Bug#990512: unblock: mirtop/0.4.23-2
Package: release.debian.org
Severity: normal
User: release.debian.org@packages.debian.org
Usertags: unblock
X-Debbugs-Cc: debian-med-packaging@lists.alioth.debian.org
Please unblock package mirtop
our GSoC Student Shruti Sridhar has written an autopkgtest for
this package which uncovers a real bug. This is fixed in the
really late upload.
[ Reason ]
The upload fixes a circular import in the code which was fixed
in a patch. The according autopkgtest is included in the change
as well.
[ Impact ]
The program would not work without the patch.
[ Tests ]
The autopkgtest is part of the changes of this upload.
[ Risks ]
There are no real risks since the package is a leaf package.
[ Checklist ]
[x] all changes are documented in the d/changelog
[x] I reviewed all changes and I approve them
[x] attach debdiff against the package in testing
unblock mirtop/0.4.23-2
diff -Nru mirtop-0.4.23/debian/changelog mirtop-0.4.23/debian/changelog
--- mirtop-0.4.23/debian/changelog 2019-12-05 11:43:49.000000000 +0100
+++ mirtop-0.4.23/debian/changelog 2021-06-30 20:18:19.000000000 +0200
@@ -1,3 +1,15 @@
+mirtop (0.4.23-2) unstable; urgency=medium
+
+ * Team Upload.
+
+ [ Shruti Sridhar ]
+ * Add autopkgtests
+
+ [ Nilesh Patra ]
+ * d/p/fix-circular-import.patch: Fix circular import
+
+ -- Nilesh Patra <nilesh@debian.org> Wed, 30 Jun 2021 18:18:19 +0000
+
mirtop (0.4.23-1) unstable; urgency=medium
* New upstream version
diff -Nru mirtop-0.4.23/debian/patches/fix-circular-import.patch mirtop-0.4.23/debian/patches/fix-circular-import.patch
--- mirtop-0.4.23/debian/patches/fix-circular-import.patch 1970-01-01 01:00:00.000000000 +0100
+++ mirtop-0.4.23/debian/patches/fix-circular-import.patch 2021-06-30 20:18:19.000000000 +0200
@@ -0,0 +1,29 @@
+Description: import module in needed functions to fix circular import
+Author: Nilesh Patra <nilesh@debian.org>
+Last-Update: 2021-06-30
+--- a/mirtop/bam/bam.py
++++ b/mirtop/bam/bam.py
+@@ -15,7 +15,6 @@
+ from mirtop.mirna.realign import isomir, hits, reverse_complement
+ from mirtop.mirna.mapper import get_primary_transcript, guess_database
+ from mirtop.bam import filter
+-from mirtop.gff import body
+ from mirtop.mirna.annotate import annotate
+ from mirtop.libs import sql
+
+@@ -72,6 +71,7 @@
+ def low_memory_bam(bam_fn, sample, out_handle, args):
+ if args.genomic:
+ raise ValueError("low-memory option is not compatible with genomic coordinates.")
++ from mirtop.gff import body
+ precursors = args.precursors
+ bam_fn = _sam_to_bam(bam_fn)
+ bam_fn = _bam_sort(bam_fn)
+@@ -100,6 +100,7 @@
+ def low_memory_genomic_bam(bam_fn, sample, out_handle, args):
+ logger.info("Reading BAM file in low memory mode.")
+ logger.warning("This is under development and variants can be unexact.")
++ from mirtop.gff import body
+ precursors = args.precursors
+ bam_fn = _sam_to_bam(bam_fn)
+ bam_fn = _bam_sort(bam_fn)
diff -Nru mirtop-0.4.23/debian/patches/series mirtop-0.4.23/debian/patches/series
--- mirtop-0.4.23/debian/patches/series 2019-12-05 11:42:13.000000000 +0100
+++ mirtop-0.4.23/debian/patches/series 2021-06-30 20:18:19.000000000 +0200
@@ -1 +1,2 @@
spelling
+fix-circular-import.patch
diff -Nru mirtop-0.4.23/debian/tests/control mirtop-0.4.23/debian/tests/control
--- mirtop-0.4.23/debian/tests/control 1970-01-01 01:00:00.000000000 +0100
+++ mirtop-0.4.23/debian/tests/control 2021-06-30 20:18:19.000000000 +0200
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @, python3-nose, samtools, bedtools, seqan-apps
+Restrictions: allow-stderr
diff -Nru mirtop-0.4.23/debian/tests/run-unit-test mirtop-0.4.23/debian/tests/run-unit-test
--- mirtop-0.4.23/debian/tests/run-unit-test 1970-01-01 01:00:00.000000000 +0100
+++ mirtop-0.4.23/debian/tests/run-unit-test 2021-06-30 20:18:19.000000000 +0200
@@ -0,0 +1,20 @@
+#!/bin/bash
+set -e
+
+CUR_DIR=`pwd`
+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 ${CUR_DIR}/test/ $AUTOPKGTEST_TMP
+cp -a ${CUR_DIR}/data/ $AUTOPKGTEST_TMP
+
+cd $AUTOPKGTEST_TMP
+
+for py in $(py3versions -s 2> /dev/null)
+do
+ echo "Testing with $py in $(pwd):"
+ nosetests3 -v
+
+done
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