[med-svn] [iqtree] branch master updated (030aee3 -> a2e119e)
Andreas Tille
tille at debian.org
Mon Dec 14 08:24:13 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository iqtree.
from 030aee3 Typo
new ddc6b1a Project now moved to Github
new 073d744 Imported Upstream version 1.3.11+dfsg
new 8cc4e6f Merge tag 'upstream/1.3.11+dfsg'
new fbff0d7 Use current upstream version for next upload to new
new 9f93690 Examples are now inside the package source
new 2fd0411 Add license for Files: fmemopen*
new 28a8f46 Add missing license for Files: gzstream.*
new a2e119e Manual source is under debian/* so specify this separatel
The 8 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:
CMakeLists.txt | 125 +-
FindEigen3.cmake | 81 +
License.txt => LICENSE | 46 +-
README.md | 6 +
alignment.cpp | 20 +-
alignmentpairwise.cpp | 8 +-
bionj.h | 10 +-
debian/Documents_source/example.nex | 8 -
debian/changelog | 4 +-
debian/copyright | 39 +-
debian/examples | 3 +-
debian/watch | 2 +-
eigendecomposition.cpp | 19 +-
example/example.nex | 9 +
{debian/Documents_source => example}/example.phy | 0
{model => example}/models.nex | 0
{debian/Documents_source => examples}/example.phy | 0
gss.cpp | 2 +-
gzstream.h | 3 +-
iqtree.cpp | 662 +-
iqtree.h | 29 +-
iqtree_config.h.in | 4 +-
mexttree.cpp | 22 +
mexttree.h | 9 +
model/modelcodon.cpp | 68 +-
model/modelcodon.h | 3 +-
model/modeldna.cpp | 56 +-
model/modeldna.h | 3 +-
model/modelfactory.cpp | 53 +-
model/modelfactory.h | 3 +-
model/modelgtr.cpp | 160 +-
model/modelgtr.h | 19 +-
model/modelmixture.cpp | 279 +-
model/modelmixture.h | 35 +-
model/modelprotein.cpp | 4 +-
model/modelset.cpp | 6 +-
model/modelset.h | 3 +-
model/modelsubst.h | 13 +-
model/partitionmodel.cpp | 41 +-
model/partitionmodel.h | 13 +
model/ratefree.cpp | 135 +-
model/ratefree.h | 12 +-
model/ratefreeinvar.cpp | 8 +-
model/ratefreeinvar.h | 3 +-
model/rategamma.cpp | 49 +-
model/rategamma.h | 14 +-
model/rategammainvar.cpp | 40 +-
model/rategammainvar.h | 3 +-
model/rateheterogeneity.h | 19 +-
model/rateinvar.cpp | 12 +-
model/rateinvar.h | 21 +-
model/ratekategory.cpp | 22 +-
model/ratekategory.h | 3 +-
msetsblock.cpp | 5 +
mtree.cpp | 103 +-
mtree.h | 20 +
mtreeset.cpp | 29 +
mtreeset.h | 2 +
ncl/nxstoken.h | 6 +-
ngs.cpp | 7 +-
ngs.h | 3 +-
optimization.cpp | 5 +-
optimization.h | 2 +-
pda.cpp | 21 +
pdnetwork.cpp | 4 +-
phyloanalysis.cpp | 164 +-
phylokernel.h | 6 +-
phylokernelmixrate.h | 2 +
phylokernelmixture.h | 2 +
phylolib.h | 26 -
phylonode.cpp | 10 +-
phylosupertree.cpp | 27 +-
phylosupertree.h | 4 +-
phylosupertreeplen.cpp | 351 +-
phylosupertreeplen.h | 43 +-
phylotesting.cpp | 299 +-
phylotesting.h | 4 +-
phylotree.cpp | 556 +-
phylotree.h | 51 +-
phylotreepars.cpp | 2 +
phylotreesse.cpp | 103 +-
pllnni.cpp | 61 +-
pllnni.h | 6 +-
pllrepo/AUTHORS | 0
pllrepo/COPYING | 674 --
pllrepo/ChangeLog | 0
pllrepo/Doxyfile | 2299 ------
pllrepo/INSTALL | 370 -
pllrepo/Makefile.am | 7 -
pllrepo/NEWS | 0
pllrepo/README | 0
pllrepo/configure.ac | 123 -
pllrepo/sources.am | 2 -
pllrepo/src/CMakeLists.txt | 67 -
pllrepo/src/Makefile.ALL | 54 -
pllrepo/src/Makefile.ARM | 51 -
pllrepo/src/Makefile.AVX | 60 -
pllrepo/src/Makefile.AVX-MPI | 59 -
pllrepo/src/Makefile.AVX-PTHREADS | 61 -
pllrepo/src/Makefile.AVX.clang | 57 -
pllrepo/src/Makefile.AVX.shared | 68 -
pllrepo/src/Makefile.MIC-PTHREADS | 62 -
pllrepo/src/Makefile.SSE3 | 52 -
pllrepo/src/Makefile.SSE3-MPI | 50 -
pllrepo/src/Makefile.SSE3-PTHREADS | 52 -
pllrepo/src/Makefile.am | 53 -
pllrepo/src/alignment.c | 754 --
pllrepo/src/avxLikelihood.c | 4111 ---------
pllrepo/src/bipartitionList.c | 434 -
pllrepo/src/cycle.h | 516 --
pllrepo/src/errcodes.h | 69 -
pllrepo/src/evaluateGenericSpecial.c | 3321 --------
pllrepo/src/evaluatePartialGenericSpecial.c | 1378 ---
pllrepo/src/fastDNAparsimony.c | 1941 -----
pllrepo/src/genericParallelization.c | 2283 -----
pllrepo/src/genericParallelization.h | 127 -
pllrepo/src/globalVariables.h | 170 -
pllrepo/src/hardware.c | 165 -
pllrepo/src/hardware.h | 48 -
pllrepo/src/hash.c | 219 -
pllrepo/src/hash.h | 50 -
pllrepo/src/lexer.c | 299 -
pllrepo/src/lexer.h | 88 -
pllrepo/src/makenewzGenericSpecial.c | 3145 -------
pllrepo/src/mem_alloc.c | 228 -
pllrepo/src/mem_alloc.h | 70 -
pllrepo/src/mic_native.h | 56 -
pllrepo/src/mic_native_aa.c | 1254 ---
pllrepo/src/mic_native_dna.c | 676 --
pllrepo/src/models.c | 4377 ----------
pllrepo/src/newick.c | 583 --
pllrepo/src/newick.h | 61 -
pllrepo/src/newviewGenericSpecial.c | 8736 --------------------
pllrepo/src/optimizeModel.c | 3145 -------
pllrepo/src/parsePartition.c | 388 -
pllrepo/src/parsePartition.h | 51 -
pllrepo/src/parsimony.c | 865 --
pllrepo/src/pll.h | 1692 ----
pllrepo/src/pllInternal.h | 313 -
pllrepo/src/pthread.h | 1368 ---
pllrepo/src/queue.c | 96 -
pllrepo/src/queue.h | 48 -
pllrepo/src/randomTree.c | 177 -
pllrepo/src/recom.c | 689 --
pllrepo/src/restartHashTable.c | 357 -
pllrepo/src/sched.h | 183 -
pllrepo/src/searchAlgo.c | 3310 --------
pllrepo/src/semaphore.h | 169 -
pllrepo/src/ssort.c | 121 -
pllrepo/src/stack.c | 85 -
pllrepo/src/stack.h | 48 -
pllrepo/src/topologies.c | 778 --
pllrepo/src/trash.c | 129 -
pllrepo/src/treeIO.c | 236 -
pllrepo/src/treeIO.h | 23 -
pllrepo/src/utils.c | 3734 ---------
stoprule.cpp | 4 +-
test_scripts/README | 19 +
test_scripts/compile.sh | 120 +
test_scripts/gen_test_standard.py | 92 +
test_scripts/gen_test_webserver.py | 85 +
test_scripts/generate_test_cmds.py | 97 +
test_scripts/jobmanager.py | 102 +
test_scripts/submit_jobs.sh | 45 +
test_scripts/submitjob.sh | 2 +
test_scripts/test_configs.txt | 27 +
test_scripts/test_data/d59_8.nex | 13 +
test_scripts/test_data/d59_8.phy | 60 +
test_scripts/test_data/example.nex | 5 +
.../test_data}/example.phy | 0
test_scripts/test_data/prot_M126_27_269.phy | 28 +
tools.cpp | 193 +-
tools.h | 68 +-
vectorclass/changelog.txt | 25 +-
vectorclass/special.zip | Bin 34472 -> 34477 bytes
vectorclass/vectorclass.h | 6 +-
vectorclass/vectorclass.pdf | Bin 466946 -> 476370 bytes
vectorclass/vectorf128.h | 32 +-
vectorclass/vectorf256.h | 30 +-
vectorclass/vectorf256e.h | 8 +-
vectorclass/vectorf512.h | 29 +-
vectorclass/vectori128.h | 103 +-
vectorclass/vectori256.h | 529 +-
vectorclass/vectori256e.h | 68 +-
vectorclass/vectori512.h | 4 +-
vectorclass/vectormath_exp.h | 94 +-
vectorclass/vectormath_hyp.h | 120 +-
vectorclass/vectormath_trig.h | 86 +-
188 files changed, 4103 insertions(+), 59511 deletions(-)
create mode 100644 FindEigen3.cmake
copy License.txt => LICENSE (95%)
create mode 100644 README.md
delete mode 100644 debian/Documents_source/example.nex
create mode 100644 example/example.nex
copy {debian/Documents_source => example}/example.phy (100%)
rename {model => example}/models.nex (100%)
copy {debian/Documents_source => examples}/example.phy (100%)
delete mode 100755 phylolib.h
delete mode 100644 pllrepo/AUTHORS
delete mode 100644 pllrepo/COPYING
delete mode 100644 pllrepo/ChangeLog
delete mode 100644 pllrepo/Doxyfile
delete mode 100644 pllrepo/INSTALL
delete mode 100644 pllrepo/Makefile.am
delete mode 100644 pllrepo/NEWS
delete mode 100644 pllrepo/README
delete mode 100644 pllrepo/configure.ac
delete mode 100644 pllrepo/sources.am
delete mode 100644 pllrepo/src/CMakeLists.txt
delete mode 100644 pllrepo/src/Makefile.ALL
delete mode 100644 pllrepo/src/Makefile.ARM
delete mode 100644 pllrepo/src/Makefile.AVX
delete mode 100644 pllrepo/src/Makefile.AVX-MPI
delete mode 100644 pllrepo/src/Makefile.AVX-PTHREADS
delete mode 100644 pllrepo/src/Makefile.AVX.clang
delete mode 100644 pllrepo/src/Makefile.AVX.shared
delete mode 100644 pllrepo/src/Makefile.MIC-PTHREADS
delete mode 100644 pllrepo/src/Makefile.SSE3
delete mode 100644 pllrepo/src/Makefile.SSE3-MPI
delete mode 100644 pllrepo/src/Makefile.SSE3-PTHREADS
delete mode 100644 pllrepo/src/Makefile.am
delete mode 100644 pllrepo/src/alignment.c
delete mode 100644 pllrepo/src/avxLikelihood.c
delete mode 100644 pllrepo/src/bipartitionList.c
delete mode 100644 pllrepo/src/cycle.h
delete mode 100644 pllrepo/src/errcodes.h
delete mode 100644 pllrepo/src/evaluateGenericSpecial.c
delete mode 100644 pllrepo/src/evaluatePartialGenericSpecial.c
delete mode 100644 pllrepo/src/fastDNAparsimony.c
delete mode 100644 pllrepo/src/genericParallelization.c
delete mode 100644 pllrepo/src/genericParallelization.h
delete mode 100644 pllrepo/src/globalVariables.h
delete mode 100644 pllrepo/src/hardware.c
delete mode 100644 pllrepo/src/hardware.h
delete mode 100644 pllrepo/src/hash.c
delete mode 100644 pllrepo/src/hash.h
delete mode 100644 pllrepo/src/lexer.c
delete mode 100644 pllrepo/src/lexer.h
delete mode 100644 pllrepo/src/makenewzGenericSpecial.c
delete mode 100644 pllrepo/src/mem_alloc.c
delete mode 100644 pllrepo/src/mem_alloc.h
delete mode 100644 pllrepo/src/mic_native.h
delete mode 100644 pllrepo/src/mic_native_aa.c
delete mode 100644 pllrepo/src/mic_native_dna.c
delete mode 100644 pllrepo/src/models.c
delete mode 100644 pllrepo/src/newick.c
delete mode 100644 pllrepo/src/newick.h
delete mode 100644 pllrepo/src/newviewGenericSpecial.c
delete mode 100644 pllrepo/src/optimizeModel.c
delete mode 100644 pllrepo/src/parsePartition.c
delete mode 100644 pllrepo/src/parsePartition.h
delete mode 100644 pllrepo/src/parsimony.c
delete mode 100644 pllrepo/src/pll.h
delete mode 100644 pllrepo/src/pllInternal.h
delete mode 100644 pllrepo/src/pthread.h
delete mode 100644 pllrepo/src/queue.c
delete mode 100644 pllrepo/src/queue.h
delete mode 100644 pllrepo/src/randomTree.c
delete mode 100644 pllrepo/src/recom.c
delete mode 100644 pllrepo/src/restartHashTable.c
delete mode 100644 pllrepo/src/sched.h
delete mode 100644 pllrepo/src/searchAlgo.c
delete mode 100644 pllrepo/src/semaphore.h
delete mode 100644 pllrepo/src/ssort.c
delete mode 100644 pllrepo/src/stack.c
delete mode 100644 pllrepo/src/stack.h
delete mode 100644 pllrepo/src/topologies.c
delete mode 100644 pllrepo/src/trash.c
delete mode 100644 pllrepo/src/treeIO.c
delete mode 100644 pllrepo/src/treeIO.h
delete mode 100644 pllrepo/src/utils.c
create mode 100644 test_scripts/README
create mode 100755 test_scripts/compile.sh
create mode 100755 test_scripts/gen_test_standard.py
create mode 100755 test_scripts/gen_test_webserver.py
create mode 100755 test_scripts/generate_test_cmds.py
create mode 100755 test_scripts/jobmanager.py
create mode 100755 test_scripts/submit_jobs.sh
create mode 100755 test_scripts/submitjob.sh
create mode 100644 test_scripts/test_configs.txt
create mode 100644 test_scripts/test_data/d59_8.nex
create mode 100644 test_scripts/test_data/d59_8.phy
create mode 100644 test_scripts/test_data/example.nex
rename {debian/Documents_source => test_scripts/test_data}/example.phy (100%)
create mode 100644 test_scripts/test_data/prot_M126_27_269.phy
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