[med-svn] [Git][med-team/physamp][upstream] New upstream version 1.1.0
Julien Y. Dutheil
gitlab at salsa.debian.org
Wed Apr 18 15:35:51 BST 2018
Julien Y. Dutheil pushed to branch upstream at Debian Med / physamp
Commits:
62913cc6 by Julien Y. Dutheil at 2018-04-18T16:05:29+02:00
New upstream version 1.1.0
- - - - -
7 changed files:
- CMakeLists.txt
- ChangeLog
- docs/_config.yml
- docs/physamp.texi
- physamp.spec
- physamp/AlignmentOptimizer.cpp
- physamp/PhyloSampler.cpp
Changes:
=====================================
CMakeLists.txt
=====================================
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -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
=====================================
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,8 @@
+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
=====================================
docs/_config.yml
=====================================
--- a/docs/_config.yml
+++ b/docs/_config.yml
@@ -1 +1,5 @@
-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
=====================================
--- a/docs/physamp.texi
+++ b/docs/physamp.texi
@@ -1,7 +1,7 @@
\input texinfo @c -*-texinfo-*-
@c %**start of header
@setfilename physamp.info
- at settitle PhySamp Manual 1.0.3
+ at 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
=====================================
--- a/physamp.spec
+++ b/physamp.spec
@@ -1,34 +1,31 @@
-%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 at 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 at evolbio.mpg.de> 1.0.1-1
- Compatibility update with Bio++ 2.3.1
* Fri May 26 2017 Julien Dutheil <dutheil at evolbio.mpg.de> 1.0.0-1
=====================================
physamp/AlignmentOptimizer.cpp
=====================================
--- a/physamp/AlignmentOptimizer.cpp
+++ b/physamp/AlignmentOptimizer.cpp
@@ -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
=====================================
--- a/physamp/PhyloSampler.cpp
+++ b/physamp/PhyloSampler.cpp
@@ -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;
View it on GitLab: https://salsa.debian.org/med-team/physamp/commit/62913cc63d6f099877a1a99b0d1fbf31cf746603
---
View it on GitLab: https://salsa.debian.org/med-team/physamp/commit/62913cc63d6f099877a1a99b0d1fbf31cf746603
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