diff --git a/debian/README.Debian b/debian/README.Debian new file mode 100644 index 000000000..f96e0bb8b --- /dev/null +++ b/debian/README.Debian @@ -0,0 +1,90 @@ +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 `__. + +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 `__. + +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 `__ +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 `_ +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 +`_ + +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: tvb-users@googlegroups.com +- Raw demo IPython Notebooks can be found under: + https://github.com/the-virtual-brain/tvb-documentation/tree/master/demos diff --git a/debian/changelog b/debian/changelog new file mode 100644 index 000000000..5a163eb8d --- /dev/null +++ b/debian/changelog @@ -0,0 +1,5 @@ +tvb-framework (1.5.6-1) unstable; urgency=low + + * Initial release. Closes: #901868 + + -- umar haruna abdullahi Thu, 05 Jul 2018 17:29:23 +0100 diff --git a/debian/compat b/debian/compat new file mode 100644 index 000000000..b4de39476 --- /dev/null +++ b/debian/compat @@ -0,0 +1 @@ +11 diff --git a/debian/control b/debian/control new file mode 100644 index 000000000..93bf0a0ab --- /dev/null +++ b/debian/control @@ -0,0 +1,40 @@ +Source: tvb-framework +Maintainer: the virtual brain +Uploaders: umar haruna abdullahi +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 diff --git a/debian/copyright b/debian/copyright new file mode 100644 index 000000000..afc279992 --- /dev/null +++ b/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 +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 . + . + 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'. diff --git a/debian/rules b/debian/rules new file mode 100644 index 000000000..285bde54d --- /dev/null +++ b/debian/rules @@ -0,0 +1,9 @@ +#!/usr/bin/make -f + +#export DH_VERBOSE = 1 +export PYBUILD_NAME = tvb-framework + +%: + dh $@ --with python2 --buildsystem=pybuild + +override_dh_auto_test: diff --git a/debian/source/format b/debian/source/format new file mode 100644 index 000000000..163aaf8d8 --- /dev/null +++ b/debian/source/format @@ -0,0 +1 @@ +3.0 (quilt) diff --git a/debian/source/lintian-overrides b/debian/source/lintian-overrides new file mode 100644 index 000000000..6cccc49c2 --- /dev/null +++ b/debian/source/lintian-overrides @@ -0,0 +1,9 @@ +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 diff --git a/debian/tvb-framework.lintian-overrides b/debian/tvb-framework.lintian-overrides new file mode 100644 index 000000000..a4c14c6d6 --- /dev/null +++ b/debian/tvb-framework.lintian-overrides @@ -0,0 +1,8 @@ +# 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 diff --git a/debian/watch b/debian/watch new file mode 100644 index 000000000..7c7bbff49 --- /dev/null +++ b/debian/watch @@ -0,0 +1,3 @@ +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)))