Update with lint formatting

.github/ISSUE_TEMPLATE/10-bug-report.yml

@@ -11,12 +11,12 @@ body:
         Please, before submitting, make sure that:
 
         - There is not an [existing issue](https://github.com/TulipaEnergy/TulipaClustering.jl/issues) with the same question
-        
+
         - You have read the [contributing guide](https://TulipaEnergy.github.io/TulipaClustering.jl/dev/90-contributing/)
-        
-        
+
+
         - You are following the [code of conduct](https://github.com/TulipaEnergy/TulipaClustering.jl/blob/main/CODE_OF_CONDUCT.md)
-        
+
 
         The form below should help you in filling out this issue.
   - type: textarea

.github/ISSUE_TEMPLATE/20-feature-request.yml

@@ -9,12 +9,12 @@ body:
         Please, before submitting, make sure that:
 
         - There is not an [existing issue](https://github.com/TulipaEnergy/TulipaClustering.jl/issues) with the same question
-        
+
         - You have read the [contributing guide](https://TulipaEnergy.github.io/TulipaClustering.jl/dev/90-contributing/)
-        
-        
+
+
         - You are following the [code of conduct](https://github.com/TulipaEnergy/TulipaClustering.jl/blob/main/CODE_OF_CONDUCT.md)
-        
+
 
         The form below should help you in filling out this issue.
   - type: textarea

.github/ISSUE_TEMPLATE/30-usage.yml

@@ -11,12 +11,12 @@ body:
 
         - You have checked the [documentation](https://TulipaEnergy.github.io/TulipaClustering.jl) and haven't found enough information
         - There is not an [existing issue](https://github.com/TulipaEnergy/TulipaClustering.jl/issues) with the same question
-        
+
         - You have read the [contributing guide](https://TulipaEnergy.github.io/TulipaClustering.jl/dev/90-contributing/)
-        
-        
+
+
         - You are following the [code of conduct](https://github.com/TulipaEnergy/TulipaClustering.jl/blob/main/CODE_OF_CONDUCT.md)
-        
+
 
         The form below should help you in filling out this issue.
   - type: textarea

.github/ISSUE_TEMPLATE/99-general.yml

@@ -9,12 +9,12 @@ body:
         Please, before submitting, make sure that:
 
         - There is not an [existing issue](https://github.com/TulipaEnergy/TulipaClustering.jl/issues) with the same question
-        
+
         - You have read the [contributing guide](https://TulipaEnergy.github.io/TulipaClustering.jl/dev/90-contributing/)
-        
-        
+
+
         - You are following the [code of conduct](https://github.com/TulipaEnergy/TulipaClustering.jl/blob/main/CODE_OF_CONDUCT.md)
-        
+
 
         The form below should help you in filling out this issue.
   - type: textarea

README.md

@@ -17,12 +17,10 @@
 
 If you use TulipaClustering.jl in your work, please cite using the reference given in [CITATION.cff](https://github.com/TulipaEnergy/TulipaClustering.jl/blob/main/CITATION.cff).
 
-
 ## Contributing
 
 If you want to make contributions of any kind, please first that a look into our [contributing guide directly on GitHub](docs/src/90-contributing.md) or the [contributing page on the website](https://TulipaEnergy.github.io/TulipaClustering.jl/dev/90-contributing/).
 
-
 ---
 
 ### Contributors

docs/make.jl

@@ -1,21 +1,28 @@
 using TulipaClustering
 using Documenter
 
-DocMeta.setdocmeta!(TulipaClustering, :DocTestSetup, :(using TulipaClustering); recursive = true)
+DocMeta.setdocmeta!(
+  TulipaClustering,
+  :DocTestSetup,
+  :(using TulipaClustering);
+  recursive = true,
+)
 
 const page_rename = Dict("developer.md" => "Developer docs") # Without the numbers
 const numbered_pages = [
-  file for
-  file in readdir(joinpath(@__DIR__, "src")) if file != "index.md" && splitext(file)[2] == ".md"
+  file for file in readdir(joinpath(@__DIR__, "src")) if
+  file != "index.md" && splitext(file)[2] == ".md"
 ]
 
 makedocs(;
-    modules = [TulipaClustering],
-    authors = "Greg Neustroev <[email protected]> and contributors",
-    repo = "https://github.com/TulipaEnergy/TulipaClustering.jl/blob/{commit}{path}#{line}",
-    sitename = "TulipaClustering.jl",
-    format = Documenter.HTML(; canonical = "https://TulipaEnergy.github.io/TulipaClustering.jl"),
-    pages = ["index.md"; numbered_pages],
+  modules = [TulipaClustering],
+  authors = "Greg Neustroev <[email protected]> and contributors",
+  repo = "https://github.com/TulipaEnergy/TulipaClustering.jl/blob/{commit}{path}#{line}",
+  sitename = "TulipaClustering.jl",
+  format = Documenter.HTML(;
+    canonical = "https://TulipaEnergy.github.io/TulipaClustering.jl",
+  ),
+  pages = ["index.md"; numbered_pages],
 )
 
 deploydocs(; repo = "github.com/TulipaEnergy/TulipaClustering.jl")

docs/src/90-contributing.md

@@ -4,10 +4,8 @@ First of all, thanks for the interest!
 
 We welcome all kinds of contribution, including, but not limited to code, documentation, examples, configuration, issue creating, etc.
 
-
 Be polite and respectful, and follow the code of conduct.
 
-
 ## Bug reports and discussions
 
 If you think you found a bug, feel free to open an [issue](https://github.com/TulipaEnergy/TulipaClustering.jl/issues).

src/cluster.jl

@@ -106,7 +106,10 @@ julia> TulipaClustering.split_into_periods!(df)
    3 │      1          3      3
 ```
 """
-function split_into_periods!(df::AbstractDataFrame; period_duration::Union{Int, Nothing} = nothing)
+function split_into_periods!(
+  df::AbstractDataFrame;
+  period_duration::Union{Int, Nothing} = nothing,
+)
   # If the periods already exist, combine them into the time steps if necessary
   combine_periods!(df)
 
@@ -197,9 +200,15 @@ function find_auxiliary_data(clustering_data::AbstractDataFrame)
   key_columns = validate_df_and_find_key_columns(clustering_data)
   n_periods = maximum(clustering_data.period)
   period_duration = maximum(clustering_data.timestep)
-  last_period_duration = maximum(clustering_data[clustering_data.period .== n_periods, :timestep])
+  last_period_duration =
+    maximum(clustering_data[clustering_data.period .== n_periods, :timestep])
 
-  return AuxiliaryClusteringData(key_columns, period_duration, last_period_duration, n_periods)
+  return AuxiliaryClusteringData(
+    key_columns,
+    period_duration,
+    last_period_duration,
+    n_periods,
+  )
 end
 
 """
@@ -409,7 +418,11 @@ function find_representative_periods(
   # Check that the number of RPs makes sense. The first check can be done immediately,
   # The second check is done after we compute the auxiliary data
   if n_rp < 1
-    throw(ArgumentError("The number of representative periods is $n_rp but has to be at least 1."))
+    throw(
+      ArgumentError(
+        "The number of representative periods is $n_rp but has to be at least 1.",
+      ),
+    )
   end
 
   # Find auxiliary data and pre-compute additional constants that are used multiple times alter

src/io.jl

@@ -7,7 +7,9 @@ Converts a weight matrix from a (sparse) matrix, which is more convenient for
 internal computations, to a dataframe, which is better for saving into a file.
 Zero weights are dropped to avoid cluttering the dataframe.
 """
-function weight_matrix_to_df(weights::Union{SparseMatrixCSC{Float64, Int64}, Matrix{Float64}})
+function weight_matrix_to_df(
+  weights::Union{SparseMatrixCSC{Float64, Int64}, Matrix{Float64}},
+)
   weights = sparse(weights)
   periods, rep_periods, values = weights |> findnz
   result = DataFrame(; period = periods, rep_period = rep_periods, weight = values)
@@ -39,7 +41,11 @@ function write_clustering_result_to_tables(
   period_duration[end] = aux.last_period_duration
   DuckDB.register_data_frame(
     connection,
-    DataFrame(; rep_period = 1:num_rep_periods, num_timesteps = period_duration, resolution = 1.0),
+    DataFrame(;
+      rep_period = 1:num_rep_periods,
+      num_timesteps = period_duration,
+      resolution = 1.0,
+    ),
     "rep_periods_data",
   )
   return nothing

src/structures.jl

@@ -8,7 +8,12 @@ mutable struct AuxiliaryClusteringData
   last_period_duration::Int
   n_periods::Int
 
-  function AuxiliaryClusteringData(key_columns, period_duration, last_period_duration, n_periods)
+  function AuxiliaryClusteringData(
+    key_columns,
+    period_duration,
+    last_period_duration,
+    n_periods,
+  )
     return new(key_columns, period_duration, last_period_duration, n_periods)
   end
 end
@@ -23,7 +28,13 @@ mutable struct ClusteringResult
   rp_matrix::Union{Matrix{Float64}, Nothing}
   auxiliary_data::Union{AuxiliaryClusteringData, Nothing}
 
-  function ClusteringResult(profiles, weight_matrix, clustering_matrix, rp_matrix, auxiliary_data)
+  function ClusteringResult(
+    profiles,
+    weight_matrix,
+    clustering_matrix,
+    rp_matrix,
+    auxiliary_data,
+  )
     return new(profiles, weight_matrix, clustering_matrix, rp_matrix, auxiliary_data)
   end
 

src/weight_fitting.jl

@@ -220,7 +220,8 @@ function fit_rep_period_weights!(
     else
       x = Vector(weight_matrix[period, 1:n_rp])
     end
-    x = projected_subgradient_descent!(x; subgradient, projection, tol = tol * 0.01, args...)
+    x =
+      projected_subgradient_descent!(x; subgradient, projection, tol = tol * 0.01, args...)
     x[x .< tol] .= 0.0  # replace insignificant small values with zeros
     if weight_type == :convex || weight_type == :conical_bounded
       # Because some values might have been removed, convexity can be lost.

test/test-cluster.jl

@@ -67,7 +67,8 @@ end
 @testset "Data valudation" begin
   @testset "Make sure that when the columns are right validation works and the key columns are found" begin
     @test begin
-      df = DataFrame([:period => [1, 1, 2], :timestep => [1, 2, 1], :a .=> "a", :value => 1:3])
+      df =
+        DataFrame([:period => [1, 1, 2], :timestep => [1, 2, 1], :a .=> "a", :value => 1:3])
       keys = TulipaClustering.validate_df_and_find_key_columns(df)
 
       keys == [:timestep, :a]

test/test-io.jl

@@ -21,8 +21,11 @@
     TulipaClustering.write_clustering_result_to_tables(connection, clustering_data)
 
     tables = DBInterface.execute(connection, "SHOW TABLES") |> DataFrame |> df -> df.name
-    @test sort(tables) ==
-          Union{Missing, String}["profiles_rep_periods", "rep_periods_data", "rep_periods_mapping"]
+    @test sort(tables) == Union{Missing, String}[
+      "profiles_rep_periods",
+      "rep_periods_data",
+      "rep_periods_mapping",
+    ]
 
     @testset "rep_periods_data" begin
       rep_periods_data_df =
@@ -36,8 +39,10 @@
     end
 
     @testset "ClusteringResult constructor without auxiliary data" begin
-      clustering_result =
-        TulipaClustering.ClusteringResult(clustering_data.profiles, clustering_data.weight_matrix)
+      clustering_result = TulipaClustering.ClusteringResult(
+        clustering_data.profiles,
+        clustering_data.weight_matrix,
+      )
 
       @test clustering_result.profiles == clustering_data.profiles
       @test clustering_result.weight_matrix == clustering_data.weight_matrix

test/test-weight-fitting.jl

@@ -71,7 +71,11 @@ end
         distance = SqEuclidean(),
         init = :kmcen,
       )
-      TulipaClustering.fit_rep_period_weights!(clustering_result; weight_type = :dirac, niters = 5)
+      TulipaClustering.fit_rep_period_weights!(
+        clustering_result;
+        weight_type = :dirac,
+        niters = 5,
+      )
       all(sum(clustering_result.weight_matrix[1:(end - 1), :]; dims = 2) .== 1.0)
     end
   end
@@ -88,7 +92,11 @@ end
         distance = SqEuclidean(),
         init = :kmcen,
       )
-      TulipaClustering.fit_rep_period_weights!(clustering_result; weight_type = :convex, niters = 5)
+      TulipaClustering.fit_rep_period_weights!(
+        clustering_result;
+        weight_type = :convex,
+        niters = 5,
+      )
       sum(clustering_result.weight_matrix) ≈ round(365 / 7, RoundUp) &&
         all(sum(clustering_result.weight_matrix[1:(end - 1), :]; dims = 2) .≈ 1.0)
     end