Added debian directory for building debian package

debian/README.Debian

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+tvb-library for Debian
+
+THE VIRTUAL BRAIN SCIENTIFIC LIBRARY
+====================================
+
+The Virtual Brain Project (TVB Project) has the purpose of offering some
+modern tools to the Neurosciences community, for computing, simulating
+and analyzing functional and structural data of human brains.
+
+"TVB Scientific Library" is the most important scientific contribution
+of TVB Project, but only a part of our code. In order to use this TVB
+Python Library (modify/run/test), you are advised to follow the steps
+described here:
+http://docs.thevirtualbrain.com/manuals/ContributorsManual/ContributorsManual.html#contributors-manual
+
+The interaction with TVB source code is recommended for advanced users
+only, for which the concepts proposed by TVB are known and understood,
+and which also have some programming knowledge.
+
+"TVB Scientific Library" comes in two major forms for code-contributors:
+as a light-weight Python library, or plugged into TVB framework
+(including Web interface and Persistence of data layers). Depending on
+your needs and resources, you could use any of the two available options
+for contributing and testing new code.
+
+"TVB Scientific Library" is a light-weight, stand-alone Python library
+that contains all the needed packages in order to run simulations and
+analysis on data without the need for the entire TVB Framework. This
+implies that no storage will be provided so data from each session will
+be lost on close. You need to either persist it yourself in some manner
+or use the full TVBFramework where HDF5 / database storage is provided
+as default.
+
+For more details, check: http://www.thevirtualbrain.org/
+
+"TVB Scientific Library" contains the following packages: basic,
+datatypes, simulator and analyzers. The dependencies between these
+packages can be seen in tvb-package-diagram.jpg . Following is a short
+description of each of these packages:
+
+-  tvb.basic
+
+This package is the base of TVB and holds sub-packages that are used by
+most of the other packages like logging, global settings and the TVB
+traits package. You should rarely (if at all) need to change code in
+this package, and should know exactly what you are doing before
+attempting to change anything from here.
+
+-  tvb.datatypes
+
+The simulator and analyzers packages (as well as uploaders and
+visualizers in TVB Framework) will need to have a common "language" in
+order to work with the same data. In TVB architecture, that "common
+language" is represented by Data Types. TVB Data Types declarations are
+located in this package.
+
+Most of the datatypes here have a diamond like inheritance structure of
+the following form:
+
+::
+
+                            DataTypeData
+                                 |
+                                / \\
+               DataTypeFramework   DataTypeScientific
+                                \ /
+                                 |
+                              DataType
+
+
+The DataTypeData holds the actual structure of the datatype.
+DataTypeScientific holds any methods required from a scientific point of
+view. DataTypeFramework should just be ignored from a library user point
+of view as it holds framework related methods and will be removed
+altogether in the near future. DataType just brings all the above
+together and is the class you should actually use in your code.
+
+-  tvb.simulator
+
+The Simulation Component is the most important component in The Virtual
+Brain solution, as it is the component responsible for all the
+scientific computation related to brain models and data.
+
+You can find various demos of using the simulator under
+tvb/simulator/demos as well as some nice tutorials under
+tvb/simulator/doc/tutorials/ .
+
+-  tvb.analyzers
+
+Holds modules that can run various analysis of data resulted from the
+simulator. There are a few demos which use the PCA analyzer like
+tvb/simulator/demos/pca\_analyse\_view\_region and
+tvb/simulator/demos/pca\_analyse\_view\_surface . TVB is not strong in
+doing data analysis, we barely have a minimum set of analyzers for
+immediate needs.
+
+NOTE:
+
+To contribute to this repo, you are advised to first fork it under
+GitHub (through the web ui), and next clone that fork on your machine,
+and use it as you use any other git repository.
+
+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-library::
+
+    cd [folder_where_tvb_library_is]
+    pytest tvb/test [--junitxml=path]
+
+The second alternative form of running TVB tests, when installing TVB from Pypi, is::
+
+    pip install -U tvb-library
+    pytest --pyargs tvb.tests.library
+
+
+Coverage
+--------
+
+A coverage report can be generated with::
+
+    pip install pytest-cov
+    cd [folder_where_tvb_library_is]
+    py.test --cov-config .coveragerc --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: tvb-users@googlegroups.com
+-  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-library (1.5.5.1-1) unstable; urgency=medium
+
+  * Initial release. Closes: #901866
+
+ -- umar haruna abdullahi <umarbrowser20@gmail.com>  Sun, 01 Jul 2018 10:25:24 +0100

debian/compat

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+11

debian/control

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+Source: tvb-library
+Maintainer: the virtual brain <tvb.debian@codemart.ro>
+Uploaders: umar haruna abdullahi <umarbrowser20@gmail.com>
+Section: python
+Priority: optional
+Build-Depends: debhelper (>=11),
+               dh-python,
+               python-all,
+               python-setuptools,
+               python-networkx,
+               python-numpy,
+               python-numba,
+               python-numexpr,
+               python-matplotlib,
+               python-sklearn,
+               python-scipy,
+               tvb-gdist,
+               tvb-data
+Standards-Version: 4.1.4
+Vcs-Browser: https://github.com/the-virtual-brain/tvb-library
+Vcs-Git: https://github.com/the-virtual-brain/tvb-library.git
+Homepage: http://www.thevirtualbrain.org
+
+Package: tvb-library
+Architecture: all
+Depends: ${misc:Depends},
+         ${python:Depends}
+Description: most important scientific contribution of TVB Project
+ This package is the base of TVB and holds sub-packages that are used by
+ most of the other packages like logging, global settings and the TVB
+ traits package.

debian/copyright

@@ -0,0 +1,31 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: tvb-library
+Upstream-Contact: TVB TEAM <tvb.admin@thevirtualbrain.org>
+Source: https://github.com/the-virtual-brain/tvb-library
+
+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+
+
+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'.

debian/rules

@@ -0,0 +1,7 @@
+#!/usr/bin/make -f
+
+#export DH_VERBOSE = 1
+export PYBUILD_NAME = tvb-library
+
+%:
+	dh $@ --with python2 --buildsystem=pybuild

debian/source/format

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+3.0 (quilt)

debian/source/lintian-overrides

@@ -0,0 +1 @@
+tvb-library source: debian-watch-does-not-check-gpg-signature

debian/tvb-library.lintian-overrides

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+tvb-library: no-upstream-changelog
+tvb-library: 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-library/tvb-library-(.+)\.(?:zip|tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz)))

setup.py

@@ -44,7 +44,7 @@
 
 TVB_TEAM = "Stuart Knock, Marmaduke Woodman, Paula Sanz Leon, Laurent Pezard, Viktor Jirsa"
 
-TVB_INSTALL_REQUIREMENTS = ["networkx", "numpy", "numba", "numexpr", "matplotlib",
+TVB_INSTALL_REQUIREMENTS = ["networkx", "numpy", "numba", "numexpr", "matplotlib==2.1.2",
                             "pytest", "scikit-learn", "scipy", "tvb-gdist", "tvb-data"]
 
 with open(os.path.join(os.path.dirname(__file__), 'README.rst')) as fd: