Remove State struct #17
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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.
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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:
filled::Boolfield.Fixes BioJulia/Automa.jl#103
Broader considerations
See the comment here: BioJulia/Automa.jl#103 (comment) . @TransGirlCodes suggested removing this entire package, but I kind of like #14 (even though it needs to be reworked because I've found out macros don't support interpolating, but that's another story), and I can't really think of any other place to add these definitions. Maybe it's fine to have this as a very lightweight, zero dependency package that defines common supertypes and interfaces.
Looking through the code of BioGenerics, really it's only the code in the IO module I feel like we need to keep.
For now, let's just remove the TranscodingStreams dependency. Since this package is not user-facing, we can break the API as much as we want, so I don't think we need to lose any sleep about making yet another breaking release.
Comments welcome - @BioJulia/maintainers