debian/0000755000000000000000000000000012216633542007172 5ustar debian/compat0000644000000000000000000000000212171561472010372 0ustar 9 debian/copyright0000644000000000000000000000230012171561472011122 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: python-freecontact Upstream-Contact: Laszlo Kajan Source: ftp://rostlab.org/free/ Files: debian/* Copyright: 2013 Laszlo Kajan , Technical University of Munich, Germany License: GPL-3+ Files: * Copyright: 2013 Laszlo Kajan , 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 . . 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/examples0000644000000000000000000000001712171561472010733 0ustar examples/*.aln debian/rules0000755000000000000000000000153512171561472010260 0ustar #!/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 debian/source/0000755000000000000000000000000012216631336010471 5ustar debian/source/format0000644000000000000000000000001412171561472011702 0ustar 3.0 (quilt) debian/source/options0000644000000000000000000000002412216631336012103 0ustar single-debian-patch debian/upstream0000644000000000000000000000047712171561472010767 0ustar Name: python-freecontact Contact: Laszlo Kajan 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: debian/watch0000644000000000000000000000022112171561472010220 0ustar # Compulsory line, this is a version 3 file version=3 opts=passive \ ftp://rostlab.org/free/python-freecontact-([0-9.]+)\.tar\.gz debian uupdate debian/Description0000644000000000000000000000155212216630606011401 0ustar 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, 8-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. debian/control0000644000000000000000000000141112216630704010567 0ustar Source: python-freecontact Section: python Priority: extra Maintainer: Debian Med Packaging Team Uploaders: Laszlo Kajan Build-Depends: debhelper (>= 9~), libboost-python-dev, libfreecontact0-dev, python-all-dev (>= 2.6.6-3~), python-all-dbg Standards-Version: 3.9.4 Homepage: http://rostlab.org/ Vcs-Git: git://anonscm.debian.org/debian-med/python-freecontact.git Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/python-freecontact.git 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. debian/changelog0000644000000000000000000000024012216633241011034 0ustar python-freecontact (1.1-1) unstable; urgency=low * Initial release (Closes: #723771). -- Laszlo Kajan Wed, 17 Jul 2013 19:03:32 +0200 debian/README.source0000644000000000000000000000057412171561472011361 0ustar 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.