text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
value | license stringclasses 15
values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
# -*- coding: utf-8 -*-
#
# This file is a plugin for EventGhost.
# Copyright © 2005-2016 EventGhost Project <http://www.eventghost.net/>
#
# EventGhost 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 v... | WoLpH/EventGhost | plugins/X10/__init__.py | Python | gpl-2.0 | 10,254 | [
"Firefly"
] | b0c2f2256a202b20580e3519b379eb1a20af0a2cfaa5fb879b008e9427fda754 |
"""
DICEseq - Dynamic Isoform spliCing Estimator via sequencing data
See: http://diceseq.sourceforge.net
"""
import sys
if sys.version_info >= (3,):
sys.exit('diceseq requires Python 2')
# Always prefer setuptools over distutils
from setuptools import setup, find_packages, Extension
# To use a consistent encoding... | huangyh09/diceseq | setup.py | Python | apache-2.0 | 2,532 | [
"Gaussian",
"pysam"
] | f361cf1742436ea899c1751d717e1b3907812196b19702544dc16c250e0b757a |
sobrenomes_list = [
"Aaron"
,
"Ab"
,
"Abba"
,
"Abbe"
,
"Abbey"
,
"Abbie"
,
"Abbot"
,
"Abbott"
,
"Abby"
,
"Abdel"
,
"Abdul"
,
"Abe"
,
"Abel"
,
"Abelard"
,
"Abeu"
,
"Abey"
,
"Abie"
,
"Abner"
,
"Abraham"
,
"Abrahan"
,
"Abram"
,
"Abramo"
,
"Abran"
,
"Ad"
,
"Adair"
,
"Adam"
,
"Adamo"
,
"Adams"
,
"Adan"
,
"Addie"
,
"Addison"... | Pharaoh00/Pharaoh-Toolkit | 0.0.6/modulos/listas/nomesLista_Second.py | Python | mit | 42,218 | [
"ASE",
"Brian",
"Dalton",
"Desmond",
"MOE"
] | e31567479d44c0cbd98af852514b6867cf2b376ca1588e0edcc7e7b8ed3ef41c |
# (c) 2012-2014, Michael DeHaan <michael.dehaan@gmail.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) an... | muravjov/ansible | lib/ansible/utils/__init__.py | Python | gpl-3.0 | 60,718 | [
"Galaxy",
"VisIt"
] | 0fda91c0b108d5d738e039c566a23526f385a30a348fad15c447d273bb054a97 |
# -*- coding: utf-8 -*-
#
# Copyright 2008 - 2019 Brian R. D'Urso
#
# This file is part of Python Instrument Control System, also known as Pythics.
#
# Pythics 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, e... | dursobr/Pythics | pythics/help/help.py | Python | gpl-3.0 | 80,574 | [
"Brian"
] | d6e7aaa0e6fb090ac1b06696d65888105c3e3fd8dadf070004e425f4ea4fb009 |
###############################################################################
##
## Copyright (C) 2014-2016, New York University.
## Copyright (C) 2011-2014, NYU-Poly.
## Copyright (C) 2006-2011, University of Utah.
## All rights reserved.
## Contact: contact@vistrails.org
##
## This file is part of VisTrails.
##
## ... | VisTrails/VisTrails | vistrails/packages/spreadsheet/spreadsheet_tabcontroller.py | Python | bsd-3-clause | 33,837 | [
"VTK"
] | 57288f156ed4a6475c1f44cbc8c5b7ecb6893627f1c688324ba6786cad8f9381 |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | SKIRT/PTS | dustpedia/core/sample.py | Python | agpl-3.0 | 8,168 | [
"Galaxy"
] | 28ef6388f2b5fdac10d59feffa273fb85659747db67e4330763e61b5da7fc66b |
#!/usr/bin/python
import math
import argparse
from string import maketrans
#Script used in order to obtain primers.
parser = argparse.ArgumentParser()
parser.add_argument('-file', action="store", dest = 'File', required = "True")
parser.add_argument('-fasta', action = "store", dest = "genome", required = "True")
parse... | sergioSEa/Developed_scripts | primer-generation.py | Python | gpl-3.0 | 16,460 | [
"Biopython"
] | eeee12407169eff47a30b8de41e1ce6450ef1a5e0b8d62f29bf62fbf609bfe5e |
# Code from Chapter 6 of Machine Learning: An Algorithmic Perspective (2nd Edition)
# by Stephen Marsland (http://stephenmonika.net)
# You are free to use, change, or redistribute the code in any way you wish for
# non-commercial purposes, but please maintain the name of the original author.
# This code comes with no... | Anderson-Lab/anderson-lab.github.io | csc_466_2021_spring/MLCode/Ch6/ecoli.py | Python | mit | 1,737 | [
"Gaussian"
] | cc3f85b90c7e95fcc95c414ecd93fd965d752010ca22f629a045942e89418ced |
#
# This file is part of the CCP1 Graphical User Interface (ccp1gui)
#
# (C) 2002-2005 CCLRC Daresbury Laboratory
#
# 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 ... | alexei-matveev/ccp1gui | interfaces/daltonio.py | Python | gpl-2.0 | 15,263 | [
"Dalton"
] | d3cc06095776816ef41f78fb252c2f039f07793e55a9e175b9f5479aa39c7649 |
# -*- coding: utf-8 -*-
from zope.interface import Interface, implements
from twisted.application import service
from twisted.internet import defer
class IBasicDispatcherService(Interface):
def my_func(self, value):
"""Return a deferred returning a string"""
class BasicDispatcherService(service.Service... | christoforov/edusensors | edusensors/dispatchers/service/BasicDispatcherService.py | Python | mit | 1,202 | [
"MOE"
] | f13eaf479c170ac96562e723f76e3277018a4d976dc1df71347db05fef67071d |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | anderspitman/scikit-bio | skbio/io/format/tests/test_clustal.py | Python | bsd-3-clause | 12,297 | [
"scikit-bio"
] | bea78cc1297d078d49a748e15258ca1653ada84ef0f254e777558564dbfa536f |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Useful tool for image reduction."""
import os
import copy
import numpy as np
from scipy import ndimage
from scipy.ndimage.filters import gaussian_filter
from astropy.io import fits
from astropy.nddata import Cutout2D
from astropy.stats import SigmaClip
from astropy.t... | dr-guangtou/KungPao | kungpao/imtools.py | Python | gpl-3.0 | 28,670 | [
"Gaussian"
] | c1e6102ad7c844adc9e47bdad41c3a15f3a1454ec72c115526fe3aa2349c8977 |
# Copyright (c) 2012 Spotify AB
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may not
# use this file except in compliance with the License. You may obtain a copy of
# the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, s... | ivannotes/luigi | setup.py | Python | apache-2.0 | 3,092 | [
"VisIt"
] | 325856004fdd1a64c106de83027d11a0351d449d94ad38f4fe7b33f500bf17a9 |
# ################################################################
#
# Active Particles on Curved Spaces (APCS)
#
# Author: Silke Henkes
#
# ICSMB, Department of Physics
# University of Aberdeen
# Author: Rastko Sknepnek
#
# Division of Physics
# School of Engineering, Physics and Mathem... | sknepneklab/SAMoS | analysis/batch_nematic/batch_analyze_nematic_phi0.75b.py | Python | gpl-3.0 | 2,491 | [
"VTK"
] | 073c833d7532a5f4dd0242a2b5f859f305f4e163c98523079e86122e1325ac8b |
#!/usr/bin/env python
from __future__ import division, absolute_import, print_function
import os
import sys
import argparse
import redmapper
if __name__ == '__main__':
parser = argparse.ArgumentParser(description='Calibrate the redMaGiC red galaxy selection')
parser.add_argument('-c', '--configfile', action... | erykoff/redmapper | bin/redmagic_run.py | Python | apache-2.0 | 828 | [
"Galaxy"
] | f91da979b9e739ac8cb487403dd67f10117fe015df5a077cc7feaf90d913fc89 |
#! /usr/bin/env python3
# -*- coding: utf-8 -*-
import os,sys,traceback
import re,shutil
from pyramid.view import view_config, view_defaults
from pyramid.response import FileResponse
import logging
from pprint import pformat
import textwrap
import datetime
import humanize
from pygments import highlight
from pygment... | ofilangi/askomics | askomics/ask_view.py | Python | agpl-3.0 | 72,805 | [
"Galaxy"
] | a33d324d5c14dd47df67d3ad7cd4f18930d68654cc1cd43b3a1f9b3e338c6c0f |
#! /usr/bin/env python
from __future__ import division, print_function
import pandas as pd
import sys
import os
import dill
import numpy as np
file_path = os.path.dirname(os.path.realpath(__file__))
lib_path = os.path.abspath(os.path.join(file_path, './'))
sys.path.append(lib_path)
import candle
additional_defini... | ECP-CANDLE/Benchmarks | common/calibration_main.py | Python | mit | 8,705 | [
"Gaussian"
] | 77bc66b7d1829f57fcdb24092899def872ae53e6109f1a6c382b8280a621805c |
#!/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/settings.py | Python | gpl-2.0 | 5,371 | [
"VisIt"
] | d3c786ff6fbf6b3b97e3e439a00086fc2af12cdaa09c21e55df4a70ea19dcdd2 |
from ase.units import Bohr, AUT, _me, _amu
from gpaw import *
from gpaw.tddft import *
from gpaw.tddft.units import attosec_to_autime
from gpaw.mpi import world
###############################################################################
# EHRENFEST DYNAMICS WITHIN THE PAW METHOD
# WORKS WITH PAW AS LONG THERE ISN'... | ajylee/gpaw-rtxs | gpaw/tddft/ehrenfest.py | Python | gpl-3.0 | 7,612 | [
"ASE",
"GPAW"
] | 72f554315da3807201e4cd5e86cb8eb77cd2b3678586668b68b183650f17203d |
import matplotlib
import matplotlib.pyplot as plt
from matplotlib.transforms import IdentityTransform,Affine2D
from matplotlib import pylab
from shapely import geometry
from shapely.ops import cascaded_union
import rdkit
from rdkit import Chem
import fileinput
import sys
class Draw(object):
def __init__(self,topolo... | ldomic/lintools | lintools/draw.py | Python | gpl-3.0 | 12,545 | [
"RDKit"
] | 55e92767094f58cdb88e71638076ad1ff1dff6494af239005a7288c76c883864 |
"""
Courseware views functions
"""
import logging
import urllib
import json
from collections import defaultdict
from django.utils.translation import ugettext as _
from django.conf import settings
from django.core.context_processors import csrf
from django.core.exceptions import PermissionDenied
from django.core.urlr... | carsongee/edx-platform | lms/djangoapps/courseware/views.py | Python | agpl-3.0 | 37,259 | [
"VisIt"
] | 64be7b909230cfb0331e325e2a3f285b5859203cd8b9303a05fd62543c03e406 |
# Principal Component Analysis Code :
from numpy import mean,cov,double,cumsum,dot,linalg,array,rank,size,flipud
from pylab import *
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import ro... | tapomayukh/projects_in_python | classification/Classification_with_kNN/Single_Contact_Classification/Spatial_Resolution/space_resolution_per_meter_percent_1200ms.py | Python | mit | 3,503 | [
"Mayavi"
] | e73a2ee1222dda6f2869cc50450969e01b573ce4b8d76cca1699fc69557102ca |
# (C) British Crown Copyright 2010 - 2015, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | mo-g/iris | lib/iris/io/__init__.py | Python | gpl-3.0 | 14,069 | [
"NetCDF"
] | 249903c5d59247c34e08b415d3934a301c53375f305bbad300cacd0e22e20f50 |
"""
@file bible/seed.py
@author Brian Kim
@brief initialize the database with the good stuff
"""
from model import *
import requests
def mk_en_lang():
return Language(u'en',u'English')
def mk_niv():
en = mk_en_lang()
return Version(en,u'NIV',u'New International Version')
def mk_rsv():
en = mk_en_la... | briansan/bible | bible/seed.py | Python | bsd-2-clause | 2,115 | [
"Brian"
] | 1a20be1b24a2b04ba3d52a7268d86a391a54fee3ab9168437cea6d710e3ef5a5 |
import collections
import numpy as np
def gaussian_grad(im_input, sigma):
"""Performs smoothing with derivative gaussian kernel.
Uses seperable convolution to simultaneously smooth and calculate the
gradient of a grayscale image.
Parameters
----------
im_input : array_like
An intens... | DigitalSlideArchive/HistomicsTK | histomicstk/filters/edge/gaussian_grad.py | Python | apache-2.0 | 1,900 | [
"Gaussian"
] | cdb147eedeba5e63fd1bf6bfb4366e60e71b55d91f0b40c3cbb893eacc7166d6 |
#!/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... | druss316/G-Harvestor | html/getCurrentUserNames.py | Python | gpl-3.0 | 1,648 | [
"Galaxy"
] | 607817dc8f85f195551018580dc2bd06b2a627a1ea310a3b70fd7f05f8eee5bd |
import math
import sys
import random
import numpy as np
class Estimation:
"""Estimate realMatition probabilities from observation,
Generate new observation according to the estimator
"""
def __init__(self):
"""Class Initialization"""
self.nrows = 2
self.ncols = 2
sel... | arongdari/digbeta | tour/src/estimate.py | Python | gpl-3.0 | 2,653 | [
"Gaussian"
] | 1e3dd1fae6eea8414ba7a0ad8f1ce00d14dd87e033e4a9f8fc4656c65d8e2064 |
import md5
import os
from twisted.python import util
from twisted.trial.test import packages
from twisted.trial import runner, reporter, unittest
from twisted.python.modules import getModule
# XXX - this is used in test_script, perhaps it should be in a utility module
def testNames(test):
"""
Return the i... | santisiri/popego | envs/ALPHA-POPEGO/lib/python2.5/site-packages/twisted/trial/test/test_loader.py | Python | bsd-3-clause | 19,124 | [
"VisIt"
] | 10eb5fd2a0f7d89a5d7fa219b0f19350890a05028a2a6d64d932c7c46406f148 |
# -*- coding: utf-8 -*-
import os
import shutil
from lettuce import step, world
from django.conf import settings
from lettuce.django import django_url
from should_dsl import should
from model_mommy import mommy
from apps.members.models import Member
from apps.members.models import Participation
from apps.projects.model... | nsi-iff/nsi_site | apps/members/features/steps.py | Python | mit | 3,842 | [
"VisIt"
] | e681cfd55887b0c1bf25f5880c5f2b0886f0c94aff78a1379d88acd2d12f3fe4 |
# -*- coding: utf-8 -*-
# rdesignerProtos.py ---
#
# Filename: rdesignerProtos.py
# Description:
# Author: Subhasis Ray, Upi Bhalla
# Maintainer:
# Created: Tue May 7 12:11:22 2013 (+0530)
# Version:
# Last-Updated: Wed Dec 30 13:01:00 2015 (+0530)
# By: Upi
# URL:
# Keywords:
# Compatibility:
#
#
# Comment... | BhallaLab/moose | moose-core/python/rdesigneur/rdesigneurProtos.py | Python | gpl-3.0 | 32,040 | [
"MOOSE",
"NEURON"
] | fb4276a25fecc43704263d0c053775dea467d746c2c0fd83ebad21896350ab72 |
# This file is part of fedmsg.
# Copyright (C) 2012 Red Hat, Inc.
#
# fedmsg is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#... | opoplawski/fedmsg_meta_fedora_infrastructure | fedmsg_meta_fedora_infrastructure/tests/anitya.py | Python | lgpl-2.1 | 31,211 | [
"ADF"
] | b1840110e4962e1de468f76ffd150c728b77ca295222fc3cd8d913f3f7e1a06d |
"""Routes configuration
The more specific and detailed routes should be defined first so they
may take precedent over the more generic routes. For more information
refer to the routes manual at http://routes.groovie.org/docs/
"""
import types
import os
import re
from pylons import config
from routes import Mapper
def... | DIRACGrid/DIRACWeb | dirac/config/routing.py | Python | gpl-3.0 | 2,840 | [
"DIRAC"
] | bb4bfcae0a396e72f20cf512cdf1204093ae7c1e2c7e8703a2715e49af8b3949 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import json
import os
import unittest
import numpy as np
import pandas as pd
from pymatgen.io.lammps.outputs import LammpsDump, parse_lammps_dumps, parse_lammps_log
from pymatgen.util.testing import PymatgenTest
test_dir = o... | vorwerkc/pymatgen | pymatgen/io/lammps/tests/test_outputs.py | Python | mit | 6,712 | [
"LAMMPS",
"pymatgen"
] | 257060793f167bf0659f86174b0940f28dbf4826d165e90770c5d3c9d16a923e |
#!/usr/bin/env python
# Copyright 2014-2019 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/hf.py | Python | apache-2.0 | 29,364 | [
"CRYSTAL",
"PySCF"
] | 531620f1cfce8ea10570c7ae507d58361e0fa8270f2b49ecb67a225428f0b6dc |
import os
import discord
from .utils import checks
from discord.ext import commands
from cogs.utils.dataIO import dataIO
try:
import spotipy
from spotipy.oauth2 import SpotifyClientCredentials
except:
spotipy = None
class Spotify:
def __init__(self, bot):
self.bot = bot
self.settings ... | atiwiex/Ati-Cogs | spotify/spotify.py | Python | gpl-3.0 | 3,554 | [
"VisIt"
] | e4aac19839958168cfe59ec85fe56317b13baddc21315ffdfe1754fe911db68e |
"""Single-trials covariance-based Granger Causality for gaussian variables.
-------------------- Total Granger interdependence ----------------------
Total Granger interdependence:
TGI = GC(x,y)
TGI = sum(GC,2):
TGI = GC(x->y) + GC(y->x) + GC(x.y)
TGI = GC(x->y) + GC(y->x) + GC(x.y) = Hycy + Hxcx - Hxxcyy
This quantit... | EtienneCmb/brainpipe | brainpipe/connectivity/stgc.py | Python | gpl-3.0 | 6,960 | [
"Gaussian"
] | 18f1ee649df2cb6e6737fe3ba6e8ac7d8e9a69419c2b55be188ba7155531bdc8 |
#!/usr/bin/env python
"""
LAMMPS Replica Exchange Molecular Dynamics (REMD) trajectories are arranged by
replica, i.e., each trajectory is a continuous replica that records all the
ups and downs in temperature. However, often the requirement is trajectories
that are continuous in temperature, which is achieved by this... | jeremiahyan/lammps | tools/replica/reorder_remd_traj.py | Python | gpl-2.0 | 20,166 | [
"LAMMPS"
] | af5d3b5760186f521888611c42ade1711f2025734bd848c0e719e89c413c719e |
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2003-2006 Donald N. Allingham
# Copyright (C) 2008,2012 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2012 Paul Franklin
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | dermoth/gramps | gramps/plugins/textreport/custombooktext.py | Python | gpl-2.0 | 6,713 | [
"Brian"
] | cd249ac85cd564b67f24f3e13ec2411941b5526bebdf9c19a748abf8f1d8679b |
#
# Copyright (c) 2009-2015, Jack Poulson
# All rights reserved.
#
# This file is part of Elemental and is under the BSD 2-Clause License,
# which can be found in the LICENSE file in the root directory, or at
# http://opensource.org/licenses/BSD-2-Clause
#
import El
m = 2000
n = 4000
k = 3000
testMehrotra = Tru... | mcopik/Elemental | examples/interface/QPAffine.py | Python | bsd-3-clause | 4,828 | [
"Gaussian"
] | 403780fd957a823469703b53edf34f34897fec6b1408edc114d2d3a10db40434 |
#!/usr/bin/env python
"""
Example script using OnsagerCalc to compute the elasto-diffusion tensor for
an interstitial. It also shows how to both construct an input YAML file for
an FCC, BCC, or HCP crystal with octahedral / tetrahedral network, and
read from that same YAML file as input. It's actually *extremely genera... | DallasTrinkle/Onsager | bin/OctaTetra-interstitial.py | Python | mit | 8,833 | [
"CRYSTAL"
] | ac3663f210f8aecaf355f5ae6e23b00213ba295dc2aa37e3fa491ac0780102b8 |
from ase import Atoms
from ase.optimize import QuasiNewton
from gpaw import GPAW
a = 6
b = a / 2
mol = Atoms('H2O',
[(b, 0.7633 + b, -0.4876 + b),
(b, -0.7633 + b, -0.4876 + b),
(b, b, 0.1219 + b)],
cell=[a, a, a])
calc = GPAW(nbands=4,
h=0.2,
... | qsnake/gpaw | doc/documentation/lcao/lcao_h2o.py | Python | gpl-3.0 | 455 | [
"ASE",
"GPAW"
] | 1c41d55fcc7016fee05c62920ca1df363c426979a3be03199b0e6868fa689c63 |
# -*- coding: utf-8 -*-
"""
sphinx.writers.texinfo
~~~~~~~~~~~~~~~~~~~~~~
Custom docutils writer for Texinfo.
:copyright: Copyright 2007-2013 by the Sphinx team, see AUTHORS.
:license: BSD, see LICENSE for details.
"""
import re
import string
import textwrap
from os import path
from docutils imp... | nirmeshk/oh-mainline | vendor/packages/sphinx/sphinx/writers/texinfo.py | Python | agpl-3.0 | 45,335 | [
"VisIt"
] | 2142f76d785970ad7010c1b476103ea36f7f4a016d1d107e77cbb8160dd5ef2f |
"""
Edits the Gromacs .mdp file.
A Gromacs .mdp file contains various informations about the simulation setup
ranging from the Molecular Dynamics timestep to the thermostat parameters,
output management and so on. A Dimer simulation in Gromacs requires some of these
settings to be set in a particular way. This pack... | marckn/dimerizer | dimerizer/mdp/__init__.py | Python | gpl-3.0 | 1,952 | [
"Gromacs"
] | eab26fefdf9f38a30a649de67c1c24722aa37c2c0b387e0be07a938b05c11a3a |
# Principal Component Analysis Code :
from numpy import mean,cov,double,cumsum,dot,linalg,array,rank,size,flipud
from pylab import *
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import ro... | tapomayukh/projects_in_python | sandbox_tapo/src/skin_related/BMED_8813_HAP/Scaling/results/cross_validate_objects_BMED_8813_HAP_scaled_method_I.py | Python | mit | 3,959 | [
"Mayavi"
] | 495cba3f4fca068d8e912b1783a441fa97ea1a67f8eaa317a83f98f773089c2e |
#Using Scrapy with Selenium to scape a rendered page [Updated]
from scrapy.contrib.spiders.init import InitSpider
from scrapy.http import Request, FormRequest
from scrapy.contrib.linkextractors.sgml import SgmlLinkExtractor
from scrapy.contrib.spiders import CrawlSpider, Rule
from scrapy.spider import BaseSpider... | InfiniteRandomVariable/hello-world | tutorial/tutorial/spiders/guardian.py | Python | apache-2.0 | 3,904 | [
"VisIt"
] | fb65dd6cea0bdecaa99986586affc8a5fc71c6ae7552cb91a4d3380909743864 |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class PyAse(PythonPackage):
"""The Atomic Simulation Environment (ASE) is a set of tools
and... | LLNL/spack | var/spack/repos/builtin/packages/py-ase/package.py | Python | lgpl-2.1 | 2,182 | [
"ASE"
] | a05e963aaa0a6d7172b3a7fdcb7390221dfa66417e3eaeeec7bc86b9f59e1fdf |
#!/usr/bin/env python
#
# ex43.py
#
# Author: Billy Wilson Arante
# Created: 2016/05/15 PHT
# Citation: http://learnpythonthehardway.org/book/ex43.html
#
from sys import exit
from random import randint
class Scene(object):
def enter(self):
print "This scene is not yet configured. Subclass it and " + \
... | arantebillywilson/python-snippets | py2/lpthw/ex43.py | Python | mit | 9,859 | [
"BLAST"
] | ec89740df42fb6f08f3df48f59571667c55533664f0c1023d2a483fb2aeafc11 |
import os
import tarfile
from flyingpigeon.subset import clipping
from flyingpigeon.subset import countries, countries_longname
from flyingpigeon.log import init_process_logger
from pywps.Process import WPSProcess
import logging
logger = logging.getLogger(__name__)
class ClippingProcess(WPSProcess):
def __init... | KatiRG/flyingpigeon | flyingpigeon/processes/wps_subset_countries.py | Python | apache-2.0 | 5,682 | [
"NetCDF"
] | 100ada56b7b2620c001b40f028e136e2c1da19a58b109ee4ccfa3254cf0cfd4a |
# -*- coding: utf-8 -*-
import datetime
import json
import os
import shutil
from django.conf import settings
from django.core.files.storage import default_storage as storage
from django.core.urlresolvers import reverse
import mock
from nose.tools import eq_, ok_
from pyquery import PyQuery as pq
import mkt
from mkt.... | mstriemer/zamboni | mkt/submit/tests/test_views.py | Python | bsd-3-clause | 38,838 | [
"exciting"
] | 6fe5170568b059a31a76fce46e41e81148c5f437254ae2a096b6400daf812f28 |
import logging
from igraph import Graph
from more_itertools import unique_everseen
from .base_writer import BaseWriter
class DRTTripletsWriter(BaseWriter):
_logger = logging.getLogger(__name__)
def visit(self, g):
triplets = self.__get_relations_and_entities_from_graph(g)
return triplets
... | fractalego/pynsett | pynsett/writer/drt_triplets_writer.py | Python | mit | 1,471 | [
"VisIt"
] | d8f98884d301b5d09517217a21f7d5d6a8e18ca9f4d4639ea4c456e2e9047b2d |
"""Contains the parent classes for MPF's display system, including the
DisplayController, MPFDisplay, DisplayElement, Transition, and Decorator.
"""
# display.py
# Mission Pinball Framework
# Written by Brian Madden & Gabe Knuth
# Released under the MIT License. (See license info at the end of this file.)
# Documenta... | spierepf/mpf | mpf/media_controller/core/display.py | Python | mit | 30,607 | [
"Brian"
] | 8a631e0fb0234161a3c23f7634c28cf6d886e1d6eb773081acc8a6ef69d977ce |
""" DIRAC Basic MySQL Class
It provides access to the basic MySQL methods in a multithread-safe mode
keeping used connections in a python Queue for further reuse.
These are the coded methods:
__init__( host, user, passwd, name, [maxConnsInQueue=10] )
Initializes the Queue and tries to connect to... | fstagni/DIRAC | Core/Utilities/MySQL.py | Python | gpl-3.0 | 52,142 | [
"DIRAC"
] | cd26f588bc2cbf015f81e2279f4b40776d4a5a4e5b8549cd67a9db7b1b709b3b |
# Copyright (c) 2014-2015 Brett Cannon <brett@python.org>
# Copyright (c) 2014-2016 Claudiu Popa <pcmanticore@gmail.com>
# Copyright (c) 2015 Pavel Roskin <proski@gnu.org>
# Licensed under the GPL: https://www.gnu.org/licenses/old-licenses/gpl-2.0.html
# For details: https://github.com/PyCQA/pylint/blob/master/COPYING
... | rogalski/pylint | pylint/checkers/python3.py | Python | gpl-2.0 | 42,745 | [
"VisIt"
] | 0e456b4f41a8540b066b3c8d67b79d54e2e419415921756efbb91a37e8d58902 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# module builder script
#
import os, sys, shutil, tempfile, subprocess, platform
this_dir = os.path.dirname(__file__)
scripts_root_dir = os.path.dirname(this_dir)
scripts_common_dir = os.path.join(scripts_root_dir, "common")
scripts_android_dir = os.path.join(scripts_roo... | appcelerator/titanium_mobile_tooling | scripts/module/builder.py | Python | apache-2.0 | 8,032 | [
"VisIt"
] | c77a33ee8b8f1e2ced1a905662610457f339202e2979a6dd0b4aa0e5546f054e |
from simphony.api import CUBA
from .pair_style import PairStyle
from .atom_type_fixes import get_per_atom_type_fixes
from ..common.atom_style import (get_lammps_string, AtomStyle)
class ConfigurationError(RuntimeError):
pass
class ScriptWriter(object):
""" Writer of a LAMMPS-commands script
The Scrip... | simphony/simphony-lammps-md | simlammps/config/script_writer.py | Python | bsd-2-clause | 8,010 | [
"LAMMPS"
] | eff4109289988d270232e83c1389b1760bb7cae097d51fe9a0090022f0cbc46a |
# -*- coding: utf-8 -*-
# Copyright 2007-2021 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at... | thomasaarholt/hyperspy | hyperspy/misc/eds/utils.py | Python | gpl-3.0 | 25,314 | [
"Avogadro",
"Gaussian"
] | 9644449bf5f39892cd0ccaf81bb48243d81036ab7a12c111903c3afd0b0309a1 |
"""Galaxy Cluster Ensemble Calculations.
Cluster mass-richness and mass-concentration scaling relations, and NFW
halo profiles for weak lensing shear and magnification, including the
effects of cluster miscentering offsets.
This framework calculates properties and profiles for every individual
cluster, storing the da... | jesford/cluster-lensing | clusterlensing/clusters.py | Python | mit | 20,488 | [
"Galaxy",
"Gaussian"
] | 34af47ada2c543aafe218f5e9b9140cd9abb5c0867fbed94d63723d9f1556f0b |
"""
===============================================================
Customized sampler to implement an outlier rejections estimator
===============================================================
This example illustrates the use of a custom sampler to implement an outlier
rejections estimator. It can be used easily wi... | fmfn/UnbalancedDataset | examples/applications/plot_outlier_rejections.py | Python | mit | 4,354 | [
"Gaussian"
] | 0596806ed0bbb6669650f2a1a51c962609aad2cd595feac8a3530f1f0c53c5b2 |
"""Contains a dictionary that maps file extensions to VTK readers."""
import pathlib
import os
import warnings
import numpy as np
import pyvista
from pyvista import _vtk
READERS = {
# Standard dataset readers:
'.vtk': _vtk.vtkDataSetReader,
'.pvtk': _vtk.lazy_vtkPDataSetReader,
'.vti': _vtk.vtkXMLIm... | akaszynski/vtkInterface | pyvista/utilities/fileio.py | Python | mit | 20,039 | [
"VTK"
] | d4d1c7a669cda94fa98fe13ea858384c54b4d2b2f4a6af6bb93a7faa93d9696c |
#!/usr/bin/python
# Find API usage in benchmark programs
import sys
import os
flist = [
"../sunspider_v0.9.1/3d-cube.js",
"../sunspider_v0.9.1/3d-morph.js",
"../sunspider_v0.9.1/3d-raytrace.js",
"../sunspider_v0.9.1/access-binary-trees.js",
"../sunspider_v0.9.1/access-fannkuch.js",
"../sunspider_v0.9.1/access-nbody.... | darkrsw/safe | benchmarks/apiusage/apiusage.py | Python | bsd-3-clause | 2,428 | [
"Gaussian"
] | b98ab86ea7db2d79c2c5f6b7b71955f1f0aa835bf362304425761390fe762d9d |
#!/usr/bin/env python
#
# Creates and displays a box plot.
#
#
# agomez (at) tacc.utexas.edu
# 30 Oct 2014
#
# ---------------------------------------------------------------------
import numpy as np
import matplotlib.pyplot as plt
#gaussian distributions
dataset_1 = np.random.normal(5.0, 3.0, 1000)
dataset_2 = np.ran... | antoniogi/HPC | Python/TACC_HPC/3_matplotlib/boxes.py | Python | apache-2.0 | 529 | [
"Gaussian"
] | 69b93c397b3a71c9c192f569cc5147566fc8e80f3d8f2c274700dc5f6e3540ad |
# Copyright: (c) 2013, James Cammarata <jcammarata@ansible.com>
# Copyright: (c) 2018, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import os.path
import re
import sh... | shsingh/ansible | lib/ansible/cli/galaxy.py | Python | gpl-3.0 | 68,922 | [
"Galaxy"
] | 0a8be36bcc5d3d3bb570fab634d8b8a04003425ed9a090e03ffd53cfc8fe586d |
# -*- coding: utf-8 -*-
'''
Created on Nov 19, 2015
Modified on Nov 19, 2015
Version 0.01.a
@author: rainier.madruga@assurant.com
A simple Python Program to review an Excel file and parse stats for a database
'''
# Import and Load Libraries for Script
import datetime
import os
import openpyxl
import zipfile
import r... | rainier-m/python-soccer | parse_SoccerStats.py | Python | gpl-2.0 | 6,458 | [
"CRYSTAL"
] | 116519721bf570f0ed1d05180a3c0759a502b8668dee6afc265c566f51287f14 |
#!/usr/bin/env python
# encoding: utf-8
"""
mygis.py
Series of routines for reading / writing various GIS formats
(added as I need them)
Requires GDAL and netCDF4 (both the libraries and the Python bindings)
if GDAL is not available it will still import, but libraries that require gdal will raise an import e... | gutmann/icar | helpers/lib/mygis.py | Python | mit | 21,405 | [
"NetCDF"
] | 0cb167b68841235e53fa2062f959b626729eb03e5bfa287c45a76d0967766026 |
'''
This is the application scheduler.
It defines scheduled tasks and runs them as per their defined schedule.
This scheduler is started and stopped when the app is started and stopped.
Unless RUN_SCHEDULE is set to False in the config. In which case it must be started manually / managed by supervisor.
It is presume... | JiscPER/jper | service/scheduler.py | Python | apache-2.0 | 16,454 | [
"Octopus"
] | da7a652a505feac2fa5559f284bae44a1b893ed3eba9b287805d6b3695356655 |
# ----------------------------------------------------------------------------
# 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_genbank.py | Python | bsd-3-clause | 15,587 | [
"scikit-bio"
] | dd486acaee5a4e019baccced698f5a22363f8e11701fb03c1f5f7a1e3c812ae2 |
"""QE calculator interface."""
# Copyright (C) 2014 Atsushi Togo
# All rights reserved.
#
# This file is part of phonopy.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# * Redistributions of source code must retai... | atztogo/phonopy | phonopy/interface/qe.py | Python | bsd-3-clause | 20,630 | [
"CRYSTAL",
"VASP",
"phonopy"
] | a054bfd72883ad6def33cca60de685efffb6fdeaf7ea65506b0dc0b71244fe90 |
# Copyright 2007 by Tiago Antao <tiagoantao@gmail.com>. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""
This module provides code to work with FDist.
See http://www.rubic.... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/PopGen/FDist/__init__.py | Python | apache-2.0 | 4,332 | [
"Biopython"
] | 2dd112111b800ba61ec9835898fae302ee282809e98cb4a9b086d974df02636b |
from __future__ import print_function
import os
os.environ['THEANO_FLAGS'] = "mode=FAST_COMPILE"
__author__ = 'http://stackoverflow.com/questions/25967922/pybrain-time-series-prediction-using-lstm-recurrent-nets'
from sys import stdout
from itertools import cycle
from random import random, choice, sample
from time i... | w0nk0/LSTMtest1 | keras_gen_from_model.py | Python | gpl-2.0 | 11,958 | [
"NEURON"
] | db4c06c11d49189957f179cc4fa3626fe24e19c9f2f00a4bab31c80eed5aa6a7 |
from typing import Iterable
import gempy as gp
import pandas as pd
import numpy as np
def loop2gempy(
contacts_file: str,
orientations_file: str,
bbox: Iterable,
groups_file: str,
model_base: float,
model_top: float, dtm_reproj_file: str = None,
faults_contact: ... | cgre-aachen/gempy | gempy/addons/map2gempy.py | Python | lgpl-3.0 | 7,684 | [
"VTK"
] | 32333f04505110f67b21a80b95da269c55c19a49743fe2c1ddc6b333f39092a7 |
""" DIRAC API Base Class """
__RCSID__ = '$Id$'
import pprint
import sys
from DIRAC import gLogger, gConfig, S_OK, S_ERROR
from DIRAC.Core.Security.ProxyInfo import getProxyInfo, formatProxyInfoAsString
from DIRAC.ConfigurationSystem.Client.Helpers.Registry import getDNForUsername
from DIRAC.Core.Utilities.Version i... | andresailer/DIRAC | Core/Base/API.py | Python | gpl-3.0 | 5,421 | [
"DIRAC"
] | 156ceddd77201be11841bfca1147ec321fd7cc1fd0696c02b0aa611fd891d93a |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=80 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# -------------------------------------------------------... | marmyshev/transitions | resources/pyinstaller/hook-openlp.plugins.presentations.presentationplugin.py | Python | gpl-2.0 | 2,322 | [
"Brian"
] | 51003daaa0ce5dd6ea3c619b22197388fc3d5b4cf986c51432751aeb116f7d53 |
"""
visit https://morvanzhou.github.io/tutorials/ for more!
Build two networks.
1. Without batch normalization
2. With batch normalization
Run tests on these two networks.
"""
# 23 Batch Normalization
import numpy as np
import tensorflow as tf
import matplotlib.pyplot as plt
ACTIVATION = tf.nn.relu
N_LAYERS = 7
N... | del680202/MachineLearning-memo | src/tensorflow/BN.py | Python | apache-2.0 | 6,157 | [
"VisIt"
] | 546a6af4d926c1847df1dffe2afd1c528bf7717da3364c08b2db08624e392673 |
"""
Traits View definition file.
The view trait of the parent class is extracted from the model definition
file. This file can either be exec()ed or imported. See
core/base.py:Base.trait_view() for what is currently used. Using exec()
allows view changes without needing to restart Mayavi, but is slower than
importi... | dmsurti/mayavi | mayavi/sources/ui/parametric_surface.py | Python | bsd-3-clause | 1,083 | [
"Mayavi"
] | cbeeb592686c3fef33e859268b7e3069e813fc4ecd2f814ad149180783df7b3c |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# This file lib_nrf24.py is a slightly tweaked version of Barraca's "pynrf24".
# So this is my tweak for Raspberry Pi and "Virtual GPIO" ...
# ... of Barraca's port to BeagleBone python ... (Joao Paulo Barraca <jpbarraca@gmail.com>)
# ... of maniacbug... | rahulpopuri/plants | scripts/lib_nrf24.py | Python | apache-2.0 | 25,861 | [
"Brian"
] | 074071b0dfc0f27c2148f0929611f26872be6525128392b444a29b246499f41d |
import numpy.random as random
import numpy as np
from ase import Atoms
from ase.calculators.neighborlist import NeighborList
from ase.lattice import bulk
atoms = Atoms(numbers=range(10),
cell=[(0.2, 1.2, 1.4),
(1.4, 0.1, 1.6),
(1.3, 2.0, -0.1)])
atoms.set_scaled_po... | grhawk/ASE | tools/ase/test/neighbor.py | Python | gpl-2.0 | 2,397 | [
"ASE"
] | 75c0b2c892d0d99bddb9d0f657d64d794d3a53831823809db70ef51b8afa4524 |
#!/usr/bin/env python
#JSON {"lot": "RHF/6-31G",
#JSON "scf": "PlainSCFSolver",
#JSON "linalg": "CholeskyLinalgFactory",
#JSON "difficulty": 1,
#JSON "description": "Basic RHF example with Cholesky matrices, includes export of Hamiltonian"}
from horton import *
import numpy as np
# Hartree-Fock calculation
# ---... | eustislab/horton | data/examples/hf_dft/rhf_h2_cholesky.py | Python | gpl-3.0 | 2,421 | [
"Gaussian"
] | 32b3502bc91b7d6d0f272990f6860d2663d4f50792a1d1161bceaed91e6c2fe5 |
"""
=====================================
Blind source separation using FastICA
=====================================
An example of estimating sources from noisy data.
:ref:`ICA` is used to estimate sources given noisy measurements.
Imagine 3 instruments playing simultaneously and 3 microphones
recording the mixed si... | RPGOne/Skynet | scikit-learn-c604ac39ad0e5b066d964df3e8f31ba7ebda1e0e/examples/decomposition/plot_ica_blind_source_separation.py | Python | bsd-3-clause | 2,228 | [
"Gaussian"
] | 35f67b098b33ed66df5851fa35719fcdbe08a4fa27a15675c175da41c1438888 |
"""
============================================================
Empirical evaluation of the impact of k-means initialization
============================================================
Evaluate the ability of k-means initializations strategies to make
the algorithm convergence robust as measured by the relative stan... | cdegroc/scikit-learn | examples/cluster/plot_kmeans_stability_low_dim_dense.py | Python | bsd-3-clause | 4,364 | [
"Gaussian"
] | 09ec6a4a2b6817d0eebccc279c01c5c38cc89cad6acbf88b61c1c05c07f6b1a6 |
#!/usr/bin/env python
from vtk import *
reader1 = vtkXMLTreeReader()
reader1.SetFileName("treetest.xml")
reader1.Update()
view = vtkTreeMapView()
view.SetAreaSizeArrayName("size")
view.SetAreaColorArrayName("level")
view.SetAreaLabelArrayName("name")
view.SetAreaLabelVisibility(True)
view.SetAreaHoverArra... | hlzz/dotfiles | graphics/VTK-7.0.0/Examples/Infovis/Python/treemap_view.py | Python | bsd-3-clause | 616 | [
"VTK"
] | 07d17edf885922e01e3f5d98221436d510170aadfed0089458a1002d595f10dc |
import ast
from jaspyx.ast_util import ast_load, ast_call
from jaspyx.visitor import BaseVisitor
class BinOp(BaseVisitor):
def visit_BinOp(self, node):
attr = getattr(self, 'BinOp_%s' % node.op.__class__.__name__, None)
attr(node.left, node.right)
for key, value in {
'Add': '+',
... | iksteen/jaspyx | jaspyx/visitor/binop.py | Python | mit | 1,001 | [
"VisIt"
] | 57e512c2874233badc8854d4355887b62231d99d08d025aa07464eb08c4bd30b |
# -*- coding: utf-8 -*-
# Copyright 2007-2011 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at... | sillvan/hyperspy | hyperspy/io.py | Python | gpl-3.0 | 16,870 | [
"NetCDF"
] | 3f419b2f497eb3bc7d5d6c0f84030aa25ae0ef582e449439ff540d647a059661 |
##############################################################################
# Copyright (c) 2013-2018, 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... | EmreAtes/spack | var/spack/repos/builtin/packages/r-fgsea/package.py | Python | lgpl-2.1 | 2,167 | [
"Bioconductor"
] | c5baa0bb75d5b02a8ca2256ddaec9858eee7832a9d84eb9e6d820f4b12627069 |
#
# dnfhelper.py
#
# Copyright (C) 2010-2015 Red Hat, Inc.
#
# 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... | bcl/lorax | src/pylorax/dnfhelper.py | Python | gpl-2.0 | 3,578 | [
"Brian"
] | ac2ed1ad2fa1c6b3681198d71f7d2671f6bbc2051f1524b5b643c0b9569eabe6 |
#!/usr/bin/env python
from pyDFTutils.ase_utils import symbol_number, symnum_to_sym
import numpy as np
import re
import os
import sys
import pickle
from scipy.integrate import trapz
from collections import OrderedDict
int_keys = ("num_bands", "num_wann", 'bands_num_points',
"fermi_surface_num_points", "num... | mailhexu/pyDFTutils | pyDFTutils/wannier90/wannier.py | Python | lgpl-3.0 | 25,028 | [
"ASE",
"Wannier90"
] | f3adb316f21fc34d3912e552320db9c2aeba178f3bdf1d6bce2b770ee64e43e8 |
#!/usr/bin/env python
#print __name__
import optparse
import os
usage_line = """
homology_BESThit_parsing.py
Version 1.0 (28 August, 2014)
License: GNU GPLv2
To report bugs or errors, please contact Daren Card (dcard@uta.edu).
This script is provided as-is, with no support and no guarantee of proper or desirable fu... | darencard/ContigAnnotator | homology_BESThit_parsing.py | Python | gpl-2.0 | 5,698 | [
"BLAST"
] | d1873a07e3d5ca573edc04573efbc98f7fb2c7b9d857d51a158f42fb60e12cee |
"""
Display Activation Contours
===========================
Load a statistical overlay as a "topographic" contour map.
"""
print __doc__
import os.path as op
from surfer import Brain
"""
Bring up the visualization.
Contour maps looks best with the "low_contrast" cortex
colorscheme, so we will pass that as an optio... | aestrivex/PySurfer | examples/plot_topographic_contours.py | Python | bsd-3-clause | 1,851 | [
"Mayavi"
] | bcc1149702e98c656f683d8953f08186b439320aa5c73b36cb40e90b066093d1 |
""" DIRAC FileCatalog plug-in class to manage dynamic datasets defined by a metadata query
"""
import hashlib
import os
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Core.Utilities.List import stringListToString
class DatasetManager(object):
_tables = dict()
_tables["FC_MetaDatasets"] = {
"Fie... | DIRACGrid/DIRAC | src/DIRAC/DataManagementSystem/DB/FileCatalogComponents/DatasetManager/DatasetManager.py | Python | gpl-3.0 | 31,158 | [
"DIRAC"
] | 22aa6ac1d4f718d31f817a796069c54cb7bd24381eaaa6161c926ac74e1cc810 |
#!/usr/bin/env python
########################################################################
# File : dirac-platform
# Author : Adria Casajus
########################################################################
"""
The *dirac-platform* script determines the "platform" of a certain node.
The platform is a string... | DIRACGrid/DIRAC | src/DIRAC/Core/scripts/dirac_platform.py | Python | gpl-3.0 | 5,709 | [
"DIRAC"
] | 87e4246a88b1ae4a8e47a25b6feb4ce51f9877568e923288073c155de9a5423c |
# Copyright 2014 SolidBuilds.com. All rights reserved
#
# Authors: Ling Thio <ling.thio@gmail.com>
from __future__ import print_function # Use print() instead of print
from flask import url_for
from StringIO import StringIO
import json
import random
import string
import pytest
import shutil
import os
import re
from... | livro-aberto/BookCloud | tests/test_page_urls.py | Python | gpl-3.0 | 20,254 | [
"VisIt"
] | a990fbe02e254e523fb8ab22daff6e72d92f2c6ab3988d68cbea496aee33b763 |
from __future__ import absolute_import, division, print_function
# ----------------------------------------------------------------------------
# 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 ... | Kleptobismol/scikit-bio | skbio/util/_exception.py | Python | bsd-3-clause | 538 | [
"scikit-bio"
] | a39464d97c29ff8ec432f1ba70fce98364ab1a2f4a9ea4f854f1b376fddb6cdb |
import Sire.Config
import argparse
import os
import sys
try:
numpy = Sire.try_import("numpy")
except:
pass
from Sire.Tools import OpenMMMD
from Sire.Tools import readParams
parser = argparse.ArgumentParser(description="Perform molecular dynamics single topology free energy calculations "
... | chryswoods/Sire | wrapper/python/scripts/somd-freenrg.py | Python | gpl-2.0 | 5,014 | [
"Amber",
"OpenMM",
"VisIt"
] | 2cd708a48ae762351bcfa57c6c97935eb34cb0b8d60a5dd8e2fddca43e1d6b02 |
from .. import Availability, Class, Constant, Define, Method, Parameter, Type
gx_class = Class('VOX',
doc="""
High Performance 3D Grid. Designed for accessing
3D grids quickly using slices. It designed arround
non-uniform multi-resolution compressed ... | GeosoftInc/gxapi | spec/core/VOX.py | Python | bsd-2-clause | 107,579 | [
"Gaussian"
] | 363e26d7a1144f1cd09925058fbb23a3590029ce178517ba3ebb2df5ac46b416 |
#get the default AMI's and titles for the 8 EC2 datacenters through endless screen scraping
#please destroy me when EC2 provides this data through JSON ;)
import time, datetime, sys, re
try:
from splinter import Browser
except:
sys.exit('install splinter, ./bin/pip install splinter')
EC2_USER = ""
EC2_PASS = "... | munkiat/mist.io | scripts/get_ec2_amis.py | Python | agpl-3.0 | 2,107 | [
"VisIt"
] | efba057bac01600eebdfef331163776c350c0fab2ac4a0e71487287207c86d90 |
import ase.db
from ase.structure import molecule
from ase.optimize.bfgs import BFGS
from ase.calculators.nwchem import NWChem
from ase.data.g2_1 import molecule_names, atom_names
c = ase.db.connect('g2-1.db')
for name in molecule_names + atom_names:
id = c.reserve(name=name, calculator='nwchem')
if id is Non... | robwarm/gpaw-symm | gpaw/test/big/g2_1/g21nwchem.py | Python | gpl-3.0 | 1,064 | [
"ASE",
"NWChem"
] | a78f8b87cb89457e0d88c2f11c339b6107abf990f88d9985a7f014b4db574580 |
import os
import numpy as np
from ase.structure import bulk
from gpaw import GPAW
from gpaw.response.df import DF
from ase.dft import monkhorst_pack
from gpaw.response.bse import BSE
from gpaw.mpi import rank, size
# generate kmesh
kpts =(2,2,2)
bzk_kc = monkhorst_pack(kpts)
shift_c = []
for Nk in kpts:
if Nk % 2... | ajylee/gpaw-rtxs | gpaw/test/bse_sym.py | Python | gpl-3.0 | 1,884 | [
"ASE",
"GPAW"
] | 021aa3525788bc26527d13d539aa33706833024454f820c83cfe6839a13d7da7 |
#
# Copyright 2018 Analytics Zoo 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... | intel-analytics/analytics-zoo | pyzoo/zoo/orca/automl/auto_estimator.py | Python | apache-2.0 | 11,592 | [
"ORCA"
] | b32b049ea3856a6f2ca3b2c9729618bb1bf238d7d28e0c3c26269b07755d65f3 |
# Copyright 2019-present, GraphQL Foundation
# All rights reserved.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
from casing import title
from license import C_LICENSE_COMMENT
class Printer(object):
def __init__(self):
self._fields... | graphql/libgraphqlparser | ast/cxx_json_visitor_impl.py | Python | mit | 2,312 | [
"VisIt"
] | 72867dca86601479141de4bd9a67820db29982bb787580ae3c79761146ee7042 |
# coding=utf-8
import logging
import traceback
import gevent
from gevent.hub import Waiter
from gevent import Timeout
import time
from octopus.service.octp_client import OctpClient
from octopus.service.service import Service
from octopus import err
from octopus import constant
log = logging.getLogger(constant.LOGGER_... | ideascf/octopus | service/selector/_base.py | Python | mit | 2,620 | [
"Octopus"
] | d4d5687f41cbfffe33aa8aade7ccd03320ec1351105405265d0f44acd5b342c0 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.