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Add QNs (#7)
* Add QN creation and sampling * Clarify vector of vals in grammar * Add tests * Fix QN tests * Add methods, tests for QN properties * Fix target function depth tests * Refactor QN tests * Add interpreter, async_step for QNs * Remove `Avg(...)` from grammar for now * Fix rounding of activation levels * Add documentation * Remove single letter functions * Fix notebook failing linting * SynthBN -> Synth * Updates to experiments * Switch to srun * Use SLURM_NTASKS * Update job name * Use Julia 1.10.2 to match cluster * Use SlurmClusterManager * Use SlurmClusterManager dynamically * Move SlurmClusterManager usage inside try block * Don't use @quickactivate macro in slurm context * Delete boilerplate script * Update trajectory script * Increase memory for sampling trajectories * Even more memory * Clean up scripts * Split script use distributed * Clean up bash scripts * Fix new version of split script * Fix new version of split script, pt2 * Updated synth process * Fewer steps per trajectory * Support 1.10 Statistics * Use QN version of GDS * Try split up @Everywhere * Reorganize synth script * Remove nested pmap * Increase resources * Fewer levels of trajectories * More memory * Add constraints * Restructure synthesis experiments * Increase max depth * Don't load files in main process * Trying lower memory * Re-up memory * Catch an error with some extra info * Catch an error and don't fail * Error message causing more errors... * Don't fail on link checker * Add compat * Uncomment tests * Fix QN errors in testing * Add Aqua and JET
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‎.github/workflows/Lint.yml‎

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id: lychee
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uses: lycheeverse/lychee-action@v2
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with:
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fail: false
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args: --config '.lychee.toml' .

‎.gitignore‎

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.DS_Store
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.benchmarkci
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Manifest.toml
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!experiments/SynthBN/Manifest.toml
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!experiments/Synth/Manifest.toml
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benchmark/*.json
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‎Project.toml‎

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name = "GraphDynamicalSystems"
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uuid = "13529e2e-ed53-56b1-bd6f-420b01fca819"
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authors = ["Reuben Gardos Reid <[email protected]>"]
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version = "0.1.0"
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version = "0.2.0"
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[deps]
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AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"
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DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
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DynamicalSystems = "61744808-ddfa-5f27-97ff-6e42cc95d634"
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FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
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Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
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HerbConstraints = "1fa96474-3206-4513-b4fa-23913f296dfc"
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HerbCore = "2b23ba43-8213-43cb-b5ea-38c12b45bd45"
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HerbGrammar = "4ef9e186-2fe5-4b24-8de7-9f7291f24af7"
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HerbSearch = "3008d8e8-f9aa-438a-92ed-26e9c7b4829f"
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MLStyle = "d8e11817-5142-5d16-987a-aa16d5891078"
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MetaGraphsNext = "fa8bd995-216d-47f1-8a91-f3b68fbeb377"
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Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
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SoleLogics = "b002da8f-3cb3-4d91-bbe3-2953433912b5"
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Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
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[compat]
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AbstractTrees = "0.4.5"
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DocStringExtensions = "0.9.3"
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DynamicalSystems = "3"
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FileIO = "1"
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Graphs = "1.12"
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HerbConstraints = "0.2.4"
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HerbCore = "0.3.4"
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HerbGrammar = "0.5"
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HerbSearch = "0.4.1"
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MLStyle = "0.4.17"
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MetaGraphsNext = "0.7"
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SoleLogics = "0.9, 0.10"
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Random = "1.11"
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SoleLogics = "0.12"
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Statistics = "1.10,1.11.1"
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julia = "1.6"

‎docs/Project.toml‎

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# Don't forget to run
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#
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# pkg> dev ..
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#
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[deps]
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Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
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LiveServer = "16fef848-5104-11e9-1b77-fb7a48bbb589"
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GraphDynamicalSystems = "13529e2e-ed53-56b1-bd6f-420b01fca819"
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LiveServer = "16fef848-5104-11e9-1b77-fb7a48bbb589"
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Revise = "295af30f-e4ad-537b-8983-00126c2a3abe"
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‎docs/make.jl‎

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using Revise
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Revise.revise()
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using GraphDynamicalSystems
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using Documenter
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‎docs/src/95-reference.md‎

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```
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```@autodocs
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Modules = [GraphDynamicalSystems]
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Modules = [GraphDynamicalSystems, GraphDynamicalSystems.BooleanNetworks]
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```

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use flake

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