[med-svn] [python-freecontact] 02/10: 1.0-1 ready
Laszlo Kajan
lkajan at alioth.debian.org
Thu Sep 19 17:37:19 UTC 2013
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 <lkajan at debian.org>
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 <lkajan at debian.org> 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 <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Laszlo Kajan <lkajan at debian.org>
+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
+ ${Description}
+ .
+ This package contains the Python binding.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..5441151
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,29 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: python-freecontact
+Upstream-Contact: Laszlo Kajan <lkajan at rostlab.org>
+Source: ftp://rostlab.org/free/
+
+Files: debian/*
+Copyright: 2013 Laszlo Kajan <lkajan at rostlab.org>, Technical University of Munich, Germany
+License: GPL-3+
+
+Files: *
+Copyright: 2013 Laszlo Kajan <lkajan at rostlab.org>, Technical University of Munich, Germany
+License: GPL-3+
+
+License: GPL-3+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+ .
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 3 can be found in `/usr/share/common-licenses/GPL-3'.
diff --git a/debian/examples b/debian/examples
new file mode 100644
index 0000000..d4e7101
--- /dev/null
+++ b/debian/examples
@@ -0,0 +1 @@
+examples/*.aln
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..a06fcc3
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,27 @@
+#!/usr/bin/make -f
+#export DH_VERBOSE=1
+
+export CPPFLAGS:=$(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 <lkajan at rostlab.org>
+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
--
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