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CMakeLists.txt
View file @ 0f9aa36a
......@@ -59,6 +59,7 @@ else ()
# Generate command line args (always add -c to output compressed file to stdout)
if (${COMPRESS_PROGRAM} STREQUAL "gzip")
# -n for no timestamp in files (reproducible builds)
# -9 for maximum compression (lintian error)
set (COMPRESS_ARGS -c9n)
else ()
set (COMPRESS_ARGS -c)
......@@ -73,7 +74,7 @@ IF (CMAKE_INSTALL_PREFIX)
ENDIF (CMAKE_INSTALL_PREFIX)
include (GNUInstallDirs)
find_package (bpp-phyl 11.0.0 REQUIRED)
find_package (bpp-phyl 12.0.0 REQUIRED)
# Subdirectories
......@@ -86,10 +87,10 @@ ENDIF(NO_DEP_CHECK)
# Packager
SET(CPACK_PACKAGE_NAME "physamp")
SET(CPACK_PACKAGE_VENDOR "Julien Y. Dutheil")
SET(CPACK_PACKAGE_VERSION "1.0.3")
SET(CPACK_PACKAGE_VERSION "1.1.0")
SET(CPACK_PACKAGE_VERSION_MAJOR "1")
SET(CPACK_PACKAGE_VERSION_MINOR "0")
SET(CPACK_PACKAGE_VERSION_PATCH "3")
SET(CPACK_PACKAGE_VERSION_MINOR "1")
SET(CPACK_PACKAGE_VERSION_PATCH "0")
SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "The Phylogenetic Sampler package")
SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/LICENSE")
SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS")
......
ChangeLog
View file @ 0f9aa36a
14/03/18 -*- Version 1.1.0 -*-
14/03/18 Julien Dutheil
* Compatibility update Bio++ 2.4.0.
30/03/15 -*- Version 0.2.0 -*-
30/03/15 Julien Dutheil
......
debian/changelog
View file @ 0f9aa36a
physamp (1.0.3-2) UNRELEASED; urgency=medium
physamp (1.1.0-1) UNRELEASED; urgency=medium
[ Steffen Moeller ]
* shortened single line description
* debian/upstream/metadata:
- reference to paper
- stated that there are no entries in catalogs
-- Steffen Moeller <moeller@debian.org> Mon, 25 Sep 2017 14:46:05 +0200
[ Julien Y. Dutheil ]
* New upstream version.
* Compiles with -DCMAKE_BUILD_TYPE=RelWithDebInfo to generate debug info
(lintian warning)
* Point Vcs-fields to salsa.debian.org
* Standards-Version: 4.1.4
-- Julien Dutheil <julien.dutheil@univ-montp2.fr> Wed, 18 Apr 2018 16:28:13 +0200
physamp (1.0.3-1) unstable; urgency=medium
......
debian/control
View file @ 0f9aa36a
......@@ -4,13 +4,13 @@ Uploaders: Andreas Tille <tille@debian.org>,
Julien Dutheil <julien.dutheil@univ-montp2.fr>
Section: science
Priority: optional
Build-Depends: debhelper (>= 10),
Build-Depends: debhelper (>= 11~),
cmake,
texinfo,
libbpp-phyl-dev (>= 2.3.1)
Standards-Version: 4.1.0
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/physamp.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/physamp.git
libbpp-phyl-dev (>= 2.4.0)
Standards-Version: 4.1.4
Vcs-Browser: https://salsa.debian.org/med-team/physamp.git
Vcs-Git: https://salsa.debian.org/med-team/physamp.git
Homepage: https://jydu.github.io/physamp/
Package: physamp
......
debian/rules
View file @ 0f9aa36a
......@@ -7,3 +7,8 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+bindnow
%:
dh $@
override_dh_auto_configure:
dh_auto_configure -- -DCMAKE_BUILD_TYPE=RelWithDebInfo
docs/_config.yml
View file @ 0f9aa36a
theme: jekyll-theme-slate
\ No newline at end of file
theme: jekyll-theme-slate
title: PhySamp
description: Phylogenetic Sampling and Optimization of Sequence Alignments
show_downloads: true
share: true
docs/physamp.texi
View file @ 0f9aa36a
\input texinfo @c -*-texinfo-*-
@c %**start of header
@setfilename physamp.info
@settitle PhySamp Manual 1.0.3
@settitle PhySamp Manual 1.1.0
@documentencoding UTF-8
@afourpaper
@dircategory Science Biology Genetics
......@@ -13,9 +13,9 @@
@copying
This is the manual of the PhySamp package, version 1.0.3.
This is the manual of the PhySamp package, version 1.1.0.
Copyright @copyright{} 2017 Julien Y. Dutheil
Copyright @copyright{} 2018 Julien Y. Dutheil
@end copying
@titlepage
......
physamp.spec
View file @ 0f9aa36a
%define _basename physamp
%define _version 1.0.1
%define _release 1
%define _prefix /usr
URL: https://github.com/jydu/maffilter
URL: https://github.com/jydu/physamp
Name: %{_basename}
Version: %{_version}
Release: %{_release}
Name: physamp
Version: 1.1.0
Release: 1%{?dist}
License: GPL-3.0
Vendor: Julien Dutheil
Source: %{_basename}-%{_version}.tar.gz
Source: %{name}-%{version}.tar.gz
Summary: The PhySamp package
Group: Productivity/Scientific/Other
Requires: libbpp-phyl11 = 2.3.1
Requires: libbpp-seq11 = 2.3.1
Requires: libbpp-core3 = 2.3.1
Requires: libbpp-phyl12 = 2.4.0
Requires: libbpp-seq12 = 2.4.0
Requires: libbpp-core4 = 2.4.0
BuildRoot: %{_builddir}/%{_basename}-root
BuildRoot: %{_builddir}/%{name}-root
BuildRequires: cmake >= 2.8.11
BuildRequires: gcc-c++ >= 4.7.0
BuildRequires: groff
BuildRequires: texinfo >= 4.0.0
BuildRequires: libbpp-core3 = 2.3.1
BuildRequires: libbpp-core-devel = 2.3.1
BuildRequires: libbpp-seq11 = 2.3.1
BuildRequires: libbpp-seq-devel = 2.3.1
BuildRequires: libbpp-phyl11 = 2.3.1
BuildRequires: libbpp-phyl-devel = 2.3.1
BuildRequires: libbpp-core4 = 2.4.0
BuildRequires: libbpp-core-devel = 2.4.0
BuildRequires: libbpp-seq12 = 2.4.0
BuildRequires: libbpp-seq-devel = 2.4.0
BuildRequires: libbpp-phyl12 = 2.4.0
BuildRequires: libbpp-phyl-devel = 2.4.0
AutoReq: yes
......@@ -80,6 +77,9 @@ rm -rf $RPM_BUILD_ROOT
%{_prefix}/share/man/man1/bppphysamp.1.*
%changelog
* Wed Mar 14 2018 Julien Dutheil <dutheil@evolbio.mpg.de> 1.1.0-1
- Compatibility update with Bio++ 2.4.0
- More options in branch panel
* Tue Jun 06 2017 Julien Dutheil <dutheil@evolbio.mpg.de> 1.0.1-1
- Compatibility update with Bio++ 2.3.1
* Fri May 26 2017 Julien Dutheil <dutheil@evolbio.mpg.de> 1.0.0-1
......
physamp/AlignmentOptimizer.cpp
View file @ 0f9aa36a
......@@ -401,8 +401,8 @@ class InputSelector: public Selector {
int main(int args, char ** argv)
{
cout << "******************************************************************" << endl;
cout << "* Bio++ Alignment Optimizer, version 1.0.2. *" << endl;
cout << "* Author: J. Dutheil Last Modif. 20/07/17 *" << endl;
cout << "* Bio++ Alignment Optimizer, version 1.1.0. *" << endl;
cout << "* Author: J. Dutheil Last Modif. 14/03/18 *" << endl;
cout << "* E. Figuet *" << endl;
cout << "******************************************************************" << endl;
cout << endl;
......
physamp/PhyloSampler.cpp
View file @ 0f9aa36a
......@@ -83,8 +83,8 @@ class Test {
int main(int args, char ** argv)
{
cout << "******************************************************************" << endl;
cout << "* Bio++ Phylogenetic Sampler, version 1.0.2. *" << endl;
cout << "* Author: J. Dutheil Last Modif. 20/07/17 *" << endl;
cout << "* Bio++ Phylogenetic Sampler, version 1.1.0. *" << endl;
cout << "* Author: J. Dutheil Last Modif. 14/03/18 *" << endl;
cout << "******************************************************************" << endl;
cout << endl;
......