text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
import mixtape.featurizer, mixtape.tica, mixtape.cluster, mixtape.markovstatemodel
import numpy as np
import mdtraj as md
from parameters import load_trajectories, build_full_featurizer
import sklearn.pipeline, sklearn.externals.joblib
import mixtape.utils
n_iter = 50
n_choose = 40
stride = 4
lag_time = 1
trj0, traj... | kyleabeauchamp/PMTStuff | code/NSD1_rmsd.py | Python | gpl-2.0 | 721 | [
"MDTraj"
] | 18435fa359468675535414bda39462ba6641f61b5fc548e3dfe7d33447fb12cf |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkCleanPolyData(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.... | nagyistoce/devide | modules/vtk_basic/vtkCleanPolyData.py | Python | bsd-3-clause | 487 | [
"VTK"
] | 61e97691b5b84e7c94c94554586086e231af57878ce5fcf5e652de3404a16e52 |
# -*- coding: utf-8 -*-
"""
QASuite
"""
import ConfigParser
import inspect
import os
import re
import twill.commands
import twill.extensions.check_links
import urllib
import urllib2
import urlparse
from BSXPath import BSXPathEvaluator, XPathResult, XPathExpression
from BeautifulSoup import BeautifulSoup
from datet... | PanDAWMS/panda-mon-qa | pandamonqa/qasuite/suite.py | Python | apache-2.0 | 10,827 | [
"VisIt"
] | 84757d40b26566d2aee2cc45550896e85a7831556e69f89c092ab909df0a6847 |
#
# GFSK modulation and demodulation.
#
#
# Copyright 2005-2007,2012 Free Software Foundation, Inc.
#
# This file is part of GNU Radio
#
# GNU Radio 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 versi... | iohannez/gnuradio | gr-digital/python/digital/gfsk.py | Python | gpl-3.0 | 11,583 | [
"Gaussian"
] | 8cf2436128df4b49f1d4e9d8ba2e7c3d795c32f9ca2b12154e7acb69732cb9df |
import copy
import functools
import sys
import warnings
from collections import defaultdict
from html import escape
from numbers import Number
from pathlib import Path
from typing import (
TYPE_CHECKING,
Any,
Callable,
DefaultDict,
Dict,
Hashable,
Iterable,
Iterator,
List,
Mappin... | jhamman/xarray | xarray/core/dataset.py | Python | apache-2.0 | 200,716 | [
"NetCDF"
] | 67a4f4f21f7116de3656d6519a590f3aa40576a2b0244f0fe026d5593ac4bfb3 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# freeseer - vga/presentation capture software
#
# Copyright (C) 2011, 2014 Free and Open Source Software Learning Centre
# http://fosslc.org
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as... | Freeseer/freeseer | src/freeseer/frontend/reporteditor/reporteditor.py | Python | gpl-3.0 | 9,795 | [
"VisIt"
] | 3505cefa96faff96dece5b4f814b3c4f61b1c070bd31807757f1dec6ac6c3486 |
"""
DIRAC API Class
All DIRAC functionality is exposed through the DIRAC API and this
serves as a source of documentation for the project via EpyDoc.
The DIRAC API provides the following functionality:
- A transparent and secure way for users
to submit jobs to the Grid, monitor them and
re... | andresailer/DIRAC | Interfaces/API/Dirac.py | Python | gpl-3.0 | 100,755 | [
"DIRAC"
] | ca5847a246ac9351540845339dd02f7b77fab799040e503528bf3ad34ee24f7e |
# ============================================================================
#
# Copyright (C) 2007-2012 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | jeroendierckx/Camelot | camelot/admin/action/base.py | Python | gpl-2.0 | 14,022 | [
"VisIt"
] | 18f6be4d78b5cf27c0ce435b2f0e0dbce85bd9eb31ba29904dcb37ce2a4bb4b0 |
"""Tools for working with Gaussian grids. Copied from ajdawson on github on 24/05/17"""
from __future__ import (absolute_import, division, print_function)
import functools
import numpy as np
import numpy.linalg as la
from numpy.polynomial.legendre import legcompanion, legder, legval
def __single_arg_fast_cache(func... | jamesp/Isca | src/extra/python/scripts/gauss_grid.py | Python | gpl-3.0 | 2,930 | [
"Gaussian"
] | 567a737ec952312a4383d18cfae1528b932c01f3757e08a8288bf643132933b8 |
#################################################################
# $HeadURL$
#################################################################
"""
.. module:: Pfn
:synopsis: ProcessPool and related classes
ProcessPool
-----------
ProcessPool creates a pool of worker subprocesses to handle a queue of tasks
much lik... | avedaee/DIRAC | Core/Utilities/ProcessPool.py | Python | gpl-3.0 | 30,302 | [
"DIRAC"
] | 8af15628344e494c3abc36200d056af8952e38a65c713c7940997ac870aa382b |
# ============================================================================
#
# Copyright (C) 2007-2010 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | kurtraschke/camelot | camelot/container/__init__.py | Python | gpl-2.0 | 3,635 | [
"VisIt"
] | fc2435d88563759f169108ecc1307b8ca5f05a0e5f555bb13d43d9ed553c4bcf |
# 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... | kobejean/tensorflow | tensorflow/contrib/data/python/kernel_tests/sql_dataset_op_test_base.py | Python | apache-2.0 | 4,382 | [
"MOE"
] | 968cbe72fb6f5b7b0bfbadcd0f32b1e4c7fa81954226ef8ab731697fb7a129a5 |
#! /usr/bin/env python
"""
Module with frame/cube filtering functionalities.
"""
__author__ = 'Carlos Alberto Gomez Gonzalez'
__all__ = ['frame_filter_highpass',
'frame_filter_lowpass',
'cube_filter_highpass',
'cube_filter_lowpass',
'cube_filter_iuwt']
import warnings
tr... | carlgogo/vip_exoplanets | vip_hci/var/filters.py | Python | bsd-3-clause | 15,228 | [
"Gaussian"
] | cdfa31c7aa8994c3dde89ee4d830283c34b380a3ea99f29e895473e1486b9834 |
# mako/pyparser.py
# Copyright (C) 2006-2014 the Mako authors and contributors <see AUTHORS file>
#
# This module is part of Mako and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""Handles parsing of Python code.
Parsing to AST is done via _ast on Python > 2.5, otherwise th... | grepme/CMPUT410Lab01 | virt_env/virt1/lib/python2.7/site-packages/Mako-1.0.0-py2.7.egg/mako/pyparser.py | Python | apache-2.0 | 7,737 | [
"VisIt"
] | bd637eab1fe8cd9028787baf380b0a4bb77ba74d945ee7e5c5ee9fe1feb5fa38 |
#!/usr/bin/env python
""" Get a proxy from the proxy manager
"""
import os
from DIRAC.Core.Base import Script
Script.setUsageMessage( '\n'.join( [ __doc__.split( '\n' )[1],
'Usage:',
' %s [option|cfgFile] UserName Role' % Script.scriptName,
... | Andrew-McNab-UK/DIRAC | tests/Jenkins/dirac-proxy-download.py | Python | gpl-3.0 | 1,243 | [
"DIRAC"
] | 15367c1c825632a0c9cd8b07c5779ab8ce1ceaaa0384ba289c7af4d6f5dfc180 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Gary Burton
# Copyright (C) 2010 Jakim Friant
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | dermoth/gramps | gramps/plugins/tool/relcalc.py | Python | gpl-2.0 | 10,831 | [
"Brian"
] | 906f3b352132dc3e427c05c5b6ed7e369d68b34622e8a9d9a91fd178b8661ccb |
"""
Reads:
- 2D prediction clusters from previous step
- location: see output from previous step
- format: see output from previous step
- 3D mesh
- location: defined in settings file
- format: ply or STL
- library: VTK
- Camera calibration parameters
Tasks:
- For each prediction cluster in each... | mmmatthew/raycast | code/s08__cast_rays_3d.py | Python | apache-2.0 | 5,904 | [
"VTK"
] | d905c53ddc2c4933c8505580fd4dadb3263622cb70480ce48a3b4b823a7920cc |
# pylint: disable=missing-docstring
# pylint: disable=redefined-outer-name
from lettuce import world, step
from nose.tools import assert_true, assert_equal
from selenium.common.exceptions import StaleElementReferenceException
############### ACTIONS ####################
@step('I select Checklists from the Tools menu... | pomegranited/edx-platform | cms/djangoapps/contentstore/features/checklists.py | Python | agpl-3.0 | 4,725 | [
"VisIt"
] | 5cdfc0dfdaf361b7601ced8ddc64a54919c93998d8775532d320f5fe9289bde0 |
#
# fourcc are codes to specify the encoding method a audio or video string
# in RIFF file (.avi and .wav).
#
# The following lists come from mmpython project:
# file: mmpython/video/fourcc.py
# url: http://sourceforge.net/projects/mmpython/
#
# List of codecs with no compression (compression rate=1.0)
UNCOMPRE... | goofwear/raspberry_pwn | src/pentest/metagoofil/hachoir_parser/video/fourcc.py | Python | gpl-3.0 | 13,511 | [
"CRYSTAL"
] | 35c3724d432057ec032c0a210620f5bff17e89c7a624e49c404f0959c9c3eabd |
# -*- coding: utf-8 -*-
# @Author: zpriddy
# @Date: 2016-04-17 20:28:40
# @Last Modified by: Zachary Priddy
# @Last Modified time: 2016-10-08 19:14:03
from core.models.device import Device
from core.services import ffIndigo
from core.templates import ffTemplates
class Device(Device):
def __init__(self, deviceI... | zpriddy/Firefly | Firefly/devices/ffIndigo/ffIndigo_switch.py | Python | apache-2.0 | 2,451 | [
"Firefly"
] | 9889557a50b54044eab1d546f72a0cec0b2f760e17b7a0a54f51e8eb9280f4a5 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | skosukhin/spack | var/spack/repos/builtin/packages/orthomcl/package.py | Python | lgpl-2.1 | 2,025 | [
"BLAST"
] | 61cf4526345c2f68637d327b57d5fad5f4a058b59b81dd2b1367e0e2b0abafe1 |
# ConnPlotter --- A Tool to Generate Connectivity Pattern Matrices
#
# This file is part of ConnPlotter.
#
# Copyright (C) 2009 Hans Ekkehard Plesser/UMB
#
# ConnPlotter 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 Fou... | gewaltig/cython-neuron | extras/ConnPlotter/tcd_nest.py | Python | gpl-2.0 | 6,829 | [
"NEURON"
] | b544946e538651d72b6c46154971280b0dbd771bdae6de17abbd7c368b68de95 |
# -*- coding: utf-8 -*-
r"""Testing of core library
"""
from copy import deepcopy
import numpy as np
import pytest
from matplotlib import use
from mock import patch
from neutronpy import Data, Energy, functions
from neutronpy.constants import BOLTZMANN_IN_MEV_K
from scipy.integrate import simps
use('Agg')
def buil... | neutronpy/neutronpy | tests/test_data.py | Python | mit | 12,333 | [
"Gaussian"
] | 393534915767a4c09ea2e67103d695b1f1f46dc29bc00d13e18a3d6386a1b4ed |
import random
import numpy as np
from collections import defaultdict
from environment import Action
#graph
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
from matplotlib import cm
from matplotlib.ticker import LinearLocator, FormatStrFormatter
class MCLearning:
def __init__(self, env):
... | ywk991112/easy21-RL | MCLearning.py | Python | mit | 3,838 | [
"VisIt"
] | 02b3d6f55f9e2e76af6559c5c229d953055e60062ff76d6faf89edf103ea86f3 |
# -*- coding: utf-8 -*-
'''
Torrent-tv.ru Playlist Downloader Plugin configuration file
'''
# Insert your Torrent-tv.ru playlist URL here
url = ''
# TV Guide URL
tvgurl = 'http://api.torrent-tv.ru/ttv.xmltv.xml.gz'
# Shift the TV Guide time to the specified number of hours
tvgshift = 0
# Download playlist every N ... | cosynus/python | plugins/config/torrenttv.py | Python | mit | 39,235 | [
"Galaxy"
] | e51eb4cddb0499651ebaf87c194ca5f42e7cec93f71c8a3d1bbf2fe91f4aee1f |
import unittest
import pysal
import numpy as np
#from pysal.spreg import probit as PB
from pysal.contrib.handler import Model
from functools import partial
Probit = partial(Model, mtype='Probit')
class TestProbit(unittest.TestCase):
def setUp(self):
db=pysal.open(pysal.examples.get_path("columbus.dbf"),"... | TaylorOshan/pysal | pysal/contrib/handler/tests/test_probit.py | Python | bsd-3-clause | 2,700 | [
"COLUMBUS"
] | 0ba4bed66ae110f95fb59c9c2a94b103877eef0375f349ebc7e1a66d67a2527c |
#!/usr/bin/env python
"""
Radionuclides
=============
"""
from opendrift.readers import reader_netCDF_CF_generic, reader_ROMS_native
from opendrift.models.radionuclides import RadionuclideDrift
from datetime import timedelta, datetime
import numpy as np
o = RadionuclideDrift(loglevel=0, seed=0) # Set loglevel to 0 ... | OpenDrift/opendrift | examples/example_radionuclides.py | Python | gpl-2.0 | 6,939 | [
"NetCDF"
] | 4a280e8bd38814cc4539b3f98e72b0d9af900117a825664ace6a314e6d1451df |
#!/usr/bin/env drgn
#
# Copyright (C) 2019 Tejun Heo <tj@kernel.org>
# Copyright (C) 2019 Facebook
desc = """
This is a drgn script to monitor the blk-iocost cgroup controller.
See the comment at the top of block/blk-iocost.c for more details.
For drgn, visit https://github.com/osandov/drgn.
"""
import sys
import re
... | penberg/linux | tools/cgroup/iocost_monitor.py | Python | gpl-2.0 | 10,097 | [
"VisIt"
] | 8acb914f238d11b8048f850446f0a06b751dc7dc85b25bfce6766d736f375ca0 |
import os
from datetime import datetime
from collections import OrderedDict
#-------------------------------------------------------------------------------
class SpecfitParser:
"""Parse and modify parameter files for the SpecFit task"""
def __init__(self, filename, ext=-1):
self.filename = filename
... | justincely/pyspecfit | pyspecfit/parser.py | Python | bsd-3-clause | 9,570 | [
"Gaussian"
] | 61466f6c4ed393c409ef7dddc0f1b785735e7d326c097f37fcf4c4920af45893 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
import time
# !! This is the configuration of Nikola. !! #
# !! You should edit it to your liking. !! #
# ! Some settings can be different in different languages.
# ! A comment stating (translatable) is used to denote those.
# ! There are two ways to... | ravikiranj/rkjnet | conf.py | Python | bsd-2-clause | 32,612 | [
"VisIt"
] | 8e3fc1185c1979c7b97c2067ed9725ece29351ab4b104d814b1eee7d12f4dc2f |
from __future__ import print_function
# Copyright (C) 2010, Jesper Friis
# (see accompanying license files for details).
"""Utility tools for convenient creation of slabs and interfaces of
different orientations."""
import numpy as np
def wrap_positions(positions, cell, pbc=True, center=(0.5, 0.5, 0.5),
... | suttond/MODOI | ase/utils/geometry.py | Python | lgpl-3.0 | 23,688 | [
"ASE",
"CRYSTAL"
] | 7e429ad96792d2c264f16f9ba8807b539228f30c92d8a52754756846da20c2fd |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2012-2013, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License ... | zenoss/ZenPacks.zenoss.CloudStack | ZenPacks/zenoss/CloudStack/VirtualMachine.py | Python | gpl-2.0 | 4,523 | [
"VisIt"
] | e3d91de6968e029cd27f84078e28a6175b9eaef8530c42de8b50a82ad6282cca |
"""The single layer SOINN algorithm procedures, for developers only."""
from numpy import *
from . import __grouping2 as grouping2
from math import isnan
from oldgraph.classes.graph import graph
winner_index = 0
winner_2nd_index = 0
setN = [] #:neuron weights
gr = graph() #:topology structure implemented by p... | sbxzy/pygks | pygks/isoinn2.py | Python | bsd-3-clause | 6,967 | [
"NEURON"
] | e4fcabb9537e6a6d909ea71f03130ccfeda771a59d5757a1c14fa846b296bcd4 |
"""
Adapted from https://github.com/bytefish/facerec
"""
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 /= fl... | idf/scipy_util | scipy_util/normalization.py | Python | bsd-3-clause | 1,473 | [
"Gaussian"
] | a400c819eb69677d1ea566d43adf46e3eb5f3ea269e8908d174c7faaf4e3c01b |
#
# Copyright (C) 2013-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | mkuron/espresso | testsuite/python/cluster_analysis.py | Python | gpl-3.0 | 6,975 | [
"ESPResSo"
] | 8c8f616bef379910fc97415fba044bc6cc365520b5b17d03e111fd9fdbb4bbd9 |
import logging
handler = logging.StreamHandler()
handler.setLevel(logging.INFO)
handler.setFormatter(logging.Formatter('{levelname}:{name}:{msg}', style='{'))
root_logger = logging.getLogger()
root_logger.setLevel(logging.INFO)
root_logger.addHandler(handler)
from fluggo.media import process, libav, x264, matroska, f... | fluggo/Canvas | scripts/encode-video.py | Python | gpl-3.0 | 8,900 | [
"Brian"
] | 48ad270bf664b6b82569d481f284f4b6905860702734f67785d438702e30f890 |
#--------------------------------------------------------------------------
# Software: InVesalius - Software de Reconstrucao 3D de Imagens Medicas
# Copyright: (C) 2001 Centro de Pesquisas Renato Archer
# Homepage: http://www.softwarepublico.gov.br
# Contact: invesalius@cti.gov.br
# License: GNU ... | fabio-otsuka/invesalius3 | invesalius/data/editor.py | Python | gpl-2.0 | 8,420 | [
"VTK"
] | d5de8a394a7e057188ad4936ef6452b936308ec29f4ef1ff2f66063daeea756f |
#import the simple module from the paraview
from paraview.simple import *
#### disable automatic camera reset on 'Show'
paraview.simple._DisableFirstRenderCameraReset()
<<<<<<< HEAD
total_proc=2
maindirectory='/eng/home/zhixuanc/Desktop/rohit-zhixuanc/Documents/C_plusplus/Resutls/'
subdirectory='ccr/comp_erupt/sym_200/... | zhixuanc/Volcano_Plume_SPH | bin/post_paraview.py | Python | gpl-3.0 | 2,744 | [
"ParaView"
] | 26fdae6c89c38729ecc6a2657224a036b7327b317dcd7599c4721c1ecfe61dee |
# -*- 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
from w... | drxos/kuiqblog | config/urls.py | Python | bsd-3-clause | 1,655 | [
"VisIt"
] | 13689203de96e91138a28650d7f47944a054a99b2cab1315c186544072df8dae |
"""
Tests for listingvisit endpoints
"""
from django.test import override_settings
from rest_framework import status
from tests.ozp.cases import APITestCase
from tests.ozpcenter.helper import APITestHelper
from ozpcenter import model_access as generic_model_access
from ozpcenter.scripts import sample_data_generator as... | aml-development/ozp-backend | tests/ozpcenter_api/test_api_profile_listingvisit.py | Python | apache-2.0 | 4,208 | [
"VisIt"
] | 3bba7e4a61b6222ff92ff1eab3d5e049d6e88da0e325f0ee4a38e7b9fb83ae38 |
#!/usr/bin/env python
# encoding: utf-8
# Thomas Nagy, 2005-2008 (ita)
"base for all c/c++ programs and libraries"
import os, sys, re
import TaskGen, Task, Utils, preproc, Logs, Build, Options
from Logs import error, debug, warn
from Utils import md5
from TaskGen import taskgen, after, before, feature
from Constants ... | mosaic-cloud/mosaic-distribution-dependencies | dependencies/nodejs/0.8.22/tools/wafadmin/Tools/ccroot.py | Python | apache-2.0 | 18,685 | [
"VisIt"
] | c69bef3732a0de4865dc62159382eb701a1b80db2bdc3bde5411570523ae96b1 |
# $Id$
#
# Copyright (c) 2010, 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 | rdkit/Chem/SaltRemover.py | Python | bsd-3-clause | 6,011 | [
"RDKit"
] | eb5e87a656b27253f374894a0793f267be687f877f5ee86e591dfc4a2997cd79 |
#!/usr/bin/python
import sys
# python script to extract read id from the id column and pick up the corresponding sequence in a fasta reference read library.
# to use when 3' trimming in bowtie has degraded the information of the initial sequence read
# The script takes a bowtie standard output and create a dictionary... | JuPeg/tools-artbio | unstable/local_tools/id_to_fasta_in_bowtie.py | Python | mit | 1,821 | [
"Bowtie"
] | 89cc61b0a9d772671be1d701c07e7dd3230c93cb869b8302255bdafaadf0b1cb |
import sys
sys.path.insert(1,"../../../")
import h2o
from tests import pyunit_utils
import random
from h2o.estimators.glm import H2OGeneralizedLinearEstimator
def random_attack():
def attack(family, train, valid, x, y):
kwargs = {}
kwargs['family'] = family
gaussian_links = ["inverse", "log", "identity"... | pchmieli/h2o-3 | h2o-py/tests/testdir_algos/glm/pyunit_NOPASS_random_attack_medium.py | Python | apache-2.0 | 5,041 | [
"Gaussian"
] | 6bd306b858476612a00c11e4f562bd1a5acc15f960d36944e057f17cac692093 |
#!/usr/bin/env python
import re
import os
import argparse
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Alphabet import generic_dna
import Bio.pairwise2 as pw
#from Bio.Blast.Applications import NcbiblastxCommandline
import pandas as pd
from IPython.core.debugger import T... | shiva1387/metamaps | inst/python/simBlast.py | Python | gpl-2.0 | 8,233 | [
"BLAST"
] | fd4ac92bf5dcb622a42c3d69133388ec46b92e55c9099d18a66cfbf5423257de |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | wdwvt1/scikit-bio | skbio/sequence/tests/test_iupac_sequence.py | Python | bsd-3-clause | 21,183 | [
"scikit-bio"
] | d1b933e3820b8ad9c0e2ddce6c7b15bf210aadc1621d9778b910cf8f546ae8f1 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkGroupLeafVertices(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | nagyistoce/devide | modules/vtk_basic/vtkGroupLeafVertices.py | Python | bsd-3-clause | 487 | [
"VTK"
] | 4e353d6325baa5f7e54325b15ebdf283c7140ab70f3983a5b9a46c081801827d |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | Kleptobismol/scikit-bio | skbio/parse/tests/test_record_finder.py | Python | bsd-3-clause | 9,666 | [
"scikit-bio"
] | d3fd93cef1822d38d1e7aeb80e3842b8209790f3b41c3399d41c8ebbd356cc51 |
# -*- coding: utf-8 -*-
"""Importer for Hetionet JSON."""
import unittest
import pybel.io.hetionet.constants as hioc
from pybel import dsl
from pybel.io.hetionet import from_hetionet_json
class TestHetionet(unittest.TestCase):
def test_import(self):
self._help(
h_type=hioc.ANATOMY,
... | pybel/pybel | tests/test_io/test_hetionet.py | Python | mit | 1,886 | [
"Pybel"
] | cde241ff2938901e49331154f09db074d3d994185a8093a75850a3ae36363876 |
# -*- coding: utf-8 -*-
"""
@file
@brief Overwrites latex writer as Sphinx's version is
bugged in version 1.8.0.
"""
import os
from docutils import nodes
from docutils.frontend import OptionParser
from sphinx.locale import __
from sphinx.builders.latex import LaTeXBuilder
from sphinx.writers.latex import (
LaTeXWri... | sdpython/pyquickhelper | src/pyquickhelper/sphinxext/sphinx_latex_builder.py | Python | mit | 10,372 | [
"VisIt"
] | 87cea26db783252408b7e802493e3ad81866d862c7728cab59c5ed807c1c97a2 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
from pymatgen.analysis.local_env import CrystalNN
from pymatgen.analysis.structure_prediction.dopant_predictor import (
get_dopants_from_shannon_radii,
get_dopants_from_substitution_probabilities,
)
f... | vorwerkc/pymatgen | pymatgen/analysis/structure_prediction/tests/test_dopant_predictor.py | Python | mit | 3,225 | [
"pymatgen"
] | b164314f9e683fa419b5a2898592948d7ced46c304884118a585b5e90aeacb10 |
"""Structure optimization. """
import sys
import pickle
import time
from math import sqrt
from os.path import isfile
from ase.parallel import rank, barrier
from ase.io.trajectory import Trajectory
import collections
class Dynamics:
"""Base-class for all MD and structure optimization classes."""
def __init__... | andrew031191/pyneb | optimize.py | Python | lgpl-3.0 | 6,203 | [
"ASE"
] | 3fff8c816dec8f4aa8587a8d91f221c89c4061d5bc82ae61bab9ec122b0d90ea |
"""Trains a CNN to detect the current steering wheel angle from images."""
from __future__ import print_function, division
import sys
import os
sys.path.append(os.path.join(os.path.dirname(__file__), '..'))
import models
from lib import replay_memory
from lib import util
from lib.util import to_variable, to_cuda, to_... | aleju/self-driving-truck | train_steering_wheel/train.py | Python | mit | 12,677 | [
"Gaussian"
] | e10042e8b390c715a250168232d7e12d1434b86e881d5eb9ac809a48a3cd7e9a |
"""
These tests exposes lower level functions than needed -- see tests_multiple_queries for simpler constructions
using glm_target
"""
import numpy as np
from scipy.stats import norm as ndist
import regreg.api as rr
from ...tests.flags import SMALL_SAMPLES, SET_SEED
from ...tests.decorators import (wait_for_return_va... | selective-inference/selective-inference | sandbox/randomized_tests/test_greedy_step.py | Python | bsd-3-clause | 5,920 | [
"Gaussian"
] | 09598fec9d551c06e8094ac87f89eaa23400c177f87c45899a1b700b8ba30f04 |
# -*- coding: utf-8 -*-
############################ Copyrights and license ############################
# #
# Copyright 2012 Andrew Bettison <andrewb@zip.com.au> #
# Copyright 2012 Dima Kukushkin <dima@kukushkin.me> ... | mgorny/PyGithub | github/Requester.py | Python | lgpl-3.0 | 23,024 | [
"Brian"
] | 3195686023ceb36136b9d71c2291872654281b3dc6b4a0060a59d7efe1265431 |
from rdkit.Chem import Draw
from rdkit import Chem
def writeToFile(mols, names, comments, fileName):
fid = open("CheckStandardizationTmp.txt", "a")
idx = 0
for mol in mols:
smiles = Chem.MolToSmiles(mol, isomericSmiles=True)
name = names[idx]
comment = comments[idx]
idx = i... | JonnaStalring/AZOrange | tests/standardizationTestSuite/sdf2smiles.py | Python | lgpl-3.0 | 1,862 | [
"RDKit"
] | f0f80ea44583276898bf7eaede5803ef7ce6ea0ed29dc660ffdb9df3c6dc8f81 |
# 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.
#
"""Command line wrapper for bwa
"""
from __future__ import print_function
from Bio._py3k import basestring
__docformat__ = "restructuredtext en"
f... | updownlife/multipleK | dependencies/biopython-1.65/build/lib.linux-x86_64-2.7/Bio/Sequencing/Applications/_bwa.py | Python | gpl-2.0 | 20,544 | [
"BWA",
"Biopython"
] | 5db96e2b35af24ff9a425e60f6fabd36eb0b7d793253f6a9a7506d385359e78d |
input_name = '../examples/linear_elasticity/linear_elastic_iga.py'
output_name = 'test_linear_elastic_iga.vtk'
from tests_basic import TestInput
class Test(TestInput):
pass
| RexFuzzle/sfepy | tests/test_input_linear_elastic_iga.py | Python | bsd-3-clause | 178 | [
"VTK"
] | 37a6cd1e7b547c6244198a8c06268ce5bbe12f90fb2b7388176a6f4febbf7df3 |
#! /usr/bin/env python
# -*- coding: UTF-8 -*-
import numpy as np
from synthfbmcircul import synth_fgn as synth_fgn
## The downsample parameter (K) is actually the index of the process,
## which when it tends to infinity, converges in distribution to
## the Rosenblatt process (or in general to a Hermite pro... | ivannz/study_notes | year_14_15/course_project/code/python/hsssi_processes.py | Python | mit | 3,424 | [
"Gaussian"
] | 6617fb24ac74e71c8822ff100b8c98f93db3fc08c91783e0274519ac6699638c |
from __future__ import division, absolute_import, print_function
import warnings
import numpy as np
from numpy.testing import (
TestCase, run_module_suite, assert_, assert_raises, assert_equal,
assert_warns, assert_no_warnings, assert_array_equal,
assert_array_almost_equal, suppress_warnings)
f... | ssanderson/numpy | numpy/random/tests/test_random.py | Python | bsd-3-clause | 62,177 | [
"Gaussian"
] | 989eaa2ef40a55feb42be0d20ae0da0e9b3e89b92ab555afe297a6d0415e058a |
try: paraview.simple
except: from paraview.simple import *
from paraview.simple import *
paraview.simple._DisableFirstRenderCameraReset()
soln_pvd = GetActiveSource()
Calculator1 = Calculator()
RenderView1 = GetRenderView()
DataRepresentation1 = GetDisplayProperties(soln_pvd)
DataRepresentation2 = Show()
DataRepres... | davidshepherd7/oomph-lib-micromagnetics | etc/paraview_helpers/m_vec.py | Python | gpl-2.0 | 2,433 | [
"ParaView"
] | ae8fdced3165581d0f10e3c03fb47d1e4758d3071a7ae30566cc404b780739db |
#!/usr/bin/env python
from __future__ import print_function
import os
import sys
import argparse
import multiprocessing
from os.path import exists, join
from tempfile import mkdtemp
import pysam
from dark.process import Executor
from dark.bowtie2 import Bowtie2
DEFAULT_SAMTOOLS_VIEW_FLAGS = (
pysam.FUNMAP | pys... | terrycojones/dark-matter | bin/run-bowtie2.py | Python | mit | 14,642 | [
"pysam"
] | 267c26dbff88c3f7ac7ef9be315cacab5f3367e63d3bfca56360b663698c8a63 |
# -*- coding: utf-8 -*-
# Copyright (C) 2017 by Pedro Mendes, Virginia Tech Intellectual
# Properties, Inc., University of Heidelberg, and University of
# of Connecticut School of Medicine.
# All rights reserved.
# Copyright (C) 2010 - 2016 by Pedro Mendes, Virginia Tech Intellectual
# Properties, Inc., Universit... | jonasfoe/COPASI | copasi/bindings/python/unittests/Test_CState.py | Python | artistic-2.0 | 2,101 | [
"COPASI"
] | 1db0b9d27be15878715dc37fd9db1a1348f3a328cf91a0ab5c2e39a0eeceee76 |
#
# CCLib_proxy Interface Library for High-Level operations
# Copyright (c) 2014-2016 Ioannis Charalampidis
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
... | wavesoft/CCLib | Python/cclib/extensions/bluegiga.py | Python | gpl-3.0 | 3,261 | [
"cclib"
] | d82fe562db68da6deef0c388d6878b16ca950673c87b72692f6b4f0f5c0622be |
'''
SASSIE: Copyright (C) 2011 Joseph E. Curtis, Ph.D.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
... | madscatt/zazzie | src_2.7/sassie/test_sassie/simulate/complex_monte_carlo/test_smaller1.py | Python | gpl-3.0 | 13,508 | [
"CHARMM"
] | aafcbe24a6aa5dbcd36399e06252a40d17fd8471be24a8e89dda6fe72962f541 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# @allow-sane-utf8
#
# Copyright (c) 2004-present, Facebook, Inc.
# All rights reserved.
#
# This source code is licensed under the BSD-style license found in the
# LICENSE file in the root directory of this source tree. An additional grant
# of patent rights can be... | peterlei/fboss | fboss/py/fboss/cli/data/oui_to_vendor_ieee.py | Python | bsd-3-clause | 828,050 | [
"ASE",
"Amber",
"BWA",
"CRYSTAL",
"Firefly",
"Galaxy",
"Jaguar",
"NEURON",
"Octopus"
] | 848f60f31acc531622a3e1042aff0e835eb2f64a62b5f4ef52e5859931ef94b2 |
#!/bin/env python
"""
Create a production to replicate files from some storage elements to others
:since: May 31, 2018
:author: A. Sailer
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
from DIRAC.Core.Utilities.DIRACScript import ... | ic-hep/DIRAC | src/DIRAC/TransformationSystem/scripts/dirac_transformation_replication.py | Python | gpl-3.0 | 1,560 | [
"DIRAC"
] | 488a9428ff88dd27b8a295e2e415ee2ff5821f33e318ebfc8dea13fd3f6b98ab |
# -*- coding: utf-8 -*-
# Unit tests for cache framework
# Uses whatever cache backend is set in the test settings file.
from __future__ import unicode_literals
import copy
import os
import re
import shutil
import tempfile
import threading
import time
import unittest
import warnings
from django.conf import settings
... | gchp/django | tests/cache/tests.py | Python | bsd-3-clause | 85,722 | [
"Brian"
] | 01f98b53a65008a1a94985686a662d8096157719e11efbfb04ae632420f57bed |
#!/usr/bin/env python
# This example demonstrates the use and manipulation of lookup tables.
import vtk
from vtk.util.colors import *
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# First create pipeline a simple pipeline that reads a structure grid
# and then extracts a plane f... | hlzz/dotfiles | graphics/VTK-7.0.0/Examples/Rendering/Python/rainbow.py | Python | bsd-3-clause | 3,210 | [
"VTK"
] | 7aa627548f61fe0d8fc4927f74f71003d9afc6c970b7bd730db3f58d00046ecb |
# -*- coding: utf-8 -*-
#
# gPrime - A web-based genealogy program
#
# Copyright (C) 2003-2006 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2008 Peter G. LAndgren
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General P... | sam-m888/gprime | gprime/plugins/rel/rel_sv.py | Python | gpl-2.0 | 23,598 | [
"Brian"
] | 3d3ebcf1605fb414b8977170f33402c0b6307abc92da10ac15af75aa8e563d49 |
# -*- 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... | sfriesel/suds | tests/test_cache.py | Python | lgpl-3.0 | 12,811 | [
"Firefly"
] | 1e7117dad3c81a3108150ddb4b8bbeec904a92ed572a8723a48ce36647b843bb |
#! /usr/bin/env python
#Parser for blast -m 8 or blast+ -m 6 and 7 output file with description inserted
import sys
##Query id,Subject id,Description, % identity, alignment length,mismatches,gap openings,q. start,q. end,s. start,s. end,e-value,bit score
dict1={}
for line in open(sys.argv[1]):
data = line.split('\t'... | fandemonium/code | blast_parser_b_multi.py | Python | mit | 1,213 | [
"BLAST"
] | 798673c98711e799f4d07ffc4bd012a72c04586cdd7b263a2ba7aac0390dd290 |
# 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 ... | olafhauk/mne-python | mne/cov.py | Python | bsd-3-clause | 78,828 | [
"Gaussian"
] | 3b0cf60c8edfabfb581e059569b46bfcc7514ebdab1ad06913abf4038b2f3e2f |
#!/usr/bin/env python
# CPIP is a C/C++ Preprocessor implemented in Python.
# Copyright (C) 2008-2017 Paul Ross
#
# 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... | paulross/cpip | src/cpip/CppCondGraphToHtml.py | Python | gpl-2.0 | 5,812 | [
"VisIt"
] | 85710bec22762070cdfa20e6d2c18f621b974eba041070010ea8ff6b4c4f1045 |
#!/usr/bin/env python
#-*- coding:utf-8 -*-
'''
Multivariate time series
TISEAN's multivariate section is still growing - like the research body
in this area. As a convention, program names for ``cross-'' quantities
computed between two signals start with x. Those programs that can handle
scalar as well as mult... | sdia/tisane | multivariate.py | Python | gpl-3.0 | 21,756 | [
"Gaussian"
] | 5503a7a96a64fb1de47f4ad75e85494227a479470b261437d0f1bd443ba93a1c |
# coding=utf-8
PARTNERS_PRICE = """
{
"prices": [
{
"currency_code": "USD",
"display_name": "POOL",
"distance": 10.93,
"duration": 1320,
"estimate": "$13-17",
"high_estimate": 18,
"localized_display_name": "POOL",
... | darina/omim | tools/python/jsons.py | Python | apache-2.0 | 27,319 | [
"Galaxy"
] | 761a2baed72fcc769094f82b74a459805fec9120d6ca7dd37a46b44374d9a245 |
# -*- coding: utf-8 -*-
# Copyright 2007-2021 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy 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... | erh3cq/hyperspy | hyperspy/tests/signals/test_1D_tools.py | Python | gpl-3.0 | 15,138 | [
"Gaussian"
] | 89b13d549c7708c0b9cc3cca988231193ac99135c22b003ec3ee22a153b8826e |
import unittest
from mock import MagicMock
import sys
mocked_gfal2 = MagicMock()
sys.modules['gfal2'] = mocked_gfal2
from DIRAC.Resources.Storage.GFAL2_XROOTStorage import GFAL2_XROOTStorage
class XROOTStorage_TestCase(unittest.TestCase):
def setUp(self):
'''
Setup
'''
# Mock external libraries /... | chaen/DIRAC | Resources/Storage/test/Test_GFAL2_XROOTStorage.py | Python | gpl-3.0 | 1,520 | [
"DIRAC"
] | 61cc16dbb120358cd1306e41e771608c6103007165fe65051dd3318c3f31b1ec |
#!/usr/bin/env python
# Copyright 2013 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""The frontend for the Mojo bindings system."""
import argparse
import imp
import os
import pprint
import sys
# Disable lint check ... | sencha/chromium-spacewalk | mojo/public/tools/bindings/mojom_bindings_generator.py | Python | bsd-3-clause | 7,110 | [
"VisIt"
] | fdcbf49811fa788c019164583a2e94af1a25b296819138cb2d2bf4dde77945ea |
#!/usr/bin/env python3 -tt
"""
This file defines the event types used in the Stanford Portable Graphics Libraries.
The structure of this package is adapted from the Java event model.
EventClassType
==============
This _enumeration definest the vent classes. The element values are each a single bit
and can be a... | sredmond/acmpy | campy/graphics/gevents.py | Python | mit | 19,357 | [
"Galaxy"
] | 077f2419f42932a5498ee3f63c755da7461f2732a5f88e189dedd86d517f411e |
# Copyright 2017 Amazon.com, Inc. or its affiliates. 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. A copy of the License
# is located at
#
# http://aws.amazon.com/apache2.0/
#
# or in the "license" file acc... | KellenSunderland/sockeye | sockeye/layers.py | Python | apache-2.0 | 3,685 | [
"NEURON"
] | 190c41085f431ca9179b1b07d69afb82bf6b475620938ec226423b7537f496ce |
#
# Copyright Amazon.com, Inc. or its affiliates. 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.
# A copy of the License is located at
#
# http://aws.amazon.com/apache2.0
#
# or in the "license" file accompanyi... | wcs1only/s2n | tests/integration/s2n_test_constants.py | Python | apache-2.0 | 23,597 | [
"Octopus"
] | c297540939f175570c225e18e691d50db70a990882016d7da684d14d473161e6 |
# ===============================================================================
# Copyright 2021 ross
#
# 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/LICE... | USGSDenverPychron/pychron | pychron/processing/sclf.py | Python | apache-2.0 | 6,915 | [
"Gaussian"
] | 73686dadfc5b5843994886eb6f1f73e31c08016d3ee9a34977a737d6a7a39cb8 |
# 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 t... | kkreis/espressopp | src/interaction/LennardJonesAutoBonds.py | Python | gpl-3.0 | 9,989 | [
"ESPResSo"
] | 640a34c6932c2fad2435b78f47008bd106315abf6d8b13070b2cfa0211e96696 |
"""Support for the ipygany plotter."""
from array import array
import warnings
import numpy as np
from IPython import display
# not to be imported at the init level
try:
import ipygany
except ImportError: # pragma: no cover
raise ImportError('Install ``ipygany`` to use this feature.')
try:
from ipywid... | akaszynski/vtkInterface | pyvista/jupyter/pv_ipygany.py | Python | mit | 7,927 | [
"VTK"
] | 8aa1ea5239db22db82361c41802a29665dd1a885fd351e33c40123df6bd0cf2e |
from __future__ import annotations
import argparse
import ast
import traceback
from typing import NamedTuple
from typing import Sequence
DEBUG_STATEMENTS = {
'ipdb',
'pdb',
'pdbr',
'pudb',
'pydevd_pycharm',
'q',
'rdb',
'rpdb',
'wdb',
}
class Debug(NamedTuple):
line: int
... | pre-commit/pre-commit-hooks | pre_commit_hooks/debug_statement_hook.py | Python | mit | 2,198 | [
"VisIt"
] | dce3cba702f58dff4f61088d4cee25cea6f582bf8191f88e3099a652860f687e |
# pylint: disable=missing-docstring
from django.test import TestCase
from common.util import slugify, clean_html
class PagesTest(TestCase):
def test_get_homepage(self):
response = self.client.get("/")
self.assertEqual(response.status_code, 200)
def test_non_existent(self):
response =... | lutris/website | common/tests.py | Python | agpl-3.0 | 1,431 | [
"VisIt"
] | ae7085a139b12c2b9e9cf485487dccffee37e1e9b6326361bcafa24e3e9a59dd |
from django.db import models
class RegisteredSubjectManager(models.Manager):
def get_by_natural_key(self, subject_identifier_as_pk):
return self.get(subject_identifier_as_pk=subject_identifier_as_pk)
def get_for_subject_identifier(self, subject_identifier):
"""Returns a queryset for the give... | botswana-harvard/edc-registration | edc_registration/managers.py | Python | gpl-2.0 | 583 | [
"VisIt"
] | 27e5a01d65ef3f1921236cc6a5a404ebc364f5ed3599f36b02f43b584b77c93d |
from SDST.snpeff import effNames,snpEffEffects
import itertools
import vcf
import math
import fisher
def vcfMelt(reader,outfile,samplename=None,includeGenotypes=False):
"""Melt a VCF file into a tab-delimited text file
:param reader: a vcf.Reader object (from the pyvcf package)
:param outfile: a stream to... | seandavi/SDST | SDST/seqvcf.py | Python | mit | 6,760 | [
"pysam"
] | 8f2d15605d27cabe7e29850366b8b3450e05b956de2ec3d8dec7c05ad66735c1 |
# -*- coding: utf-8 -*-
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import os.path
import numpy as np
import matplotlib.pyplot as plt
import abel
# This example demonstrates a BASEX transform of an image obtained... | stggh/PyAbel | examples/example_basex_photoelectron.py | Python | mit | 2,708 | [
"Gaussian"
] | 30d5db0a142dfe821223d5bb98413b6e6c793ca3cddfb9cff7c9c5184a44e6dc |
"""RabbitMQSynchronizer
RabbitMQSynchronizer keeps the RabbitMQ user database synchronized with the CS
RabbitMQ user database is updated according to changes in CS.
"""
from DIRAC import S_OK
from DIRAC.ConfigurationSystem.Client.Helpers.Registry import hostHasProperties
from DIRAC.ConfigurationSystem.Client.Help... | DIRACGrid/DIRAC | src/DIRAC/FrameworkSystem/Utilities/RabbitMQSynchronizer.py | Python | gpl-3.0 | 5,263 | [
"DIRAC"
] | f81354c726f3f7fc1d45d486e113a0414de323e3dd3b3d66cc9b4f4ef28049ee |
# The DF of a gap in a tidal stream
from functools import wraps
import copy
import warnings
import multiprocessing
import numpy
from scipy import integrate, interpolate, special
from ..util import galpyWarning, coords, multi, conversion
from ..util import _rotate_to_arbitrary_vector
from ..orbit import Orbit
from ..pot... | jobovy/galpy | galpy/df/streamgapdf.py | Python | bsd-3-clause | 72,880 | [
"Galaxy",
"Gaussian"
] | 0e59e7cd2604c14f11566f08684ee8e466e1673cb954e763b614da8f0fbb608f |
"""
Analyze data in a pickle file by maximum time / width / height and similar
features.
"""
# Core Library modules
import logging
import pickle
import sys
# Third party modules
import numpy
# Local modules
from . import data_analyzation_metrics as dam
from . import features, handwritten_data, utils
logger = loggi... | MartinThoma/hwrt | hwrt/analyze_data.py | Python | mit | 4,439 | [
"Bowtie"
] | 853ca04f6a04b342774fa1f698e65cff6ecd196921e7c1fc440e3d956e5d0457 |
# $Id$
#
# Copyright (C) 2003 Rational Discovery LLC
# All Rights Reserved
#
from rdkit import Chem
from rdkit.VLib.Output import OutputNode as BaseOutputNode
class OutputNode(BaseOutputNode):
""" dumps smiles output
Assumptions:
- destination supports a write() method
- inputs (parents) ... | greglandrum/rdkit | rdkit/VLib/NodeLib/SmilesOutput.py | Python | bsd-3-clause | 2,131 | [
"RDKit"
] | 82372bd1fc517b1759a9cf1c9ce195be2fbf16cb7e43d2712ef2fca715f57843 |
import pickle
from gpaw import GPAW
from gpaw.transport.jstm import STM
# tip data
tip = GPAW('tip', txt=None)
h1, s1 = pickle.load(open('tip_hs.pckl')) # h and s matrix
h10, s10 = pickle.load(open('tip_p_hs.pckl')) #principal layer h and s matrix
# surface data
srf = GPAW('srf', txt=None)
h2, s2 = pickle.load(open(... | qsnake/gpaw | doc/tutorials/negfstm/scan.py | Python | gpl-3.0 | 1,067 | [
"GPAW"
] | e88ada8849ae7e4d04b7a3c0e8fd2575e533c53fd8930422ad0fbdb42f41b722 |
#!/usr/bin/env python
#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#
#
# Name: generate_gaussian_samples.py
#
# Author: Constantin Weisser (weisser@mit.edu)
#
# Purpose: This is a python script to write a file containing 10000 data points
# sampled from a 2D Gaussian
#
#-#-... | weissercn/MLTools | Dalitz/gaussian_samples/generate_gaussian_samples.py | Python | mit | 1,468 | [
"Gaussian"
] | da5cd6f22bc56c2536571bc5261d2af8707e3ad22ad4b0d1744a272bede8e752 |
"""Python bindings for 0MQ."""
#-----------------------------------------------------------------------------
# Copyright (C) 2010-2012 Brian Granger, Min Ragan-Kelley
#
# This file is part of pyzmq
#
# Distributed under the terms of the New BSD License. The full license is in
# the file COPYING.BSD, distributed ... | skycucumber/Messaging-Gateway | webapp/venv/lib/python2.7/site-packages/zmq/__init__.py | Python | gpl-2.0 | 2,167 | [
"Brian"
] | ce9448c0103b5029560ec825489a699fc624735bd811882a96aab135d37de505 |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# 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... | googleapis/python-compute | tests/unit/gapic/compute_v1/test_regions.py | Python | apache-2.0 | 52,676 | [
"Octopus"
] | 25e5d3abfa7d92574788c5ac832d5b8fb6d740192d795e3beae64c91f9ddc612 |
#
# Copyright (C) 2001-2006 greg Landrum and Rational Discovery LLC
#
# @@ 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.
#
""" Functionality for SATIS t... | bp-kelley/rdkit | rdkit/Chem/SATIS.py | Python | bsd-3-clause | 2,807 | [
"RDKit"
] | fb3eb7b6caf383e363f26025f9a1216b26e01bb6974a99b0397080474e243667 |
#!/usr/bin/python
#Trecias Bioinformatikos laboratorinis darbas
#Rytis Karpuska PS1
import os
import time
import string
import Bio.SubsMat.MatrixInfo
import Bio.Blast.NCBIWWW
import Bio.Blast.NCBIXML
from Bio import Entrez
#run ncbi blast
print "Running Blast..."
fasta_seq_file = open("3uzd_seq.fasta", "r");
fasta_se... | jauler/VU_MIF_tasks | BakalauroStudijos/BioInformatika/3uzd.py | Python | gpl-2.0 | 3,837 | [
"BLAST"
] | 1fd31516bb5183a64e8696e4701f3fbfd7e34fd52d439534b515037453926c65 |
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