[med-svn] [Git][med-team/kineticstools][master] 9 commits: routine-update: New upstream version
Étienne Mollier
gitlab at salsa.debian.org
Wed Nov 25 22:47:00 GMT 2020
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 <etienne.mollier at mailoo.org> 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 <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>
+Uploaders: Andreas Tille <tille at debian.org>,
+ Étienne Mollier <etienne.mollier at mailoo.org>
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
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