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# Natural Language Toolkit: Logic
#
# Author: Dan Garrette <dhgarrette@gmail.com>
#
# Copyright (C) 2001-2013 NLTK Project
# URL: <http://www.nltk.org>
# For license information, see LICENSE.TXT
"""
A version of first order predicate logic, built on
top of the typed lambda calculus.
"""
from __future__ import print_fu... | bbengfort/TextBlob | textblob/nltk/sem/logic.py | Python | mit | 67,597 | [
"VisIt"
] | 440dc8645195de21ef7612edf857a1e927399dadeb5fbf03e1369a43dca15cc0 |
# Copyright 2014 The Oppia 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 applicable ... | AllanYangZhou/oppia | core/controllers/reader_test.py | Python | apache-2.0 | 70,581 | [
"VisIt"
] | 270dfb898836bb250bcac8c586717239ce957c9115631286653792936fc9d75a |
#!/usr/bin/env python
# Copyright 2014-2019 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/prop/hfc/uhf.py | Python | apache-2.0 | 12,140 | [
"PySCF"
] | c4a4fe7dd8debb611cba8c2fe4ce75a146c028fd7fbec7736f89a32e76c22518 |
"""
PHYLIP multiple sequence alignment format (:mod:`skbio.io.format.phylip`)
=========================================================================
.. currentmodule:: skbio.io.format.phylip
The PHYLIP file format stores a multiple sequence alignment. The format was
originally defined and used in Joe Felsenstein's... | wdwvt1/scikit-bio | skbio/io/format/phylip.py | Python | bsd-3-clause | 13,510 | [
"BioPerl",
"scikit-bio"
] | 8880b1009cc6f5a50abfc32eee42bd0a73fa8cdb02d15a8c8c01d13fefbf2a5f |
"""
This file is a prebuilt library to wrap splinter. It goes with the environments.py
You can use it to quickly setup tests using only feature files. For more splinter documentation
visit their site at http://splinter.cobrateam.info/
The browser object you would use in splinter is available via context.browser
It is ... | mc706/prog-strat-game | core/features/steps/webseed.py | Python | mit | 7,496 | [
"VisIt"
] | 1602e4c85bd7dacf535cbeee660e50e94b2369b02d4e44a23e4f14db6ed2dfef |
"""openmoltools: Tools for Small Molecules, Antechamber, OpenMM, and More.
"""
from __future__ import print_function
DOCLINES = __doc__.split("\n")
import os
import sys
import shutil
import tempfile
import subprocess
from distutils.ccompiler import new_compiler
from setuptools import setup, Extension
import numpy
tr... | Clyde-fare/openmoltools | setup.py | Python | gpl-2.0 | 1,905 | [
"OpenMM"
] | b1189cd3e064cf18bd5fa91b6a4a26640050ac3afcb6897497f25908b816d7b1 |
r"""XML-RPC Servers.
This module can be used to create simple XML-RPC servers
by creating a server and either installing functions, a
class instance, or by extending the SimpleXMLRPCServer
class.
It can also be used to handle XML-RPC requests in a CGI
environment using CGIXMLRPCRequestHandler.
The Doc* classes can b... | yotchang4s/cafebabepy | src/main/python/xmlrpc/server.py | Python | bsd-3-clause | 36,661 | [
"Brian"
] | 902a09d52754874b68b669d19cfc223074af61f0bd0bb39559ae476ccf9bd28b |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
import os
import numpy as np
import random
from pymatgen.analysis.defects.utils import QModel, eV_to_k, \
generate_reciprocal_vectors_squared, genrecip, \
closestsites, StructureMotifI... | dongsenfo/pymatgen | pymatgen/analysis/defects/tests/test_utils.py | Python | mit | 15,852 | [
"VASP",
"pymatgen"
] | df39e754551ac5f138cec72592bb680b25d3ae7b079a06c450f85def9adb7ce4 |
import numpy as np
import mayavi.mlab as mlab
import moviepy.editor as mpy
duration= 2 # duration of the animation in seconds (it will loop)
fig_myv = mlab.figure(size=(220,220), bgcolor=(1,1,1))
X, Y = np.linspace(-2,2,200), np.linspace(-2,2,200)
XX, YY = np.meshgrid(X,Y)
ZZ = lambda d: np.sinc(XX**2+YY*... | solvery/lang-features | python/use_lib/video_1/mayavi_3.py | Python | gpl-2.0 | 625 | [
"Mayavi"
] | fc42ee7fd1d59bd6208577fbf63805585f2bf8e589f852a33b313c60957e0685 |
# Orca
#
# Copyright 2005-2008 Sun Microsystems Inc.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/scripts/apps/gtk-window-decorator/script.py | Python | gpl-3.0 | 4,550 | [
"ORCA"
] | 6e73709e3409cdf34ea76330474cfe337bd486d0fc1549734f9865bb31b21be0 |
import os, sys, re, inspect, types, errno, pprint, subprocess, io, shutil, time, copy
import path_tool
path_tool.activate_module('FactorySystem')
path_tool.activate_module('argparse')
from ParseGetPot import ParseGetPot
from socket import gethostname
#from options import *
from util import *
from RunParallel import R... | jinmm1992/moose | python/TestHarness/TestHarness.py | Python | lgpl-2.1 | 40,239 | [
"MOOSE",
"VTK"
] | 645fdd2342f471a5564969759b25fa62c2ed021e4e5fcf28eb77bab3a7d1d952 |
# Author: Meduri Venkata Shivaditya
import superimport
import numpy as np
import matplotlib.pyplot as plt
from scipy.stats import norm, multivariate_normal
import bayes_logistic # pip install bayes_logistic
import warnings
import pyprobml_utils as pml
warnings.filterwarnings("ignore", category=RuntimeWarning)
np.ran... | probml/pyprobml | scripts/logreg_laplace_demo.py | Python | mit | 5,192 | [
"VisIt"
] | f413b8c53ed575e6bbc6308f6cbf042d4d3fdd7671ad6c02d91f654632a3a0d8 |
class ClauseVisitor(object):
"""Traverses and visits ``ClauseElement`` structures.
Calls visit_XXX() methods dynamically generated for each particular
``ClauseElement`` subclass encountered. Traversal of a
hierarchy of ``ClauseElements`` is achieved via the
``traverse()`` method, which is pass... | santisiri/popego | envs/ALPHA-POPEGO/lib/python2.5/site-packages/SQLAlchemy-0.4.3-py2.5.egg/sqlalchemy/sql/visitors.py | Python | bsd-3-clause | 3,851 | [
"VisIt"
] | 0f113e0468ff6c80d3bceb42abf6d7bf07e41ff09e3e6c90a31dd0ad1f4bfb72 |
#!/usr/bin/env python
########################################
#Globale Karte fuer tests
# from Rabea Amther
########################################
# http://gfesuite.noaa.gov/developer/netCDFPythonInterface.html
import math
import numpy as np
import pandas as pd
from pandas import *
import pylab as pl
import Scient... | CopyChat/Plotting | Python/climate_change/swio_changes_rsds_rcp85.py | Python | gpl-3.0 | 8,465 | [
"NetCDF"
] | 1a87595c204392d6ea40443f581c8b594cf0aa897215ef696db1a27f9611418e |
#===============================================================================
# Hangman, in Python
#-------------------------------------------------------------------------------
# Version: 1.1.0
# Updated: 24-01-2014
# Author: Alex Crawford
# License: MIT
#==========================================================... | Trebek/hangman-python | hangman.py | Python | mit | 15,596 | [
"exciting"
] | f0611da69715a53a5293437cfa079da7d1ceb99d367796e9c38aa3bb2daf6e85 |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/scf/test/test_addons.py | Python | apache-2.0 | 20,192 | [
"PySCF"
] | bcfcc9dfb749e7a9a32785380e31854a434fa2ca55d90f111956caf1c1031683 |
# -*- coding: utf-8 -*-
"""
solace.forms
~~~~~~~~~~~~
Implements the form handling. The code here largely comes from the
Zine form handling system, without the Zine dependency.
:copyright: (c) 2010 by the Solace Team, see AUTHORS for more details.
(c) 2009 by Plurk Inc., see AUTHO... | mitsuhiko/solace | solace/utils/forms.py | Python | bsd-3-clause | 62,177 | [
"VisIt"
] | 3204b089b2d0053da93f6c2c99ef6d92add5fc822bff6b8393d7f620b910a02b |
import os
from config import *
from copy import deepcopy
from geometry import *
class Min3p:
"""A class that gathers thhe actions for min3p chemistry, except writing that is left to
min3pwriter"""
def __init__(self, core):
self.core = core
self.initBase()
self.nodes = None
... | ORTI3D/ORTI3D_code | iliblast/Min3p.py | Python | gpl-3.0 | 16,931 | [
"VTK"
] | d10142e4078476789e4ecd5a0f88163076d0018a9e4e63d9e4fe84889a3d7b08 |
from module_base import ModuleBase
from module_mixins import NoConfigModuleMixin
import module_utils
import vtk
class testModule(NoConfigModuleMixin, ModuleBase):
def __init__(self, module_manager):
# initialise our base class
ModuleBase.__init__(self, module_manager)
# we'll be playing ... | chrisidefix/devide | modules/user/testModule.py | Python | bsd-3-clause | 2,148 | [
"VTK"
] | 1a75095240ca885a6a38350c0b5cb51d2b01e0154c87ff883c8baeb65e4c3f9d |
"""
Channelend module
Copyright (c) 2009 John Markus Bjoerndalen <jmb@cs.uit.no>,
Brian Vinter <vinter@nbi.dk>, Rune M. Friborg <rune.m.friborg@gmail.com>.
See LICENSE.txt for licensing details (MIT License).
"""
from pycsp.greenlets.exceptions import *
from pycsp.common.const import *
def retire(*list_of_cha... | runefriborg/pycsp | pycsp/greenlets/channelend.py | Python | mit | 3,002 | [
"Brian"
] | 2588f2656fb091e15413b521df834ed1f8fb74563b093f6fc315ab06859fcc19 |
from pymol import cmd
from random import random
import time
# this shows how you can efficiently update the coordinates
# of an existing model for real-time viewing
# for asychronous execution, you want to run this using the "spawn"
# command from inside PyMOL or with the "-l" option from the unix shell
# WARNING: ... | gratefulfrog/lib | python/pymol/pymol_path/examples/devel/chempy_model02.py | Python | gpl-2.0 | 1,862 | [
"PyMOL"
] | 9a186a1c27b275a66c562b37802c37ac7b9b8751c9b360e031573e0efb4bb177 |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | fweik/espresso | testsuite/python/pressure.py | Python | gpl-3.0 | 14,993 | [
"ESPResSo"
] | a8dcb46ee0ae9e55bee9534eb7f5db636292315fca8ca32890259e71310823f0 |
"""
.. autoclass:: revscoring.scorer_models.nb.GaussianNB
:members:
:member-order:
.. autoclass:: revscoring.scorer_models.nb.MultinomialNB
:members:
:member-order:
.. autoclass:: revscoring.scorer_models.nb.BernoulliNB
:members:
:member-order:
"""
import logging
from sklearn import naive_bay... | eranroz/revscoring | revscoring/scorer_models/nb.py | Python | mit | 3,031 | [
"Gaussian"
] | 9e147570030a84e608450d08005146c9ad9c6fd5aa2e6fd6a7ce52b7c1a27896 |
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in ... | Charley-fan/metaArray | misc.py | Python | gpl-3.0 | 43,576 | [
"Gaussian"
] | 13ea45bec5db9063ce6306b4b7cdcae449fe705a768ee397cdab152f755b6242 |
from player import Player
import inputcontroller
import outputcontroller
from mapgenerator import MapGenerator
from itemgenerator import ItemGenerator
from dungeon import Map
import monstergenerator
import battle
class Game:
def __init__(self):
self._maps = []
self._player = Player("")
se... | V3n0M93/Rogue-like-like | src/game.py | Python | gpl-2.0 | 4,793 | [
"VisIt"
] | 80bceb03fa7d0569064f6cf98872ee1d98ab694ae101b2ba7c56c041c6d2554e |
#!/usr/bin/env python
"""
Artificial Intelligence for Humans
Volume 1: Fundamental Algorithms
Python Version
http://www.aifh.org
http://www.jeffheaton.com
Code repository:
https://github.com/jeffheaton/aifh
Copyright 2013 by Jeff Heaton
Licensed under the Apache License, Version 2... | PeterLauris/aifh | vol1/python-examples/examples/example_distance.py | Python | apache-2.0 | 2,517 | [
"VisIt"
] | 75e679dbd07a6abb6b77add16c9f57d63b63f98cf046911d0c245fae32adf876 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module define a WulffShape class to generate the Wulff shape from
a lattice, a list of indices and their corresponding surface energies,
and the total area and volume of the wulff shape,the weighted surface energy,
th... | materialsproject/pymatgen | pymatgen/analysis/wulff.py | Python | mit | 27,721 | [
"pymatgen"
] | 848f21a4a416b7d3e11300f8e2555d3d99acc4117ff1742a273e696aa7f17958 |
import os
import copy
import pytest
import logging
from moult import log
from moult.utils import installed_packages
from py._path.local import LocalPath
log.set_level(logging.DEBUG)
class ScriptData(object):
def __init__(self, tmpdir):
self.tmpdir = tmpdir
self.tmpdata = None
self.pri... | tweekmonster/moult | tests/conftest.py | Python | mit | 2,513 | [
"VisIt"
] | 53a07db94d36ccb8d4126fd3553da67cf10181c29dbdf2a7c89fa951dc469f48 |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | SKIRT/PTS | core/prep/creator.py | Python | agpl-3.0 | 18,018 | [
"Galaxy"
] | 998bb26ab4092201d4d65d5e7dee5597be58b5da2ce25f06a39aa771763f837c |
import gzip
import itertools
import os
import re
import subprocess
import sys
import tempfile
import zipfile
from collections import namedtuple
import numpy as np
from openbabel import pybel
from openbabel.pybel import Atom
from plip.basic import config, logger
logger = logger.get_logger()
def tmpfile(prefix, direc... | pharmai/plip | plip/basic/supplemental.py | Python | gpl-2.0 | 15,220 | [
"PyMOL",
"Pybel"
] | 4864454c878e10d31413b60da2c5727a2e6a2cb3d7a31cce765d2dcc9425e692 |
#!/usr/bin/env python
"""Automatically install required tools and data to run bcbio-nextgen pipelines.
This automates the steps required for installation and setup to make it
easier to get started with bcbio-nextgen. The defaults provide data files
for human variant calling.
Requires: git, Python 3.x, Python 2.7 or a... | lpantano/bcbio-nextgen | scripts/bcbio_nextgen_install.py | Python | mit | 13,032 | [
"BWA",
"Bioconda",
"Biopython",
"Bowtie",
"Galaxy",
"pysam"
] | 3fd25d4c4af3e3703994247d7a7db823962e79098820ee9a81827c55ed7c70b6 |
# -*- coding: utf-8 -*-
{
' iw-12: Werkdruck / 090 gr / 1,30 Volumen': ' iw-12: Werkdruck / 090 gr / 1,30 Volumen',
' iw-12: Werkdruck / 090 gr / 1,30 Volumen ': ' iw-12: Werkdruck / 090 gr / 1,30 Volumen ',
' iw-13: Matt MC / 115 gr / 0,93 Volumen ': ' iw-13: Matt MC / 115 gr / 0,93 Volumen ',
' iw-2: ... | UB-Heidelberg/UBHD-OMPArthistorikum | languages/nl.py | Python | gpl-3.0 | 26,740 | [
"Elk"
] | 0d0f36e452814f10b62c1baf85c683c8e7ae04494db7a8f3c3a5aa6dd706a717 |
import unittest
import numpy as np
import pysal
from pysal.spreg.ols import OLS
from pysal.spreg.ols_regimes import OLS_Regimes
PEGP = pysal.examples.get_path
class TestOLS_regimes(unittest.TestCase):
def setUp(self):
db = pysal.open(pysal.examples.get_path('columbus.dbf'),'r')
self.y_var = 'CRIME... | darribas/pysal | pysal/spreg/tests/test_ols_regimes.py | Python | bsd-3-clause | 7,672 | [
"COLUMBUS"
] | 8465236dd97cd43b882d0273eb17dade96eaaf7a44281e442d117448d78de84a |
"""Base module for all operators that create offspring."""
import numpy as np
from random import random
from ase import Atoms
from ase.ga.atoms_attach import enable_raw_score_methods
class OffspringCreator(object):
"""Base class for all procreation operators
Parameters:
verbose: Be verbose and print so... | suttond/MODOI | ase/ga/offspring_creator.py | Python | lgpl-3.0 | 2,819 | [
"ASE"
] | a3667c7afce039c402d0b98df895d35530baf6d0857768474cf9834ef896d722 |
#
# libtcod 1.6.0 python wrapper
# Copyright (c) 2008,2009,2010,2012,2013 Jice & Mingos
# 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... | nerdyLawman/pyhack | src/libtcodpy.py | Python | gpl-3.0 | 61,315 | [
"Amber"
] | 4feb2dd982f10cfa1cb68ae339a03d5370d904c05e10b8d2e1c72635367dc5b0 |
"""Functions to simulate scans and maps."""
import numpy as np
import numpy.random as ra
import os
from astropy.io import fits
from astropy.table import Table, vstack
import astropy.units as u
from collections.abc import Iterable
from .io import mkdir_p, locations
from .utils import tqdm, jit
from astropy.coordinate... | matteobachetti/srt-single-dish-tools | srttools/simulate.py | Python | bsd-3-clause | 31,364 | [
"Gaussian"
] | c3de87876c818f664bf147e5efb136c2d1e2c9257b7b54891492e423a419e080 |
#!/usr/bin/env python
#
# Appcelerator Titanium Module Packager
#
#
import os, subprocess, sys, glob, string
import zipfile
from datetime import date
cwd = os.path.abspath(os.path.dirname(sys._getframe(0).f_code.co_filename))
os.chdir(cwd)
required_module_keys = ['name','version','moduleid','description','copyright','... | dezinezync/TiStoreView | build.py | Python | mit | 6,787 | [
"VisIt"
] | 103c755cb290d16b2f88cc774d00f4d112cab8020a2fa16709af843a430fcaed |
#!/usr/bin/env python
"""
Calculate the radial distribution function (RDF) from files.
It takes statistical averaging over atoms in a file and over files.
Usage:
rdf.py [options] INFILE [INFILE...]
Options:
-h, --help Show this help message and exit.
-d DR Width of the bin. [default: 0.1]
-r,--rmax RMA... | ryokbys/nap | nappy/rdf.py | Python | mit | 23,439 | [
"Gaussian"
] | 9fe0c5247888468614a9cfb2955469489136fe751d5a85b4786f7797ba2a54dc |
"""
"""
import os
from tempfile import tempdir
from pulsar.manager_factory import build_managers
from pulsar.cache import Cache
from pulsar.tools import ToolBox
from pulsar.tools.authorization import get_authorizer
from pulsar import messaging
from galaxy.objectstore import build_object_store_from_config
from galaxy.t... | natefoo/pulsar | pulsar/core.py | Python | apache-2.0 | 6,319 | [
"Galaxy"
] | 85063d6bc5b87d54cd7421ef8702f46a0469d4381636be4792806b1dc6831f5e |
#===============================================================================
# LICENSE XOT-Framework - CC BY-NC-ND
#===============================================================================
# This work is licenced under the Creative Commons
# Attribution-Non-Commercial-No Derivative Works 3.0 Unported Lic... | SMALLplayer/smallplayer-image-creator | storage/.xbmc/addons/net.rieter.xot.smallplayer/resources/libs/cache/filecache.py | Python | gpl-2.0 | 6,904 | [
"VisIt"
] | 1a30a424483ffd0f95538f2fd47bbbcae34f1bd6d4738571a47d49521918fd04 |
#pylint: disable=missing-docstring
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/... | nuclear-wizard/moose | python/chigger/geometric/GeometricSourceMeta.py | Python | lgpl-2.1 | 1,889 | [
"MOOSE",
"VTK"
] | 7c27a6a8ca20bb54b25d97597608b011187cb47df4c45bd07a252ef9ab8eaeba |
#!/usr/bin/env python
#
# Copyright (C) 2013-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ 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, ei... | espressopp/espressopp | testsuite/AdResS/TDforce/test_TDforce.py | Python | gpl-3.0 | 16,457 | [
"ESPResSo"
] | 50f937de53d6ee67f4431cf65e8ff3e7670186a3afc5a0fd8dc7e9600be67ff4 |
"""
A collection of assorted utility functions.
"""
from builtins import range
from collections import Counter
import importlib
import json
import warnings
from itertools import product, combinations
import numpy
from scipy.spatial.distance import cdist
from scipy.special import expit
import scipy.stats
from .consta... | crcollins/molml | molml/utils.py | Python | mit | 26,163 | [
"CRYSTAL"
] | de66c16244eb1161f4830fc46735a86165f37583ee924bc00dc4570ca23e96bf |
"""
MultiVolumeVisualization
:Authors:
Berend Klein Haneveld
"""
from PySide.QtCore import QObject
from PySide.QtCore import Signal
from vtk import vtkColorTransferFunction
from vtk import vtkPiecewiseFunction
# Define render types for multi render
MultiVisualizationTypeMix = "Default mix"
MultiVisualizationTypeMIP ... | berendkleinhaneveld/Registrationshop | ui/visualizations/MultiVolumeVisualization.py | Python | mit | 2,648 | [
"VTK"
] | 707635d7bd1d7e5a94bd65d9d3321644eb7dc66703cf16b5d93ed57a7de57183 |
import pymbar
import blib
import pymc
import numpy as np
import pandas as pd
import simtk.openmm.app as app
import simtk.openmm as mm
import simtk.unit as u
import mdtraj as md
mass = 12.01078 * u.daltons + 4 * 35.4532 * u.daltons
sigma = pymc.Uniform("sigma", 0.53, 0.57, value=0.545)
epsilon = pymc.Uniform("epsilon"... | kyleabeauchamp/DBayes | dbayes/test_pymc_2values.py | Python | gpl-2.0 | 1,834 | [
"MDTraj",
"OpenMM"
] | 035b4e6e290301b47028fcb8f4cf103b9c862d366199cda1e83a65ac141d76a9 |
"""
==============================
Probability Calibration curves
==============================
When performing classification one often wants to predict not only the class
label, but also the associated probability. This probability gives some
kind of confidence on the prediction. This example demonstrates how to di... | jjx02230808/project0223 | examples/calibration/plot_calibration_curve.py | Python | bsd-3-clause | 5,902 | [
"Gaussian"
] | 97f827d4cba26a271eafe5b44dff69549d26b659aa960ed7bb0cefa0a02c2d70 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2006-2011 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 | stoq/gui/config.py | Python | gpl-2.0 | 37,495 | [
"VisIt"
] | 138814c4b377344e09a4e5052ea3b9b41b043c23ec590cb0af939e9b73a4e4fc |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under t... | alejob/mdanalysis | package/MDAnalysis/lib/mdamath.py | Python | gpl-2.0 | 13,812 | [
"Gromacs",
"MDAnalysis"
] | 7673f5e7cd04e8c2c86785e4aa49b0a5eec2a234706a22b4206da9ec1b4eccb0 |
# -*- coding: utf-8 -*-
import collections
import datetime
import hashlib
import json
import os
import stat
import tarfile
from copy import deepcopy
from tempfile import mkdtemp
from django.conf import settings
from django.core import mail
from django.core.files.storage import default_storage as storage
from django.co... | ngokevin/zamboni | mkt/webapps/tests/test_tasks.py | Python | bsd-3-clause | 31,914 | [
"exciting"
] | 163f5a65e76148cbc9ccda3e2371cb705f7c809d3862b7ea9de3192374ab20e1 |
#!/usr/bin/env python
"""Adaoted from the "wall" demo client for Open Pixel Control
http://github.com/zestyping/openpixelcontrol
Creates a shifting rainbow plaid pattern by overlaying different sine waves
in the red, green, and blue channels.
To run:
First start the gl simulator using the included "wall" layout
... | TheGentlemanOctopus/thegentlemanoctopus | octopus_code/core/octopus/patterns/rainbowPlaidEqPattern.py | Python | gpl-3.0 | 2,810 | [
"Octopus"
] | 4fae8a0d96e5f52420461a2209159dbb7449789f18cec0de2c4cf58ab8a98834 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
from distutils.core import setup
setup(
name='ASE-QE',
version='0.1.1',
author='Paweł T. Jochym',
author_email='pawel.jochym@ifj.edu.pl',
packages=['ase-qe', 'ase-qe.test'],
scripts=[],
url='http://pypi.python.org/pypi/ASE-QE/',
license='LICENS... | jochym/ase-qe | setup.py | Python | gpl-3.0 | 541 | [
"ASE",
"ESPResSo"
] | 97544dfe05ff65c34021d39d7c71615820c5599329f1582cc5905064b0727ba0 |
####################################################################################################
# neuropythy/optimize/__init__.py
# Initialization code for neuropythy's optimization module.
# By Noah C. Benson
from .core import (fapply, finto,
PotentialFunction, is_potential, to_potential,
... | noahbenson/neuropythy | neuropythy/optimize/__init__.py | Python | agpl-3.0 | 759 | [
"Gaussian"
] | 2a17f6c62a6235ed3e189710034fc293bb7e81a9c5216fa6c7a441a3b0ff36c7 |
# -*- coding: utf-8 -*-
"""
ast
~~~
The `ast` module helps Python applications to process trees of the Python
abstract syntax grammar. The abstract syntax itself might change with
each Python release; this module helps to find out programmatically what
the current grammar looks like and allows... | MalloyPower/parsing-python | front-end/testsuite-python-lib/Python-3.0/Lib/ast.py | Python | mit | 11,340 | [
"VisIt"
] | 88c089e134625809311a529f0286f2bb35403d85046ddac1a0cbb99f989764db |
"""Ops and optimizations for using BLAS calls
BLAS = Basic Linear Algebra Subroutines
Learn more about BLAS here:
http://www.netlib.org/blas/blast-forum/
The standard BLAS libraries implement what is called "legacy BLAS" in that
document.
This documentation describes Theano's BLAS optimization pipeline.
Where th... | marcsans/cnn-physics-perception | phy/lib/python2.7/site-packages/theano/tensor/blas.py | Python | mit | 92,331 | [
"BLAST"
] | db0b3bdc440bbc00b072e87d1c95fdad9cd8bdbdcca6721813452bd8b1fa6963 |
import mimetypes
print(mimetypes.guess_type('test.jpg'))
# ('image/jpeg', None)
print(type(mimetypes.guess_type('test.jpg')))
# <class 'tuple'>
print(mimetypes.guess_type('test.jpg')[0])
# image/jpeg
print(type(mimetypes.guess_type('test.jpg')[0]))
# <class 'str'>
print(mimetypes.guess_type('test.tar.gz'))
# ('app... | nkmk/python-snippets | notebook/mimetypes_test.py | Python | mit | 40,568 | [
"NetCDF"
] | fda7b6a11a4cdee5ac2eda6e3ef6837b39caccff413e05a55d60dfbeeec1a36f |
from __future__ import division
import numpy as np
from nose.plugins.attrib import attr
import pybasicbayes.distributions as distributions
from pybasicbayes.testing.mixins import BigDataGibbsTester, MaxLikelihoodTester, \
GewekeGibbsTester, BasicTester
@attr('regression')
class TestRegression(
BasicTest... | mattjj/pybasicbayes | tests/test_regression.py | Python | mit | 3,403 | [
"Gaussian"
] | 86a85c16b32c59508f6b244e9c39ea6368b32f83ab0dde0662fc7e654fef864f |
#!/usr/bin/python
import httplib2
import os
import sys
from apiclient.discovery import build
from oauth2client.file import Storage
from oauth2client.client import flow_from_clientsecrets
from oauth2client.tools import run
# CLIENT_SECRETS_FILE, name of a file containing the OAuth 2.0 information for
# this applicat... | lhongskie/yt-samples-python | my_uploads.py | Python | apache-2.0 | 3,001 | [
"VisIt"
] | cba897111aa0f0f332889323c0c827fc0206a57128c77f4e4bce84733e10c9a3 |
#!/usr/bin/env python
__author__ = "Vivek <vivek.balasubramanian@rutgers.edu>"
__copyright__ = "Copyright 2014, http://radical.rutgers.edu"
__license__ = "MIT"
__use_case_name__ = "'Amber + CoCo' simulation-analysis proof-of-concept (ExTASY)."
from radical.ensemblemd import Kernel
from radical.ensem... | radical-cybertools/ExTASY | examples/coam-on-stampede/extasy_amber_coco.py | Python | mit | 9,260 | [
"Amber"
] | 0dbc8eac18a744e43917394fc6cffda32be0f2bd6e7c0a62b9bf65657a01ccad |
# $HeadURL$
import os
import time
from DIRAC import gConfig, S_OK, S_ERROR, gLogger
from DIRAC.Core.Utilities import List
from DIRAC.Core.Utilities.Subprocess import pythonCall
from DIRAC.Core.Utilities.ThreadPool ... | myco/VMDIRAC | WorkloadManagementSystem/private/OutputDataExecutor.py | Python | gpl-3.0 | 11,568 | [
"DIRAC"
] | 2566716b63cdcaf6a4ba8907008aedd07ab4e729a6fca6de416ceba31583e3f6 |
# This file is part of pyfesom
#
################################################################################
#
# Original code by Dmitry Sidorenko, 2013
#
# Modifications:
# Nikolay Koldunov, 2016
# - optimisation of reading ASCII fies (add pandas dependency)
# - move loading and processing of ... | FESOM/pyfesom | pyfesom/load_mesh_data.py | Python | mit | 20,823 | [
"NetCDF"
] | e916efd7aba7c6353f2f736cf9f7be4796cc11190306a7e22181723d46282324 |
########################################################################
# Author: Stuart Paterson
# eMail : Stuart.Paterson@cern.ch
########################################################################
""" The Watchdog class is used by the Job Wrapper to resolve and monitor
the system CPU and memory consumed... | vmendez/DIRAC | WorkloadManagementSystem/JobWrapper/WatchdogLinux.py | Python | gpl-3.0 | 4,029 | [
"DIRAC"
] | 1557393ecc8b34cb58367567ee6bd50cbd0dcab976d32397f35c17eb55def3b9 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright (C) 2018 David Arroyo Menéndez
# Author: David Arroyo Menéndez <davidam@gnu.org>
# Maintainer: David Arroyo Menéndez <davidam@gnu.org>
# This file is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as p... | davidam/python-examples | numpy/gmm.py | Python | gpl-3.0 | 3,134 | [
"Gaussian"
] | 394a1dd43c200169d3075239bcc31fff0fe4cc4f92f4ad642a53d327acb04427 |
"""
Physical units and dimensions.
The base class is Unit, where all here defined units (~200) inherit from.
"""
from sympy import Rational, pi
from sympy.core import AtomicExpr
class Unit(AtomicExpr):
"""
Base class for all physical units.
Create own units like:
m = Unit("meter", "m")
"""
i... | Cuuuurzel/KiPyCalc | sympy_old/physics/units.py | Python | mit | 5,275 | [
"Avogadro"
] | 6059323bfb01aaa6cbbd7d51a0be12f57041e04feb45a251db4c35d012bde355 |
# piddlePIL.py -- a Python Imaging Library backend for PIDDLE
# Copyright (C) 1999 Joseph J. Strout
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2 of the License, o... | rdkit/rdkit | rdkit/sping/PIL/pidPIL.py | Python | bsd-3-clause | 15,697 | [
"RDKit"
] | ab7c37535a1f1c1d9e7e73726693a1b778add0feecf5d6994f6c822a89ca02a7 |
# -*- coding: utf-8 -*-
# HORTON: Helpful Open-source Research TOol for N-fermion systems.
# Copyright (C) 2011-2017 The HORTON Development Team
#
# This file is part of HORTON.
#
# HORTON is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by th... | theochem/horton | horton/io/test/test_cp2k.py | Python | gpl-3.0 | 8,623 | [
"CP2K"
] | 58ec1ad4d2cff7e5901bc6d8d9c9c647cce27c4588fbc76919a3f5a8d209006e |
#!/usr/bin/env python
import httplib,requests
from bs4 import BeautifulSoup
from pprint import pprint,pformat
from random import randrange
from optparse import OptionParser, OptionGroup
import sys, re
def process_opts():
usage = """
Put text into a format yospos can read.
usage %prog test
"""
par... | ursineasylum/yospos | sparklee.py | Python | mit | 14,209 | [
"BLAST",
"CRYSTAL",
"Galaxy"
] | a1423e37d5ccd76ef513aee87353e8b95b3d2662544ae8a17cfe70fe0bfc562a |
import warnings
warnings.warn("pymatgen.serializers.pickle_coders has been moved to "
"pymatgen.util.serialization. This stub will be removed in pmg "
"2018.01.01.")
from pymatgen.util.serialization import *
| matk86/pymatgen | pymatgen/serializers/pickle_coders.py | Python | mit | 238 | [
"pymatgen"
] | a300b4cd249996e6996ae0daa2204f0b7a98170f7472da905bc5c93bcc4234ee |
from __future__ import print_function
### READING FILES
file_name = 'data.txt'
# Reading in and parsing file contents
data_list = []
with open(file_name) as f:
# SKip the header (the first line)
next(f)
for line in f:
# Remove newline char
line = line.replace('\n', ... | dvida/UWO-PA-Python-Course | Lecture 3/L3_lecture.py | Python | mit | 5,075 | [
"Gaussian"
] | 511134fb33b06ad75e77488c4c0511c60523f8a33259705ba23bb994d76a3dd1 |
#!/usr/bin/env python
import argparse
import glob
import pysam
"""
improved algorithm for comparing two variants:
if different chromosome? different variant
if position of two variants is more than 300 bp apart? different variant
if:
restore the common sequence between the two variants (e.g. ... | BD2KGenomics/brca-website | python_scripts/overlap_string_comparison.py | Python | apache-2.0 | 7,248 | [
"pysam"
] | a18f7bf3df5d9b85cbc2bb97c82c337ffec3ee1f99ea0cef12f1a509c0fe8c7d |
"""
Numerical python functions written for compatability with matlab(TM)
commands with the same names.
Matlab(TM) compatible functions
-------------------------------
:func:`cohere`
Coherence (normalized cross spectral density)
:func:`csd`
Cross spectral density uing Welch's average periodogram
:func:`detrend`... | tkaitchuck/nupic | external/linux64/lib/python2.6/site-packages/matplotlib/mlab.py | Python | gpl-3.0 | 104,273 | [
"Gaussian"
] | 11954ad76b57a5fe9d3156737260141b26a8408a5c2e94790ef544375c0e8a50 |
# Copyright 2012 by Wibowo Arindrarto. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Bio.SearchIO objects to model high scoring regions between query and hit."""
from __fu... | zjuchenyuan/BioWeb | Lib/Bio/SearchIO/_model/hsp.py | Python | mit | 45,621 | [
"BLAST",
"Biopython"
] | e1005a64f75d4b6d78e30aa01d9d9ac12dc0a318c051851c3fe41a753f1bdfc8 |
# Compacted basis set labels as strings for GUI
# Author: Evgeny Blokhin
import six
# hierarchy API: __order__ to apply classifier
__order__ = 5
def classify(tilde_obj):
if not tilde_obj.electrons['basis_set'] or tilde_obj.info['ansatz'] == 0x1:
return tilde_obj
if tilde_obj.info['ansatz'] == 0x2:... | tilde-lab/tilde | tilde/classifiers/basisset.py | Python | mit | 2,385 | [
"CRYSTAL",
"Gaussian"
] | 5637117ba8f9146f5b497d97ebb25830e50346118964ecb6dcca5c4e4f0aa797 |
"""
Implementation of a function to read NetCDF files from Integrated Marine Observing System (IMOS)
"""
import xarray as xr
from ..waterframe import WaterFrame
def read_nc_imos(path, clean_data=True):
"""
Open a NetCDF file from Integrated Marine Observing System (IMOS). All QC flags are 0.
P... | rbardaji/oceanobs | mooda/input/read_nc_imos.py | Python | mit | 1,997 | [
"NetCDF"
] | 3cb6c43534519371d081f9745e0d096c4fff5547f0e6e8aef8c00bd831732d19 |
import base64
import re
import os
import sys
import urllib.request, urllib.parse, urllib.error
PY3 = sys.version_info[0] == 3
if PY3:
from io import StringIO
str = str
else:
from io import StringIO
try:
import json
except ImportError:
import simplejson as json
from .rest import ErrorResponse,... | ArcherSys/ArcherSys | Lib/site-packages/dropbox/client.py | Python | mit | 67,600 | [
"VisIt"
] | e21a0fd4bb26267911b3b2343d360075d99546a37e93bb69feb2c56d02e25fab |
#! /usr/bin/python
# remove_long_name.py
# Checks fasta file for the long name in the lines starting with ">" (i.e. > read_short_name read_long name) and deletes the long name. Some tools (such as bwa) do not like the long name having white spaces, which will lead to a messed up sam file.
# Usage: ./remove_long_name... | schimar/hts_tools | remove_long_name.py | Python | gpl-2.0 | 1,155 | [
"BWA"
] | 628d13025457d97ce27fffceb3cd77f14ff029d35461655b3b909f190a7ff39b |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import os
import random
import unittest
import json
import six
from monty.os.path import which
from pymatgen import Lattice, PeriodicSite
from monty.json impor... | xhqu1981/pymatgen | pymatgen/transformations/tests/test_standard_transformations.py | Python | mit | 19,196 | [
"VASP",
"pymatgen"
] | 16b981e28dac30d8f5e1991bd40cb807c4216e133fca5f51cac6282cdd735572 |
#!/usr/bin/python
#=============================================================================================
# MODULE DOCSTRING
#=============================================================================================
"""
Tools for constructing OpenMM System objects from various convenient input file formats... | jchodera/yank | Yank/systembuilder.py | Python | lgpl-3.0 | 45,075 | [
"MDTraj",
"OpenMM"
] | 71546c97e4710146a61a7dfab2ace9aa001272637c68e2c6185f0b1ae7ebf6f9 |
# Orca
#
# Copyright 2004-2008 Sun Microsystems Inc.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/orca_prefs.py | Python | gpl-3.0 | 30,374 | [
"ORCA"
] | f1b1f604d33f596f8259e0820d8a78c39100bada0a246cd5320282631d93c93a |
########################################################################
#
# (C) 2015, Brian Coca <bcoca@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation... | danieljaouen/ansible | lib/ansible/galaxy/role.py | Python | gpl-3.0 | 15,345 | [
"Brian",
"Galaxy"
] | 3399f65736e7acefb34162f3fe3983261445b90a7dcd88ae97f5e592dc3aa686 |
import unittest
import numpy as np
import pysal.lib
import pysal.model.spreg as EC
from scipy import sparse
from pysal.lib.common import RTOL
PEGP = pysal.lib.examples.get_path
class TestBaseOLS(unittest.TestCase):
def setUp(self):
db = pysal.lib.io.open(PEGP('columbus.dbf'),'r')
y = np.array(db.b... | lixun910/pysal | pysal/model/spreg/tests/test_ols_sparse.py | Python | bsd-3-clause | 4,989 | [
"COLUMBUS"
] | dceadd8ec324054ac0774e5373826b604baf9acf38f816dab2211a87ef4bb6f2 |
# -*- coding: utf-8 -*-
# (c) Nelen & Schuurmans. GPL licensed, see LICENSE.rst.
import datetime
import re
import pathlib
# directories
PACKAGE_DIR = pathlib.Path(__file__).parent.parent
SOURCE_DIR = PACKAGE_DIR / "var" / "source"
LOG_DIR = PACKAGE_DIR / "var" / "log"
# make sure they exist - there must be a bette... | nens/openradar | openradar/config.py | Python | gpl-3.0 | 4,533 | [
"ASE"
] | f44cba2dc04d85b3e41ecc716f94f75457412e85784dab4da3472689f490767b |
# coding: utf-8
#
# Copyright 2012 NAMD-EMAP-FGV
#
# This file is part of PyPLN. You can get more information at: http://pypln.org/.
#
# PyPLN 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 o... | NAMD/pypln.backend | pypln/backend/workers/pos/__init__.py | Python | gpl-3.0 | 1,840 | [
"NAMD"
] | bda78f1a1fe86dbb9e79f4ef9df32f25bb39f38a5c9855cd960b3dd0d0a3c8c2 |
from django import forms
from django.forms.util import ErrorList
from edc_constants.constants import NO, YES
from ..models import MaternalSrh
from .base_maternal_model_form import BaseMaternalModelForm
class MaternalSrhForm(BaseMaternalModelForm):
class Meta:
model = MaternalSrh
fields = '__al... | botswana-harvard/microbiome | microbiome/apps/mb_maternal/forms/maternal_srh_form.py | Python | gpl-2.0 | 3,445 | [
"VisIt"
] | aa10e479c3b66bc4c3cc13c75ff3c537cb3b04dd26603fff9e504bcf755a5ec9 |
#!/usr/bin/env python
import unittest
import os
import numpy as np
import dynaphopy.interface.iofile as io
import dynaphopy
from dynaphopy.interface.phonopy_link import get_force_constants_from_file
class TestDynaphopy(unittest.TestCase):
def setUp(self):
import phonopy
print ('Using phonopy {}'.... | abelcarreras/DynaPhoPy | unittest/Si_test.py | Python | mit | 3,738 | [
"phonopy"
] | 615e96b8291d140fbd1fd984525bb14ba79a05ea914f3b2a1da67a135df89215 |
#!/usr/bin/env python
"""
This is a script for quick Mayavi-based visualizations of finite element
computations results.
Examples
--------
The examples assume that run_tests.py has been run successfully and the
resulting data files are present.
- view data in output-tests/test_navier_stokes.vtk
$ python po... | RexFuzzle/sfepy | postproc.py | Python | bsd-3-clause | 19,662 | [
"Mayavi",
"VTK"
] | e8f00e3e2999e31d55785b2c9eeb25bc11ee8b94b4d42ff72b5c2265a8e8782d |
""" DIRAC JobDB class is a front-end to the main WMS database containing
job definitions and status information. It is used in most of the WMS
components
The following methods are provided for public usage:
getJobAttribute()
getJobAttributes()
getAllJobAttributes()
getDistinctJobAttributes... | coberger/DIRAC | WorkloadManagementSystem/DB/JobDB.py | Python | gpl-3.0 | 85,525 | [
"DIRAC"
] | 93871952ddee5ba2cbde97e0fe86576b4c54b09198360fdd10fbe0e9a564b0e3 |
# -*- coding: utf-8 -*-
from datetime import date
from workalendar.tests import GenericCalendarTest
from workalendar.canada import Canada, Ontario, Quebec, BritishColumbia
from workalendar.canada import Alberta, Saskatchewan, Manitoba, NewBrunswick
from workalendar.canada import NovaScotia, PrinceEdwardIsland, Newfound... | sayoun/workalendar | workalendar/tests/test_canada.py | Python | mit | 15,258 | [
"Desmond"
] | 004cba9812bfb165ef7ed2942363e0668ae8a21d6eb7c5b598897f746e199804 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2019, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Test single point logfiles in cclib."""
import datetime
import os
import unittest
import numpy
import p... | cclib/cclib | test/data/testSP.py | Python | bsd-3-clause | 24,236 | [
"ADF",
"Dalton",
"GAMESS",
"Gaussian",
"Jaguar",
"MOLCAS",
"Molpro",
"NWChem",
"ORCA",
"Psi4",
"TURBOMOLE",
"cclib"
] | 6238f0de83d842e1998e26d3fed6d9e022bafdf99d3716cd0389d456152d8d2d |
# -*- coding: utf-8 -*-
"""
Support for calculating D spacing for powder diffraction lines as
as function of pressure and temperature, given symmetry, zero-pressure lattice
constants and equation of state parameters.
Author:
Mark Rivers
Created:
Sept. 10, 2002 from older IDL version
Modifications:
Sept. 26,... | erangre/Dioptas | dioptas/model/util/jcpds.py | Python | gpl-3.0 | 36,565 | [
"CRYSTAL"
] | 51a02772334dd87ca4752282fb5f983b3c6ef549efb2c57ab93dafaa53bf60fb |
# encoding: utf-8
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding field 'Indicator.last_modified_at'
db.add_column(u'profiles_indicator', 'last_modified_at', self.... | 216software/Profiles | communityprofiles/profiles/oldmigrations/0087_auto__add_field_indicator_last_modified_at.py | Python | mit | 26,523 | [
"MOE"
] | 07706899c37826fc6dc08c8f924a7fc0189059bb17982ecee41b7326bad80193 |
#!/usr/bin/env python
#
# Appcelerator Titanium Module Packager
#
#
import os, subprocess, sys, glob, string
import zipfile
from datetime import date
cwd = os.path.abspath(os.path.dirname(sys._getframe(0).f_code.co_filename))
os.chdir(cwd)
required_module_keys = ['name','version','moduleid','description','copyright','... | trd-paolo/TiGrowingTextField | build.py | Python | apache-2.0 | 6,860 | [
"VisIt"
] | a8cb1e1db0b87b9b78f6d52af7dd97007305ce932cae08467469fe34250633db |
"""Runs the Raykar et al. (2010) algorithm on the galaxy classification task.
Matthew Alger
The Australian National University
2016
"""
import argparse
import logging
import time
import h5py
import matplotlib
import matplotlib.pyplot as plt
import numpy
import sklearn
import sklearn.decomposition
import sklearn.metr... | chengsoonong/crowdastro | crowdastro/experiment/experiment_rgz_raykar.py | Python | mit | 9,572 | [
"Galaxy"
] | 6e5ef9783e58a91210fde29c19ac6da032d5abd7653de02f52e1e5f00638c0df |
## ENVISIoN
##
## Copyright (c) 2021 Gabriel Anderberg, Didrik Axén, Adam Engman,
## Kristoffer Gubberud Maras, Joakim Stenborg
## All rights reserved.
##
## Redistribution and use in source and binary forms, with or without
## modification, are permitted provided that the following conditions are met:
##
## 1. ... | rartino/ENVISIoN | envisionpy/hdf5parser/ELK/force_parser_elk.py | Python | bsd-2-clause | 6,351 | [
"Elk"
] | 6d569585a8c9f957f81981a509ebe53cfe7a7a314f1c8f1898305a757a9b9e4b |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkElevationFilter(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vt... | nagyistoce/devide | modules/vtk_basic/vtkElevationFilter.py | Python | bsd-3-clause | 489 | [
"VTK"
] | 97faa2d8e3c157713d4e024be1b87b727bdfa169dcccf8d56408b4334744d3a9 |
'''Body Composition is a Slicer module that allows to segment different parts of the lungs in a manual or semi-automatic basis
with the help of a customized Slicer Editor.
It also performs a set of operations to analyze the different structures of
the volume based on its label map, like Area, Mean, Std.Dev., etc.
First... | acil-bwh/SlicerCIP | Scripted/CIP_BodyComposition/CIP_BodyComposition.py | Python | bsd-3-clause | 83,135 | [
"VTK"
] | 73a4be06fa3439efa3ae974b64078d723cec8e5bb755a0023c3d3629a6ff1248 |
'''
SASSIE: Copyright (C) 2011 Joseph E. Curtis, Ph.D.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
... | madscatt/zazzie | src_2.7/sassie/simulate/energy_minimization/write_namd_input.py | Python | gpl-3.0 | 5,081 | [
"NAMD"
] | de2b719579721eb6d39ee2a6ce1f5fa7dc9594f8a0c9bdead6ab786fd333cb0a |
from sys import exit
from sys import path as syspath
from bisect import bisect_left
from os import path
from argparse import ArgumentParser as parser
from ConfigParser import ConfigParser
import time
import numpy as np
import numpy.random as nprand
from scipy import integrate
from scipy.optimize import brentq
from sn... | ruggiero/wubclus | clustep/clustep.py | Python | gpl-2.0 | 10,500 | [
"Galaxy"
] | 48aa013bba6e8ea4eec74dcc29ed5e7ed0d0ee3a6431c484e294f77b5a1ead5e |
'''
Theme layer template.
New Section
===========
Additional information goes here.
@warning: THIS IS A TEMPLATE SHOWING THE BASIC STRUCTURE OF A THEME_LAYER SCRIPT! DO NOT OVERWRITE!
ALWAYS USE "SAVE AS..."!
@todo: point one
@todo: point two
@author: kmu
@since: 6. sep. 2010
'''
# Built-i... | kmunve/pysenorge | pysenorge/themes/theme_layer_template.py | Python | gpl-3.0 | 1,999 | [
"NetCDF"
] | f6f735051b68a2f686927b89ff6e0df6c7948e3e298ab55efb509f73e7677540 |
# LIBTBX_PRE_DISPATCHER_INCLUDE_SH export PHENIX_GUI_ENVIRONMENT=1
# DIALS_ENABLE_COMMAND_LINE_COMPLETION
from __future__ import annotations
import copy
import sys
import wx
import gltbx
import gltbx.gl as gl
import libtbx.phil
import wxtbx.utils
from dxtbx.model import MultiAxisGoniometer
from scitbx.array_family ... | dials/dials | command_line/geometry_viewer.py | Python | bsd-3-clause | 24,262 | [
"CRYSTAL"
] | e051de187338aa7e758725abdce7d4f2b2e3b983277c65b81f82ab945f498803 |
# -*- coding: utf-8 -*-
"""
Created on Mon Mar 7 14:38:46 2011
Plot pca test error vs train error
@author: -
"""
# Computes the gaussian gradients on a boxm_alpha_scene
import os;
import optparse;
import time;
import sys;
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.cm as cmt
import glob
#P... | mirestrepo/voxels-at-lems | dbrec3d/bof/general/classify/collect_classification_results.py | Python | bsd-2-clause | 2,653 | [
"Gaussian"
] | 0cce4eccafae50b156009235b16c32fd2771bdb1d9719fb2c25531d57b1da146 |
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