Update package with latest version of Bestie Template (#62)

.JuliaFormatter.toml

@@ -10,7 +10,7 @@ format_docstrings = false
 format_markdown = false
 import_to_using = true
 indent = 2
-margin = 100
+margin = 92
 normalize_line_endings = "unix"
 remove_extra_newlines = true
 separate_kwargs_with_semicolon = true

.copier-answers.yml

@@ -1,12 +1,13 @@
 # Changes here will be overwritten by Copier
 AnswerStrategy: recommended
-AuthorEmail: [email protected]
-AuthorName: Greg Neustroev
-Indentation: 2
-JuliaMinVersion: '1.6'
+Authors: Greg Neustroev <[email protected]> and contributors
+CodeOfConductContact: G.Neustroev@tudelft.nl
+JuliaIndentation: 2
+JuliaMinVersion: 1.10.5
 License: Apache-2.0
+LicenseCopyrightHolders: Greg Neustroev
 PackageName: TulipaClustering
 PackageOwner: TulipaEnergy
 PackageUUID: 314fac8b-c762-4aa3-9d12-851379729163
-_commit: v0.7.0
+_commit: v0.12.0
 _src_path: https://github.com/JuliaBesties/BestieTemplate.jl

.editorconfig

@@ -5,6 +5,14 @@ root = true
 end_of_line = lf
 insert_final_newline = true
 charset = utf-8
-indent_size = 2
 indent_style = space
 trim_trailing_whitespace = true
+
+[*.jl]
+indent_size = 2
+
+[*.md]
+indent_size = 2
+
+[*.{yml,toml,json}]
+indent_size = 2

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

@@ -11,9 +11,13 @@ 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
     id: description

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

@@ -9,9 +9,13 @@ 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
     id: description

.github/ISSUE_TEMPLATE/30-usage.yml

@@ -11,9 +11,13 @@ 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
     id: description

.github/ISSUE_TEMPLATE/99-general.yml

@@ -9,9 +9,13 @@ 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
     id: description

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,7 +1,9 @@
 <!--
 Thanks for making a pull request to TulipaClustering.jl.
 We have added this PR template to help you help us.
-Make sure to read the contributing guidelines and abide to the code of conduct.
+
+Make sure to read the contributing guidelines and abide by the code of conduct.
+
 See the comments below, fill the required fields, and check the items.
 -->
 
@@ -21,7 +23,9 @@ There is no related issue.
 
 <!-- mark true if NA -->
 <!-- leave PR as draft until all is checked -->
+
 - [ ] I am following the [contributing guidelines](https://github.com/TulipaEnergy/TulipaClustering.jl/blob/main/docs/src/90-contributing.md)
+
 - [ ] Tests are passing
 - [ ] Lint workflow is passing
 - [ ] Docs were updated and workflow is passing

.github/workflows/Docs.yml

@@ -35,19 +35,23 @@ jobs:
           version: "1"
       - name: Use Julia cache
         uses: julia-actions/cache@v2
-      - run: |
+      - name: Instantiate environment with development version of the package
+        run: |
           julia --project=docs -e '
             using Pkg
             Pkg.develop(PackageSpec(path=pwd()))
             Pkg.instantiate()'
-      - run: |
+      - name: Run doctest
+        run: |
           julia --project=docs -e '
             using Documenter: DocMeta, doctest
             using TulipaClustering
             DocMeta.setdocmeta!(TulipaClustering, :DocTestSetup, :(using TulipaClustering); recursive=true)
             doctest(TulipaClustering)'
-      - run: julia --project=docs docs/make.jl
+      - name: Generate and deploy documentation
+        run: julia --project=docs docs/make.jl
         env:
           JULIA_PKG_SERVER: ""
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
+          GKSwstype: "100" # https://discourse.julialang.org/t/generation-of-documentation-fails-qt-qpa-xcb-could-not-connect-to-display/60988

.github/workflows/Lint.yml

@@ -28,10 +28,15 @@ jobs:
         uses: julia-actions/cache@v2
       - name: Install JuliaFormatter.jl
         run: julia -e 'using Pkg; pkg"add JuliaFormatter"'
+      - name: Hack for setup-python cache # https://github.com/actions/setup-python/issues/807
+        run: touch requirements.txt
       - name: Setup Python
         uses: actions/setup-python@v5
         with:
           cache: "pip"
+          python-version: "3.11"
+      - name: Hack for setup-python cache # https://github.com/actions/setup-python/issues/807
+        run: rm requirements.txt
       - name: Cache pre-commit
         uses: actions/cache@v4
         with:
@@ -53,3 +58,4 @@ jobs:
         uses: lycheeverse/lychee-action@v1
         with:
           fail: true
+          args: --config '.lychee.toml' .

.github/workflows/PreCommitUpdate.yml

@@ -10,10 +10,15 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
+      - name: Hack for setup-python cache # https://github.com/actions/setup-python/issues/807
+        run: touch requirements.txt
       - name: Setup Python
         uses: actions/setup-python@v5
         with:
           cache: pip
+          python-version: "3.11"
+      - name: Hack for setup-python cache # https://github.com/actions/setup-python/issues/807
+        run: rm requirements.txt
       - name: Install pre-commit
         run: pip install pre-commit
       - name: Run pre-commit's autoupdate

.github/workflows/Test.yml

@@ -5,7 +5,6 @@ on:
     branches:
       - main
     tags: ["*"]
-
   workflow_dispatch:
 
 jobs:
@@ -23,7 +22,7 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - "1.6"
+          - "1.10.5"
           - "1"
         os:
           - ubuntu-latest

.gitignore

@@ -1,13 +1,14 @@
 *.jl.*.cov
 *.jl.cov
 *.jl.mem
+*.rej
+.DS_Store
+.benchmarkci
 Manifest.toml
+benchmark/*.json
+coverage
 docs/build/
 env
-/.benchmarkci
-/benchmark/*.json
-coverage/
-*.rej
-node_modules
-.DS_Store
+debugging
 .vscode
+node_modules

.pre-commit-config.yaml

@@ -44,6 +44,6 @@ repos:
     hooks:
       - id: yamllint
   - repo: https://github.com/domluna/JuliaFormatter.jl
-    rev: v1.0.61
+    rev: v1.0.60
     hooks:
       - id: julia-formatter

CODE_OF_CONDUCT.md

@@ -60,7 +60,7 @@ representative at an online or offline event.
 ## Enforcement
 
 Instances of abusive, harassing, or otherwise unacceptable behavior may be
-reported to the community leaders responsible for enforcement at
+reported to the community leaders responsible for enforcement:
 `[email protected]`.
 All complaints will be reviewed and investigated promptly and fairly.
 

README.md

@@ -11,6 +11,7 @@
 [![DOI](https://zenodo.org/badge/712902842.svg)](https://zenodo.org/doi/10.5281/zenodo.10419235)
 [![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg)](CODE_OF_CONDUCT.md)
 [![All Contributors](https://img.shields.io/github/all-contributors/TulipaEnergy/TulipaClustering.jl?labelColor=5e1ec7&color=c0ffee&style=flat-square)](#contributors)
+[![BestieTemplate](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/JuliaBesties/BestieTemplate.jl/main/docs/src/assets/badge.json)](https://github.com/JuliaBesties/BestieTemplate.jl)
 
 ## How to Cite
 

docs/make.jl

@@ -1,37 +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
-
-function nice_name(file)
-  file = replace(file, r"^[0-9]*-" => "")
-  if haskey(page_rename, file)
-    return page_rename[file]
-  end
-  return splitext(file)[1] |> x -> replace(x, "-" => " ") |> titlecase
-end
+const numbered_pages = [
+  file for file in readdir(joinpath(@__DIR__, "src")) if
+  file != "index.md" && splitext(file)[2] == ".md"
+]
 
 makedocs(;
   modules = [TulipaClustering],
-  doctest = true,
-  linkcheck = false, # Rely on Lint.yml/lychee for the links
   authors = "Greg Neustroev <[email protected]> and contributors",
   repo = "https://github.com/TulipaEnergy/TulipaClustering.jl/blob/{commit}{path}#{line}",
   sitename = "TulipaClustering.jl",
   format = Documenter.HTML(;
-    prettyurls = true,
     canonical = "https://TulipaEnergy.github.io/TulipaClustering.jl",
-    assets = ["assets/style.css"],
   ),
-  pages = [
-    "Home" => "index.md"
-    [
-      nice_name(file) => file for
-      file in readdir(joinpath(@__DIR__, "src")) if file != "index.md" && splitext(file)[2] == ".md"
-    ]
-  ],
+  pages = ["index.md"; numbered_pages],
 )
 
-deploydocs(; repo = "github.com/TulipaEnergy/TulipaClustering.jl", push_preview = true)
+deploydocs(; repo = "github.com/TulipaEnergy/TulipaClustering.jl")

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