Étienne Mollier pushed to branch master at Debian Med / kineticstools
Commits: b3474d5e by Etienne Mollier at 2020-11-25T22:02:51+01:00 routine-update: New upstream version - - - - - cde48152 by Etienne Mollier at 2020-11-25T22:02:53+01:00 New upstream version 0.6.1+git20200729.e3723e0+dfsg - - - - - 206db447 by Etienne Mollier at 2020-11-25T22:03:06+01:00 Update upstream source from tag 'upstream/0.6.1+git20200729.e3723e0+dfsg' Update to upstream version '0.6.1+git20200729.e3723e0+dfsg' with Debian dir ef9cde02667253c37aca078c45b264daa427f224 - - - - - 695b67a3 by Etienne Mollier at 2020-11-25T22:03:06+01:00 routine-update: Standards-Version: 4.5.1 - - - - - d21c7bc0 by Etienne Mollier at 2020-11-25T22:03:06+01:00 routine-update: debhelper-compat 13 - - - - - 1f625d1c by Etienne Mollier at 2020-11-25T22:20:54+01:00 add myself to Uploaders - - - - - b55cedef by Etienne Mollier at 2020-11-25T23:17:50+01:00 fix resources migration to kineticstools-data - - - - - 11d7480a by Etienne Mollier at 2020-11-25T23:32:24+01:00 declare kineticstools-data Multi-Arch: foreign - - - - - e015e687 by Etienne Mollier at 2020-11-25T23:45:27+01:00 ready to upload to unstable - - - - - 5 changed files: - debian/changelog - debian/control - debian/rules - kineticsTools/MultiSiteCommon.py - test/test_integration.py Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,15 @@ +kineticstools (0.6.1+git20200729.e3723e0+dfsg-1) unstable; urgency=medium + + * Add myself to Uploaders + * New upstream version + * Standards-Version: 4.5.1 (routine-update) + * debhelper-compat 13 (routine-update) + * Fix resources migration to data package when several python versions are + provided by Debian. (Closes: #973058) + * Declare kineticstools-data Multi-Arch: foreign. + + -- Étienne Mollier <[email protected]> Wed, 25 Nov 2020 23:45:13 +0100 + kineticstools (0.6.1+git20200325.3558942+dfsg-1) unstable; urgency=medium [ Etienne Mollier ] ===================================== debian/control ===================================== @@ -1,9 +1,10 @@ Source: kineticstools Maintainer: Debian Med Packaging Team <[email protected]> -Uploaders: Andreas Tille <[email protected]> +Uploaders: Andreas Tille <[email protected]>, + Étienne Mollier <[email protected]> Section: science Priority: optional -Build-Depends: debhelper-compat (= 12), +Build-Depends: debhelper-compat (= 13), dh-python, python3-all, python3-setuptools, @@ -17,7 +18,7 @@ Build-Depends: debhelper-compat (= 12), python3-pytest <!nocheck>, python3-pytest-runner <!nocheck>, python3-pytest-xdist <!nocheck> -Standards-Version: 4.5.0 +Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/kineticstools Vcs-Git: https://salsa.debian.org/med-team/kineticstools.git Homepage: https://github.com/PacificBiosciences/kineticsTools @@ -41,6 +42,7 @@ Description: detection of DNA modifications Package: kineticstools-data Architecture: all +Multi-Arch: foreign Depends: ${misc:Depends} Description: detection of DNA modifications -- data files Tools for detecting DNA modifications from single molecule, real-time (SMRT®) ===================================== debian/rules ===================================== @@ -15,6 +15,7 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all INSTDIR = $(CURDIR)/debian/$(DEB_SOURCE) BINDIR = $(INSTDIR)/usr/bin MANDIR = $(INSTDIR)/usr/share/man/ +DATADIR = $(CURDIR)/debian/kineticstools-data/usr/share/kineticstools/resources %: dh $@ --with python3 --buildsystem=pybuild @@ -26,7 +27,12 @@ override_dh_auto_install: mkdir -p $(MANDIR)/man1 rst2man doc/manual.rst > $(MANDIR)/man1/ipdSummary.1 mkdir -p debian/kineticstools-data/usr/share/kineticstools - mv debian/python3-kineticstools/usr/lib/python3.*/dist-packages/kineticsTools/resources debian/kineticstools-data/usr/share/kineticstools/ + # There is probably a simpler way, but that should do for the moment. + set -e \ + ; for libdir in debian/python3-kineticstools/usr/lib/python3.* \ + ; do rm -rf $(DATADIR) \ + ; mv $${libdir}/dist-packages/kineticsTools/resources $(DATADIR) \ + ; done rm debian/python3-kineticstools/usr/lib/python3.*/dist-packages/nosetests.xml override_dh_auto_clean: ===================================== kineticsTools/MultiSiteCommon.py ===================================== @@ -143,7 +143,7 @@ class MultiSiteCommon(object): def getContextMeans(self, start, end, sequence): meanVector = [] for pos in range(start, end + 1): - ctx = sequence[(pos - self.pre):(pos + self.post + 1)].tostring() + ctx = sequence[(pos - self.pre):(pos + self.post + 1)].tostring().decode("ascii") if ctx in self.contextMeanTable: meanVector.append(self.contextMeanTable[ctx]) else: ===================================== test/test_integration.py ===================================== @@ -13,10 +13,10 @@ EXPECTED_GFF = """\ Escherichia_coli_K12\tkinModCall\tmodified_base\t6307\t6307\t34\t-\t.\tcoverage=56;context=CAGATTAGCACGCTGATGCGCATCAGCGACAAACTGGCGGG;IPDRatio=1.92 Escherichia_coli_K12\tkinModCall\tmodified_base\t6455\t6455\t32\t-\t.\tcoverage=53;context=CCTGCAAGGACTGGATATGCTGATTCTTATTTCACCTGCGA;IPDRatio=1.78 Escherichia_coli_K12\tkinModCall\tmodified_base\t6512\t6512\t32\t-\t.\tcoverage=55;context=GTAATCACAACTATCGATCAACTCATTCTCATTTTTTGCTA;IPDRatio=1.81 -Escherichia_coli_K12\tkinModCall\tm6A\t6984\t6984\t34\t-\t.\tcoverage=56;context=TACTGGCGGGTAACGGCACAACCTACATGCCGCTGGAAGGT;IPDRatio=2.02;identificationQv=5 -Escherichia_coli_K12\tkinModCall\tm4C\t7111\t7111\t24\t+\t.\tcoverage=19;context=GGAGGCCAGGACGCCGCTGCCGCTGCCGCGTTTGGCGTCGA;IPDRatio=2.45;identificationQv=4 +Escherichia_coli_K12\tkinModCall\tm6A\t6984\t6984\t34\t-\t.\tcoverage=56;context=TACTGGCGGGTAACGGCACAACCTACATGCCGCTGGAAGGT;IPDRatio=2.02;frac=0.627;fracLow=0.321;fracUp=0.911;identificationQv=5 +Escherichia_coli_K12\tkinModCall\tm4C\t7111\t7111\t24\t+\t.\tcoverage=19;context=GGAGGCCAGGACGCCGCTGCCGCTGCCGCGTTTGGCGTCGA;IPDRatio=2.45;frac=1.000;fracLow=0.370;fracUp=1.000;identificationQv=4 Escherichia_coli_K12\tkinModCall\tmodified_base\t20051\t20051\t44\t+\t.\tcoverage=19;context=ACGTCAAAGGGTGACAGCAGGCTCATAAGACGCCCCAGCGT;IPDRatio=2.54 -Escherichia_coli_K12\tkinModCall\tm4C\t20296\t20296\t24\t-\t.\tcoverage=17;context=GGATGCCGGGCAACAGCCCGCATTATGGGCGTTGGCCTCAA;IPDRatio=1.86;identificationQv=9 +Escherichia_coli_K12\tkinModCall\tm4C\t20296\t20296\t24\t-\t.\tcoverage=17;context=GGATGCCGGGCAACAGCCCGCATTATGGGCGTTGGCCTCAA;IPDRatio=1.86;frac=1.000;fracLow=0.379;fracUp=1.000;identificationQv=9 Escherichia_coli_K12\tkinModCall\tmodified_base\t20449\t20449\t31\t+\t.\tcoverage=18;context=TGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGT;IPDRatio=2.49""" @@ -39,6 +39,7 @@ class TestKineticsTools(PbIntegrationBase): "--csv", csv_out, "--pvalue", "0.001", "--identify", "m6A,m4C", + "--methylFraction", "--reference", ref_set, alignments ] @@ -46,6 +47,7 @@ class TestKineticsTools(PbIntegrationBase): assert op.isfile(gff_out) assert op.isfile(csv_out) records = [] + print(gff_out) with open(gff_out, "rt") as gff: for line in gff.read().splitlines(): if not line.startswith("##"): @@ -58,4 +60,4 @@ class TestKineticsTools(PbIntegrationBase): csv_records.append(line) assert len(csv_records) == 3222 assert csv_records[1] == \ - r'"Escherichia_coli_K12",6214,0,C,8,0.784,0.144,0.631,1.242,33' + r'"Escherichia_coli_K12",6214,0,C,8,0.784,0.144,0.631,1.242,33,,,' View it on GitLab: https://salsa.debian.org/med-team/kineticstools/-/compare/e6a7696dcc7071456c0a162231c5c2b656f4b7a8...e015e6876b40ee5754be8fc14e0aa57bdcfb9ad1 -- View it on GitLab: https://salsa.debian.org/med-team/kineticstools/-/compare/e6a7696dcc7071456c0a162231c5c2b656f4b7a8...e015e6876b40ee5754be8fc14e0aa57bdcfb9ad1 You're receiving this email because of your account on salsa.debian.org.
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