Re: RFS: added autopkgtest for pplacer
Hi Mohd,
Am Sun, Apr 10, 2022 at 08:08:42PM -0000 schrieb Mohd Bilal:
> I've added autopkgtest for pplacer[1] . As suggested in the matrix room , I've used the test prescribed in the Makefile as well as included some of the commands from the pplacer tutorial[2] .
Thanks a lot for your effort to write a test for pplacer.
> Requesting someone to review and sponsor my changes.
I have some remarks here.
1. There is no information given where you obtained the data in
debian/tests/data from. It is good style to add some script that
fetches the data from somewhere (may be via wget or whaterver
tool you prefer.
2. The data should be also mentioned in d/copyright.
3. Since the size of the data exceedes the size of the other files
it might make sense to create a separate tarball as it is
described in the Debian Med team policy[3]. Alternatively
you might consider xz compressing the data files (which needs
adding them in debian/source/include-binaries) and uncompressing
them once they are needed. The compression rate might be
sufficiently high to tolerate the size of the compressed data
files.
It might be also be sensible to create an extra pplacer-examples
binary package in case the compression rate is not high enough.
A sign for the issue is also given by lintian:
I: pplacer: arch-dep-package-has-big-usr-share 12192kB 39%
4. Unfortunately the test does not work in my pbuilder environment.
I've added a `set -x` to run-unit-test and so I'Ve got:
autopkgtest [07:44:44]: test run-unit-test: [-----------------------
+ export LC_ALL=C.UTF-8
+ LC_ALL=C.UTF-8
+ '[' /tmp/autopkgtest.W5By5K/autopkgtest_tmp = '' ']'
+ cp -a /usr/share/doc/pplacer/examples/src /usr/share/doc/pplacer/examples/vaginal_16s.refpkg /tmp/autopkgtest.W5By5K/autopkgtest_tmp
+ cp -a /tmp/autopkgtest.W5By5K/tree/ /tmp/autopkgtest.W5By5K/autopkgtest_tmp
+ cd /tmp/autopkgtest.W5By5K/autopkgtest_tmp
+ echo -e '\e[93m\e[1mTest 1\e[0m'
+ cd src
+ make test
Test 1
make: *** No rule to make target 'test'. Stop.
autopkgtest [07:44:45]: test run-unit-test: -----------------------]
There is no Makefile provided and if I'm checking the build directory
the Makefile would need a binary _build/tests/tests.native which
contains the according calls to the pplacer binaries. Thus the test
only works in a full source tree ... and I admit I'm quite baffled
why the Salsa-CI test is passing. It obviously rebuilds the needed
binary but I have no idea why.
I think what we should do instead is to read the text of the upstream
test and implement (part of) the calls to the tools as shell script.
Kind regards and thanks again for your work on this anyway
Andreas.
> [1] - https://salsa.debian.org/med-team/pplacer
> [2] - https://fhcrc.github.io/microbiome-demo/
[3] https://med-team.pages.debian.net/policy/#embedding-large-test-data
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http://fam-tille.de
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