CMakeLists.txt

@@ -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(${PROJECT_NAME}_VERSION_CURRENT "7")
+SET(${PROJECT_NAME}_VERSION_CURRENT "8")
 SET(${PROJECT_NAME}_VERSION_REVISION "0")
 SET(${PROJECT_NAME}_VERSION_AGE "0")
 
@@ -53,7 +53,7 @@ if (CMAKE_INSTALL_PREFIX)
 endif (CMAKE_INSTALL_PREFIX)
 
 include (GNUInstallDirs)
-find_package (bpp-seq 11.0.0 REQUIRED)
+find_package (bpp-seq 12.0.0 REQUIRED)
 
 # CMake package
 set (cmake-package-location ${CMAKE_INSTALL_LIBDIR}/cmake/${PROJECT_NAME})
@@ -95,10 +95,10 @@ ENDIF(NO_DEP_CHECK)
 # Packager
 SET(CPACK_PACKAGE_NAME "libbpp-popgen")
 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++ Population Genetics library")
 SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING.txt")
 SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS.txt")
@@ -107,6 +107,8 @@ SET(CPACK_SOURCE_GENERATOR "TGZ")
 # /!\ This assumes that an external build is used
 SET(CPACK_SOURCE_IGNORE_FILES 
        "/build/" 
+       "/html/" 
+       "/PopGen.tag" 
        "/\\\\.git/" 
        "/\\\\.gitignore" 
        ${CPACK_SOURCE_IGNORE_FILES}

ChangeLog

+26/02/18 -*- Version 2.4.0 -*-
+
+25/02/18 Julien Dutheil
+* Removed all dynamic exception specification (gcc 7)
+
 24/11/17 Julien Dutheil
 * Fixed error in tajima83.
 

Doxyfile

@@ -38,7 +38,7 @@ PROJECT_NAME           = bpp-popgen
 # 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-popgen.spec

-%define _basename bpp-popgen
-%define _version 2.3.1
-%define _release 1
 %define _prefix /usr
 
-URL: http://biopp.univ-montp2.fr/
+URL: https://github.com/BioPP/bpp-seq
 
-Name: %{_basename}
-Version: %{_version}
-Release: %{_release}
+Name: bpp-popgen
+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++ Population Genetics library
 Group: Development/Libraries/C and C++
-Requires: bpp-core = %{_version}
-Requires: bpp-seq = %{_version}
+Requires: bpp-core = %{version}
+Requires: bpp-seq = %{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-core4 = %{version}
+BuildRequires: libbpp-core-devel = %{version}
+BuildRequires: libbpp-seq12 = %{version}
+BuildRequires: libbpp-seq-devel = %{version}
 
 AutoReq: yes
 AutoProv: yes
@@ -31,26 +28,26 @@ AutoProv: yes
 This library contains utilitary and classes for population genetics analysis. 
 It is part of the Bio++ project.
 
-%package -n libbpp-popgen7
+%package -n libbpp-popgen8
 Summary: Bio++ Population Genetics library
 Group: Development/Libraries/C and C++
 
-%description -n libbpp-popgen7
+%description -n libbpp-popgen8
 This library contains utilitary and classes for population genetics and molecular evolution analysis.
 It is part of the Bio++ project.
 
 %package -n libbpp-popgen-devel
 Summary: Libraries, includes to develop applications with %{_basename}
 Group: Development/Libraries/C and C++
-Requires: libbpp-popgen7 = %{_version}
-Requires: libbpp-seq11 = %{_version}
-Requires: libbpp-seq-devel = %{_version}
-Requires: libbpp-core3 = %{_version}
-Requires: libbpp-core-devel = %{_version}
+Requires: libbpp-popgen8 = %{version}
+Requires: libbpp-seq12 = %{version}
+Requires: libbpp-seq-devel = %{version}
+Requires: libbpp-core4 = %{version}
+Requires: libbpp-core-devel = %{version}
 
 %description -n libbpp-popgen-devel
 The libbpp-popgen-devel package contains the header files and static libraries for
-building applications which use %{_basename}.
+building applications which use %{name}.
 
 %prep
 %setup -q
@@ -67,11 +64,11 @@ make DESTDIR=$RPM_BUILD_ROOT install
 %clean
 rm -rf $RPM_BUILD_ROOT
 
-%post -n libbpp-popgen7 -p /sbin/ldconfig
+%post -n libbpp-popgen8 -p /sbin/ldconfig
 
-%postun -n libbpp-popgen7 -p /sbin/ldconfig
+%postun -n libbpp-popgen8 -p /sbin/ldconfig
 
-%files -n libbpp-popgen7
+%files -n libbpp-popgen8
 %defattr(-,root,root)
 %doc AUTHORS.txt COPYING.txt INSTALL.txt ChangeLog
 %{_prefix}/%{_lib}/lib*.so.*
@@ -87,6 +84,9 @@ rm -rf $RPM_BUILD_ROOT
 %{_prefix}/include/*
 
 %changelog
+* Mon Mar 12 2018 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.4.0-1
+- Remove deprecated dynamic exception specifications
+- Increased interface number
 * 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-popgen (2.4.0-1) UNRELEASED; urgency=medium
+
+  * New upstream version
+
+ -- Julien Y. Dutheil <julien.dutheil@univ-montp2.fr>  Tue, 27 Mar 2018 21:46:45 +0200
+
 libbpp-popgen (2.3.2-1) unstable; urgency=medium
 
   [ Julien Dutheil ]

debian/control

@@ -7,8 +7,8 @@ Priority: optional
 Build-Depends: debhelper (>= 11~),
                cmake,
                d-shlibs (>= 0.80),
-               libbpp-core-dev (>= 2.3.2),
-               libbpp-seq-dev (>= 2.3.2)
+               libbpp-core-dev (>= 2.4.0),
+               libbpp-seq-dev (>= 2.4.0)
 Standards-Version: 4.1.3
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libbpp-popgen.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/libbpp-popgen.git
@@ -17,10 +17,10 @@ Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
 Package: libbpp-popgen-dev
 Architecture: any
 Section: libdevel
-Depends: libbpp-popgen7 (= ${binary:Version}),
+Depends: libbpp-popgen8 (= ${binary:Version}),
          ${misc:Depends},
-         libbpp-core-dev (>= 2.3.2),
-         libbpp-seq-dev (>= 2.3.2)
+         libbpp-core-dev (>= 2.4.0),
+         libbpp-seq-dev (>= 2.4.0)
 Description: Bio++ Population Genetics library development files
  Bio++ is a set of C++ libraries for Bioinformatics, including sequence
  analysis, phylogenetics, molecular evolution and population genetics.
@@ -31,7 +31,7 @@ Description: Bio++ Population Genetics library development files
  This package contains the static library and the header files of the
  Bio++ Population Genetics classes.
 
-Package: libbpp-popgen7
+Package: libbpp-popgen8
 Architecture: any
 Multi-Arch: same
 Section: libs

debian/copyright

 Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Name: B++-Popgen
+Upstream-Name: Bpp-PopGen
 Upstream-Contact: Julien Yann Dutheil <julien.dutheil@univ-montp2.fr>
-Source: http://biopp.univ-montp2.fr/Repositories/sources/
+Source: https://github.com/BioPP/bpp-popgen/
 
 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

src/Bpp/PopGen/BiAlleleMonolocusGenotype.cpp

@@ -52,7 +52,7 @@ BiAlleleMonolocusGenotype::BiAlleleMonolocusGenotype(
   allele_index_[1] = second_allele_index;
 }
 
-BiAlleleMonolocusGenotype::BiAlleleMonolocusGenotype(std::vector<size_t> allele_index) throw (BadSizeException) : allele_index_(vector<size_t>(2))
+BiAlleleMonolocusGenotype::BiAlleleMonolocusGenotype(std::vector<size_t> allele_index) : allele_index_(vector<size_t>(2))
 {
   if (allele_index.size() != 2)
     throw BadSizeException("BiAlleleMonolocusGenotype::BiAlleleMonolocusGenotype: allele_index must contain two values.", allele_index.size(), 2);

src/Bpp/PopGen/BiAlleleMonolocusGenotype.h

@@ -72,7 +72,7 @@ public:
   /**
    * @brief Build a monolocus genotype containing two alleles.
    */
-  BiAlleleMonolocusGenotype(std::vector<size_t> allele_index) throw (BadSizeException);
+  BiAlleleMonolocusGenotype(std::vector<size_t> allele_index);
 
   /**
    * @brief Copy constructor.

src/Bpp/PopGen/DataSet/AnalyzedLoci.cpp

@@ -77,7 +77,6 @@ AnalyzedLoci::~AnalyzedLoci()
 void AnalyzedLoci::setLocusInfo(
   size_t locus_position,
   const LocusInfo& locus)
-throw (IndexOutOfBoundsException)
 {
   if (locus_position < loci_.size())
     loci_[locus_position] = new LocusInfo(locus);
@@ -90,7 +89,6 @@ throw (IndexOutOfBoundsException)
 
 size_t AnalyzedLoci::getLocusInfoPosition(
   const std::string& locus_name) const
-throw (BadIdentifierException)
 {
   for (size_t i = 0; i < loci_.size(); i++)
   {
@@ -104,7 +102,6 @@ throw (BadIdentifierException)
 
 const LocusInfo& AnalyzedLoci::getLocusInfoByName(
   const std::string& locus_name) const
-throw (BadIdentifierException)
 {
   for (size_t i = 0; i < loci_.size(); i++)
   {
@@ -119,7 +116,6 @@ throw (BadIdentifierException)
 
 const LocusInfo& AnalyzedLoci::getLocusInfoAtPosition(
   size_t locus_position) const
-throw (Exception)
 {
   if (locus_position >= loci_.size())
     throw IndexOutOfBoundsException("AnalyzedLoci::getLocusInfoAtPosition: locus_position out of bounds.", locus_position, 0, loci_.size());
@@ -134,7 +130,6 @@ throw (Exception)
 // AlleleInfo
 void AnalyzedLoci::addAlleleInfoByLocusName(const std::string& locus_name,
                                             const AlleleInfo& allele)
-throw (Exception)
 {
   bool locus_found = false;
   for (vector<LocusInfo*>::iterator it = loci_.begin(); it != loci_.end(); it++)
@@ -161,7 +156,6 @@ throw (Exception)
 
 void AnalyzedLoci::addAlleleInfoByLocusPosition(size_t locus_position,
                                                 const AlleleInfo& allele)
-throw (Exception)
 {
   if (locus_position < loci_.size())
   {
@@ -194,7 +188,6 @@ std::vector<size_t> AnalyzedLoci::getNumberOfAlleles() const
 /******************************************************************************/
 
 unsigned int AnalyzedLoci::getPloidyByLocusName(const std::string& locus_name) const
-throw (LocusNotFoundException)
 {
   for (size_t i = 0; i < loci_.size(); i++)
   {
@@ -208,7 +201,6 @@ throw (LocusNotFoundException)
 /******************************************************************************/
 
 unsigned int AnalyzedLoci::getPloidyByLocusPosition(size_t locus_position) const
-throw (IndexOutOfBoundsException)
 {
   if (locus_position >= loci_.size())
     throw IndexOutOfBoundsException("AnalyzedLoci::getPloidyByLocusPosition: locus_position out of bounds.", locus_position, 0, loci_.size());

src/Bpp/PopGen/DataSet/AnalyzedLoci.h

@@ -90,24 +90,21 @@ public:
    *
    * @throw IndexOutOfBoundsException if locus_position is out of bounds.
    */
-  void setLocusInfo(size_t locus_position, const LocusInfo& locus)
-  throw (IndexOutOfBoundsException);
+  void setLocusInfo(size_t locus_position, const LocusInfo& locus);
 
   /**
    * @brief Get the position of a LocusInfo.
    *
    * @throw BadIdentifierException if locus_name is not found.
    */
-  size_t getLocusInfoPosition(const std::string& locus_name) const
-  throw (BadIdentifierException);
+  size_t getLocusInfoPosition(const std::string& locus_name) const;
 
   /**
    * @brief Get a LocusInfo by name.
    *
    * @throw BadIdentifierException if locus_name is not found.
    */
-  const LocusInfo& getLocusInfoByName(const std::string& locus_name) const
-  throw (BadIdentifierException);
+  const LocusInfo& getLocusInfoByName(const std::string& locus_name) const;
 
   /**
    * @brief Get a LocusInfo by its position.
@@ -115,8 +112,7 @@ public:
    * @throw NullPointerException if the LocusInfo is not difined.
    * @throw IndexOutOfBoundsException if locus_position is out of bounds.
    */
-  const LocusInfo& getLocusInfoAtPosition(size_t locus_position) const
-  throw (Exception);
+  const LocusInfo& getLocusInfoAtPosition(size_t locus_position) const;
 
   /**
    * @brief Add an AlleleInfo to a LocusInfo by LocusInfo name.
@@ -125,8 +121,7 @@ public:
    * @throw LocusNotFoundException if locus_name is not found.
    */
   void addAlleleInfoByLocusName(const std::string& locus_name,
-                                const AlleleInfo& allele)
-  throw (Exception);
+                                const AlleleInfo& allele);
 
   /**
    * @brief Add an AlleleInfo to a LocusInfo by its position.
@@ -135,8 +130,7 @@ public:
    * @throw IndexOutOfBoundsException if locus_position is out of bounds.
    */
   void addAlleleInfoByLocusPosition(size_t locus_position,
-                                    const AlleleInfo& allele)
-  throw (Exception);
+                                    const AlleleInfo& allele);
 
   /**
    * @brief Get the number of loci.
@@ -153,16 +147,14 @@ public:
    *
    * @throw LocusNotFoundException if locus_name is not found.
    */
-  unsigned int getPloidyByLocusName(const std::string& locus_name) const
-  throw (LocusNotFoundException);
+  unsigned int getPloidyByLocusName(const std::string& locus_name) const;
 
   /**
    * @brief Get the ploidy of a locus by its position.
    *
    * @throw IndexOutOfBoundsException if locus_position is out of bounds.
    */
-  unsigned int getPloidyByLocusPosition(size_t locus_position) const
-  throw (IndexOutOfBoundsException);
+  unsigned int getPloidyByLocusPosition(size_t locus_position) const;
 };
 } // end of namespace bpp;
 

src/Bpp/PopGen/DataSet/AnalyzedSequences.cpp

@@ -90,7 +90,7 @@ void AnalyzedSequences::setAlphabet(const Alphabet* alpha)
   autoset_ = false;
 }
 
-void AnalyzedSequences::setAlphabet(const std::string& alpha_type) throw (Exception)
+void AnalyzedSequences::setAlphabet(const std::string& alpha_type)
 {
   if (alpha_type != string("DNA") && alpha_type != string("RNA") && alpha_type != string("PROTEIN"))
     throw Exception(string("AnalyzedSequences::setAlphabet: bad alphabet type. (") + alpha_type + string(")."));

src/Bpp/PopGen/DataSet/AnalyzedSequences.h

@@ -95,7 +95,7 @@ public:
   /**
    * @brief Set the alphabet used for the sequences by alphabet type.
    */
-  void setAlphabet(const std::string& alpha_type) throw (Exception);
+  void setAlphabet(const std::string& alpha_type);
 
   /**
    * @brief Get the alphabet.

src/Bpp/PopGen/DataSet/DataSetTools.cpp

@@ -42,7 +42,7 @@
 using namespace bpp;
 using namespace std;
 
-std::unique_ptr<DataSet> DataSetTools::buildDataSet(const OrderedSequenceContainer& osc) throw (Exception)
+std::unique_ptr<DataSet> DataSetTools::buildDataSet(const OrderedSequenceContainer& osc)
 {
   unique_ptr<DataSet> d_s(new DataSet());
   d_s->addEmptyGroup(0);
@@ -61,7 +61,7 @@ std::unique_ptr<DataSet> DataSetTools::buildDataSet(const OrderedSequenceContain
   return d_s;
 }
 
-std::unique_ptr<DataSet> DataSetTools::buildDataSet(const PolymorphismSequenceContainer& psc) throw (Exception)
+std::unique_ptr<DataSet> DataSetTools::buildDataSet(const PolymorphismSequenceContainer& psc)
 {
   unique_ptr<DataSet> d_s(new DataSet());
   set<size_t> grp_ids = psc.getAllGroupsIds();

src/Bpp/PopGen/DataSet/DataSetTools.h

@@ -67,12 +67,12 @@ public:
   /**
    * @brief General method to build a DataSet from an OrderedSequenceContainer.
    */
-  static std::unique_ptr<DataSet> buildDataSet(const OrderedSequenceContainer& osc) throw (Exception);
+  static std::unique_ptr<DataSet> buildDataSet(const OrderedSequenceContainer& osc);
 
   /**
    * @brief Specific methode to build a DataSet from a PolymorphismSequenceContainer.
    */
-  static std::unique_ptr<DataSet> buildDataSet(const PolymorphismSequenceContainer& psc) throw (Exception);
+  static std::unique_ptr<DataSet> buildDataSet(const PolymorphismSequenceContainer& psc);
 };
 } // end of namespace bpp;
 

src/Bpp/PopGen/DataSet/Date.cpp

@@ -47,7 +47,7 @@ using namespace std;
 
 // ** Class constructor: *******************************************************/
 
-Date::Date(const int day, const int month, const int year) throw (BadIntegerException) : day_(day),
+Date::Date(const int day, const int month, const int year) : day_(day),
   month_(month),
   year_(year)
 {
@@ -75,7 +75,7 @@ Date& Date::operator=(const Date& date)
   return *this;
 }
 
-void Date::setDate(const int day, const int month, const int year) throw (BadIntegerException)
+void Date::setDate(const int day, const int month, const int year)
 {
   if (day >= 1 && day <= 31)
     day_ = day;
@@ -93,7 +93,7 @@ void Date::setYear(const int year)
   year_ = year;
 }
 
-void Date::setMonth(const int month) throw (BadIntegerException)
+void Date::setMonth(const int month)
 {
   if (month >= 1 && month <= 12)
     month_ = month;
@@ -101,7 +101,7 @@ void Date::setMonth(const int month) throw (BadIntegerException)
     throw (BadIntegerException("Date::Date: month must be in [1;12].", month));
 }
 
-void Date::setDay(const int day) throw (BadIntegerException)
+void Date::setDay(const int day)
 {
   if (day >= 1 && day <= 31)
     day_ = day;