Hey Fabian,
Thank you for the follow-ups :D
On Sat, Mar 7, 2020 at 9:56 PM Fabian Klötzl <kloe...@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.
