precommit hook

Author: jchiquet

.Rbuildignore

@@ -1,18 +1,19 @@
-^.*\.Rproj$
-^\.Rproj\.user$
-cran-comments.md
-figure
+.travis.yml
+AUTHORS
 README.md
 README.rmd
-.travis.yml
 README_cache
+^.*\.Rproj$
 ^CRAN-RELEASE$
+^CRAN-SUBMISSION$
+^\.Rproj\.user$
 ^\.github$
+^\.pre-commit-config\.yaml$
 ^_pkgdown\.yml$
-^pkgdown$
 ^docs
-^docs/*.*
 ^docs/*
-^CRAN-SUBMISSION$
+^docs/*.*
+^pkgdown$
 ^revdep
-AUTHORS
+cran-comments.md
+figure

.github/workflows/linting.yaml

@@ -45,4 +45,4 @@ src/*.so
 src/*.dll
 
 # revdep testing
-revdep/
+revdep/

.gitignore

@@ -0,0 +1,91 @@
+# All available hooks: https://pre-commit.com/hooks.html
+# R specific hooks: https://github.com/lorenzwalthert/precommit
+repos:
+-   repo: https://github.com/lorenzwalthert/precommit
+    rev: v0.4.3.9021
+    hooks:
+    -   id: style-files
+        args: [--style_pkg=styler, --style_fun=tidyverse_style]
+    # -   id: roxygenize
+    #     # roxygen requires loading pkg -> add dependencies from DESCRIPTION
+    #     additional_dependencies:
+    #     -    Matrix
+    #     -    Rcpp
+    -   id: use-tidy-description
+    -   id: spell-check
+        exclude: >
+          (?x)^(
+          .*\.[rR]|
+          .*\.feather|
+          .*\.jpeg|
+          .*\.pdf|
+          .*\.png|
+          .*\.py|
+          .*\.RData|
+          .*\.rds|
+          .*\.Rds|
+          .*\.Rproj|
+          .*\.sh|
+          (.*/|)\.gitignore|
+          (.*/|)\.gitlab-ci\.yml|
+          (.*/|)\.lintr|
+          (.*/|)\.pre-commit-.*|
+          (.*/|)\.Rbuildignore|
+          (.*/|)\.Renviron|
+          (.*/|)\.Rprofile|
+          (.*/|)\.travis\.yml|
+          (.*/|)appveyor\.yml|
+          (.*/|)NAMESPACE|
+          (.*/|)renv/settings\.dcf|
+          (.*/|)renv\.lock|
+          (.*/|)WORDLIST|
+          \.github/workflows/.*|
+          data/.*|
+          )$
+    -   id: lintr
+        args: [--warn_only]
+        verbose: false
+    -   id: readme-rmd-rendered
+    -   id: parsable-R
+    -   id: no-browser-statement
+    -   id: no-print-statement
+    -   id: no-debug-statement
+    -   id: deps-in-desc
+    -   id: pkgdown
+- repo: https://github.com/pre-commit/mirrors-clang-format
+  rev: v22.1.2
+  hooks:
+    - id: clang-format
+      args: ["--style=Google"]
+      exclude: ./src/RcppExports.cpp
+- repo: https://github.com/cpplint/cpplint
+  rev: 2.0.2
+  hooks:
+    - id: cpplint
+      args:
+        - --exclude=src/RcppExports.cpp
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+    -   id: check-added-large-files
+        args: ['--maxkb=200']
+    -   id: file-contents-sorter
+        files: '^\.Rbuildignore$'
+    # -   id: end-of-file-fixer
+    #     exclude: '\.Rd,R/RcppExports.R'
+-   repo: https://github.com/pre-commit-ci/pre-commit-ci-config
+    rev: v1.6.1
+    hooks:
+    # Only required when https://pre-commit.ci is used for config validation
+    -   id: check-pre-commit-ci-config
+-   repo: local
+    hooks:
+    -   id: forbid-to-commit
+        name: Don't commit common R artifacts
+        entry: Cannot commit .Rhistory, .RData
+        language: fail
+        files: '\.(Rhistory|RData|)$'
+        # `exclude: <regex>` to allow committing specific files
+
+ci:
+    autoupdate_schedule: monthly

.pre-commit-config.yaml

@@ -28,7 +28,9 @@ Imports:
     Rcpp
 Suggests: 
     testthat,
-    spelling
+    spelling,
+    mclust, 
+    ggplot2
 LinkingTo: Rcpp
 RoxygenNote: 7.3.3
 Language: en-US

DESCRIPTION

@@ -1,5 +1,6 @@
 ---
-title: "aricode: fast computations of clustering comparison measures"
+title: "aricode"
+subtitle: "fast computations of clustering comparison measures"
 format: gfm
 ---
 
@@ -10,8 +11,6 @@ knitr::opts_chunk$set(
 )
 ```
 
-# aricode
-
  <!-- badges: start -->
 [![R-CMD-check](https://github.com/jchiquet/aricode/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/jchiquet/aricode/actions/workflows/R-CMD-check.yaml)
 [![CRAN Status](https://www.r-pkg.org/badges/version/aricode)](https://CRAN.R-project.org/package=aricode)
@@ -121,4 +120,3 @@ p.timings <- ggplot(timings, aes(x = n, y = time, colour = method)) +
 
 p.timings + ggtitle("number of classes grows with n") + theme_bw()
 ```
-

README.qmd

@@ -1,6 +1,7 @@
 templates:
   params:
     bootswatch: readable
+url: https://github.com/jchiquet/aricode
 
 navbar:
   title: "aricode"
@@ -16,4 +17,3 @@ navbar:
   right:
     - icon: fa-github
       href: https://github.com/jchiquet/aricode
-

_pkgdown.yml

@@ -1,23 +1,155 @@
+agroparistech
+al
+Alain
 AMI
 ARI
+aricode
+Arlot
+aut
+automatiquement
+bersani
+Bersani
+bfeebcaf
+bootswatch
+BugReports
+Calcul
+calcul
+CallEntries
+CallMethodDef
+cb
+Celisse
+cerr
+Changelog
+chiquet
+Chiquet
+classe
+classi
+classiSEXP
+clustComp
 CMD
+commencent
+compileAttributes
+comptage
+Comptage
+const
+countPairs
+cout
+cpp
+cre
+ctb
+de
+dervieux
+Dervieux
+des
+DL
+dll
+DllInfo
+doi
+du
+emi
+endif
+entropies
 Epps
+et
+factorielles
+faf
+fd
+florent
+Florent
+gagner
+gcc
+getRank
+ggplot
+github
+gmail
+guillem
+Guillem
+Harchaoui
+href
+https
+hypergéométrique
+idx
+ifdef
+indexCur
+individus
+inrae
+IntegerVector
+jchiquet
 JMLR
+jSEXP
+julien
+Julien
+Lajugie
+les
+lfactorial
+lgamma
+libérée
 Lifecycle
+LinkingTo
+LogicalVector
+LTS
 MARIraw
+martina
+mclust
+nameClassi
+navbar
+nb
+nbIndex
+ni
 NID
+nij
+nj
 NMI
+Nmni
+Nmnj
+Nombre
+numberPair
+NumericVector
 NVI
+oldrel
 ORCID
-SortPairs
-Vinh
-Xuan
-al
-clustComp
-doi
-entropies
-et
-mclust
+paires
+params
+PMLR
+Probabilité
+Pré
 radix
+Rcerr
+Rcout
+rcpp
+Rcpp
+RCPP
+RcppExport
+registerRoutines
+rigaill
+Rigaill
+rngScope
+RNGScope
+RObject
+Rostream
+ROSTREAM
 roxygen
+RoxygenNote
+Rémi
+selon
+SEXP
+SHA
+SortPairs
 sortPairs
+sundqvist
+Sundqvist
+Sylvain
+temporaire
+terme
+testthat
+tmp
+Tri
+ubuntu
+uniques
+useDynamicSymbols
+valentin
+Vinh
+Xuan
+Zaid
+à
+Équivalent