setup.py | 6 3 + 3 - 0 !
1 file changed, 3 insertions(+), 3 deletions(-)

 do not check existence of third party tools since these are
 removed.  We are using Debian packaged tools

sepp-package/run-sepp.sh | 2 1 + 1 - 0 !
setup.py | 15 11 + 4 - 0 !
test/unittest/testConfig.py | 6 3 + 3 - 0 !
test/unittest/testMidpoint.py | 3 1 + 2 - 0 !
test/unittest/testSepp.py | 3 1 + 2 - 0 !
5 files changed, 17 insertions(+), 12 deletions(-)

 use debian packaged guppy and hmm*
 An if statement is added because copy_tool_to_lib is also called for the jar
 that is generated before the Python part of the build.

tools/merge/build.xml | 2 1 + 1 - 0 !
tools/merge/tipp.xml | 2 1 + 1 - 0 !
2 files changed, 2 insertions(+), 2 deletions(-)

 more recent version of java suppresses some warnings

tools/merge/src/phylolab/taxonamic/JSONMerger.java | 10 7 + 3 - 0 !
tools/merge/src/phylolab/taxonamic/PPlacerJSONMerger.java | 4 3 + 1 - 0 !
2 files changed, 10 insertions(+), 4 deletions(-)

 fix build issue

tools/merge/build.xml | 6 1 + 5 - 0 !
tools/merge/tipp.xml | 6 1 + 5 - 0 !
2 files changed, 2 insertions(+), 10 deletions(-)

 adapting the build.xml file of ant to debian policy
 There are no embedded jars to include.
 The classpath thus has to be changed to include Debian-packaged jars.
 The .java files should not be included in the target jars.

run_tipp_tool.py | 9 5 + 4 - 0 !
sepp/config.py | 9 5 + 4 - 0 !
sepp/ensemble.py | 6 5 + 1 - 0 !
sepp/exhaustive_tipp.py | 11 5 + 6 - 0 !
sepp/exhaustive_upp.py | 8 5 + 3 - 0 !
5 files changed, 25 insertions(+), 18 deletions(-)

 using configuration files that are in /etc or in ~/.sepp

tools/merge/src/phylolab/taxonamic/JSONMerger.java | 10 8 + 2 - 0 !
tools/merge/src/phylolab/taxonamic/PPlacerJSONMerger.java | 9 7 + 2 - 0 !
2 files changed, 15 insertions(+), 4 deletions(-)

 looking for the right index in placements jsonarray
 Original code assumes the edge_num information is in the first position in the
 JSONArray placements, which is not always the case. We insert a loop to look
 for the right position.

test/unittest/testConfig.py | 4 2 + 2 - 0 !
1 file changed, 2 insertions(+), 2 deletions(-)

 deactivating minor test relative to log verbosity level

split_sequences.py | 1 1 + 0 - 0 !
1 file changed, 1 insertion(+)

 marking split_sequences.py with a #! line

run_abundance.py | 2 1 + 1 - 0 !
run_sepp.py | 2 1 + 1 - 0 !
run_tipp.py | 2 1 + 1 - 0 !
run_tipp_tool.py | 2 1 + 1 - 0 !
run_upp.py | 2 1 + 1 - 0 !
sepp-package/run-sepp.sh | 9 8 + 1 - 0 !
6 files changed, 13 insertions(+), 6 deletions(-)

 marking the python interpreter as python3
 This is to conform to Debian Python policy.