[med-svn] [Git][med-team/rdp-readseq][master] 5 commits: Install examples

Pranav Ballaney gitlab at salsa.debian.org
Sat Aug 8 00:19:58 BST 2020 


Pranav Ballaney pushed to branch master at Debian Med / rdp-readseq


Commits:
7e69b74e by Pranav Ballaney at 2020-08-08T04:44:58+05:30
Install examples

- - - - -
e7ae37c7 by Pranav Ballaney at 2020-08-08T04:45:15+05:30
Add autopkgtests

- - - - -
fa500533 by Pranav Ballaney at 2020-08-08T04:46:32+05:30
Install docs

- - - - -
8860d5be by Pranav Ballaney at 2020-08-08T04:47:00+05:30
Add Pranav Ballaney to Uploaders

- - - - -
ec36969b by Pranav Ballaney at 2020-08-08T04:47:16+05:30
Update changelog

- - - - -


10 changed files:

- + debian/README.test
- debian/changelog
- debian/control
- debian/docs
- + debian/examples
- + debian/tests/control
- + debian/tests/data/ids
- + debian/tests/data/random.fa
- + debian/tests/data/random.fq
- + debian/tests/run-unit-test


Changes:

=====================================
debian/README.test
=====================================
@@ -0,0 +1,14 @@
+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.
+
+Notes on the files used for testing this package.
+─────────────────────────────────────────────────
+
+random.fa, random.fq and ids were written with random
+content just to test the package.
\ No newline at end of file


=====================================
debian/changelog
=====================================
@@ -1,3 +1,16 @@
+rdp-readseq (2.0.2-3) UNRELEASED; urgency=medium
+
+  [ Steffen Möller ]
+  * Add new d/u/metadata file with ref to conda
+
+  [ Pranav Ballaney ]
+  * Install examples
+  * Add autopkgtests
+  * Install docs
+  * Add Pranav Ballaney to Uploaders
+
+ -- Pranav Ballaney <ballaneypranav at gmail.com>  Sat, 08 Aug 2020 04:47:04 +0530
+
 rdp-readseq (2.0.2-6) unstable; urgency=medium
 
   * Fix Uploaders lint errors


=====================================
debian/control
=====================================
@@ -2,7 +2,8 @@ Source: rdp-readseq
 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>,
-           Olivier Sallou <osallou at debian.org>
+           Olivier Sallou <osallou at debian.org>,
+           Pranav Ballaney <ballanepranav at gmail.com>
 Section: java
 Priority: optional
 Build-Depends: debhelper (>= 11~),


=====================================
debian/docs
=====================================
@@ -1 +1,3 @@
 README
+debian/README*
+debian/tests/run-unit-test
\ No newline at end of file


=====================================
debian/examples
=====================================
@@ -0,0 +1,2 @@
+debian/tests/data/random.*
+debian/tests/data/ids
\ No newline at end of file


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


=====================================
debian/tests/data/ids
=====================================
@@ -0,0 +1,2 @@
+randomsequence1
+randomsequence2
\ No newline at end of file


=====================================
debian/tests/data/random.fa
=====================================
@@ -0,0 +1,12 @@
+>randomsequence1
+atgcatgcatgccgattagccatgacatgacaccccccaatg
+>randomsequence2
+agacacagatagacagatagacagagatagatggtgtgccca
+>randomsequence3
+aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
+>randomsequence4
+agagagaagaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
+>randomsequence3
+aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
+>randomsequence5
+agagagaagaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa


=====================================
debian/tests/data/random.fq
=====================================
@@ -0,0 +1,24 @@
+ at randomsequence1
+atgcatgcatgccgattagccatgacatgacaccccccaatg
++randomsequence1
+atgcatgcatgccgattagccatgacatgacaccccccaatg
+ at randomsequence2
+agacacagatagacagatagacagagatagatggtgtgccca
++randomsequence2
+agacacagatagacagatagacagagatagatggtgtgccca
+ at randomsequence3
+aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
++randomsequence3
+aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
+ at randomsequence4
+agagagaagaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
++randomsequence4
+agagagaagaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
+ at randomsequence3
+aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
++randomsequence3
+aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
+ at randomsequence5
+agagagaagaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
++randomsequence5
+agagagaagaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa


=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,68 @@
+#!/bin/bash
+set -e
+
+pkg=rdp-readseq
+
+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}"
+
+gunzip -r *
+
+echo -e "\e[93m\e[1mTest 1\e[0m"
+rdp-readseq random-sample -n 2 -s 25 random.fa random-sample
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 2\e[0m"
+rdp-readseq reverse-comp -i random.fa -o reverse-comp
+echo "de07af6b256364aee08e500d595bf4f0  reverse-comp" >> checksums
+md5sum --check checksums
+
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 3\e[0m"
+rdp-readseq rm-dupseq -d -i random.fa -o rm-dupseq
+echo "d978407aaee481974d60be19ba88be81  rm-dupseq" >> checksums
+md5sum --check checksums
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 4\e[0m"
+rdp-readseq split random.fa split 3
+echo "5e7e68143bd6c75810222dad4f7fafdf  split/0_random.fa" >> checksums
+echo "a38c212d74660b3b8b7978b34a65969a  split/1_random.fa" >> checksums
+md5sum --check checksums
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 5\e[0m"
+rdp-readseq to-fasta random.fq > to-fasta
+echo "c1a68f563e86516970219a34ace03f18  to-fasta" >> checksums
+md5sum --check checksums
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 6\e[0m"
+rdp-readseq to-fastq random.fq > to-fastq
+echo "1a8570b3f4122f5131b0983c2d98653f  to-fastq" >> checksums
+md5sum --check checksums
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 7\e[0m"
+rdp-readseq select-seqs ids select-seqs fasta keep random.fa
+echo "b13a011f049ecbb73988bc9ba53e587d  select-seqs" >> checksums
+md5sum --check checksums
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo



View it on GitLab: https://salsa.debian.org/med-team/rdp-readseq/-/compare/d7c2855e189cb2be2dfaed1524d1b07cdb9701be...ec36969baf791e2e5ebd1dbd6b7e3040de91aeb5

-- 
View it on GitLab: https://salsa.debian.org/med-team/rdp-readseq/-/compare/d7c2855e189cb2be2dfaed1524d1b07cdb9701be...ec36969baf791e2e5ebd1dbd6b7e3040de91aeb5
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