Merge branch 'setup-netlogo-project' into 'main'

Setup for a minimal NetLogo model

See merge request !2

.gitignore

+/model/
+/odd/

README.md

@@ -2,4 +2,49 @@
 
 This is an example project to demonstrate Literate Programming to create [NetLogo](https://ccl.northwestern.edu/netlogo/) models from ODD+C protocols. 
 
+## Rabies model - ODD protocol
 
+### Purpose
+
+
+
+### Entities, state variables, and scales
+
+### Process overview and scheduling
+
+```netlogo
+;- file:Code.nls
+; ==> Setup.
+; ==> Go.
+```
+
+```netlogo
+;- Go
+to go
+  tick
+end
+```
+
+### Design concepts
+
+### Initialization
+
+```netlogo
+;- Setup
+to setup
+  reset-ticks
+end
+```
+
+### Input data
+
+### Submodels
+
+## Appendix
+
+### NetLogo file
+
+In the main `nlogo` file, we only "include" an `nls` file to allow for the reverse mode.
+The file `Model.nlogo` is simply copied from the `nlogo` directory via option `code_files` in the `[paths]` section of the `Yarner.toml`.
+
+This separation of model code and user interface also allows to edit the model's UI elements in NetLogo's GUI builder tool, while using Literate Programming for the code.

Yarner.toml

@@ -2,9 +2,9 @@
 fence_sequence = "```"
 fence_sequence_alt = "~~~"
 
-block_name_prefix = "//-"
+block_name_prefix = ";-"
 
-macro_start = "// ==>"
+macro_start = "; ==>"
 macro_end = "."
 
 transclusion_start = "@{{"
@@ -15,29 +15,25 @@ link_prefix = "@"
 file_prefix = "file:"
 hidden_prefix = "hidden:"
 
-# default_language = "rust"
-
 [paths]
-root = "lp/"
-code = "../model/"
-docs = "../odd/"
-
-files = ["ODD.md"]
-# entrypoint = "Main"
-
-# code_files = ["**/*.rs"]
-# code_paths = ["_"]
-
-# doc_files = ["**/*.png", "**/*.jpg"]
-# doc_paths = ["_"]
-
-# [language.rs]
-# clear_blank_lines = true
-# eof_newline = true
-
-    # [language.rs.block_labels]
-    # comment_start = "//"
-    ## comment_end = "*/"
-    # block_start = "<@"
-    # block_next = "<@>"
-    # block_end = "@>"
+root = "."
+code = "model/"
+docs = "odd/"
+
+files = ["README.md"]
+entrypoint = "Main" # Avoids writing unnamed code blocks
+
+# NetLogo is not suited to generate the UI from code.
+# We therefore use the copy files feature for the base .nlogo file, and for UI.
+code_files = ["nlogo/Model.nlogo"]
+code_paths = ["-"]
+
+[language.nls]
+clear_blank_lines = true
+eof_newline = true
+
+    [language.nls.block_labels]
+    comment_start = ";"
+    block_start = "<@"
+    block_next = "<@>"
+    block_end = "@>"

lp/ODD.md

-# Rabies model - ODD protocol

nlogo/Model.nlogo

+__includes["Code.nls"]
+@#$#@#$#@
+GRAPHICS-WINDOW
+220
+10
+733
+524
+-1
+-1
+5.0
+1
+10
+1
+1
+1
+0
+1
+1
+1
+0
+100
+0
+100
+1
+1
+1
+ticks
+30.0
+
+BUTTON
+10
+10
+80
+50
+NIL
+setup
+NIL
+1
+T
+OBSERVER
+NIL
+NIL
+NIL
+NIL
+1
+
+BUTTON
+90
+10
+160
+50
+NIL
+go
+T
+1
+T
+OBSERVER
+NIL
+NIL
+NIL
+NIL
+1
+
+@#$#@#$#@
+## WHAT IS IT?
+
+## HOW IT WORKS
+
+## HOW TO USE IT
+@#$#@#$#@
+default
+true
+0
+Polygon -7500403 true true 150 5 40 250 150 205 260 250
+@#$#@#$#@
+NetLogo 6.1.0
+@#$#@#$#@
+@#$#@#$#@
+@#$#@#$#@
+@#$#@#$#@
+@#$#@#$#@
+default
+0.0
+-0.2 0 0.0 1.0
+0.0 1 1.0 0.0
+0.2 0 0.0 1.0
+link direction
+true
+0
+Line -7500403 true 150 150 90 180
+Line -7500403 true 150 150 210 180
+@#$#@#$#@
+0
+@#$#@#$#@