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#
# commands.py - the GraalVM specific commands
#
# ----------------------------------------------------------------------------------------------------
#
# Copyright (c) 2007, 2012, Oracle and/or its affiliates. All rights reserved.
# DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
#
# This code is free ... | rjsingh/graal | mx/commands.py | Python | gpl-2.0 | 55,430 | [
"VisIt"
] | b172cfbe599b59eebe36d7f46d085b7ceede5b3cb6fa68d1c72965977ec7f99c |
"""
Distribution functions used in GLM
"""
# Author: Christian Lorentzen <lorentzen.ch@googlemail.com>
# License: BSD 3 clause
from abc import ABCMeta, abstractmethod
from collections import namedtuple
import numbers
import numpy as np
from scipy.special import xlogy
DistributionBoundary = namedtuple("Distribution... | shyamalschandra/scikit-learn | sklearn/_loss/glm_distribution.py | Python | bsd-3-clause | 11,891 | [
"Gaussian"
] | 46abaaa1818f3a232f4de41c603971216a9a6db985390b86671285e0de400b5e |
#!/usr/bin/env python
# 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
#
# U... | sunqm/pyscf | pyscf/solvent/ddcosmo_grad.py | Python | apache-2.0 | 14,634 | [
"PySCF"
] | c7232b5aed9bc912b1ce14e2642f78888f8a893fde4565c212ea0f90353f175e |
# Orca
#
# Copyright 2014 Igalia, S.L.
#
# Author: Joanmarie Diggs <jdiggs@igalia.com>
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your o... | ruibarreira/linuxtrail | usr/lib/python3/dist-packages/orca/colornames.py | Python | gpl-3.0 | 39,049 | [
"ORCA"
] | 5f605b43a348349d6df3035ca61009c2c2894d3f8ede917ca642c07f6ae9c123 |
#!/usr/bin/env python
#---------------- EDIT JOB NAME -------------------
#$ -N SiteAnalysis
#--------------------------------------------------
#$ -S /usr/bin/python
#$ -v PYTHONPATH=/home/oliver/Library/python-lib
#$ -v LD_LIBRARY_PATH=/opt/intel/cmkl/8.0/lib/32:/opt/intel/itc60/slib:/opt/intel/ipp41/ia32_itanium/sha... | iwelland/hop | doc/examples/siteanalysis.py | Python | lgpl-3.0 | 2,916 | [
"MDAnalysis"
] | 50760a5376dc75b216b7a3abd9a67aff2cf8b72222660459883881e770dde1be |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# ommprotocol: A command line application to launch
# MD protocols with OpenMM
# By Jaime RGP <@jaimergp>
import os
from distutils.spawn import find_executable
import pytest
import numpy as np
from ommprotocol.io import SystemHandler, Positions, Restart, pr... | insilichem/ommprotocol | tests/test_io.py | Python | lgpl-3.0 | 2,851 | [
"OpenMM"
] | 583a7338015b8699ddfaa35cf022e13e5c676da35ebcee2bd6bd9e3f4cf9d708 |
""" This is a simple example of implementation of a Ping/Pong service for executors.
This service does not any specific configuration to run, only the Port number, and authz e.g.:
{
Port = 9145
{
Authorization
{
Default = all
}
}
}
"""
from __future__ im... | yujikato/DIRAC | docs/source/DeveloperGuide/Systems/Framework/stableconns/service.py | Python | gpl-3.0 | 1,757 | [
"DIRAC"
] | fcf753443a62090eae394480cab8a7f3528280ecc3ab56151c4138704d7aff23 |
# -*- coding: utf-8 -*-
"""
Plot mitoskel network in with various scalar values
"""
import sys
import os
import os.path as op
import matplotlib.pyplot as plt
from mayavi import mlab
from pipeline.make_networkx import makegraph as mg
from mombud.functions import vtkvizfuncs as vz
from wrappers import swalk, UsageError
#... | moosekaka/sweepython | cell_pick_viz/vtk_make_single_fig.py | Python | mit | 2,723 | [
"Mayavi",
"VTK"
] | 6af71faad99f11902c8820fedeb3a9c788cb16edff87d6b3f0b1530915d5554a |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
This module implements input and output processing from Nwchem.
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"... | sonium0/pymatgen | pymatgen/io/nwchem.py | Python | mit | 26,287 | [
"Gaussian",
"NWChem",
"pymatgen"
] | 4af3220c24174e1e6fc3b8c045a09535fdfca4229ec984532c258fa17c7610a3 |
## D3PO (Deonoiseing, Deconvolving, and Decomposing Photon Observations) has
## been developed at the Max-Planck-Institute for Astrophysics.
##
## Copyright (C) 2014 Max-Planck-Society
##
## Author: Marco Selig
## Project homepage: <http://www.mpa-garching.mpg.de/ift/d3po/>
##
## This program is free software: you can ... | information-field-theory/d3po | d3po.py | Python | gpl-3.0 | 70,808 | [
"Gaussian"
] | bbb1178803d79785526e8e50aa3f61f5db79227284d4ee1c86293fa9167de949 |
# -*- coding: utf-8 -*-
# TAMkin is a post-processing toolkit for normal mode analysis, thermochemistry
# and reaction kinetics.
# Copyright (C) 2008-2012 Toon Verstraelen <Toon.Verstraelen@UGent.be>, An Ghysels
# <An.Ghysels@UGent.be> and Matthias Vandichel <Matthias.Vandichel@UGent.be>
# Center for Molecular Modeling... | molmod/tamkin | tamkin/io/charmm.py | Python | gpl-3.0 | 10,581 | [
"Avogadro",
"CHARMM"
] | dedfadc61934a06ba8ad602afe06ade3552666a8107752ca292bd9d746fc8a18 |
# -*- encoding: utf-8 -*-
import sys
import os
import os.path
import glob
import logging
import utils
def ribosomal_reduction( T, configs, audit ):
logging.debug( "Attempting to remove ribosomal RNA (rRNA)..." )
# create the destination for unaligned reads if not exists
if not audit:
utils.create_directory( con... | polarise/breeze | breeze/ribosomal_reduction.py | Python | gpl-2.0 | 2,785 | [
"Bowtie"
] | d98acc12335fd5dc8d0f32d3490eb80e217f43a98598c4e1d24b83b53f27c62b |
from ..cg.kdtree import KDTree
from .weights import W
from .util import isKDTree, get_ids, get_points_array_from_shapefile, get_points_array
import copy
from warnings import warn as Warn
import numpy as np
__all__ = ["KNN", "Kernel", "DistanceBand"]
__author__ = "Sergio J. Rey <srey@asu.edu>, Levi John Wolf <levi.john... | TaylorOshan/pysal | pysal/weights/Distance.py | Python | bsd-3-clause | 30,148 | [
"COLUMBUS",
"Gaussian"
] | f523e4eac39ccf6f80d6ec2d168919d4fdd67f2612be86500653069ed3a94ed4 |
class VehicleInfo(object):
def __init__(self):
"""
make_target: option passed to make to create binaries. Usually sitl, and "-debug" may be appended if -D is passed to sim_vehicle.py
default_params_filename: filename of default parameters file. Taken to be relative to autotest dir.
... | ranqingfa/ardupilot | Tools/autotest/pysim/vehicleinfo.py | Python | gpl-3.0 | 11,087 | [
"Firefly"
] | 263f3145200cc3dd3a9cb89f9cbde355b5ea69e3084097d705152931fecf0090 |
#!/usr/bin/env python3
# creates an ASE xyz file from a cp2k restart file
import os
from ase import io
def main(inFile,outFile):
if not os.path.isfile(inFile):
raise ValueError('File {:} does not exist'.format(str(inFile)))
#if output exists mv to .bak
if os.path.isfile(outFile):
print('AT... | patrickmelix/Python4ChemistryTools | cp2krestart2xyz.py | Python | mit | 1,683 | [
"ASE",
"CP2K",
"Gaussian"
] | fb98f87f04d966d0464448753996ebcb6eb62265471a53620a4e054751eef427 |
"""
Extensions of the nrn.Section class.
$Id:$
"""
import nrn
import neuron
import sys
import StringIO
class ExtendedSection(nrn.Section):
def __init__(self, name=None):
nrn.Section.__init__(self)
self.hoc_name = nrn.Section.name(self)
if name:
self._name = name
e... | neurodebian/pkg-neuron | share/lib/python/neuron/sections.py | Python | gpl-2.0 | 2,486 | [
"NEURON"
] | cbd019336f33e5cd5c06fdac99e8a823191357ae74ea55fa64d05cb56f7a9887 |
# pylint: disable=arguments-differ
""" Models for the shopping cart and assorted purchase types """
from collections import namedtuple
from datetime import datetime
from datetime import timedelta
from decimal import Decimal
import json
import analytics
from io import BytesIO
from django.db.models import Q, F
import py... | simbs/edx-platform | lms/djangoapps/shoppingcart/models.py | Python | agpl-3.0 | 90,362 | [
"VisIt"
] | ef11bae085766fdb4c0c90b376a6d8cbefcd24333f29985f62b193fd97663b95 |
#######################################
#Neural Network Main Module
#NeuralNetwork.py
#
#(c) 2017 Carter N. Plasek
#######################################
#######################################
#This program is free software; you can redistribute it and/or modify it under
#the terms of the GNU General Public License ... | NerdyYoungMen/Neural-Network-PythonLib | Module/NeuralNetwork.py | Python | gpl-3.0 | 9,066 | [
"NEURON"
] | f7706c7fa83ccbb5bd3e37381ffa3a16581c107c39c12225c6e2186d732b41ae |
# -*- coding: utf-8 -*-
# ***********************************************************************
# Copyright (C) 2016 - 2017 Oscar Gerardo Lazo Arjona *
# <oscar.lazoarjona@physics.ox.ac.uk> *
# ***********************************************************************
... | oscarlazoarjona/quantum_memories | examples/orca/svd/simple_example_svd.py | Python | gpl-3.0 | 916 | [
"ORCA"
] | 722e22ac0428086f7d83e2e963cb11c7cc174113543399dc8fd0b3b6d8baba5a |
def check_prob_params(params):
"""
Sets parameter values pertaining to components of probability
Parameters
----------
params: dict
dictionary containing key/value pairs for probability
Returns
-------
params: dict
dictionary containing key/value pairs for probability
... | aimalz/chippr | research/scripts/cosmolike_inf_script.py | Python | mit | 6,349 | [
"Gaussian"
] | b71f5c2aac54889275e299b72680075830067b2bae7361b624a453fbfbe2ebba |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
'''
Multipole integrals. (Be careful with the gauge origin of the multipole
integrals). An implementation of multipoles (up to hexadecapole) can be found
in
https://github.com/cuanto/pyscf-scripts/blob/master/props/multipole_rhf.py
See also 20-ao... | sunqm/pyscf | examples/gto/25-multipole-integrals.py | Python | apache-2.0 | 806 | [
"PySCF"
] | 0b24c5281ba8d41bc170323f12a18663c4a3b60e753364f9333f6fe90395ee45 |
../../../../../../share/pyshared/orca/scripts/toolkits/__init__.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/scripts/toolkits/__init__.py | Python | gpl-3.0 | 66 | [
"ORCA"
] | 4eede4a1b8cf9d9ff97162cfacdaffda33cccb25402884813a123f885bc59acc |
import os
import logging
if __name__ == "__main__":
import sys
sys.path.append("..")
del sys
import fenalib.logging_setup as logging_setup
from fenalib.assert_utils import assert_type
from fenalib.parser import Parser
from fenalib.token_classes import TypedToken
from fenalib.str_utils import encode_s... | Aquafina-water-bottle/Command-Compiler-Unlimited | fenalib/interpreter.py | Python | mit | 6,128 | [
"VisIt"
] | 27481488450613c0d5cab0384b312cc59cd9314565ac20ca994077cfead9cac1 |
#!/usr/bin/env python
# Copyright 2002 Google Inc. All Rights Reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list of c... | joachimmetz/python-gflags | gflags/flagvalues.py | Python | bsd-3-clause | 41,280 | [
"MOE"
] | 4018d3cf87247de0ea344fe776f9e59fd40126058a6274127ee80bb8c00fb139 |
import numpy as np
import networkx as nx
from collections import defaultdict
from models import ( ClassInstance, ClassInstanceClassInstance, Relation,
Review, Treenode, TreenodeConnector, TreenodeClassInstance )
class Neuron(object):
def __init__(self, neuron_id, project_id):
self.neuron = Cla... | catsop/CATMAID | django/applications/catmaid/objects.py | Python | gpl-3.0 | 17,770 | [
"NEURON"
] | 724ae1da8f5836dc7e4417503f9661591008cc35ab538eef24a2aca16727d2db |
import collections
import functools
import operator
import os
import re
from random import randint
from time import time
from ase.atoms import Atoms, symbols2numbers
from ase.calculators.calculator import get_calculator, all_properties, \
all_changes
from ase.calculators.singlepoint import SinglePointCalculator
fr... | askhl/ase | ase/db/core.py | Python | gpl-2.0 | 19,447 | [
"ASE"
] | aa182cb8777c2a3b17a09fd4df637b57fbc23710333381fa094ac6e912b309b0 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2004-2007 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Contribution 2009 by Brad Crittenden <brad [AT] bradcrittenden.net>
# Copyright (C) 2008 Benny Malengier
# Copyright (C) 2010 Jakim Friant
#
# This program is free... | gramps-project/gramps | gramps/gui/plug/export/_exportassistant.py | Python | gpl-2.0 | 24,263 | [
"Brian"
] | 0c3a80f407279584b2fa8120ff270d5418dfd8a16dc81aebe08e375cbed253c1 |
"""
Generates predictions on test-dev or test using an ensemble of nets. The
ensemble is produced using the average of the pre-softmax output from each net.
Place each model in its own folder. The folder must contain:
- The .caffemodel file
- proto_test.prototxt
- adict.json
- vdict.json
- aux.json
aux.json should c... | ronghanghu/vqa-mcb | eval/ensemble.py | Python | bsd-2-clause | 10,501 | [
"NEURON"
] | 03ec8498493630ec230fe582a2b1d528f5aa6ca7c613146a726fe8246b3e1335 |
# S.D. Peckham
# Sept 2014 (new version to use netCDF4)
# June 2010 (streamlined a bit more)
# December 2, 2009 (updated open_new_file to use "info")
# October 13, 2009
import os
import sys
import time
import numpy as np
import bov_files
import file_utils
import rti_files
import netCDF4 as nc
#--------------------... | peckhams/topoflow | topoflow/utils/ncgs_files.py | Python | mit | 19,923 | [
"NetCDF"
] | d3f05d225fe147fe4ef519064d3ef5a61c5d538ba6d188d3ebcb1e48a4b18c6a |
#!/usr/bin/env python
# encoding: utf-8
# ddd
import numpy as np
# -------- GLOBAL SCALAR DEFINITIONS -----------------------------
# ======== all definitions are in m,s,g unit system.
n_frames = 30
# ....... dimensions .............................................
x_lower = 0.0
x_upper = 10.0e-6 # l... | nthakkar/emclaw | maxwell_3d_source/maxwell.py | Python | gpl-2.0 | 13,528 | [
"Gaussian"
] | bef07bbfa51d5d9157ccd70c0d4ce24f5d40adca295fe90fc488511dbb21e995 |
"""
=========================
Bayesian Ridge Regression
=========================
Computes a :ref:`bayesian_ridge_regression` on a synthetic dataset.
Compared to the OLS (ordinary least squares) estimator, the coefficient
weights are slightly shifted toward zeros, wich stabilises them.
As the prior on the weights is... | seckcoder/lang-learn | python/sklearn/examples/linear_model/plot_bayesian_ridge.py | Python | unlicense | 2,481 | [
"Gaussian"
] | f5796a54e6e721e892e08afc21ed30eb649f227910b9976beecf2bb522e68a19 |
# Copyright (c) 2008-2016 MetPy Developers.
# Distributed under the terms of the BSD 3-Clause License.
# SPDX-License-Identifier: BSD-3-Clause
"""
Four Panel Map
===============
By reading model output data from a netCDF file, we can create a four panel plot showing:
* 300 hPa heights and winds
* 500 hPa heights and ... | metpy/MetPy | v0.5/_downloads/Four_Panel_Map.py | Python | bsd-3-clause | 5,567 | [
"NetCDF"
] | b287e153f0b969f95a6ed340bc927b56f98657d54044e1713c3de9466cf975e9 |
import pysam
import scipy.stats as stats
import iInfo
#import multiprocessing
import warnings
import math
def Sequence_Annotator(variant, Sample_dict, H_CHR, Reference, Variant_Class, SNVMinBaseQuality, SNVMinMappingQuality, IndelMinBaseQuality, IndelMinMappingQuality, Bam_opts, Genotype_opts, opts):
CHR = variant[H... | Matteodigg/iEVA | iEVA/iBam.py | Python | mit | 15,864 | [
"pysam"
] | 9ec426c4890086dde7a08fdbf2805497a76445f247938b3577c9fde96898dbbe |
# Author: Yang Long <longyang_123@yeah.net>
#
# License: LGPL-2.1
import numpy as np
def Uniform(chromes,LB,UB,mutationrate,IntCon,args):
'''
Uniform random mutation (Default)
'''
preal = 0.1
pint = 0.2
if 'preal' in args:
preal = args['preal']
if 'pint' in args:
pint = arg... | longyangking/Husky | Husky/SA/MultiUtils/Mutation.py | Python | lgpl-2.1 | 2,217 | [
"Gaussian"
] | 22a34ede06101eecf5104a5cbbd56a3ab42e1938170fd9eff2a790cea19d4702 |
# Orca
#
# Copyright 2011. Orca Team.
# Author: Joanmarie Diggs <joanmarie.diggs@gmail.com>
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at y... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/script_manager.py | Python | gpl-3.0 | 9,667 | [
"ORCA"
] | ed1f0800c18f1556af004e78ba7530bb957d070b76b42820987f526fed60e7ec |
import unittest
import numpy
import os
import mdarray as mt
class TestTrajectoryXTC(unittest.TestCase):
def setUp(self):
if not mt.__config__['gromacs']:
self.skipTest('Skipping tests since gromacs support was not compiled')
self.testDir = os.path.dirname(os.path.realpath(__file__))
... | boryszef/moltools-python | tests/test_trajectory_xtc.py | Python | gpl-3.0 | 2,510 | [
"Gromacs"
] | 04905190a61a0ab38c1799166047f7373aa8b9fde4ffdfaaf2f481509bef5a79 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2017 Lenovo, Inc.
#
# 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
# ... | andreaso/ansible | lib/ansible/modules/network/lenovo/cnos_save.py | Python | gpl-3.0 | 5,059 | [
"VisIt"
] | 07cffcd84770e631701e08741b5f1bea9e2f5acc584e833389a974a3ae3a9415 |
import logging
import os
import shutil
import urllib.request as request
import zipfile
from contextlib import closing
from datetime import datetime
from time import sleep
from urllib.parse import urljoin, urlsplit
import requests
from django.conf import settings
from django.db.models import Q
from rest_framework impor... | linea-it/dri | api/product_register/ImportProcess.py | Python | gpl-3.0 | 36,802 | [
"Galaxy"
] | 494be027780bfbb6138c5fbe3fc33528c83f4423e7a4890a56a878dd480be5cb |
# -*- coding: utf-8 -*-
import numpy as np
try:
import seawater.gibbs
except ImportError, e:
pass # module doesn't exist, deal with it.
from altimetry.tools import deriv, calcul_distance, interp1d, loess
if __debug__ : import matplotlib.pyplot as plt
def track_orient(x,y,orient=False):
# ;Calculate... | rdussurget/py-altimetry | altimetry/tools/altimetry_tools.py | Python | lgpl-3.0 | 31,527 | [
"Brian"
] | 569e3c5a6cd2e77ad9e7649fe9a4efeb89f5ebb9bd90fbbaabc3c81caedb4944 |
"""
"""
__author__='Xun Li <xunli@asu.edu>'
__all__=[]
from mt_densitymap import *
import ctypes
import numpy as np
import wx
def call_kde(n,x,y,pts_ids, extent,bandwidth,cellsize,kernel, gradient, opaque):
_x = VecDouble(x)
_y = VecDouble(y)
_pts_ids = VecInt(pts_ids)
_extent = VecDouble(extent)
... | GeoDaCenter/CAST | stars/core/DKDEWrapper.py | Python | gpl-3.0 | 4,601 | [
"Gaussian"
] | d91f03f6842725c78b069835689f061ab9aa7a3a63d70086fbad631e0214ca44 |
#!/usr/bin/env python
import sysconfig
import subprocess
import json
import os
import sys
import platform
if os.path.dirname(__file__):
os.chdir(os.path.dirname(__file__))
if platform.system() in ('Windows', 'Darwin') or platform.system().startswith('CYGWIN'):
sys.exit(0) # test not supported on windows or os... | dgrunwald/rust-cpython | tests/check_symbols.py | Python | mit | 2,955 | [
"VisIt"
] | 386bcd0e73c9cc4932b359218eb60333a2f82b55232c2decb2ab38afa3b20c83 |
# -*- coding: latin-1 -*-
"""
Hydrogen Models
---------------
Hydrogen in HII regions is typically assumed to follow Case B recombination
theory.
The values for the Case B recombination coefficients are given by `Hummer &
Storey (1987)
<http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=1987MNRAS.224..801H&db_ke... | mikelum/pyspeckit | pyspeckit/spectrum/models/hydrogen.py | Python | mit | 10,727 | [
"Gaussian"
] | d56009e233c3918218820be42b853e91bec9d5054bf400b0d1ad4da4c8c7d81e |
#!/usr/bin/env python
import argparse
import copy
import logging
import re
import sys
from cpt_gffParser import gffParse, gffWrite, gffSeqFeature
logging.basicConfig(level=logging.INFO)
log = logging.getLogger(name="blast2gff3")
__doc__ = """
BlastXML files, when transformed to GFF3, do not normally show gaps in the
... | TAMU-CPT/galaxy-tools | tools/blast/blast_to_gapped_gff3.py | Python | gpl-3.0 | 10,128 | [
"BLAST"
] | 69472394339e76e12b0a7c1dd30275f4ea2f857c0025b128693eb8437b04c2b7 |
"""
WSGI config for neuron project.
It exposes the WSGI callable as a module-level variable named ``application``.
For more information on this file, see
https://docs.djangoproject.com/en/1.10/howto/deployment/wsgi/
"""
import os
from django.core.wsgi import get_wsgi_application
os.environ.setdefault("DJANGO_SETTI... | chugunovyar/factoryForBuild | neuron/wsgi.py | Python | gpl-3.0 | 390 | [
"NEURON"
] | 028b83922cb1258a953621c038e8e26996d115f785a290d9cc7805f27affd59a |
# coding: utf-8 -*-
from __future__ import absolute_import
from flask import url_for
import pytest
from firefly.models.topic import Category, Post, Comment
@pytest.mark.usefixtures('client_class')
class TestPost:
def setup(self):
c = Category.objects.create(
name='python', description='描述',... | ruitian/firefly | tests/test_post.py | Python | mit | 1,504 | [
"Firefly"
] | cc35f3f88dfc26ec9949fc287899ea652a6d93b9d35c002dac9db1a3d4e83c55 |
#
# 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... | bravo-zhang/spark | examples/src/main/python/ml/generalized_linear_regression_example.py | Python | apache-2.0 | 2,505 | [
"Gaussian"
] | b6eadfe264e2f71b616f11de674b9b59855c496725ef38f3b39075a1e91cdfc7 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class Athena(AutotoolsPackage):
"""Athena is a grid-based code for astrophysical magnetohydrodyn... | iulian787/spack | var/spack/repos/builtin/packages/athena/package.py | Python | lgpl-2.1 | 9,787 | [
"BLAST"
] | e7bd832c6494ba7c5a14300791b07107d712fdb3e1bc4c9a21648e9bb0b39a59 |
#!/usr/bin/python
########################################################################
# 20 Oct 2014
# Patrick Lombard, Centre for Stem Stem Research
# Core Bioinformatics Group
# University of Cambridge
# All right reserved.
########################################################################
import argparse... | pdl30/pychiptools | pychiptools/call_alignment.py | Python | gpl-2.0 | 3,630 | [
"Bowtie"
] | 577e8f75a18e7f503369c7e95d87295c344d87f4ad30bafc8bd9ce4cfa3a8f55 |
#!/usr/bin/env python3
#pylint: disable=missing-docstring
#* 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
... | nuclear-wizard/moose | python/chigger/tests/transform/translate.py | Python | lgpl-2.1 | 1,376 | [
"MOOSE"
] | 3abd5900c20c8d4c8964026f82e17a043e56c0183e01b5cbe9ab2d9852ab44f8 |
"""
Copyright (c) 2014, Austin R. Benson, David F. Gleich,
Purdue University, and Stanford University.
All rights reserved.
This file is part of MRNMF and is under the BSD 2-Clause License,
which can be found in the LICENSE file in the root directory, or at
http://opensource.org/licenses/BSD-2-Cl... | arbenson/mrnmf | RunNMF.py | Python | bsd-2-clause | 4,146 | [
"Gaussian"
] | 527abcff4d26c0715e82ccf0ec3ae699f375fef3e68116fdd75a36d52f3fbea0 |
# -*- encoding: utf-8 -*-
__author__ = 'chris'
import math
import numpy as np
from scipy.stats import linregress
from scipy.special import binom
"""
All normalization steps are based on the following two papers:
Liwicki, M. ; Bunke, H.: HMM-based on-line recognition of handwritten whiteboard notes.
In: Tenth... | cwiep/online-handwriting-tools | traj/trajnorm.py | Python | apache-2.0 | 7,282 | [
"Gaussian"
] | 80793e70bdabe4860a923be9626162ace6b3b3a4e6be32cabf7f7ae1e84aa632 |
"""
Module containing many types of independence testing methods.
"""
__author__ = 'wittawat'
from abc import ABCMeta, abstractmethod
from fsic.data import PairedData
import matplotlib.pyplot as plt
import numpy as np
#from numba import jit
import fsic.data as data
import fsic.util as util
import fsic.feature as fea
... | wittawatj/fsic-test | fsic/indtest.py | Python | mit | 56,608 | [
"Gaussian"
] | 62ee0ae26aa54ee0faf737d0fa4b1f4a385e41abeedd36ba4e759cc4284140bf |
#!/usr/bin/env python
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Makes sure files have the right permissions.
Some developers have broken SCM configurations that flip the executable
permission... | Teamxrtc/webrtc-streaming-node | third_party/webrtc/src/chromium/src/tools/checkperms/checkperms.py | Python | mit | 13,388 | [
"Galaxy",
"xTB"
] | 4fe122e59e655b928a895d9d97dfd7628a1cd69b4f8a33a9027598aeb7ec2fe7 |
## \package GODiGraph A directed graph representation of the Gene Ontology.
# \author Brian Muller <mullerb@musc.edu>
# \edited by Andrew Warren <aswarren@gmail.com> The makeGraph function returns the dictionary of nodes
#import networkx
from networkx import DiGraph, dfs_postorder_nodes, is_directed_acyclic_graph
fro... | aswarren/GOGranny | GOGranny/GODiGraph.py | Python | gpl-2.0 | 10,018 | [
"Brian",
"Cytoscape"
] | e58ad275996d65e023eeac9858064313b46a77ca06887c079bab041231387d0f |
def superExtract(*args, **kw):
"""
Optimally extract curved spectra, following Marsh 1989.
:INPUTS:
data : 2D Numpy array
Appropriately calibrated frame from which to extract
spectrum. Should be in units of ADU, not electrons!
variance : 2D Numpy array
Variances o... | bkaiser94/red_cam_pipeline | superextract.py | Python | mit | 26,909 | [
"Gaussian"
] | f133406d00f51bdc62ebfa19af173a44da94fd033be2536c718c90ced68885cc |
# Portions Copyright (c) Facebook, Inc. and its affiliates.
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2.
# changelog bisection for mercurial
#
# Copyright 2007 Matt Mackall
# Copyright 2005, 2006 Benoit Boissinot <benoit.boissinot@ens-lyon.org>
#
#... | facebookexperimental/eden | eden/hg-server/edenscm/mercurial/hbisect.py | Python | gpl-2.0 | 12,462 | [
"VisIt"
] | 6fe686c48c40ff44fa9cff02726e2495a05bbbefc553bfee728a128a2243804f |
"""Updates packages when new upstream releases become available
Overview:
- The `Scanner` initializes the `asyncio` loop and for each recipe,
loads the ``meta.yaml`` using `Recipe` and executes its `Filter`
objects for each recipe.
- The `Recipe` handles reading, modification and writing of
``meta.yaml`` files... | bioconda/bioconda-utils | bioconda_utils/autobump.py | Python | mit | 48,775 | [
"BLAST",
"Bioconda"
] | 08259e8fb6d328b0d8e5221828adb442c35ae9848591498dcd87b18a2b1a5b9d |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Perform fragmentation of molecules.
"""
import logging
import copy
from monty.json import MSONable
from pymatgen.analysis.graphs import MoleculeGraph, MolGraphSplitError
from pymatgen.analysis.local_env im... | fraricci/pymatgen | pymatgen/analysis/fragmenter.py | Python | mit | 19,296 | [
"pymatgen"
] | 488d48bcc559b9d458575e02ddde647be47cef27adf22f8868c9b6add632789e |
# cython: infer_types=True
#
# Tree visitor and transform framework
#
import inspect
import TypeSlots
import Builtin
import Nodes
import ExprNodes
import Errors
import DebugFlags
import cython
class TreeVisitor(object):
"""
Base class for writing visitors for a Cython tree, contains utilities for
recur... | JulienMcJay/eclock | windows/Python27/Lib/site-packages/Cython/Compiler/Visitor.py | Python | gpl-2.0 | 26,447 | [
"VisIt"
] | a4f44052c3e662bdad2144fcc7040237cd406615f2368ffec0697b394c1ca4a2 |
import os
import site
import sys
# Add
site.addsitedir(os.path.normpath(sys.argv[0] + "/../.."))
import rotamer.io.amber as amber_io
import rotamer.io.gmin as gmin_io
if __name__ == "__main__":
if sys.argv[1] == "init":
pass
elif sys.argv[1] == "move":
coords = amber_io.read_amber_restart(".coo... | khs26/rotamer_library | rotamer/driver.py | Python | mit | 440 | [
"Amber"
] | 8c5cd6e3fbb5867bc6b3bbd2765781cd39fb75b025bb49c308dcc0930d141e1c |
# $HeadURL: svn+ssh://svn.cern.ch/reps/dirac/DIRAC/trunk/DIRAC/Core/DISET/private/Transports/SSL/ThreadSafeSSLObject.py $
""" SAMResultsClient class is a client for the SAM Results DB.
"""
__RCSID__ = "$Id: ThreadSafeSSLObject.py 18161 2009-11-11 12:07:09Z acasajus $"
# it crashes epydoc
#__docformat__ = "restructuredt... | Sbalbp/DIRAC | Core/LCG/SAMResultsClient.py | Python | gpl-3.0 | 4,485 | [
"DIRAC"
] | 77ab3afa58fcea57bcca46b495cdc851f27f9c77c33519b460d06c8ebb2c77f2 |
'''
Testing of the BSE CLI interface
'''
import os
import sys
import subprocess
import pytest
from .common_testvars import cli_dir, fake_data_dir
def _test_cli_cmd(cmd):
# NOTE: We do not enforce any encoding here. What is returned will be a byte string
# For our purposes here, that is ok. We don't know wha... | MOLSSI-BSE/basis_set_exchange | basis_set_exchange/tests/test_cli.py | Python | bsd-3-clause | 2,412 | [
"NWChem",
"Psi4",
"TURBOMOLE"
] | 309bd3d0fced6bb028c73877f8d75147e334a6b865dab27110172b4d1712fbc0 |
# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
# All rights reserved.
#
# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are ... | wizmer/NeuroM | neurom/check/morphtree.py | Python | bsd-3-clause | 8,899 | [
"NEURON"
] | b4b8feacce322691a01c172eab10e85dbefac67c199e644ea9387ae439de256e |
"""
A test of the Gaussian elimination kernel used for the BoundaryRecoverer.
"""
from firedrake import (IntervalMesh, FunctionSpace, Function, RectangleMesh,
VectorFunctionSpace, FiniteElement, SpatialCoordinate)
from gusto import kernels
import numpy as np
import pytest
@pytest.fixture
def ... | firedrakeproject/gusto | tests/kernel_tests/test_gauss_elim_kernel.py | Python | mit | 5,081 | [
"Gaussian"
] | 96d9a501466468e41e4e468071fab1480588206d3d2d6df7ea3ae43924aa99a6 |
#!/usr/bin/env python
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Implementation for `pmg structure` CLI.
"""
import sys
from tabulate import tabulate
from pymatgen.core.structure import Structure
from pymatgen.analysis.structure_matcher import El... | davidwaroquiers/pymatgen | pymatgen/cli/pmg_structure.py | Python | mit | 3,810 | [
"pymatgen"
] | 13b4b087c945d318ede7e1b8c60c240a62d4ac8ee919dee6346ff0eba90f98c5 |
# Orca
#
# Copyright (C) 2011-2013 Igalia, S.L.
#
# Author: Joanmarie Diggs <jdiggs@igalia.com>
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (... | h4ck3rm1k3/orca-sonar | src/orca/label_inference.py | Python | lgpl-2.1 | 19,516 | [
"ORCA"
] | cc42b1563039f5241cb488e7b3f77f89b0407a7df34e1bc722146d3e68e8d0b7 |
# This demo solves the Stokes equations, using stabilized
# first order elements for the velocity and pressure. The
# sub domains for the different boundary conditions used
# in this simulation are computed by the demo program in
# src/demo/mesh/subdomains.
#
# Original implementation: ../cpp/main.cpp by Anders Logg
#... | MiroK/dolfin | demo/documented/stokes-stabilized/python/demo_stokes-stabilized.py | Python | gpl-3.0 | 2,361 | [
"VTK"
] | e66567b145028cbf0dceb8ae7cb96e03b2b71ed46d44f1c346cc5f8091ce89f2 |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | jbedorf/tensorflow | tensorflow/python/autograph/converters/break_statements.py | Python | apache-2.0 | 4,733 | [
"VisIt"
] | 203f20c90982be9be1335093ef17861f1cff42b9e5093cecdd6b31b57eb8f208 |
# Autodetecting setup.py script for building the Python extensions
#
__version__ = "$Revision$"
import sys, os, imp, re, optparse
from glob import glob
import sysconfig
from distutils import log
from distutils import text_file
from distutils.errors import *
from distutils.core import Extension, setup
from distutils.... | BeATz-UnKNoWN/python-for-android | python3-alpha/python3-src/setup.py | Python | apache-2.0 | 84,771 | [
"VisIt"
] | ec6f62f77044bafe8f6d86c138e178cef3e67be1f711346c112aed6d979de750 |
import ldap3
class CERNLDAPSyncPlugin(object):
"""Synchronization plugin for mapping new users to CERN accounts.
This plugin results in new users having two additional fields in the CS,
CERNAccountType and PrimaryCERNAccount. If the new nickname does not have a
corresponding CERN account it will be r... | DIRACGrid/DIRAC | src/DIRAC/ConfigurationSystem/Client/SyncPlugins/CERNLDAPSyncPlugin.py | Python | gpl-3.0 | 3,360 | [
"DIRAC"
] | 1fb6fc2d4d9a42938f4d22bf48b7bafe42b9a93ff507f19309b9dd67359bcdc9 |
"""User-friendly public interface to polynomial functions. """
from __future__ import print_function, division
from sympy.core import (
S, Basic, Expr, I, Integer, Add, Mul, Dummy, Tuple
)
from sympy.core.mul import _keep_coeff
from sympy.core.symbol import Symbol
from sympy.core.basic import preorder_traversal
... | madan96/sympy | sympy/polys/polytools.py | Python | bsd-3-clause | 175,595 | [
"Gaussian"
] | 943c309ece1d614bf23e3ad9cdf74ec5f0a3b0edce73b60da5c7ff2b26004810 |
"""
=============================================
Whitening evoked data with a noise covariance
=============================================
Evoked data are loaded and then whitened using a given
noise covariance matrix. It's an excellent
quality check to see if baseline signals match the assumption
of Gaussian white... | effigies/mne-python | examples/plot_evoked_whitening.py | Python | bsd-3-clause | 1,513 | [
"Gaussian"
] | 2e66c720abf8fd140b62a3e14b07caff31419850287675dbff4e1eef220b91b6 |
"""
Implementation of neural network
Core implementations
Tianqi Chen
"""
import numpy as np
import sys
# Full connected layer
# note: all memory are pre-allocated, always use a[:]= instead of a= in assignment
class FullLayer:
def __init__( self, i_node, o_node, init_sigma, rec_gsqr = False ):
asser... | aurora1625/bayesnn | nnet.py | Python | apache-2.0 | 12,457 | [
"Gaussian"
] | 4ecff0a109df32b5160ff57381a22f79961738965421ea8031aeed807fe56447 |
#!/usr/bin/env python
"""
PanGenome
Genome library
Uses a serial-BBH approach to compute a pangenome of the desired organisms list
"""
from Bio import SeqIO
from ductape.common.commonmultiprocess import CommonMultiProcess
from ductape.genome.blast import Blaster, RunBBH
import sys
if sys.version_info[0] < 3:
impo... | combogenomics/DuctApe | ductape/genome/pangenome.py | Python | bsd-2-clause | 13,168 | [
"BLAST"
] | b4934b49a3623cc5d6c56d83cec567889890858cb1ee60897d3b2fdae2fa2761 |
#!/usr/bin/python
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.2
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses... | ravibhure/ansible | lib/ansible/modules/network/avi/avi_vsvip.py | Python | gpl-3.0 | 4,713 | [
"VisIt"
] | ed2788e840d1a1884dd33f824e96663522b7c0e9587d0d3737e2e20811923bb3 |
import sys, os.path, logging
new_path = [ os.path.join( os.getcwd(), "lib" ) ]
new_path.extend( sys.path[1:] ) # remove scripts/ from the path
sys.path = new_path
from galaxy import eggs
import pkg_resources
pkg_resources.require( "sqlalchemy-migrate" )
from migrate.versioning.shell import main
from ConfigParser im... | volpino/Yeps-EURAC | scripts/manage_db.py | Python | mit | 1,484 | [
"Galaxy"
] | 85e4f0244c3853e6a83e31a7fbf94e3e42d1446c491e5e07250dc2f1422ff547 |
## serpent.py - pure Python implementation of the Serpent algorithm.
## Bjorn Edstrom <be@bjrn.se> 13 december 2007.
##
## Copyrights
## ==========
##
## This code is a derived from an implementation by Dr Brian Gladman
## (gladman@seven77.demon.co.uk) which is subject to the following license.
## This Python ... | gray-panda/grayrepo | 2020_flareon/11_rabbithole/serpent.py | Python | gpl-2.0 | 71,724 | [
"Brian"
] | ead66f29f72e05567331977ecd7cc399fd697537f7c4cf5593ea2832483c5be6 |
#!/usr/bin/env python
#-*- coding:utf-8 -*-
#
# This file is part of the NNGT project to generate and analyze
# neuronal networks and their activity.
# Copyright (C) 2015-2019 Tanguy Fardet
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License a... | Silmathoron/NNGT | doc/examples/introduction_to_groups.py | Python | gpl-3.0 | 8,292 | [
"NEURON"
] | d2837b0aebc02c72ba6a31bf8d66592dc11d49f30a4d5df6ffbfbf9e89162245 |
from __future__ import division ## true division in Python 2 (NOT NEEDED FOR PYTHON3)
import numpy as np ## package for scientific computing with Python
from scipy import sparse as sp ## package for sparse matrices
from scipy import stats as st ## package for stats
import matplotlib.pyplot as plt #... | degoldschmidt/QIF | network_spik.py | Python | gpl-3.0 | 5,090 | [
"Gaussian",
"NEURON"
] | 8e65c13a7420ae8dd712a88eefd67bdf9e9abf34d629a3655325c20bf03f679f |
# Outdoor Solar Adjusted Temperature Calculator
#
# Ladybug: A Plugin for Environmental Analysis (GPL) started by Mostapha Sadeghipour Roudsari
#
# This file is part of Ladybug.
#
# Copyright (c) 2013-2015, Chris Mackey <Chris@MackeyArchitecture.com>
# Ladybug is free software; you can redistribute it and/or modify ... | samuto/ladybug | src/Ladybug_Outdoor Solar Temperature Adjustor.py | Python | gpl-3.0 | 84,683 | [
"EPW"
] | e659d3ef260be33fbd75e53283967af0b05f2fe72053bd260032df58f58a4903 |
################################################################################
# Copyright (C) 2013 Jaakko Luttinen
#
# This file is licensed under the MIT License.
################################################################################
r"""
General functions random sampling and distributions.
"""
import ... | jluttine/bayespy | bayespy/utils/random.py | Python | mit | 11,769 | [
"Gaussian"
] | 5de774b5ec7eee86c557e9519280f288519b6b28e2ff6e8d35db506177b79f66 |
#! /usr/bin/env python
# FIXME: it has to be seen if this is any useful
# FIXME: to bring back to life
from DIRAC.Core.Base.Script import parseCommandLine
parseCommandLine()
from DIRAC.Resources.Catalog.FileCatalog import FileCatalog
from DIRAC.Core.Utilities.File ... | andresailer/DIRAC | tests/Integration/Resources/Catalog/FIXME_Test_CatalogPlugin.py | Python | gpl-3.0 | 18,130 | [
"DIRAC"
] | 6a73b0d07aaa6d68b38e7735baa9f322e418541c0f182e19ef8f17ac15751599 |
""" File catalog class. This is a simple dispatcher for the file catalog plug-ins.
It ensures that all operations are performed on the desired catalogs.
The File Catalog plug-ins are supposed to implement a certain number of methods of
the File Catalog interface. The names of the implemented methods classi... | yujikato/DIRAC | src/DIRAC/Resources/Catalog/FileCatalog.py | Python | gpl-3.0 | 19,117 | [
"DIRAC"
] | 11d861d9189a0555005a92f4c7d11a711691586fa3be9757e5859fd66edcd391 |
#!/usr/bin/env python
# encoding: utf-8
"""
paper1.py
Scripts for G. Brammer's first paper with the 3D-HST data. General utilities for redshift fitting, etc. are also in 'unicorn.analysis'.
$URL: https://subversion.assembla.com/svn/threedhst_internal/trunk/reduce.py $
$Author: gbrammer $
$Date: 2011-05-22 02:01:43 -... | gbrammer/unicorn | paper1.py | Python | mit | 17,567 | [
"Galaxy"
] | d4d2a955b8bbf49a78ce675c21b959598736b0927986039812be9d5af5609914 |
# moosehandler.py ---
#
# Filename: moosehandler.py
# Description:
# Author: subhasis ray
# Maintainer:
# Created: Tue Jun 16 12:25:40 2009 (+0530)
# Version:
# Last-Updated: Wed Feb 10 10:02:44 2010 (+0100)
# By: Subhasis Ray
# Update #: 229
# URL:
# Keywords:
# Compatibility:
#
#
# Commentar... | BhallaLab/moose-thalamocortical | pymoose/gui/moosehandler.py | Python | lgpl-2.1 | 6,160 | [
"MOOSE"
] | 0fcc4c1b7959a93a3b4c9d44ceee65775ad093c16cd0d90bcc85a8539e9e7671 |
# Copyright (c) Charl P. Botha, TU Delft
# All rights reserved.
# See COPYRIGHT for details.
from module_base import ModuleBase
from module_mixins import ScriptedConfigModuleMixin
import module_utils
import vtk
import math
class MarschnerLobb(ScriptedConfigModuleMixin, ModuleBase):
def __init__(self, module_mana... | nagyistoce/devide | modules/misc/MarschnerLobb.py | Python | bsd-3-clause | 3,289 | [
"VTK"
] | 6c49a19541207d6b056ef5d8bf5143386121bea4b9e70353c165bbaeccbbf861 |
#!/usr/bin/env python
import sys
import os
import re
import glob
import xmltodict
import json
import yaml
import copy
import logging
from argparse import ArgumentParser
from argparse import RawDescriptionHelpFormatter
from elasticsearch1 import Elasticsearch
from collections import OrderedDict
import datetime
import ... | ICGC-TCGA-PanCancer/pcawg-central-index | pcawg_metadata_parser/generate_ceph_transfer_json.py | Python | gpl-2.0 | 27,134 | [
"BWA"
] | 3799810d3e0f9faa4711c0768cdde6ecbc0a51c35a0977daa654436205b42cc3 |
# Copyright 2010 Google Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... | arjunsatyapal/lantern | demo1/demo/views.py | Python | apache-2.0 | 47,752 | [
"VisIt"
] | 4bde0993e4eb2250da56b76fbc359ce6cd18cf5ad27f8214c65a99d9dc860177 |
#__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... | matthew-brett/scipy | scipy/optimize/_optimize.py | Python | bsd-3-clause | 135,580 | [
"Gaussian"
] | 87922f16a9175f911a430cd06256c1372b2a0b91673748caa409e9b317ee7198 |
import numpy as np
import unittest
from caffe2.python import core, workspace, test_util
class TestToyRegression(test_util.TestCase):
def testToyRegression(self):
"""Tests a toy regression end to end.
The test code carries a simple toy regression in the form
y = 2.0 x1 + 1.5 x2 + 0.5
... | xzturn/caffe2 | caffe2/python/toy_regression_test.py | Python | apache-2.0 | 2,822 | [
"Gaussian"
] | d3e00883760b98200155b20886a79e317c41cc053b96bb6014513dff7d19fac8 |
import threading
from ase.test import World
from ase.io import PickleTrajectory
from ase.neb import NEB
from ase.calculators.lj import LennardJones as Calculator
from ase.optimize import BFGS
fmax = 0.05
nimages = 3
print [a.get_potential_energy() for a in PickleTrajectory('H.traj')]
images = [PickleTrajectory('H.t... | JConwayAWT/PGSS14CC | lib/python/multimetallics/ase/test/neb.py | Python | gpl-2.0 | 1,489 | [
"ASE"
] | e87a5282b1f56eb5fe51e2dbc39bd1ee139c629c2153e58032f5e6a37b00963c |
from __future__ import division, print_function
import os
import numpy as np
import netCDF4 as n4
import time as ttime
from collections import OrderedDict as OD
import matplotlib.dates as dates
from utilities import get_nv
def _file_factory(self, casename, endname, filetype='ascii'):
"""
Code to crea... | moflaher/fvcom_pyprocessor | fvcom_pyprocessor/save_fvcom.py | Python | agpl-3.0 | 37,519 | [
"NetCDF"
] | 969982ed28d4b7cdabc47016f0a50e44fbc256335febbae1a9103587825d55b4 |
""" The SystemAdministratorIntegrator is a class integrating access to all the
SystemAdministrator services configured in the system
"""
__RCSID__ = "$Id$"
from DIRAC import S_OK
from DIRAC.Core.Utilities.ThreadPool import ThreadPool
from DIRAC.FrameworkSystem.Client.SystemAdministratorClient import SystemAdminis... | fstagni/DIRAC | FrameworkSystem/Client/SystemAdministratorIntegrator.py | Python | gpl-3.0 | 3,045 | [
"DIRAC"
] | ac65dce25eab97777f415943f5236081e8a48a5be58e7cbeeae6599f25bcc9d7 |
from matplotlib import pyplot as plt
from evaluation import evaluate,evalDensity
import numpy
class Visualizer(object):
def __init__(self,evaluator,extent,xn,yn,incWave=None):
self.evaluator=evaluator
self.incWave=incWave
self.f=None
self.setGrid(extent,xn,yn)
... | tbetcke/PyBEM2D | pybem2d/core/visualization.py | Python | mit | 5,843 | [
"Mayavi"
] | 50e1d84fe5b76c6efbc7b2b11a7bdd4cf4cff76333807dc4f8288e645cd3300b |
#!/usr/bin/env python
__license__ = 'GPL v3'
__copyright__ = '2008, Kovid Goyal <kovid at kovidgoyal.net>'
''' Create an OSX installer '''
import sys, re, os, shutil, subprocess, stat, glob, zipfile, plistlib
from setup import __version__ as VERSION, __appname__ as APPNAME, SRC, Command, \
scripts, basenames... | nozuono/calibre-webserver | setup/installer/osx/freeze.py | Python | gpl-3.0 | 18,558 | [
"VisIt"
] | b028d028ac601a4bbbf18ffea8e7fe25ac1e6650428482330647a355ac215e66 |
import os.path
import ast
import annotators
import llvm_builder
import compiler
import hpcs_builtins
from optparse import OptionParser
import llvmlite.binding as llvm
def compile_source(source_file_name):
checker = compiler.ConstraintChecker()
with open(source_file_name) as source_file:
source = ast.... | Jokymon/hpcs | hpcs.py | Python | gpl-3.0 | 2,297 | [
"VisIt"
] | 6713c1c4f722cb3eececbe0c204267f9b3429723f8be194663bd3ed857c3f522 |
#!/usr/bin/env python
# add paths
import os, sys, traceback
sys.path.append('../utils')
# import modules
from co2 import CO2
from fillgaps import fill
from dewpoint import dewpoint
import os, re, stat, datetime
from netCDF4 import Dataset as nc
from optparse import OptionParser
from collections import OrderedDict as ... | RDCEP/psims | pysims/translators/dssat45/psims2wth.py | Python | agpl-3.0 | 12,520 | [
"NetCDF"
] | e8b904415e0c94ea7405cc5df8f7a9bc69452304fb03acf6021297127d3f259a |
import os
import sys
import time
from math import sin, cos, radians, atan2, degrees
import numpy as np
from ase.data import chemical_symbols
class DevNull:
def write(self, string):
pass
def flush(self):
pass
def seek(self, offset, whence=0):
return 0
def tell(self):
... | askhl/ase | ase/utils/__init__.py | Python | gpl-2.0 | 6,523 | [
"ASE"
] | 86e063b52af1b7ca11c23c4e3f26eb4359de2f3003b2247f9959161e159bc64a |
"""
Extensions to SQLAlchemy for altering existing tables.
At the moment, this isn't so much based off of ANSI as much as
things that just happen to work with multiple databases.
"""
import StringIO
import sqlalchemy as sa
from sqlalchemy.schema import SchemaVisitor
from sqlalchemy.engine.default import Defa... | razzius/sqlalchemy-migrate | migrate/changeset/ansisql.py | Python | mit | 11,385 | [
"VisIt"
] | 07f0410d9e477c1e1512c9cf4ab8df1e911ad733605535a77f3a2bbb0250be3d |
# Orca
#
# Copyright 2009 Sun Microsystems Inc.
# Copyright 2015-2016 Igalia, S.L.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your optio... | GNOME/orca | src/orca/generator.py | Python | lgpl-2.1 | 62,265 | [
"ORCA"
] | e4ee40b26e423d2b774be86d7dd83bf3d975d8edd1a33242542ac02083979e26 |
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