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#!/usr/bin/env python
from core import geo, pmap
import numpy as np
from datetime import timedelta
import glob
import os
from netcdf import netcdf as nc
from cache import Cache, Loader
from helpers import short
import logging
class Heliosat2(object):
def __init__(self, config, strategy_type):
self.confi... | scottlittle/solar_radiation_model | models/heliosat.py | Python | mit | 6,744 | [
"NetCDF"
] | cef22d1d1c45f76e03b5735602cf4526344495b7e88302b2e65c47f5472033cc |
import numpy as np
import bayesianoracle as bo
import bayesianoracle.plot as boplotter
import matplotlib.pyplot as plt
from matplotlib.collections import LineCollection
from matplotlib import colors as cl
from matplotlib import gridspec, ticker
# Import function information
from function_data import *
execfile("func... | altaetran/bayesianoracle | tests/quadraticBayesianAveraging/paper_examples/StatisticalQuadraticModels1D.py | Python | apache-2.0 | 9,162 | [
"Gaussian"
] | da8f934861a5c4ea131128b95281e3e89e57f2cf692a86a3f30d17ec6af60550 |
########################################################################
# $HeadURL$
########################################################################
""" X509Certificate is a class for managing X509 certificates alone
"""
__RCSID__ = "$Id$"
import GSI
import os
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.U... | Sbalbp/DIRAC | Core/Security/X509Certificate.py | Python | gpl-3.0 | 6,252 | [
"DIRAC"
] | 3efcdfafe5f500b27c43fae5729b71eba460bf51c4435e57107c08cf8ff3de70 |
#!/usr/bin/env python
"""
Tests for writing and reading UGRID compliant netCDF.
"""
from __future__ import (absolute_import, division, print_function)
import os
import numpy as np
import pytest
from gridded.pyugrid.ugrid import UGrid
from gridded.pyugrid.uvar import UVar
from .utilities import chdir, two_triangl... | NOAA-ORR-ERD/gridded | gridded/tests/test_ugrid/test_write_read.py | Python | unlicense | 2,320 | [
"NetCDF"
] | 362535126de50cb7f96f36e7a3013b44ffbcf6d369b256e9bb74124da4d25901 |
# coding=utf-8
# constants.py: Kort's Spellcrafting Calculator
#
# See http://www.github.com/artomason/KortsCalculator/ for updates
#
# See NOTICE.txt for copyrights and grant of license
from Character import *
from tuple2 import *
from dict2 import *
import sys
__all__ = [
'ScVersion', 'GemLists', 'DropLists', ... | artomason/KortsCalculator | Constants.py | Python | gpl-2.0 | 42,919 | [
"CRYSTAL"
] | bfd95840120c524da7c22c6035bc6d0fac05792194e1054d506eeadbe0bc859b |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | Jorge-C/bipy | skbio/maths/stats/ordination/canonical_correspondence_analysis.py | Python | bsd-3-clause | 8,563 | [
"scikit-bio"
] | a026a2d64f298b3fd393c6e2bcb7ec80d197976120ce8dbfa76d9da3d30bc52c |
import moose
import numpy as np
import rdesigneur as rd
def test_21_vclamp():
"""Test vclamp.
"""
rdes = rd.rdesigneur(
stimList = [['soma', '1', '.', 'vclamp', '-0.065 + (t>0.1 && t<0.2) * 0.02' ]],
plotList = [
['soma', '1', '.', 'Vm', 'Soma membrane potential'],
[... | dilawar/moose-core | tests/rdesigneur/test_21_vclamp.py | Python | gpl-3.0 | 854 | [
"MOOSE"
] | 300d444b40c654eef6f7eb9169d6a99ab6fa9cb3d71759cfd6bdfbeaab459101 |
"""
Test the Studio help links.
"""
from flaky import flaky
from unittest import skip
from common.test.acceptance.fixtures.course import XBlockFixtureDesc
from common.test.acceptance.tests.studio.base_studio_test import StudioCourseTest, ContainerBase
from common.test.acceptance.pages.studio.index import DashboardPag... | jzoldak/edx-platform | common/test/acceptance/tests/studio/test_studio_help.py | Python | agpl-3.0 | 48,761 | [
"VisIt"
] | 322224003833c3d35f128639b7c0debde92248014a9e4cb0f7a9f0ebacb929c3 |
# Copyright 2008-2013 Nokia Siemens Networks Oyj
#
# 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... | ktan2020/legacy-automation | win/Lib/site-packages/robot/result/testsuite.py | Python | mit | 5,583 | [
"VisIt"
] | dd4d940729e57a25437a50472b8c3b9ad2546be95f774c0caf07da6d45c4c87a |
## Aditya Gilra, NCBS, Bangalore, 2012
## Dilawar Singh, NCBS, 2015
import os
os.environ['NUMPTHREADS'] = '1'
import sys
sys.path.append('../../../python/')
import moose
from moose.utils import *
import moose.utils as mu
import count
import numpy as np
from moose.neuroml.NeuroML import NeuroML
import unittest
simdt... | dilawar/moose-full | moose-core/tests/python/neuroml/CA1.py | Python | gpl-2.0 | 1,046 | [
"MOOSE"
] | 6b7754ded773df0b46639c228db65ecf9fe9e4b214531103494c6fa310a9c9be |
from PyQt4.Qt import *
import Avogadro
class Tool(QObject):
# constructor
def __init__(self):
QObject.__init__(self)
# widget = GLWidget
def paint(self, widget):
# Painter
# print("paint(", widget, ")")
return None
# widget = GLWidget
# mouseEvent = QMouseEvent
def mousePressEvent(self,... | rcplane/periodicdisplay | reference/avogadro/libavogadro/examples/python/tooltemplate.py | Python | gpl-2.0 | 902 | [
"Avogadro"
] | f2c1834810f244495def2a16feef03166f5be584a42808dd843b89df7695093f |
# ./sdf_model.py
# -*- coding: utf-8 -*-
# PyXB bindings for NM:e92452c8d3e28a9e27abfc9994d2007779e7f4c9
# Generated 2016-09-25 19:01:05.718182 by PyXB version 1.2.5 using Python 3.5.1.final.0
# Namespace AbsentNamespace0
from __future__ import unicode_literals
import pyxb
import pyxb.binding
import pyxb.binding.saxer... | HBPNeurorobotics/BlenderRobotDesigner | robot_designer_plugin/export/urdf/generic/sdf_model_dom.py | Python | gpl-2.0 | 893,051 | [
"Gaussian"
] | 926ad06c0efa7eb7ffb2a57573983b24c3375f326eb125d8da6bae6a4648d145 |
import logging
import sys
import socket
import codecs
import json
import hashlib
import shutil
import urlparse
import urllib
import os
import webbrowser
import subprocess
import requests
import requesocks
def idle_port():
s = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
s.bind(("", 0))
s.listen(1... | Jonavin/firefly-proxy | lib/utils.py | Python | bsd-2-clause | 5,423 | [
"Firefly"
] | 10a51bea8b70ec5c9ff7cfbeec4ac20f4e76bbe172fd1c4e357bc3b873bac823 |
from playground.molecule.molecule import Molecule, Atom
from playground.molecule.molecularsystem import MolecularSystem
import pele.utils.elements as elem
import networkx as nx
import numpy as np
import unittest
import os
class TestMolecule(unittest.TestCase):
"""
a base class for molecular system unit tests... | cjforman/pele | playground/molecule/test/molecule_test.py | Python | gpl-3.0 | 6,230 | [
"PyMOL"
] | d5062a2c4250a33bd0ffd9819c5434bed44b6dcf1f8a568c9ea888ccf2fc78f4 |
"""
This file contains a library of automated image processing effects that borrow
heavily from the simpler effects found in viztools.py
"""
from __future__ import print_function
from __future__ import division
from os import listdir
from os.path import join, isfile
import cv2
import numpy as np
from vidviz.effects im... | themattinthehatt/vid-viz | vidviz/auto.py | Python | mit | 20,553 | [
"Gaussian"
] | 437a54b52ef6859d6e8c106a6dc4622b71884fd282d2ede8f6ab9c1b3ad1dceb |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2020, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Generic output file parser and related tools"""
import bz2
import fileinput
import gzip
import inspect
import io
impor... | cclib/cclib | cclib/parser/logfileparser.py | Python | bsd-3-clause | 20,759 | [
"ADF",
"Avogadro",
"Dalton",
"GAMESS",
"Gaussian",
"Jaguar",
"MOPAC",
"Molpro",
"NWChem",
"ORCA",
"Q-Chem",
"cclib"
] | 9052c0a2f45d240615d46bf4a072dc0148cda5ea4a9d19db15ad97a325dbfdf6 |
#
# Copyright (C) 2013,2014,2015,2016 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option)... | KonradBreitsprecher/espresso | testsuite/interactions_bonded.py | Python | gpl-3.0 | 5,159 | [
"ESPResSo"
] | 7044a2031c324d19d4ba3f31244a0ad155a691ae9e6d7099d36bd39a0ebee4b5 |
# Copyright 2015 47Lining LLC.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing... | 47lining/nucleator-core | lib/nucleator/core/update/commands/update.py | Python | apache-2.0 | 9,520 | [
"Galaxy"
] | 7e7c72193144be9e702f7ed9199d823548b86f1b8f64482d8716f4b2d84644e4 |
import ddt
from django.template import Context, Template
import unittest
@ddt.ddt
class OAExtrasTests(unittest.TestCase):
template = Template(
"{% load oa_extras %}"
"{{ text|link_and_linebreak }}"
)
@ddt.data(
("", ""),
('check this https://dummy-url.com', 'https://dummy... | Stanford-Online/edx-ora2 | openassessment/tests/test_templatetags.py | Python | agpl-3.0 | 1,368 | [
"VisIt"
] | 92d0c44269a0f8d6346a1e0e83ea96867395721c99e44db674dfc5a645f71413 |
"""
=================================
Gaussian Mixture Model Sine Curve
=================================
This example demonstrates the behavior of Gaussian mixture models fit on data
that was not sampled from a mixture of Gaussian random variables. The dataset
is formed by 100 points loosely spaced following a noisy ... | scikit-learn/scikit-learn | examples/mixture/plot_gmm_sin.py | Python | bsd-3-clause | 6,076 | [
"Gaussian"
] | 39d185c6f1961632fa48c1020ae0cc953f01c6767aaeeb0a8ab5a6b6ec93eaeb |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#... | MDAnalysis/mdanalysis | testsuite/MDAnalysisTests/auxiliary/test_xvg.py | Python | gpl-2.0 | 5,850 | [
"MDAnalysis"
] | 9bb954c55902019cd8b2b517dfbc6fcb9fe9d5965770ba8fc2e5690666ef013d |
from .estimator_base import *
class H2ONaiveBayesEstimator(H2OEstimator):
"""
The naive Bayes classifier assumes independence between predictor variables
conditional on the response, and a Gaussian distribution of numeric predictors with
mean and standard deviation computed from the training dataset. Wh... | YzPaul3/h2o-3 | h2o-py/h2o/estimators/naive_bayes.py | Python | apache-2.0 | 4,328 | [
"Gaussian"
] | 7ca23c4e639eb8efec40d5d9dd58061e95c95c6cf0205e89b528a4c0f01deb91 |
# mako/codegen.py
# Copyright 2006-2021 the Mako authors and contributors <see AUTHORS file>
#
# This module is part of Mako and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""provides functionality for rendering a parsetree constructing into module
source code."""
import j... | sqlalchemy/mako | mako/codegen.py | Python | mit | 47,147 | [
"VisIt"
] | b129a3a740b7ba41a7d266777c6a9b70a2ecf5139f35ed3e90e20146bca0d4f8 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
urlpat... | hjwp/cookiecutter-example-project | config/urls.py | Python | mit | 1,452 | [
"VisIt"
] | 464426c7d547aeeb1ff9c72152279e3830f115b0097374c46a00c2806f74c9f2 |
#
#
# File to test current configuration of GranuleCell project.
#
# To execute this type of file, type '..\..\..\nC.bat -python XXX.py' (Windows)
# or '../../../nC.sh -python XXX.py' (Linux/Mac). Note: you may have to update the
# NC_HOME and NC_MAX_MEMORY variables in nC.bat/nC.sh
#
# Author: Padr... | pgleeson/TestArea | models/MooseDemo/pythonScripts/RunTests.py | Python | gpl-2.0 | 11,129 | [
"MOOSE",
"NEURON"
] | 8fbcef167635095021339781302d7020f07d5f9d0c825cb5fe4d844d3c552a92 |
#!/usr/bin/env python
########################################################################
# File : dirac-wms-get-queue-cpu-time.py
# Author : Federico Stagni
########################################################################
""" Report CPU length of queue, in seconds
This script is used by the dirac-... | vmendez/DIRAC | WorkloadManagementSystem/scripts/dirac-wms-get-queue-cpu-time.py | Python | gpl-3.0 | 1,226 | [
"DIRAC"
] | b9c3077ae1424ab8a92644a6bf88e2a5794d9f67eac8d0cc52a22ddd3f2c7673 |
from django.core import serializers
from questionnaire.models import Questionnaire, Section, SubSection, Question, QuestionGroup, QuestionOption, QuestionGroupOrder
questionnaire = Questionnaire.objects.get(name="JRF 2013 Core English", description="From dropbox as given by Rouslan")
section_1 = Section.objects.creat... | testvidya11/ejrf | questionnaire/fixtures/questionnaire/section_4a.py | Python | bsd-3-clause | 15,470 | [
"VisIt"
] | c7bea4781061ab4b03823e01198923917fe7429ab52c3d15025a8ebb8ca12e0e |
# -*- coding: utf-8 -*-
#
# LatentStrainAnalysis documentation build configuration file, created by
# sphinx-quickstart on Tue Apr 28 10:49:47 2015.
#
# 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
# autogenerate... | brian-cleary/LatentStrainAnalysis | docs/source/conf.py | Python | mit | 8,288 | [
"Brian"
] | de1057c526bdbf6cdf3aee19aa5db7c6509ff932a9593ab5dad089d1f2bffe92 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2011 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... | tiagocardosos/stoq | stoqlib/reporting/callsreport.py | Python | gpl-2.0 | 1,653 | [
"VisIt"
] | 24d3bf0ac77fd7800a775dfc8317b6694f2d1808f28c99e311dc891f9cdc91c6 |
#!/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/dft/rks.py | Python | apache-2.0 | 7,989 | [
"PySCF"
] | 670c775e87af5eeed13b2b6c82fab52d4abc1385f534ec56605139df466045eb |
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | gkc1000/pyscf | pyscf/nao/m_conv_ac_dp.py | Python | apache-2.0 | 871 | [
"PySCF"
] | c4261d9049240959e85ceaf4041a9e2b6d7de0ddcddb8383633549504ba4e60b |
#!/usr/bin/env python
'''
Consensus Maker
Version 2.0
By Brendan Kohrn and Scott Kennedy(1)
(1) Department of Pathology, University of Washington School of Medicine, Seattle, WA 98195
Based on work by Scott Kennedy
January 21, 2014
Written for Python 2.7.3
Required modules: Pysam, Samtools
Inputs:
A position-sor... | mwschmit/Duplex-Sequencing | ConsensusMaker.py | Python | bsd-3-clause | 22,894 | [
"pysam"
] | 133d1cfb0c7afae31590925892fefbcb6f26e70e1823943ff4fad7002543b8e1 |
'''
Created on Oct 28, 2014
@author: ic4
'''
import unittest
import mock
import serapis.irods.api_wrapper as irods_api
from serapis.irods import exceptions as irods_exc
from serapis.storage.irods import _data_types as irods_types
def run_ils_fake1(output):
m = mock.Mock()
m.return_value = output
class... | wtsi-hgi/serapis | tests/irods/test_api_wrapper.py | Python | agpl-3.0 | 9,717 | [
"BWA"
] | 3b00a8e29d7c53da0ae031652a20bd4fe257df05d502c6f560bf0b0b707d2a61 |
'''
Takes a TLE at a certain time epoch and then computes the state vectors and
hence orbital elements at every time epoch (at every second) for the next 8
hours.
'''
import numpy as np
import math
import sys
import os
sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), os.path.pardir)))
from kep_d... | aerospaceresearch/orbitdeterminator | orbitdeterminator/propagation/sgp4.py | Python | mit | 15,629 | [
"EPW"
] | 08c8979e57f815e1f729963823eb70e68b9b2a0d9c4ecba1122eff64f26e53ab |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# This file is part of the SPORCO package. Details of the copyright
# and user license can be found in the 'LICENSE.txt' file distributed
# with the package.
"""
Basis Pursuit DeNoising
=======================
This example demonstrates the use of classes :class:`.admm.bpd... | bwohlberg/sporco | examples/scripts/sc/bpdn_cmp.py | Python | bsd-3-clause | 3,586 | [
"Gaussian"
] | 4bb6976f2cd2f501fc02bc92b915163de52da2fc8c4ef295e5795d9462383a62 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
def test_duccsd():
"""Test projective factorized UCCSDT on Ne using RHF/cc-pVDZ orbitals"""
import pytest
import forte.proc.scc as scc
import forte
import psi4
ref_energy = -128.677997285129
geom = "Ne"
scf_energy, psi4_wfn = forte.util... | evangelistalab/forte | tests/pytest/sparse_ci/srcc/test_duccsd.py | Python | lgpl-3.0 | 988 | [
"Psi4"
] | 170b29d4a0d9fa0a8d4a1e7467522afc01bbeaca17ad872de3c936c2c063a854 |
D=16
subdim=4
N=100
seed=7
import nef.nef_theano as nef
import nef.convolution
import hrr
import math
import random
random.seed(seed)
vocab=hrr.Vocabulary(D,max_similarity=0.1)
net=nef.Network('Question Answering') #Create the network object
net.make('A',1,D,mode='direct') #Make some pseudo populations (so they
... | jaberg/nengo | examples/question.py | Python | mit | 2,681 | [
"NEURON"
] | 8fcc4e707435b86c039c497f2622c3d6f7cf3cfcce6f931f06073f5899f00fb3 |
#!/usr/bin/env python
########################################################################
# File : dirac-wms-job-get-jdl
# Author : Stuart Paterson
########################################################################
"""
Retrieve the current JDL of a DIRAC job
Usage:
dirac-wms-job-get-jdl [options] ... ... | ic-hep/DIRAC | src/DIRAC/Interfaces/scripts/dirac_wms_job_get_jdl.py | Python | gpl-3.0 | 2,025 | [
"DIRAC"
] | 8c2599dfdd8783af36c3d7fde241a01102489bbb983e3e7ca4dd0d7663e4ab95 |
from __future__ import unicode_literals
import numpy as np
from astropy.io import ascii, fits
import matplotlib as mp
import matplotlib.pyplot as plt
from matplotlib.colors import LogNorm
import pandas as pd
import pylab as py
import scipy as sp
from scipy import optimize
import string as s
from statsmodels impor... | themiyan/zfire_survey | zfire_utils.py | Python | mit | 25,333 | [
"Galaxy"
] | e1e079476336a3ab124432f43e0f02559e8e0a583cbd468123323f90beb58723 |
# This is a module for Server Manager testing using Python.
# This provides several utility functions useful for testing
import os
import re
import sys
import exceptions
from vtkPVServerManagerDefaultPython import *
# we get different behavior based on how we import servermanager
# so we want to import servermanager t... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/Wrapping/Python/paraview/smtesting.py | Python | gpl-3.0 | 4,598 | [
"ParaView"
] | 163e5d7e336b4e35b82979fbfe4e58a7418edee376262e8fb44946eec9b8cfc0 |
# -*- coding: utf-8 -*-
"""
Module for animating solutions in 1D.
Can also save them but requieres ffmpeg package
see save_animation method.
"""
import numpy as nm
from os.path import join as pjoin
from glob import glob
from matplotlib import animation
from matplotlib import pyplot as plt
from matplotlib import colors... | vlukes/sfepy | sfepy/discrete/dg/dg_1D_vizualizer.py | Python | bsd-3-clause | 20,407 | [
"VTK"
] | f962c7e34f2a22d8c221b671c52515129a1d85082915f2c74185718ec3314dca |
"""
Tests for the course home page.
"""
from datetime import datetime, timedelta
from unittest import mock
from urllib.parse import quote_plus
import ddt
from django.conf import settings
from django.http import QueryDict
from django.test.utils import override_settings
from django.urls import reverse
from django.util... | eduNEXT/edx-platform | openedx/features/course_experience/tests/views/test_course_home.py | Python | agpl-3.0 | 43,964 | [
"VisIt"
] | 2de007671331509bc6395f3ce4617ec950cb9ecbd6bb5402807f13a8a3afadba |
# Implementation of KNN algorithm with default K = 5
# This script expects a directory as argument.
# Given directory should have a file called train_set.csv and
# another file called test_set.csv
import helpers.files as files
import helpers.normalizers as normalizers
import helpers.ann as ann
from config.constants im... | queirozfcom/ml201401 | train_and_apply_ann.py | Python | mit | 5,209 | [
"NEURON"
] | 9ac5e047bfcbe40df6130947caf3f0e0e49a0c1e2488994c22b9cd66aa7eaa5c |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | espressomd/espresso | doc/tutorials/electrokinetics/scripts/plot.py | Python | gpl-3.0 | 1,736 | [
"ESPResSo"
] | af0598b1e7fb5679a02041b22b753f07c9adcaa9520d972146d3dc34123e9e6f |
#!/usr/bin/env python
import sys
sys.path.append(".")
from netcdf import netcdf as nc
from models.helpers import to_datetime, short
from glob import glob
from itertools import groupby
import os
from functools import partial
from datetime import datetime
import numpy as np
rev_key = {}
TO_RAD = 30. * 60.
TO_MJ = 10 *... | gersolar/solar_radiation_model | models/utils/radiance.py | Python | mit | 4,308 | [
"NetCDF"
] | 5774ca206baa6bed58022a616a0fb78c4eeaeea6a049f1cf92b4a2d15b683eaf |
"""
# Notes:
- This simulation seeks to emulate the COBAHH benchmark simulations of (Brette
et al. 2007) using the Brian2 simulator for speed benchmark comparison to
DynaSim. However, this simulation does NOT include synapses, for better
comparison to Figure 5 of (Goodman and Brette, 2008) - although it uses the... | asoplata/dynasim-benchmark-brette-2007 | output/Brian2/brian2_benchmark_COBAHH_nosyn_0004/brian2_benchmark_COBAHH_nosyn_0004.py | Python | gpl-3.0 | 3,341 | [
"Brian"
] | a13a8c03479379c11eb0910a35776ac515e72a71ba0c75c8d4d4c43e6d35ce89 |
"""Interface to the CaImAn package (https://github.com/simonsfoundation/CaImAn)."""
import numpy as np
import multiprocessing as mp
from caiman import components_evaluation
from caiman.utils import visualization
from caiman.source_extraction.cnmf import map_reduce, initialization, pre_processing, \
... | cajal/pipeline | python/pipeline/utils/caiman_interface.py | Python | lgpl-3.0 | 32,356 | [
"Gaussian",
"NEURON"
] | db9d3b2139eea713b955f84ce0de3666b543864ee7e12d3ecd087e6443c291ac |
import netCDF4 as nc4
import numpy as np
# Model datatype
float_type = "f8"
# Set the height
kmax = 512
zsize = 0.5
dz = zsize / kmax
# Set the profiles
z = np.linspace(0.5*dz, zsize-0.5*dz, kmax)
b = np.zeros(np.size(z))
b[0:int(kmax/2)] = 1.
# Write input NetCDF file
nc_file = nc4.Dataset('rayleightaylor_input.n... | microhh/microhh2 | cases/rayleightaylor/rayleightaylor_input.py | Python | gpl-3.0 | 615 | [
"NetCDF"
] | 7dacda58ad5ed11453ca56375becc3c5145c6f4a0f6b5a157780b7cf3f53fb8d |
# -*- coding: utf-8 -*-
#
# 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 "L... | adrian-ionescu/apache-spark | python/pyspark/ml/tests.py | Python | apache-2.0 | 99,066 | [
"Gaussian"
] | 5ee57300719831913ff00af90c559b3a469f902cc8d6130444c9c836235935ad |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# -*- Python -*-
"""
Chat program
ROSPEEX あるいは jsk ROS Voice Recognition
から入力された文章を使い、DoCoMoAPIで会話する
The project is hosted on GitHub where your could fork the project or report
issues. Visit https://github.com/roboworks/
:copyright: (c) 2015,201... | okadahiroyuki/trcp | trcp_chat/nodes/ChatTRCP.py | Python | mit | 16,700 | [
"VisIt"
] | 6ebb484ba6674d4a80f76d0917340397aad7c7167bf7dbc32e7ece15871f668e |
#!/usr/bin/env python
import argparse
import binascii
import copy
import datetime
import hashlib
import json
import logging
import os
import shutil
import struct
import subprocess
import tempfile
import xml.etree.ElementTree as ET
from collections import defaultdict
from Bio.Data import CodonTable
logging.basicConfig(... | martenson/tools-iuc | tools/jbrowse/jbrowse.py | Python | mit | 52,886 | [
"BLAST",
"Galaxy"
] | 9481ff71a3dd3d78c710622945766b1fbb17b7d397447ec2199269a26014c812 |
##
## @file numfig.py
##
## @brief For numbering figures in Sphinx
##
## @version $Id: numfig.py 10 2012-10-07 14:39:47Z jrobcary $
##
## Started from https://bitbucket.org/arjones6/sphinx-numfig/wiki/Home
##
## Copyright © 2005-2012, Tech-X Corporation, Boulder, CO
## Free for any use whatsoever.
##
from do... | WASP-System/central | wasp-doc/src/sphinx/sphinx-plugins/numfig/numfig.py | Python | agpl-3.0 | 4,026 | [
"VisIt"
] | df4d748acd8e0ccc0399b9c8bb922b76d9fa63755eca89477d910c335fa8a8bb |
# -*- coding: utf-8 -*-
# Author: Óscar Nájera
# License: 3-clause BSD
"""
Backreferences Generator
========================
Parses example file code in order to keep track of used functions
"""
from __future__ import print_function
import ast
import os
# Try Python 2 first, otherwise load from Python 3
try:
im... | bthirion/nistats | doc/sphinxext/sphinx_gallery/backreferences.py | Python | bsd-3-clause | 6,560 | [
"VisIt"
] | 3aea118113af58cd423c49c9b422118b85b3154aca7d72c5a92fb5f0e76f458f |
"""Gromacs molecular dynamics simulation datasets.
"""
from .access import load_benzene
from .access import (load_benzene, load_ABFE,
load_expanded_ensemble_case_1,
load_expanded_ensemble_case_2,
load_expanded_ensemble_case_3,
load_wa... | alchemistry/alchemtest | src/alchemtest/gmx/__init__.py | Python | bsd-3-clause | 473 | [
"Gromacs"
] | 81d509b47df54f53afe8c2626a3f086eaabe228f4c7048d3d033c56697ae6b8e |
""" NotificationDB class is a front-end to the Notifications database
"""
__RCSID__ = "$Id$"
import time
import types
from DIRAC import gConfig, gLogger, S_OK, S_ERROR
from DIRAC.Core.Utilities.Mail import Mail
from DIRAC.Core.Base.DB import DB
from DIRAC.Core.Utilities import DEncode
from DIRAC.ConfigurationSystem.... | andresailer/DIRAC | FrameworkSystem/DB/NotificationDB.py | Python | gpl-3.0 | 34,270 | [
"DIRAC"
] | ebf8994f822fccf19867b3c5abdb0afac49cf58bb0097b841218a4037552db61 |
import numpy as np
import matplotlib.pyplot as plt
import fitsio
import h5py
from K2pgram import K2pgram, eval_freq, K2pgram_basis
from gatspy.periodic import LombScargle
import fitsio
import glob
import emcee
import scipy.interpolate as spi
import scipy.signal as sps
plotpar = {'axes.labelsize': 10,
'text.... | RuthAngus/K2rotation | find_delta_nu.py | Python | mit | 4,393 | [
"Gaussian"
] | 40f02bc461403dfc26a16a0b5d77feca6d38f9ea323931d6915bfcb8bede8fea |
"""
This module provides a way to pass information between passes as metadata.
* add attaches a metadata to a node
* get retrieves all metadata from a particular class attached to a node
"""
from gast import AST # so that metadata are walkable as regular ast nodes
class Metadata(AST):
""" Base class to add in... | pombredanne/pythran | pythran/metadata.py | Python | bsd-3-clause | 1,989 | [
"VisIt"
] | 67ce0b82d228f51be21ccb087dbbe85d1b51c152c8a81bd3fc3b8bf5a512fccb |
from apiclient import discovery
from apiclient import model
import json
import Image
import os
api_key = open(os.environ['HOME'] + "/.freebase_api_key").read()
model.JsonModel.alt_param = ""
freebase = discovery.build('freebase', 'v1sandbox', developerKey=api_key)
response = freebase.image(id='/en/espresso').execut... | tfmorris/freebase-python-samples | client-library/image.py | Python | bsd-3-clause | 379 | [
"ESPResSo"
] | 2f4d5fec3b3ea132c0aa74ecc9034e92e87fe7dd341b18bdc60ea7d03d97cae8 |
import operator
from six import ensure_text, iteritems, iterkeys, text_type
from ..node import NodeVisitor, DataNode, ConditionalNode, KeyValueNode, ListNode, ValueNode, BinaryExpressionNode, VariableNode
from ..parser import parse
class ConditionalValue(object):
def __init__(self, node, condition_func):
... | UK992/servo | tests/wpt/web-platform-tests/tools/wptrunner/wptrunner/wptmanifest/backends/conditional.py | Python | mpl-2.0 | 13,137 | [
"VisIt"
] | 97408b4678a539fb994cacc896c1d166c6b97371598590a41968bc6c55392b56 |
import hashlib
import json
import os
import shutil
import tempfile
import traceback
import zlib
from typing import Dict, List
from urllib.parse import unquote
from fsbc.paths import Paths
from fsbc.task import TaskFailure, current_task
from fsbc.util import is_sha1
from fscore.resources import Resources
from fsgamesys... | FrodeSolheim/fs-uae-launcher | fsgamesys/amiga/launchhandler.py | Python | gpl-2.0 | 46,150 | [
"ADF"
] | 355ad9fe5d9352ceba4ea0d11d18ff52c61274c3395fd09642acf5b41600bcb9 |
#!/usr/bin/env python
__author__ = 'Mike McCann,Duane Edgington,Reiko Michisaki'
__copyright__ = '2013'
__license__ = 'GPL v3'
__contact__ = 'duane at mbari.org'
__doc__ = '''
cron loader for CANON wave gliders slocum, OA and TEX in September 2013
Mike McCann; Modified by Duane Edgington and Reiko Michisaki... | stoqs/stoqs | stoqs/loaders/CANON/wg_loadsep2013.py | Python | gpl-3.0 | 5,101 | [
"NetCDF"
] | a88e669d30fcbc52aa3bbc9cd831f28506fb8fae4d292031ad20cf2f36b6d133 |
#!/usr/bin/env python
# Copyright 2020 Google, LLC.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-kms | samples/attestations/verify_attestation.py | Python | apache-2.0 | 3,178 | [
"VisIt"
] | d04c745af26ac46b2ce9dd406afb43139f563586181646f06b6e709901d9a2be |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
This module contains the classes for configuration of the chemenv package.
"""
__author__ = "David Waroquiers"
__copyright__ = "Copyright 2012, The Materi... | tallakahath/pymatgen | pymatgen/analysis/chemenv/utils/chemenv_config.py | Python | mit | 8,193 | [
"pymatgen"
] | d9fc4f0b024ed9b59cea899c290919b639f28df23e5ca1ffde30905022f37cac |
from instagram.client import InstagramAPI
import sys
if len(sys.argv) > 1 and sys.argv[1] == 'local':
try:
from config import *
#InstagramAPI.host = test_host
#InstagramAPI.base_path = test_base_path
InstagramAPI.access_token_field = "access_token"
InstagramAPI.authorize_ur... | haukurk/Partify | other/get_instagram_access_token.py | Python | mit | 1,274 | [
"VisIt"
] | 13679e9ac927d7d3d11362072ba71387fddce5e7ab6c97d600a11737faa8e575 |
#!/usr/bin/env python
# Copyright 2010-2013 by Peter Cock.
# 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.
r"""Read and write BGZF compressed files (the GZIP variant used in BAM... | updownlife/multipleK | dependencies/biopython-1.65/build/lib.linux-x86_64-2.7/Bio/bgzf.py | Python | gpl-2.0 | 34,085 | [
"Biopython"
] | 606c38c87cf818fd7b78232a021c0d9fc2ccc5f095d49338363997c6eb69f51b |
#!/bin/env python
"""
tests for SSHComputingElement module
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import os
import shutil
import subprocess32 as subprocess
import shlex
import pytest
import DIRAC
from DIRAC.Resources.Computing.SSHComputingElem... | ic-hep/DIRAC | src/DIRAC/Resources/Computing/test/Test_SSHComputingElement.py | Python | gpl-3.0 | 2,569 | [
"DIRAC"
] | 7b3e4964b8852bffe1c7c4a56c08a671168903df577fcb6518ec15ed88ff94a3 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 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
#... | jturney/psi4 | psi4/driver/p4util/writer.py | Python | lgpl-3.0 | 16,954 | [
"Psi4"
] | 7e4dbfcdd2b5f2886da8fb28b83d26e2a127b558c3c371a88d43e3e920b66b0f |
#!/usr/bin/env python
# encoding: utf-8
"""Legacy metrics script."""
import os
import tabulate
from modularodm import Q
from framework.analytics import get_basic_counters
from website import models
from website import settings
from website.app import init_app
from website.addons.osfstorage.model import OsfStorageFi... | barbour-em/osf.io | scripts/metrics.py | Python | apache-2.0 | 4,068 | [
"Brian"
] | cfdc5910b0153efa8120ab45bbb59435b26dfda0cae04fe9ab0cc1ed684e88a1 |
# Copyright (C) 2013-2016 Martin Vejmelka, UC Denver
#
# 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, mer... | openwfm/wrfxpy | src/rtma_cycler.py | Python | mit | 32,003 | [
"NetCDF"
] | 9214e2804d313ac3289428a9ccf18fa05633a1eb3414b2fb2e8deabf0847fad8 |
# -*- coding: utf-8 -*-
# Copyright (c) 2015-2022, Exa Analytics Development Team
# Distributed under the terms of the Apache License 2.0
"""
QE Type Conversions
######################
"""
lengths = {'alat': 'alat', 'bohr': 'au', 'crystal': 'crystal',
'angstrom': 'A', 'crystal_sg': 'crystal_sg'}
def to_qe_... | exa-analytics/exatomic | exatomic/qe/types.py | Python | apache-2.0 | 1,774 | [
"CRYSTAL"
] | fae1193c8734c2ba5dbc2251429fc6c48804c323cbd0f9efade0710ab5cef289 |
# The MIT License (MIT)
#
# Copyright (c) 2015 Christofer Hedbrandh
#
# 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, co... | chedbrandh/glabra | glabra/graph.py | Python | mit | 11,799 | [
"VisIt"
] | 273628069a3c8b62073401b80d34d6d29dab48a6f65ee223b34a8fbf943367b8 |
# pylint: skip-file
import sys, os
import argparse
import mxnet as mx
import numpy as np
import logging
import seg_carv_7_init_from_cls
from symbols.irnext_v2_deeplab_v3_dcn_w_hypers import *
from symbols.unet_dcn_w_hypers import *
from seg_carv_1_data_loader import FileIter
from seg_carv_1_data_loader import BatchFil... | deepinsight/Deformable-ConvNets | deeplab/runs_carv/seg_carv_4_train.py | Python | apache-2.0 | 6,827 | [
"Gaussian"
] | 8168aaf2116e7a52742b8771d9fdd3a7908e78c2e1d4decc48fa1da55bfdb0a7 |
# Copyright 2002 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.
# get set abstraction for graph representation
from Bio.Pathway.Rep.HashSet import *
class... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/Pathway/Rep/Graph.py | Python | apache-2.0 | 6,168 | [
"Biopython"
] | 75c6142e76f2dafd02d748e9dcadb5467fdf4a6d03cc02e6ec5d0b3b0f69d660 |
# Copyright 2008-2011 by Peter Cock. 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.
"""
Bio.AlignIO support for "fasta-m10" output from Bill Pearson's FASTA tools.
You are ex... | bryback/quickseq | genescript/Bio/AlignIO/FastaIO.py | Python | mit | 23,159 | [
"Biopython"
] | 5715a40f55bf58a8e465adbe4a5d373c376775e45d0251bf2368f50d87e088b6 |
import json
import sys
from copy import copy
from decimal import Decimal, InvalidOperation
from math import isclose, isfinite
from typing import Type
from zlib import compress
import pytest
from conftest import needs_libqpdf_v, skip_if_pypy
from hypothesis import assume, example, given
from hypothesis.strategies impor... | pikepdf/pikepdf | tests/test_object.py | Python | mpl-2.0 | 23,196 | [
"Brian"
] | 7bd2a8ec428f497d6a3620e921819a16669c47819024da0ea7400894f9831ec8 |
from bok_choy.page_object import PageObject, PageLoadError, unguarded
from bok_choy.promise import BrokenPromise, EmptyPromise
from .course_page import CoursePage
from ...tests.helpers import disable_animations
from selenium.webdriver.common.action_chains import ActionChains
class NoteChild(PageObject):
url = Non... | B-MOOC/edx-platform | common/test/acceptance/pages/lms/edxnotes.py | Python | agpl-3.0 | 20,547 | [
"VisIt"
] | baf88cc29c24a5227913383de3697c408f2055769836a17a3d5ee2632fe1c923 |
import json
import os
from International import Languages
class Keys:
last_idf_folder = 'last_idf_folder'
last_epw_folder = 'last_epw_folder'
last_idf = 'last_idf'
last_epw = 'last_epw'
language = 'language'
def load_settings(settings_file_name):
try:
settings = json.load(open(setti... | Myoldmopar/EPLaunchLight | EPLaunchLite/Settings.py | Python | bsd-3-clause | 1,038 | [
"EPW"
] | 3bdc051035044e4b66cd923319710eef9c87f66b593040315d21aea41a39eafe |
'''
This module contains database routines that may be accessed with or without using a web framework. All use SQLObject; this
adds a bit of overhead, but provides nice exception management.
The connection object is set locally based on parameters in the projectSpecs import. We're using MySQL. The database
schema i... | pbarton666/buzz_bot | djangoproj/djangoapp/b_dbRoutines.py | Python | mit | 30,740 | [
"VisIt"
] | 76fe5b07e5671681ffaa5e975b0f286009458bfa932efedc151603bc64077afb |
r"""
Package handling SV solvers in yaplf.
Package yaplf.algorithms.svm.solvers contains all the classes handling solvers
in SV learning algorithms. A solver is specialized in finding the solution of
one of the peculiar constrained optimization problems rising when dealing with
SV algorithms.
TODO:
- SV regression ... | dariomalchiodi/yaplf | yaplf/algorithms/svm/classification/solvers.py | Python | lgpl-3.0 | 33,875 | [
"Gaussian"
] | bf555ea1ad6b33a2b37a39cd3130adb49963eee54d9e5c8bcf30ffb4651f904e |
from ase import *
from gpaw import *
from ase.transport.calculators import TransportCalculator as TC
from gpaw.lcao.tools import get_lead_lcao_hamiltonian, remove_pbc
"""
1. calculate the transmission function of Sodium bulk with one atom in the
unit cell and sampling over (n, m) k-points in the transverse ibz.
2.... | qsnake/gpaw | oldtest/transport_transverse_k2.py | Python | gpl-3.0 | 1,907 | [
"ASE",
"GPAW"
] | d25a32068ae8a3f2957dcf56d52f8d7d7bb6bee94992987effe189f3fed659e2 |
""" Collection of DIRAC useful adler32 related tools.
By default on Error they return None.
.. warning::
On error False is returned.
.. warning::
All exceptions report to the stdout.
"""
from __future__ import print_function
from __future__ import absolute_import
from __future__ import divisi... | yujikato/DIRAC | src/DIRAC/Core/Utilities/Adler.py | Python | gpl-3.0 | 3,230 | [
"DIRAC"
] | 132cc15e8abe9529a0e362777f768357d65f93f931d66518c7f14e891294cf78 |
""" Code that calculates clutter by using running stats. """
from copy import deepcopy
from distributed import Client, LocalCluster
from .config import get_field_names
import warnings
import numpy as np
import pyart
try:
from dask import delayed
import dask.array as da
except ImportError:
warnings.warn(... | zssherman/cmac2.0 | cmac/radar_clutter.py | Python | bsd-3-clause | 10,230 | [
"NetCDF"
] | d3e5d4efb372adf7e7e289ad5f6d621f2e73f9df306e35487f4183b6237d3672 |
#! /usr/bin/env python
from MDAnalysis import *
import numpy
import math
import sys
my_traj = sys.argv[1]
u = Universe("init.pdb",my_traj)
v = Universe("init.pdb")
end = my_traj.find('.pdb')
fout_angle1 = my_traj[0:end] + '_betafloor_glob_angle1.dat'
fout_angle2 = my_traj[0:end] + '_betafloor_glob_angle2.dat'
c = ... | demharters/git_scripts | angle_betafloor_indiv_glob_mhcii.py | Python | apache-2.0 | 1,523 | [
"MDAnalysis"
] | 5bb3dd63bd7ae43c55da434d3b01e0b67d4dacbb2ec5ef33303fe7e88ec55d91 |
#!/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/geomopt/test/test_addons.py | Python | apache-2.0 | 1,179 | [
"PySCF"
] | bb856028e34b8c878b4f981db254698d9e20daeaf2827bbd005dc5004e75126c |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | espressomd/espresso | testsuite/python/tune_skin.py | Python | gpl-3.0 | 1,674 | [
"ESPResSo"
] | 4d87c0bc3a19d620a18aa1e8d886856f69e6e185fb516a4a2aaeb0a7b38c092e |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (c) 2017 Brian McClure
#
# django-octopus is free software under terms of the MIT License.
#
from setuptools import setup, find_packages
description = """"""
setup(
name='django-octopus',
version='0.4.1',
packages=find_packages(),
include_... | brmc/django-octopus | setup.py | Python | mit | 985 | [
"Brian",
"Octopus"
] | 8176ce79293dc38ce44c57067a8d946bc8c66d9d57c41a01fe7e3dd6903c0274 |
#!/usr/bin/python
"""
PyMOL plugin that provides show_contacts command and GUI
for highlighting good and bad polar contacts.
Factored out of clustermols by Matthew Baumgartner.
The advantage of this package is it requires many fewer dependencies.
Modified: Marcin Magnus 2020
Source <https://pymolwiki.org/index.p... | m4rx9/rna-pdb-tools | rna_tools/tools/PyMOL4RNA/libs/show_contacts.py | Python | mit | 15,707 | [
"PyMOL"
] | fbbcee215b72c66bf78fb27a321046c7b5abcfe60bfce12c60d73bd92a177b24 |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-admin-sort-cs-sites
# Author : Matvey Sapunov
########################################################################
"""
Sort site names at CS in "/Resources" section. Sort can be alphabetic... | sposs/DIRAC | Core/scripts/dirac-admin-sort-cs-sites.py | Python | gpl-3.0 | 4,921 | [
"DIRAC"
] | 8018b5d582afab527f6eff340cfbaf2d670ab5e40238fa505ebe90477d76d179 |
from galaxy.web.base.controller import *
class Mobile( BaseUIController ):
@web.expose
def index( self, trans, **kwargs ):
return trans.fill_template( "mobile/index.mako" )
@web.expose
def history_list( self, trans ):
return trans.fill_template( "mobile/history/list.mako" )
@web.e... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/webapps/galaxy/controllers/mobile.py | Python | gpl-3.0 | 2,554 | [
"Galaxy"
] | f596e961a3d8ddc98dac7161af634a52d317db8956861e7fdd6a676b50df79e6 |
#-------------------------------------------------------------------------------
# Cloud-COPASI
# Copyright (c) 2013 Edward Kent.
# All rights reserved. This program and the accompanying materials
# are made available under the terms of the GNU Public License v3.0
# which accompanies this distribution, and is available... | edkent/cloud-copasi | cloud_copasi/web_interface/aws/resource_views.py | Python | gpl-3.0 | 3,715 | [
"COPASI"
] | 69c141d8562887e85f0e62a7bb890cde6a077fd099f408be25a4d925682de8b6 |
# (C) British Crown Copyright 2010 - 2016, 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... | jswanljung/iris | lib/iris/io/__init__.py | Python | lgpl-3.0 | 15,376 | [
"NetCDF"
] | 92a6cf6f3ca65c573c5f25c6f30b634f2ae9e6b0dd551f2f2cc78412c03cd718 |
import csv,os,os.path,sys
from time import strftime
from collections import OrderedDict
import argparse
import dotenv
import math
from constants import OMOP_CONSTANTS, OMOP_MAPPING_RECORD, BENEFICIARY_SUMMARY_RECORD, OMOP_CONCEPT_RECORD, OMOP_CONCEPT_RELATIONSHIP_RECORD
from utility_classes import Table_ID_Values
from ... | OHDSI/ETL-CMS | python_etl/CMS_SynPuf_ETL_CDM_v5.py | Python | apache-2.0 | 121,037 | [
"VisIt"
] | 7fa21fe0e02cefbd4e780208dad17e82d4dc537e0ccbf391269822fcb1ccbcf1 |
paraview_plugin_version = '1.1.6'
# This is module to import. It provides VTKPythonAlgorithmBase, the base class
# for all python-based vtkAlgorithm subclasses in VTK and decorators used to
# 'register' the algorithm with ParaView along with information about UI.
from paraview.util.vtkAlgorithm import smproperty, smpro... | banesullivan/ParaViewGeophysics | PVPlugins/PVGeo_OMF.py | Python | bsd-3-clause | 3,699 | [
"ParaView",
"VTK"
] | 95d4ed47d7e7ea03df6c4b200d66ca7e47ae0ffc2de2f26662c486bb0309a693 |
""" :mod: SRM2Storage
=================
.. module: python
:synopsis: SRM v2 interface to StorageElement
"""
# # imports
import os
import re
import time
import errno
from stat import S_ISREG, S_ISDIR, S_IMODE, ST_MODE, ST_SIZE
# # from DIRAC
from DIRAC import gLogger, gConfig
from DIRAC.Core.Utilities imp... | andresailer/DIRAC | Resources/Storage/SRM2Storage.py | Python | gpl-3.0 | 82,153 | [
"DIRAC"
] | 8827c4db553d09e99476f299f4104909f644ea6d1425774940f744de7974ac2d |
#!/usr/bin/env python
import os
try:
__IPYTHON__
import sys
del sys.argv[1:]
except:
pass
import srwl_bl
import srwlib
import srwlpy
import math
import srwl_uti_smp
def set_optics(v, names=None, want_final_propagation=True):
el = []
pp = []
if not names:
names = ['S1', 'S1_HCM', 'H... | radiasoft/sirepo | tests/template/srw_generate_data/nsls-ii-hxn-beamline-ssa-closer.py | Python | apache-2.0 | 38,894 | [
"CRYSTAL",
"Gaussian"
] | e99e873b7eb80131fd1fa93d49b3b122b502a311accafc938da1645893498f3b |
#!/bin/py
#
# Combustion Theory Final Exam: Turbulent Diffusion Flames
#
import sys
import numpy as np
import pylab
import scipy.special as ss
def beta(a, b, mew):
e1 = ss.gamma(a + b)
e2 = ss.gamma(a)
e3 = ss.gamma(b)
e4 = mew ** (a - 1)
e5 = (1 - mew) ** (b - 1)
return (e1/(e2*e3)) * e4 * e5
... | nicholasmalaya/paleologos | combustion/final/flow.py | Python | mit | 5,810 | [
"Gaussian"
] | 5d2a599a3a5cf528e80a93233bdcda186261015be55e2168e6cde0051006731e |
###############################################################################
##
## Copyright (C) 2014-2015, 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.
##
## ... | hjanime/VisTrails | vistrails/packages/vtk/inspectors.py | Python | bsd-3-clause | 7,975 | [
"VTK"
] | d86c6413e3f8659667cfc93ce6966c4a35af286efe5fca7394a174e4a3bcf8be |
#!/usr/bin/python2
'''
Makes list of all Drosophila species out of list of files, submits makeblastdb
for the .fasta files
'''
import subprocess
import os
def get_list_of_all_files():
'''Puts filenames of files in 02_raw_input into a list'''
p = subprocess.Popen(['ls', '../02_raw_input'], stdout=subprocess.... | CoderMatthias/ortholog-assignment | 05_scripts/00_mk_db_N_sp_list.py | Python | gpl-2.0 | 1,598 | [
"BLAST"
] | b5e064efb5d3b1e0a7e82f7ef2f205f126266fa3d4d980830c7004ae7de0f62c |
# Copyright 2010-2017, The University of Melbourne
# Copyright 2010-2017, Brian May
#
# This file is part of Karaage.
#
# Karaage 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... | brianmay/karaage | karaage/apps.py | Python | gpl-3.0 | 821 | [
"Brian"
] | 3489994e9b32a02c80dd6f0194d6b5e0772c41578c5efe504337fc443614312b |
# Custom GPAW setup for Puhti (Bull cluster)
import os
# compiler
compiler = './gcc.py'
mpicompiler = './gcc.py'
mpilinker = 'mpicc'
extra_compile_args = ['-std=c99', '-O3', '-fopenmp-simd']
extra_link_args = ['-fno-lto']
# libz
libraries = ['z']
# libxc
library_dirs += [os.environ['LIBXCDIR'] + '/lib']
include_dirs... | mlouhivu/build-recipes | gpaw-conda/setup/customize-puhti.py | Python | mit | 774 | [
"GPAW"
] | d64052a0f1f0a78da1ca9da0d145f7e9975bf0467b282166d0fdd5a9e692e3a8 |
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