Your message dated Sun, 4 Jul 2021 22:25:27 +0200
with message-id <[email protected]>
and subject line Re: Bug#990512: unblock: mirtop/0.4.23-2
has caused the Debian Bug report #990512,
regarding unblock: mirtop/0.4.23-2
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
990512: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=990512
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: release.debian.org
Severity: normal
User: [email protected]
Usertags: unblock
X-Debbugs-Cc: [email protected]
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 <[email protected]> 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 <[email protected]>
+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
--- End Message ---
--- Begin Message ---
On 2021-07-01 06:28:18 +0200, Andreas Tille wrote:
> Package: release.debian.org
> Severity: normal
> User: [email protected]
> Usertags: unblock
> X-Debbugs-Cc: [email protected]
>
> 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
Aged to 7 days.
Cheers
> 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 <[email protected]> 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 <[email protected]>
> +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
--
Sebastian Ramacher
signature.asc
Description: PGP signature
--- End Message ---
