refactor: avoid deprecation warnings after update

[romanc]

Description

This is a follow-up from updating NDSL in PR #156. We get rid of deprecation warnings to avoid future problems when the API changes.

Quick note on the extra_dim_lengths: We can remove empty dictionaries {} because that's now the default. Previously that default wasn't re-entrant so many places specified the option explicitly. Now there's no need anymore for this.

How Has This Been Tested?

This is a pure refactor. All good as long as current tests don't complain.

Checklist:

• My code follows the style guidelines of this project
• I have performed a self-review of my own code
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation: N/A
• My changes generate no new warnings
• Any dependent changes have been merged and published in downstream modules
• New check tests, if applicable, are included: N/A

[romanc]

/cc @twicki & @FlorianDeconinck FYI