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""" Class that contains client access to the PilotsLogging handler. """
__RCSID__ = "$Id$"
from DIRAC.Core.Base.Client import Client, createClient
@createClient('WorkloadManagement/PilotsLogging')
class PilotsLoggingClient(Client):
"""Implementation of interface of Pilots Logging service. Client class should be u... | fstagni/DIRAC | WorkloadManagementSystem/Client/PilotsLoggingClient.py | Python | gpl-3.0 | 1,358 | [
"DIRAC"
] | 485a2701b65b425cb7db5c337860a0629ad5d67297d561c4be088c6abd55fd72 |
from __future__ import print_function
import sklearn.mixture
from numpy.linalg import inv, eig
from numpy import ix_, array, inf, sqrt, linspace, zeros, arctan2, matrix, pi
from .gaussian import Gaussian
def schur_complement(mat, row, col):
""" compute the schur complement of the matrix block mat[row:,col:] of t... | flowersteam/explauto | explauto/models/gmminf.py | Python | gpl-3.0 | 10,065 | [
"Gaussian"
] | b63e3b1f620dc4d66e7c8dc584b522cefa96b3e8ec584dfde54d5a577fbc2e46 |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
#
# This file is part of SPORE.
#
# Copyright (C) 2016, the SPORE team (see AUTHORS).
#
# SPORE 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 ... | IGITUGraz/spore-nest-module | unittests/test_dbl_exp_neuron.py | Python | gpl-2.0 | 3,752 | [
"NEURON"
] | 81ddfe7362679f9da01f43aa69254288b43d95898d6dc11064e660b3b553c544 |
'''
The one parameter exponential family distributions used by GLM.
'''
# TODO: quasi, quasibinomial, quasipoisson
# see http://www.biostat.jhsph.edu/~qli/biostatistics_r_doc/library/stats/html/family.html
# for comparison to R, and McCullagh and Nelder
import numpy as np
from scipy import special
from . import links ... | yl565/statsmodels | statsmodels/genmod/families/family.py | Python | bsd-3-clause | 51,421 | [
"Gaussian"
] | d3545201c5436e42a67492463c86f98d7522069b7b5226bb9326efadedcdecb9 |
import urllib.parse
import logging
import importlib
logger = logging.getLogger(__name__ + '.' + 'unshorten')
formatter = logging.Formatter('%(levelname)s: [UNSHORTEN] %(message)s')
handler = logging.StreamHandler()
handler.setFormatter(formatter)
# Prevent the messages from being propagated to the root logger
logge... | vivescere/yajuu | yajuu/unshorteners/__init__.py | Python | gpl-3.0 | 1,409 | [
"MOE"
] | 4556a3506e5613f0a60a0fa76edb05b86f8c6d472a59b442a0b7faf209b4a7b5 |
""" Test functions for stats module
"""
from __future__ import division, print_function, absolute_import
import warnings
import re
import sys
import pickle
from numpy.testing import (TestCase, run_module_suite, assert_equal,
assert_array_equal, assert_almost_equal, assert_array_almost_equal,
assert_allclose,... | Newman101/scipy | scipy/stats/tests/test_distributions.py | Python | bsd-3-clause | 109,483 | [
"Gaussian"
] | 12aba072efbf33747290d62fd99af3033b842d039673459479f5898909cfc1b3 |
# -*- coding: utf-8 -*-
#!/usr/bin/python
"""Test of the fix for one of the two issues in bug 552887a."""
from macaroon.playback import *
import utils
sequence = MacroSequence()
########################################################################
# Load the local test case.
#
sequence.append(KeyComboAction("<Co... | h4ck3rm1k3/orca-sonar | test/keystrokes/firefox/bug_552887a.py | Python | lgpl-2.1 | 13,710 | [
"ORCA"
] | 1cd2d55a66a8ddd432121ea1075f3a0db6184162db3d6af06c22a3d4d04c14c0 |
from __future__ import unicode_literals
import base64
import json
import re
from .common import InfoExtractor
from .theplatform import ThePlatformIE
from .adobepass import AdobePassIE
from ..compat import compat_urllib_parse_unquote
from ..utils import (
int_or_none,
parse_duration,
smuggle_url,
try_g... | yan12125/youtube-dl | youtube_dl/extractor/nbc.py | Python | unlicense | 20,766 | [
"Brian"
] | def41744ce7c07689823d15eeee22988209b3a3a9c26323f162934ce10516491 |
#
# Copyright (c) 2017 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | yashdsaraf/scancode-toolkit | src/commoncode/command.py | Python | apache-2.0 | 12,195 | [
"VisIt"
] | 6fe7c4e3c4e5f116d7a887e1d9b497a07d967c2acd8470bfd8d80ab2feaa5a50 |
import re
from ._gen import LXScriptParser, LXScriptVisitor
from . import error
from antlr4 import CommonTokenStream
class Parser(LXScriptParser.LXScriptParser):
"""A parser for the LXScript language"""
def __init__(self, input):
super(Parser, self).__init__(input=CommonTokenStream(input))
#... | frenchie16/lxscript | lexparse/parser.py | Python | unlicense | 1,053 | [
"VisIt"
] | 624d620374d425781e100c038bc6f2dca25f887e9ebfaef44f5a86d6ed91de91 |
#!/usr/bin/env ganga
import getpass
from distutils.util import strtobool
polarity='MagDown'
datatype='MC'
substitution='None'
channel='kstar_eta_3pi'
b=Job()
b.application=DaVinci(version="v36r5")
if datatype=='MC':
b.application.optsfile='NTupleMaker_{0}.py'.format(polarity)
if datatype=='Data':
if substit... | Williams224/davinci-scripts | ksteta3pi/JobSubmit.py | Python | mit | 2,011 | [
"DIRAC"
] | fb56b01277fbf9c6496bfb0dbc3e00049febc3c358de72181c1667d08661bc4f |
# $Id$
#
# Copyright (C) 2007 Greg Landrum
# All Rights Reserved
#
import copy
class pySparseIntVect(object):
""" this class is pretty much obsolete (it's in C++ now) """
size=0
container={}
def __init__(self,size):
self.size=size
self.container={}
def UpdateFromSequence(self,seq):
"""
>>... | soerendip42/rdkit | rdkit/DataStructs/SparseIntVect.py | Python | bsd-3-clause | 9,458 | [
"RDKit"
] | ce50a73a4982a670d30d1ed8f6c832a217898760a7cd81251f5b67f8f2232620 |
#!/usr/bin/env python3
"""
This is the new SONAR setup/install script. It will check for
prerequisites and configure some helper files.
Usage: setup.py
"""
import os,subprocess,sys,glob
SONAR_HOME = os.path.abspath( os.path.dirname( sys.argv[0] ) )
if len(glob.glob("%s/commonVars.py"%SONAR_HOME))==0:
sys.exit(... | scharch/SONAR | setup.py | Python | gpl-3.0 | 7,141 | [
"BLAST",
"BioPerl",
"Biopython"
] | 793ec42b95a5b3e1ff7b336880b69176d88769a00e60478541af75b67db03b24 |
import numpy as np
from mdtraj.testing import eq
from mdtraj.utils import uniform_quaternion, rotation_matrix_from_quaternion
def test_quaternion_0():
q = uniform_quaternion(random_state=2)
eq(np.sum(q**2), np.float64(1.0))
eq(q.shape, (4,))
q2 = uniform_quaternion(size=2)
eq(np.sum(q2**2, axis=1)... | leeping/mdtraj | tests/test_quaternion.py | Python | lgpl-2.1 | 1,071 | [
"MDTraj"
] | d27f60a946987494c2569e063c8f7d638fdbb3080b9e0bf2f1e2d1175d0a140d |
"""
TODO
"""
import numpy
from theano import function, shared
from theano import tensor as TT
import theano
sharedX = (lambda X, name:
shared(numpy.asarray(X, dtype=theano.config.floatX), name=name))
def kinetic_energy(vel):
"""Returns the kinetic energy associated with the given velocity
and ma... | dungtn/hackspace-2016 | source/convolutional_net/LearningAlgorithm/hmc/hmc.py | Python | gpl-3.0 | 15,117 | [
"Gaussian"
] | 9da1703f74d7f34879de5e618ff22df7f851cc02e8ec3d6b27b40c24249ba6da |
# Copyright 2018 the GPflow 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 in writi... | GPflow/GPflow | tests/gpflow/utilities/test_traversal.py | Python | apache-2.0 | 21,203 | [
"Gaussian"
] | d21ebe0d4bcae9c3be8150001d6e5aa89d6af72977d584d3a0c54c7d79e9ecf8 |
########################################################################
# File : ARCComputingElement.py
# Author : A.T.
########################################################################
""" ARC Computing Element
"""
__RCSID__ = "58c42fc (2013-07-07 22:54:57 +0200) Andrei Tsaregorodtsev <atsareg@in2p3.fr>"
... | coberger/DIRAC | Resources/Computing/ARCComputingElement.py | Python | gpl-3.0 | 10,905 | [
"DIRAC"
] | 077bfd10affa0fbf3f5008d45b4c390ebaacb537bce2a5fd93819c51fa8547c7 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import rdkit
from rdkit.Chem import AllChem
from rdkit import DataStructs
__license__ = "X11"
METADATA = {
"id": "method_rdkit_ecfp2_2048_tanimoto",
"representation": "ecfp2_2048",
"similarity": "tanimoto"
}
def _compute_fingerprint(molecule):
return Al... | skodapetr/lbvs-environment | methods/ecfp/ecfp2_2048_tanimoto.py | Python | mit | 1,396 | [
"RDKit"
] | cb6aedd1775a8a51aa8b4b5e47daa91fd1e7592d73a153e64a0906a4162ea9a7 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
__author__ = "Jifu Zhao"
__email__ = "jzhao59@illinois.edu"
__date__ = "04/07/2017"
__modify__ = "04/24/2017"
"""
import warnings
import numpy as np
import pandas as pd
from itertools import product
import matplotlib.pyplot as plt
from sklearn.metrics.p... | JifuZhao/Poisson-Kriging | old/kriging2.py | Python | mit | 11,291 | [
"Gaussian"
] | 9d896f4152758320c445fdf28f863045382fa278ccb2d855548eeb8ff4ceead4 |
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'GaussianFitter.ui'
#
# Created by: PyQt4 UI code generator 4.11.4
#
# WARNING! All changes made in this file will be lost!
from PyQt4 import QtCore, QtGui
try:
_fromUtf8 = QtCore.QString.fromUtf8
except AttributeError:
def _fromUtf... | tboudreaux/PHY-2002 | GaussianFitter.py | Python | lgpl-3.0 | 7,629 | [
"Gaussian"
] | 2b4a3bcc1270dc3094c8a97a4231fb8c9833527a248250019b6126c50c682162 |
"""Standard test images.
For more images, see
- http://sipi.usc.edu/database/database.php
"""
import os as _os
from .. import data_dir
from ..io import imread, use_plugin
from .._shared._warnings import expected_warnings
from ._binary_blobs import binary_blobs
from .. import img_as_bool
__all__ = ['load',
... | rjeli/scikit-image | skimage/data/__init__.py | Python | bsd-3-clause | 7,832 | [
"ESPResSo"
] | dfbbe82c361a11a3582d8a94ea31e431e0cdf7e2f7de0b748bd473ce6486880f |
#
# Brian C. Lane <bcl@redhat.com>
#
# Copyright 2014 Red Hat, Inc.
#
# This copyrighted material is made available to anyone wishing to use, modify,
# copy, or redistribute it subject to the terms and conditions of the GNU
# General Public License v.2. This program is distributed in the hope that it
# will be useful,... | marmarek/pykickstart | tests/commands/sshkey.py | Python | gpl-2.0 | 1,819 | [
"Brian"
] | 2dd19aef4a987aa89eddfe3f6458735ef2b6aced1a314be188a5be5384766cc9 |
import six.moves.cPickle as pickle
from copy import copy
from nose.tools import assert_raises
from syn.five import STR
from syn.base.b import Base, Attr, init_hook, coerce_hook, setstate_hook, \
pre_create_hook, Harvester
from syn.type.a import Type, Schema, List, Set
from syn.schema.b.sequence import Sequence
from... | mbodenhamer/syn | syn/base/b/tests/test_base.py | Python | mit | 21,684 | [
"VisIt"
] | 4a9151aea814981ad20d6fcfed740d0726f24b9c4716f8af6302b8b163be1c89 |
# Copyright 2021 The Distla 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 applicable ... | google/distla_core | distla/distla_core/distla_core/analysis/initializers.py | Python | apache-2.0 | 14,414 | [
"Gaussian"
] | 617a0a5418f4928b8ddd31616493ec58b48acd9930ea8664133a9a6717d350ee |
#!/usr/bin/python -O
#PBS -N myjob
#PBS -l select=1:ncpus=1:mem=12GB
#PBS -l walltime=70:00:00
import subprocess
import os
import sys
def module_add(modulen... | hjanime/mrcchip | sampe.py | Python | gpl-2.0 | 2,081 | [
"BWA"
] | ce29333f8015d1c9dd1cbfb16c3deef57f00701e69a0fc976f22e3d44434d239 |
#!/usr/bin/env python
from itertools import combinations, izip, product, chain, repeat
from os.path import basename, dirname, isfile, join, relpath
from sys import stdout, stderr, exit, maxint, argv
from ConfigParser import ConfigParser
from optparse import OptionParser
from math import floor
import networkx as nx
fro... | danydoerr/PSyCHO | scripts/pairwise_similarities.py | Python | mit | 18,112 | [
"BLAST"
] | 8c75825bdc3982a0f5173462bb2ecce64fc4e506d28e95b0acb9a3b0b612d846 |
# This program is free software; you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the Free Software
# Foundation; either version 2 of the License, or (at your option) any later
# version.
#
# This program is distributed in the hope that it will be usefu... | dbbhattacharya/kitsune | vendor/packages/logilab-astng/inspector.py | Python | bsd-3-clause | 10,260 | [
"VisIt"
] | 6abae848ffbc7acc8bff3a27c17dcd9a0c3e540202e01285614994d1a8e64ad5 |
"""
Helper functions to run with OpenMM, these function could be methods of the
MDSimulation class however because of limitations imposed by the
multiprocessing they need to be functions
"""
from __future__ import absolute_import, division, print_function
import os
import sys
import time
import functools
import traceb... | AdaptivePELE/AdaptivePELE | AdaptivePELE/simulation/openmm_simulations.py | Python | mit | 41,215 | [
"Amber",
"Dalton",
"Gromacs",
"MDTraj",
"OpenMM"
] | 29f17ef53d83262992784263277e148f4c2e4f9054072492f279724dbbc6afea |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the LMS Instructor Dashboard.
"""
import requests
from bok_choy.web_app_test import WebAppTest
from ...fixtures.course import CourseFixture
from ...fixtures.ga_course_team import CourseTeamFixture
from ...pages.biz.ga_contract import BizContractPage
from ...pages.common... | nttks/edx-platform | common/test/acceptance/tests/lms/test_ga_instructor_dashboard.py | Python | agpl-3.0 | 21,634 | [
"VisIt"
] | e1453e551f2fc71c51b6f4b79040cdc598783cc356e0e8c7dba88969a80225b1 |
"""
Python implementation of the fast ICA algorithms.
Reference: Tables 8.3 and 8.4 page 196 in the book:
Independent Component Analysis, by Hyvarinen et al.
"""
# Authors: Pierre Lafaye de Micheaux, Stefan van der Walt, Gael Varoquaux,
# Bertrand Thirion, Alexandre Gramfort, Denis A. Engemann
# License: BS... | depet/scikit-learn | sklearn/decomposition/fastica_.py | Python | bsd-3-clause | 17,407 | [
"Gaussian"
] | cbc8dea524363187fa32b9dce00612b336b800eb59099620adc4c3c1065acf99 |
"""
Title: WGAN-GP with R-GCN for the generation of small molecular graphs
Author: [akensert](https://github.com/akensert)
Date created: 2021/06/30
Last modified: 2021/06/30
Description: Complete implementation of WGAN-GP with R-GCN to generate novel molecules.
"""
"""
## Introduction
In this tutorial, we implement a... | keras-team/keras-io | examples/generative/wgan-graphs.py | Python | apache-2.0 | 22,181 | [
"RDKit"
] | ce301c2f657c4d0dd46a8bc8002fb97c07675e5893a15c93970261847eed6052 |
"""
EIIE A3C training script
You must have an instance of FeedDaemon running in order to use this script.
If you want to use a direct connection for data, change the papi data feed instance.
"""
import sys
sys.path.insert(0, '../')
from os import listdir
import logging
logging.basicConfig(level=logging.ERROR)
impor... | naripok/cryptotrader | scripts/eiie_rl_train.py | Python | mit | 9,437 | [
"VisIt"
] | 62e5b0b46f738eeb447dbeaa5619bbbfef99dfdd591abbb52c8e763e2bc76323 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
## we set up default information.
## first, easy to maintain lists which can eventually be moved to
## files.
# TRANSLATOR WARNING: DO NOT TRANSLATE THE FIELD NAMES: ONLY THE VALUES!!!
CREDITS = "Gregory"
# only translate the items in the list [..] (and feel free to create ... | Linutux/Gourmet | gourmet/defaults/defaults_nl.py | Python | gpl-2.0 | 23,366 | [
"Octopus"
] | e758154824e95a2c1db4b19d6de72bb07db5c27a80e2c94c09f0fb119b9a13fe |
from core.images import *
# Name, Image, Tier, Importance
GAME_ITEMS = [
("A King's Crown", IMG_A_KINGS_CROWN, 1, 1),
("Aegis", IMG_AEGIS, 4, 44),
("Awakening Armor", IMG_AWAKENING_ARMOR, 2, 35),
("Awakening Armor +1", IMG_AWAKENING_ARMOR_PLUS_1, 2, 36),
("Awakening Sword", IMG_AWAKENING_SWORD, 2,... | Varkalas/Tower-of-Hero-Assistant | core/constants.py | Python | mit | 3,020 | [
"CRYSTAL"
] | dc1f5f4537b5603b3493afd7ed1b217ed4e9b2401c243dfbaecdc5aed5f680f0 |
# -*- coding: utf-8 -*-
# Copyright (c) 2007, 2008, Benoît Chesneau
# Copyright (c) 2007 Simon Willison, original work on django-openid
#
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# ... | openpgh/askpgh | askbot/deps/django_authopenid/views.py | Python | gpl-3.0 | 56,379 | [
"VisIt"
] | bb5ec79de116355ba040851b66148aecf31fdc809404222abc1484a4ba8f7c58 |
'''
Created on Jul 6, 2011
@author: mkiyer
'''
'''
Created on Jun 3, 2011
@author: mkiyer
'''
import logging
import chimerascan.pysam as pysam
def extend_and_pad_sam(input_fastq_files, input_sam_file, output_sam_file):
infh = pysam.Samfile(input_sam_file, "r")
outfh = pysam.Samfile(output_sam_file, "w", tem... | tectronics/chimerascan | chimerascan/deprecated/extend_and_pad_sam.py | Python | gpl-3.0 | 3,290 | [
"pysam"
] | f026956a4c2c5c22626ced56e560753ecec09f1c148ce288f3a8f54e33861f46 |
from ruffus import follows, transform, regex, mkdir,\
pipeline_printout, pipeline_printout_graph,\
pipeline_run, files, merge,\
touch_file, posttask, jobs_limit
import os
import sys
from subprocess import check_call
from pipeline_config import POINTS_H5_DIR,\
PCD_DIR, PCD_DOWNSAMPLED_DIR... | sameeptandon/sail-car-log | mapping/pipeline/pipeline.py | Python | bsd-2-clause | 12,901 | [
"VTK"
] | 9a1d3fe5b7046de842dc7ada6ab1bfdc32a443879d8c0d51ce92b53336951b27 |
# -*- coding:utf-8 -*-
#
# Copyright 2012 NAMD-EMAP-FGV
#
# This file is part of PyPLN. You can get more information at: http://pypln.org/.
#
# PyPLN 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 vers... | flavioamieiro/pypln.web | pypln/web/settings.py | Python | gpl-3.0 | 5,457 | [
"NAMD"
] | cfa9f653fc645aa27499d511f5a24928dd3950e455d436cf06e929c63fa59e17 |
#
# Gaussian Mixture Model, swiped from scikit-learn then tweaked -
# 1) eliminate need do initialization so we can specify a previous set
# of parameters.
# 2) add last two functions to allow fixed means and axis-aligned
# covariance.
#
# Tweaks by - Ross Fadely
#
"""
Gaussian Mixture Models.
This implementat... | rossfadely/xd-demo | gmm_wrapper.py | Python | mit | 28,323 | [
"Gaussian"
] | d2839e7316e28635152c93b295992b1b3c57e198a6656c88bb03d06311747984 |
# 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... | maxrp/autopsy | pythonExamples/dataSourceIngestModule.py | Python | apache-2.0 | 7,443 | [
"Brian"
] | 1d09b28710738b86c132f928b9d569461634c0440fed4737f8e4d19b4ab658b8 |
# Copyright 2015 datawire. 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 applicable law or agr... | bozzzzo/quark | quarkc/ast.py | Python | apache-2.0 | 22,591 | [
"VisIt"
] | 0ea027c340de34f8114c1323ecd976ffe514da70c2f1e0bfa6d71ace4c9907ff |
# -*- coding: UTF-8 -*-
# @author JoseMariaRomeroARK visit my gitHub site at: https://github.com/JoseMariaRomeroARK
from tkinter import *
import Utilidades
import os, shutil, threading
from VentanAux import createNew
listaFormatos =[".mp3",".aac",".m4a",".mp4",".wma",".wav",".atrac",".m4p",".m3p",".flac",".midi",... | JoseMariaRomeroARK/Movil-Music-Mananger-M3 | VentanaMain.py | Python | cc0-1.0 | 8,249 | [
"VisIt"
] | a28275e037cf32a0b79761343da0f294a488476c468b5202a52a50fcae40315c |
import math
import numpy as np
import random
def get_ff_fun(start_flattop, filling_ff, flattop_ff):
'''
get the feed forward table function
'''
def ff_(time):
if time < start_flattop:
return filling_ff
else:
return flattop_ff
return ff_
def get_sp_f... | Bellaz/ModuleSimulator | python/utils.py | Python | gpl-3.0 | 2,615 | [
"Gaussian"
] | 438e3d6dda7264390b682c2b487858bca10368e34ed90dd550eb474e00123c09 |
# Copyright 2014-2020 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
#
# Unless required by appl... | sunqm/pyscf | pyscf/cc/__init__.py | Python | apache-2.0 | 7,633 | [
"PySCF"
] | 71e55c27cee069e8e3abda3af95ca1f7b79e2511a5808b0637b7711b3472d600 |
#!/usr/bin/env python3
"""
Copyright 2020 Paul Willworth <ioscode@gmail.com>
This file is part of Galaxy Harvester.
Galaxy Harvester is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 ... | pwillworth/galaxyharvester | html/getUserAttr.py | Python | gpl-3.0 | 2,268 | [
"Galaxy"
] | cdfc0faff682653cb455397da546b84a7b4e0d4c157e4404952696ea89200dd3 |
"""
Application: HealthNet
File: models.py
Authors:
- Nathan Stevens
- Philip Bedward
- Daniel Herzig
- George Herde
- Samuel Launt
Description:
- This file contains all the class definitions for each
model within the HealthNet application
"""
f... | blackpan2/HealthNet | src/healthnet/base/models.py | Python | mit | 28,881 | [
"VisIt"
] | d9dece1a7c0b222ce6b1c759966215aee2542238af01cba6fb3a95649aef774b |
'''variantAnalysisAlign.py
Usage:
variantAnalysisAlign.py <sampledata> <indir> <outdir> <index>
<indelvcf> <snpvcf> <pathfile> [--threads=<threads>]
Options:
--threads=<threads> Number of threads [default: 1]
--pair=<pair> Input reads should be paired
--help ... | adam-rabinowitz/ngs_python | scripts/Variants/variantAnalysisAlign.py | Python | gpl-2.0 | 4,135 | [
"BWA"
] | 1cac2ae14c5b65f4fd94a4535417dcf790c2202905f5dc71ba7318626f60fa63 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
import warnings
import requests
from monty.os.path import which
from pymatgen.ext.cod import COD
website_is_up = requests.get("https://www.crystallography.net").status_code == 200
@unitte... | gmatteo/pymatgen | pymatgen/ext/tests/test_cod.py | Python | mit | 1,215 | [
"pymatgen"
] | ca63b070d3e31e8e6a2cfd6b82627dbe7c173e7d7ee9ac7bbf2530602d64b94e |
'''
Conversion of basis sets to deMon2K format
'''
from .. import lut, manip, sort, misc, printing
def write_demon2k(basis):
'''Converts a basis set to deMon2K format
'''
if 'gto_spherical' in basis['function_types']:
s = '# This basis set uses spherical components\n\n'
else:
s = '# ... | MOLSSI-BSE/basis_set_exchange | basis_set_exchange/writers/demon2k.py | Python | bsd-3-clause | 3,538 | [
"deMon2k"
] | 0f62c4d05e480bcb32c7c62c03995f01ba3917193eafea70cb3a0b6946d9238a |
'''Command line options for attractor networks.
Use this to effectively define/select which command line arguments should be
used for the network.
Classes / Functions
-------------------
.. autosummary::
DOptionParser
ParameterSelector
getOptParser
'''
from __future__ import absolute_import, print_functi... | MattNolanLab/ei-attractor | grid_cell_model/models/parameters.py | Python | gpl-3.0 | 16,390 | [
"Gaussian",
"NEURON"
] | 9a944084a4d5e589664041c11c6edfda66509e57ab26f4fba5bce0e3be9a4ed4 |
import clang_util
import cpp
import file_parser
import re
import util
import parser_addition
from clang.cindex import TypeKind
def sequence_from_text(text):
return [cpp.SimpleToken(entry) for entry in text.split(' ')]
def get_alias_from_text(name, text):
return cpp.Alias(name, [cpp.SimpleToken(spelling) for... | lubkoll/friendly-type-erasure | type_erasure/cpp_file_parser.py | Python | mit | 16,956 | [
"VisIt"
] | 83bc3505f7693aa4eea87c8d39c95d56742309f45014cb018aac36d83c4d982c |
"""Utilities to assist with commerce tasks."""
import json
import logging
from urllib import urlencode
from urlparse import urljoin
import requests
import waffle
from django.conf import settings
from django.contrib.auth import get_user_model
from django.urls import reverse
from django.utils.translation import ugettext... | a-parhom/edx-platform | lms/djangoapps/commerce/utils.py | Python | agpl-3.0 | 15,603 | [
"VisIt"
] | ca33d1c7063bec5a1a527237c21d38390cd20ed748ec6affdba8ab225ebdf418 |
"""Constants for the Amazon Polly text to speech service."""
from __future__ import annotations
from typing import Final
CONF_REGION: Final = "region_name"
CONF_ACCESS_KEY_ID: Final = "aws_access_key_id"
CONF_SECRET_ACCESS_KEY: Final = "aws_secret_access_key"
DEFAULT_REGION: Final = "us-east-1"
SUPPORTED_REGIONS: Fi... | mezz64/home-assistant | homeassistant/components/amazon_polly/const.py | Python | apache-2.0 | 3,092 | [
"Brian"
] | a8e8cc60f938e2df847031d8a597bfa7f1cff31f63e0bfb3622a9ef1ab309f95 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from setuptools import setup
def readme():
with open('README.md') as f:
return f.read()
setup(
name='bowtie-content',
version='0.0.1',
packages=['bowtie_content'],
include_package_data=True,
zip_safe=False,
license='MIT License',
d... | django-bowtie/bowtie-content | setup.py | Python | mit | 896 | [
"Bowtie"
] | a23f2afb1d4247fa7722740534effa6419a6d1109b35462fe30ca6473965ee78 |
'''
Example of a spike receptor (only receives spikes)
In this example spikes are received and processed creating a raster plot at the end of the simulation.
'''
from brian import *
import numpy
from brian_multiprocess_udp import BrianConnectUDP
# The main function with the NeuronGroup(s) and Synapse(s) must be na... | ricardodeazambuja/BrianConnectUDP | examples/OutputNeuronGroup_multiple_inputs.py | Python | cc0-1.0 | 2,862 | [
"Brian",
"NEURON"
] | 6b4c26a0dd295801133111839d0dfa67dd39f4a5af5abd1b394ea51f56d9528a |
#!/usr/bin/env python
import sys
import math
import numpy as np
import matplotlib.pyplot as plt
import os.path
try:
import gi
gi.require_version('NumCosmo', '1.0')
gi.require_version('NumCosmoMath', '1.0')
except:
pass
from gi.repository import GObject
from gi.repository import NumCosmo as Nc
from gi.reposit... | NumCosmo/NumCosmo | examples/example_rosenbrock.py | Python | gpl-3.0 | 4,314 | [
"Gaussian"
] | be5c908fcb3cde652a0a02e6a5b9c3b1036c2ad819ff3b113bc1819e84347782 |
#
# Code to process gcdataconcepts accelerometer data.
#
# Based on:
# https://gist.github.com/sixtenbe/1178136
# http://nbviewer.ipython.org/urls/raw.github.com/duartexyz/bmc/master/DataFiltering.ipynb
# http://commons.wikimedia.org/wiki/File:HilbertTransform_EnvelopePhase.png
#
#
# (c) 2013, Wannes Meert, KU Leuven
#... | toonn/mlii | classifyrunner/accproc.py | Python | bsd-2-clause | 38,858 | [
"TINKER"
] | 7dd40dc285843f0e1fbe285db116de33bdf0a9aac387d3fa192489282414f2e3 |
import numpy as np
from ase.optimize.optimize import Optimizer
class FIRE(Optimizer):
def __init__(self, atoms, restart=None, logfile='-', trajectory=None,
dt=0.1, maxmove=0.2, dtmax=1.0, Nmin=5, finc=1.1, fdec=0.5,
astart=0.1, fa=0.99, a=0.1, master=None):
"""Parameters... | suttond/MODOI | ase/optimize/fire.py | Python | lgpl-3.0 | 2,416 | [
"ASE"
] | 6cafbe7a2db96fa23264fbf94b00b2df9056d8a4e67718193292eeaddbbd2c22 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""Test suit for the CP2K ASE calulator.
http://www.cp2k.org
Author: Ole Schuett <ole.schuett@mat.ethz.ch>
"""
from __future__ import division, print_function
import os
from ase.test import NotAvailable
from ase import units
from ase.atoms import Atoms
from ase.md.velocityd... | misdoro/python-ase | ase/test/cp2k/cp2k_MD.py | Python | gpl-2.0 | 1,332 | [
"ASE",
"CP2K"
] | 096b5ea6eedc4aadeb1dea316ad2a49442783a61a763e8e794452f33d0edeb72 |
# coding: utf-8
#!/usr/bin/env python
from __future__ import division, unicode_literals
"""
#TODO: Write module doc.
"""
__author__ = 'Shyue Ping Ong'
__copyright__ = 'Copyright 2013, The Materials Virtual Lab'
__version__ = '0.1'
__maintainer__ = 'Shyue Ping Ong'
__email__ = 'ongsp@ucsd.edu'
__date__ = '8/1/15'
i... | rousseab/pymatgen | pymatgen/io/xyzio.py | Python | mit | 481 | [
"pymatgen"
] | ada89b0734c54f453d5e1b92b7f50c34a44433853db582883c2a33c3ce048972 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Written by Lucas Sinclair.
MIT Licensed.
Contact at www.sinclair.bio
"""
# Built-in modules #
import os
# First party modules #
from seqsearch.databases import Database
# Third party modules #
# Constants #
home = os.environ.get('HOME', '~') + '/'
###############... | xapple/seqsearch | seqsearch/databases/ncbi_16s.py | Python | mit | 1,295 | [
"BLAST"
] | 87077a8fc9b609b9b9a370353cccc52ee4e10a12f3132da88371f19c51294dfc |
#!/usr/bin/env python
"""
oa
Objective analysis. This function will interpolate data using the
fortran routines written by Emanuelle Di Lorenzo and Bruce Cornuelle
Written by Brian Powell on 10/08/13
Copyright (c)2017 University of Hawaii under the BSD-License.
"""
import numpy as np
import seapy.oalib
_... | dalepartridge/seapy | oa.py | Python | mit | 4,466 | [
"Brian"
] | f75923e674635de61ff0a9647bd9b8d7ce6b055cedd444e62704d694c4ef1f68 |
"""
Generate samples of synthetic data sets.
"""
# Authors: B. Thirion, G. Varoquaux, A. Gramfort, V. Michel, O. Grisel,
# G. Louppe
# License: BSD 3 clause
from itertools import product
import numbers
import numpy as np
from scipy import linalg
from ..utils import array2d, check_random_state
from ..utils i... | seckcoder/lang-learn | python/sklearn/sklearn/datasets/samples_generator.py | Python | unlicense | 40,691 | [
"Gaussian"
] | d130c9abf7ffec90293a1c67ba37221ed37b6806c590248973d60ca02d98d70d |
'''
modified by Chongxuan Li (chongxuanli1991@gmail.com)
'''
import numpy as np
import theano
import theano.tensor as T
import collections as C
import anglepy as ap
import anglepy.ndict as ndict
from anglepy.misc import lazytheanofunc
import math, inspect
import theano.sandbox.cuda.rng_curand as rng_curand
def shar... | zhenxuan00/mmdgm | mlp-mmdgm/anglepy/models/GPUVAE_YZ_X.py | Python | mit | 14,360 | [
"Gaussian"
] | db5906dc2500edb95e17ffc3b6787677b1d63b66e5fa335f5e434842533ebc30 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module defines classes to generate point defect structures
"""
import logging
from abc import ABCMeta, abstractmethod
from monty.json import MSONable
from pymatgen.analysis.bond_valence import BVAna... | gmatteo/pymatgen | pymatgen/analysis/defects/generators.py | Python | mit | 10,969 | [
"pymatgen"
] | 00ef77d5c5427a5cb002b137662ed9594f345a28494122446afec54dc23e0654 |
import numpy as np
import h5py
import matplotlib.pyplot as plt
from itertools import compress
from astropy.io import fits
import pandas as pd
from .utils import fit_continuum
# attributes!
REQUIRED_3D = ['xs', 'ys', 'ivars'] # R-order lists of (N-epoch, M-pixel) arrays
REQUIRED_1D = ['bervs', 'airms'] # N-epoch array... | megbedell/wobble | wobble/data.py | Python | mit | 31,151 | [
"ESPResSo"
] | b000a70a7ba9087e91653def8878b0b6095e3bc7cf48c1bf3e35f78d019c2a6b |
import functools
import inspect
import itertools
import sys
import warnings
from collections import defaultdict
from collections import deque
from types import TracebackType
from typing import Any
from typing import Callable
from typing import cast
from typing import Dict
from typing import Generator
from typing import... | JoelMarcey/buck | third-party/py/pytest/src/_pytest/fixtures.py | Python | apache-2.0 | 65,720 | [
"VisIt"
] | fc7be80bbb137c81fe76714278d3098abc6bfb85c1332cd6ffd1ba72af4b1b4e |
#!/usr/bin/env python
#
# $File: reichstat.py $
#
# This file is part of simuPOP, a forward-time population genetics
# simulation environment. Please visit http://simupop.sourceforge.net
# for details.
#
# Copyright (C) 2004 - 2010 Bo Peng (bpeng@mdanderson.org)
#
# This program is free software: you can redistribute ... | BoPeng/simuPOP | docs/reichstat.py | Python | gpl-2.0 | 2,134 | [
"VisIt"
] | e8f43a4eec1c461d9aac6d80cce0688e938cd0804de0e9143851a24b62d7b58f |
import dateutil.parser
import json
import ldap
import pickle
import pika
import re
import traceback
from pyramid_addons.helpers import http_created, http_ok
from pyramid_addons.validation import (SOURCE_MATCHDICT, EmailAddress,
TextNumber, Validator)
from pyramid.httpexceptions im... | ucsb-cs/submit | submit/helpers.py | Python | bsd-2-clause | 20,238 | [
"VisIt"
] | 9bf377483c3aacbbc71181b7808ccb3fb46d372dbe57b02c6df41b99fc745b41 |
"""This implementation is based on the oryginal MATLAB implementation.
TODO: Unit test against the oryginal.
"""
from __future__ import division, print_function, absolute_import
import numpy as np
from numpy.random import randn
from scipy.signal import resample
from numpy.fft import fft, ifft
# sigma has been remo... | mrkrd/cochlea | cochlea/zilany2009/ffGn_module.py | Python | gpl-3.0 | 2,018 | [
"Gaussian"
] | 8f235dcfb83b5c5211270e30bdfda5278ce58879eca565df28a5869400480627 |
"""
This Service provides functionality to access and modify the
InstalledComponentsDB database
"""
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.FrameworkSystem.DB.InstalledComponentsDB import InstalledComponentsDB, Component, Host, InstalledComponent, HostLogging
from DIRAC.Core.DISET.RequestHandler import Re... | andresailer/DIRAC | FrameworkSystem/Service/ComponentMonitoringHandler.py | Python | gpl-3.0 | 14,091 | [
"DIRAC"
] | 39412914957473a8b464c921f233cc1aee7cf4e92995e9179a0ddbc2244f1d34 |
#!/usr/bin/env python
# $Id: codegen.py 60 2002-12-19 06:35:28Z miles $
import compiler
import dis
import operator
from parser import ParserError
class MyCodeGenerator(compiler.pycodegen.ModuleCodeGenerator):
def visitDiscard(self, node):
self.visit(node.expr)
self.emit('RETURN_VALUE') ... | milesegan/lython | codegen.py | Python | bsd-3-clause | 1,075 | [
"VisIt"
] | c184967209ac0d62438c191015841eabcfacdd5301a63e5da1fdb3e7291331f2 |
# Filename: ciderD.py
#
# Description: Describes the class to compute the CIDEr-D (Consensus-Based Image Description Evaluation) Metric
# by Vedantam, Zitnick, and Parikh (http://arxiv.org/abs/1411.5726)
#
# Creation Date: Sun Feb 8 14:16:54 2015
#
# Authors: Ramakrishna Vedantam <vrama91@vt.edu> and Tsu... | ramakrishnavedantam928/cider | pyciderevalcap/ciderD/ciderD.py | Python | bsd-2-clause | 1,697 | [
"Gaussian"
] | f30ab8cbc09e9a5d3ca4d6b6852e0366044a8a06f3d11db3521b9606f6aee7d7 |
"""Plotting the 1-D profile from isophotal analysis."""
import numpy as np
import matplotlib.pyplot as plt
from matplotlib import gridspec
from matplotlib import rcParams
from matplotlib.patches import Ellipse
from matplotlib.ticker import NullFormatter
from kungpao.display import display_single
plt.rc('text', use... | dr-guangtou/KungPao | kungpao/isophote/plotting.py | Python | gpl-3.0 | 8,047 | [
"Galaxy"
] | 5de9f5472c91512bcaaac4ffbc665cb1a4958ab261430a711c4cfc3ad159653e |
#!/usr/bin/env python
#-*- coding:utf-8 -*-
# test_attributes.py
"""
Test the validity of the plotting functions.
"""
import os
import numpy as np
import pytest
import nngt
import nngt.generation as ng
import nngt.plot as nplt
# absolute directory path
dirpath = os.path.abspath(os.path.dirname(__file__))
# te... | Silmathoron/NNGT | testing/test_plots.py | Python | gpl-3.0 | 5,861 | [
"Gaussian"
] | 0f2bd5cb2ded41a4849e26b2424c8343645bb6df8760af46d694946b73e6322b |
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2006-2014, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public version 2.1 or l... | Clyde-fare/cclib | test/bettertest.py | Python | lgpl-2.1 | 3,232 | [
"ADF",
"GAMESS",
"Gaussian",
"Jaguar",
"Molpro",
"cclib"
] | ff5ca10f6e226556c7b0ed595047fe00b291a2c7a43ce07f77a29a9f1218b4e1 |
# Copyright (C) 2016
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, o... | espressopp/espressopp | src/tools/energy.py | Python | gpl-3.0 | 4,388 | [
"ESPResSo"
] | 8191f875c4d48e12b2907f2af276fa2f17ac4fe57af9c308ab8c3738836d57b5 |
# -*- coding: utf-8 -*-
# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
A "grab bag" of relatively small general-purpose utilities that don't have
a clear module/package to live in.
"""
import abc
import contextlib
import difflib
import inspect
import json
import os
import signal
import sys
import ... | aleksandr-bakanov/astropy | astropy/utils/misc.py | Python | bsd-3-clause | 30,026 | [
"ESPResSo"
] | 8d573dcdfe2e7a090aea9795a2a6ddd6d60327c1eb46504a01ce29b22b046db5 |
#Guru
#takes fasta alignments, a distance metric and builds neighbor joining trees
import os, sys
from galaxy import eggs
from galaxy.tools.util import hyphy_util
#Retrieve hyphy path, this will need to be the same across the cluster
tool_data = sys.argv.pop()
HYPHY_PATH = os.path.join( tool_data, "HYPHY" )
H... | volpino/Yeps-EURAC | tools/hyphy/hyphy_dnds_wrapper.py | Python | mit | 1,959 | [
"Galaxy"
] | a95b241297594a5b0a9766a4ce3b7ff6ca70af33525af19692b2f0a61f9ccf0b |
'''
High-level editor interface that communicates with underlying editor (like
Espresso, Coda, etc.) or browser. Basically, you should call set_context(obj)
method to set up undelying editor context before using any other method.
This interface is used by zen_actions.py for performing different
actions like Expand ab... | Bruno-sm/fguess | training_files/Python/zen_editor.py | Python | gpl-3.0 | 11,683 | [
"ESPResSo"
] | 71b21fe54f5d06abb99d9a8c36bce1290eee4b812de4863eacccef9915354765 |
#!/usr/bin/env python2.7
import sys
import amr
from amr import *
import amr_parser
from amr_parser import *
import amr_fragment
from amr_fragment import *
from collections import deque, defaultdict
from re_utils import extract_patterns, delete_pattern
class AMREdge(object):
def __init__(self, label, graph, h_node,... | masterkeywikz/seq2graph | scripts/amr_graph.py | Python | mit | 49,613 | [
"VisIt"
] | 78897b1b50bc5632507623c8b7f7bd48a4dc877d2cbbe0fd46974bc44ca3ce90 |
# 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 | mol_dqn/experimental/optimize_qed_t.py | Python | apache-2.0 | 9,688 | [
"RDKit"
] | 2f2464f517ebbbe1034b5eb7f7bdfbc3f606f7fbdcb9e10db2b472b265a34190 |
# -*- coding: utf-8 -*-
"""
Created on Sun Jun 24 20:53:29 2018
@author: butenko
"""
#adapt_mesh is the manager function (called in Launcher)
import h5py #testing
import time as time_lib
from dolfin import *
from pandas import read_csv
from tissue_dielectrics import DielectricProperties
import numpy as np
impo... | andreashorn/lead_dbs | ext_libs/OSS-DBS/OSS_platform/Mesh_adaption_hybrid.py | Python | gpl-3.0 | 47,682 | [
"NEURON"
] | e6fca0bef0e1860d77d239ec302d7ea25b47a415cfcae583f24cbc3c2882d44d |
# -*- coding: utf-8 -*-
# ------------------------------------------------------------
# streamondemand.- XBMC Plugin
# Canale per I Cavalieri Dello Zodiaco
# http://blog.tvalacarta.info/plugin-xbmc/streamondemand.
# ------------------------------------------------------------
import re
from core import config
from co... | orione7/Italorione | channels/saintseiya.py | Python | gpl-3.0 | 8,833 | [
"CRYSTAL"
] | 0bc8e455eb3dd59c1191ed7efcd89eb492f306c2dcc4a8f5ee03b84cfdb826fe |
import vtk
import os
import os.path
from vis.vtkpoly import VtkPolyModel
from vis.vtkvol import VtkVolumeModel
from IO.obj import OBJReader
class VtkIO:
def __get_reader(self, file_extension):
'''Returns a reader that can read the file type having the provided extension. Returns None if no such reader.'''
lo... | zibneuro/brainvispy | IO/vtkio.py | Python | bsd-3-clause | 1,198 | [
"VTK"
] | 679d54fdcc51cec42d71deab550becf354125e67b29e6e97310d9f18fd1183a5 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import logging
import trimeshpy
from trimeshpy.trimesh_vtk import TriMesh_Vtk
from trimeshpy.trimeshflow_vtk import TriMeshFlow_Vtk
def main():
# Test files
file_name = trimeshpy.data.brain_lh
logging.basicConfig(level=logging.DEBUG)
# Load VTK surface
... | StongeEtienne/trimeshpy | examples/visu_test.py | Python | mit | 1,442 | [
"VTK"
] | 103321e01cac2a05effa83276876a4b9447a08c688d498e67c1b5744b3dbc06e |
# Copyright (C) 2009 by Eric Talevich (eric.talevich@gmail.com)
# Based on Bio.Nexus, copyright 2005-2008 by Frank Kauff & Cymon J. Cox.
# 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 pa... | poojavade/Genomics_Docker | Dockerfiles/gedlab-khmer-filter-abund/pymodules/python2.7/lib/python/Bio/Phylo/NewickIO.py | Python | apache-2.0 | 12,742 | [
"Biopython"
] | 83c7c4cbaeea70fecabff6224e9df6a6ff024880755b5a455109dfe9a2732b47 |
#!/usr/bin/env python
# test_cursor.py - unit test for cursor attributes
#
# Copyright (C) 2010-2011 Daniele Varrazzo <daniele.varrazzo@gmail.com>
#
# psycopg2 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 Foun... | EricNeedham/assignment-1 | venv/lib/python2.7/site-packages/psycopg2/tests/test_cursor.py | Python | mit | 19,167 | [
"GULP"
] | 4087bb65ea5c793522a24213ae9f2ca4f2f81215f04984312ea2be38f85d4c5a |
"""Configuration file for eruption scenario
Tephra modelling validation worksheet
Scenario Name: Mount Mayon 2000 (VEI3_eruption)
Run Date: 2010_05_18
Run number:1 ... | GeoscienceAustralia/PF3D | testing/mayon.py | Python | gpl-3.0 | 3,497 | [
"Gaussian"
] | 8f1bc2e36e5fb9f44694a6ec7f16ea47f6755c15270961fad669f05336585264 |
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Mathieu Blondel <mathieu@mblondel.org>
# Olivier Grisel <olivier.grisel@ensta.org>
# Andreas Mueller <amueller@ais.uni-bonn.de>
# Eric Martin <eric@ericmart.in>
# Giorgio Patrini <giorgio.patrini@anu.edu.au>
# ... | sergeyf/scikit-learn | sklearn/preprocessing/_data.py | Python | bsd-3-clause | 118,327 | [
"Gaussian"
] | 9f30bfec04c5c8cb5660316a8091ee2a6f2d076709ef49706eb3d0abcac1b208 |
########################################################################
# $Id$
########################################################################
""" Definitions of a standard set of pilot commands
Each commands is represented by a class inheriting CommandBase class.
The command class constructor takes... | sposs/DIRAC | WorkloadManagementSystem/PilotAgent/pilotCommands.py | Python | gpl-3.0 | 29,040 | [
"DIRAC"
] | 925ce1a7b861abb294f1b8f19172911c98e59f63be32406227fa3e6cdbd553d5 |
#!/usr/bin/env python
from sys import argv, exit
from getopt import getopt, GetoptError
## @package nccmp
## Compares NetCDF files by absolute max norms of difference of variables
##
## Without options,
## \code
## nccmp.py foo.nc bar.nc
## \endcode
## compares all the variables in \c foo.nc and \c bar.nc.
##
## Opt... | JohannesFeldmann/pism | util/nccmp.py | Python | gpl-2.0 | 4,477 | [
"NetCDF"
] | 4c365de852036fd2110cfbda4e2c05bcbd84708776ce41d100df7b9ebb420c06 |
#! CCSD dipole with user-specified basis set
import psi4
h2o = psi4.geometry("""
0 1
H
O 1 0.957
H 2 0.957 1 104.5
""")
psi4.set_options({'freeze_core': 'false'})
psi4.basis_helper("""
# Sadlej-pVTZ
spherical
****
H 0
S 4 1.00
33.8650140000 0.0060680000
5.0947880000 0.045... | amjames/psi4 | samples/python/cc54/input.py | Python | lgpl-3.0 | 2,897 | [
"Psi4"
] | ff851c7c7f859efed365094aaf9168e480afa2db31d2a1db31199bd7859e2149 |
from vtk import *
import numpy as np
from matplotlib import pyplot as plt
import itkutilities
import sys
xwidth = 256
ywidth = 256
zwidth = 256
xscale = 1
yscale = 1
zscale = 1
input_file_name = sys.argv[1]
output_file_name = sys.argv[2]
reader = vtkPolyDataReader()
reader.SetFileName(input_file_name)
reader.ReadAl... | velizarefremov/vascularnetworks | createBifurcs.py | Python | gpl-3.0 | 1,907 | [
"VTK"
] | a7eddeb5caf47b57953e583595d0f5b04477e0d5e5e953d464970a43edb317ff |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | Laurawly/tvm-1 | python/tvm/contrib/cutlass/build.py | Python | apache-2.0 | 13,892 | [
"VisIt"
] | 93ef9e4c6cbda44967fa3596e69ce28af555f2dacb206b8c2f1a78a1f9f1f8ae |
#!/usr/bin/env python
# -*- coding:utf-8 -*-
# @author:Hieda no Chiaki <i@wind.moe>
import codecs
import json
import logging
import os
import sys
from src.init import system
logging.basicConfig(level=logging.INFO)
def getID3(file):
"""获取音乐文件的ID3"""
if system() == "Windows":
f = os.path.split(os.path... | forblackking/PyBiu | src/id3.py | Python | apache-2.0 | 2,443 | [
"MOE"
] | f1a0db9e3c9f918062608d125c46227151d617e16eddeb619943051563f37459 |
#!/usr/bin/python
import re
import sys
print "require(OpenMx)"
print "#################################################"
print "# THIS IS AN AUTOGENERATED FILE"
print "# ANY CHANGES MADE TO THIS FILE WILL NOT BE SAVED"
print "#################################################"
p = re.compile("\.\. code-block:: r.*?\r?\n... | mhunter1/OpenMx | inst/tools/sphinxToR.py | Python | apache-2.0 | 448 | [
"OpenMX"
] | 3c5f9e1186b20ef5720f7da92447753c69fbf722de32e53a0478fece3704c78c |
# c: 14.04.2008, r: 14.04.2008
from sfepy.fem.periodic import *
filename_mesh = 'database/tests/plane.mesh'
material_2 = {
'name' : 'm',
'mode' : 'here',
'region' : 'Omega',
'K' : [[3.0, 0.1], [0.3, 1.0]],
}
field_1 = {
'name' : 'pressure',
'dim' : (1,1),
'domain' : 'Omega',
'bases' :... | certik/sfepy | tests/test_assembling.py | Python | bsd-3-clause | 3,875 | [
"VTK"
] | e8c30f8ed25b7f3086dac65837ba5c0dcc0aa54903ecc8119af57cee5e8f0aa9 |
"""
canny.py - Canny Edge detector
Reference: Canny, J., A Computational Approach To Edge Detection, IEEE Trans.
Pattern Analysis and Machine Intelligence, 8:679-714, 1986
Originally part of CellProfiler, code licensed under both GPL and BSD licenses.
Website: http://www.cellprofiler.org
Copyright (c) 2003-2009 M... | rjeli/scikit-image | skimage/feature/_canny.py | Python | bsd-3-clause | 11,196 | [
"Gaussian"
] | 5cfa3da678da711603205b46683b8c737529e92852c0c05c13741d7ce236d094 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
import copy
import glob
import json
import os
import unittest
import sys
from pymatgen import Molecule
from pymatgen.io.qchem import QcTask, QcInput, QcOutput, QcNucVel... | xhqu1981/pymatgen | pymatgen/io/tests/test_qchem.py | Python | mit | 85,888 | [
"pymatgen"
] | 2b7882d3b19a4fa318c17c8539392e3a03f62437242a0189fb459ff0ac3cf9a6 |
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