JSON ACSetTransformations

[lukem12345]

Currently, ACSets.jl supports serialization of ACSets to JSON to export ACSets to other languages that support complementary parsers.

Due to new features in Decapodes being encoded as ACSetTransformations, and these features needing to be exported across systems, the JSON serialization of ACSetTransformations should be supported. The serialization of ACSetTransformations being generic, this serialization should be upstreamed to Catlab rather than stay in the Decapodes library.

So, this PR adds support for the serialization of ACSetTransformations to JSON. Incidentally, FinFunction serialization is also supported.

The generate-parse & write-read interface is copied from the pattern for serialization currently used by ACSets.jl

Support for VarFunctions is outside of the current scope of this PR, and so an issue should be created pending merge of this PR that adds such support.

[jpfairbanks]

Looks good to me except for the white space question.

[lukem12345]

Test file passes when ran via include. I'll fix the ]test on the next commit

[epatters]

I'm fine if you want to merge this as-is (once all the CI is passing) as long as you are OK with me possibly revisiting the API later once I have more time.

[lukem12345]

I'm fine if you want to merge this as-is (once all the CI is passing) as long as you are OK with me possibly revisiting the API later once I have more time.

Certainly. I tried to follow the serialization scheme set forth in ACSets.jl, but I am sure that there are improvements to be made both to this code and where it lives.

ACSets.jl has a /src/serialization/ folder, and I did not create one here, for one thing.

[lukem12345]

I have just marked this PR as ready to review.

I made one change to parsing that explicitly checks whether the mapping in a FinFunction is empty (input["dom"]["n"] != 0 ? Int.(input["map"]) : 1:0), due to the following behavior:

julia> FinFunction(1:0, 0, 4)
FinFunction(1:0, 0, 4)

julia> FinFunction([], 0, 4)
ERROR: MethodError: no method matching (SetFunction{Dom, Codom} where {S, S′, Dom<:(FinSet{S}), Codom<:(FinSet{S′})})(::Vector{Any}, ::Int64, ::Int64)

[github-actions]

Review Checklist

Does this PR follow the development guidelines? Following is a partial checklist:

Tests

• New features and bug fixes have unit tests
• New modules have tests that are ultimately called by the test runner (test/runtests.jl)
• Existing tests have not been deleted
• Code coverage >= 90% or reduction justified in PR

Documentation

• All exported functions, types, and constants have docstrings, written in complete sentences
• Citations are given for any constructions, algorithms, or code drawn from external sources

Other

• Style guidelines are followed, including indent width 2
• Changes breaking backwards compatibility have been approved