From 6c0aaab4199047c1b72276848fb81ee2047e3d0f Mon Sep 17 00:00:00 2001 From: umar abdullahi Date: Sat, 7 Jul 2018 17:35:33 +0100 Subject: [PATCH 1/5] Added debian directory for building from source Update and added lintian overrides --- debian/README.Debian | 46 ++++++++++++++++++++++++++++++ debian/changelog | 5 ++++ debian/compat | 1 + debian/control | 23 +++++++++++++++ debian/copyright | 31 ++++++++++++++++++++ debian/rules | 11 +++++++ debian/source/format | 1 + debian/source/lintian-overrides | 1 + debian/tvb-gdist.lintian-overrides | 2 ++ debian/watch | 3 ++ 10 files changed, 124 insertions(+) create mode 100644 debian/README.Debian create mode 100644 debian/changelog create mode 100644 debian/compat create mode 100644 debian/control create mode 100644 debian/copyright create mode 100644 debian/rules create mode 100644 debian/source/format create mode 100644 debian/source/lintian-overrides create mode 100644 debian/tvb-gdist.lintian-overrides create mode 100644 debian/watch diff --git a/debian/README.Debian b/debian/README.Debian new file mode 100644 index 00000000..e3942b38 --- /dev/null +++ b/debian/README.Debian @@ -0,0 +1,46 @@ +tvb-gdist for Debian + +External Library Geodesic +========================= + +The `gdist` module is a Cython interface to a C++ library +(http://code.google.com/p/geodesic/) for computing +geodesic distance which is the length of shortest line between two +vertices on a triangulated mesh in three dimensions, such that the line +lies on the surface. + +The algorithm is due Mitchell, Mount and Papadimitriou, 1987; the implementation +is due to Danil Kirsanov and the Cython interface to Gaurav Malhotra and +Stuart Knock. + + +Original library (published under MIT license): +http://code.google.com/p/geodesic/ + +We added a python wrapped and made small fixes to the original library, to make it compatible with cython. + +To install this, either run `pip install gdist` or download +sources from Github and run `python setup.py install` in current folder. + +Basic test could be:: + + python + import gdist + + +Python 2.7, Cython, and a C++ compiler are required. + +Debian package +============== + +In order to produce a Debian package, assuming you have the requisite tools +installed (`apt-get install devscripts python-all-dev python-stdeb`):: + + cd debian + debuild -us -uc + cd ../../ + + +and you should find a suitable deb file for your system. + + -- umar haruna abdullahi Sun, 01 Jul 2018 12:24:32 +0100 diff --git a/debian/changelog b/debian/changelog new file mode 100644 index 00000000..b1dd78e3 --- /dev/null +++ b/debian/changelog @@ -0,0 +1,5 @@ +tvb-gdist (1.5.6-1) unstable; urgency=medium + + * Initial release. Closes: #896927 + + -- umar haruna abdullahi Sun, 01 Jul 2018 12:24:32 +0100 diff --git a/debian/compat b/debian/compat new file mode 100644 index 00000000..b4de3947 --- /dev/null +++ b/debian/compat @@ -0,0 +1 @@ +11 diff --git a/debian/control b/debian/control new file mode 100644 index 00000000..c0ac8e8f --- /dev/null +++ b/debian/control @@ -0,0 +1,23 @@ +Source: tvb-gdist +Maintainer: umar haruna abdullahi +Section: python +Priority: optional +Build-Depends: cython, + debhelper (>=11), + dh-python, + python-all, + python-numpy, + python-scipy, + python-setuptools +Standards-Version: 4.1.4.2 +Vcs-Browser: https://github.com/the-virtual-brain/tvb-geodesic +Vcs-Git: https://github.com/the-virtual-brain/tvb-geodesic.git +Homepage: http://www.thevirtualbrain.org + +Package: tvb-gdist +Architecture: any +Depends: ${misc:Depends}, ${python:Depends}, ${shlibs:Depends} +Description: gdist module is a Cython interface + computing geodesic distance which is the length of shortest + line between two vertices on a triangulated mesh in three + dimensions, such that the line lies on the surface diff --git a/debian/copyright b/debian/copyright new file mode 100644 index 00000000..1305519a --- /dev/null +++ b/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 +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 . + . + 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'. diff --git a/debian/rules b/debian/rules new file mode 100644 index 00000000..5f16329f --- /dev/null +++ b/debian/rules @@ -0,0 +1,11 @@ +#!/usr/bin/make -f + +#export DH_VERBOSE = 1 +export PYBUILD_NAME = tvb-gdist +export DEB_BUILD_MAINT_OPTIONS = hardening=+all +DPKG_EXPORT_BUILDFLAGS = 1 + +include /usr/share/dpkg/buildflags.mk + +%: + dh $@ --with python2 --buildsystem=pybuild diff --git a/debian/source/format b/debian/source/format new file mode 100644 index 00000000..163aaf8d --- /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 00000000..7d2edfcc --- /dev/null +++ b/debian/source/lintian-overrides @@ -0,0 +1 @@ +tvb-gdist source: debian-watch-does-not-check-gpg-signature diff --git a/debian/tvb-gdist.lintian-overrides b/debian/tvb-gdist.lintian-overrides new file mode 100644 index 00000000..eec8f18b --- /dev/null +++ b/debian/tvb-gdist.lintian-overrides @@ -0,0 +1,2 @@ +tvb-gdist: no-upstream-changelog +tvb-gdist: dependency-on-python-version-marked-for-end-of-life diff --git a/debian/watch b/debian/watch new file mode 100644 index 00000000..82af55fa --- /dev/null +++ b/debian/watch @@ -0,0 +1,3 @@ +version=3 +opts=uversionmangle=s/(rc|a|b|c)/~$1/ \ +https://pypi.debian.net/tvb-gdist/tvb-gdist-(.+)\.(?:zip|tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz))) From add1da4a185d460317b58f2d62a8c0e6ebf64626 Mon Sep 17 00:00:00 2001 From: umar abdullahi Date: Wed, 11 Jul 2018 11:30:52 +0100 Subject: [PATCH 2/5] Upadate maintainer and added uploader --- debian/control | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/debian/control b/debian/control index c0ac8e8f..7e62480a 100644 --- a/debian/control +++ b/debian/control @@ -1,5 +1,6 @@ Source: tvb-gdist -Maintainer: umar haruna abdullahi +Maintainer: the virtual brain +Uploaders: umar haruna abdullahi Section: python Priority: optional Build-Depends: cython, From 4e4638ed83dcf74fcdbc130d7437e286808afede Mon Sep 17 00:00:00 2001 From: umar abdullahi Date: Thu, 12 Jul 2018 07:43:28 +0100 Subject: [PATCH 3/5] remove email and name --- debian/README.Debian | 2 -- 1 file changed, 2 deletions(-) diff --git a/debian/README.Debian b/debian/README.Debian index e3942b38..d9bb8be7 100644 --- a/debian/README.Debian +++ b/debian/README.Debian @@ -42,5 +42,3 @@ installed (`apt-get install devscripts python-all-dev python-stdeb`):: and you should find a suitable deb file for your system. - - -- umar haruna abdullahi Sun, 01 Jul 2018 12:24:32 +0100 From 1c60420fc91ed242e62a4a11e33f19fdfe688937 Mon Sep 17 00:00:00 2001 From: umar abdullahi Date: Thu, 12 Jul 2018 07:45:54 +0100 Subject: [PATCH 4/5] update readme --- debian/README.Debian | 13 ------------- 1 file changed, 13 deletions(-) diff --git a/debian/README.Debian b/debian/README.Debian index d9bb8be7..9e4f02d6 100644 --- a/debian/README.Debian +++ b/debian/README.Debian @@ -29,16 +29,3 @@ Basic test could be:: Python 2.7, Cython, and a C++ compiler are required. - -Debian package -============== - -In order to produce a Debian package, assuming you have the requisite tools -installed (`apt-get install devscripts python-all-dev python-stdeb`):: - - cd debian - debuild -us -uc - cd ../../ - - -and you should find a suitable deb file for your system. From 415f9b184b5baca27b3c166d6804bc7a0f3c84b2 Mon Sep 17 00:00:00 2001 From: umar abdullahi Date: Thu, 12 Jul 2018 07:46:47 +0100 Subject: [PATCH 5/5] update source field --- debian/copyright | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/debian/copyright b/debian/copyright index 1305519a..c2434ab1 100644 --- a/debian/copyright +++ b/debian/copyright @@ -1,7 +1,7 @@ Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: tvb-library Upstream-Contact: TVB TEAM -Source: https://github.com/the-virtual-brain/tvb-library +Source: https://github.com/the-virtual-brain/tvb-geodesic Files: * Copyright: 2012-2017 Baycrest Centre for Geriatric Care ("Baycrest") and others