Merge branch 'master' of https://github.com/JuliaTeachingCTU/Scientific-Programming-in-Julia

Author: pevnak

Manifest.toml

@@ -21,14 +21,14 @@ uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
 
 [[Compat]]
 deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "SHA", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"]
-git-tree-sha1 = "4866e381721b30fac8dda4c8cb1d9db45c8d2994"
+git-tree-sha1 = "31d0151f5716b655421d9d75b7fa74cc4e744df2"
 uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
-version = "3.37.0"
+version = "3.39.0"
 
 [[DataAPI]]
-git-tree-sha1 = "bec2532f8adb82005476c141ec23e921fc20971b"
+git-tree-sha1 = "cc70b17275652eb47bc9e5f81635981f13cea5c8"
 uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a"
-version = "1.8.0"
+version = "1.9.0"
 
 [[DataStructures]]
 deps = ["Compat", "InteractiveUtils", "OrderedCollections"]
@@ -56,9 +56,9 @@ version = "0.8.5"
 
 [[Documenter]]
 deps = ["ANSIColoredPrinters", "Base64", "Dates", "DocStringExtensions", "IOCapture", "InteractiveUtils", "JSON", "LibGit2", "Logging", "Markdown", "REPL", "Test", "Unicode"]
-git-tree-sha1 = "fe0bc46b27cd3413df55859152fd70e50744025f"
+git-tree-sha1 = "8b43e37cfb4f4edc2b6180409acc0cebce7fede8"
 uuid = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
-version = "0.27.6"
+version = "0.27.7"
 
 [[DocumenterTools]]
 deps = ["AbstractTrees", "Base64", "DocStringExtensions", "Documenter", "FileWatching", "Gumbo", "LibGit2", "Sass"]
@@ -72,7 +72,7 @@ uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
 
 [[EcosystemCore]]
 deps = ["StatsBase"]
-git-tree-sha1 = "6673d8009ca36aedd7a37b6f6cfbde0e179b2a59"
+git-tree-sha1 = "9b3a25d787bcd5974160b1c7064096b8fb37a88c"
 repo-rev = "main"
 repo-url = "https://github.com/JuliaTeachingCTU/EcosystemCore.jl.git"
 uuid = "3e0d8730-8ea0-4ee2-afe6-c85384c618a2"
@@ -171,9 +171,9 @@ version = "1.4.1"
 
 [[Parsers]]
 deps = ["Dates"]
-git-tree-sha1 = "438d35d2d95ae2c5e8780b330592b6de8494e779"
+git-tree-sha1 = "a8709b968a1ea6abc2dc1967cb1db6ac9a00dfb6"
 uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
-version = "2.0.3"
+version = "2.0.5"
 
 [[Pkg]]
 deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"]

Project.toml

@@ -11,3 +11,9 @@ StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 
 [compat]
 julia = "1.6"
+
+[extras]
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[targets]
+test = ["Test"]

docs/Manifest.toml

@@ -57,15 +57,15 @@ version = "1.16.1+0"
 
 [[ChainRulesCore]]
 deps = ["Compat", "LinearAlgebra", "SparseArrays"]
-git-tree-sha1 = "bd4afa1fdeec0c8b89dad3c6e92bc6e3b0fec9ce"
+git-tree-sha1 = "a325370b9dd0e6bf5656a6f1a7ae80755f8ccc46"
 uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
-version = "1.6.0"
+version = "1.7.2"
 
 [[ColorSchemes]]
 deps = ["ColorTypes", "Colors", "FixedPointNumbers", "Random"]
-git-tree-sha1 = "9995eb3977fbf67b86d0a0a0508e83017ded03f2"
+git-tree-sha1 = "a851fec56cb73cfdf43762999ec72eff5b86882a"
 uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4"
-version = "3.14.0"
+version = "3.15.0"
 
 [[ColorTypes]]
 deps = ["FixedPointNumbers", "Random"]
@@ -81,9 +81,9 @@ version = "0.12.8"
 
 [[Compat]]
 deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "SHA", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"]
-git-tree-sha1 = "1a90210acd935f222ea19657f143004d2c2a1117"
+git-tree-sha1 = "31d0151f5716b655421d9d75b7fa74cc4e744df2"
 uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
-version = "3.38.0"
+version = "3.39.0"
 
 [[CompilerSupportLibraries_jll]]
 deps = ["Artifacts", "Libdl"]
@@ -131,9 +131,9 @@ version = "0.8.5"
 
 [[Documenter]]
 deps = ["ANSIColoredPrinters", "Base64", "Dates", "DocStringExtensions", "IOCapture", "InteractiveUtils", "JSON", "LibGit2", "Logging", "Markdown", "REPL", "Test", "Unicode"]
-git-tree-sha1 = "fe0bc46b27cd3413df55859152fd70e50744025f"
+git-tree-sha1 = "8b43e37cfb4f4edc2b6180409acc0cebce7fede8"
 uuid = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
-version = "0.27.6"
+version = "0.27.7"
 
 [[DocumenterTools]]
 deps = ["AbstractTrees", "Base64", "DocStringExtensions", "Documenter", "FileWatching", "Gumbo", "LibGit2", "Sass"]
@@ -153,7 +153,7 @@ version = "2.2.3+0"
 
 [[EcosystemCore]]
 deps = ["StatsBase"]
-git-tree-sha1 = "43c67ffceba411b843d9d7237d9210e7b075d934"
+git-tree-sha1 = "9b3a25d787bcd5974160b1c7064096b8fb37a88c"
 repo-rev = "main"
 repo-url = "https://github.com/JuliaTeachingCTU/EcosystemCore.jl.git"
 uuid = "3e0d8730-8ea0-4ee2-afe6-c85384c618a2"
@@ -283,9 +283,9 @@ version = "0.10.1+1"
 
 [[HTTP]]
 deps = ["Base64", "Dates", "IniFile", "Logging", "MbedTLS", "NetworkOptions", "Sockets", "URIs"]
-git-tree-sha1 = "60ed5f1643927479f845b0135bb369b031b541fa"
+git-tree-sha1 = "14eece7a3308b4d8be910e265c724a6ba51a9798"
 uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3"
-version = "0.9.14"
+version = "0.9.16"
 
 [[HarfBuzz_jll]]
 deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"]
@@ -539,9 +539,9 @@ version = "8.44.0+0"
 
 [[Parsers]]
 deps = ["Dates"]
-git-tree-sha1 = "9d8c00ef7a8d110787ff6f170579846f776133a9"
+git-tree-sha1 = "a8709b968a1ea6abc2dc1967cb1db6ac9a00dfb6"
 uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
-version = "2.0.4"
+version = "2.0.5"
 
 [[Pixman_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
@@ -561,15 +561,15 @@ version = "2.0.1"
 
 [[PlotUtils]]
 deps = ["ColorSchemes", "Colors", "Dates", "Printf", "Random", "Reexport", "Statistics"]
-git-tree-sha1 = "2537ed3c0ed5e03896927187f5f2ee6a4ab342db"
+git-tree-sha1 = "b084324b4af5a438cd63619fd006614b3b20b87b"
 uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043"
-version = "1.0.14"
+version = "1.0.15"
 
 [[Plots]]
 deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "GeometryBasics", "JSON", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "PlotThemes", "PlotUtils", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs"]
-git-tree-sha1 = "457b13497a3ea4deb33d273a6a5ea15c25c0ebd9"
+git-tree-sha1 = "6841db754bd01a91d281370d9a0f8787e220ae08"
 uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
-version = "1.22.2"
+version = "1.22.4"
 
 [[Preferences]]
 deps = ["TOML"]
@@ -682,9 +682,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 
 [[StaticArrays]]
 deps = ["LinearAlgebra", "Random", "Statistics"]
-git-tree-sha1 = "3240808c6d463ac46f1c1cd7638375cd22abbccb"
+git-tree-sha1 = "3c76dde64d03699e074ac02eb2e8ba8254d428da"
 uuid = "90137ffa-7385-5640-81b9-e52037218182"
-version = "1.2.12"
+version = "1.2.13"
 
 [[Statistics]]
 deps = ["LinearAlgebra", "SparseArrays"]
@@ -719,9 +719,9 @@ version = "1.0.1"
 
 [[Tables]]
 deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "TableTraits", "Test"]
-git-tree-sha1 = "1162ce4a6c4b7e31e0e6b14486a6986951c73be9"
+git-tree-sha1 = "fed34d0e71b91734bf0a7e10eb1bb05296ddbcd0"
 uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
-version = "1.5.2"
+version = "1.6.0"
 
 [[Tar]]
 deps = ["ArgTools", "SHA"]

docs/make.jl

@@ -60,6 +60,7 @@ lecture_03 = [
 lecture_04 = [
     "Lecture" => "./lecture_04/lecture.md"
     "Lab" => "./lecture_04/lab.md"
+    "Homework" => "./lecture_04/hw.md"
 ]
 
 lecture_05 = [
@@ -109,7 +110,7 @@ makedocs(;
         "1: Introduction" => lecture_01,
         "2: The power of Type System & multiple dispatch" => lecture_02,
         "3: Design patterns" => lecture_03,
-        "4: Packages development, environments, etc..." => lecture_04,
+        "4: Packages development, Unit Tests & CI" => lecture_04,
         "5: Benchmarking, profiling, and performance gotchas" => lecture_05,
         "6: Language introspection" => lecture_06,
         "7: Macros" => lecture_07,

docs/src/lecture_02/hw.md

@@ -55,15 +55,15 @@ end
 
 function agent_step!(a::Animal, w::World)
     incr_energy!(a,-1)
-    if rand() <= food_prob(a)
+    if rand() <= foodprob(a)
         dinner = find_food(a,w)
         eat!(a, dinner, w)
     end
     if energy(a) <= 0
         kill_agent!(a,w)
         return
     end
-    if rand() <= reproduction_prob(a)
+    if rand() <= reprprob(a)
         reproduce!(a,w)
     end
     return a
@@ -79,16 +79,16 @@ mutable struct Sheep <: Animal
     id::Int
     energy::Float64
     Δenergy::Float64
-    reproduction_prob::Float64
-    food_prob::Float64
+    reprprob::Float64
+    foodprob::Float64
 end
 
 mutable struct Wolf <: Animal
     id::Int
     energy::Float64
     Δenergy::Float64
-    reproduction_prob::Float64
-    food_prob::Float64
+    reprprob::Float64
+    foodprob::Float64
 end
 
 id(a::Agent) = a.id  # every agent has an ID so we can just define id for Agent here
@@ -100,8 +100,8 @@ grow!(a::Plant) = a.size += 1
 # get field values
 energy(a::Animal) = a.energy
 Δenergy(a::Animal) = a.Δenergy
-reproduction_prob(a::Animal) = a.reproduction_prob
-food_prob(a::Animal) = a.food_prob
+reprprob(a::Animal) = a.reprprob
+foodprob(a::Animal) = a.foodprob
 
 # set field values
 energy!(a::Animal, e) = a.energy = e

docs/src/lecture_02/lab.md

@@ -91,15 +91,15 @@ removed from the world. If it has positive energy it will try to reproduce.
 ```@example non_parametric_agents
 function agent_step!(a::Animal, w::World)
     incr_energy!(a,-1)
-    if rand() <= food_prob(a)
+    if rand() <= foodprob(a)
         dinner = find_food(a,w)
         eat!(a, dinner, w)
     end
     if energy(a) <= 0
         kill_agent!(a,w)
         return
     end
-    if rand() <= reproduction_prob(a)
+    if rand() <= reprprob(a)
         reproduce!(a,w)
     end
     return a
@@ -179,8 +179,8 @@ mutable struct Sheep <: Animal
     id::Int
     energy::Float64
     Δenergy::Float64
-    reproduction_prob::Float64
-    food_prob::Float64
+    reprprob::Float64
+    foodprob::Float64
 end
 ```
 Again we will use `Sheep` as a generic example for an `Animal` which
@@ -190,8 +190,8 @@ all other fields of our animals will stay constant.
 # get field values
 energy(a::Animal) = a.energy
 Δenergy(a::Animal) = a.Δenergy
-reproduction_prob(a::Animal) = a.reproduction_prob
-food_prob(a::Animal) = a.food_prob
+reprprob(a::Animal) = a.reprprob
+foodprob(a::Animal) = a.foodprob
 
 # set field values
 energy!(a::Animal, e) = a.energy = e
@@ -275,8 +275,8 @@ mutable struct Wolf <: Animal
     id::Int
     energy::Float64
     Δenergy::Float64
-    reproduction_prob::Float64
-    food_prob::Float64
+    reprprob::Float64
+    foodprob::Float64
 end
 
 function eat!(wolf::Wolf, sheep::Sheep, w::World)

docs/src/lecture_03/hw.md

@@ -22,16 +22,6 @@ delicious looks but decreases the energy of the sheep by
 ```@raw html
 </div></div>
 ```
-```@setup hw03
-abstract type Mushroom <: PlantSpecies end
-Base.show(io::IO,::Type{Mushroom}) = print(io,"🍄")
-
-EcosystemCore.eats(::Animal{Sheep},::Plant{Mushroom}) = true
-function EcosystemCore.eat!(s::Animal{Sheep}, m::Plant{Mushroom}, w::World)
-    incr_energy!(s, -size(m)*Δenergy(s))
-    EcosystemCore.kill_agent!(m,w)
-end
-```
 Your new species should give you results like below
 ```@repl hw03
 s = Sheep(1,2,2,1,1);
@@ -74,20 +64,6 @@ calls to the function `fn` that is returned by `every_nth(f,n)`.
 ```@raw html
 </div></div>
 ```
-```@setup hw03
-function every_nth(f::Function, n::Int)
-    i = 1
-    function callback(w::World)
-        # display(i) # comment this out to see how the counter increases
-        if i == n
-            f(w)
-            i = 1
-        else
-            i += 1
-        end
-    end
-end
-```
 You can use `every_nth` to log and save the agent count only every couple of
 steps of your simulation. Using `every_nth` will look like this:
 ```@repl hw03