Merge pull request #68 from cesmix-mit/update-doc

Documentation update

.github/workflows/CI.yml

@@ -13,7 +13,6 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - "1.9"
           - "1.10"
         os:
           - ubuntu-latest

Project.toml

@@ -26,5 +26,5 @@ YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"
 Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
 
 [compat]
-julia = ">= 1.9"
+julia = ">= 1.10"
 InteratomicPotentials = ">= 0.2.9"

docs/Project.toml

@@ -1,9 +1,11 @@
 [deps]
 AtomsBase = "a963bdd2-2df7-4f54-a1ee-49d51e6be12a"
+CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 DocumenterCitations = "daee34ce-89f3-4625-b898-19384cb65244"
-GLMakie = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a"
-ImageMagick = "6218d12a-5da1-5696-b52f-db25d2ecc6d1"
+InteratomicPotentials = "a9efe35a-c65d-452d-b8a8-82646cd5cb04"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
-Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
 PotentialLearning = "82b0a93c-c2e3-44bc-a418-f0f89b0ae5c2"
+Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
+UnitfulAtomic = "a7773ee8-282e-5fa2-be4e-bd808c38a91a"

docs/make.jl

@@ -21,15 +21,20 @@ const EXAMPLES_DIR = joinpath(@__DIR__, "..", "examples")
 const OUTPUT_DIR   = joinpath(@__DIR__, "src/generated")
 
 examples = [
-    "Subsampling, compute descriptors, and fit ACE" => "Na/fit-dpp-ace-na"
+    "Compute ACE descriptors, subsample, and fit ACE" => "Na/fit-dpp-ace-na.jl"
 ]
 
-for (_, name) in examples
-    example_filepath = joinpath(EXAMPLES_DIR, string(name, ".jl"))
-    Literate.markdown(example_filepath, OUTPUT_DIR, documenter=true)
+for (_, example_path) in examples
+    s = split(example_path, "/")
+    sub_path, file_name = string(s[1:end-1]...), s[end]
+    example_filepath = joinpath(EXAMPLES_DIR, example_path)
+    Literate.markdown(example_filepath,
+                      joinpath(OUTPUT_DIR, sub_path),
+                      documenter = true)
 end
 
-examples = [title=>joinpath("generated", string(name, ".md")) for (title, name) in examples]
+examples = [title => joinpath("generated", replace(example_path, ".jl" => ".md"))
+            for (title, example_path) in examples]
 
 
 makedocs(
@@ -43,7 +48,7 @@ makedocs(
       highlightsig = true,
       sitename = "PotentialLearning.jl",
       expandfirst = [],
-      draft = false,    
+      draft = false,
       pages = ["Home" => "index.md",
                "How to run the examples" => "how-to-run-the-examples.md",
                "Examples" => examples,

examples/Na/fit-dpp-ace-na.jl

@@ -1,11 +1,12 @@
-push!(Base.LOAD_PATH, "../../")
+#push!(Base.LOAD_PATH, "../../")
 
 using Unitful, UnitfulAtomic
 using AtomsBase, InteratomicPotentials, PotentialLearning
 using LinearAlgebra, CairoMakie
 
 # Load dataset
-confs, thermo = load_data("data/liquify_sodium.yaml", YAML(:Na, u"eV", u"Å"))
+path = joinpath(dirname(pathof(PotentialLearning)), "../examples/Na/")
+confs, thermo = load_data("$path/data/liquify_sodium.yaml", YAML(:Na, u"eV", u"Å"))
 confs, thermo = confs[220:end], thermo[220:end]
 
 # Split dataset
@@ -61,7 +62,7 @@ scatter!(ax1, e_test, e_err_test, label = "Test", markersize = 5.0)
 scatter!(ax1, e_train[dpp_inds2], e_err_train[dpp_inds2], markersize = 5.0,
          color = :darkred, label = "DPP Samples")
 axislegend(ax1)
-save("figures/energy_error_training_test_scatter.pdf", fig)
+save("$path/figures/energy_error_training_test_scatter.pdf", fig)
 display(fig)