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#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | MOA-2011/e2openplugin-OpenWebif | plugin/controllers/views/web/tvbrowser.py | Python | gpl-2.0 | 5,187 | [
"VisIt"
] | 7d64fb5cedbad31fa108ef84749cccf25f7c1dcf301ad3c2aaabfd7891ec00ce |
# Copyright (c) 2013 Mark Dickinson
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, dist... | bpsinc-native/src_third_party_chromite | third_party/digraph.py | Python | bsd-3-clause | 3,002 | [
"VisIt"
] | 948392c97de00df77682366cf21b99f5c66563e5b19a6deff81b8c2aac5f9335 |
# $Id$
#
# Copyright (c) 2007, Novartis Institutes for BioMedical Research Inc.
# 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... | soerendip42/rdkit | Projects/DbCLI/CreateDb.py | Python | bsd-3-clause | 20,854 | [
"RDKit"
] | e5e009378037e301bf9969678c028d16587c89a0675fb76d1e07b692da08d7e5 |
# Script to run a second derivative gaussian kernel on a grid
# Author : Isabel Restrepo
# 6-14-2009
import bvpl_batch
import time
#time.sleep(30);
bvpl_batch.register_processes();
bvpl_batch.register_datatypes();
class dbvalue:
def __init__(self, index, type):
self.id = index # unsigned integ... | mirestrepo/voxels-at-lems | bvpl/appearance_gauss3d_xx_batch.py | Python | bsd-2-clause | 3,514 | [
"Gaussian"
] | b731ddc6e619f63e12191fee08907837ff71cb4f14801e0c5ca6797a5dcae9db |
# -*- coding: utf-8 -*-
"""
jinja2.compiler
~~~~~~~~~~~~~~~
Compiles nodes into python code.
:copyright: (c) 2017 by the Jinja Team.
:license: BSD, see LICENSE for more details.
"""
from itertools import chain
from copy import deepcopy
from keyword import iskeyword as is_python_keyword
from functo... | facelessuser/sublime-markdown-popups | st3/mdpopups/jinja2/compiler.py | Python | mit | 65,351 | [
"VisIt"
] | 17ea9fe4c40e4e9750806ae8d87b811ce240b2ff805895ab9206bb2926ef6996 |
import pickle
import scipy.io
import numpy as np
import matplotlib.pyplot as plt
from scipy.integrate import simps
from sklearn.neighbors.kde import KernelDensity
from scipy.interpolate import griddata, RegularGridInterpolator, interp1d
from weather.scraper.flight_conditions import properties, Airframe
def expected_v... | leal26/AeroPy | examples/morphing/flight_conditions/expected_range_constant_aoa.py | Python | mit | 2,664 | [
"Gaussian"
] | 8012c51e2465c9c997fbb8d76b60f10af76f903b23850d9f60bf68233b489fd8 |
'''
(c) 2010-2011 Thomas Holder, MPI for Developmental Biology
Python parser for AAindex: Amino Acid Index Database
http://www.genome.jp/aaindex/
PyMOL commands:
aaindex2b
pmf
'''
from __future__ import print_function
import sys, os
_aaindex = dict()
_pymol_auto_arg_update = lambda: None
def search(... | weitzner/Dotfiles | pymol_scripts/aaindex.py | Python | mit | 13,956 | [
"ChemPy",
"PyMOL"
] | 468fe548a758018d586503fcb9dd345574ef8723ce97bd10ab2ce86a7653a2eb |
#------------------------------------------------------------------------------
# Copyright (c) 2005, Enthought, Inc.
# All rights reserved.
#
# This software is provided without warranty under the terms of the BSD
# license included in enthought/LICENSE.txt and may be redistributed only
# under the conditions describe... | dmsurti/mayavi | tvtk/pyface/picker.py | Python | bsd-3-clause | 16,816 | [
"VTK"
] | e9d37766a39891fcc25eb5a02993f549a7977b2277982c360c6a868516b3ad50 |
import os
from ase.units import Hartree
from gpaw.lrtddft import LrTDDFT
from gpaw.lrtddft.spectrum import spectrum, rotatory_spectrum
def check_convergence(lr, # LrTDDFT object
dirname='conv', # directory name to store the files
title=None, # title for gnu... | robwarm/gpaw-symm | gpaw/lrtddft/convergence.py | Python | gpl-3.0 | 5,244 | [
"ASE",
"GPAW"
] | 4d032821ff8e015778f453e9e38d76632309f56be701acbd92a71f256f1ed3df |
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Matti Hämäläinen <msh@nmr.mgh.harvard.edu>
# Denis A. Engemann <denis.engemann@gmail.com>
#
# License: BSD (3-clause)
from copy import deepcopy
from distutils.version import LooseVersion
import itertools as itt
from math import log
import ... | cjayb/mne-python | mne/cov.py | Python | bsd-3-clause | 79,004 | [
"Gaussian"
] | 013ccfb1f48f96f56ce672fa21479b6ba98d850d1d8a2c9ee94cc57c4cb294f6 |
"""Martel expression for the hmmpfam database search program in hmmer.
This has been tested with version 2.2g. I should also make it work with
2.1.1 output.
XXX This isn't completely finished and doesn't do everything quite right.
The main two problems being that it isn't well tested for a wide variety of
outputs and... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/expressions/hmmpfam.py | Python | apache-2.0 | 9,388 | [
"Biopython"
] | 7c23761eb6259a5a15307468ea12b8ea359ce433ff7d902b5c64c056fdb53aa9 |
#!/usr/bin/env python
import __future__
import gtk
import os
import numpy as np
import sys
from ase.gui.languages import translate as _
from ase.gui.widgets import pack, Help
class Execute(gtk.Window):
""" The Execute class provides an expert-user window for modification
and evaluation of system properties wi... | slabanja/ase | ase/gui/execute.py | Python | gpl-2.0 | 9,029 | [
"ASE"
] | ee0b2a3e938d236f841863c6823331cf33372e3d10b66087a2a1194d1d8ec3f1 |
# unit tests for python synapse client
############################################################
from datetime import datetime as Datetime
from math import pi
import time
import uuid
import pytest
from unittest.mock import patch
from synapseclient import annotations
from synapseclient.annotations import (
Ann... | thomasyu888/synapsePythonClient | tests/unit/synapseclient/unit_test_annotations.py | Python | apache-2.0 | 15,840 | [
"MOOSE"
] | b4c33df65df73520e69d90e0f79c78c7a9ee6ce6c87ab17371a13edbbdfe2de0 |
# -*- coding: utf-8 -*-
from django.shortcuts import render
from django.http import HttpResponseRedirect, HttpResponse, Http404
from django.template import RequestContext
from django.contrib import messages
from django.shortcuts import render_to_response, get_object_or_404
from django.contrib.auth.decorators import lo... | entpy/beauty-and-pics | beauty_and_pics/website/views.py | Python | mit | 57,493 | [
"VisIt"
] | 48566c7639c216359f6d2efa0a89b12ac186c2845dab2d3baf3f6ca24d9ccb53 |
# Copyright (c) 2012, Cloudscaling
# All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable... | cloudbase/nova-virtualbox | nova/hacking/checks.py | Python | apache-2.0 | 21,658 | [
"VisIt"
] | 523ba539f683a5c122ba9f641954ad1c1a16c50055c15a0fed79e7daeb333c8e |
# 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)
class PyTorchGeometric(PythonPackage):
"""PyTorch Geometric (PyG) is a geometric deep learning extension
library ... | LLNL/spack | var/spack/repos/builtin/packages/py-torch-geometric/package.py | Python | lgpl-2.1 | 3,350 | [
"ASE"
] | 33372a8d1ab22edf119d3b9c4655514e3931cb4ac18278866a7943680e7d75b3 |
import glob
import mixtape.featurizer, mixtape.tica, mixtape.cluster, mixtape.markovstatemodel
import numpy as np
import mdtraj as md
from mixtape import ghmm, feature_selection, subset_featurizer
import sklearn.pipeline, sklearn.externals.joblib
import mixtape.utils
n_iter = 1000
n_rounds = 100
n_choose = 50
stride =... | kyleabeauchamp/PMTStuff | code/optimize.py | Python | gpl-2.0 | 1,227 | [
"MDTraj"
] | 882a41966fed22fd807761179adc7d52da12240e57320b4f944c96c7be3d5558 |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
#
# Copyright 2021 The NiPreps Developers <nipreps@gmail.com>
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may... | poldracklab/mriqc | mriqc/config.py | Python | bsd-3-clause | 19,461 | [
"VisIt"
] | 010f252f1647ce95f5c11a71d92a1e6c96de49a2ae1b476995f36dc9ef1b6f30 |
"""Langevin dynamics class."""
import sys
import numpy as np
from numpy.random import standard_normal
from ase.md.md import MolecularDynamics
from ase.parallel import world
class Langevin(MolecularDynamics):
"""Langevin (constant N, V, T) molecular dynamics.
Usage: Langevin(atoms, dt, temperature, friction... | grhawk/ASE | tools/ase/md/langevin.py | Python | gpl-2.0 | 4,378 | [
"ASE"
] | a8e835cd5a5aacaff95dd010ccb28030bb002388d9f7278834148bb3f08362a1 |
#!/usr/bin/env python3
#* 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/licenses/lgp... | harterj/moose | python/mooseutils/tests/test_yaml_load.py | Python | lgpl-2.1 | 3,207 | [
"MOOSE"
] | b6fa9cbe16d1e9356efa0d366d103e8c731dfa6c250305e8cd671fd71063a28e |
# Jython Database Specification API 2.0
#
# $Id: runner.py 2094 2002-05-09 01:03:37Z bzimmer $
#
# Copyright (c) 2001 brian zimmer <bzimmer@ziclix.com>
"""
To run the tests, simply invoke this script from the commandline:
jython runner.py <xml config file> [vendor, ...]
If no vendors are given, then al... | DarioGT/OMS-PluginXML | org.modelsphere.sms/lib/jython-2.2.1/Lib/test/zxjdbc/runner.py | Python | gpl-3.0 | 5,434 | [
"Brian"
] | 83fee9f1caf09e9d0c7a378e9a7a6aa39847b7f8199ec88dc00abc918fbf52b9 |
# Copyright 2009-2016 by Peter Cock. All rights reserved.
# Based on code contributed and copyright 2009 by Jose Blanca (COMAV-UPV).
#
# 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.SeqIO sup... | zjuchenyuan/BioWeb | Lib/Bio/SeqIO/SffIO.py | Python | mit | 62,493 | [
"Biopython"
] | bd0435ff7a28f8efc212b80990be746051a95d69bf03574de13f31c6e054e2d8 |
#
# Post-processing script QE --> EPW
# 14/07/2015 - Samuel Ponce
#
from builtins import input
import numpy as np
import os
# Enter the number of irr. q-points
prefix = input('Enter the prefix used for PH calculations (e.g. diam)\n')
# Enter the number of irr. q-points
nqpt = input('Enter the number of irreducible q... | QEF/q-e_schrodinger | EPW/examples/sic/phonons/pp.py | Python | gpl-2.0 | 899 | [
"EPW"
] | 5aef3d150ed78ac12f3e1c1632cfa57e73c4f5696e7457148e237b6bcb88c3d6 |
# -*- coding: utf-8 -*-
"""
Output Plugin for MusePack encoder
Copyright (c) 2006-2008 by Nyaochi
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 you... | rinrinne/cueproc-alternative | src/ce_mpc.py | Python | gpl-2.0 | 2,414 | [
"VisIt"
] | 04002ee530b65fce923b8667ea503fddd251d7137d35c8519e73eab58539c28f |
"""
Tests a variety of potentially problematic disulfides. Disulfides between
two same resids on different chains, disulfides on the same chain, and
unrelated disulfides on different chains.
Also tests how chains are handled when Maestro puts a capping group
with resid -1 on them
"""
import os
from vmd import molecul... | Eigenstate/dabble | dabble/test/relaxin/test_relaxin.py | Python | gpl-2.0 | 2,430 | [
"Amber",
"CHARMM",
"VMD"
] | 893c999f8ed4ec57c67e05bb47e8255e097e1b20b670e7837153dd3c708c6e7b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Módulo interfaz con Brutefir, usado por el módulo presets.py,
también funciona en línea de comandos.
Se lee brutefir_config y se conecta con el proceso brutefir.
Se proporcionan CUATRO listas:
outputsMap: lista de salidas y su correspondiente puer... | AudioHumLab/FIRtro | bin/read_brutefir_process.py | Python | gpl-3.0 | 8,369 | [
"DIRAC"
] | 9c112e2aef5aa3573070ff67691f9249f5d63aa4185ae2b60db439afa8cae7fd |
import os
import unittest
import pymatgen
from pymatgen.apps.battery.analyzer import BatteryAnalyzer
from pymatgen.core.structure import Structure
from pymatgen.util.testing import PymatgenTest
module_dir = os.path.join(os.path.dirname(pymatgen.__file__), "..", "test_files")
class BatteryAnalyzerTest(PymatgenTest):... | davidwaroquiers/pymatgen | pymatgen/apps/battery/tests/test_analyzer.py | Python | mit | 4,075 | [
"pymatgen"
] | 8625313fdb3cf8fb76e7d7037cee21cecf35e95d3ea29193ae2669a614993a9f |
########################################################################## #
# This file is part of OCEMR.
#
# OCEMR 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,... | ph1l/ocemr | ocemr/urls.py | Python | gpl-3.0 | 10,187 | [
"VisIt"
] | 57fdc164dd0a9f5fc4770fc326fb7ab8af90738df7bfea0429e756c33af97ec5 |
#!/usr/bin/env python
"""CSP Commstime benchmark.
See F.R.M. Barnes (2006) Compiling CSP. In Proceedings of
Communicating Process Architectures 2006.
Code adapted from PyCSP by John Markus Bjorndalen, available:
http://www.cs.uit.no/~johnm/code/PyCSP/
PyCSP - Communicating Sequential Processes for Python. John Mark... | futurecore/python-csp | csp/cchannels/tests/commstime.py | Python | gpl-2.0 | 1,797 | [
"Brian"
] | 94644ce7187a0e3b59c51a5b908fbcdc5869a2419ae293597249a4d5998a3a0e |
########################################################################
# File: StorageElementProxyHandler.py
########################################################################
"""
:mod: StorageElementProxyHandler
.. module: StorageElementProxyHandler
:synopsis: This is a service which represents a DISET p... | coberger/DIRAC | DataManagementSystem/Service/StorageElementProxyHandler.py | Python | gpl-3.0 | 11,964 | [
"DIRAC"
] | bb9fbf2255307b5e07021127e243cc33a11296de3e76672f822ebbe28301a69c |
# -*- coding: utf-8 -*-
##
## This file is part of Harvesting Kit.
## Copyright (C) 2013, 2014 CERN.
##
## Harvesting Kit 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, o... | kaplun/harvesting-kit | harvestingkit/contrast_out.py | Python | gpl-2.0 | 15,340 | [
"VisIt"
] | 5c4c63b733b5ef25919a691e73cdce475d0864db909f39c03d52903d2d09360f |
import os
import sys
import datetime
import math
import tinctest
import re
import shutil
from time import gmtime, strftime, sleep
import unittest2 as unittest
from fnmatch import fnmatch
from tinctest.runner import TINCTextTestResult
from tinctest.lib import run_shell_command, Gpdiff
from mpp.models import SQLTestCas... | cjcjameson/gpdb | src/test/tinc/tincrepo/query/indexapply/__init__.py | Python | apache-2.0 | 11,199 | [
"ORCA"
] | d3be0887a37f9d0d82af653c8ea8fb92aef82397c4d9424ce28915fb53b0b159 |
"""
Generate AST node definitions from an ASDL description.
"""
import sys
import os
import asdl
class ASDLVisitor(asdl.VisitorBase):
def __init__(self, stream, data):
super(ASDLVisitor, self).__init__()
self.stream = stream
self.data = data
def visitModule(self, mod, *args):
... | alvin319/CarnotKE | jyhton/ast/asdl_py.py | Python | apache-2.0 | 25,123 | [
"VisIt"
] | d0b05e84ef6c2fe4ef6a2869b15b77db84916331e3fd9ea3c6fed00b10e4850d |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License
"""
This module implements reading and writing of ShengBTE CONTROL files.
"""
import warnings
from typing import Any, Dict, List, Optional, Union
import numpy as np
from monty.dev import requires
from monty.js... | gmatteo/pymatgen | pymatgen/io/shengbte.py | Python | mit | 9,230 | [
"CRYSTAL",
"ESPResSo",
"VASP",
"pymatgen"
] | b302055a706e0245e976d353923e70ba172a8eb4b238234d2c75ac6aa93e91cf |
#!/usr/bin/python
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
#
ANSIB... | noroutine/ansible | lib/ansible/modules/network/avi/avi_scheduler.py | Python | gpl-3.0 | 5,238 | [
"VisIt"
] | 25fd4e114df6d45da5f0ee2f110039366f260d5cbc49edb889f2b34d5cb1abc5 |
#!/usr/local/bin/env python
#=============================================================================================
# MODULE DOCSTRING
#=============================================================================================
"""
Yank
====
Interface for automated free energy calculations.
"""
#=========... | sonyahanson/yank | Yank/yank.py | Python | lgpl-3.0 | 24,235 | [
"NetCDF",
"OpenMM"
] | c2a61514b86ab19b82f0bbf1e83521d6df4bf4aad1efdfee13ac384c633dd710 |
# (c) 2015, 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 published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | ravello/ansible | v2/ansible/plugins/action/patch.py | Python | gpl-3.0 | 2,389 | [
"Brian"
] | 0c2dd2a29c7bca72e323d32874725870e4b4bd52013d27c3f2f48fa8ebf75ab1 |
# Kevin van Rensburg 6/11/2021
# Copyright 2001
# Testing Startup Script version 0.13
# kstart13.py
# Creating new def Kvep1()-Kvep10()- Episodes for game and clean up all related def's
# updated the following def's : Adventure(), Continue()
# Adding script and lines to Kvep1-10, Adventure()
# Completed Kvep6 and worki... | kurg/KendyVerse | kstart13.py | Python | gpl-3.0 | 58,911 | [
"BLAST"
] | 5a9b49ef460c1f6bfc2b69392f666eab111ab12f226ec51789824a8190cee2ff |
import os #used to work on an entire directory of xml files
import datetime
currentOCA = ""
seeChargesTrue = False #some forms put the OCA number in the charges section for some reason
logfile = None
def getFileLinesList(filepath):
"""Simple function that takes a filepath to one of the converted .xml file... | OpenData-NC/PoliceReportScraper | odnc_police/xmlScraper.py | Python | bsd-2-clause | 62,648 | [
"MOE"
] | dc52883ab43453ea9015f747d7a8eccd4b7ed960b63edbafc2fa9c58e88c276c |
"""
Module simplifying manipulation of XML described at
http://libvirt.org/formatdomain.html
"""
import logging
import platform
import re
from .. import xml_utils
from .. import utils_misc
from ..libvirt_xml import base, accessors, xcepts
from ..libvirt_xml.devices import librarian
LOG = logging.getLogger('avocado.'... | avocado-framework/avocado-vt | virttest/libvirt_xml/vm_xml.py | Python | gpl-2.0 | 159,021 | [
"VisIt"
] | b87087d7dda7ce912d73c89a240672c219aaaacf603c8ded8bbb5a63f86e6cac |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
urlpat... | ylitormatech/terapialaskutus | config/urls.py | Python | bsd-3-clause | 1,837 | [
"VisIt"
] | c31da87c936b1633b2d334b6728477f5521032f74806f868f301f3259804f800 |
# -*- coding: utf-8 -*-
from urlreplacer import emails
from urlreplacer.tlds import TLDs
def test_different_marker_func():
assert emails(
'test@example.com',
lambda a, b: u'<{}|{}>'.format(a, b)
) == '<mailto:test@example.com|test@example.com>'
assert emails(
'mailto:test@example... | tictail/urlreplacer | tests/test_emails.py | Python | mit | 2,002 | [
"ADF"
] | cdd938e830ed4865e356b65e66d62fdcbb739c016149b2c593c54f9eba5e9de0 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
## Copyright 2015 Rasmus Scholer Sorensen, rasmusscholer@gmail.com
##
## This program is free software: you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundation, either version ... | scholer/nascent | bin/simulator_tests.py | Python | agpl-3.0 | 23,933 | [
"Cytoscape"
] | 4e87473961fdff487bb1a9d09ae5d13ac11aa6f970475ea4987fe8ed29a3b718 |
# 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 writing, software
# distributed under t... | aforalee/RRally | tests/hacking/checks.py | Python | apache-2.0 | 16,059 | [
"VisIt"
] | bf61abbd1482187dc337432edc74829c17a81d77096474b80df6e81a17811e2a |
__author__ = 'tylin'
__version__ = '2.0'
# Interface for accessing the Microsoft COCO dataset.
# Microsoft COCO is a large image dataset designed for object detection,
# segmentation, and caption generation. pycocotools is a Python API that
# assists in loading, parsing and visualizing the annotations in COCO.
# Pleas... | ptrendx/mxnet | example/ssd/dataset/pycocotools/coco.py | Python | apache-2.0 | 17,747 | [
"VisIt"
] | dd05e0c3bb21b344b32624bfd6be8fd9da6d07c04310ea5f49b1ffc9211d05b1 |
"""K-means clustering"""
# Authors: Gael Varoquaux <gael.varoquaux@normalesup.org>
# Thomas Rueckstiess <ruecksti@in.tum.de>
# James Bergstra <james.bergstra@umontreal.ca>
# Jan Schlueter <scikit-learn@jan-schlueter.de>
# Nelle Varoquaux
# Peter Prettenhofer <peter.prettenh... | RPGOne/scikit-learn | sklearn/cluster/k_means_.py | Python | bsd-3-clause | 59,475 | [
"Gaussian"
] | a79d0d069f9a8891900496b891f939bbb6f192066c04891b413a48889de26925 |
"""
Extract biologically relevant states from alanine dipeptide data.
"""
import seaborn as sns
import pandas as pd
from msmbuilder import example_datasets, cluster, msm, featurizer, lumping
from sklearn.pipeline import make_pipeline
sns.set(style="white")
# Load an example dataset from the cloud
dataset = example_da... | kyleabeauchamp/TechDemo | src/msm_analysis.py | Python | gpl-2.0 | 1,907 | [
"MDTraj"
] | f7e51d4e48576a94fc46fad3cdd5efb33f9386fc1ee4ffd50a45717e3f5fb585 |
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publi... | thica/ORCA-Remote | src/ORCA/widgets/core/TouchImage.py | Python | gpl-3.0 | 1,293 | [
"ORCA"
] | c37e3413d1cc44d92682e208fd57188f856369d97caab65dec4d21f0b0f7ef77 |
from rdkit.Chem.Descriptors import MolWt, ExactMolWt
from ._base import Descriptor
__all__ = ("Weight",)
class Weight(Descriptor):
r"""molecular weight descriptor.
:type averaged: bool
:param averaged: averaged by number of atom
"""
def description(self):
return "{}{}molecular weight".... | mordred-descriptor/mordred | mordred/Weight.py | Python | bsd-3-clause | 1,141 | [
"RDKit"
] | f4d9a3e90772f34f3d64945cfaad786b458801b2faca0403274f2b9e4749d4aa |
"""
Parse a genbank entry that we download from NCBI or a file that is on our hard drive.
This example uses BioPython
"""
import os
import sys
from Bio import Entrez, SeqIO
import re
import argparse
if __name__ == '__main__':
parser = argparse.ArgumentParser(description="Parse a GenBank record from NCBI or a loc... | linsalrob/EdwardsLab | ncbi/parse_genbank.py | Python | mit | 3,660 | [
"Biopython"
] | 54d5ba250a041279cee7199ee6647331db958a984b962753d3e6a831d6f09fdd |
"""
NetCDF reader/writer module.
This module is used to read and create NetCDF files. NetCDF files are
accessed through the `netcdf_file` object. Data written to and from NetCDF
files are contained in `netcdf_variable` objects. Attributes are given
as member variables of the `netcdf_file` and `netcdf_variable` objects... | ogrisel/scipy | scipy/io/netcdf.py | Python | bsd-3-clause | 31,228 | [
"NetCDF"
] | 8ad48165fd5faebf0ef68f3fd7be3b2cf06e3e960d611d395d41821b36e0b335 |
import vtk
# create a rendering window and renderer
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
# create a renderwindowinteractor
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
# create source
source = vtk.vtkDiskSource()
source.SetInnerRadius(1)
source.SetOute... | Nefarin/SODM | tests/conf/vtkTest.py | Python | gpl-2.0 | 689 | [
"VTK"
] | fdf9a56d57e97a3a20049f3aadf722ba718634fab10f9ac2c550515eccc9461f |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | theflofly/tensorflow | tensorflow/contrib/gan/python/eval/python/classifier_metrics_impl.py | Python | apache-2.0 | 45,015 | [
"Gaussian"
] | ce2aa2cfc7ca778e217e8bbe02e0d2fe9b55c1409c697c5b9807d804c1a0ccd9 |
from neuron import Neuron
# The Layer class
#################
class Layer(object):
def __init__(self,neuron_number,weight_number):
self.neuron_number = neuron_number # number of neurons
self.weight_number = weight_number # number of weights
self.randomize()
# randomize all ... | gsideris/genetic-train-neural | neural/layer.py | Python | apache-2.0 | 1,277 | [
"NEURON"
] | 024e8e84cffe62dc295f1d6c069400d0792f4f1fb942025fbc3d4f3d23565d1d |
import logging
from datetime import datetime
import couchdb
from couchdb.client import ResourceConflict
from couchdb.schema import Document, Schema, BooleanField, DateTimeField, \
IntegerField, TextField, DictField, ListField, View
from gearshift import config
from gearshift.util import loa... | dbrattli/python-gearshift | gearshift/visit/cdvisit.py | Python | mit | 2,639 | [
"VisIt"
] | 502cb4e28eb5148904d058db1660a7ca933061357dc533a2ed30efc8d9129ff7 |
"""Given a FASTQ (or BAM) and a long-qnames file trancate the qnames to
whatever length we want and push the too-long qnames to the overflow
file. Also convert any old style qnames (not ending in a *) to new style
ones with a proper termination character"""
import time
import logging
import pysam
from mitty.benchmark... | sbg/Mitty | mitty/empirical/qnametruncate.py | Python | apache-2.0 | 2,210 | [
"pysam"
] | 469576efd68e0197fe310ea1451a0553d5c40dca1339d25b95791c039faf7c98 |
from flask.ext.login import UserMixin
from werkzeug import generate_password_hash, check_password_hash
from octopus.core import app
from service import dao
from octopus.lib import dataobj
class Account(dataobj.DataObj, dao.AccountDAO, UserMixin):
'''
{
"id" : "<unique persistent account id>",
... | JiscPER/jper | service/models/account.py | Python | apache-2.0 | 7,386 | [
"Octopus"
] | 56b9567b3bce86a0441abb55ac2e68be829c19511420254445c56eab6d2275ac |
# -*- coding: utf-8 -*-
from __future__ import division, print_function
__all__ = ["BasicSolver"]
import numpy as np
from scipy.linalg import cholesky, cho_solve
class BasicSolver(object):
"""
This is the most basic solver built using :func:`scipy.linalg.cholesky`.
kernel (george.kernels.Kernel): A su... | dfm/george | george/solvers/basic.py | Python | mit | 3,421 | [
"Gaussian"
] | e9e4b7c3be6d0b484269fee692ded233bbf5ea8ccbdccea3ef255cc9cf24dd71 |
import os.path
import unittest
import shutil
from subprocess import check_output, check_call
from tempfile import NamedTemporaryFile
import pysam
from bam_crumbs.utils.test import TEST_DATA_DIR
from bam_crumbs.utils.bin import BIN_DIR
from bam_crumbs.bam_tools import (filter_bam, calmd_bam, realign_bam,
... | pziarsolo/bam_crumbs | test/test_bam_tools.py | Python | gpl-3.0 | 5,387 | [
"pysam"
] | f7ec8a671193fe456fcfdd8514e25d0fff5df655349bcae2a99b09acd2d6f2a5 |
"""
Basic molecular features.
"""
from __future__ import division
from __future__ import unicode_literals
__author__ = "Steven Kearnes"
__copyright__ = "Copyright 2014, Stanford University"
__license__ = "MIT"
from rdkit.Chem import Descriptors
from deepchem.feat import Featurizer
class MolecularWeight(Featurizer):... | Agent007/deepchem | deepchem/feat/basic.py | Python | mit | 3,268 | [
"RDKit"
] | 5132f3d928b72790e397c091ea349dbee4da911ee6425658690706908ea62c1f |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | corburn/scikit-bio | skbio/io/format/tests/test_blast6.py | Python | bsd-3-clause | 6,321 | [
"scikit-bio"
] | 8ac8d5cd2a4a6f9d761f921b43310c082a69f96eb05fd5e5602945be3a813af2 |
"""Support for Ecobee Thermostats."""
import collections
from typing import Optional
import voluptuous as vol
from homeassistant.components.climate import ClimateEntity
from homeassistant.components.climate.const import (
ATTR_TARGET_TEMP_HIGH,
ATTR_TARGET_TEMP_LOW,
CURRENT_HVAC_COOL,
CURRENT_HVAC_DRY... | partofthething/home-assistant | homeassistant/components/ecobee/climate.py | Python | apache-2.0 | 27,928 | [
"VisIt"
] | 38c1f778dab6812e8b1505323271aa06a0db80d43829631173718472064a3545 |
try:
from rdkit.ML.FeatureSelect import CMIM
except ImportError:
CMIM = None
from rdkit import DataStructs as DS
from rdkit import RDConfig
import unittest
class TestCase(unittest.TestCase):
def setUp(self) :
pass
def test0FromList(self) :
if CMIM is None:
return
examples = []
b... | rdkit/rdkit-orig | rdkit/ML/FeatureSelect/UnitTestCMIM.py | Python | bsd-3-clause | 1,087 | [
"RDKit"
] | 9153afa2dc16911ee4e1621f3dee72389ef966baa6ca1ea7953608a230415a27 |
# Copyright 2014 Cloudera Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, so... | mahantheshhv/ibis | ibis/expr/format.py | Python | apache-2.0 | 8,433 | [
"VisIt"
] | 648c7dea5e8751e571830a1db3bf7b64f40c9f1c3a4dbc90b885536d5e27eec8 |
#!/usr/bin/python
#
# Find 4 sided polygons from a kinect
#
# Copyright (C) 2012 Mike Stitt
#
# Permission is hereby granted, free of charge, to any person obtaining a copy of
# this software and associated documentation files (the "Software"), to deal in
# the Software without restriction, including without limitatio... | MikeStitt/simple-object-tracker | test_kinect.py | Python | mit | 12,728 | [
"Gaussian"
] | f43a17f4e2ea7752facdbfd5623b6d42da8bfd6558a3b0aee98eb8e0dff8de06 |
# Copyright 2015 Curtis Sand
#
# 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 writing, ... | fretboardfreak/space | tests/lib/model/test_query.py | Python | apache-2.0 | 2,789 | [
"Galaxy"
] | d18126f6fff94b7a2a9b694cf415aa9a3cfd59a4636476de80acde4610880e26 |
# encoding: utf-8
"""
Adf.ly shortener implementation
Needs api key and uid
"""
from ..exceptions import ShorteningErrorException
from .base import BaseShortener
class AdflyShortener(BaseShortener):
api_url = 'http://api.adf.ly/api.php'
def __init__(self, **kwargs):
if not all([kwargs.get('key', Fals... | YarnSeemannsgarn/pyshorteners | pyshorteners/shorteners/adfly.py | Python | mit | 1,083 | [
"ADF"
] | dd02825eebf8f29fdd78e106b2c6c33c093520ae9b46033f8cd2fbe13c349042 |
from unittest import TestCase
import numpy as np
import scipy.signal as sps
from pylinac.core import image
from pylinac.core.image_generator.simulators import Simulator
from pylinac.core.profile import SingleProfile, MultiProfile, CircleProfile, CollapsedCircleProfile, Normalization, \
Interpolation
from tests_ba... | jrkerns/pylinac | tests_basic/core/test_profile.py | Python | mit | 8,435 | [
"Gaussian"
] | 55407e99980aa1312a6e378e4578cb3df6769274c0e8d8782caab600d9f06f1e |
#!/usr/bin/python
from datetime import date,datetime
import sqlalchemy
import json
import pprint
import uuid
import logging
import os
import utils
from config import ComicStreamerConfig
from comicstreamerlib.folders import AppFolders
from sqlalchemy.orm import scoped_session
from sqlalchemy.orm import sessionmaker... | davide-romanini/ComicStreamer | comicstreamerlib/database.py | Python | apache-2.0 | 16,523 | [
"VisIt"
] | 21a52cc2f06e4c9ef80cdd689074189ce1dff28a4aa69805f45c033438e11002 |
"""
=====================================================
Community analysis of metgenomic shotgun sequencing
=====================================================
Pipeline_metagenomecommunities.py takes as input a set of fastq
files from a shotgun sequencing experiment of environmental samples
and assesses community... | CGATOxford/CGATPipelines | obsolete/pipeline_metagenomecommunities.py | Python | mit | 81,942 | [
"BLAST",
"Bioconductor",
"Gaussian"
] | 06e9f549907c5719b37d4ff0ce3b5cfd3cc8ef685b75eeb773f998fc7dc1f738 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Low-level objects providing an abstraction for the objects involved in the calculation.
"""
from __future__ import unicode_literals, division, print_function
import collections
import abc
import six
import ... | gpetretto/pymatgen | pymatgen/io/abinit/abiobjects.py | Python | mit | 50,583 | [
"ABINIT",
"CRYSTAL",
"Gaussian",
"pymatgen"
] | 45816e06c5c282122888adcb1002e516fcbd571899fc2f1db0b7c4277856e030 |
#!/usr/bin/env python
###############################################################################
# #
# This program is free software: you can redistribute it and/or modify #
# it under the terms of the GNU General Public License... | dparks1134/CommunityM | deprecated/mapReadsToGreenGenes.py | Python | gpl-3.0 | 3,552 | [
"BWA"
] | 227abd155092b7d4c54f0d8b3ef17fea519565e9fb0ac40c7746fe83d605b9d2 |
import lxml.etree
from calmjs.parse.parsers.es5 import Parser
from .jsonlike import *
from .xmlvisitor import XmlVisitor
__version__ = "0.4.0"
_parser = Parser()
_visitor = XmlVisitor()
def parse(text, encoding="utf8", debug=False):
if not isinstance(text, str):
text = text.decode(encoding)
tree =... | redapple/js2xml | js2xml/__init__.py | Python | mit | 502 | [
"VisIt"
] | 1b6c3d097331018fc6d852ba0cd71121399b783a6aa50c1df8bb1c77aa3f04d1 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# .. py:currentmodule:: dolfin_adjoint
#
# Mathematical Programs with Equilibrium Constraints
# ==================================================
#
# .. sectionauthor:: Simon W. Funke <simon@simula.no>
#
# This demo solves example 5.2 of :cite:`hintermueller2011`.
#
# Pro... | live-clones/dolfin-adjoint | examples/mpec/mpec.py | Python | lgpl-3.0 | 10,606 | [
"ParaView"
] | 31d70cdc047e22082aed7b34a13861356788036ff6f3d5560d9ea62ac827092e |
"""
Helps to implement authentication and authorization using Auth0.
Offers functions for generating the view functions needed to implement Auth0,
a login screen, callback maker, and a function decorator for protecting
endpoints.
"""
import flask
import requests
import functools
import json
import jwt
import ga4gh.s... | saupchurch/server | ga4gh/server/auth/__init__.py | Python | apache-2.0 | 11,539 | [
"VisIt"
] | 23dcb53406d53010118d9e633ea9054a25a32bc5dcf72fffa72d4b594cce584f |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkExtractTensorComponents(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | nagyistoce/devide | modules/vtk_basic/vtkExtractTensorComponents.py | Python | bsd-3-clause | 505 | [
"VTK"
] | f45d588033a2998eb85d1e1590353577148f112147f6ef9a5f6576588a082ac2 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2012 Radim Rehurek <radimrehurek@seznam.cz>
# Copyright (C) 2017 Mohit Rathore <mrmohitrathoremr@gmail.com>
# Licensed under the GNU LGPL v2.1 - http://www.gnu.org/licenses/lgpl.html
"""This module implements functionality related to the `Term Frequency -... | napsternxg/gensim | gensim/models/tfidfmodel.py | Python | gpl-3.0 | 21,861 | [
"VisIt"
] | cd2b54e6826eaac84535e6f00a5744b69b402d123d22ed26c5f7af56d28e4475 |
# -*- coding: utf-8 -*-
"""
functions.py - Miscellaneous functions with no other home
Copyright 2010 Luke Campagnola
Distributed under MIT/X11 license. See license.txt for more infomation.
"""
from __future__ import division
from .python2_3 import asUnicode
from .Qt import QtGui, QtCore, USE_PYSIDE
Colors = {
'b... | Rareson/LammpsRelated | pyqtgraph/functions.py | Python | gpl-3.0 | 83,247 | [
"Gaussian"
] | fc11c159414e2debb4bb0496f9f944532170935fca2c2ad4ab1fa21c646c2e61 |
#!/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/lib/linalg_helper.py | Python | apache-2.0 | 65,487 | [
"PySCF"
] | 55d504b3a119b83591d953cdac5f00f5933bc5e291741ea33c08f37324da9a83 |
# Copyright (c) Charl P. Botha, TU Delft
# All rights reserved.
# See COPYRIGHT for details.
# FIXME: def show() should really be moved a level up!!
# left click on glyph: select and drag
# left click on canvas: rubberband select
# right click on glyph: glyph context menu
# right click on canvas: canvas context menu
... | chrisidefix/devide | interfaces/wx_interface/graph_editor.py | Python | bsd-3-clause | 116,718 | [
"VTK"
] | ad7c2683d6b012bfd5297a9beb450a0c71639ee9698bee0fd62423b6d736ada7 |
# -*- coding: utf-8 -*-
"""upload_docs
Implements a Distutils 'upload_docs' subcommand (upload documentation to
PyPI's packages.python.org).
"""
import os
import socket
import zipfile
import httplib
import urlparse
import tempfile
import sys
import shutil
from base64 import standard_b64encode
from pkg_resources impo... | xbianonpi/xbian-package-development | content/usr/local/lib/python2.7/dist-packages/distribute-0.6.30-py2.7.egg/setuptools/command/upload_docs.py | Python | gpl-2.0 | 6,868 | [
"VisIt"
] | 8b630c369e4118a6f3cf649f96ea1bf860b4f6e735d3cb8fe195ba347883ec76 |
# vim: tabstop=4 shiftwidth=4 softtabstop=4
# Copyright (c) 2012 OpenStack Foundation
# All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.a... | DirectXMan12/nova-hacking | nova/tests/compute/test_resource_tracker.py | Python | apache-2.0 | 33,658 | [
"exciting"
] | 4db0cf653ddf2bc6a3ab215a8892e0e9f3191c7f45eb3fe33e749bb6655754ac |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from django.conf.urls import patterns
from django.conf.urls import url
from .views import index
from .views import visit_url
from .views import add_url
from .views import delete_url
from .views import search
urlpatterns = patterns(
'later.views',
url(r'^$', index... | mozillazg/open-it-later | openitlater/later/urls.py | Python | mit | 530 | [
"VisIt"
] | aeabe48b80e77227074b221568f12a946dd275929c7deadd89b67ab74b858510 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under t... | MDAnalysis/mdanalysis | package/MDAnalysis/coordinates/TRJ.py | Python | gpl-2.0 | 50,608 | [
"Amber",
"CHARMM",
"MDAnalysis",
"NetCDF"
] | f10140c1b324f4c20685a07d108e626c0ded646e965ca0eed5b91ede4edfd5fd |
##
# Copyright 2009-2013 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
# the Hercules foundation (htt... | geimer/easybuild-easyblocks | easybuild/easyblocks/n/ncl.py | Python | gpl-2.0 | 7,189 | [
"NetCDF"
] | d241b4b84d30a7233d48b23edeb2c107802ca46c24c600159b4ad85ec439a877 |
# -*- coding: utf-8 -*-
# Copyright 2013-2014 Victor Amin, http://vamin.net/
"""MESS.DB main module
This module runs MESS.DB. The primary responibility of this code is to load a
mess tool and execute it.
"""
from __future__ import print_function
from __future__ import unicode_literals
import argparse
import inspect... | vamin/MESS.DB | mess/__main__.py | Python | agpl-3.0 | 2,217 | [
"Open Babel",
"Pybel"
] | 2cf147cdd67c47ef5559403e8f6cf094d351e625eb24a42d06f74e0434c12f9a |
from vtk import *
from vtk.web.camera import *
from vtk.web.query_data_model import *
import json, os, math, gzip, shutil
# Global helper variables
encode_codes = 'ABCDEFGHIJKLMNOPQRSTUVWXYZ'
arrayTypesMapping = ' bBhHiIlLfd'
jsMapping = {
'b': 'Int8Array',
'B': 'Uint8Array',
'h': 'Int16Array',
'H': ... | keithroe/vtkoptix | Web/Python/vtk/web/dataset_builder.py | Python | bsd-3-clause | 22,138 | [
"VTK"
] | 3ae92f7160d3ba5490b242cc5d79c7d9853359f90cc2309a30d68f06825d8538 |
class PickerPlacement:
def __init__(self,tape,board,placement):
self.tape=tape
self.board=board
self.placement=placement
class Picker:
def __init__(self,config):
self.config=config
self.tapeTemplates={}
self.tapes=[];
def addTape(self,tape):
self.tapes.append(tape)
def organizeTap... | celer/picktor | src/picker.py | Python | mit | 2,385 | [
"VisIt"
] | 69a87ebc7fb9795100b5e903fd64eec20ee21017b787c27ff5fd753fa10c552b |
"""
Tests for materialized_variant_filter.py.
"""
import os
from django.db import connection
from django.contrib.auth.models import User
from django.test import TestCase
from sympy.core.function import sympify
from main.models import AlignmentGroup
from main.models import Chromosome
from main.models import Dataset
f... | woodymit/millstone | genome_designer/variants/tests/test_materialized_variant_filter.py | Python | mit | 25,917 | [
"BWA"
] | c987d0d1ef9fda92e94b6865eabe7c9c1f28dcd37eab6c5e07be065bd4fc3a8e |
# -*- coding: utf-8 -*-
"""
The :mod:`sklearn.naive_bayes` module implements Naive Bayes algorithms. These
are supervised learning methods based on applying Bayes' theorem with strong
(naive) feature independence assumptions.
"""
# Author: Vincent Michel <vincent.michel@inria.fr>
# Minor fixes by Fabian Pedre... | beepee14/scikit-learn | sklearn/naive_bayes.py | Python | bsd-3-clause | 28,476 | [
"Gaussian"
] | 9837d24def10ce2cacb00bd3044aed67a36af8adcf3b432d7b4c24f312b44029 |
import warnings
import multiprocessing
from collections import OrderedDict
import numpy as np
import scipy.stats as ss
from scipy.optimize import leastsq
import upsilon.extract_features.period_LS_pyfftw as pLS
from upsilon.extract_features.feature_set import get_feature_set
from upsilon.extract_features.feature_set ... | dwkim78/upsilon | upsilon/extract_features/extract_features.py | Python | mit | 20,863 | [
"Gaussian"
] | a8aa38aa182a6224075ce3c3b6f3d1f4e14a31d52d4180d9816e58c37dc509ed |
# The MIT License
#
# Copyright 2014, 2015 Piotr Dabkowski
#
# Permission is hereby granted, free of charge, to any person obtaining
# a copy of this software and associated documentation files (the 'Software'),
# to deal in the Software without restriction, including without limitation the rights
# to use, copy, modif... | Aravinthu/odoo | doc/_extensions/pyjsparser/parser.py | Python | agpl-3.0 | 107,855 | [
"VisIt"
] | 389416f8c30f3e5323682867e4ad48a2c39840178de73f47be1160102959489f |
# -*- coding: utf-8 -*-
# $Id: manpage.py 7321 2012-01-20 06:50:44Z grubert $
# Author: Engelbert Gruber <grubert@users.sourceforge.net>
# Copyright: This module is put into the public domain.
"""
Simple man page writer for reStructuredText.
Man pages (short for "manual pages") contain system documentation on unix-li... | superdesk/Live-Blog | documentor/libraries/docutils-0.9.1-py3.2/docutils/writers/manpage.py | Python | agpl-3.0 | 34,868 | [
"VisIt"
] | f91ae524536d707d22093218c221a5e92951f2e9a5c8cf3417c56b3e75838358 |
import argparse
import logging
import os
from bioblend import galaxy
logging.basicConfig(level=logging.DEBUG)
log = logging.getLogger('search')
def main():
parser = argparse.ArgumentParser()
"""
--galaxy-url $galaxy_url
--api_keys $api_keys
--fastq_files_list $slx_library_fastq_file
"""
... | pajanne/galaxy-kickstart | search_tool/import.py | Python | mit | 3,408 | [
"Galaxy"
] | 717f6f0800b0cc80c377a60580c50c9331bea4e467a2e31db05f4e881df0b655 |
from __future__ import annotations
import ast
import pytest
from pre_commit_hooks.check_builtin_literals import Call
from pre_commit_hooks.check_builtin_literals import main
from pre_commit_hooks.check_builtin_literals import Visitor
BUILTIN_CONSTRUCTORS = '''\
import builtins
c1 = complex()
d1 = dict()
f1 = float... | pre-commit/pre-commit-hooks | tests/check_builtin_literals_test.py | Python | mit | 3,680 | [
"VisIt"
] | c167d7c36f4cc71088344a4ce8eb9caea607554602ae2be7f827d9857de9743c |
# -*- coding: utf-8 -*-
# parts of pygchem (Python interface for GEOS-Chem Chemistry Transport Model)
#
# Copyright (C) 2014 Benoît Bovy
# see license.txt for more details
#
"""
GEOS-Chem datasets I/O using one of the available
backends ('iris', 'netcdf', 'bpch').
"""
import importlib
from contextlib import context... | benbovy/PyGChem | pygchem/datasets.py | Python | gpl-3.0 | 2,440 | [
"NetCDF"
] | 25cd08da2d42f88830d191fd5d24798392f72b2d015c2043b8071611b535613b |
from numpy import array, arange, random
from tvtk.api import tvtk
from mayavi.scripts import mayavi2
def single_type_ug():
"""Simple example showing how to create an unstructured grid
consisting of cells of a single type.
"""
points = array([[0,0,0], [1,0,0], [0,1,0], [0,0,1], # tets
... | kayarre/dicomwrangle | unstructured_grid.py | Python | bsd-2-clause | 3,256 | [
"Mayavi",
"VTK"
] | e856e796f4fb6ff236153ad8b41f4487e3877a55d0067c7737b8ecbe0720c171 |
# encoding: utf-8
import os
import numpy as np
import glob
try:
import netCDF4 as netCDF
except:
import netCDF3 as netCDF
import pyroms
import pyroms_toolbox
import _remapping
import matplotlib.pyplot as plt
import datetime
def remapping(varname, srcfile, wts_files, srcgrd, dstgrd, \
rotate_uv=Fa... | dcherian/pyroms | pyroms_toolbox/pyroms_toolbox/remapping.py | Python | bsd-3-clause | 19,676 | [
"NetCDF"
] | f3ef393ab4f9291fe2a665e0d6f86ec91337480f517b2d14f7e4221e26d67906 |
"""Probabilistic arithmetic on independent random variables."""
from __future__ import print_function
import itertools
from functools import partial
import bisect
import operator
from numpy import asfarray
from numpy import multiply, add, divide
from numpy import unique, isnan, isscalar, size, flatnonzero
from numpy... | jszymon/pacal | pacal/indeparith.py | Python | gpl-3.0 | 57,776 | [
"DIRAC"
] | 815a66d3daacbe8234f9766e2981aa2d9a5383d72b220198c2a3285d356cf9ac |
from __future__ import division, print_function
import numpy as np, matplotlib.pyplot as plt, pandas as pd
import plotting as pl, gus_utils as gu, models as m, fits as f, corner_plot as cp,\
matplotlib as mpl, dwarf as d, matplotlib.ticker as ticker
from scipy.special import gammaincinv
from palettable.colo... | anguswilliams91/OnTheRun | code/plots.py | Python | mit | 22,062 | [
"Galaxy"
] | 9b43015c061d8c1632451e332fc5d3ec0bb84bac67b990878d2560d54aed1b76 |
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