[med-svn] [Git][med-team/emmax][master] 8 commits: routine-update: Packaging update

[Mohd Bilal (@rmb)]

Mohd  Bilal pushed to branch master at Debian Med / emmax


Commits:
d0ce860c by Mohammed Bilal at 2022-07-12T17:33:20+00:00
routine-update: Packaging update

- - - - -
7fa8edb4 by Mohammed Bilal at 2022-07-12T17:33:25+00:00
routine-update: Standards-Version: 4.6.1

- - - - -
4dd9afd4 by Mohammed Bilal at 2022-07-12T17:33:26+00:00
routine-update: debhelper-compat 13

- - - - -
f08446ba by Mohammed Bilal at 2022-07-12T17:33:33+00:00
routine-update: Remove trailing whitespace in debian/copyright

- - - - -
c8822632 by Mohammed Bilal at 2022-07-12T17:33:34+00:00
routine-update: Add salsa-ci file

- - - - -
08b3a4f7 by Mohammed Bilal at 2022-07-12T17:33:35+00:00
routine-update: Rules-Requires-Root: no

- - - - -
720ca911 by Mohammed Bilal at 2022-07-12T23:11:56+05:30
Add autopkgtests

- - - - -
492ea076 by Mohammed Bilal at 2022-07-12T23:16:47+05:30
Update changelog

- - - - -


7 changed files:

- debian/changelog
- − debian/compat
- debian/control
- debian/copyright
- + debian/salsa-ci.yml
- + debian/tests/control
- + debian/tests/run-unit-test


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,20 @@
+emmax (0~beta.20100307-2) UNRELEASED; urgency=medium
+
+  [ Steffen Möller ]
+  * Team upload.
+  * Update metadata with ref to conda
+
+  [ Mohammed Bilal ]
+  * routine-update: Packaging update
+  * routine-update: Standards-Version: 4.6.1
+  * routine-update: debhelper-compat 13
+  * routine-update: Remove trailing whitespace in debian/copyright
+  * routine-update: Add salsa-ci file
+  * routine-update: Rules-Requires-Root: no
+  * Add autopkgtests
+
+ -- Mohammed Bilal <mdbilal at disroot.org>  Tue, 12 Jul 2022 23:16:02 +0530
+
 emmax (0~beta.20100307-1) unstable; urgency=low
 
   * Initial release (Closes: #925158)


=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-12


=====================================
debian/control
=====================================
@@ -4,17 +4,18 @@ Uploaders: SteffenSteffen Moeller <moeller at debian.org>,
            Andreas Tille <tille at debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 12~),
+Build-Depends: debhelper-compat (= 13),
                libatlas-base-dev,
                liblapack-dev,
                zlib1g-dev,
                libblas3,
                liblapack3,
                libatlas3-base
-Standards-Version: 4.3.0
+Standards-Version: 4.6.1
 Vcs-Browser: https://salsa.debian.org/med-team/emmax
 Vcs-Git: https://salsa.debian.org/med-team/emmax.git
 Homepage: http://genome.sph.umich.edu/wiki/EMMAX
+Rules-Requires-Root: no
 
 Package: emmax
 Architecture: any


=====================================
debian/copyright
=====================================
@@ -1,6 +1,6 @@
 Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: emmax
-Upstream-Contact: Hyun Min Kang <hmkang at umich.edu> 
+Upstream-Contact: Hyun Min Kang <hmkang at umich.edu>
 Source: http://genetics.cs.ucla.edu/emmax/
 
 Files: *


=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml


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


=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,35 @@
+#!/bin/bash
+set -e
+
+pkg=plink
+
+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}"
+
+echo "247395d4cfd4bef03befd9672a2afe0a  test.emmax.ps" >> checksums
+
+p-link --noweb  --file test --recode12 --output-missing-genotype 0 --transpose --out test
+
+awk '{print $1,$2,$6}' test.ped > test.emmax_phenotypes
+sed -i 's/-9$/NA/' test.emmax_phenotypes
+sed -i 's/0$/NA/' test.emmax_phenotypes
+
+echo -e "\e[93m\e[1mRunning Tests\e[0m"
+
+echo -e "\e[93m\e[1mTest 1\e[0m"
+
+emmax-kin -v -d 10 test
+
+echo -e "\e[93m\e[1mTest 2\e[0m"
+
+emmax -v -d 10 -t test -p test.emmax_phenotypes -k test.BN.kinf -o test.emmax
+
+md5sum --check checksums
+echo -e "\e[92m\e[1mPASS\e[0m"



View it on GitLab: https://salsa.debian.org/med-team/emmax/-/compare/2e9ee3883a705fa511a09504bd98cab6eb553907...492ea076f0958ce65cbdf9ec8dae52560af00797

-- 
View it on GitLab: https://salsa.debian.org/med-team/emmax/-/compare/2e9ee3883a705fa511a09504bd98cab6eb553907...492ea076f0958ce65cbdf9ec8dae52560af00797
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