Remove unused tests that are not part of the CI

The CI still contains a test for the prepare_inputs.py script. However, this script is no longer used and this function is transferred in the zarp-cli. I thus propose we remove it. @gypas @kanitz or anyone else in disagreement with this statement?

added Bug Discuss labels

mentioned in merge request !97 (merged)

Currently, at the time of me writing this, there are three lines which are commented out in the CI:

    #- bash tests/test_scripts_prepare_inputs_table/test.sh
    #- bash tests/test_scripts_prepare_inputs_labkey/test.sh
    #- bash tests/test_alfa/test.sh

I'm OK with removing all of them...

Hi. It's fine for me to remove the prepare_inputs.py script and the corresponding tests.

added To Do label

I added To Do label since we should decide on the content of CI before we move to GitHub (i.e. at the end of the development cycle here).

changed title from Remove prepare inputs test from the ci to Remove unused tests that are not part of the CI

From what I saw there is an ALFA test in the input folder that has not been used as a ci test for quite some time (https://git.scicore.unibas.ch/zavolan_group/pipelines/zarp/-/tree/dev/tests/test_alfa) . Do we want to keep it? Is it still usable? @burri0000 what do you think?

That above is a test for ALFA functionality that runs one-rule pipeline, correct?
I think we decided to move away from unit testing in zarp; if not - we will need to write such tests for every rule(?) But what about rules which do have their unit tests in their respective repositories (like TIN calculation or PCA plotting). Also - is this really our job to write such unit tests for: ALFA, STAR, cutadapt etc.?

I don't think we need them anymore. The example files in ALFA test were recently helpful when we had the discussion about directionality. But I guess this is also reported and saved in the corresponding issue and no additional files are needed.

Also, the test (at least ALFA) would need some adaptation because the structure changed. So from my side, I'm fine to remove this test.

As for the third test (since we are already discussing them all here and present our opinions):
If I recall correctly we decided to drop official support for LabKey parsing (we might have this internally, just not in the public repo). So, IMO, that script and test should be out too.

mentioned in merge request !99 (merged)

assigned to @bakma

added Doing label and removed To Do label

Fixed in !99 (merged)

closed

removed Doing label

I know that the issue is closed, but I think that we should have also removed the following part from the documentation: https://git.scicore.unibas.ch/zavolan_group/pipelines/zarp#additional-information

What do you think?

OK, my bad, we overlooked it :(
I will push a fix branch in a minute.

reopened

mentioned in merge request !100 (merged)

Fixed in !100 (merged)