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## Automatically adapted for numpy.oldnumeric Jun 27, 2008 by -c
# $Id$
#
# Copyright (C) 2001-2008 greg Landrum and Rational Discovery LLC
# All Rights Reserved
#
"""
"""
from __future__ import print_function
import numpy
import random
from rdkit.ML.DecTree import QuantTree, ID3
from rdkit.ML.InfoTheory import e... | jandom/rdkit | rdkit/ML/DecTree/BuildQuantTree.py | Python | bsd-3-clause | 12,053 | [
"RDKit"
] | 58a185d9cb17621b38cfc25c342e819997b1f40de7daca8638e611628d9839cb |
#!/usr/bin/python2.4
# Copyright (c) 2011 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
'''Collections of messages and their translations, called cliques. Also
collections of cliques (uber-cliques).
'''
import types
f... | paul99/clank | tools/grit/grit/clique.py | Python | bsd-3-clause | 16,436 | [
"xTB"
] | fc97e977162c7df6d2c6f780d1f9e30dead1080fbc52a8f63b20ce2e0c5c3ec6 |
from __main__ import vtk, qt, ctk, slicer
import string
class FeatureDescriptionLabel(qt.QLabel):
def __init__(self, parent=None):
super(FeatureDescriptionLabel, self).__init__(parent)
self.setFixedWidth(300)
self.setFrameStyle(qt.QFrame.Box)
self.setWordWrap(True)
def setDescription(self... | acil-bwh/SlicerCIP | Scripted/CIP_LesionModel/FeatureWidgetHelperLib/FeatureDescriptionLabel.py | Python | bsd-3-clause | 15,593 | [
"VTK"
] | 89766709464a760b57c05b4951bc66f78bcdc6ba10ccf3ce2d8fcdec9b1c0ff5 |
"""A Martel format to parse the output from transfac.
Formats:
format Format for a whole file.
"""
import warnings
warnings.warn("Bio.expressions was deprecated, as it does not work with recent versions of mxTextTools. If you want to continue to use this module, please get in contact with the Biopython d... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/expressions/transfac.py | Python | apache-2.0 | 2,579 | [
"Biopython"
] | 743a39156440213abced5d2182eeea3046190fec97d624b36b59879c956f19d6 |
#!/usr/bin/env python
"""
Get status of the available Storage Elements
Usage:
dirac-dms-show-se-status [<options>]
Example:
$ dirac-dms-show-se-status
Storage Element Read Status Write Status
DIRAC-USER Active Active
IN2P3-disk Active... | ic-hep/DIRAC | src/DIRAC/DataManagementSystem/scripts/dirac_dms_show_se_status.py | Python | gpl-3.0 | 3,318 | [
"DIRAC"
] | c3ef8641f699ff07eaf325afdec3dfb385e7c2f03d2b4adf2263ad62e43c7cba |
'''
This script will format masscan results from file ready for import
into elastic search db
Argument 1:
e|k|c. e represents erase scan result file after import
k means keep file
c means csv which can be used in a logstash fashion with elk
'''
import os
from os import path
import re
import datetime
from ScanRecord imp... | muttiopenbts/nazar | data-import.py | Python | gpl-2.0 | 7,739 | [
"Elk"
] | b1c7776b8d6a14a3a66f26c631769d9f3c565c8976ae062f92d8bbc1eb260033 |
#!/usr/local/bin/yade-trunk -x
# -*- encoding=utf-8 -*-
# CWBoon 2015
# Uses the following algorithm:
# CW Boon, GT Houlsby, S Utili (2012). A new algorithm for contact detection between convex polygonal and polyhedral particles in the discrete element method. Computers and Geotechnics 44, 73-82.
#Display is saved... | cosurgi/trunk | examples/PotentialBlocks/cubePBscaled.py | Python | gpl-2.0 | 13,634 | [
"ParaView",
"VTK"
] | 0bc8629d913f428ce2efee3322686309a2d2082f674afd94a6745681c87f4acf |
from datetime import date
from dateutil.relativedelta import MO, TH
from dateutil.relativedelta import relativedelta as rd
from holidays import HolidayBase
class NYCHolidays(HolidayBase):
def __init__(self, **kwargs):
self.country = 'US'
HolidayBase.__init__(self, **kwargs)
def _populate(self... | CityOfNewYork/NYCOpenRecords | app/lib/__init__.py | Python | apache-2.0 | 3,891 | [
"COLUMBUS"
] | ce56eb4b41b10874c9e5a8792208b7b6ea446fbadbf99cccdc04a599a8b8f215 |
from datetime import datetime
import logging
import os
from pathlib import Path
import re
import subprocess
from tqdm import tqdm
import warnings
import cftime
import netCDF4
import yaml
from sqlalchemy import create_engine
from sqlalchemy import (
Column,
Integer,
String,
Text,
Boolean,
DateT... | OceansAus/cosima-cookbook | cosima_cookbook/database.py | Python | apache-2.0 | 29,832 | [
"NetCDF"
] | a0c86c34661d957e4e71c6ed2aab5efbeeffe2a23a9c6d989d8e062760c7675e |
#__docformat__ = "restructuredtext en"
# ******NOTICE***************
# optimize.py module by Travis E. Oliphant
#
# You may copy and use this module as you see fit with no
# guarantee implied provided you keep this notice in all copies.
# *****END NOTICE************
# A collection of optimization algorithms. Version 0... | aeklant/scipy | scipy/optimize/optimize.py | Python | bsd-3-clause | 115,217 | [
"Gaussian"
] | 0aadb5e2b9525ca16b7e848c577b5a5b61e19a19f3aa692eb21fc11c0ef0105b |
# -*- coding: utf-8 -*-
"""
Unit tests for instructor.api methods.
"""
import datetime
import ddt
import functools
import random
import pytz
import io
import json
import shutil
import tempfile
from urllib import quote
from django.conf import settings
from django.contrib.auth.models import User
from django.core import ... | ampax/edx-platform | lms/djangoapps/instructor/tests/test_api.py | Python | agpl-3.0 | 217,955 | [
"VisIt"
] | 3a05b570bc19bcc40dd410f4f4fe06d4cfaa4a04c0e01b5862ee11e770d21c3f |
'''
package docstring
author: Jyh-Miin Lin (Jimmy), Cambridge University
address: jyhmiinlin at gmail.com
Created on 2013/1/21
================================================================================
This file is part of pynufft.
pynufft is free software: you can redistribute it and/or modify
it under the t... | jyhmiinlin/cineFSE | CsTransform/Copy of pynufft.py | Python | gpl-3.0 | 105,189 | [
"Mayavi"
] | 2cdb8328999abe58f5600a92323730f2e156ace42dcc1aecffc1ff7dae55e926 |
# Copyright (C) 2003 CAMP
# Please see the accompanying LICENSE file for further information.
"""Grid transformers.
This module defines tools for doing interpolations/restrictions between
differentt uniform 3D grids.
"""
from __future__ import division
from math import pi
import numpy as np
from gpaw import debug
... | robwarm/gpaw-symm | gpaw/transformers.py | Python | gpl-3.0 | 4,809 | [
"GPAW"
] | d21cf41fafed767c419d95007d7413b301cacd9bc7dda4540f0decf596a8e7f6 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# OpenAddress.py is a Python script that summarizes a unique list of street names with their asscociated
# cities and zip codes from csv files you can download from the Open Address project (https://openaddresses.io/).
# Download a region and place this script into a folder ... | johnhickok/streetzip | OpenAddress.py | Python | gpl-2.0 | 1,641 | [
"VisIt"
] | a70c5be213a2c2a9a83e68d1a8aba3ad8c0676fa84cf38fd0d66e7a564dbbd1c |
"""
Put Canvas specific configuration here.
Note that this project has three different configuration files:
/var/canvas/website/settings.py
That is where we keep all Django specific settings.
/var/canvas/common/configuration.py
That is where we keep AWS and infrastructure related settings. No... | canvasnetworks/canvas | website/canvas/knobs.py | Python | bsd-3-clause | 5,468 | [
"VisIt"
] | 28483c944d9c8148d12ccd3f07ec2c5e4e82c53b93d773322c7830846ddbaf33 |
#
# This file is part of Bakefile (http://bakefile.org)
#
# Copyright (C) 2008-2013 Vaclav Slavik
#
# 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... | vslavik/bakefile | src/bkl/model.py | Python | mit | 32,477 | [
"VisIt"
] | a7ff27e6afe2530c9ecba960d3e69dc1520b67636e326ab86dfb29dfd91faba3 |
from kivy.app import App
from time import time
from kivy.uix.button import Button
from kivy.uix.scrollview import ScrollView
from kivy.uix.behaviors import ButtonBehavior
from kivy.uix.label import Label
from random import randrange
from kivy.metrics import cm
from kivy.lang import Builder
from kivy.uix.recycleview.vie... | Bakterija/log_fruit | src/app_modules/widgets/databox/recycleview_example.py | Python | unlicense | 5,302 | [
"VisIt"
] | 46accf61e7a59273bcefe06fe1604e090756012a42e709e1ed26dc7bfc81598f |
import numpy as np
class Scheduler:
def __init__(self,first_date,presenters,avoid=[]):
# Options.
self.avoid=avoid
self.next_date=first_date
self.presenters=presenters
# Hard code.
self.months = ["Jan.","Feb.","March","April","May","June","July","August","Sept.","Oct.","Nov.","Dec."]
sel... | bbusemeyer/busempyer | busempyer/schedule.py | Python | gpl-2.0 | 1,501 | [
"Brian"
] | 4aabb6e9380ee62ddb0c36f600dc821936bbf3f4b90df78fae194ab9c8f25484 |
#
# 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... | mistercrunch/airflow | airflow/www/utils.py | Python | apache-2.0 | 23,576 | [
"VisIt"
] | 15eaea74617862de213a93cdf1d23507ff47e7997bd1054caa9bcec78b890496 |
#
# 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 us... | spark-test/spark | python/pyspark/ml/classification.py | Python | apache-2.0 | 117,534 | [
"Gaussian"
] | 3e8798ee809e7e378a29605322967e849e4fa7520faf19a75b604ca2a05254bf |
# -*- coding: utf-8 -*-
from __future__ import absolute_import
from PyQt5 import QtCore, QtWidgets
import gr
from qtgr import GRWidget
import csv
from util.logger import Logger
import sys
from statistics.pdf import PDF, Kernels
import numpy as np
import os
logger = Logger("gui.pdf_widget")
logger.setstream("defaul... | sciapp/pyMolDyn | src/gui/pdf_widget.py | Python | mit | 10,235 | [
"Gaussian"
] | c53f8417a58887170359289a598d224a7160d3eb5a5dc073554ab3f7b84e0d45 |
import six
import unittest
from restkiss.exceptions import HttpError, NotFound, MethodNotImplemented
from restkiss.preparers import Preparer, FieldsPreparer
from restkiss.resources import Resource
from restkiss.utils import json
from .fakes import FakeHttpRequest, FakeHttpResponse
class GenericResource(Resource):
... | CraveFood/restkiss | tests/test_resources.py | Python | bsd-3-clause | 12,204 | [
"Galaxy"
] | fc75951aa01ff9648cd8c304597b730825be4b7589643229af29c04993c4f2e2 |
#!/bin/env python
from config import DATA_DIR, LATS, LONS, GRIDS, MONTHS_YEAR
from netCDF4 import Dataset
from local_utils import get_month_slice, get_grid_subset, days_year, get_day_of_year_index, is_leap_year
import numpy as np
from mpi4py import MPI
import argparse
import sys
comm = MPI.COMM_WORLD
mpi_rank = com... | abuddenb/agu2015 | calc_daily_mean_current.py | Python | mit | 4,778 | [
"NetCDF"
] | 6428539100e0030f629d32e2ba3e06f5b18612fa99a70da459431b66b999627f |
#!/usr/bin/env python
# vim: set fileencoding=utf-8 :
# Elie Khoury <Elie.Khoury@idiap.ch>
# Fri Aug 30 11:53:40 CEST 2013
#
# Copyright (C) 2012-2013 Idiap Research Institute, Martigny, Switzerland
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public ... | guker/spear | spear/tools/IVector.py | Python | gpl-3.0 | 16,016 | [
"Gaussian"
] | 70f1e64616b940e96d445fb11f4b799d9a04e8b06d5d746e97408a813f0f1684 |
#!/usr/bin/env python
#------------------------------------------------------------------------------
#
# This tool tries to smooth mask edges by blurring and thresholding.
# While blur makes the edges smooth the thresholding produces new binary
# mask.
#
# For blurring is made by the (separated) Gaussian convo... | DREAM-ODA-OS/tools | imgproc/smooth_mask.py | Python | mit | 5,082 | [
"Gaussian"
] | 2b1fd6a39769d56dc21785a36e8edc9383c39939607a6de28dbe7a90ff1fbc88 |
#!/usr/bin/env python
# This simple example shows how to do basic rendering and pipeline
# creation.
import vtk
def main():
colors = vtk.vtkNamedColors()
# Set the background color.
bkg = map(lambda x: x / 255.0, [26, 51, 102, 255])
colors.SetColor("BkgColor", *bkg)
# This creates a polygonal c... | lorensen/VTKExamples | src/Python/GeometricObjects/CylinderExample.py | Python | apache-2.0 | 2,160 | [
"VTK"
] | d5562dac41040204b01d3cf4bac3206e6a96a3d8d322a813dd5a4204347a56de |
# being a bit too dynamic
# pylint: disable=E1101
from __future__ import division
from collections import namedtuple
from distutils.version import LooseVersion
import re
import warnings
import numpy as np
import pandas.compat as compat
from pandas.compat import lrange, map, range, string_types, zip
from pandas.error... | GuessWhoSamFoo/pandas | pandas/plotting/_core.py | Python | bsd-3-clause | 128,312 | [
"Gaussian"
] | 2e2953c6b8864a15619eaa1970280c1da1473f327e6cfa225c54b6e1110bae85 |
#A* -------------------------------------------------------------------
#B* This file contains source code for the PyMOL computer program
#C* Copyright (c) Schrodinger, LLC.
#D* -------------------------------------------------------------------
#E* It is unlawful to modify or remove this copyright notice.
#F* -------... | gratefulfrog/lib | python/pymol/selecting.py | Python | gpl-2.0 | 6,826 | [
"PyMOL"
] | 10e3d62d3f7b5369d0019047cb19ca63f7e70be1dea54190c319c0826eadf016 |
# GromacsWrapper: formats.py
# Copyright (c) 2009-2010 Oliver Beckstein <orbeckst@gmail.com>
# Released under the GNU Public License 3 (or higher, your choice)
# See the file COPYING for details.
"""
:mod:`gromacs.formats` -- Accessing various files
=================================================
This module contai... | pslacerda/GromacsWrapper | gromacs/formats.py | Python | gpl-3.0 | 1,338 | [
"Gromacs"
] | c282e5d2830cf65a6bb3c7af8c6502214a3f51b24b63dda6313f9b585acc1194 |
from __future__ import division
from pylab import *
from scipy.special.orthogonal import p_roots
def gauss1(f, n):
"""gaussian quadrature for weight=1 on (-1,1)"""
[x,w] = p_roots(n+1)
result = 0
for i in range(n+1):
result = result + w[i]*f(x[i])
return result
def gauss(f, a, b, n... | startupjing/MathTools | GaussianQuadrature.py | Python | mit | 589 | [
"Gaussian"
] | 6f6a6426999885edb313a0a5f7028a826b40850a9fdd077df6f7cee45149464f |
#!/usr/bin/python3
# -*- coding: utf-8 -*-
""" --- Day 9: All in a Single Night ---
Every year, Santa manages to deliver all of his presents in a single night.
This year, however, he has some new locations to visit;
his elves have provided him the distances between every pair of locations.
He can start and end at an... | coolharsh55/advent-of-code | 2015/day09/all_in_a_single_night_part_2.py | Python | mit | 5,896 | [
"VisIt"
] | a33779df9b18e95fc3b94ad26beb5767509a253192277e2963b085b6bb4a333d |
#
# Original authors: Richard Hall and Guillaume Godin
# 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.
#
#
# Richard hall 2017
# IFG main code
# Guillaume Godin 2017
# refine out... | bp-kelley/rdkit | Contrib/IFG/ifg.py | Python | bsd-3-clause | 4,145 | [
"RDKit"
] | 71dd96489ef477eb9225dc4b38006bbff78f67d42b82bcae9d0f820756d4ccb1 |
# Copyright 2020 The Google Earth Engine Community 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 ... | google/earthengine-community | samples/python/guides/images14.py | Python | apache-2.0 | 1,732 | [
"Gaussian"
] | 572deb96fe48de3fab7eb820ff0fe5f0f1c66e8ac365e70578b61aa22b475dc7 |
# Copyright 2000-2002 Brad Chapman.
# Copyright 2004-2005 by M de Hoon.
# Copyright 2007-2014 by Peter Cock.
# 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.
"""Provides objects ... | poojavade/Genomics_Docker | Dockerfiles/gedlab-khmer-filter-abund/pymodules/python2.7/lib/python/Bio/Seq.py | Python | apache-2.0 | 86,490 | [
"Biopython"
] | 167d3442949c6c8c0d4f23cd614ff496f8ef9a640f8dcece3cdabb51edb9e415 |
"""
Recurrent layers.
TODO: write more documentation
"""
__docformat__ = 'restructedtext en'
__authors__ = ("Razvan Pascanu "
"KyungHyun Cho "
"Caglar Gulcehre ")
__contact__ = "Razvan Pascanu <r.pascanu@gmail>"
import numpy
import copy
import theano
import theano.tensor as TT
# Nicer i... | bartvm/groundhog-private | groundhog/layers/rec_layers.py | Python | bsd-3-clause | 48,042 | [
"Gaussian"
] | 57f2a2ddfa3733449742afaa2891cb13904fcc5a14becd8d9c072737c83de728 |
# coding: utf-8
from __future__ import division, unicode_literals
"""
This module implements more advanced transformations.
"""
__author__ = "Shyue Ping Ong, Stephen Dacek"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "1.0"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyuep@gmail.com"
__... | Dioptas/pymatgen | pymatgen/transformations/advanced_transformations.py | Python | mit | 24,206 | [
"pymatgen"
] | a30b34e3f4da912edd2a1c1c15dd0e93226ad59376197a458deebba1de9ce9d1 |
import itertools
import pandas as pd
import mdtraj as md
import glob
import simtk.unit as u
import numpy as np
debye = 3.33564E-30 * u.coulomb * u.meter # simtk.unit debye is messed up, using http://en.wikipedia.org/wiki/Debye
ke = 8.98755E9 * u.meter / u.farad # Coulomb constant (http://en.wikipedia.org/wiki/Coulom... | choderalab/LiquidBenchmark | src/misc/onsager.py | Python | gpl-2.0 | 1,069 | [
"MDTraj"
] | e6db5dd6298b97b56c6d572c6bb8f29beecddd2240264642f0e85eac665f889f |
import numpy as np
from gpaw.xc.functional import XCFunctional
class LDA(XCFunctional):
def __init__(self, kernel):
self.kernel = kernel
XCFunctional.__init__(self, kernel.name)
self.type = kernel.type
def calculate(self, gd, n_sg, v_sg=None, e_g=None):
if gd is not self.gd:
... | qsnake/gpaw | gpaw/xc/lda.py | Python | gpl-3.0 | 1,530 | [
"GPAW"
] | 3ade20a471bd3d1087acf1678036e479efc2df9bade2939f34afeaef6b74618c |
"""
perform exon-level counting using DEXSeq
"""
import sys
import os
from bcbio.utils import R_sitelib, file_exists, safe_makedir, which
from bcbio.distributed.transaction import file_transaction
from bcbio.provenance import do
from bcbio import bam
from bcbio.log import logger
import bcbio.pipeline.datadict as dd
... | lbeltrame/bcbio-nextgen | bcbio/rnaseq/dexseq.py | Python | mit | 4,425 | [
"BWA"
] | c786a224eee7bdda5301f8b2e7e49851128dc922e661b9f9c616b952342cd3b2 |
# -*- coding: utf-8 -*-
################################################################################
# Copyright 2014, The Open Aggregator
# GNU General Public License, Ver. 3 (see docs/license.txt)
################################################################################
"""Mean-Size Model
In Mean-Size ... | jrising/open-estimate | models/mean_size_model.py | Python | gpl-3.0 | 6,870 | [
"Gaussian"
] | 23c1ab91447327ef6cb2e8ef921773f3cc9e80cc70fc23b80fe781b27a9d5910 |
#!/bin/env python3
# AUTHORS:
# Hakan Ozadam
# Rachel Brown
#
# Moore Laboratory
# UMASS Medical School / HHMI
# RNA Therapeutics Institute
# Albert Sherman Center, ASC4-1009
# 368 Plantation Street
# Worcester, MA 01605
# USA
#
###########################... | hakanozadam/bal | main.py | Python | gpl-2.0 | 1,125 | [
"pysam"
] | 6045f1e5d10c85fa1b229694973bc36712dfa1e396c770eff0dd04b8ff8b06f2 |
# -*- coding: utf-8 -*-
"""Convert the `CausalBionet (CBN) <http://causalbionet.com>`_ for Hipathia."""
import json
import os
import zipfile
from urllib.request import urlretrieve
import click
from pyobo.cli_utils import verbose_option
from tqdm import tqdm
import pybel
import pybel.grounding
HERE = os.path.dirnam... | pybel/pybel | notebooks/hipathia_demo/cbn/_convert_cbn.py | Python | mit | 1,211 | [
"Pybel"
] | 8e436fbc6be890a02817295dd88211415effdc86956f5e6f046c6aa6b4ebee78 |
import numpy as np
from ase.units import Hartree
from Scientific.IO.NetCDF import NetCDFFile
from ase.lattice.spacegroup import Spacegroup
from gpaw.wavefunctions.pw import PWDescriptor
class ETSFWriter:
def __init__(self, filename='gpaw', title='gpaw'):
if not filename.endswith('-etsf.nc'):
... | qsnake/gpaw | gpaw/io/etsf.py | Python | gpl-3.0 | 8,576 | [
"ASE",
"DIRAC",
"GPAW",
"NetCDF"
] | 0a18df702cd1977743e45f29e56eb9374b0aa52c8ba2fea9c5aa09a553279f82 |
''' TaskManager contains WorkflowsTasks and RequestTasks modules, for managing jobs and requests tasks
'''
__RCSID__ = "$Id$"
COMPONENT_NAME = 'TaskManager'
import time, types, os
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Core.Security.ProxyInfo ... | Sbalbp/DIRAC | TransformationSystem/Client/TaskManager.py | Python | gpl-3.0 | 23,360 | [
"DIRAC"
] | eef6af195ec578fec6e7b3a4d2e6f94129c6e66e19a516e71880fd219c8ba2ca |
import os
import itertools
os.chdir('c:/mypysces/kraken')
## os.chdir('/home/bgoli/mypysces/kraken')
## import pysces
from . import *
## from Kraken import *
# investigate using vstack with type/range checking
def concatenateArrays(array_list):
output = None
for arr in range(len(array_list)):
if ... | bgoli/pysces | pysces/kraken/controllers/kraken_continuation_eigen.py | Python | bsd-3-clause | 11,564 | [
"Mayavi",
"PySCeS",
"VTK"
] | ac70bbebe96aa8c88ff68f77f4c4223ab286f408ef1c77228b43a232a9bd3e54 |
# Draw samples from the distribution
loc, scale = 0., 1.
s = np.random.laplace(loc, scale, 1000)
# Display the histogram of the samples, along with
# the probability density function:
import matplotlib.pyplot as plt
count, bins, ignored = plt.hist(s, 30, normed=True)
x = np.arange(-8., 8., .01)
pdf = np.exp(-abs(x-l... | platinhom/ManualHom | Coding/Python/numpy-html-1.10.1/reference/generated/numpy-random-laplace-1.py | Python | gpl-2.0 | 490 | [
"Gaussian"
] | edf923a4ad3bee04fce51c00c1fcab7ef015fb96331996584f41a5ba831c73ca |
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2014,2015, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public version 2.1 or later. ... | ghutchis/cclib | test/method/testnuclear.py | Python | lgpl-2.1 | 1,500 | [
"cclib"
] | c173a94c49669344d80e900e73ea451b71a3a4d4cd9449a6461b6a82d3815724 |
"""
API operations for for querying and recording user metrics from some client
(typically a user's browser).
"""
#TODO: facade or adapter to fluentd
import datetime
from galaxy import exceptions
from galaxy.web import require_admin
from galaxy.web import _future_expose_api as expose_api
from galaxy.web import _futur... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/webapps/galaxy/api/metrics.py | Python | gpl-3.0 | 4,524 | [
"Galaxy"
] | 9fff4a2a8f0b0f28badeb8f10d7203a6c0bdb9c69d9c5d98cfd7304e4beeea32 |
"""
This is only meant to add docs to objects defined in C-extension modules.
The purpose is to allow easier editing of the docstrings without
requiring a re-compile.
NOTE: Many of the methods of ndarray have corresponding functions.
If you update these docstrings, please keep also the ones in
core/fromnum... | tdsmith/numpy | numpy/add_newdocs.py | Python | bsd-3-clause | 218,580 | [
"Brian"
] | c85c19f8dadb79f47cf0085c4d2ed2e4169f0ba579a0378189f54c99ed2c9a74 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2005-2013 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## 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 Softw... | tiagocardosos/stoq | stoqlib/domain/product.py | Python | gpl-2.0 | 63,417 | [
"VisIt"
] | 7349e5cbfec37046e6970284577fb3d1e5fc84db94188685e48981f2a8ade7b8 |
#!/usr/bin/env python
# Copyright (c) 2014 Pivotal Software, Inc. All Rights Reserved
#
# This software contains the intellectual property of Pivotal Software, Inc.
# or is licensed to Pivotal Software, Inc. from third parties. Use of this
# software and the intellectual property contained therein is expressly
# limit... | lintzc/gpdb | gpMgmt/bin/gppylib/operations/persistent_rebuild.py | Python | apache-2.0 | 66,629 | [
"VisIt"
] | 348e4df9b50ac4c410763321f527590f6ecdd30c7d519000b965bec5456fa7a6 |
#
#@BEGIN LICENSE
#
# uhfno by Psi4 Developer, a plugin to:
#
# PSI4: an ab initio quantum chemistry software package
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the Li... | lothian/uhfno | pymodule.py | Python | gpl-2.0 | 1,720 | [
"Psi4"
] | 22df0749c3474cfdffdd3ca8dbd85121914df91a46dfe7bb553ac8f3abd55476 |
""" DIRAC File Catalog components
"""
| DIRACGrid/DIRAC | src/DIRAC/DataManagementSystem/DB/FileCatalogComponents/__init__.py | Python | gpl-3.0 | 38 | [
"DIRAC"
] | f5c5de899c74a08a46503355ff101a939793445f1082ef070ed2d595bded7250 |
import supybot.utils as utils
from supybot.commands import *
import supybot.plugins as plugins
import supybot.ircutils as ircutils
import supybot.callbacks as callbacks
import requests
import os.path
import psycopg2
from random import shuffle
class TagproTestMap(callbacks.Plugin):
"""This plugin allows you to cre... | steppin/some_bot | irc/plugins/TagproTestMap/plugin.py | Python | gpl-3.0 | 7,141 | [
"VisIt"
] | d5eeff85bba019ac95588deb26f4c6b9eb71f477643961edb704dd9068fd5c7f |
#!/usr/bin/python
import unittest
import os
import random
import json
import numpy as np
from pymatgen.core.structure import Structure
from pymatgen.core.lattice import Lattice
from pymatgen.core.surface import Slab, SlabGenerator, generate_all_slabs, \
get_symmetrically_distinct_miller_indices, ReconstructionG... | johnson1228/pymatgen | pymatgen/core/tests/test_surface.py | Python | mit | 25,452 | [
"pymatgen"
] | 8e0e6c7e8cfe56f039ad91725689bcf1685598ff9d30acaa469b1ce278d502e5 |
# TODO check num_threads before testing / 8 for Cisco Server
# TODO ATTTENTION! Maybe there are some mistakes in neuron parameters!
from func import *
logger = logging.getLogger('neuromodulation')
startbuild = datetime.datetime.now()
nest.ResetKernel()
nest.SetKernelStatus({'overwrite_files': True, 'local_num_threa... | magnastrazh/NEUCOGAR | nest/GDP/scripts/neuromodulaton.py | Python | gpl-2.0 | 3,320 | [
"NEURON"
] | 8f30642852a14ef40c3806ecb4614ffd13a53ba1fb8cfc6eac69c45ad62c707f |
"""
this file does variant calling for DNAseq
"""
#============= import required packages =================
import os
import sys,subprocess
sys.stdout = os.fdopen(sys.stdout.fileno(), 'w', 0) # disable buffer so that in the log file all information is printed in order.
from f00_Message import Message
from f01_list_tr... | shl198/Pipeline | Human_GATK_vari_call/Human_GATK_DNA_vari_call.py | Python | mit | 8,046 | [
"BWA"
] | 9f66088e955c2664e6baa043dc66749793e2df4c1f58f0f05fea5ef0117b132e |
#!/usr/bin/env python
################################################################################
#
# esc_switch.py
#
# Convenience tool to switch files between QE, FHI-aims, CASTEP and pdb format.
#
################################################################################
#
# Copyright 2014 Kane O'Donnell
... | HSINWEI/physics | python/esc_switch.py | Python | gpl-3.0 | 3,328 | [
"CASTEP",
"FHI-aims"
] | 46f0beb650927f9cd78380852a8ad22d48592430c9663b65b445c983bff87475 |
# -*- coding: utf-8 -*-
from __future__ import absolute_import
from typing import List, Any
import numpy as np
from scipy.stats import entropy
from sklearn.pipeline import Pipeline
from sklearn.utils import check_random_state, issparse
from sklearn.utils.metaestimators import if_delegate_has_method
from sklearn.utils ... | TeamHG-Memex/eli5 | eli5/lime/utils.py | Python | mit | 6,513 | [
"Gaussian"
] | 587d1993212d3c84dce13f6ad41c8eea5af7910862bfe6b00f47d5dcb4260325 |
# -*- coding: utf-8 -*-
"""
trueskill
~~~~~~~~~
The video game rating system.
:copyright: (c) 2012-2013 by Heungsub Lee
:license: BSD, see LICENSE for more details.
"""
from __future__ import absolute_import
from itertools import chain, imap, izip
import math
from .backends import c... | Manwe56/trueskill-ai-contest-test-tool | trueskill/trueskill/__init__.py | Python | gpl-2.0 | 27,692 | [
"Gaussian"
] | 605cfd409675a6c4e64e8793a6e405d62b5fef216f8ea091a94fba9c25fcb38d |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#################################################################################
# LAYMAN CONSTANTS
#################################################################################
# File: constants.py
#
# Handles layman actions via the command line interfac... | jmesmon/layman | layman/constants.py | Python | gpl-2.0 | 1,493 | [
"Brian"
] | 28f34f45bcf00896a09ca936a5283dcde6962c262fba0796c17b4842fe2d1e6e |
#
# 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 us... | WeichenXu123/spark | python/pyspark/pandas/generic.py | Python | apache-2.0 | 105,677 | [
"Elk"
] | 104158496f9b460c38f6ae0eda965a337fee2947a5ba918a1799508d38bece9a |
from distutils.core import setup
setup(name='pbs', \
version='VERSION_ID (git sha COMMIT_ID)', \
description='PBS job submission and management', \
author='Brian Puchala',\
author_email='bpuchala@umich.edu',\
url='REPO_URL', \
packages=['pbs'])
| tallakahath/pbs | setup.template.py | Python | lgpl-2.1 | 281 | [
"Brian"
] | 3c9d23e00ee9b2cf8b5aa3b5ae24efaf7295b8a2d9fe5957dcc0c9716386c18a |
"""
========
briandoc
========
Sphinx extension that handles docstrings in the Numpy standard format with some
brian-specific tweaks. [1]
It will:
- Convert Parameters etc. sections to field lists.
- Convert See Also section to a See also entry.
- Renumber references.
- Extract the signature from the docstring, if i... | brian-team/brian2cuda | brian2cuda/sphinxext/briandoc.py | Python | gpl-2.0 | 9,577 | [
"Brian"
] | b8b08da6c903d663d51fe8177376fb3402f06c53232327c7ec361bd18f24bd81 |
''' file name : pointpolygontest.py
Description : This sample shows how to find distance from a point to a contour
This is Python version of this tutorial : http://opencv.itseez.com/doc/tutorials/imgproc/shapedescriptors/point_polygon_test/point_polygon_test.html
Level : Beginner
Benefits : Learn to use cv2.pointPo... | asrob-uc3m/rpc_rpi | src/python/opencv_python_tutorials/Official_Tutorial_Python_Codes/3_imgproc/pointpolygontest.py | Python | gpl-3.0 | 2,208 | [
"VisIt"
] | 74c4e609856f90f8b541fe0471493bca597ff603c2eab10a6788521951772123 |
"""A useful collection of functions to read in different data files.
Supported file types are:
- geometry: cube, molden, xyz
- orbital data: molden
- volumetric data: cube, dx, xyz
- frequencies: aims, terachem
"""
# This file is part of ManipulateAggregates.
#
# Copyright (C) 2016 by Torsten Sachse
#
# Manip... | razziel89/ManipulateAggregates | ManipulateAggregates/collection/read.py | Python | gpl-3.0 | 71,228 | [
"Gaussian",
"TeraChem",
"VMD"
] | ccd49e7435038c4c7c5a40f1fa3697c4b1ad7a6de8045e44ec1a69bb41f4d969 |
from pyo import *
import Resources._global as gl
import Resources.preferences as pref
import Resources.variables as vars
from Resources.midi_routing import Midi
from Resources.audio_class import Freeze, Granul, LorenzChaotic, RosslerChaotic
from Resources.misc_class import Inputs
from Resources.trigger_class import So... | Infrabass/Black-Bass | BlackBass.py | Python | gpl-3.0 | 4,749 | [
"BLAST"
] | 3ec1b7a68e7e5a3f1f26f33a9750470de5f01d04b5b40fc0ba9829fa977f1100 |
from __future__ import division
from __future__ import print_function
import numpy as np
np.seterr(invalid='raise')
from matplotlib import pyplot as plt
import copy
import pybasicbayes
from pybasicbayes import models, distributions
from pybasicbayes.util.text import progprint_xrange
alpha_0=5.0
obs_hypparams=dict(mu_... | michaelpacer/pybasicbayes | examples/demo.py | Python | mit | 1,636 | [
"Gaussian"
] | 86255d7235d8f2204aa3d4a5ec3c3de6857e10b96ae1dd711a0ed3dc3047da6e |
from __future__ import (absolute_import, division, print_function)
import os
import numpy
from mantid import mtd
from mantid.kernel import StringListValidator, Direction, FloatBoundedValidator, \
FloatArrayMandatoryValidator, IntBoundedValidator
from mantid.api import PythonAlgorithm, MultipleFileProperty, FilePro... | ScreamingUdder/mantid | Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/IndirectILLReductionQENS.py | Python | gpl-3.0 | 25,141 | [
"CRYSTAL"
] | b80cec86148631239da719cc8e62f265b09fd2654ad68332be81650eb61b3690 |
import sys
import getopt
import os
import pandas as pd
import numpy as np
import shutil
import Bio
import pandas
from Bio import SeqIO
###############################################
#CRUX PSM SPLITTER
#William Barshop - 2015/07/13
#Updated for fractionated data processing...
date="2015/10/22"
#Laboratory of James A. ... | wohllab/milkyway_proteomics | galaxy_milkyway_files/tools/wohl-proteomics/MSGFcrux/crux_psm_splitter_fractionated.py | Python | mit | 29,971 | [
"Galaxy"
] | cd8572c708ee21229db7abcac5d9daf2c5aaf05ccda5fa67739aadce87d6ffa4 |
"""
An example for single parameter classification methods
"""
import common.statistics as stats
from random import random
from math import log, pi, sqrt
#first generate sample data
# x = salary between (1000 - 5000)
# r = car type (1-5)
def discriminant(class_variance, sample_mean, prior, x):
return (-0.5 * lo... | ocozalp/machine-learning | single_parameter/classification.py | Python | mit | 1,813 | [
"Gaussian"
] | 18644a457db90447d40e550839a3a88ac2de20b6b232a04e29e88f00f123f72b |
# Main Room class using to encapsulate the room acoustics simulator
# Copyright (C) 2019 Robin Scheibler, Ivan Dokmanic, Sidney Barthe, Cyril Cadoux
#
# 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 ... | LCAV/pyroomacoustics | pyroomacoustics/room.py | Python | mit | 101,166 | [
"Gaussian"
] | 7d8242fcb0500d1cee957744070e09cd6cd10ab0c8430be9f73b0ac1d92b9e2c |
import espressopp
# try to run this script with force_capping switched on and off
forceCapping = True
# specify number of particles
num_particles = 200
rho = 0.85
L = pow(num_particles/rho, 1.0/3.0)
# setup random LennardJones system
# this system is likely to explode on integration, because particles can strongly... | fedepad/espressopp | examples/force_capping/force_capping.py | Python | gpl-3.0 | 1,206 | [
"VMD"
] | 9e70b2ee3bc4ea777a3a3a1d0136f34d1c511c80c759e05899984364a1c0a663 |
import pytest
from .addons import using_networkx
from .utils import *
import math
import numpy as np
import qcelemental as qcel
import psi4
from psi4.driver import qcdb
pytestmark = pytest.mark.quick
def hide_test_xtpl_fn_fn_error():
psi4.geometry('He')
with pytest.raises(psi4.UpgradeHelper) as e:
... | jgonthier/psi4 | tests/pytests/test_misc.py | Python | lgpl-3.0 | 3,658 | [
"Psi4"
] | ce812cd990f43acd0408127d36ffb83f928099a0300813cff15a69121334f97c |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
#======================================================================
#
# fzf_cd.py - Change Directory in Total Commander with fzf
#
# Created by skywind on 2020/10/31
# Last Modified: 2020/10/31 22:15:03
#
#======================================================... | skywind3000/collection | script/fzf_cd.py | Python | mit | 41,907 | [
"VisIt"
] | 868586c04d3eb4915d333f5c23f7c3f22aba28889212c0c8f70f27c25dbd4113 |
#!/Library/Frameworks/Python.framework/Versions/2.7/bin/python
##!/mnt/lustre_fs/users/mjmcc/apps/python2.7/bin/python
# ----------------------------------------
# USAGE:
# ----------------------------------------
# PREAMBLE:
import numpy as np
from numpy.linalg import *
import MDAnalysis
from MDAnalysis.analysis.ali... | rbdavid/Wat_diffusion | test_suite/water_diffusion.py | Python | gpl-3.0 | 13,599 | [
"MDAnalysis",
"VMD"
] | 18de8d7c513e84b1fb63394cf529acc63052328f507b03dda950c004bcee738a |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | nuclear-wizard/moose | tutorials/darcy_thermo_mech/step05_heat_conduction/problems/step5c.py | Python | lgpl-2.1 | 1,602 | [
"MOOSE",
"VTK"
] | a6aef1c21bc650768c4eb3fa527ae61d622fdf531e15911d216c0b0904905f76 |
"""
Univariate Kernel Density Estimators
References
----------
Racine, Jeff. (2008) "Nonparametric Econometrics: A Primer," Foundation and
Trends in Econometrics: Vol 3: No 1, pp1-88.
http://dx.doi.org/10.1561/0800000009
http://en.wikipedia.org/wiki/Kernel_%28statistics%29
Silverman, B.W. Density Estimation... | wesm/statsmodels | scikits/statsmodels/nonparametric/kde.py | Python | bsd-3-clause | 17,158 | [
"Gaussian"
] | d57f9fe1e66ff8bd152aea632548c466eb582939bed2a70c8f1435d15560128f |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import (absolute_import, division, print_function,
unicode_literals)
"""
This module provides classes and methods used to describe deformations and
strains, including ap... | setten/pymatgen | pymatgen/analysis/elasticity/strain.py | Python | mit | 9,443 | [
"pymatgen"
] | 8a7f8175b797aa19b7e9712f458338991a45f63d2d74e9fbfdd964569c355df1 |
# Copyright (c) 2016, Henrique Miranda
# All rights reserved.
#
# This file is part of the yambopy project
#
from yambopy import *
from yambopy.plot import *
from itertools import product
from netCDF4 import Dataset
max_exp = 50
ha2ev = 27.211396132
atol = 1e-3
def isbetween(a,b,c):
"""
Check if cartesian poi... | henriquemiranda/yambopy | yambopy/dbs/savedb.py | Python | bsd-3-clause | 13,141 | [
"DIRAC",
"Yambo"
] | ed748e5217b2cd77d2dc2f59d719a1781dcf7c8dc0fe05dbd2ce889647ff004c |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | CDSherrill/psi4 | psi4/driver/driver_util.py | Python | lgpl-3.0 | 16,545 | [
"Psi4"
] | 2dad2926b2a96bd46483337e9a00144696788addc94de58515ee0c20528c0845 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#... | MDAnalysis/mdanalysis | testsuite/MDAnalysisTests/utils/test_persistence.py | Python | gpl-2.0 | 4,584 | [
"MDAnalysis"
] | 2fc66de7cdacbc3d1cbe6614ecf7b19821c54db4dcd3295b44f39b0baa507905 |
# Copyright Iris contributors
#
# This file is part of Iris and is released under the LGPL license.
# See COPYING and COPYING.LESSER in the root of the repository for full
# licensing details.
# Historically this was auto-generated from
# SciTools/iris-code-generators:tools/gen_rules.py
import cf_units
import numpy ... | pp-mo/iris | lib/iris/fileformats/pp_load_rules.py | Python | lgpl-3.0 | 46,304 | [
"NetCDF"
] | a15bafb7ce9689f4446f0d36040df07d2262685a23c2ddb711c1999e411a81c3 |
#!/usr/bin/env python
#
# Copyright (C) 2014
# Brian Caswell <bmc@lungetech.com>
# Narf Industries <info@narfindustries.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 res... | f0rki/cb-multios | original-challenges/FASTLANE/poller/for-release/machine.py | Python | mit | 9,589 | [
"Brian"
] | 2d71b2b8549e13abdebe72d6d16215527987a48923b385e79b8130eb86847eec |
#!/usr/bin/python
# 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 Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# Ansible is distributed... | haad/ansible-modules-core | cloud/amazon/elasticache.py | Python | gpl-3.0 | 21,536 | [
"Dalton"
] | dac0b6662492e75b4c345190d27ff730e02273e0a5beac0187996b270bc9cb97 |
# Copyright (c) 2014-present PlatformIO <contact@platformio.org>
#
# 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 appli... | platformio/platformio-core | scripts/docspregen.py | Python | apache-2.0 | 33,421 | [
"VisIt"
] | c075650c21f8e5c55360d95c9984b70c16b0142e42f1641446a65c3fb98daa76 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (c) 2011-2015 Slack
#
# 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
... | Slack06/yadg | descgen/visitor/misc.py | Python | mit | 11,545 | [
"VisIt"
] | 06f6de278010f2b54aa29da02894ae0ee60cadca73ce8a0dae4cf27b0f3aef9b |
#!/usr/bin/env python
"""Inference engine for drawing inferences on the Gene Ontology."""
__author__ = "Tamas Nepusz"
__email__ = "tamas@cs.rhul.ac.uk"
__copyright__ = "Copyright (c) 2010, Tamas Nepusz"
__version__ = "0.1"
__all__ = ["InferenceEngine", "Rules", "Query", "UNBOUND"]
from annotations.GO.ontology i... | marco-mariotti/selenoprofiles | libraries/annotations/GO/inference.py | Python | gpl-2.0 | 20,418 | [
"VisIt"
] | e57310854aa39c534e30a9ee3a19021e27cae3b488d398438b3aa38a58ea2c33 |
from __future__ import annotations
import copy
import functools
import os
import pytest
from cctbx import sgtbx, uctbx
from dxtbx.model import Crystal
from dxtbx.serialize import load
from dials.algorithms.indexing import model_evaluation
from dials.algorithms.indexing.assign_indices import AssignIndicesGlobal
from... | dials/dials | tests/algorithms/indexing/test_model_evaluation.py | Python | bsd-3-clause | 9,591 | [
"CRYSTAL"
] | 1a72969918180944787c22d6201fa345a30436b832be381311f0a917960a505c |
"""
Contains OpenID provider functionality
"""
import logging, os
from galaxy.util import parse_xml, string_as_bool
from galaxy.util.odict import odict
log = logging.getLogger( __name__ )
NO_PROVIDER_ID = 'None'
RESERVED_PROVIDER_IDS = [ NO_PROVIDER_ID ]
class OpenIDProvider( object ):
'''An OpenID Provider ob... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/openid/providers.py | Python | gpl-3.0 | 6,125 | [
"Galaxy"
] | de1cd1c191941ccf1000d56194787e35bba500890d44984592dbed9f1708c64e |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | fedepad/espressopp | src/io/__init__.py | Python | gpl-3.0 | 1,053 | [
"ESPResSo"
] | 7fa5e1d605349bbe1fc22c93d6b96eccace8a3cff5af1c91f24552663a6561b9 |
# clortho - A simple key/value server
#
# Copyright 2014-2018 by Brian C. Lane <bcl@brianlane.com>
# All Rights Reserved
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the... | bcl/clortho | src/clortho.py | Python | gpl-2.0 | 6,314 | [
"Brian"
] | dbbe13c2087dc48a3c97ba9cef42af021e6846f9430c9293f4209b68eacf2af3 |
__doc__ = """Code by Benjamin S. Murphy
bscott.murphy@gmail.com
Dependencies:
numpy
scipy
matplotlib
Classes:
OrdinaryKriging3D: Support for 3D Ordinary Kriging.
References:
P.K. Kitanidis, Introduction to Geostatistcs: Applications in Hydrogeology,
(Cambridge University Press, 1997) 272 p.
... | yejingxin/PyKrige | pykrige/ok3d.py | Python | bsd-3-clause | 33,404 | [
"Gaussian"
] | 30a4d2fcc76c1aa5db526d5c5e61ac03d3dfe0effbba742f720cfb34c7864879 |
################################################################################
# This is a setuptools setup file. For more info please see:
# http://peak.telecommunity.com/DevCenter/setuptools
#
# TODO: Check that matplotlib is downloaded/installed
# TODO: Check that long_description works
# * is pkgutil ... | mscook/Banzai-controller | setup.py | Python | apache-2.0 | 2,630 | [
"Biopython"
] | 5a0566ac8cb1678b35444b16a30fbe1560af57551e2f65ffcbe18d02d1799697 |
import datetime
import os
import sys
from SearchDistribute.GoogleSearch import GoogleSearch
from SearchDistribute.GoogleSearchQuery import GoogleSearchQuery
def print_cli_help_message():
x = os.system("clear; clear;")
print("\n<<<<<-------------------------COMMAND-LINE INTERFACE TO THIS MODULE---------------------... | ARDivekar/SearchDistribute | SearchDistribute/cli.py | Python | mit | 26,482 | [
"VisIt"
] | 970ab5b9480813e15f0e14c8536c81347dc221897e07d8b8fe20834e6345a618 |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | nuclear-wizard/moose | python/peacock/tests/utils/test_ExeFinder.py | Python | lgpl-2.1 | 2,344 | [
"MOOSE"
] | 94bc71b06fde9702dce42e948a8daff3fcb418d48e33a47c2b36800d0ba6d80c |
#! /usr/bin/python
"""versioneer.py
(like a rocketeer, but for versions)
* https://github.com/warner/python-versioneer
* Brian Warner
* License: Public Domain
* Version: 0.7+
This file helps distutils-based projects manage their version number by just
creating version-control tags.
For developers who work from a V... | kalikaneko/leap_mx | versioneer.py | Python | agpl-3.0 | 26,422 | [
"Brian"
] | 0a2a19fbf60dc3abed239708a6e5d1569dff96d7433fc6fdeee4acf1fa259c49 |
""" PilotsLoggingDB class is a front-end to the Pilots Logging Database.
This database keeps track of all the submitted grid pilot jobs.
It also registers the mapping of the DIRAC jobs to the pilot
agents.
Available methods are:
addPilotsLogging()
getPilotsLogging()
deletePilotsLoggin()
"... | yujikato/DIRAC | src/DIRAC/WorkloadManagementSystem/DB/PilotsLoggingDB.py | Python | gpl-3.0 | 7,256 | [
"DIRAC"
] | 34c4893c965a0d0ea82e0b38249620e9fd93ab63cd6c8ecfb2f76a6ecfdab5a5 |
"""
# Notes:
- This simulation seeks to emulate the CUBA benchmark simulations of (Brette
et al. 2007) using the Brian2 simulator for speed benchmark comparison to
DynaSim. However, this simulation does NOT include synapses, for better
comparison to Figure 5 of (Goodman and Brette, 2008).
- The time taken to si... | asoplata/dynasim-benchmark-brette-2007 | output/Brian2/brian2_benchmark_CUBA_nosyn_32000/brian2_benchmark_CUBA_nosyn_32000.py | Python | gpl-3.0 | 2,009 | [
"Brian"
] | f962ecf2f5e19e532aef82974cc4f77e6dcdaa4472f3564465b7dfd9b2ea2607 |
#!/usr/bin/env python
# Copyright 2014-2021 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/dft/multigrid.py | Python | apache-2.0 | 70,557 | [
"PySCF"
] | 36501f79faba044a4f61aed45702fda0417660d67c6e6d3b67bf39be9d5e5b8d |
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