Add QNs

.github/workflows/Lint.yml

@@ -52,5 +52,5 @@ jobs:
               id: lychee
               uses: lycheeverse/lychee-action@v2
               with:
-                  fail: true
+                  fail: false
                   args: --config '.lychee.toml' .

.gitignore

@@ -5,7 +5,7 @@
 .DS_Store
 .benchmarkci
 Manifest.toml
-!experiments/SynthBN/Manifest.toml
+!experiments/Synth/Manifest.toml
 benchmark/*.json
 coverage
 docs/build/

Project.toml

@@ -1,18 +1,37 @@
 name = "GraphDynamicalSystems"
 uuid = "13529e2e-ed53-56b1-bd6f-420b01fca819"
 authors = ["Reuben Gardos Reid <[email protected]>"]
-version = "0.1.0"
+version = "0.2.0"
 
 [deps]
+AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"
+DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
 DynamicalSystems = "61744808-ddfa-5f27-97ff-6e42cc95d634"
 FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
+Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
+HerbConstraints = "1fa96474-3206-4513-b4fa-23913f296dfc"
+HerbCore = "2b23ba43-8213-43cb-b5ea-38c12b45bd45"
+HerbGrammar = "4ef9e186-2fe5-4b24-8de7-9f7291f24af7"
+HerbSearch = "3008d8e8-f9aa-438a-92ed-26e9c7b4829f"
+MLStyle = "d8e11817-5142-5d16-987a-aa16d5891078"
 MetaGraphsNext = "fa8bd995-216d-47f1-8a91-f3b68fbeb377"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 SoleLogics = "b002da8f-3cb3-4d91-bbe3-2953433912b5"
+Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 
 [compat]
+AbstractTrees = "0.4.5"
+DocStringExtensions = "0.9.3"
 DynamicalSystems = "3"
 FileIO = "1"
+Graphs = "1.12"
+HerbConstraints = "0.2.4"
+HerbCore = "0.3.4"
+HerbGrammar = "0.5"
+HerbSearch = "0.4.1"
+MLStyle = "0.4.17"
 MetaGraphsNext = "0.7"
-SoleLogics = "0.9, 0.10"
+Random = "1.11"
+SoleLogics = "0.12"
+Statistics = "1.10,1.11.1"
 julia = "1.6"

docs/Project.toml

@@ -1,11 +1,8 @@
-# Don't forget to run
-#
-#     pkg> dev ..
-#
 [deps]
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
-LiveServer = "16fef848-5104-11e9-1b77-fb7a48bbb589"
 GraphDynamicalSystems = "13529e2e-ed53-56b1-bd6f-420b01fca819"
+LiveServer = "16fef848-5104-11e9-1b77-fb7a48bbb589"
+Revise = "295af30f-e4ad-537b-8983-00126c2a3abe"
 
 [compat]
 Documenter = "1"

docs/make.jl

@@ -1,3 +1,7 @@
+using Revise
+
+Revise.revise()
+
 using GraphDynamicalSystems
 using Documenter
 

docs/src/95-reference.md

@@ -13,5 +13,5 @@ Pages = ["95-reference.md"]
 ```
 
 ```@autodocs
-Modules = [GraphDynamicalSystems]
+Modules = [GraphDynamicalSystems, GraphDynamicalSystems.BooleanNetworks]
 ```

experiments/Synth/.envrc

@@ -0,0 +1 @@
+use flake

experiments/SynthBN/CondaPkg.toml → experiments/Synth/CondaPkg.toml

@@ -1,4 +1,3 @@
-channels = ["bioconda"]
 
 [pip.deps]
 biodivine-aeon = ""

experiments/Synth/LocalPreferences.toml

@@ -0,0 +1,3 @@
+[CondaPkg]
+backend = "MicroMamba"
+pip_backend = "uv"