[med-svn] [Git][med-team/perm][master] 4 commits: Add testdata

[Shruti Sridhar (@shruti_sridhar)]

Shruti Sridhar pushed to branch master at Debian Med / perm


Commits:
a961c0a0 by Shruti Sridhar at 2021-08-01T19:30:13+05:30
Add testdata

- - - - -
2b0098c9 by Shruti Sridhar at 2021-08-01T19:30:30+05:30
Add autopkgtest

- - - - -
0509f410 by Shruti Sridhar at 2021-08-01T19:30:44+05:30
Install docs

- - - - -
1746f4b6 by Shruti Sridhar at 2021-08-01T19:32:52+05:30
Update changelog

- - - - -


9 changed files:

- + debian/README.test
- debian/changelog
- debian/copyright
- + debian/docs
- + debian/examples
- + debian/tests/control
- + debian/tests/data/Reads.fasta
- + debian/tests/data/Ref.fasta
- + 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 
+────────────────────────────────────────
+Files: debian/tests/data/*
+
+The Ref.fasta and Reads.fasta file were written for testing this package. 
\ No newline at end of file


=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+perm (0.4.0-6) UNRELEASED; urgency=medium
+
+  * Team Upload.
+  * Add testdata
+  * Add autopkgtest
+  * Install docs
+
+ -- Shruti Sridhar <shruti.sridhar99 at gmail.com>  Sun, 01 Aug 2021 19:32:02 +0530
+
 perm (0.4.0-5) unstable; urgency=medium
 
   * Standards-Version: 4.5.1 (routine-update)


=====================================
debian/copyright
=====================================
@@ -12,6 +12,10 @@ Copyright: (c) 2012-2014 Hyun Soon Gweon <hyugwe at ceh.ac.uk>
                2014-2017 Andreas Tille <tille at debian.org>
 License: Apache-2.0
 
+Files: debian/tests/data
+Copyright: Shruti Sridhar <shruti.sridhar99 at gmail.com>
+License: Apache-2.0
+
 License: Apache-2.0
  Unless required by applicable law or agreed to in writing, software
  distributed under the License is distributed on an "AS IS" BASIS,


=====================================
debian/docs
=====================================
@@ -0,0 +1,2 @@
+debian/README*
+debian/tests/run-unit-test
\ No newline at end of file


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


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


=====================================
debian/tests/data/Reads.fasta
=====================================
@@ -0,0 +1,2 @@
+>reads
+ATGCGCATCGACATGACATACGACATCA
\ No newline at end of file


=====================================
debian/tests/data/Ref.fasta
=====================================
@@ -0,0 +1,2 @@
+>ref
+ATGCTAGCATACGACTACAGCATACAGCATCAGACTACGACATCAGACTACAGCATACAGCAATACGACTACAGCATACGACTACAGCATCAGATGCTACGCAGACTACGACATCAGACTACAGCATACGACATCAGACTACTACAGACACAGACACGACGACGACGACTACGACACGACGACTACATCAGACGACGACAGCAGCAGCGACAGCAGACGACATACGACAGCATACGACGACAGACATCAGACGACGACGACGACGACGACGACGACCAGACGCATCAGCAGACACGACGAAAAAAAGGAGCATCAGCA
\ No newline at end of file


=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,17 @@
+#!/bin/bash
+set -e
+
+pkg=perm
+
+export LC_ALL=C.UTF-8
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+  trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
+
+cd "${AUTOPKGTEST_TMP}"
+
+perm Ref.fasta Reads.fasta -v 100 -A -o out.sam  
+[ -s "out.sam" ] || exit 1 && echo "PASS test"
\ No newline at end of file



View it on GitLab: https://salsa.debian.org/med-team/perm/-/compare/fcab8a503500cd6ac7cf18060ce20ced6fc5c314...1746f4b67efdc264aae4df95520a9266600fcc5e

-- 
View it on GitLab: https://salsa.debian.org/med-team/perm/-/compare/fcab8a503500cd6ac7cf18060ce20ced6fc5c314...1746f4b67efdc264aae4df95520a9266600fcc5e
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