Accept repository changes for apt

When a repository changes its Suite value from 'testing' to 'stable',
this change needs to be accepted or the repository will not be used.
This leads to errors in the gitlab-ci testing since the latest version
of pip3 is not installed.

.gitlab-ci.yml

@@ -35,7 +35,7 @@ test_dry_run:
 # most docker runners will not do this
 test_integration_singularity:
   before_script:
-    - apt-get update && apt-get install -y python3-pip
+    - apt-get update -y && apt-get install -y python3-pip
     - pip3 install pyfaidx
     - pip3 install -r requirements-dev.txt
   script:
@@ -70,3 +70,4 @@ test_functional:
   stage: functional
   only:
     - schedules
+