Re: HYPHY and tests
Hi Saira & Liubov,
On Fri, Jul 05, 2019 at 04:32:44PM +0200, Liubov Chuprikova wrote:
> On Fri, 5 Jul 2019 at 15:15, Saira Hussain <saira.h0213@zoho.com> wrote:
>
> > My first step was to replicate some of the test suites inside Hyphy. In
> > order to do that I copied the SimpleAnalysis suite inside the tests and
> > configured them to run through autobuild.
>
> There is no need to replicate files that are already inside the source
> package. From this source, we are building three binary packages [1] and
> one of them [2] contains all the files, you need for the tests. Just add
> into run-unit-test a line to copy them to you temporary testing directory.
That's correct. If some files from the source distribution might be
needed for testing we can copy these into a dedicated data package - in
the hyphy case into hyphy-common where we have the examples directory
anyway.
> [1] https://packages.debian.org/en/source/sid/hyphy
> [2] https://packages.debian.org/sid/all/hyphy-common/filelist
@Liubov: Good hint to the filelist! (I was not aware of this and I love
to learn from my students!)
I had a *quick* look into the autopkgtest of hyphy. I pushed a fix
for a typo. When I now run the tests it starts nicely but than one
test seems to expect some user input:
...
3). 3 proportional equiprobable rates
R = 1.
Sample mean = 4.666666666666666 (sample variance = 16.33333333333333)
Rate[0]= 1.00000000 (weight=0.3333333)
Rate[1]= 4.00000000 (weight=0.3333333)
Rate[2]= 9.00000000 (weight=0.3333333)
------------------------------------------------
R = 5.
Sample mean = 23.33333333333333 (sample variance = 408.3333333333334)
Rate[0]= 5.00000000 (weight=0.3333333)
Rate[1]= 20.00000000 (weight=0.3333333)
Rate[2]= 45.00000000 (weight=0.3333333)
------------------------------------------------
4). User defined discrete distribution
Enter the number of categories: <<<<<================ here I just pressed enter
0 is an invalid number of categories
+ for i in *.bf
+ '[' -f definitions+MLE.bf ']'
+ hyphympi definitions+MLE.bf
Error:
Master node received an error:Could not read batch file '/tmp/hyphy-common-test.oGNZo5/displayfunction.bf'.
Path stack:
/usr/lib/hyphy/
/tmp/hyphy-common-test.oGNZo5/
/tmp/hyphy-common-test.oGNZo5/--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
@Saira: Please either patch the test to set some fixed
number or simply drop any test that might require user
interaction.
Kind regards
Andreas.
--
http://fam-tille.de
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