setup.py | 65 32 + 33 - 0 !
1 file changed, 32 insertions(+), 33 deletions(-)

 use debian packages dependencies for extension build

ariba/ext/fml-asm_ariba.cpp | 4 2 + 2 - 0 !
1 file changed, 2 insertions(+), 2 deletions(-)

 adapt to fermi-lite which does not conflict with bwa
  An issue on fermi-lite upstream tracker
    https://github.com/lh3/fermi-lite/issues/5
  suggests to take over a patch for the Debian package which would
  enable making it co-usable with libbwa-dev (which is needed in
  libseqlib).  This patch adapts ariba to the potential change in
  fermi-lite.

setup.py | 38 37 + 1 - 0 !
1 file changed, 37 insertions(+), 1 deletion(-)

 include testdata in package

ariba/tests/ncbi_getter_test.py | 24 12 + 12 - 0 !
1 file changed, 12 insertions(+), 12 deletions(-)

 disable tests that need internet access

ariba/tests/assembly_variants_test.py | 98 49 + 49 - 0 !
ariba/tests/data/assembly_variants_test_get_variants_presence_absence.snps | 6 3 + 3 - 0 !
ariba/tests/data/assembly_variants_test_get_variants_variants_only.snps | 6 3 + 3 - 0 !
3 files changed, 55 insertions(+), 55 deletions(-)

 adapt test cases for new pymummer version

ariba/assembly.py | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 run debian spades wrapper
 Debian's /usr/bin/spades.py is not a Python script, but a wrapper
 around a common executable only provided for compatibility reasons.
 Ariba is trying to execute it explicitly as a Python script.
 This patch just calls the executable without forcing it through the
 Python interpreter.