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#!python
# coding=utf-8
import os
import re
import itertools
from datetime import datetime
from .utils import all_subclasses, is_url
from .dataset import EnhancedDataset
from . import logger
class CFDataset(EnhancedDataset):
default_fill_value = -9999.9
default_time_unit = 'seconds since 1990-01-01 00:00:00... | pyoceans/pocean-core | pocean/cf.py | Python | mit | 6,355 | [
"NetCDF"
] | 1dcb04e1b7d7523e4717ac729bbb3a0768253c87f2fc8083483334dba39920b3 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2008-2009 Gary Burton
# Copyright (C) 2008 Robert Cheramy <robert@cheramy.net>
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2010 Nick Ha... | gramps-project/gramps | gramps/plugins/export/exportgedcom.py | Python | gpl-2.0 | 61,377 | [
"Brian"
] | 8fea5cc8b4c311a7a3ba8b1910aef00ffac19471e4a70fc336d992d0ca03fc02 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
NeuroKitEditor for NeuroKit plugin.
"""
__author__ = "Aviral Goel"
__credits__ = ["Upi Lab"]
__license__ = "GPL3"
__version__ = "1.0.0"
__maintainer__ = "Aviral Goel"
__email__ = "goel.aviral@gmail.com"
__status__ = "Developm... | dilawar/moose-full | moose-gui/plugins/NeuroKitEditor.py | Python | gpl-2.0 | 11,841 | [
"MOOSE",
"NEURON"
] | 79a7ae358497fb65f781a7e53ba2db85fe3b9b198c653467b72fe5ae64ba1c46 |
# pylint: disable=missing-docstring
# pylint: disable=redefined-outer-name
from lettuce import world, step
from lettuce.django import django_url
import time
@step('I register for the course "([^"]*)"$')
def i_register_for_the_course(_step, course):
url = django_url('courses/%s/about' % world.scenario_dict['COURS... | olexiim/edx-platform | lms/djangoapps/courseware/features/registration.py | Python | agpl-3.0 | 2,032 | [
"VisIt"
] | c1b32f54b1e8de7f3bfb4c44f60a1a13fcf001bfedede3b754d1fab952efc792 |
#!/usr/bin/env python
import os
try:
__IPYTHON__
import sys
del sys.argv[1:]
except:
pass
import srwl_bl
import srwlib
import srwlpy
import math
import srwl_uti_smp
def set_optics(v, names=None, want_final_propagation=True):
el = []
pp = []
if not names:
names = ['VFM', 'VFM_HFM', ... | radiasoft/sirepo | tests/template/srw_generate_data/mask-example.py | Python | apache-2.0 | 26,164 | [
"Gaussian"
] | 47f0f5f5b57a08613359e65738ca257a8ec02409fa5afc17a8449c58bca651bf |
#!/usr/bin/en python
import os
import sys
import glob
import json
import numpy as np
import pandas as pd
from lxml import objectify
def read_xml_sidecar(filepath):
"""
Read a CMTK xml sidecar file.
Returns
=======
lxml.objectify
"""
abs_path = os.path.abspath(filepath)
with open(abs_p... | abonil91/ncanda-data-integration | scripts/xnat/check_gradient_tables.py | Python | bsd-3-clause | 6,786 | [
"VisIt"
] | 70b23d9a1bb7347960f26760aed7a3891509e2ef2a2551d6f5d03b36fcc624c5 |
#!/usr/bin/env python
# -----------------------------------------------------------------------------
# Copyright (c) 2013, The Qiita Development Team.
#
# Distributed under the terms of the BSD 3-clause License.
#
# The full license is in the file LICENSE, distributed with this software.
# ---------------------------... | squirrelo/qiita | setup.py | Python | bsd-3-clause | 4,890 | [
"scikit-bio"
] | 15047999cb2be5fd4ab28b12b93b7af065535202349fa201e9db6709bb8eca00 |
"""
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 .base import LinearModel
from ..base import RegressorMixin
from ..utils.extmath import fast_logdet, p... | valexandersaulys/airbnb_kaggle_contest | venv/lib/python3.4/site-packages/sklearn/linear_model/bayes.py | Python | gpl-2.0 | 15,248 | [
"Gaussian"
] | ad9552c34e7f60c363fed263829c9976e7576c8f14796fc033398048c63b14d4 |
from os.path import abspath, basename, join, exists
from os.path import dirname
from os.path import relpath
from os import listdir, sep
from re import findall
from io import open
from ..staging import COMMAND_VERSION_FILENAME
from ..action_mapper import FileActionMapper
from ..action_mapper import path_type
from ..act... | jmchilton/lwr | lwr/lwr_client/staging/up.py | Python | apache-2.0 | 17,093 | [
"Galaxy"
] | 752112fd069692b7edfb514328c5266e33d61218f80281fe2120c0495fb34647 |
"""
network/shape.py
Network class methods to deal with the each population's cell shape (morphology)
Contributors: salvadordura@gmail.com
"""
from __future__ import unicode_literals
from __future__ import print_function
from __future__ import division
from __future__ import absolute_import
from future import sta... | thekerrlab/netpyne | netpyne/network/shape.py | Python | mit | 1,508 | [
"NEURON"
] | ce59e3c0bd1291284c76cd98d4b5d56fa60f2c77edb897ce0a97e7d324bee29e |
from __future__ import print_function
from caffe import layers as L, params as P, to_proto
from caffe.proto import caffe_pb2
import caffe
def res_group(bottom, ks, nout, stride, pad, dropout, weight_filler=dict(type='msra'), project=False):
# branch 1
branch1 = bottom
if project == True:
branch1 ... | albertxavier001/graduation-project | caffe/3 deep supervision pure dense/make_albedo_net.py | Python | mit | 13,847 | [
"Gaussian"
] | 694f4a578d4c310aed94a77cab03dae3d308a00e55bf3eb52f06fc0089f7cf6c |
"""Basic UI test that checks if the stack analysis is visible for the newly created project."""
from splinter import Browser
import time
import os
from urllib.parse import urljoin
SLEEP_BETWEEN_PAGES = 15
SLEEP_BEFORE_CLICK = 15
class Context:
"""Class that holds context for the UI tests."""
def __init__(s... | jpopelka/fabric8-analytics-common | ui-tests/test.py | Python | apache-2.0 | 10,288 | [
"VisIt"
] | 87c02e91f8e598bf45ceef7d9313ad670e051952617c13aeb56f1d9e4b8608a0 |
# ============================================================================
#
# Copyright (C) 2007-2010 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... | kurtraschke/camelot | camelot/view/controls/delegates/floatdelegate.py | Python | gpl-2.0 | 2,971 | [
"VisIt"
] | 66beec19b22d6b749541931bd58f6adc6755fe40c99eee01a2b8ab5218743228 |
""" ResourceManagementClient
Client to interact with the ResourceManagementDB.
"""
__RCSID__ = '$Id$'
from DIRAC.Core.DISET.RPCClient import RPCClient
def uppercase_first_letter(key):
""" a method that makes the first letter uppercase only (and leaves the remaining letters unaffected)
"""
return key[0].up... | arrabito/DIRAC | ResourceStatusSystem/Client/ResourceManagementClient.py | Python | gpl-3.0 | 27,731 | [
"DIRAC"
] | a6b0268ea9acd3e77ebb27508642997fe7f9f6e5fc2c5085c0ecce8aa5815402 |
from functools import partial
from client.player import Player
from client.updater import fetchClientUpdate
from config import Settings
import fa
from fa.factions import Factions
'''
Created on Dec 1, 2011
@author: thygrrr
'''
from PyQt4 import QtCore, QtGui, QtNetwork, QtWebKit
from PyQt4.QtCore import QDataStream
... | madformuse/client | src/client/_clientwindow.py | Python | gpl-3.0 | 60,723 | [
"VisIt"
] | 8af7791e873571e5ee76df9c542d7c5d72c2415ea0d1d27ca39b6db79c970832 |
import pytest
from functools import partial
import numpy as np
import psi4
from psi4.driver import qcdb
pytestmark = pytest.mark.quick
_arrs = {
'a1234_14': np.arange(4),
'blip14': np.arange(4) + [0., 0.02, 0.005, 0.02],
'a1234_22': np.arange(4).reshape((2, 2)),
'blip22': (np.arange(4) + [0., 0.02,... | psi4/psi4 | tests/pytests/test_testing.py | Python | lgpl-3.0 | 11,875 | [
"Psi4"
] | ab08d793fa49e43611df8b2ff5c777c42e2d17b29898bae707b9ec3b8811cfe5 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides classes to store, generate, and manipulate material interfaces.
"""
import warnings
from pymatgen.analysis.interfaces import CoherentInterfaceBuilder # noqa
from pymatgen.core.interface import Inter... | materialsproject/pymatgen | pymatgen/analysis/interface.py | Python | mit | 797 | [
"pymatgen"
] | ec1d85acffee96ba4dcf6341d5d8eecfa26cb149e002563aae0fdcbc28c982f0 |
# -*- coding: utf-8 -*-
#
# Moonstone is platform for processing of medical images (DICOM).
# Copyright (C) 2009-2011 by Neppo Tecnologia da Informação LTDA
# and Aevum Softwares LTDA
#
# This file is part of Moonstone.
#
# Moonstone is free software: you can redistribute it and/or modify
# it under the terms of the GN... | aevum/moonstone | src/moonstone/bloodstone/scenes/data/slice.py | Python | lgpl-3.0 | 7,771 | [
"VTK"
] | 83bccba576a1a271b58fd94dc1e4ddd9238bad5e091d63028b640f2fc7baab69 |
from vtk.web import testing
from vtk.web.testing import BrowserBasedWebTest
dependencies_met = True
try:
# import modules for automating web testing using a real browser
import selenium
except:
dependencies_met = False
# =============================================================================
# De... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/Web/Applications/TestApp/test/test_pv_web_testapp_all.py | Python | gpl-3.0 | 2,795 | [
"VTK"
] | 0c2582a16f5b1d15b06f1b9b815d6435868e9de777cc94ca0c8dd780adb32ae7 |
#!/usr/bin/env python
#
# $File: PyParentsChooser.py $
#
# This file is part of simuPOP, a forward-time population genetics
# simulation environment. Please visit http://simupop.sourceforge.net
# for details.
#
# Copyright (C) 2004 - 2010 Bo Peng (bpeng@mdanderson.org)
#
# This program is free software: you can redist... | BoPeng/simuPOP | docs/PyParentsChooser.py | Python | gpl-2.0 | 2,369 | [
"VisIt"
] | 25512b53dcaedffec58269b94aab258b4c4f33fa30b05900e5e1398cc0961854 |
#
# model_parser.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST 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... | kperun/nestml | pynestml/utils/model_parser.py | Python | gpl-2.0 | 19,642 | [
"NEURON",
"VisIt"
] | ed569215e9e1bafc412abdd4b6bf79edecc9f55ff4789f296af0f26925cab0ea |
# !/usr/local/bin/python3.4.2
# ----Copyright (c) 2017 Carnegie Hall | The MIT License (MIT)----
# ----For the full license terms, please visit https://github.com/CarnegieHall/linked-data/blob/master/LICENSE----
## Argument[0] is script to run
## Argument[1] is path to json query results from data.carnegiehall.org
## ... | CarnegieHall/linked-data | scripts/dbp_findWikidataURI.py | Python | mit | 1,682 | [
"VisIt"
] | 61ce1380429da530ba653c34e65141be9707b65a0481ba0155b5c0d5857ac746 |
#-------------------------------------------------------------------------------------------------------------------#
#
# IB2d is an Immersed Boundary Code (IB) for solving fully coupled
# fluid-structure interaction models. This version of the code is based off of
# Peskin's Immersed Boundary Method Paper in Acta N... | nickabattista/IB2d | data_analysis/analysis_in_python/DA_Blackbox/read_vtk_data.py | Python | gpl-3.0 | 4,272 | [
"VTK"
] | 3cbb7782a443c42770fd4e763fb41b83ef9289c24a9a74aacace76676f4a6a7c |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
La Niña
Command Line Weather using the http://wunderground.com API
Author: Brian Carter
http://github.com/robotmachine/La_Nina
Originally forked from niño || https://github.com/drbunsen/nino
"""
import os, sys, urllib, urllib.request, http.client, configparser, textwr... | robotmachine/La_Nina | la_nina.py | Python | mit | 5,136 | [
"Brian"
] | e463d6ee1293619c0a5732c448358f1372debee28e085928e629e30a7341896f |
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publi... | thica/ORCA-Remote | src/ORCA/widgets/Border.py | Python | gpl-3.0 | 4,647 | [
"ORCA"
] | 843857fa4ad138b81f587860356a7645834f8ecbcfb3e1979f93850e474a0df1 |
import pymol
from pymol import cmd
import sys,os
from MoleculeUtils import selectPolarProtons
from MoleculeUtils import selectApolarProtons
from MoleculeUtils import colorCPK
from PackingMeasureUtils import loadPackingPDB
def loadSurfaceInterfacePDB( file,name=None,native=None,wt=None):
print " Loading int... | weitzner/Dotfiles | pymol_scripts/InterfaceUtils-network.py | Python | mit | 20,814 | [
"PyMOL"
] | c7dcf7ec5ecdc50be2b562ad15d1b72d4cf7f791319dc0023e8b4a5c4b5273c2 |
"""psi4 module
The Sphinx documentation system scans all Python modules for docstrings
and class structure (good) but in doing so imports modules it finds in
input statements and follows any exposed code like the procedures
dictionary (bad for Psi4 b/c of psi4). So, this fake psi4 module
exists to appease Sphinx when i... | spring01/libPSI | doc/sphinxman/source/psi4.py | Python | gpl-2.0 | 3,840 | [
"Psi4"
] | 0682a7b8764137d97f28f7083afb7fb360562d9eb2242c303b30d0af46380a33 |
"""Reads quantum espresso files. Tested for output on PWSCF v.5.0.2, only
for typical output of input files made with ASE -- that is, ibrav=0."""
import numpy as np
from ase.atoms import Atoms, Atom
from ase import units
from ase.calculators.singlepoint import SinglePointCalculator
def read_espresso_out(fileobj, ind... | grhawk/ASE | tools/ase/io/espresso.py | Python | gpl-2.0 | 8,127 | [
"ASE",
"CRYSTAL",
"ESPResSo",
"Quantum ESPRESSO"
] | 7e47ed32628574d16a64dae6f81f0d9f471393836ecf75cb49f4b1516cbb1525 |
= Docker How To =
docker run -t -i centos /bin/bash
Hi, Brian,
This seems to be an issue related to Docker running out of disk space. A few
general solutions which seem to work for others include simply waiting and
retrying to pull the image, removing the contents of your /var/lib/docker
directory and restar... | loolwv7/scripts | Linux_Tricks/Docker_how_to.py | Python | gpl-3.0 | 1,023 | [
"Brian"
] | 68143809e0a4f8d22d1e0c2bc6267a99741d786903dbb10602547ffeaaca4ee6 |
"""
Ax_Metrics - EROut plugin 'geckoboard_text'
Writes Geckoboard JSON output for various charts for use with
http://www.geckoboard.com.
Contents:
- EROut_geckoboard_text - pages of text, optionally flagged
See:
- https://developer.geckoboard.com/#geck-o-meter
----------------------------------------------... | axonchisel/ax_metrics | py/axonchisel/metrics/io/erout/plugins/ero_geckoboard/text.py | Python | mit | 7,614 | [
"Amber"
] | 9004f06838e824e003eb020a2be3517369065ee877a75546e62d53af307fb753 |
"""
A robot exclusion rules parser for Python by Philip Semanchuk
Full documentation, examples and a comparison to Python's robotparser module
reside here:
http://NikitaTheSpider.com/python/rerp/
Comments, bug reports, etc. are most welcome via email to:
philip@semanchuk.com
Simple usage examples:
import ro... | chfoo/wpull | wpull/thirdparty/robotexclusionrulesparser.py | Python | gpl-3.0 | 29,545 | [
"VisIt"
] | 4002b26c3647a13b40aa13bbf3ccee270b31fc86f8de17731aa389214d44249e |
""" RabbitMQSync service to synchronize the internal RabbitMQ database.
according to CS content. The whole work is done by the RabbitMQSynchronizer
that is activated when the CS was changed.
"""
from DIRAC.Core.DISET.RequestHandler import RequestHandler
from DIRAC import S_OK
from DIRAC import gConfig
from DIRA... | DIRACGrid/DIRAC | src/DIRAC/FrameworkSystem/Service/RabbitMQSyncHandler.py | Python | gpl-3.0 | 859 | [
"DIRAC"
] | 12575fdca68f825e2184f1e5ddcfb43eadfa1bf455c88c342e3cfd1071d927a7 |
import os
from astropy.table import Table
import matplotlib.pyplot as plt
# setup information sources
stack = Table.read(os.path.join(os.environ['ANALYSISDIR'],'stack_test','stack_IR6p1_mom1.fits'))
plotDir = os.path.join(os.environ['ANALYSISDIR'],'plots','radial_plots')
degas = Table.read(os.path.join(os.environ['SC... | low-sky/degas | scripts/plot_radial_trends.py | Python | gpl-3.0 | 5,821 | [
"Galaxy"
] | 2736969bd47781141501dc4f350095cc766c75d4a183633f9288c5d8a33c7528 |
#!/usr/bin/env python
"""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... | Gschlotter/planet.opensuse.org | rawdoglib/feedparser.py | Python | gpl-2.0 | 157,078 | [
"NetCDF",
"VisIt"
] | 15bcb939012c71e97d3203adbeee8cfc229c0d27d0ca6f904aded437cb25ed3d |
"""Main entry point for distributed next-gen sequencing pipelines.
Handles running the full pipeline based on instructions
"""
import abc
from collections import defaultdict
import copy
import os
import sys
import resource
import tempfile
import toolz as tz
import yaml
from bcbio import log, heterogeneity, hla, stru... | lpantano/bcbio-nextgen | bcbio/pipeline/main.py | Python | mit | 25,515 | [
"Bowtie"
] | a741da6c0a431823979a5044f5f96e88fd01c9ad376ffa7793effe0f6452d4b9 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2007-2008 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU Lesser General Public License as published by
## the Free Softw... | andrebellafronte/stoq | plugins/ecf/test/test_cat52.py | Python | gpl-2.0 | 4,403 | [
"VisIt"
] | 9d7be635ec9f7b4cc6a53dd63f32b6cc372ab3e5fc4649c6e8fdb6c21d48f882 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements a core class LammpsData for generating/parsing
LAMMPS data file, and other bridging classes to build LammpsData from
molecules. This module also implements a subclass CombinedData for
merging LammpsD... | vorwerkc/pymatgen | pymatgen/io/lammps/data.py | Python | mit | 62,358 | [
"LAMMPS",
"pymatgen"
] | fbd5b342b9aeeb48b6b06b374343a90af23eac38fada776cd3d0b24b5b4a311a |
from json import load
from os import makedirs
from os.path import exists
from os.path import abspath
from os.path import dirname
from os.path import join
from os.path import basename
from os.path import sep
import fnmatch
from re import compile
from re import escape
import galaxy.util
from galaxy.util.bunch import Bunc... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/pulsar/client/action_mapper.py | Python | gpl-3.0 | 19,930 | [
"Galaxy"
] | be02a4de24c0655008cf09abf307faca12d2ef4bb9f873b8778c1ecf1b621134 |
#!/usr/bin/env python3
########################################################################
# Solves problem 4 from projectEuler.net.
# Finds the largest palindrome product of two 3-digt numbers.
# Copyright (C) 2010 Santiago Alessandri
#
# This program is free software: you can redistribute it and/or mod... | sanSS/programming-contests | project-euler/problem004.py | Python | gpl-3.0 | 1,398 | [
"VisIt"
] | 7f23203104038bc03bda7eeac1ed3c7e86e88719bbcc7ca5c605d20e270dee0c |
import pycasso
import numpy as np
from sklearn.preprocessing import scale
## Sparse linear regression
## Generate the design matrix and regression coefficient vector
n = 100 # sample number
d = 80 # sample dimension
c = 0.5 # correlation parameter
s = 20 # support size of coefficient
X = scale(np.random.randn(n,d)+c... | jasonge27/picasso | tutorials/tutorial.py | Python | gpl-3.0 | 4,212 | [
"Gaussian"
] | e8f6f7f034f36a7c7e5d05dc28ad9907a0f7c164debac80508dbe69eb38732b6 |
#!/usr/bin/env python3
"""
Generation of XML for Galaxy from https://bio.tools based on the Tooldog model using
galaxyxml library.
"""
# Import ------------------------------
# General libraries
import os
import copy
import logging
# External libraries
from lxml import etree
import galaxyxml.tool as gxt
import ga... | khillion/ToolDog | tooldog/annotate/galaxy.py | Python | mit | 10,519 | [
"Galaxy"
] | 80082aebfde478e3e2960265af14b7777641bc8eac41100adcf9883187120f86 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright: (c) 2015, Heyo
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
# this is a windows documentation stub. actual code lives in the .ps1
# file of the same name
ANSIBLE_METADATA = {'metadata_version': '1.1',
... | Jorge-Rodriguez/ansible | lib/ansible/modules/windows/win_nssm.py | Python | gpl-3.0 | 5,307 | [
"ADF"
] | 7e244983d23b4c32c5fe892f161f7192a3eee76fab28b0a481acb67e8b765103 |
import os
from glutton.utils import get_log, tmpfasta, tmpfasta_orfs, tmpfile, rm_f, threadsafe_io, fasta_stats
from glutton.prank import Prank
from glutton.pagan import Pagan
from glutton.blast import Blastx, Tblastx
from abc import abstractmethod
from os.path import basename, isfile, join
from sys import exit
impo... | ajm/glutton | glutton/job.py | Python | gpl-3.0 | 8,540 | [
"BLAST"
] | 7f9b4f8094b218f1d5e9e0b90b10e63568acb072a7c21ff08086de539e214714 |
"""Collection of function implementations.
Functions are either implemented as :class:`~chainer.Function`\\ s or
:class:`~chainer.FunctionNode`\\ s.
"""
from chainer.functions.activation.clipped_relu import clipped_relu # NOQA
from chainer.functions.activation.clipped_relu import ClippedReLU # NOQA
from chainer.fun... | anaruse/chainer | chainer/functions/__init__.py | Python | mit | 20,455 | [
"Gaussian"
] | b8ffa4bc770c4d485f5dda57551aeec4d35ac1aef561fc9f85393e184d7fcf0a |
"""Model definition for base class for Linear Time-varying systems
@author: Jerker Nordh
"""
from pyparticleest.interfaces import FFBSi, ParticleFiltering
try:
import pyparticleest.utils.ckalman as kalman
import pyparticleest.utils.cmlnlg_compute as mlnlg_compute
except ImportError:
print("Falling back to ... | jerkern/pyParticleEst | pyparticleest/models/ltv.py | Python | lgpl-3.0 | 22,845 | [
"Gaussian"
] | d4e28255d6c76fa0008db48ae133edf9ab659a1dc479e1618ac41e2df1e65926 |
# reinforcementTestClasses.py
# ---------------------------
# Licensing Information: You are free to use or extend these projects for
# educational purposes provided that (1) you do not distribute or publish
# solutions, (2) you retain this notice, and (3) you provide clear
# attribution to UC Berkeley, including a li... | omardroubi/Artificial-Intelligence | Projects/Project3/reinforcement/reinforcementTestClasses.py | Python | apache-2.0 | 46,566 | [
"VisIt"
] | a8d8a207837481997b5b9ddf4f24dfe7261dbcfe5b2a4e083d6428fec319a635 |
#!/usr/bin/env python
#
# setup for TreeFix library packages
#
# use the following to install:
# python setup.py build
# python setup.py install
#
import os,sys
from distutils.core import setup, Extension
import numpy
sys.path.insert(0, os.path.realpath(
os.path.join(os.path.dirname(__file__), "lib")))
USE_C... | UdeM-LBIT/GAPol | setup.py | Python | gpl-3.0 | 2,392 | [
"Biopython"
] | 4b8f2cd39ee3ba1908d21e35d1d58a0bcde0dfe8c83ec09d96ea6d73aba42ea2 |
#!/usr/bin/env python
"""
Read simplified JSON BLAST records and report the elapsed time.
"""
from __future__ import print_function
from dark.conversion import JSONRecordsReader
from time import time
import sys
if __name__ == '__main__':
if len(sys.argv) != 2:
print('Usage: %s file.json' % sys.argv[0],... | bamueh/dark-matter | bin/read-blast-json.py | Python | mit | 729 | [
"BLAST"
] | d69fade41b1761134f782e96663d8034d2b6418dd912b84153529c36dd8f7c8d |
#! CCSD dipole with user-specified basis set
import psi4
psi4.set_output_file("output.dat", False)
h2o = psi4.geometry("""
0 1
H
O 1 0.957
H 2 0.957 1 104.5
""")
psi4.set_options({'freeze_core': 'false'})
psi4.basis_helper("""
# Sadlej-pVTZ
spherical
****
H 0
S 4 1.00
33.8650140000 0.00606... | ashutoshvt/psi4 | samples/python/cc54/input.py | Python | lgpl-3.0 | 2,940 | [
"Psi4"
] | 2c22b8f9408c4a56bf9087f415cde365d52e9f06f108242ed2dbff76f066a931 |
# -*- coding: utf-8 -*-
#
# Copyright (C) 2007 Marcos Mobley ('markybob') <markybob@gmail.com>
#
# This file is part of Deluge and is licensed under GNU General Public License 3.0, or later, with
# the additional special exception to link portions of this program with the OpenSSL library.
# See LICENSE for more details... | Arzie/deluge | deluge/ui/gtkui/aboutdialog.py | Python | gpl-3.0 | 17,911 | [
"Gaussian"
] | 211b22696c69ecd497fc253588115827e3c75de459baf44a08baeb2411c504f8 |
"""
Exponential Integrate-and-Fire model.
See Neuronal Dynamics, `Chapter 5 Section 2 <http://neuronaldynamics.epfl.ch/online/Ch5.S2.html>`_
"""
# This file is part of the exercise code repository accompanying
# the book: Neuronal Dynamics (see http://neuronaldynamics.epfl.ch)
# located at http://github.com/EPFL-LCN/n... | EPFL-LCN/neuronaldynamics-exercises | neurodynex3/exponential_integrate_fire/exp_IF.py | Python | gpl-2.0 | 4,520 | [
"NEURON"
] | fbfc1c89f29f81d59d1a20319ef1797bb4cfe07be0ff78b03b5aadf99c20a961 |
#!/usr/bin/env python
"""
C.7 Mathematical Formulas (p187)
"""
from Arrays import Array
from plasTeX import Command, Environment, sourceChildren
from plasTeX import DimenCommand, GlueCommand
from plasTeX.Logging import getLogger
#
# C.7.1
#
class MathEnvironment(Environment):
mathMode = True
class ThinSpa... | nibrahim/PlasTeX | plasTeX/Base/LaTeX/Math.py | Python | mit | 14,996 | [
"Bowtie"
] | 319d1c68b97fe119f2922b9a3031897f05cb910697fd48bc3ef362f896a37ac3 |
"""
Parser function parse() to parse the _u.mat output file of Wannier90 (u matrices).
"""
from __future__ import print_function
import inspect
import re
from collections import defaultdict
from . import show_output
def parse(fname):
"""
Open the file, parses it and return the values
For now, I just che... | mostofi/wannier90 | test-suite/tools/parsers/parse_umat.py | Python | gpl-2.0 | 947 | [
"Wannier90"
] | e2d0c949da12d16baa986144e206c81e0f6515b822b61a6843ff2c6166aade60 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# QuickFF is a code to quickly derive accurate force fields from ab initio input.
# Copyright (C) 2012 - 2019 Louis Vanduyfhuys <Louis.Vanduyfhuys@UGent.be>
# Steven Vandenbrande <Steven.Vandenbrande@UGent.be>,
# Jelle Wieme <Jelle.Wieme@UGent.be>,
# Toon Verstraelen <Toon.... | molmod/QuickFF | quickff/scripts.py | Python | gpl-3.0 | 21,393 | [
"Gaussian",
"VASP"
] | ac2a9b7ef5d839c6e2d615c4f31ee9dbc3fe2c241bceb4713d3d6162d9b5c30d |
# -*- coding: utf-8 -*-
#
# This program is designed to plot an interactive 3D cube of the HI gas in
# the compact group of galaxies HCG91 using the Mayavi module. It is an example
# of "real" astrophsyical data plotted interactively in 3-D using Mayavi.
# In particular, the code does not shy away from the intricasi... | fpavogt/x3d-pathway | fits_to_x3d/HCG91/HCG91.py | Python | gpl-3.0 | 18,943 | [
"Galaxy",
"Mayavi"
] | 7ab08880e4ec206ee334c810b4f63d2fa860d33145f3d8d22282eeaaaef7b310 |
import importlib
import click
import os
import numpy
from PIL.Image import ANTIALIAS
from pyproj import Proj
from netCDF4 import Dataset
from trefoil.utilities.color import Color
from trefoil.netcdf.utilities import collect_statistics, resolve_dataset_variable
from trefoil.render.renderers.stretched import StretchedR... | consbio/clover | trefoil/cli/utilities.py | Python | bsd-3-clause | 5,125 | [
"NetCDF"
] | e26576b265b859b27b1b4892c42f866c7c9e705a51c9f18f1bae6f6dd8f1918f |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/item_title | openlp/plugins/presentations/lib/powerpointcontroller.py | Python | gpl-2.0 | 12,163 | [
"Brian"
] | bff57752cbb561ceb8e5a22ee4af8bae810f56c20554d09a0e4d4b109e24f07a |
# Copyright (c) 2014 Google Inc. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""
This script is intended for use as a GYP_GENERATOR. It takes as input (by way of
the generator flag config_path) the path of a json file that dictates the file... | kishikawakatsumi/Mozc-for-iOS | src/third_party/gyp/pylib/gyp/generator/analyzer.py | Python | apache-2.0 | 20,997 | [
"VisIt"
] | c7dcce8fcaf7bdcc79355a5ab4b586706afeb38ff6aa10eb64b31661f41d6bb4 |
# -*- coding: utf-8
# pylint: disable=line-too-long
"""Lonely, helper functions that are broadly used and don't fit anywhere"""
import os
import sys
import ssl
import yaml
import gzip
import time
import copy
import socket
import shutil
import smtplib
import tarfile
import hashlib
import textwrap
import linecache
impo... | meren/anvio | anvio/utils.py | Python | gpl-3.0 | 183,298 | [
"BLAST",
"Bioconda",
"Bioconductor",
"Biopython"
] | b771c73387d078afedae5c123c958986ad749dd352e6c5490cea94f0f2dbd09d |
#
# Copyright 2018 Analytics Zoo 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... | intel-analytics/analytics-zoo | pyzoo/zoo/chronos/model/Seq2Seq_pytorch.py | Python | apache-2.0 | 5,226 | [
"ORCA"
] | 96269bc924ddb14060157aca6f1cbc03fb410c2994b41e5632b50304ae2589cc |
########################################################################
# File : ServerUtils.py
# Author : Ricardo Graciani
########################################################################
"""
Provide uniform interface to backend for local and remote clients.return
There's a pretty big assumption here: ... | yujikato/DIRAC | src/DIRAC/WorkloadManagementSystem/Client/ServerUtils.py | Python | gpl-3.0 | 1,336 | [
"DIRAC"
] | 31b19e197f97e0ca663832234dd752a79eda7d12e5457a64a9a3c862e35ea470 |
# -*- coding: utf-8 -*-
from __future__ import with_statement
import bson
import os
import pickle
import pymongo
import sys
import unittest
import uuid
import warnings
from nose.plugins.skip import SkipTest
from datetime import datetime
from tests.fixtures import Base, Mixin, PickleEmbedded, PickleTest
from mongoeng... | depop/mongoengine-stripped | tests/test_document.py | Python | mit | 116,392 | [
"exciting"
] | a974f401d21fa1c29f0229bbc4f8cc5e550b088bddcc335d0dda9f6eaf6ba287 |
#!/usr/bin/env python
'''
TDDFT with k-point sampling or at an individual k-point
(This feature is in testing. We observe numerical stability problem in TDDFT
diagonalization.)
'''
from pyscf.pbc import gto
from pyscf.pbc import scf
from pyscf.pbc import df
from pyscf.pbc import tdscf
cell = gto.Cell()
cell.unit =... | gkc1000/pyscf | examples/pbc/22-k_points_tddft.py | Python | apache-2.0 | 1,002 | [
"PySCF"
] | d91f8efa1bdfbb3a739cd1afaa21bfb78551405e1ca0f728b7317dde1d30cfaf |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# freeseer - vga/presentation capture software
#
# Copyright (C) 2013, 2014 Free and Open Source Software Learning Centre
# http://fosslc.org
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as... | Freeseer/freeseer | src/freeseer/framework/util.py | Python | gpl-3.0 | 5,638 | [
"VisIt"
] | 684defdf93e7d606215dd4131828a7aa202bcb9d60546531d4be74b38cf7e441 |
"""Payload management for sending Ansible files and test content to other systems (VMs, containers)."""
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import atexit
import os
import stat
import tarfile
import tempfile
import time
from . import types as t
from .config import (... | Dhivyap/ansible | test/lib/ansible_test/_internal/payload.py | Python | gpl-3.0 | 4,516 | [
"Galaxy"
] | 59f06d54c3ec8d24740dadd581b5b0d7599679f8c3cf7d1e3c4159c3ac5d0573 |
#!/usr/bin/env python
from __future__ import division
import os
import itertools as it
import pytest
import numpy as np
import minipnm as mini
def test_print():
network = mini.Delaunay.random(100)
print( network )
def test_prune():
delaunay = mini.Delaunay(np.random.rand(100,3))
original_size = dela... | RodericDay/MiniPNM | test_minipnm.py | Python | mit | 2,708 | [
"VTK"
] | 9e6e5421b26cc7c39958749bd0f4f69dd574a35a48377647ab892c8ea336d564 |
# Copyright (C) 2011, 2012, 2013, 2014, 2015, 2016, 2017 David Maxwell and Constantine Khroulev
#
# This file is part of PISM.
#
# PISM 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 L... | talbrecht/pism_pik | site-packages/PISM/invert/ssa.py | Python | gpl-3.0 | 27,277 | [
"NetCDF"
] | cc94554c51249b6d8ecb4dec2ac46d2613cd1f8dbebd1bd8e81a2e5cb0c58ea4 |
# -*- coding: utf-8 -*-
""" Python package of code for Gaussian process classification experiments. """
__authors__ = 'Matt Graham'
__copyright__ = 'Copyright 2015, Matt Graham'
__license__ = 'MIT'
| matt-graham/auxiliary-pm-mcmc | gpdemo/__init__.py | Python | mit | 199 | [
"Gaussian"
] | 61e71f35764fd70d478636285510d6bca512790b65838d5e3b525af380022648 |
from collections import defaultdict
import networkx as nx
__all__ = ["check_planarity", "PlanarEmbedding"]
def check_planarity(G, counterexample=False):
"""Check if a graph is planar and return a counterexample or an embedding.
A graph is planar iff it can be drawn in a plane without
any edge intersecti... | kenshay/ImageScript | ProgramData/SystemFiles/Python/Lib/site-packages/networkx/algorithms/planarity.py | Python | gpl-3.0 | 37,593 | [
"VisIt"
] | e41f2882609408b9295f92df213ce00849585c4f9de38ff8a6336ef10e933092 |
#!/usr/bin/env python
#ryan g. coleman ryan.g.coleman ATSYMBOL gmail.com ryangc ATSYMBOL mail.med.upenn.edu
#kim sharp lab http://crystal.med.upenn.edu
#finds all inter-atom distances
import string
import sys
import geometry
import pdb
if -1 != string.find(sys.argv[0], "pdbDistances.py"):
try:
for pdbName in s... | ryancoleman/traveldistance | src/pdbDistances.py | Python | gpl-2.0 | 710 | [
"CRYSTAL"
] | fdf0ffc537d731692c8435201a83a2d8a1cd145fc84bb294f8763b38af4e7e1f |
#!/usr/bin/env python
# Copyright 2017 Google Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | kawych/k8s-stackdriver | hack/boilerplate/boilerplate.py | Python | apache-2.0 | 6,502 | [
"VisIt"
] | d1f9274d60afcd2b37fbe283f13cc0f08b19a9c8da985770e3b297abe96e2a47 |
import math
import numpy as np
try:
from tcpb.tcpb import TCProtobufClient
except ImportError:
pass
import os
#################################################
### electronic structure routines go here #######
#################################################
# each electronic structure method requires at lea... | blevine37/pySpawn17 | pyspawn/potential/terachem_cas.py | Python | mit | 11,239 | [
"TeraChem"
] | aa2a294f1f2342090cc945fa5cf79796f9f1bb30a82e3ee63ec66dc4beb2a65c |
# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
# All rights reserved.
#
# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are ... | lidakanari/NeuroM | neurom/fst/tests/test_feature_compat.py | Python | bsd-3-clause | 10,193 | [
"NEURON"
] | 0052091b3f19a9b8e93779ab4245a27b6a034e026885b54aa1da05377fb8e72e |
# -*- encoding:ascii -*-
from mako import runtime, filters, cache
UNDEFINED = runtime.UNDEFINED
__M_dict_builtin = dict
__M_locals_builtin = locals
_magic_number = 6
_modified_time = 1417089926.323608
_template_filename=u'templates/webapps/galaxy/dataset/display.mako'
_template_uri=u'/dataset/display.mako'
_template_ca... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/database/compiled_templates/dataset/display.mako.py | Python | gpl-3.0 | 17,557 | [
"Galaxy"
] | e8230d29125c4ff8c711f66e82dc9cbb86ffcbc198a9b07e637eda7862163e68 |
from __future__ import print_function
import os
import vtk
from vtk.qt4.QVTKRenderWindowInteractor import QVTKRenderWindowInteractor
from PyQt4 import QtCore, QtGui, uic
class GlyphViewerApp(QtGui.QMainWindow):
def __init__(self, data_dir):
#Parent constructor
super(GlyphViewerApp,self).__init__()... | diego0020/tutorial-vtk-pyqt | 02_embed_in_qt.py | Python | mit | 4,664 | [
"VTK"
] | fad487e9937b2d1443ab10bf78cb88a4cc8849451ce7c22391b1fdabbad09ab9 |
# -*- coding: utf-8 -*-
#
# multimeter_file.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST 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... | synergetics/nest | pynest/examples/multimeter_file.py | Python | gpl-2.0 | 2,713 | [
"NEURON"
] | d12cd957141b64b8b56d1eeb35acd32dfe1b305728e745cea925191c67942381 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
.. versionadded:: 1.9.0
This module implements the abstract base class for PMGSONable pymatgen objects,
i.e., objects that can be converted to a json repr... | sonium0/pymatgen | pymatgen/serializers/json_coders.py | Python | mit | 4,577 | [
"pymatgen"
] | 1fb9e7a538c6260caccdc19e6b45d46885475bbbc6e7241781465fa0e3094368 |
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
import os
from io import StringIO
from itertools import chain, groupby, product, repeat
import numpy as np
from numpy im... | azag0/pyberny | src/berny/geomlib.py | Python | mpl-2.0 | 11,144 | [
"CRYSTAL",
"MOPAC"
] | 04437b1f458341e33d4bc93b8e0f35f0582c0547023d1c7c001c7000a865f0ce |
import pandas as pd
from ctc_observ import *
from ctc_arrays import *
from scipy.interpolate import pchip
from statsmodels.nonparametric.smoothers_lowess import lowess
# load HSC catalog first
# hsc = pd.read_csv('/cuc36/xxl/multiwavelength/HSC/wide.csv')
def pdf_sep_gen(sep_arcsec, xposerr, opterr, pdf='Rayleigh'):
... | CTJChen/ctc_astropylib | mlematch.py | Python | apache-2.0 | 23,653 | [
"Gaussian"
] | 1a07d2f0cdaa6650ef81eae31625ab2f8bb61bf0914c6fa9741d3a73d8d1d472 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | pli3/e2-openwbif | plugin/controllers/views/web/serviceplayable.py | Python | gpl-2.0 | 5,360 | [
"VisIt"
] | b54f428d706f63fb2adc9bf13e7c03dd7880c6c3ff37a9609b332b9bee1f7a5f |
from ...tests.instance import gaussian_instance
import numpy as np
from regreg.atoms.slope import slope as slope_atom
import regreg.api as rr
from ..slope import slope
from ..lasso import full_targets
from ...tests.decorators import rpy_test_safe
try:
from rpy2.robjects.packages import importr
from rpy2 imp... | selective-inference/selective-inference | selectinf/randomized/tests/test_slope.py | Python | bsd-3-clause | 7,374 | [
"Gaussian"
] | a2f84396cf7727a40528739bb6cf1e46a799fddb4d44a57f28a1ee40b054c302 |
# -*- coding: utf-8 -*-
# Copyright 2019 The GraphicsFuzz Project 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless requi... | google/graphicsfuzz | gfauto/gfauto/signature_util.py | Python | apache-2.0 | 17,596 | [
"Amber"
] | 4a12b538025e9cb2afbcf5d91ae9f7545bfa1685546b54f5b9bc2cb1e8dda2a0 |
#!/usr/bin/env python3
'''
Implementations of the various surrogate model options for use with Bayesian
optimisation. Currently, only different Gaussian process implementations are
available, however other machine learning models and variations of Gaussian
processes are possible so long as they can predict uncertainty ... | mbway/Bayesian-Optimisation | old_library/surrogates.py | Python | gpl-3.0 | 5,378 | [
"Gaussian"
] | 4e6c527624e1b8de03c28e373873fb847e12f9a2eb11cfbe8db9323ac37aa15d |
# -----------------------------------------------------------------------------
# Name: iodefs.py (part of PyGMI)
#
# Author: Patrick Cole
# E-Mail: pcole@geoscience.org.za
#
# Copyright: (c) 2013 Council for Geoscience
# Licence: GPL-3.0
#
# This file is part of PyGMI
#
# PyGMI is free software:... | Patrick-Cole/pygmi | pygmi/raster/iodefs.py | Python | gpl-3.0 | 49,696 | [
"ADF",
"NetCDF"
] | bee071ce4da88c26e348b184b24a5bb92c7c3c1a637f6ef55b8a6c4fe463b7b8 |
from packaging import version
import warnings
import sys
from matplotlib import pyplot as plt
from matplotlib.colors import LinearSegmentedColormap
import matplotlib as mpl
import matplotlib.colors as mplcolors
import numpy as np
import matplotlib.ticker as mtik
import types
try:
import scipy.ndimage
from scipy... | SebastianBocquet/pygtc | pygtc/pygtc.py | Python | mit | 53,321 | [
"Gaussian"
] | 89754d0b0884ddf55c6ea8a241f8766170fcd60e2cc64b8a13970a0c057282d5 |
#
# CoCoEachBlockUnique.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST 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 opti... | kperun/nestml | pynestml/cocos/co_co_each_block_unique_and_defined.py | Python | gpl-2.0 | 7,234 | [
"NEURON"
] | 3887fa14180b970a814f0644e560cb55b7c992d3c2aacc28d8a3f0474cdc8762 |
#!/usr/bin/env python3
import curses
import logging
import os
import re
import time
from socket import socket, socket_collection
class screen:
def __init__(self, stdscr, sockets, config):
self.scr = stdscr
self.sockets = sockets
self.config = config
def refresh(self):
self.scr.clear()
i = 1
for sock in... | maczniak/dalshabet | dalshabet.py | Python | apache-2.0 | 4,604 | [
"VisIt"
] | 293a8828f117f38afa596bea6d4010f8ea309b92b185719ce496056b53e184eb |
import nipype.interfaces.utility as util # utility
import nipype.pipeline.engine as pe # pypeline engine
import nipype.interfaces.camino as camino
import nipype.interfaces.fsl as fsl
import nipype.interfaces.camino2trackvis as cam2trk
import nipype.algorithms.misc as misc
from ...misc.utils import get_affi... | mick-d/nipype_source | nipype/workflows/dmri/camino/diffusion.py | Python | bsd-3-clause | 10,475 | [
"ParaView",
"VTK"
] | 8564bdc92886b72b1a2fa9cb0d560d5d7a3fdf5ea4966118aa07c75138cb0d8f |
# Natural Language Toolkit: Conditional Random Fields
#
# Copyright (C) 2001-2010 NLTK Project
# Author: Edward Loper <edloper@gradient.cis.upenn.edu>
# URL: <http://www.nltk.org/>
# For license information, see LICENSE.TXT
#
# $Id: hmm.py 5994 2008-06-02 12:07:07Z stevenbird $
"""
An interface to U{Mallet <http://ma... | markgw/jazzparser | lib/nltk/tag/crf.py | Python | gpl-3.0 | 31,850 | [
"Gaussian"
] | dd323f04d70a7d75b50046e2427c7bd120ab92cf183462891293afe5b7c376f9 |
"""
Callable objects that generate numbers according to different distributions.
"""
import random
import operator
import hashlib
import struct
import fractions
from math import e,pi
import param
from param import __version__ # noqa: API import
class TimeAware(param.Parameterized):
"""
Class of objects t... | ioam/param | numbergen/__init__.py | Python | bsd-3-clause | 26,699 | [
"Gaussian"
] | 0f4aa47885e46a4611a788aa78b98a5bf46e3bcbd4a69c165676e8b1d8dca246 |
import __builtin__
import glob
import operator
import string
import itertools
import copy
import collections
import random
import csv
from cStringIO import StringIO
import subprocess
import tempfile
import os
import numpy
import sys
from distutils.version import StrictVersion
import dendropy
import time
import math
imp... | psathyrella/partis | python/treeutils.py | Python | gpl-3.0 | 219,586 | [
"Bioconductor"
] | 427a53fafe7a3ab7075a077fabea4900ecadb3022162d40f5d562a9fcbb30268 |
# -*- coding: utf-8 -*-
# This file is part of the Fluggo Media Library for high-quality
# video and audio processing.
#
# Copyright 2010 Brian J. Crowell <brian@fluggo.com>
#
# 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
# ... | fluggo/Canvas | fluggo/editor/ui/ruler.py | Python | gpl-3.0 | 5,325 | [
"Brian"
] | ce996b32d2bf9ee895dd51b236d2977b0945297c368e533e5f929a32af7acc15 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
urlpat... | HBCompass/temp | config/urls.py | Python | bsd-3-clause | 1,275 | [
"VisIt"
] | 5cf9bc2ac66f447b63c9fc50da47c7005fe50b3d5e7c96d834f89c8be70a44f4 |
# Copyright (C) 2010, Joao Rodrigues (anaryin@gmail.com)
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Code for dealing with Structural Biology Web Servers.
""" | SBRG/ssbio | ssbio/biopython/Bio/Struct/WWW/__init__.py | Python | mit | 286 | [
"Biopython"
] | 724cc228f53948fd09f081e8c29b94cce87b80214bcb485054013097f96f636e |
import urllib2
from madcow import __version__ as current_version
from madcow.conf import settings
from madcow.util import Task
class Main(Task):
url = 'http://dis.gruntle.org/app/madcow/latest/'
agent = 'Madcow Updater v' + current_version
msg_fmt = 'Madcow v%(new_version)s is available, you have v%(curre... | ToxicFrog/lancow | madcow/tasks/updater.py | Python | gpl-3.0 | 1,325 | [
"VisIt"
] | f96ef9a666533b1601c94c09f6f01e3318a4aaa524f8a6c18baf679564650f72 |
##############################################################################
# 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... | mfherbst/spack | var/spack/repos/builtin/packages/r-analysispageserver/package.py | Python | lgpl-2.1 | 1,883 | [
"Bioconductor"
] | b09a3e4451ce126a7e7a7d16208da47adfb48976902ce2bfc99f11a9272a6132 |
import copy
import csv
import datetime
import json
import mock
import os
import re
import shutil
import tempfile
import urllib
import pyquery
from cStringIO import StringIO
from nose.tools import eq_, ok_, assert_raises
from nose.plugins.skip import SkipTest
from django.test.client import RequestFactory
from django.t... | rhelmer/socorro-webapp | crashstats/crashstats/tests/test_views.py | Python | mpl-2.0 | 222,462 | [
"VisIt"
] | 4dbe2af9f2948618d7453f758224aeef385ad7969468cd3fd492e988e2d18144 |
import sys
tests = [
("testExecs/test.exe", "", {}),
("python", "test_list.py", {'dir': 'Wrap'}),
]
if sys.platform != 'win32':
pass
longTests = []
if __name__ == '__main__':
import sys
from rdkit import TestRunner
failed, tests = TestRunner.RunScript('test_list.py', 0, 1)
sys.exit(len(failed))
| jandom/rdkit | Code/GraphMol/SLNParse/test_list.py | Python | bsd-3-clause | 314 | [
"RDKit"
] | 8345e63da62acd529fa708e0c4748fd479bcad5bfd420e1ca4d5d62a1e1416fe |
# -*- coding: utf-8 -*-
# -----------------------------------------------------------------------
# Copyright (c) 2009 Jendrik Seipp
#
# RedNotebook is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either vers... | dustincys/rednotebook | rednotebook/util/utils.py | Python | gpl-2.0 | 6,182 | [
"VisIt"
] | af192bc015b47fef170d5088f198d1e796f01c7626c779bc5c4e9c07c2766b81 |
#!/usr/bin/env python
"""
Visualise Changes in Edge Weights
=================================
Here, we demonstrate how to visualise changes in edge weights over time.
We change both, the colour and the width of the edges depending on the weight.
"""
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.a... | paulbrodersen/netgraph | docs/source/sphinx_gallery_animations/plot_02_animate_edges.py | Python | gpl-3.0 | 1,627 | [
"Gaussian"
] | bfd1b5cbd0f79402291c0c1e62b31d4b74d970072726de2822297c920b72d91f |
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