distutils.ext/obidistutils/command/build.py | 3 1 + 2 - 0 !
distutils.ext/obidistutils/core.py | 4 0 + 4 - 0 !
distutils.ext/obidistutils/serenity/__init__.py | 2 1 + 1 - 0 !
distutils.ext/obidistutils/serenity/checkpackage.py | 97 3 + 94 - 0 !
setup.py | 4 2 + 2 - 0 !
5 files changed, 7 insertions(+), 103 deletions(-)

 installer uses pip and virtualenv for install,
 this patch removes this specific install to install in Debian dirs
 and use Debian libs

src/ali2consensus.py | 2 1 + 1 - 0 !
src/ecodbtaxstat.py | 2 1 + 1 - 0 !
src/ecotag.py | 2 1 + 1 - 0 !
src/ecotaxspecificity.py | 2 1 + 1 - 0 !
src/ecotaxstat.py | 2 1 + 1 - 0 !
src/extractreads.py | 1 1 + 0 - 0 !
src/extractreads2.py | 1 1 + 0 - 0 !
src/illuminapairedend.py | 2 1 + 1 - 0 !
src/ngsfilter.py | 2 1 + 1 - 0 !
src/obiaddtaxids.py | 2 1 + 1 - 0 !
src/obiannotate.py | 2 1 + 1 - 0 !
src/obiclean.py | 2 1 + 1 - 0 !
src/obicomplement.py | 2 1 + 1 - 0 !
src/obiconvert.py | 2 1 + 1 - 0 !
src/obicount.py | 2 1 + 1 - 0 !
src/obicut.py | 2 1 + 1 - 0 !
src/obidistribute.py | 2 1 + 1 - 0 !
src/obiextract.py | 2 1 + 1 - 0 !
src/obigrep.py | 2 1 + 1 - 0 !
src/obihead.py | 2 1 + 1 - 0 !
src/obijoinpairedend.py | 2 1 + 1 - 0 !
src/obipr2.py | 2 1 + 1 - 0 !
src/obisample.py | 2 1 + 1 - 0 !
src/obiselect.py | 2 1 + 1 - 0 !
src/obisilva.py | 2 1 + 1 - 0 !
src/obisort.py | 2 1 + 1 - 0 !
src/obisplit.py | 2 1 + 1 - 0 !
src/obistat.py | 2 1 + 1 - 0 !
src/obitab.py | 2 1 + 1 - 0 !
src/obitail.py | 2 1 + 1 - 0 !
src/obitaxonomy.py | 2 1 + 1 - 0 !
src/obitools/barcodecoverage/calcBc.py | 2 1 + 1 - 0 !
src/obitools/barcodecoverage/drawBcTree.py | 2 1 + 1 - 0 !
src/obitools/barcodecoverage/findErrors.py | 2 1 + 1 - 0 !
src/obitools/barcodecoverage/readFiles.py | 2 1 + 1 - 0 !
src/obitools/barcodecoverage/writeBcTree.py | 2 1 + 1 - 0 !
src/obitools/solexaPairEnd.py | 2 1 + 1 - 0 !
src/obiuniq.py | 2 1 + 1 - 0 !
src/oligotag.py | 2 1 + 1 - 0 !
39 files changed, 39 insertions(+), 37 deletions(-)

 use debian python

distutils.ext/obidistutils/command/__init__.py | 2 1 + 1 - 0 !
distutils.ext/obidistutils/command/build_cexe.py | 13 6 + 7 - 0 !
distutils.ext/obidistutils/command/build_exe.py | 31 12 + 19 - 0 !
distutils.ext/obidistutils/command/build_ext.py | 17 8 + 9 - 0 !
distutils.ext/obidistutils/command/build_scripts.py | 12 6 + 6 - 0 !
distutils.ext/obidistutils/core.py | 6 3 + 3 - 0 !
distutils.ext/obidistutils/serenity/__init__.py | 6 3 + 3 - 0 !
distutils.ext/obidistutils/serenity/checkpackage.py | 2 1 + 1 - 0 !
distutils.ext/obidistutils/serenity/getcython.py | 2 1 + 1 - 0 !
distutils.ext/obidistutils/serenity/rerun.py | 2 1 + 1 - 0 !
distutils.ext/obidistutils/serenity/virtual.py | 4 2 + 2 - 0 !
doc/sphinx/source/conf.py | 12 6 + 6 - 0 !
doc/sphinx/source/welcome.rst | 4 2 + 2 - 0 !
doc/sphinx/sphinxext/apigen.py | 2 1 + 1 - 0 !
doc/sphinx/sphinxext/docscrape.py | 20 10 + 10 - 0 !
doc/sphinx/sphinxext/docscrape_sphinx.py | 2 1 + 1 - 0 !
doc/sphinx/sphinxext/numpydoc.py | 4 2 + 2 - 0 !
setup.py | 2 1 + 1 - 0 !
src/ali2consensus.py | 6 3 + 3 - 0 !
src/ecodbtaxstat.py | 10 5 + 5 - 0 !
src/ecotag.py | 10 5 + 5 - 0 !
src/ecotaxspecificity.py | 16 8 + 8 - 0 !
src/ecotaxstat.py | 9 5 + 4 - 0 !
src/extractreads.py | 28 14 + 14 - 0 !
src/extractreads2.py | 8 4 + 4 - 0 !
src/illuminapairedend.py | 14 7 + 7 - 0 !
src/ngsfilter.py | 17 9 + 8 - 0 !
src/obiaddtaxids.py | 14 7 + 7 - 0 !
src/obiclean.py | 22 11 + 11 - 0 !
src/obiconvert.py | 2 1 + 1 - 0 !
src/obicount.py | 6 3 + 3 - 0 !
src/obicut.py | 2 1 + 1 - 0 !
src/obidistribute.py | 9 5 + 4 - 0 !
src/obiextract.py | 2 1 + 1 - 0 !
src/obihead.py | 2 1 + 1 - 0 !
src/obijoinpairedend.py | 6 3 + 3 - 0 !
src/obipr2.py | 28 14 + 14 - 0 !
src/obisample.py | 2 1 + 1 - 0 !
src/obiselect.py | 15 8 + 7 - 0 !
src/obisilva.py | 30 15 + 15 - 0 !
src/obisplit.py | 7 4 + 3 - 0 !
src/obistat.py | 19 10 + 9 - 0 !
src/obisubset.py | 2 1 + 1 - 0 !
src/obitab.py | 6 3 + 3 - 0 !
src/obitaxonomy.py | 14 7 + 7 - 0 !
src/obitools/SVGdraw.py | 266 133 + 133 - 0 !
src/obitools/align/ssearch.py | 2 1 + 1 - 0 !
src/obitools/alignment/__init__.py | 9 5 + 4 - 0 !
src/obitools/alignment/ace.py | 2 1 + 1 - 0 !
src/obitools/barcodecoverage/calcBc.py | 2 1 + 1 - 0 !
src/obitools/barcodecoverage/drawBcTree.py | 4 2 + 2 - 0 !
src/obitools/barcodecoverage/writeBcTree.py | 2 1 + 1 - 0 !
src/obitools/blast/__init__.py | 12 6 + 6 - 0 !
src/obitools/carto/__init__.py | 17 9 + 8 - 0 !
src/obitools/collections.py | 14 7 + 7 - 0 !
src/obitools/distances/__init__.py | 2 1 + 1 - 0 !
src/obitools/distances/observed.py | 7 4 + 3 - 0 !
src/obitools/distances/phylip.py | 8 4 + 4 - 0 !
src/obitools/distances/r.py | 6 3 + 3 - 0 !
src/obitools/dnahash/__init__.py | 4 2 + 2 - 0 !
src/obitools/ecobarcode/ecotag.py | 2 1 + 1 - 0 !
src/obitools/ecobarcode/rawdata.py | 6 3 + 3 - 0 !
src/obitools/ecobarcode/taxonomy.py | 22 11 + 11 - 0 !
src/obitools/ecopcr/__init__.py | 6 3 + 3 - 0 !
src/obitools/ecopcr/annotation.py | 2 1 + 1 - 0 !
src/obitools/ecopcr/options.py | 1 1 + 0 - 0 !
src/obitools/ecopcr/sequence.py | 6 3 + 3 - 0 !
src/obitools/ecopcr/taxonomy.py | 53 27 + 26 - 0 !
src/obitools/ecotag/parser.py | 14 7 + 7 - 0 !
src/obitools/eutils/__init__.py | 8 4 + 4 - 0 !
src/obitools/fast.py | 4 2 + 2 - 0 !
src/obitools/fnaqual/quality.py | 6 3 + 3 - 0 !
src/obitools/format/__init__.py | 4 2 + 2 - 0 !
src/obitools/format/ontology/go_obo.py | 4 2 + 2 - 0 !
src/obitools/format/options.py | 12 6 + 6 - 0 !
src/obitools/format/sequence/__init__.py | 12 6 + 6 - 0 !
src/obitools/goa/parser.py | 6 3 + 3 - 0 !
src/obitools/graph/__init__.py | 21 11 + 10 - 0 !
src/obitools/graph/algorithms/clique.py | 2 1 + 1 - 0 !
src/obitools/graph/algorithms/compact.py | 4 2 + 2 - 0 !
src/obitools/graph/rootedtree.py | 2 1 + 1 - 0 !
src/obitools/gzip.py | 40 20 + 20 - 0 !
src/obitools/location/__init__.py | 1 1 + 0 - 0 !
src/obitools/location/feature.py | 2 1 + 1 - 0 !
src/obitools/metabarcoding/__init__.py | 10 5 + 5 - 0 !
src/obitools/obischemas/kb/extern.py | 10 5 + 5 - 0 !
src/obitools/obo/parser.py | 13 7 + 6 - 0 !
src/obitools/options/_bioseqfilter.pyx | 2 1 + 1 - 0 !
src/obitools/options/bioseqedittag.py | 12 6 + 6 - 0 !
src/obitools/parallel/__init__.py | 2 1 + 1 - 0 !
src/obitools/parallel/jobqueue.py | 2 1 + 1 - 0 !
src/obitools/phylogeny/__init__.py | 4 2 + 2 - 0 !
src/obitools/phylogeny/newick.py | 2 1 + 1 - 0 !
src/obitools/sample.py | 14 7 + 7 - 0 !
src/obitools/seqdb/__init__.py | 2 1 + 1 - 0 !
src/obitools/seqdb/dnaparser.py | 2 1 + 1 - 0 !
src/obitools/seqdb/embl/parser.py | 2 1 + 1 - 0 !
src/obitools/seqdb/genbank/ncbi.py | 12 6 + 6 - 0 !
src/obitools/seqdb/genbank/parser.py | 2 1 + 1 - 0 !
src/obitools/sequenceencoder/__init__.py | 6 3 + 3 - 0 !
src/obitools/solexa/__init__.py | 2 1 + 1 - 0 !
src/obitools/solexaPairEnd.py | 8 4 + 4 - 0 !
src/obitools/statistics/hypergeometric.py | 9 5 + 4 - 0 !
src/obitools/statistics/noncentralhypergeo.py | 13 7 + 6 - 0 !
src/obitools/svg.py | 2 1 + 1 - 0 !
src/obitools/table/__init__.py | 77 36 + 41 - 0 !
src/obitools/table/csv.py | 4 2 + 2 - 0 !
src/obitools/tagmatcher/parser.py | 14 7 + 7 - 0 !
src/obitools/thermo/__init__.py | 26 13 + 13 - 0 !
src/obitools/tree/dot.py | 2 1 + 1 - 0 !
src/obitools/tree/newick.py | 2 1 + 1 - 0 !
src/obitools/unit/__init__.py | 2 1 + 1 - 0 !
src/obitools/unit/obitools/__init__.py | 12 6 + 6 - 0 !
src/obitools/utils/__init__.py | 52 26 + 26 - 0 !
src/obitools/utils/bioseq.py | 6 3 + 3 - 0 !
src/obitools/utils/crc64.py | 24 12 + 12 - 0 !
src/obitools/word/__init__.py | 5 3 + 2 - 0 !
src/obitools/zipfile.py | 117 55 + 62 - 0 !
src/obiuniq.py | 2 1 + 1 - 0 !
src/oligotag.py | 32 16 + 16 - 0 !
120 files changed, 775 insertions(+), 779 deletions(-)

 use 2to3 to port to python3
 Unfortunately this does not work and the build fails with

...
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/obitools-1.2.13+dfsg/src/obitools/options/_bioseqfilter.pyx
  tree = Parsing.p_module(s, pxd, full_module_name)

Error compiling Cython file:

distutils.ext/obidistutils/core.py | 1 1 + 0 - 0 !
src/obitools/SVGdraw.py | 10 3 + 7 - 0 !
src/obitools/__init__.py | 2 1 + 1 - 0 !
src/obitools/_obitools.pyx | 31 22 + 9 - 0 !
src/obitools/align/__init__.py | 22 11 + 11 - 0 !
src/obitools/align/_assemble.pxd | 4 2 + 2 - 0 !
src/obitools/align/_assemble.pyx | 2 1 + 1 - 0 !
src/obitools/align/_codonnws.pxd | 2 1 + 1 - 0 !
src/obitools/align/_codonnws.pyx | 150 77 + 73 - 0 !
src/obitools/align/_dynamic.pyx | 6 3 + 3 - 0 !
src/obitools/align/_freeendgap.pxd | 2 1 + 1 - 0 !
src/obitools/align/_freeendgap.pyx | 2 1 + 1 - 0 !
src/obitools/align/_freeendgapfm.pxd | 2 1 + 1 - 0 !
src/obitools/align/_freeendgapfm.pyx | 2 1 + 1 - 0 !
src/obitools/align/_gprofilenws.pxd | 4 2 + 2 - 0 !
src/obitools/align/_gprofilenws.pyx | 2 1 + 1 - 0 !
src/obitools/align/_lcs.pyx | 8 4 + 4 - 0 !
src/obitools/align/_nws.pxd | 2 1 + 1 - 0 !
src/obitools/align/_nws.pyx | 3 2 + 1 - 0 !
src/obitools/align/_nwsdnabyprot.pxd | 2 1 + 1 - 0 !
src/obitools/align/_nwsdnabyprot.pyx | 28 14 + 14 - 0 !
src/obitools/align/_profilenws.pxd | 4 2 + 2 - 0 !
src/obitools/align/_profilenws.pyx | 2 1 + 1 - 0 !
src/obitools/align/_qsassemble.pyx | 4 2 + 2 - 0 !
src/obitools/align/_qsrassemble.pyx | 4 2 + 2 - 0 !
src/obitools/align/_rassemble.pxd | 4 2 + 2 - 0 !
src/obitools/align/_rassemble.pyx | 2 1 + 1 - 0 !
src/obitools/align/_upperbond.pyx | 4 2 + 2 - 0 !
src/obitools/blast/__init__.py | 15 9 + 6 - 0 !
src/obitools/distances/phylip.py | 4 2 + 2 - 0 !
src/obitools/distances/r.py | 4 2 + 2 - 0 !
src/obitools/fasta/__init__.py | 2 1 + 1 - 0 !
src/obitools/fasta/_fasta.pyx | 10 5 + 5 - 0 !
src/obitools/fastq/__init__.py | 16 8 + 8 - 0 !
src/obitools/fastq/_fastq.pyx | 2 1 + 1 - 0 !
src/obitools/format/genericparser/__init__.py | 4 2 + 2 - 0 !
src/obitools/format/genericparser/_genericparser.pyx | 26 17 + 9 - 0 !
src/obitools/obischemas/kb/extern.py | 19 9 + 10 - 0 !
src/obitools/options/__init__.py | 14 7 + 7 - 0 !
src/obitools/options/_options.pyx | 15 8 + 7 - 0 !
src/obitools/profile/_profile.pyx | 14 7 + 7 - 0 !
src/obitools/seqdb/__init__.py | 4 2 + 2 - 0 !
src/obitools/table/__init__.py | 6 3 + 3 - 0 !
src/obitools/unit/__init__.py | 2 1 + 1 - 0 !
src/obitools/unit/obitools/__init__.py | 20 14 + 6 - 0 !
src/obitools/utils/__init__.py | 14 10 + 4 - 0 !
src/obitools/utils/_utils.pyx | 4 2 + 2 - 0 !
src/obitools/word/__init__.py | 2 1 + 1 - 0 !
src/obitools/word/_binary.pyx | 6 3 + 3 - 0 !
src/obitools/word/_readindex.pyx | 66 33 + 33 - 0 !
50 files changed, 310 insertions(+), 270 deletions(-)

 fix to port to python3,
 upstream not maintained nor porting to py3.

distutils.ext/obidistutils/command/build_scripts.py | 3 2 + 1 - 0 !
1 file changed, 2 insertions(+), 1 deletion(-)

 the readline function is somehow returning bytes instead of str, and so just decode
 to get string if readline returns bytes