[med-svn] [Git][med-team/libbpp-phyl-omics][upstream] New upstream version 2.4.0
Julien Y. Dutheil
gitlab at salsa.debian.org
Sat Mar 31 18:34:31 UTC 2018
Julien Y. Dutheil pushed to branch upstream at Debian Med / libbpp-phyl-omics
Commits:
37e12ef4 by Julien Y. Dutheil at 2018-03-29T14:08:44+02:00
New upstream version 2.4.0
- - - - -
14 changed files:
- CMakeLists.txt
- ChangeLog
- Doxyfile
- bpp-phyl-omics.spec
- src/Bpp/Seq/Io/Maf/AbstractDistanceEstimationMafIterator.h
- src/Bpp/Seq/Io/Maf/AbstractPhylogenyReconstructionMafIterator.h
- src/Bpp/Seq/Io/Maf/DistanceBasedPhylogenyReconstructionMafIterator.cpp
- src/Bpp/Seq/Io/Maf/DistanceBasedPhylogenyReconstructionMafIterator.h
- src/Bpp/Seq/Io/Maf/FilterTreeMafIterator.cpp
- src/Bpp/Seq/Io/Maf/FilterTreeMafIterator.h
- src/Bpp/Seq/Io/Maf/OutputDistanceMatrixMafIterator.h
- src/Bpp/Seq/Io/Maf/OutputTreeMafIterator.h
- src/Bpp/Seq/Io/Maf/TreeManipulationMafIterators.cpp
- src/Bpp/Seq/Io/Maf/TreeManipulationMafIterators.h
Changes:
=====================================
CMakeLists.txt
=====================================
--- a/CMakeLists.txt
+++ b/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(${PROJECT_NAME}_VERSION_CURRENT "2")
+SET(${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
=====================================
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,9 @@
+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
=====================================
--- a/Doxyfile
+++ b/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
=====================================
--- a/bpp-phyl-omics.spec
+++ b/bpp-phyl-omics.spec
@@ -1,34 +1,31 @@
-%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 at univ-montp2.fr> 2.4.0-1
+- Increased interface number
+- Removed dynamic exceptions specifications.
* Tue Jun 06 2017 Julien Dutheil <julien.dutheil at univ-montp2.fr> 2.3.1-1
- Increased interface number
* Wed May 10 2017 Julien Dutheil <julien.dutheil at univ-montp2.fr> 2.3.0-1
=====================================
src/Bpp/Seq/Io/Maf/AbstractDistanceEstimationMafIterator.h
=====================================
--- a/src/Bpp/Seq/Io/Maf/AbstractDistanceEstimationMafIterator.h
+++ b/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
=====================================
--- a/src/Bpp/Seq/Io/Maf/AbstractPhylogenyReconstructionMafIterator.h
+++ b/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
=====================================
--- a/src/Bpp/Seq/Io/Maf/DistanceBasedPhylogenyReconstructionMafIterator.cpp
+++ b/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
=====================================
--- a/src/Bpp/Seq/Io/Maf/DistanceBasedPhylogenyReconstructionMafIterator.h
+++ b/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
=====================================
--- a/src/Bpp/Seq/Io/Maf/FilterTreeMafIterator.cpp
+++ b/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
=====================================
--- a/src/Bpp/Seq/Io/Maf/FilterTreeMafIterator.h
+++ b/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
=====================================
--- a/src/Bpp/Seq/Io/Maf/OutputDistanceMatrixMafIterator.h
+++ b/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
=====================================
--- a/src/Bpp/Seq/Io/Maf/OutputTreeMafIterator.h
+++ b/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
=====================================
--- a/src/Bpp/Seq/Io/Maf/TreeManipulationMafIterators.cpp
+++ b/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
=====================================
--- a/src/Bpp/Seq/Io/Maf/TreeManipulationMafIterators.h
+++ b/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);
};
View it on GitLab: https://salsa.debian.org/med-team/libbpp-phyl-omics/commit/37e12ef4f91f6d4b2ef0c7ac2865780166586c73
---
View it on GitLab: https://salsa.debian.org/med-team/libbpp-phyl-omics/commit/37e12ef4f91f6d4b2ef0c7ac2865780166586c73
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