[med-svn] [Git][med-team/sumatra][master] 9 commits: New upstream version 1.0.36+ds
Pierre Gruet
gitlab at salsa.debian.org
Tue Apr 14 16:42:43 BST 2020
Pierre Gruet pushed to branch master at Debian Med / sumatra
Commits:
2fad3e13 by Pierre Gruet at 2020-04-13T15:25:26+02:00
New upstream version 1.0.36+ds
- - - - -
b252eee7 by Pierre Gruet at 2020-04-13T15:25:26+02:00
Update upstream source from tag 'upstream/1.0.36+ds'
Update to upstream version '1.0.36+ds'
with Debian dir 844a838b63d483ead3fab60313e6084c4cb12002
- - - - -
a4af1e01 by Pierre Gruet at 2020-04-13T15:35:22+02:00
Indicating in debian/copyright that sumalibs/ was removed
- - - - -
2ddf50be by Pierre Gruet at 2020-04-13T17:54:03+02:00
Updating debian/watch to fit new +ds version
- - - - -
bd71edef by Pierre Gruet at 2020-04-13T18:04:43+02:00
Passing -g flag to the compiler
- - - - -
df8a93c4 by Pierre Gruet at 2020-04-13T18:05:17+02:00
Adding autopkgtests
- - - - -
49561822 by Pierre Gruet at 2020-04-13T18:08:40+02:00
Providing autopkgtests as examples
- - - - -
fb6492f3 by Pierre Gruet at 2020-04-14T14:08:19+02:00
Adding new uploader
- - - - -
34ec1756 by Pierre Gruet at 2020-04-14T15:47:28+02:00
Updating changelog
- - - - -
15 changed files:
- ._sumatra_user_manual.md
- + debian/README.test
- debian/changelog
- debian/control
- debian/copyright
- + debian/patches/fix_build.patch
- debian/patches/series
- + debian/sumatra.examples
- + debian/tests/alignmentIdenticalInputs
- + debian/tests/alignmentOneInput
- + debian/tests/alignmentTwoInputsTwoThresholds
- + debian/tests/control
- + debian/tests/run-unit-test
- debian/watch
- sumatra.c
Changes:
=====================================
._sumatra_user_manual.md
=====================================
Binary files a/._sumatra_user_manual.md and b/._sumatra_user_manual.md differ
=====================================
debian/README.test
=====================================
@@ -0,0 +1,8 @@
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+This package can be tested by running the provided test:
+
+ sh run-unit-test
+
+in order to confirm its integrity.
=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+sumatra (1.0.36+ds-1) UNRELEASED; urgency=medium
+
+ * New upstream version 1.0.36+ds
+ * Updating debian/watch to fit new +ds version
+ * Passing -g flag to the compiler
+ * Adding autopkgtests
+ * Providing autopkgtests as examples
+
+ -- Pierre Gruet <pgtdebian at free.fr> Tue, 14 Apr 2020 14:09:09 +0200
+
sumatra (1.0.34-1) unstable; urgency=medium
* New upstream version
=====================================
debian/control
=====================================
@@ -1,7 +1,8 @@
Source: sumatra
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Tim Booth <tbooth at ceh.ac.uk>,
- Andreas Tille <tille at debian.org>
+ Andreas Tille <tille at debian.org>,
+ Pierre Gruet <pgtdebian at free.fr>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 12),
=====================================
debian/copyright
=====================================
@@ -1,6 +1,8 @@
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Contact: Céline Mercier <celine.mercier at metabarcoding.org>
Source: https://github.com/mesocentrefc/sumatra
+Files-Excluded: sumalibs/*
+Comment: Ths libs in sumalibs/ are already packaged in Debian.
Files: *
Copyright: 2013-2015 Tiayyba Riaz
@@ -11,6 +13,7 @@ License: CeCILL-2
Files: debian/*
Copyright: 2015 Tim Booth <tbooth at ceh.ac.uk>
2015 Andreas Tille <tille at debian.org>
+ 2020 Pierre Gruet <pgtdebian at free.fr>
License: CeCILL-2
License: CeCILL-2
=====================================
debian/patches/fix_build.patch
=====================================
@@ -0,0 +1,18 @@
+Description: Providing -g flag to the compiler
+Author: Pierre Gruet <pgtdebian at free.fr>
+Last-Update: 2020-04-13
+
+--- a/global.mk
++++ b/global.mk
+@@ -8,9 +8,9 @@
+
+
+ ifeq ($(CC),gcc)
+- CFLAGS += -O3 -s -DOMP_SUPPORT -w
++ CFLAGS += -g -O3 -s -DOMP_SUPPORT -w
+ else
+- CFLAGS += -O3 -w
++ CFLAGS += -g -O3 -w
+ endif
+
+
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
hardening.patch
use_debian_packaged_sumalibs.patch
+fix_build.patch
=====================================
debian/sumatra.examples
=====================================
@@ -0,0 +1,3 @@
+debian/README.test
+debian/tests/run-unit-test
+debian/tests/alignment*
=====================================
debian/tests/alignmentIdenticalInputs
=====================================
@@ -0,0 +1,39 @@
+#!/bin/sh
+# autopkgtest check: Run sumatra on two identical files with three sequences
+# in each. We use a threshold of 1 and check that
+# * 3 sequences are read in each one;
+# * 5 lines are output with a score of 1.
+# (C) 2020 Pierre Gruet.
+# Author: Pierre Gruet <pgtdebian at free.fr>
+
+set -e
+
+WORKDIR=$(mktemp -d)
+trap "rm -rf $WORKDIR" 0 INT QUIT ABRT PIPE TERM
+cd $WORKDIR
+cat <<EOF > input.fasta
+>SEQ1
+ATGTGATCAATGCTGCTAGCTGCTAGCTGCTACGCACACGTGCATCGCTGCATGCACTGCTGCTGATGCTCAGCTAG
+>SEQ2
+AGGTATCTCGATCGATCACTCGCATCGTGTGCTAGCTGCTAGCTGCTACGATCGCATCGC
+>SEQ3
+AGGTATCTCGATCGATCACTCGCATCGTGTGCTAGCTGCTAGCTGCTACGATCGCATCGC
+EOF
+
+sumatra -t 1. input.fasta input.fasta 2>&1 | \
+ sed -n 's/^3.sequences//p' | \
+ wc -l |
+ grep -q "2"
+
+if [ $? -ne 0 ]; then
+ exit 1
+fi
+
+sumatra -t 1. input.fasta input.fasta 2>&1 | \
+ sed -n 's/^SEQ.*SEQ.*1.00//p' | \
+ wc -l |
+ grep -q "5"
+
+if [ $? -ne 0 ]; then
+ exit 1
+fi
=====================================
debian/tests/alignmentOneInput
=====================================
@@ -0,0 +1,50 @@
+#!/bin/sh
+# autopkgtest check: Run sumatra on one single file with three sequences to
+# test alignment against itself. We use a threshold of 0.5 and then a
+# threshold of 0.6, and we check that
+# * 3 sequences are read in the file;
+# * 3 lines are output with a threshold of 0.5;
+# * 1 line is output with a threshold of 1.
+# (C) 2020 Pierre Gruet.
+# Author: Pierre Gruet <pgtdebian at free.fr>
+
+set -e
+
+WORKDIR=$(mktemp -d)
+trap "rm -rf $WORKDIR" 0 INT QUIT ABRT PIPE TERM
+cd $WORKDIR
+cat <<EOF > input.fasta
+>SEQ1
+ATGTGATCAATGCTGCTAGCTGCTAGCTGCTACGCACACGTGCATCGCTGCATGCACTGCTGCTGATGCTCAGCTAG
+>SEQ2
+AGGTATCTCGATCGATCACTCGCATCGTGTGCTAGCTGCTAGCTGCTACGATCGCATCGC
+>SEQ3
+AGGTATCTCGATCGATCACTCGCATCGTGTGCTAGCTGCTAGCTGCTACGATCGCATCGC
+EOF
+
+sumatra -t 0.5 input.fasta 2>&1 | \
+ sed -n 's/^3.sequences//p' | \
+ wc -l |
+ grep -q "1"
+
+if [ $? -ne 0 ]; then
+ exit 1
+fi
+
+sumatra -t 0.5 input.fasta 2>&1 | \
+ sed -n 's/^SEQ.*SEQ//p' | \
+ wc -l |
+ grep -q "3"
+
+if [ $? -ne 0 ]; then
+ exit 1
+fi
+
+sumatra -t 0.6 input.fasta 2>&1 | \
+ sed -n 's/^SEQ.*SEQ//p' | \
+ wc -l |
+ grep -q "1"
+
+if [ $? -ne 0 ]; then
+ exit 1
+fi
=====================================
debian/tests/alignmentTwoInputsTwoThresholds
=====================================
@@ -0,0 +1,58 @@
+#!/bin/sh
+# autopkgtest check: Run sumatra on two different files with three sequences
+# in each. We use a threshold of 0.7 and then 0.8, and we check that
+# * 3 sequences are read in each file;
+# * 5 lines are output if the threshold is 0.7;
+# * 3 lines are output if the threshold is 0.8.
+# (C) 2020 Pierre Gruet.
+# Author: Pierre Gruet <pgtdebian at free.fr>
+
+set -e
+
+WORKDIR=$(mktemp -d)
+trap "rm -rf $WORKDIR" 0 INT QUIT ABRT PIPE TERM
+cd $WORKDIR
+cat <<EOF > input1.fasta
+>SEQ1
+ATGTGATCAATGCTGCTAGCTGCTAGCTGCTACGCACACGTGCATCGCTGCATGCACTGCTGCTGATGCTCAGCTAG
+>SEQ2
+AGGTATCTCGATCGATCACTCGCATCGTGTGCTAGCTGCTAGCTGCTACGATCGCATCGC
+>SEQ3
+AGGTATCTCGATCGATCACTCGCATCGTGTGCTAGCTGCTAGCTGCTACGATCGCATCGC
+EOF
+
+cat <<EOF > input2.fasta
+>SEQ1
+ATGTATATCGTAGCTCTGCTGCTACGCACACGTGCATCGCTGCATGCACTGCTGCTGATGCTCAGCTAG
+>SEQ2
+AGGTACTCGATCGATCATCCACGTGTCTAGCTGCTAGCTGCTACGATCGCATCGC
+>SEQ3
+AGGTAGATCGATCACTCGCATCGTGCTGCTACGATCGCATCGC
+EOF
+
+sumatra -t 0.7 input1.fasta input2.fasta 2>&1 | \
+ sed -n 's/^3.sequences//p' | \
+ wc -l |
+ grep -q "2"
+
+if [ $? -ne 0 ]; then
+ exit 1
+fi
+
+sumatra -t 0.7 input1.fasta input2.fasta 2>&1 | \
+ sed -n 's/^SEQ.*SEQ//p' | \
+ wc -l |
+ grep -q "5"
+
+if [ $? -ne 0 ]; then
+ exit 1
+fi
+
+sumatra -t 0.8 input1.fasta input2.fasta 2>&1 | \
+ sed -n 's/^SEQ.*SEQ//p' | \
+ wc -l |
+ grep -q "3"
+
+if [ $? -ne 0 ]; then
+ exit 1
+fi
=====================================
debian/tests/control
=====================================
@@ -0,0 +1,2 @@
+Tests: alignmentIdenticalInputs, alignmentOneInput, alignmentTwoInputsTwoThresholds
+Depends: @
=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,39 @@
+#!/bin/bash
+set -e
+
+pkg=sumatra
+
+export LC_ALL=C.UTF-8
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+ AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+ # Double quote below to expand the temporary directory variable now versus
+ # later is on purpose.
+ # shellcheck disable=SC2064
+ trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
+
+cd "${AUTOPKGTEST_TMP}"
+
+sh alignmentIdenticalInputs
+if [ $? -eq 0 ]; then
+ echo "Test alignmentIdenticalInputs PASSED"
+else
+ echo "Test alignmentIdenticalInputs FAILED"
+fi
+
+sh alignmentOneInput
+if [ $? -eq 0 ]; then
+ echo "Test alignmentOneInput PASSED"
+else
+ echo "Test alignmentOneInput FAILED"
+fi
+
+sh alignmentTwoInputsTwoThresholds
+if [ $? -eq 0 ]; then
+ echo "Test alignmentTwoInputsTwoThresholds PASSED"
+else
+ echo "Test alignmentTwoInputsTwoThresholds FAILED"
+fi
+
=====================================
debian/watch
=====================================
@@ -1,3 +1,4 @@
version=4
+opts=dversionmangle=s/\+ds// \
https://git.metabarcoding.org/obitools/sumatra/wikis/home .*/sumatra/uploads/.*/sumatra_v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
=====================================
sumatra.c
=====================================
@@ -20,7 +20,7 @@
#include "libutils/utilities.h"
#include "mtcompare_sumatra.h"
-#define VERSION "1.0.34"
+#define VERSION "1.0.36"
/* ----------------------------------------------- */
View it on GitLab: https://salsa.debian.org/med-team/sumatra/-/compare/71edddbf0175461a92c6d1286b3c46d7ed60a104...34ec1756225c185bc493924c57868fdc8148ef36
--
View it on GitLab: https://salsa.debian.org/med-team/sumatra/-/compare/71edddbf0175461a92c6d1286b3c46d7ed60a104...34ec1756225c185bc493924c57868fdc8148ef36
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