Re: Help with autopkgtest for package andi

[Fabian Klötzl <kloetzl@evolbio.mpg.de>]

Hi Samyak,

By accident I noticed that you opened a pull request on Salsa. Note that
most communication in this team happens via mail. Thus, your changes
flew under the radar.

The update to v0.13 looks fine to me. You can push that directly to the
repository and ask for a sponsorship on the mailing list. As I have some
free time on my hand now, I will look closer at the autopkgtests. We can
then add them in a -2.

Best,
Fabian



On 07.03.20 20:12, Samyak Jain wrote:
> Hey Fabian,
> Thank you for the follow-ups :D
> 
> On Sat, Mar 7, 2020 at 9:56 PM Fabian Klötzl <kloetzl@evolbio.mpg.de
> <mailto:kloetzl@evolbio.mpg.de>> wrote:
> 
>     Hi,
> 
>     Adding autopackagetests for andi has been on my TODO list for a long
>     time, as I am both its upstream author and maintainer. However, as my
>     dissertation is due in two weeks, that currently takes priority.
> 
>     If you want to go forward with the tests, here are some pointers: The
>     package comes with eight tests, all located in the test directory. Of
>     these test_esa, test_process, and test_seq are compile time only. Don't
>     worry about them.
>      
> 
>     The shell scripts verify andi in different conditions. To that end, andi
>     has to be fed simulated sequences as I didn't want to check in large
>     data into git. So the shell scripts use a program called test_fasta,
>     which basically simulates genetic sequences. So you first have to figure
>     out how to build that simulator during the autopackgetest. Next, run the
>     shell scripts. Finally, make the tests reproducible, as they can
>     randomly fail. Check test_random.sh for some documentation on that. You
>     probably also have to patch the path to andi currently hard coded in the
>     scripts.
> 
>     Feel free to ask any question you like; I am happy to assist you.
> 
> 
> I went through the files, andi-manual.pdf and went through the
> test/directory.
> For that, I have added a file (debian/tests/run-unit-test) which is as
> follows:
> 
>  #!/bin/bash
> set -e
> 
> pkg=andi
> 
> 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
> 
> mkdir ${AUTOPKGTEST_TMP}/test
> cp -a test/* "${AUTOPKGTEST_TMP}/test"
> 
>  cd "${AUTOPKGTEST_TMP}"
> 
> ./test/*.sh
> 
> Following error was encountered:
> 
> autopkgtest [00:00:12]: test run-unit-test: [-----------------------
> Triggering low homology failed
> a_low.fa:>S0 (base_seed: 744030346)
> a_low.fa:>S1 (base_seed: 744030346)
> b_low.fa:>S0 (base_seed: 2613208344)
> b_low.fa:>S1 (base_seed: 2613208344)
> both_low.fa:>S0 (base_seed: 2592210513)
> both_low.fa:>S1 (base_seed: 2592210513)
> autopkgtest [00:00:13]: test run-unit-test: -----------------------]
> autopkgtest [00:00:13]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
> run-unit-test        FAIL non-zero exit status 1
> 
> 
> I'm not really sure about it, can you please help me with it?
> 
> Thanks and regards,
> Samyak Jain.