[med-svn] [Git][med-team/pbbarcode][master] 7 commits: Use 2to3 to port to Python3
Andreas Tille
gitlab at salsa.debian.org
Sat Nov 30 17:09:01 GMT 2019
Andreas Tille pushed to branch master at Debian Med / pbbarcode
Commits:
5c83377b by Andreas Tille at 2019-11-30T17:01:28Z
Use 2to3 to port to Python3
- - - - -
a311b52a by Andreas Tille at 2019-11-30T17:03:12Z
Change build system to Python3
- - - - -
8668fc4d by Andreas Tille at 2019-11-30T17:03:36Z
debhelper-compat 12
- - - - -
981d2121 by Andreas Tille at 2019-11-30T17:03:39Z
Standards-Version: 4.4.1
- - - - -
b2e467d6 by Andreas Tille at 2019-11-30T17:03:40Z
autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g
- - - - -
3e072a37 by Andreas Tille at 2019-11-30T17:03:42Z
Set upstream metadata fields: Repository, Repository-Browse.
- - - - -
aad2d78e by Andreas Tille at 2019-11-30T17:08:44Z
TODO
- - - - -
9 changed files:
- debian/changelog
- − debian/compat
- debian/control
- + debian/patches/2to3.patch
- debian/patches/series
- debian/rules
- debian/tests/control
- debian/tests/run-unit-test
- debian/upstream/metadata
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,15 @@
+pbbarcode (0.8.0-6) UNRELEASED; urgency=medium
+
+ * Use 2to3 to port to Python3
+ Closes: #937253
+ * debhelper-compat 12
+ * Standards-Version: 4.4.1
+ * autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g
+ * Set upstream metadata fields: Repository, Repository-Browse.
+ TODO: #938009 (python-pbcore)
+
+ -- Andreas Tille <tille at debian.org> Sat, 30 Nov 2019 17:59:51 +0100
+
pbbarcode (0.8.0-5) unstable; urgency=medium
* Team upload.
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11
=====================================
debian/control
=====================================
@@ -2,18 +2,18 @@ Source: pbbarcode
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
dh-python,
- python-setuptools,
+ python3-setuptools,
python3-docutils,
- python-all-dev,
- python-pbcore,
- python-numpy,
- python-h5py,
+ python3-all-dev,
+ python3-pbcore,
+ python3-numpy,
+ python3-h5py,
# Test-Depends:
- python-nose,
+ python3-nose,
pbh5tools
-Standards-Version: 4.2.1
+Standards-Version: 4.4.1
Vcs-Browser: https://salsa.debian.org/med-team/pbbarcode
Vcs-Git: https://salsa.debian.org/med-team/pbbarcode.git
Homepage: https://github.com/PacificBiosciences/pbbarcode
@@ -22,8 +22,8 @@ Package: pbbarcode
Architecture: any
Depends: ${misc:Depends},
${shlibs:Depends},
- ${python:Depends},
- python-pkg-resources
+ ${python3:Depends},
+ python3-pkg-resources
Suggests: pbdagcon
Description: annotate PacBio sequencing reads with barcode information
The pbbarcode package provides tools for annotating PacBio sequencing reads
=====================================
debian/patches/2to3.patch
=====================================
@@ -0,0 +1,398 @@
+Description: Use 2to3 to port to Python3
+Bug-Debian: https://bugs.debian.org/937253
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Sat, 30 Nov 2019 17:59:51 +0100
+
+--- a/Makefile
++++ b/Makefile
+@@ -5,17 +5,17 @@ SHELL = /bin/bash -e
+ all: build install
+
+ build:
+- python setup.py build --executable="/usr/bin/env python"
++ python3 setup.py build --executable="/usr/bin/python3"
+
+ bdist:
+- python setup.py build --executable="/usr/bin/env python"
+- python setup.py bdist --formats=egg
++ python3 setup.py build --executable="/usr/bin/python3"
++ python3 setup.py bdist --formats=egg
+
+ install:
+- python setup.py install
++ python3 setup.py install
+
+ develop:
+- python setup.py develop
++ python3 setup.py develop
+
+ test:
+ find tests -name "*.py" | xargs nosetests
+--- a/doc/conf.py
++++ b/doc/conf.py
+@@ -40,8 +40,8 @@ source_suffix = '.rst'
+ master_doc = 'index'
+
+ # General information about the project.
+-project = u'pbbarcode'
+-copyright = u'2012, PacBio'
++project = 'pbbarcode'
++copyright = '2012, PacBio'
+
+ # The version info for the project you're documenting, acts as replacement for
+ # |version| and |release|, also used in various other places throughout the
+@@ -183,8 +183,8 @@ latex_elements = {
+ # Grouping the document tree into LaTeX files. List of tuples
+ # (source start file, target name, title, author, documentclass [howto/manual]).
+ latex_documents = [
+- ('index', 'pbbarcode.tex', u'pbbarcode Documentation',
+- u'PacBio', 'manual'),
++ ('index', 'pbbarcode.tex', 'pbbarcode Documentation',
++ 'PacBio', 'manual'),
+ ]
+
+ # The name of an image file (relative to this directory) to place at the top of
+@@ -213,8 +213,8 @@ latex_documents = [
+ # One entry per manual page. List of tuples
+ # (source start file, name, description, authors, manual section).
+ man_pages = [
+- ('index', 'pbbarcode', u'pbbarcode Documentation',
+- [u'PacBio'], 1)
++ ('index', 'pbbarcode', 'pbbarcode Documentation',
++ ['PacBio'], 1)
+ ]
+
+ # If true, show URL addresses after external links.
+@@ -227,8 +227,8 @@ man_pages = [
+ # (source start file, target name, title, author,
+ # dir menu entry, description, category)
+ texinfo_documents = [
+- ('index', 'pbbarcode', u'pbbarcode Documentation',
+- u'PacBio', 'pbbarcode', 'One line description of project.',
++ ('index', 'pbbarcode', 'pbbarcode Documentation',
++ 'PacBio', 'pbbarcode', 'One line description of project.',
+ 'Miscellaneous'),
+ ]
+
+--- a/src/python/pbbarcode/BarcodeLabeler.py
++++ b/src/python/pbbarcode/BarcodeLabeler.py
+@@ -35,8 +35,9 @@ import numpy as n
+
+ from pbcore.io.BarcodeH5Reader import LabeledZmw, \
+ BARCODE_DELIMITER
++from functools import reduce
+
+-__RC_MAP__ = dict(zip('ACGTacgt-N','TGCAtgca-N'))
++__RC_MAP__ = dict(list(zip('ACGTacgt-N','TGCAtgca-N')))
+
+ class BarcodeScorer(object):
+ def __init__(self, basH5, barcodeFasta,
+@@ -53,8 +54,7 @@ class BarcodeScorer(object):
+ self.basH5 = basH5
+ self.barcodeFasta = list(barcodeFasta)
+ self.aligner = Aligner.SWaligner()
+- self.barcodeLength = n.unique(map(lambda x : len(x.sequence),
+- self.barcodeFasta))
++ self.barcodeLength = n.unique([len(x.sequence) for x in self.barcodeFasta])
+ if len(self.barcodeLength) > 1:
+ raise Exception("Currently, all barcodes must be the same length.")
+ else:
+@@ -96,7 +96,7 @@ class BarcodeScorer(object):
+ if self.scoreMode == 'paired':
+ return n.array([self.makeBCLabel(self.barcodeFasta[i].name,
+ self.barcodeFasta[i+1].name) for i
+- in xrange(0, len(self.barcodeSeqs), 2)])
++ in range(0, len(self.barcodeSeqs), 2)])
+ else:
+ return n.array([self.makeBCLabel(x.name, x.name) for x in self.barcodeFasta])
+
+@@ -193,7 +193,7 @@ class BarcodeScorer(object):
+ def choosePaired(o):
+ if o[1] == 1:
+ s = n.array([max(o[2][i], o[2][i + 1]) for i in \
+- xrange(0, len(self.barcodeSeqs), 2)])
++ range(0, len(self.barcodeSeqs), 2)])
+ p = n.argsort(-s)
+ s = s[p]
+ else:
+@@ -202,9 +202,9 @@ class BarcodeScorer(object):
+ # missed adapter will confuse this computation.
+ scores = o[3]
+ results = n.zeros(len(self.barcodeSeqs)/2)
+- for i in xrange(0, len(self.barcodeSeqs), 2):
++ for i in range(0, len(self.barcodeSeqs), 2):
+ pths = [0,0]
+- for j in xrange(0, len(scores)):
++ for j in range(0, len(scores)):
+ pths[j % 2] += scores[j][i]
+ pths[1 - j % 2] += scores[j][i + 1]
+ results[i/2] = max(pths)
+--- a/src/python/pbbarcode/SWaligner.py
++++ b/src/python/pbbarcode/SWaligner.py
+@@ -65,7 +65,7 @@ class SWaligner(object):
+ self.dpMat,
+ query,
+ targetSeqs)
+- return numpy.array([scores[i] for i in xrange(0, len(scores))])
++ return numpy.array([scores[i] for i in range(0, len(scores))])
+ return scorer
+
+
+--- a/src/python/pbbarcode/main.py
++++ b/src/python/pbbarcode/main.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ #################################################################################$$
+ # Copyright (c) 2011,2012, Pacific Biosciences of California, Inc.
+ #
+@@ -55,6 +55,7 @@ from pbbarcode.BarcodeLabeler import *
+ from pbbarcode._version import __version__
+
+ from pbh5tools.CmpH5Utils import copyAttributes
++from functools import reduce
+
+ # Paths to the Barcode Datasets in the cmp.h5 file.
+ BC_ALN_INFO_DS = "AlnInfo/Barcode"
+@@ -110,7 +111,7 @@ def makeBarcodeFofnFromBasFofn():
+
+ logging.debug("Using %d processes." % runner.args.nProcs)
+ if runner.args.nProcs <= 1:
+- newFiles = map(mpWrapper, inFiles)
++ newFiles = list(map(mpWrapper, inFiles))
+ else:
+ pool = Pool(runner.args.nProcs)
+ newFiles = pool.map(mpWrapper, inFiles)
+@@ -158,7 +159,7 @@ def labelAlignments():
+ # we use the first one to get the labels, if somehow they
+ # don't have all of the same stuff that will be an issue.
+ bcLabels = n.concatenate((bcFofn.barcodeLabels, n.array([BARCODE_DELIMITER])))
+- H5.create_dataset(BC_INFO_ID, data = n.array(range(0, len(bcLabels))),
++ H5.create_dataset(BC_INFO_ID, data = n.array(list(range(0, len(bcLabels)))),
+ dtype = 'int32')
+ H5.create_dataset(BC_INFO_NAME, data = bcLabels, dtype = h5.new_vlen(str))
+ if BC_ALN_INFO_DS in H5:
+@@ -180,17 +181,17 @@ def zipFofns(*inFofns):
+ return lines
+
+ sortedFofns = [readAndSort(inFofn) for inFofn in inFofns]
+- l = map(len, sortedFofns)
++ l = list(map(len, sortedFofns))
+ if len(n.unique(l)) != 1:
+ raise Exception("Fofns don't match, unequal number of inputs.")
+ else:
+- for i in xrange(0, n.unique(l)):
++ for i in range(0, n.unique(l)):
+ if len(n.unique([movieNameFromFile(sortedFofn[i]) for
+ sortedFofn in sortedFofns])) != 1:
+ raise Exception("Fofn elements don't match, movies differ.")
+
+ # need to un-arrayify these guys
+- return zip(*map(list, sortedFofns))
++ return list(zip(*list(map(list, sortedFofns))))
+
+ def filterZmws(zmwsForBCs):
+ """Apply various filterings passed by the user. There are somewhat
+@@ -209,7 +210,7 @@ def filterZmws(zmwsForBCs):
+
+ def molLenGuess(zmw):
+ if zmw.baxH5.hasRawBasecalls:
+- return max(map(len, zmw.subreads)) if zmw.subreads else 0
++ return max(list(map(len, zmw.subreads))) if zmw.subreads else 0
+ else:
+ return len(zmw.ccsRead) if zmw.ccsRead else 0
+
+@@ -237,7 +238,7 @@ def filterZmws(zmwsForBCs):
+ else:
+ return True
+
+- return { k:filter(zmwFilterFx, v) for k,v in zmwsForBCs.items() }
++ return { k:list(filter(zmwFilterFx, v)) for k,v in list(zmwsForBCs.items()) }
+
+ def _warnOnce():
+ var = []
+@@ -276,18 +277,18 @@ def getFastqRecords(zmw, lZmw = None):
+ def getFastqs():
+ zmwsByBarcode = getZmwsForBarcodes()
+ logging.debug("Pre-filter: Average number of ZMWs per barcode: %d" %
+- n.mean([len(zmwsByBarcode[k]) for k in zmwsByBarcode.keys()]))
++ n.mean([len(zmwsByBarcode[k]) for k in list(zmwsByBarcode.keys())]))
+
+ zmwsByBarcode = filterZmws(zmwsByBarcode)
+ logging.debug("Post-filter: Average number of ZMWs per barcode: %d" %
+- n.mean([len(zmwsByBarcode[k]) for k in zmwsByBarcode.keys()]))
++ n.mean([len(zmwsByBarcode[k]) for k in list(zmwsByBarcode.keys())]))
+
+ def getReadData(zmws):
+ recs = [getFastqRecords(zmw,lZmw) for zmw,lZmw in zmws]
+- recs = filter(lambda x : x, recs)
++ recs = [x for x in recs if x]
+ return [elt for sublst in recs for elt in sublst]
+
+- return {k:getReadData(zmws) for k, zmws in zmwsByBarcode.iteritems()}
++ return {k:getReadData(zmws) for k, zmws in zmwsByBarcode.items()}
+
+ def emitFastqs():
+ outFiles = getFastqs()
+@@ -309,7 +310,7 @@ def emitFastqs():
+ record = FastqRecord
+
+ l = 'a' if runner.args.fasta else 'q'
+- for k in outFiles.keys():
++ for k in list(outFiles.keys()):
+ if outFiles[k]:
+ with writer("%s/%s.fast%s" % (runner.args.outDir, k, l)) as w:
+ for e in outFiles[k]:
+@@ -328,7 +329,7 @@ def getUnlabeledZmws():
+ basH5 = BasH5Reader(basFile)
+ bcH5 = BarcodeH5Reader(barcodeFile)
+ sdiff = basH5.sequencingZmws[~n.in1d(basH5.sequencingZmws,
+- bcH5.labeledZmws.keys())]
++ list(bcH5.labeledZmws.keys()))]
+ for hn in sdiff:
+ unlabeledZmws.append(basH5[hn])
+
+@@ -351,7 +352,7 @@ def getZmwsForBarcodes(labels = None):
+ lZmws = bcH5.labeledZmwsFromBarcodeLabel(label)
+ for lZmw in lZmws:
+ zmw = basH5[lZmw.holeNumber]
+- if not label in zmwsForBCs.keys():
++ if not label in list(zmwsForBCs.keys()):
+ zmwsForBCs[label] = []
+ zmwsForBCs[label].append((zmw, lZmw))
+
+@@ -424,13 +425,13 @@ def subsampleReads(e):
+ k = int(len(e)*runner.args.subsample)
+ else:
+ k = len(e)
+- i = n.array(random.sample(range(0, len(e)), k), dtype = int)
++ i = n.array(random.sample(list(range(0, len(e))), k), dtype = int)
+ logging.debug("subsampled down to: %d" % len(i))
+ return [e[j] for j in i]
+
+ def callConsensus():
+ def makeReadAndReads(zmwsForBC):
+- ccsData = filter(lambda x:x, [zmw.ccsRead for _,_,zmw in zmwsForBC if zmw])
++ ccsData = [x for x in [zmw.ccsRead for _,_,zmw in zmwsForBC if zmw] if x]
+ srData = reduce(lambda x,y : x+y, [zmw.subreads for zmw,_,_ in
+ zmwsForBC if zmw], [])
+ if not srData and not ccsData:
+@@ -438,7 +439,7 @@ def callConsensus():
+
+ def getSeedRead(reads, lq = 80, uq = 90,
+ sLambda = lambda x : -x.zmw.readScore):
+- lens = map(len, reads)
++ lens = list(map(len, reads))
+ candidateRange = (n.percentile(lens, lq),
+ n.percentile(lens, uq))
+ pfReads = [read for read,l in zip(reads, lens) if
+@@ -476,16 +477,16 @@ def callConsensus():
+ zmwsForBCs = getZmwsForBarcodes()
+
+ # subsample
+- zmwsForBCs = {k:subsampleReads(v) for k,v in zmwsForBCs.items()}
++ zmwsForBCs = {k:subsampleReads(v) for k,v in list(zmwsForBCs.items())}
+
+ logging.info("unfiltered average zmws per barcode: %g" %
+- n.round(n.mean(map(len, zmwsForBCs.values()))))
++ n.round(n.mean(list(map(len, list(zmwsForBCs.values()))))))
+
+ # filter ZMWs
+ zmwsForBCs = filterZmws(zmwsForBCs)
+
+ logging.info("filtered average zmws per barcode: %g" %
+- n.round(n.mean(map(len, zmwsForBCs.values()))))
++ n.round(n.mean(list(map(len, list(zmwsForBCs.values()))))))
+
+ # now choose the best subread to seed the assembly
+ if runner.args.ccsFofn:
+@@ -496,7 +497,7 @@ def callConsensus():
+ open(runner.args.ccsFofn).read().splitlines()}
+
+ # fill in the CCS spot.
+- for k,v in zmwsForBCs.items():
++ for k,v in list(zmwsForBCs.items()):
+ l = []
+ for zmw,lZmw in v:
+ r = ccsReaders[movieNameFromFile(zmw.baxH5.file.filename)]
+@@ -505,17 +506,17 @@ def callConsensus():
+ else:
+ # add none to the CCS spot.
+ zmwsForBCs = {k:[(zmw,lZmw,None) for zmw,lZmw in v]
+- for k,v in zmwsForBCs.iteritems()}
++ for k,v in zmwsForBCs.items()}
+
+- readAndReads = { k:makeReadAndReads(v) for k,v in zmwsForBCs.items() }
++ readAndReads = { k:makeReadAndReads(v) for k,v in list(zmwsForBCs.items()) }
+
+ # remove barcodes that don't have a seed read and a set of useable reads.
+- readAndReads = { k:v for k,v in readAndReads.items() if v[0] and v[1] }
++ readAndReads = { k:v for k,v in list(readAndReads.items()) if v[0] and v[1] }
+
+ # generate FASTA files
+ outDir = runner.args.outDir
+
+- for barcode, reads in readAndReads.items():
++ for barcode, reads in list(readAndReads.items()):
+ bcdir = '/'.join((outDir, barcode))
+ if not os.path.exists(bcdir):
+ os.makedirs(bcdir)
+@@ -537,8 +538,7 @@ def callConsensus():
+ for inFof, in zipFofns(runner.args.inputFofn):
+ bh5 = BaxH5Reader(inFof)
+ reg = bh5.file['/PulseData/Regions']
+- inMovie = filter(lambda z : z.baxH5.movieName == bh5.movieName,
+- subreads)
++ inMovie = [z for z in subreads if z.baxH5.movieName == bh5.movieName]
+ holes = n.in1d(reg[:,0], n.array([a.holeNumber for a in inMovie]))
+ if any(holes):
+ nreg = reg[holes,:]
+@@ -558,12 +558,12 @@ def callConsensus():
+ ofile.close()
+
+ ## call gcon
+- outDirs = [ (outDir, k) for k in readAndReads.keys() ]
++ outDirs = [ (outDir, k) for k in list(readAndReads.keys()) ]
+ if runner.args.nProcs == 1:
+- outFasta = filter(lambda z: z, map(gconFunc, outDirs))
++ outFasta = [z for z in map(gconFunc, outDirs) if z]
+ else:
+ pool = Pool(runner.args.nProcs)
+- outFasta = filter(lambda z : z, pool.map(gconFunc, outDirs))
++ outFasta = [z for z in pool.map(gconFunc, outDirs) if z]
+
+ ## write the results
+ with FastaWriter('/'.join((outDir, "consensus.fa"))) as w:
+@@ -572,7 +572,7 @@ def callConsensus():
+
+ ## optionally cleanup
+ if not runner.args.keepTmpDir:
+- for barcode, reads in readAndReads.items():
++ for barcode, reads in list(readAndReads.items()):
+ bcdir = '/'.join((outDir, barcode))
+ shutil.rmtree(bcdir)
+
+--- a/tests/cram/consensus.t.disabled
++++ b/tests/cram/consensus.t.disabled
+@@ -1,6 +1,6 @@
+- $ export INH5=`python -c "from pbcore import data ; print data.getCmpH5()"`
+- $ export INBH51=`python -c "from pbcore import data ; print data.geBasH5s[0]"`
+- $ export INBH52=`python -c "from pbcore import data ; print data.getBasH5s[1]"`
++ $ export INH5=`python3 -c "from pbcore import data ; print data.getCmpH5()"`
++ $ export INBH51=`python3 -c "from pbcore import data ; print data.geBasH5s[0]"`
++ $ export INBH52=`python3 -c "from pbcore import data ; print data.getBasH5s[1]"`
+ $ export BARCODE_FASTA=$TESTDIR/../../etc/barcode.fasta
+ $ echo $INBH51 > bas.fofn
+ $ echo $INBH52 >> bas.fofn
+--- a/tests/cram/sanity.t
++++ b/tests/cram/sanity.t
+@@ -1,6 +1,6 @@
+- $ export INH5=`python -c "from pbcore import data ; print data.getCmpH5()"`
+- $ export INBH51=`python -c "from pbcore import data ; print data.getBasH5s()[0]"`
+- $ export INBH52=`python -c "from pbcore import data ; print data.getBasH5s()[1]"`
++ $ export INH5=`python3 -c "from pbcore import data ; print data.getCmpH5()"`
++ $ export INBH51=`python3 -c "from pbcore import data ; print data.getBasH5s()[0]"`
++ $ export INBH52=`python3 -c "from pbcore import data ; print data.getBasH5s()[1]"`
+ $ export BARCODE_FASTA=$TESTDIR/../../etc/barcode.fasta
+ $ echo $INBH51 > bas.fofn
+ $ echo $INBH52 >> bas.fofn
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
format-manpage.patch
module-multiarch-path.patch
spelling.patch
+2to3.patch
=====================================
debian/rules
=====================================
@@ -9,12 +9,12 @@ include /usr/share/dpkg/default.mk
PYBUILD_NAME = pbbarcode
%:
- LC_ALL=C.UTF-8 dh $@ --with python2 --buildsystem=pybuild
+ LC_ALL=C.UTF-8 dh $@ --with python3 --buildsystem=pybuild
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
PYBUILD_SYSTEM=custom \
- PYBUILD_TEST_ARGS="find tests -name '*.py' | xargs nosetests -v" \
+ PYBUILD_TEST_ARGS="find tests -name '*.py' | xargs nosetests3 -v" \
dh_auto_test
endif
=====================================
debian/tests/control
=====================================
@@ -1,3 +1,3 @@
Tests: run-unit-test
-Depends: @, pbh5tools, python-nose, python-cram
+Depends: @, pbh5tools, python3-nose, python3-cram
Restrictions: allow-stderr
=====================================
debian/tests/run-unit-test
=====================================
@@ -2,15 +2,15 @@
pkg=pbbarcode
-if [ "$ADTTMP" = "" ] ; then
- ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
- trap "rm -rf $ADTTMP" 0 INT QUIT ABRT PIPE TERM
+if [ "$AUTOPKGTEST_TMP" = "" ] ; then
+ AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+ trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
fi
-cp -a /usr/share/doc/${pkg}/etc $ADTTMP
-cp -a /usr/share/doc/${pkg}/tests $ADTTMP
+cp -a /usr/share/doc/${pkg}/etc $AUTOPKGTEST_TMP
+cp -a /usr/share/doc/${pkg}/tests $AUTOPKGTEST_TMP
-cd $ADTTMP
+cd $AUTOPKGTEST_TMP
find . -name "*.gz" -exec gunzip \{\} \;
find tests -name "*.py" | xargs nosetests
@@ -22,8 +22,8 @@ find tests/cram -name "*.t" | grep -v consensus.t | xargs cram --verbose
# I have tried the very first part of this test which translates to
cd etc
-python -c "from pbcore import data ; print data.getBasH5s()[0]" > bas.fofn
-python -c "from pbcore import data ; print data.getBasH5s()[1]" >> bas.fofn
+python3 -c "from pbcore import data ; print data.getBasH5s()[0]" > bas.fofn
+python3 -c "from pbcore import data ; print data.getBasH5s()[1]" >> bas.fofn
pbbarcode labelZmws barcode.fasta bas.fofn
# and even this takes long enough that I decided to kill the process
# So probably this is nothing we should push to the autopkgtest infrastructure
=====================================
debian/upstream/metadata
=====================================
@@ -1,7 +1,9 @@
Registry:
- - Name: bio.tools
- Entry: NA
- - Name: OMICtools
- Entry: OMICS_18566
- - Name: SciCrunch
- Entry: NA
+- Name: bio.tools
+ Entry: NA
+- Name: OMICtools
+ Entry: OMICS_18566
+- Name: SciCrunch
+ Entry: NA
+Repository: https://github.com/PacificBiosciences/pbbarcode
+Repository-Browse: https://github.com/PacificBiosciences/pbbarcode
View it on GitLab: https://salsa.debian.org/med-team/pbbarcode/compare/ea7b3c2a84cca6d4d93eb93db15a90f26eb3f78c...aad2d78ed8af4705f7c983f57d6007a1ea805ea4
--
View it on GitLab: https://salsa.debian.org/med-team/pbbarcode/compare/ea7b3c2a84cca6d4d93eb93db15a90f26eb3f78c...aad2d78ed8af4705f7c983f57d6007a1ea805ea4
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