Re: [Outreachy] predictprotein and other RostLab packages

Hi Andreas,

2016-07-02 0:32 GMT+03:00 Andreas Tille <andreas@an3as.eu>:

Hi Tanya,

On Fri, Jul 01, 2016 at 12:09:36PM +0300, merlettaia wrote:
> .... That's why I think there
> should be different order of commands, and this should fix that problem. At
> least I tried to reproduce, it doesn't appear any more. Please check my
> recent commit, and tell me if the error still appears.

Looks good now

> There is also 1 problem with this package - in last test it can't load apbs
> package, even if it is installed.

Shouldn't it in the Depends of the test control file if it is needed?

It's optional in debian/control file, and it should be - pdb2pqr works without it, and it simply shows warning message. All my tests pass without apbs. Some of pdb2pqr upstream tests won't pass, because they suppose that this optional package is installed and compare output file with expected output, which differs when apbs is present or is not (I don't use these tests).

For now installation of apbs is considered by pdb2pqr to be correct if in python REPL command "from apbslib import *" doesn't fail with "ImportError: No module named apbslib". For now even when apbs is built with -DENABLE_PYTHON=ON flag (as suggested by pdb2pqr) and installed, this command still fails.

I'll spend some time on apbs tomorrow and if I'll fail, I'll probably continue working on other packages.

> pdb2pqr doesn't fail, still some
> functionality which involves apbs call, is not available. For the moment I
> worked on that package I decided to postpone it and to fix later. Now I'll
> try to install apbs from sources and check where the problem is - if you
> don't mind.

As I said previously its perfectly fine if you do further research on
this specific issue. May be it might uncover some problems either in
pdb2pqr or apbs. However, for the moment I follow your hint and
deactivate the test. It now simply echos a message that explains why
the test is not run. So for the moment we have a better package than
before (at least some testing) and we can add more and better testing
later.

Thanks a lot for your fine work

Andreas.

PS: Please let me know what packages from rostlab are ready for upload.

For now I made simple tests are ready for these packages:
librg-blast-parser-perl, librg-utils-perl,
librostlab, librostlab-blast,
libzerg, libzerg-perl,
profisis, disulfinder,

rate4site, reprof.

For some of them I haven't wrote correct descriptions\README.test yet. There is a simple test in disulfinder with Readme.test, but I wanted to check this package if I could improve tests somehow (and probably do the same for profisis and rate4site). All current tests should pass when packages are installed correctly.

I haven't wrote tests for these packages yet: pssh2, profnet, profphd, profphd-utils, predictprotein.

--
http://fam-tille.de

Best wishes,

Tanya.