[med-svn] [Git][med-team/physamp][master] 4 commits: Merge branch 'upstream' of ssh://git.debian.org/git/debian-med/physamp into upstream

Julien Y. Dutheil gitlab at salsa.debian.org
Wed Apr 18 15:35:46 BST 2018


Julien Y. Dutheil pushed to branch master at Debian Med / physamp


Commits:
1fb8db55 by Julien Y. Dutheil at 2017-09-04T20:13:21+02:00
Merge branch 'upstream' of ssh://git.debian.org/git/debian-med/physamp into upstream

- - - - -
62913cc6 by Julien Y. Dutheil at 2018-04-18T16:05:29+02:00
New upstream version 1.1.0
- - - - -
8c0f6598 by Julien Y. Dutheil at 2018-04-18T16:05:31+02:00
Update upstream source from tag 'upstream/1.1.0'

Update to upstream version '1.1.0'
with Debian dir f6b44ccc8bc13c79e99d1ec09f2af68a25b143bb
- - - - -
0f9aa36a by Julien Y. Dutheil at 2018-04-18T16:35:20+02:00
Drafted version 1.1.0.

- - - - -


10 changed files:

- CMakeLists.txt
- ChangeLog
- debian/changelog
- debian/control
- debian/rules
- 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


=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,11 +1,19 @@
-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 at 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 at univ-montp2.fr>  Wed, 18 Apr 2018 16:28:13 +0200
 
 physamp (1.0.3-1) unstable; urgency=medium
 


=====================================
debian/control
=====================================
--- a/debian/control
+++ b/debian/control
@@ -4,13 +4,13 @@ Uploaders: Andreas Tille <tille at debian.org>,
            Julien Dutheil <julien.dutheil at 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
=====================================
--- a/debian/rules
+++ b/debian/rules
@@ -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
=====================================
--- 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/compare/e826a62c1ccf54fac927dddd3831a4c2e24452b8...0f9aa36ad817145a2f563db298720039740259f6

---
View it on GitLab: https://salsa.debian.org/med-team/physamp/compare/e826a62c1ccf54fac927dddd3831a4c2e24452b8...0f9aa36ad817145a2f563db298720039740259f6
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