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Why are consensus committee only functions not wrapped?

The group of users that can make use of this is very limited. By ommitting these functions the API list stays short and relevant to the biggest group of users. Those who do wish to use these functions can always use the generic call_function() method on the contract of choice to call them.

Why is the native ContractManagement contract not wrapped?

The contract deploy, update and destroy functionality is already part of the GenericContract base class used in all contract wrappers.

Why is the native Ledger contract not wrapped?

All information that can be obtained from the Ledger contract can also be obtained using the NeoRpcClient. In some cases the Ledger contract returns even incomplete data. For example Ledger.GetBlock returns a TrimmedBlock without transactions as opposed to NeoRpcClient.get_block() which returns the complete block. The Ledger contract is really intended to be consumed by smart contracts.

Why does the IJson interface consume and produce dictionaries?

This was originally used in the full node version of Mamba. However, it seems like the standard in the Python community if judged by looking at popular packages/frameworks like requests and aiohttp. Also, frameworks like FastAPI, Django and Flask all have ways of consuming a dict when returning a json response. It seems like the best choice for these reasons.

How do I prevent 'error: "as_none" of "StackItem" does not return a value' when type checking with MyPy?

The mypy team made an unfortunate choice to include a restriction on something that is actually a code style choice. They refuse to change the default behaviour despite the raised complaints and other type checkers like pyright not falling over this. The error can be disabled with --disable-error-code func-returns-value or by adding it to your configuration file i.e. for pyproject.toml use

disable_error_code = "func-returns-value"

How do I <insert topic>?

Have a look at the examples on GitHub if the documentation doesn't cover your question. If the examples also don't answer your question then feel free to ask on GitHub or ask in #python on the NEO Discord server.