Re: Help with autopkgtest for package andi

[Andreas Tille <andreas@an3as.eu>]

Hi Fabian,

sponsored - but since you are upstream please fix

  I: andi: spelling-error-in-binary usr/bin/andi exlusive exclusive

in your next release.

Thank you for your preparation

      Andreas.

On Mon, Mar 23, 2020 at 04:27:33PM +0100, Fabian Klötzl wrote:
> 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.
> 
> 

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