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#
# Copyright 2016 The BigDL Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in ... | intel-analytics/BigDL | python/orca/example/torchmodel/train/resnet_finetune/resnet_finetune.py | Python | apache-2.0 | 4,379 | [
"ORCA"
] | 0fc7b84b7eef99c8a15d4d51313a45c79fb2633ae86ae36cb904bb1274aad466 |
# -*- coding: utf-8 -*-
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""Interfaces to assorted Freesurfer utility programs.
Change directory to provide relative paths for doctests
>>> import os
>>> filepath = os.path.dirname( os.path.realpat... | carolFrohlich/nipype | nipype/interfaces/freesurfer/utils.py | Python | bsd-3-clause | 125,235 | [
"Gaussian",
"VTK"
] | 69bac34ad457c92634a569138e380bbfbc5fdc14a4c4d4e028c9cdc453f5777c |
"""Open Drug Discovery Toolkit
==============================
Universal and easy to use resource for various drug discovery tasks,
ie docking, virutal screening, rescoring.
Attributes
----------
toolkit : module,
Toolkits backend module, currenlty OpenBabel [ob] and RDKit [rdk].
This setting is toolkit-wide, a... | oddt/oddt | oddt/__init__.py | Python | bsd-3-clause | 2,562 | [
"RDKit"
] | 2e9f9db8ae4a3c492ebb8a12121826866c02321b8eaf5a8a2a75a45256af8e0f |
# coding: utf-8
# In[1]:
import numpy as np
import networkx as nx
import som_functions as som
import math
import sklearn.metrics as met
import sklearn.manifold as man
from time import time
import matplotlib.pyplot as plt
##visualise network
def visualise(G, network, layer):
##randomly generate colours for ... | DavidMcDonald1993/ghsom | GHSOM projected.py | Python | gpl-2.0 | 14,427 | [
"NEURON",
"VisIt"
] | a248cbf4f4cc21845962ee936d2722cb733d647b180f260d61a387e65c5bace9 |
''' DIRACAccountingCommand
The DIRACAccountingCommand class is a command class to
interrogate the DIRAC Accounting.
'''
# FIXME: NOT Usable ATM
# missing doNew, doCache, doMaster
__RCSID__ = '$Id$'
from datetime import datetime, timedelta
from DIRAC import S_OK, S_ERROR
from DIRAC.AccountingSystem.Client.Repo... | arrabito/DIRAC | ResourceStatusSystem/Command/DIRACAccountingCommand.py | Python | gpl-3.0 | 10,012 | [
"DIRAC"
] | a9ea69a582022235e871e904d4b160978c7078036daaea32dbb43d9b3b11be7c |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
"""
Versioneer 2
============
* Like a rocketeer, but for versions!
* Based on https://github.com/warner/python-versioneer
* Brian Warner
* License: Public Domain
* Compatible With: python2.6, 2.7, 3.2, 3.3, 3.4, and pypy
* Edited by Ryan Dwyer
This is a... | ryanpdwyer/hdf5plotter | versioneer.py | Python | mit | 38,263 | [
"Brian"
] | 008ccee0fdb4993c724a919c1b7b5653a94db07a65885c60014246cb8bc8f544 |
"""
This module provides the generic functionality of tracing code by
modifying its AST. Eventually this will become a separate package.
This is similar to the standard library module bdb, while birdseye
itself would correspond to pdb.
Most of the work is in TreeTracerBase.
"""
from __future__ import print_function, d... | alexmojaki/executing | tests/samples/tracer.py | Python | mit | 26,009 | [
"VisIt"
] | 01be136864046cf03af02c10275891d69b7344184b513dea064f2e65846ab45a |
#!/usr/bin/env python
# CREATED:2013-03-08 15:25:18 by Brian McFee <brm2132@columbia.edu>
# unit tests for librosa.filters
#
# This test suite verifies that librosa core routines match (numerically) the output
# of various DPWE matlab implementations on a broad range of input parameters.
#
# All test data is generated... | librosa/librosa | tests/test_filters.py | Python | isc | 16,300 | [
"Brian"
] | d9d059673449a696881eab66c6ceb1906940e290dbd30ed1bcc3e8f657e8ecb4 |
from galaxy.util import permutations
from galaxy import model
from galaxy import util
from galaxy import exceptions
import logging
log = logging.getLogger( __name__ )
def expand_meta_parameters( trans, tool, incoming ):
"""
Take in a dictionary of raw incoming parameters and expand to a list
of expanded ... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/tools/parameters/meta.py | Python | gpl-3.0 | 5,696 | [
"Galaxy"
] | 3f3c754c46f0073f150d42eb1c83e5911225f8a1144d2198f11d64d757745b04 |
# -*- coding: utf-8 -*-
"""
Objetos Arbol de Sintaxis Abstracto (AST - Abstract Syntax Tree).
Este archivo define las clases para los diferentes tipos de nodos del
árbol de sintaxis abstracto. Durante el análisis sintático, se debe
crear estos nodos y conectarlos. En general, usted tendrá diferentes
nodos AST para ... | Alecardv/College-projects | MiniPascal/mpasast.py | Python | gpl-3.0 | 8,600 | [
"VisIt"
] | e139a6478c2133e838e7981e2edfdc4fa522425504dd9e365e5dc3076205f7f8 |
##############################################################################
# Copyright (c) 2013-2018, 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... | EmreAtes/spack | var/spack/repos/builtin/packages/r-annotationforge/package.py | Python | lgpl-2.1 | 2,180 | [
"Bioconductor"
] | 4cb3b02429c24f52efebc150542c933ce3e505d04452bc0e425d643aa7df155c |
from node import NodeVisitor, ValueNode, ListNode, BinaryExpressionNode
from parser import atoms, precedence
atom_names = {v:"@%s" % k for (k,v) in atoms.iteritems()}
named_escapes = set(["\a", "\b", "\f", "\n", "\r", "\t", "\v"])
def escape(string, extras=""):
rv = ""
for c in string:
if c in named_... | youtube/cobalt | third_party/web_platform_tests/tools/wptrunner/wptrunner/wptmanifest/serializer.py | Python | bsd-3-clause | 4,257 | [
"VisIt"
] | ec9e8ed67975b6c74e1448efacc478c1f783f4d408ac78c8e059310a98f338f2 |
#!/usr/bin/env python
""" MultiQC module to parse output from Bowtie 1 """
from __future__ import print_function
from collections import OrderedDict
import logging
import re
from multiqc import config
from multiqc.plots import bargraph
from multiqc.modules.base_module import BaseMultiqcModule
# Initialise the logge... | ahvigil/MultiQC | multiqc/modules/bowtie1/bowtie1.py | Python | gpl-3.0 | 6,177 | [
"Bowtie"
] | 34e76a24f72854ceeb3ad2b021e373e0568dfffe229036c0a8ae9a2b7cb7186a |
""" Author: Ning Guo <ceguo@connect.ust.hk>
run `mv footing.yade.gz 0.yade.gz`
to generate initial RVE packing
"""
from esys.escript import *
from esys.finley import ReadGmsh
from esys.weipa import saveVTK
from esys.escript.pdetools import Projector
from msFEM import MultiScale
from saveGauss import saveGauss2D... | anna-effeindzourou/trunk | examples/FEMxDEM/footing.py | Python | gpl-2.0 | 3,553 | [
"VTK"
] | ba3d9bd20accbc3c0cf74ab8439fe8a54304db0ec7ed0fbee3b808232b37eb69 |
import os
import glob
from setuptools import setup, find_packages
SETUP_PTH = os.path.dirname(os.path.abspath(__file__))
def readme():
with open('README.rst') as f:
return f.read()
setup(
name="pydii",
packages=find_packages(),
version="1.9.0",
install_requires=["pymatgen... | pydii/pydii | setup.py | Python | mit | 2,291 | [
"pymatgen"
] | 9295db3a26f20b8bd44d7e0d91992ecc1a249efccb977a14db8beee283a1bb0a |
## load dependencies - third party
import numpy as np
import pandas as pd
import random as rd
from tqdm import tqdm
## load dependencies - internal
from smogn.box_plot_stats import box_plot_stats
from smogn.dist_metrics import euclidean_dist, heom_dist, overlap_dist
## generate synthetic observations
def over_samplin... | nickkunz/smogn | smogn/over_sampling.py | Python | gpl-3.0 | 19,219 | [
"Gaussian"
] | b82bba498288b18d26b2c00b7664428917b31ffb2664c68a2387fa2678d902e9 |
from behave import given, then
from common import DEFAULT_WAIT
# Unique to Scenario: Moderator invites new user
@given('I invite a new user, with the name "First Last"')
def impl(context):
context.execute_steps('''
when I visit the "invite user" page
when I enter "First Last" into the "full name" ... | nlhkabu/connect | bdd/features/steps/invite_user.py | Python | bsd-3-clause | 990 | [
"VisIt"
] | 3c2cc5d17bf79dede2ad73e6d8990f6060e864189ae61ed482ae4447f23e8e76 |
#!/usr/bin/env python
# coding: utf-8
#
# Copyright 2007 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 ... | QingkaiLu/RAMCloud | scripts/upload.py | Python | isc | 99,760 | [
"VisIt"
] | dd963a273a872eca8e22803f1ee485413610fd1cbec0a2c8e60c9e5c8d9de5ef |
from __future__ import absolute_import, division
import textwrap
from copy import copy
import six
import os
from distutils.version import LooseVersion
from plotly import optional_imports
from plotly.io._base_renderers import (
MimetypeRenderer,
ExternalRenderer,
PlotlyRenderer,
NotebookRenderer,
... | plotly/python-api | packages/python/plotly/plotly/io/_renderers.py | Python | mit | 16,189 | [
"ORCA"
] | 9855bc5d4168aec7dc5f643a2f3e5883a7cdc82801a0c52ba8b16b8a9cc7f8d4 |
from typing import Sequence, Union, Any
from collections import OrderedDict
from numpy import Inf, exp
import pandas as pd
from hbayesdm.base import TaskModel
from hbayesdm.preprocess_funcs import prl_multipleB_preprocess_func
__all__ = ['prl_rp_multipleB']
class PrlRpMultipleb(TaskModel):
def __init__(self, *... | CCS-Lab/hBayesDM | Python/hbayesdm/models/_prl_rp_multipleB.py | Python | gpl-3.0 | 10,195 | [
"NEURON"
] | 1a8b57631c41eb668c4c51ca69de1becda6c9dcc429fedc077a779c8ee2bbea5 |
r"""
QSeq format (:mod:`skbio.io.format.qseq`)
=========================================
.. currentmodule:: skbio.io.format.qseq
The QSeq format (`qseq`) is a record-based, plain text output format produced
by some DNA sequencers for storing biological sequence data, quality scores,
per-sequence filtering information... | wdwvt1/scikit-bio | skbio/io/format/qseq.py | Python | bsd-3-clause | 10,430 | [
"scikit-bio"
] | 32a335c6d392f95e2ce654b005c33f25413e1751e64539fbfc0cc9db8b0f855e |
# NOTE: This example uses the next generation Twilio helper library - for more
# information on how to download and install this version, visit
# https://www.twilio.com/docs/libraries/python
from twilio.rest import Client
# Your Account Sid and Auth Token from twilio.com/user/account
account = "ACXXXXXXXXXXXXXXXXXXXXX... | teoreteetik/api-snippets | notifications/rest/services/list-service/list-service.6.x.py | Python | mit | 450 | [
"VisIt"
] | dfe42458726dadc01e8c78dcbba6e55b73dfa1f4d4aad4ead0f1bae112526278 |
##
# 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... | hpcuantwerpen/easybuild-easyblocks | easybuild/easyblocks/w/wrf.py | Python | gpl-2.0 | 19,534 | [
"NetCDF"
] | 955f23e39039c93b854ed50c84d94804f56f0e4fa0fc87b39f1ffeaeda407dba |
import os
os.chdir('c:/mypysces/kraken')
## os.chdir('/home/bgoli/mypysces/kraken')
from pysces.kraken.Kraken import *
## from Kraken import *
# build controller
blob = getBasicController()
Model_File = '2006_isola2.psc'
Model_Dir = 'c:\\mypysces\\pscmodels\\isola06'
## Model_Dir = '/home/bgoli/mypysces/pscmodels/i... | bgoli/pysces | pysces/kraken/controllers/kraken_continuation.py | Python | bsd-3-clause | 5,975 | [
"Mayavi",
"PySCeS",
"VTK"
] | bc5eb7929318003bbd5247ba9fba4d809b1e80f0d03db7025e499b5060026897 |
# -*- coding: UTF-8 -*-
"""
``Qualimap``
-----------------------
:Authors: Liron Levin
:Affiliation: Bioinformatics core facility
:Organization: National Institute of Biotechnology in the Negev, Ben Gurion University.
Short Description
~~~~~~~~~~~~~~~~~~~~~
Runs Qualimap in RNASeq or BAM qc modes, in RNASeq mod... | bioinfo-core-BGU/neatseq-flow_modules | neatseq_flow_modules/Liron/Qualimap/Qualimap.py | Python | gpl-3.0 | 11,454 | [
"HTSeq"
] | 636ef91b15ff7dc099da22727e48f7c6fdb01bfd297350fa4fe7d7b4dc94bc1d |
"""Predicates providing information about the state of the current player."""
import datetime
from apps.managers.challenge_mgr import challenge_mgr
from apps.managers.player_mgr.models import Profile
from apps.widgets.badges.models import BadgeAward
from apps.widgets.resource_goal.models import EnergyGoal
from apps.man... | yongwen/makahiki | makahiki/apps/managers/predicate_mgr/player_predicates.py | Python | mit | 3,290 | [
"VisIt"
] | a0626fabd89322d8457801b4063dcab6ca1a87aa23f053e422420d3c71058028 |
# -*- coding: utf-8 -*-
"""
This module implements :class:`SpikeTrainList`, a pseudo-list
which supports a multiplexed representation of spike trains
(all times in a single array, with a second array indicating which
neuron/channel the spike is from).
"""
import numpy as np
import quantities as pq
from .spiketrain imp... | samuelgarcia/python-neo | neo/core/spiketrainlist.py | Python | bsd-3-clause | 13,644 | [
"NEURON"
] | 906c301376be05533fffb65fa5cb6a897090cfc4d4f6bb9e0daf142e9503798a |
# This file comes from wad2pdf / thingdics.pdf
# Dictionaries for mapping thing numbers to sprite names
# Wad2PDF is a program that converts Doom levels into PDF files.
# (C) 2005-8 Jussi Pakkanen
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public L... | Palats/wadcraft | wadcraft/waddata.py | Python | gpl-2.0 | 47,643 | [
"Brian",
"CRYSTAL"
] | f6357969ee7f6bf7ee5cffdd39a3d9b81652143b1c22533aebe0609b029c2bbb |
#!/usr/bin/env python3
########################################################################
# Solves problem 124 from projectEuler.net.
# Finds the n of the 10000th rad(n) of the first 100000 rads.
# Copyright (C) 2011 Santiago Alessandri
#
# This program is free software: you can redistribute it and/or m... | sanSS/programming-contests | project-euler/problem124.py | Python | gpl-3.0 | 1,445 | [
"VisIt"
] | 6338a1d8e60dff3c9c91e201b556bb579c76e45d8dca2b9bde34a8d6b7d44579 |
# Copyright 2014 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.
"""Application context management for the cr tool.
Contains all the support code to enable the shared context used by the cr tool.
This includes the configu... | dednal/chromium.src | tools/cr/cr/base/context.py | Python | bsd-3-clause | 6,668 | [
"VisIt"
] | 4ebfa14ec236c91f184d5c920edcf48158be328c8c3bdaf8ae0b18be5765bf3f |
# Copyright 2018 The TensorFlow Probability Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law o... | tensorflow/probability | tensorflow_probability/python/util/seed_stream.py | Python | apache-2.0 | 9,734 | [
"Gaussian"
] | e2e99faf4f24eeffb076b6b9aff1b6a2c873c6e34b0c79fdd9b85842ba7296ea |
#!/usr/bin/python
#Audio Tools, a module and set of tools for manipulating audio data
#Copyright (C) 2007-2012 Brian Langenberger
#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... | Excito/audiotools | audiotools/accuraterip.py | Python | gpl-2.0 | 6,002 | [
"Brian"
] | c050f03622072c573cc697d0396393bd71131632c478f895c1a44feadd2c1e8f |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright: (c) 2018, F5 Networks Inc.
# GNU General Public License v3.0 (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
ANSIBLE_METADATA = {'metadata_version': '1.1',
... | alxgu/ansible | lib/ansible/modules/network/f5/bigip_asm_policy_signature_set.py | Python | gpl-3.0 | 25,535 | [
"Galaxy"
] | ecde08b9ceacc66674e8bdfb0abaf9f94899618c6765ae43fa93ad9c6a3b14f3 |
'''
Created on Mar 19, 2015
@author: ayan
'''
from __future__ import (absolute_import, division, print_function)
import re
from .lookup import X_COORDINATES, Y_COORDINATES
from .utils import GridPadding
def find_grid_topology_var(nc):
"""
Get the variable from a netCDF dataset
that have a `cf_role `at... | ayan-usgs/pysgrid | pysgrid/read_netcdf.py | Python | bsd-3-clause | 10,954 | [
"NetCDF"
] | 222b58434060caa866b88ef7ba460910c524e8a9d90f1fa3afa03c12083f4c9f |
#!/usr/bin/env python
import os, sys, time
import string, math
from scipy.io import netcdf
#-----------------------------------------------------------------|
def moy (file_in) :
#-----------------------------------------------------------------|
FILE_IN = open(file_in, 'r')
neff= len(FILE_IN.readlines())
FILE_IN... | SamKChang/abinit-7.10.5_multipole | doc/tutorial/lesson_paral_moldyn/diag_moldyn.py | Python | gpl-3.0 | 7,919 | [
"NetCDF"
] | c3d5868a59750f670003d3adb5e0d06a081cf8e5e7235bafe745fb1ca27c3719 |
# -*- coding: us-ascii -*-
#------------------------------------------------------
#Build an index for all input variables
#inside the given input files of the ABINIT distribution.
#Date: 22/09/2004
#
#------------------------------------------------------
# Copyright (C) 2004-2017 ABINIT group (td)
# This file is dist... | jmbeuken/abinit | developers/various/var-file-index.py | Python | gpl-3.0 | 6,731 | [
"ABINIT"
] | 8472e605a9d5d47b804023294c7dcd8fce67386729ba07262a4812b22ad63e6c |
"""
Renderer for the FilterList object.
@author: Chris Scott
"""
from __future__ import absolute_import
from __future__ import unicode_literals
import copy
import logging
import numpy as np
from PySide2 import QtCore
from . import _rendering
from . import utils
from ..algebra import vectors as vectorslib
from .ren... | chrisdjscott/Atoman | atoman/rendering/filterListRenderer.py | Python | mit | 34,138 | [
"VTK"
] | b47551a54100813a64fc2ad8f3d6a4fdc984d6ca18418eb4c337394dd03e78a1 |
# 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 applicab... | jiaphuan/models | research/pcl_rl/env_spec.py | Python | apache-2.0 | 5,998 | [
"Gaussian"
] | 1573d0701eaacc8696450db52acb0ed356906fd41cb3ae342288c63864698e47 |
# -*- coding: utf-8 -*-
#
# Copyright © 2012 Pierre Raybaut
# Licensed under the terms of the MIT License
# (see winpython/__init__.py for details)
"""
WinPython Package Manager
Created on Fri Aug 03 14:32:26 2012
"""
from __future__ import print_function
import os
import os.path as osp
import shutil
import re
impo... | PopCap/GameIdea | Engine/Source/ThirdParty/HTML5/emsdk/Win64/python/2.7.5.3_64bit/Lib/site-packages/winpython/wppm.py | Python | bsd-2-clause | 19,944 | [
"VTK"
] | 4233bf18a433bfe88f4a51d150f9edbfe8e8a932aa491ade1975c593f54d5909 |
##############################################################################
# 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-ensembldb/package.py | Python | lgpl-2.1 | 3,177 | [
"Bioconductor"
] | ded0de63b35d24784daef8c5fc759fe2d7234ddf581d4cce2a6d614694bc2cdd |
try: paraview.simple
except: from paraview.simple import *
def RequestDataDescription(datadescription):
"Callback to populate the request for current timestep"
if datadescription.GetForceOutput() == True:
for i in range(datadescription.GetNumberOfInputDescriptions()):
datadescription.GetIn... | openmichigan/PSNM | CubicNonlinearSchrodinger/Programs/NLS3dFortranMPIParaView/pipeline_image.py | Python | bsd-2-clause | 35,589 | [
"ParaView"
] | 1b6c09ea1d9c016d2cc08ee77138707d6c2c9445e43184d085ab4e5ea72c8b7b |
import numpy as np
from simulations import single_experiment, params_variations_calc
import models
import sys
sys.path.append('../analysis/')
from measures import measuring_subthre_dynamics
def make_simulation_for_model(MODEL, args, return_output=False,\
sampling='low'):
if samplin... | yzerlaut/heterogenous_firing_response | numerical_simulations/run_3d_scan_stim.py | Python | gpl-2.0 | 6,124 | [
"NEURON"
] | 9936b1ef47ad8ba9b522bc3d574b1e3ec04a0fc3da4df7f54a114b33babb51fd |
# python 3
#
# Author: Kate Willett
# Created: 18 January 2019
# Last update: 24 January 2019
# Location: /data/local/hadkw/HADCRUH2/MARINE/EUSTACEMDS/EUSTACE_SST_MAT/
# GitHub: https://github.com/Kate-Willett/HadISDH_Marine_Build
# -----------------------
# CODE PURPOSE AND OUTPUT
# -----------------------
# Th... | Kate-Willett/HadISDH_Marine_Build | EUSTACE_SST_MAT/gridbox_sampling_uncertainty.py | Python | cc0-1.0 | 34,644 | [
"Gaussian"
] | 086f7dcf070a83f858695e50a1416d859619c09479b4be374c9ef51cbc91c821 |
import os
import re
# Get rid of intel-dependent modules using "module purge" command and
# then capture list of available modules in single column format
stream = os.popen("module purge; module avail -t 2>&1 >/dev/null")
# Print header
print 'Name,Version,Default,Type,Domain,Handle Type,Handle Key,Description'
# Se... | sinkovit/parse-modules | gensoft.py | Python | gpl-3.0 | 17,849 | [
"Amber",
"BLAST",
"Biopython",
"Bowtie",
"CP2K",
"CPMD",
"GAMESS",
"Gaussian",
"Gromacs",
"HTSeq",
"LAMMPS",
"MOPAC",
"NAMD",
"NWChem",
"Q-Chem",
"Quantum ESPRESSO",
"VisIt",
"pysam"
] | 970892ec3a696db238eb11dd647403aad2654a98f7bcb12803ac5986590e2dc3 |
# -*- coding: iso-8859-1 -*-
import time
import select
import socket
import pyglet
from pyglet.window import key
import cocos
from cocos.director import *
from cocos.scene import *
from cocos.layer import *
from cocos.sprite import *
from cocos.actions.interval_actions import *
from cocos.actions.basegrid_actions im... | Kauko/TripMan | game.py | Python | mit | 12,858 | [
"GULP"
] | 2ec7e23e2a7813994698ad835483d5f74e4b304e163aac2d31ef212185aa3af9 |
#!/usr/bin/env python
from Bio import SeqIO
from dna_features_viewer import BiopythonTranslator, GraphicRecord
from matplotlib import rc_context
import matplotlib
import matplotlib.pyplot as plt
from itertools import cycle
import re
import sys
import argparse
class CPTTranslator(BiopythonTranslator):
"""
This ... | TAMU-CPT/galaxy-tools | tools/genome_viz/linear_genome_plot.py | Python | gpl-3.0 | 12,778 | [
"Galaxy"
] | 66e9757baa2e8a67de9c5abe7d59c99a58b501fd47838205d5b7f42209983edd |
# -*- coding: utf-8 -*-
from collections import OrderedDict
# The documents are referenced by page content, via the database IDs,
# so these must be ordered.
document_data = {
1: {
'file': 'Table 1.pdf',
'title': "Table 1 'First editions' with revised music text"
},
2: {
'file': '... | kcl-ddh/chopin-online | catalogue/management/commands/page_data.py | Python | gpl-3.0 | 6,049 | [
"ADF"
] | b4dd3eda8ab809830638704fa6b3bd2fc01f08ab7f6de954fefd9574a9b0724f |
# th.po
val = {"" : "Project-Id-Version: sheltermanager\nReport-Msgid-Bugs-To: FULL NAME <EMAIL@ADDRESS>\nPOT-Creation-Date: 2013-01-24 10:55+0000\nPO-Revision-Date: 2010-09-02 16:40+0000\nLast-Translator: Robin Rawson-Tetley <db@sheltermanager.com>\nLanguage-Team: Thai <th@li.org>\nMIME-Version: 1.0\nContent-Type: te... | aubzen/sheltermanager | src/locale/locale_th.py | Python | gpl-3.0 | 88,765 | [
"Amber",
"VisIt"
] | 77e4c1c91e76be3927ab8bad7f18de778af839ca24f18f34c527c5e8dac82b2d |
#!/usr/bin/env python
import io
import netCDF4
import numpy
import m6plot
import m6toolbox
import matplotlib.pyplot as plt
import os
import sys
def run():
try: import argparse
except: raise Exception('This version of python is not new enough. python 2.7 or newer is required.')
parser = argparse.ArgumentParser(d... | nicjhan/MOM6-examples | tools/analysis/meridional_overturning.py | Python | gpl-3.0 | 6,978 | [
"NetCDF"
] | 400aec6a5f4e96d115d4f67bdefc2a85d01fd99f696b3afd731311ae1f7228b7 |
#!/usr/bin/env python
# The MIT License (MIT)
#
# Copyright (c) 2016 Paul Watkins, National Institutes of Health / NINDS
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction... | elhuhdron/emdrp | emdrp/emdrp/dpLabelMesher.py | Python | mit | 59,110 | [
"VTK"
] | 7fcf1fa5543819e7eb0b0795936eae42ddafd5d707d1c7b17c2390b93a472fcc |
# Copyright 2009 Brian Quinlan. All Rights Reserved.
# Licensed to PSF under a Contributor Agreement.
"""Implements ProcessPoolExecutor.
The follow diagram and text describe the data-flow through the system:
|======================= In-process =====================|== Out-of-process ==|
+----------+ +----------... | FFMG/myoddweb.piger | monitor/api/python/Python-3.7.2/Lib/concurrent/futures/process.py | Python | gpl-2.0 | 26,955 | [
"Brian"
] | 40697ac1b0b86211afe9421ee49633efce82bc14682a306f550972db30b28156 |
# coding=utf-8
"""
Unit Tests for sickbeard/numdict.py
"""
# pylint: disable=line-too-long
import os.path
import sys
import unittest
sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), '../lib')))
sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), '..')))
from sickbea... | Jusedawg/SickRage | tests/numdict_tests.py | Python | gpl-3.0 | 19,644 | [
"Octopus"
] | a80f5605726ecd02637de3749d31c8a52f7d6e7932931fc7155239ea3cf259a8 |
__version__ = '1.0'
import os
from setuptools import setup, find_packages
here = os.path.abspath(os.path.dirname(__file__))
README = open(os.path.join(here, 'README.rst')).read()
setup(name='dalton',
version=__version__,
description="An httplib injection library for recording and playing back HTTP inte... | bbangert/Dalton | setup.py | Python | mit | 1,090 | [
"Dalton"
] | de86263f9aa96fe001c97ccacf4c1623e5a0d8099ae68a809ec9c927b9297e42 |
# Copyright 2016 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or a... | e4p/dsub | test/integration/e2e_io_tasks.py | Python | apache-2.0 | 3,774 | [
"BWA"
] | 471e4f577dade3a1e548f5341ac381c5143a1008de7088bce605daeb1ff1e18c |
#! /usr/bin/env python2
# -*- coding: utf-8 -*-
#======================================================================
#
# emake.py - emake version 3.6.5
#
# history of this file:
# 2009.08.20 skywind create this file
# 2009.11.14 skywind new install() method
# 2009.12.22 skywind implementation execute int... | skywind3000/AsyncNet | tools/emake.py | Python | apache-2.0 | 90,621 | [
"VisIt"
] | 080fde9971b6825f3c21b4373db1113d3ac3be9931f2a19fbca563c70c27a82f |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# sobtc_app_beta_beta_beta_beta_beta_beta_beta_beta.py
#
# Replicated by Billy Wilson Arante
# Replicated on 2016/11/22 EDT
#
# Attribution: GUIs with Tkinter (intermediate) by sentdex (YouTube)
import matplotlib
from matplotlib.backends.backend_tkagg import FigureCanvas... | arantebillywilson/python-snippets | py3/tkinter/sobtc-app/sobtc_app_beta.py | Python | mit | 4,599 | [
"VisIt"
] | 62b4db7134aa7dd6cc0c10525fc0fdadabd5ec8b20066dbe1a3f86073127c8b5 |
import pytest
from brian2 import *
from brian2.tests.utils import assert_allclose
from brian2.devices.device import reinit_devices, set_device, reset_device
import brian2cuda
# CUDA version of brian2.tests.test_cpp_standalone.test_openmp_consistency
@pytest.mark.cuda_standalone
@pytest.mark.standalone_only
def test_... | brian-team/brian2cuda | brian2cuda/tests/test_cpp_cuda_consistency.py | Python | gpl-2.0 | 7,021 | [
"NEURON"
] | 589c345f8a31199ef372820c4277a7c5db2b1b7fc2789580b1eaa1994e565a9b |
""" Base class for MyProxy and VOMS
"""
__RCSID__ = "$Id$"
import types
import os
import tempfile
import DIRAC
from DIRAC import gConfig, S_OK, S_ERROR
from DIRAC.Core.Utilities import DErrno
from DIRAC.Core.Security.X509Chain import X509Chain # pylint: disable=import-error
from DIRAC.Core.Security import Locations... | fstagni/DIRAC | Core/Security/BaseSecurity.py | Python | gpl-3.0 | 2,871 | [
"DIRAC"
] | df8daa4211ed7ccf88f95ef2a39d315a278d4385068713c993623a51141f0364 |
from kivy.uix.label import Label
from kivy.uix.treeview import TreeView, TreeViewLabel
from kivy.uix.scrollview import ScrollView
from kivy.properties import ListProperty
from kivy.uix.tabbedpanel import TabbedPanel
from kivy.uix.gridlayout import GridLayout
from kivy.uix.floatlayout import FloatLayout
from kivy.lang i... | missionpinball/mpf-wizard | mpfwiz/mpf_wizard_ui.py | Python | mit | 7,108 | [
"Brian"
] | c21974b1fd2f21b6ca057e16ee2710a9e634382c6c241819293c7f2f771d35ea |
# pylint: disable-msg=I0011,C0301,W0611
"""I found some of my scripts trigger off an AttributeError in pylint
0.8.1 (with common 0.12.0 and astng 0.13.1).
Traceback (most recent call last):
File "/usr/bin/pylint", line 4, in ?
lint.Run(sys.argv[1:])
File "/usr/lib/python2.4/site-packages/pylint/lint.py", line ... | GbalsaC/bitnamiP | venv/lib/python2.7/site-packages/logilab/astng/test/regrtest_data/package/import_package_subpackage_module.py | Python | agpl-3.0 | 2,214 | [
"VisIt"
] | f3eae58971d6cbc15939055b6e8c67517016805583574c0440d0046079eb4553 |
##############################################################################
# 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-organismdbi/package.py | Python | lgpl-2.1 | 2,431 | [
"Bioconductor"
] | 2ba2a54c6b1192688668dd0de4c2cf6c79f511a6df2cd59007e13eb438d908f7 |
# -*- coding: utf-8 -*-
#
# Copyright (C) Pootle contributors.
#
# This file is a part of the Pootle project. It is distributed under the GPL3
# or later license. See the LICENSE file for a copy of the license and the
# AUTHORS file for copyright and authorship information.
import locale
from collections import Ordere... | claudep/pootle | pootle/apps/pootle_language/models.py | Python | gpl-3.0 | 8,793 | [
"VisIt"
] | 58471ec5c02c616b16923a8503ee2c5c619fd38a870096b7fe55591c33a5a306 |
from numpy import exp, array, random, dot
class NeuralNetwork():
def __init__(self):
# seed the randomg number generator
random.seed(1)
# we model a single neuron with 3 input connections and 1 output connections
# we assign random weights to a 3x1 matrix, with values in the range of -1 to 1
# and mean 0
... | paulmorio/grusData | neuralNetwork/NeuralNetwork.py | Python | mit | 3,063 | [
"NEURON"
] | 18d75c625396ee0065b19ed6bd8c44b6b5b0ca1ba8badf22031d57fb721b00ae |
"""
Defines the plugin to perform evaluation on the user in the proxy
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id $"
import re
from DIRAC.Resources.Catalog.ConditionPlugins.FCConditionBasePlugin import FCConditionBasePlugin
from ... | yujikato/DIRAC | src/DIRAC/Resources/Catalog/ConditionPlugins/ProxyPlugin.py | Python | gpl-3.0 | 3,693 | [
"DIRAC"
] | d07090b41c57fa6af8969a12c23a3a8d797067b08922ad22aed92ccf9435ad24 |
"""
Custom AST NodeVisitor classes uses for Python xss linting.
"""
import ast
import re
from xsslint.reporting import ExpressionRuleViolation
from xsslint.rules import RuleSet
from xsslint.utils import Expression, ParseString, StringLines
ruleset = RuleSet(
python_concat_html='python-concat-html',
python_de... | jolyonb/edx-platform | scripts/xsslint/xsslint/visitors.py | Python | agpl-3.0 | 12,636 | [
"VisIt"
] | 4e54950a1a2c1f18aab8359566d1a828a9ac82ed8f3359552bd8a9df079888c2 |
import neovim
import subprocess
from typing import List
import enum
import functools
import ast
import logging
from .py_ast import PrettyReader
# Logging config
logger = logging.getLogger('neoreader')
_handler = logging.FileHandler('/tmp/neoreader.log', 'a')
_handler.setFormatter(logging.Formatter(
'%(asctime)s -... | MaxwellBo/neoreader | rplugin/python3/neoreader/plugin.py | Python | gpl-3.0 | 11,426 | [
"VisIt"
] | 5dacc833ff96a5476c998f3359bf9e704d0b7ddd1b00d4ca1098d774e0c01ab5 |
from cis.data_io.products import NetCDF_Gridded
import cis.data_io.gridded_data as gd
import logging
from cis.utils import demote_warnings
def _get_cubes(filenames, constraints=None, callback=None):
import iris
# Removes warnings and prepares for future Iris change
iris.FUTURE.netcdf_promote = True
... | duncanwp/cis_plugins | mri_esm.py | Python | lgpl-3.0 | 3,533 | [
"NetCDF"
] | e02167056f6ef218dc0a442310ad6477df50d0fbdecd51106bb330a12b620555 |
from copy import deepcopy
from networkx import MultiDiGraph
from numpy import array, hstack, where
from sklearn.neighbors import KernelDensity # StatsModels works better
from src.utils.dag_utils.adjacency_matrix_utils import get_emit_and_trans_adjacency_mats
from ..gp_utils import fit_gp
def fit_sem_emit_fncs(G: ... | neildhir/DCBO | src/utils/sem_utils/emissions.py | Python | mit | 3,638 | [
"Gaussian"
] | 433e118d1306b0709f1734ca26c4811d2cef7833a0bac9b562b765741175a9d1 |
from scipy.integrate.quadrature import quadrature
from scipy.integrate import quad
def gaussian(f, a, b, y=None):
try:
if y:
y_est, err_est = quadrature(f, a, b, args=(y))
y_actual, err_actual = quad(f, a, b, args=(y))
err = err_est + err_actual
else:
... | protocol114/numerical-2.2 | algorithms/gaussian.py | Python | mit | 860 | [
"Gaussian"
] | 68759ad0975d4073abe4ffd630cddd9fa96a307cd72f1ab810860de89c5e9110 |
# Please do not change this widgets module for Quisk. Instead copy
# it to your own quisk_widgets.py and make changes there.
#
# This module is used to add extra widgets to the QUISK screen.
from __future__ import print_function
import wx, time
import _quisk as QS
class BottomWidgets: # Add extra widgets to the bot... | shenki/quisk | n2adr/uhfrx_widgets.py | Python | gpl-2.0 | 5,879 | [
"ADF"
] | 9f49b4b6c650c0a408fc15ecf63acaf002ec53715c8fc8bad7eb0971e399fb63 |
#! /usr/bin/env python
from __future__ import absolute_import
import argparse
import ase.io
def convert(input_filename, output_filename, from_format=None, to_format=None):
"""Wrap ASE functions to read structure from file and write new format"""
try:
structure = ase.io.read(input_filename, format=from... | ajjackson/mctools | mctools/ase_convert.py | Python | gpl-3.0 | 1,470 | [
"ASE",
"CRYSTAL"
] | 4efd74c45f365b745d3cf22e957b0c8dcf97955507e1e0ea5364c73de1da8204 |
# -*- coding: latin-1 -*-
# PyWin32 Internet Explorer Toolbar
#
# written by Leonard Ritter (paniq@gmx.net)
# and Robert Förtsch (info@robert-foertsch.com)
"""
This sample implements a simple IE Toolbar COM server
supporting Windows XP styles and access to
the IWebBrowser2 interface.
It also demonstrates how to hij... | sserrot/champion_relationships | venv/Lib/site-packages/win32com/demos/ietoolbar.py | Python | mit | 10,752 | [
"VisIt"
] | c8949c2caac541f1ef366d0ebb7f83bbdd4537c37a436157eb59fd55960a902d |
# -*- coding: UTF-8 -*-
import nltk
topic = {}
topic[0] = set(['name'])
topic[1] = set(['home address', 'residence'])
topic[2] = set(['e-mail address', "email address"])
topic[3] = set(["national identification", "identification number"])
topic[4] = set(["passport"])
topic[5] = set(["ip"])
topic[6] = set(["vehicle reg... | mindbergh/PrivacyPolicyAnalyser | www/ppa/classifier/keywords_extractor.py | Python | apache-2.0 | 5,555 | [
"VisIt"
] | 1373f6b39a242791ce179570a3b4da31d68d520f80adac2122cb5c78919149f3 |
import sys
import argparse
import numpy as np
import math
import matplotlib.pyplot as plt
import matplotlib as mp
import os
from scipy import interpolate
import xes_energies
import pdb
from scipy.ndimage.filters import gaussian_filter as filt
data_extractor = np.genfromtxt
# backsatter energy for graphite 002
e0 = ... | hoidn/LCLS | xes/build/lib/xes/xes_process.py | Python | gpl-3.0 | 10,719 | [
"Gaussian"
] | 9d2349b23b4b5d1468ed85217f45adebdb8a519e29f3c4afc8ad1b54422c9168 |
"""Nodes that make up parse trees
Parsing spits out a tree of these, which you can then tell to walk itself and
spit out a useful value. Or you can walk it yourself; the structural attributes
are public.
"""
# TODO: If this is slow, think about using cElementTree or something.
from inspect import isfunction
from sys ... | lucaswiman/parsimonious | parsimonious/nodes.py | Python | mit | 13,091 | [
"VisIt"
] | 514d0b109bc0b1df1e3a380df2b29bba594816f28d896ac3c9d92d4d53f66a69 |
# pylint: disable=arguments-differ
""" Models for the shopping cart and assorted purchase types """
import csv
import json
import logging
import smtplib
import StringIO
from collections import namedtuple
from datetime import datetime, timedelta
from decimal import Decimal
from io import BytesIO
import analytics
impor... | procangroup/edx-platform | lms/djangoapps/shoppingcart/models.py | Python | agpl-3.0 | 91,262 | [
"VisIt"
] | ed76b2768847ce2b9e23234c6bd3e9de942066189e962f812f68f2cada1178bd |
""" CEAvailabilityPolicy module
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = '$Id$'
from DIRAC import S_OK
from DIRAC.ResourceStatusSystem.PolicySystem.PolicyBase import PolicyBase
class CEAvailabilityPolicy(PolicyBase):
"""
The C... | yujikato/DIRAC | src/DIRAC/ResourceStatusSystem/Policy/CEAvailabilityPolicy.py | Python | gpl-3.0 | 1,394 | [
"DIRAC"
] | 8e9af4d69f5b7d8937aa29546bd131e5bbeef33732c4074ff3dacf24001564aa |
from __future__ import annotations
import copy
import itertools
import json
import math
import numpy as np
from cctbx import uctbx
import dials.util.log
from dials.algorithms.scaling.model.model import plot_scaling_models
from dials.algorithms.scaling.scaling_library import (
merging_stats_from_scaled_array,
... | dials/dials | command_line/report.py | Python | bsd-3-clause | 91,783 | [
"CRYSTAL"
] | 0da7de4fb0006e1af4826104cdc90c409107dcf9f97ff4ff054fab17845c145c |
# PEEL is released under the GNU General Public License (see http://www.gnu.org/licenses/gpl.html).
# This code is currently being developed by Jeff Wagner (j5wagner [at] ucsd [dot] edu)
# If you have any questions, comments, or suggestions, please don't hesitate to contact Jeff.
# This code is very heavily based on Ja... | j-wags/POVME | binana/peel.py | Python | gpl-3.0 | 214,481 | [
"VMD"
] | e1ddfd3435448b6663073715b2a96c49bff07d0dcf42cabf7f13ede44997d380 |
# this program corresponds to special.py
### Means test is not done yet
# E Means test is giving error (E)
# F Means test is failing (F)
# EF Means test is giving error and Failing
#! Means test is segfaulting
# 8 Means test runs forever
### test_besselpoly
### test_mathieu_a
### test_mathieu_even_coef
##... | anntzer/scipy | scipy/special/tests/test_basic.py | Python | bsd-3-clause | 141,977 | [
"Elk"
] | c9c6777c3687a230d276c421a61fb4b39a93a476689822b19fae833ed494ff94 |
###
# #%L
# ImgLib2: a general-purpose, multidimensional image processing library.
# %%
# Copyright (C) 2009 - 2016 Tobias Pietzsch, Stephan Preibisch, Stephan Saalfeld,
# John Bogovic, Albert Cardona, Barry DeZonia, Christian Dietz, Jan Funke,
# Aivar Grislis, Jonathan Hale, Grant Harris, Stefan Helfrich, Mark Hiner,
... | imglib/imglib2-tests | src/test/scripts/chart-gen.py | Python | gpl-2.0 | 5,836 | [
"Brian"
] | dc410a7d42820e585fd7cc58e80f708bb92f2e7337d7ac6dfafe8cb3621bce06 |
import PyV8
from PyV8 import JSClass
import logging
import jsonpickle
import json
log = logging.getLogger("Untangle");
def var_dump(obj, indent = 0):
ind = " " * indent
print ind+"%s" % type(obj)
if type(obj) is str:
print ind+" - %s" % obj
elif type(obj) is list:
for o in obj:
... | qistoph/jsuntangle | jsuntangler/Parser.py | Python | gpl-3.0 | 21,678 | [
"VisIt"
] | 73542081ab68570d14afb114adbd76a95a882abd80b0fe4e4049d61f5996510c |
#!/usr/bin/env python
"""
Unit tests for run_compute_precision_recall.py
==============================================
"""
# ----------------------------------------------------------------------------
# Copyright (c) 2015--, Evguenia Kopylova
#
# Distributed under the terms of the Modified BSD License.
#
# The full ... | ekopylova/OTU-clustering | python_scripts/tests/test_run_compute_precision_recall.py | Python | bsd-3-clause | 56,071 | [
"BLAST"
] | 9606d323b1093be513d9cf6f67b8a703cfae534d65b4ec03412122eba6c972f5 |
import os
from .. import DataType
from ..step1.data_handler import DataHandler
from ..step1.gui_handler import Step1GuiHandler
from ..step2.plot import Step2Plot
from ..utilities.gui_handler import GuiHandler
from ..utilities.pyqrgraph import Pyqtgrah as PyqtgraphUtilities
class LoadLoadDataTab:
def __init__(se... | ornlneutronimaging/iBeatles | src/iBeatles/session/load_load_data_tab.py | Python | mit | 7,263 | [
"CRYSTAL"
] | b66937e6fde555f14d7dd05884e14424588f1dea06feb87770a2cb2c96d3cacb |
"""Utility functions for plotting M/EEG data
"""
from __future__ import print_function
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Denis Engemann <denis.engemann@gmail.com>
# Martin Luessi <mluessi@nmr.mgh.harvard.edu>
# Eric Larson <larson.eric.d@gmail.com>
# ... | aestrivex/mne-python | mne/viz/utils.py | Python | bsd-3-clause | 18,022 | [
"Mayavi"
] | 62304deff91d455b41f38773a359ba19c45dcd74f36b7f7e7a8fedb466948715 |
# ============================================================================
#
# Copyright (C) 2007-2012 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | jeroendierckx/Camelot | camelot/core/utils.py | Python | gpl-2.0 | 9,051 | [
"VisIt"
] | 568630ac4dabd7f01b610b08cecf5cc74a541b8dda8c08eea2942008e551569f |
########################################################################
# File : SSHComputingElement.py
# Author : Dumitru Laurentiu
########################################################################
""" SSH (Virtual) Computing Element: For a given list of ip/cores pair it will send jobs
directly through ... | ic-hep/DIRAC | src/DIRAC/Resources/Computing/SSHBatchComputingElement.py | Python | gpl-3.0 | 8,663 | [
"DIRAC"
] | 1c1a2f5e4e1f942c0e5b1e61d28d0ab3a0d4a1cea5c238bc6cf2818c94e646b4 |
# -*- coding: utf-8 -*-
"""Implementation of probability distributions.
"""
# Author: Taku Yoshioka, Shohei Shimizu
# License: MIT
import numpy as np
from numpy import log, sqrt, abs, power, sign
from scipy.special import gamma, gammaln
from pymc3.distributions import Continuous
from theano import tensor a... | taku-y/bmlingam | bmlingam/prob.py | Python | mit | 5,814 | [
"Gaussian"
] | cc2ca8286d41d1b5e05d9407afabf531324cc3f1539d341710ffecfa2c3376ff |
# -*- coding: utf-8 -*-
# encoding: utf-8
"""
Plotting functions for pymzML.
The Factory object can hold several plots with several data traces each.
The data can be visualized as an interactive plotly plot or be exported as JSON.
"""
# Python mzML module - pymzml
# Copyright (C) 2010-2019 M. Kösters, C. Fufezan
# ... | pymzml/pymzML | pymzml/plot.py | Python | mit | 24,726 | [
"ORCA"
] | d2dac05352281cd7a1d4d95536a918167bb3f688077e24e1d0b5f2348b726e86 |
#Main GWR classes
#Offset does not yet do anyhting and needs to be implemented
__author__ = "Taylor Oshan Tayoshan@gmail.com"
import numpy as np
import numpy.linalg as la
from scipy.stats import t
from kernels import *
from diagnostics import get_AIC, get_AICc, get_BIC
import pysal.spreg.user_output as USER
from pys... | ljwolf/pysal | pysal/contrib/gwr/gwr.py | Python | bsd-3-clause | 31,293 | [
"Gaussian"
] | c14abb114d2163979f2fd24c0310b535c16da7489c6a2c2763202a912c65062f |
from scholar import *
from BeautifulSoup import BeautifulSoup
from html2text import *
import string
import random
import Queue
import Levenshtein
import urllib2
import networkx as nx
import time
import mechanize
import cookielib
from functools import wraps
def get_random_id(size = 16, chars = string.ascii_letters + st... | w1ndy/comap-mcm | MCM 2014/BuildCitationNetwork.py | Python | mit | 6,234 | [
"VisIt"
] | 9e39ae5d6f00696e8fd2176a04be49fd99901053697eab5d213d3744cdfc6649 |
'''
Created
@author: Andrew Roth
JointSNVMix-0.6.2
joint_snv_mix.pre_processing.bam_to_jcnt.BamToJcntConverter
joint_snv_mix.pre_processing.bam_to_jcnt.JointPileupIterator
================================================================================
Modified on 2013-07-20
@author: Yi Li
pyloh.preprocess.io
==... | uci-cbcl/MixClone | mixclone/preprocess/io.py | Python | gpl-2.0 | 6,158 | [
"pysam"
] | 9475c2d863edc527c28e52116e761f3a17541b92ece045b395e9bdab5426a118 |
'''
Example of a spike receptor (only receives spikes)
In this example spikes are received and processed creating a raster plot at the end of the simulation.
'''
from brian import *
import numpy
from brian_multiprocess_udp_mono import BrianConnectUDP
# The main function with the NeuronGroup(s) and Synapse(s) must ... | ricardodeazambuja/BrianConnectUDP | examples/OutputNeuronGroup_Liquid_mono.py | Python | cc0-1.0 | 2,757 | [
"Brian",
"NEURON"
] | 6b4cb3a7c3cdadc85ef8bd40d6279928688b6e4a366a09bbb9615269c9277f9b |
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'electrodeParasDialog.ui'
#
# Created: Tue Jun 28 11:16:43 2011
# by: PyQt4 UI code generator 4.8.3
#
# WARNING! All changes made in this file will be lost!
from PyQt4 import QtCore, QtGui
try:
_fromUtf8 = QtCore.QString.fromUtf8
e... | BhallaLab/moose-thalamocortical | pymoose/gui/qt/electrodeParasDialog.py | Python | lgpl-2.1 | 9,047 | [
"MOOSE"
] | 4a1c7a3340e789f2dda7a7ba4892724862c7ca6dc6fd760c6de25b637e0944a9 |
"""Main qcl Application called when qcl script is invoked """
from argparse import ArgumentParser, \
ArgumentDefaultsHelpFormatter, \
ArgumentTypeError
from qcl import conformers, obconformers, minima, \
stretch, templates, zmatrix, figs, rmsd, job
def get_arguments(args=None):
"""
Parse command li... | ben-albrecht/qcl | qcl/application.py | Python | mit | 7,446 | [
"Open Babel",
"Q-Chem"
] | e1df27b022f62add8c4348b2fe907af5455d245f368a28bec5b6fffd92432528 |
"""
DIRAC.Resources.Computing package
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
| yujikato/DIRAC | src/DIRAC/Resources/Computing/__init__.py | Python | gpl-3.0 | 171 | [
"DIRAC"
] | d6e6428692e9c3cef4024cd5fde31c991293dbaf1b2b216dc3fac0db357e7368 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import io
import re
from setuptools import setup
VERSIONFILE = "ncml/__init__.py"
verstrline = open(VERSIONFILE, "rt").read()
VSRE = r"^__version__ = ['\"]([^'\"]*)['\"]"
mo = re.search(VSRE, verstrline, re.M)
if mo:
verstr = mo.group(1)
else:
raise RuntimeError("... | ioos/ncml | setup.py | Python | cc0-1.0 | 2,012 | [
"NetCDF"
] | 2160b9d4e1c12e1d779c084b53923d4b358d31561bd26fdb9bce0c72be852ab0 |
#!/usr/bin/env python
"""
Runs checkTransformationIntegrity from ValidateOutputDataAgent on selected Tranformation
"""
from DIRAC.Core.Base.Script import Script
@Script()
def main():
# Registering arguments will automatically add their description to the help menu
Script.registerArgument(["transID: transforma... | DIRACGrid/DIRAC | src/DIRAC/TransformationSystem/scripts/dirac_transformation_verify_outputdata.py | Python | gpl-3.0 | 851 | [
"DIRAC"
] | 9107a6096a36fba5ec9215e366e0a1fb5766b7279fab97d883189b56bd6e0217 |
# -*- coding: utf-8 -*-
"""
Models used to implement SAML SSO support in third_party_auth
(inlcuding Shibboleth support)
"""
from __future__ import absolute_import
import json
import logging
import re
from config_models.models import ConfigurationModel, cache
from django.conf import settings
from django.contrib.sites... | Lektorium-LLC/edx-platform | common/djangoapps/third_party_auth/models.py | Python | agpl-3.0 | 32,725 | [
"VisIt"
] | 6adb3654256598293b295771dc92a39318e7b20fae5474ac1e65d8f494c2466b |
"""
Copyright (c) 2004, CherryPy Team (team@cherrypy.org)
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 o... | bieschke/nuffle | lib/python/cherrypy/test/test_cache_filter.py | Python | gpl-2.0 | 2,225 | [
"VisIt"
] | c6db3359f6b3e07d71cfac0313dce481cc025629d9c16117d775decaea94a6d8 |
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