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|---|---|---|---|---|---|---|---|
# -*- coding: utf-8 -*-
"""
@author: AlexBourassa
This is based on old code. It works, but may not be optimal or simple...
"""
from A_Lab.Widgets.GraphWidget.Graph_Widget_Plugin import *
from PyQt4 import QtGui as _gui
from PyQt4 import QtCore as _core
from PyQt4 import uic as _uic
import os as _os
import numpy as _n... | AlexBourassa/A-Lab | A_Lab/Widgets/GraphWidget/Fitter.py | Python | gpl-2.0 | 14,054 | [
"Gaussian"
] | 61dba5114ce43af0520700da49178dfd1df7f6354045bced83af1f46a467447a |
"""
View for Courseware Index
"""
# pylint: disable=attribute-defined-outside-init
import logging
import urllib
from django.conf import settings
from django.contrib.auth.decorators import login_required
from django.contrib.auth.models import User
from django.core.context_processors import csrf
from django.core.urlre... | Lektorium-LLC/edx-platform | lms/djangoapps/courseware/views/index.py | Python | agpl-3.0 | 21,509 | [
"VisIt"
] | 5bd3fc9ad0d2eea43ba2432e1a87f52aecea928f89b3bb1a435aed2badd2d92d |
#!/usr/bin/env python
'''
Parse logged data from BEDs .EVT or .WAT file to compute translations in x, y, z and rotations
about these axes. Output as NetCDF with the intention of of loading into a STOQS database.
The resulting Netcdf file will be of featureType timeSeries for stationary events (the default).
If the --t... | stoqs/stoqs | stoqs/loaders/CCE/bed2netcdf/bed2netcdf.py | Python | gpl-3.0 | 41,983 | [
"NetCDF"
] | 36b1067237efe4420b5f5239755b079c6f55261772526a34638bba52444d150f |
# -*- coding: utf-8 -*-
'''
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is dis... | repotvsupertuga/repo | plugin.video.zen/resources/lib/sources/phdmovies_mv_tv.py | Python | gpl-2.0 | 8,060 | [
"ADF"
] | 4f96dd4aa3344d2b3dd0cdba053fb5e21ff7829b812fe101dd831898c9d940c6 |
from pyneuroml.neuron import export_to_neuroml1
export_to_neuroml1("test.hoc", "test.level1.xml", 1)
export_to_neuroml1("test.hoc", "test.level2.xml", 2)
| 34383c/pyNeuroML | examples/export_neuroml1.py | Python | lgpl-3.0 | 158 | [
"NEURON"
] | 28ab94e263f3899c21a14b5a27d186458ace523c747baff64bc014dc5a7492b4 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# notifypassword - Send forgotten password from user database to user
# Copyright (C) 2003-2011 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of... | heromod/migrid | mig/server/notifypassword.py | Python | gpl-2.0 | 4,268 | [
"Brian"
] | 46ca55ac7d38e599d68988d8576e48cde12e22fe3a9f9da59a90665d3a25b0e8 |
#!/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 that all files contain proper licensing information."""
import json
import optparse
import os.path
import subproces... | Just-D/chromium-1 | tools/checklicenses/checklicenses.py | Python | bsd-3-clause | 19,353 | [
"Galaxy"
] | 9942cd8942c82adde65e9b3b5c91e4ac85c74349effe40ced49fd00f78735697 |
import numpy, pylab, scipy, scipy.optimize, scipy.interpolate, copy
from xrd_diffraction_conversion_fcns import *
import matplotlib.delaunay as dlny
def numtostring(x, n=0): #exponential notation with n significnat digits. if n not specified then trivial string conversion
if n < 1:
return str(x)
return... | johnmgregoire/vanDover_CHESS | xrd_math_fcns.py | Python | bsd-3-clause | 112,346 | [
"Gaussian"
] | 71db6ea5d5ab04ec60edc5528701776d190d4837740b67151d2e472a14cbac6f |
"""Builds the CIFAR-10 network.
Summary of available functions:
# Compute input images and labels for training. If you would like to run
# evaluations, use input() instead.
inputs, labels = distorted_inputs()
# Compute inference on the model inputs to make a prediction.
predictions = inference(inputs)
# Compu... | kcartier/tensorflow-toe-in-the-water | tensorflow/models/image/cifar10/cifar10.py | Python | apache-2.0 | 17,878 | [
"Gaussian"
] | 068ffef01c6e9eec52c010dd1fb7ccf862fd85de846c2127d039b5715cc6e72a |
import logging
import datetime
import simplejson
import tempfile
try:
from hashlib import md5
except:
from md5 import md5
from dirac.lib.base import *
from dirac.lib.diset import getRPCClient, getTransferClient
from dirac.lib.credentials import getUsername, getSelectedGroup, getSelectedSetup
from DIRAC import S_O... | DIRACGrid/DIRACWeb | dirac/controllers/systems/accountingPlots.py | Python | gpl-3.0 | 10,892 | [
"DIRAC"
] | 98ac951e95c16becad5c291e3481c4eab1c882e45356ee3804587bec74e8e005 |
#
# This module contains messages
#
from ige.ospace.Const import *
from ige import NoSuchObjectException
import client, types, string, res, gdata
from ige import log
#
# Transform routines
#
def techID2Name(techID):
if techID >= 1000:
return _(client.getTechInfo(techID).name.encode())
else:
return... | mozts2005/OuterSpace | client-msg-wx/lib/messages.py | Python | gpl-2.0 | 9,437 | [
"Galaxy"
] | eee42ccc7e4b0bb4c2041ae52e83c42d8b97ef5da804dc5e1fa3ac4aac5b4c42 |
"""Unit test for roman72.py
This program is part of "Dive Into Python", a free Python book for
experienced programmers. Visit http://diveintopython.org/ for the
latest version.
"""
__author__ = "Mark Pilgrim (mark@diveintopython.org)"
__version__ = "$Revision: 1.3 $"
__date__ = "$Date: 2004/05/05 21:57:20 $"
__copyr... | tapomayukh/projects_in_python | sandbox_tapo/src/refs/diveintopython-pdf-5.4/diveintopython-5.4/py/roman/stage7/romantest72.py | Python | mit | 5,848 | [
"VisIt"
] | 82d8e83649c5d4fdb9fb37300b607ba0c2d299cc0eff77a1e8dd5563f14798b9 |
#
# QAPI types generator
#
# Copyright IBM, Corp. 2011
#
# Authors:
# Anthony Liguori <aliguori@us.ibm.com>
#
# This work is licensed under the terms of the GNU GPLv2.
# See the COPYING.LIB file in the top-level directory.
from ordereddict import OrderedDict
from qapi import *
import sys
import os
import getopt
impor... | piyushroshan/xen-4.3.2 | tools/qemu-xen/scripts/qapi-types.py | Python | gpl-2.0 | 7,559 | [
"VisIt"
] | 4cc861370b086f5f874974ef19ce016a9b900c1524b2a2898eabf8757a1a8a2b |
# Copyright (C) 2013-2020 2ndQuadrant Limited
#
# This file is part of Barman.
#
# Barman is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later versio... | 2ndquadrant-it/barman | barman/output.py | Python | gpl-3.0 | 65,249 | [
"ESPResSo"
] | d1549a26efc2bfa159ed14e541d2471311362379d30b70d3ef804fbab0f3610f |
# Copyright (c) 2012, Cloudscaling
# All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable... | klmitch/nova | nova/hacking/checks.py | Python | apache-2.0 | 32,078 | [
"VisIt"
] | 14c3ef46bda7b430dcce20833de11793c8e5f746fb72166270d70c15b5dd3784 |
import version
version.append ('$Revision: 91660 $')
del version
# This file is 'kImage' instead of 'Image' because of the potential
# conflict with the Python Imaging Library.
try:
import Image
import ImageColor
import ImageDraw
except ImportError:
import PIL.Image as Image
import PIL.ImageColor as ImageColor
... | alexrudy/Cauldron | Cauldron/bundled/GUI/kImage.py | Python | bsd-3-clause | 18,912 | [
"MOE"
] | 8a89c286f63ea80c72ccdd3952273a6b252087de9357ae2a2c0fdba02dc0cce8 |
''' DIRAC.ResourceStatusSystem.Policy package
'''
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = '$Id$'
| yujikato/DIRAC | src/DIRAC/ResourceStatusSystem/Policy/__init__.py | Python | gpl-3.0 | 179 | [
"DIRAC"
] | dfb9380fe4a10570c3e7b23b795c6e545a03df1c4caf5ac0c40defada2ff653f |
from sys import exit
from random import randint
class Scene(object):
def enter(self):
print "This scene is not yet configured. Subclass it and implement enter()."
exit(1)
class Engine(object):
def __init__(self, scene_map):
self.scene_map = scene_map
def play(self):
curr... | liggettla/python | ex43.py | Python | mit | 8,807 | [
"BLAST"
] | 07c56b711cb1c687479e50dffd7027d1635494c4488465cd00f0a43231cc65bc |
"""Implements the graph generation for computation of gradients."""
import collections
import warnings
import tensorflow.python.platform
import numpy as np
from tensorflow.python.framework import ops
from tensorflow.python.framework import tensor_shape
from tensorflow.python.framework import tensor_util
from tensor... | liyu1990/tensorflow | tensorflow/python/ops/gradients.py | Python | apache-2.0 | 24,255 | [
"VisIt"
] | edbb5460e2e3b6ca69df83bfe1c151f0659330559d48e4e3160cdd7345cb94be |
#!/usr/bin/env python2
# vim:fileencoding=UTF-8:ts=4:sw=4:sta:et:sts=4:ai
from __future__ import with_statement
__license__ = 'GPL v3'
__copyright__ = '2009, Kovid Goyal <kovid@kovidgoyal.net>'
__docformat__ = 'restructuredtext en'
import sys, os, shutil, plistlib, subprocess, glob, zipfile, tempfile, \
py_comp... | ashang/calibre | setup/installer/osx/app/main.py | Python | gpl-3.0 | 27,912 | [
"VisIt"
] | d1f6493b7e7dd50bf4d6ecdc6e9ba96b2a3fed0ab0d0f50fca12a78a5d29e001 |
import matplotlib.pyplot as plt
import os
from astropy.table import Table
import numpy as np
# setup information sources
degas = Table.read(os.path.join(os.environ['SCRIPTDIR'],'degas_base.fits'))
stack = Table.read('/lustre/cv/users/akepley/degas/stack_test/stack_IR6p0_mom1.fits')
plotDir = os.path.join(os.environ['... | low-sky/degas | scripts/plot_fdense_vs_molmass_combined.py | Python | gpl-3.0 | 2,487 | [
"Galaxy"
] | b858d5ba32bfd64fa6d81b720480e7006dab090908f18f0b41d32d59ffe351bd |
"""
Various bayesian regression
"""
from __future__ import print_function
# Authors: V. Michel, F. Pedregosa, A. Gramfort
# License: BSD 3 clause
from math import log
import numpy as np
from scipy import linalg
from scipy.linalg import pinvh
from .base import LinearModel
from ..base import RegressorMixin
from ..util... | MechCoder/scikit-learn | sklearn/linear_model/bayes.py | Python | bsd-3-clause | 19,650 | [
"Gaussian"
] | 92c54dbc0c5cdc6c1c9efc739832fa32cfb5abea69cfb55782fafb24809fd2c2 |
words=[
u"James", u"John", u"Robert", u"Michael", u"William", u"David", u"Richard", u"Joseph",
u"Charles", u"Thomas", u"Christopher", u"Daniel", u"Matthew", u"Donald", u"Anthony",
u"Paul", u"Mark", u"George", u"Steven", u"Kenneth", u"Andrew", u"Edward", u"Brian",
u"Joshua", u"Kevin", u"Ronald", u"Timothy", u"Jason... | Ivacker/swift | utils/benchmark/Phonebook/Phonebook.py | Python | apache-2.0 | 1,595 | [
"Brian"
] | 39988a41020106409708e3da4aa8604bb5e03198dbb4f487052bc29be722bd88 |
#!/usr/bin/env python
"""Collect daily reference desk statistics in a database
Display the stats in a useful way with charts and download links"""
from flask import Flask, abort, request, redirect, url_for, \
render_template, make_response, g, session
from flask_babelex import Babel
from flask_lo... | dbs/refdeskstats | refdesk.py | Python | gpl-3.0 | 22,461 | [
"VisIt"
] | fe8eb08de4638843d245070187fc4264e992b5e16403dbc0c80d579378d0f109 |
"""
The B{0install} command-line interface.
"""
# Copyright (C) 2011, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from __future__ import print_function
from zeroinstall import _, logger
import os, sys
from optparse import OptionParser
import logging
from zeroinstall import SafeEx... | AlexanderRyzhko/0install-TUF | zeroinstall/cmd/__init__.py | Python | lgpl-2.1 | 12,927 | [
"VisIt"
] | 7985e05ba4ad54662a3b96f69b0cb552ad4a428f8e7ba9aa7489ac97c2c30a62 |
from rdkit import RDConfig
import os, sys
import unittest
from rdkit import Chem
from rdkit.Chem import rdMolHash
class TestCase(unittest.TestCase):
def setUp(self):
pass
def test1(self):
m = Chem.MolFromSmiles('C1CCCC(O)C1c1ccnc(OC)c1')
self.assertEqual(rdMolHash.MolHash(m, rdMolHash.HashFunction.A... | greglandrum/rdkit | Code/GraphMol/MolHash/Wrap/testMolHash.py | Python | bsd-3-clause | 1,896 | [
"RDKit"
] | 243216bf4ba2fdc4c02b4420a7ac182f8aaaf2bb84d7a276c10ae3a19dd72ad9 |
"""Universal feed parser
Handles RSS 0.9x, RSS 1.0, RSS 2.0, CDF, Atom 0.3, and Atom 1.0 feeds
Visit http://feedparser.org/ for the latest version
Visit http://feedparser.org/docs/ for the latest documentation
Required: Python 2.1 or later
Recommended: Python 2.3 or later
Recommended: CJKCodecs and iconv_codec <http... | virtuald/exaile | plugins/podcasts/_feedparser.py | Python | gpl-2.0 | 122,472 | [
"NetCDF",
"VisIt"
] | 5177664d3d7fc98623f344e4e520208c8326202b8e27c0b18c540cbbccda6305 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
The initial version of this module was based on a similar implementation
present in FireWorks (https://pypi.python.org/pypi/FireWorks).
Work done by D. Waroquiers, A. Jain, and M. Kocher.
The main differenc... | montoyjh/pymatgen | pymatgen/io/abinit/qadapters.py | Python | mit | 87,473 | [
"ABINIT",
"pymatgen"
] | 2456e6e5eef1bf0e211c2a552bc00907392e0e0559e2b07baef02e431fd95ffd |
###
# Utilities used in RunMC.py for its Monte Carlo algorithm.
# -Tristan Truttmann (tristan.truttmann@gmail.com)
###
# Note: Possible future improvement is to record density matrices for faster convergence.
# The followign ~20 lines define imporant files and directories to write to and get from.
# It also extends t... | ttruttmann/monte-carlo | MC_Util.py | Python | mit | 58,383 | [
"Molpro",
"SIESTA"
] | 9eb294482ef1236f55e904c395402d7f0c47680411c958835329c1f4b144f576 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | lgarren/spack | var/spack/repos/builtin/packages/r-affyio/package.py | Python | lgpl-2.1 | 1,756 | [
"Bioconductor"
] | 345b1f35c6690a74c9b8f1986ec15aec5489d2e394f3d15e7a8913d9a1b71b6d |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkFieldDataToAttributeDataFilter(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,... | nagyistoce/devide | modules/vtk_basic/vtkFieldDataToAttributeDataFilter.py | Python | bsd-3-clause | 519 | [
"VTK"
] | 8f111d5cbc205cc4db76c171364e0e84fb8969aeed66da6d12e1b9eb6c8cb338 |
from gpaw.xc.libxc import LibXC
from math import pi
import numpy as np
nspins = 1
for name in [
'LDA', 'PBE', 'revPBE', 'RPBE',
'LDA_X', 'GGA_X_PBE_R', 'GGA_X_RPBE',
'LDA_C_PW',
]:
xc = LibXC(name)
xc.initialize(nspins)
libxc = xc.xc
lxc_fxc = libxc.calculate_fxc_spinpaired
lxc_fxc_... | qsnake/gpaw | gpaw/test/lxc_fxc.py | Python | gpl-3.0 | 1,639 | [
"GPAW"
] | cb8bf0afd11c421f33645c34c2439a1fa99c0be83d51f0099912b4e5ae803164 |
"""Utilities allowing for high-level testing throughout Pulsar."""
import traceback
import sys
import threading
import os
from contextlib import contextmanager
from stat import S_IXGRP, S_IXOTH
from os import pardir, stat, chmod, access, X_OK, pathsep, environ
from os import makedirs, listdir
from os.path import join... | galaxyproject/pulsar | test/test_utils.py | Python | apache-2.0 | 16,551 | [
"Galaxy"
] | 44b6333673cfc52b498eeac2a68f7b02aac5c9591b828a2481a6221d1724db82 |
# pmx Copyright Notice
# ============================
#
# The pmx source code is copyrighted, but you can freely use and
# copy it as long as you don't change or remove any of the copyright
# notices.
#
# ----------------------------------------------------------------------
# pmx is Copyright (C) 2006-2013 by Daniel ... | tectronics/pmx | pmx/xtc.py | Python | lgpl-3.0 | 5,230 | [
"Gromacs"
] | acdafc2d304defb630c524c16d42bee9da5f0db90c5d15556fbc81f8214e416d |
SU_ITEMS = [
'The Xiphos',
"Kraken's Cutlass",
'Saber of the Stormsail',
'Aeterna',
'The Defender',
'Aurumvorax',
'Durandal the Blazing Sword',
"Qarak's Will",
"Tylwulf's Betrayal",
'Blacktongue',
'Feltongue',
'Shadowsabre',
'Grotesque Bite',
'The Captain',
'N... | baiumbg/useless-cogs | mxl/constants.py | Python | mit | 31,567 | [
"CRYSTAL",
"Firefly",
"Jaguar",
"TINKER"
] | 67de4deb3c27b94c28b889321f81f3f9191306a4d4086a037b49cb2bffac83e6 |
# Copyright 2012, 2013 The GalSim developers:
# https://github.com/GalSim-developers
#
# This file is part of GalSim: The modular galaxy image simulation toolkit.
#
# GalSim 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... | mardom/GalSim | tests/test_base.py | Python | gpl-3.0 | 79,805 | [
"Galaxy",
"Gaussian"
] | c25ac072e1d45c1f043a62f1ffd7d0ca5195590f2823be8c32628adbaa48eaf2 |
###############################################################################
# Copyright 2016 - Climate Research Division
# Environment and Climate Change Canada
#
# This file is part of the "EC-CAS diags" package.
#
# "EC-CAS diags" is free software: you can redistribute it and/or modify
# it under... | neishm/EC-CAS-diags | eccas_diags/common.py | Python | lgpl-3.0 | 28,889 | [
"CDK"
] | 8bd012a6e6b7f812157d540a9b2a8b0952f7b83b586bd7d12256d090e6e0e2ff |
# -*- coding: utf-8 -*-
# Copyright 2021 El Nogal - Pedro Gómez <pegomez@elnogal.com>
# License AGPL-3.0 or later (http://www.gnu.org/licenses/agpl).
from openerp import models, fields, api, exceptions, _
from openerp.osv import expression
from datetime import datetime
from dateutil.relativedelta import relativedelta
... | ELNOGAL/CMNT_00040_2016_ELN_addons | commercial_route/models/commercial_route.py | Python | agpl-3.0 | 5,588 | [
"VisIt"
] | 4ca4dfb3534ab151ebe54066a02b872abbe0d06c04d24f032b794d213fbf78ea |
#!/bin/env python2.7
import sys
import os
import os.path
import glob
import copy
import traceback
import time
import re
import csv
import tempfile
import urllib.request, urllib.parse, urllib.error
import shutil
import atexit
import subprocess
import time
import math
from collections import defaultdict
from os.path impo... | HorvathLab/NGS | RNA2DNAlign/src/LoH.py | Python | mit | 10,447 | [
"pysam"
] | 9ea46797d2c4be7d21f252742e12328d975d574557869d938ee0a99a65ff74f1 |
#!/usr/bin/env python
# Extract fasta files by their descriptors stored in a separate file.
# Requires biopython
# TODO:
# - Create more sophisticated logic for matching IDs/Descriptions/Partial matches etc.
# - Create a mode variable to encapsulate invert/partial/description/id etc?
from Bio import SeqIO
import s... | jrjhealey/bioinfo-tools | fastafetcher.py | Python | gpl-3.0 | 4,793 | [
"Biopython"
] | bf34fbde69ffe09d20fdb8b4d845c00cba0ba4ee87fb85ae96a8ece485587181 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Simple volume rendering example.
reader = vtk.vtkSLCReader()
reader.SetFileName(VTK_DATA_ROOT + "/Data/sphere.slc")
# Create transfer functions for opacity and color
opa... | hlzz/dotfiles | graphics/VTK-7.0.0/Rendering/Volume/Testing/Python/volTM2DCropRegions.py | Python | bsd-3-clause | 3,520 | [
"VTK"
] | 4a00635b55ebb8e992e072d6855a6a9eafcd0c7a1ec99b5d33731c4676463c9f |
#
# 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... | maropu/spark | python/pyspark/ml/regression.py | Python | apache-2.0 | 91,559 | [
"Gaussian"
] | ef98bce5ef3ecb36b4b49069e5aef7d15f1fd879e41a512a0e1b55659c7282ae |
# Compute a particle concentration
# and save as netCDF
import datetime
import numpy as np
from netCDF4 import Dataset
from postladim import ParticleFile
# import gridmap
# ----------------
# User settings
# ----------------
particle_file = "/hexagon/vol1/bjorn_rhea/out.nc"
grid_file = "/data/model_data006/anneds... | bjornaa/ladim | models/zladim/agg2nc.py | Python | mit | 2,415 | [
"NetCDF"
] | 0ae3533efc2af9bdc014394a3ecbdf2109ad4396c7a762e1960a0586ffa86e18 |
import sys
import logging
import ast
import constants as c
import copy
import numpy
import os
import qcck
import qcgf
import qcio
import qcrp
import qcts
import qcutils
import time
import xlrd
import meteorologicalfunctions as mf
log = logging.getLogger('qc.ls')
def l1qc(cf):
# get the data series from the Excel ... | OzFlux/OzFluxQC | scripts/qcls.py | Python | gpl-3.0 | 17,765 | [
"NetCDF"
] | f6c50d3f23fd390d0d8ab6b29bcc9cf2c616ac2a4198e774346d94aec3d1a563 |
"""
Views for user API
"""
from django.shortcuts import redirect
from django.utils import dateparse
from rest_framework import generics, views
from rest_framework.decorators import api_view
from rest_framework.response import Response
from opaque_keys.edx.keys import UsageKey
from opaque_keys import InvalidKeyError
... | kamalx/edx-platform | lms/djangoapps/mobile_api/users/views.py | Python | agpl-3.0 | 9,333 | [
"VisIt"
] | 47eeebff832d135724609e26afe59291ba189d35b557c55bda112496470aa6a9 |
"""
=========================
Bayesian Ridge Regression
=========================
Computes a Bayesian Ridge Regression on a synthetic dataset.
See :ref:`bayesian_ridge_regression` for more information on the regressor.
Compared to the OLS (ordinary least squares) estimator, the coefficient
weights are slightly shift... | JT5D/scikit-learn | examples/linear_model/plot_bayesian_ridge.py | Python | bsd-3-clause | 2,553 | [
"Gaussian"
] | e0bda6d2f77ae647e003c518a1535d011b7927ca06e9d12579da3f83ab55a5bc |
from __future__ import division, absolute_import, print_function
import numpy as np
from .common import run_monitored, set_mem_rlimit, Benchmark
try:
from scipy.stats import spearmanr
except ImportError:
pass
try:
import scipy.interpolate as interpolate
except ImportError:
pass
class Leaks(Benchma... | pnedunuri/scipy | benchmarks/benchmarks/interpolate.py | Python | bsd-3-clause | 6,314 | [
"Gaussian"
] | db6d2dec72ba08c7c3cb2a39f3eeff5f6b45f3f615ad0880f08c48006588c406 |
##
# Copyright 2009-2017 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (F... | ULHPC/easybuild-easyblocks | easybuild/easyblocks/c/cp2k.py | Python | gpl-2.0 | 35,231 | [
"CP2K"
] | ea20fbf891e152848d3c52eefee03765ecf5ffe24f9650bfbde72d955f58972a |
# Rekall Memory Forensics
#
# Copyright 2014 Google Inc. 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 License, or (at
# your option) any later v... | chen0031/rekall | rekall-core/rekall/entities/lookup_table.py | Python | gpl-2.0 | 7,824 | [
"VisIt"
] | 38faceb8e86d244bd87b6f6b27a39003f7025a62ff8f9177324eebd3be461140 |
"""
Import functions for EPW data files.
"""
import io
from urllib.request import urlopen, Request
import pandas as pd
def read_epw(filename, coerce_year=None):
r'''
Read an EPW file in to a pandas dataframe.
Note that values contained in the metadata dictionary are unchanged
from the EPW file.
... | mikofski/pvlib-python | pvlib/iotools/epw.py | Python | bsd-3-clause | 17,255 | [
"EPW"
] | 3029268c3287ef3031b54801c8b56ea3e9979787ed8fc06dadfc01157970b7d4 |
# -*- coding: utf-8 -*-
"""
=====================================================================
Extracting artifact and evoked response atoms from the sample dataset
=====================================================================
This example illustrates how to learn rank-1 [1]_ atoms on the multivariate
sampl... | alphacsc/alphacsc | examples/multicsc/plot_sample_evoked_response.py | Python | bsd-3-clause | 12,769 | [
"Gaussian"
] | bb79d4ba0c37cdd00c748862ac7e5687c4538a6bbaf555f4a27beb1f620618be |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | MJJoyce/climate | ocw/tests/test_local.py | Python | apache-2.0 | 8,555 | [
"NetCDF"
] | 6d52317dd896d695bc9b62f149961b6f8444ae794f1b8a523a3e9bedba946f27 |
"""
Test Logger Wrapper
"""
__RCSID__ = "$Id$"
import unittest
import logging
from StringIO import StringIO
from DIRAC.FrameworkSystem.private.standardLogging.LoggingRoot import LoggingRoot
from DIRAC.FrameworkSystem.private.standardLogging.Logging import Logging
gLogger = LoggingRoot()
def cleaningLog(log):
"... | andresailer/DIRAC | FrameworkSystem/private/standardLogging/test/TestLoggingBase.py | Python | gpl-3.0 | 1,257 | [
"DIRAC"
] | a5ebdc938d6fcdaa51465765a28c11c934ca3c97354d4eb8db6bc6038efb6dd7 |
########################################################################
#
# (C) 2015, Brian Coca <bcoca@ansible.com>
#
# 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... | wenottingham/ansible | lib/ansible/galaxy/role.py | Python | gpl-3.0 | 14,007 | [
"Brian",
"Galaxy"
] | 465e4d37baaf34a47f5ec8b6859167139768d76a7a4f5f2774fe095149168dfa |
"""
This is the play
"""
import numpy as np
import matplotlib.pyplot as plt
import math
from sklearn.cluster import KMeans
from sklearn.datasets import make_blobs
from functions import selection_algorithm, scl
from csl import CSL
plot = True
verbose = False
tracking = True
selection = False
# Generate the data
n_sa... | h-mayorquin/competitive_and_selective_learning | play.py | Python | mit | 1,250 | [
"NEURON"
] | 72c1c64460742a00eb20ce37ff8748a13573dce46eb491893bb94aa47638e1ef |
from __future__ import print_function, division
import unittest, numpy as np
from pyscf import gto, scf
from pyscf.nao import mf as nao_mf
mol = gto.M( verbose = 1, atom = '''Mn 0 0 0;''', basis = 'cc-pvdz', spin = 5, )
#gto_mf_rhf = scf.RHF(mol)
#gto_mf_rhf.kernel()
gto_mf_uhf = scf.UHF(mol)
gto_mf_uhf.kernel()
clas... | gkc1000/pyscf | pyscf/nao/test/test_0084_mn_mf.py | Python | apache-2.0 | 1,226 | [
"PySCF"
] | 7171f724bf8781e7e5064296b0f19fe388460e6a1dd549e78e6d6762cf9b5f5f |
# Copyright (C) 2011-2018 Free Software Foundation, Inc.
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option) any later version.
#
# This progr... | BPI-SINOVOIP/BPI-Mainline-kernel | toolchains/gcc-linaro-7.3.1-2018.05-x86_64_arm-linux-gnueabihf/share/gdb/system-gdbinit/elinos.py | Python | gpl-2.0 | 3,080 | [
"CDK"
] | 15c89f29a916366d71c7c1b8618e1ed0fa821c3ce9b1671cb74135241e9e6311 |
import os
from ast import parse
import pytest
from smother.python import PythonFile
from smother.python import Visitor
case_func = """
def a():
pass
"""
ctx_func = ['', 'a', 'a']
case_class = """
class A:
def method(self):
pass
x = 3
"""
ctx_class = ['', 'A', 'A', 'A.method', 'A.method', 'A',... | ChrisBeaumont/smother | smother/tests/test_python.py | Python | mit | 2,513 | [
"VisIt"
] | 609d41da563193d085da7849aebb833de819c4e731fc57676d810f2b309ce54e |
import numpy as np
import netCDF4 as netCDF
from datetime import datetime
import pyroms
import pyroms_toolbox
# load 2-dimentional interannual discharge data
# from Hill and Beamer.
print 'Load interannual discharge data'
nc_data = netCDF.Dataset('runoff.nc', 'r')
time = nc_data.variables['time'][:]
data = nc_data.... | dcherian/pyroms | examples/rivers/make_runoff_clim.py | Python | bsd-3-clause | 5,338 | [
"NetCDF"
] | 3f4b04c3e5d6d885105e838f29287d97f7f43df5421288eb95cbc1c71e699494 |
"""
Perform Levenberg-Marquardt least-squares minimization, based on MINPACK-1.
AUTHORS
The original version of this software, called LMFIT, was written in FORTRAN
as part of the MINPACK-1 package by Jorge More' et al, available from NETL... | tomevans/wfc3 | mpfit.UNSTABLE.py | Python | mit | 90,154 | [
"Gaussian"
] | 1750bf85e8dd378219c9567914a6e7d8a41d1f41d38fe2d500463294a6dba27b |
#!/usr/bin/env python
# This uses jobTree (https://github.com/benedictpaten/jobTree) to run analysis on the CNAVG output.
from jobTree.scriptTree.target import Target
from jobTree.scriptTree.stack import Stack
from optparse import OptionGroup
from optparse import OptionParser
from sonLib.bioio import logger
from so... | dzerbino/cn-avg | paper_figures/scripts/cnavg_post_analysis_jobtree.py | Python | bsd-3-clause | 14,248 | [
"pysam"
] | 207d837a5e6cd3974144450926daff3221ed5bbaabed739b23e9aa81a7532d9b |
# 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... | drpngx/tensorflow | tensorflow/contrib/distributions/python/ops/bijectors/real_nvp.py | Python | apache-2.0 | 12,719 | [
"Gaussian"
] | f4ce03c2bbc5412dcb6e61327c52c65901b6d4304c709aa9378f59806c6def91 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
This module defines PDEntry, which wraps information (composition and energy)
necessary to create phase diagrams.
"""
__author__ = "Shyue Ping Ong"
__cop... | xhqu1981/pymatgen | pymatgen/phasediagram/entries.py | Python | mit | 9,519 | [
"pymatgen"
] | 3ef961da4198eb9f51cdc14decd539c84a6cffcd1a7303c3153a8b675405ed5f |
##
# Copyright 2009-2021 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (F... | boegel/easybuild-easyblocks | easybuild/easyblocks/t/trinity.py | Python | gpl-2.0 | 14,495 | [
"BWA"
] | 90ab7a3a3ad0ce231d7be41a9d92e9ad36cc17ae968f3286e4cc519f9fd67bb2 |
'''
Main "pipeline" script for the Legacy Survey (DECaLS, MzLS, BASS)
data reductions.
For calling from other scripts, see:
- :py:func:`run_brick`
Or for much more fine-grained control, see the individual stages:
- :py:func:`stage_tims`
- :py:func:`stage_refs`
- :py:func:`stage_outliers`
- :py:func:`stage_halos`
- ... | legacysurvey/legacypipe | py/legacypipe/runbrick.py | Python | bsd-3-clause | 165,331 | [
"Galaxy",
"Gaussian"
] | 64a35c5d7a707e8f585aa8470b806be32df22ccfebdeedbb9c41aa43ffda9140 |
#!/usr/bin/env python
#-----------------------------------------------------------------------------
# Copyright (c) 2013--, biocore development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
#-------------------------... | ekopylova/burrito-fillings | bfillings/blat.py | Python | bsd-3-clause | 16,807 | [
"BLAST"
] | f5c90cbc20ce14fa057cb6b44d845ee2486ddd86f5bab331a178d7e746cb1888 |
"""Steps used throughout lettuce tests for story app"""
from datetime import datetime
from django.core.urlresolvers import reverse
from lettuce import step, world
from lettuce.django import django_url
from nose.tools import assert_equal
from storybase_story.models import Story
@step(u'Then the Story\'s title should... | denverfoundation/storybase | apps/storybase_story/features/steps.py | Python | mit | 2,647 | [
"VisIt"
] | 0ec16046c3776d5674c34d6e8a34ece21e9518f5703424fba1e1d59916849ced |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2007 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 Software F... | tiagocardosos/stoq | plugins/ecf/deviceconstanteditor.py | Python | gpl-2.0 | 7,045 | [
"VisIt"
] | c4f65ed69979635453e175d22b768dc579a80892ded94c7c4845b11168869d37 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2014 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 Software F... | tiagocardosos/stoq | stoqlib/reporting/person.py | Python | gpl-2.0 | 1,262 | [
"VisIt"
] | 270bba5dd23f3bff4735a6b214063b20230b14e6a19635f47dd52a5906bb94dd |
"""
Support for the Amazon Polly text to speech service.
For more details about this component, please refer to the documentation at
https://home-assistant.io/components/tts.amazon_polly/
"""
import logging
import voluptuous as vol
from homeassistant.components.tts import Provider, PLATFORM_SCHEMA
import homeassistan... | MungoRae/home-assistant | homeassistant/components/tts/amazon_polly.py | Python | apache-2.0 | 6,145 | [
"Brian"
] | 80c21d0e26641ef88971990430c6b0c2d0dcfbfdd45dfa2f1cb300e4c5224be7 |
# Copyright (C) 2016 Alex Nitz
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 3 of the License, or (at your
# option) any later version.
#
# This program is distributed in the ... | ahnitz/pycbc | pycbc/events/stat.py | Python | gpl-3.0 | 69,021 | [
"Gaussian"
] | 9278214ad51d3c06ffd407c1017278c605d31cd2ff799ae9e058b5afd8d2f3b5 |
# Copyright 2020 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... | karllessard/tensorflow | tensorflow/compiler/mlir/tfr/python/op_reg_gen.py | Python | apache-2.0 | 5,172 | [
"VisIt"
] | 568dc2e06873f1da92d4d9507edd571ceaee797bedcd888affd6053fb8982178 |
import sys, os
from getIQU import IQU
from subprocess import call
import sys, os
import numpy as np
import glob
import matplotlib.pyplot as plt
from astropy.convolution import convolve_fft, Gaussian2DKernel
from astropy.visualization import AsinhStretch
from astropy.io import fits
from astropy.wcs import WCS
import sci... | sbg2133/miscellaneous_projects | carina/planck_lic_aplpy.py | Python | gpl-3.0 | 7,820 | [
"Gaussian"
] | cf0f06ed2d8bdb1b6f6fa0630fef0fdca2ab5fc5ee5eb449d6e3cc7ad7845074 |
"""
Distributions
-------------
A widget for plotting attribute distributions.
"""
from math import sqrt
import sys
import collections
from xml.sax.saxutils import escape
from AnyQt.QtWidgets import QSizePolicy, QLabel, QListView,QToolTip
from AnyQt.QtGui import QColor, QPen, QBrush, QPainter, QPicture, QPalette
fro... | cheral/orange3 | Orange/widgets/visualize/owdistributions.py | Python | bsd-2-clause | 28,245 | [
"Gaussian"
] | d1203974fc004cf1d266054eeb1786087b1ebc50be3726ac6657a3d05165f2fe |
def main():
from brian2 import start_scope,mvolt,ms,NeuronGroup,StateMonitor,run
import matplotlib.pyplot as plt
import neo
import quantities as pq
start_scope()
# Izhikevich neuron parameters.
a = 0.02/ms
b = 0.2/ms
c = -65*mvolt
d = 6*mvolt/ms
I = 4*mvolt/ms
# Standard Izhikevich neur... | etorre/elephant | elephant/test/make_spike_extraction_test_data.py | Python | bsd-3-clause | 1,574 | [
"NEURON"
] | 3264abe39962dd796ba4c4882083cc1b3d1df235ec57b4cf52d1cbaf664df8fe |
from asyncio import gather, Lock, Semaphore, sleep, CancelledError
from collections import deque
from time import time, monotonic
from queue import Empty
from itertools import cycle
from sys import exit
from distutils.version import StrictVersion
from aiopogo import PGoApi, HashServer, json_loads, exceptions as ex
fro... | evenly-epic-mule/Monocle | monocle/worker.py | Python | mit | 60,070 | [
"VisIt"
] | 2490629a7529b13a4ed610346999021a929c78de0308559e9bb42f6962852839 |
from datetime import datetime
import json
from twisted.internet import reactor
from twisted.python.failure import Failure
from twisted import logger
from twisted.web.resource import Resource, NoResource
from twisted.web.server import NOT_DONE_YET, Site
import urllib
from matrix_gitter.markup import gitter_to_matrix
fr... | remram44/matrix-appservice-gitter-twisted | matrix_gitter/matrix.py | Python | bsd-3-clause | 32,619 | [
"VisIt"
] | 1548d4a32ee6f30507f40965cf8bb9baa19bcee0e257456b4050f42f99f84631 |
# -*- coding: utf-8 -*-
# SyConn - Synaptic connectivity inference toolkit
#
# Copyright (c) 2016 - now
# Max Planck Institute of Neurobiology, Martinsried, Germany
# Authors: Philipp Schubert, Joergen Kornfeld
import glob
import os
import re
import shutil
import time
from collections import Counter, defaultdict
from t... | StructuralNeurobiologyLab/SyConn | syconn/reps/super_segmentation_object.py | Python | gpl-2.0 | 159,389 | [
"NEURON"
] | c670d4d7edb9980ea0793316a915829238a3180245687b2a71a405be69c5b73d |
import numpy as np
import os
try:
import netCDF4 as netCDF
except:
import netCDF3 as netCDF
import matplotlib.pyplot as plt
import time
from datetime import datetime
from matplotlib.dates import date2num, num2date
import pyroms
import pyroms_toolbox
import _remapping
class nctime(object):
pass
def remap_bdry... | kshedstrom/pyroms | examples/Arctic_HYCOM/remap_bdry_uv.py | Python | bsd-3-clause | 16,837 | [
"NetCDF"
] | ddeed37a7635dbbb91cce51990a2a2b98627bb1f6f14e94e1e9dfd94a641315c |
# -*-coding:utf8-*-
from __future__ import print_function
"""
This file is part of SkyLab
Skylab 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 ve... | coenders/skylab | skylab/ps_model.py | Python | gpl-3.0 | 25,950 | [
"Gaussian"
] | d556d3b1b089b4da280fd96e02508d0fe45ae4e6fbbf62ba1667bdeb79d7f062 |
"""
CBMPy: fluxmodules decomposiiton test module
This module only exists for testing purposes
=====================
PySCeS Constraint Based Modelling (http://cbmpy.sourceforge.net)
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... | SystemsBioinformatics/cbmpy | cbmpy/fluxmodules/TestDecomposition.py | Python | gpl-3.0 | 13,673 | [
"PySCeS"
] | f833dfc37250caeb34afd07dc31e75b91facf53b9022d2b29bd043d679f5e75c |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides classes to interface with the Materials Project REST
API v2 to enable the creation of data structures and pymatgen objects using
Materials Project data.
To make use of the Materials AP... | gmatteo/pymatgen | pymatgen/ext/matproj.py | Python | mit | 67,879 | [
"ABINIT",
"VASP",
"pymatgen"
] | 1a1c25d400a27434d923289e410875e083860d483f895721bd1e03c8835a355b |
##############################################################################
# adaptiveMD: A Python Framework to Run Adaptive Molecular Dynamics (MD)
# Simulations on HPC Resources
# Copyright 2017 FU Berlin and the Authors
#
# Authors: Jan-Hendrik Prinz
# Contributors:
#
# `adaptiveMD` is free software: ... | jrossyra/adaptivemd | adaptivemd/engine/openmm/openmmrun.py | Python | lgpl-2.1 | 12,440 | [
"MDTraj",
"OpenMM"
] | 3a043db568cc6604de2ff06378905e1413bd3d959bc16851ebd498d627a37ee9 |
# Copyright 2011 OpenStack Foundation
# 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 requ... | saeki-masaki/cinder | cinder/tests/unit/api/test_xmlutil.py | Python | apache-2.0 | 27,333 | [
"VisIt"
] | 2d43c5821ce2ecb03abcd5d7ccf593c3b160040dbab25ab6b5ac16adc4658414 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 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
#... | jH0ward/psi4 | conda/_conda_vers.py | Python | lgpl-3.0 | 1,480 | [
"Psi4"
] | 8d6656a374a61898b4583768d38b3408913f8a4d1ec2fbf37fe2801adcd9d350 |
'''Connection weight figures.
.. currentmodule:: noisefigs.plotters.connections
Classes
-------
.. autosummary::
WeightExamplesHists
WeightOutE2IPlotter
WeightOutI2EPlotter
WeightInE2IPlotter
WeightInI2EPlotter
WeightGridPlotter
Burak2009ConnectionPlotter
'''
from __future__ import absol... | MattNolanLab/ei-attractor | noisefigs/noisefigs/plotters/connections.py | Python | gpl-3.0 | 16,318 | [
"NEURON"
] | 910a86fc0dc2df2a26335160a37628e1a48d2593f00f19e7ccc0eb5278489c5b |
"""Kernels for Gaussian process regression and classification.
The kernels in this module allow kernel-engineering, i.e., they can be
combined via the "+" and "*" operators or be exponentiated with a scalar
via "**". These sum and product expressions can also contain scalar values,
which are automatically converted to... | bnaul/scikit-learn | sklearn/gaussian_process/kernels.py | Python | bsd-3-clause | 84,172 | [
"Gaussian"
] | 82d279f2856f16638d1e53d3fd96156c03f1e593f8803b960434fb2b52f41cf6 |
"""
Simple wrapper class for a Basic GP.
"""
from __future__ import division
from __future__ import absolute_import
from __future__ import print_function
import numpy as np
from ..utils.models import printable
from ..likelihoods import Gaussian
from ..kernels import SE, Matern
from .exact import ExactGP
__all__ = [... | mwhoffman/pygp | pygp/inference/basic.py | Python | bsd-2-clause | 2,189 | [
"Gaussian"
] | 5a2bba8d0c638a9dce4155feb3e1549756a3d487573ed3eaf9514ec0e4a97ccd |
#!/usr/bin/env python
import os
import sys
import argparse
from src.ipr import read_ipr
from src.sprot import read_sprot
from src.sprot import get_fasta_info
from src.sprot import get_blast_info
from src.sprot import get_gff_info
from src.annotation import write_annotations
from src.fix import fix_anno
def main(args):... | genomeannotation/annie | annie.py | Python | mit | 4,465 | [
"BLAST"
] | 5521ade3720a38720f6ab8aa7cd42cc6cc724009cceec58a37d4be0f33dd8add |
# -*- coding: utf-8 -*-
""" GIS Module
@requires: U{B{I{gluon}} <http://web2py.com>}
@requires: U{B{I{shapely}} <http://trac.gispython.org/lab/wiki/Shapely>}
@copyright: (c) 2010-2012 Sahana Software Foundation
@license: MIT
Permission is hereby granted, free of charge, to any person
obtaini... | ashwyn/eden-message_parser | modules/s3/s3gis.py | Python | mit | 274,540 | [
"Amber"
] | dd24024183d256a8da79201d705e6a2e04a9727998f421cbf88d1ce8862b2079 |
# monitor.py
#
# Copyright (C) 2011-2015 Red Hat, Inc.
#
# 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 License, or
# (at your option) any later version.
#
# This progr... | bcl/lorax | src/pylorax/monitor.py | Python | gpl-2.0 | 6,715 | [
"Brian"
] | c789d9e0fa371516911d9ed191cbdd61c54533c7f707ce1fa5c991ea027ffdfb |
#!/usr/bin/env python3
# Copyright (c) 2018 The Bitsend Core developers
# Distributed under the MIT software license, see the accompanying
# file COPYING or http://www.opensource.org/licenses/mit-license.php.
"""Verify commits against a trusted keys list."""
import argparse
import hashlib
import os
import subprocess
im... | LIMXTEC/BitSend | contrib/verify-commits/verify-commits.py | Python | mit | 7,876 | [
"Octopus"
] | e1040c247e98e62c1a17cf4852d6018d90f98806be599a1e8f058a1110eb8e18 |
from . import nodes
class Visitor:
""" Visit ast nodes """
def visit(self, node):
if isinstance(node, nodes.Program):
for variable in node.variables:
self.visit(variable)
for statement in node.statements:
self.visit(statement)
elif isins... | windelbouwman/ppci-mirror | ppci/lang/fortran/utils.py | Python | bsd-2-clause | 1,713 | [
"VisIt"
] | fa8c088af466b41d177902ae1c7191c43ed07e0df02622df26e4577141daf034 |
import numpy as np
import math
from scipy.special import kn
from scipy.interpolate import interp1d
from scipy.interpolate import SmoothBivariateSpline
from scipy.optimize import brentq
from scipy.integrate import quad
from scipy.interpolate import griddata
#import matplotlib.pyplot as plt
from Hidden_Sec_Utilities imp... | pgdeniverville/Hidden-Sector-Limits | Hidden_Sec_Physics.py | Python | mit | 14,590 | [
"Brian"
] | ad3e0fd4e651adf913ce345809d07cbb80bc131bcf7d42efcfe2eb0f32dffbea |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2011-2012 Async Open Source
##
## This program is free software; you can redistribute it and/or
## modify it under the terms of the GNU Lesser General Public License
## as published by the Free Software Foundation; either version 2
## of the License... | tiagocardosos/stoq | stoqlib/reporting/boleto.py | Python | gpl-2.0 | 34,454 | [
"VisIt"
] | c4b0fe803716f1243ec9661133f8741c1f87f58cc71a4ac5a1f971fc1e94d658 |
# -*- coding: utf-8 -*-
from __future__ import absolute_import, division, print_function, unicode_literals
import warnings
import deepiv.samplers as samplers
import deepiv.densities as densities
from deepiv.custom_gradients import replace_gradients_mse
from keras.models import Model
from keras import backend as K
f... | jhartford/DeepIV | deepiv/models.py | Python | mit | 18,271 | [
"Gaussian"
] | f019c70b5d8d457a8c0b4df829cb9d1eb3edf26c5595e89cfb9a26a010f97e7c |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/dft/test/test_xcfun.py | Python | apache-2.0 | 20,515 | [
"PySCF"
] | 1b7d2b7792aee07846f438ad48359c3b9f59ddca3af5807503913f19d7890418 |
# OUTCARToGULP_ModeMap.py by J. M. Skelton
import csv;
import math;
import os;
from argparse import ArgumentParser;
# Import IO routines from OUTCARToGULP.py.
from OUTCARToGULP import _ReadOUTCARFile, _WriteGULPInputFile;
# Default base for the automatically-determined output file name.
_DefaultOutputFileNameBa... | JMSkelton/VASPToGULP | OUTCARToGULP_ModeMap.py | Python | gpl-3.0 | 10,936 | [
"GULP",
"VASP"
] | 70b8f8c8d0e30167ac5acff7392fa12dac41fc8f9887ee8585c63cad53d0fa42 |
from mayavi.version import version, version as __version__
from mayavi.core.engine import Engine
from mayavi.core.off_screen_engine import OffScreenEngine
from mayavi.tests.runtests import m2_tests as test
| dmsurti/mayavi | mayavi/api.py | Python | bsd-3-clause | 206 | [
"Mayavi"
] | c5562d4d22d9436a4b2ac8b908935ed4b5faccabbad05c42edb7f84d20996d24 |
# Copyright 2000-2010 Michael Hudson-Doyle <micahel@gmail.com>
# Antonio Cuni
#
# All Rights Reserved
#
#
# Permission to use, copy, modify, and distribute this software and
# its documentation for any purpose is hereby granted without fee,
# provided that the above copyri... | timm/timmnix | pypy3-v5.5.0-linux64/lib_pypy/pyrepl/completing_reader.py | Python | mit | 9,446 | [
"Galaxy"
] | 9a5d89d29dbb8d9139f1cdbb3806f451a374499d647964d1103d66ca4a08168a |
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