[med-svn] [Git][med-team/king-probe][master] 8 commits: Add test and reference data
Pranav Ballaney
gitlab at salsa.debian.org
Wed Jul 15 16:19:45 BST 2020
Pranav Ballaney pushed to branch master at Debian Med / king-probe
Commits:
6a3e113d by Pranav Ballaney at 2020-07-15T17:39:23+05:30
Add test and reference data
- - - - -
bf22e709 by Pranav Ballaney at 2020-07-15T17:39:40+05:30
Add autopkgtests
- - - - -
2f45becc by Pranav Ballaney at 2020-07-15T18:55:58+05:30
Install docs and examples
- - - - -
e30a2f99 by Pranav Ballaney at 2020-07-15T20:02:05+05:30
Add notes about files used for autopkgtests
- - - - -
57eb2d1a by Pranav Ballaney at 2020-07-15T20:02:48+05:30
Add partial copyright info about files used for autopkgtests
- - - - -
57d7f1ae by Pranav Ballaney at 2020-07-15T20:03:14+05:30
Update changelog
- - - - -
846a5a4b by Pranav Ballaney at 2020-07-15T20:05:55+05:30
Fix an error in d/docs
- - - - -
e4b068bf by Pranav Ballaney at 2020-07-15T20:08:26+05:30
Add Pranav Ballaney to Uploaders
- - - - -
16 changed files:
- + debian/README.test
- debian/changelog
- debian/control
- debian/copyright
- + debian/docs
- + debian/examples
- + debian/tests/control
- + debian/tests/data/1zni.pdb1.gz
- + debian/tests/data/6ins.pdb1.gz
- + debian/tests/ref/6ins.dotinfo.table.gz
- + debian/tests/ref/6ins.kin.gz
- + debian/tests/ref/6ins.rawinfo.table.gz
- + debian/tests/ref/6ins.surfacedots.kin.gz
- + debian/tests/ref/6insEF.kin.gz
- + debian/tests/ref/6ins_1zni.kin.gz
- + debian/tests/run-unit-test
Changes:
=====================================
debian/README.test
=====================================
@@ -0,0 +1,22 @@
+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.
+─────────────────────────────────────────────────
+
+Files: debian/tests/data/6ins.pdb1.gz
+Source: https://www.rcsb.org/structure/6INS
+
+Files: debian/tests/data/1zni.pdb1.gz
+Source: https://www.rcsb.org/structure/1ZNI
+
+Files: debian/tests/ref/*
+These files were produced by running the data files
+ listed above through king-probe as described in
+ run-unit-test.
=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+king-probe (2.16.160404+git20200121.9b198c1-3) UNRELEASED; urgency=medium
+
+ * Add test and reference data
+ * Add autopkgtests
+ * Install docs and examples
+ * Add notes about files used for autopkgtests
+ * Add partial copyright info about files used for autopkgtests
+
+ -- Pranav Ballaney <ballaneypranav at gmail.com> Wed, 15 Jul 2020 20:02:54 +0530
+
king-probe (2.16.160404+git20200121.9b198c1-2) unstable; urgency=medium
* Do not hard code the build architecture compiler
=====================================
debian/control
=====================================
@@ -2,7 +2,8 @@ Source: king-probe
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Malihe Asemani <ml.asemani at gmail.com>,
Andreas Tille <tille at debian.org>,
- Michael Prisant <michael.prisant at gmail.com>
+ Michael Prisant <michael.prisant at gmail.com>,
+ Pranav Ballaney <ballaneypranav at gmail.com>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 12)
=====================================
debian/copyright
=====================================
@@ -10,6 +10,19 @@ Files: debian/*
Copyright: 2015 Malihe Asemani <ml.asemani at gmail.com>, Andreas Tille <tille at debian.org>
License: probe
+Files: debian/tests/data/6ins.pdb1.gz
+Source: https://www.rcsb.org/structure/6INS
+
+Files: debian/tests/data/1zni.pdb1.gz
+Source: https://www.rcsb.org/structure/1ZNI
+
+Files: debian/tests/ref/*
+Copyright: 2020 Pranav Ballaney <ballaneypranav at gmail.com>
+License: probe
+Comment: These files were produced by running the data files
+ listed above through king-probe as described in
+ debian/tests/run-unit-test
+
License: probe
This is free software and the source code is freely
available. You are free to redistribute or modify under the
=====================================
debian/docs
=====================================
@@ -0,0 +1,3 @@
+debian/README*
+debian/tests/run-unit-test
+README*
\ No newline at end of file
=====================================
debian/examples
=====================================
@@ -0,0 +1,2 @@
+debian/tests/data
+debian/tests/ref
\ No newline at end of file
=====================================
debian/tests/control
=====================================
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr
=====================================
debian/tests/data/1zni.pdb1.gz
=====================================
Binary files /dev/null and b/debian/tests/data/1zni.pdb1.gz differ
=====================================
debian/tests/data/6ins.pdb1.gz
=====================================
Binary files /dev/null and b/debian/tests/data/6ins.pdb1.gz differ
=====================================
debian/tests/ref/6ins.dotinfo.table.gz
=====================================
Binary files /dev/null and b/debian/tests/ref/6ins.dotinfo.table.gz differ
=====================================
debian/tests/ref/6ins.kin.gz
=====================================
Binary files /dev/null and b/debian/tests/ref/6ins.kin.gz differ
=====================================
debian/tests/ref/6ins.rawinfo.table.gz
=====================================
Binary files /dev/null and b/debian/tests/ref/6ins.rawinfo.table.gz differ
=====================================
debian/tests/ref/6ins.surfacedots.kin.gz
=====================================
Binary files /dev/null and b/debian/tests/ref/6ins.surfacedots.kin.gz differ
=====================================
debian/tests/ref/6insEF.kin.gz
=====================================
Binary files /dev/null and b/debian/tests/ref/6insEF.kin.gz differ
=====================================
debian/tests/ref/6ins_1zni.kin.gz
=====================================
Binary files /dev/null and b/debian/tests/ref/6ins_1zni.kin.gz differ
=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,70 @@
+#!/bin/bash
+set -e
+
+pkg=king-probe
+
+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 *
+ls -R
+cd data
+#do_stuff_to_test_package#
+echo -e "\e[93m\e[1mTest 1\e[0m"
+king-probe 6ins.pdb1 >> 6ins.kin
+tail +2 6ins.kin > 6ins.kin.head
+tail +2 ../ref/6ins.kin > ../ref/6ins.kin.head
+diff 6ins.kin.head ../ref/6ins.kin.head
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 2\e[0m"
+king-probe -count -self all 6ins.pdb1 > 6ins.dotinfo.table
+tail +2 6ins.dotinfo.table > 6ins.dotinfo.table.head
+tail +2 ../ref/6ins.dotinfo.table > ../ref/6ins.dotinfo.table.head
+diff 6ins.dotinfo.table.head ../ref/6ins.dotinfo.table.head
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 3\e[0m"
+king-probe -unformated -self "all" 6ins.pdb1 > 6ins.rawinfo.table
+tail +2 6ins.rawinfo.table > 6ins.rawinfo.table.head
+tail +2 ../ref/6ins.rawinfo.table > ../ref/6ins.rawinfo.table.head
+diff 6ins.rawinfo.table.head ../ref/6ins.rawinfo.table.head
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 4\e[0m"
+king-probe -out all 6ins.pdb1 >> 6ins.surfacedots.kin
+tail +2 6ins.surfacedots.kin > 6ins.surfacedots.kin.head
+tail +2 ../ref/6ins.surfacedots.kin > ../ref/6ins.surfacedots.kin.head
+diff 6ins.surfacedots.kin.head ../ref/6ins.surfacedots.kin.head
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 5\e[0m"
+king-probe -both chainE chainF 6ins.pdb1 >> 6insEF.kin
+tail +2 6insEF.kin > 6insEF.kin.head
+tail +2 ../ref/6insEF.kin > ../ref/6insEF.kin.head
+diff 6insEF.kin.head ../ref/6insEF.kin.head
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 6\e[0m"
+king-probe -once all all 6ins.pdb1 1zni.pdb1 >> 6ins_1zni.kin
+tail +2 6ins_1zni.kin > 6ins_1zni.kin.head
+tail +2 ../ref/6ins_1zni.kin > ../ref/6ins_1zni.kin.head
+diff 6ins_1zni.kin.head ../ref/6ins_1zni.kin.head
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
View it on GitLab: https://salsa.debian.org/med-team/king-probe/-/compare/38834d13fe946c17e840ff76ec82c73ca4950c03...e4b068bf1fa442da75a41ab4166419d0cd709148
--
View it on GitLab: https://salsa.debian.org/med-team/king-probe/-/compare/38834d13fe946c17e840ff76ec82c73ca4950c03...e4b068bf1fa442da75a41ab4166419d0cd709148
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