[Debian-med-packaging] Bug#990512: unblock: mirtop/0.4.23-2

[Andreas Tille]

Package: release.debian.org
Severity: normal
User: release.debian.org at packages.debian.org
Usertags: unblock
X-Debbugs-Cc: debian-med-packaging at 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
-------------- next part --------------
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 at 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 at 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