Package: obitools | Debian Sources

Package: obitools / 1.2.13+dfsg-3

Metadata

Package	Version	Patches format
obitools	1.2.13+dfsg-3	3.0 (quilt)

Patch series

view the series file

Patch	File delta	Description
use_debian_libs \| (download)	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
fix_path_interpreter \| (download)	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
2to3.patch \| (download)	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:
port_python3.patch \| (download)	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.

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