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 <[email protected]> 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
