CMakeLists.txt

@@ -9,7 +9,7 @@ cmake_minimum_required (VERSION 2.8.11)
 project (bpp-phyl-omics CXX)
 
 # Compile options
-set (CMAKE_CXX_FLAGS "-std=c++11 -Wall -Weffc++ -Wshadow -Wconversion")
+#set (CMAKE_CXX_FLAGS "-std=c++11 -g")
 
 IF(NOT CMAKE_BUILD_TYPE)
   SET(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING
@@ -35,7 +35,7 @@ ELSE(NO_DEP_CHECK)
 #           library implements.
 # In other words, the library implements all the interface numbers in the
 # range from number current - age to current.
-SET(${PROJECT_NAME}_VERSION_CURRENT "2")
+SET(${PROJECT_NAME}_VERSION_CURRENT "3")
 SET(${PROJECT_NAME}_VERSION_REVISION "0")
 SET(${PROJECT_NAME}_VERSION_AGE "0")
 
@@ -53,8 +53,8 @@ if (CMAKE_INSTALL_PREFIX)
 endif (CMAKE_INSTALL_PREFIX)
 
 include (GNUInstallDirs)
-find_package (bpp-seq-omics 2.0.0 REQUIRED)
-find_package (bpp-phyl 11.0.0 REQUIRED)
+find_package (bpp-seq-omics 3.0.0 REQUIRED)
+find_package (bpp-phyl 12.0.0 REQUIRED)
 
 # CMake package
 set (cmake-package-location ${CMAKE_INSTALL_LIBDIR}/cmake/${PROJECT_NAME})
@@ -96,10 +96,10 @@ ENDIF(NO_DEP_CHECK)
 # Packager
 SET(CPACK_PACKAGE_NAME "libbpp-phyl-omics")
 SET(CPACK_PACKAGE_VENDOR "Bio++ Development Team")
-SET(CPACK_PACKAGE_VERSION "2.3.1")
+SET(CPACK_PACKAGE_VERSION "2.4.0")
 SET(CPACK_PACKAGE_VERSION_MAJOR "2")
-SET(CPACK_PACKAGE_VERSION_MINOR "3")
-SET(CPACK_PACKAGE_VERSION_PATCH "1")
+SET(CPACK_PACKAGE_VERSION_MINOR "4")
+SET(CPACK_PACKAGE_VERSION_PATCH "0")
 SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "The Bio++ Phylogen-Omics library")
 SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING.txt")
 SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS.txt")
@@ -108,6 +108,8 @@ SET(CPACK_SOURCE_GENERATOR "TGZ")
 # /!\ This assumes that an external build is used
 SET(CPACK_SOURCE_IGNORE_FILES 
        "/build/" 
+       "/html/"
+       "/BppPhylOmics.tag" 
        "/\\\\.git/" 
        "/\\\\.gitignore" 
        ${CPACK_SOURCE_IGNORE_FILES}

ChangeLog

+09/03/18 -*- Version 2.4.0 -*-
+
+09/03/18 Julien Dutheil
+* Removed all dynamic exception specifications
+* Increased interface number.
+
 10/12/17 -*- Version 2.3.2 -*-
 
 10/05/17 -*- Version 2.3.0. -*-

Doxyfile

@@ -38,7 +38,7 @@ PROJECT_NAME           = bpp-phyl-omics
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 2.3.0
+PROJECT_NUMBER         = 2.4.0
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a

bpp-phyl-omics.spec

-%define _basename bpp-phyl-omics
-%define _version 2.3.1
-%define _release 1
 %define _prefix /usr
 
-URL: http://biopp.univ-montp2.fr/
+URL: https://github.com/BioPP/bpp-phyl-omics
 
-Name: %{_basename}
-Version: %{_version}
-Release: %{_release}
+Name: bpp-phyl-omics
+Version: 2.4.0
+Release: 1%{?dist}
 License: CECILL-2.0
 Vendor: The Bio++ Project
-Source: http://biopp.univ-montp2.fr/repos/sources/%{_basename}-%{_version}.tar.gz
+Source: %{name}-%{version}.tar.gz
 Summary: Bio++ Sequence library: genomics components
 Group: Development/Libraries/C and C++
-Requires: bpp-core = %{_version}
-Requires: bpp-seq = %{_version}
-Requires: bpp-phyl = %{_version}
-Requires: bpp-seq-omics = %{_version}
+Requires: bpp-core = %{version}
+Requires: bpp-seq = %{version}
+Requires: bpp-phyl = %{version}
+Requires: bpp-seq-omics = %{version}
 
-BuildRoot: %{_builddir}/%{_basename}-root
+BuildRoot: %{_builddir}/%{name}-root
 BuildRequires: cmake >= 2.8.11
 BuildRequires: gcc-c++ >= 4.7.0
-BuildRequires: libbpp-core3 = %{_version}
-BuildRequires: libbpp-core-devel = %{_version}
-BuildRequires: libbpp-seq11 = %{_version}
-BuildRequires: libbpp-seq-devel = %{_version}
-BuildRequires: libbpp-phyl11 = %{_version}
-BuildRequires: libbpp-phyl-devel = %{_version}
-BuildRequires: libbpp-seq-omics2 = %{_version}
-BuildRequires: libbpp-seq-omics-devel = %{_version}
+BuildRequires: libbpp-core4 = %{version}
+BuildRequires: libbpp-core-devel = %{version}
+BuildRequires: libbpp-seq12 = %{version}
+BuildRequires: libbpp-seq-devel = %{version}
+BuildRequires: libbpp-phyl12 = %{version}
+BuildRequires: libbpp-phyl-devel = %{version}
+BuildRequires: libbpp-seq-omics3 = %{version}
+BuildRequires: libbpp-seq-omics-devel = %{version}
 
 AutoReq: yes
 AutoProv: yes
@@ -37,30 +34,30 @@ AutoProv: yes
 This library contains the genomics components of the Bio++ phylogenetics library.
 It is part of the Bio++ project.
 
-%package -n libbpp-phyl-omics2
+%package -n libbpp-phyl-omics3
 Summary: Bio++ Phylogenetics library: genomics components
 Group: Development/Libraries/C and C++
 
-%description -n libbpp-phyl-omics2
+%description -n libbpp-phyl-omics3
 This library contains the genomics components of the Bio++ phylogenetics library.
 It is part of the Bio++ project.
 
 %package -n libbpp-phyl-omics-devel
 Summary: Bio++ Phylogenetics library: genomics components
 Group: Development/Libraries/C and C++
-Requires: libbpp-phyl-omics2 = %{_version}
-Requires: libbpp-seq11 = %{_version}
-Requires: libbpp-seq-devel = %{_version}
-Requires: libbpp-core3 = %{_version}
-Requires: libbpp-core-devel = %{_version}
-Requires: libbpp-phyl11 = %{_version}
-Requires: libbpp-phyl-devel = %{_version}
-Requires: libbpp-seq-omics2 = %{_version}
-Requires: libbpp-seq-omics-devel = %{_version}
+Requires: libbpp-phyl-omics3 = %{version}
+Requires: libbpp-seq12 = %{version}
+Requires: libbpp-seq-devel = %{version}
+Requires: libbpp-core4 = %{version}
+Requires: libbpp-core-devel = %{version}
+Requires: libbpp-phyl12 = %{version}
+Requires: libbpp-phyl-devel = %{version}
+Requires: libbpp-seq-omics3 = %{version}
+Requires: libbpp-seq-omics-devel = %{version}
 
 %description -n libbpp-phyl-omics-devel
 The libbpp-phyl-omics-devel package contains the header files and static libraries for
-building applications which use %{_basename}.
+building applications which use %{name}.
 
 %prep
 %setup -q
@@ -77,11 +74,11 @@ make DESTDIR=$RPM_BUILD_ROOT install
 %clean
 rm -rf $RPM_BUILD_ROOT
 
-%post -n libbpp-phyl-omics2 -p /sbin/ldconfig
+%post -n libbpp-phyl-omics3 -p /sbin/ldconfig
 
-%postun -n libbpp-phyl-omics2 -p /sbin/ldconfig
+%postun -n libbpp-phyl-omics3 -p /sbin/ldconfig
 
-%files -n libbpp-phyl-omics2
+%files -n libbpp-phyl-omics3
 %defattr(-,root,root)
 %doc AUTHORS.txt COPYING.txt INSTALL.txt ChangeLog
 %{_prefix}/%{_lib}/lib*.so.*
@@ -97,6 +94,9 @@ rm -rf $RPM_BUILD_ROOT
 %{_prefix}/include/*
 
 %changelog
+* Mon Mar 12 2018 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.4.0-1
+- Increased interface number
+- Removed dynamic exceptions specifications.
 * Tue Jun 06 2017 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.3.1-1
 - Increased interface number
 * Wed May 10 2017 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.3.0-1

debian/changelog

+libbpp-phyl-omics (2.4.0-1) UNRELEASED; urgency=medium
+
+  * New upstream version
+  * Versioned Build-Depends: d-shlibs (>= 0.82)
+
+ -- Julien Dutheil <julien.dutheil@univ-montp2.fr>  Thu, 29 Mar 2018 14:10:42 +0200
+
 libbpp-phyl-omics (2.3.2-1) unstable; urgency=medium
 
   [ Julien Dutheil ]

debian/control

@@ -6,9 +6,9 @@ Section: science
 Priority: optional
 Build-Depends: debhelper (>= 11~),
                cmake,
-               d-shlibs (>= 0.80),
-               libbpp-phyl-dev (>= 2.3.2),
-               libbpp-seq-omics-dev (>= 2.3.2)
+               d-shlibs (>= 0.82),
+               libbpp-phyl-dev (>= 2.4.0),
+               libbpp-seq-omics-dev (>= 2.4.0)
 Standards-Version: 4.1.3
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libbpp-phyl-omics.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/libbpp-phyl-omics.git
@@ -17,10 +17,10 @@ Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
 Package: libbpp-phyl-omics-dev
 Architecture: any
 Section: libdevel
-Depends: libbpp-phyl-omics2 (= ${binary:Version}),
+Depends: libbpp-phyl-omics3 (= ${binary:Version}),
          ${misc:Depends},
-         libbpp-phyl-dev (>= 2.3.2),
-         libbpp-seq-omics-dev (>= 2.3.2)
+         libbpp-phyl-dev (>= 2.4.0),
+         libbpp-seq-omics-dev (>= 2.4.0)
 Description: Bio++ Phylogenetics library: genomics components (development files)
  Bio++ is a set of C++ libraries for Bioinformatics, including sequence
  analysis, phylogenetics, molecular evolution and population genetics.
@@ -31,11 +31,13 @@ Description: Bio++ Phylogenetics library: genomics components (development files
  This package contains the static library and the header files of the
  Bio++ classes dedicated to genomic phylogeny.
 
-Package: libbpp-phyl-omics2
+Package: libbpp-phyl-omics3
 Architecture: any
+Multi-Arch: same
 Section: libs
 Depends: ${shlibs:Depends},
          ${misc:Depends}
+Pre-Depends: ${misc:Pre-Depends}
 Description: Bio++ Phylogenetics library: genomics components
  Bio++ is a set of C++ libraries for Bioinformatics, including sequence
  analysis, phylogenetics, molecular evolution and population genetics.

debian/copyright

 Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Name: B++-Phyl-Omics
+Upstream-Name: Bpp-Phyl-Omics
 Upstream-Contact: Julien Yann Dutheil <julien.dutheil@univ-montp2.fr>
-Source: http://biopp.univ-montp2.fr/Repositories/sources/
+Source: https://github.com/BioPP/bpp-phyl-omics/
 
 Files: *
 Copyright: 2010-2016 Julien Yann Dutheil <julien.dutheil@univ-montp2.fr>

debian/patches/unforce-cxxflags.patch

@@ -11,7 +11,7 @@ Comment: Upstream version 2.3.0 now has additional -std=c++11 which might
  
  # Compile options
 -set (CMAKE_CXX_FLAGS "-std=c++11 -Wall -Weffc++ -Wshadow -Wconversion")
-+set (CMAKE_CXX_FLAGS "-std=c++11 -Wno-deprecated -g")
++#set (CMAKE_CXX_FLAGS "-std=c++11 -g")
  
  IF(NOT CMAKE_BUILD_TYPE)
    SET(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING

debian/rules

@@ -4,6 +4,8 @@
 
 export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 
+CMAKE_EXTRA_FLAGS += -DBUILD_TESTING=OFF
+
 %:
 	dh $@
 

src/Bpp/Seq/Io/Maf/AbstractDistanceEstimationMafIterator.h

@@ -69,7 +69,7 @@ class AbstractDistanceEstimationMafIterator:
     {}
 
   private:
-    MafBlock* analyseCurrentBlock_() throw (Exception)
+    MafBlock* analyseCurrentBlock_()
     {
       MafBlock* block = iterator_->nextBlock();
       if (!block) return 0;

src/Bpp/Seq/Io/Maf/AbstractPhylogenyReconstructionMafIterator.h

@@ -63,7 +63,7 @@ class AbstractPhylogenyReconstructionMafIterator:
   virtual ~AbstractPhylogenyReconstructionMafIterator() {}
 
   private:
-    MafBlock* analyseCurrentBlock_() throw (Exception)
+    MafBlock* analyseCurrentBlock_()
     {
       MafBlock* block = iterator_->nextBlock();
       if (!block) return 0;

src/Bpp/Seq/Io/Maf/DistanceBasedPhylogenyReconstructionMafIterator.cpp

@@ -44,7 +44,7 @@ knowledge of the CeCILL license and that you accept its terms.
 using namespace bpp;
 using namespace std;
 
-Tree* DistanceBasedPhylogenyReconstructionMafIterator::buildTreeForBlock(const MafBlock& block) throw (Exception)
+Tree* DistanceBasedPhylogenyReconstructionMafIterator::buildTreeForBlock(const MafBlock& block)
 {
   //First get the distance matrix for this block:
   if (!block.hasProperty(distanceProperty_))

src/Bpp/Seq/Io/Maf/DistanceBasedPhylogenyReconstructionMafIterator.h

@@ -79,7 +79,7 @@ class DistanceBasedPhylogenyReconstructionMafIterator:
     const std::string& getDistanceProperty() const { return distanceProperty_; }
 
     std::string getPropertyName() const { return builder_->getName(); }
-    Tree* buildTreeForBlock(const MafBlock& block) throw (Exception);
+    Tree* buildTreeForBlock(const MafBlock& block);
 };
 
 } //end of namespace bpp.

src/Bpp/Seq/Io/Maf/FilterTreeMafIterator.cpp

@@ -42,7 +42,7 @@ knowledge of the CeCILL license and that you accept its terms.
 using namespace bpp;
 using namespace std;
 
-MafBlock* FilterTreeMafIterator::analyseCurrentBlock_() throw (Exception)
+MafBlock* FilterTreeMafIterator::analyseCurrentBlock_()
 {
   bool test = false;
   currentBlock_ = iterator_->nextBlock();

src/Bpp/Seq/Io/Maf/FilterTreeMafIterator.h

@@ -88,9 +88,9 @@ class FilterTreeMafIterator:
 
 
   public:
-    MafBlock* analyseCurrentBlock_() throw (Exception);
+    MafBlock* analyseCurrentBlock_();
 
-    MafBlock* nextRemovedBlock() throw (Exception) {
+    MafBlock* nextRemovedBlock() {
       if (trashBuffer_.size() == 0) return 0;
       MafBlock* block = trashBuffer_.front();
       trashBuffer_.pop_front();

src/Bpp/Seq/Io/Maf/OutputDistanceMatrixMafIterator.h

@@ -87,7 +87,7 @@ class OutputDistanceMatrixMafIterator:
 
 
   public:
-    MafBlock* analyseCurrentBlock_() throw (Exception) {
+    MafBlock* analyseCurrentBlock_() {
       currentBlock_ = iterator_->nextBlock();
       if (output_ && currentBlock_)
         writeBlock_(*output_, *currentBlock_);

src/Bpp/Seq/Io/Maf/OutputTreeMafIterator.h

@@ -95,7 +95,7 @@ class OutputTreeMafIterator:
 
 
   public:
-    MafBlock* analyseCurrentBlock_() throw (Exception) {
+    MafBlock* analyseCurrentBlock_() {
       currentBlock_ = iterator_->nextBlock();
       if (output_ && currentBlock_)
         writeBlock_(*output_, *currentBlock_);

src/Bpp/Seq/Io/Maf/TreeManipulationMafIterators.cpp

@@ -42,7 +42,7 @@ knowledge of the CeCILL license and that you accept its terms.
 using namespace bpp;
 using namespace std;
 
-MafBlock* TreeManipulationMafIterator::analyseCurrentBlock_() throw (Exception)
+MafBlock* TreeManipulationMafIterator::analyseCurrentBlock_()
 {
   currentBlock_ = iterator_->nextBlock();
   if (currentBlock_) {
@@ -60,7 +60,7 @@ MafBlock* TreeManipulationMafIterator::analyseCurrentBlock_() throw (Exception)
 }
 
 
-void NewOutgroupMafIterator::manipulateTree_(TreeTemplate<Node>* tree) throw (Exception)
+void NewOutgroupMafIterator::manipulateTree_(TreeTemplate<Node>* tree)
 {
   vector<Node*> leaves = tree->getLeaves();
   Node* outgroup = 0;
@@ -79,7 +79,7 @@ void NewOutgroupMafIterator::manipulateTree_(TreeTemplate<Node>* tree) throw (Ex
 }
 
 
-void DropSpeciesMafIterator::manipulateTree_(TreeTemplate<Node>* tree) throw (Exception)
+void DropSpeciesMafIterator::manipulateTree_(TreeTemplate<Node>* tree)
 {
   vector<Node*> leaves = tree->getLeaves();
   for (size_t i = 0; i < leaves.size(); ++i) {

src/Bpp/Seq/Io/Maf/TreeManipulationMafIterators.h

@@ -64,10 +64,10 @@ class TreeManipulationMafIterator:
     {}
 
   public:
-    MafBlock* analyseCurrentBlock_() throw (Exception);
+    MafBlock* analyseCurrentBlock_();
 
   protected:
-    virtual void manipulateTree_(TreeTemplate<Node>* tree) throw (Exception) = 0;
+    virtual void manipulateTree_(TreeTemplate<Node>* tree) = 0;
 
 };
 
@@ -89,7 +89,7 @@ class NewOutgroupMafIterator:
     {}
 
   private:
-    void manipulateTree_(TreeTemplate<Node>* tree) throw (Exception);
+    void manipulateTree_(TreeTemplate<Node>* tree);
 
 };
 
@@ -111,7 +111,7 @@ class DropSpeciesMafIterator:
     {}
 
   private:
-    void manipulateTree_(TreeTemplate<Node>* tree) throw (Exception);
+    void manipulateTree_(TreeTemplate<Node>* tree);
 
 };