[med-svn] [Git][med-team/seqkit][master] 5 commits: Add autopkgtests

[Nilesh Patra]

Nilesh Patra pushed to branch master at Debian Med / seqkit


Commits:
abd67fc5 by Nilesh Patra at 2020-08-03T15:46:36+00:00
Add autopkgtests

- - - - -
ae9eb5c8 by Nilesh Patra at 2020-08-03T15:46:55+00:00
Add missing sources for repack bam files

- - - - -
91a69c40 by Nilesh Patra at 2020-08-03T15:47:34+00:00
Convert to bam files during install

- - - - -
c1f42c1b by Nilesh Patra at 2020-08-03T15:48:15+00:00
Add new binary: seqkit-examples

- - - - -
620e9103 by Nilesh Patra at 2020-08-03T21:22:40+05:30
Add myself to uploaders

- - - - -


11 changed files:

- debian/control
- − debian/install
- + debian/missing-sources/pcs109_5k.sam
- + debian/missing-sources/pcs109_5k_prim.sam
- + debian/missing-sources/pcs109_5k_spliced.sam
- debian/rules
- + debian/seqkit-examples.docs
- + debian/seqkit.install
- debian/links → debian/seqkit.links
- + debian/tests/control
- + debian/tests/run-unit-test


Changes:

=====================================
debian/control
=====================================
@@ -1,8 +1,7 @@
 Source: seqkit
 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>, Nilesh Patra <npatra974 at gmail.com>
 Section: science
-Testsuite: autopkgtest-pkg-go
 Priority: optional
 Build-Depends: debhelper-compat (= 13),
                dh-golang,
@@ -22,7 +21,8 @@ Build-Depends: debhelper-compat (= 13),
                golang-github-op-go-logging-dev,
                golang-github-logrusorgru-aurora-dev,
                golang-github-tatsushid-go-prettytable-dev,
-               golang-github-bsipos-thist-dev
+               golang-github-bsipos-thist-dev,
+               samtools
 Standards-Version: 4.5.0
 Vcs-Browser: https://salsa.debian.org/med-team/seqkit
 Vcs-Git: https://salsa.debian.org/med-team/seqkit.git
@@ -43,3 +43,19 @@ Description: cross-platform and ultrafast toolkit for FASTA/Q file manipulation
  demonstrates competitive performance in execution time and memory usage
  compared to similar tools. The efficiency and usability of SeqKit enable
  researchers to rapidly accomplish common FASTA/Q file manipulations.
+
+Package: seqkit-examples
+Architecture: all
+Depends: ${shlibs:Depends},
+         ${misc:Depends}
+Description: examples for seqkit: cross-platform and ultrafast toolkit for FASTA/Q file manipulation
+ SeqKit describes a cross-platform ultrafast comprehensive toolkit for
+ FASTA/Q processing. SeqKit provides executable binary files for all
+ major operating systems, including Windows, Linux, and Mac OS X, and can
+ be directly used without any dependencies or pre-configurations. SeqKit
+ demonstrates competitive performance in execution time and memory usage
+ compared to similar tools. The efficiency and usability of SeqKit enable
+ researchers to rapidly accomplish common FASTA/Q file manipulations.
+ .
+ This package contains a test data set as well as sample scripts
+ running some test suite provided by Debian also as autopkgtest.


=====================================
debian/install deleted
=====================================
@@ -1,2 +0,0 @@
-build/bin/seqkit	usr/bin
-build/bin/benchmark	usr/lib/seqkit


=====================================
debian/missing-sources/pcs109_5k.sam
=====================================
The diff for this file was not included because it is too large.

=====================================
debian/missing-sources/pcs109_5k_prim.sam
=====================================
The diff for this file was not included because it is too large.

=====================================
debian/missing-sources/pcs109_5k_spliced.sam
=====================================
The diff for this file was not included because it is too large.

=====================================
debian/rules
=====================================
@@ -9,4 +9,13 @@ include /usr/share/dpkg/default.mk
 
 override_dh_auto_install:
 	dh_auto_install -- --no-source
-	rm debian/seqkit/usr/bin/benchmark
+
+override_dh_installdocs:
+	# Regenerate bam and bam index files
+	cat debian/missing-sources/pcs109_5k_prim.sam | samtools view -Sb - > tests/pcs109_5k_prim.bam
+	cat debian/missing-sources/pcs109_5k.sam | samtools view -Sb - > tests/pcs109_5k.bam
+	cat debian/missing-sources/pcs109_5k_spliced.sam | samtools view -Sb - > tests/pcs109_5k_spliced.bam
+	samtools index tests/pcs109_5k_prim.bam tests/pcs109_5k_prim.bam.bai
+	samtools index tests/pcs109_5k.bam tests/pcs109_5k.bam.bai
+	samtools index tests/pcs109_5k_spliced.bam tests/pcs109_5k_spliced.bam.bai
+	dh_installdocs


=====================================
debian/seqkit-examples.docs
=====================================
@@ -0,0 +1,3 @@
+tests
+debian/missing-sources/*
+debian/tests/run-unit-test


=====================================
debian/seqkit.install
=====================================
@@ -0,0 +1,2 @@
+debian/tmp/usr/bin/seqkit	usr/bin
+debian/tmp/usr/bin/benchmark	usr/lib/seqkit


=====================================
debian/links → debian/seqkit.links
=====================================


=====================================
debian/tests/control
=====================================
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr


=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,36 @@
+#!/bin/bash
+set -e
+
+pkg=seqkit
+
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+  trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -Rf /usr/share/doc/${pkg}-examples/* "${AUTOPKGTEST_TMP}"
+
+cd "${AUTOPKGTEST_TMP}"
+gunzip -r *
+file=tests/hairpin.fa
+
+seqkit seq -w 60 $file > testfile
+
+echo "Test 1"
+filegrep=`grep -c '^>' $file`
+testfilegrep=`grep -c '^>' $file`
+if [ "$filegrep" != "$testfilegrep" ]
+then
+	exit 1
+fi
+echo "PASS"
+
+cksumfile=`cat $file | md5sum | cut -d" " -f 1`
+cksumtestfile=`cat testfile | md5sum | cut -d' ' -f 1`
+echo "Test 2"
+if [ "$cksumfile" != "$cksumtestfile" ]
+then
+	exit 1
+fi
+echo "PASS"
+



View it on GitLab: https://salsa.debian.org/med-team/seqkit/-/compare/2c2feb26d8ef4fcd2a031b0000a55afe731027d6...620e910307418ba637a0882a732c9b3623c52466

-- 
View it on GitLab: https://salsa.debian.org/med-team/seqkit/-/compare/2c2feb26d8ef4fcd2a031b0000a55afe731027d6...620e910307418ba637a0882a732c9b3623c52466
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