Added debian directory

debian/README.Debian

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+tvb-framework for Debian
+
+TVB FRAMEWORK
+=============
+
+The Virtual Brain framework is a complete framework including:
+
+-  a plugable workflow manager;
+-  a data persistence layer (with a relational DB and File Storage);
+-  an HTML5 based user interface;
+-  visualizers for neuro-science related entities.
+
+The easiest way to make use of this code, is to obtain
+a Distribution of TVB with Python and all the necessary packages linked,
+and then clone this repo nearby. More details `in our
+documentation <http://docs.thevirtualbrain.org/manuals/ContributorsManual/ContributorsManual.html>`__.
+
+Alternatively, if you plan to develop long term with TVB, extensively
+modify code, add new dependencies, or you simply prefer to use your own
+Python installation, you may want to read this:
+`here <http://docs.thevirtualbrain.org/manuals/ContributorsManual/ContributorsManual.html#the-unaided-setup>`__.
+
+If you don't require the framework features listed above, the simulator
+and associated scientific modules can be used independently; please see
+the `tvb-library <https://github.com/the-virtual-brain/tvb-library>`__
+repo.
+
+Usage
+-----
+
+To use TVB code, clone from GitHub (https://github.com/the-virtual-brain/tvb-framework), or get from Pypi::
+
+    pip install tvb-framework
+    python -m tvb.interfaces.web.run WEB_PROFILE tvb.config
+
+
+Your port **8080** should be free, as a CherryPy service will try to run there.
+Your default browser should automatically open http://localhost:8080/ which is the way to
+interact with TVB Web Interface.
+
+When using from sources (pypi or Github, not TVB_Distribution), if you want BCT adapters enabled, you should
+manually download BCT https://sites.google.com/site/bctnet/
+and set env variable **BCT_PATH** towards the directory where you unzip BCT, plus also have Octave or
+Matlab installed with command line API enabled.
+
+
+Testing
+=======
+
+For testing the package, the `Pytest  <https://docs.pytest.org/>`_
+framework is used. Pytest can be installed using pip.
+
+Pytest will run all files in the current directory and its subdirectories
+of the form test_*.py or \*_test.py.
+More generally, it follows `standard test discovery rules
+<https://docs.pytest.org/en/latest/getting-started.html>`_
+
+The command for running our tests has two forms.
+Recommendation when working with a git clone of tvb-framework::
+
+    cd [folder_where_tvb_framework_is]
+    pytest tvb/test/framework [--profile=TEST_POSTGRES_PROFILE] [--junitxml=path]
+    # default profile value is TEST_SQLITE_PROFILE
+
+The second alternative form of running TVB tests, when installing TVB from Pypi, is::
+
+    pip install -U tvb-framework
+    pytest --pyargs tvb.tests.framework
+
+
+Coverage
+========
+
+A coverage report can be generated with::
+
+    pip install pytest-cov
+    cd [folder_where_tvb_framework_is]
+    py.test --cov=tvb tvb/tests/ --cov-branch --cov-report xml:[file_where_xml_will_be_generated]
+
+
+Further Resources
+=================
+
+-  For issue tracking we are using Jira: http://req.thevirtualbrain.org
+-  For API documentation and live demos, have a look here:
+   http://docs.thevirtualbrain.org
+-  A public mailing list for users of The Virtual Brain can be joined
+   and followed using: [email protected]
+-  Raw demo IPython Notebooks can be found under:
+   https://github.com/the-virtual-brain/tvb-documentation/tree/master/demos

debian/changelog

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+tvb-framework (1.5.6-1) unstable; urgency=low
+
+  * Initial release. Closes: #901868
+
+ -- umar haruna abdullahi <[email protected]>  Thu, 05 Jul 2018 17:29:23 +0100

debian/compat

@@ -0,0 +1 @@
+11

debian/control

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+Source: tvb-framework
+Maintainer: the virtual brain <[email protected]>
+Uploaders: umar haruna abdullahi <[email protected]>
+Section: python
+Priority: optional
+Build-Depends: debhelper (>=11),
+               dh-python,
+               python-all,
+               python-setuptools,
+               python-bs4,
+               python-cfflib,
+               python-cherrypy,
+               python-formencode,
+               python-genshi,
+               python-h5py,
+               python-nibabel,
+               python-pil,
+               python-psutil,
+               python-simplejson,
+               python-sqlalchemy,
+               python-migrate,
+               python-networkx,
+               python-pytest,
+               python-numpy,
+               python-scipy,
+               tvb-library,
+               tvb-data
+Standards-Version: 4.1.4
+Vcs-Browser: https://github.com/the-virtual-brain/tvb-framework
+Vcs-Git: https://github.com/the-virtual-brain/tvb-framework.git
+Homepage: http://www.thevirtualbrain.org
+
+Package: tvb-framework
+Architecture: all
+Depends: ${misc:Depends},
+         ${python:Depends}
+Description: virtual brain framework is a complete framework
+ including a plugable workflow manager,a data persistence layer
+ (with a relational DB and File Storage),an HTML5 based user
+ interface, visualizers for neuro-science related entities

debian/copyright

@@ -0,0 +1,119 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: tvb-framework
+Upstream-Contact: TVB TEAM <[email protected]>
+Source: https://github.com/the-virtual-brain/tvb-framework
+
+Files: *
+Copyright: 2012-2017 Baycrest Centre for Geriatric Care ("Baycrest") and others
+License: GPL-3.0+
+
+Files: debian/*
+Copyright: 2018 Baycrest Centre for Geriatric Care ("Baycrest") and others
+License: GPL-3.0+
+
+Files: tvb/interfaces/web/static/js/d3.v3.js
+       tvb/interfaces/web/static/js/d3.v4.min.js
+Copyright: 2012, Michael Bostock
+License: BSD-2-clause 
+
+Files: tvb/interfaces/web/static/jquery/*
+Copyright: 2011 John Resig
+License: MIT-2.1.1
+
+Files: tvb/interfaces/web/static/mathjax/*
+Copyright: __UNKNOWN__
+License: Apache-2.0
+
+License: GPL-3.0+
+ This program is free software: you can redistribute it and/or modify it under the
+ terms of the GNU General Public License as published by the Free Software Foundation,
+ either version 3 of the License, or (at your option) any later version.
+ This program is distributed in the hope that it will be useful, but WITHOUT ANY
+ WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+ PARTICULAR PURPOSE.  See the GNU General Public License for more details.
+ You should have received a copy of the GNU General Public License along with this
+ program.  If not, see <http://www.gnu.org/licenses/>.
+ .
+ When using The Virtual Brain for scientific publications, please cite it as follows:
+ Paula Sanz Leon, Stuart A. Knock, M. Marmaduke Woodman, Lia Domide,
+ Jochen Mersmann, Anthony R. McIntosh, Viktor Jirsa (2013)
+ The Virtual Brain: a simulator of primate brain network dynamics.
+ Frontiers in Neuroinformatics (7:10. doi: 10.3389/fninf.2013.00010)
+ .
+ On Debian systems, the complete text of the GNU General Public License
+ Version 3 can be found in `/usr/share/common-licenses/GPL-3'.
+
+License: MIT-2.1.1
+ 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, publish,
+ distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so, subject to
+ the following conditions:
+ .
+ The above copyright notice and this permission notice shall be
+ included in all copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+ LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+ OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+ WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+License: BSD-2-clause
+ Copyright (c) The Regents of the University of California.
+ All rights reserved.
+ .
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+ 1. Redistributions of source code must retain the above copyright
+   notice, this list of conditions and the following disclaimer.
+ 2. Redistributions in binary form must reproduce the above copyright
+   notice, this list of conditions and the following disclaimer in the
+   documentation and/or other materials provided with the distribution.
+ 3. Neither the name of the copyright holder nor the names of its contributors
+   may be used to endorse or promote products derived from this software without
+   specific prior written permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE REGENTS AND CONTRIBUTORS ``AS IS'' AND
+ ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ ARE DISCLAIMED.  IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE
+ FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
+ OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+ LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+ OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGE.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+ ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+License: Apache-2.0
+ 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, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+ .
+ On Debian systems, the complete text of the GNU General Public License
+ Version 3 can be found in `/usr/share/common-licenses/Apache-2.0'.

debian/rules

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+#!/usr/bin/make -f
+
+#export DH_VERBOSE = 1
+export PYBUILD_NAME = tvb-framework
+
+%:
+	dh $@ --with python2 --buildsystem=pybuild
+
+override_dh_auto_test:

debian/source/format

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+3.0 (quilt)

debian/source/lintian-overrides

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+tvb-framework source: debian-watch-does-not-check-gpg-signature
+
+# Source is present in there places
+tvb-framework source: source-is-missing
+
+# This is not a minified JS file and might contain long lines
+tvb-framework source: insane-line-length-in-source-file
+tvb-framework source: source-contains-prebuilt-javascript-object
+tvb-framework source: embedded-javascript-library

debian/tvb-framework.lintian-overrides

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+# Is Ok for the duplicate fonts
+tvb-framework: duplicate-font-file
+tvb-framework: embedded-javascript-library
+tvb-framework: executable-not-elf-or-script
+tvb-framework: privacy-breach-generic
+tvb-framework: image-file-in-usr-lib
+tvb-framework: no-upstream-changelog
+tvb-framework: dependency-on-python-version-marked-for-end-of-life

debian/watch

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+version=3
+opts=uversionmangle=s/(rc|a|b|c)/~$1/ \
+https://pypi.debian.net/tvb-framework/tvb-framework-(.+)\.(?:zip|tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz)))