This is the last PR of the plasnet integration into pling.
This is a small PR that looks very long because of test data (95% of the changes are just adding a minimal bakta db so that we can run integration tests on the annotation workflow).
The main changes are:
CI tests just run now on ubuntu runners as pling now depends on singularity, which is not available for mac-os runners;
Added a Makefile to make installation and testing easier;
Downgraded pandas from 2.1.1 to 2.0.3 to allow pling to run on python 3.8;
Added 3 integration tests, 1 for the align workflow and two for the annotation workflow: test_pling_align_end_to_end, test_pling_anno_with_dedup_end_to_end, and test_pling_anno_without_dedup_end_to_end;
Please just merge if the CI tests pass. We now have CI tests back and running! However, we have a limit of 2000 minutes/month on private repos, if we hit the limit and still want CI to run, we will have to make this repo public.
This is the last PR of the
plasnetintegration intopling.This is a small PR that looks very long because of test data (95% of the changes are just adding a minimal
baktadb so that we can run integration tests on the annotation workflow).The main changes are:
ubunturunners asplingnow depends onsingularity, which is not available formac-osrunners;Makefileto make installation and testing easier;pandasfrom2.1.1to2.0.3to allowplingto run onpython 3.8;test_pling_align_end_to_end,test_pling_anno_with_dedup_end_to_end, andtest_pling_anno_without_dedup_end_to_end;Please just merge if the CI tests pass. We now have CI tests back and running! However, we have a limit of 2000 minutes/month on private repos, if we hit the limit and still want CI to run, we will have to make this repo public.