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#!/usr/bin/env python
"""
Trying to apply MSM analysis on my trajectories
http://msmbuilder.org/latest/
This script takes trajectories and topology from AMBER and saves in a directory
different transicion matrices for a combination of lag times and cluster
centers
"""
import mdtraj as md
from msmbuilder.dataset impor... | jeiros/Scripts | MSManalysis/msm_builder.py | Python | mit | 4,762 | [
"Amber",
"MDTraj"
] | 672ac16d46fead6153b635f429b56fe0f3629d0a86ead521cd5bd5dd3c48d66f |
#
# ImageViewTk.py -- classes for the display of FITS files in Tk surfaces
#
# Eric Jeschke (eric@naoj.org)
#
# Copyright (c) Eric R. Jeschke. All rights reserved.
# This is open-source software licensed under a BSD license.
# Please see the file LICENSE.txt for details.
import numpy
import PIL.Image as PILimage
i... | Rbeaty88/ginga | ginga/tkw/ImageViewTk.py | Python | bsd-3-clause | 11,656 | [
"FLEUR"
] | 4c3b02d27f2bb9d61e40ac582689d2e4dc03d3b5b6de027508fa22a5a952d866 |
# -*- coding: utf-8 -*-
#
# DiracDocs documentation build configuration file, created by
# sphinx-quickstart on Sun Apr 25 17:34:37 2010.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# A... | fstagni/DIRACDocs | source/conf.py | Python | gpl-3.0 | 7,096 | [
"DIRAC"
] | d37ee5e11c056f02212481814ea172c94d5ca2378816b1820826c0ed11bc6abe |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides some useful functions for dealing with magnetic Structures
(e.g. Structures with associated magmom tags).
"""
import logging
import os
import warnings
from collections import namedtuple
from enum impo... | materialsproject/pymatgen | pymatgen/analysis/magnetism/analyzer.py | Python | mit | 46,760 | [
"VASP",
"pymatgen"
] | 29cc2e702dbe3aa88c8b00806124db5e9020d8115952007937ec394307ccd693 |
#!/usr/bin/env python
"""
globals.py 9.00 PrivateEyePi Globals Parameters
---------------------------------------------------------------------------------
Works conjunction with host at www.privateeyepi.com
Visit projects.privateeyepi.com for full details ... | az-max/dht22-web-monitor | globals.py | Python | gpl-2.0 | 6,284 | [
"VisIt"
] | a37d37072587902acfbbb51846424790622bde9527d96b45476f2e0571e6792d |
"""Convert BAM/SAM to tab-format
NAME SEQ1 QUAL1 SEQ2 QUAL2
files may be SAM or BAM (autodetected)
Output is always to stdout (err goes to stderr, redirect it if you need to)"""
import pysam
import os
import select
from scripter import path_to_executable
from argparse import ArgumentParser
from copy imp... | benjschiller/seriesoftubes | seriesoftubes/converters/bamtotab.py | Python | artistic-2.0 | 1,450 | [
"pysam"
] | 5d545161c5d8886cdca2f7cdfb4a3c94035f7bd894570dbca97557d875a4759a |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | pli3/e2-openwbif | plugin/controllers/views/web/mediaplayerplay.py | Python | gpl-2.0 | 5,214 | [
"VisIt"
] | af4fc6e50abb39fa5a6cd5854a839a45270bdbf8def82424cecb20072d31cb09 |
import unittest
import math
import torch
import os
import tempfile
import uuid
import shutil
import pyprob
from pyprob import util, Model, LearningRateScheduler, Optimizer
from pyprob.distributions import Normal, Uniform
class ModelTestCase(unittest.TestCase):
def __init__(self, *args, **kwargs):
# http:... | probprog/pyprob | tests/test_train.py | Python | bsd-2-clause | 10,914 | [
"Gaussian"
] | 8fea59305efd88ea2bdf5d8fb3e57df256f76bb802c8842104ceca90b18b4094 |
# -----------------------------------------------------------------------------
# Import packages
import numpy as np
import multiprocessing
from itertools import repeat
from collections import Iterable
from scipy.integrate import cumtrapz
# noinspection PyPackageRequirements
from sklearn.mixture import GaussianMixture... | smeingast/PNICER | pnicer/utils/gmm.py | Python | gpl-3.0 | 22,248 | [
"Gaussian"
] | dd668560cd371988ea41448d8da461b4dd817fae8bad0ccfbd9cd31afc02edc3 |
import os
import numpy as np
import pytest
import vtk
import pyvista
from pyvista import examples
from pyvista.plotting import system_supports_plotting
ffmpeg_failed = False
try:
try:
import imageio_ffmpeg
imageio_ffmpeg.get_ffmpeg_exe()
except ImportError:
import imageio
imag... | akaszynski/vtkInterface | tests/test_examples.py | Python | mit | 10,724 | [
"VTK"
] | f80052806f68bdacd75ed79d3c33e62fbea1cd21ae45be7a0d0ddfd330284aca |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2012 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundati... | andrebellafronte/stoq | stoqlib/gui/test/test_supplierdetails.py | Python | gpl-2.0 | 2,678 | [
"VisIt"
] | fbc3b3642adc50d53353f26442f951e03856b712bfb60dfa35e0453658d20dca |
"""Support for Konnected devices."""
import copy
import hmac
from http import HTTPStatus
import json
import logging
from aiohttp.hdrs import AUTHORIZATION
from aiohttp.web import Request, Response
import voluptuous as vol
from homeassistant import config_entries
from homeassistant.components.binary_sensor import DEVI... | mezz64/home-assistant | homeassistant/components/konnected/__init__.py | Python | apache-2.0 | 14,293 | [
"VisIt"
] | 8e5fd7e0db8038ad8afeb11869ae1205773267978e65dca8905f3c13a2877de2 |
# -*- coding: utf-8 -*-
# Author: Óscar Nájera
# License: 3-clause BSD
"""
========================
Backreferences Generator
========================
Reviews generated example files in order to keep track of used modules
"""
from __future__ import print_function
import ast
import os
# Try Python 2 first, otherwise ... | pprett/scikit-learn | doc/sphinxext/sphinx_gallery/backreferences.py | Python | bsd-3-clause | 6,073 | [
"VisIt"
] | 37d6d70fab0141102526788c5e205b2e15a2da9a0297383b7da6db6a4050a47c |
#
# Author: Travis Oliphant 2002-2011 with contributions from
# SciPy Developers 2004-2011
#
from __future__ import division, print_function, absolute_import
from scipy._lib.six import string_types, exec_, PY3
from scipy._lib._util import getargspec_no_self as _getargspec
import sys
import keyword
import r... | mbayon/TFG-MachineLearning | venv/lib/python3.6/site-packages/scipy/stats/_distn_infrastructure.py | Python | mit | 118,645 | [
"Gaussian"
] | 205cfb18847b1786a063ce8dc95eccd11327ae6a0be5709f53322e26beb7f0f4 |
import logging
import urllib
from functools import partial
from django.conf import settings
from django.core.context_processors import csrf
from django.core.exceptions import PermissionDenied
from django.core.urlresolvers import reverse
from django.contrib.auth.models import User
from django.contrib.auth.decorators i... | TsinghuaX/edx-platform | lms/djangoapps/courseware/views.py | Python | agpl-3.0 | 32,409 | [
"VisIt"
] | b5c7744a497f343660f39943aaf841312caf752d9d9dfc666fe2059c0daf7837 |
# Copyright 2009 Brian Quinlan. All Rights Reserved.
# Licensed to PSF under a Contributor Agreement.
from __future__ import with_statement
import functools
import logging
import threading
import time
try:
from collections import namedtuple
except ImportError:
from concurrent.futures._compat import namedtuple... | ychen820/microblog | y/google-cloud-sdk/platform/google_appengine/lib/concurrent/concurrent/futures/_base.py | Python | bsd-3-clause | 19,656 | [
"Brian"
] | ada06d94a0cd7b447c70dc08579363e16899e4d8f2a42b6cdb7a2be38ee8c035 |
# -*- encoding: utf-8 -*-
#############################################################################
################## awmstools : Common functions for python ###################
##############################################################################
##
## o author: Alexander Schmolck (A.Schmolck@gmx.net)
##... | bmcfee/gordon | examples/feature_extractors/matlab_feature_extractor_with_dependencies/mlabwrap-1.1/awmstools.py | Python | gpl-3.0 | 60,530 | [
"Brian"
] | eeadaefb4323ac905ad8f54aeb8e8ad3725cdde02773b4affe61d6195ec98649 |
../../../../../../../share/pyshared/orca/scripts/apps/Thunderbird/script_utilities.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/scripts/apps/Thunderbird/script_utilities.py | Python | gpl-3.0 | 85 | [
"ORCA"
] | 7370fab60294b895fd182595a4d9165beda7b8b75cecb29c88a55fa69dbd763c |
# -*- 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-pubsublite | tests/unit/gapic/pubsublite_v1/test_admin_service.py | Python | apache-2.0 | 228,548 | [
"Octopus"
] | fc56f90697384c08a1147dad0340df7a2e9a170dcfdedaae1d510d23b398d4ee |
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Mathieu Blondel <mathieu@mblondel.org>
# Olivier Grisel <olivier.grisel@ensta.org>
# Andreas Mueller <amueller@ais.uni-bonn.de>
# Eric Martin <eric@ericmart.in>
# License: BSD 3 clause
from itertools import chain, combina... | WangWenjun559/Weiss | summary/sumy/sklearn/preprocessing/data.py | Python | apache-2.0 | 51,987 | [
"Gaussian"
] | ec29a88cc47dc1a083659e17e9ab2383ad693ec3d03e33dc56c13cd664b6d5aa |
"""
Test the about xblock
"""
import datetime
import pytz
from django.conf import settings
from django.core.urlresolvers import reverse
from django.test.utils import override_settings
from mock import patch
from opaque_keys.edx.locations import SlashSeparatedCourseKey
from course_modes.models import CourseMode
from x... | beni55/edx-platform | lms/djangoapps/courseware/tests/test_about.py | Python | agpl-3.0 | 23,322 | [
"VisIt"
] | fbd938e7a4e1beb58b7069cbdf1ac0d23d303e42b7dd2b088f6b3753b1baf5a8 |
##----------------------------------------------------------------------------------------------------------------------
##-- Copyright (C) Huawei Technologies Co., Ltd. 2008-2011. All rights reserved.
##----------------------------------------------------------------------------------------------------------------... | HuaweiSNC/OPS2 | src/python/selflearn.py | Python | mit | 206,556 | [
"VisIt"
] | 754af308d65103be3ca8a709efa6fa41651eeabfd573a1b9c0aed3f88cb17637 |
import asyncio
import discord
import json
import aiohttp
from time import strftime
from discord.ext import commands
from utils import checks
from mods.cog import Cog
class Changes(Cog):
def __init__(self, bot):
super().__init__(bot)
self.cursor = bot.mysql.cursor
self.proxy_request = bot.proxy_request
async d... | NotSoSuper/NotSoBot | mods/Changes.py | Python | mit | 7,250 | [
"MOE"
] | 9ef4fd37ee2432660ef02627d1ed55ee7d518e8b2d263e2f316ac0731d5affbb |
# drizzle/base.py
# Copyright (C) 2005-2013 the SQLAlchemy authors and contributors <see AUTHORS file>
# Copyright (C) 2010-2011 Monty Taylor <mordred@inaugust.com>
#
# This module is part of SQLAlchemy and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""Support for the Driz... | rooi/CouchPotatoServer | libs/sqlalchemy/dialects/drizzle/base.py | Python | gpl-3.0 | 15,314 | [
"VisIt"
] | 86dd0ec91eef84bd7efb9745f099e627fe326900627967a5be533cbf945fe950 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Note: To use the 'upload' functionality of this file, you must:
# $ pip install twine
import io
import os
import sys
from shutil import rmtree
from setuptools import find_packages, setup, Command
# Package meta-data.
NAME = 'amptk'
DESCRIPTION = 'AMPtk: amplicon too... | nextgenusfs/ufits | setup.py | Python | bsd-2-clause | 3,886 | [
"Biopython"
] | d11398933e4b0dd4ab191d5fbe354190de8f9e89aef050f6c7bfab6ed89c5892 |
# -*- 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 ... | MDAnalysis/mdanalysis | package/MDAnalysis/coordinates/NAMDBIN.py | Python | gpl-2.0 | 4,813 | [
"MDAnalysis",
"NAMD"
] | 8d82521a2172b01405c6bde4afaf337a4663e51095a8e798976d84b7d8b0a62a |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the LMS Instructor Dashboard.
"""
import time
from flaky import flaky
from nose.plugins.attrib import attr
from bok_choy.promise import EmptyPromise
from ..helpers import UniqueCourseTest, get_modal_alert, EventsTestMixin
from ...pages.common.logout import LogoutPage
... | IndonesiaX/edx-platform | common/test/acceptance/tests/lms/test_lms_instructor_dashboard.py | Python | agpl-3.0 | 51,165 | [
"VisIt"
] | 99904f6943b52b9b5ebbec80f7645b4100309879139dd244c427407fea855075 |
# Copyright 2012-2014 Brian May
#
# This file is part of python-tldap.
#
# python-tldap 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.... | brianmay/python-tldap | tldap/backend/__init__.py | Python | gpl-3.0 | 2,141 | [
"Brian"
] | e572ba0606d5d9986a86d0dc48a4348714a1c8b6165ae02d880e3d484ce3a556 |
import ast
import io
import Utils.unparse as unparse
# Extract information from an eval'able expression
class ExpressionInfo(ast.NodeVisitor):
def __init__(self, expr):
self.expr = expr
self.names = []
self.components = []
self.onlyNames = True
tree = ast.parse(self.expr)
self.visit(tree)
... | yliu120/dbsystem | HW3/dbsys-hw3/update/dbsys-hw3/Utils/ExpressionInfo.py | Python | apache-2.0 | 1,063 | [
"VisIt"
] | 758bf6b88680413d7c4e3ed32c1c485d0947a24f6e2c9ac7860be9cbe9d4e260 |
# encoding: utf-8
'''
PYROMS is a toolkit for working with ROMS ocean models
pyroms is based on the python/numpy/matplotlib scientific python suite.
NetCDF I/O is based on the NetCDF4-python package. The toolkit contains
general modeling tools for dealing with arrays, diagnosing standard
properties, curvilinear gr... | kshedstrom/pyroms | pyroms/pyroms/__init__.py | Python | bsd-3-clause | 616 | [
"NetCDF"
] | ed2ad9396fcf2f2b37739b53ee96b4336fbbb5b0183ca0b698ed83ee1bfa4f66 |
# -*- coding: utf-8 -*-
"""
- this will run webtests in TESTING database (db.testuri= from appconfig.ini)
- use sessions inside database: session.connect(request, response, db=db)
--or-- if you use shared file system sessions then always have same auth_user rows for used users in both databases
- pip install sele... | zvolsky/codex2020 | modules/plugin_splinter.py | Python | agpl-3.0 | 29,236 | [
"VisIt"
] | 13fc6155640e3f2d37e338600993b076fa1b07ac657c384376d26191378fd55f |
from random import random, randint
import math
import numpy as np
import plotly.plotly as py
import plotly.graph_objs as go
weightdomain = [(0, 20)] * 4
def wineprice(rating, age):
peak_age = rating - 50
price = float(rating) / 2
if age > peak_age:
price = price * (5 - (age - peak_age))
else... | luoshao23/ML_algorithm | Clustering/Pred_KNN.py | Python | mit | 4,903 | [
"Gaussian"
] | 684d5c5adcf1c9d7977c5c89a8021eca9952ed1bf26e08862ca50ccdc90d0e79 |
#!/usr/bin/env python
#-*- coding:utf-8 -*-
#
# This file is part of the NNGT project to generate and analyze
# neuronal networks and their activity.
# Copyright (C) 2015-2019 Tanguy Fardet
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License a... | Silmathoron/NNGT | nngt/lib/sorting.py | Python | gpl-3.0 | 6,483 | [
"NEURON"
] | 54fa21ff80d9886ce1b9d33ca1f1671543ab161885b9502df4a46e53a2fa6329 |
from firefly.core.common import config
from firefly.qt import QWidget
__all__ = ["BaseModule"]
class BaseModule(QWidget):
def __init__(self, parent):
super(BaseModule, self).__init__(parent)
self.main_window = self.parent().parent()
@property
def app_state(self):
return self.main... | immstudios/firefly | firefly/base_module.py | Python | gpl-3.0 | 686 | [
"Firefly"
] | c8d048e8303f1ceaa3d277219e67471caadaaa57045be5e921458de421d0493e |
## \file
## \ingroup tutorial_roofit
## \notebook
##
## \brief Multidimensional models: usage of full p.d.f. with per-event errors
##
## \macro_code
##
## \date February 2018
## \authors Clemens Lange, Wouter Verkerke (C++ version)
import ROOT
# B-physics pdf with per-event Gaussian resolution
# ---------------------... | karies/root | tutorials/roofit/rf307_fullpereventerrors.py | Python | lgpl-2.1 | 3,482 | [
"Gaussian"
] | 296f261f0d65506dac231bf9d65032cdc27a9bf183b78dac304c5571afba5b54 |
"""This generates urls to download climate data from the specified lat/lon coordinate and curls the
data at the address."""
import os
import sys
arguments = sys.argv[1:]
if arguments[0] == '-h' or arguments[0] == '--h' or arguments[0] == '--help':
print "MakeRequests.py arguments:"
print "(1) Latitude coordi... | ksaxberg/final_teamAZ | DataCollection/MakeRequests.py | Python | mit | 4,639 | [
"NetCDF"
] | 174b68dccf460c10038dcc1f986358f3e047582bda9e644ef0a7a661abc2b5e0 |
# coding=utf-8
# Copyright 2022 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... | google-research/google-research | jax_dft/jax_dft/neural_xc_test.py | Python | apache-2.0 | 16,276 | [
"Gaussian"
] | 29de7d7b27780eb9ab22e5806b69998f2b2ac6caf7e468ec376cb3debef1ef2c |
'''
Created on Aug 17, 2009
@author: Olivier Derpierre
'''
import logging
import re
import os
from octopus.dispatcher.poolman import IPoolManager, PoolDescription, ComputerDescription, ComputerNotFoundError, PoolNotFoundError
from octopus.dispatcher import settings
LOGGER = logging.getLogger("main.dispatcher")
WORKE... | mikrosimage/OpenRenderManagement | src/octopus/dispatcher/poolman/filepoolman.py | Python | bsd-3-clause | 6,156 | [
"Octopus"
] | e6a70ebff2a822b14aa8cfafb8dd3d00ad4ab5121f899630c62d6ab30bf7eff3 |
import os, sys
import rethinkdb as r
import hashlib
from mutation_stability import mutation_stability
class run_stability():
def __init__(self, split_number):
try:
self.sequence_file = open(split_number + "_sequences_file.txt", 'r')
except:
print("That sequence file does no... | blab/stability | augur/stability-data/foldx_essentials/run_stability_cluster.py | Python | agpl-3.0 | 9,538 | [
"FoldX"
] | 97e53d9da248cd2aaf11a6e0743d12c6ab9b74f2c2a17e9492bb84f568613e68 |
"""genetic.py
Library for Genetic Algorithm
"""
DEFLIMIT = 2.0
import random
class Generation(object):
"""Generation is used as easy interface to interact with the
library.
Keyword arguments:
vallstlst -- list of list with values of chromosomes
fitnesslst -- list of fitness respectivily of... | osergeev/bike | genetic.py | Python | gpl-2.0 | 11,384 | [
"Gaussian"
] | 70251770b8322857f27ffa6ab7ba53cf92a52c031e2edfce8fd9cd2f013274a0 |
#
# Copyright (C) 2017-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | pkreissl/espresso | testsuite/python/force_cap.py | Python | gpl-3.0 | 1,992 | [
"ESPResSo"
] | 80131c1fa95dd3ef0fca6785029b5ccc3ff61f3fd7a2416fb731c6e7cd919d00 |
from Task import Task
from learning.featureBuilders import *
class CAFA3Task(Task):
def __init__(self):
Task.__init__(self)
# Task settings
self.allowMissing = False
self.limitTrainingToAnnotated = True
# Data files
self.sequencesPath = "Swiss_Prot/Swissprot_sequence... | TurkuNLP/CAFA3 | task/tasks.py | Python | lgpl-3.0 | 5,680 | [
"BLAST"
] | fecc5bff7d417d3a1df368851bfe04b2a3cbc3888084f65a0cd0b73cebcbdfe7 |
##############################################################################
# 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/r-vsn/package.py | Python | lgpl-2.1 | 2,743 | [
"Bioconductor"
] | 9b6b0b429d5ae783f9af519d201452b33a74f9b105a01c7ba2aa829d171b4621 |
import asyncio
import importlib
import json
import signal
import sys
from concurrent.futures import ThreadPoolExecutor
from os import path
from pathlib import Path
from typing import Any
from time import sleep
from aiohttp import web
from Firefly import aliases, logging, scheduler
from Firefly.const import COMPONENT_... | Firefly-Automation/Firefly | Firefly/core/core.py | Python | apache-2.0 | 16,522 | [
"Firefly"
] | 0196d6ad754382b1bb213266c6fd02d00b9971c019eab63a6bf92a954aab2640 |
"""Utilities used in the Kadenze Academy Course on Deep Learning w/ Tensorflow.
Creative Applications of Deep Learning w/ Tensorflow.
Kadenze, Inc.
Parag K. Mital
Copyright Parag K. Mital, June 2016.
"""
import matplotlib.pyplot as plt
import tensorflow as tf
import urllib
import numpy as np
import zipfile
import os
... | niazangels/CADL | session-3/libs/utils.py | Python | apache-2.0 | 20,961 | [
"Gaussian"
] | 5d8a6928b112047f4a630478ff513e11748041aad709a964b59ecf87f8636334 |
"""
NL2BR Extension
===============
A Python-Markdown extension to treat newlines as hard breaks; like
StackOverflow and GitHub flavored Markdown do.
Usage:
>>> import markdown
>>> print markdown.markdown('line 1\\nline 2', extensions=['nl2br'])
<p>line 1<br />
line 2</p>
Copyright 2011 [Brian Neal]... | isnowfy/pydown | markdown/extensions/nl2br.py | Python | mit | 781 | [
"Brian"
] | eeb5b70a584334239896164b40ccb98c65d37ae55afc217d931ed385cd5a4599 |
"""
Tests i18n in courseware
"""
import re
from django.conf import settings
from django.contrib.auth.models import User
from django.core.urlresolvers import reverse
from django.test import TestCase
from django.test.client import Client
from django.utils import translation
from nose.plugins.attrib import attr
from op... | caesar2164/edx-platform | lms/djangoapps/courseware/tests/test_i18n.py | Python | agpl-3.0 | 8,577 | [
"VisIt"
] | 855afdf93e18c411b150c02615e7be2b8acb9ebaf9f3badcc781f508d046c671 |
"""
AST nodes for C constructs.
"""
import os
import types
import subprocess
import logging
log = logging.getLogger(__name__)
from ctypes import CFUNCTYPE
from ..nodes import CtreeNode, File
from .. import CONFIG
from ..util import singleton, highlight, truncate
from ..types import get_ctype, get_common_ctype, get_... | alphaFred/Sejits4Fpgas | sejits4fpgas/src/vhdl_ctree/c/nodes.py | Python | gpl-3.0 | 18,561 | [
"VisIt"
] | 417e2bbc12251e9ad01026077b34dc7711ba65b35260fc6a24660d4d562158e6 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Simulation framework for testing LDSC
Models for SNP effects:
- Infinitesimal (can simulate n correlated traits)
- Spike & slab (can simulate up to 2 correlated traits)
- Annotation-informed
Features:
- Field aggregation tools for annotation-informed m... | hail-is/hail | hail/python/hail/experimental/ldscsim.py | Python | mit | 41,334 | [
"Gaussian"
] | c31a6197b6612fff36fb8f4ae55a453a27c7a2c8b4984bd9af4393e8ad96d0b5 |
#
# This script receives a list of fasta files, reads the content of each one
# and writes it to a single fasta-formatted file.
#
import argparse, os, shutil, fnmatch
# Process command arguments
parser = argparse.ArgumentParser()
parser.add_argument('-gnm', action="store", dest='basename')
parser.add_argument('-out_... | davidwilson-85/easymap | process_input/fasta-concat.py | Python | gpl-3.0 | 1,982 | [
"Biopython"
] | 867922d59982d45e8c4fa7871871e31377cd616a6f758fb5506a42c35e730806 |
# -*- test-case-name: "industrialise.tests.test_browser" -*-
import urllib
import urllib2
import urlparse
import cookielib
import robotparser
from lxml.html import fromstring, submit_form
import wsgi_intercept
from wsgi_intercept.urllib2_intercept.wsgi_urllib2 import WSGI_HTTPHandler
from industrialise import __vers... | rweir/industrialise | industrialise/browser.py | Python | bsd-3-clause | 6,483 | [
"VisIt"
] | cb042b9cb30f2a2579664402721ea41560c57a4cf9b3bf38dbbfc48de6740545 |
import os
import numpy as np
import deepchem as dc
from rdkit import Chem
seed = 123
np.random.seed(seed)
base_dir = os.getcwd()
data_dir = os.path.join(base_dir, "refined_atomconv")
train_dir = os.path.join(base_dir, "train")
test_dir = os.path.join(base_dir, "test")
pdbbind_dir = os.path.join(base_dir, "v2015")
pri... | deepchem/deepchem | contrib/atomicconv/splits/pdbbind_scaffold_split.py | Python | mit | 2,309 | [
"RDKit"
] | d88bc18f1493bf0de899290e09713a04c2be9ebcd62a2f6d136ec2e26b4eae88 |
#!/usr/bin/env python
# Authors: Andrew Jewett (jewett.aij at g mail)
# http://www.chem.ucsb.edu/~sheagroup
# License: 3-clause BSD License (See LICENSE.TXT)
# Copyright (c) 2011, Regents of the University of California
# All rights reserved.
"""
ttree Ttree is a simple program for recursively composing and ... | takaakiaoki/my-lammps | tools/moltemplate/src/ttree.py | Python | gpl-2.0 | 209,799 | [
"LAMMPS",
"NAMD",
"VisIt"
] | 3354ff4c1069df70c6792aab1c1555c862ae095bfc9b9306176c2df83ae0ba60 |
""" Test class for Pilot Status Agent
"""
# imports
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import pytest
from mock import MagicMock
# DIRAC Components
from DIRAC.WorkloadManagementSystem.Agent.PilotStatusAgent import PilotStatusAgent
from DIRAC imp... | yujikato/DIRAC | src/DIRAC/WorkloadManagementSystem/Agent/test/Test_Agent_PilotStatusAgent.py | Python | gpl-3.0 | 3,770 | [
"DIRAC"
] | ff865e75b00708f38b0dc4d6e599b1ddbbdfbe5aa467f870d6c61ed21baa91a8 |
# -*- coding: utf-8 -*-
# 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 opt... | madscatt/zazzie | src/sassie/contrast/multi_component_analysis/stoichiometry.py | Python | gpl-3.0 | 12,811 | [
"Avogadro"
] | 275e54b8f5a97e8455abf6d0a1e895b51aa104c1e2a167262e22f565035acfc9 |
import mock
from django.test import TestCase
from django.utils import timezone
from myvoice.clinics.models import Visit
from myvoice.core.tests import factories
from .. import tasks
from .. import models
from ..textit import TextItException
@mock.patch('myvoice.survey.tasks.importer.import_responses')
class TestIm... | myvoice-nigeria/myvoice | myvoice/survey/tests/test_tasks.py | Python | bsd-2-clause | 7,690 | [
"VisIt"
] | 75a205ea4bd4174d94d6518a890aae748eb8738030772da72fd3f41c96ce64cb |
# pylint: disable=I0011, C0111, no-self-use
from parsimonious.nodes import NodeVisitor
class Transformer(object):
def __init__(self, parser):
self.visitor = Visitor([expr for expr in parser.grammar])
def transform(self, parsed):
self.visit(parsed)
return self.visits()
def visit... | teleological/camxes-py | transformers/node_coverage.py | Python | mit | 1,142 | [
"VisIt"
] | a15f8e4e3a6f5b776f315eb7765b45aecf3c6dbbce7b325f024cc33824cfae88 |
import argparse
import sys
import logging
import os
import shutil
import math
from collections import OrderedDict
import pysam
import csv
class LocusItem(object):
def __init__(self, chromosome, TSS_start, TSS_end, name, score, strand, gene_body_start, gene_body_end):
self.Chromosome = chromosome
self.TSS_sta... | shengqh/ngsperl | lib/Chipseq/getReadCount.py | Python | apache-2.0 | 8,837 | [
"pysam"
] | 680a50bbabfa238193e16b3fe8b714229db78f30717198ad2b0b73c89bb82896 |
""" Model definition for base class for Mixed Linear/Nonlinear Gaussian systems
@author: Jerker Nordh
"""
from pyparticleest.models.rbpf import RBPSBase
import scipy.linalg
import numpy.random
import math
try:
import pyparticleest.utils.ckalman as kalman
import pyparticleest.utils.cmlnlg_compute as mlnlg_comp... | jerkern/pyParticleEst | pyparticleest/models/mlnlg.py | Python | lgpl-3.0 | 53,683 | [
"Gaussian"
] | aa7f9ce11c92ec57e91d9ac7dc7195b3ca665b5f8ab699d4a7245b2b656617ca |
#!/usr/bin/env python
"""Bash completion for ase-db, ase-run, ase-build, ase-info and ase-gui.
Put this in your .bashrc::
complete -o default -C _ase_bash_complete.py ase-db ase-run \
ase-build ase-info ase-gui
"""
import os
import sys
from glob import glob
command, word, previous = sys.argv[1:]
line = ... | misdoro/python-ase | tools/_ase_bash_complete.py | Python | gpl-2.0 | 2,250 | [
"ASE",
"CRYSTAL"
] | 0c5d106ad52950b9cb31a42e797b17166450bca2ac547bbd77775be9a05d70ac |
""" Given a force field in Tinker format this script will write out a C++ source
file for that force field
"""
from FManII import *
class ForceField:
def __init__(self):
self.rad_type=""
self.rad_size=""
self.params={}
self.type2class={}
self.terms={}
self.orderrules... | ryanmrichard/ForceManII | bin/ParseFF.py | Python | lgpl-3.0 | 11,829 | [
"TINKER"
] | b0244f467a6655ed7e85d77082dad3d818fb3cfcf62b79ba7c26e82b35d50e87 |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
MAST Authentication
===================
This file contains functionality related to
authenticating MAST users.
"""
import os
import keyring
import warnings
from getpass import getpass
from astroquery import log
from ..exceptions import Authenticat... | imbasimba/astroquery | astroquery/mast/auth.py | Python | bsd-3-clause | 3,939 | [
"VisIt"
] | c3d7ea682ae26ebaf2ed5e2d186cadc1e71b2bafd95c5d0135d8b0d8db3badf5 |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | highfei2011/spark | examples/src/main/python/sql/datasource.py | Python | apache-2.0 | 9,076 | [
"COLUMBUS"
] | af4108f93bbd74ce2bf0464421027766db47cb643f8b02a4c4ba60754338d224 |
#!/usr/bin/env python
"""
Reads a list of intervals and a maf. Produces a new maf containing the
blocks or parts of blocks in the original that overlapped the intervals.
If a MAF file, not UID, is provided the MAF file is indexed before being processed.
NOTE: If two intervals overlap the same block it will be written... | martenson/tools-iuc | tools/interval2maf/interval2maf.py | Python | mit | 6,030 | [
"Galaxy"
] | d8f433dd2f1317f51515b76e845f2afba013d4750cf839614706ca95e6de4252 |
# encoding: utf-8
# Written for Python 3.6
import os
import sys
import math
import cage
import numpy as np
import pymatgen as pmg
import pymatgen.io.nwchem as nwchem
"""
Script to set up the calculations for a chain of paths connecting the non
equivalent facets of a cage molecule.
"""
# TODO Make these parameters ... | mbercx/cage | cage/scripts/twocats/chain_old.py | Python | mit | 9,142 | [
"NWChem",
"pymatgen"
] | e9aded0003ca11dffbc12fc450e9ccdf14161af49364fee23e328cf50a067056 |
# Copyright (C) 2010-2018 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 v... | hmenke/espresso | testsuite/python/thole.py | Python | gpl-3.0 | 2,420 | [
"ESPResSo"
] | 936941444cc4ca6cba139672434d8e3a42d6b3c5366e12719f2f6d1f3c8a5947 |
from __future__ import absolute_import, division, print_function, unicode_literals
import json
import warnings
from tonnikala.languages.base import LanguageNode, ComplexNode, BaseGenerator
from slimit.parser import Parser
from slimit import ast
from slimit.ast import *
from collections.abc import Iterable
from slimit... | tetframework/Tonnikala | tonnikala/languages/javascript/generator.py | Python | apache-2.0 | 23,014 | [
"VisIt"
] | 8bcfaaf00fc421bc197cedc6929b4bb93c9714e4272963009478d6f711364b26 |
# Copyright 2013 Allen Institute
# This file is part of dipde
# dipde 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.
#
# dipde is dis... | AllenInstitute/dipde | dipde/examples/cortical_column.py | Python | gpl-3.0 | 9,045 | [
"Brian"
] | e0da2a21587b0cc6b5f7e15ddd6a7fb7e1d9f21c1d213eabcb256bb74932ec74 |
# -*- coding: utf-8 -*-
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding the extended fields to the base model,
# since there are fewer of them and I know what
# ... | neuroelectro/neuroelectro_org | neuroelectro/south_migrations/0069_user_fixes.py | Python | gpl-2.0 | 31,632 | [
"NEURON"
] | fccd6bf4711a62c1e6c91e0aeabe28165cf5ac9113dabd9305194a1424838cf8 |
"""
.. _ref_geometric_example:
Geometric Objects
~~~~~~~~~~~~~~~~~
The "Hello, world!" of VTK
"""
import pyvista as pv
###############################################################################
# This runs through several of the available geometric objects available in
# VTK which PyVista provides simple conven... | akaszynski/vtkInterface | examples/00-load/create-geometric-objects.py | Python | mit | 1,355 | [
"VTK"
] | 960c5fca10b2208048e0f728cc8e5c36ddf14cc8d8f59eeee6c4440f50aacd74 |
""" DIRAC Graphs package provides tools for creation of various plots to provide
graphical representation of the DIRAC Monitoring and Accounting data
The DIRAC Graphs package is derived from the GraphTool plotting package of the
CMS/Phedex Project by ... <to be added>
"""
import importlib.resources
# Mak... | DIRACGrid/DIRAC | src/DIRAC/Core/Utilities/Graphs/__init__.py | Python | gpl-3.0 | 6,033 | [
"DIRAC"
] | a5302fdcd133b31e1f1aea5a831b98c8f76cfe0cbb27fc878833220fe03ed4c1 |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | gregcaporaso/scikit-bio | skbio/io/format/tests/test_blast7.py | Python | bsd-3-clause | 9,968 | [
"scikit-bio"
] | 015a92c79ddd349ee4cf7c561183c6e55fad1696e684c22279200f5b48bd20c7 |
import numpy as np
import matplotlib
from matplotlib import pyplot as plt
import pyfits as pf
from lmfit import minimize, Parameters, fit_report
from lmfit.models import GaussianModel
############# Functions to perform #############
def plot_spec(data_file):
plt.figure()
plt.imshow(data_file, cmap = 'gray', vmin ... | UCBerkeleySETI/breakthrough | APF/Tutorial/tutorial_code_final_github.py | Python | gpl-3.0 | 4,926 | [
"Gaussian"
] | 26a3d3d03e83cb4184911612f884f9ea07def6ed8c9ce8f75e24a871040c0807 |
import numpy as np
class GaussianNaiveBayes(object):
def __init__(self, class_priors=None):
self.mean, self.variance, self.classes = None, None, None
self.class_priors_provided = False
self.class_priors = None
if class_priors:
self.class_priors_provided = True
self.class_priors = class_priors
def... | MayankAgarwal/MachineLearning | ml/classification/naive_bayes/GaussianNaiveBayes.py | Python | gpl-3.0 | 6,154 | [
"Gaussian"
] | 48f38c648106a251e9fe7ab448960eb4938e3772f71b183f72dcb17324779584 |
# Copyright 2015 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... | seanli9jan/tensorflow | tensorflow/python/ops/gradients_impl.py | Python | apache-2.0 | 51,512 | [
"VisIt"
] | 20c217a366072da4f4563bfb2e66c730b02f72a1945bde9f874772a19946c55e |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | jensreeder/scikit-bio | skbio/diversity/alpha/tests/test_lladser.py | Python | bsd-3-clause | 7,629 | [
"scikit-bio"
] | 0691e239f145675ef9c9519b42531bcbc752307b4a1e482970f23e4e5e726429 |
"""Build a RNN model """
from __future__ import absolute_import
from __future__ import print_function
from __future__ import division
import os
import sklearn as sk
import tensorflow as tf
from tensorflow.contrib import rnn
from tensorflow.contrib import seq2seq as s2s
import numpy as np
from decorators import *
... | jeremy24/rnn-classifier | model.py | Python | mit | 32,171 | [
"Gaussian"
] | be7cc94932e479446cc139e80d26a643c98163dcba8f82740fa88bf5bfb4d616 |
#!/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/ajax/radio.py | Python | gpl-2.0 | 5,838 | [
"VisIt"
] | 7188d5cc320a095c4878d2b86197e112f027f6a1858d3f9c8368f0ba6ee18fd9 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from pymatgen.analysis.prototypes import AflowPrototypeMatcher
from pymatgen.util.testing import PymatgenTest
class AflowPrototypeMatcherTest(PymatgenTest):
def test_prototype_matching(self):
af ... | gmatteo/pymatgen | pymatgen/analysis/tests/test_prototypes.py | Python | mit | 1,391 | [
"pymatgen"
] | 8b0680f4a3a6c1c0088bf3b112abc6fbc2e2327ef859bf3d34e4a72b9f47a79e |
"""
The main client API you'll be working with most often. You'll need to
configure a dropbox.session.DropboxSession for this to work, but otherwise
it's fairly self-explanatory.
"""
import re
import simplejson as json
from dropbox.rest import ErrorResponse
from dropbox.rest import RESTClient
def format_path(path):... | AlphaX2/FotoShareN9 | 1.6.1/fotoshare/opt/FotoShareN9/plugins/dropbox/libs/dropbox/client.py | Python | gpl-3.0 | 29,287 | [
"VisIt"
] | 98a35bbb4997f57b8fb5f011f58b4ef20a917a7845102f548dc01b38a89e6ef9 |
# -*- coding: utf-8 -*-
"""Generate the attributes.rst and attributes_dev.rst files from the
ccData docstring that describes attributes."""
from docs_common import check_cclib
import cclib
check_cclib(cclib)
def generate_attributes():
"""Generate a string containing a reStructuredText table
representation ... | cclib/cclib | doc/sphinx/attributes.py | Python | bsd-3-clause | 3,056 | [
"cclib"
] | 6722e028148e552772a058e5fd7d665374b2e5388a3885c9c9f33bc73a95f8f4 |
#!/usr/bin/env python
'''By Ryan Gao, 2014 '''
from splinter import Browser
from sys import argv
url = "http://THE_DEFAULT_URL/{0}"
path = "/THE_DEFAULT_AJAX_AFTER_SHEBANG"
def load_by_firefox(path):
with Browser() as browser:
# Visit URL
path = url.format(path)
print 'Vi... | wolf0403/ajax-for-dummies | sp.py | Python | unlicense | 713 | [
"VisIt"
] | d5b8f8ceeb51e9ac58711454a1ea76afd3f3cb0d6457a59236ba787b8a1e5f2c |
from json import loads as _parseJSON
from datetime import datetime as _datetime
from dateutil import tz as _tz
from shutil import rmtree as _rmtree
from urllib.request import urlopen as _urlopen
from subprocess import getstatusoutput as _getstatusoutput
from subprocess import call as _call
import os as _os
import re as... | LeoIannacone/npm2deb | npm2deb/__init__.py | Python | gpl-3.0 | 24,379 | [
"CRYSTAL"
] | d85cd576794a9ed207b9783426972169e88c60dfe0e3d877ab424ba98f4dae7d |
'''
fs.contrib.tahoelafs
====================
This modules provides a PyFilesystem interface to the Tahoe Least Authority
File System. Tahoe-LAFS is a distributed, encrypted, fault-tolerant storage
system:
http://tahoe-lafs.org/
You will need access to a Tahoe-LAFS "web api" service.
Example (it wil... | GbalsaC/bitnamiP | venv/lib/python2.7/site-packages/fs/contrib/tahoelafs/__init__.py | Python | agpl-3.0 | 15,448 | [
"VisIt"
] | 75476d702fb129a682009bf63923f589d6a9f1dd24d5c0220b1a2dfce6b5d922 |
# Copyright (c) 2018 PaddlePaddle 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 app... | PaddlePaddle/Paddle | python/paddle/fluid/initializer.py | Python | apache-2.0 | 42,337 | [
"Gaussian"
] | 9d4c4d0066ba1e94e9f494481dc0271a7be30e44cb0165420a1cae7be8622a96 |
"""
Authors: Damien Irving (irving.damien@gmail.com)
Copyright 2015 CSIRO
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 l... | taerwin/cwsl-mas | cwsl/vt_modules/vt_ensemble_agg.py | Python | apache-2.0 | 3,631 | [
"NetCDF"
] | c707e69a4884b52ea583dcd185ecf2679c57eeb6cb2f63cc57185c453af22867 |
__all__ = [
'TopoReader',
'GravObsReader',
'GravGradReader',
'MagObsReader',
'GeologyMapper',
]
__displayname__ = 'General Tools'
import numpy as np
import pandas as pd
import vtk
from vtk.numpy_interface import dataset_adapter as dsa
from .. import _helpers, interface
from ..base import FilterPr... | banesullivan/ParaViewGeophysics | PVGeo/ubc/general.py | Python | bsd-3-clause | 10,897 | [
"VTK"
] | d4853993303c07d20772f3bc45db3ad090d0fd56fb4e942c4f67b9ae3b636bcf |
""" Testing the API and a bit more.
It will submit a number of test jobs locally (via runLocal), using the python unittest to assess the results.
Can be automatized.
"""
# pylint: disable=protected-access, wrong-import-position, invalid-name, missing-docstring
import os
import sys
import unittest
import multi... | andresailer/DIRAC | tests/Workflow/Integration/Test_UserJobs.py | Python | gpl-3.0 | 6,666 | [
"DIRAC"
] | 3689284521c842b991a33c884e75a2126844663a7310d08dd9fbbb8c421ddf32 |
#
# QAPI command marshaller generator
#
# Copyright IBM, Corp. 2011
# Copyright (C) 2014 Red Hat, Inc.
#
# Authors:
# Anthony Liguori <aliguori@us.ibm.com>
# Michael Roth <mdroth@linux.vnet.ibm.com>
# Markus Armbruster <armbru@redhat.com>
#
# This work is licensed under the terms of the GNU GPL, version 2.
# See ... | VishalRohra/orp | third-party/qemu-orp/scripts/qapi-commands.py | Python | apache-2.0 | 12,372 | [
"VisIt"
] | e70d9ce4b34205e4ac909de9f7359f8467f78f1070569e74127f25ea7a76427d |
import numpy as np
import pickle
from numpy import fromfile
import pylab as pl
from operator import itemgetter
import scipy.io as io
import numpy as np
# print readicecube(fin,(1,35,52),(5,),(3,))
def readicecube(filestream,shp,dimiterref,dimpos,icecube,mode='read',dimnoiterref=None):
"""
read data icecube fro... | hendrikwout/pynacolada | trash/pynacolada-20130924.py | Python | gpl-3.0 | 19,038 | [
"NetCDF"
] | 62171bc2f40e8633198ad60f9de49da7498b45ee04ca5542710bc772fa6fd123 |
"""
Python code clone detector,
using Abstract Syntax Trees.
"""
import ast
import collections
__author__ = 'FBV'
__license__ = 'MIT'
__version__ = '0.0.2'
__status__ = 'alpha'
class Position(ast.NodeVisitor):
'''
Find a clone position in the code (its line-span).
Count child nodes.
'''
def ini... | ActiveState/code | recipes/Python/578206_Pythcode_clone_detector_Dont_Repeat/recipe-578206.py | Python | mit | 5,290 | [
"VisIt"
] | 81ec16f8a0bef88f1ad1598cdff4124b29df5f763a65c25287251f9bb1e42e96 |
"""Reaction.py: Methods to execute reactions."""
import collections
import multiprocessing
from functools import partial
from typing import Tuple
import rdkit.rdBase as rkrb
import rdkit.RDLogger as rkl
from rdkit.Chem.AllChem import (
AddHs,
CalcMolFormula,
Kekulize,
MolFromSmiles,
MolToSmiles,
... | JamesJeffryes/MINE-Database | minedatabase/reactions.py | Python | mit | 18,262 | [
"RDKit"
] | c8858880fb536a1191562367d9921d9885ad4ada9b8a4ea697580c0b3016af99 |
import pylab
import nest
nest.ResetKernel()
neuron = nest.Create("iaf_neuron")
nest.SetStatus(neuron, {"I_e": 376.0})
multimeter = nest.Create("multimeter")
nest.SetStatus(multimeter, {"withtime": True, "record_from": ["V_m"]})
nest.GetStatus(multimeter)
spikedetector = nest.Create("spike_detector", params={"withgid"... | rlopc/datcom-labs | ugr-datcom-ncc_ni-labs/ugr-datcom-ncc_ni-lab_01/ejemplo1.py | Python | gpl-3.0 | 742 | [
"NEURON"
] | e95bef88d72eead5d3a489d6be34cd3c538545fa400658a93771a02718df2c07 |
#
# Copyright 2016 The BigDL Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in ... | intel-analytics/BigDL | python/chronos/src/bigdl/chronos/data/experimental/xshards_tsdataset.py | Python | apache-2.0 | 8,852 | [
"ORCA"
] | e27b0a81a17805808e1b8a82f028d003165cde8cc7d5fea8c59e4d1ec2ccca74 |
# This file is part of Androguard.
#
# Copyright (C) 2012, Geoffroy Gueguen <geoffroy.gueguen@gmail.com>
# 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:/... | kanpol/abugfinder | tools/modified/androguard/decompiler/dad/instruction.py | Python | gpl-3.0 | 38,522 | [
"VisIt"
] | 36c11d1953c4a001a6868a17bc9771184a15dba92a5a9c6d5f083fe1f79c771d |
#!/usr/bin/env python
# Copyright NumFOCUS
#
# 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.txt
#
# Unless required by applicable law or ... | InsightSoftwareConsortium/ITKExamples | src/Bridge/VtkGlue/ConvertvtkImageDataToAnitkImage/Code.py | Python | apache-2.0 | 1,236 | [
"VTK"
] | 111415662c471a3a3fa63b0ff1aa89b91155d83b513131a87f11eaeb98ea22a2 |
import os
import os.path as op
from os.path import join as pjoin
import sys
import warnings
import pytest
from mayavi import mlab
import nibabel as nib
import numpy as np
from numpy.testing import assert_array_equal, assert_array_less
from unittest import SkipTest
from surfer import Brain, io, utils
from surfer.util... | Eric89GXL/PySurfer | surfer/tests/test_viz.py | Python | bsd-3-clause | 16,479 | [
"Mayavi"
] | b57864f01cd3e7a80e31d465339e44bd827abff60ae0a3a8a38643f17385d668 |
#! /usr/bin/python
# -*- coding: utf-8 -*-
"""The base class of game entities."""
from collections import ChainMap
from copy import copy as cp
from itertools import chain
import re
from .player_operation import PlayerOps, PlayerOpTree, translate_po_tree
from ..utils.game import Zone, Type, DHBonusType
from ..utils.m... | fyabc/MiniGames | HearthStone2/MyHearthStone/game/game_entity.py | Python | mit | 27,053 | [
"BLAST"
] | fe55febb7a7608c916bd875220cce093bf4f93e21149a455e321d126dd00352b |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2003-2007 Donald N. Allingham
# Copyright (C) 2007-2012 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2012 Nick Hall
# Copyright (C) 2011-2016 Paul Franklin
#
# This program is free software; you can redistribute it... | SNoiraud/gramps | gramps/gui/plug/report/_bookdialog.py | Python | gpl-2.0 | 42,854 | [
"Brian"
] | 650aefb62985389bcccb7ce488c85f52ca4bec05d47af31bf06d1e3f78fb5b6c |
"""
font data tables for truetype and afm computer modern fonts
"""
latex_to_bakoma = {
'\\__sqrt__' : ('cmex10', 0x70),
'\\bigcap' : ('cmex10', 0x5c),
'\\bigcup' : ('cmex10', 0x5b),
'\\bigodot' : ('cmex10', 0x4b),
'\\bigoplus' ... | iproduct/course-social-robotics | 11-dnn-keras/venv/Lib/site-packages/matplotlib/_mathtext_data.py | Python | gpl-2.0 | 56,423 | [
"Bowtie"
] | fc4c26622876d94a690e5c90ef3865b55bbc8699cc4bdc7a8a23135d54d1dc11 |
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