overhaul of input-output functionality

[guyvdbroeck]

• replaced LoadSave module by io directory
• removed logistic circuit loaders
• rewrite of .psdd parser using Lerche.jl
• use parse, read and write from Base to do IO, no custom function names
• add our own flexible file format .jpc which can be read as either ProbCircuit or StructProbCircuit
• allow read/write in combination with a .vtree file for IO of StructProbCircuit

I used the occasion for some general cleanup:

• got rid of all things LogisticCircuit, regression circuit, circuit pairs, etc., these should go into their own package and receive more dedicated attention
• removed some tests that were too slow

[codecov-commenter]

Codecov Report

Merging #87 (1061b7d) into master (d456ce6) will increase coverage by 0.96%. The diff coverage is 72.33%.

@@            Coverage Diff             @@
##           master      #87      +/-   ##
==========================================
+ Coverage   69.05%   70.02%   +0.96%     
==========================================
  Files          45       37       -8     
  Lines        3490     2802     -688     
==========================================
- Hits         2410     1962     -448     
+ Misses       1080      840     -240     

Impacted Files	Coverage Δ
src/ProbabilisticCircuits.jl	100.00% <ø> (ø)
src/factor_graph/factor_graph.jl	100.00% <ø> (ø)
src/factor_graph/fg_compile.jl	56.41% <ø> (ø)
src/io/ensemble_io.jl	0.00% <0.00%> (ø)
src/io/plot.jl	0.00% <ø> (ø)
src/param_bit_circuit.jl	93.10% <ø> (-1.64%)	:arrow_down:
src/parameters.jl	61.22% <0.00%> (ø)
src/io/clt_io.jl	73.68% <73.68%> (ø)
src/io/io.jl	88.88% <88.88%> (ø)
src/io/jpc_io.jl	93.15% <93.15%> (ø)
... and 16 more

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[guyvdbroeck]

I agree it would be useful to already move the commented-out slow tests to the slow test functionality.

For the logistic circuits, it didn't make sense to wait because the logistic circuit parser was removed from LogicCircuits.jl, and without it the expectations etc. don't work anyway. Better bite the bullet, and check out the older commit when making LogisticCircuits.jl in future. Also, who is maintaining the logistic circuit functionality? In the past we have never had that stuff functioning in Juice.

[khosravipasha]

Sounds good, we can merge this then. I can make the new package. I only wrote the parser to read logistic circuits. I think yitao wrote the paramter learning, we don't support anything else yet for logistic/regression circuits.