Commit 0f9752d1 authored by Julien Y. Dutheil's avatar Julien Y. Dutheil
Browse files

New upstream version 2.4.0

parent 7e007750

CMakeLists.txt

+7 −5
Original line number Diff line number Diff line
@@ -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 "11")

SET(${PROJECT_NAME}_VERSION_CURRENT "12")

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-phyl")

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++ Phylogenetics 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/" 

       "/BppPhyl.tag" 

       "/\\\\.git/" 

       "/\\\\.gitignore" 

       ${CPACK_SOURCE_IGNORE_FILES}

ChangeLog

+4 −0
Original line number Diff line number Diff line 
20/02/18 -*- Version 2.4.0 -*-



10/12/17 -*- Version 2.3.2 -*-



10/05/17 -*- Version 2.3.0 -*-



23/09/16 Laurent Gueguen

Doxyfile

+1 −1
Original line number Diff line number Diff line
@@ -38,7 +38,7 @@ PROJECT_NAME = bpp-phyl 
# 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.spec

+26 −26
Original line number Diff line number Diff line 
%define _basename bpp-phyl

%define _version 2.3.1

%define _release 1

%define _prefix /usr



URL: http://biopp.univ-montp2.fr/

URL: https://github.com/BioPP/bpp-phyl



Name: %{_basename}

Version: %{_version}

Release: %{_release}

Name: bpp-phyl

Version: 1.4.0

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++ Phylogenetics 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
@@ -31,11 +28,11 @@ AutoProv: yes 
This library contains utilitary and classes for phylogenetics and molecular evolution analysis.

It is part of the Bio++ project.



%package -n libbpp-phyl11

%package -n libbpp-phyl12

Summary: Bio++ Phylogenetics library

Group: Development/Libraries/C and C++



%description -n libbpp-phyl11

%description -n libbpp-phyl12

This library contains utilitary and classes for phylogenetics and molecular evolution analysis.

It is part of the Bio++ project.
@@ -43,15 +40,15 @@ It is part of the Bio++ project. 
%package -n libbpp-phyl-devel

Summary: Libraries, includes to develop applications with %{_basename}

Group: Development/Libraries/C and C++

Requires: libbpp-phyl11 = %{_version}

Requires: libbpp-seq11 = %{_version}

Requires: libbpp-seq-devel = %{_version}

Requires: libbpp-core3 = %{_version}

Requires: libbpp-core-devel = %{_version}

Requires: libbpp-phyl12 = %{version}

Requires: libbpp-seq12 = %{version}

Requires: libbpp-seq-devel = %{version}

Requires: libbpp-core4 = %{version}

Requires: libbpp-core-devel = %{version}



%description -n libbpp-phyl-devel

The libbpp-phyl-devel package contains the header files and static libraries for

building applications which use %{_basename}.

building applications which use %{name}.



%prep

%setup -q
@@ -68,11 +65,11 @@ make DESTDIR=$RPM_BUILD_ROOT install 
%clean

rm -rf $RPM_BUILD_ROOT



%post -n libbpp-phyl11 -p /sbin/ldconfig

%post -n libbpp-phyl12 -p /sbin/ldconfig



%postun -n libbpp-phyl11 -p /sbin/ldconfig

%postun -n libbpp-phyl12 -p /sbin/ldconfig



%files -n libbpp-phyl11

%files -n libbpp-phyl12

%defattr(-,root,root)

%doc AUTHORS.txt COPYING.txt INSTALL.txt ChangeLog

%{_prefix}/%{_lib}/lib*.so.*
@@ -88,6 +85,9 @@ 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

src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp

+23 −20
Original line number Diff line number Diff line
@@ -102,7 +102,7 @@ Tree* PhylogeneticsApplicationTools::getTree( 
  const string& suffix,

  bool suffixIsOptional,

  bool verbose,

  int warn) throw (Exception)

  int warn)

{

  string format = ApplicationTools::getStringParameter(prefix + "tree.format", params, "Newick", suffix, suffixIsOptional, warn);

  string treeFilePath = ApplicationTools::getAFilePath(prefix + "tree.file", params, true, true, suffix, suffixIsOptional, "none", warn);
@@ -126,7 +126,7 @@ vector<Tree*> PhylogeneticsApplicationTools::getTrees( 
  const string& suffix,

  bool suffixIsOptional,

  bool verbose,

  int warn) throw (Exception)

  int warn)

{

  string format = ApplicationTools::getStringParameter(prefix + "trees.format", params, "Newick", suffix, suffixIsOptional, warn);

  string treeFilePath = ApplicationTools::getAFilePath(prefix + "trees.file", params, true, true, suffix, suffixIsOptional, "none", warn);
@@ -163,7 +163,7 @@ SubstitutionModel* PhylogeneticsApplicationTools::getSubstitutionModel( 
  const string& suffix,

  bool suffixIsOptional,

  bool verbose,

  int warn) throw (Exception)

  int warn)

{

  BppOSubstitutionModelFormat bIO(BppOSubstitutionModelFormat::ALL, true, true, true, verbose, warn + 1);

  string modelDescription;
@@ -192,7 +192,7 @@ TransitionModel* PhylogeneticsApplicationTools::getTransitionModel( 
  const string& suffix,

  bool suffixIsOptional,

  bool verbose,

  int warn) throw (Exception)

  int warn)

{

  BppOTransitionModelFormat bIO(BppOSubstitutionModelFormat::ALL, true, true, true, verbose, warn + 1);

  string modelDescription;
@@ -221,7 +221,7 @@ void PhylogeneticsApplicationTools::setSubstitutionModelParametersInitialValuesW 
  size_t modelNumber,

  const SiteContainer* data,

  std::map<std::string, std::string>& sharedParams,

  bool verbose) throw (Exception)

  bool verbose)

{

  string initFreqs = ApplicationTools::getStringParameter(model.getNamespace() + "initFreqs", unparsedParameterValues, "", "", true, 2);
@@ -258,7 +258,7 @@ void PhylogeneticsApplicationTools::setSubstitutionModelParametersInitialValuesW 
  for (size_t i = 0; i < pl.size(); ++i)

  {

    AutoParameter ap(pl[i]);

    ap.setMessageHandler(ApplicationTools::warning);

    ap.setMessageHandler(ApplicationTools::warning.get());

    pl.setParameter(i, ap);

  }
@@ -311,7 +311,7 @@ FrequenciesSet* PhylogeneticsApplicationTools::getRootFrequenciesSet( 
  const std::string& suffix,

  bool suffixIsOptional,

  bool verbose,

  int warn) throw (Exception)

  int warn)

{

  string freqDescription = ApplicationTools::getStringParameter("nonhomogeneous.root_freq", params, "Full(init=observed)", suffix, suffixIsOptional, warn);

  if (freqDescription == "None")
@@ -347,7 +347,7 @@ FrequenciesSet* PhylogeneticsApplicationTools::getFrequenciesSet( 
  std::map<std::string, std::string>& sharedparams,

  const std::vector<double>& rateFreqs,

  bool verbose,

  int warn) throw (Exception)

  int warn)

{

  map<string, string> unparsedParameterValues;

  BppOFrequenciesSetFormat bIO(BppOFrequenciesSetFormat::ALL, verbose, warn);
@@ -698,7 +698,7 @@ DiscreteDistribution* PhylogeneticsApplicationTools::getRateDistribution( 
  map<string, string>& params,

  const string& suffix,

  bool suffixIsOptional,

  bool verbose) throw (Exception)

  bool verbose)

{

  string distDescription = ApplicationTools::getStringParameter("rate_distribution", params, "Constant()", suffix, suffixIsOptional);
@@ -733,7 +733,6 @@ TreeLikelihood* PhylogeneticsApplicationTools::optimizeParameters( 
  bool suffixIsOptional,

  bool verbose,

  int warn)

throw (Exception)

{

  string optimization = ApplicationTools::getStringParameter("optimization", params, "FullD(derivatives=Newton)", suffix, suffixIsOptional, warn);

  if (optimization == "None")
@@ -747,7 +746,7 @@ throw (Exception) 
  string mhPath = ApplicationTools::getAFilePath("optimization.message_handler", params, false, false, suffix, suffixIsOptional, "none", warn + 1);

  OutputStream* messageHandler =

    (mhPath == "none") ? 0 :

    (mhPath == "std") ? ApplicationTools::message :

    (mhPath == "std") ? ApplicationTools::message.get() :

    new StlOutputStream(new ofstream(mhPath.c_str(), ios::out));

  if (verbose)

    ApplicationTools::displayResult("Message handler", mhPath);
@@ -755,7 +754,7 @@ throw (Exception) 
  string prPath = ApplicationTools::getAFilePath("optimization.profiler", params, false, false, suffix, suffixIsOptional, "none", warn + 1);

  OutputStream* profiler =

    (prPath == "none") ? 0 :

    (prPath == "std") ? ApplicationTools::message :

    (prPath == "std") ? ApplicationTools::message.get() :

    new StlOutputStream(new ofstream(prPath.c_str(), ios::out));

  if (profiler)

    profiler->setPrecision(20);
@@ -978,10 +977,15 @@ throw (Exception) 
          }

          string pname  = stp.nextToken();

          string pvalue = stp.nextToken();

          try {

            size_t p = pl.whichParameterHasName(pname);

            pl.setParameter(p, AutoParameter(pl[p]));

            pl[p].setValue(TextTools::toDouble(pvalue));

          }

          catch(Exception& e)

          {

          }

        }

      }

      bck.close();

      tl->setParameters(pl);
@@ -1156,7 +1160,6 @@ void PhylogeneticsApplicationTools::optimizeParameters( 
  bool suffixIsOptional,

  bool verbose,

  int warn)

throw (Exception)

{

  string optimization = ApplicationTools::getStringParameter("optimization", params, "FullD(derivatives=Newton)", suffix, suffixIsOptional, warn);

  if (optimization == "None")
@@ -1170,7 +1173,7 @@ throw (Exception) 
  string mhPath = ApplicationTools::getAFilePath("optimization.message_handler", params, false, false, suffix, suffixIsOptional, "none", warn + 1);

  OutputStream* messageHandler =

    (mhPath == "none") ? 0 :

    (mhPath == "std") ? ApplicationTools::message :

    (mhPath == "std") ? ApplicationTools::message.get() :

    new StlOutputStream(new ofstream(mhPath.c_str(), ios::out));

  if (verbose)

    ApplicationTools::displayResult("Message handler", mhPath);
@@ -1178,7 +1181,7 @@ throw (Exception) 
  string prPath = ApplicationTools::getAFilePath("optimization.profiler", params, false, false, suffix, suffixIsOptional, "none", warn + 1);

  OutputStream* profiler =

    (prPath == "none") ? 0 :

    (prPath == "std") ? ApplicationTools::message :

    (prPath == "std") ? ApplicationTools::message.get() :

    new StlOutputStream(new ofstream(prPath.c_str(), ios::out));

  if (profiler)

    profiler->setPrecision(20);
@@ -1398,7 +1401,7 @@ void PhylogeneticsApplicationTools::writeTree( 
  bool suffixIsOptional,

  bool verbose,

  bool checkOnly,

  int warn) throw (Exception)

  int warn)

{

  string format = ApplicationTools::getStringParameter(prefix + "tree.format", params, "Newick", suffix, suffixIsOptional, warn);

  string file = ApplicationTools::getAFilePath(prefix + "tree.file", params, false, false, suffix, suffixIsOptional, "none", warn);
@@ -1424,7 +1427,7 @@ void PhylogeneticsApplicationTools::writeTrees( 
  bool suffixIsOptional,

  bool verbose,

  bool checkOnly,

  int warn) throw (Exception)

  int warn)

{

  string format = ApplicationTools::getStringParameter(prefix + "trees.format", params, "Newick", suffix, suffixIsOptional, warn);

  string file = ApplicationTools::getAFilePath(prefix + "trees.file", params, true, false, suffix, suffixIsOptional, "none", warn);