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#-------------------------------------------------------------------------------
#
# Define classes for (uni/multi)-variate kernel density estimation.
#
# Currently, only Gaussian kernels are implemented.
#
# Written by: Robert Kern
#
# Date: 2004-08-09
#
# Modified: 2005-02-10 by Robert Kern.
# Contr... | arokem/scipy | scipy/stats/kde.py | Python | bsd-3-clause | 21,796 | [
"Gaussian"
] | 59920931facd930396270182a63c8f486e305cb35e17414c6aeb967e279bac3e |
#!/usr/bin/env python
"""
Reads a list of intervals and a maf. Produces a new maf containing the
blocks or parts of blocks in the original that overlapped the intervals.
If a MAF file, not UID, is provided the MAF file is indexed before being processed.
NOTE: If two intervals overlap the same block it will be writte... | dbcls/dbcls-galaxy | tools/maf/interval2maf.py | Python | mit | 5,001 | [
"Galaxy"
] | 674835560534cd41239a38cf6a540ba038febfd55898d64cd8bae7ef75a66b48 |
import numpy as np
def gaussian_kernel(x1, x2, sigma):
x1 = x1.flatten()
x2 = x2.flatten()
sim = 0
# ===================== Your Code Here =====================
# Instructions : Fill in this function to return the similarity between x1
# and x2 computed using a Gaussian kernel ... | nsoojin/coursera-ml-py | machine-learning-ex6/ex6/gaussianKernel.py | Python | mit | 430 | [
"Gaussian"
] | 58c53801ca189b0cf9f3ad7e59da9d84a757fb74cf80fd8369b87d56a9537a5e |
# $Id$
#
# Copyright (C) 2006 greg Landrum
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
from contextlib import closing
import unittest
from ... | bp-kelley/rdkit | rdkit/Chem/FeatMaps/UnitTestFeatMapParser.py | Python | bsd-3-clause | 4,564 | [
"RDKit"
] | ebf17fa6f57551a8aa5456012b7d541ae7a3a47261f08dbb14b54159337fd969 |
# -*- coding: utf-8 -*-
# Copyright (C) 2012, Almar Klein, Ant1, Marius van Voorden
#
# This code is subject to the (new) BSD license:
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of s... | curtiszimmerman/deepdreamer | deepdreamer/images2gif.py | Python | gpl-3.0 | 36,702 | [
"NEURON"
] | d335e144cf87605521268454c2ceefe98a9dbbfddc586ed079cc6537ceb2eb27 |
# -#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#
# these are system modules
import commands
import numpy
import os
import sys
# these are my local modules
from env import gidgetConfigVars
import miscIO
import miscTCGA
import path
import tsvIO
# -#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#... | cancerregulome/gidget | commands/feature_matrix_construction/main/new_Level3_miRNAseq.py | Python | mit | 11,860 | [
"ADF"
] | d76bc066092a26e711f9e35cad83f2523a6d235f340e738edba5c1fa081007b7 |
#!/usr/bin/python
# -*- encoding: utf-8; py-indent-offset: 4 -*-
# +------------------------------------------------------------------+
# | ____ _ _ __ __ _ __ |
# | / ___| |__ ___ ___| | __ | \/ | |/ / |
# | | | | '_ \ / _ \/ __| |/ /... | xorpaul/check_mk | web/plugins/wato/notifications.py | Python | gpl-2.0 | 10,848 | [
"VisIt"
] | d417c710c8d035b845da19e8672d3a469bf93bbb0b687d079679836eefcfcd3e |
"""
Tests to try and ensure that important mayavi imports work with no UI.
"""
# Author: Prabhu Ramachandran <prabhu@aero.iitb.ac.in>
# Copyright (c) 2009, Enthought, Inc.
# License: BSD Style.
import sys
import unittest
from traits.etsconfig.api import ETSConfig
class TestNoUIToolkit(unittest.TestCase):
"""Te... | liulion/mayavi | mayavi/tests/test_no_ui_toolkit.py | Python | bsd-3-clause | 2,037 | [
"Mayavi"
] | 1fc1c09fe3c20dd2d97769e0476c2be49c8faac7ce07ace4c02d6fc85b90e230 |
from .estimator_base import H2OEstimator
class H2ODeepLearningEstimator(H2OEstimator):
def __init__(self, model_id=None, overwrite_with_best_model=None, checkpoint=None,
use_all_factor_levels=None, activation=None, hidden=None, epochs=None,
train_samples_per_iteration=None, seed=None, ... | madmax983/h2o-3 | h2o-py/h2o/estimators/deeplearning.py | Python | apache-2.0 | 22,893 | [
"Gaussian"
] | 4e88d00becf16ed8211e9cb4cd0226752bc1572769249aeff794ff421feea178 |
import chainerx
from chainerx import _docs
def set_docs():
_docs_creation()
_docs_evaluation()
_docs_indexing()
_docs_linalg()
_docs_logic()
_docs_loss()
_docs_manipulation()
_docs_math()
_docs_sorting()
_docs_statistics()
_docs_connection()
_docs_normalization()
_d... | hvy/chainer | chainerx/_docs/routines.py | Python | mit | 127,369 | [
"Gaussian"
] | 39c6c047602574d716bc3211414de4c45c21397d2fdf357e82569c360490d028 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | ashutoshvt/psi4 | psi4/driver/qcdb/bfs.py | Python | lgpl-3.0 | 8,260 | [
"Psi4"
] | d4852bf6eb6175fe568e316d8cbd1c752eb1de86719399c64719c5417c1d1ecd |
#! /usr/bin/env python
################################################################################
# Ruth Lunt 2013 #
################################################################################
import numpy as np
import matplotlib.pyplot as plt
... | WMD-group/mixed_metal_oxide_potentials | metal_oxide_mix.py | Python | gpl-3.0 | 11,526 | [
"GULP"
] | 94068d8850e4a54a652eb0c698c29fc5a3f5473058ecd544c2704d40ac26bdb7 |
import unittest
from hypothesis import given
from paraview import servermanager
from paraview.simple import Disconnect
from simphony.core.cuba import CUBA
from simphony_paraview.show import show
from simphony_paraview.core.testing import (
cuds_containers,
create_example_mesh, create_example_lattice, create_e... | simphony/simphony-paraview | simphony_paraview/tests/test_show.py | Python | bsd-2-clause | 3,134 | [
"ParaView"
] | 5156368ebb7e2eaa7386bde69931427acf3fcb2583dbba5f9891cecbb9cc64a6 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# create a rendering window and renderer
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
renWin.StereoCapableWindowOn()
iren = vtk.vtkRende... | hlzz/dotfiles | graphics/VTK-7.0.0/IO/EnSight/Testing/Python/EnSightTensorsInversion.py | Python | bsd-3-clause | 1,611 | [
"VTK"
] | 002c5054ad725b7d0721480e1e8f0e4e57341ea226f1d5d966291f595b0b4bc0 |
# -*- coding: utf-8 -*-
"""
Created on Wed Feb 25 201 - 04:24:26
@author: Yoan BOUZIN email : yoan.bouzin@gmail.com
"""
try:
import time
import subprocess
import platform
import os
import Tkinter # Python 2
import ttk
from tkFileDialog import askopenfilename
from Tkinter import *
fr... | Tuisto59/Blast-LP | BLAST-LP v1.2.py | Python | gpl-2.0 | 48,327 | [
"BLAST"
] | eacd89b5b2b0b363b97fc0af8ea9f28daf0ac4c4801cbabc571e96aa034445bd |
#! /usr/bin/env python
import sys, shutil
from numpy import *
from os import path, makedirs
from glob import glob
import subprocess
class color:
"""
define colors in the terminal
"""
purple = '\033[95m'
cyan = '\033[96m'
darkcyan = '\033[36m'
blue = '\033[94m'
green = '\033[92m'
ye... | chunshen1987/superMC | scripts/generate_3d_profiles/generate_ebe_3d_profiles.py | Python | gpl-3.0 | 7,993 | [
"Gaussian"
] | f8d5a3b99032eccc36a02a0c71e685f035112b00e3e13226b2891f03055d1bf1 |
#!/usr/bin/env python
# copy LAMMPS src/libliggghts.so and liggghts.py to system dirs
instructions = """
Syntax: python install.py [-h] [libdir] [pydir]
libdir = target dir for src/libliggghts.so, default = /usr/local/lib
pydir = target dir for liggghts.py, default = Python site-packages dir
"""
impo... | schrummy14/LIGGGHTS_Flexible_Fibers | python/install.py | Python | gpl-2.0 | 2,198 | [
"LAMMPS"
] | 845e62c6bd26aeebeec8aa935d872dfb4ab20d6167db11bda88466ef28d20656 |
""" :mod: OperationTests
====================
.. module: OperationTests
:synopsis: Operation test cases
.. moduleauthor:: Krzysztof.Ciba@NOSPAMgmail.com
Operation test cases
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ ... | ic-hep/DIRAC | src/DIRAC/RequestManagementSystem/Client/test/Test_Operation.py | Python | gpl-3.0 | 3,935 | [
"DIRAC"
] | 8e080d03ac3600330705f7ee08ce4ca3aafa8a0b5228ffa714ea11b2a0fbed89 |
## This file is part of Invenio.
## Copyright (C) 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2012, 2014 CERN.
##
## Invenio 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, ... | egabancho/invenio | invenio/legacy/websession/templates.py | Python | gpl-2.0 | 114,091 | [
"VisIt"
] | 4ede93c786f12a6b4f805e67144f65bcf3c791badcffab7fea96aa75eafb98b6 |
# -*- coding: utf-8 -*-
# This program is free software; you can redistribute it and/or modify
# it under the terms of the (LGPL) GNU Lesser General Public License as
# published by the Free Software Foundation; either version 3 of the
# License, or (at your option) any later version.
#
# This program is distri... | pexip/os-python-suds-jurko | tests/test_cache.py | Python | lgpl-3.0 | 12,799 | [
"Firefly"
] | 1a1bed0ec4528ae7f15d66aea1beabfad33273cf0204fdb0c2cda11ce79d81ed |
# Hidden Markov Model Implementation
import pylab as pyl
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy as scp
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import rospy
#import hrl_lib.mayavi2_util as mu
import hrl_lib.viz ... | tapomayukh/projects_in_python | classification/Classification_with_HMM/Single_Contact_Classification/Variable_Stiffness_Variable_Velocity/HMM/with padding 3s/hmm_crossvalidation_force_20_states.py | Python | mit | 29,288 | [
"Mayavi"
] | 9e1f70c6ed37637e65e52327de6fda193ef47bfbe4cc39b0c79ffca8e4a7a376 |
import inspect
import logging
import os
from six import with_metaclass
from kalliope.core.ConfigurationManager import SettingLoader
from kalliope.core.ConfigurationManager.ConfigurationChecker import ConfigurationChecker
from kalliope.core.Models import Singleton
from kalliope.core.Models.Brain import Brain
from kall... | kalliope-project/kalliope | kalliope/core/ConfigurationManager/BrainLoader.py | Python | gpl-3.0 | 6,353 | [
"NEURON"
] | b603f6941843a9df623d0e6256fd0dc6d8479c8ae721b02ac9fba3d6483958c8 |
from Biskit import *
import Biskit.tools as T
import numpy as N
###############################
## Creating a Trajectory
## Example 1:
## starting from several single structures
###############################
m = PDBModel( '3TGI' )
t = Trajectory( 20 * [ m ] ) ## trajectory of 20 identical structures
t.ref ... | ostrokach/biskit | doc/tutorial_md/tutorial_md.py | Python | gpl-3.0 | 2,885 | [
"Amber"
] | c1eb7822891b999b54e1585362699049e9db75192aba76c95a5468e0b3c74d48 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements various transmuter classes.
Transmuters are essentially classes that generate TransformedStructures from
various data sources. They enable the high-throughput generation of new
struc... | gmatteo/pymatgen | pymatgen/alchemy/transmuters.py | Python | mit | 15,098 | [
"VASP",
"pymatgen"
] | 5d039b6a2108d60e96d034101b8a007cb3e6f6b2873b597ac7e8955710c56fd0 |
# Copyright 2021 Lawrence Livermore National Security, LLC
"""
This script is used by cmec-driver to run the ASoP-Spectral metrics.
It is based on the workflow in ASoP1_spectral_main.py and
can be called with the aruments listed below. Keys that can be set
in the config or settings dictionary are: region, timescale-all... | nick-klingaman/ASoP | ASoP-Spectral/ASoP1_Spectral/ASoP1_spectral_cmec_workflow.py | Python | apache-2.0 | 25,029 | [
"NetCDF"
] | 08bb1a7d1abf95fc299ad193d304eda938cbc611f5894cc731facb92d18aa571 |
"""
Put Canvas specific configuration here.
Note that this project has three different configuration files:
/var/canvas/website/settings.py
That is where we keep all Django specific settings.
/var/canvas/common/configuration.py
That is where we keep AWS and infrastructure related settings. No... | drawquest/drawquest-web | website/canvas/knobs.py | Python | bsd-3-clause | 5,123 | [
"VisIt"
] | 4699092ae353005e6b7dfb43dbd058ddccda13e167c3dda3fdfb2c67b343dc07 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2009 Brian G. Matherly
# Copyright (C) 2009 Gary Burton
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publis... | gramps-project/gramps | gramps/gui/dbman.py | Python | gpl-2.0 | 45,626 | [
"Brian"
] | 498bc381cefe082547efe382877cf295f7936c6fa83d0b8f4aa6f56bc052ca3a |
import errors
import executer
from phpbuiltins import constants
from scope import scope
class PHPFunction():
def __init__(self, name, modifiers, params, body, context = None, filename = None, line_num = 0):
self.name = name
self.modifiers = modifiers
self.params = params
self.body = body
self.conte... | g-i-o-/pyphp | pyphp/phpfunction.py | Python | mit | 2,442 | [
"VisIt"
] | b6a9de753560206d8a46a7c1a9ce9463170080039d395a30a18c1ac6fb6feceb |
#!/usr/env/bin/python
from distutils.core import setup
from distutils.extension import Extension
from Cython.Build import cythonize
from Cython.Distutils import build_ext
import pysam
import numpy
import glob
import os
def two_dot(version):
v = version.split('.')
return '.'.join(v[0:min(3,len(v))])
def get_ve... | timothyjamesbecker/FusorSV | setup.py | Python | gpl-3.0 | 2,213 | [
"pysam"
] | b662d5d3afad9416d704ab098dd50c14ecc94f4473d541281d9da10aa8673f0a |
"""General Tools for use throughout RLPy"""
def module_exists(module_name):
try:
__import__(module_name)
except ImportError:
return False
else:
return True
import sys
import numpy as np
# print "Numpy version:", numpy.__version__
# print "Python version:", sys.version_info
import ... | BerkeleyAutomation/rlpy | rlpy/Tools/GeneralTools.py | Python | bsd-3-clause | 40,682 | [
"Gaussian"
] | e870d2f220ca344571b7bcd7edeb65f60c1e6fac3bc9184aadb4323e0bbc665e |
"""
Functions related to creating the engine or the figures.
"""
# Author: Gael Varoquaux <gael.varoquaux@normalesup.org>
# Copyright (c) 2007, Enthought, Inc.
# License: BSD Style.
# Standard library imports.
import gc
import warnings
import copy
import numpy as np
# Enthought imports
from pyface.timer.api import... | dmsurti/mayavi | mayavi/tools/figure.py | Python | bsd-3-clause | 11,152 | [
"Mayavi"
] | fc3940e7837efd7756dfc9042cef26c854700947ff42c30b44e8b84aee2a2440 |
#! /usr/bin/env python
sources = """
eNrsvWuT40iSINZ3ku501Eq7J51Op8edMEzlAqhiojKzH7NLa9ZsTXX1TN30dLdVVc/WWnYuB0ki
MzFJEiwAzGROW49Jpi/6Z/dH9Av0C+SvCEQEAiCr+jVrdjVjnSAQ4RHh4eHh4eGP//Off/vmvej1
v3jvvffW93VW1W/+2ev/75+9995B8OU/vPr1F59Pn7z41dMvfvvlZ89ePZt+8ZvBcDgccMFxsFnl
dZCu5sHlZjWr82KVLgL8kq+ugru8vg6+vK+vi1VClabTdLGYToN... | s-m-i-t-a/sales_flatpages | runtests.py | Python | bsd-3-clause | 228,439 | [
"EPW"
] | 0bb38163d8d23ba3b7e758297d40860ee5038ecaa962e5eed409c42bb39265ef |
"""
Simple GUI for Quantum ESPRESSO
"""
from PyQt5.QtWidgets import (QApplication, QCheckBox, QComboBox, QDialog,
QDialogButtonBox, QFormLayout, QGridLayout, QGroupBox, QHBoxLayout,
QLabel, QLineEdit, QMenu, QMenuBar, QPushButton, QScrollArea, QSpinBox,
QTextEdit, QVBoxLayout, QWidget, QPlainT... | taylor-a-barnes/test-gui | window.py | Python | bsd-3-clause | 55,650 | [
"DIRAC",
"Gaussian",
"Quantum ESPRESSO"
] | 638e1ec75d7524c94897cc03d5c358d28685d702b47845a63b2549b711679d7d |
from flask import jsonify, Flask, request, Response
from flask.ext.sqlalchemy import SQLAlchemy
from flask.ext.httpauth import HTTPBasicAuth
import time
import json
auth = HTTPBasicAuth()
import os
"""Provides an API for models, intended for use with javascript and electron"""
app = Flask(__name__)
app.config.from_ob... | schinke/solid-fortnight-ba | flask/app.py | Python | mit | 19,346 | [
"VisIt"
] | 60c53bc3818775d3fa16a32bf3c789759c5b1a3eb6929240159a2aee499e4bfd |
import ispyb.model
class Sample(ispyb.model.DBCache):
def __init__(self, sample_id, db_conn, preload=None):
"""Create a Sample object for a defined sample_id. Requires
a database connection object exposing further data access methods.
:param sample_id: bLSampleId
:param db_conn: I... | DiamondLightSource/ispyb-api | src/ispyb/model/sample.py | Python | apache-2.0 | 2,810 | [
"CRYSTAL"
] | c8f72095655347b626a1dd38613c531d30a71c43f3f4c109a038b6e963719c8e |
#User provided customizations for the gpaw setup
import os
# compiler
compiler = './gcc.py'
mpicompiler = './gcc.py'
mpilinker = 'cc'
extra_compile_args = ['-std=c99']
# libz
libraries = ['z']
# libxc
library_dirs += [os.environ['LIBXCDIR'] + '/lib']
include_dirs += [os.environ['LIBXCDIR'] + '/include']
libraries +=... | mlouhivu/build-recipes | gpaw/examples/sisu-git-2016-04-01/customize-gnu.py | Python | mit | 583 | [
"GPAW"
] | 994ff2f62dcb0b86a25cbc25e8e98d5ab0960ba46beae30cf4a82f7931e55788 |
import os
import numpy as np
from pychemia.utils.periodic import atomic_symbol, covalent_radius, atomic_number
from pychemia.utils.constants import bohr_angstrom, angstrom_bohr
from pychemia.utils.mathematics import unit_vectors
from .parser import parser
from pychemia.utils.netcdf import netcdf2dict
from pychemia.cor... | MaterialsDiscovery/PyChemia | pychemia/code/abinit/input.py | Python | mit | 28,922 | [
"ABINIT",
"NetCDF"
] | 126270ee7bbc0a7e027aab3c7960e37f9d4d6a39b4ef2f881a059c10fb9d7509 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# grid_events - event handler to monitor files and trigger actions
# Copyright (C) 2003-2015 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of t... | heromod/migrid | mig/server/grid_events.py | Python | gpl-2.0 | 37,280 | [
"Brian"
] | 6b3570c78f4e5f690c0149045a3665a0f31ccf073ede1810481855d6d3e829d8 |
# -*- coding: utf-8 -*-
# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
This package defines miscellaneous units. They are also
available in the `astropy.units` namespace.
"""
from . import si
from astropy.constants import si as _si
from .core import (UnitBase, def_unit, si_prefixes, binary_prefi... | pllim/astropy | astropy/units/misc.py | Python | bsd-3-clause | 3,393 | [
"Dalton"
] | 993c714f2008288a714601027ad005de4d23245e3e460918c66069eb7966a3f1 |
# -*- coding: utf-8 -*-
"""This class contains an alternate implementation of the PyBEL database manager that only stores graphs in memory."""
from dataclasses import dataclass
from typing import Iterable, List
from pybel import BELGraph
@dataclass
class _Namespace:
id: int
class DictManager:
"""A dictio... | pybel/pybel-tools | src/pybel_tools/dict_manager.py | Python | mit | 1,150 | [
"Pybel"
] | 05c275ef77a366064f37e69db384e082c78bf77429ca8ddc3322d9890beeaa53 |
from twisted.internet import defer
from nevow import livepage, loaders, tags, rend, static, entities, util
from nevow.livepage import js
testFrameNode = js.testFrameNode
contentDocument = testFrameNode.contentDocument
gid = contentDocument.getElementById
XPathResult = js.XPathResult
null = js.null
class xpath(obje... | UstadMobile/exelearning-ustadmobile-work | nevow/livetest.py | Python | gpl-2.0 | 13,641 | [
"VisIt"
] | 4ca6d327ea02eaf650c3f46e46c62205674e5e45a1a17c1aee1988c4602bac0d |
# coding: utf8
{
' (leave empty to detach account)': ' (leave empty to detach account)',
' Module is the main communications hub of the Sahana system. It is used to send alerts and/or messages using SMS & Email to various groups and individuals before, during and after a disaster.': ' Module is the main communications ... | dotskapes/wikiSkapes | languages/en-gb.py | Python | mit | 231,317 | [
"VisIt"
] | e9451dc4a54c3ddedc447e08d6e3b022a5970af9088368d0a2cb9a24e78ed530 |
#
# Copyright 2016 The BigDL Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in ... | intel-analytics/BigDL | python/dllib/test/bigdl/caffe/caffe_layers.py | Python | apache-2.0 | 12,755 | [
"Gaussian"
] | c7dd41f7660c84d9faa02bc8043982ecf9bb0f8f4dcbb06d628cc30736c0f887 |
##############################################################################
# #
# NodeBox 1.9.5 -> Pycairo wrapper #
# #
... | johnnovak/twyg | twyg/cairowrapper.py | Python | mit | 19,681 | [
"Gaussian"
] | 674323a71c52c0d091d68c51f24ac4f38b44788753c1a5798310709dbdf78691 |
import logging
import os
import string
import tempfile
from time import gmtime
from time import strftime
from datetime import date
from datetime import datetime
from galaxy import util
from galaxy import web
from galaxy.web.base.controller import BaseUIController
from galaxy.web.form_builder import CheckboxField
from ... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/webapps/tool_shed/controllers/repository.py | Python | gpl-3.0 | 230,844 | [
"Galaxy"
] | 65264e37d4f78a3141ca74f95d77282584f7eaacaa8312312c166ce50e8ee57c |
# pylint: disable=E1103
import pandas as pd
import os.path
from . import resource_usage as ru
TRANSCRIPT_GTF_FILE = "TRANSCRIPT_GTF_FILE"
GENOME_FASTA_DIR = "GENOME_FASTA_DIR"
SIMULATED_READS = "SIMULATED_READS"
LEFT_SIMULATED_READS = "LEFT_SIMULATED_READS"
RIGHT_SIMULATED_READS = "RIGHT_SIMULATED_READS"
FASTQ_READS... | lweasel/piquant | piquant/quantifiers.py | Python | mit | 19,357 | [
"Bowtie"
] | a87f38ae1b01936e05102f7d09bcf45678409a06085d8ef6480fb8fdbabbc8f9 |
# ----------------------------------------------------------------------
# Numenta Platform for Intelligent Computing (NuPIC)
# Copyright (C) 2013, Numenta, Inc. Unless you have purchased from
# Numenta, Inc. a separate commercial license for this software code, the
# following terms and conditions apply:
#
# This pro... | Petr-Kovalev/nupic-win32 | py/nupic/swarming/permutationhelpers.py | Python | gpl-3.0 | 26,130 | [
"Gaussian"
] | 66e6cbfa246b66cb4c27beeefca9153ee5c953545d5f351690bf9567fc9b01b8 |
# Copyright (C) 2011-2012 CRS4.
#
# This file is part of Seal.
#
# Seal 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.
#
# Seal is dis... | QwertyManiac/seal-cdh4 | tests/seal/lib/aligner/test_bwa_aligner.py | Python | gpl-3.0 | 3,040 | [
"BWA"
] | 2c8b54e9117c4f5d9e1e653c662ed0898d96f2e6a35c810d2d11a055f3a314c3 |
# Define constants
import os
script_dir = os.path.dirname(os.path.realpath(__file__)).replace("/utils", "")
available_snp_callers = ["bcftools", "freebayes"]
analysis_types = ["trim",
"align",
"merge",
"snps",
"indels",
"transpos... | AndersenLab/pyPipeline | utils/constants.py | Python | mit | 751 | [
"BWA"
] | 53f3f38073eec11ffdfdeaaf1ad8e621931ad9ad1b3e083bd09e64c39be57c4b |
from neuron import h, gui
import math
import random
#neuron.load_mechanisms("./mod")
class cfiber(object):
'''
C-fiber class with parameters:
L: int (mkM)
length of compartment
d: float
diameter of fiber
num: int
number of compartments
coordinates: dict (updates by posi... | research-team/robot-dream | Nociception/cfiber.py | Python | mit | 9,526 | [
"NEURON"
] | bd7bc511c6974ba71609543ff4cfa33d74b3fe7af1362024bf788acd374a0fac |
"""
API for initiating and tracking requests for credit from a provider.
"""
import datetime
import logging
import uuid
import pytz
import six
from django.db import transaction
from edx_proctoring.api import get_last_exam_completion_date
from openedx.core.djangoapps.credit.exceptions import (
CreditProviderNotC... | edx-solutions/edx-platform | openedx/core/djangoapps/credit/api/provider.py | Python | agpl-3.0 | 16,195 | [
"VisIt"
] | 6166a7720639f4cd3fc247ec23e6f0523d759ba492730edc135994a7a5160422 |
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
from Objects.CAdaline import AdalineGD, AdalineSGD
# Getting Iris data again...
df = pd.read_csv('https://archive.ics.uci.edu/ml/machine-learning-databases/iris/iris.data', header=None)
df.tail()
y = df.iloc[0:100, 4].values
y = np.whe... | petritn/MachineLearning | AdalineLearning.py | Python | gpl-3.0 | 1,945 | [
"NEURON"
] | d4f62450665a07a92ea2d97ddc058016bffb91a74f9b099a897daa8b99ca613e |
# -*- coding: utf-8 -*-
#_____________________________________________________________________________
#
# Copyright (c) 2012 Berlin Institute of Technology
# All rights reserved.
#
# Developed by: Neural Information Processing Group (NI)
# School for Electrical Engineering and Computer Science
# ... | pmeier82/BOTMpy | botmpy/test/_test_cluster_methods.py | Python | mit | 10,851 | [
"Gaussian"
] | f1005ef960eb4726126893b9fba24b124c418f5eff3633bf10d1f852f9be42dc |
#!/usr/bin/env python3
"""
emep_readcdf contains:
class:
EmepFileClass - which defines objects with name,proj,x0, etc.
methods:
readcdf - reads EMEP cdf file, and figures out projection.
returns : EmepFile (object), and values of a
specified variable for the full... | mifads/pyscripts | emxcdf/readcdf.py | Python | gpl-3.0 | 24,851 | [
"NetCDF"
] | b4ab592cb7228d14c81dc26a80eee22596ee594f061c9217eb0807ec5234031a |
import GPy
import GPyOpt
import argparse
import os
import numpy as np
import time
import FireflyAlgorithm as ffa
def func(var):
hist = []
gamma = var[:,0][0]
alpha = var[:,1][0]
fireflies = int(var[:,2][0] * 100)
step = int(var[:,3][0] * 100)
iterations = int(var[:,4][0] * 1000)
if args.v ... | OPU-Surveillance-System/monitoring | master/scripts/planner/solvers/bo_firefly_iteration.py | Python | mit | 4,015 | [
"Firefly"
] | 5404648a134ef950eb9503a04b4e6e5dc795638a3e05a2abe4e8f1b1f9659bcf |
# (c) 2013-2014, Michael DeHaan <michael.dehaan@gmail.com>
# Stephen Fromm <sfromm@gmail.com>
# Brian Coca <briancoca+dev@gmail.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 publish... | pilwon/ansible | lib/ansible/runner/action_plugins/assemble.py | Python | gpl-3.0 | 5,570 | [
"Brian"
] | 130b20b0718345b839a135e4bb78fd3f109e2f217bf29d0166ff850548c5a370 |
# -*- encoding: utf-8 -*-
"""
General helper functions that don't fit neatly under any given category.
They provide some useful string and conversion methods that might
be of use when designing your own game.
"""
from __future__ import division, print_function
from builtins import object, range
from future.utils impo... | MarsZone/DreamLand | evennia/evennia/utils/utils.py | Python | bsd-3-clause | 59,803 | [
"VisIt"
] | 0c7a5787a0a24829e5da4022e8de7b09cdedd1b7e907c46dfa43bfe939a5c555 |
# pylint: disable=missing-docstring
# pylint: disable=redefined-outer-name
from lettuce import step, world
from nose.tools import assert_equal, assert_in, assert_not_equal
from selenium.common.exceptions import InvalidElementStateException
from common import *
from contentstore.utils import reverse_course_url
from te... | Stanford-Online/edx-platform | cms/djangoapps/contentstore/features/grading.py | Python | agpl-3.0 | 7,162 | [
"VisIt"
] | 63b4b73340eb858d5e94bf926c2d78734521accaa79436060ee933fad3389fe1 |
"""
Copyright 2016 Brian Quach
Licensed under MIT (https://github.com/brianquach/udacity-nano-fullstack-catalog/blob/master/LICENSE) # noqa
"""
from catalog import app
app.secret_key = 'development'
app.run(host='0.0.0.0', port=8000, debug=False)
| brianquach/udacity-nano-fullstack-catalog | vagrant/catalog/runserver.py | Python | mit | 250 | [
"Brian"
] | 1a4201bdbe439cfb08a9c668ffe339ab9399fe9f6e26704e0c03ff4897b99ac0 |
x = []
##########################################################################
#
# QGIS-meshing plugins.
#
# Copyright (C) 2012-2013 Imperial College London and others.
#
# Please see the AUTHORS file in the main source directory for a
# full list of copyright holders.
#
# Dr Adam S. Candy, adam.candy@... | adamcandy/QGIS-Meshing | extras/raster_tools/RastorTools_obs.py | Python | lgpl-2.1 | 5,555 | [
"NetCDF"
] | ae5f1a0b73d614524b8be0e4595e41308c9d0864e5878cf313d9170238726abc |
'''
Created on Aug 29, 2012
@author: jchen
'''
from google.appengine.api import mail
import web2
def sendmailfunc(available, ticketurl, email):
avail_text=""
if available==1:
avail_text =" available"
else:
avail_text =" unavailable"
title="You have ticket becomes %s"%avail_text
body... | godosou/barcaticketsinform | tasks/informclient.py | Python | lgpl-3.0 | 924 | [
"VisIt"
] | d909a620efc10998618cd9b8e1bbdfbdfb5b58de36a6c369f16bb2d22cafcf43 |
# -*- coding: utf-8 -*-
#!/usr/bin/env python
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007 Johan Gonqvist <johan.gronqvist@gmail.com>
# Copyright (C) 2007-2009 Gary Burton <gary.burton@zen.co.uk>
# Copyright (C) 2007-2009 Stephane Charet... | sam-m888/gramps | gramps/plugins/webreport/download.py | Python | gpl-2.0 | 7,780 | [
"Brian"
] | 7bdca47ce96aedaf126138c72f07044557e50d61d99ccbd7f1e7429934df7d4c |
## Copyright (c) 2009-2011, Noel O'Boyle
## All rights reserved.
##
## This file is part of Cinfony.
## The contents are covered by the terms of the BSD license
## which is included in the file LICENSE_BSD.txt.
"""
webel - A Cinfony module that runs entirely on web services
webel can be used from all of CPython, J... | cinfony/cinfony | cinfony/webel.py | Python | bsd-2-clause | 13,004 | [
"CDK",
"CHARMM",
"Gaussian",
"Gromacs",
"Hyperchem",
"MacroModel"
] | 7a17eccba53c43d4d96fce09f21a303aaf942eeaf17ef33fbab93efa2fe94622 |
# Copyright 2001 by Katharine Lindner. 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.
"""Martel based parser to read ECell formatted files.
This is a huge regular regular expr... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/ECell/ecell_format.py | Python | apache-2.0 | 2,780 | [
"Biopython"
] | 6a64f9acd2f334f60e7f7d233a01d5df3a06f6191e0c9915a0dda7cdf500fe9f |
# Copyright 2014-2020 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | sunqm/pyscf | pyscf/agf2/uagf2_slow.py | Python | apache-2.0 | 10,460 | [
"PySCF"
] | 55eac0bf526a6d927e1b024f72e0da429c2ac505914a3b410e59661754f79ee2 |
# Player Variables
def major_bonus(stat):
stat += 10
return stat
def minor_bonus(stat):
stat += 5
return stat
#player variables
age = (18, 38)
potential = (30, 100)
def_iq = (35, 100)
off_iq = (35, 100)
decision_making = (39, 100)
court_awareness = (39, 100)
strength = (39, 100)
fatigue =... | benkul/BBA | game_variables.py | Python | mit | 2,072 | [
"MOOSE"
] | 6ab0fa9e55b383a83471278460208fdb4319c07e90bd7f679a090da809c4728f |
#!/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/gto/basis/parse_molpro.py | Python | apache-2.0 | 4,032 | [
"Molpro",
"PySCF"
] | 673a7f5b865b7833d74c5cdbb27399ebfa6e43fdf20da5d1a5a4a482e1f97755 |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class Visit(CMakePackage):
"""VisIt is an Open Source, interactive, scalable, visualization,
... | LLNL/spack | var/spack/repos/builtin/packages/visit/package.py | Python | lgpl-2.1 | 12,706 | [
"NetCDF",
"VTK",
"VisIt"
] | 0fd32f7984f040b89c36595fcf2661a07e97ef8a681c67e620e142d414ff2019 |
#!/usr/bin/env python
from __future__ import print_function
import vtk
import numpy
from icqsol.shapes.icqRefineSurface import RefineSurface
from icqsol.util.icqDataFetcher import getArrayIndexFromNameAndProjectOntoCells
class BaseSolver:
def __init__(self, pdata, max_edge_length, order=5):
"""
C... | gregvonkuster/icqsol | bem/icqBaseSolver.py | Python | mit | 5,012 | [
"VTK"
] | b970df6d6cd2905bb2695af2907a93cd74dfd8b865b6b4eabdf5cfa0e868f0df |
# this program corresponds to special.py
### Means test is not done yet
# E Means test is giving error (E)
# F Means test is failing (F)
# EF Means test is giving error and Failing
#! Means test is segfaulting
# 8 Means test runs forever
### test_besselpoly
### test_mathieu_a
### test_mathieu_even_coef
##... | jamestwebber/scipy | scipy/special/tests/test_basic.py | Python | bsd-3-clause | 132,935 | [
"Elk"
] | 84837d8f0b02367ec3560009b34fb07376cd1bc57a894d31c9be03d7c43bb153 |
# -*- coding: utf-8 -*-
import sys
import numpy as np
from ase.optimize.optimize import Optimizer
from ase.utils.linesearch import LineSearch
class LBFGS(Optimizer):
"""Limited memory BFGS optimizer.
A limited memory version of the bfgs algorithm. Unlike the bfgs algorithm
used in bfgs.py, the inverse... | slabanja/ase | ase/optimize/lbfgs.py | Python | gpl-2.0 | 11,107 | [
"ASE"
] | f305cbed7b9cbd531915161f076fb49d08e5259bca8f1ef2f1e96b83317bdf19 |
#!/usr/bin/python
#----------------------------------------------------
# Program to convert VIC fluxes files to NetCDF file
# will ask the user wich variable he wants to export
# and also for wich years. Assumes there is data
# for the entire time period, from 1-jan to 31-dec
# SET UP FOR DAILY TIME STEP. FLUX FILE S... | yixinmao/VIC | tools/post_processing/flux2nc.py | Python | gpl-2.0 | 4,980 | [
"NetCDF"
] | 703cddb3580d0394f1413a325be85b23cc1db9cb8c792939e66036b93395bebf |
# -*- coding: utf-8 -*-
import codecs
import warnings
import re
from contextlib import contextmanager
from parso.normalizer import Normalizer, NormalizerConfig, Issue, Rule
from parso.python.tree import search_ancestor
from parso.python.tokenize import _get_token_collection
_BLOCK_STMTS = ('if_stmt', 'while_stmt', 'f... | sserrot/champion_relationships | venv/Lib/site-packages/parso/python/errors.py | Python | mit | 48,022 | [
"VisIt"
] | 122cdc20a7e5965ad31d854408521b8ae3859cd02511d40dd5e95705e2b9dad0 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
'''
**********************************************************
*
* SpectraLearnPredict - SKlearn Neural Networks
* Perform Machine Learning on Spectroscopy Data.
*
* Uses: Deep Neural Networks, TensorFlow, SVM, PCA, K-Means
*
* By: Nicola Ferralis <feranick@hotmail.com>
*
... | feranick/SpectralMachine | Archive/SpectraLearnPredict/SpectraLearnPredict/slp/slp_nn.py | Python | gpl-3.0 | 5,308 | [
"NEURON"
] | 04664b3c9b6b0d883c04fd0c5aceb5171488071dfe0e9a8b0dfbb42e2bf23353 |
# (c) 2014 Michael DeHaan, <michael@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, either version 3 of the License, or
# (at your option) any later ve... | onitake/ansible | lib/ansible/playbook/role/requirement.py | Python | gpl-3.0 | 6,765 | [
"Galaxy"
] | b96f79399731de110c804b51a34af0a21ec92c105b7202d16eddf804b2e2a086 |
'''Functions that implement the prior for the spline coefficients of
an isentrope for F_UNCLE
'''
import numpy as np
def k_g(
tau, # log of ratio of volumes
alpha, # Characteristic length of correlation
beta # log of fractional uncertainty
):
'''Kernel function in log-log coordinates i... | fraserphysics/F_UNCLE | F_UNCLE/Models/gram.py | Python | gpl-2.0 | 2,492 | [
"Gaussian"
] | 6d6abf7c8512e6bd6fc5be848536e6e2e61900c9aee4e9bc23eef3368a010607 |
"""
Functionality to read and write the Newick serialization format for trees.
.. seealso:: https://en.wikipedia.org/wiki/Newick_format
"""
import re
import pathlib
__version__ = "1.0.1.dev0"
RESERVED_PUNCTUATION = ':;,()'
COMMENT = re.compile(r'\[[^\]]*\]')
def length_parser(x):
return float(x or 0.0)
def l... | glottobank/python-newick | src/newick.py | Python | apache-2.0 | 16,032 | [
"VisIt"
] | 48e84cf1c5e857a8e7e0153ea3883404e4626d0366e85c23d95d67868140ff41 |
import click
import pysam
import gzip
import sys
from itertools import izip
@click.command()
@click.option('--baf', help='path for bamfile')
@click.option('--rf', help='path for readfile')
@click.option('--out', help='out file path directory')
def subsample(rf, baf, out):
readList = set([])
bam = pysam.Alig... | k3yavi/alevin | testing/src-py/subsampleExReadsByBam.py | Python | gpl-3.0 | 1,148 | [
"pysam"
] | 15874272a06134fe6dd046e555596159b8844f9a35439a6341fe421f5add7ca0 |
# Internal HTSeq functions, not part of the API
import HTSeq
import numpy
def GenomicInterval_range(gi, step):
for pos in range(gi.start, gi.end, step):
yield HTSeq.GenomicPosition(gi.chrom, pos, gi.strand)
def GenomicInterval_xranged(gi, step):
if gi.strand == "-":
step *= -1
for pos in... | simon-anders/htseq | python3/HTSeq/_HTSeq_internal.py | Python | gpl-3.0 | 1,504 | [
"HTSeq"
] | 55809a87c7dd9e0fd668b224ab0995e057004e1cb5e585ef8b0c655ebe89c2f3 |
# -*- coding: utf-8 -*-
from __future__ import division, print_function
import h5py
import six
import re
import collections
import copy
import numpy as np
import pint
u = pint.UnitRegistry()
# Probably easier to get a list of all the attrs, then parse appropriately.
def h5ls_str(g, offset='', print_types=False):
... | ryanpdwyer/hdf5plotter | hdf5plotter/_util.py | Python | mit | 5,826 | [
"VisIt"
] | 8e4f1f03788c2af1fa47764d144273aac5c59f7d072e81d178cab63c4356bbe1 |
from views import *
from lookups import *
import requests
import re
from utils import *
import itertools
from config import config
if config.IMPORT_PYSAM_PRIMER3:
import pysam
import csv
#hpo lookup
import random
from flask import Response, request
import os
from werkzeug.datastructures import Headers
import re
@a... | logust79/phenopolis | views/igv.py | Python | mit | 3,126 | [
"pysam"
] | be7ca93b5ad50426930d9a58c01371fbca98a3ef674e34e4768bb648dfa02061 |
# -*- coding: utf-8 -*-
'''
Copyright (c) 2015 by Tobias Houska
This file is part of Statistical Parameter Estimation Tool (SPOTPY).
:author: Tobias Houska
Holds functions to analyse results out of the database.
Note: This part of SPOTPY is in alpha status and not yet ready for production use.
'''
import numpy as n... | bees4ever/spotpy | spotpy/analyser.py | Python | mit | 37,517 | [
"Gaussian"
] | e8b8ad4c2f236d1308b94266901a34651b9c0deb13b456586db6cefac421531a |
"""
========================================
Special functions (:mod:`scipy.special`)
========================================
.. currentmodule:: scipy.special
Nearly all of the functions below are universal functions and follow
broadcasting and automatic array-looping rules.
.. seealso::
`scipy.special.cython_s... | pizzathief/scipy | scipy/special/__init__.py | Python | bsd-3-clause | 27,440 | [
"Gaussian"
] | 79e04dca320900f62213136481e2972e5189aa3fe0d77695761f5d6a1817470f |
# This code is part of Ansible, but is an independent component.
# This particular file snippet, and this file snippet only, is BSD licensed.
# Modules you write using this snippet, which is embedded dynamically by Ansible
# still belong to the author of the module, and may assign their own license
# to the complete wo... | nrwahl2/ansible | lib/ansible/module_utils/basic.py | Python | gpl-3.0 | 112,326 | [
"VisIt"
] | 1dc2ec95757abdc9c425efb69e51c4145cfebd9f5aea8abfc6f67d326341fac8 |
# -*- coding: utf-8 -*-
"""
Regression tests for the Test Client, especially the customized assertions.
"""
from __future__ import unicode_literals
import os
import itertools
from django.conf import settings
from django.core.urlresolvers import reverse, NoReverseMatch
from django.template import (TemplateSyntaxError,... | liavkoren/djangoDev | tests/test_client_regress/tests.py | Python | bsd-3-clause | 64,722 | [
"VisIt"
] | ae2da23a5c320e2a55b9705b0f866e5ba61b2b0c59456aff91f1d24b2dcc4ea8 |
"""
A simple VTK widget for PyQt or PySide.
See http://www.trolltech.com for Qt documentation,
http://www.riverbankcomputing.co.uk for PyQt, and
http://pyside.github.io for PySide.
This class is based on the vtkGenericRenderWindowInteractor and is
therefore fairly powerful. It should also play nicely with the
vtk3DWi... | sankhesh/VTK | Wrapping/Python/vtk/qt/QVTKRenderWindowInteractor.py | Python | bsd-3-clause | 18,051 | [
"CRYSTAL",
"VTK"
] | 64838acf55113263796a030717cc81ea5044d9c2dd2c39e8b9e11b279b038c66 |
""" Bokeh is a Python interactive visualization library that targets modern
web browsers for presentation.
Its goal is to provide elegant, concise construction of novel graphics in the
style of d3.js, but also deliver this capability with high-performance
interactivity over very large or streaming datasets. Bokeh can ... | Ziqi-Li/bknqgis | bokeh/bokeh/__init__.py | Python | gpl-2.0 | 2,025 | [
"VisIt"
] | ff7740c520bd1fbe9168292fa573c0a9a55fe6bbb95491d417d0c79053caecc2 |
"""Defines a set of test problems.
This module complements the More, Garbow and Hillstrom
problem set implemented in OTK++ and implements a Python
interface. Whereas OTK++ implements only evaluators for
these functions, this module also contains the following
definitions:
- symbolic expressions and expression ge... | tbs1980/otkpp | pyotk/pyotk/testproblems.py | Python | gpl-3.0 | 15,187 | [
"Gaussian"
] | 00e4888b7186e39d6799541db63e68a93746cf2f85adc7f4d2bb2da8bc8b10f7 |
"""
A set of functions for various types of fitting.
"""
import logging
import os
import glob
import json
from george import kernels
import FittingUtilities
from astropy import units as u, constants
from scipy.optimize import fmin, brute, minimize
from scipy.interpolate import InterpolatedUnivariateSpline as spline
f... | kgullikson88/General | Fitters.py | Python | gpl-3.0 | 88,851 | [
"Gaussian"
] | c15ab895ab8024d9bf47d6097f4ba162e9d63fbfab93f685207241933825a71f |
import numpy as np
def minmax(X, low, high, minX=None, maxX=None, dtype=np.float):
X = np.asarray(X)
if minX is None:
minX = np.min(X)
if maxX is None:
maxX = np.max(X)
# normalize to [0...1].
X -= float(minX)
X /= float((maxX - minX))
# scale to [low...high].
X = X... | idf/FaceReader | facerec_py/facerec/normalization.py | Python | mit | 1,416 | [
"Gaussian"
] | 8207329490b48de597f5cd5c86d6aecabc199d86209b440ceabbd795e5834742 |
from __future__ import division
import random
import math
import itertools
from collections import Counter,defaultdict
try:
from Bio import SeqIO
from Bio.Data.IUPACData import protein_letters as PROTEIN_ALPHABET
except ImportError:
raise ImportError("Failed to import necessary Biopython components. "\
... | romansloutsky/weightedSDP | wsdp.py | Python | mit | 2,131 | [
"Biopython"
] | ac4577fbde043dd9ed995c9ce50cfff0242fbed72103e17efac3b6f67381a9bf |
#!/usr/bin/python
# graph.py
# Graph algorithms for TSP Art
#
# Author: Tommy Tracy II
# Created: 11/2/2013
#
from math import *
from scipy.spatial import Delaunay
import numpy as np
VERBOSE = False
# ---------- Generate Graph from Nodes ---------- #
# Returns all of the edges (point_0, point_1, weight) in t... | tjt7a/TSart | graph.py | Python | gpl-2.0 | 13,771 | [
"VisIt"
] | fba46f5e686fb0164d187240a017987160e77959c9949e9a65421fc404e18bd7 |
# -*- coding: utf-8 -*-
"""
Fields for Discontinous Galerkin method
"""
import numpy as nm
import six
from numpy.lib.stride_tricks import as_strided
from six.moves import range
from sfepy.base.base import (output, assert_, Struct)
from sfepy.discrete import Integral, PolySpace
from sfepy.discrete.common.fields import ... | rc/sfepy | sfepy/discrete/dg/fields.py | Python | bsd-3-clause | 49,854 | [
"MCell"
] | bbc239f6feb451a5c8f9952af8a5ef4914b993741b9897962ffba5597fef0a70 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/bug_1117098 | openlp/core/lib/serviceitem.py | Python | gpl-2.0 | 24,844 | [
"Brian"
] | 1a2afe7b1db90eb65823bb77f1e6783a6076466ab1bcebeda0d72d7ac3908063 |
"""Fetches all the freely available WMT14 data
Visit: http://www.statmt.org/wmt14/translation-task.html"""
import os
import anna.data.utils as utils
CORPORA = {
"europarl-parallel.tgz":
"http://www.statmt.org/wmt13/training-parallel-europarl-v7.tgz",
"europarl-monolingual.tgz":
"http://www.s... | jpbottaro/anna | anna/data/dataset/wmt.py | Python | mit | 1,573 | [
"VisIt"
] | e212c9a469e3adc163f2f872a59c2802b0945fcbffb3df41328d54dacdde2448 |
r"""
.. warning:: This model and this model description are under review following
concerns raised by SasView users. If you need to use this model,
please email help@sasview.org for the latest situation. *The
SasView Developers. September 2018.*
Definition
----------
Calculates ... | SasView/sasmodels | sasmodels/models/bcc_paracrystal.py | Python | bsd-3-clause | 6,955 | [
"CRYSTAL",
"Gaussian"
] | 5ed97bdb0f9ee13ce004a751a803cfdcc2b6f696f137aecd238cd605cac86641 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the G... | fedepad/espressopp | src/analysis/AnalysisBase.py | Python | gpl-3.0 | 3,322 | [
"ESPResSo"
] | 5611299eadc4f40780ceb9870ab69c9d241aa268f5fb3cd5cc0bd88e12062b4e |
"""
=======================================
Signal processing (:mod:`scipy.signal`)
=======================================
Convolution
===========
.. autosummary::
:toctree: generated/
convolve -- N-dimensional convolution.
correlate -- N-dimensional correlation.
fftconvolve --... | gertingold/scipy | scipy/signal/__init__.py | Python | bsd-3-clause | 14,599 | [
"Gaussian"
] | 3b6b513e69412fd8e2cdf9825a05c7c798512bca61253e3895a98a78c154d054 |
from __future__ import print_function
import unittest as ut
import espressomd
import numpy as np
from espressomd.electrostatics import *
from espressomd import electrostatic_extensions
@ut.skipIf(not espressomd.has_features(["ELECTROSTATICS"]),
"Features not available, skipping test!")
class ELC_vs_MMM2D_n... | KonradBreitsprecher/espresso | testsuite/elc_vs_mmm2d_neutral.py | Python | gpl-3.0 | 4,613 | [
"ESPResSo"
] | e871c223284494a2438e451b6f68541219243198e5224660a46d6fd6974a7e33 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the LMS.
"""
from datetime import datetime, timedelta
from flaky import flaky
from textwrap import dedent
from unittest import skip
from nose.plugins.attrib import attr
import pytz
import urllib
from bok_choy.promise import EmptyPromise
from ..helpers import (
Uniqu... | waheedahmed/edx-platform | common/test/acceptance/tests/lms/test_lms.py | Python | agpl-3.0 | 53,038 | [
"VisIt"
] | bbffdf811884c5c30aaefbde19ef648e5ff2624e1843fa6b90c650739cfeeda2 |
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