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"""
Krige CV
--------
Searching for optimal kriging parameters with cross validation
"""
import numpy as np
from pykrige.rk import Krige
from pykrige.compat import GridSearchCV
# 2D Kring param opt
param_dict = {"method": ["ordinary", "universal"],
"variogram_model": ["linear", "power", "gaussian", "... | rth/PyKrige | examples/krige_cv.py | Python | bsd-3-clause | 1,902 | [
"Gaussian"
] | 4fafcdfa29d64cdbd595bf914073a5d05b7b9a6b1fe88b21700ddafa6d9ec96b |
import os
import textwrap
from io import StringIO
import numpy as np
from mock import patch
from nose.tools import eq_, ok_
import neurom.io as io
import neurom.io.neurolucida as nasc
from neurom.core.dataformat import COLS
from neurom.io.datawrapper import DataWrapper
_path = os.path.dirname(os.path.abspath(__file_... | juanchopanza/NeuroM | neurom/io/tests/test_neurolucida.py | Python | bsd-3-clause | 7,736 | [
"NEURON"
] | 9e96ea029424114255ad607b285d3b252d7de982a886658ebb84d0cc791d4fa4 |
# Author: Samuel Genheden samuel.genheden@gmail.com
"""
Program to create a hybrid MARTINI topology
The AA structure should have the same order as the structure
created by automartini. This is important since antechamber reshuffles
the atoms.
This script requires the branch write_virtualn of my version of parmed
ava... | SGenheden/Scripts | Mol/make_hybridtop.py | Python | mit | 2,749 | [
"Gromacs"
] | c3f3e56c24551ba7c9d2e053873a5a55f6c9bffb45b6db3872e5e8106395aa29 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
import time
# Configuration, please edit
# Data about this site
BLOG_AUTHOR = "Laurent Perrinet"
BLOG_TITLE = "SciBlog"
# This is the main URL for your site. It will be used
# in a prominent link
SITE_URL = "http://blog.invibe.net/"
# This is the URL wh... | meduz/invibe | conf.py | Python | artistic-2.0 | 24,248 | [
"VisIt"
] | 6c84d68cde3c8d057719e6c5f6df293222bff2120db259d9cd400a46600633bc |
"""A source object that computes stress tensors on a volume.
The tensors are computed from the application of a point load on a
semi-infinite domain.
"""
# Authors: KK Rai (kk.rai [at] iitb.ac.in)
# R. Ambareesha (ambareesha [at] iitb.ac.in)
# Prabhu Ramachandran (prabhu [at] aero.iitb.ac.in... | dmsurti/mayavi | mayavi/sources/point_load.py | Python | bsd-3-clause | 2,160 | [
"Mayavi"
] | be9b8183a62d0b01273a4fcc682e1eca79d62329745b5d2010bb2d40757f2b74 |
# -*- coding: utf-8 -*-
from __future__ import absolute_import, print_function, division
# standard library dependencies
import io
import itertools
import json
import inspect
from json.encoder import JSONEncoder
from petl.compat import PY2
from petl.io.sources import read_source_from_arg, write_source_from_arg
# inte... | alimanfoo/petl | petl/io/json.py | Python | mit | 9,874 | [
"VisIt"
] | 5cbe0a5ece6caa417e6fde1c2a92540aff544ca2520b1f4ebad89d143d096f16 |
""" Models for the shopping cart and assorted purchase types """
from collections import namedtuple
from datetime import datetime
from datetime import timedelta
from decimal import Decimal
import analytics
from io import BytesIO
import pytz
import logging
import smtplib
import StringIO
import csv
from boto.exception i... | jazkarta/edx-platform-for-isc | lms/djangoapps/shoppingcart/models.py | Python | agpl-3.0 | 73,304 | [
"VisIt"
] | 72167d38ce4b044acff67573687907c7b26454282834a07d1a193f1adb6718c0 |
# -*- coding: utf-8 -*-
#
# Copyright (C) Pootle contributors.
# Copyright (C) Zing contributors.
#
# This file is a part of the Zing project. It is distributed under the GPL3
# or later license. See the LICENSE file for a copy of the license and the
# AUTHORS file for copyright and authorship information.
import loca... | evernote/zing | pootle/apps/pootle_language/models.py | Python | gpl-3.0 | 8,648 | [
"VisIt"
] | 1b273881d152ec4ba6d8bc5c17be7db305158ae39c6c1e7b108208fa4af6d5e5 |
"""
Implements compartmental model of a passive cable. See Neuronal Dynamics
`Chapter 3 Section 2 <http://neuronaldynamics.epfl.ch/online/Ch3.S2.html>`_
"""
# This file is part of the exercise code repository accompanying
# the book: Neuronal Dynamics (see http://neuronaldynamics.epfl.ch)
# located at http://github.c... | EPFL-LCN/neuronaldynamics-exercises | neurodynex3/cable_equation/passive_cable.py | Python | gpl-2.0 | 6,153 | [
"NEURON"
] | 625e9a37b74e205b643f88a05c915988f95a9b1ca4aab30b657291fdf42d7a5f |
#!/bin/python
import subprocess
import socket
from SCons.Script import DefaultEnvironment
env = DefaultEnvironment()
def before_build_spiffs(source, target, env):
env.Execute("node node_modules/gulp/bin/gulp.js")
env.AddPreAction(".pioenvs/%s/spiffs.bin" % env['PIOENV'], before_build_spiffs)
| dgunther/espurna_blynk | code/pio_hooks.py | Python | gpl-3.0 | 300 | [
"GULP"
] | 3412ee0ab8917c9196085df97989af00ceac0f8ab7c546b64934851357397dd0 |
import os.path
import subprocess
import time
import signal
# From this package
import lib.error as error
import lib.util as util
import lib.test_framework as test_framework
class Runner(test_framework.AbstractRunner):
LEVEL = 4
DURATION = "30s"
OPEN_CUT = '-' * 20 + '8<' + '-' * 20
CLOSE_CUT = '-' * 2... | xthexder/stripe-ctf-3.0 | level5/test/runner.py | Python | mit | 4,034 | [
"Octopus"
] | 8022eeb644026d277a9b766cf7a9c625929471057afe572ffa6b7e9d8bc81c8b |
# Miro - an RSS based video player application
# Copyright (C) 2005, 2006, 2007, 2008, 2009, 2010, 2011
# Participatory Culture Foundation
#
# 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; eithe... | debugger06/MiroX | tv/lib/frontends/widgets/gtk/window.py | Python | gpl-2.0 | 24,475 | [
"VisIt"
] | 4e0c5e901dfe4e7aa63c39caac907164ed2a758776b5b0900ce82318786a1ce8 |
# -*- coding: utf-8 -*-
# Copyright (c) 2016-2021 Wintermute0110 <wintermute0110@gmail.com>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; version 2 of the License.
#
# This program is distr... | Wintermute0110/plugin.program.advanced.emulator.launcher | resources/scrap.py | Python | gpl-2.0 | 242,932 | [
"VisIt"
] | c1ba966d81a2658be5605cd7108abce9c92733dab1501b8bd43599ee78fdea2b |
#-*- coding:utf-8 -*-
phb_spell = {
"Acid splash": "Брызги кислоты",
"Aid": "Подмога",
"Alarm": "Сигнал тревоги",
"Alter self": "Смена обличья",
"Animal friendship": "Дружба с животными",
"Animal messenger": "Почтовое животное",
"Animal shapes": "Превращение в животных",
"Animate dead":... | kestel/dndmonstertrans | dicts/spells.py | Python | bsd-2-clause | 29,706 | [
"BLAST"
] | 2bece18cff0a5381d70af2c9afa0ca3fd7d74ec4e512684955540e504bd92f43 |
# This file is part of MOOSE simulator: http://moose.ncbs.res.in.
# MOOSE 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.
# MOOSE is ... | rahulgayatri23/moose-core | python/libmumbl/nml_parser/NetworkML.py | Python | gpl-3.0 | 39,148 | [
"MOOSE",
"NEURON"
] | e664ddb3def1d091032b7b9e396d04e58f226a66d1f5a472486af11da1e0fe76 |
#
# This file is part of Bakefile (http://www.bakefile.org)
#
# Copyright (C) 2006-2008 Vaclav Slavik, Kevin Powell, Steven Van Ingelgem,
# Kevin Ollivier, Aleksander Jaromin
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated d... | aponxi/libmysqlpp | bakefile-0.2.9/output/msvs200xprj.py | Python | lgpl-2.1 | 42,048 | [
"VTK"
] | b31538bc6e8bdea48f9c711663e9e267721c68df6ab782e537dbdc904747de7b |
#! /usr/bin/env python3
# -*- 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 requi... | googleapis/python-documentai | scripts/fixup_documentai_v1beta2_keywords.py | Python | apache-2.0 | 6,175 | [
"VisIt"
] | dab5adf7036566bf25acee559ffbc8cfeef9914d71c30caa0675a14cafd95dfa |
import numpy
from chainer import cuda
from chainer import function
from chainer.utils import type_check
from chainer import variable
def _as_mat(x):
if x.ndim == 2:
return x
return x.reshape(len(x), -1)
def _matmul(a, b, xp):
if xp is numpy:
# numpy 1.9 does not support matmul.
... | kiyukuta/chainer | chainer/functions/noise/simplified_dropconnect.py | Python | mit | 5,385 | [
"Gaussian"
] | 32e86a2d7ab074c1411b234948ab931f815ba45c1322b6e10194672f24fbdda2 |
"""
End-to-end tests for certificate on dashboard
"""
import datetime
from bok_choy.web_app_test import WebAppTest
from ...fixtures.course import CourseFixture
from ...pages.lms.auto_auth import AutoAuthPage
from ...pages.lms.ga_dashboard import DashboardPage
from ..ga_helpers import GaccoTestMixin
class Certificat... | nttks/edx-platform | common/test/acceptance/tests/lms/test_ga_certificate.py | Python | agpl-3.0 | 1,763 | [
"VisIt"
] | 71468a82288e38c77c3665410cc18cb20cb43b31cd4ef06e861afb4b257a69ed |
import argparse
from amber.amber16.cpptraj.command import exec_cpptraj
from utilities.path import which
from tempfile import mkstemp
import numpy
from pdb import set_trace as tr
if __name__ == '__main__':
parser = argparse.ArgumentParser(description="""Obtain MSD(t) averaged over different chunks of the trajectory... | jmborr/confinedBSA | simulation/silica/cristobalite/confineBSA/poretop/yesbonds/wholesystem/diffusion_t0average.py | Python | mit | 2,748 | [
"Amber"
] | 551ba7f90f8276774c1f6f394bb580159dd627c155f9dad8528dcf9658aa9d65 |
""" Graph package.
"""
import abc
from collections import defaultdict
from ..utils.collections import OrderedSet
def topological_sort(nodes):
""" Sort nodes topological, use Tarjan algorithm here
See: https://en.wikipedia.org/wiki/Topological_sorting
"""
unmarked = set(nodes)
marked = set()
... | windelbouwman/ppci-mirror | ppci/graph/graph.py | Python | bsd-2-clause | 4,821 | [
"VisIt"
] | 1db74a57e2b0f09877b4010c5efce5172f9e1ff701d2ddce3df5476fe5883f50 |
#
# 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/virtual_sites_tracers_common.py | Python | gpl-3.0 | 9,436 | [
"ESPResSo"
] | 9cec797d2c4deb57e66871850bc79cfd652e6b96e9b71dc98760ee821358701b |
#!/usr/bin/python
# (C) 2013, Markus Wildi, markus.wildi@bluewin.ch
#
# 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, or (at your option)
# any later version.
#
# Thi... | xyficu/rts2 | scripts/rts2saf/rts2saf/acquire.py | Python | gpl-2.0 | 19,243 | [
"VisIt"
] | 420e956ecc35831a3955528679f168fa4fb1de6178f82556d93e79301bb94b86 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import warnings
import unittest
import os
from pymatgen.alchemy.transmuters import CifTransmuter, PoscarTransmuter
from pymatgen.alchemy.filters import ContainsSpecieFilter
from pymatgen.transformations.standa... | tschaume/pymatgen | pymatgen/alchemy/tests/test_transmuters.py | Python | mit | 4,306 | [
"pymatgen"
] | 1d6f6f0ad227dd8196fa7725b0660009227d4d1e95689723311dd75b3b4ea419 |
import ocl
import pyocl
import camvtk
import vtk
import math
if __name__ == "__main__":
print(ocl.version()) # print out git version tag
# set up VTK visualization
myscreen = camvtk.VTKScreen()
myscreen.setAmbient(20,20,20)
myscreen.camera.SetPosition(4, 4, 3)
myscreen.camera.SetFocalPoi... | aewallin/opencamlib | examples/python/drop-cutter/drop_cutter_one-triangle_1.py | Python | lgpl-2.1 | 3,071 | [
"VTK"
] | f373e95f8810ee564b5b8e6a57bf80c0b8cb1be90cfad0ac16bb928e8c05031a |
# -*- coding: utf-8 -*-
"""
Unit tests for instructor.api methods.
"""
import datetime
import ddt
import random
import pytz
import io
import json
import requests
import shutil
import tempfile
from urllib import quote
from django.conf import settings
from django.contrib.auth.models import User
from django.core import m... | jazztpt/edx-platform | lms/djangoapps/instructor/tests/test_api.py | Python | agpl-3.0 | 194,402 | [
"VisIt"
] | 79810aa3198308944c23849a11db65358be44718f9f11ecaf24d2479742074b2 |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
import numpy as np
from scipy import ndimage as nd
from scipy.ndimage import morphology
from skimage import feature as skft
from skimage import morphology as skmorph
from scipy.spatial import distance
def... | liuzhaoguo/FreeROI | froi/algorithm/imtool.py | Python | bsd-3-clause | 5,610 | [
"Gaussian"
] | 30c249d4defb78d06f525b264bc04d5b6c5e7521e85b45398dc3cda7d1676041 |
# Usage:
# insert consumer and app keys as well as filepaths below
# run (eg in Terminal): python3 scriptname.py
# inputfile is a list of userids
# cc-by-nc Felix Victor Muench (fvmuench@gmail.com)
ckey = ''
csecret = ''
atoken = ''
asecret = ''
tweets_per_user = 42 # max 3200, rate limit adds 1 call per 200 tweets,... | FlxVctr/twitterscripts | get_timelines_from_userids.py | Python | mit | 2,049 | [
"exciting"
] | 97b6086b75dde0cb0c8e833831d12fcc28eb077547b1e7462056520a3171ecc8 |
# gPrime - A web-based genealogy program
#
# Copyright (C) 2012 Nick Hall
# Copyright (C) 2012 Brian G. Matherly
# Copyright (C) 2012-2014 Paul Franklin
#
# 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... | sam-m888/gprime | gprime/plugins/textreport/tableofcontents.py | Python | gpl-2.0 | 4,874 | [
"Brian"
] | ca9bef65c44ce91c0430b58bc913f533b22b3661a3a2abae562b9b866617dcfd |
#!/usr/bin/env python
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2008, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU Genera... | zenoss/ZenPacks.zenoss.Memcached | ZenPacks/zenoss/Memcached/libexec/check_memcached.py | Python | gpl-2.0 | 2,650 | [
"VisIt"
] | eee6f4e6dff93b4ef164499486e888baa086fc3c5090d158ee1075c4167e5d8d |
import time
from datetime import datetime
from cybox.common import Hash
from cybox.objects.address_object import Address
from cybox.objects.uri_object import URI
from pymisp import PyMISP
from .base import StixTransform
class StixMispTransform(StixTransform):
"""Insert data from a STIX package into a MISP event... | thisismyrobot/cti-toolkit | certau/transform/misp.py | Python | bsd-3-clause | 7,504 | [
"Amber"
] | 7b286db81c9c1637f2f284a4a6928b8b752a4419037ba30fa13f0a76e5d653dd |
# Author: Samuel Genheden samuel.genheden@gmail.com
"""
Program to do hydrogen mass repartition on a lammps datafile
Will increase the mass of the hydrogen and decrease mass of the heavy atoms bonded to
them.
The default output is the input data file with a "_heavyh" string appended
Examples
lmp_massrepart.py da... | SGenheden/Scripts | Lammps/lmp_massrepart.py | Python | mit | 4,723 | [
"LAMMPS"
] | f9b618c98dd57451e377d65e2c7f957a556c2cf3ba0eaf12106c876b3fb1fde1 |
# coding=utf-8
#-----------------------------------------------------
# Author: Yaqiang Wang
# Date: 2016-7-10
# Purpose: MeteoInfoLab random module
# Note: Jython
#-----------------------------------------------------
from org.meteoinfo.math import RandomUtil
from mipylib.numeric.miarray import MIArray
... | meteoinfo/meteoinfolab | pylib/mipylib/numeric/random/random.py | Python | lgpl-3.0 | 3,861 | [
"Gaussian"
] | bb11675ba786103f45c6ac5dfcf464bd8431f7c213290a9dd7f2e5dcd3a7637f |
import os
import pprint
import sys
import textwrap
import py
import pytest
from _pytest.config import ExitCode
from _pytest.main import _in_venv
from _pytest.main import Session
from _pytest.pytester import Testdir
class TestCollector:
def test_collect_versus_item(self):
from pytest import Collector, It... | markshao/pytest | testing/test_collection.py | Python | mit | 44,970 | [
"VisIt"
] | 7356e4e30c5d0b271871dc54e3b72b68d0fd30d98d94713f6f0999bf1f299b6b |
#!/usr/bin/env python
from __future__ import print_function
import re
import sys
import os
import os.path
from optparse import OptionParser
import pysam
readKeyRe = re.compile('(.*)\s[1-2](.*)')
readNumRe = re.compile('.*\s([1-2]).*')
# upper and lower limit of the paired reads length
upperLimit = 2000
lowerLimit ... | dlmeduLi/rmdup | rmdup.py | Python | mit | 10,121 | [
"pysam"
] | 6fa6c566e17079c6b4fc82869babb536d842200b9055668b06f32dc369904797 |
import logging, os, random, ConfigParser, datetime
logging.basicConfig(level=logging.INFO, format='%(asctime)s - %(name)s - %(levelname)s - %(message)s')
from telegram import ForceReply, InlineKeyboardButton, InlineKeyboardMarkup, InlineQueryResultArticle, ParseMode, InputTextMessageContent
from telegram.ext import Upd... | awuwu/yuukibot | yuuki.py | Python | mit | 21,469 | [
"VisIt"
] | acd350e510c52a960727d2535c09903adeb72f23e2acddcd7f5e84ac16cfb845 |
""" This is the Proxy storage element client """
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import os
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Resources.Storage.Utilities import checkArgumentFormat
from DIRAC.Resources.Storage.StorageBase im... | yujikato/DIRAC | src/DIRAC/Resources/Storage/ProxyStorage.py | Python | gpl-3.0 | 7,523 | [
"DIRAC"
] | ba188415087a5081be7c64266cd6e4cac7f9f126e21d1d03312200090893d6da |
# Copyright 2018 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... | jbedorf/tensorflow | tensorflow/tools/compatibility/update/generate_v2_renames_map.py | Python | apache-2.0 | 7,161 | [
"VisIt"
] | 958a870e250ee0bfbf31e1f621bfa971eeeb33ef274800edec9f880669ac3fe3 |
""" Contains the Mode parent class for the Media Controller"""
# modes.py
# Mission Pinball Framework
# Written by Brian Madden & Gabe Knuth
# Released under the MIT License. (See license info at the end of this file.)
# Documentation and more info at http://missionpinball.com/mpf
import logging
import os
from colle... | spierepf/mpf | mpf/media_controller/core/mode.py | Python | mit | 6,739 | [
"Brian"
] | fdf3064804e65b99984efdb1880d8a6b275aa95793cac3178cdcb56a2b46ed61 |
# spud - keep track of photos
# Copyright (C) 2008-2013 Brian May
#
# 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.
#
# ... | brianmay/spud | spud/wsgi.py | Python | gpl-3.0 | 858 | [
"Brian"
] | 4b30b0bf91438205f59c7b7747b800ad59482ac01f1b92ba9cba6478cdfd6f17 |
"""Forest of trees-based ensemble methods
Those methods include random forests and extremely randomized trees.
The module structure is the following:
- The ``BaseForest`` base class implements a common ``fit`` method for all
the estimators in the module. The ``fit`` method of the base ``Forest``
class calls the ... | pypot/scikit-learn | sklearn/ensemble/forest.py | Python | bsd-3-clause | 62,431 | [
"Brian"
] | 487a8572b006466bc05ae4bd715da72954b468a532e0681c15282a5fe3593fb8 |
import sys,string,os
sys.path.insert(1, os.path.join(sys.path[0], '..')) ### import parent dir dependencies
import pysam
import copy,getopt
import time
import traceback
try: import export
except Exception: pass
try: import unique
except Exception: pass
import Bio; from Bio.Seq import Seq
def cleanUpLine(line):
lin... | nsalomonis/AltAnalyze | import_scripts/SAMtoBarcode.py | Python | apache-2.0 | 3,705 | [
"pysam"
] | 57d6b97c66853ed73a8a354b0d2dde8ac2928be0e3006d1a6a7a635522c0d163 |
import numpy as np, theano.tensor as TT
import theano
from control4.maths.symbolic import floatX,join_columns,lmatrix,fmatrix,is_symbolic_tensor
import cycontrol
import scipy.stats
class CPD(object):
"""
Conditional Probability Distribution
"""
def mls(self, a_na):
"""
Most likely samp... | SFPD/rlreloaded | control4/core/cpd.py | Python | mit | 9,302 | [
"Gaussian"
] | e3b883de1be945e0e4a455b6e1ddc2f55a8fb613fe6dc48718f6b555e2616aaf |
#!/usr/bin/python
"""
Copyright 2010 Paul Willworth <ioscode@gmail.com>
This file is part of Galaxy Harvester.
Galaxy Harvester is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 of th... | clreinki/GalaxyHarvester | logout.py | Python | agpl-3.0 | 1,966 | [
"Galaxy"
] | a02846300c782447d3c9c06d56d1ac80666cabd219707e43d659dfd593381118 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkThresholdTable(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk... | nagyistoce/devide | modules/vtk_basic/vtkThresholdTable.py | Python | bsd-3-clause | 483 | [
"VTK"
] | 08e9292094a1395769da0a485f1b50b64aa70ac92d4ad6c8b173ca1daf239256 |
"""Sphinx configuration of phonopy documentation."""
# -*- coding: utf-8 -*-
#
# phonopy documentation build configuration file, created by
# sphinx-quickstart on Mon Apr 13 15:11:21 2009.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# Note that not all possible configuration val... | atztogo/phonopy | doc/conf.py | Python | bsd-3-clause | 9,196 | [
"phonopy"
] | 03f87ca03cc0e06cfa5f7cd4ffd92276ffb5f3a9d852937bef09c359499c66e6 |
"""0MQ Error classes and functions."""
#-----------------------------------------------------------------------------
# Copyright (C) 2013 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, distribut... | skycucumber/Messaging-Gateway | webapp/venv/lib/python2.7/site-packages/zmq/error.py | Python | gpl-2.0 | 3,545 | [
"Brian"
] | a1c4bebe566ecc436258e5fde8da63ce7b82bcc3fb7037bce1e24a22a3f7e4ee |
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at https://mozilla.org/MPL/2.0/.
import pytest
import math as m
import numpy as np
from sisl.physics.distribution import *
pytestmark = [pytest.mark.p... | zerothi/sisl | sisl/physics/tests/test_distribution.py | Python | mpl-2.0 | 2,167 | [
"Gaussian"
] | 434e7b21e3b24f21ad5d36ccc6ea14ab0970ab8f0778b63908a78f60f3e5af97 |
#!/usr/bin/python
import os, sys, getopt, string, math
from Bio.Seq import Seq
from Bio.Blast import NCBIXML
from Bio.Alphabet import IUPAC
OUTFILEPART2 = 'tmp.orf.part2.fasta'
#==============================================================================
def show_help():
print """%s uses parsed BLASTX output to ... | lotharwissler/bioinformatics | python/openreadingframe/orf_prediction_part1.py | Python | mit | 7,760 | [
"BLAST"
] | fcdec97869af2d4d64f5492deb9d47b82c53a60fd35f87f3e93e2df65ec504d8 |
import pandas as pd
from sklearn.ensemble import RandomForestRegressor
from sklearn.ensemble import BaggingRegressor
from sklearn.ensemble import ExtraTreesRegressor
from sklearn.ensemble import AdaBoostRegressor
from sklearn.ensemble import GradientBoostingRegressor
from sklearn.ensemble import RandomTreesEmbedding
fr... | rupakc/Kaggle-Compendium | Mercari Price Suggestion Challenge/mercari_baseline.py | Python | mit | 5,943 | [
"Gaussian"
] | df3baa3aecc693951707c6a7062ef0370351ea6a182c83e1de3f748f4dacabe0 |
import numbers
from copy import copy
try:
from statsmodels.genmod.families.family import (Gaussian, Binomial, Poisson)
except ImportError:
Gaussian = None
Binomial = None
Poisson = None
from .links import *
from ..model import modelcontext
from ..distributions import Normal, T, Uniform, Bernoulli, Poi... | kyleam/pymc3 | pymc/glm/families.py | Python | apache-2.0 | 2,934 | [
"Gaussian"
] | 9c28f7006cf8308990511bd5ff5ca54ecbcc95e61c55b7dacee09cef6de88444 |
from octopus.modules.es import testindex
from service import sheets
import os, csv
from StringIO import StringIO
TEST_SUBMISSION = os.path.join(os.path.dirname(os.path.realpath(__file__)), "..", "resources", "test_submission.csv")
BLANK_LINES = os.path.join(os.path.dirname(os.path.realpath(__file__)), "..", "resources... | CottageLabs/oacwellcome | service/tests/unit/test_sheet.py | Python | apache-2.0 | 5,554 | [
"Octopus"
] | 089aed00963b5cf37823594ef5277403fee4983bfeee925535ef3dc7a4201d33 |
import numpy as np
import rdkit
import tensorflow as tf
from tensorflow.python.framework import test_util
from deepchem.feat.graph_features import ConvMolFeaturizer
from deepchem.feat.mol_graphs import ConvMol
from deepchem.models.tensorgraph.layers import Add, MaxPool2D, MaxPool3D, GraphCNN, GraphEmbedPoolLayer, Cast... | Agent007/deepchem | deepchem/models/tensorgraph/tests/test_layers.py | Python | mit | 36,929 | [
"RDKit"
] | 057d446505721f2afeaf228d5489e70206b77ba3646f27d0e50b2f860e7e4842 |
import sys
import os
def extractPDBInfo(input1,input2):
""" read the PDB file and chainId to map the residue serial number with residue number & chain info """
keyList = []
valueList = []
pdbTups = ()
pdbInfoMap = {}
index = 0
fileName = open(input1,'r')
if fileName:
for... | gersteinlab/Frustration | read.py | Python | gpl-3.0 | 5,449 | [
"BLAST"
] | 8d31a2908be8b905cfd600c03546158d23595e3824e3b111a6fa1848008cb866 |
import genson
import time
from os import path
my_path = path.dirname(path.abspath(__file__))
def parse_and_report_error(doc):
try:
genson.loads(doc)
except Exception as e:
print("Caught exception: %s" % e)
return
print("Did not catch exception")
def test_main():
testdata =... | davidcox/genson | test/test_basic.py | Python | mit | 2,889 | [
"Gaussian"
] | 01e20b8e9052eb698bbbbe0e174e3ba1b3e641dd244371a1b11cae6d31d63c9e |
import json
import time
from nxtools import logging
from firefly.api import api
from firefly.core.common import config
from firefly.dialogs.rundown import PlaceholderDialog, SubclipSelectDialog
from firefly.objects import Asset, Item, Event, asset_cache
from firefly.view import FireflyViewModel
from firefly.qt import... | immstudios/firefly | firefly/modules/rundown_model.py | Python | gpl-3.0 | 10,343 | [
"Firefly"
] | 5c98f96f4c3f43122cdeb8d953c64995c018f4ef0bd4d2e151830d46c018f0f7 |
raise Exception
#this is not ready to work on tscc yet. placeholder.
__author__ = 'lovci'
import os,sys
import StringIO
import bx.pwm.position_weight_matrix as pwm ###Vital: commented sections of position_weight_matrix.py to ignore reverse strand
from bx.pwm.pwm_score_maf import MafBlockScorer, MafMotifScorer ###V... | YeoLab/gscripts | gscripts/conservation/maf_scorer.py | Python | mit | 8,840 | [
"Biopython"
] | 5d9442a593c03c4d52c96fdb8938d48f4f43abab78cd9a05f00f732113ab5b5e |
from flask import Flask, render_template, session, request, redirect
import random
app = Flask(__name__)
app.secret_key = 'my_secret_key'
@app.route('/')
def index():
if not 'gold' in session:
session['gold'] = 0
if not 'activities' in session:
session['activities'] = []
return render_temp... | jiobert/python | Francisco_Trujillo/Assignments/flaskolympics/olympics8/server.py | Python | mit | 1,645 | [
"CASINO"
] | d39e7ea416a33a023ee0a95b20041b2500469bb355bd64d3406ea4fa748ed1b1 |
from __future__ import absolute_import, division, unicode_literals
import string
EOF = None
E = {
'null-character':
'Null character in input stream, replaced with U+FFFD.',
'invalid-codepoint':
'Invalid codepoint in stream.',
'incorrectly-placed-solidus':
'Solidus (/) incorrectly ... | hoosteeno/fjord | vendor/src/html5lib-python/html5lib/constants.py | Python | bsd-3-clause | 86,873 | [
"Bowtie"
] | 43658b8398c8b8d64690f2ca1484a5b3f9124e8af2ea79b6da121a5b615eca03 |
# (c) Dan La Russa & Randy Taylor
# routines for fitting histograms
import numpy as np
import matplotlib.mlab as mlab
from scipy.optimize import curve_fit
np.seterr("ignore")
def gauss_fit(data, freq, bins, binwidth):
"""
Fits a Gaussian pdf to a histogram using
the method of least squares.
data = a... | sharifelguindi/qatrackplus | qatrack/qa/control_chart/leastsquaresfit.py | Python | mit | 1,435 | [
"Gaussian"
] | e95f8f1a42ce71f64cf40a67cba68295c690614ad3770ead8c475cbca1540583 |
"""
# Majic
# Copyright (C) 2014 CEH
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This pr... | NERC-CEH/jules-jasmin | majic/joj/websetup_chess_driving_dataset.py | Python | gpl-2.0 | 15,035 | [
"NetCDF"
] | 534edb673c655c7acfabb06c064e73343ff6f7c330c3c090bc77ab0007b4a87a |
#!/usr/bin/env python
##
## @file addCustomValidator.py
## @brief Example creating a custom validator to be called during validation
## @author Frank T. Bergmann
##
##
## This file is part of libSBML. Please visit http://sbml.org for more
## information about SBML, and the latest version of libSBML.
##
##
i... | dilawar/moose-full | dependencies/libsbml-5.9.0/examples/python/addCustomValidator.py | Python | gpl-2.0 | 3,174 | [
"VisIt"
] | e57473ac1b037b296b7bfe43b01a0fdfd69f73b745dc4620b52105b93a7c893b |
# -*- coding: utf-8 -*-
from south.utils import datetime_utils as datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
from sentry.utils.db import is_postgres
class Migration(SchemaMigration):
is_dangerous = True
def forwards(self, orm):
# Changing fiel... | mvaled/sentry | src/sentry/south_migrations/0354_auto__chg_field_commitfilechange_filename.py | Python | bsd-3-clause | 83,209 | [
"Elk"
] | 70cc02f0b161f116995c5a9d91a21bec5bbe7ebf512e2bb3924a84e69200d078 |
# How many galaxies from the gold standard sample are necessary to establish whether a user agrees with the experts?
# Hm - not many have done more than 1. Might have to expand the experiment to the full expert data set of 100 galaxies ...
# Plot (N/2 - M/2) vs. (M+N) and see where agreement lies!!
# Read in the lis... | willettk/rgz-analysis | python/gold_standard.py | Python | mit | 9,570 | [
"Galaxy"
] | f1b1e0d00f66cab89d2e695f3af97c7ad71a70d72661358500d7e9a37039a45c |
#!/usr/bin/env python
##############################################################################################
#
#
# regrid_emissions_N96e.py
#
#
# Requirements:
# Iris 1.10, time, cf_units, numpy
#
#
# This Python script has been written by N.L. Abraham as part of the UKCA Tutorials:
# http://www.ukca.ac.u... | acsis-project/emissions | emissions/python/timeseries_1950-2020/regrid_Me2CO_emissions_n96e_360d.py | Python | gpl-3.0 | 19,238 | [
"NetCDF"
] | cabae2ac7c0313d51011bb19cf87b74543441b859b277d69035a26463400bc91 |
from bcpp_subject_form_validators import MedicalDiagnosesFormValidator
from ..constants import ANNUAL
from ..models import MedicalDiagnoses
from .form_mixins import SubjectModelFormMixin
class MedicalDiagnosesForm (SubjectModelFormMixin):
form_validator_cls = MedicalDiagnosesFormValidator
optional_labels =... | botswana-harvard/bcpp-subject | bcpp_subject/forms/medical_diagnoses_form.py | Python | gpl-3.0 | 622 | [
"VisIt"
] | 1f34767079007fa64a70f991b4ce7d44220b349b48d50fe0d2cc850f486dbac0 |
# $HeadURL$
__RCSID__ = "$Id$"
import os
try:
import hashlib
md5 = hashlib
except:
import md5
import types
import threading
import cStringIO
import tarfile
import tempfile
from DIRAC.Core.Utilities.ReturnValues import S_OK, S_ERROR
from DIRAC.FrameworkSystem.Client.Logger import gLogger
gLogger = gLogger.getSub... | miloszz/DIRAC | Core/DISET/private/FileHelper.py | Python | gpl-3.0 | 12,697 | [
"DIRAC"
] | 097ce4259b116daef1f1c040a57fd1715743ac7b80d5d04ec5fc901711a558fe |
"""
Acceptance tests for Studio related to the split_test module.
"""
from __future__ import absolute_import
import math
from bok_choy.promise import Promise
from selenium.webdriver.support.ui import Select
from common.test.acceptance.fixtures.course import XBlockFixtureDesc
from common.test.acceptance.pages.lms.co... | ESOedX/edx-platform | common/test/acceptance/tests/studio/test_studio_split_test.py | Python | agpl-3.0 | 47,091 | [
"VisIt"
] | bbc112c08cc7f1f94df8c79a382cdbea9281f428165562834df81cb0a0edc4a2 |
from rope.base import libutils
from rope.base import pyobjects, exceptions, stdmods
from rope.refactor import occurrences
from rope.refactor.importutils import importinfo
class ImportInfoVisitor(object):
def dispatch(self, import_):
try:
method_name = 'visit' + import_.import_info.__class__._... | ruchee/vimrc | vimfiles/bundle/vim-python/submodules/rope/rope/refactor/importutils/actions.py | Python | mit | 14,204 | [
"VisIt"
] | 3f73f2c3a5a72a5570b0d2df03b6023dfe0eabd9b96b198cc5262a162043dc8d |
"""Creates a 2D hyperspectrum consisting of two gaussians and plots it.
This example can serve as starting point to test other functionalities on the
simulated hyperspectrum.
"""
# Create an empty spectrum
s = signals.Spectrum(np.zeros((32, 32, 1024)))
# Generate some simple data: two Gaussians with random centers... | pburdet/hyperspy | examples/simple_simulations/two_gaussians.py | Python | gpl-3.0 | 1,405 | [
"Gaussian"
] | 7dc71b4f172ccb78fdd260cf001124fd159ac33311328e59a02e9cb8a0d5a4c1 |
"""This module defines an ASE interface to GROMACS.
http://www.gromacs.org/
It is VERY SLOW compared to standard Gromacs
(due to slow formatted io required here).
Mainly intended to be the MM part in the ase QM/MM
Markus.Kaukonen@iki.fi
To be done:
1) change the documentation for the new file-io-calculator (test wo... | suttond/MODOI | ase/calculators/gromacs.py | Python | lgpl-3.0 | 17,658 | [
"ASE",
"GROMOS",
"Gromacs"
] | 4e89cdfe8fa417c4cc562c9190fa56f20f54170d59ded1fce61349b8271a0292 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2017, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
import os
import unittest
from cclib.parser import ccData
from cclib.bridge import cclib2openbabel
class OpenbabelTest(... | gaursagar/cclib | test/bridge/testopenbabel.py | Python | bsd-3-clause | 738 | [
"cclib"
] | d2ce7e18eca77500769debd8b4eadfd5bad4ce5c18def908185ce532d1b82490 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
""" functions that creates image from a video file
Primarily intended for plotting, returns correlation images ( local or max )
See Also:
------------
@author andrea giovannucci
"""
from builtins import range
import cv2
import logging
import numpy as np
from scipy.ndim... | simonsfoundation/CaImAn | caiman/summary_images.py | Python | gpl-2.0 | 33,025 | [
"Gaussian"
] | 19dfb6fe4a869cdc2700ee9b7549bce427f45eefe6cd7369ca9854fa193490a4 |
# This software is distributed under BSD 3-clause license (see LICENSE file).
#
# Authors: Heiko Strathmann
#
from numpy import *
from pylab import *
from scipy import *
from shogun import RealFeatures
from shogun import MeanShiftDataGenerator
from shogun import GaussianKernel, CombinedKernel
from shogun import Linear... | sorig/shogun | examples/undocumented/python/graphical/statistics_linear_time_mmd.py | Python | bsd-3-clause | 6,141 | [
"Gaussian"
] | 1c27cf9d0d1441540a38995e35c634cacfc4bae2edea88567499010acfb98db9 |
#!/usr/bin/env python
###############################################################################
#
# ptgraph2.py - generate protein topology graphs from PDB atomic co-ordinates
# plus STRIDE or DSSP information.
#
# File: ptgraph2.py
# Author: Alex Stivala
# Created: July 2007
#
# $Id: ptgraph2.py 4642 2013-04... | NirBenTalLab/proorigami-ptgraph | ptgraph2.py | Python | mit | 341,545 | [
"Biopython",
"PyMOL"
] | e481278745a39d64acffdcb2a382efe5a0dfea96596db0b879386eba358d097f |
# -*- coding: utf-8 -*-
#-------------------------------------------------------------------------------
# Name: configure.py
# Purpose: Installation and Configuration Utilties
#
# Authors: Christopher Ariza
#
# Copyright: Copyright © 2011-2012 Michael Scott Cuthbert and the music21 Project
# Licen... | arnavd96/Cinemiezer | myvenv/lib/python3.4/site-packages/music21/configure.py | Python | mit | 60,161 | [
"exciting"
] | 63702a4fdd270861a80cee1601d2ecfe405ab3eb1be74aabebf89802928ed4fd |
""" TransformationPlugin is a class wrapping the supported transformation plugins
"""
import random
import time
from DIRAC import gConfig, S_OK, S_ERROR
from DIRAC.Core.Utilities.SiteSEMapping import getSitesForSE, getSEsForSite
from DIRAC.Core.Utilities.List import breakListIntoChunks
from DIRAC.Resources.Catalog.... | arrabito/DIRAC | TransformationSystem/Agent/TransformationPlugin.py | Python | gpl-3.0 | 9,419 | [
"DIRAC"
] | a5cd7a2fa2ccb9324556f77c2ead9da521cc55fc3f7b1e93ae43e24c0a8d02be |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# -----------------------------------------------------------------------------
#
# FreeType high-level python API - Copyright 2011-2015 Nicolas P. Rougier
# Distributed under the terms of the new BSD license.
#
# ----------------------------------------------------------... | psychopy/psychopy | psychopy/visual/textbox2/textbox2.py | Python | gpl-3.0 | 53,737 | [
"Gaussian"
] | 2f7f19a49fc0971f2fbcbe258b877545871fa7c4ba3dd3b199417861f570b882 |
# coding: utf-8
# Copyright 2017 CERN. This software is distributed under the
# terms of the GNU General Public Licence version 3 (GPL Version 3),
# copied verbatim in the file LICENCE.md.
# In applying this licence, CERN does not waive the privileges and immunities
# granted to it by virtue of its status as an In... | blond-admin/BLonD | blond/beam/profile.py | Python | gpl-3.0 | 20,384 | [
"Gaussian"
] | 4cf6bcac0e9bbd3df600c88e52add43e76a2d1e054494812b682b3f329c70c44 |
import numpy as np
import os
import subprocess
# from time import sleep
# Rotates input xyz file and generates 100 output xyz files at random orientations along with input.scan for each of them to give as input to mechAFM
def makeIt(output_folder = "randomRotateOutput/"):
fileNumber = 0
for i in range(24... | SINGROUP/readAFM | databaseCode/toyDB/twoDiffAtomsHC/makeXYZ.py | Python | gpl-3.0 | 4,633 | [
"CHARMM"
] | ca84f3a622642114a6b58244934b7fd4715b9ab4f5320ac70f9693991b2847e3 |
import pytest
import os
import glob, os, re, shutil
import numpy as np
from flare.otf import OTF
from flare.otf_parser import OtfAnalysis
from flare.gp import GaussianProcess
from flare.struc import Structure
cmd = {"cp2k": "CP2K_COMMAND", "qe": "PWSCF_COMMAND"}
software_list = ["cp2k", "qe"]
example_list = [1, 2]
... | mir-group/flare | tests/test_otf.py | Python | mit | 7,770 | [
"CP2K"
] | baa0bbfc098e347342b0690db898d65f14753210e72036fab6f0957d37fb4de2 |
#!/usr/bin/env python3
# generation of up to N low energy conformers
# from 2D input (smi) to 3D output (sdf)
# see Ebejer et. al.
# "Freely Available Conformer Generation Methods: How Good Are They?"
# JCIM, 2012, DOI: 10.1021/ci2004658 for technical details
#
# Copyright (C) 2018 Francois Berenger
# System Cohort Di... | UnixJunkie/smi2sdf3d | smi2sdf.py | Python | gpl-3.0 | 7,577 | [
"RDKit"
] | 2f71289ca8fad68c8cac2d27f0044e0888d175f3496325af399ff3f545450564 |
from distutils.core import setup
setup(
name='PiCloud-Client',
version='4.0.0',
author='Brian Hines',
author_email='brian@projectweekend.net',
packages=['picloud_client'],
url='https://github.com/exitcodezero/picloud-client-python',
license='LICENSE.txt',
description='A Python client fo... | exitcodezero/picloud-client-python | setup.py | Python | mit | 479 | [
"Brian"
] | c1418c50457db11d03279bc30cc7327ee21b4b505d52fe8fb3621493986d1f18 |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/pbc/scf/test/test_scfint.py | Python | apache-2.0 | 3,460 | [
"PySCF"
] | 0000500e562d1451fa9208368105ca4085130fd346c4f1dbcec52813587b0190 |
"""
Stripplot
---------
This example shows how to make a Stripplot.
"""
# category: scatter plots
import altair as alt
from vega_datasets import data
source = data.movies.url
stripplot = alt.Chart(source, width=40).mark_circle(size=8).encode(
x=alt.X(
'jitter:Q',
title=None,
axis=alt.Axis... | altair-viz/altair | altair/examples/stripplot.py | Python | bsd-3-clause | 950 | [
"Gaussian"
] | b272df97bc9fd1f5649a82ec94c78523fb9672a84491c618db19028099c8c09c |
#!/usr/bin/env python
"""A class for handling 5C read data."""
import os
import sys
import numpy
import h5py
try:
import pysam
except:
pass
class FiveCData(object):
"""
This class handles interaction count data for 5C experiments.
The FiveCData class contains all of the interaction informati... | bxlab/hifive | hifive/fivec_data.py | Python | mit | 20,887 | [
"pysam"
] | cf2c7a6fc05206c32029b81876eb54c3b334e14b1d427b03039f4848d848f2e5 |
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | gkc1000/pyscf | pyscf/pbc/df/test/test_incore.py | Python | apache-2.0 | 2,410 | [
"PySCF"
] | 4240befbbe75e7d04cb5af7464ceab59008db70d3116e0b76c22998817efbfee |
#
# This file is a part of Siesta Help Scripts
#
# (c) Andrey Sobolev, 2013
#
from collections import defaultdict
import numpy as np
class PlotData(object):
def __init__(self, data, **kwds):
self.title = data.title
self.y = []
self.y_titles = tuple(data.y_titles)
class FunctionData(Plot... | ansobolev/shs | shs/data/plotdata.py | Python | mit | 4,073 | [
"SIESTA"
] | 918d8257d26ccc801d45099720fd2aadb55b0d05136e8c63ddc525874b830c6f |
""" Soft implementation of a Direct Acyclic Graph (DAG)
Nota Bene: It is NOT fully checked if valid (i.e. some cycle can be introduced)!
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import copy
from DIRAC import gLogger
__RCSID__ = "$Id $"
cla... | ic-hep/DIRAC | src/DIRAC/Core/Utilities/DAG.py | Python | gpl-3.0 | 3,728 | [
"DIRAC"
] | 4f1a43eccbfe38e286243784b79cc246c2b8ea9330c4dd7bf0a7e4791def8678 |
import sys
import unittest
# Run from the root dir
sys.path.insert(0, '.')
from pycparser import c_parser, c_generator
_c_parser = c_parser.CParser(
lex_optimize=False,
yacc_debug=True,
yacc_optimize=False,
yacctab='yacctab')
def compare_asts(ast1, a... | pombredanne/pycparser-1 | tests/test_c_generator.py | Python | bsd-3-clause | 3,383 | [
"VisIt"
] | a3b237b399026f46268fc5a97afdfa3da44d3c23424421f1b445e08c35d10df4 |
from __future__ import print_function
import psi4
from psi4.driver import qcdb
#! A test of the basis specification. Various basis sets are specified outright and in blocks, both
#! orbital and auxiliary. Constructs libmints BasisSet objects through the constructor that calls
#! qcdb.BasisSet infrastructure. Checks th... | CDSherrill/psi4 | samples/python/mints9/input.py | Python | lgpl-3.0 | 4,478 | [
"Psi4"
] | 45143c79674ea1a36395e655c313120445491f2f981cd7adf1acd4e9493f38b3 |
"""Handle extraction of final files from processing pipelines into storage.
"""
import datetime
import os
import toolz as tz
from bcbio import log, utils
from bcbio.upload import shared, filesystem, galaxy, s3
from bcbio.pipeline import run_info
import bcbio.pipeline.datadict as dd
_approaches = {"filesystem": files... | lpantano/bcbio-nextgen | bcbio/upload/__init__.py | Python | mit | 18,835 | [
"Galaxy"
] | c9d4f098effb9505bc7dbaaaa4a81361a5f607b9cd7114bacbd42bb3f5a2d169 |
from ase import *
a = 3.6
b = a / 2
initial = Atoms('Cu4',
positions=[(0, 0, 0),
(0, b, b),
(b, 0, b),
(b, b, 0)],
cell=(a, a, a),
pbc=True)
initial *= (4, 4, 4)
del initial[0]
images = [ini... | freephys/python_ase | ase/test/vacancy.py | Python | gpl-3.0 | 945 | [
"ASE"
] | b23bfb5b9aedc3c03886dee7e6e2a8231a0c1f75f49a94bd2ab508b48f9cf553 |
########################################################################
# $HeadURL$
########################################################################
"""
"""
__RCSID__ = "$Id$"
import time
import types
import sys
import random
import hashlib
import urlparse
import base64
from DIRAC import gConfig, gLogger, S... | DIRACGrid/RESTDIRAC | RESTSystem/DB/OATokenDB.py | Python | gpl-3.0 | 12,839 | [
"DIRAC"
] | f688726a8ce37fd21c1032ba54989d589eacac4e3d13444139a8f64ef0c211ad |
# -*- coding: utf-8 -*-
"""SQLite parser plugin for Google Chrome history database files."""
from dfdatetime import posix_time as dfdatetime_posix_time
from dfdatetime import webkit_time as dfdatetime_webkit_time
from plaso.containers import events
from plaso.containers import time_events
from plaso.lib import defini... | kiddinn/plaso | plaso/parsers/sqlite_plugins/chrome_history.py | Python | apache-2.0 | 51,316 | [
"VisIt"
] | 66afd7f6c143f31c9e0c4a0ac2e51cdf697272aac35c1982432507937d1ffcfa |
from __future__ import division
import warnings
import numpy as np
from scipy.stats import multivariate_normal
from menpo.base import name_of_callable
from menpo.feature import no_op
from menpo.visualize import print_dynamic, print_progress
from menpo.model import GMRFModel
from menpo.shape import (DirectedGraph, Undi... | yuxiang-zhou/menpofit | menpofit/aps/base.py | Python | bsd-3-clause | 39,189 | [
"Gaussian"
] | 574d151e531ee4495740fc7ca9ad5f8b519622c6b75672f683edbc93d0e1f444 |
import os
import shutil
import unittest
import random
import json
import numpy
import urllib
from pytest import raises
from datetime import datetime, timedelta
from paegan.transport.models.transport import Transport
from paegan.transport.models.behavior import LarvaBehavior
from paegan.transport.particles.particle impo... | asascience-open/paegan-transport | tests/test_model_controller.py | Python | gpl-3.0 | 18,023 | [
"NetCDF"
] | 0a8ff66c5e4cea3cbd4b7c9e4906c970fb5283b103b4bedbce17f9cac24e754e |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
See __doc__ for setup_com_from_mae.
Job Types
---------
cs - Conformational search
Appends "_cs".
mini - Minimization
Appends "_mini".
re - Redundant conformer elimination
Appends "_re".
"""
import argparse
import os
import sys
import schrod... | ericchansen/q2mm | screen/setup_com_from_mae_many.py | Python | mit | 3,206 | [
"MacroModel"
] | fc643490651da65a5dd2ca360d838b8dcaca27e741428e5e652763805adb0691 |
"""
Common methods used by the API sample scripts.
"""
import json
import logging
import os
import sys
import urllib2
#new_path = [ os.path.join( os.path.dirname( __file__ ), '..', '..', 'lib' ) ]
new_path = [ '/apps/sys/galaxy/production/lib' ]
new_path.extend( sys.path[1:] )
sys.path = new_path
from galaxy import e... | golharam/rgtools | scripts/galaxy/api/common.py | Python | lgpl-3.0 | 5,958 | [
"Galaxy"
] | 13e683c419ce23f43742e2bb3d2548c20f4eb92d1a4e90b14e74ef232d4d594b |
#! /usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-admin-ce-info
# Author : Vladimir Romanovsky
########################################################################
"""
Retrieve Site Associated to a given CE
"""
from __future__ import pri... | fstagni/DIRAC | Interfaces/scripts/dirac-admin-ce-info.py | Python | gpl-3.0 | 1,602 | [
"DIRAC"
] | 13d40f8e64a96699c079eec868269bf8e1885f7a64cee88ca09a32555744e492 |
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