[med-svn] [libbpp-popgen] branch upstream updated (bbfffd4 -> fbdbf41)
Andreas Tille
tille at debian.org
Tue Jun 13 21:08:08 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository libbpp-popgen.
from bbfffd4 Imported Upstream version 2.2.0
new fbdbf41 New upstream version 2.3.1
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.gitignore | 14 +
AUTHORS.txt | 2 +
CMakeLists.txt | 165 +-
ChangeLog | 10 +
Doxyfile | 2662 ++++++++++++--------
INSTALL.txt | 19 +-
bpp-popgen.spec | 131 +-
debian/changelog | 61 -
debian/compat | 1 -
debian/control | 25 -
debian/copyright | 66 -
debian/docs | 0
debian/libbpp-popgen-dev.install | 3 -
debian/libbpp-popgen6.install | 1 -
debian/postinst | 57 -
debian/postrm | 59 -
debian/prerm | 41 -
debian/rules | 121 -
debian/source/format | 1 -
header.html | 27 +
package.cmake.in | 26 +
src/Bpp/PopGen/{ => DataSet}/AnalyzedLoci.cpp | 0
src/Bpp/PopGen/{ => DataSet}/AnalyzedLoci.h | 4 +-
src/Bpp/PopGen/{ => DataSet}/AnalyzedSequences.cpp | 0
src/Bpp/PopGen/{ => DataSet}/AnalyzedSequences.h | 0
src/Bpp/PopGen/{ => DataSet}/DataSet.cpp | 0
src/Bpp/PopGen/{ => DataSet}/DataSet.h | 7 +-
src/Bpp/PopGen/{ => DataSet}/DataSetTools.cpp | 8 +-
src/Bpp/PopGen/{ => DataSet}/DataSetTools.h | 8 +-
src/Bpp/PopGen/{ => DataSet}/Date.cpp | 0
src/Bpp/PopGen/{ => DataSet}/Date.h | 0
src/Bpp/PopGen/{ => DataSet}/Group.cpp | 8 +-
src/Bpp/PopGen/{ => DataSet}/Group.h | 8 +-
src/Bpp/PopGen/{ => DataSet}/Individual.cpp | 28 +-
src/Bpp/PopGen/{ => DataSet}/Individual.h | 12 +-
.../PopGen/{ => DataSet/Io}/AbstractIDataSet.cpp | 0
src/Bpp/PopGen/{ => DataSet/Io}/AbstractIDataSet.h | 0
.../PopGen/{ => DataSet/Io}/AbstractODataSet.cpp | 0
src/Bpp/PopGen/{ => DataSet/Io}/AbstractODataSet.h | 0
.../PopGen/{ => DataSet/Io/Darwin}/DarwinDon.cpp | 0
src/Bpp/PopGen/{ => DataSet/Io/Darwin}/DarwinDon.h | 4 +-
.../{ => DataSet/Io/Darwin}/DarwinVarSingle.cpp | 0
.../{ => DataSet/Io/Darwin}/DarwinVarSingle.h | 2 +-
.../Io/GeneMapper}/GeneMapperCsvExport.cpp | 0
.../Io/GeneMapper}/GeneMapperCsvExport.h | 6 +-
.../PopGen/{ => DataSet/Io/Genepop}/Genepop.cpp | 0
src/Bpp/PopGen/{ => DataSet/Io/Genepop}/Genepop.h | 6 +-
.../PopGen/{ => DataSet/Io/Genetix}/Genetix.cpp | 0
src/Bpp/PopGen/{ => DataSet/Io/Genetix}/Genetix.h | 6 +-
src/Bpp/PopGen/{ => DataSet/Io}/IDataSet.h | 0
src/Bpp/PopGen/{ => DataSet/Io}/IODataSet.h | 4 +-
src/Bpp/PopGen/{ => DataSet/Io}/ODataSet.h | 0
src/Bpp/PopGen/{ => DataSet/Io}/PopgenlibIO.cpp | 0
src/Bpp/PopGen/{ => DataSet/Io}/PopgenlibIO.h | 2 +-
src/Bpp/PopGen/{ => DataSet}/Locality.h | 0
.../PopGen/{ => DataSet}/MultiSeqIndividual.cpp | 0
src/Bpp/PopGen/{ => DataSet}/MultiSeqIndividual.h | 8 +-
src/Bpp/PopGen/MonolocusGenotypeTools.cpp | 8 +-
src/Bpp/PopGen/MonolocusGenotypeTools.h | 2 +-
src/Bpp/PopGen/MultilocusGenotype.h | 2 +-
src/Bpp/PopGen/MultilocusGenotypeStatistics.cpp | 4 +-
src/Bpp/PopGen/MultilocusGenotypeStatistics.h | 2 +-
src/Bpp/PopGen/PolymorphismSequenceContainer.cpp | 100 +
src/Bpp/PopGen/PolymorphismSequenceContainer.h | 48 +-
.../PopGen/PolymorphismSequenceContainerTools.cpp | 53 +
.../PopGen/PolymorphismSequenceContainerTools.h | 25 +-
src/Bpp/PopGen/SequenceStatistics.cpp | 450 ++--
src/Bpp/PopGen/SequenceStatistics.h | 142 +-
src/CMakeLists.txt | 131 +-
69 files changed, 2422 insertions(+), 2158 deletions(-)
create mode 100644 .gitignore
delete mode 100644 debian/changelog
delete mode 100644 debian/compat
delete mode 100644 debian/control
delete mode 100644 debian/copyright
delete mode 100644 debian/docs
delete mode 100644 debian/libbpp-popgen-dev.install
delete mode 100644 debian/libbpp-popgen6.install
delete mode 100755 debian/postinst
delete mode 100755 debian/postrm
delete mode 100755 debian/prerm
delete mode 100755 debian/rules
delete mode 100644 debian/source/format
create mode 100644 header.html
create mode 100644 package.cmake.in
rename src/Bpp/PopGen/{ => DataSet}/AnalyzedLoci.cpp (100%)
rename src/Bpp/PopGen/{ => DataSet}/AnalyzedLoci.h (98%)
rename src/Bpp/PopGen/{ => DataSet}/AnalyzedSequences.cpp (100%)
rename src/Bpp/PopGen/{ => DataSet}/AnalyzedSequences.h (100%)
rename src/Bpp/PopGen/{ => DataSet}/DataSet.cpp (100%)
rename src/Bpp/PopGen/{ => DataSet}/DataSet.h (99%)
rename src/Bpp/PopGen/{ => DataSet}/DataSetTools.cpp (90%)
rename src/Bpp/PopGen/{ => DataSet}/DataSetTools.h (89%)
rename src/Bpp/PopGen/{ => DataSet}/Date.cpp (100%)
rename src/Bpp/PopGen/{ => DataSet}/Date.h (100%)
rename src/Bpp/PopGen/{ => DataSet}/Group.cpp (98%)
rename src/Bpp/PopGen/{ => DataSet}/Group.h (98%)
rename src/Bpp/PopGen/{ => DataSet}/Individual.cpp (98%)
rename src/Bpp/PopGen/{ => DataSet}/Individual.h (98%)
rename src/Bpp/PopGen/{ => DataSet/Io}/AbstractIDataSet.cpp (100%)
rename src/Bpp/PopGen/{ => DataSet/Io}/AbstractIDataSet.h (100%)
rename src/Bpp/PopGen/{ => DataSet/Io}/AbstractODataSet.cpp (100%)
rename src/Bpp/PopGen/{ => DataSet/Io}/AbstractODataSet.h (100%)
rename src/Bpp/PopGen/{ => DataSet/Io/Darwin}/DarwinDon.cpp (100%)
rename src/Bpp/PopGen/{ => DataSet/Io/Darwin}/DarwinDon.h (96%)
rename src/Bpp/PopGen/{ => DataSet/Io/Darwin}/DarwinVarSingle.cpp (100%)
rename src/Bpp/PopGen/{ => DataSet/Io/Darwin}/DarwinVarSingle.h (98%)
rename src/Bpp/PopGen/{ => DataSet/Io/GeneMapper}/GeneMapperCsvExport.cpp (100%)
rename src/Bpp/PopGen/{ => DataSet/Io/GeneMapper}/GeneMapperCsvExport.h (97%)
rename src/Bpp/PopGen/{ => DataSet/Io/Genepop}/Genepop.cpp (100%)
rename src/Bpp/PopGen/{ => DataSet/Io/Genepop}/Genepop.h (95%)
rename src/Bpp/PopGen/{ => DataSet/Io/Genetix}/Genetix.cpp (100%)
rename src/Bpp/PopGen/{ => DataSet/Io/Genetix}/Genetix.h (95%)
rename src/Bpp/PopGen/{ => DataSet/Io}/IDataSet.h (100%)
rename src/Bpp/PopGen/{ => DataSet/Io}/IODataSet.h (96%)
rename src/Bpp/PopGen/{ => DataSet/Io}/ODataSet.h (100%)
rename src/Bpp/PopGen/{ => DataSet/Io}/PopgenlibIO.cpp (100%)
rename src/Bpp/PopGen/{ => DataSet/Io}/PopgenlibIO.h (99%)
rename src/Bpp/PopGen/{ => DataSet}/Locality.h (100%)
rename src/Bpp/PopGen/{ => DataSet}/MultiSeqIndividual.cpp (100%)
rename src/Bpp/PopGen/{ => DataSet}/MultiSeqIndividual.h (99%)
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