Commits on Oct 14, 2023

1. Remove State struct …

   The State struct is presumably intended to be used by users of Automa, such that
   all the information related to the state of an Automa machine, which needs to be
   stored in a BioJulia Reader type, is implemented one place.
   Presumably, the idea was that it would make it easier for users to reason about
   what is needed when implementing a reader.
   
   However, it's not a good idea for several reasons:
   1. It hardly makes it easier to reason about that users need to bring in this
      package in order to store a state related to Automa - if this struct should
      exist at all, it should be in Automa.jl
   2. It's debatable what kind of information needs to be stored, and this also
      depends on the specific reader type. For example, FASTX does not need to
      to store the `filled::Bool` field.
   3. It's easier to reason about for users and authors if all state related to a
      reader is stored in the reader itself, instead of in a field defined in
      another package
   4. This forces a dependency on TranscodingStreams on this package, which is
      unnecessary for most users of BioGenerics.

   

   jakobnissen committed Oct 14, 2023
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