Merge pull request #83 from cesmix-mit/fix-path

test: fix paths using ENV
cesmix-mit · Jul 14, 2024 · 1e7fae5 · 1e7fae5
2 parents b49be2e + cc4f9c0
commit 1e7fae5
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Showing 9 changed files with 22 additions and 21 deletions.
diff --git a/docs/make.jl b/docs/make.jl
@@ -10,22 +10,22 @@ DocMeta.setdocmeta!(
     recursive = true,
 )
 
-# Citations ####################################################################
+ENV["BASE_PATH"]    = joinpath(@__DIR__, "../") 
 
+# Citations ####################################################################
 bib = CitationBibliography(joinpath(@__DIR__, "citation.bib"))
 
-# Generate examples ############################################################
 
-const EXAMPLES_DIR = joinpath(@__DIR__, "..", "examples")
-const OUTPUT_DIR   = joinpath(@__DIR__, "src/generated")
-
-function create_examples(examples, EXAMPLES_DIR, OUTPUT_DIR)
+# Generate examples ############################################################
+const examples_path = joinpath(@__DIR__, "..", "examples")
+const output_path   = joinpath(@__DIR__, "src/generated")
+function create_examples(examples, examples_path, output_path)
     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)
+        example_filepath = joinpath(examples_path, example_path)
         Literate.markdown(example_filepath,
-                          joinpath(OUTPUT_DIR, sub_path),
+                          joinpath(output_path, sub_path),
                           documenter = true)
     end
     examples = [title => joinpath("generated", replace(example_path, ".jl" => ".md"))
@@ -37,32 +37,32 @@ end
 examples = [
     "Fit a-HfO2 dataset with ACE" => "ACE-aHfO2/fit-ace-ahfo2.jl",
 ]
-basic_examples = create_examples(examples, EXAMPLES_DIR, OUTPUT_DIR)
+basic_examples = create_examples(examples, examples_path, output_path)
 
 # Subsampling examples
 examples = [
     "Subsample a-HfO2 dataset with DPP and fit with ACE" => "DPP-ACE-aHfO2-1/fit-dpp-ace-ahfo2.jl",
     "Subsample Na dataset with DPP and fit with ACE" => "DPP-ACE-Na/fit-dpp-ace-na.jl",
     "Subsample Si dataset with DPP, fit with ACE, and cross validate" => "DPP-ACE-Si/fit-dpp-ace-si.jl",
 ]
-ss_examples = create_examples(examples, EXAMPLES_DIR, OUTPUT_DIR)
+ss_examples = create_examples(examples, examples_path, output_path)
 
 # Optimization examples
 examples = [
     "Optimize ACE hyper-parameters: minimize force time and fitting error" => "Opt-ACE-aHfO2/fit-opt-ace-ahfo2.jl",
 ]
-opt_examples = create_examples(examples, EXAMPLES_DIR, OUTPUT_DIR)
+opt_examples = create_examples(examples, examples_path, output_path)
 
 # Dimension reduction examples
 examples = [
     "Reduce ACE descriptors with PCA and fit a-HfO2 dataset" => "PCA-ACE-aHfO2/fit-pca-ace-ahfo2.jl",
 ]
-dr_examples = create_examples(examples, EXAMPLES_DIR, OUTPUT_DIR)
+dr_examples = create_examples(examples, examples_path, output_path)
 
 examples = [
     "Load Ar+Lennard-Jones dataset and postprocess" => "LJ-Ar/lennard-jones-ar.jl"
 ]
-misc_examples = create_examples(examples, EXAMPLES_DIR, OUTPUT_DIR)
+misc_examples = create_examples(examples, examples_path, output_path)
 
 
 # Make and deploy docs #########################################################

diff --git a/examples/ACE-aHfO2/fit-ace-ahfo2.jl b/examples/ACE-aHfO2/fit-ace-ahfo2.jl
@@ -8,11 +8,12 @@ using Unitful, UnitfulAtomic
 using LinearAlgebra, Random, DisplayAs
 
 # Define paths.
-base_path = match(r"^(.*/PotentialLearning/)", @__DIR__).match
+base_path = haskey(ENV, "BASE_PATH") ? ENV["BASE_PATH"] : "../../"
 ds_path   = "$base_path/examples/data/a-HfO2/a-HfO2-300K-NVT-6000.extxyz"
 res_path  = "$base_path/examples/ACE-aHfO2/results/";
 
 # Load utility functions.
+
 include("$base_path/examples/utils/utils.jl")
 
 # Create experiment folder.

diff --git a/examples/DPP-ACE-Na/fit-dpp-ace-na.jl b/examples/DPP-ACE-Na/fit-dpp-ace-na.jl
@@ -8,7 +8,7 @@ using AtomsBase, InteratomicPotentials, PotentialLearning
 using LinearAlgebra, Plots
 
 # Define paths.
-base_path = match(r"^(.*/PotentialLearning/)", @__DIR__).match
+base_path = haskey(ENV, "BASE_PATH") ? ENV["BASE_PATH"] : "../../"
 ds_path   = "$base_path/examples/data/Na/liquify_sodium.yaml"
 
 # ## b. Load atomistic dataset and split it into training and test.

diff --git a/examples/DPP-ACE-Si/fit-dpp-ace-si.jl b/examples/DPP-ACE-Si/fit-dpp-ace-si.jl
@@ -13,7 +13,7 @@ using CSV, JLD, DataFrames
 elname, elspec = "Si", [:Si] 
 
 # Define paths.
-base_path = match(r"^(.*/PotentialLearning/)", @__DIR__).match
+base_path = haskey(ENV, "BASE_PATH") ? ENV["BASE_PATH"] : "../../"
 inpath   = "$base_path/examples/data/Si-3Body-LAMMPS/"
 outpath  = "$base_path/examples/DPP-ACE-Si/output/$elname/";
 

diff --git a/examples/DPP-ACE-aHfO2-1/fit-dpp-ace-ahfo2.jl b/examples/DPP-ACE-aHfO2-1/fit-dpp-ace-ahfo2.jl
@@ -8,7 +8,7 @@ using Unitful, UnitfulAtomic
 using LinearAlgebra, Random, DisplayAs
 
 # Define paths.
-base_path = match(r"^(.*/PotentialLearning/)", @__DIR__).match
+base_path = haskey(ENV, "BASE_PATH") ? ENV["BASE_PATH"] : "../../"
 ds_path   = "$base_path/examples/data/a-HfO2/a-HfO2-300K-NVT-6000.extxyz"
 res_path  = "$base_path/examples/DPP-ACE-aHfO2-1/results/";
 

diff --git a/examples/DPP-ACE-aHfO2-2/fit-dpp-ace-ahfo2.jl b/examples/DPP-ACE-aHfO2-2/fit-dpp-ace-ahfo2.jl
@@ -6,7 +6,7 @@ using JLD, CairoMakie
 
 #################### Importing Data ###################
 
-base_path = match(r"^(.*/PotentialLearning/)", @__DIR__).match
+base_path = haskey(ENV, "BASE_PATH") ? ENV["BASE_PATH"] : "../../"
 ds_path   = "$base_path/examples/data/a-HfO2/aHfO2_diverse_descriptors_3600.jld"
 res_path  = "$base_path/examples/DPP-ACE-aHfO2-2/results/";
 

diff --git a/examples/LJ-Ar/lennard-jones-ar.jl b/examples/LJ-Ar/lennard-jones-ar.jl
@@ -8,7 +8,7 @@ using AtomsBase, InteratomicPotentials, PotentialLearning
 using LinearAlgebra, Plots, DisplayAs
 
 # Define paths.
-base_path = match(r"^(.*/PotentialLearning/)", @__DIR__).match
+base_path = haskey(ENV, "BASE_PATH") ? ENV["BASE_PATH"] : "../../"
 ds_path   = "$base_path/examples/data/LJ-AR/lj-ar.yaml"
 
 # ## b. Load atomistic dataset.

diff --git a/examples/Opt-ACE-aHfO2/fit-opt-ace-ahfo2.jl b/examples/Opt-ACE-aHfO2/fit-opt-ace-ahfo2.jl
@@ -9,7 +9,7 @@ using LinearAlgebra, Random, DisplayAs
 using DataFrames, Hyperopt
 
 # Define paths.
-base_path = match(r"^(.*/PotentialLearning/)", @__DIR__).match
+base_path = haskey(ENV, "BASE_PATH") ? ENV["BASE_PATH"] : "../../"
 ds_path   = "$base_path/examples/data/a-HfO2/a-HfO2-300K-NVT-6000.extxyz"
 res_path  = "$base_path/examples/Opt-ACE-aHfO2/results/";
 

diff --git a/examples/PCA-ACE-aHfO2/fit-pca-ace-ahfo2.jl b/examples/PCA-ACE-aHfO2/fit-pca-ace-ahfo2.jl
@@ -8,7 +8,7 @@ using Unitful, UnitfulAtomic
 using LinearAlgebra, Random, DisplayAs
 
 # Define paths.
-base_path = match(r"^(.*/PotentialLearning/)", @__DIR__).match
+base_path = haskey(ENV, "BASE_PATH") ? ENV["BASE_PATH"] : "../../"
 ds_path   = "$base_path/examples/data/a-HfO2/a-HfO2-300K-NVT-6000.extxyz"
 res_path  = "$base_path/examples/PCA-ACE-aHfO2/results/";