This is an automated email from the git hooks/post-receive script. lkajan pushed a commit to branch master in repository python-freecontact.
commit 375aa10da4ee83ea212ef77abcf2292488c63190 Author: Laszlo Kajan <[email protected]> Date: Wed Jul 17 20:30:57 2013 +0200 1.0-1 ready --- .gitignore | 6 ++++++ debian/Description | 17 +++++++++++++++++ debian/README.source | 6 ++++++ debian/changelog | 6 ++++++ debian/compat | 1 + debian/control | 19 +++++++++++++++++++ debian/copyright | 29 +++++++++++++++++++++++++++++ debian/examples | 1 + debian/rules | 27 +++++++++++++++++++++++++++ debian/source/format | 1 + debian/upstream | 10 ++++++++++ debian/watch | 4 ++++ 12 files changed, 127 insertions(+) diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..5149cf0 --- /dev/null +++ b/.gitignore @@ -0,0 +1,6 @@ +build +*.swp +files +*.debhelper.log +*.substvars +python-freecontact diff --git a/debian/Description b/debian/Description new file mode 100644 index 0000000..4a4cba2 --- /dev/null +++ b/debian/Description @@ -0,0 +1,17 @@ +FreeContact is a protein residue contact predictor optimized for speed. +Its input is a multiple sequence alignment. FreeContact can function as an +accelerated drop-in for the published contact predictors +EVfold-mfDCA of DS. Marks (2011) and +PSICOV of D. Jones (2011). + +FreeContact is accelerated by a combination of vector instructions, multiple +threads, and faster implementation of key parts. +Depending on the alignment, 10-fold or higher speedups are possible. + +A sufficiently large alignment is required for meaningful results. +As a minimum, an alignment with an effective (after-weighting) sequence count +bigger than the length of the query sequence should be used. Alignments with +tens of thousands of (effective) sequences are considered good input. + +jackhmmer(1) from the hmmer package, or hhblits(1) from hhsuite +can be used to generate the alignments, for example. diff --git a/debian/README.source b/debian/README.source new file mode 100644 index 0000000..ffd2a7d --- /dev/null +++ b/debian/README.source @@ -0,0 +1,6 @@ +python-freecontact - fast protein contact predictor - binding for Python +======================================================================== + +hardening-no-fortify-functions usr/lib/python*/dist-packages/freecontact*.so +---------------------------------------------------------------------------- +These are false positives. blhc ../python-freecontact*build does not complain. diff --git a/debian/changelog b/debian/changelog new file mode 100644 index 0000000..27f9da0 --- /dev/null +++ b/debian/changelog @@ -0,0 +1,6 @@ +python-freecontact (1.0-1) UNRELEASED; urgency=low + + * Source package automatically created by stdeb 0.6.0+git. + * Initial release (Closes: #12345) + + -- Laszlo Kajan <[email protected]> Wed, 17 Jul 2013 19:03:32 +0200 diff --git a/debian/compat b/debian/compat new file mode 100644 index 0000000..ec63514 --- /dev/null +++ b/debian/compat @@ -0,0 +1 @@ +9 diff --git a/debian/control b/debian/control new file mode 100644 index 0000000..5ba0ce7 --- /dev/null +++ b/debian/control @@ -0,0 +1,19 @@ +Source: python-freecontact +Section: python +Priority: extra +Maintainer: Debian Med Packaging Team <[email protected]> +Uploaders: Laszlo Kajan <[email protected]> +Build-Depends: debhelper (>= 9~), libboost-python-dev, libfreecontact0-dev, python-all-dev (>= 2.6.6-3~), python-all-dbg +Standards-Version: 3.9.4 +Vcs-Git: git://git.debian.org/debian-med/python-freecontact.git +Vcs-Browser: http://git.debian.org/?p=debian-med/python-freecontact.git +Homepage: http://rostlab.org/ +X-Python-Version: >= 2.6 + +Package: python-freecontact +Architecture: any +Depends: ${misc:Depends}, ${python:Depends}, ${shlibs:Depends} +Description: fast protein contact predictor - binding for Python + ${Description} + . + This package contains the Python binding. diff --git a/debian/copyright b/debian/copyright new file mode 100644 index 0000000..5441151 --- /dev/null +++ b/debian/copyright @@ -0,0 +1,29 @@ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: python-freecontact +Upstream-Contact: Laszlo Kajan <[email protected]> +Source: ftp://rostlab.org/free/ + +Files: debian/* +Copyright: 2013 Laszlo Kajan <[email protected]>, Technical University of Munich, Germany +License: GPL-3+ + +Files: * +Copyright: 2013 Laszlo Kajan <[email protected]>, Technical University of Munich, Germany +License: GPL-3+ + +License: GPL-3+ + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + . + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + . + You should have received a copy of the GNU General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + . + On Debian systems, the complete text of the GNU General + Public License version 3 can be found in `/usr/share/common-licenses/GPL-3'. diff --git a/debian/examples b/debian/examples new file mode 100644 index 0000000..d4e7101 --- /dev/null +++ b/debian/examples @@ -0,0 +1 @@ +examples/*.aln diff --git a/debian/rules b/debian/rules new file mode 100755 index 0000000..a06fcc3 --- /dev/null +++ b/debian/rules @@ -0,0 +1,27 @@ +#!/usr/bin/make -f +#export DH_VERBOSE=1 + +export CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS) +export CFLAGS:=$(shell dpkg-buildflags --get CFLAGS) +export CXXFLAGS:=$(shell dpkg-buildflags --get CXXFLAGS) +export LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS) + +Description := $(shell sed -e ':a; N; s/\n/$${Newline}/; ta' < debian/Description) + +.PHONY: override_dh_gencontrol +override_dh_gencontrol: + dh_gencontrol -- '-VDescription=$(Description)' + +.PHONY: get-orig-source +get-orig-source: + uscan --verbose --force-download --destdir=.. + +PYVER = $(shell echo -e 'import sys\nprint(str(sys.version_info.major)+"."+str(sys.version_info.minor))' | /usr/bin/python) +PYVERBDIR = $(wildcard ./build/lib.*-2.7) + +.PHONY: override_dh_auto_test +override_dh_auto_test: + PYTHONPATH=$(PYVERBDIR) ./test/test01.py + +%: + dh $@ --with python2 --buildsystem=python_distutils diff --git a/debian/source/format b/debian/source/format new file mode 100644 index 0000000..163aaf8 --- /dev/null +++ b/debian/source/format @@ -0,0 +1 @@ +3.0 (quilt) diff --git a/debian/upstream b/debian/upstream new file mode 100644 index 0000000..a0a2a48 --- /dev/null +++ b/debian/upstream @@ -0,0 +1,10 @@ +Name: python-freecontact +Contact: Laszlo Kajan <[email protected]> +Homepage: http://rostlab.org/ +Reference: + - Author: László Kaján and Thomas A. Hopf and Matúš Kalaš and Debora S. Marks and Burkhard Rost + Title: 'FreeContact: ...' + Journal: BMC Bioinformatics + Year: '201?' + +# vim:et:ts=2:ai:syntax=yaml: diff --git a/debian/watch b/debian/watch new file mode 100644 index 0000000..fbf5de4 --- /dev/null +++ b/debian/watch @@ -0,0 +1,4 @@ +# Compulsory line, this is a version 3 file +version=3 +opts=passive \ +ftp://rostlab.org/free/python-freecontact-([0-9.]+)\.tar\.gz debian uupdate -- Alioth's /git/debian-med/git-commit-notice on /srv/git.debian.org/git/debian-med/python-freecontact.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
