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import datetime
from collections import namedtuple
import pytest
import pycds
from pycds import *
from pydap.handlers.pcic import RawPcicSqlHandler
import testing.postgresql
from pycds.util import *
from sqlalchemy import create_engine, event
from sqlalchemy.orm import sessionmaker
from sqlalchemy.schema import DDL, ... | pacificclimate/pydap.handlers.pcic | tests/conftest.py | Python | gpl-3.0 | 9,249 | [
"MOE"
] | bbcace5991ee38437abaa8f1546b4fa02065ac0b238145a783cdb01f03d45a39 |
import sys
import getopt
caffe_root = '../../lib/caffe/'
sys.path.insert(0, caffe_root + 'python')
import numpy as np
import caffe
from caffe import layers as L, params as P
from caffe.coord_map import crop
import site
site.addsitedir('./oylmpic_layer')
def conv(name, bottom, nout, ks=3, stride=1, pad=0, group=1, bias... | mrtukkin/ifp | BuildTrainNet.py | Python | gpl-3.0 | 7,244 | [
"Gaussian"
] | 98409e37bd14fa223ec888b4556e5b1e2283b45916e673b9a2d399fa536adc99 |
import traceback
import pyglet
from geoplotlib.core import GeoplotlibApp
class AppConfig:
def __init__(self):
self.reset()
def reset(self):
self.layers = []
self.bbox = None
self.savefig = None
self.tiles_provider = 'mapquest'
self.smoothing = False
s... | lucciano/geoplotlib | geoplotlib/__init__.py | Python | mit | 9,984 | [
"Gaussian"
] | 235646bdac0b61539e12ee58f6beb9eeda563df07103d3167e0c8c9a969ef320 |
"""
Visit the Twitter developer page and create a new application:
https://dev.twitter.com/apps/new
This will get you a CONSUMER_KEY and CONSUMER_SECRET.
Twitter only supports the application-only flow of OAuth2 for certain
API endpoints. This OAuth2 authenticator only supports the application-only
flow right no... | crashbit/twitter | twitter/oauth2.py | Python | mit | 2,813 | [
"VisIt"
] | 8d2cf309d0c72b133417d3f87d9fd7e92f9b87399ddee2b5d632fb41ac62f74c |
# Copyright 2015 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or ag... | flgiordano/netcash | +/google-cloud-sdk/lib/googlecloudsdk/core/resource/resource_expr.py | Python | bsd-3-clause | 15,555 | [
"VisIt"
] | dbe706da243792d74264afedfec8298ddaa26602057ee93e6dd851ff4683df8a |
import traceback
import types
import os
import sys
class toolPlugin():
def pluginEXE(self):
'''Respond to the "tblastx" type command.
'''
plugin_exe = r"C:/Program Files/NCBI/blast-2.2.24+/bin/tblastx.exe"
return plugin_exe
def GetExec():
'''Stand-alone "tblastx"... | fxb22/BioGUI | plugins/Tools/BLASTPlugins/TBLASTX.py | Python | gpl-2.0 | 613 | [
"BLAST"
] | 2fdf647ab988248803aeeaae263bf9beddc6b476e6476849852e5d0b569dfdaa |
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 i1 in range(5... | SINGROUP/readAFM | databaseCode/toyDB/threeAtoms/makeXYZ.py | Python | gpl-3.0 | 4,866 | [
"CHARMM"
] | a86159464119f6a5d311c36abbc962c27bfc341beb9e22641a9b170027659038 |
#! /usr/bin/python2
import subprocess
import sys
import os
import time
from subprocess import PIPE
import socket
default_params = ''
output_file_prefix = 'output'
if len(sys.argv) > 1:
output_file_prefix = sys.argv[1]
#
# SCENARIO
#
# 0: radial dam break
# 1: gaussian
# 2: balanced steady state u
# 3: balanced ste... | schreiberx/sweet | archive/benchmarks_plane/rexi_tests_lrz/2016_01_03_scalability_rexi_fd_high_core_res_run3/params.py | Python | mit | 5,634 | [
"Gaussian"
] | da6bec9687f93deba4fa5b9beb38eaf104ca1a92afc80099c4515743c843c90e |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
# REF [site] >>
# http://scikit-learn.org/stable/modules/clustering.html
# https://docs.scipy.org/doc/scipy-0.14.0/reference/cluster.hierarchy.html
# http://scikit-learn.org/stable/auto_examples/cluster/plot_kmeans_digits.html
# http://scikit-learn.org/stable/auto_examples... | sangwook236/general-development-and-testing | sw_dev/python/rnd/test/machine_learning/sklearn/sklearn_clustering.py | Python | gpl-2.0 | 6,484 | [
"Gaussian"
] | 16420fa6c742a0d1fa0c0ea1d189e08c0db0955bf04c18c5ab08d6591262ff67 |
import sys
import os
import numpy as np
import h5py
import multiprocessing
import cPickle
import ephem
import matplotlib.pyplot as plt
import types
from sklearn.gaussian_process import GaussianProcess
from sklearn.cross_validation import train_test_split
from sklearn import metrics, linear_model, tree, ensemble
# NOTE... | acbecker/solar | regress2.py | Python | mit | 10,935 | [
"Gaussian"
] | 5fb9e87d09691226f0d40f2b7929f3f9020f57f88baa1f0b159a24f91b70cfe7 |
# gtkvtk.py -- A Gtk Widget for Rendering VTK Scenes
# -*- coding: utf-8 -*-
#
# Written by Jonathan Kleinehellefort <jk@molb.org>, based on
# GtkVTKRenderWindow.py from VTK <http://www.vtk.org/> by Prabhu
# Ramachandran, in turn based on vtkTkRenderWidget.py by David Gobbi.
#
# Copyright 2008 Lehrstuhl Bildverstehen u... | arcoslab/roboview | gtkvtk.py | Python | gpl-3.0 | 16,005 | [
"VTK"
] | 8970ce59f7235061f7077b008015ec095e9fa1ccf931111f1ab6b638c3b7227b |
"""Simple tests for the color transfer function utilities in tvtk."""
import unittest
from tvtk.util.ctf import (load_ctfs, save_ctfs, \
rescale_ctfs, ColorTransferFunction, PiecewiseFunction)
from tvtk.api import tvtk
def make_volume_prop(mins=255, maxs=355):
"""Make a volume property for the testing."... | dmsurti/mayavi | tvtk/tests/test_ctf_util.py | Python | bsd-3-clause | 2,321 | [
"VTK"
] | 4ff4798ff68784893b9181ebde58da5cefa628f7fa16c831288dd774013230a2 |
#!/usr/bin/env python
"""
This file will take arguments which will fill in a programme for working.
"""
import argparse
from docx import *
import sys, calendar
if __name__ == '__main__':
parser = argparse.ArgumentParser(description = 'Create a word document for a school booking.', epilog="(c)2014 A Cripps"... | kabads/CreateProgramme | createprogramme.py | Python | gpl-2.0 | 3,101 | [
"VisIt"
] | c8d7eb8fd4b46522b628534a3dcfa99995a92c957830c88bf64a6eb184fd373b |
#!/usr/bin/env python
##
## @file test.py
## @brief AutoRunner for Python test scripts
## @author Akiya Jouraku
##
## $Id: test.py 8704 2009-01-04 02:26:05Z mhucka $
## $HeadURL: https://sbml.svn.sourceforge.net/svnroot/sbml/trunk/libsbml/src/bindings/python/test.py $
##
##<!--------------------------------------... | alexholehouse/SBMLIntegrator | libsbml-5.0.0/src/bindings/python/test.py | Python | gpl-3.0 | 2,890 | [
"VisIt"
] | 5f6c563ebf5efa63903ab03d47592039da03e87dc9e7ad64a57fb81bc8158b8e |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
urlpatterns = [
url(r'^$', TemplateView.as_view(templ... | kdagley/publicrelations | config/urls.py | Python | bsd-3-clause | 1,224 | [
"VisIt"
] | cd19029fb2de653065e61569a1d9bbfe322db5549df8b87a3b063cbb1fa2f22c |
# -*- coding: utf-8 -*-
# TAMkin is a post-processing toolkit for normal mode analysis, thermochemistry
# and reaction kinetics.
# Copyright (C) 2008-2012 Toon Verstraelen <Toon.Verstraelen@UGent.be>, An Ghysels
# <An.Ghysels@UGent.be> and Matthias Vandichel <Matthias.Vandichel@UGent.be>
# Center for Molecular Modeling... | molmod/tamkin | tamkin/test/test_nma.py | Python | gpl-3.0 | 38,724 | [
"CP2K",
"CPMD",
"Gaussian"
] | 6080211c6d76941b743ee8b77a0d7fdbdbcc4d5ba9f2a6e9672589cb0f95cfd3 |
################################################
# Permanent Orienteering Course WebApp
#
# (c) 2014 Eric Jones
# Licensed under the MIT License
# https://github.com/ercjns/o-webapp
################################################
# imports
#to-do better way to access the db, these imports feel wrong
from ap... | ercjns/O-PermanentCourseApp | application/views.py | Python | mit | 6,852 | [
"VisIt"
] | 940db1ab0162f6592e84a8907a523550ef25937212c67bb0888be6d244ab79c2 |
# Copyright (C) 2010-2014 CEA/DEN, EDF R&D
#
# This library 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.
#
# This library ... | FedoraScientific/salome-paravis | src/PV_SWIG/presentations.py | Python | lgpl-2.1 | 88,784 | [
"ParaView"
] | 6f7209f013e9a6fd34a4bc503db0249ff7607be40a78c6d8a3b297dab3c8812f |
#
# Copyright 2002 by Michael Hoffman. 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.
#
# note:
# I used Lincoln Stein's perl Bio::DB::GFF::Util::Binning as a model for this
"... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/GFF/binning.py | Python | apache-2.0 | 1,761 | [
"Biopython"
] | 522d6e61a492c80c53201abb83797eec9faaff44c72e9b099381df9e47203bbb |
# Copyright 2001 by Tarjei Mikkelsen. 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 data from the KEGG database.
References:
Kaneh... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/KEGG/__init__.py | Python | gpl-2.0 | 2,713 | [
"Biopython"
] | 338f4970142b6dbe5ce667dbe668c0f570f1fd43531da4d2af784fc8d35df62f |
#!/usr/bin/python
import HTSeq
import sys
from Bio.Seq import Seq
from Bio.Alphabet import generic_dna
from Bio.Blast import NCBIXML
from Bio.Blast.Applications import NcbiblastnCommandline
from Bio.Blast.Applications import NcbiblastpCommandline
from Counter import Counter # --- Counter.py from python3 is needed to ... | mickaelsilva/pythonscripts | AlleleCalling/cluster_versions/alleleCalling_probe_based_main.py | Python | gpl-2.0 | 7,665 | [
"BLAST",
"HTSeq"
] | 9cce2c861aa6d0e4516b6822d90da04487011456ec7d028503ff38cd1c0d4c5a |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the G... | espressopp/espressopp | src/analysis/MeanSquareInternalDist.py | Python | gpl-3.0 | 2,081 | [
"ESPResSo"
] | 208ab49609cdd3115ab4051587ce8f2da27f06207db3803ca68b5e97dba6328d |
#
# Copyright (c) 2012-2014 Jonathan Topf
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publis... | ckod3/mayaseed | scripts/ms_export.py | Python | mit | 145,332 | [
"Gaussian"
] | 40a7054a0820daad9882310f1886e3d92030ff03c1762258d0f1b0d6a748bd3b |
#!/usr/bin/env python
"""rallpack3_moose_vs_neuron.py:
This file compares moose and neuron for rallpack3.
Last modified: Sun May 25, 2014 07:05AM
"""
from __future__ import print_function
__author__ = "Dilawar Singh"
__copyright__ = "Copyright 2013, NCBS Bangalore"
__credits__ =... | subhacom/moose-core | tests/python/Rallpacks/moose_vs_neuron/rallpack3/neuron_sim.py | Python | gpl-3.0 | 4,632 | [
"MOOSE",
"NEURON"
] | e69901989c140192bed848a407fa81609597681a5d1794b1583181eaa73053b6 |
#!/usr/bin/env python
import os,sys
account_file = 'account.txt'
lock_file = 'lock_file.txt'
while True:
f = file(account_file,'r')
lf = file(lock_file,'r')
# f.close()
username = raw_input('Please input username:').strip()
for luser in lf.readlines():
luser = luser.strip().split()
if username == luser[0]:
... | lichengshuang/createvhost | python/others/oldboy/day1/bak.login2.py | Python | apache-2.0 | 1,390 | [
"VisIt"
] | 797008f967a358a3cfe0475a7bae4fe15985b45ad0c7769138c7061c47ff1a8d |
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'historical_map_dialog_base.ui'
#
# Created by: PyQt4 UI code generator 4.11.4
#
# WARNING! All changes made in this file will be lost!
from PyQt4 import QtCore, QtGui
try:
_fromUtf8 = QtCore.QString.fromUtf8
except AttributeError:
... | lennepkade/HistoricalMap | historical_map_dialog_base.py | Python | gpl-2.0 | 44,082 | [
"Gaussian"
] | fed6c8cd12a998e31819ab0cbaf424ec1fe27f764a47a146b7a63b1f9dfe477b |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals, division, absolute_import, print_function
from builtins import * # noqa pylint: disable=unused-import, redefined-builtin
from past.builtins import basestring
import logging
import re
import time
from datetime import datetime, timedelta
from dateutil.pa... | sean797/Flexget | flexget/plugins/internal/api_trakt.py | Python | mit | 49,025 | [
"VisIt"
] | e3e44033588dd5181651a8a0e93fdaa9b538e446c51133aed40d2ccb1a90a90e |
# 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 PyRnacocktail(PythonPackage):
"""RNACocktail: A comprehensive framework
for accurate a... | LLNL/spack | var/spack/repos/builtin/packages/py-rnacocktail/package.py | Python | lgpl-2.1 | 1,042 | [
"pysam"
] | 77d0c208277ff16f68c63685490f379b435062a8bcc06b9807880d24d92c5e35 |
#!/usr/bin/env python
""" The dirac-pilot.py script is a steering script to execute a series of
pilot commands. The commands may be provided in the pilot input sandbox, and are coded in
the pilotCommands.py module or in any <EXTENSION>Commands.py module.
The pilot script defines two switches in order to ch... | wkrzemien/Pilot | Pilot/dirac-pilot.py | Python | gpl-3.0 | 2,409 | [
"DIRAC"
] | 395ccb2bd0d45fbd2255d21c59796f46afeb19df8f8376aeb3f6fe4bd615de99 |
# -*- coding: utf-8 -*-
# SyConn - Synaptic connectivity inference toolkit
#
# Copyright (c) 2016 - now
# Max Planck Institute of Neurobiology, Martinsried, Germany
# Authors: Philipp Schubert, Joergen Kornfeld
import os
import shutil
import time
from logging import Logger
from typing import Optional, Dict, List, Tupl... | StructuralNeurobiologyLab/SyConn | syconn/extraction/object_extraction_wrapper.py | Python | gpl-2.0 | 18,111 | [
"Gaussian"
] | c44e8acb3960578a7d9204e9b1d6ed161a9c3b54fc4f1ae29d045509172cb611 |
#!/usr/bin/env python
"""
obs.py
State Estimation and Analysis for PYthon
Module to handle the observation structure within ROMS. The ROMS structure
defines the obs_provenance, which is a numeric ID for tracking the source
of the observations you use. This module defines a dictionary to translate
between ... | powellb/seapy | seapy/roms/obs.py | Python | mit | 32,264 | [
"Brian",
"NetCDF"
] | cf90ad0cff9bf045a55cfa6f10431a30f06089cd821d0d364efac86a31e8c51b |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""Functional tests using WebTest."""
import datetime as dt
from rest_framework import status as http_status
import logging
import unittest
import markupsafe
import mock
import pytest
from nose.tools import * # noqa: F403
import re
from django.utils import timezone
from... | baylee-d/osf.io | tests/test_webtests.py | Python | apache-2.0 | 50,489 | [
"VisIt"
] | a9401b71468948be2201ae7d415b5f884c32b2138dc5fdfbbb7b9d31bc748ebd |
"""
The GA4GH data model. Defines all the methods required to translate
data in existing formats into GA4GH protocol types.
"""
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import glob
import os
import json
import tempfile
import shutil
import atexit
imp... | UMMS-Biocore/ga4gh-server | ga4gh/datamodel/__init__.py | Python | apache-2.0 | 16,158 | [
"pysam"
] | 8887c1dda328fb43023ff0ea6dfd9ff998200f417c627fdc66e9152257ee2463 |
import unittest
from pymatgen.util.testing import PymatgenTest
from pymatgen.analysis.adsorption import *
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from pymatgen import Structure, Lattice, Molecule
from pymatgen.util.coord import in_coord_list
test_dir = os.path.join(os.path.dirname(__file__), "..", ... | dongsenfo/pymatgen | pymatgen/analysis/tests/test_adsorption.py | Python | mit | 8,097 | [
"pymatgen"
] | 5eb656bcb3eec23de293aa862273610957c7f3f1ddc26ec0d9f31bc8065902f3 |
# Copyright (c) 2012, Cloudscaling
# All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable... | vmturbo/nova | nova/hacking/checks.py | Python | apache-2.0 | 30,393 | [
"VisIt"
] | ebc72977478b3d26ff5ed80a2c914a0200a4edc54d3615aa5f39e116f7981a1a |
import openmoltools
import mdtraj as md
from simtk.openmm import app
import simtk.openmm as mm
from simtk import unit as u
temperature = 300. * u.kelvin
equil_friction = 5 / u.picoseconds
equil_timestep = 1 * u.femtoseconds
pressure = 1.0 * u.atmospheres
barostat_frequency = 25
discard_steps = 10000
n_steps = 500000
c... | jchodera/LiquidBenchmark | src/test_stepsize/old/equilibrate.py | Python | gpl-2.0 | 2,153 | [
"MDTraj",
"OpenMM"
] | a9d803920bad12450d227352bb3d281e459cbd23e811b0a6a8443ca2d5788884 |
from galaxy.util.bunch import Bunch
from galaxy.tools.parameters import *
from galaxy.tools.parameters.grouping import *
from galaxy.util.template import fill_template
from galaxy.util.none_like import NoneDataset
from galaxy.web import url_for
from galaxy.jobs import JOB_OK
import galaxy.tools
from types import *
imp... | volpino/Yeps-EURAC | lib/galaxy/tools/actions/__init__.py | Python | mit | 16,716 | [
"Galaxy"
] | 660710be6668639947f583e5ebc9fc2a38a61d77b4283fe8849542de773258d2 |
# coding: utf-8
# pylint: disable = C0103
"""Plotting Library."""
from __future__ import absolute_import
import warnings
from copy import deepcopy
from io import BytesIO
import numpy as np
from .basic import Booster
from .sklearn import LGBMModel
def check_not_tuple_of_2_elements(obj, obj_name='obj'):
"""check... | wxchan/LightGBM | python-package/lightgbm/plotting.py | Python | mit | 16,550 | [
"VisIt"
] | 73d1efec24dc0e83c9f5b4c84f716462ae9680ef41839ef3f4621cfb89dcdf49 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# restartMaker_v0.py
#
# Copyright 2015 Carlos Eduardo Sequeiros Borja <casebor@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 Foundati... | casebor/labioscripts | python/restartMaker.py | Python | gpl-3.0 | 7,200 | [
"Amber",
"MDTraj"
] | 870a39b4b93f9b555bd910b1c5438c33bdf4398755fae5aaae93b0dc3e661427 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Created on Mon Aug 8 18:02:10 2016
@author: agiovann
"""
from __future__ import division
from __future__ import print_function
# analysis parallel
from builtins import next
from builtins import filter
from builtins import str
from builtins import zip
from builtins ... | agiovann/Constrained_NMF | use_cases/granule_cells/analysis_parallel_multisession.py | Python | gpl-2.0 | 135,666 | [
"NEURON"
] | b096c8dcff577b806423cbe42a4f886dc606b1155699565bca2754c552890bb3 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | skosukhin/spack | var/spack/repos/builtin/packages/r-rtracklayer/package.py | Python | lgpl-2.1 | 2,610 | [
"Bioconductor"
] | 7573b9a0a99bb7ad3d7caeca40ae8e4307feef8d79ad54929ba6f6a2c536e36f |
# -*- coding:utf-8 -*-
#
# Copyright 2013 NAMD-EMAP-FGV
#
# This file is part of PyPLN. You can get more information at: http://pypln.org/.
#
# PyPLN 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 vers... | rsouza/pypln.web | pypln/web/settings/production.py | Python | gpl-3.0 | 3,767 | [
"NAMD"
] | 5135e29cc63a99a037650d2639ecd03600acd1cc8c39cbfd9a961776aa824f2c |
#
# co_co.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST 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 ... | kperun/nestml | pynestml/cocos/co_co.py | Python | gpl-2.0 | 1,614 | [
"NEURON"
] | a99bfe0edcb86e43ee51b2ee266adaed5c668c6fee4bbe5bf520932976c16251 |
# Copyright (C) 2013, Thomas Leonard
# See the README file for details, or visit http://0install.net.
import os
from os.path import dirname, join, relpath
import collections
from xml.dom import minidom
from xml.dom import XMLNS_NAMESPACE
from zeroinstall.injector.namespaces import XMLNS_IFACE
from zeroinstall impor... | 0install/0repo | repo/catalog.py | Python | lgpl-2.1 | 3,403 | [
"VisIt"
] | eb13c6e1f8d5663d3e2b1adcbc00200cb9608cbbe472a6b5d1b714705bfa20bf |
programs_list = ["ani_depthplot.py=programs.ani_depthplot:main",
"core_depthplot.py=programs.core_depthplot:main",
"dir_redo.py=programs.dir_redo:main",
"huji_sample_magic.py=programs.conversion_scripts.huji_sample_magic:main",
"install_etopo.py=programs.install_etopo:main",
"iodp_samples_magic.py=programs.conversion_s... | lfairchild/PmagPy | programs_list.py | Python | bsd-3-clause | 7,568 | [
"Gaussian"
] | e55bb66a41b53a29a9508e0a9a3c5af3e161948e669375d020ee27f46e5e02ea |
"""
You can use this form to update your NSF conflicts form. You'll need to do some editing, but
this will help.
First, go to Google Scholar, and visit your profile.
Select all your references by clicking the square box next to Title
Choose Export --> BibTex and then "All my articles"
That will possibly open in a n... | linsalrob/EdwardsLab | bin/NSF_conflicts.py | Python | mit | 6,881 | [
"VisIt"
] | 9ed145f8057f1c541aaac7d7d228c17d857228bcc4a948b710480dc8df742904 |
"""Convenience function to create a context for the built in error functions"""
import logging
import copy
import symengine
from pycalphad import variables as v
from pycalphad.codegen.callables import build_callables
from pycalphad.core.utils import instantiate_models, filter_phases, unpack_components
from espei.error... | PhasesResearchLab/ESPEI | espei/error_functions/context.py | Python | mit | 4,910 | [
"pycalphad"
] | fd596f7d23783cb6d28f8d2a8d1ee9103a27232c5bfe008343deae819096d3fb |
#!/usr/bin/env python
__author__ = "Mike McCann"
__copyright__ = "Copyright 2012, MBARI"
__license__ = "GPL"
__maintainer__ = "Mike McCann"
__email__ = "mccann at mbari.org"
__doc__ = '''
Script to read data from CSV formatted data from the Liquid Robotics Waveglider
platform and write them to netCDF files. There ar... | josephmfaulkner/stoqs | stoqs/loaders/CANON/toNetCDF/wgToNetcdf.py | Python | gpl-3.0 | 10,363 | [
"NetCDF"
] | 4fa9d6b950ab13ad875e9c65320fb72fc82214c4b881b0eb836b78b862183cf8 |
# -*- coding: utf-8 -*-
"""Copyright 2015 Roger R Labbe Jr.
Code supporting the book
Kalman and Bayesian Filters in Python
https://github.com/rlabbe/Kalman-and-Bayesian-Filters-in-Python
This is licensed under an MIT license. See the LICENSE.txt file
for more information.
"""
from __future__ import (absolute_imp... | zaqwes8811/micro-apps | self_driving/deps/Kalman_and_Bayesian_Filters_in_Python_master/kf_book/pf_internal.py | Python | mit | 12,107 | [
"Gaussian"
] | b37aab06c62645993d6b5a158deb29b7809490324b6da8a08d9ad295bb8320d5 |
from django import forms
import requests, json
from bdo_platform.settings import PARSER_JWT, PROFILES_URL
class DatasetsForm(forms.Form):
choices = (
(None, ""),
(u'{"observation": "trip", "source": "anek", "dataType": "csv"}', "ANEK - Trips"),
(u'{"observation": "history", "source": "anek... | dipapaspyros/bdo_platform | uploader/forms.py | Python | mit | 4,308 | [
"NetCDF"
] | 9c3f2c58d6dad4bf4caa8ab0d5c1fb0a0e997701db6f670ce98f02f7cd0c3694 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for playback feature
"""
from bok_choy.web_app_test import WebAppTest
from ..biz.test_ga_contract_operation import BizStudentRegisterMixin
from ...fixtures.course import CourseFixture
from ...pages.biz.ga_contract import BizContractPage
from ...pages.biz.ga_navigation impor... | nttks/edx-platform | common/test/acceptance/tests/lms/test_ga_playback.py | Python | agpl-3.0 | 5,430 | [
"VisIt"
] | 428efc2695da072b6bbce985fe26039508efbea3710e2d9f8d4f36b0282662c9 |
##############################################################################
# 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-acme/package.py | Python | lgpl-2.1 | 2,300 | [
"Bioconductor"
] | faecf460abf7cc9e99125e58a03b2b0b6b28853bc143b9b328f244e9b1904a9b |
from docutils.nodes import figure, caption, Text, reference, raw, SkipNode, Element
from sphinx.roles import XRefRole
# Element classes
class page_ref(reference):
pass
class num_ref(reference):
pass
# Visit/depart functions
def skip_page_ref(self, node):
raise SkipNode
def latex_visit_page_ref(self,... | MrCreosote/KBaseSearchEngine | docsource/_ext/numfig.py | Python | mit | 3,273 | [
"VisIt"
] | 7ead7fa696c23e26e58457f5b17f3bc0b15d76ab8611d8d1defab42504beb4b7 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""This is a utility script for LibidoMechanica. It's designed to go through the
poems in the source corpus and correct problems in the source texts. There are
a variety of textual transformations applied.
This is a utility script for LibidoMechanica and, like the other p... | patrick-brian-mooney/LibidoMechanica | check_corpus.py | Python | gpl-3.0 | 11,801 | [
"Brian"
] | 29b951cea3f5ccf4da33ee8fef2e904cfa080d56b439dd5b664f16cb1c47ba9d |
import pytest
from pytest_bdd import (
scenarios,
then,
when,
)
from . import browsersteps
pytestmark = [
pytest.mark.bdd,
pytest.mark.usefixtures('workbook'),
]
scenarios('generics.feature')
# https://github.com/pytest-dev/pytest-bdd/issues/124
@when('I visit "/<type_name>/"')
def i_visit_the... | T2DREAM/t2dream-portal | src/encoded/tests/features/test_generics.py | Python | mit | 936 | [
"VisIt"
] | f15eb694a7203872a65378d6c1d084ce8d3cf2a015cd5ac54bbcf420cf3dc33f |
import os
import urlparse
import requests
import splinter
from selenium.webdriver.common.by import By
from selenium.webdriver.support.wait import WebDriverWait
from selenium.webdriver.support import expected_conditions as EC
from tests.common.utils import urljoin
class Browser(object):
'''Drives the browser in the... | saukrIppl/seahub | tests/ui/driver.py | Python | apache-2.0 | 2,783 | [
"VisIt"
] | 819c9b44a1e2467e8cd7cd63a5b5e558e956c40ce639083e86c02f932dd69185 |
#
# Copyright Capita Translation and Interpreting 2013
#
# This file is part of Pipeline Creation Language (PCL).
#
# Pipeline Creation Language (PCL) 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 ve... | ianj-als/pcl | src/pclc/visitors/third_pass_resolver_visitor.py | Python | gpl-3.0 | 11,888 | [
"VisIt"
] | 5e00e52c7aabfea1149bd426a19182006665b1cd3667fed3ea0a54a985c0ef1c |
#
# basic run through the PDB with labels, checking to make sure
# they don't leak RAM
#
from glob import glob
import threading
import time
from pymol import cmd
import sys, os, os.path
import traceback
ent_dir = "pdb"
def load():
cmd.set("valence")
r = 0
list = glob("pdb/*/*")
# while list[0]!="... | gratefulfrog/lib | python/pymol/pymol_path/test/inp/B08.py | Python | gpl-2.0 | 1,170 | [
"PyMOL"
] | a325af71311a2772fcc3ba4e80b4db0f27079eb3673c14b3a1989053031abe68 |
#!/usr/bin/env python
"""
Vehicle speed prediction model.
Example invocations:
# Run verbose training
./cnn_lstm_prediction.py --verbosity 2
# Only run the test phase
./cnn_lstm_prediction.py --skipTraining --test
# Continue training a checkpointed model
./cnn_lstm_prediction.py --loadModel speed_checkp... | BoltzmannBrain/self-driving | models/cnn_lstm_prediction.py | Python | mit | 13,942 | [
"Gaussian"
] | 1d264f7f97338e364ecd4a54d2bfd3795bb204051c0026c6a1113d61273e87dc |
import sys
sys.path.insert(1,"../../../")
import h2o
from tests import pyunit_utils
import random
def cars_checkpoint():
cars = h2o.upload_file(pyunit_utils.locate("smalldata/junit/cars_20mpg.csv"))
s = cars.runif()
train = cars[s > .2]
valid = cars[s <= .2]
print "\n*** Description (chunk distr... | madmax983/h2o-3 | h2o-py/tests/testdir_algos/gbm/pyunit_NOPASS_cars_checkpointGBM.py | Python | apache-2.0 | 9,718 | [
"Gaussian"
] | 363835415a13f4cd7065cba6db5940fcd9fa5e64bfd100dbcc485bd7f531ecaa |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
import datetime
from django.core.exceptions import ImproperlyConfigured
from django.test import TestCase, override_settings
from django.utils.encoding import force_str
from django.views.generic.base import View
from .models import Artist, Author, Book, ... | DONIKAN/django | tests/generic_views/test_list.py | Python | bsd-3-clause | 12,129 | [
"MOOSE"
] | e573fd7ba5c31552e13b4f76dd12be528e7b264950102e405f35a9dff4407463 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2010 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU Lesser General Public License as published by
## the Free Software F... | andrebellafronte/stoq | plugins/books/__init__.py | Python | gpl-2.0 | 905 | [
"VisIt"
] | 48260cdfbb6c2b79933073fffa02daca0d7c01734b9913f31878a0d3c657d8b4 |
# -*- coding: utf-8 -*-
# Licensed under a 3-clause BSD style license - see LICENSE.rst
#
# Astropy documentation build configuration file.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# Note that not all possible configuration values are present in this file.
#
# All configurati... | Cadair/solarbextrapolation | docs/conf.py | Python | mit | 8,691 | [
"Mayavi"
] | 41401bebb6d08aab9f8ad4ef51f20b0b99cf486c3c68f3f17d413b76d17e7091 |
# test_tuftedib.py ---
#
# Filename: test_tuftedib.py
# Description:
# Author:
# Maintainer:
# Created: Mon Jul 16 16:12:55 2012 (+0530)
# Version:
# Last-Updated: Wed Jun 26 09:58:42 2013 (+0530)
# By: subha
# Update #: 522
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
#
#
#... | BhallaLab/moose-examples | traub_2005/py/test_tuftedib.py | Python | gpl-2.0 | 1,538 | [
"MOOSE"
] | 128fdc4b9e34bea6df09ad2a7362ee784174beaddfb6277997a6d71464c31902 |
import unittest
import numpy as np
from np_gaussian_2d_loss import np_r2_bivariate_gaussian_loss, np_r4_bivariate_gaussian, softmax, epsilon, \
np_r4_bivariate_gaussian_loss
class TestNumpy2DGaussianLoss(unittest.TestCase):
def test_r2_2d_loss(self):
vec_in = np.array([[1, 1, 0, 0, 0]])
vec_ou... | reinvantveer/Topology-Learning | model/topoml_util/test_np_gaussian_2d_loss.py | Python | mit | 2,071 | [
"Gaussian"
] | ca30c62f3a3ef5f097993fa9d9e222981087cef3d0d351b6e8e4add9e198a619 |
# coding: utf-8
# In[13]:
import tkinter as tk
import sqlite3
import numpy as np
import pandas as pd
from pandas import HDFStore
#import pubchempy as pcp
#import json
#from urllib.request import urlopen
#import urllib
#from urllib.request import urlopen
#from bs4 import BeautifulSoup
#from rdkit import Chem
#fro... | bbqtaco/matinsy | mksdswebsite.py | Python | gpl-3.0 | 28,123 | [
"RDKit"
] | 109716195071a4c49994a7bcad145ef8b35fa1fb2bd1b6c094449ec067679d26 |
#!/usr/bin/env python
"""dirac-docs-build-commands.py
Build scripts documentation from the scripts docstrings. The scripts are not
very uniform
"""
import sys
from diracdoctools.cmd.commandReference import run
from diracdoctools.Config import CLParser
sys.exit(run(**(CLParser().optionDict())))
| chaen/DIRAC | docs/diracdoctools/scripts/dirac-docs-build-commands.py | Python | gpl-3.0 | 302 | [
"DIRAC"
] | ba4f999d32b911ae125784f0cd6c4af6c5e1d2dc5a18cfaf80e4b6ae61724551 |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | rahul003/mxnet | python/mxnet/initializer.py | Python | apache-2.0 | 24,963 | [
"Gaussian"
] | d37b87bbf029369e9a5ffff92126cee0712e93529e040f24c343400fca1dc4fc |
import numpy as np
import psi4
psi4.core.set_output_file("output.dat", False)
mol = psi4.geometry("""
He 0 0 1
He 0 0 -1
no_reorient
symmetry c1
""")
e, wfn = psi4.energy("PBE/cc-pVDZ", molecule=mol, return_wfn=True)
# Yank some things from the wavefunction
V = wfn.V_potential()
D = np.asarray(wfn.Da())
points_fu... | jH0ward/psi4 | tests/libxc/devl/grid_test.py | Python | lgpl-3.0 | 4,419 | [
"Psi4"
] | e2d3a167cc1d1059076b90f3123d87da2b755f1dba5e1332c5e6b075cb5500e0 |
"""
Project
FPGA-Imaging-Library
Design
ErosionDilationBin
Function
Erosion or Dilation for binary images.
Module
Software simulation.
Version
1.0
Modified
2015-05-22
Copyright (C) 2015 Tianyu Dai (dtysky) <dtysky@outlook.com>
This library is free software; you can redistribute it and/or
modify it under the ter... | jaechoon2/FPGA-Imaging-Library | LocalFilter/ErosionDilationBin/SoftwareSim/sim.py | Python | lgpl-2.1 | 4,672 | [
"MOE"
] | 9c3da9a06b0d5b5916578a1313064ca39dad3f12856f418eff66774d655a44af |
"""Structure optimization. """
import sys
import pickle
import time
from math import sqrt
from os.path import isfile
import numpy as np
from ase.parallel import rank, barrier
from ase.io.trajectory import Trajectory
import collections
class Dynamics:
"""Base-class for all MD and structure optimization classes.... | suttond/MODOI | ase/optimize/optimize.py | Python | lgpl-3.0 | 6,994 | [
"ASE"
] | 2eaa7c23244ea54e933f36e8953a736638677eb21a3a7f695cdeede27df647b1 |
#!/usr/bin/python
#-*- coding: utf-8 -*-
from collections import OrderedDict
from unidecode import unidecode
from bs4 import BeautifulSoup
from getpass import getpass
from html import unescape
from sys import platform
from sys import argv
from sys import exit
from time import sleep
from re import findall
import request... | shellterlabs/lug | extract-dryscrape.py | Python | gpl-3.0 | 8,353 | [
"VisIt"
] | ad56d6aded87b1402e9cdbeb9231e0b774edfdebde15d95b830fe477ed442eeb |
#!/usr/bin/env python
"""
remove files from the FileCatalog (and all replicas from Storage Elements)
"""
import os
import DIRAC
from COMDIRAC.Interfaces import critical
from COMDIRAC.Interfaces import DSession
from COMDIRAC.Interfaces import DCatalog
from COMDIRAC.Interfaces import pathFromArgument
if __name__ ==... | pigay/COMDIRAC | Interfaces/scripts/drm.py | Python | gpl-3.0 | 1,535 | [
"DIRAC"
] | a335d80b27ce9cc3d169a219be5c0932902b3755bb6ee0250933e7685a32565a |
from numpy.testing import assert_equal, assert_array_equal
from nose.tools import assert_true, assert_raises, assert_not_equal
from copy import deepcopy
import os.path as op
import numpy as np
from scipy import sparse
import os
import warnings
from mne.utils import (set_log_level, set_log_file, _TempDir,
... | trachelr/mne-python | mne/tests/test_utils.py | Python | bsd-3-clause | 16,252 | [
"Mayavi"
] | d4a498f60774b649e6963ece1947dc7fbdd7d71bc65c794ec177a364c6352735 |
"""
This is our testing framework.
Goals:
* it should be compatible with py.test and operate very similarly
(or identically)
* doesn't require any external dependencies
* preferably all the functionality should be in this file only
* no magic, just import the test file and execute the test functions, that's it
* po... | wxgeo/geophar | wxgeometrie/sympy/utilities/runtests.py | Python | gpl-2.0 | 85,989 | [
"VisIt"
] | 24bf1e2c9695f55936b9582611e233c27afdbd520417176211be55c5816f20bc |
"""
PlugNPlay module
Copyright (c) 2009 John Markus Bjoerndalen <jmb@cs.uit.no>,
Brian Vinter <vinter@nbi.dk>, Rune M. Friborg <rune.m.friborg@gmail.com>.
See LICENSE.txt for licensing details (MIT License).
"""
import pycsp.current
@pycsp.current.process
def Identity(cin, cout):
"""Copies its input stream... | runefriborg/pycsp | pycsp/common/plugNplay.py | Python | mit | 1,701 | [
"Brian"
] | 1fc68a9173da6556d67f57984e10adff405f357d14e557f22841d1e63df35ec5 |
from __future__ import print_function
from distutils.core import setup
from distutils.extension import Extension
import numpy as np
from distutils.ccompiler import new_compiler
import os
import sys
import tempfile
"""
Check for OpenMP based on
https://github.com/MDAnalysis/mdanalysis/tree/develop/package/setup.py
retr... | kfogel/batman | setup.py | Python | gpl-3.0 | 3,398 | [
"MDAnalysis"
] | c41a77fbf235fe45fe59363de7b99794139d20003f75ece0597515421e044f75 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import sys
import platform
from setuptools import setup, find_packages, Extension
from setuptools.command.build_ext import build_ext as _build_ext
class build_ext(_build_ext):
def finalize_options(self):... | gpetretto/pymatgen | setup.py | Python | mit | 8,449 | [
"ABINIT",
"ASE",
"FEFF",
"Gaussian",
"NWChem",
"VASP",
"VTK",
"pymatgen"
] | 744f8268c1f88b8f6520912b65dd20af5c9c594bc3ef14564eb92549130dea81 |
#!/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/gto/__init__.py | Python | apache-2.0 | 1,004 | [
"PySCF"
] | c2e51a8376ce07f636f9c3cd2262a0a08f42e23ac00ee4cefd8b840cce274d7e |
# Author: Samuel Genheden, samuel.genheden@gmail.com
"""
Program to draw 2D structures on a grid with RDKit
"""
import argparse
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import Draw
if __name__ == '__main__' :
parser = argparse.ArgumentParser(description="Draw molecules")
parser... | SGenheden/Scripts | Plot/draw_mols.py | Python | mit | 795 | [
"RDKit"
] | 7aa3b7af19289a136b5f6a9fc4871fe1df76f181d2768998f4120d6b300f50be |
#!/usr/bin/env python
# CREATED:2013-03-08 15:25:18 by Brian McFee <brm2132@columbia.edu>
# unit tests for librosa core (__init__.py)
#
# Run me as follows:
# cd tests/
# nosetests -v --with-coverage --cover-package=librosa
#
from __future__ import print_function
# Disable cache
import os
try:
os.environ.pop(... | yunque/librosa | tests/test_core.py | Python | isc | 24,090 | [
"Brian"
] | 9e0b6232b868fe0178870ee68e71a2d253f173c031ebb9b4d3219baafcc6a50f |
#!/usr/bin/env python
#
# Copyright (c) 2008-2015 by Enthought, Inc.
# All rights reserved.
"""
The Mayavi scientific data 3-dimensional visualizer.
The Mayavi *project* includes two related *packages* for 3-dimensional
visualization:
- **Mayavi2**: A tool for easy and interactive visualization of data.
- **TVTK**: ... | dmsurti/mayavi | setup.py | Python | bsd-3-clause | 16,436 | [
"Mayavi",
"VTK"
] | 83f47131f5274365024f712fa78d8155cf781877eedc4b1b8ca346b01448e30f |
# Created by: Aditya Dua
# 18 August 2017
import pkg_resources
import vtk
import math
import numpy as np
class VtkPipeline:
def __init__(self, background=(0.15, 0.15, 0.15), total_time_steps=None, timer_rate=60, gif_file=None):
self.ren = vtk.vtkRenderer()
self.ren.SetBackground(background[0], bac... | adityadua24/robopy | robopy/base/graphics.py | Python | mit | 6,302 | [
"VTK"
] | 4cc6f986b462ec0749c620c3741a0c71e0bc239c487ccad0a5ca8b1ea1b7db08 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# A script to test the threshold filter.
# Values above 2000 are set to 255.
# Values below 2000 are set to 0.
# Image pipeline
imageCanvas = vtk.vtkImageCanvasSource2D()
imageCanvas.... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Imaging/Core/Testing/Python/TestImageCanvas.py | Python | gpl-3.0 | 1,476 | [
"VTK"
] | e6fd4abad2d6e58b5990e6e717966b8fd57647e7769238166b21111b38357572 |
# coding: utf-8
# # Logistic Regression with a Neural Network mindset
#
# Welcome to your first (required) programming assignment! You will build a logistic regression classifier to recognize cats. This assignment will step you through how to do this with a Neural Network mindset, and so will also hone your intuiti... | KrisCheng/ML-Learning | archive/MOOC/Deeplearning_AI/NeuralNetworksandDeepLearning/LogisticRegressionWithaNeuralNetworkMindset/Logistic+Regression+with+a+Neural+Network+mindset+v3.py | Python | mit | 29,124 | [
"NEURON"
] | 781aeca308fdc8fa10ed36d564b42645eaf278d8c47d9d13cbb4e6004cef9716 |
########################################################################
# $HeadURL $
# File: StorageElementProxyHandler.py
########################################################################
"""
:mod: StorageElementProxyHandler
.. module: StorageElementProxyHandler
:synopsis: This is a service which represents... | avedaee/DIRAC | DataManagementSystem/Service/StorageElementProxyHandler.py | Python | gpl-3.0 | 11,735 | [
"DIRAC"
] | 3cc60b441767dd02f265e0430d750ec0194d419cbb6db9bc4929d4efef2fbd75 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under t... | kain88-de/mdanalysis | package/MDAnalysis/coordinates/DLPoly.py | Python | gpl-2.0 | 8,956 | [
"DL_POLY",
"MDAnalysis"
] | 700315993eacaf625301696ed82d9e0e22f4606704a84e7cb1fe7193e0413a7f |
#!/opt/local/bin/python
# a sample script to create input data for wkb from a .mat file
import os,sys
from netCDF4 import Dataset as netcdf
import numpy as np
import matplotlib.pyplot as plt
import datetime
from matplotlib import rcParams
from random import randrange
import scipy.io
#- offshore side (west preferred .... | rblod/OPTIBAT | PREPRO/mat2cdf.py | Python | gpl-3.0 | 2,915 | [
"NetCDF"
] | 036199efe41eb5e97459909718324283e8bf5c29d3fdda4dd5f7d83ca717b263 |
# Hidden Markov Model Implementation
import math
import pylab as pyl
import numpy as np
import matplotlib.pyplot as pp
import matplotlib.cm as cm
#from enthought.mayavi import mlab
import scipy as scp
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import rospy
#import hrl_lib... | tapomayukh/projects_in_python | rapid_categorization/misc/hmm_online_force_10_states.py | Python | mit | 10,110 | [
"Gaussian",
"Mayavi"
] | d98a9cf346bc9fda7ce99ba310499c1f92629663f7a26f001a55b31c8380e815 |
import os.path
ATTR_KEYS = [
'activity',
'product',
'institute',
'model',
'experiment',
'frequency',
'modeling_realm',
'mip_table',
'ensemble_member',
'version_number',
'variable_name',
'temporal_subset',
'geographical_info',
't_start',
't_end',
'temporal... | pacificclimate/climdir | cfmeta/cmipfile.py | Python | gpl-3.0 | 5,297 | [
"NetCDF"
] | fd6fb626332bab0b82648ad9fefdc53f671661ea030c540bebc4f6bc7c4b823a |
# -*- coding: utf-8 -*-
'''Helper functions for importing the nzdc database from the old server.'''
'''This file may be safely removed once all data pre-processing is completed'''
import subprocess
import datetime as dt
import fileinput
from DictionaryOfNewZealandEnglish.user.models import *
from DictionaryOfNewZea... | Matt--/DictionaryOfNewZealandEnglish | DictionaryOfNewZealandEnglish/nzdc_data_massage.py | Python | bsd-3-clause | 16,146 | [
"Amber"
] | b5040742ac42d03a131c0393460cf770335dba1b04edece7d485ce263462a2d8 |
#!/usr/bin/env python
'''
This little example shows how a cursor can be created in
image viewers, and renderers. The standard TkImageViewerWidget and
TkRenderWidget bindings are used. There is a new binding:
middle button in the image viewer sets the position of the cursor.
'''
import sys
from functools import p... | sumedhasingla/VTK | Rendering/Tk/Testing/Python/cursor3D.py | Python | bsd-3-clause | 9,418 | [
"VTK"
] | 3fc615286e1d731202968111e1fcd3b449049de4406ad57db49ff536518b98de |
#!/usr/bin/env python
#
# Copyright 2007 Google Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law o... | rev2004/android2cloud.app-engine | google_appengine/google/appengine/tools/appcfg.py | Python | mit | 95,156 | [
"VisIt"
] | 73b90040b161133facc0caa71cd371f7a55c1eb80f17a2811cd9f5983030302f |
from __future__ import print_function, division
import unittest, numpy as np
from pyscf import gto, scf
from pyscf.nao import gw_iter
from pyscf.nao import gw as gw_c
import numpy as np
class KnowValues(unittest.TestCase):
def test_sf_iter(self):
""" This compares matrix element of W calculated by G0W0 and G0W0... | gkc1000/pyscf | pyscf/nao/test/test_0055_gw_sf_iter.py | Python | apache-2.0 | 883 | [
"PySCF"
] | 7b5fc45447a8fe1d20c1d85d63a79040e863a6cb35bb510df518348d6e6070f2 |
#### PATTERN | WEB #################################################################################
# -*- coding: utf-8 -*-
# Copyright (c) 2010 University of Antwerp, Belgium
# Author: Tom De Smedt <tom@organisms.be>
# License: BSD (see LICENSE.txt for details).
# http://www.clips.ua.ac.be/pages/pattern
############... | clips/pattern | pattern/web/__init__.py | Python | bsd-3-clause | 171,164 | [
"VisIt"
] | e8e0d66f5362513bf9b877840d73c88010061540e063eff23938bca006fe6c30 |
# -*- coding: utf-8 -*-
""" core implementation of testing process: init, session, runtest loop. """
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import contextlib
import fnmatch
import functools
import os
import pkgutil
import sys
import warnings
import... | cloudera/hue | desktop/core/ext-py/pytest-4.6.11/src/_pytest/main.py | Python | apache-2.0 | 26,903 | [
"VisIt"
] | 9b76ec4f59d76da3eee52435c8094629c2119510712a99756975d83e9efedc43 |
#!/usr/bin/env python
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import os
import subprocess
from builtins import dict
from builtins import str
from chado.client import Client
from future import standard_library... | abretaud/python-chado | chado/util/__init__.py | Python | mit | 1,650 | [
"Galaxy"
] | 30a491cb95f89a9aa34a0d0bbf52a471cafc1742b04627494fd69e7210171962 |
#==========================================================================
#
# Copyright NumFOCUS
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/l... | richardbeare/ITK | Wrapping/Generators/Python/Tests/extras.py | Python | apache-2.0 | 14,042 | [
"VTK"
] | 32919259f634f34985468415eb9aaca4d627fa5dc9976c245c70d761a23b49aa |
# -*- coding: utf-8 -*-
"""
Created on Sun Aug 17 17:44:17 2014
@author: worker
"""
import numpy as np
from numpy.fft import fftshift,ifftshift,fft,ifft
from numpy.fft import fft2 as fast_fft2
from numpy.fft import ifft2 as fast_ifft2
from numpy.fft import fftn as fast_fftn
from numpy.fft import ifftn as fast_ifftn
... | KryoEM/relion2 | python/myutils/image.py | Python | gpl-2.0 | 43,002 | [
"Gaussian"
] | 1583f6d03a58d543c9722d31af09261b6aa03ba73bff14a2a1c93b51d7de9e0c |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2022 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | psi4/psi4 | psi4/driver/qcdb/util/__init__.py | Python | lgpl-3.0 | 984 | [
"Psi4"
] | bdf80cfb28734f1f9317aa84516289601bf62f4074637414366b9cc696f62a63 |
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