 |
#
# Honeybee: A Plugin for Environmental Analysis (GPL) started by Mostapha Sadeghipour Roudsari
#
# This file is part of Honeybee.
#
# Copyright (c) 2013-2015, Mostapha Sadeghipour Roudsari <Sadeghipour@gmail.com>
# Honeybee is free software; you can redistribute it and/or modify
# it under the terms of the GNU Ge... | samuto/Honeybee | src/Honeybee_Generate Cumulative Sky.py | Python | gpl-3.0 | 6,928 | [
"EPW"
] | d0cdeb785081309653543ab25485faf742cecaae6a815f261752196e5b6eea40 |
#!/usr/bin/env python
from setuptools import setup
"""
Documentation can be found at https://docs.python.org/2/distutils/index.html, but usually you only need to do the
following steps to publish a new package version to PyPI::
# Update the version tag in this file (setup.py)
python setup.py register
pyth... | brki/cleanerversion | setup.py | Python | apache-2.0 | 2,094 | [
"Brian"
] | f8661abc8557a3dadd9c42b940e22b9dc50334b536763f0fbc26e5e7cce05145 |
import unittest
import warnings
import numpy as np
from pymatgen.analysis.elasticity.strain import (
Deformation,
DeformedStructureSet,
Strain,
convert_strain_to_deformation,
)
from pymatgen.core.lattice import Lattice
from pymatgen.core.structure import Structure
from pymatgen.core.tensors import Ten... | vorwerkc/pymatgen | pymatgen/analysis/elasticity/tests/test_strain.py | Python | mit | 6,871 | [
"pymatgen"
] | 256af8e1fd9b31149c85c49d3a5786f000be4154c4bceef7cdca645b0cb2258c |
#!/usr/bin/env python3
#
# This file is part of Radicale Server - Calendar Server
# Copyright © 2009-2017 Guillaume Ayoub
#
# This library 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 th... | jaesivsm/Radicale | setup.py | Python | gpl-3.0 | 3,596 | [
"VisIt"
] | 0ee277e9fdc201ff453f3f53f063feb3413091143bab29a8a5b191e4702e8468 |
# Copyright: (c) 2013, James Cammarata <jcammarata@ansible.com>
# Copyright: (c) 2018-2021, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import json
import os.path
im... | s-hertel/ansible | lib/ansible/cli/galaxy.py | Python | gpl-3.0 | 79,637 | [
"Galaxy"
] | c5af12fdc09d05fc3afac485ad144a738f485ab781b03e826388ab53a26ed756 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkPolyDataNormals(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vt... | nagyistoce/devide | modules/vtk_basic/vtkPolyDataNormals.py | Python | bsd-3-clause | 491 | [
"VTK"
] | 3ba5102730c58bd55e268b26c8021431c0ded015d563b91a6a62b9e314aa52eb |
# (c) 2012-2018, Ansible by Red Hat
#
# This file is part of Ansible Galaxy
#
# Ansible Galaxy is free software: you can redistribute it and/or modify
# it under the terms of the Apache License as published by
# the Apache Software Foundation, either version 2 of the License, or
# (at your option) any later version.
#
... | chouseknecht/galaxy | galaxy/main/urls.py | Python | apache-2.0 | 2,412 | [
"Galaxy"
] | c6e099a682021aa979a15e54b552ae7546a5558623a9acdbb73db4f082e17cff |
"""
Class: Bacteria.py
Description: This class models a bacteria with a single neuron brain. This bacteria could make only
two movements in response to enviroment's food concentration: Run, in which it will walk
in the same direction it was and Tumble, when it changes the dir... | abreufernandof/NeuralNets | Bacteria.py | Python | gpl-3.0 | 15,422 | [
"NEURON"
] | 091be958967c8049225509cff8a6634a68e0425a6f040a6c16f89ef8eeab5848 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Copyright (C) 2012 Computational Neuroscience Group, NMBU.
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 you... | LFPy/LFPy | LFPy/test/test_pointprocess.py | Python | gpl-3.0 | 14,292 | [
"NEURON"
] | 2b6827e01e001554ed5243a0eb0e076dfd38809402d6e075ef90443b4da4a498 |
# -*- coding: utf-8 -*-
"""
<DefineSource>
@Date : Fri Nov 14 13:20:38 2014 \n
@Author : Erwan Ledoux \n\n
</DefineSource>
A Brianer
"""
#<DefineAugmentation>
import ShareYourSystem as SYS
BaseModuleStr="ShareYourSystem.Standards.Recorders.Simulater"
DecorationModuleStr="ShareYourSystem.Standards.Classors.Classer... | Ledoux/ShareYourSystem | Pythonlogy/ShareYourSystem/Standards/Recorders/Brianer/draft/__init__ copy 5.py | Python | mit | 34,952 | [
"Brian",
"NEURON"
] | 31719288929aabbd9a5aa7d581f49956563669533599bbcebbf3f79ff3e90234 |
###############################################################################
##
## Copyright (C) 2006-2011, University of Utah.
## All rights reserved.
## Contact: contact@vistrails.org
##
## This file is part of VisTrails.
##
## "Redistribution and use in source and binary forms, with or without
## modification, ... | CMUSV-VisTrails/WorkflowRecommendation | vistrails/packages/vtk/inspectors.py | Python | bsd-3-clause | 10,741 | [
"VTK"
] | 40e8bab960be26b8d87b49e0343c58b6846595fdcda1c41a28370deee746292b |
""" This is a test of the chain
PilotsLoggingClient -> PilotsLoggingHandler -> PilotsLoggingDB
It supposes that the DB is present, and that the service is running
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import unittest
import sys
from D... | yujikato/DIRAC | tests/Integration/WorkloadManagementSystem/Test_PilotsLoggingClient.py | Python | gpl-3.0 | 5,212 | [
"DIRAC"
] | 36e217d54b7913447fd184b5377a976da0e8e35ec6d8e40b9d95f9c08dd49026 |
"""
FEniCS tutorial demo program: Poisson equation with Dirichlet conditions.
Simplest example of computation and visualization with FEniCS.
-Laplace(u) = f on the unit square.
u = u0 on the boundary.
u0 = u = 1 + x^2 + 2y^2, f = -6.
"""
from dolfin import *
# Create mesh and define function space
mesh = UnitSquareM... | akshmakov/Dolfin-Fijee-Fork | test/unit/book/python/chapter_1_files/stationary/poisson/d1_p2D.py | Python | lgpl-3.0 | 918 | [
"VTK"
] | 541f086da974ef7fdefb28b947a7ca7293ef2185214c02ccd2fa4b3ccd92ef13 |
# -*- coding: utf-8 -*-
"""test_app.py - ???
Author: Paul Brian
(C) 2012 Rice University
This software is subject to the provisions of the GNU Lesser General
Public License Version 2.1 (LGPL). See LICENSE.txt for details.
"""
from rhaptos2.repo import dolog, set_logger, set_app
from rhaptos2.repo.run import make_app... | philschatz/rhaptos2.repo | rhaptos2/repo/tests/test_app.py | Python | lgpl-2.1 | 592 | [
"Brian"
] | 4b876f3f7e906901525d76989f342ec075e4f6cc549f94e7167aeb305a3ead72 |
"""
Mind: Specify path for your bader executable in main with the needed options
"""
import numpy as np
from pymatgen import Structure
from pymatgen.analysis.energy_models import EnergyModel
from pymatgen.analysis.ewald import EwaldSummation
from pymatgen.io.vaspio import Chgcar, Potcar
from mpinterfaces import *
... | henniggroup/MPInterfaces | dev_scripts/coulomb_summer_test.py | Python | mit | 13,109 | [
"VASP",
"pymatgen"
] | e44d1f1dea65e22a09ec3dc693a5f4b92c243aa02c220bfb42e537af976f9bfb |
"""
Views related to the Custom Courses feature.
"""
import csv
import datetime
import functools
import json
import logging
import pytz
from contextlib import contextmanager
from copy import deepcopy
from cStringIO import StringIO
from django.core.urlresolvers import reverse
from django.http import (
HttpResponse... | vikas1885/test1 | lms/djangoapps/ccx/views.py | Python | agpl-3.0 | 20,956 | [
"VisIt"
] | 6820ead0792eadf87364adce5ecacd1b2affc664f5acb4d07d52bc1dfd74f6bb |
# 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... | junghans/espressopp | src/interaction/SoftCosine.py | Python | gpl-3.0 | 6,535 | [
"ESPResSo"
] | 4e5b8a03bdc02d55ec358b28ea29962bc53dec598356316e3d012b11e815320e |
from fitensemble import belt, ensemble_fitter
from mdtraj.testing import eq
from unittest import skipIf
import os
import numpy as np
regularization_strength = 1.5 # Strength of prior when testing BELT
def generate_gaussian_data(num_frames, num_measurements):
prior_pops = ensemble_fitter.get_prior_pops(num_frames... | kyleabeauchamp/FitEnsemble | fitensemble/test/test_belt.py | Python | gpl-3.0 | 4,197 | [
"MDTraj"
] | 349c229c3742ad65d2e8507c4905429c094006a1e714397ef5ad6545e8807b35 |
#!/usr/bin/env python
# This version is created at Mon Mar 17 12:54:44 CET 2014
# Author: Asli I. Ozen (asli@cbs.dtu.dk)
# License: GPL 3.0 (http://www.gnu.org/licenses/gpl-3.0.txt)
import sys, gzip
import re, string
import argparse
import os
from Bio.Blast import NCBIStandalone
from operator import itemgetter, attrget... | MG-group-tools/MGFunc | mgfunc_v2/clustergenes.py | Python | gpl-3.0 | 20,467 | [
"BLAST"
] | 5ce155a1199982cc7153d73d086f119f8e7c3b8c02a49dd6a545b556f7c71031 |
#
# Author: Travis Oliphant 2002-2011 with contributions from
# SciPy Developers 2004-2011
#
from __future__ import division, print_function, absolute_import
from scipy._lib.six import string_types, exec_, PY3
from scipy._lib._util import getargspec_no_self as _getargspec
import sys
import keyword
import r... | josephcslater/scipy | scipy/stats/_distn_infrastructure.py | Python | bsd-3-clause | 119,658 | [
"Gaussian"
] | 29bc50796f41660f69a4c2325dcb6c11002405cb84a0922ccbdd0b99a36fc0c8 |
#!/usr/bin/env python
from __future__ import print_function, unicode_literals
import argparse
import imp
import json
import logging
import os
import pkg_resources
import platform
import re
import shutil
import sys
import textwrap
import subprocess
import warnings
from collections import OrderedDict
from importlib imp... | chipx86/reviewboard | reviewboard/cmdline/rbsite.py | Python | mit | 97,643 | [
"VisIt"
] | 3f27a53ddb6a60d8a41b1e11be4e10112bf800a9c77e3db6cd3e9092342ff081 |
# Portions Copyright (c) Facebook, Inc. and its affiliates.
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2.
# encoding.py - character transcoding support for Mercurial
#
# Copyright 2005-2009 Matt Mackall <mpm@selenic.com> and others
#
# This softwar... | facebookexperimental/eden | eden/hg-server/edenscm/mercurial/encoding.py | Python | gpl-2.0 | 21,692 | [
"FEFF"
] | 181da507e864fd461279118639f4e704dc720c44ecad31f80289392f8ededf11 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/item_title | openlp/core/utils/languagemanager.py | Python | gpl-2.0 | 6,722 | [
"Brian"
] | c9517d6cf3f503b2e26c4c6ca87cb7d1a2d4e38158238ec034284e05703c97d9 |
""" Command line script analyse_image
"""
# Author: Ilya Patrushev ilya.patrushev@gmail.com
# License: GPL v2.0
import os
import argparse
from isimage import Image
import matplotlib.pyplot as plt
import cv2
import numpy as np
import numpy.linalg as la
import tempfile
import shutil
import pptx
def draw_paint(img1, i... | ilyapatrushev/isimage | isimage/analyse_image/analyse_image.py | Python | gpl-2.0 | 8,326 | [
"Gaussian"
] | 422218ebf891db91e2c7d8e5cc283f0f41058a7fe126d0bfae1a634bd4d5cee4 |
"""
=========================================
Image denoising using dictionary learning
=========================================
An example comparing the effect of reconstructing noisy fragments
of the Lena image using firstly online :ref:`DictionaryLearning` and
various transform methods.
The dictionary is fitted o... | depet/scikit-learn | examples/decomposition/plot_image_denoising.py | Python | bsd-3-clause | 5,773 | [
"Gaussian"
] | c110a1cbb3a58a2f47426d2c1a343357459e279bd4bd9ea25c9a8cca5a1b08dc |
"""slinkPredicates.py
The nominal, adjectival and verbal predicates that can be the subordinating
event in an SLINK. All entries are associated with one or more patterns from
slinketPatters.py.
This file is not used by the runtime system, but it is used by create_dicts.py
when it pickles the dictionaries.
Each entr... | tarsqi/ttk | library/slinket/slinkPredicates.py | Python | apache-2.0 | 200,886 | [
"exciting"
] | 7bbccdaebe74f964e1ebb51f6d8cf85ed0d4d1f6c446cc9108118ac330f75b2d |
from galaxy_analysis.plot.plot_styles import *
import matplotlib.pyplot as plt
"-----------------------------------------"
import sys
from joblib import Parallel, delayed
import multiprocessing
import deepdish as dd
from galaxy_analysis.utilities import utilities
import numpy as np
import glob as glob
from galaxy_an... | aemerick/galaxy_analysis | plot/plot_velocity_distribution.py | Python | mit | 2,545 | [
"Galaxy"
] | 2325db641391ac319ce1e6e69d240425c89be10e1938d26da8180422ad78835e |
#!/usr/bin/env python
"""
A linting tool to check if templates are safe
"""
from __future__ import print_function
import argparse
import ast
import os
import re
import sys
import textwrap
from enum import Enum
class StringLines(object):
"""
StringLines provides utility methods to work with a string in terms... | fintech-circle/edx-platform | scripts/safe_template_linter.py | Python | agpl-3.0 | 101,151 | [
"VisIt"
] | bfabbd2ae2b893bfac620735ff8ff34f49ec455318aba2e0e1dc627c70f6f8cb |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2013 Radim Rehurek <me@radimrehurek.com>
# Licensed under the GNU LGPL v2.1 - http://www.gnu.org/licenses/lgpl.html
"""
Deep learning via word2vec's "skip-gram and CBOW models", using either
hierarchical softmax or negative sampling [1]_ [2]_.
The train... | ivanvladimir/gensim | gensim/models/word2vec.py | Python | gpl-3.0 | 76,317 | [
"VisIt"
] | a48ad5a8559fd4330c4eed92b89596d16d21cdc304fd33a6ca9c24809657268d |
#!/usr/bin/env python
#-*- coding:utf-8 -*-
#
# This file is part of the NNGT project to generate and analyze
# neuronal networks and their activity.
# Copyright (C) 2015-2019 Tanguy Fardet
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License a... | Silmathoron/NNGT | nngt/core/neural_pop_group.py | Python | gpl-3.0 | 41,885 | [
"NEURON"
] | dfce96bc0efdadb692accc0ecadeb5044b731a2628f598afc206c999fa05361b |
#* 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 TestHa... | harterj/moose | python/TestHarness/tests/test_Allocations.py | Python | lgpl-2.1 | 4,994 | [
"MOOSE"
] | 956bbbab4f42cfaee017aac734252d51bbe6cbe8797600eb04e8ee13eba60a66 |
# Copyright 2014-2017 CERN. This software is distributed under the
# terms of the GNU General Public Licence version 3 (GPL Version 3),
# copied verbatim in the file LICENCE.md.
# In applying this licence, CERN does not waive the privileges and immunities
# granted to it by virtue of its status as an Intergovernment... | blond-admin/BLonD | __EXAMPLES/mpi_main_files/EX_09_Radial_Loop.py | Python | gpl-3.0 | 5,222 | [
"Gaussian"
] | 6bd36aa37e0537e38873d14a66cff6bd7ca9ec4051f5b33eb4df015c21ffe66a |
# 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.
"""Pair Potentials for molecular dynamics.
For anisotropic potentials see `hoomd.md.pair.aniso`
"""
from . import aniso
from .pair import (Pair, LJ, Gauss, SLJ... | joaander/hoomd-blue | hoomd/md/pair/__init__.py | Python | bsd-3-clause | 553 | [
"HOOMD-blue"
] | 5705e7624d53a81544605e01798303df1e511d6494d49e0f709940625aa59dcc |
import numpy as np
from scipy.io import netcdf
def genNetCDF(wavelength, stI, stQ, stU, stV, sigmaI, sigmaQ, sigmaU, sigmaV, boundary, height, obsTheta, obsGamma, mask, pars, normalization, outputFile):
"""
This routine generates a NetCDF file with the observations ready for Hazel-MPI
Args:
wa... | aasensio/pyiacsun | pyiacsun/hazel/genNetCDF.py | Python | mit | 4,509 | [
"NetCDF"
] | a4b339c0dfff9e42c1bcf5c46028567881a9b07c68bb26dde3e0916b0bcba940 |
import numpy
from scipy.interpolate import InterpolatedUnivariateSpline
class interp1d(InterpolatedUnivariateSpline):
""" this replaces the scipy interp1d which do not always
pass through the points
note that kind has to be an integer as it is actually
a UnivariateSpline.
"""
def __init__(self,... | DonRegan/nbodykit | nbodykit/corrfrompower.py | Python | gpl-3.0 | 2,158 | [
"Gaussian"
] | 8b72fd5ad0e033d39246f7f47b5bcf3cc73d4fd925d78c1d1d5ea6f9ff87f242 |
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