Netqasm

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- Added docstrings to a large part of the codebase
- Some refactoring based on inconsistencies found while documenting

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- Added type hints to most of the code.
- Now using the `black` and `isort` formatters for the whole repo.
- Extracted pre-subroutine construction out of the Connection class and moved to the Builder class.
- Improved type hints related to numpy types.
- Added convenience methods to the `SharedMemory` class.
- Added support for single-threaded SquidASM simulator.
- Bumped qlink-layer requirement to 1.0.0. Arrays for EPR instructions still use the 0.1.0 format.
- Added a compatibility module for simulators that use qlink-layer 1.0.0 themselves but want to interpret EPR arrays using 0.1.0.
- Updated code that is deprecated in NetSquid 1.0 (it is now compatible with 1.0).

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- Added support for choosing the measurement basis for M-type EPR generation.
- Added the ability to manually create a Register in the SDK. Further use with these Registers is limited for now.
- Added interfaces for applications and the runtime environment, to make it easier to instantiate and run apps.
- Added the `netqasm qne login` and `netqasm qne logout` commands.
- Renamed `Executioner` to `Executor`.
- Optimized initialization of arrays when all elements have the same initial value (use a loop).
- Fixed NV compilation when doing sequential EPR create commands.
- Fixed NV compilation of `K` gates.
- Fixed bug where multiple branch labels with the same name could appear.

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- Reverted patches 0.5.1 and 0.5.2.
0.5.3 is exactly the same as 0.5.0.

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- Added support for choosing the measurement basis for M-type EPR generation.
- Added the ability to manually create a Register in the SDK. Further use with these Registers is limited for now.
- Added interfaces for applications and the runtime environment, to make it easier to instantiate and run apps.
- Added the `netqasm qne login` and `netqasm qne logout` commands.

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- Renamed `Executioner` to `Executor`.
- Fixed NV compilation when doing sequential EPR create commands.