Dev/fix typing
This PR:
- enable type-checking on all Python code (except in the docs)
- fix all type-check errors due to the first point
- update pre-check tools
- update flake8 repo
Git-LFS is now available on our GitLab instance.
Please note that the quota check is now in blocking mode. More informations about quotas: https://gitlab.inria.fr/siteadmin/doc/-/wikis/faq#quota-management-policy-to-monitor-disk-space-by-project-on-gitlab
GitLab upgrade completed. Current version is 17.8.2.
This PR: