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# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
import exchange.views
urlpatterns = [
url(r'^$', exch... | muratby/cashbox | config/urls.py | Python | bsd-3-clause | 1,328 | [
"VisIt"
] | 0aca068d7c31a715974f84cb0cb9a4e8363cb0b7eb1ebc8cb66be2f6155feae6 |
"""
Tests for traits defined in mayavi.core.traits
"""
# Author: Prabhu Ramachandran <prabhu@aero.iitb.ac.in>
# Copyright (c) 2008, Prabhu Ramachandran Enthought, Inc.
# License: BSD Style.
import unittest
import numpy
from traits.api import (HasTraits, Either, Array, Any,
TraitError, Float, Int)
from ... | dmsurti/mayavi | mayavi/tests/test_mayavi_traits.py | Python | bsd-3-clause | 4,382 | [
"Mayavi"
] | 8003c9de80bc686ea984d5f66c3632a12bd903976abc0236bd1604b4defdf294 |
#-*. coding: utf-8 -*-
"""cinfony: a common API to several cheminformatics toolkits
cinfony is a Python library that provides a common API to several
open source cheminformatics toolkits.
"""
doclines = __doc__.split("\n")
# My code is BSD
# Open Babel is GPL v2
# OPSIN is Artistic License v2.0 (not viral)
# CDK is ... | cinfony/cinfony | setup.py | Python | bsd-2-clause | 1,419 | [
"CDK",
"Open Babel",
"RDKit"
] | 1baeb2a9eebe69af52e2999a931556753ed5134fe4ded3c3dcf04720fc37a791 |
#!/usr/bin/env python
import argparse
import logging
import sys
from BCBio import GFF
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqFeature import (
FeatureLocation,
SeqFeature
)
from Bio.SeqRecord import SeqRecord
logging.basicConfig(level=logging.INFO)
log = logging.getLogger(__name__)
def par... | blankclemens/tools-iuc | tools/progressivemauve/xmfa2gff3.py | Python | mit | 5,559 | [
"Biopython"
] | 1c16e9a26dae83380f27714b963d48c79ac4c5f0635dc164f792490385d5fbb6 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import collections
import abc
import numpy as np
from pymatgen.core.spectrum import Spectrum
from pymatgen.util.plotting import add_fig_kwargs
"""
This module implements core classes for calculation of diff... | fraricci/pymatgen | pymatgen/analysis/diffraction/core.py | Python | mit | 7,522 | [
"CRYSTAL",
"pymatgen"
] | 6bcf5db7f80f2c23c8b8412cce5f385fe9b610d618e378d4488cd4085bf55516 |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | KaiSzuttor/espresso | testsuite/python/engine_langevin.py | Python | gpl-3.0 | 2,305 | [
"ESPResSo"
] | 40889019fc94b4c3f25f94c15152c57176a9be302eea27c5175f58362cb0378c |
# ancestor.py - generic DAG ancestor algorithm for mercurial
#
# Copyright 2006 Matt Mackall <mpm@selenic.com>
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2 or any later version.
import heapq
import util
from node import nullrev
def commonancestorsh... | hekra01/mercurial | mercurial/ancestor.py | Python | gpl-2.0 | 12,290 | [
"VisIt"
] | 9086dffdcad0968da6d092b6b303ec1e8277e3c02a772c9c8d4ac32047179703 |
#!/usr/bin/env python
'''
Generation of LFP like signal from spike data
---------------------------------------------
Generates "LFP" like signal for demonstration with the VIOLA tool, using a
simplified biophysics based approach.
In short, the signals are generated by
1. Computing the extracellular potential a... | espenhgn/VIOLA | test_data/fake_LFP_signal.py | Python | gpl-2.0 | 18,981 | [
"NEURON"
] | afc6e4f590cf9fea0dbb8b92a36067b4565ec2c21472a6cdb965e8d99c51158e |
# Copyright (c) 2006-2014 LOGILAB S.A. (Paris, FRANCE) <contact@logilab.fr>
# Copyright (c) 2013-2015 Google, Inc.
# Copyright (c) 2014-2016 Claudiu Popa <pcmanticore@gmail.com>
# Copyright (c) 2014 Michal Nowikowski <godfryd@gmail.com>
# Copyright (c) 2015 Mike Frysinger <vapier@gentoo.org>
# Copyright (c) 2015 Mihai ... | arju88nair/projectCulminate | venv/lib/python3.5/site-packages/pylint/checkers/format.py | Python | apache-2.0 | 43,690 | [
"VisIt"
] | cc5578ff9760bfe1bf665ce3441032633ee4366ce2e24c1a2e78f8bbb7071c79 |
from pylab import *
from brian import *
from abstract_neuron_group import *
from util import *
class MLIGroup(AbstractNeuronGroup):
'''
Group of Molecular Layer Interneurons (MLIs).
This model assumes the physiological properties of basket and stellate
cells are similar enough to share the same m... | blennon/MLI_PKJ_net | MLI_PKJ_net/molecular_layer.py | Python | mit | 3,602 | [
"Brian"
] | b763f0ae7d059eb419d860e823e2d12b4a9b69fffcfcb864a4c529ee24c5e1c8 |
"""
ASSET is a statistical method [1] for the detection of repeating sequences
of synchronous spiking events in parallel spike trains.
Given a list `sts` of spike trains, the analysis comprises the following
steps:
1) Build the intersection matrix `imat` (optional) and the associated
probability matrix `pmat` with t... | dholstein/elephant | elephant/asset.py | Python | bsd-3-clause | 68,871 | [
"NEURON"
] | 376099238f46a6f04de23678fe5a0e2facbcffcc15bc9f3ca86b231d43cf0f73 |
# 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 the G... | espressopp/espressopp | src/interaction/LennardJonesAutoBonds.py | Python | gpl-3.0 | 10,620 | [
"ESPResSo"
] | cc9f9465908b47e663c0a46504316cc954e752b6d0b463e4112f8f20b9213cf2 |
"""Header value parser implementing various email-related RFC parsing rules.
The parsing methods defined in this module implement various email related
parsing rules. Principal among them is RFC 5322, which is the followon
to RFC 2822 and primarily a clarification of the former. It also implements
RFC 2047 enco... | prefetchnta/questlab | bin/x64bin/python/36/Lib/email/_header_value_parser.py | Python | lgpl-2.1 | 103,074 | [
"CRYSTAL"
] | 1e1e0d7a83e5b6bcd695e769fdbfc6fd53181c5361f7519461737417d2933bb8 |
# 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 t... | mtougeron/python-openstacksdk | openstack/object_store/v1/_proxy.py | Python | apache-2.0 | 8,617 | [
"Brian"
] | 017c60693f6b5d2564a406a47c28398c82f7e11f5619bf7967e6a112b9d84f84 |
###################################################################################
## ##
## With this retina model our aim is to show an overview of the main features ##
## that can be configured in the retina script. The retina model imp... | pablomc88/COREM | COREM/Retina_scripts/example_1.py | Python | gpl-3.0 | 4,955 | [
"NEURON"
] | 9e4170025efe520687c41cf68961c46671071dfed0f99a0d9339d61986c4a0df |
#!/usr/bin/env python
import os
import sys
if __name__ == "__main__":
os.environ.setdefault("DJANGO_SETTINGS_MODULE", "octopus.settings")
from django.core.management import execute_from_command_line
execute_from_command_line(sys.argv)
| gregorianzhang/octopus | manage.py | Python | apache-2.0 | 250 | [
"Octopus"
] | da395257770f965d5b7bb09d85f4a50d4949bb17d8ba4e5e407e4c98bb9fdc8e |
""" DIRAC Workload Management System Client class encapsulates all the
methods necessary to communicate with the Workload Management System
"""
import os
from io import StringIO
import time
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.ConfigurationSystem.Client.Helpers.Operations import Operations
from DIR... | DIRACGrid/DIRAC | src/DIRAC/WorkloadManagementSystem/Client/WMSClient.py | Python | gpl-3.0 | 9,263 | [
"DIRAC"
] | 0118df9316d26164aac9fc8fd66654d4df250f32fc4c4635909069b475a23836 |
"""
Contains testing infrastructure for QCFractal.
"""
import os
import pkgutil
import shutil
import signal
import socket
import subprocess
import sys
import threading
import time
from collections import Mapping
from contextlib import contextmanager
import numpy as np
import pandas as pd
import pytest
import qcengine... | psi4/DatenQM | qcfractal/testing.py | Python | bsd-3-clause | 18,053 | [
"Psi4",
"RDKit"
] | a88aa75f02d1425da03950d7484b2bbd4870077d16783b9c00d9d4833a910752 |
# Copyright 1999-2000 by Jeffrey Chang. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
# Patches by Mike Poidinger to support multiple databases.
# Updated by Peter Cock in 2007... | asherkhb/coge | bin/last_wrapper/Bio/Blast/NCBIStandalone.py | Python | bsd-2-clause | 90,834 | [
"BLAST",
"Biopython"
] | 07530697a979beee1c5f16b328361fd905e87e7288ac347dff57991e9c20dca2 |
# ancestor.py - generic DAG ancestor algorithm for mercurial
#
# Copyright 2006 Matt Mackall <mpm@selenic.com>
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2 or any later version.
from __future__ import absolute_import
import collections
import heapq... | dscho/hg | mercurial/ancestor.py | Python | gpl-2.0 | 12,410 | [
"VisIt"
] | 3d284823c5ec95d2474599b0a543612eabbe170a22034667a5b226eea0bca337 |
#!/usr/bin/env python
import numpy as np
import matplotlib.pyplot as plt
from scipy.optimize import curve_fit
import scipy.optimize as opt
import json
try:
import prosail
except ImportError:
print "We need to have the prosail Python bindings installed"
print "Available from http://github.com/jgomezdans/pro... | jgomezdans/barrax_2015 | prosail_functions.py | Python | gpl-2.0 | 34,357 | [
"Gaussian"
] | 6fc7774bc35adbaf86c7e6966294d17623ec0e47d4f003aa33bd814ecc97f8a5 |
"""
Copyright (c) 2004-Present Pivotal Software, Inc.
This program and the accompanying materials are made available under
the terms of the 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.... | edespino/gpdb | src/test/tinc/tincrepo/mpp/models/regress/sql_related/regress_sql_concurrency_test_case/regress_sql_concurrency.py | Python | apache-2.0 | 6,826 | [
"ORCA"
] | 0d29b3562e95c4ad49d067a7d9a40206c7edb21a857171099a0fdb6267502f7f |
#!/usr/bin/env python
# Copyright 2018 The Amber 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 ... | GPUOpen-Drivers/llpc | test/run_amber.py | Python | mit | 6,867 | [
"Amber"
] | 8b5ef8fb8c3789cd9ebc2c8e76b87162b01d86988797d4ee1b94604451a1b1e8 |
"""Task.py
Functionality for running multiple tasks simultaneously.
Classes:
Task Processing that can be forked off in a separate process.
"""
import warnings
warnings.warn("Bio.MultiProc is deprecated. If you want to use this code, please let the Biopython developers know by sending an email to biopython-dev@bi... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/MultiProc/Task.py | Python | apache-2.0 | 2,988 | [
"Biopython"
] | d87baf0dd3ddf0c9d2a95bacb081c5f8b3b30f880778be4e1b3f201bd9d25a02 |
#
#
#Custom filename tags to distinguish from other runs
project = "Project"
runVers = "Run"
#Default plot
#Select ONE only:
#makePlot = "structure"
#makePlot = "sed"
makePlot = "spectrum"
#makePlot = "ldc"
#makePlot = "ft"
#makePlot = "tlaLine"
#Spectrum synthesis mode
# - uses model in Restart.py... | sevenian3/ChromaStarPy | A0Halpha.py | Python | mit | 2,745 | [
"Gaussian"
] | 00bd7328334c361f16f2c05ccaf401c331b6692e995c777bccb80f37b82609d8 |
import orderedset
def find_cycle(nodes, successors):
path = orderedset.orderedset()
visited = set()
def visit(node):
# If the node is already in the current path, we have found a cycle.
if not path.add(node):
return (path, node)
# If we have otherwise already visit... | apple/swift-llbuild | products/ui/llbuildui/graphalgorithms.py | Python | apache-2.0 | 960 | [
"VisIt"
] | 90323204bfdbb547d5409e3f428c03a18f1c10b43d2eefd8e4201532e88e481e |
##
# Copyright 2013 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (FWO) (... | ocaisa/easybuild-easyblocks | easybuild/easyblocks/f/foldx.py | Python | gpl-2.0 | 3,012 | [
"FoldX"
] | 384912ce2968786cc581d264a68fc6a694efbf217c0eab5b989cf86742911822 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# cleanallexes - [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/cleanallexes.py | Python | gpl-2.0 | 1,126 | [
"Brian"
] | 9588ef1dfbc5592b43350aaf8ce5b0b856a6620f74f3c8699965be204f552d36 |
#!/usr/bin/env python
"""
Make plot of data containing a quadratic with Gaussian noise, but fit a straight line to it
"""
import matplotlib.pyplot as pl
import numpy as np
# x values
x = np.linspace(-5, 5, 8)
a = 1.
b = 0.5
c = 0.75
# quadratic
y = a + b*x + c*x**2
# noise with sigma = 1
n = np.random.randn(len(x... | mattpitkin/GraWIToNStatisticsLectures | figures/scripts/quadratic_data.py | Python | mit | 1,057 | [
"Gaussian"
] | 867a5103f1fab877ab806c907a6d218b05b63573aaa913121465c00850022cf1 |
#
# Copyright (C) 2002-2006 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
"""unit testing code for the... | rvianello/rdkit | rdkit/Chem/Pharm2D/UnitTestUtils.py | Python | bsd-3-clause | 10,234 | [
"RDKit"
] | bf02ca5ed47be803248cab2a7565cf5298679601563915097a6efe96b6ad7d40 |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | sunqm/pyscf | pyscf/pbc/gto/_pbcintor.py | Python | apache-2.0 | 2,371 | [
"PySCF"
] | 8cb982d3baa0bfd18bb09e763a4e6deab85fdc17a2e2956a20733d0a6fdb0e82 |
from brian.stdunits import *
from brian.units import *
F = 1
N_SUBPOP = 2
INTERCO_RATE = .9
INTERCO_STRENGTH = .05
PARAMETERS = {
'Common':
{'simu_dt' : 0.05*msecond,
'simu_length' : 2000*msecond,
'N_subpop' : N_SUBPOP,
'N_mitral' : N_SUBPOP*100*F,
'inter_conn_rate' : {0: {1: INTERCO_... | neuro-lyon/multiglom-model | src/test_beta.py | Python | mit | 1,549 | [
"Brian"
] | e8096cecc2721139c43ededc7be03b4935d0650dc8e53dacf542314257bd0e9b |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | SKIRT/PTS | magic/catalog/synchronizer.py | Python | agpl-3.0 | 19,613 | [
"Galaxy"
] | 773046c8b506537cfaeafdcff4724a11473304a2a4da76ebb9402d6e475b859a |
""". regress totemp gnpdefl gnp unemp armed pop year
Source | SS df MS Number of obs = 16
-------------+------------------------------ F( 6, 9) = 330.29
Model | 184172402 6 30695400.3 Prob > F = 0.0000
Residual | 836424.129 ... | hlin117/statsmodels | statsmodels/iolib/stata_summary_examples.py | Python | bsd-3-clause | 4,614 | [
"Gaussian"
] | cbc41a78247768ebdfa18eebc4e1d9a0be669f31f71259169ea701c42784d935 |
"""Unit test for apihelper.py
This program is part of "Dive Into Python", a free Python book for
experienced programmers. Visit http://diveintopython.org/ for the
latest version.
"""
__author__ = "Mark Pilgrim (mark@diveintopython.org)"
__version__ = "$Revision: 1.4 $"
__date__ = "$Date: 2004/05/05 21:57:19 $"
__cop... | tapomayukh/projects_in_python | sandbox_tapo/src/refs/diveintopython-pdf-5.4/diveintopython-5.4/py/apihelpertest.py | Python | mit | 1,891 | [
"VisIt"
] | c9e1d5421e78924c21e3d68e84f80a8d1f64f9488020107ca0eeee0c4f10e763 |
#!/usr/bin/env python
# -*- Mode: Python; coding: utf-8; indent-tabs-mode: nil; tab-width: 4 -*-
### BEGIN LICENSE
# Copyright (C) 2013 Brian Douglass bhdouglass@gmail.com
# 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 publishe... | bhdouglass/remindor-common | setup.py | Python | gpl-3.0 | 1,434 | [
"Brian"
] | 25baceac68034fd17db123d7f67c275d8960832011a96186a20c58337a484da4 |
#
# Copyright (C) 2008, Brian Tanner
#
# http://rl-glue-ext.googlecode.com/
#
# 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 req... | evenmarbles/rlglued | examples/mines-sarsa-example/sample_sarsa_agent.py | Python | bsd-3-clause | 7,885 | [
"Brian"
] | c9d4d0bc76ed6f9c73367cbf0fc4cff1a679501233b5762dcbbd8e7c148ed512 |
from __future__ import annotations
import pytest
from dxtbx.model import Detector
from dials.algorithms.refinement import DialsRefineConfigError
from dials.algorithms.refinement.parameterisation.autoreduce import AutoReduce
from dials.algorithms.refinement.parameterisation.autoreduce import (
phil_scope as ar_ph... | dials/dials | tests/algorithms/refinement/test_parameter_auto_reduction.py | Python | bsd-3-clause | 8,297 | [
"CRYSTAL"
] | 3b502d1aba60175709704f709546f17e168746ded35a0e0460d19806dd5a7336 |
#
# Copyright (C) 2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later vers... | espressomd/espresso | doc/tutorials/convert.py | Python | gpl-3.0 | 12,717 | [
"ESPResSo",
"Mayavi",
"VisIt"
] | 179ba280e8226a5b3e9baca28c125bf209e43f2940f1d16b81e0be036dfd4da8 |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General... | le9i0nx/ansible | lib/ansible/modules/network/avi/avi_microservicegroup.py | Python | gpl-3.0 | 4,447 | [
"VisIt"
] | a875bf503f85f8b7b41ae1aa2375f1ce19a82f64faaf7f88ce205f303c63ac12 |
#!/usr/bin/python
# (C) 2013, Markus Wildi, markus.wildi@bluewin.ch
#
# 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, or (at your option)
# any later version.
#
# Thi... | xyficu/rts2 | scripts/rts2saf/rts2saf/sextract.py | Python | gpl-2.0 | 10,808 | [
"VisIt"
] | 0da4fcda965cb226e9ee9399fabb8955b530dd50e680ec64d73fbb404de806be |
# -*- coding: utf-8 -*-
"""
File related views, including view_file, view_history_file, view_trash_file,
view_snapshot_file, view_shared_file, file_edit, etc.
"""
import os
import hashlib
import json
import stat
import urllib2
import chardet
import logging
import posixpath
import re
from django.core.cache import cach... | Chilledheart/seahub | seahub/views/file.py | Python | apache-2.0 | 56,425 | [
"VisIt"
] | 02a240f836bc492c87bc338f73ad14ff3f25ffa90ea1259c1b7e85bb96ae5cda |
# -*- coding: utf-8 -*-
#!/usr/bin/python
"""Test of find output of Firefox on the Orca wiki."""
from macaroon.playback import *
import utils
sequence = MacroSequence()
########################################################################
# We wait for the focus to be on a blank Firefox window.
#
sequence.append... | h4ck3rm1k3/orca-sonar | test/keystrokes/firefox/find_wiki.py | Python | lgpl-2.1 | 6,794 | [
"ORCA"
] | 685907f55e7602e3fa3dbc01f0348ae5a699f4f2f11ace56ded5ff71e80f4aca |
# 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/dataSourceIngestModule.py | Python | apache-2.0 | 8,071 | [
"Brian"
] | fde29a76a6dfec7f99d318c68c59a344ecb18ad07640018f562e0faf81c23105 |
import functools
import math
from ...core import Dummy, E, Function, Integer, cacheit, oo, sympify, zoo
from ...core.function import ArgumentIndexError
from ...ntheory import sieve
class CombinatorialFunction(Function):
"""Base class for combinatorial functions."""
def _eval_simplify(self, ratio, measure):
... | skirpichev/omg | diofant/functions/combinatorial/factorials.py | Python | bsd-3-clause | 18,024 | [
"VisIt"
] | d737193cf42e399f6bc29a5a6a8dc8783a818eaa4abae24a1cd60e1393b835bd |
#!/usr/bin/env python
import pysam
import sys
from re import sub
from random import random
if len(sys.argv) == 5:
assert sys.argv[1].endswith('.bam')
inbamfn = sys.argv[1]
outbam1fn = sys.argv[3]
outbam2fn = sys.argv[4]
inbam = pysam.Samfile(inbamfn, 'rb')
outbam1 = pysam.Samfile(outbam1fn, '... | MischaLundberg/bamsurgeon | scripts/bamsplit_proportion.py | Python | mit | 1,321 | [
"pysam"
] | 86886e458caa5abfbfbd015ecc3834ad2db1c59ecb48a3c8ec7e7f53feead8fe |
#!/usr/bin/python
#
# Copyright 2010 Brian Dolbec <brian.dolbec@gmail.com>
# Copyright 2010 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
#
# $Header$
from __future__ import print_function
__version__= "0.0.1"
__author__ = "Brian Dolbec"
__email__ = "brian.dolbec@gmail.com"
fro... | bacher09/Gentoolkit | pym/gentoolkit/test/eclean/test_clean.py | Python | gpl-2.0 | 3,899 | [
"Brian"
] | 9924bd660411fde994e9b168ea674520b15b5ff4d2e63bf07f773a127434fc40 |
""" JSON schema definitions for splice
* default schema:
the imageURI and enhancedImageURI are not re-used, Splice versions prior to
1.1.23 use this schema
* compact schema:
the imageURI and enhancedImageURI are re-used, a "URI id" to "URI" mapping
is stored in the "assets" property
"""
ISO_8061_patte... | mostlygeek/splice | splice/schemas.py | Python | mpl-2.0 | 5,796 | [
"VisIt"
] | 1999fbeef8f2c93cdcc33a8d302ad99311b0542a1ca038645524cc7af3feda55 |
""" Within this module is defined the class from which all other accounting types are defined
"""
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Utilities import Time
from DIRAC.Core.Base.Client import Client
from DIRAC.AccountingSystem.Client.DataStoreClient import gDataStoreClient
class BaseAccountingType(object):... | DIRACGrid/DIRAC | src/DIRAC/AccountingSystem/Client/Types/BaseAccountingType.py | Python | gpl-3.0 | 6,399 | [
"DIRAC"
] | 5e42822514a7dd2cd648c7ad6a4f5515b59c406bb087393dc08f84ca8bf220fb |
import numpy as np
from imagediff import kernels, util
def do_subtraction(image,template,cutoff=1.0,radius=10,boundary=None,maskreg=None, kerneltype=None,method=None,sqrt=False,rdnoise=False):
"""
image: fits object
template: fits object
"""
if kerneltype is None: #- Gaussian poly as default
... | gdhungana/ImageDiff | py/imagediff/difference.py | Python | mit | 6,409 | [
"Gaussian"
] | 73bbb7303075fcab5de3c674b2a00c645545c6fc0e630bf0e37678506810a9e1 |
###BAMtoJunctionBED
#Author Nathan Salomonis - nsalomonis@gmail.com
#Permission is hereby granted, free of charge, to any person obtaining a copy
#of this software and associated documentation files (the "Software"), to deal
#in the Software without restriction, including without limitation the rights
#to use... | kdaily/altanalyze | BAMtoJunctionBED.py | Python | apache-2.0 | 10,339 | [
"pysam"
] | a430d7d0dac5c970aa9ad566efb1019056871625d123077ebf857a975c5e46e6 |
""" JobManagerHandler is the implementation of the JobManager service
in the DISET framework
The following methods are available in the Service interface
submitJob()
rescheduleJob()
deleteJob()
killJob()
"""
__RCSID__ = "$Id$"
from DIRAC import gConfig, gLogger, S_OK, S_ERROR
from DIRAC.Cor... | arrabito/DIRAC | WorkloadManagementSystem/Service/JobManagerHandler.py | Python | gpl-3.0 | 19,733 | [
"DIRAC"
] | 106d033c321fd199eb24aaaab1fb98ac1a74099df5efeeb78fdda3e088cf59e8 |
# -*- coding: utf-8 -*-
'''
diacamma.member test_tools package
@author: Laurent GAY
@organization: sd-libre.fr
@contact: info@sd-libre.fr
@copyright: 2015 sd-libre.fr
@license: This file is part of Lucterios.
Lucterios is free software: you can redistribute it and/or modify
it under the terms of the GNU General Publi... | Diacamma2/asso | diacamma/member/test_tools.py | Python | gpl-3.0 | 6,877 | [
"Dalton"
] | 2ca8f1d9abf7399e42e8a1a433a1d66020f29d53a783b3f1d40dbee7c6bc65ca |
# -*- coding: utf-8 -*-
'''
This module provides an access to the HITRAN data.
Data is downloaded and cached.
This module serves as a simple database manager frontend.
API is aimed to be RESTful, which means that interaction
between local API and remote data-server will be held
via sending RESTful queries (API->rem... | dp7-PU/QCLAS_public | src/hapi.py | Python | mit | 751,958 | [
"Gaussian"
] | 128cf25824c94f02cc8d7c9c15f3e6ee05ccdd423ef3ccf1190f358362c64017 |
"""
Various bayesian regression
"""
# Authors: V. Michel, F. Pedregosa, A. Gramfort
# License: BSD 3 clause
from math import log
import numpy as np
from scipy import linalg
from ._base import LinearModel, _rescale_data
from ..base import RegressorMixin
from ._base import _deprecate_normalize
from ..utils.extmath imp... | glemaitre/scikit-learn | sklearn/linear_model/_bayes.py | Python | bsd-3-clause | 26,708 | [
"Gaussian"
] | 273d7b1a9db727b3084f380c80ea4ff148a83ae701f8e0d8a704ff320db9aa77 |
# coding: utf-8
from __future__ import division, unicode_literals
"""
This module defines classes to represent the density of states, etc.
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "2.0"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyuep@gmail.com"
__... | Dioptas/pymatgen | pymatgen/electronic_structure/dos.py | Python | mit | 17,289 | [
"Gaussian",
"pymatgen"
] | 5c1258502f8a8c33f986c81702fb6c157548572549b377d1e162969a4e1b91a9 |
"""
Gaussian Mixture Models.
This implementation corresponds to frequentist (non-Bayesian) formulation
of Gaussian Mixture Models.
"""
# Author: Ron Weiss <ronweiss@gmail.com>
# Fabian Pedregosa <fabian.pedregosa@inria.fr>
# Bertrand Thirion <bertrand.thirion@inria.fr>
# Important note for the deprec... | mbayon/TFG-MachineLearning | venv/lib/python3.6/site-packages/sklearn/mixture/gmm.py | Python | mit | 32,607 | [
"Gaussian"
] | 8f8571a43707367a6630f69687e7d9d8fbc0fb56813b8815225ba1a0281388fc |
#!/usr/bin/python
# Script: angle_distribute.py
# Purpose: binned angle distributions by angle type
# Syntax: angle_distribute.py datafile nbin theta_min theta_max outfile files ...
# datafile = lammps data file
# nbin = # of bins per angle type
# theta_min = min expected angle
# ... | eddiejessup/pizza | scripts/angle_distribute.py | Python | gpl-2.0 | 3,931 | [
"LAMMPS"
] | a3304126dda528eb27cf003bbcbc27b06fed87e9c005ef9fb2130c6ef5f0d07e |
# -*- coding: utf-8 -*-
import sys
from naoqi import ALProxy
def main(robotIp, volume):
tts = ALProxy("ALTextToSpeech", robotIp, 9559)
tts.say("Ciao quinto B, mi abbasso il volume")
tts.setVolume(volume)
tts.say("Ora il volume è al {}%% scusate il disturbo per prima!".format(volume*100))
if __name_... | feroda/play-nao | setvolume.py | Python | agpl-3.0 | 814 | [
"ESPResSo"
] | 902091bf6ef41cca8840ebd3647abd51c82cbfc8c7b6ff3111fee891aee1852f |
from django.shortcuts import render
from django.contrib.auth.decorators import login_required
from django.template import RequestContext
from django.shortcuts import render, render_to_response
from django.views.generic import View
from django.http import HttpResponse
from customers import models as m
import sys, json
f... | abhaystoic/barati | barati/customers/views_cluster/beautician.py | Python | apache-2.0 | 9,535 | [
"VisIt"
] | cd1af6d69307de42fe05fbe114730aa34a24ac8a08cc8eb5ad75d652cbcc0689 |
"""
Hurricane Electric DNS library module
Inspired by EveryDNS Python library by Scott Yang:
http://svn.fucoder.com/fucoder/pyeverydns/everydnslib.py
"""
try:
from http.cookiejar import CookieJar
except ImportError:
from cookielib import CookieJar
try:
from urllib.parse import urlencode
from urlli... | tresni/pyHurricaneDNS | HurricaneDNS.py | Python | mit | 12,188 | [
"Brian"
] | 6c9d846daab2dd36a3fd5f67eeed0cfb28cfadd858878288a648e95dc6a11aea |
#!/tools/Python/Current/bin/python
'''
This python script accepts .csv data set, .bms configurations, and output directory then produces statistical analysis results from the processed data
'''
from optparse import OptionParser
import csv
import os,os.path,re,sys
import system
'''
concatToColumns.py
'''
def countLi... | NIRALUser/RodentThickness | Applications/RodentThickness/Data/pythonscript/run.py | Python | gpl-3.0 | 32,182 | [
"VTK"
] | ec470d009b66ecab3f9a61e4dc5741ab9e18fca7594fce282a5af8abbcdd8e0f |
# main/view.py
from django.shortcuts import render_to_response, get_object_or_404
from django.contrib.auth import authenticate, login
from django.contrib.auth.models import User, Group
from django.contrib.auth.decorators import login_required
from django.shortcuts import render
from django.template import RequestConte... | CarlFK/veyepar | dj/main/views.py | Python | mit | 86,771 | [
"Brian"
] | 5ab522f27ae16808e58fa917381761226adbc8737be8e30b9bc67a1776094e62 |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the te... | le9i0nx/ansible | lib/ansible/modules/network/avi/avi_role.py | Python | gpl-3.0 | 3,902 | [
"VisIt"
] | 25fee9b8de2e887330c4bfac5b9e87d10832d75914b7d7150e8756fcb5115df4 |
#
# One-dimensional netCDF sample file generator
# Author: Andrew Dunn
# Last modified: 27 Apr 2014
#
# This file is part of Climate Analyser.
#
# Climate Analyser 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 Fo... | climate-analyser-team/sample_data_generator | generate1D.py | Python | gpl-3.0 | 1,836 | [
"NetCDF"
] | 8fc2808e31dddfb1fe558aa0839b510198250c73037fd4682732f8e543a2e5cb |
# Copyright (c) 2016, Henrique Miranda
# All rights reserved.
#
# This file is part of the yambopy project
#
from yambopy import *
from yambopy.plot import *
ha2ev = 27.211396132
class YamboRTDB():
"""
Open the RT databases and store it in a RTDB class
"""
def __init__(self,folder='.',calc='.',save=No... | alexmoratalla/yambo-py | yambopy/dbs/rtdb.py | Python | bsd-3-clause | 9,212 | [
"Yambo"
] | 9ceff06b72f4bd3d4774d9d1a4cf35a06276b7dd519ea160e61ddf2bd900e8c5 |
#
# QAPI types generator
#
# Copyright IBM, Corp. 2011
#
# Authors:
# Anthony Liguori <aliguori@us.ibm.com>
#
# This work is licensed under the terms of the GNU GPLv2.
# See the COPYING.LIB file in the top-level directory.
from ordereddict import OrderedDict
from qapi import *
import sys
import os
import getopt
impor... | jds2001/qemu-kvm | scripts/qapi-types.py | Python | gpl-2.0 | 7,543 | [
"VisIt"
] | 86c094e1fe21e5dc8b49173c3217c161ac482d1234acf3bba7ee4bbb785d7276 |
class CyberpunkQuestGenerator:
@classmethod
def generate_quest_giver(cls):
"""
a
1. WHITE COLLAR WORKING FOR
1. Artificial intelligence research institute
2. City-government office
3. Tax office
4. Cyberparts industry
5. Weapons factory
6.... | d2emon/generator-pack | src/genesys/generator/_unknown/cyberpunk_quest.py | Python | gpl-3.0 | 16,648 | [
"CRYSTAL"
] | e5f7f37c9d0097fc963d52a9517d19d28de0a14c2c63757b5062c7ea1f134404 |
from Tkinter import *
import tkMessageBox
from FreesteelPython import *
import code
class MainFrame(Frame):
def selectNone(self):
self.vtkwindow.display()
def selectCone(self):
self.vtkwindow.display(self.conedata)
def selectSphere(self):
self.vtkwindow.display(self.spheredata)
def showConsole(self):
con... | play113/swer | libactp-read-only/freesteel/test/test-PolydataWindow.py | Python | mit | 2,576 | [
"VTK"
] | df706ad8d0b733f5312b9000429c8ea30c4b2dcef250b3552f59d0f93f23a868 |
# Copyright (C) 2020 Equinor ASA, Norway.
#
# The file 'test_row_scaling.py' is part of ERT - Ensemble based Reservoir Tool.
#
# ERT 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... | joakim-hove/ert | tests/libres_tests/res/enkf/test_row_scaling.py | Python | gpl-3.0 | 3,263 | [
"Gaussian"
] | bb6c1099f1b6fd37681304337cbab66ea2f5512aaf8507f4fdf3103732948cd8 |
# Copyright 2016 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... | mixturemodel-flow/tensorflow | tensorflow/contrib/bayesflow/python/kernel_tests/monte_carlo_test.py | Python | apache-2.0 | 8,131 | [
"Gaussian"
] | 79b835711a95e7fb95a6623413401c65d63b8d81bdefd03e4f0ee8852f621910 |
"""
Copyright (C) 2014 Delft University of Technology, The Netherlands
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 lat... | jkokorian/ODMAnalysis | odmanalysis/fitfunctions/FitFunctions.py | Python | gpl-3.0 | 14,974 | [
"Gaussian"
] | 36203eeba74e6b5fcab50ef55bfd2d5871569e7a68cd1101598cafb01451afbc |
# coding: utf-8
from __future__ import division, unicode_literals
"""
A module to perform experimental thermochemical data analysis.
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyuep@gmail.com"
__date__... | rousseab/pymatgen | pymatgen/analysis/thermochemistry.py | Python | mit | 3,242 | [
"pymatgen"
] | fea73605bdcf51f05ce4a04e3f4b8a2885dd41ed752bc03af985f36f702039ce |
"""
tsptw.py: solve the asymmetric traveling salesman problem with time window constraints
minimize the travel cost for visiting n customers exactly once;
each customer has a time window within which the salesman must visit him
formulations based on Miller-Tucker-Zemlin's formulation, for the atsp;
one- and two-index... | mattmilten/PySCIPOpt | examples/unfinished/tsptw.py | Python | mit | 7,537 | [
"VisIt"
] | 6911505d5a16246978c712d79d6169747c22f2676a25b826ebf01dc4b8bd828a |
#!/usr/bin/env python
# -------------------------------------------------------------
# file: combine_xmf.py
#
# Combines xmf files from restarted runs into one VisIt readable file.
#
import sys,os
import numpy as np
def loadFile(filename, directory):
return np.loadtxt(os.path.join(directory, filename))
def com... | amanzi/ats-dev | tools/utils/combine_obs.py | Python | bsd-3-clause | 1,671 | [
"VisIt"
] | 40d3d74d547639e740aeab3e1e7ba12b8cf870fbf24e8a81f2cb577a1a657590 |
from paraview.simple import *
from vtk.web.query_data_model import *
from paraview.web import camera as pv
dataset_destination_path = '/tmp/cylinder'
# Initial ParaView scene setup
Cylinder(Resolution = 30, Height = 10.0, Center = (1,2,3))
rep = Show()
view = Render()
ResetCamera()
view.CenterOfRotation = view.Came... | Kitware/arctic-viewer | scripts/examples/paraview/samples/camera-cylindrical.py | Python | bsd-3-clause | 908 | [
"ParaView",
"VTK"
] | cbc2d89a18dde7c516b7c5a10169a32078360b5bc5a146e313dd3cdf9668ae29 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
"""
This module provides utility classes for io operations.
"""
__author__ = "Shyue Ping Ong, Rickard Armiento, Anubhav Jain, G Matteo, Ioannis Petousis"
__copyright__ ... | aykol/pymatgen | pymatgen/util/io_utils.py | Python | mit | 5,752 | [
"pymatgen"
] | a50d269ede9a359760d9e050a0076e6c83c90fbaa74d292aa5536ad29a15f423 |
import numpy as np
from tqdm import trange
from dt_central import dt_central
import copy
def timefreq_analysis_prelims(time,tau,scale,w0,gauss_spread,eps,dt_GCD,shannonnyquistexclusionzone,weighted_CWT,smoothing_coeff,smoothing_type):
""" timefreq_analysis_prelims returns some variables for the time-frequency analys... | guillaumelenoir/WAVEPAL | wavepal/timefreq_analysis_prelims.py | Python | mit | 13,428 | [
"Gaussian"
] | 32bcfd522f889a3791e9c27d9f9ddbefd74ed98f75c116b802a86fd0fe15f4b8 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# This module is also sponsored by E.T.A.I. (www.etai.fr)
# 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
ANSIBLE_METADATA = {'metadata_version... | Dhivyap/ansible | lib/ansible/modules/cloud/vmware/vmware_guest.py | Python | gpl-3.0 | 147,284 | [
"VisIt"
] | b326db3b85b2d9f061a98e11e4c6e7ce524631d589201257114f5110277b94d3 |
# Copyright 2001 by Tarjei Mikkelsen. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
# get set abstraction for graph representation
from Bio.Pathway.Rep.HashSet import *
class... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/Pathway/Rep/MultiGraph.py | Python | apache-2.0 | 7,057 | [
"Biopython"
] | b8ad1ebca9aa01f8e74fea24494e3f3598b871a4616280852887e50e97ce6ff3 |
from __future__ import print_function
__author__ = """Alex "O." Holcombe, Charles Ludowici, """ ## double-quotes will be silently removed, single quotes will be left, eg, O'Connor
import time, sys, platform, os
from math import atan, atan2, pi, cos, sin, sqrt, ceil, radians, degrees
import numpy as np
import psychopy, ... | alexholcombe/dot-jump | dataRaw/Fixed Cue/test_dot-jump15Nov2016_14-23.py | Python | gpl-3.0 | 25,543 | [
"Gaussian"
] | aa5ca9fbecb4c4bf8b5d43c95e1dd34db10404c43e9e29c4201993020e50d415 |
"""
General helper functions that don't fit neatly under any given category.
They provide some useful string and conversion methods that might
be of use when designing your own game.
"""
import os
import sys
import imp
import types
import math
import re
import textwrap
import datetime
import random
import traceback
... | google-code-export/evennia | src/utils/utils.py | Python | bsd-3-clause | 34,830 | [
"VisIt"
] | de42c44209df9dc65fcbafec808f8d1e002a0150ba9cc22557912748aa0838b8 |
"""SCons.Tool.javac
Tool-specific initialization for javac.
There normally shouldn't be any need to import this module directly.
It will usually be imported through the generic SCons.Tool.Tool()
selection method.
"""
#
# Copyright (c) 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009 The SCons Foundation
#
# Per... | kuiche/chromium | third_party/scons/scons-local/SCons/Tool/javac.py | Python | bsd-3-clause | 8,568 | [
"VisIt"
] | 940d57da941d5c19268bc00e2cce2d820214fa128aae7495d1a66947313ddfa6 |
from ..libtcod import libtcod
black = libtcod.black
darkest_grey = libtcod.darkest_grey
darker_grey = libtcod.darker_grey
dark_grey = libtcod.dark_grey
grey = libtcod.grey
light_grey = libtcod.light_grey
lighter_grey = libtcod.lighter_grey
lightest_grey = libtcod.lightest_grey
darkest_gray = libtcod.darkest_gray
darke... | v4nz666/7drl2016 | RoguePy/UI/Colors.py | Python | gpl-3.0 | 6,793 | [
"Amber"
] | b9bb7be9d809fd52bf1bfe815b9e59eea373787aea611867c2fda7f48a1a6dd3 |
from django.utils.translation import ugettext_lazy as _
INVALID_MESSAGE = _('Sorry, I could not understand your message.'
' Please contact your DHIO for help, or visit http://www.ewsghana.com')
INVALID_PRODUCT_CODE = _('%s is not a recognized commodity code. Please contact your DHIO or RHIO for he... | qedsoftware/commcare-hq | custom/ewsghana/handlers/__init__.py | Python | bsd-3-clause | 1,365 | [
"VisIt"
] | 3b28fa7f446e8a359e8a1d825dd2580d4eaeceea9397884d7674213e4d7f7aae |
"""
Run many trilegal simulations and cull scaled LF functions to compare with data
"""
import argparse
import logging
import numpy as np
import os
import sys
import time
import matplotlib as mpl
mpl.use('Agg')
import matplotlib.pylab as plt
import ResolvedStellarPops as rsp
from IPython import parallel
from ..pop_sy... | philrosenfield/TPAGB-calib | tpagb_calibration/sfhs/vary_sfh.py | Python | bsd-3-clause | 30,558 | [
"Galaxy"
] | f0b5dcc91e311894fa8d3870709e9127595f7dbeffee66a63980ad20ea3eaced |
# -*- coding: utf-8 -*-
import glob
import os
import textwrap
from distutils.version import StrictVersion
import setuptools
from setuptools.package_index import PackageIndex
import pytest
from . import *
from ..utils import silence
TEST_SETUP_PY = """\
#!/usr/bin/env python
from __future__ import print_function
... | larrybradley/astropy-helpers | astropy_helpers/tests/test_ah_bootstrap.py | Python | bsd-3-clause | 14,549 | [
"VisIt"
] | 2d2e1c51db8492ddf06d7f119d1a9012ee29dade9f552ccac71b506ade193905 |
import numpy as np
from ase.structure import molecule
from ase.dft import Wannier
from gpaw import GPAW
from gpaw.test import equal
# Test of ase wannier using gpaw
calc = GPAW(gpts=(32, 32, 32), nbands=4)
atoms = molecule('H2', calculator=calc)
atoms.center(vacuum=3.)
e = atoms.get_potential_energy()
niter = calc.ge... | robwarm/gpaw-symm | gpaw/test/asewannier.py | Python | gpl-3.0 | 1,356 | [
"ASE",
"GPAW"
] | 568a96efdeb070b14b0d680e7e3436d782c981958b3d2d5780716da698827312 |
import os
import sys
from ase import Atom, Atoms
from ase.units import Bohr, Hartree
from ase.io.cube import write_cube
from gpaw import GPAW
from gpaw.test import equal
from gpaw.cluster import Cluster
from gpaw.point_charges import PointCharges
from gpaw.external_potential import ConstantPotential
cp = ConstantPot... | qsnake/gpaw | gpaw/test/external_potential.py | Python | gpl-3.0 | 2,481 | [
"ASE",
"GPAW"
] | 4454ae81ca9b44b91f2bab700ffd7afc0dc4393881444ae24bdf73c053582d01 |
#! /usr/bin/python2
# -*- coding: utf-8; -*-
#
# (c) 2013 booya (http://booya.at)
#
# This file is part of the OpenGlider project.
#
# OpenGlider 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 ... | hiaselhans/OpenGlider | openglider/graphics/functions.py | Python | gpl-3.0 | 1,372 | [
"VTK"
] | 0c708217942ce6e97de910dbc703e9f93bcddd8eced4e4d113aa296012892251 |
"""This module provides a disc feeder class."""
# Imports
# If wpilib not available use pyfrc
try:
import wpilib
except ImportError:
from pyfrc import wpilib
import common
import datalog
import parameters
import stopwatch
class Direction(object):
"""Enumeration for the directions of the feeder."""
S... | TechnoJays/robot2014 | src/robot/feeder.py | Python | gpl-2.0 | 12,997 | [
"Jaguar"
] | 63d36e4063a454ea7857196c622729c59012163150f9cea640cff12569f74512 |
#
# Copyright (C) 2000-2008 greg Landrum and Rational Discovery LLC
#
""" Informational Entropy functions
The definitions used are the same as those in Tom Mitchell's
book "Machine Learning"
"""
import numpy
import math
from rdkit.six.moves import xrange
# try to get the C versions of these routines
try:
... | soerendip42/rdkit | rdkit/ML/InfoTheory/entropy.py | Python | bsd-3-clause | 2,823 | [
"RDKit"
] | 5f4dea953b6c717aee3ae4fa4e2ed1b3b30bb32ce394b55c2b57ff56c7299be3 |
import copy
from django.core.exceptions import ImproperlyConfigured
from django.db import models
from django.db.models.deletion import PROTECT
from edc_appointment.constants import IN_PROGRESS_APPT, COMPLETE_APPT
from edc_base.model_managers.historical_records import HistoricalRecords
from edc_constants.constants impor... | botswana-harvard/edc-visit-tracking | edc_visit_tracking/model_mixins/visit_model_mixin/visit_model_mixin.py | Python | gpl-2.0 | 6,440 | [
"VisIt"
] | abafc6fd27d78cddcdca5c6f4a699fc39a34d4d4dc53467eb78e74d9c58b4413 |
""" DIRAC Multi VO FileCatalog plugin class to manage file metadata for multiple VO.
"""
from DIRAC import S_OK
from DIRAC.DataManagementSystem.DB.FileCatalogComponents.FileMetadata.FileMetadata import FileMetadata
from DIRAC.DataManagementSystem.DB.FileCatalogComponents.DirectoryMetadata.MultiVODirectoryMetadata impor... | DIRACGrid/DIRAC | src/DIRAC/DataManagementSystem/DB/FileCatalogComponents/FileMetadata/MultiVOFileMetadata.py | Python | gpl-3.0 | 4,903 | [
"DIRAC"
] | e421df260687dd0892ce180909c2efd5da0b1236da9f6fb62c79014b6b01af5c |
"""
Python/Numeric version of this module was called mpfit. This version was modified to use numpy.
"""
from __future__ import division # confidence medium
__version__ = '0.2'
"""
Perform Levenberg-Marquardt least-squares minimization, based on MINPACK-1.
... | pkgw/pwkit | lmmin_reference/nmpfit.py | Python | mit | 96,774 | [
"Gaussian"
] | a99ed9bd55bfa15dfef888f789190168fabe669087ca7ae5813ea3d2b9f99625 |
import numpy as np
from gpaw.utilities import unpack
from gpaw.utilities.blas import gemm
import gpaw.mpi as mpi
class LCAO:
"""Eigensolver for LCAO-basis calculation"""
def __init__(self, diagonalizer=None):
self.diagonalizer = diagonalizer
# ??? why should we be able to set
# this ... | ajylee/gpaw-rtxs | gpaw/lcao/eigensolver.py | Python | gpl-3.0 | 4,553 | [
"GPAW"
] | e4a23fa78e504e7968c9261255323aad7f992de9b3cde3d2137d4ec2df81b04f |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-configure
# Author : Ricardo Graciani
########################################################################
"""
Main script to write dirac.cfg for a new DIRAC installation and initial downl... | calancha/DIRAC | Core/scripts/dirac-configure.py | Python | gpl-3.0 | 20,098 | [
"DIRAC"
] | dfd8150311666e7e2324b93393efa099a1011ad00d0aaa0174316c8fd03f3d76 |
# coding=utf-8
import cv2
import numpy as np
# Basic functions
def get_background(img, mask, scale_factor=10, gauss=False, gauss_sigma=0):
"""
Automatically generates a background based on the image and the stars (found through the
threshold function). The algorithm is self-developed. Though mostly robust... | drpython/StaryPython | Orion/clean.py | Python | unlicense | 3,495 | [
"Gaussian"
] | facf9c452d3564a2680104691dc28ab8b9389ca33a890723b7d9d5d623221ce9 |
import gzip
import sys
import os
from .config import get_db_dir
defaultdir = get_db_dir()
'''
From nodes.dmp
tax_id -- node id in GenBank taxonomy database
parent tax_id -- parent node id in GenBank taxonomy database
rank ... | linsalrob/PhageHosts | code/taxon/taxon.py | Python | mit | 7,139 | [
"BLAST"
] | fce14504c5134c6f1c35d2010ee24fa3837c6c40c2c08c79dd4f50a7c451f1bf |
# $Id$
#
# Copyright (C) 2000-2008 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.
#
""" command line util... | greglandrum/rdkit | rdkit/ML/BuildComposite.py | Python | bsd-3-clause | 35,858 | [
"RDKit"
] | f160b77999f2e9aace2ff76d3b716b946ee3407104cef539458660ac9cb2b745 |
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