gh-36708: CI Linux: Fixes for tests of optional packages
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Fixes test failure of `database_knotinfo` seen in GH Actions, as
reported by @soehms in
https://github.com/sagemath/sage/pull/36668#issuecomment-1806273609
Fixes same also for `database_cubic_hecke` and `mathics`.
To test: `FROM_DOCKER_TARGET=with-targets-pre TARGETS_PRE=config.status
tox -e docker-ubuntu-bionic-gcc_8-maximal-incremental --
database_knotinfo database_cubic_hecke mathics`
We also remove packages starting with `_` from the list of tested
packages. The dependencies of `_develop` pulled in the dummy package
`github_cli`.
We also use output groups to fold away some repetitive output.
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URL: https://github.com/sagemath/sage/pull/36708
Reported by: Matthias Köppe
Reviewer(s): Dima Pasechnik, Sebastian Oehms
